From 28efab6af3088c1b8f1bdabb8131c0e3d09bcb56 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 16 Jan 2024 13:09:17 +0100 Subject: [PATCH 001/446] added setting for https forwading --- conf/template_settings.txt | 3 +++ 1 file changed, 3 insertions(+) diff --git a/conf/template_settings.txt b/conf/template_settings.txt index 5f01c644d..8cf15d092 100644 --- a/conf/template_settings.txt +++ b/conf/template_settings.txt @@ -192,3 +192,6 @@ CRONTAB_COMMAND_SUFFIX = "2>&1" DEFAULT_AUTO_FIELD = "django.db.models.AutoField" DATA_UPLOAD_MAX_MEMORY_SIZE = 7000000 + +# Needed when using a proxy for https forwading +SECURE_PROXY_SSL_HEADER = ('HTTP_X_FORWARDED_PROTO', 'https') \ No newline at end of file From f19784188f46e555a23490481953bacd3e9aada2 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 23 Oct 2023 12:04:00 +0000 Subject: [PATCH 002/446] Bump wheel from 0.37.1 to 0.38.1 in /conf Bumps [wheel](https://github.com/pypa/wheel) from 0.37.1 to 0.38.1. - [Changelog](https://github.com/pypa/wheel/blob/main/docs/news.rst) - [Commits](https://github.com/pypa/wheel/compare/0.37.1...0.38.1) --- updated-dependencies: - dependency-name: wheel dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- conf/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/requirements.txt b/conf/requirements.txt index cdea7bb12..7f2e62cac 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -1,4 +1,4 @@ -wheel==0.37.1 +wheel==0.38.1 asn1crypto==1.5.0 bcrypt==4.0.1 biopython==1.79 From 52b282d4c0736fd8e1b279aee44c90d4d71712c1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 2 Nov 2023 21:39:04 +0000 Subject: [PATCH 003/446] Bump django from 4.2 to 4.2.7 in /conf Bumps [django](https://github.com/django/django) from 4.2 to 4.2.7. - [Commits](https://github.com/django/django/compare/4.2...4.2.7) --- updated-dependencies: - dependency-name: django dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- conf/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/requirements.txt b/conf/requirements.txt index 7f2e62cac..51e25de6b 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -3,7 +3,7 @@ asn1crypto==1.5.0 bcrypt==4.0.1 biopython==1.79 cryptography==38.0.3 -Django==4.2 +Django==4.2.7 django-crispy-forms==2.0 crispy-bootstrap5==0.7 django-crontab==0.7.1 From c088706cadf98ca3e53985d9b72116966b60f0ad Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 18 Apr 2024 13:12:27 +0200 Subject: [PATCH 004/446] Resolving conflicts --- README.md | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/README.md b/README.md index d585518e6..bea4aeb23 100644 --- a/README.md +++ b/README.md @@ -21,6 +21,7 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Create iskylims database and grant permissions](#create-iskylims-database-and-grant-permissions) - [Configuration settings](#configuration-settings) - [Run installation script](#run-installation-script) +<<<<<<< HEAD - [Upgrade to iSkyLIMS version 3.0.0](#upgrade-to-iskylims-version-300) - [Pre-requisites](#pre-requisites-1) - [Clone github repository](#clone-github-repository-1) @@ -33,6 +34,19 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [SAMBA configurarion](#samba-configurarion) - [Email verification](#email-verification) - [Configure Apache server](#configure-apache-server) +======= + - [Configure Apache server](#configure-apache-server) + - [Installation verification](#installation-verification) + - [Upgrade to iSkyLIMS version 3.0.0](#upgrade-to-iskylims-version-300) + - [Pre-requisites](#pre-requisites-1) + - [Executing the upgrade](#executing-the-upgrade) + - [Clone github repository](#clone-github-repository-1) + - [Configuration settings](#configuration-settings-1) + - [Running upgrade script](#running-upgrade-script) + - [Final configuration steps](#final-configuration-steps) + - [SAMBA configurarion](#samba-configurarion) + - [Email verification](#email-verification) +>>>>>>> 12e92359 (readme mods) - [Verification of the installation](#verification-of-the-installation) - [iSkyLIMS documentation](#iskylims-documentation) @@ -48,7 +62,10 @@ Before starting the installation make sure : - Database MySQL > 8.0 or MariaDB > 10.4 - Local server configured for sending emails - Apache server v2.4 +<<<<<<< HEAD - git > 2.34 +======= +>>>>>>> 12e92359 (readme mods) - Python > 3.8 - Connection to samba shared folder where run folders are stored (p.e galera/NGS_Data) - Dependencies: @@ -137,6 +154,17 @@ bash install.sh --install app sudo bash install.sh --install full ``` +<<<<<<< HEAD +======= +#### Configure Apache server + +Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf + +#### Installation verification + +After installation is completed and apache server is up and running open you navigator typing "localhost" or the "server local IP". + +>>>>>>> 12e92359 (readme mods) ### Upgrade to iSkyLIMS version 3.0.0 If you have already iSkyLIMS on version 2.3.0 you can upgrade to the latest stable version 3.0.0. @@ -152,10 +180,19 @@ Because in this upgrade many tables in database are modified it is required that It is highly recomended that you made these backups and keep them safely in case of upgrade failure, to recover your system. +<<<<<<< HEAD #### Clone github repository We've also change the way that iSkyLIMS is installed and upgraded. From now on iskylims is downloaded in a user folder and installed elsewhere (p.e /opt/). +======= +#### Executing the upgrade + +We've also change the way that iSkyLIMS is installed and upgraded. From now on iskylims is downloaded in a user folder and installed elsewhere (p.e /opt/). + +##### Clone github repository + +>>>>>>> 12e92359 (readme mods) Open a linux terminal and move to a directory where iSkyLIMS code will be downloaded @@ -165,7 +202,11 @@ git clone https://github.com/BU-ISCIII/iSkyLIMS.git iskylims cd iskylims ``` +<<<<<<< HEAD #### Configuration settings +======= +##### Configuration settings +>>>>>>> 12e92359 (readme mods) Copy the initial setting template into a file named install_settings.txt @@ -181,7 +222,11 @@ database ,email settings and the local IP of the server where iSkyLIMS will run. sudo nano install_settings.txt ``` +<<<<<<< HEAD #### Running upgrade script +======= +##### Running upgrade script +>>>>>>> 12e92359 (readme mods) If your organization requires that dependencies / stuff that needs root are installed by a different person that install the application the you can use the install script in several steps as follows. @@ -211,6 +256,7 @@ sudo bash install.sh --upgrade dep sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables ``` +<<<<<<< HEAD ##### Steps not requiring root Next you need to upgrade iskylims app. Please use the command below: @@ -243,6 +289,8 @@ mysql -u iskylims -h dmysqlps.isciiides.es mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` +======= +>>>>>>> 12e92359 (readme mods) ### Final configuration steps #### SAMBA configurarion @@ -260,10 +308,13 @@ mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/b - Go to Configuration -> Email configuration - Fill the form with the needed params for your email configuration and try to send a test email. +<<<<<<< HEAD #### Configure Apache server Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf +======= +>>>>>>> 12e92359 (readme mods) #### Verification of the installation Open the navigator and type "localhost" or the "server local IP" and check that iSkyLIMs is running. From 975303886a2ca339a0ad218128a9de31af4cd297 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 18 Apr 2024 13:14:42 +0200 Subject: [PATCH 005/446] Resolving conflicts --- README.md | 51 --------------------------------------------------- image.png | Bin 0 -> 90700 bytes 2 files changed, 51 deletions(-) create mode 100755 image.png diff --git a/README.md b/README.md index bea4aeb23..d585518e6 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,6 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Create iskylims database and grant permissions](#create-iskylims-database-and-grant-permissions) - [Configuration settings](#configuration-settings) - [Run installation script](#run-installation-script) -<<<<<<< HEAD - [Upgrade to iSkyLIMS version 3.0.0](#upgrade-to-iskylims-version-300) - [Pre-requisites](#pre-requisites-1) - [Clone github repository](#clone-github-repository-1) @@ -34,19 +33,6 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [SAMBA configurarion](#samba-configurarion) - [Email verification](#email-verification) - [Configure Apache server](#configure-apache-server) -======= - - [Configure Apache server](#configure-apache-server) - - [Installation verification](#installation-verification) - - [Upgrade to iSkyLIMS version 3.0.0](#upgrade-to-iskylims-version-300) - - [Pre-requisites](#pre-requisites-1) - - [Executing the upgrade](#executing-the-upgrade) - - [Clone github repository](#clone-github-repository-1) - - [Configuration settings](#configuration-settings-1) - - [Running upgrade script](#running-upgrade-script) - - [Final configuration steps](#final-configuration-steps) - - [SAMBA configurarion](#samba-configurarion) - - [Email verification](#email-verification) ->>>>>>> 12e92359 (readme mods) - [Verification of the installation](#verification-of-the-installation) - [iSkyLIMS documentation](#iskylims-documentation) @@ -62,10 +48,7 @@ Before starting the installation make sure : - Database MySQL > 8.0 or MariaDB > 10.4 - Local server configured for sending emails - Apache server v2.4 -<<<<<<< HEAD - git > 2.34 -======= ->>>>>>> 12e92359 (readme mods) - Python > 3.8 - Connection to samba shared folder where run folders are stored (p.e galera/NGS_Data) - Dependencies: @@ -154,17 +137,6 @@ bash install.sh --install app sudo bash install.sh --install full ``` -<<<<<<< HEAD -======= -#### Configure Apache server - -Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf - -#### Installation verification - -After installation is completed and apache server is up and running open you navigator typing "localhost" or the "server local IP". - ->>>>>>> 12e92359 (readme mods) ### Upgrade to iSkyLIMS version 3.0.0 If you have already iSkyLIMS on version 2.3.0 you can upgrade to the latest stable version 3.0.0. @@ -180,19 +152,10 @@ Because in this upgrade many tables in database are modified it is required that It is highly recomended that you made these backups and keep them safely in case of upgrade failure, to recover your system. -<<<<<<< HEAD #### Clone github repository We've also change the way that iSkyLIMS is installed and upgraded. From now on iskylims is downloaded in a user folder and installed elsewhere (p.e /opt/). -======= -#### Executing the upgrade - -We've also change the way that iSkyLIMS is installed and upgraded. From now on iskylims is downloaded in a user folder and installed elsewhere (p.e /opt/). - -##### Clone github repository - ->>>>>>> 12e92359 (readme mods) Open a linux terminal and move to a directory where iSkyLIMS code will be downloaded @@ -202,11 +165,7 @@ git clone https://github.com/BU-ISCIII/iSkyLIMS.git iskylims cd iskylims ``` -<<<<<<< HEAD #### Configuration settings -======= -##### Configuration settings ->>>>>>> 12e92359 (readme mods) Copy the initial setting template into a file named install_settings.txt @@ -222,11 +181,7 @@ database ,email settings and the local IP of the server where iSkyLIMS will run. sudo nano install_settings.txt ``` -<<<<<<< HEAD #### Running upgrade script -======= -##### Running upgrade script ->>>>>>> 12e92359 (readme mods) If your organization requires that dependencies / stuff that needs root are installed by a different person that install the application the you can use the install script in several steps as follows. @@ -256,7 +211,6 @@ sudo bash install.sh --upgrade dep sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables ``` -<<<<<<< HEAD ##### Steps not requiring root Next you need to upgrade iskylims app. Please use the command below: @@ -289,8 +243,6 @@ mysql -u iskylims -h dmysqlps.isciiides.es mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` -======= ->>>>>>> 12e92359 (readme mods) ### Final configuration steps #### SAMBA configurarion @@ -308,13 +260,10 @@ mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/b - Go to Configuration -> Email configuration - Fill the form with the needed params for your email configuration and try to send a test email. -<<<<<<< HEAD #### Configure Apache server Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf -======= ->>>>>>> 12e92359 (readme mods) #### Verification of the installation Open the navigator and type "localhost" or the "server local IP" and check that iSkyLIMs is running. diff --git a/image.png b/image.png new file mode 100755 index 0000000000000000000000000000000000000000..cac5ffb4c285dcd40ab5e7395c64143c151889ca GIT binary patch literal 90700 zcmc$_2T)U8+bD`k5fu~>kt(l9Z_**5h^QzKdPj=VTPPu+7ePc(KAfU$kQWi@ zA|;Rz0#X7Aq4#>DpZ;^soqy)ubI#1YYX-9R+H0@&l=alNI$COUmsl@RP*Bi4eezI` zf`Y1pg5vz-MQU5JHB@S z_k{2Gk^ct?|9%pel9l}L8)PNq|MdCK7r&k@f?ABVhA1e`WS%}$G4Qoq!O{la*ui#h zh&gawyLb&ef9;0KqwnW)Z!uBjKY3Jqr--Q}D0@MmC^nZV)*rzXWZ+n>v%^rDTf~3q z29<%PE@cT9{~IsH)%5${&eIMZJDk-5n<+wjpO|9 zEm2T#(I?i2{5qvyR&{{X8u$|8y;O_|5LwK-^&4= zfTh~mZ#>b8fvpVv(8lZua(g`4iN6jtIx#EB)ag+YbT?ItS=ymeUebZZaKxvZUUnD- z8O6$gNGVmFgIh2M>g~B*EIMHQ1L3aG@MJWBU*N0DZ9rT(iKeE``H0g&>1wIxfHR=h zvgW!FvqIM2b;LpSC_6ykkJ9Nd2-^`YD*D^iHu(jJxY47jn_wC7p% zEI8SDU496g(~|XAb25}QHLiCm5v1zp`!j#GZQ_9!zr0$k^C`OAETc{F4h7hCGP&4| zg@&XvO+Y;v9dk=x#yiNOhSJ7sZMb<1i$C2IkY3UGKx-4y`aC^gi{^85`JhWBwsDC5 zX=JP|u@qrm=dEu`F*Q-Q7mBpEMgQ|>s?QsGi;^9n>;r6<5J~6Lt0<;XV#ZBCtJXc= z)?nk;$hD!-%<#wrlCV)?6w_E83<^)m_;hKZuTh1>WDave@3~;R1A3E%3T5b=mp3J~ zA({FeF^Mv3z--x@6;-N@JB}loB-Sxcj1Y2lcy!IEndE3FWc*_YBcp#A`1`y==Y+0Z zoER?__~)MvBn5@sPQroa`dJyy*}T!P*g!?P)L`5v-G@+K8R8v|IkRk?9ALGo@r=A# zfys5km5;S2l|wbMQ_#~cu!!1v#Y7<^op%6f?(;KWubS^o7=fSCCXN-^=W@g?0xJ`f zofCyhz&j5<_CmZ|GPZ3PBe|2ka6(U`SD=)*MmS;qR?D z+u(EwUS%+*d`*TlIvswl{*`*2nW0drQ#k>~?;5+cZz3o+qEz{mBj4aM4RX(J0dBZn zJ3?S8xuE@Ls{1{HTPo{I0PJIVyuEWkI@jLMXbe`^eMG7GIfsRZnIhiEc)*!2HL^*w zBYEIR0^zrIPWBonY3i|ndRYeWiG{L&&o0uBRLho%D!$GBT>2?}duF#mTH|p)uQR3! z$#LP&L~@zEf!7oecHD3yp{HZl1&hrV)Ju{RiZq5Ce~zzPHh@cOAe#HYZwZgZS!NOi z4RrF-#-@|PB2Uv>?v1zMBe;$x1fP5Sf%XYnp zZ-zbxEYV|MQimSmJ$Z?kmf)e<^wOZYrksO6tDs=FvTL)^etsT=fW3n`*b8*|4VvyaFSoiIH=53IGN#GE%`;tq z_3sxx_>qEWGEg7m;HYwo@~Bq6`U{ct%?n1oi9&@ykCVgZhd3|A%;+xy zwmEQ|1O&C)C9~bylPc2%$)2oe*4x*Agx)oegquIezhqVgD`mT}SDKYjq=biSRk8kB z`%iWi4>Csz)i+KRi;QDtJdBCKx#L1~lwBw7B0mW-3Go-J+ZhU4S>jwL?7OK`@A*}Y z(w_79v+Xy=e4uMnubNNtwOL1>T(Jubh?$>v-1y3Y_M6G(VBE$oS^yH@Hj!b@Mj#L1 zkT70LKJEHKjP?{LIv+CQvxzJl|Q|sUK$<9W0U(sd~U}wuwvq!z-hEo?IjCufjpCz&#f_GV8nNZ>4^+)t~_Jo)xjX_@~mYVwk8BLjGQ_v z-amT;(hNO7L(CmJGf&d$?Q3fw|He96Hox}I#A*gy<@|vcl6CHDyRhmT@5iYK-(oE+ zIx+>3bT-OxjoN!{Ta8A5J|E-QET{W;8Sx84oVB9U2Sb;l&jPFajaaem=>Vy6_qD`n z%l+`v-Q_#7M<=@#ctVn>+ZH@Ci?&SpxZ_z++lz2f$MO5xIFD3k13HwNERon<-n`xM zGcj$oZ0@WKOQ6P*$);qL%BOV5L=J-Wr9ec$U*5DpzjVUuLV%+eJBoTAkvvI>rq6|Kd7sQ;_?T zAtr0~c0P`J#&{WZ-Naj!K3~q}Ur2EH3?6v4-gKW>q|Ui~$v8butWSpYJxn?s+fEl> ziU|nY83OTTUmkZIZVypMu~~_X*gK?NA|{HpjX-Ko^D0qphE3*zyk7EnVC4bMy??w@ zf3e9*;@MP5wSNZo8KTs1_)~`uiK$%sA6M8#v~W3HY{=4} z_$I<|K{4xSk^LH7saazjfiI$4w%F9dVZ1c|5-)&rp^y}Sa63~uh{qCnc$!|W*CnzU z7Md|xj1{Dk+4sjmZSc(0a z^n63T)K?Sh36WGeN^2`4wxr-4H~~M~G6gQ!^nUP_xDbhOvntq1VfQ&m0#B{lgPC8` zW++SB1Ut$P0?RW?jA@6422V`=Ul5WHkGtub3M@2Qy)lOVb~@U7GP5W}>HQyDb$pT< zw23k0$G_yuUxnS>j`w1lz47Zdvu0DgjMi{|Icup`#3itfyjfoYD?^9z2pE$MtDqn= zXp3}L=UCc=bd!TJCbrQ}Mo^2%L#eTP6;H-%GN!Y^OudOC0Eae9tE#DT#nUyzbSb|L z!SboLZaRgdRIbx@WAJFChOx^kVc^iZ$2q9>x%oq`Dax3EIZYYp3G3JtS3t0)eTxA6 z#dx@Y>d&j&>3RZ3ShLvx(sz2n;=n)*Z{sryt_8HBwa!yh07mH`NtpXh) z!}{mI%M)e@#?pq4_3nb;V%^&!I^BzO+v79SfL3r#kgcnW&&rsH7zo8IBuhBWgzpp* z^%rhnHlX~lr%d*nfKn4$z6%Imte|8$Rwd0$mkzgY4Q||q1^Kz*-Ds1}Qx9b;C zL>6q`-uP+#V7-lnxzhI!mm`UJCVLT?c*tIW8Blmr7o*Ic8`G)eWma7OYZe5zape2Ey!k6YC!*_U2GD&?;AA6B!sNWHn8%=||0PWyv_} z`r8&W$l3r(AZp6`{$Fh0`#6ttkyQtYtg}|myx*>QPaLN2gY92C9!p1n z@zXOLzpx{8>gEY(An(G=*IE>C?ySIl#rl)O_QD;^m4nAtP3P7ntg*cw-xuZ*%^cFH z(sSCUw@Pjvh;f7NFJu;FXKj$!{G|@7?LN?cU%V6szq^(B4v5QQ@7&!^`Rw+7X9m0$ zu>JHLqcD(o@9U}Q1I?MW%v&A3EFrCGm7={D>2EBzRvEYlHhh~r&%>iC)V_u6(i1V| zaOve;PeaKF^`1g98j13|$OZ?arvpK=yZKP%*Z3D-W2-Hj>&Bsyh$g`absSS`bm!6i zA<1{Qaw}lSiuQwNg|jPJmyaRKAPi-9pAp3rfBcTHChc{7dLA*}h8F&yW{H}x{KuM~ zVfdHA^;2q=nn7#hJ1(V0FYf8MonK0aqf)B_;YMo{g=Fz^sq7Hp4NWfqBX?4F;-MBt zMr2uw+c3KKl}rb04WU?2_RXp1W4>yMamD=mtJEo1?Hrmb9a64%R&x3TYZj)MMutOs zfmzf12~=R$X~<_fe?GYpiPS}A`K`%MMsfDS7I_QlK4>+nR6BUJH^TDFIW=vpIOn;s zWp<~U*VLet3t6BbMh9p{?{GTE`h*|yUN}Kj_J7wnv&>Dz>^g>U!90EgQVWDzaz{1cG?3iY3{GNhh<-}imKJ&Dr zAAoYHqf32a!AyS=hf{%Ei z4gINMo$b$vHz}2c1|icJU1F6mKSaetAKqmf5YS=ONf`o~nZWtw(OwH_ldw>B#gbq} zjnDUjeOhP%>7m|rp9B*}OTZqNR}^o3|GCX^INwbNwmy8{)I)&TGg=HEO4Un6J)H)l z_#Y+qCi_^SN;y`=SqPR!^@T4Eyh_qFG-3c-EZYJFWUdn5A{(xrBD7KZ3-)l%NtIR6Yr<`)a` zC_$gjDu=yvVa$%<5Atd|#aw=+os}b2-@sj73LU~4YYd&L-roNjvgIzBUkZg*&aA(+ zxgd)lGb$ayG@e6Du)H5mD~@NA+S@pPhxaohL(x;cNb}Yi^=Xw|M(~g*TiyFBOARXB ztAm?2?tGJkENWsQLy8B}{Wj`WzDL5?>b?_meg>75q8aO2p(%=IwQ1E4Jd9||I^$+n zAjLAD+w6=hKD&GFhgZ}?*UK-o&INxR)q6-15 z3n2jACwHT#+VWc~(h--ai^<5cm)TNc_{D`2D27ou?n+BOn3j}=S)V=(;Y@1e+CNo| z#7c0S>hbZqG`XFioiW)+4#qmKBg=uq=dEp)?N~a(c$t|gNBS6~FZH41OVT4Yq!Zf5 zWqbCAbXv1>9_F8UX}lCFu{^y9dSV8y!cZoIOp~Z(?ma8_dc?!?3K+9(%Nf&8DI4)n z6WQ2Jxk8r5UrTg=Kpy&oUEW|a^ND^F8f+;;!md&O3*zt&>A7x$f2m28VF%9C8=)&h zRTw=ohGVB%-FIscXuI%jUX9bvuF`~Eo2Ef`BdZHy05!6D=sa0qjr7frT7V2_bf%4M zKWhhr>AXh77pKD`w|AP#!CWUOM*F3=%UgA8*3SvQ?X~xh(N!`g#YcovQ9XM5odcrRnYds3FSqqk5QIs*=n(zt0H1lSS!{+(A)Rr^WB%z2qk@9cHKAC z$vANxl?|h%e4x0i!Oi$>CBf%O_0n2|QHPjV#?GFl0rgq+mbxLOWN3KmzaM#Yqgq?F z<#0{g$+-d|2P+yKp&sj7_XNH&N9DIyv~um}kGgn{;_A%-H)4W_kpIMUi%1f>b8DF9bYt9-o2*T8R zx!AEW!P|Mc70k3^+YcOxnwKdzNXJKC6BogUNZAu3|@MIJhJ=Dvg5MQ z3%05a$}*?VcY?F7R`r;)mqGPqtK0zt$Mz>Odr%NQtupuk4lFM`END`JbS41ACzm>0 zcfL_Hdzz8%VzF}$=zD~E|2bJyk^Z~a;8qX)*LEv~@3yC9l^04Tf15HkW?3w7EsbeM z?u~%LsR}xwuyRO-%MTMRmte%vULJyNs{Nlri%*%Y85_4lScDT_Xyi;mdYsVru+%OF&k9=5{bJY!$s0iPfMvGWLy7$`Wuo%lB2o1m+yXdtO*>Ns z^$86Mi@rYCFCstS9buf=X$sIkLkknDsmC`jtt7xc^F1iCRomCNq&*Mw23JPZ#@M)Z zTA#S!=C;afpGgq!>G=Yt%d?y2c}-5M+#LFo^(8(=gYAeCIwa5{# z{Wcv1P9j?9?REOLfUQI|fdm`F+Hld@c7Bs8u3Mu+LYJo?ca*R88C;vP6$!8d9cyMc zeJrnclgJcv9@c3ca?1%OV+L{1rC7sUdfch!DY!mmIbgRrU+)+#Rg|Z~jP$H+J?X%U z9ML;=9F{Yf;)gYhKVA~=Eq&#c8YGA!`c_s(9tV!?*m4kD9ExnReb%*KI$en*P9+}0pS@?WH z>Z2rAB1>#=9jf4@ref|@s$&~*F<>@?Eof6&me82q)OhX~n`-(?=U(0Xbv;nT7+P3( zkB#N%34jF>Ec3=H!&{GD^>A?Ya6Ih6{g9mo9su6=#|j*5yf1(5*7#D|D!buc?gfQz z?wL6lJ>`*fUJorv+X+5|Au+nq*gM6#ncwRhje=&WOpeiTgP>--xw zIin#xXXCKe%XfKd?O`A%tDWFQa2T?H@=X@)o%Bt1-pY?~h<*Wi9z>!1o^5ozfx3(+0Ndi6K*Nx8? zQIs(tIHXpgfWH19{dW8U3F_e&BZ(_`^|qUAcQjwUyH5)IV2V`YFcXj$SIH_jsg%Ww zp_G-Za%)*f$19sMNcQiVGmVyEA&zS=AuzO)DpAQ0-tJH~z3UOs>VeAqLVlbgQLOcv2^T>+14(NZgJm8ftCGU(@6EZfv&S5C&t8&RpRnZNG<6zGy43OFihi_U8Cw9@l997_YZ zTfBF9)|jOa_bXu*xV-izt9yVg>vkOlQ6l;%w{w*&X*^JuIGXCC_PLQjwd!+6>1vwqZ5WTL0`G1htP=oxVpi=I3&Ai+24HMorn91h3q*b3&W2MkEWr>Cv&AR! z&K)>gh{# z3EY_GrKJP7i!LQVrSH~c<@6?=jjLo*1;v~n{*>rT9q50mbZc}=qUxQV7WbK($-}N^ zkr7OnRs$AH)V)|9{0mLSnS9toEAH++kg6=}zcOH|lK@?8;lqadxROywZ*scJ=y)i? z9@|>Be%xO6t*@G-F*_)4Q)9)?nFWR0x_qK(U%HrN-D7cm`JsGfR^;Qk!O!qVwQPWq2iHbpYY_T}c(X!Ht~*Zd{4^IH^8T_h&Y2*bvvNUH_DRcdbdUD84z;cuW(HNOv@nx zuq36)!YFyhTLqSwZ?$eUjSRR-?Nx3b>oC;yBk-+mGg*^ z!Pm;xNQaL@ww&MW5sKfvuy@78@juRtmCtO^9EL!*RAp$MLhgTl}`DOdU~k zEtwGAeZrDLwwk1g2ylhCnN?CZZkaiq>ap;c4ozMzdPF5+GuCgp_cpzQ#k3uep&L*$ z3Zh3n$;@eAG;asKe&e=JsHP$I{tIx0MGR2VpQ-2E_2UWG9Cx4h0vwgsu7GJ{Y=XtU zd@qY{=12}!=uGVuzm$mI5Bd@SG?4gmq{lyWAhot;tkL=kZL(s6A$YO1mID*rwhPanvV z)NZd@kPFPe)RH#YM369-1ggIK5%#?H+rsu@YoX{nU9(TFn_`gFvXLdy()5FKa%VD9 z9RQq73pAQM_yjFvR_d#z(uO&3$md1}ge^QgHUi`Fe3;7((7n+mmicl1bxs88YHrmZ zKVmVv4ITE%`Zb*isvFAVwn+gzipRS&^e(F<(df3b>~sbtvhN;b(e#*Q(3fnb@d2&p zfw`vcZ8eAyKOCjhvW>$mxg~&@1nJ2JzFXF^3nrS65j{U*+EU|$d0nQ~Ykq*neZ3bO z{4yF-L;Vr2zM&*Em*b1u*GebPAbFz7LO!I%Z7d6zqCGg;nQRIl;P6@h&Jca*_|h`< z2o4Te;8rBnwU&9rcPNo>W+>{DHuj*UY{yAmajQ;;TK<;|lTpL^tklzm+1XnRxYBr} zSZ;BI1K{Yt!rD#)NM_MTU2nxAYQQf^a^gmzcMbL$$OKMSq`x(dbTqYCf~K#@YHT8J z!KKo=16bmfc*DnxOPfrbVc*>t;EPm^JXaq;gF&IaS*^=+_9HiMR0-QW;CZ6Sbz~yh z6ps0htIqEhX^eAlo3E*(Z}qw}XnBk}4$pWrI}VK1<;Gel=bY@C;4X_#xUSpO_OBA7fyEAEEa6rWn zZU$<}@Zr101H}H%&s*EQ5$R4G0}0CFEI)XG$M5~6$A~L8(NzKM1;8!)^9z|~VUTedPjRK;1Ext=1cs zcjII$CX0AnutUn5r~VXj@GlLk_eLWt_UsbguiGfe_FraP+M5++fnX#4m6;vpt_2)#%31qfQRbXfTpO1P=mBwcX&m35PI9&OTl+KRQO?Gt zxg*5U_mj&uFCOqf!A4fm&PMu)>K!P_N*DB)ps{yf(6b*U)fM28sh}1XE9s`~?%_Oe zXz)qJ6I;3%=Nu#ljL1It^A1XEe39+> zJ%c^NWM9Z?&;VgnC;w7+W^}6}xBh@L$|D@d+dO^G6f1jNhOj(=YVWKCCZPd+FTxIa zo7+-rIh!-4pM>lmM5JxvPz)5mc1Hd2J@>gQC26M=H## zLQf2Mm3{QJ1q(W!MQ41Ldv&fqP|9bKyK;y2*Us!%QfF+#E>LJ$kUe_f6jO0YoAX`W zH^)T)YtnRL_c>0`1=D-oWM`jC76UUr%xY_c$(w&~OelF5I%P~10taINJ-u4FEV zfknT*#bWNp*tfh+tv_!+zkNi0TVhz@X#TvgaMWN6EgjQnqyG2ph6?$uGoO*}Ley;2 z4B|TDXtk-LVet)9p}zrKI2_%k$$J!-zb(|(Xg3_Dn7~VZR`;iNgG`6u9pm$`7^!8b@I2Nos;s1 z!CP8xWCx&hiGdM0m?SYlXL9=TpHBRJ7sHsX7j|3CT0A2)f9@rgYwLHij;$#Ec^_J{ znm`}sK#sK_OLs@IW-zT7qqV8hA>#re{E}`y(z$Fz-?^#dZ)C^ko}4M&NVhCKdQLzt zSuGp?s(3_>ERu#Bwj;?V67RJ>Kt{P8IVNiMPy~z_rC6IPds$*oGBf={HZeJ2U!eWNqJ%@Xy`5ZS@lAKj(+ZE7KR0jJoMd)!odR;s*zty@Nf~s_PnMX*0)GT84tg2Bi7Bh7|?^zG}2` z^JSZ{vQKcUawS276=5x79!5ug0t?<_PI?R1wH6fpw~KaHv85Mi==p&_Ow1!wgPaFc zhNVUzX_s+>Mz4jH2^-Zvp_SPw^tT6%4wFcN?qSkz4GoK5Pz7jDB8F3O^bT3iBd>`_ zZe=4$Q>ChrS4*E`(Iw9sb6X3SG${h7YVw>j4YVxSo*+PF9DZn~4~yWB` z!q>p(XUyxth7TTuIgb|2Qk&|+QpE&zNtnX>T-k>^L}r0&TJkr3pFrpfbX!1WZ?ahB zJnNWt6ouTSq!bgw0d1G;SG|dKE^A6aq^~A*18wM8F3Y*~fA0~$l?l}j_BRO$@Lrgr z{OmGT@`&R2t~K)Gq>+7ks+;kRzsM8SF&ab94w$C~F@zAtp29SyQdVYvO7Q4tQp?3e zn>yHI6L09B@3IY@n}2~!orFD7`Fkd}`o*?DfpuQ_Ka>0JPwFF_nNojVepLQw#lbl= z{#@`%KR~GGaJis`nq`LXcI`lvSv&ksFzbEs#2u}Bx(cZ@7m!plwh#Y@0M`EoDgF=8 z-tNg)ZAt0XVH^=T8#3D9gmZF0wsLC)N|uyswcFGnF|)atoccA70_Y-tkWDwmec`{y z()&ggcWT&vFm_vdHm?%#qC*qpyV>rIJ<&%944$9m;kFPO>Bo(kHFj|@>>sB)v|R`D~ecxD-Se%Nn-CV}Of?!o4( zXML>5|AcbhH`OVONHa!|_?e~MZOwIm6cSd`S5az2`bmcF;iR6!ozw!}dLOpjdPpMA z1_6e_6m`K`VuA1(2-bgAHx{ep_r&*^fyl}=Oz{2n`gm)HYb;nq3_j3J~} zhS}*)VM1b@(_4jBiY&L3zxo{Att-huZcR<>vFx7a>)L6JA8--}-)(O&IAOq4g^ZA3 zEhVPw*9}f}jBNd4`!%V&1p6BM0NJEvzXYwx)-IN;3Q{UeE^M!5T_h-A^`{^WvJiii zqG*1nu(~U&aW&Cx13bK7zH-7aK?tvC*+@tF`}WNbOWcLiy^K6nrK6tsJ~w45aK zH-y?wB?7Yj4wq>|6Iil4CRSNQlJOZ#FDh1^2(2g6lXEVsqP&snU@<$pPfN;YC_&f) zZr}Tn(tU0EW5LnwZJJ^bg@WN8(Q}|a)-i}bcqIp>BKhYw{Gmy%ot&mbj>$Fm)`&K=6xh7AhA+Yz61nUf&y^}OHc zq9TcJ(kUA1>eBXZEtfMdMILM{w#gcdj*I}D#qG4zHV|7E0 zo~jOC#+m8one4&QtV~y(9dun__!PW-aTMGLUb4WwDBGywkx~0O=fG)Z6!Ls>cXChJ$zt)0lcsf|SmMUR&p4cU=Xkyvrv zGZZSi7l0-@JIrUWWU1MP<7IT#PURlpF*!{^k#ZyIBWhM(0%Z1egKCV>Mxdrbs60>$ zus3CW?a-#urWfjU;is|mHmAOpaSEOH7Z!KpVI)(>3d#KB9MOKkyHt{tkD23+Z{9Bv z5bvLZ0>FrBk>_B-MLB^?s7Ya`#6(@cwS%BP- zv#u@maUWLNI{w7l#^qnbDn&)AEAP- zSj6-?U<;~;EXu@Ak5}Jb4pm!E1U?OV0!b)HWDDPOHA&>nhoKf85$bB*n&qQ;FF8ck zExj=iL&cu&Ee?`)GJg%Jwb|4gvVSQiExjnDzB7C7TB?=Z-H=bi{o#u^)3oD z9DymcuiE8^ z1B~nxdttcZ!y*T>s%KBpb4~rzE~{1td0Y7Yq*-APcIKVZSGAwH**_xF+6TfGw3Vh; z#x|8ov^AZB5Y}IPpM-4+o7V_%=6!lJYwt&+0Z;kteemjGEh~i9{&A#6E+v^_XdRr? zHo|bg3$!J3Nmq-x>(ky?9bAf{w^1uH5m;>T6*TIfo6c~hQYCFf{JGpdzfEY>usXx7 zjkP+2U{AJ7{r9$RBYsA%yA1|}jKr%37Yosxn35xS)ixXIvu6&UM*UqV zE#!&DnUaC3)v;N@`A5O@CsKymr;At9nkHl9hBrl^ak+f~1?oxKC`ff>$uu-)C0=nhI+g`7ex=cWSN_TJ=w+{*A} z5`OEYLzAd>z#t^w@vx(|j&G}~*7>qvM4Z)qtd`JYhjbO>vAWi01ErpUasEB^(pOaB zTYh%6%*Kc)J{TX@ABoo^_jtR2)6WLZ!T&0JYkMAtzj5oHm>V=bOY{KHF-pF!5ax^u zWvg9SXe#ega^6jhcub|*a~cBZ8RDN8~mn{NZ{Ril=wo2MaOKmBD$ta zp(%|pUQx0cxhsH0(Jp3+98Cch###p@TIm(9zACJC=<_Ej>wWR?dO(#pBr6Ee<1*SQmme=-fj_)MN=P@hRF;cx^AYF+>PuCuPO@0`euU20^poN_ z)6N|HTZAi6Qxd!%Wo56y^|bctyiQkl)#2=8F6WjrFZV?dgMhIIh9b*ziH(KgFN&EJ z#0rIic`X*|GB;K+?EReW2-9_j*UZ9KK`vQRC5^2k_-FX8A;s&NM*NPPd~s}2hKyol zceeFwn3k5-biU5B9_J4Rrt&mCXf1Jgv}tp(bISbM2j>#Zm-oO=L8~@la0lvya!uK9 zE1I373@8=S6|DP@{i`ly6TNm>DX)NG{&$x$R2#RUVWHCnE01aFKFGf#-_#vT%xHI4 zZ5CSW%S#rZ{GEfbY#)?^d+qEN4Eg^gr9@P_F8E7>bzX^b$qtRA4A1RAy|Hf~@mv6D;!o%I-*J(0bl$HjMu&{*RJ|nU;uf?!4pnZ{kpWxdZLqH_{Kt}yA zw7W;a$qaKJZc|+_L{OhwXMFiL@yjEs2-TFa+GEK03{7~?#$<7as>?w=JB4+EMa@7u z|1E(Ry&+fe7gZ<340;{Y%$6R~C8`^~YYRquZ57VpJ3+n{4V!ySDYFS?H-~X!tUVliTpj1U}`Ky6ZP+Y73e*hUdoACc{Gr|9us%R)GBt$H7 z%km&2jN#+Qujx4ziZU|Tfj7zSIqic@GU_`U^6>B!KWp@Yt!#8`+@c80X7p1ar;+j$ zlEdEzsP3w6#sQncw*L*KkuYd*mOAgfa<6N?BZqagk2P?=A`4@|n;^`Tu#8zd{VTztn%# z|L082{|^C|5Egnf_IA-AY0wyR`G}a4%0}{?=LsS_$+ui8tArJ^NC; z*MpP1+5l7QDfaF)bLTQ{rQ0t}uUbs)+2T7Yo%{+otm0z2UG{CuQgU>CcI&$-@JVRn zaL$xZ3+xxwDe&CgQClD5YWGc#GG*#BARC=gHt@QSnGvCFaBkfiia8;{n!98YliRTClv+lZqJsQ7WPdD>$ zqH;1%&G~TLdV<$x8p5gwDa44%ch5=xE3v4Qe@^!O=qqjG37b%xA=ZI2@4WL&q^hrvAQ?KfK&SBfvnwOE z=l!~w@Z4nnF2@4Dqp}`q1oG1i64NqVd#>&Dvrs7G-OBn^iVNn(j=P@caDbz z%vKAo%vXn_k~4owy8KI_Me6sNyd9?>Sn!(lHtc3AzAD~fNo^oiZy zMSG$O&LmkqO*wevNS|PX!6&7#4j>sb`{8D7EBc^7uTMujP+axp#E(SD%BBkT)A!VM zrK@#}2|u=!u$Vlp^@{5d1xs%Js_&-LI>m{U`O{|wi(-e5`)&^Cqi>5E#kJB@+dhqS zl~m4%WoH{y`)U49y%^aF(;}FhmKTzMxI(9bfMp4nm>lGpHsQ+%Nr7_;Hn4G^OM8|ab! z0};#<#zhZ35~v5&$k6rhidy5^k3#Ky_qC#Ed88bjzFWY#hSCDX{cD^~`!ssYZ{2qw zYxfi9+0h6A^KJTE0t<_}m3=zZCC7tT9fYaD(dOI5Z#dI~(P<}+AyAJ&H2`k2><4UOgS>#xwAZ>-)=$z-f0|fD z>XWu-w)O<1+j0NMkc!(lE`ih3S)W=yVmUcs|5)uG=%W>QMYg%L4{=8z_pn5a^&g%dv=dV$>q@Qz4 z9w7q1nqYwqm26AUtT}KvDyAGV@@VKaUc52}fz%rQ@ZDw*^+5ng;>e7fL^8m?o`9ns zpx$a&>f>DW;TzLKZQ;CAivcZ=Egwy$l)V;eh34;#nozX4!_r%|!W#e+kHFp7s?P;H zX$r7U)Y$LX)+aEl<|>SYO+-ODzKO`UKQ)M=A8%z`bT+hvp2R|NZ_%eYI~lDH<|^r9 z*FNBsGB=7>=|G*PmDOQ10lCRM`<%Wn^g4*w-tdW-BkD!CpGt#79NPa41P34iSz<$n zu_DEUpm>ODYR$vtgCJRx?=JhRYa2Bu*;iagk7-Z$s>5d~nymiZNV6QTH z1^%(`Hc`AZ+kx9;xm4%-?&5zn9W{P9e26dO>{cu+rC4UbKM zDxiIYFAwy!Oksu%6XtY;J^hv9PFJ7MrMEn=U+Xp5Y2#kkpuB69cR0<&slg(!)B7-h>1{E}KWt5C!IN$kJq(&}ewN*rdiRG6= zPHJv4`^Git2Gmy$Z>zx>57}PycTaQ>g5xFO_wSeTV)F*EG%llc5oQQJg18Sz*Izf> zJJm&MvgH)fx&7snb`U&~y3VGnFwG+if&&dXw}qHWBs*?{2L0RC>_A!gXTB4|9d7Fx zq$%&m!}wy8s75!Np6QB(?&}jiwyxM)jaNk{Zynv?v&wG?kz;n7i-e*gjIWNW&N(=q zM!{$O=-v9VTqZ`NVYZ(>=T;9=S%qL-GKuEOEG{>l4{JL|F^y|EEV@G?Jwb&JTpU`Z zkQWAz`=1pp_$i3lO!K9IG0vlE#cdCbxr4si3{v@R*HGdvFlMorjrOe#Z-Zb`*HGup z6oziH%AgS=rjM36Bm&xRrdxG-`zTrQ?#GH8A)Heou71AR{?7n9bII%&2N&VxW~5Ni zU@alQ$(_!B{EQQ3=`wvKx@nG;E|rz3Y-#}rV}AUWV^6Y9cEq&X=BV^&1}_!#@nmX1 z!2(3UYf;?mL-rm7dMUe{5Qn{A94?#CH6hz;=`UP5mU`MLy2jafoYQ?}WZoppiq}yo zI7JV>BQx`yjG$J0Ff1LhRA}wpq2}Ne!*I3V+sRq>_!R)>8Zaqh(aysM+SVz%?UwW#ZOBzN+=f*Y)apt}X@bi;{Rrw!~fU5C^l5c)@9JY70rt5u2b5ozasz zu0i>Sl`69_$P4;P0}yjt;gr%zBq>w14&kPDI68A++z)ZYLqvBrJJLMfXF==&exqt; z16>$RoB4GmCxfsHZ;de_~?2OS2avnI7lF3H8A;4!RcymNS%BsXQ9*dt6BZs>E5a1}KA z$5;CCY}#qOO&IkR0rfNXb0VBU=1Zu1eiGf;=HQW{z}V%8b@aWRTf6>BS!#n0L-Arx z!Mauj4`YumOB0s^q#XlC@%}G>i1&ungQhZD2MPEZyNd5iXR8&XZQ4#Sen zNtVX{i@EoVYO-J6M)46rL_kGAkm6$j5$Qdl*Z`#?N)ZAoy@cK&1VKPVK&5vO=}lTf zkBERsC!vPk0s#^rbdqpxeD>b&e&2J>I%}Oz|9oLB79_cUW#*b|X0Ab~yqwbDlJIhR zV@_w;&0Q$)1@-8*U8=S1=uU`qeUPVV`M^riDvxQT2RA6=cl*I(^?8@9k;k^6T8^b}bhL)aDlK;1aL)p=@?YlUgC7NJlLfvmW~G#w z&6I=ZCB7~tzL1cNRFikC)9m=8(bSd$BPkvI%r(x79=}E{M6xbnmWIVs>=I?6ny7cZ zUDkd3d*aqy^ws{v-=?xt>d;`r<12N-BF}EC(zkFrPIo&8*^9KO06=(rR9b9M^*R~3eBi} zk8xLC2D>nnruUgTAJ{|<&>V{rt$TkxX9Q)h^7wr#Mn87SH}j4e!04>I_c&-q1_X}R z3T87u)j#~ephOrlS-X-`%$vy;;Itv53R}fCoU7JHA8#dzz9Vw?9fG=6dt#7%9`!nX zEG*@#*LlLV-?9cM4K5_=*ncqQ&;}Py3Uk5KUa>xX@11cWl~m{E?SqP$N<6JkO<(1J zs7&fG-l|J=;=N#Yl{G)`6F7^t2u>MWy|(b=Jw&yzTHU}0%W~i>cQ%pJn0Fb%ah5vQW78OSW|4H*vby3Mt8!}H zA?~kSSFbclROh7laF7TJA4Y0TV7IvVo4$6guHVz_t!xD8#q8Pfq{W8kJPk~d{<0q$Q>JF)dSF7t=jIonSfa@PbYix@5wQ72-x<% zN$;7DC|<`$YDT>(0n-}_$&0e-MOsucBx?EDD4OzAHx6ntmlo+`liDN8AzYP#36gwY zucYpJEY@=+tt6Vg0k(v zOg;-*u$`7kyea-j+ahFrZJncD%&e+@U%Q>l-YYhwIZ z6!tqz9+-o;^}qck7g4jed6iPBKly;(>4%K{R_&A7Yu^}#$uQfW6}b@yKRh+}VOA1i z9c&~_paX7V5xv@B@I>zD{i4oon2WX#PeVtQTH4~yQU^hjwPR0T!#_>@Jz!#| ze*ZXl9NJz#Xv`6rM*4J64nF!-LB3mh1;N(yI(Nc#k& zuq%2yw%}u5|FOGaa)c{Y3v2sJkuC_85tE(Oq;#8My(8TOn^PQ(vQyd3T2O5MBIhTL z1Zs5I^`-lz(i@2tm3C>Yc=JPbDccBZ;cncV(o!Wxugd_jQm?|Y^!s{Y89PpeO-70C zQ`ex;!)~1^i}bH*F~#r>_;oi!5dUH3&~P`{UOrI+Ste>Rj_*>~53aCb1yx(6y`JM*gnHnwyBiA{B+5!L7tSB>s_i1V8rp*WdE=_tRK z-wsolFA#kceZn2e4C0@n&Qkkq0iu8miYXZ@SU34P-@oZKm>F}KqVP9|yArySE&`U4 zMo>0%MVNo^)GIo&!xl@6Z9@+8Q$QW?^$Y!Tb^4Ab_R|dxKSeiRAc(9}hWQFvf6u3n zOzSnmHolJju{(bQcIOEbSpeZsQ*_1n(MmCl$Fm2fStu^i(Nnr-evahc{o_TkhqfmI zf)09mxEWOBQld_v`suQjFNng^p2ShX7mb3$Bn_auI~Z4=qNXR>>#Cjgt8 z_$yP~p~JqEnX(|4#ei(1YT994jpP{5zq?8u%E@aq;8sJ0lwq+7l}Znrx?=P>&91(USvPp zL$~8$?y}f~!Kri}<|VZNgX%{WKVJjA+PG7uDKTy zbAMuO1mFWI+MpL2&3>;StmFg`;+2w(^=U2GyNbL!jMK6D7B$ys3eE`iPu zEwE_Hr+}In4=67b)~yshOq?M;Xp58#qE3q*J8eQ!$*IYs)hPxiuUvDNLthA-MM+YlTt@{`)-RjvZJxQEq7zlIu=dI6c1;UD`bfim~~Zl4{blL zZ#bOVs~?;Qvi7V&EqN&_1y&9YE-e;;A-k8?<=*}fn(}?XAkTbc_Y@h(HADIQy7PRl zFYa#*>s2ix_ZKytop&OuM%fj9iaVlOfhC#aN6n24j_Jh_I?Vb+%rmBxZwsS=TCIUh zfL@g;**aK_d|5VYj8XlzMgzJvWu?!oYhI=-hQfezMd}rkJ1yc_15Tmj^iVl;G0C~* zN`Cq})06t^FabP&>)zDWa63Q2Ar=*evv)CQ6mN0c?p!bCWx6vS%DkS_D-4L{sU8Fy zJ*}T8bLHz9=tgE>-Z_j5-r81(ZIXK0L`?YvZm7DvoBmbAa9JHYJQ4cB(H|k9T(u`r z{{`O84V}@bP*%I{Y-ZzoPeDT$CnSo5s&#{!+BlM}AS*YIBaS=0CRl8#NpHBCeud$+ zv^GTtr8adQPMUXry_u5*4nO2z2rPF-)ezD z3zq;uV-S%~N3{zcOp8Q!?s+qvf&b-h*1w?O6>@3P`?KhP=mXgIo_@pW6h-SO_MR>L z76L5|xejkHiEH0FHn7_L^7(EqZQ24e7S&NiUHN2nKLO{NHBn$SJ(@SL;=!W?r$B91vg?l}8EyaKw?T-dV z3)Aywq~L?A&5^TS_$l!_`v!DU^3x;tvt;ZiY6UCcFYMY?qFC;xWLIBFu73hOvilX~ z_5Bldy<*rWy?9YsrE~yb56Ox7Qq#-{x4H~*=*{F#OtP3!IySwWc~Z^(^|o93%Qu?S zsbY23gp@f>#vOS1KAJ1%OtnwD>H51V8%^*RnY~w3~r?Pbfa$|UkBM#zU3+DE*Wp#H>6|TfiSDaS07!r0& zUsB~6n%rC5+k!WjADCV15%~7z5ai9HoCBPJZxYylsv8(?9l|F=_AakXmkjg%8{ji^{B0&7S=3OD!slmBKQobeGDQsaifEg7rR&tQVd_ z@Fdmg+D(IG!D)wGLKd{6moNwQV9X$Ma#jbc?C!|J*t9-=qT>2po%X|908xC8X#>R) zjlqiQSYI*J!{SZ?Wd%ZmbZaG2c3cCe}Yy zEO;`(1&2B0#V?Z-vLD6$3*nC z#&tohZEph4XknXv-hMENXQ=2ClpQ#MCwE_hzbs^i{~_tOa#L}KC@EcuU|hh!!tyL8 zvY`OlKng)JHWcrDOMF;E-_r@P9FCAoS8I33B0dmot@|i*s)m_|jJ{G_Ev+wA|19uE zQWmCxOahSGX2{U|1LBUq1CWTIi!Frs81CmsT18eVg&(Qw%5@)dTl!_mb`54nK6U0Q zWFYN23;~@xU;Lvg^s9~)o}znX+(aq|9Yy!2WY+pe>O`Lr@?(B@e;#vHrLq??(wxB zc+v#JS$;zM+^b^r?=S9uar)RNlF0Z(pR_N&vlD%hphQZ`D<3UiVFBZOtfvJBT?=Rc z^1ad`hbX`i{rxbic@5vlwyKc*HST+03MQ)tDlY@TEFM3H0N%v2RAvbd(TY{!ikSM$ z%p)EshzaK6Ax4u~Vfh(=#oqgVUoE_uu3R-EGAJJ1t`VDFOKd*@FuLtOeJ@PtWmg<3 z$!f3?30E5QlWjYBq{+EN#oo;Jb3 zBU1Yh*`xdqoN7d?ICi5|VN!%98w~Qhm0dnRA*?t@h%dRI;|L)#^B1bVEWqsp-BB5M z%K*|8D2egjyb2H*yl|`|iEO^P?~>r~c!7id)hS`BU>ZZxGnDHB$liM`xhJ>CPC06e z9-ecvnvj#<0q(L7zwy-r&04N#IumGtm_)--5a@(xmAb`rL_*eX;%)_cy1+xUU@9ly z4})C4lCsU2Q>X(3%70B2Kf$G!eZAoYG;q{*RP6B%$A=1sUYcv<2tR%}?<71!A#fMd zH*c^+E$e=_>5O34>7aaU=MuxuHlhMt5L(mu?W-+iUUGTtc)p8`yQ#%QL#*}RH$7@i zh|QjfAdYY4w>+VQ?m7T8We5Mnoe-11VprbgMKOAdn5B{4UeYI1su$TPUzS{R49dE0 z_+<3!!RS?}cW!0t$kxPET)H$qRkkV0Byj+505BGo;44y+4zIpSVsAee^UEsCe6drIi++ zC*HAz_QL%&JJ|_PEY1*qjPnUoW;kxsSF0@KJUBWnKgM9$ESGdb7n0Wfts$N(g}Xb& zqZfP0-gT1OxjGLh8Gaj|l&s38N*SoVT<}Cc&jO2Sp*;Qk3@&l&$`iJ;36#z|;QH14 z2PZ6z((cRh(~l2?zOvTH(t}uCJU(!?TLbG|0_{9IE{I$dDzE+eJ+hBqk#BgxI9A%p zQW-KfZo+4cP43HWkRpUg_3*(PK$+)>c3HnJ#SPZil&yJZW_U$2MotN~yOuoQ$(?eT zBF?AxbvfDVD{q&%ndPL?ec&eY7OQzEJ_+pQ)9HW#-QF-Uvm0f094~nHs`d%uDWER- z82m~A;z**&!Zl$(HW1Y4JJ~D(LatWbL0Rll2?0VM^W-S+-dO0_3oW5 z$>C{0(qqM|S6m~@yLEsJMf~2O`ie(GRbO6cZ}!8ZlD)c_vi$6h?KY!-outP=KTJsu z0`>qp)o9GbCH3tgkP5D{>SC969PMY07m4nmaUq`p3L%(Lsh7EJrJlv+$GSq;dHUwX zfy|w8zUn{SIdLjuSEZp}n1aCLEcGcgK*!EKh8zEsSa#?mD5-UNb~-HRhwkexuXQMg zMPCwafL5V06E=0`%e**oYS!V z0SYR4^FEX=W@K5(@(u7FadiJw!nic9jTUUL(Smg$!VTM)cbjM_Ut6%R1we4>R-Tkz z@zkud+LM-g?EACcoG7Gc2%8`ZUbTjK6?nJ;6+PDw|4R2qYX1N2T>9^lr2ke=|KDqJ z;uQa>eZe3m5AX{6(!zb!^T3xpdCgq8NUO$KWnQHggV`=U<$e3#RC$J&Tocv-#=>J}? z0fiJqh-wWk$eY_93SYO< z|7=p=KH_w^2t^heI_Ot{_&6QnWDagc`OoVM%ao@YsjW9q)E@@Ar$04W8(IMSt!AHD zdV{o```j=z1^Zl~9}6FWu=Lb~oEEShn_OSJH#%q2Hv-gtTpN+Penv(ZvtUSG&8mOl zRrknn*LC=Q%&_|J8fG%7U*DqH=cyq-AQk5rMy1BU?NcCp3_B*PpEFQ{8-FV@-ZlPQ zVO^G|o%Y!uOg@x7gl;P&MK?M5PcnN9%~!P-IK#lU`vhkRvQ|%HQ%%*!tJ23k98v@d z+<}@x=~Zm8TJt}eDLm-cUTIb*WbJpe=D5o+(n%QQ}p>TFok zo%H3tp>p2A(wn;Is#^ivBE4>x@!ZxC{1e*+RI`5ZyMFSOdkzQPhC6V5rRU=cN2cD* zhqfR6%btGsWu{3Bj>i2{cUId=tCQ&$1M=o85#Wc}i}FSVd6n!xW98*7z;w|&{J6v_ z7WKK}(L5ZM>~}s;omIJpqoh4UIz@TiYSRCq_YP0P&*Z0$Z>&Te?(H>mZLNKHNi*?l zqOc8}f&S1kpU6am1@o z{;AlaUfC!N?eyVUM@aS)-m`C+>6wobEc3KI+6tjWNe( z07Z4pTBlWUJSDP!^^%$E;p$2p^^7||wJ1A3yRVqD`wTah=v54d*8OUR2JxmeUZ3{W zZAA~&7Nnau%V;WwHI*&;mJxwealjK&j?K%ye7}v6Gcdry+&2DC?$!10iu4yUmFus0 z!xK>o_h2OOu6*XPj)GzvbKIA?yJ~uUugs7VB5XU4?t1!CcP9HO(c|=ypY%c6Ls{XbYU-o?h zCw;s6nzd59Ek2+0VD;tFK6Yq|F5|R&#^BpCXG~QE5X0Z|`5mZVW-5W?s_oCdW)66> zF4z%#JFBf+fy?z%I>xHNESWtcyc)@CFg;9>IuwOrZkAU{g~nm#MYPDjwEbr-6(_4I znmRrKSwhh&sKdbmPD=4IjdS)Xi#+>J5QGY!R{us%K6_;(K&1WSkZJ{j)(E^VfP7LFEl&hyJB4&84#ST0JK3YJ^V zdXkvU<&HvLJEfJ8sAKb@_ssshGpg{SqRCr(ZvoF*NUJjw0^)8cG${k=t>>0j;(qtI zcI}l`;7MAJDgMl2C|Nws zGf`~gqN0zn#jQ~*4O@(M2ocq%q?}bkub^v|0P|O9TCpw3<-3%$`5he5{*i$5 z%@fy^MxK*7J5>qeOMSJNv=tQgA+z{7_(!r%n0L?m*k%vMY$UD>i65ad*FV4)z($4< zJe;Nw@*+6e71oF-^!!Aj6c_!%UgWS;IO^Ecy(iPI|V|n81nu_)BzlZda zCzSqIMv59IX~Wh0`Od}Fr%}?Dk9j#(RqBFbUM7@V5PB7_rt`j#x$!aG%0$)kR_>_v zE64FwY#B|^>lOFRFx*gG9JgY@l zBckFhQ-NnvFS|&JG|mC6Ezi{(hvByFRAYg)ssj5A3X4;)LnY>3GTIo^z#t@y9{TPG#(6J#ERJq6y!m_tUXzF%Qxd( z&izq3@bl=f$UXd}?w8h~5NRdMC*xp0N`2xBVDid6&Ul_=L5OTc7&QH@`T;k8cB`%y z^?RIc;r!8q*C=)!e`A)(VH1w2?WDYNWX{QzyvF>~`NBkjE(CfwkspznYlq(tm;PqL zXl^hX*aP>Rm)G@oBeB`)FD};BujN{G|!+T?9#H+T4)SU4v z4gN(iii_NYW%#uJyqMOs{Ym-giQ{Pwnc>wBZ_wb2@(HY55=|>|J^e$v&M+$TE8K<_ zE7${~yV@RHcetAr=wzxUY%-Qt;TSPIx{?qU0538<_At-?$hdQWJc1tWM;Ij@YLX~C z?-I@cu>OGB!gU;r)^^OtIF-h~hI3`;qG~|q?uqR%F^$;p_Og6tn%ll@AZEae!V8Iu z(`9;sykR6oW)5P&b@jjdUcJAQt>>`Awf~jBHzogo+FK-vv)`@`0QH>U+Mw9SWV)8B zk=xMr_Y=x&+JDH?J44LsnfN2=7K7O6NsQ8{M*zTNi*z65w~MzU74q|;oRZsw?kL21 zY?B@dH^y=I!F+cia8MZW(m?`{uL8 z`HdBj@|>80ilpoqVmj~4p?wXML-k^GYnx)`?ceg6B3%Z6JI&acnC|JEOpZ^tYKlDo`b$77b zKa3QJHosaT1mCM199}!Gto(-&r+PmlZT_F-K7JK%oVqv2wJ{Jp76%QRxf)k@T(Jk;`9~wv7flypx#WJ%7(=c1n7Df z;3?U%*5jwt9;~+K8x=~Oobk;fQv-uxJ*-l;jPq0p9TV4R_8h}qf8*0mT*ZrCa>@*f znR?^;lRrFVBol3)9luG@eP_9z&^nF5U`?>uS=*hhnE8P^uL3crfuFa$k0jc;d&zq) zOUmWvMRKgdz0Tcz@tTj-g6o{^X4Pq_EHTEx*9H72?}qVb-&)5DJ5j4;;f-xq66SHtq59B1%1YOcgn|BFq#~)#Qn0j%wu>f|XGq<4MdU~m2_PU6gYwxSiB25q$ zGj{*x(~+9KaiIFGPZ55N&Oj(ohOgi16sP@ua?yT9)e47y9_*}>BcEg+C-P4mp)^(Pj}=Ct`CK$GcHEkbJkxdElYql*v(k5N|8viz#IkkI??Mw zKyE7A8H5gedin;)#PNi`8tFEkA40m`Z!(hS$b_fl84?JEz1eFPxSEE^FZt8r>C#@$ zo>JP+(6;dOHdgb=nUQR?`sYI^=yTR`=JFe_w8*y6{K|uB!WO0BpZf~{($m4f7W{TN z7s=DEGi2yIS&Esb_^+--9qy(^wPZbXW2`C6gv))m9L}d$eP;JpenL+ZmjN7#Sde|K z`$RGsBV1qU$>R?XehS*goW&)@?mpm?j<}=z*@S^7JhGNsMJZg|{4WJrEmpN%QV+6f ztrT2j7=HP=c*uYFyNX_>v<@b(UMA~YJ56UelW|nJo3BSCJCJW-96dAwZB%OQ|@KQemH1_*RoE~>dP1*hjnwi`v z`hDk{O%A(`pXO;o=If5f42tFN(#8L!Rg=|y{cNj}PU--HHlR)d;8n6s z!ZA}^8w-~Ka)rfVKuu?wXDH&%Kc5pM0Z<&;ifk_&Hq7~k;)7A0p!M2koxY2(bCdbl>s%rA&B>6F3=RZn&D5Vh&d~9c%sruW3RmP z{PFZLW%}Jqgdp^Fwez%@A;dEtD`Qal!ph{8GIc)(+R0P~uu1>Y--t_cMo|oE?1u)2 z49!b{mQ?$h?{Dy!!dRz-K0(Ymf^m0@~f2W@3 zRTve9z6Mp67*%|6b939Cixjo*{Cw+TO`}#27X9@JtLNJ205r8jCrPXYdNfpGj7GSP z(3TsNra;dmj{uT}@4Bw-M+!+ud5xJVHrpbpM_oMi2USqKl0}tBO8pb~fme*z8Mn26 zZ1Nd#D^=hmC?FdUwyRTbLLy~F45Ej{Vx=)k=hKdsh(dbD8N)?H6e1deEbky(z z_9Q+j$u``LzNlwgk$<1JM|pDjTJ1o!oj&$lFBn*HL1Wg5I2Gd>;x`kK+z~aCiM5UA zoZ<2A+dtzpI+a}Rg(IB}hsSGvn`^FIVznHTxQUNfV$MvnD4}3V+oEYkCh)scIA# zBEEt9{XjF!AN!el01W8_QU`MJZB`e^xfnmLaYR^|gPB&T{lfIc-`Qz7PF_C57^E%c zbCZ|j3ihatIqq49^{l(&er_o9fNU4jz3t&2?*3sM zZ$~!}>bpwYV3eJa)hOAiZx*fOTiW9_4mhf`m2QUb5+@SsW2NyqHg*!#{+><9QAnZz zJNoTah*R@{HTWiFMF(CftP*D!5tuRC_h65HT#-d-KMVTAqWwdK@QLM!1P+eM&Lyd8 zsFvbE)%f8zwbQW4{EEC?+X8i>Vs4ZBl%DoX7R>S{>v`hAfHf>F!>%KaJ9emPDLZ_- zr;WqGsr1DQOii&&^G0wg1#*Fvtj(u5&J>o4OR-C`V_T{_S@#Q(onNSnqVSdBwcVs3 z9}lmcrJhu%kOZmT9oLIsy9?f;>`kwJknH_t;Wk2b8Y+qhjiuss3ANOAYK#GeaGm0fO(E27 zEv|)>cpk+pmz8_jcklUoZam)X%31T&UT8*bs>&AoPqOORPA8hM*iGuu;qGst$!iUTxBlS6zzTf8RrjTC*W(nfaVQqy zi48Lx|LIPs!;L3wx3VaY8uSO9I_)TA)V@$uT;_Hf6V}NEpLs(+feD?H3k3ecu%@GeI$mJ_o(9c}>Ysa+&9#Uq^Uh{2@1e9_ZWcgFhY?JTNfc0bi6pWi%|Lz{ZdM>(mbo}46Y2>-Iek2(>%fiI!h zWUIS63Y%{Mx0rK=k^PYZe|tP_^BR7CL$7;r+u!X)`(d%Fjh63vHu?a*6mx2qo1*xQrF z9g61DekBwe4Md-zNh=vHgB1UR6g?GyRCLgwl?1B1aZ5cnH+M{YaKs#5O6pUdW)4ku zgz6_^E$xtYXjQdnTGk-VmlK(b@S?ITePf>!^m(?wC0YjKxpeVao zr=w5~vwqm#WIp9+uc1{nS3Q1$Ynp!s(o<(GKgRv+3p&UYy(;y8(%0;eQwh@;eC$y%p3f@vFA)`6}u2$ z(M5(HnGSiIRe)cfO_9#FJ4n`a(H9C>+?e$`e{#?CLm7;YfN^ZcRO0ct!Oe0Db+lcs zpw%2F*sBD3rYB7v&Gh;zf5k7$$kdldAuLME(UOgW0`0`WJ#eX6(>T+IR5zg|B8PcE zHh_TA;(*K-&{uxrEN>g_cX$!{{_`S0jgU5Z@b<$cr;+Tm3C@M9=05kQA^xR2=Zc>p z%ciLA4itQ5%RQgh2ao)9`m;+-pc+o?UOkbbh=;E^J+u(Z2*j z&@l+R2|3|)bVsSq$+f#iRitdAvwMYf!0W)M32}$vyV&2UDAp&j41~nAG+@~3EQ{A; zE_t`F_9JCHex+rQhWZvKW%Ool=XvvL+fPTb<>QmNo#qw*MoFtb8+>F5KK_scDnWS^ zWeaf`dWI|7nN&*oYFRcx^-~t|vmbg|n#=i5&{nTbx`d<_HXY)6Jmr$avboqCXs;$H z%R%Y_VewVTY#9I)sg>c6Wc165}T9G7m&4xoKnAb z5&^!uLC?(XvKnY(Ltp+%Asy`PC5h;n)=@gR8P^2mb@*%Kpl z7mQqyFda~J5?Rr>NHhR=deU!#pT^Pt8H&^k-sKgPmVSN=Jis3i2)LnlxAnI2l_{M} zVYpn^`F1C@z_nXtTv;mj*JF-mS#%^Jai6|dFv&T~oK zURq6^L9N)LG2G@AuR|LY@>X1M9R6YsJunX4tzuqFYFNoYP; zx(W$ASga@1uS&i8K?|cE;D9g$z_4#6Fg^2hEWB%os0Ly)77=_3-dYUg*J-q&v@MJ; zC0dUAn-lINirREM#>zMjkEDZC;;s}vYe0-Q?xs8~Ycg2;9d5YVy!J9Vu09@L^tA4m zn*dc?JSSwhJ>`Ro;szsrNy#_0#y`P}XUZx(jdkGb%cv$iEq$lsu{5hzQo2 z#UaD>D<@AXz!GDLv)#A4 z&K);y;9}hE=6~uqS0k~$JT@bP;5B7u>bn?EFb9s7{f)C`XA7B%mSt^1SACJ0yM3n8 z2ooUODMXaZdg@#gNa}%k)l^NQ0_ox80mRo7Nd2h6=u)=}429^d)5s>n&#Fcujf`djzli$OG z$GO$qz;gCS=*2e+Mj1YH43uTl;v{BaY_*+52YXB>mn_LfJu%?QJZNzl5Mlp5Nju$S z_5OLi6;Kw0STsE?A0r7&5vg@bnrZG#$dq-?06V6=>y-l{#4&eux)w(L@-nBzUmX(@ zMfE0$N7d5Pg-79Vq(#UJ#p6c&HUS!b-FHz}M5`G?Sw;4Z%=?vSy1*}xs{z?>Ff*|~ zO>s8GyRYV4#{L1+OZ#lkic{?!-~QjTt>N^>96!Q;JvqmGW6sZBAsAMhaCB#`&A8Qf3 zfShoPG`X~hQ$DT(_bP}O=qjglUfcV5CmXo`F2JK`(MxpPsdMvHba!Hd9FJ!{lXvNl z_H5sy~=d@$Y3xe z9U2PzMhJpF8Idl}JJ+1D(B9ZIo4KE^zs`+)Zy9*bR$+AlQCoTqEx&|R^jlt@b?Nz& zb`?nIOmPBmacTsmLz$`voX^s$&t%dcrM#HrEhmTLyirH#(9ZQ=5(YD)v{_ASgtaxt zy_)x3-5rdgjTbK3%G@#uW8vdXp(lE3ab9K}-3uUZb|B)hOtKR%P3j~Yw7z5KMH8O_ zg3k^jibte_^Du1<&mC8v>#>81Vk<%AT*Is8M?>z~~< z94H-I$MyXzyO^UrxfV6MvTK(BD9ZB@&W{Wl@lC+TP@|89* zyI*t107?chErTC8B{7Bi0Xbjx4qyx}jtw7(j{#PfFEVix`nxnqg1=Asxbcp``2<%fo|k_2?PKc#S8@}J?9h3H zZ?mGrOOc6VJWY2`$`FO^I-+?HY}O!>l=)3e!NoOnCq^2${@2cCgumUI&Flx-(maF$ zk4(Uqs~5hQy?`IqjR%UE++bgO=Jn0($=i5(!+N;G^O8mCPM0ZXW8Y&BZ7vGJ%1Q_b z&#`63b&b96@t566**z%@vPqwu{#uhAYUqR>Q2-}UCA_kSI&R`J^G+{%G_->~JY4-# z`8M;Yes9Wu5|HnmYTo)SL?~5>WZyNj1LWfXW?%$GmHuLe=xi2w$BmPSv#t-r%3d_R-F1sU@h!@G4@mAJTjCYJS6twFHO;ty?*#j>z(ubEV2a-Hw+| z0wRKW)d#citT5Eq-vGv4r%IPw1@DBdoJG^lm7}PB-afg+dcbO&AS7J2YUs#JWq2lFp~a`v)A^-S&hEb10L{{@@#`;~a0Tjyl?F@W;M zMXL#2gkuiwn^MFgzM6j}|3LfzLeWL)&jB%I_ig*RTj2Gg=0l(M=)Klco_`K^0xCca zf&;x8uLi^?etjURM_)-ab&II?TwSsTrkPQv$xE_M4Fy2ujYsiV9Vx#2PJ=zytZhb??ngqg)+Q~3Li`R>VsAWHH)K!ww_3jO_v{m`U%oE; z4v^h{d4aaCHM=LZhCFN%U+0+2!wQVBaV<*si^y0vHQ6bq1DlHjdhP=`({ClOF!}ewZt3Z_uZV0mG@^(?>XPiLm&m}clU0@D9mZ+ z+Yc3GYs-VZ32SCYKAK}}XxDr=0KNZMvavw9fH~y$oJNh%9rx@A_pPz-)RHp$wyneR zsvo!XKdfAp*rATU^!?PGrny)C$yD6?0=Yjy7_pd^rD7EfUl%HMyRU9}A)xP*;)_q5 zgv+=zd)%nO$Ijl3K=m;o zZT=c**e3SS*UY=fnPgkV|GIQDukpQMWCMYzH}W9q^PR3eI>}#G`3;^GbG1ZUDCm>} zW7fWcbsF^Jf2&L>1EX}YpHCQM?73pLAx82n5bOyp&wS#BRY+@;Q{%EbIM#O4@xGb#TndN}aR5^js77DKEN)LCK%9JL6UFP8cpfGtkY!=IHbktki_C^y@r3eB4!ll=pDv zW%b!>B&>R%0IC_mmI_zO0h70rM#$S}U@p^+nQ}s;X!GbvVe*#hg$a<~{x?6edp>nL z2yjFW4M6E>;;Gp}U<5~4y1wL>yT3o>3{sBAaz&Br)fPbX{dRSclN0EXu*CY;+l*zj z{_b_mLw#_}Fp zBd_N$j~S}RWfXj_Ns$o5fX_bjMuP?xifqwn!NW;pE0ubH zDKBM$ug`YPG^#0Q%+XuloxgAm)R}3Ek|V4&Pc2F)5ofw99t5fvf<0#a?gkp=P6f2z z6s927np7sLlM(m&PvearIFM?99;#)ofHpg)BRh?K90#zY>^k=(_wdcf&C~74S>@tZ zi9tUy4`YpwYo|4i`+F5oGU2-q2-ouf^=+>~obxSUgQk9nFDg(dB9^dUpZL1S&(L_P z%)qx!Y~i|2V!+$#K_%w4urvKj`aRmp(I+MLJX;c89DQUs^ekkur5}BVpt`&Xx>hX* z1eSBy;#wa#?C_Q1vsg9etlcC-4f#fwTXXsiP;t9D>Sda*xa7|0CI~P@9*$ zTQ~9y>2fYol{QtbPiM^25m8|mAG0ueYhs-EYOnu!;$cWdfn0m5-wrEz{H5n!ZGFvQ zWTAQ~t0OgNPXGm{wy4MAAW_X`DM*ddW*W5z;?}GsnEmm*_u!>cJ<|tLwaaR_=vWq% zh_lKZxhLy;7YG~#ax9d1RtZ#ku7L2>T!K^MvEGq-W?lXkk2IIOY9+gSiK?F%K|5?9 zAvG-$S!mhe%H9si;Ztpsh2V$}~}TB5z-; z22Uwc;H)_mTqAK-Obt(YuOi!{^nsJ#AZ zDKlFX+{(RmdUm{ZI#9Ofg#C!@@Q7TgP*uCpR7tCKuv@Ea&}y;e$5oaBb>;1)Qsao< zt?0(*@;bAVc~9+95BpCMKnlY7(OtzVpdvsjaqaXRDLWm2bIn*Shj^kLjt3UlZ#{s_ zv0IPO>hnR7Zu-}9HIR)E1=OiuY3)Jyex)tYHD?foga|i4#6gP|WS+!ct7&;pxJYF? zKWMjOl4THw!ClWnlO6cKQJRdb&Cr0z%z76SgmT}kW@LgWo+y4m;+y8Cwb)Ne!lOpA z)SRqKNU42Kna&ni^4aynglCfjs`1M4%!06xG zd9rWi_uJBzdV6Ix+U2&?#gfYH-Qc_F3|IV}v5$d2KsZ>!G2rn!L0;+rhtA{6H4Hs( zJZM34$k~u0`?%kD-!RL6e{&4VPOO7`dK%3vl&!w#WkMtKj*Au=fn6+|gnx(S6%^(h z*Ie}02a+wpkw#1UFJnJiD=fF!@mD+UX&UfQTMeH!+?qOUrcW@{|2_kXn!c;Nilz!% z(bnUbZIzIBMx~bbm=K%a)!G-Wj|wf_z4KB$z3Zusduo;jUqf%|WLOodD0f;(;5BZX zW9XCHtWu&J+S#0wywsyaFNlYE^Ut?q%PLJ*JsnJj2fRvcTRv{o!~;Ao!Q;}#U?ZO? zs6WJ?KnpKDnK6qlH;v}iZ02_6Ao0!OS{aZLADRl1XM>NpY{^oW;-v++%jl%$3NS1b z*88;xv?6%@ayQU4PyZ=S&weJbn{5FMGtm}+EtDx;hg7u=%5}2f&OtI_J{l5wVFF4; zd)8m#To$s-19I^#SsMFKy}CI#Gi9X=&;OW=3MNZ8fSSCe*PLx9iDQm@=I47MD&q!g zxL~CgOdA4_UNQ;e=*H#kz9(!jX`AY}cQgi}_<;*C(9w($idSH~_bQUhcXj04=B?4| zi7+f}^qj)3^>E0470s5XK$09y%=e();|#AdQUaUrzCeY-F=>6-ig6axuwaogGfhr{fz_X>Hx3vE5_>uo)(uAYHs8Uyq@_=4lG2>vFB zVb-%9IO}eAHQPmHLd{=ndtt;qxuIWa02i#2jt^yyrVD)RPPrPUF?B6=KSfnG$)cJn}5%1PG$Yao}p9Bxfw)AobmHn1Lxn# z&P@z&CC9gZFpb{~IzMTeoy;w;(b_fzl5Ms3K?_fvdu@!SdpSu2-FRXCG5$N*$8vS-*fmI^oYSkPId@tm-rGDi)JONu7l~?TSS1z%Jf?;dvn>yjFf`emm%S zm%(GdHO2ge>f)xd@wOlRGyVzT&fuO0U$Vx(5*h2oOEoWklv<;yhFoo3!}>B#P~pdpf0BS6K5w{t6ON|b6eP6r6=kAVVLIzXX9naY)8o(&@S54y&XmC zC$G#_q%2qF!ZEfT3(jMX8P|K98`KiTb$J>uZn++H46`WU9n6hi|C5h56abZez4W-J z9?1zDs6i!5N{?j8G6zeprc^Kc=^Wg)CFw;R7O%Gu5nd|hg6Nly6~hWmqyG$0!AP>fO%Bemj(Ds{|HCLu(yEg3Y$FK@SmaoE8>E4RYSyf(ljBS?C@$dy-8g;6hJSQk`QAsC(lIUnM zheg6H2V>*S*Ynd5ivj0`#!)CMG&25f&USE`nG5ef&QuX9Cqe_C`8AF-r3l}O!rY)O z6hBEpLDJ;80@vjLS){s8>jTUWm$G6m`%^7OSIfg69Pke0!DGGzV0d{}9ShlC$UH&6 zH1V&X^evO)vnrag(g08X!?aOPD#BFtD}sD2sFicUNeGwT7n@h=^Gs^M?!Nwrz5)Jf z2a(mELNThu*+(U09v5&~Yga^YqfR0n70)tC**A-@AEfL9koAmS=z&b+%bQnaAD^l>BqF z>s@L#(t}O_)H81KdSF>-!SvFyCncDGxuw4cP{!E#icWo>btB-A+<30RfTj?#>%)!7>SE`ypGvu&NAXg9E#}Egx51Zl4dPvYf^-iSQe|`Ytx`$HHrY_@M zQJ&Jm;G_6b{BT+k2`2kXFh(r0-t|0PGL{iYN`9|i5Ocj`WL%>WB9!EGv@ESMSdolm zYPb+=hxx->{q#nDi<`dF$CjealjNu>^v88(L|a1q!cRMon0$2|_S%ZFpr?H~`Y`RB z(_W_HN-i}42L?i`$9^kSaAmHkS$OkT%Zr>6vN_`Z)Kv4@3aGuORYQduEN=X?An1#M zA3VNvu&I6FVn$xos_}-rXj=-`d7k}6w1^4k6LxBHag<$pza}Z-5EP zbQe%pS&>a32jx^752vGWSk67ArluAa71aY$JK=Ur^%9kdiHVq)m@G48jLX?h0H{Rf z9ReTUw*YMFyb`U5Zfi@?D*(mv9Yk$UN}U*)uKqn6`=vD%E%;B#ttuFZx=8ZU=1 zp<`<0>h?wu%15-JVOWNC$=O*WrmB8Pwc)-5=|yo#byT%z~b@R|es{ZW}Ze&Gm(QWn_OB_ksjpe|vb3+uK`SVJDxsGKxiS^fq8 zYd^&Uf80T_S02e~cl1^7HlwI<{*XD^Qo6euCxqqd*qj(k9<^ODwE(qv^J;4r@ur$b$K z{I8Ag?Z1Nui77Xr3U&*Nk&kGRcF4&ewxkef^HRvKI8QpfT$4?@Ygb(gPbteSSh_^S zNJR0;mb~JEHX&KkEmCZej{KnGA6sF`)R??uSK#p5*jmJuc34ZVVNj|I;ayJ@yS>(R z3rqoD0v7B!sB?NJCYE>$p^gI&P@q!t%;2C*dqf;hd8RQ#@;v9!>7-7+rDcg;Cr0^$ zEIt)3F0Lh@qO<{ema$g40Mijr`YhmfQ5eF6t5m>E5q60ct|-Bs*?P zJ1Bo+&ct&et+S(hI zaG@tXD{l&U$Nij%*z>{P%IMAkf|c%y;$Vo$vcau-wNmGxT3GNvdxFdb*fU_)1a6LI zQ@notVK8`lsC4)*kc+&4+bO>s97vm^Ay;E(0x5;2c<#+{S5;Mg?u}s}gfSda0c)!g zid7`2%zbJ0K>=JWP@CChD>wUVG6WHF6z58wYD-;KSmcX-;#V2SaHdr$@W^@RGQZ-z zy=ilC*)y0^Sw?E8os`SbTo*kRxg+K$3GF0+u=0@fa^WDJ6CJ_Z$!kCr^Hwx!V1P!; zfKzs$i)M2;z_S;hqXHw{+1XL-sN9$;p#V80uVXqq-SPhJR<72;;*a^Xe0y$O;9SHl z!!UJLsP!~KnM^7_m-EqYmn57v$K9D9Agz9!mqF}tPQ%!^IMvq<6m@o+Sab$~8)>}M zhkb$i|O!>1w}w{P8hwH9LlySI(DiBrve(-U^5 z3`5rHsfCZOQJx0-`%C@SD>k1lb#X8{TxZ6_bv&}N1k&Dkp*X0}AM|rB<}8=nnKEfs z$u896?G-3IXs=%}CL(^Q#N^AeMJyPXqAwp1&3E zywElWVvtXPt5Na%9MtIEJ0I!WZBIb$11ilXrP*D?hG${`huDxilR~jm5UnaS{>${8IB;5pZjkVvJdfkN$Gj)bHFm!e)0H>&bg8*OEP=O6AL#bw%TYjBOe@L7+f&Rf zs&F-4nSV_6;^$OCimht{6_%#X&L@TH4sq&Hl*2oX_Yc%I#8ASoCb z;ZE}1o`mTE%|VTyV6NVk69H`@wI#qBm!mn20a5m^ihh8Yw76~rz0QD&Xlgq_}*BiPHY)IZ}oE1=D|UxSxLzDL}3u%tdbCI zj?-|isDW?3+phm!y1gP$>=d2nFdq8QelCtz*_JFO+zrV5P`U`3edABvYBtZ+4j`hP zcICL9?`@sh26BfZSGmoDI*Ph|G9s!D?|vbcV6JSG#1}45&ouH<_<)p<%=b*x%Bo%$ zD!u#{3tAm@41Qd`eWz~~{o76wQ|&U?`MAKWR&i;>dwam%`egvch!_U-^smtVlI`tSM_Eyppt=tmLb`33<8rjcPOvkZ6=m;?m=(#brzlESR`O$JX~ zr`ZKqSmbegV&AFxfURJlAvI0d0rfy^+MLhfFCH3T_w}vUkdl&aX{vBEvsGKeeMqON z)`!yVHb>$>)q>6^v1@@FG(;-?_|LkOfjqNTm&hp^U^#!%x3Tm68J7tcZLBeN^`k%F z7`Uy{A@IW+qDYL4j9|Nco5A%2$tn-c5aduN;QJjT`abtGKynIM4)wl_!~Hs;GMa zohaJ=+bpaEeu6z`uKOa(o1-p|yUuti&^wjbS=X?7FfK-RK_tbpjhNM~WPk_c8khC) zkRA5MP#%8Z=7fN3fsMd|f5QOHTAC`+b1{6oUI+A41r!Tf7s)T0cUm#WdYg|L$8B|; zNlbW{ai@VLBIt0XGvD|lT^#sY5Qd#fu#=)*EqcO4KY9D=RluF=N^cb3ssHI( z<30q6oNOLA^W4QH-En_`j%o<6I{gS>`U%!0VEJn~*&IbgLVy1wte~ae7ZqlH380V} zAD#_&Vx>bpWwk(!!jDNRZzve+A0|C_Dt-D7syc>gKBEvZ+w3|!KcCE31LCr)^7Imw z{7FndE2WHP;Cc`~ld_6D0DV)2s{#5xlAM=9FCgDTNqBWv#j5cl|9#=B6K!raZi& zBGZ&%z0c+>t$5)(aWKJ3PF~suQd0U2J_$+4-`-dR%FN42*5y)(@eI=OxHO2yPniZ? zJ>H^Z?usF169u`tP{43>xz5>j9&pcD^E05F_06vdHl$R->k?5J|BLV6`9wmgKLvm2 z3MO0n}_Mlfs>&feJ9pf5G8T zs8W`cT=HT}XgvoOb_y)`%yl+juOjJih5(`))-6R5|iQW#?B*D?{BFY%UJIJVHTv12B3&BD!r1*g63ZWykiR z7A_G{zJqGE&qrMu2?FV{NJh;MJ1G#;etwc1+n4^wND>ofK0VswvfbtKMK3(Bx2#_z zS~!uYoVv7(4r3@J#(vMn76^Mo-XpE3h*MWrcd|3EJg7%b$Ec4ju{oz*s{gFvVj0bR zv4I32{^H6?6(Ws=f}_8^`IC_skqFoy!n{3}`_Rb9D2iSM1E3mFQ`0=UpE}iFQ4D&b zJ_g}2oRsCh?;1?)1V|vN61+2<`t+|vYTEMWSNBf8ar%;Ty%Qe{Ua(m5qt5HXO9DSc z^6#CjM;ry{sbc}c6nN?KS?VBsd?#BW2`be6i}1b6iLq2Xi-`RCsSSx;qa*($mz2Pjgx2OncASUMD z=pEE0K^~7xRR$te4vQHarn&><3X9pS{r(i3etafvb0wN+0vy_^^R02T{f28s4)gbW z`9cU}bLp476lG>a4Q;7@As}p;#C<+XLG!d6pTP$p0+;rg@iw-)h85EoWG6L8(RbU5 zuPj4vh<*JxK21H77LGc9Tl99oTAQ9^8q3D!?#B7lDor?jN**{nqSup&hKGmqX0HKM zZ3o~nJR%}}pE;4wnPtIg1s#&n;+2eGi9hh^e@2;|2NQlvI9}U~mz(<~bW!>7;oF&w z-`s@B!P@yu2DDy5;?Ns4BtZ4Z(`!3Uymca}po+2QKhW^4x5j93zv-G;eMi8BumTd6 zq!&hOySpKP#4TSOu5j5be|PD3*qzC}Ufmu@fh3|>BYufn8{OOaD6AI(!81Ylt+cN{ zz&_af-p>|)`DA%fJ*8iVNgUca`GcIC){MHJv+&^%Ta(BjB4+p>>3n;PKDG z&j5G{M(7o>cui<18q!P|z$PLf=?u%*N(Rb=D`noIk}jRx6D*{9o|#w*9su6!iS znQG6*&VaT7b{7#M75BL6c;1%Nsb61T>w!~BT~614w1UjaV)2?upP~=w;l!s~<3a%7 zEUm8o-v8ASY(w+!aq~8B##}h=1wT&Y*o;^E5w_Tp!P>bIA8+SzfB4x1uL<#P=6oRF zFemW&_RXpqiBW$=N<+Co)fGS7`m;d;^-Ffj-=}P_n_D6LN!`P!9b0K=C zdz1N}7$$FhI2T+0OOzE^Kvs$XK7`*~9uu${J_mozRPp}(`)xUVEl(-G*mhmI zeACd*j;*D&^^_u~_MpqL+LURi6P0!e#(_LPnV(Kl0>mMa!`&|9eG3>g+k5^Ulv)QD z^`tpEEh3A0Q87{9AA%j*1!`r1a`j62OOv^gfYc86e+HOWZXrC_vU}UXri4GN9`{Hc z0ZMJCkF3gn_Ok%3IS`=6bctxXDv&AROG{~c87(3Ief@%#qTq^BELSiz5vfw{{n?1d zAP5!Pk*MESOYjhW|9ojqucJK}%;)1Xw7T>W0FLy;W^%+AmXwtNY)b`AXliX03IWC2 zd`owCcezFnclH>K_*wY{>j5H=-}=RW!ub%@Z>37bsuD#026*GCw3wK9Ya2vP)rMcY zJxzaY*O~aQgKT6{rAPIky`$P`r zehNBPfBk#%T#PwsWg<@rjaoWM)^_vGa;o^()_eTYXIbVkw8_hYH3NtiOsQlZ+|bZa z(-2g$|K>SEAAH+HChGJRo!H_F^CYDQa|4Vdhtjh)1J~j^*6uIoLsgpm))!g_;*zg0 zxsUg!F!>ABL42BGYTQ8VV*p~|;KdUCBtOT2+jM=p?KdTU7(I8 ziP8GRNZ`Y$78G7N{UV>DkhRewm(8P&l(2noF|3WXqd*ve8`E2QN)vhCy!jYb8bNRN zj(0GV;2%D^46~tWmo-)Aq1q2?xlt%FrI5mY;>vrHvk@BW<0jkDU*#+#;ezVWzS9z> z;?Y(hS@tu^klzNjs{V|@U46N|34gey_J?+PMZSqb+YXy!SnSR?8psJF0O$0e|I2O3 z2vR?mBbQg}3Xn04QeIR;XM%8C+%l9!5(;exeMLDO?Ks}v-Z?-|>@Z9`JUsLd3~T{x z1rr}XJ8%v3d?@Mg+NyBlk|LrRIb9vV<%YkJ_>Ya*vdBUw=s)e1$T_(UveX^esW^f3 z%zIsc|4dV?#*216`}5{_CRe2K{4j&a!I!_jzY481l!!U2Z&t#%c#MCh5SBN%;D%C4 zYydJh|1<~$E9c(DMY8bl@QuYrfwh5TG*_ba22S#Jgi1&NR4aKxc!ij<6X;cD{<S8g2)>96?ope!_Y?#4aVEtA&Jb)o}WLkGotZM3QLX`P_Lwr}a?n>MYBC4_`13 zw?zAI{fS{11>PeDFIWcC@(Z$0)>+91MCQ}TsWA))oNM`A#F{+4ZoE)~6Z9wxh5)zZ zZ;t9ZrK1~=l`#N`8>a`GUTYjPYLhPxmGi%Q7065B-@+%Eo%Cpy8CYa*w04;5y`K>4 zkOUV0Ks%*d!g=W>?|zk|X+=1Tm5LX}Ag6I)&=srtszDK!Fn(ST=2u^{{-vG&ck4FXZ*W0a`y?3Xj4efG zSoLpLa$D@GgM&OaV!Rb zGs3o;BLyllSm5m*PVNNjUJPM-hBnZ)89yCidzdH0SB6R_ zE=|ru7jXLb)%T(+kqD1QCmw@AnHXXv6W+Q|{`O%HdRB z6Ct4Juokmg&Qc@S(stRY;GlIQYORjF2iVeH&zTpAPQ~L5z5LiGs^Z5c~ zg=)YvfkdQX@0h4qpeh&U#SixO^MjSnuoa*hwSm_6K4b)xkbBTf?t~eW5EB|(@nbuF z_|`!4&<)*cXM@oHffC;-o%Q=89-hLw;Qg@noOOe>*&>pJWUg=nq24xDqvCo~CE~qV z&RJb2Q_Tq)yno+bYXFj%D(Fj2Ap{P`NBech7%}hE(vNEY{;a}|6zAY@NCh>)KtW7; z<$@;APCY&~0)`_X;QI-C5>xM+|Dd9%Mi9ta2HLWgjK}ODtgqZsIf-|6m;UO9RT5pm zJsBjINo7Rsb)0nRvPk_~Y!h3pchpPO%T_fj-qAIj#`K^uP1ibp(snYnV-p1WK%!9! zDKDP*`arIIWSkTUhcqDD|G-1kJs98smixZSYitE6gStGt4wgGpog^5bJ&S1+(s{hQ|Pp@7oR| zERScm;)4ZHD>bZCcBTiMqAQ+Qw3|(x*Xct>ySO{(mG!w<2;61^N8Y>MqR(%sz-b(m ziu3y1D&Bz84r5dUWaKMMTkAg&;V3mMER6I41_p+UJ~VKuv^ujJaz2+KS|R?W7IZF7 z0RwVEFI9X5c7tL6tM7h(dO%^hSWopFb6>u)-=^pI51|Fu=O2O2Ct-%@_09e%aF4u?k z7x|<17RfMD){+jtV^b^g_59_wJqZj~Y4!cz%JbN5qy>&GgXaAf@KTP03){X0DotJ$ zRsbva*HwR)U_W@0${M%xg0-|8ph)a7Mf<=DjS%6t%r395^Fxo`2>Iq*|7a^l@JG43 zVo52fz8bV;E$ht@%Dt2nKfL6C*4g_{8-zcX{-7DTxoi_IfpXQ-r{ejesX9 zP%`Bfbg7*%%Xt;PcQ>Iz-xqGNIdM7VRNDcfF;A>8FuRbfUDHBIugTI1C65>xvYN+5 zkT^4rnwB4J>1;FA*!D3@erC~hF5?Lr9NYh1pv%8NHyX{@>CTE9>4&&oSl35D6bvuY zK7Jc3#AyTN*Nni$((bJ8{|h+$df*z^_4Q~RRLz4gMS3IX*7QZ%Q0qL7?1=+7wP$Fr z9-TC2D+!1=#~uOd?AV!pxI0YH_BIi15f?&osQpmj&pV3+S=O?#4P)YsX>2(njt$%< zK)0b7q+|b}6+#1_C&cn*0Wf4|rW{RNTz26J&6Go*CJ&{n3*HK_Yw{BJ`lrS{U ziJy*<&r}o+6yFsIk}XwXLNI~3&mco@3`7W4;$#6R^Bs(4$hq0u5&NQvIu(Ck7-ftb zpjwh?&>J&VYJip{74I{gA-b)^>dfE_b+(|Z`Y(wh@RJu7(c$#0fUoPO$|2#)A1sVI zy|`1^^|UT=lrxhj@cg|0kihxt?^m;>OWrI_Wht-}LKHvBUz1z(7sr|t>zbFF)cMF& zAbY>_`d3Tz*4w&>fim0Dd7(Kc(H^x$*acXDajqiST~1)?O&q^F4+b$;T1{srn5BcX z2jl`k4D(8GR4i~i5pOb$Rq<18Vanfe8IpCQWnf*kpSxk2Z54J;5wmizR?_sB9M5lRhc!-6P%K{WPyV;G zw*orgHWuo6$tfsK153o_K_6FN3WNyAG{WZQ<{fKsrNah_iczmLOeYHB>D(kkFF>+U z`gjAHwp#SUAik}BFY-IZCM(<0#WZ`uDMS^e0)H~vAyQZkE66?Rx(a>COHVk9OM0aRM^6_mBbK4dpC>W=?# zdYi)i%`A~~+cl);uPy?egWP;`1~i3@@Nk?wnH0VNMA`4TRY22E%R@i}a<735U+>yK z>@yu6!py*12O3#GR5#U=qAev8@Zigc(*_!_{Xeb4IV^rjM6qyjU>oygnFS%Ev@52? z%%5f%f!ps#f6FYr;-g}|tHm0AX$!yvDhMe3=RjHON$O4m)zn>h&O|gjzt4wrc`&HK zkQWXo4?JNIuao>WNpZ=u4euGrm<>X?W>COjf2UQ0gU_frM6XDEadENq%a2qLh$N>H z%}r7Ofb(t#P^UD32|Vc?;6E%`(#fcxe!M@{w}*i(fYq6of#vO;3o#I!bc&-ZF7K(Ix>^u*$+*9GN57U8UdCr zC{tvWWT*FqFrIb`n~KWTsjCJANMPggd@cE4Zt~z%4Jo@tkf%uviD>~0);R=@W;hT; z5i(66PjBcR5L&mxORhCgS4(pQ;cyU%q^q#-m}NM=B~RTFzlQMsucvDtJV8FE=wBa5}c!EJkn{noc*;`PW=+&s&m3DP@b z;V>oVJy6x+yE6BIsKVE!{qiei98L!1nm%X(pQ^T{PS40VrAQ-}*VmJz)$PrS;T*}4 zqlmt=u(AsK_T)w0B%4T%SY!_n+mtY>!2+m|cVAwDqDRQuNYRf?+}Jr-v?Z|@JI+biQL zy(h%CHz%NS3V;y&^?ECoE23}kWPgzi)GEIxCMGsa(f}1mOMJROjWrt10Nfu;ZeY}v zX;OTWl_Y+ZaE5BcvE`*pDRsclPVq-Qz~+>(hFFd$PDH}ky5Qapm$O!lAXQ6z{{=ae zOrR)mS#Vhn6HY(^(Vs9m@eNU5(J%u zzTPEJ13v=+94ydK{s-WodcQ-JjzlRaGEfU;ru)jzIKPZAvLyUV(hDU3bV?ysXCzZH zM=>`dWq5anDCPUzw$SPGob~4NSYQ^t8lgl-i3J%Q!9NL!u~ z7eKxK^W|upCMGW9V&t-01S$KbCD{COUsz2>-XcnvgO-DVoWY){sF4*!l#z-usNuAr z<|4Pyv-hz1h6*JDI99i&liLxcoeD}y%G~4cAR%DE;cypRItp+YWjw+FH^X=QX%)3^ zkpKEQs9f^v>gkQE15s0*qdh9!NqV(<#F-JrvB&fB5*QaijR23gIVk6fQgcZUGvF&7 z4smWG(Y}FX;MwC96^+^&eFD&+ z{sREmK%7hh9cH;LWtt);YDlq32cCDAqV3tMSxAgP#0mmn$_S_F?>Euz`vK?!%~y(` zO)C`C8b$si6IcQe^WC0dzex0hxde{~KTuFB#5*hXU*3V{Khr%EuDn83@8i=gxEK7l zPEC_VE{EP@QwG&EptFLHh@bh-=_(t&0sGTXGfr=j(|kg@kOn4`wWfhp#Xz zqFrum6kYZqRg)~1QR0d??=gPZ(8M4V2*o;a{Q#U=1~C2M<^A>I{g`ij0JX*!J%pAokFQd0^!C>t!?K_@gK^9U`*UhAEL;+lnx~`&T%QR2BxqX?Jv+W= zS0|HS@cL4;an%`k`>s4(Imjx0n&ODCvUKeLpEtsb1d`ymCI^hqdI_l~mI=02AvO#g zyQ8L~eG!zBc~c(&1aXIzgS5CZDkIPioD*RPBL^%&-0>n(hClaf(+`~9|DTwB^a7!6 zf-7Hlc}ABmBNaNrh-V*Li?7@)usB!qfk7YRbj5+i~1SI0R=vQP{{pD}ak zl>JB3J0tnx*mGb|P)?;Gy1HhS*Gv#zGpM}*2h!0zhWmEji}23mrOJ$0I6+dsT!(es z7$Z<-~urpt)0{ej5>-U1J=-+;}0}c!M58?yohp{@J6tmEsq;__8;qoQqb7o^+j%9`i zPf_Kk=e{ORcZJ~FY%G4GaX-W{{gEOlD@cttk&{{HUP0UFwcvf0yOuSIU8~u!tmNBdHP=1G0pLmV1JEG42kI^;V za2h_xIP0rUh_>4!UJfG}Eh92hY$3#j^jCXRXM_-4zm$9PMr$bx*~y?4Zo>7BXy7e9 zBIq5>gCT`^q8(6r$}+^nP(l=In*r;+6e3`L1gy#R(*sQeSS4hB7ZVW?G4?n2#7wViV2v@;26mG{2T0#+4cjJ=|Ch)ce?Lj9|IQ6E%kVDI9tjw#^UVm!w zi+zD;Oh!@QxiMv+#sKFk+J{{V^D(oNpvfG!#pMhY&$;GjHAH{5P$(nKJY&%%D5@#u2DL;#&FNzCyQ#w|V8x?V)V5qdJ#g z_7Hn8skssT)$8_jUg1X!s$M`2J?X1}z{LrQ7l;F}HsJo_FAnATOQAgBMcVa&W|Kvm z(aS;{$pBuarp%}C1ql)Aaa9ocUG!PUEf6s=6ORT9{b3;{Bk-&IWCTj@bzfVz7 z<>%Ld1&HANXC%<z1YVECgMQVL*?9!DJy+C+N-amO=Ic!~oW0)XXCpC0hNd-vQAgQTT9 zl6rg&5BSrE-9VlG;_iC?lf1V2Ok~J)WGEnm zxC<0oMaky@KX)uQJ7QWuXvi#a*i|oQ+-tn|=u6_pCPH7og}9yx=gMcw0s||q4tb)X zp(9Fy9Tk}@IOSl>oIk7flI9U!zSA|4#xz1kPu zU*s{%ChF5`NeQ)rjWCn?ers%i`iaXYlnxAc`ggTWKfb}8X1NsaWEMf8Vwi+_SWbQk z4@>8$>EVlQkg+{wgdH1mJ)xci8w}va9JZ=s}AwDjU06k`4 zW5gK){)ilvG+hM*66*37IjG%etXvqODBBnH2*CcxFs6#S6joU6v(D*fpz-|NbmS2< zjJUZzlG?~TiMIW8=@q+TUts2d_k_rStxeXMJl)=EsV3M%ubl*op^!dUfVI__*=UDRq@n_Hf*e`zo(MOT5y((dksEG0 z=q!#&`Zi3e#Ylj}v;yloqN4K!pbak1JH8Z`E!uLqOgo=MvGog#*6M1UTxw`SREZ5x zNFqFASOY|v508%I=NGX`$S+r7m}vkART4Std&fD7K>Bo+VDm^yhY@9qej>HsPEUY; zzdYsPS3Q;G4$k?DE^1q^j@#*2?Q|}~?9p;NJx4+-0#5~vBs)`#lU5#Cv z$k~}YoH0H(+I^F5q)X^0*wJg0i&Ue_b;pi@d)X(&xL0hi>fo8U_z_0NppVH#kl`#7HWl`yvCo5r&2SIMJhsE?12Vs@o)!Omi% z4ot8=mPx0`$ndEA6`OHdg8;aV^ku}Bdj0j(v`sCkAg~8aZWQ&!HsSp&%%I1t8Mtg2 zI^ij$a4!1mSSR-Vy zkFt@wj#8fn+*&z)YaK&pglYq?4*0SfS1`>A0zoEqUd7y*F6+!oyao!?5XBPQk8C1i zM||B0K!R~qmbT1d3vwbmiBA^*5&~3%(+=WQehMp4cM#xb5n+NlZY zcXs9`?q_?^&mVr=e-XJrZOd-oR?1P0%FcJyvpp}}nqZ;&>!yiHwHMH~6!L|Rk&<;1nHC&l~vf*K5!~hYr4KamG6M$qRIy#ZP zNOU%XjDA3-X8R6epzH>$1At@Zwp7dwB=b(v(X|WL46+)117oPLKtngeaRZ83Wbb^| z%On>)(0IY%=RrkeY2{JuZ&hPleD)`_h{lu*nUIbjztOHzlJw+%BQ3a|8X#(-Pl-qt z{^~fR^oNr9x%MZxw9~vzks}aB8A!cSp1asGrnqzzMqMMHu)eWGL?gMoeA!<LKAwF7>KwF`%TMm<3p85y;vI((j$ zl@*K7e-Qp3ePjaRki~AkZG_ zw=67>f;JvG8(PF9Ky`$yP8X{BXiyZ>H*y5zE677onXJ1deHCVZItiEPr6*AHc$>7- zr?o7|(`xj+58Yxda^hxhj$`8{vS}OK8xnc41g7ykr7J?8ye6-~1_O%R|CmwNs%S(O znbZ0pAg21)-)r7Hq+pkeu!HAHM)TKWu}v75O6 z7AXLC$j#1vQy#){RG_01md4X8kbgxesP6mOIr;Af_Rtf?vkplbC`LPpJTq;GBYQ{o zy1;n;T3pm$tsY%t^kYM=k=0w!O}0^f#o{s9ez0vak-X?ly4KGTu)!D^#L3Tw5sm5F zI?UC_-rGiT?4cptJ_6h459$|i&owgi-7B9bBEno)8tNM8s;Gg%O!Qth4G&|2<M? z^B#oK9sZX^`&j?r)8IfBW|@?{WA(FwflgTI;&5b6vs5@_<^6B5{(~Nn1AZX+hJRe}__% zuQ|I{2f+uf-J$0>!8*AbIeRR_*b|5gN#bq=0+pW4y73GPTIE!1_q}Hr8M2bj67uqa z$0t&f+uv-#K#z2CQ?D`@|CIIPbtV2CF}?o{u3msYfoe?GF4G+{DSNA(EURK6q)O!e zDRJt{TAjyUr?e~s)wY}GtN$38%?dRg@hd-)Mg3}`rn0T$B~1Hj*gD* z8oFjQS|W)q3p*y!@RL0#nf(|i%~zhQNi5gH#y&h9r8~1txx^lQNGwMXO`|&l#2Z!n z)?3jn#Cr#ZuKy>^;tNxs%`BseQt5b{a-U!B=t@wX84bhX?xIgUwLxa(2z&xE{mD`bgemK^b5~vn_6GUJsPw#+86ZbEZbVoGlYe|w2Vw08be&s zsKCi=UA1+cK`Ak(nUALH2vn9$xS^-veO@#>9A;{=TzW(brToty1`Pyc#MELLiL zX9fQA6QN!y8((W)?^@HIy3d(<(|`P05FL(^i5>0J7wHrq067win^^_+q>+=<@I4yD zunEsgS_@oKDpnnv(Vkam@n2iHZD)-4Jy9qVHOWU29Tp$+rJ{+0YV0E|g~sH@(gsD1 zB;)DB0z4;<6SA-AA(<_=@nazcra49h$`%-Egh5A2Q2r8yyM_)M1u3Kkxc&NcpT$&| zo7qV&^aS8vcSPOGj$ck7F6ozA-6iL>@B<;l7);s54Q`Pddaf99+-n9@%6$d<%Kl;-*H9q$B@uN(Bq z)89-KcGw3%7Og;WW-6y#2RJ7UYveMQE=} z(5O^6EF~ve%ji9;@omhFao+?9;NLG$gw}nFb}T;kR%P1VJT84dbr#Pf!tJ@~`Erk@9XVy-F7N}#)Ai)d zs?H-R$3#Nqt$T5rZIUtH*e(5s9)=dfBa_1%AX|?!%;h`!A`s>k6eN%1Gp#+!^B4aj z9jYr>t#BPGC#XaWx|1ccMsx}q(y(>Vwd@$$14hi#eyxiU`~xqoVODc}b$`G4ofMTa zVyZn)|@cfJ$Uv?dHjRV=5%oE?NW8J$*2uXn9OX}UYsfA#{F{p2#2Yj$hjms zegYd>G=t_G>Gj>wQNEQ}>33DC>54-yU2181da)Zv8m{=q{%52aFnL60kMCYNb;pSE zMQFklCJuQjyHfk_i4gn?tA=ClX5B@JFCS^u#Tp6u4e^Bwh1uTcF}X|FY>Cl|bc64wvkWxUU3o477{~NS!`&(B!A&rf3S@TPPR)7w_>6R=mETp5R z?Y3FtW~Dh9?4$Ip8X3|J4w_I%lU;RPeGznlLP^)+*4mP{tkq4gwGc+ZPBwiqc=}bt zKZ8HCEDS7vn#4bAA*OPAw2*{!vZtfgffU&qWO*gN!r+5~$1GI}{fbIp3)Ss(Gf-2f zN=mJeZ5oV}l-(img`p2xT7`qG`(ReyGilaaEg69xJE2o9OvJ6EMX#n4rQ5}bvrQjE zXg+5{U9l^p%!sk9`2FZj_GmGU98LW5^Yi77oHq^GXnTQN=Ch|y(cy~5=Fb;36FEX- zHxm=1P(?#bsm(1kBJ?+%a20JfH+`$qIaXKi?xt8#!DA^tId?r>=9vn=2z-i&|R_BAirS^6vPR(Ll5E z%gFEtqc-H!Qcd56hljKHEquG=IaQBQoc_G1NiCh`;ltZ?b#-JKA;UBq9J4y_|3zw8 z+Jh6Ib8JYa`I*z_$NOBuCR35jEr%q|JSt^_bKtvf$EQPZdg2l`AV!rk;x#@@3xUR>mbaQs-3Nke0nqs?x$9 zw{J4;|EyHQI~02)E=GF*5A2LJ-8JKp?b)E8RGVVD`%CDe!Glc*ENjH{+Z!I~iU~H; zjW?^WsNJFFZXSp_er#vQWkNQtUj?=O^69$j#|M)oB(Kt16F4sQ#`un_l=;twB61yFQNHucCO5_>o6*$YJ>IGKKz2~2)0NrMjviw3+F z?QwivS(nD)=5l9!yWmrldd=H?t00l=d~D?pUL<2)Sqg>?%ipKLtFJDP`o2o4Ns|&s z5Xp$Q!XRJ^YN};oZUHfL!U&e=#w%aqYs!cfthSES@nFC>gegyEM;RkHHPK?{zjzcn zFOnESDJ=ZlWb!eD|F@J$_ZL(E*-sXi!8l5#=t2R8W*mrWt4aTdAKWtGze3IeQ zfSiB7=J+J9`M@nO)`Lasp2(44XV6MOgdeNfy2@8_S+PBKN@0)w_(k>8Qu`FD(6mnt zZZ;-e>LRqs$yS;j?o)9*wt%Hj!ZosY~o=WkMM27ZVRV?#1~&eSKKNZrhrc8z)r~b=5ah z$&~l*e{!dD*O-*Vj}~BGLN6^E-)|P4RZq87dsUkMRbW`Yvu#6l(s!Tg%IMF8V_Cn` zaaZuQWaSjlHt5u5%>NY+>hR)l=Sc=l8t}IkIc!&#Dj#jA{1|ze9;~7*o0(Eyf^`E6S49fC zhT~Tq4B5OODPT3^B|5Bw<}5aMJfz zd$79kOMlhI8do_)?}94HH-{{Mx?38hfStI92f8t?4}=@QWMlgMi`w%nD}^i1-Y%Ff z`@eJW`E7fD=?ZQOwR#I=b%tClQv{>DIqK^F_$(hzu42a6%zL;a-6?8>V|=}dc0|(^ zuIg;5Wrx`~{^(^zKQ(ETg~_V|P>DrYgbkhZdTD>A=uwD3et&RgX4lWczs%-Eh+hU% z7|kJ|Hljn%bW5#t;b^9WbKASLN$(loGf{`=MMCD}^wgL^<3is zv>$`m_`&-LdbNuKF@EFa@x^gxf${QVrh!5Iq!lBR@|_G4>$`FHFgB@2qTa{RUby&U z1*oLSE-9}|YiPcH{klZTQ%=zO%w&}L%X=#PF)BW5z4uAs*$W^qA^Jps!Ml8Q8?9y& zr-RKg5M19GC&s#V^}i#SKY*DC_A!uYRwIj1&qG_J<7G_H1Kv=Ur_)2|nh|QSo@LY{ z^gEF3tJYK52wnk1@#6CBrPfyd&CLeC@%(3b#vCBq*()_pf2dYg$7gapOUN%WB8zZb zpbrrDkz{VxVCeUtL@4CpIe3_iKzOvK&!&w5;9#Yo4K7 z$xFhnlQI9aq9U7O+>~EH06w}aF#c3uiK3Iz!J62<~4=t zd3p$&^Rg>i*g`5>Gb8q1^|l%;?D;M3N93wYfjRw`IB!u=piHO&J1HbeA#6$s2m!c% z&2)K-i{`-B*ya*QG|Zjk{L3U3-JavK4mV|?P2I!{IZ@-Uo?w$0Gkd4sQGDdgV~OIP zX}-_KER#nrL6>Im^O#lBp&6O-gMDsn6U@xug7WDABkb<441gFQ5&T1yWp(-DS|V2o zl&Je?lSfq3jjZ`A(TEJ?Ehq4agUn5xC>P-`9=AGDiU((`1V_LDkxCVB>vun0hym`6 zqH7!6ZQuufg&@o3?yk6MgB$*^yDE+PELI`-<+MCrqVXz-p&uZY3=0T+9pI>i$CZ23 z7JD$!qSxSW+SeSEb*E@a*S!^e?Kj& z+InD7MK1b9>hb8g0#e+;ZPeqm+x5`R#*WAO{DE=xJ$qYwsn(yU8#(HPkt>fL?=j^5 zNwvo-TJBf6%M(}nB<;)bGUq;S;6vKv(Ic1uabr!wm$(HS8p`mM=NA;D8Qwg9B3SnE z7TJ41*=DxLv6m5*71DN%6`M!1Q6B7rI=AN87$nVEU0!Z91Aho({J{d+@nRtX3R zJ6y?~LmhaeuRXS{=IHBOEo0cATAy5iQ%#^s9v1E!X`e(9TR*I|Z zj{IV8evpp{2!3rNrI;dmc{kiH{l5)SZ&J$`!^PbQHuLqO+HkDxu9>mlo|0y=Tr2~Y zsF{(0m%po)juYS4js3>Np;|===2E|PZXJ~(YHHDG@YVPFS*KvWC%fMNx)-CmSssEr zEX&3XztKR6^;MuyW#1t@BHIG(aT=V2Jt16iB5u6b@p#WIN+c3lF*ZlT@R5aqdcp>`|N1&p+no?o%1Hj{y7hBu&y-ieDA6WG)Qs}c)|8}S&b$+C)Hlt z+sEfC07T4`ZZjL2vcHv+JOrK7{=wS-c#oGtLxq)idn2-Yoi@gU&>cFgM1_>&`wD&D zg?|DWD90QxW$`Hentcg7L9d_u^yUM3Y1!+((b}6K=MV8YaNh*G)g}a9Yw%~rC&qzj zB#YY)oX2MD(Hs}h|FMuupr$brX5UY68(fA8rB9fCn(L{k*G(Bx#Vi43J()+R!d1xg zh{QRuVR1!6#p5bbs;d(TfiKwBKU!yUnVmTuMm+FY@2W*Pg)Hb4fz-7EQ>=et@b{t6 zAp&M!bVfecO5bgbr#Q4kCze4YW|+ox@@c1lu~ElAYv@K_CLu^=Zy}8F)wC<|a5h}2 zZ>BRztVX^WO>a;=>_&_8eLuCUzADxUSb5l<#YCA89~Ts~D0%YaYp z*>e*t89RZ(ishrO>!am2aB$S(^j|SPeE2+Moqg#VhsdIc$W?S#vcxAivs~YWa6Sy0 zo#zz4U_ZytY@I*j+}5u2eD-iMAw+H9AmLAuxwV7GIx&O~xWZShm-?cZB8G-E``1Ju zFyWCG3Z(D5qdl!`2_s-qYAAYBViZodp)GBJnrr?Xt3}eCr(5~$Umxv*3GR?T{)@)K zWzz)bin~8aH#!@J@;+?M3EA7`KEXb_VUC`z$YrVwS@YLLa^e$PsoaR}WNl^Ss}_jF zWg9+ShBqSX9=o-b!pC-O6^$sRO3^aY=?$Ar_OJ6QL%7O0*&Qf*_Xsj71{uJf3&t@9mEz%G-QKzZ5ApF$TOn-km?BZbnPRxqCz zKT(BWv`rRkvf!r4{1s;)LwBbuQA0kJHih*R4uGcCaIL)dFdW_{5JI^-1-QbWR=oN; z*3#nAL<-+6WrO-4PV5--!QRdGZx1Phi`H%23bGi-v(|jT-9HmHCH|<*rYDXFuCZct zJ`T{>nBX`!SXj)^@VA(0ju}{=Z;mOE=3M}EX6pE#C=UJcc@z2VZ))rxqwYk4QQ811 zUohiv>{jzFIPo?Y(XTFq;1`;+g>~NTWfic`et{RsaF%IW-V($K?)N_q}Aei3i{ z0c?z;Si7}x72Lw%V2sLOZEt*!fsL>o?LqT9QA^2i)4*KmDmq;065j zYiQS&iIa0Qua&C*K~0wQ<>~7?`UU_Rk%k3t=F@h?4J&55{t$30D!%ezOcb~!B*j>! zW}PG0JZAog>ol%kz{sd04g$pE%!^_n4P6QKrCrXwg{QqcP2Cyesga3uNo)aLbx{&K zdk?Y)uIh17(n5!Y3V@r@0CeBwi4_PvnpQgdIiP-*2WggA#G)kg>BJU5KK*XW$BVWq zY)t5Pq5glS9l(C~FlqD94Uq`9nZ`he$z`1gGT}RD6W|)X9OA&)gj2{lD<-1h?D)Pv z#n5eHGL=JEc<@1RyWo;%`jMk27IAa?lR0KqW&0_Cz8Ej8gTM>oIsJso7vH-^?Jmco zqP=5IFRW{v;&7eQF0p6vSfIa6CSf@2v%-&g3(yk_K`7-uv{1RpJ9-1Mi7N$W6A>bZ zlON11WKh!u2fu=T4TcYT?RHD;q3z7dQ}r}1mqTMd2ZM`a3i-L5voA*Qu; z#A^4|y}>+V=yN)ruRX!FiT1)C11h|?ejanlIeG+#aTjeYv(Y3#5185) zJCHS-_N`~s-Nz&{F7C_3!kpB8Z4qz7$nORb(n?NFAoo7G%m<>Y02UpU@Z5v;vR+xW zoE)rf=YS6>s=*Yt#}T-Fv@|S=slDi7`%s~22#bnoaDLcg5e(NQB+_8AB=O31K^!&C zZQ6+rdj7T0MomK*ji9iRyIidh$9o)#el8zEc&^5F+JOX1wd#aFB{^}4udD~sv=$3$ zv1KipeQG`)Ps>k}>9Ajwe?fH3ed{{q1KwtQFeE=cjNO_EP3*wkME`bbhd#Z?2r)rX zN7L}W&Ra!}@i$9fL6p}k}e`lWX4ny=_>|YWV0vIzu zRP*hhkNNjd`0!9~jo)qH@Hv+V0P8d1y63;v%S4%3S(Cb$s*B2vBr#67e=W;T?S>rg zhuUzlil{{tfH8lht?3oHz2W*yq39>Kw{%q~fr5#SU=Ca{{QIN!((^aj;Pa(fdNZJ* zFm_8wNGPJZlw1&p>N{_RMSnK+>2Ko+88%M3cl~CI!(%hL1w`=${`WT7RG&amZKd$^ z>6MzZeQiX>^Cz!7m14OtVDQ_{F9}vbbQEmw&}9YZ^j{Z`4fEr-5~kBo6^Er?{d`@s zb~uveAVW1}62J_2s~(RX-?pTYCoMqKAaqV@T4%>zQ_oZYf`IQ*67m<)eC8rq`k_3iF7TGT0+P1WZ38Ih?&tP~uFI$jgX4r15d^Ssh^K5;AJR*|msKFed> zffBnqIVfQC=zpV|K*j`2GnGMBcR2+$q z2&DLO`wB3=a&{HjZ@(G*#_)Mc_wn+{9zX`MXN`FpmuydtFCD6R=+Bj}z~B|+K@g?R z&!2x{k(H8=xX;Cfp49jS1*zG~C4tdM57><&+(@vjZ~{euC+f-(+Bg8=-|TXtW@tTp z(HyImctJ& zFJyb04)8t&jt}O2KUn^`#&e%Ov)%YeoxI)#D@^zL5ANum9-GHsta3v+Lc{XH?2&n{ zl$Ol6QxkddUVD3ggK7v?l<(Ma;Uz^xyUf%`LAD!|#4J}NM1P5Soma8=%H4MdCojvo z@#bXR>!F7$k$Q|uiHOqesRalhL7!FM-L33#cZvUEC9ifjEB`h+O7Nei5aVMkt)h7H z488~#GP#fNuyTFkh9xm->fNxjPHJ=0RBd-kehRFeTS_Bp@DWewMAkgjk zt}7HtEb6vz!P6;EMf((V5EugUlr;4gzVu|0h9^T)XeMB}4Z+^8#fk=7gnjlmtnu`? zq~@+-Pf4kZV4G6s!H^#e0u#|SN7uFGqMOT^RX@3Ox?~oOR39Y&*L(#|?W!nFMyZtV zDHq@AHKG|PIxoPi5eR8q^gNN}Se&;l;+bHrX?x69 zD#o^mDc>se-}ey2&Yx8}N6M7ePC61v2)hn}@V)JLfg!zeu3#Jrlm0qglg*cpVBA2= z_3GT;C*24Qw&lO$dN+N;+^;stRcXSAsMz4@cgwLXQ}_olg-%_P8d4Uxx`Y-s8 zRV!Oe0Vq?rkONJ{65oB)ce$I36nodA=YdCTG3!lw3&T*!o~8mDiqJn0K!BDIeNiB6 zne3z)4#9ba=zf7UboKhJU%yT|{fU0UtT=W>(T@2urZIBkpAGa5{E?+WtE26+NvnhywGZKDl(Fupj13%l=yBE%Jg;I2pkG6`$6)O|4niG83~XV z=rN;RD^av)B6cCHf2RvAyqNP7y=oME)#F6Zu)nE3r<#69M18@UTTHcua zi_>NEC5*xlj&Y_MbZ9ah%OVWnew!VB4(OgXj6Z7JhgjKAZvp*&iFF?D&mzSBQhN95 zp)JCF2B+H4((N??m97VwIR`^Vd13Wky}X%#*xaj=^RLg1lw_3ZeudL+S$*^Z&{p5^ z9@-m#uqitkb-&!)bT+^n2-Vtau$Mm146~j10`;OnTLd!;4HyN>A&j4g^_RewhC(m+ z4(HPeHzS~3gFff8x#xRu)ea0rLjQjT@8s|Ak3plk4YzXB_ACn>JMrC%iVV}o5=v6- zrDAUj!x=JhZRDKx_cty2Za}8P7p*(@zp$_)CpjhkxFq%c{*xDVIBg)z6bp(js&`l1 zxE)RY5wFX`PsWrn^XQcER!DV@Z&r5ITvLG7c75g|{Qs1_E`BY-7`7hxR3M3R1M*Pq z8q*C}T=wBVK{z$Imy?ESaBFMDbh_*onmD|?E2Bdai9PqvBQImF;C0)xqC0m#I}SQJ z@sNyrpE@|uJaQU&Z{xSMyFGHRM@rZrhna>ojFv_rgPOiPA7xlV&m4?SR1a!R8b|ye zu=tc6d)Ma2a=R#L-1`I(B%1R_E_UuGSyu;QB`r`KygZnIk(BsCEsnb(Aj5G#HX^8 zad*nLv|h&D48I>UOBBksbmbG=Chb2d8w4td%3wA`4bmGPw6onI5C4MBBWX|x6PkZq z+Mym`y!FB0%`-cZLt=+rx8fy$`5&Or_UX_@{)j6t8wavA^9m~^c5rH^0Bl!ZYj27m z=ffQraG*^Lk*g#9n4EvA6R-Df`GFVw6UT_ozh@pSQ$&fv$8;sSBj4tUby*FK&Vn+4 z5|-KBJ)~1W*Aw31vpaurhN;mY!%3_g_$;5d7Qt)*B?C80r|g|`xQRKKYe(*UG;|UX zB}oz;(Co64;%%lBw*8ELr|37h6g+A_` zhmX(5*Z_g;=o80P4>oUq=-@P)(u~z10YTYTG*y!Zz(6!w_I2+!98g-`!S`v!4aN6A zfGX*w9i=8ius?`gWs%Tr>{25v2om8GAdd`uLh%egJpP-;mx`KbCzce$=Uf4@{!c%6 zQB2Aw=T|<%n!t>sL?lcyVB&zQlaynC`^&j6&ZedLx_o-_M+qDAi96#%tNRs4Wf&}< z2bM-EgWzX{`l~^#7k9f0N6ADjd4J}I|N{xWthF&j##T%RXtsG{V!+Y&x=f95{gUQoO9~Uq6 z;=c|hR+NCqAUNw7<$z8t-%^@eM@^^?6}ao6&!BRlD}@Ma)#|9+&(4(8#IdSTk~*zf zW-2(34O}?Bn1Y)D9vpWAD*XDUCJfLB)F|{JFZA5emqWJ#A%?ZNx7P&b_HMW+tHY|% zD~c@7A?*0L3RD%Chnq{bqu2mNM7cd33>38gcsi~a!nz7g$2v;?o<~113fDO>Faxp^ zdV6~FIi>}h*HA@m=T6Q=sz(!`l_D;S6gFv)rc6wEO3QNVk!wv9*0fzJUA;t#)*fJB zlF!eM8;n%InpC-wo*V$5hEP>C22QW?rAvknWyGH#@(0K6E_5X{U^K*?N6^Fs=(lZ} zKUjEutZjAp;>BehO$wEht|N}XY$_$_`hH7@e5dtnjX1_j#WGq(LbNqwq;OX zS-#-%ux_5h8T^o^Cn4=#^_On7=44&9lpe=x-}>l?jM_OG1nd5V5I(7=fmLZ%D+Qi3^=6-{ zQfB_A(+!xd8=-Y!cAsr9d?%0Ld}oSGt{@sb*VywtZrpt7)q7;C!Jk$4O$Q^1kD}?Hmc;zGeBlm zKr)yzvl&vXYE4`5Fx)pd+MZi3mI}P{RU@}G=>(mJ=bec7z6I`sB{vkuf4F;jId$C* z8jl`K1${ffqcxvcNm*bCC4BCo>z~;Fo2ov)9r6wXrr$WRhvmDVSdBxFJi*nCHKd})a7aZPzRhK3O-!W3?z`qcV&Lw zb}|)l*@(>gD=zG@SX0W%|$aPsMy)eTHUK@RHDMxybt)pt#;fc|L z;n{s&d}7_6*Z1%l?a-b_-LKr>5{Tf?*Bh&~8WSwCp3oz11k>7Au6l*LC*QtrRZVYf zfv_@G>1-;lE~8gE z>-<~59VYnPyu}v%S&T2NQ{F~=yZ2`h4bRRu|Moz0={h5UUDG9Eb_j>)RaYQ)*x&_^yl7U--VEv+1|Zz&s@U5fLIsv*Bc%K2fPdXMdjIO`(fI zARoL3OV6@fJMv&X2xjTPJ%pcU@is(U5ke1ZZ5v@&+gp-Dajd~p)!mVrRZ8e-rh%na z6~Bur=Jq$;+Db2DtbpIUf5#>1}lzQ8qjm7Rl*@VTJ-oQjme#`E8-G}vaW^9!HI`#}1TII7&8VuVOs=eC^ZpH$WB1>FuT4uGah5|OTdjffDt*9P zgLEd2x6MoC5{GiKcOpKq!n)}B>mj4JiE}th*Tg)2Tq5>cT{T!}$1C(hQ9!tY*q#Ps z9n!VvRU{Kvi@&Bhxbp#c5G?4vED>_)Wx0#o{-VN8t1*d}VLYUg#~M2wSdO+zPrrwz z?APyBDlbQ7Y%kIkvBXTw?*`|Ynj+jUi1V>5_lvr@Q{ri!&!##B=t>!|*22@Wu3V)-QcxYNetYO{yGRas zt0j$;`p)s+_?}mIri`^d+3^w*WF<=L^+C2AiU#TRE08H zXr;)6_Slf>ha;Sjt#=Gej1ZiW=0_(0kefe5?9(=?8*@9}_gfZKhvv z!4Ut}M3U!Ih61Xn7?hE3i)D3~U#wJex0go-@-7)Qs_Hwnj8CZcGio{shUqr_h1*{2 zB%yU*{f6vrCf?Nw>`>aSQ-AsL-s)=mh39SJSNpiZE|cYaXcr#5wAuF;cHwVezjcXH zcQ5Cqv_^W!>4DFpqU%lvpPE#u_?`XLVM281e+AY}petWak7Ea(;Gm!;bgaumKmhpV z6}hkt4W-CwnZs$u|S+p=NmGGUs>iy5;rco~ERRDP@6Cz-X_I>%M`MKH;QNp<7jdG73Wp}O}}Mc*tbtdq*-D;00@N%y*>7gJ55M=!e) zIYLNis|I4OP>2c=@lg8mDN3J$j(_6tK%leu%2N+*nqf}!cI}rAGkNVHT$?;^0GXHZC1RZJ4iwc;)el*upVWJI3;2F-1V%Ln4bN`aXRm<#egP3D~a z%Jg=$;Kfq6XMU@cX;>rN(*qfD$Oz(zTtz$XiUky{WJdiPW7_#f$NkKo-eQRt_46Hx z`Wj$LBiXmD+|mF(y!piP`xu*6+3ZHpd9h$8V1*17PuXnSNp|=v+}?cYitwnWa$kx5 zS?m+NOS`CO=j0>_;b`D}xh$V`lCm(KI_cu%pS`p3EI44Ht@K*fs{3TM;rB?0(c6tr zJjcBAVqE%(I;x4&>R|e_)LvkU$yjqnZ-x)c+sg6@9Ub)|ZDJk!+OGM~Mas7bOujSe zhVn22wicSQ579{Ztm-3ya)Z+s0~-9TgVpPc(OcEVqRC^~S$WZB8#ze^boRXmp+}!K zbl16^#wlbtwbui>bgp&H57Ok_UqSZ{Jw9VVL{gii;xfJw_TYPSM7uS!Q=Ify9r72c z&)GDbKLZlUGA5Q#U?WMup5bp1rxX+9yIWYU%w?u0_OO}|go7al&GZIO`&Ia^$EQpw zEw-8^x|DvUcIR^J6--x`JX*Bwrg?*txOYJm{Og!Ou|f`=iGc5SrYp$%TL5Ov2y!Y2 zCo&&9+UnwQi`!zT@!d#&a+6fpGY?bLT<;3&#zEa~egdb7gGSXuXUcCy4}##b?dQzT zFTXeS()we_t)0P@!(?@Tm((HCwUSC8vF(u({+ZeM9pfQ<{pRpo_VagPQJ+xewYt7i zWE`U>7Ho(8EdDWb2GTX3GN_+8qfQf|aIDg9DH98TnpZ@}*7MQ)GOY)&`kS*&*MqGG&h-&Ez#8FdrRvcm{bDVrMoJ>%Q zs8U#b9vT@*0l^vFas2Q+L!ymv5@z|M=ZWaD{Y&ZHCPwF&JLdIeZ z-_O-|TdZ-^*wVS3cFdy3tS?(QGUk7q@ad5S1$96Vjx)}QqD zdZx3B#L3*BT0U?8wi;6Z7UwI#26RtLq`eh|{pC_ZrrQn){j^>MuYMJhLX+kgxx$_v z`jt~y3(=k;pT4J>gS6OCt4WL##?GS-b`j#V6kb@iNaSfv6hwnDsiLgS9jst}F24DV zLWZY}nj$C-SUELDzfT>k2fmEx z%N-pd9?#}T=}02&zaH&Ln(O?j7V(uFaNt`eBKokK<9aqVO91Y>SoYGfLQHToC>w#B zW9svgxW_w*2-ypk`3*0LGTW3Sb9U_fjBvghOTw4jymNpljs*RK=0rirAC>L4UXDpc zwMs-U!2YcH+b2!fyIRwpg4*-wHJ6&UGs^3 zyMjJ&ENepVn8cJI2;<=Uxvui>9lau!HB?$c+e-&s{RrE_&b)}6P0|vbroW#m`(mXK zKZk~gzk+;Zvf9`-l$2u`29l51W6NzaQ0fe7k?uB)yr1-$trboS6_E?m=86=iK+=X3HL`8TYc);pIVvRDpIaxHT z=7esi5<+k+SoEd7xOY)#OIv=G;(T`FERT@mGMe$GlK0Of3qgKTySr`W1`30AhhHt3 zh1G`%6BPxl6(b3UU3UE4M3m=`JLb$1PiilEX(tmojdp*%KBKpnbZrP@CzDvKrM*xu zO^#GzJrpEYI%Jcvt*xh?xqZIChisDG|Fv4V&y}K_p}DiOGxJSNoUd-Ih5AGKnXjHv zIt)9R&=NO-l zW4P}3rX%?)fp}FKwb8b*d-{WW$QWCDMT!Y+Zw-+%X_jER6K%m#?NTetVhtq|m9nTI zLfFs;%MXpBR&BKDBqewUiNdz-l9Bm?^@Z4)hLbT$&+E)l{_`Ul$a}*B2Oh!Zxi!bSy?gZRurM0-A^91ci=qLu^7YX z>d^63Y?zRE*>T;*p=8We_bc-DX!W{9-*Y5VkRW{ewj-OorLR_uK&t*n^KG@%5rKQd zt*3P*AF4&%69_^RqkMlEYdFSN68Qhtuo58@?ieTAVxKFZT$hPP1n=i=b7%>UGz@P} zC@Q*72WR3uCQP_$;c0!7{Z;7dVp@$ei>K)Mp%LVvP5INQ_-(!{{{nP>Jw16^^i+&vbVK;0tA+Pi(xMLcz(_lZee`>ScAQv~f zy{pT>=v(3>l73p6t}CQ7Ql{MXmH`v5o)(tMg1wJ%4szuxM(J-a6=C7184(UUsB*RV zSU53jO&C7wyIwRgq8G$ku3o=1pWe^UEilaI`2E-V0bUI!ne~Nvf(Co}A_4ZZQg#Lg z$+NTHI7^brm2w4w8^BTtyizu5!dDW}JM*B0L0~M&wc`;%4>#cy zzZebS4H3D?7%ddtkq{My%2<3z$4HT9#-g1aUQyk9<*I$@(tOAH0m+gUX1-M<;u=bS z^>VdY`^CD*%RBG+awRwCdCb`QO4F9-ac|YyI-8r^rx$Es=8<%aHgyu6H0TettWcWY z9^%5M=!2xPqFi*zGJ;Qdqlt5#b%aa1e33C;*zDA?bp_c%t>LpV8m8lL_L+khH0E64Rt61jmqmUjio5>F z-PzqOV&NZzJu|?Q>fs(q&0wQ=@tFnz{o4mHf@bHl_1t9F@Q=;Wuhnz()(*3 z_6BN*N*5E~|Gdsl?^Q`~W4Eso7A~om1FQpi?b_~Aij)cVc|bockY{%2=fXQbbJSAW zhd8>U=$S=hrSWwHTlH}Z*4uY<#s?h!HDLx)H?d)K|Ur);pq$_M8|Ko?mKRsq}L8p?R6uD8Aj$)zu z%@D)zy>-e)vE27sw4F5D_ytSF_2En(b8Oh@08UB9>XX()U)V#UutsIlKKKw8?5=k&CKTVnr|uA8yv zGS$Khd@BD11ZLUnhqylLzt6n3e#@0rLvy%Yv`+W(+!6{Jp`qC6EKABHBJr6# zSzgbb%^6o&B=G5g9<`YrkGmnluiAs$In%D@V=$<@^yLm7Fp@vsKAChOkv zHOQ|p@=F831+(qy|LOw8&{)s(QVs5qol^T7p#i3}6{7=1ds)e?NN-cXA}Vd#~v$j@nbt)7Hk+zdCmm|!eR#rI-dN7sHlA_(4_CEV!uE{pv; zW#stDsJ}hTo*h3-1d|;OTwG?G0$b?m8Z#6(lNl;+5NXqqj*5K=Y-{4Z8>Xs&Ku`+1 z+y;rJ^Vdey`?6KWEm#_E;$VQe$jUbN%yKxRM|}F?0qrIGXH+owcXL<@+e69vi^p=C z1}BoW9`r)}7O7x$Ohs=ZLGy31Gz!dz%-9LJyMQC4b!o`9w_?zvmY>=RKX?4YKaFPgVu6Uc*srj#;+gnch$W$i+j4@(?U;BV-8zOQPbx0C+&OOL~0 z^L!QaOGTBnu|D6hSiE6Pm4arrw7=y;?m3h<*}rwHSzSCs@egA0*7`2_+2bH6)CE)N z7ftW9>I@j^vJSf^QerUkC0J-%@{>k9Eo=-#TjhEECp4tw2Agk}wvl@Ac=)6BeaWqUta$_z`*wGyGQn858plN0e8d%w{Mr z?=Nr9k!>+0;*fvYeS6u=V*6x?zdw>K)#&8t^SojnXhL74eiqIp_NU~)#3Cj%1US+b zj^@m;X@NT7?1sU*YUr%Z)4VIu)2ds0_$z$10y2D6OJxr&$xEVGKUTvIm%yFIorS&X zQb`)adYoD*;MhX;o$@Z%wakjEev2kD2c^s-;eOka(wcPNPK&N6e3XB@pz+P{SL4RR z{p^W9rtJ=?sU+3GYgJKJ{EmUnI8_GMQ1q?6!9nHM)B9oq8}6?S9BfP5+O+V5ENkH= z9nNT>R^IG)@=~)(Rmlm!0)UTl+iTW8*d%PU^&1>uY9W!Ck-NO26;_@jr%|1|&>Cve zQhg6gu=jej$|ZeRvB|De_Nlw^{>iAcvLJWsJdhw4_HMb%hDzmp_ik65Z;@86%AFD( z=(Du~R{|k=uk28jt9`R?JepXsFi>E!EdS5N!;TJ0VK)lZ$VIacuO6mV(z-WcQ7#TB zbOnB<67)Xv4L@mAP4BA;o}#PuHn7S(SpH2$VOXQrf~lmzXX2wID0I_EiNYRp1=-j1 zy}5Go^+Lvc6q+G@vd%s44f~o^*AkP42NrW*7gt7-i>>qEoG6JUH`jOLYK|3C%2o<2 zM&_h4c{tTy^M-vj1l*3Dv*LDLx~z!j2{U}E52Ayf$&q^|WqF>Lqe7Tp8yXt+P1KG; ziJd~#oiIN??+e9WmO_ravAuk+rB!p39Ws7yh%WtvJ1@4GW@l&s3N4z-7UPFe&VRp@b&%%{nT3OV`a&BZhf zwk^3i$_H@^PdL1KmoSx|=$n^hvG?TZ=c#y>{<@CMA(w2iXd+C!hJ#nuhaORR340N+ z+L^%j;0iLT`qQV|A}r$|M%80;WE>J64d1`pPx$}Zd&{V(-uM4^OhQtSkoo`uBHc); zlz=oygLHSdK?n#)NQabkHw-z1v~)8JNOulH{_pvGf4{TVf35T6#Dm{D>&z1wXS12T z_Z`=LU)THfW>Qqwp8(p>Pjv`AE?!=BH_r_2R1SI5UN65PL7*c0F>EJ`JynSu1biNq zcE?EOh6RAH9Y@YGR`_7R``S!@z<8OLC9P)V+Q(SU>Q14kcN3Q1HlpGu{L(!8)2 zci%Rir%Is`4KEjT)5_k{Kp2)X^FCPMrC~rhL95v19mU04P7&*=_rt^Qvee!gB9HLJ zO>Ljc#ZfWA;G)dxN!T@#t}ai9S%JL zX7WKjj7ArIEA>xf19^;`rkys3-`fj+91ggqP*OO5$am2al<;e)YdNAx!&Y8Lr+rhk zPD!c7=#E~ev|$yv(le_m4VSu^xaxzDZT@t?A z2BVBjOx~Xd=i^$o)-^v3f5gWA&z~-LrsPzpJY)TLR*8l@-e)x2*im zR6=g^fTXsu-C+`xlZ9tWgcL@)pc*T&)BVob8qwNn-~->FlZ26EO3}V;bvyTl88)J8VJF_8?J@0J3M>$-~d?UPP2Y= z2w(h#y=44h^V3$X)yGGLo=HvZ_|gVFi;gaJrwy{P|x`m|c6 z@i_o%+px^`o7Hl{=3wV+_}XAeqb6^6DjKh`Ws#BDQLuY%$?DkfO{ey;*}0pXf#*pi zmG|nhV%ga4Fqq?^6|z zz-#(O@&xdtuC>EQj%GsZfCFL7qnpuUeL?4TXs?UGoIf3vm>V6AW)WHR+baJsZURO(1+FfN8wz3m{?fxXQ}=1K{mgJ zeuEv;iIQe2#{lwevN-y^gz`rEgHGQic*0iUx~?2AG&*KbuxxASC)AaJ_KEyZcjo>q zi|2r&Zvg8<;f@%B#}--(#BEqvW8^AF3=v;!oAMO(?# z#MH1}`N$>b@d#m4hxZ#blJB$}33?0S2}v7VL|;A-#?R=kqVbQyg0l@(8FCONi2~C? z%b7|Bu&(+rF|xa1Xwf65WG1JeaNDwf zlo%q%53362glrLSnvLIE%?t7_*5R9Fcs=ZgCD5}^Xi1W(cYCkjJu8(=r2^P~k7ikD3K`bB8U ztw~aINS%Y#z7V~H9$nKz95QqTm$qAuF37=vI>6I`4Y0HS2h=Oj(HRq_+UL)nYMH8_`v?Y6ybnXDlOe0?g#Wl`uc^Q5AoY zc2BHx3k`9#I>sZuqD!(?`lJZ68OafuUVF0e|hIiWf6vFN7S z4-|X)IHGQCw?8(k=KL5=U@I7RNqI0&cE0%Ts_|l|#|D(SKXw7uOHuhQ3ZbkO^OCCA zgE3`xo1nFg(`QqAtDOTTl7-}X?{?y3SKFuVdND4uKH_r}s=!5W^O=Cz7Yn9dNBadd z%MLT4`88h8jMtqZUY|MPD-;}lEGTc72 zc$E?UR~txhRvIiRtA5A%Ul|-r8>81D%$wbqk--MIBkg5ho?0+6T~)S6eHXw4sEgp{ zt|@MEKkI7m=Eso?e~L^wnyn`rpu+RZS%>pX!?5)%)ZnMi#`|Q8lH>Xfj}1tg_IiGG z8@v6r=4+YSH2_N;^L+!+yCPpcpZwmC`}|U;bNJ;p@@b6a;;X_O7g;wJxD3#1y=q9} ziGGCXYXy^tSvW?~bi^67|G-{}QNR$4md?cCGRTzl=D+j1wYe*plKZ>8h<9lpA2 zN8Zm{xG-p>_{+VCmWcGHg+8}Xg=C<5gx;a7x~Mj9YR!5=9S5%0aa70b9cT`xJBd$) zycGOt82wxCi51dT211 zvYiy|%8}tPcNdSj8T>0G;84P4aK#HBbz1Yrj9TiNT*i=d#g#qp#+tVL*_~ugHxf3%r#d zq1Ol+icc?*6dnbnL__b&U)=XN+0U2J2G&aNqCR3!d%lV)-VI&ImT9{d(?0GP4!B^Z zquI+5YF8+2s?QuvZOG?z&M~NP=RYi_zGLS*w-K!!BNY-M|I3r4AG&+#8v&du*bQ3q zWj?mXwo;SJGL4$Sb|qm(4xT0^bcbv)Ch5iE1iuyE$URM;BMuwJHyC3vzmqWhVW%db zqDb?f3)4PX(#Iih9(;i|u&Mp}2H0=*16L-^)T^yD{Hfh%LKOMtOv zIPsiTQ?ZvZI-ZLWi05Kj?PLx1ftujG3A1yG!Q~-(8+{Yh1Qs-KnpyRi$vZdYj?Jn| z*3MT+W3T@D9ryRI>8T*%>Ly8@E0G6^XJxuAIZ-##g%?fDm7@`U0 zk}m-m&v`J{*K6FM@>&1GC=LAmwoVV9HWx$A(XmlS)P>nMag(71YC|h%-+Zmq;Tm}#9%g) zsRBxXf_iy1-$Mgh4qBksv(-QC+|`)!hm8S?D#1U3%fVe@`}ne$e+!U#uv~|e4HZ#J z*h|3d{KZYkSD%;GM(R5N^_%wT_HGTOh{ol&xUusK8cm}cdA`zO_Ko1f zFxqrHD{grG`Yo+K_TZ5(aCg(IY+B`0@aaXH)1qzJpR-9>Fq0&(XetioQs|WmLfr@F z1wVu_M`IGHE!LWPr0{1FgY?=t@PeAqYT4VGSSz9cjLkrx3@WVf#jgxC145c{z+ha^ zjjCjVr$EhZi%&yLj+$jd8i5`1Ouibm4ILHY*Sj%T!;Jba_(J?Ap;~lUwQ2S9l5Q=na5xF)_eZW0ZMIW zR0z!p=JT1VJkYgNUOro_mrZtkpWsx*?wn$*D``^J?QP2F6_o{4Ntm7|D(cq*-myxX z*7#M2=3GE?b&o%=Kv(`qbl_AhWYI-D(8l*&y#2M>NbQR1#$L3o@>q%&OU9^k%OZ=FrxT)Wf1?OykZ6YZwMDpU+fjyc|1jFU5B=-1Y3gZ_a9-$W5k_?oL zrPICE$ob;QVg`aP00Dp@n?f&aFa8;K7crb^m@lngjwi&d&fVRVBNa$UwD~?`1_T70 z-uWErnx^Y-7$X3%&5Xaw(E24{#ziN%5aVq#*#@U09r=4zZRKcn#p}&}CpG5NSyK)DjBs)+Yw^ovp5u z#<1r{+KtS>FQ#azmZBS1dWJ?+>OM(3jT6bs~+if-9kPQLjfxMUnNmCihY+ONf=H5E!^hHdf?n+006gl7v2q z?!oFk;P0hmq2pqHW8lym!|-CcQ~e4k(1_bWNoe6($BB;W*Z6hJms7l}HsN54ag)&T z_ImAW^8g`Bhx$hR&OX4-6;^y-J_oI`-1E>_<88o7gg`lfE}<#6V2bep^{PB{8abDu zE;-*M>*sySykPFkiNnc!^20w%pYcS$5d-~za1}3n$yGjwUXMS875H$+=YM}p8pG-Q zl+y?EU|@^;#j=F4DtBzZA{$&;tA()Q#Ac(+kq^p*Erc28Z$;uhSsLL8qX@1Jynl^J z4|m`FbJX|b*+hP}=Ev{n#DKyNXeBmugZj>F(7}ZAux(NfbIBsX1m9ThUZD{~~j z8L9cCx0)W7miZIgTJ|{1&n_h2I?bt%*UqP^hAmm~4{_xR+HSp1zb}P zu#r@>K{g}PQ`s+;hyN5^p1~S+{U~Q85VIp8YxQ%0{*Y8_#2vfNSqlKi=nv zV$BGDv7{P`d2W1Yd{YA%+haEVPS=Tr*?2_*o}O^^qsk%I$hVPy=zqq!FpF}>roM{> z%C)U%E{EnY1a1_==EEov6ixa9vH8Ru_FuegpECKrIXnzn-IraAy~+gy~dj2z{*ZDtK5g#+$bg3_q$V5{1ZrBS%>m7QLTz0>`sgvvxxjKN6>m!evPd7#+BGB>G zMz_}eyt(&Tx&r?S#}_^6 z5vQFQ3#W2Tjvf11;yD}#PyS0(<{&<8A<;YuYBmDMyMm@bT+}u;(F_W33_IOY2jas0 zcyIEl$rn2tv`HgOJoYE)+Xk1N)rtBecPf+klSN`J_vl`%>nTPJn7S|$(a_L{a$|FX zgzvi7?cvS(dkS4SjPnFG`7C|yZM>6hQg)yN&oP;Qwj;#z>^PRVO+M~t1?NVu=ip}BW`9J&STd~#n&e3 z2U6gSXeRb&Jt916c?}HA?^C#2a+fFxjqKg)2{&KWv5v~GgcO`#1KwBBo>Oddu#0y8 zZz9?U4xyG6S8kY_{D8V|#fYvN%$f(`(ox`+DSzsK05Amy?qyXoF!XsVVS7wtV)}`w3AQ zQi@WBYxoBW_Qdy$lP=Se%rvWW(JS6)1avp<5IRWGZ*LEbz$ymrB)suQTQZ-SL{r*t z7T3=6jvav|(tc#@his4SjQa>3 zW-4?284rNLuMVI5G{q2*h}ne$$0r1+I@FZ%?WKg92~NfD_ll}rQT;ovqt_2=qrG}I zH@?+eQ0?!yG{?z*{RI}QFd{yGsj}6w+UzZyTv!^#YT@rp#Apz3=O|^Q5K!4NY;0|; zaaCAX!e*}34U<(=3z5Yl-Nt2BNU;n1C#u-tJd#GhqI$ORzLx(jG+AJZ2WI%Eo{V?K zcHk%FlfPe>3a5u+74i5;^;p9<2JW>sQBqNKjG0uMLr!(@Wu(UFlk3Q3CrbbZIlc*0uc?23T8biN7ka8upLdu?LwG z^-jktyimw_ZWr#_YN44w{O+iEm5=SX3*@5t0}}RJP+~1$quvi6z_uiXx-f8KCJAhg z?!f4yM6&oFQ1Mx-N76h;7u2bof&MT23%v+ucVk;yAUx}eR_fm74N%X#&Qe)Kt?sRTBwD~a`cxWfCUa&VelFNw>_`-P zRIi;RkcYMeIK?E_pNofokqmnK$s26CShJ_R<+uFvN-F&Ah}K)e20;F^7IEEBo=~up zO$VG4-;~zi6xuHPO%hV)NG5o!m5btG9zyRuHe!^`p6-ENzZMuW6859flh6@0n1p0x zRVMSy)?UkPSw^Y6wyr+M+N-|T+?USyn zY08yf`?Lc4(}V%<&HX*HV~UOe3i~in2k6E^@oaYMMa~V}jQg<$IfSl#H$DZQj3@tw zR+t!UnmA1W!~51KAO&0oc+)YK-_N=G8KXf_kg7@Vls~}O@L+F^irR&7MSpG?kdTm= zK(>xLwlJ$O0Zxn>5{}30El+4Lz@NI_hXm@V%5TfwIyz6$_JSHXbXJsJ@$&7yB$JOvPIMT zh{G$_tsl>qDypsc=#EeG`4x%`wr-gi$wb>2hU2JCY5m3zqWgaa`~w|Lcpb z$rz|Vye7ekcT32GS|{+ag;*8cym^_k2!t^vO)325qtM)h936$o_ELutd5F?(V>x_ zlI!Se^{B})eN@hiz-Y7Ar-g%}G=^!MuIn6WxfJogUIc2F2-7H%!v{K}`lKDa$5JY7 zWJRFIM;Rqpt-5t=DdIJ^scCqm`qxULc6xnow!3)iy8YhHEeFQKwCN{N=f6a#gRvk| zPLtXeW};QcB`R5DZ{Wa|)M^sB%zlElGBxrv5c$hpx-RbYMB*>l*ZJpB-ijxP>V0;f z!l}5fB43|9Al3UGba1FVSbr>XBP0i(Tb-L<)lHQ|8T>t*a_^z?$kDDlZ zwFi(_hJ>HhEEOVf5!W)`u*RfM{Kxq1`wfF8N!j6>OTSB$M4}4`bjE1q7?d3Lu;PyG z-pd^|wMCJ;y({$o>tg~8#soALgxkuX`wdhW9@2I&nP3f?>kxxoL+a}#4A>g{R&3CF zE~eu$cs?^RI&$gS21vYTBH1C&VvQ4EsofFcfGzEj-Z4T;yz4L@Sppba*hDy(U#!Nfyw&u1c;7Z1m8_C>U@8Wx_*WWm;`fDCT z?BLVEo=22qm&(|!w8R>e;|;srLU#?^2Vd<=H8mW4-2YfeexIUZX@TuKuUv4UxeVv|hd$q3iq{D4WKVkQ8WTv~Ui289= z#T9H)hZ~d5e?q_TAd&LBS{J?52pfD7%%HS+5j*zt#Kbq`P z3NaL|;}c1<5#X-fR?w2zi+Fc(%qM!?mKQbq@_vA+ixSHZxe()3PZ_lR8~c(>!>REykB#)XY`Gm}*lex5GF zw`ZiYhHszv(bkG5O`qoJFg@+fh$H&|K6~@3r=HiTlHGvSTh6U-g-Cd)u)2R@?aFW~~r8VRD zBG#5$3%|_z&(aBewM>*=HPvLV_mulAQ_T3C&B#FTaGuZA*?g7q3vX_u0Wk35G+BlU zvtFkjssuaLX<$!Y`+k#PaC$2zN4;n2hRiuZ1fa$dDex=vdZ0}AxIe!=RfbP$;AwQe zLUWsVeI@T4QZ~1X3;A;!xHSHQED-LoR-NV@=wP*vQCfx>sNKw1c&9iS3Ym%-gf+?(*hr4~ZkS zU)8~LN@>;f5RN4OLB4{m!#^_?A#R%{O{lb`5|_1{up4fpj=(>O+Y5M{1gt)V>m25p zi+Taqr!!2|#+Pxe=i#kyi$no(l9UA4uB|Bd$ACg@Vd3A<)d4kn~Q}r90V7mRd#bQ z3mR|QEBLB#>xk9H4kpI8r;ioWW}hxPFMZ{-c_&|gJ5z$t7x!jtqPhGOaI2tJ*=Ra; zreJguGm@FT-6Kt*G)pGU>qcXF@@JM5CVq=_F&g>OFVWv}X=bx3c9iUdD8Y!plyGjU zIp!C?a`arviS4K*{v|WG(j5eAIgBVT*~XoB7#8Nx75;lR2kUeh9^A6Dnku`zI@ykF zn!4TmyXVgAA>twRphO{O^7^PomFmaTkM#a2l^Tn_vQ-WKt$hu5243KiB<)j zZoh85qY+8mj@=>srP{BP8y5>D^8B(Mj0_Kr!fB1xrfZ^tEiOBqeWe!~V}`Bpi$35N z*->9Q)%EEaHQmcUC4dm`+D!VkYU@4Ved(L{L;;&!uDMkai=otF8Fz-(o6|CwKx2zc zs4+!-J$>Ws>!`!^3ouHiOziINBJ3P|blBLsO(I`178^7R&AZRpAyQq2uxv&fIPt~KKTKXi zpS3*f)L$8)fS-3$wN5?{-lZ9;DG0w616WKLu!N-Ct6zz%o~6H;d5V83vX!4biv2|) zpoRJ##IOHMYD-mw^>}tF@)3=&xo_h5Y*Wx%3kefXUlX76BO3m|s+Lxv)G5A}^QO~H zd(5(@V@;Z#)t&WcGwx$yN?iqa37(|Ll4mj11?CE@Yu@Ue%&CY zHXkG^n8x{S;$g2+aIhYJ?^&sUPOCSJqN6XxUXF#9_eXQPFG7kY1WsgZDdc^!VSw@B z&MTF!0~GXlsJ~;5!*5ewyNv=iFSmGmgA4&n4sPF*Y?{Gtvjlw-JfV%B2StY0FGNS! zsPV{evz$PQ-^?&oPmkDHg=<|8Fv96bvPdUyIr>p%S|Vlq5B2RR_ro!OHModWnv*)r zAe~F;gh0pRpFP~>isK-aI0XVYCIDID0FKK%CGHsKUZ{JoXgrrb83=d5ulGFi3U#k) zx?8`YClgpn-QrV4;oWM-w^K;R!>9L-L70Knb_a6ym{!oOsGx#2mCsMI-lBcnvHK2e z%-W&COm@E4Z+|OYUsYVEhJo@ZARY7g7G7xU;YpdHd(n8X#mCaIvmQXsSkl0wSN(V9 zAn4WrUKAwPP=9&3o%e3w;^Tf8GpPZYx&OtO)uhQnR6uHBn#93wnkdbQrClj?#7CNx;(69RoNe|IE8rd zy6;T0eqi_0Vc2^YFzmA!JE3AliqdSom|*o}@1;@JcHV1PH*XEz_;?TRcj*Wcczdb4 z3E!Nrs7+kAt~lJRIgGLf`XP50ZrC~Y{BMUmT4JxOR`}o&l#q`%O!q_BGX&jz&(Ex4 zVYi8*g=>*JP|tib+t|l4s5=Q0o$p`l3me;#KzkP898=Zu>{wMdH~T)jn8R}*YhEy` zZBxa8Y#|UIVuN7(Os53Xfc6r_T$DPIhiU6^+Wx@SGzg~Pmj<58p-de>U7TFf1wjQ< z*#F+zI4ukCa~DMf5>?tTI8B}AjXnH$?s9{`5BS}&t!v-Fpc}qCv>#J%A|mDj3RW$e z>*ZhU-XHGASOZ>o7KM#nwJfMwEv^r@0~TVjHBJpnpC64{d-T`qWD0`WGeI4vk(Zx0 zFezK7LqjGKS6qvePw!%D1o8V&;=&Yp5@@7==#+(3rola$ot)2$G$UpU9`u)5TUudV z>bq-uPLQ?`=yXRZ6^Z)aP6bfiTyorU7aKP62JX(my6x^|tp*t3Q1G+PJuui}!aa#% zv*QRp*GQmwb=$BU#?k@!pG1l;SL3QHt3qh}J!Oi%Ppb(BcT^a9>_q9uz|H)684^r) z-`<=W-tv{~u-1w)U#C{!yD*y$(a4ee@b(aPr7Z&r#?aO%`~Jp=42^<@8Hzw87?qp0 zuA-)^{frhvoAWJbD5A&W9WDr%;I``?hBePZOH>Rlt1@!69f};9 z*shN1S2{Qp1!+aR_Wi7WEIhdkz^|5=`e{(zT+b%_jbA+3IUCs=oP5s{C5Jc$lVX(( z!=ds*%oU;$1=Gs#-YQUcL(Yl;mWhvO%6=VH*HZJdTjt_((oqzRCU*Am5%RdTR?b)} zU?Vf+m-ci4-0O;X8XX3Oh4^#_3`O~$&^Lkp`cRNoaGZc=TP?3PSXU{T%-`?qMw=p5 z>X<1cAX$KmA|s_q>AYhbxxf|0rV)QNQ|)-0G}ZyOfr%pLkgGxK95UNGGl)~0sbH%F zgXH(#bLFm9f>&1p!8UMV4n5D6T*Q*Yt;@7}CKDqE+e4eXj?+HLDJkyQRmb${hssZz z?;XxtZcx913m&xHQ=4GhyU)>!(c$Fb-W$%*l33U$C*0^EC032r&#O()-`aQ<5Qw~} zu?Y3QInKx{l)-6Q89JFpUV#wD^L&0?jC8LVxmdjJA?Any`S9V$p1@tjwt#9bae#d6 zapZ!BCI2F44c}GoUnAkQid?yQ*~M|C6x@`R9{<}z8W18QABg0rU|Y)5q7%+1T?e)ufmky=nV*`oK|ENDJ5u^> zdeOQEGk4^)X8v^Dner7pznY~nr_5by-6Nofdfuyt(&b&@i;(pd7rPaMt%Jc0TnA5y z!ooVGP;rYLVf0eMY*%k>C~Z5H0P^wm8%(?hoHx~D9V1}z8L0;qtcG?{4BP2D+?To9 z3Uxffm*8JK5^hSc4iy!DuvCt8+dnGh?t|@*P9MG-j&%Gm+#fR9^!Sx#EdH2gnL%2i zJ!%0C;8XG%QRk%73>6Xm_yN*wDqm@+68H@wH( z)u$+$trGMeCrd{udK6NOsQWQ#HizFi2PKiCIMXS{9~Z{|@W|~dR7O8)@CjOZA}#9W z@3()`SKeez#feIuf--6}&qe*c^j^RGvLANt%Zv%HwbQM?x!A61Y;G2v2VtBxRT>z> z3bqL6%Ku87aBSZ=K2PjMz+lr}#~nMve(VE& zTLq5i`W|K&R*~t#0yrsRqP!F5=iH)TGl3jr8RE^`7AO9kW|ZFUU6hS}^>SYwDK}BK zPEb`!4=^$*{OK?*MCJk}&H`+NKr2c?3;3O!UD?$w#J`uA6#JX|cP_nCq5xoNx|J`8 zdqTvo5C>pj6`gk-QxJAf1oUi%fedl+qW)Fbq3~Wky~dBO_e>STNZ@Ei5h=L*bteNC z^2!ObJ+sYtNz|zQGjQM2h1u*k3sAP&Y71JeblXz84U5hsy568Rt>kocbx+R&@BBjA z@9R@2G)rIa-VYHifbJt{Lnt3Bg05a1DcrvDX%ti`;h{(AS`weHx4ZBgyZ2K^VA+^c zI48V#80iT5N}e{RgU{St#}iGxXmeUU*Ac0L*_mh=>LjY4s8Ww+7T*mC8o43}WSk!K z{!FsSo=Ik>&IQED*QQn*sqm@@FO^8^D>hbD+Z4&v*e z3?+9V%27~?`)|Q0P$jT&I>~+K;TPYO*dvw2Bh#MWw@f8>%I2|{Qoo-LM6Q5PPqs+Z zm}ZaWY6%0;xLw+>6PF4`J_PVx!0V4^>)*1ruSWzs4)RTzW~t!l6>xC0uH6W&DsM$*>`>~Y|Ej`g|i7XUV^Jg;*FI*U& zLfNSMi$?ZKxWA!=Un1-4M^*bXM7?9O^|NE_w;WbCwTyYe7vB)kFmA*JDOesOl-+_ z?x{$W=F099dYouda~CRsC{-S^r_1vb2IWL!C4>T?LYj~ zNO-TDkX{;m_r$o_Y-$Zx(WaizCKg3rN@9e)r|LG2xRGQ7AJsd)&2a5`dwdxu8J zD?5mO$|PuPvGv%wU&iH4lW4^R!W+l}XrR~}58+%8(vR&+8r0^EM-CdW%6pWZ$;j@Py8PccI+|Yd3?E^&>ag zlFL<_|6E@}S+@0XoMHb|mNoL&?dItZcoaswr@eLsoy#6 zQ*?xoL3i$BU^6^ScK>)Uu-tmEQ61dgaRFLEWil=ZjhL@zEfM9XBq{6vPu1xYYJ@YIO857_!E|-Vp@i4cgCZ zwqUqKFpew_`ad>6)5g)MxDJI-f_EQv(7!Q0J^dVl0p2b#V1dK)GBas~F?kHY7lQmG zp%vuJ?_8S0a|G`o?mq}9$<%dpbao&Z(+_MW?Qo*RQ1AHD{r7?nt}Ya2rt8gYyzhcv z6XUI}sd4+|T?WXv8i`_l-pO~a%|Nf4nSz%liU;@?o<)*TXUfgSB;N``|N*jb#+DwsZczZ8B z{(P@2kbn~MkYiW*Y?0P&;PYR4CZ}gF)i8H4I zH?iHwr?E_cKHn3u$i?`LJZbmWP!wT_ginN#gl-3*mz%tmcd2b^+{O~LGFUEOnNupp3fVD5_NX8&{lepHjI2}PW$e#@6S^@Q=p z|3~cr-Rq>_SYpcho?At*O_|*cbJ5v4kHDsQF_M;(4B+ims*~^@S^5P@LDO>B&NH?H z?q_gtX7(G{Z@;FkPsa&K?&uquwglnyoWa7w(c((|#-LU<~jsPwi!wjsWKD&vQ?(2x)D-u(B7C#nzWJ2Ee$ zvP@v}Bod*-Qs651$xH#=QN@0eNw9{_M4HTC4ObazzWMUVw+6RBe2nBch`m;O%+me1M%6 z^{;nHG3Gv#ulz*)w>1QE3kB_c_6v+G<<*i;OV~JSLjo?#;6X|pI?3-ZhUUNI1?$3H zbdpaie#QS0EZs&L!usd(D!~4GImnUn`dIxNEY)mBid}4|?q%?0^W z7r3On{_qW^0XCg{c8>ab*~C_i4$@{Jyl;wSLd8pevq9&-cS;LIHA{wyPW4*Y3*1_L zOa3$X9J#6QCjC2W?fSP28D<|{f{5M+XMAd^C{Km9Zp9NHNl&eQW`SvezrPj)(0P@#(zga;-LQ?XY~0& zOrm~TLia$oE!}B);96A!hleRjaUz{>|Ic-Y1&0vB;DxjZS(TrUO!DrXxw@bs+@i7j z5Xc84m}2zZr;S2#3->YGKIuEPlQRXyuZfNcnK~qLRRp{_*qEM)g+&Bh2lH-I*i1Ue zPNa{Zmb?EnSScifDQSnAR+Tk#(P=`f+K`%Wn79!&;?VPHlPGim`D>=l5tw)76}C`%%sUl) zUMBo}uWgCpeuxlK?#)3~GJ5{~nL^;ZuTyQQQfM$6TzgjDViVVKU^EzEq$Pj4RGnME zg+rs7O1;9Voa#2I{okj^1u-Y*MwkA~SU27yj7W#U?wk<`SmI=Sp#%iPCCcLH_M4o1 z|1~;RAWi^trJlUJd?EVXPfzq`#+YJYg|gD^kX|1R02WubTCk7 z^A;Hbx0i-9&K-hV=M7N$tb`6+K9qxbF0-P73xJRc_UOo2-j;Tb&O7MzU+^;@O`xap>uk7uhw{5!Cia-N{i$oX&f<$sH1&*FhI zQ#s)A0m|M*x!3VpwT__>*q#T1@ebhqDBZOVYeXr*3wD_Wq zIL-Rvc;~7fj&2_Us)*_X91@E(xA%oVJui+=$silLZycANpjJ5olKd9Vf&dXbC(PRw z_=DyZIuIWsV?kKO8n{H9^l$&76+8&jbM9sEBQXFRqm_azYAUd|U9d$Vb#?s=jG&Kb z1*I78V|;9vSNb<9gJAb7qR+le+DZn%m!Ej&M8V4L-ILSj;5l= zPC-F|ezahC83DP7%BkNs%ix*0Pr}Q3Ag|z0Im?zyN=kr82-oT%L=w363>eT~hEJJ5 zrnLiF(fJvhw!o!q=?Lr;0S7!lIUT%-r-E#0`?7s23q7piYLPx81t3|Nl4n|7tt=`R4q#C9skIPR`y0dMJ^VQj{!x^WpRV0{F{B A7XSbN literal 0 HcmV?d00001 From 9190246cc0c7ce42afec282cd453b354db3e98d2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 30 Oct 2023 18:03:51 +0100 Subject: [PATCH 006/446] deleted junk --- image.png | Bin 90700 -> 0 bytes 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100755 image.png diff --git a/image.png b/image.png deleted file mode 100755 index cac5ffb4c285dcd40ab5e7395c64143c151889ca..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 90700 zcmc$_2T)U8+bD`k5fu~>kt(l9Z_**5h^QzKdPj=VTPPu+7ePc(KAfU$kQWi@ zA|;Rz0#X7Aq4#>DpZ;^soqy)ubI#1YYX-9R+H0@&l=alNI$COUmsl@RP*Bi4eezI` zf`Y1pg5vz-MQU5JHB@S z_k{2Gk^ct?|9%pel9l}L8)PNq|MdCK7r&k@f?ABVhA1e`WS%}$G4Qoq!O{la*ui#h zh&gawyLb&ef9;0KqwnW)Z!uBjKY3Jqr--Q}D0@MmC^nZV)*rzXWZ+n>v%^rDTf~3q z29<%PE@cT9{~IsH)%5${&eIMZJDk-5n<+wjpO|9 zEm2T#(I?i2{5qvyR&{{X8u$|8y;O_|5LwK-^&4= zfTh~mZ#>b8fvpVv(8lZua(g`4iN6jtIx#EB)ag+YbT?ItS=ymeUebZZaKxvZUUnD- z8O6$gNGVmFgIh2M>g~B*EIMHQ1L3aG@MJWBU*N0DZ9rT(iKeE``H0g&>1wIxfHR=h zvgW!FvqIM2b;LpSC_6ykkJ9Nd2-^`YD*D^iHu(jJxY47jn_wC7p% zEI8SDU496g(~|XAb25}QHLiCm5v1zp`!j#GZQ_9!zr0$k^C`OAETc{F4h7hCGP&4| zg@&XvO+Y;v9dk=x#yiNOhSJ7sZMb<1i$C2IkY3UGKx-4y`aC^gi{^85`JhWBwsDC5 zX=JP|u@qrm=dEu`F*Q-Q7mBpEMgQ|>s?QsGi;^9n>;r6<5J~6Lt0<;XV#ZBCtJXc= z)?nk;$hD!-%<#wrlCV)?6w_E83<^)m_;hKZuTh1>WDave@3~;R1A3E%3T5b=mp3J~ zA({FeF^Mv3z--x@6;-N@JB}loB-Sxcj1Y2lcy!IEndE3FWc*_YBcp#A`1`y==Y+0Z zoER?__~)MvBn5@sPQroa`dJyy*}T!P*g!?P)L`5v-G@+K8R8v|IkRk?9ALGo@r=A# zfys5km5;S2l|wbMQ_#~cu!!1v#Y7<^op%6f?(;KWubS^o7=fSCCXN-^=W@g?0xJ`f zofCyhz&j5<_CmZ|GPZ3PBe|2ka6(U`SD=)*MmS;qR?D z+u(EwUS%+*d`*TlIvswl{*`*2nW0drQ#k>~?;5+cZz3o+qEz{mBj4aM4RX(J0dBZn zJ3?S8xuE@Ls{1{HTPo{I0PJIVyuEWkI@jLMXbe`^eMG7GIfsRZnIhiEc)*!2HL^*w zBYEIR0^zrIPWBonY3i|ndRYeWiG{L&&o0uBRLho%D!$GBT>2?}duF#mTH|p)uQR3! z$#LP&L~@zEf!7oecHD3yp{HZl1&hrV)Ju{RiZq5Ce~zzPHh@cOAe#HYZwZgZS!NOi z4RrF-#-@|PB2Uv>?v1zMBe;$x1fP5Sf%XYnp zZ-zbxEYV|MQimSmJ$Z?kmf)e<^wOZYrksO6tDs=FvTL)^etsT=fW3n`*b8*|4VvyaFSoiIH=53IGN#GE%`;tq z_3sxx_>qEWGEg7m;HYwo@~Bq6`U{ct%?n1oi9&@ykCVgZhd3|A%;+xy zwmEQ|1O&C)C9~bylPc2%$)2oe*4x*Agx)oegquIezhqVgD`mT}SDKYjq=biSRk8kB z`%iWi4>Csz)i+KRi;QDtJdBCKx#L1~lwBw7B0mW-3Go-J+ZhU4S>jwL?7OK`@A*}Y z(w_79v+Xy=e4uMnubNNtwOL1>T(Jubh?$>v-1y3Y_M6G(VBE$oS^yH@Hj!b@Mj#L1 zkT70LKJEHKjP?{LIv+CQvxzJl|Q|sUK$<9W0U(sd~U}wuwvq!z-hEo?IjCufjpCz&#f_GV8nNZ>4^+)t~_Jo)xjX_@~mYVwk8BLjGQ_v z-amT;(hNO7L(CmJGf&d$?Q3fw|He96Hox}I#A*gy<@|vcl6CHDyRhmT@5iYK-(oE+ zIx+>3bT-OxjoN!{Ta8A5J|E-QET{W;8Sx84oVB9U2Sb;l&jPFajaaem=>Vy6_qD`n z%l+`v-Q_#7M<=@#ctVn>+ZH@Ci?&SpxZ_z++lz2f$MO5xIFD3k13HwNERon<-n`xM zGcj$oZ0@WKOQ6P*$);qL%BOV5L=J-Wr9ec$U*5DpzjVUuLV%+eJBoTAkvvI>rq6|Kd7sQ;_?T zAtr0~c0P`J#&{WZ-Naj!K3~q}Ur2EH3?6v4-gKW>q|Ui~$v8butWSpYJxn?s+fEl> ziU|nY83OTTUmkZIZVypMu~~_X*gK?NA|{HpjX-Ko^D0qphE3*zyk7EnVC4bMy??w@ zf3e9*;@MP5wSNZo8KTs1_)~`uiK$%sA6M8#v~W3HY{=4} z_$I<|K{4xSk^LH7saazjfiI$4w%F9dVZ1c|5-)&rp^y}Sa63~uh{qCnc$!|W*CnzU z7Md|xj1{Dk+4sjmZSc(0a z^n63T)K?Sh36WGeN^2`4wxr-4H~~M~G6gQ!^nUP_xDbhOvntq1VfQ&m0#B{lgPC8` zW++SB1Ut$P0?RW?jA@6422V`=Ul5WHkGtub3M@2Qy)lOVb~@U7GP5W}>HQyDb$pT< zw23k0$G_yuUxnS>j`w1lz47Zdvu0DgjMi{|Icup`#3itfyjfoYD?^9z2pE$MtDqn= zXp3}L=UCc=bd!TJCbrQ}Mo^2%L#eTP6;H-%GN!Y^OudOC0Eae9tE#DT#nUyzbSb|L z!SboLZaRgdRIbx@WAJFChOx^kVc^iZ$2q9>x%oq`Dax3EIZYYp3G3JtS3t0)eTxA6 z#dx@Y>d&j&>3RZ3ShLvx(sz2n;=n)*Z{sryt_8HBwa!yh07mH`NtpXh) z!}{mI%M)e@#?pq4_3nb;V%^&!I^BzO+v79SfL3r#kgcnW&&rsH7zo8IBuhBWgzpp* z^%rhnHlX~lr%d*nfKn4$z6%Imte|8$Rwd0$mkzgY4Q||q1^Kz*-Ds1}Qx9b;C zL>6q`-uP+#V7-lnxzhI!mm`UJCVLT?c*tIW8Blmr7o*Ic8`G)eWma7OYZe5zape2Ey!k6YC!*_U2GD&?;AA6B!sNWHn8%=||0PWyv_} z`r8&W$l3r(AZp6`{$Fh0`#6ttkyQtYtg}|myx*>QPaLN2gY92C9!p1n z@zXOLzpx{8>gEY(An(G=*IE>C?ySIl#rl)O_QD;^m4nAtP3P7ntg*cw-xuZ*%^cFH z(sSCUw@Pjvh;f7NFJu;FXKj$!{G|@7?LN?cU%V6szq^(B4v5QQ@7&!^`Rw+7X9m0$ zu>JHLqcD(o@9U}Q1I?MW%v&A3EFrCGm7={D>2EBzRvEYlHhh~r&%>iC)V_u6(i1V| zaOve;PeaKF^`1g98j13|$OZ?arvpK=yZKP%*Z3D-W2-Hj>&Bsyh$g`absSS`bm!6i zA<1{Qaw}lSiuQwNg|jPJmyaRKAPi-9pAp3rfBcTHChc{7dLA*}h8F&yW{H}x{KuM~ zVfdHA^;2q=nn7#hJ1(V0FYf8MonK0aqf)B_;YMo{g=Fz^sq7Hp4NWfqBX?4F;-MBt zMr2uw+c3KKl}rb04WU?2_RXp1W4>yMamD=mtJEo1?Hrmb9a64%R&x3TYZj)MMutOs zfmzf12~=R$X~<_fe?GYpiPS}A`K`%MMsfDS7I_QlK4>+nR6BUJH^TDFIW=vpIOn;s zWp<~U*VLet3t6BbMh9p{?{GTE`h*|yUN}Kj_J7wnv&>Dz>^g>U!90EgQVWDzaz{1cG?3iY3{GNhh<-}imKJ&Dr zAAoYHqf32a!AyS=hf{%Ei z4gINMo$b$vHz}2c1|icJU1F6mKSaetAKqmf5YS=ONf`o~nZWtw(OwH_ldw>B#gbq} zjnDUjeOhP%>7m|rp9B*}OTZqNR}^o3|GCX^INwbNwmy8{)I)&TGg=HEO4Un6J)H)l z_#Y+qCi_^SN;y`=SqPR!^@T4Eyh_qFG-3c-EZYJFWUdn5A{(xrBD7KZ3-)l%NtIR6Yr<`)a` zC_$gjDu=yvVa$%<5Atd|#aw=+os}b2-@sj73LU~4YYd&L-roNjvgIzBUkZg*&aA(+ zxgd)lGb$ayG@e6Du)H5mD~@NA+S@pPhxaohL(x;cNb}Yi^=Xw|M(~g*TiyFBOARXB ztAm?2?tGJkENWsQLy8B}{Wj`WzDL5?>b?_meg>75q8aO2p(%=IwQ1E4Jd9||I^$+n zAjLAD+w6=hKD&GFhgZ}?*UK-o&INxR)q6-15 z3n2jACwHT#+VWc~(h--ai^<5cm)TNc_{D`2D27ou?n+BOn3j}=S)V=(;Y@1e+CNo| z#7c0S>hbZqG`XFioiW)+4#qmKBg=uq=dEp)?N~a(c$t|gNBS6~FZH41OVT4Yq!Zf5 zWqbCAbXv1>9_F8UX}lCFu{^y9dSV8y!cZoIOp~Z(?ma8_dc?!?3K+9(%Nf&8DI4)n z6WQ2Jxk8r5UrTg=Kpy&oUEW|a^ND^F8f+;;!md&O3*zt&>A7x$f2m28VF%9C8=)&h zRTw=ohGVB%-FIscXuI%jUX9bvuF`~Eo2Ef`BdZHy05!6D=sa0qjr7frT7V2_bf%4M zKWhhr>AXh77pKD`w|AP#!CWUOM*F3=%UgA8*3SvQ?X~xh(N!`g#YcovQ9XM5odcrRnYds3FSqqk5QIs*=n(zt0H1lSS!{+(A)Rr^WB%z2qk@9cHKAC z$vANxl?|h%e4x0i!Oi$>CBf%O_0n2|QHPjV#?GFl0rgq+mbxLOWN3KmzaM#Yqgq?F z<#0{g$+-d|2P+yKp&sj7_XNH&N9DIyv~um}kGgn{;_A%-H)4W_kpIMUi%1f>b8DF9bYt9-o2*T8R zx!AEW!P|Mc70k3^+YcOxnwKdzNXJKC6BogUNZAu3|@MIJhJ=Dvg5MQ z3%05a$}*?VcY?F7R`r;)mqGPqtK0zt$Mz>Odr%NQtupuk4lFM`END`JbS41ACzm>0 zcfL_Hdzz8%VzF}$=zD~E|2bJyk^Z~a;8qX)*LEv~@3yC9l^04Tf15HkW?3w7EsbeM z?u~%LsR}xwuyRO-%MTMRmte%vULJyNs{Nlri%*%Y85_4lScDT_Xyi;mdYsVru+%OF&k9=5{bJY!$s0iPfMvGWLy7$`Wuo%lB2o1m+yXdtO*>Ns z^$86Mi@rYCFCstS9buf=X$sIkLkknDsmC`jtt7xc^F1iCRomCNq&*Mw23JPZ#@M)Z zTA#S!=C;afpGgq!>G=Yt%d?y2c}-5M+#LFo^(8(=gYAeCIwa5{# z{Wcv1P9j?9?REOLfUQI|fdm`F+Hld@c7Bs8u3Mu+LYJo?ca*R88C;vP6$!8d9cyMc zeJrnclgJcv9@c3ca?1%OV+L{1rC7sUdfch!DY!mmIbgRrU+)+#Rg|Z~jP$H+J?X%U z9ML;=9F{Yf;)gYhKVA~=Eq&#c8YGA!`c_s(9tV!?*m4kD9ExnReb%*KI$en*P9+}0pS@?WH z>Z2rAB1>#=9jf4@ref|@s$&~*F<>@?Eof6&me82q)OhX~n`-(?=U(0Xbv;nT7+P3( zkB#N%34jF>Ec3=H!&{GD^>A?Ya6Ih6{g9mo9su6=#|j*5yf1(5*7#D|D!buc?gfQz z?wL6lJ>`*fUJorv+X+5|Au+nq*gM6#ncwRhje=&WOpeiTgP>--xw zIin#xXXCKe%XfKd?O`A%tDWFQa2T?H@=X@)o%Bt1-pY?~h<*Wi9z>!1o^5ozfx3(+0Ndi6K*Nx8? zQIs(tIHXpgfWH19{dW8U3F_e&BZ(_`^|qUAcQjwUyH5)IV2V`YFcXj$SIH_jsg%Ww zp_G-Za%)*f$19sMNcQiVGmVyEA&zS=AuzO)DpAQ0-tJH~z3UOs>VeAqLVlbgQLOcv2^T>+14(NZgJm8ftCGU(@6EZfv&S5C&t8&RpRnZNG<6zGy43OFihi_U8Cw9@l997_YZ zTfBF9)|jOa_bXu*xV-izt9yVg>vkOlQ6l;%w{w*&X*^JuIGXCC_PLQjwd!+6>1vwqZ5WTL0`G1htP=oxVpi=I3&Ai+24HMorn91h3q*b3&W2MkEWr>Cv&AR! z&K)>gh{# z3EY_GrKJP7i!LQVrSH~c<@6?=jjLo*1;v~n{*>rT9q50mbZc}=qUxQV7WbK($-}N^ zkr7OnRs$AH)V)|9{0mLSnS9toEAH++kg6=}zcOH|lK@?8;lqadxROywZ*scJ=y)i? z9@|>Be%xO6t*@G-F*_)4Q)9)?nFWR0x_qK(U%HrN-D7cm`JsGfR^;Qk!O!qVwQPWq2iHbpYY_T}c(X!Ht~*Zd{4^IH^8T_h&Y2*bvvNUH_DRcdbdUD84z;cuW(HNOv@nx zuq36)!YFyhTLqSwZ?$eUjSRR-?Nx3b>oC;yBk-+mGg*^ z!Pm;xNQaL@ww&MW5sKfvuy@78@juRtmCtO^9EL!*RAp$MLhgTl}`DOdU~k zEtwGAeZrDLwwk1g2ylhCnN?CZZkaiq>ap;c4ozMzdPF5+GuCgp_cpzQ#k3uep&L*$ z3Zh3n$;@eAG;asKe&e=JsHP$I{tIx0MGR2VpQ-2E_2UWG9Cx4h0vwgsu7GJ{Y=XtU zd@qY{=12}!=uGVuzm$mI5Bd@SG?4gmq{lyWAhot;tkL=kZL(s6A$YO1mID*rwhPanvV z)NZd@kPFPe)RH#YM369-1ggIK5%#?H+rsu@YoX{nU9(TFn_`gFvXLdy()5FKa%VD9 z9RQq73pAQM_yjFvR_d#z(uO&3$md1}ge^QgHUi`Fe3;7((7n+mmicl1bxs88YHrmZ zKVmVv4ITE%`Zb*isvFAVwn+gzipRS&^e(F<(df3b>~sbtvhN;b(e#*Q(3fnb@d2&p zfw`vcZ8eAyKOCjhvW>$mxg~&@1nJ2JzFXF^3nrS65j{U*+EU|$d0nQ~Ykq*neZ3bO z{4yF-L;Vr2zM&*Em*b1u*GebPAbFz7LO!I%Z7d6zqCGg;nQRIl;P6@h&Jca*_|h`< z2o4Te;8rBnwU&9rcPNo>W+>{DHuj*UY{yAmajQ;;TK<;|lTpL^tklzm+1XnRxYBr} zSZ;BI1K{Yt!rD#)NM_MTU2nxAYQQf^a^gmzcMbL$$OKMSq`x(dbTqYCf~K#@YHT8J z!KKo=16bmfc*DnxOPfrbVc*>t;EPm^JXaq;gF&IaS*^=+_9HiMR0-QW;CZ6Sbz~yh z6ps0htIqEhX^eAlo3E*(Z}qw}XnBk}4$pWrI}VK1<;Gel=bY@C;4X_#xUSpO_OBA7fyEAEEa6rWn zZU$<}@Zr101H}H%&s*EQ5$R4G0}0CFEI)XG$M5~6$A~L8(NzKM1;8!)^9z|~VUTedPjRK;1Ext=1cs zcjII$CX0AnutUn5r~VXj@GlLk_eLWt_UsbguiGfe_FraP+M5++fnX#4m6;vpt_2)#%31qfQRbXfTpO1P=mBwcX&m35PI9&OTl+KRQO?Gt zxg*5U_mj&uFCOqf!A4fm&PMu)>K!P_N*DB)ps{yf(6b*U)fM28sh}1XE9s`~?%_Oe zXz)qJ6I;3%=Nu#ljL1It^A1XEe39+> zJ%c^NWM9Z?&;VgnC;w7+W^}6}xBh@L$|D@d+dO^G6f1jNhOj(=YVWKCCZPd+FTxIa zo7+-rIh!-4pM>lmM5JxvPz)5mc1Hd2J@>gQC26M=H## zLQf2Mm3{QJ1q(W!MQ41Ldv&fqP|9bKyK;y2*Us!%QfF+#E>LJ$kUe_f6jO0YoAX`W zH^)T)YtnRL_c>0`1=D-oWM`jC76UUr%xY_c$(w&~OelF5I%P~10taINJ-u4FEV zfknT*#bWNp*tfh+tv_!+zkNi0TVhz@X#TvgaMWN6EgjQnqyG2ph6?$uGoO*}Ley;2 z4B|TDXtk-LVet)9p}zrKI2_%k$$J!-zb(|(Xg3_Dn7~VZR`;iNgG`6u9pm$`7^!8b@I2Nos;s1 z!CP8xWCx&hiGdM0m?SYlXL9=TpHBRJ7sHsX7j|3CT0A2)f9@rgYwLHij;$#Ec^_J{ znm`}sK#sK_OLs@IW-zT7qqV8hA>#re{E}`y(z$Fz-?^#dZ)C^ko}4M&NVhCKdQLzt zSuGp?s(3_>ERu#Bwj;?V67RJ>Kt{P8IVNiMPy~z_rC6IPds$*oGBf={HZeJ2U!eWNqJ%@Xy`5ZS@lAKj(+ZE7KR0jJoMd)!odR;s*zty@Nf~s_PnMX*0)GT84tg2Bi7Bh7|?^zG}2` z^JSZ{vQKcUawS276=5x79!5ug0t?<_PI?R1wH6fpw~KaHv85Mi==p&_Ow1!wgPaFc zhNVUzX_s+>Mz4jH2^-Zvp_SPw^tT6%4wFcN?qSkz4GoK5Pz7jDB8F3O^bT3iBd>`_ zZe=4$Q>ChrS4*E`(Iw9sb6X3SG${h7YVw>j4YVxSo*+PF9DZn~4~yWB` z!q>p(XUyxth7TTuIgb|2Qk&|+QpE&zNtnX>T-k>^L}r0&TJkr3pFrpfbX!1WZ?ahB zJnNWt6ouTSq!bgw0d1G;SG|dKE^A6aq^~A*18wM8F3Y*~fA0~$l?l}j_BRO$@Lrgr z{OmGT@`&R2t~K)Gq>+7ks+;kRzsM8SF&ab94w$C~F@zAtp29SyQdVYvO7Q4tQp?3e zn>yHI6L09B@3IY@n}2~!orFD7`Fkd}`o*?DfpuQ_Ka>0JPwFF_nNojVepLQw#lbl= z{#@`%KR~GGaJis`nq`LXcI`lvSv&ksFzbEs#2u}Bx(cZ@7m!plwh#Y@0M`EoDgF=8 z-tNg)ZAt0XVH^=T8#3D9gmZF0wsLC)N|uyswcFGnF|)atoccA70_Y-tkWDwmec`{y z()&ggcWT&vFm_vdHm?%#qC*qpyV>rIJ<&%944$9m;kFPO>Bo(kHFj|@>>sB)v|R`D~ecxD-Se%Nn-CV}Of?!o4( zXML>5|AcbhH`OVONHa!|_?e~MZOwIm6cSd`S5az2`bmcF;iR6!ozw!}dLOpjdPpMA z1_6e_6m`K`VuA1(2-bgAHx{ep_r&*^fyl}=Oz{2n`gm)HYb;nq3_j3J~} zhS}*)VM1b@(_4jBiY&L3zxo{Att-huZcR<>vFx7a>)L6JA8--}-)(O&IAOq4g^ZA3 zEhVPw*9}f}jBNd4`!%V&1p6BM0NJEvzXYwx)-IN;3Q{UeE^M!5T_h-A^`{^WvJiii zqG*1nu(~U&aW&Cx13bK7zH-7aK?tvC*+@tF`}WNbOWcLiy^K6nrK6tsJ~w45aK zH-y?wB?7Yj4wq>|6Iil4CRSNQlJOZ#FDh1^2(2g6lXEVsqP&snU@<$pPfN;YC_&f) zZr}Tn(tU0EW5LnwZJJ^bg@WN8(Q}|a)-i}bcqIp>BKhYw{Gmy%ot&mbj>$Fm)`&K=6xh7AhA+Yz61nUf&y^}OHc zq9TcJ(kUA1>eBXZEtfMdMILM{w#gcdj*I}D#qG4zHV|7E0 zo~jOC#+m8one4&QtV~y(9dun__!PW-aTMGLUb4WwDBGywkx~0O=fG)Z6!Ls>cXChJ$zt)0lcsf|SmMUR&p4cU=Xkyvrv zGZZSi7l0-@JIrUWWU1MP<7IT#PURlpF*!{^k#ZyIBWhM(0%Z1egKCV>Mxdrbs60>$ zus3CW?a-#urWfjU;is|mHmAOpaSEOH7Z!KpVI)(>3d#KB9MOKkyHt{tkD23+Z{9Bv z5bvLZ0>FrBk>_B-MLB^?s7Ya`#6(@cwS%BP- zv#u@maUWLNI{w7l#^qnbDn&)AEAP- zSj6-?U<;~;EXu@Ak5}Jb4pm!E1U?OV0!b)HWDDPOHA&>nhoKf85$bB*n&qQ;FF8ck zExj=iL&cu&Ee?`)GJg%Jwb|4gvVSQiExjnDzB7C7TB?=Z-H=bi{o#u^)3oD z9DymcuiE8^ z1B~nxdttcZ!y*T>s%KBpb4~rzE~{1td0Y7Yq*-APcIKVZSGAwH**_xF+6TfGw3Vh; z#x|8ov^AZB5Y}IPpM-4+o7V_%=6!lJYwt&+0Z;kteemjGEh~i9{&A#6E+v^_XdRr? zHo|bg3$!J3Nmq-x>(ky?9bAf{w^1uH5m;>T6*TIfo6c~hQYCFf{JGpdzfEY>usXx7 zjkP+2U{AJ7{r9$RBYsA%yA1|}jKr%37Yosxn35xS)ixXIvu6&UM*UqV zE#!&DnUaC3)v;N@`A5O@CsKymr;At9nkHl9hBrl^ak+f~1?oxKC`ff>$uu-)C0=nhI+g`7ex=cWSN_TJ=w+{*A} z5`OEYLzAd>z#t^w@vx(|j&G}~*7>qvM4Z)qtd`JYhjbO>vAWi01ErpUasEB^(pOaB zTYh%6%*Kc)J{TX@ABoo^_jtR2)6WLZ!T&0JYkMAtzj5oHm>V=bOY{KHF-pF!5ax^u zWvg9SXe#ega^6jhcub|*a~cBZ8RDN8~mn{NZ{Ril=wo2MaOKmBD$ta zp(%|pUQx0cxhsH0(Jp3+98Cch###p@TIm(9zACJC=<_Ej>wWR?dO(#pBr6Ee<1*SQmme=-fj_)MN=P@hRF;cx^AYF+>PuCuPO@0`euU20^poN_ z)6N|HTZAi6Qxd!%Wo56y^|bctyiQkl)#2=8F6WjrFZV?dgMhIIh9b*ziH(KgFN&EJ z#0rIic`X*|GB;K+?EReW2-9_j*UZ9KK`vQRC5^2k_-FX8A;s&NM*NPPd~s}2hKyol zceeFwn3k5-biU5B9_J4Rrt&mCXf1Jgv}tp(bISbM2j>#Zm-oO=L8~@la0lvya!uK9 zE1I373@8=S6|DP@{i`ly6TNm>DX)NG{&$x$R2#RUVWHCnE01aFKFGf#-_#vT%xHI4 zZ5CSW%S#rZ{GEfbY#)?^d+qEN4Eg^gr9@P_F8E7>bzX^b$qtRA4A1RAy|Hf~@mv6D;!o%I-*J(0bl$HjMu&{*RJ|nU;uf?!4pnZ{kpWxdZLqH_{Kt}yA zw7W;a$qaKJZc|+_L{OhwXMFiL@yjEs2-TFa+GEK03{7~?#$<7as>?w=JB4+EMa@7u z|1E(Ry&+fe7gZ<340;{Y%$6R~C8`^~YYRquZ57VpJ3+n{4V!ySDYFS?H-~X!tUVliTpj1U}`Ky6ZP+Y73e*hUdoACc{Gr|9us%R)GBt$H7 z%km&2jN#+Qujx4ziZU|Tfj7zSIqic@GU_`U^6>B!KWp@Yt!#8`+@c80X7p1ar;+j$ zlEdEzsP3w6#sQncw*L*KkuYd*mOAgfa<6N?BZqagk2P?=A`4@|n;^`Tu#8zd{VTztn%# z|L082{|^C|5Egnf_IA-AY0wyR`G}a4%0}{?=LsS_$+ui8tArJ^NC; z*MpP1+5l7QDfaF)bLTQ{rQ0t}uUbs)+2T7Yo%{+otm0z2UG{CuQgU>CcI&$-@JVRn zaL$xZ3+xxwDe&CgQClD5YWGc#GG*#BARC=gHt@QSnGvCFaBkfiia8;{n!98YliRTClv+lZqJsQ7WPdD>$ zqH;1%&G~TLdV<$x8p5gwDa44%ch5=xE3v4Qe@^!O=qqjG37b%xA=ZI2@4WL&q^hrvAQ?KfK&SBfvnwOE z=l!~w@Z4nnF2@4Dqp}`q1oG1i64NqVd#>&Dvrs7G-OBn^iVNn(j=P@caDbz z%vKAo%vXn_k~4owy8KI_Me6sNyd9?>Sn!(lHtc3AzAD~fNo^oiZy zMSG$O&LmkqO*wevNS|PX!6&7#4j>sb`{8D7EBc^7uTMujP+axp#E(SD%BBkT)A!VM zrK@#}2|u=!u$Vlp^@{5d1xs%Js_&-LI>m{U`O{|wi(-e5`)&^Cqi>5E#kJB@+dhqS zl~m4%WoH{y`)U49y%^aF(;}FhmKTzMxI(9bfMp4nm>lGpHsQ+%Nr7_;Hn4G^OM8|ab! z0};#<#zhZ35~v5&$k6rhidy5^k3#Ky_qC#Ed88bjzFWY#hSCDX{cD^~`!ssYZ{2qw zYxfi9+0h6A^KJTE0t<_}m3=zZCC7tT9fYaD(dOI5Z#dI~(P<}+AyAJ&H2`k2><4UOgS>#xwAZ>-)=$z-f0|fD z>XWu-w)O<1+j0NMkc!(lE`ih3S)W=yVmUcs|5)uG=%W>QMYg%L4{=8z_pn5a^&g%dv=dV$>q@Qz4 z9w7q1nqYwqm26AUtT}KvDyAGV@@VKaUc52}fz%rQ@ZDw*^+5ng;>e7fL^8m?o`9ns zpx$a&>f>DW;TzLKZQ;CAivcZ=Egwy$l)V;eh34;#nozX4!_r%|!W#e+kHFp7s?P;H zX$r7U)Y$LX)+aEl<|>SYO+-ODzKO`UKQ)M=A8%z`bT+hvp2R|NZ_%eYI~lDH<|^r9 z*FNBsGB=7>=|G*PmDOQ10lCRM`<%Wn^g4*w-tdW-BkD!CpGt#79NPa41P34iSz<$n zu_DEUpm>ODYR$vtgCJRx?=JhRYa2Bu*;iagk7-Z$s>5d~nymiZNV6QTH z1^%(`Hc`AZ+kx9;xm4%-?&5zn9W{P9e26dO>{cu+rC4UbKM zDxiIYFAwy!Oksu%6XtY;J^hv9PFJ7MrMEn=U+Xp5Y2#kkpuB69cR0<&slg(!)B7-h>1{E}KWt5C!IN$kJq(&}ewN*rdiRG6= zPHJv4`^Git2Gmy$Z>zx>57}PycTaQ>g5xFO_wSeTV)F*EG%llc5oQQJg18Sz*Izf> zJJm&MvgH)fx&7snb`U&~y3VGnFwG+if&&dXw}qHWBs*?{2L0RC>_A!gXTB4|9d7Fx zq$%&m!}wy8s75!Np6QB(?&}jiwyxM)jaNk{Zynv?v&wG?kz;n7i-e*gjIWNW&N(=q zM!{$O=-v9VTqZ`NVYZ(>=T;9=S%qL-GKuEOEG{>l4{JL|F^y|EEV@G?Jwb&JTpU`Z zkQWAz`=1pp_$i3lO!K9IG0vlE#cdCbxr4si3{v@R*HGdvFlMorjrOe#Z-Zb`*HGup z6oziH%AgS=rjM36Bm&xRrdxG-`zTrQ?#GH8A)Heou71AR{?7n9bII%&2N&VxW~5Ni zU@alQ$(_!B{EQQ3=`wvKx@nG;E|rz3Y-#}rV}AUWV^6Y9cEq&X=BV^&1}_!#@nmX1 z!2(3UYf;?mL-rm7dMUe{5Qn{A94?#CH6hz;=`UP5mU`MLy2jafoYQ?}WZoppiq}yo zI7JV>BQx`yjG$J0Ff1LhRA}wpq2}Ne!*I3V+sRq>_!R)>8Zaqh(aysM+SVz%?UwW#ZOBzN+=f*Y)apt}X@bi;{Rrw!~fU5C^l5c)@9JY70rt5u2b5ozasz zu0i>Sl`69_$P4;P0}yjt;gr%zBq>w14&kPDI68A++z)ZYLqvBrJJLMfXF==&exqt; z16>$RoB4GmCxfsHZ;de_~?2OS2avnI7lF3H8A;4!RcymNS%BsXQ9*dt6BZs>E5a1}KA z$5;CCY}#qOO&IkR0rfNXb0VBU=1Zu1eiGf;=HQW{z}V%8b@aWRTf6>BS!#n0L-Arx z!Mauj4`YumOB0s^q#XlC@%}G>i1&ungQhZD2MPEZyNd5iXR8&XZQ4#Sen zNtVX{i@EoVYO-J6M)46rL_kGAkm6$j5$Qdl*Z`#?N)ZAoy@cK&1VKPVK&5vO=}lTf zkBERsC!vPk0s#^rbdqpxeD>b&e&2J>I%}Oz|9oLB79_cUW#*b|X0Ab~yqwbDlJIhR zV@_w;&0Q$)1@-8*U8=S1=uU`qeUPVV`M^riDvxQT2RA6=cl*I(^?8@9k;k^6T8^b}bhL)aDlK;1aL)p=@?YlUgC7NJlLfvmW~G#w z&6I=ZCB7~tzL1cNRFikC)9m=8(bSd$BPkvI%r(x79=}E{M6xbnmWIVs>=I?6ny7cZ zUDkd3d*aqy^ws{v-=?xt>d;`r<12N-BF}EC(zkFrPIo&8*^9KO06=(rR9b9M^*R~3eBi} zk8xLC2D>nnruUgTAJ{|<&>V{rt$TkxX9Q)h^7wr#Mn87SH}j4e!04>I_c&-q1_X}R z3T87u)j#~ephOrlS-X-`%$vy;;Itv53R}fCoU7JHA8#dzz9Vw?9fG=6dt#7%9`!nX zEG*@#*LlLV-?9cM4K5_=*ncqQ&;}Py3Uk5KUa>xX@11cWl~m{E?SqP$N<6JkO<(1J zs7&fG-l|J=;=N#Yl{G)`6F7^t2u>MWy|(b=Jw&yzTHU}0%W~i>cQ%pJn0Fb%ah5vQW78OSW|4H*vby3Mt8!}H zA?~kSSFbclROh7laF7TJA4Y0TV7IvVo4$6guHVz_t!xD8#q8Pfq{W8kJPk~d{<0q$Q>JF)dSF7t=jIonSfa@PbYix@5wQ72-x<% zN$;7DC|<`$YDT>(0n-}_$&0e-MOsucBx?EDD4OzAHx6ntmlo+`liDN8AzYP#36gwY zucYpJEY@=+tt6Vg0k(v zOg;-*u$`7kyea-j+ahFrZJncD%&e+@U%Q>l-YYhwIZ z6!tqz9+-o;^}qck7g4jed6iPBKly;(>4%K{R_&A7Yu^}#$uQfW6}b@yKRh+}VOA1i z9c&~_paX7V5xv@B@I>zD{i4oon2WX#PeVtQTH4~yQU^hjwPR0T!#_>@Jz!#| ze*ZXl9NJz#Xv`6rM*4J64nF!-LB3mh1;N(yI(Nc#k& zuq%2yw%}u5|FOGaa)c{Y3v2sJkuC_85tE(Oq;#8My(8TOn^PQ(vQyd3T2O5MBIhTL z1Zs5I^`-lz(i@2tm3C>Yc=JPbDccBZ;cncV(o!Wxugd_jQm?|Y^!s{Y89PpeO-70C zQ`ex;!)~1^i}bH*F~#r>_;oi!5dUH3&~P`{UOrI+Ste>Rj_*>~53aCb1yx(6y`JM*gnHnwyBiA{B+5!L7tSB>s_i1V8rp*WdE=_tRK z-wsolFA#kceZn2e4C0@n&Qkkq0iu8miYXZ@SU34P-@oZKm>F}KqVP9|yArySE&`U4 zMo>0%MVNo^)GIo&!xl@6Z9@+8Q$QW?^$Y!Tb^4Ab_R|dxKSeiRAc(9}hWQFvf6u3n zOzSnmHolJju{(bQcIOEbSpeZsQ*_1n(MmCl$Fm2fStu^i(Nnr-evahc{o_TkhqfmI zf)09mxEWOBQld_v`suQjFNng^p2ShX7mb3$Bn_auI~Z4=qNXR>>#Cjgt8 z_$yP~p~JqEnX(|4#ei(1YT994jpP{5zq?8u%E@aq;8sJ0lwq+7l}Znrx?=P>&91(USvPp zL$~8$?y}f~!Kri}<|VZNgX%{WKVJjA+PG7uDKTy zbAMuO1mFWI+MpL2&3>;StmFg`;+2w(^=U2GyNbL!jMK6D7B$ys3eE`iPu zEwE_Hr+}In4=67b)~yshOq?M;Xp58#qE3q*J8eQ!$*IYs)hPxiuUvDNLthA-MM+YlTt@{`)-RjvZJxQEq7zlIu=dI6c1;UD`bfim~~Zl4{blL zZ#bOVs~?;Qvi7V&EqN&_1y&9YE-e;;A-k8?<=*}fn(}?XAkTbc_Y@h(HADIQy7PRl zFYa#*>s2ix_ZKytop&OuM%fj9iaVlOfhC#aN6n24j_Jh_I?Vb+%rmBxZwsS=TCIUh zfL@g;**aK_d|5VYj8XlzMgzJvWu?!oYhI=-hQfezMd}rkJ1yc_15Tmj^iVl;G0C~* zN`Cq})06t^FabP&>)zDWa63Q2Ar=*evv)CQ6mN0c?p!bCWx6vS%DkS_D-4L{sU8Fy zJ*}T8bLHz9=tgE>-Z_j5-r81(ZIXK0L`?YvZm7DvoBmbAa9JHYJQ4cB(H|k9T(u`r z{{`O84V}@bP*%I{Y-ZzoPeDT$CnSo5s&#{!+BlM}AS*YIBaS=0CRl8#NpHBCeud$+ zv^GTtr8adQPMUXry_u5*4nO2z2rPF-)ezD z3zq;uV-S%~N3{zcOp8Q!?s+qvf&b-h*1w?O6>@3P`?KhP=mXgIo_@pW6h-SO_MR>L z76L5|xejkHiEH0FHn7_L^7(EqZQ24e7S&NiUHN2nKLO{NHBn$SJ(@SL;=!W?r$B91vg?l}8EyaKw?T-dV z3)Aywq~L?A&5^TS_$l!_`v!DU^3x;tvt;ZiY6UCcFYMY?qFC;xWLIBFu73hOvilX~ z_5Bldy<*rWy?9YsrE~yb56Ox7Qq#-{x4H~*=*{F#OtP3!IySwWc~Z^(^|o93%Qu?S zsbY23gp@f>#vOS1KAJ1%OtnwD>H51V8%^*RnY~w3~r?Pbfa$|UkBM#zU3+DE*Wp#H>6|TfiSDaS07!r0& zUsB~6n%rC5+k!WjADCV15%~7z5ai9HoCBPJZxYylsv8(?9l|F=_AakXmkjg%8{ji^{B0&7S=3OD!slmBKQobeGDQsaifEg7rR&tQVd_ z@Fdmg+D(IG!D)wGLKd{6moNwQV9X$Ma#jbc?C!|J*t9-=qT>2po%X|908xC8X#>R) zjlqiQSYI*J!{SZ?Wd%ZmbZaG2c3cCe}Yy zEO;`(1&2B0#V?Z-vLD6$3*nC z#&tohZEph4XknXv-hMENXQ=2ClpQ#MCwE_hzbs^i{~_tOa#L}KC@EcuU|hh!!tyL8 zvY`OlKng)JHWcrDOMF;E-_r@P9FCAoS8I33B0dmot@|i*s)m_|jJ{G_Ev+wA|19uE zQWmCxOahSGX2{U|1LBUq1CWTIi!Frs81CmsT18eVg&(Qw%5@)dTl!_mb`54nK6U0Q zWFYN23;~@xU;Lvg^s9~)o}znX+(aq|9Yy!2WY+pe>O`Lr@?(B@e;#vHrLq??(wxB zc+v#JS$;zM+^b^r?=S9uar)RNlF0Z(pR_N&vlD%hphQZ`D<3UiVFBZOtfvJBT?=Rc z^1ad`hbX`i{rxbic@5vlwyKc*HST+03MQ)tDlY@TEFM3H0N%v2RAvbd(TY{!ikSM$ z%p)EshzaK6Ax4u~Vfh(=#oqgVUoE_uu3R-EGAJJ1t`VDFOKd*@FuLtOeJ@PtWmg<3 z$!f3?30E5QlWjYBq{+EN#oo;Jb3 zBU1Yh*`xdqoN7d?ICi5|VN!%98w~Qhm0dnRA*?t@h%dRI;|L)#^B1bVEWqsp-BB5M z%K*|8D2egjyb2H*yl|`|iEO^P?~>r~c!7id)hS`BU>ZZxGnDHB$liM`xhJ>CPC06e z9-ecvnvj#<0q(L7zwy-r&04N#IumGtm_)--5a@(xmAb`rL_*eX;%)_cy1+xUU@9ly z4})C4lCsU2Q>X(3%70B2Kf$G!eZAoYG;q{*RP6B%$A=1sUYcv<2tR%}?<71!A#fMd zH*c^+E$e=_>5O34>7aaU=MuxuHlhMt5L(mu?W-+iUUGTtc)p8`yQ#%QL#*}RH$7@i zh|QjfAdYY4w>+VQ?m7T8We5Mnoe-11VprbgMKOAdn5B{4UeYI1su$TPUzS{R49dE0 z_+<3!!RS?}cW!0t$kxPET)H$qRkkV0Byj+505BGo;44y+4zIpSVsAee^UEsCe6drIi++ zC*HAz_QL%&JJ|_PEY1*qjPnUoW;kxsSF0@KJUBWnKgM9$ESGdb7n0Wfts$N(g}Xb& zqZfP0-gT1OxjGLh8Gaj|l&s38N*SoVT<}Cc&jO2Sp*;Qk3@&l&$`iJ;36#z|;QH14 z2PZ6z((cRh(~l2?zOvTH(t}uCJU(!?TLbG|0_{9IE{I$dDzE+eJ+hBqk#BgxI9A%p zQW-KfZo+4cP43HWkRpUg_3*(PK$+)>c3HnJ#SPZil&yJZW_U$2MotN~yOuoQ$(?eT zBF?AxbvfDVD{q&%ndPL?ec&eY7OQzEJ_+pQ)9HW#-QF-Uvm0f094~nHs`d%uDWER- z82m~A;z**&!Zl$(HW1Y4JJ~D(LatWbL0Rll2?0VM^W-S+-dO0_3oW5 z$>C{0(qqM|S6m~@yLEsJMf~2O`ie(GRbO6cZ}!8ZlD)c_vi$6h?KY!-outP=KTJsu z0`>qp)o9GbCH3tgkP5D{>SC969PMY07m4nmaUq`p3L%(Lsh7EJrJlv+$GSq;dHUwX zfy|w8zUn{SIdLjuSEZp}n1aCLEcGcgK*!EKh8zEsSa#?mD5-UNb~-HRhwkexuXQMg zMPCwafL5V06E=0`%e**oYS!V z0SYR4^FEX=W@K5(@(u7FadiJw!nic9jTUUL(Smg$!VTM)cbjM_Ut6%R1we4>R-Tkz z@zkud+LM-g?EACcoG7Gc2%8`ZUbTjK6?nJ;6+PDw|4R2qYX1N2T>9^lr2ke=|KDqJ z;uQa>eZe3m5AX{6(!zb!^T3xpdCgq8NUO$KWnQHggV`=U<$e3#RC$J&Tocv-#=>J}? z0fiJqh-wWk$eY_93SYO< z|7=p=KH_w^2t^heI_Ot{_&6QnWDagc`OoVM%ao@YsjW9q)E@@Ar$04W8(IMSt!AHD zdV{o```j=z1^Zl~9}6FWu=Lb~oEEShn_OSJH#%q2Hv-gtTpN+Penv(ZvtUSG&8mOl zRrknn*LC=Q%&_|J8fG%7U*DqH=cyq-AQk5rMy1BU?NcCp3_B*PpEFQ{8-FV@-ZlPQ zVO^G|o%Y!uOg@x7gl;P&MK?M5PcnN9%~!P-IK#lU`vhkRvQ|%HQ%%*!tJ23k98v@d z+<}@x=~Zm8TJt}eDLm-cUTIb*WbJpe=D5o+(n%QQ}p>TFok zo%H3tp>p2A(wn;Is#^ivBE4>x@!ZxC{1e*+RI`5ZyMFSOdkzQPhC6V5rRU=cN2cD* zhqfR6%btGsWu{3Bj>i2{cUId=tCQ&$1M=o85#Wc}i}FSVd6n!xW98*7z;w|&{J6v_ z7WKK}(L5ZM>~}s;omIJpqoh4UIz@TiYSRCq_YP0P&*Z0$Z>&Te?(H>mZLNKHNi*?l zqOc8}f&S1kpU6am1@o z{;AlaUfC!N?eyVUM@aS)-m`C+>6wobEc3KI+6tjWNe( z07Z4pTBlWUJSDP!^^%$E;p$2p^^7||wJ1A3yRVqD`wTah=v54d*8OUR2JxmeUZ3{W zZAA~&7Nnau%V;WwHI*&;mJxwealjK&j?K%ye7}v6Gcdry+&2DC?$!10iu4yUmFus0 z!xK>o_h2OOu6*XPj)GzvbKIA?yJ~uUugs7VB5XU4?t1!CcP9HO(c|=ypY%c6Ls{XbYU-o?h zCw;s6nzd59Ek2+0VD;tFK6Yq|F5|R&#^BpCXG~QE5X0Z|`5mZVW-5W?s_oCdW)66> zF4z%#JFBf+fy?z%I>xHNESWtcyc)@CFg;9>IuwOrZkAU{g~nm#MYPDjwEbr-6(_4I znmRrKSwhh&sKdbmPD=4IjdS)Xi#+>J5QGY!R{us%K6_;(K&1WSkZJ{j)(E^VfP7LFEl&hyJB4&84#ST0JK3YJ^V zdXkvU<&HvLJEfJ8sAKb@_ssshGpg{SqRCr(ZvoF*NUJjw0^)8cG${k=t>>0j;(qtI zcI}l`;7MAJDgMl2C|Nws zGf`~gqN0zn#jQ~*4O@(M2ocq%q?}bkub^v|0P|O9TCpw3<-3%$`5he5{*i$5 z%@fy^MxK*7J5>qeOMSJNv=tQgA+z{7_(!r%n0L?m*k%vMY$UD>i65ad*FV4)z($4< zJe;Nw@*+6e71oF-^!!Aj6c_!%UgWS;IO^Ecy(iPI|V|n81nu_)BzlZda zCzSqIMv59IX~Wh0`Od}Fr%}?Dk9j#(RqBFbUM7@V5PB7_rt`j#x$!aG%0$)kR_>_v zE64FwY#B|^>lOFRFx*gG9JgY@l zBckFhQ-NnvFS|&JG|mC6Ezi{(hvByFRAYg)ssj5A3X4;)LnY>3GTIo^z#t@y9{TPG#(6J#ERJq6y!m_tUXzF%Qxd( z&izq3@bl=f$UXd}?w8h~5NRdMC*xp0N`2xBVDid6&Ul_=L5OTc7&QH@`T;k8cB`%y z^?RIc;r!8q*C=)!e`A)(VH1w2?WDYNWX{QzyvF>~`NBkjE(CfwkspznYlq(tm;PqL zXl^hX*aP>Rm)G@oBeB`)FD};BujN{G|!+T?9#H+T4)SU4v z4gN(iii_NYW%#uJyqMOs{Ym-giQ{Pwnc>wBZ_wb2@(HY55=|>|J^e$v&M+$TE8K<_ zE7${~yV@RHcetAr=wzxUY%-Qt;TSPIx{?qU0538<_At-?$hdQWJc1tWM;Ij@YLX~C z?-I@cu>OGB!gU;r)^^OtIF-h~hI3`;qG~|q?uqR%F^$;p_Og6tn%ll@AZEae!V8Iu z(`9;sykR6oW)5P&b@jjdUcJAQt>>`Awf~jBHzogo+FK-vv)`@`0QH>U+Mw9SWV)8B zk=xMr_Y=x&+JDH?J44LsnfN2=7K7O6NsQ8{M*zTNi*z65w~MzU74q|;oRZsw?kL21 zY?B@dH^y=I!F+cia8MZW(m?`{uL8 z`HdBj@|>80ilpoqVmj~4p?wXML-k^GYnx)`?ceg6B3%Z6JI&acnC|JEOpZ^tYKlDo`b$77b zKa3QJHosaT1mCM199}!Gto(-&r+PmlZT_F-K7JK%oVqv2wJ{Jp76%QRxf)k@T(Jk;`9~wv7flypx#WJ%7(=c1n7Df z;3?U%*5jwt9;~+K8x=~Oobk;fQv-uxJ*-l;jPq0p9TV4R_8h}qf8*0mT*ZrCa>@*f znR?^;lRrFVBol3)9luG@eP_9z&^nF5U`?>uS=*hhnE8P^uL3crfuFa$k0jc;d&zq) zOUmWvMRKgdz0Tcz@tTj-g6o{^X4Pq_EHTEx*9H72?}qVb-&)5DJ5j4;;f-xq66SHtq59B1%1YOcgn|BFq#~)#Qn0j%wu>f|XGq<4MdU~m2_PU6gYwxSiB25q$ zGj{*x(~+9KaiIFGPZ55N&Oj(ohOgi16sP@ua?yT9)e47y9_*}>BcEg+C-P4mp)^(Pj}=Ct`CK$GcHEkbJkxdElYql*v(k5N|8viz#IkkI??Mw zKyE7A8H5gedin;)#PNi`8tFEkA40m`Z!(hS$b_fl84?JEz1eFPxSEE^FZt8r>C#@$ zo>JP+(6;dOHdgb=nUQR?`sYI^=yTR`=JFe_w8*y6{K|uB!WO0BpZf~{($m4f7W{TN z7s=DEGi2yIS&Esb_^+--9qy(^wPZbXW2`C6gv))m9L}d$eP;JpenL+ZmjN7#Sde|K z`$RGsBV1qU$>R?XehS*goW&)@?mpm?j<}=z*@S^7JhGNsMJZg|{4WJrEmpN%QV+6f ztrT2j7=HP=c*uYFyNX_>v<@b(UMA~YJ56UelW|nJo3BSCJCJW-96dAwZB%OQ|@KQemH1_*RoE~>dP1*hjnwi`v z`hDk{O%A(`pXO;o=If5f42tFN(#8L!Rg=|y{cNj}PU--HHlR)d;8n6s z!ZA}^8w-~Ka)rfVKuu?wXDH&%Kc5pM0Z<&;ifk_&Hq7~k;)7A0p!M2koxY2(bCdbl>s%rA&B>6F3=RZn&D5Vh&d~9c%sruW3RmP z{PFZLW%}Jqgdp^Fwez%@A;dEtD`Qal!ph{8GIc)(+R0P~uu1>Y--t_cMo|oE?1u)2 z49!b{mQ?$h?{Dy!!dRz-K0(Ymf^m0@~f2W@3 zRTve9z6Mp67*%|6b939Cixjo*{Cw+TO`}#27X9@JtLNJ205r8jCrPXYdNfpGj7GSP z(3TsNra;dmj{uT}@4Bw-M+!+ud5xJVHrpbpM_oMi2USqKl0}tBO8pb~fme*z8Mn26 zZ1Nd#D^=hmC?FdUwyRTbLLy~F45Ej{Vx=)k=hKdsh(dbD8N)?H6e1deEbky(z z_9Q+j$u``LzNlwgk$<1JM|pDjTJ1o!oj&$lFBn*HL1Wg5I2Gd>;x`kK+z~aCiM5UA zoZ<2A+dtzpI+a}Rg(IB}hsSGvn`^FIVznHTxQUNfV$MvnD4}3V+oEYkCh)scIA# zBEEt9{XjF!AN!el01W8_QU`MJZB`e^xfnmLaYR^|gPB&T{lfIc-`Qz7PF_C57^E%c zbCZ|j3ihatIqq49^{l(&er_o9fNU4jz3t&2?*3sM zZ$~!}>bpwYV3eJa)hOAiZx*fOTiW9_4mhf`m2QUb5+@SsW2NyqHg*!#{+><9QAnZz zJNoTah*R@{HTWiFMF(CftP*D!5tuRC_h65HT#-d-KMVTAqWwdK@QLM!1P+eM&Lyd8 zsFvbE)%f8zwbQW4{EEC?+X8i>Vs4ZBl%DoX7R>S{>v`hAfHf>F!>%KaJ9emPDLZ_- zr;WqGsr1DQOii&&^G0wg1#*Fvtj(u5&J>o4OR-C`V_T{_S@#Q(onNSnqVSdBwcVs3 z9}lmcrJhu%kOZmT9oLIsy9?f;>`kwJknH_t;Wk2b8Y+qhjiuss3ANOAYK#GeaGm0fO(E27 zEv|)>cpk+pmz8_jcklUoZam)X%31T&UT8*bs>&AoPqOORPA8hM*iGuu;qGst$!iUTxBlS6zzTf8RrjTC*W(nfaVQqy zi48Lx|LIPs!;L3wx3VaY8uSO9I_)TA)V@$uT;_Hf6V}NEpLs(+feD?H3k3ecu%@GeI$mJ_o(9c}>Ysa+&9#Uq^Uh{2@1e9_ZWcgFhY?JTNfc0bi6pWi%|Lz{ZdM>(mbo}46Y2>-Iek2(>%fiI!h zWUIS63Y%{Mx0rK=k^PYZe|tP_^BR7CL$7;r+u!X)`(d%Fjh63vHu?a*6mx2qo1*xQrF z9g61DekBwe4Md-zNh=vHgB1UR6g?GyRCLgwl?1B1aZ5cnH+M{YaKs#5O6pUdW)4ku zgz6_^E$xtYXjQdnTGk-VmlK(b@S?ITePf>!^m(?wC0YjKxpeVao zr=w5~vwqm#WIp9+uc1{nS3Q1$Ynp!s(o<(GKgRv+3p&UYy(;y8(%0;eQwh@;eC$y%p3f@vFA)`6}u2$ z(M5(HnGSiIRe)cfO_9#FJ4n`a(H9C>+?e$`e{#?CLm7;YfN^ZcRO0ct!Oe0Db+lcs zpw%2F*sBD3rYB7v&Gh;zf5k7$$kdldAuLME(UOgW0`0`WJ#eX6(>T+IR5zg|B8PcE zHh_TA;(*K-&{uxrEN>g_cX$!{{_`S0jgU5Z@b<$cr;+Tm3C@M9=05kQA^xR2=Zc>p z%ciLA4itQ5%RQgh2ao)9`m;+-pc+o?UOkbbh=;E^J+u(Z2*j z&@l+R2|3|)bVsSq$+f#iRitdAvwMYf!0W)M32}$vyV&2UDAp&j41~nAG+@~3EQ{A; zE_t`F_9JCHex+rQhWZvKW%Ool=XvvL+fPTb<>QmNo#qw*MoFtb8+>F5KK_scDnWS^ zWeaf`dWI|7nN&*oYFRcx^-~t|vmbg|n#=i5&{nTbx`d<_HXY)6Jmr$avboqCXs;$H z%R%Y_VewVTY#9I)sg>c6Wc165}T9G7m&4xoKnAb z5&^!uLC?(XvKnY(Ltp+%Asy`PC5h;n)=@gR8P^2mb@*%Kpl z7mQqyFda~J5?Rr>NHhR=deU!#pT^Pt8H&^k-sKgPmVSN=Jis3i2)LnlxAnI2l_{M} zVYpn^`F1C@z_nXtTv;mj*JF-mS#%^Jai6|dFv&T~oK zURq6^L9N)LG2G@AuR|LY@>X1M9R6YsJunX4tzuqFYFNoYP; zx(W$ASga@1uS&i8K?|cE;D9g$z_4#6Fg^2hEWB%os0Ly)77=_3-dYUg*J-q&v@MJ; zC0dUAn-lINirREM#>zMjkEDZC;;s}vYe0-Q?xs8~Ycg2;9d5YVy!J9Vu09@L^tA4m zn*dc?JSSwhJ>`Ro;szsrNy#_0#y`P}XUZx(jdkGb%cv$iEq$lsu{5hzQo2 z#UaD>D<@AXz!GDLv)#A4 z&K);y;9}hE=6~uqS0k~$JT@bP;5B7u>bn?EFb9s7{f)C`XA7B%mSt^1SACJ0yM3n8 z2ooUODMXaZdg@#gNa}%k)l^NQ0_ox80mRo7Nd2h6=u)=}429^d)5s>n&#Fcujf`djzli$OG z$GO$qz;gCS=*2e+Mj1YH43uTl;v{BaY_*+52YXB>mn_LfJu%?QJZNzl5Mlp5Nju$S z_5OLi6;Kw0STsE?A0r7&5vg@bnrZG#$dq-?06V6=>y-l{#4&eux)w(L@-nBzUmX(@ zMfE0$N7d5Pg-79Vq(#UJ#p6c&HUS!b-FHz}M5`G?Sw;4Z%=?vSy1*}xs{z?>Ff*|~ zO>s8GyRYV4#{L1+OZ#lkic{?!-~QjTt>N^>96!Q;JvqmGW6sZBAsAMhaCB#`&A8Qf3 zfShoPG`X~hQ$DT(_bP}O=qjglUfcV5CmXo`F2JK`(MxpPsdMvHba!Hd9FJ!{lXvNl z_H5sy~=d@$Y3xe z9U2PzMhJpF8Idl}JJ+1D(B9ZIo4KE^zs`+)Zy9*bR$+AlQCoTqEx&|R^jlt@b?Nz& zb`?nIOmPBmacTsmLz$`voX^s$&t%dcrM#HrEhmTLyirH#(9ZQ=5(YD)v{_ASgtaxt zy_)x3-5rdgjTbK3%G@#uW8vdXp(lE3ab9K}-3uUZb|B)hOtKR%P3j~Yw7z5KMH8O_ zg3k^jibte_^Du1<&mC8v>#>81Vk<%AT*Is8M?>z~~< z94H-I$MyXzyO^UrxfV6MvTK(BD9ZB@&W{Wl@lC+TP@|89* zyI*t107?chErTC8B{7Bi0Xbjx4qyx}jtw7(j{#PfFEVix`nxnqg1=Asxbcp``2<%fo|k_2?PKc#S8@}J?9h3H zZ?mGrOOc6VJWY2`$`FO^I-+?HY}O!>l=)3e!NoOnCq^2${@2cCgumUI&Flx-(maF$ zk4(Uqs~5hQy?`IqjR%UE++bgO=Jn0($=i5(!+N;G^O8mCPM0ZXW8Y&BZ7vGJ%1Q_b z&#`63b&b96@t566**z%@vPqwu{#uhAYUqR>Q2-}UCA_kSI&R`J^G+{%G_->~JY4-# z`8M;Yes9Wu5|HnmYTo)SL?~5>WZyNj1LWfXW?%$GmHuLe=xi2w$BmPSv#t-r%3d_R-F1sU@h!@G4@mAJTjCYJS6twFHO;ty?*#j>z(ubEV2a-Hw+| z0wRKW)d#citT5Eq-vGv4r%IPw1@DBdoJG^lm7}PB-afg+dcbO&AS7J2YUs#JWq2lFp~a`v)A^-S&hEb10L{{@@#`;~a0Tjyl?F@W;M zMXL#2gkuiwn^MFgzM6j}|3LfzLeWL)&jB%I_ig*RTj2Gg=0l(M=)Klco_`K^0xCca zf&;x8uLi^?etjURM_)-ab&II?TwSsTrkPQv$xE_M4Fy2ujYsiV9Vx#2PJ=zytZhb??ngqg)+Q~3Li`R>VsAWHH)K!ww_3jO_v{m`U%oE; z4v^h{d4aaCHM=LZhCFN%U+0+2!wQVBaV<*si^y0vHQ6bq1DlHjdhP=`({ClOF!}ewZt3Z_uZV0mG@^(?>XPiLm&m}clU0@D9mZ+ z+Yc3GYs-VZ32SCYKAK}}XxDr=0KNZMvavw9fH~y$oJNh%9rx@A_pPz-)RHp$wyneR zsvo!XKdfAp*rATU^!?PGrny)C$yD6?0=Yjy7_pd^rD7EfUl%HMyRU9}A)xP*;)_q5 zgv+=zd)%nO$Ijl3K=m;o zZT=c**e3SS*UY=fnPgkV|GIQDukpQMWCMYzH}W9q^PR3eI>}#G`3;^GbG1ZUDCm>} zW7fWcbsF^Jf2&L>1EX}YpHCQM?73pLAx82n5bOyp&wS#BRY+@;Q{%EbIM#O4@xGb#TndN}aR5^js77DKEN)LCK%9JL6UFP8cpfGtkY!=IHbktki_C^y@r3eB4!ll=pDv zW%b!>B&>R%0IC_mmI_zO0h70rM#$S}U@p^+nQ}s;X!GbvVe*#hg$a<~{x?6edp>nL z2yjFW4M6E>;;Gp}U<5~4y1wL>yT3o>3{sBAaz&Br)fPbX{dRSclN0EXu*CY;+l*zj z{_b_mLw#_}Fp zBd_N$j~S}RWfXj_Ns$o5fX_bjMuP?xifqwn!NW;pE0ubH zDKBM$ug`YPG^#0Q%+XuloxgAm)R}3Ek|V4&Pc2F)5ofw99t5fvf<0#a?gkp=P6f2z z6s927np7sLlM(m&PvearIFM?99;#)ofHpg)BRh?K90#zY>^k=(_wdcf&C~74S>@tZ zi9tUy4`YpwYo|4i`+F5oGU2-q2-ouf^=+>~obxSUgQk9nFDg(dB9^dUpZL1S&(L_P z%)qx!Y~i|2V!+$#K_%w4urvKj`aRmp(I+MLJX;c89DQUs^ekkur5}BVpt`&Xx>hX* z1eSBy;#wa#?C_Q1vsg9etlcC-4f#fwTXXsiP;t9D>Sda*xa7|0CI~P@9*$ zTQ~9y>2fYol{QtbPiM^25m8|mAG0ueYhs-EYOnu!;$cWdfn0m5-wrEz{H5n!ZGFvQ zWTAQ~t0OgNPXGm{wy4MAAW_X`DM*ddW*W5z;?}GsnEmm*_u!>cJ<|tLwaaR_=vWq% zh_lKZxhLy;7YG~#ax9d1RtZ#ku7L2>T!K^MvEGq-W?lXkk2IIOY9+gSiK?F%K|5?9 zAvG-$S!mhe%H9si;Ztpsh2V$}~}TB5z-; z22Uwc;H)_mTqAK-Obt(YuOi!{^nsJ#AZ zDKlFX+{(RmdUm{ZI#9Ofg#C!@@Q7TgP*uCpR7tCKuv@Ea&}y;e$5oaBb>;1)Qsao< zt?0(*@;bAVc~9+95BpCMKnlY7(OtzVpdvsjaqaXRDLWm2bIn*Shj^kLjt3UlZ#{s_ zv0IPO>hnR7Zu-}9HIR)E1=OiuY3)Jyex)tYHD?foga|i4#6gP|WS+!ct7&;pxJYF? zKWMjOl4THw!ClWnlO6cKQJRdb&Cr0z%z76SgmT}kW@LgWo+y4m;+y8Cwb)Ne!lOpA z)SRqKNU42Kna&ni^4aynglCfjs`1M4%!06xG zd9rWi_uJBzdV6Ix+U2&?#gfYH-Qc_F3|IV}v5$d2KsZ>!G2rn!L0;+rhtA{6H4Hs( zJZM34$k~u0`?%kD-!RL6e{&4VPOO7`dK%3vl&!w#WkMtKj*Au=fn6+|gnx(S6%^(h z*Ie}02a+wpkw#1UFJnJiD=fF!@mD+UX&UfQTMeH!+?qOUrcW@{|2_kXn!c;Nilz!% z(bnUbZIzIBMx~bbm=K%a)!G-Wj|wf_z4KB$z3Zusduo;jUqf%|WLOodD0f;(;5BZX zW9XCHtWu&J+S#0wywsyaFNlYE^Ut?q%PLJ*JsnJj2fRvcTRv{o!~;Ao!Q;}#U?ZO? zs6WJ?KnpKDnK6qlH;v}iZ02_6Ao0!OS{aZLADRl1XM>NpY{^oW;-v++%jl%$3NS1b z*88;xv?6%@ayQU4PyZ=S&weJbn{5FMGtm}+EtDx;hg7u=%5}2f&OtI_J{l5wVFF4; zd)8m#To$s-19I^#SsMFKy}CI#Gi9X=&;OW=3MNZ8fSSCe*PLx9iDQm@=I47MD&q!g zxL~CgOdA4_UNQ;e=*H#kz9(!jX`AY}cQgi}_<;*C(9w($idSH~_bQUhcXj04=B?4| zi7+f}^qj)3^>E0470s5XK$09y%=e();|#AdQUaUrzCeY-F=>6-ig6axuwaogGfhr{fz_X>Hx3vE5_>uo)(uAYHs8Uyq@_=4lG2>vFB zVb-%9IO}eAHQPmHLd{=ndtt;qxuIWa02i#2jt^yyrVD)RPPrPUF?B6=KSfnG$)cJn}5%1PG$Yao}p9Bxfw)AobmHn1Lxn# z&P@z&CC9gZFpb{~IzMTeoy;w;(b_fzl5Ms3K?_fvdu@!SdpSu2-FRXCG5$N*$8vS-*fmI^oYSkPId@tm-rGDi)JONu7l~?TSS1z%Jf?;dvn>yjFf`emm%S zm%(GdHO2ge>f)xd@wOlRGyVzT&fuO0U$Vx(5*h2oOEoWklv<;yhFoo3!}>B#P~pdpf0BS6K5w{t6ON|b6eP6r6=kAVVLIzXX9naY)8o(&@S54y&XmC zC$G#_q%2qF!ZEfT3(jMX8P|K98`KiTb$J>uZn++H46`WU9n6hi|C5h56abZez4W-J z9?1zDs6i!5N{?j8G6zeprc^Kc=^Wg)CFw;R7O%Gu5nd|hg6Nly6~hWmqyG$0!AP>fO%Bemj(Ds{|HCLu(yEg3Y$FK@SmaoE8>E4RYSyf(ljBS?C@$dy-8g;6hJSQk`QAsC(lIUnM zheg6H2V>*S*Ynd5ivj0`#!)CMG&25f&USE`nG5ef&QuX9Cqe_C`8AF-r3l}O!rY)O z6hBEpLDJ;80@vjLS){s8>jTUWm$G6m`%^7OSIfg69Pke0!DGGzV0d{}9ShlC$UH&6 zH1V&X^evO)vnrag(g08X!?aOPD#BFtD}sD2sFicUNeGwT7n@h=^Gs^M?!Nwrz5)Jf z2a(mELNThu*+(U09v5&~Yga^YqfR0n70)tC**A-@AEfL9koAmS=z&b+%bQnaAD^l>BqF z>s@L#(t}O_)H81KdSF>-!SvFyCncDGxuw4cP{!E#icWo>btB-A+<30RfTj?#>%)!7>SE`ypGvu&NAXg9E#}Egx51Zl4dPvYf^-iSQe|`Ytx`$HHrY_@M zQJ&Jm;G_6b{BT+k2`2kXFh(r0-t|0PGL{iYN`9|i5Ocj`WL%>WB9!EGv@ESMSdolm zYPb+=hxx->{q#nDi<`dF$CjealjNu>^v88(L|a1q!cRMon0$2|_S%ZFpr?H~`Y`RB z(_W_HN-i}42L?i`$9^kSaAmHkS$OkT%Zr>6vN_`Z)Kv4@3aGuORYQduEN=X?An1#M zA3VNvu&I6FVn$xos_}-rXj=-`d7k}6w1^4k6LxBHag<$pza}Z-5EP zbQe%pS&>a32jx^752vGWSk67ArluAa71aY$JK=Ur^%9kdiHVq)m@G48jLX?h0H{Rf z9ReTUw*YMFyb`U5Zfi@?D*(mv9Yk$UN}U*)uKqn6`=vD%E%;B#ttuFZx=8ZU=1 zp<`<0>h?wu%15-JVOWNC$=O*WrmB8Pwc)-5=|yo#byT%z~b@R|es{ZW}Ze&Gm(QWn_OB_ksjpe|vb3+uK`SVJDxsGKxiS^fq8 zYd^&Uf80T_S02e~cl1^7HlwI<{*XD^Qo6euCxqqd*qj(k9<^ODwE(qv^J;4r@ur$b$K z{I8Ag?Z1Nui77Xr3U&*Nk&kGRcF4&ewxkef^HRvKI8QpfT$4?@Ygb(gPbteSSh_^S zNJR0;mb~JEHX&KkEmCZej{KnGA6sF`)R??uSK#p5*jmJuc34ZVVNj|I;ayJ@yS>(R z3rqoD0v7B!sB?NJCYE>$p^gI&P@q!t%;2C*dqf;hd8RQ#@;v9!>7-7+rDcg;Cr0^$ zEIt)3F0Lh@qO<{ema$g40Mijr`YhmfQ5eF6t5m>E5q60ct|-Bs*?P zJ1Bo+&ct&et+S(hI zaG@tXD{l&U$Nij%*z>{P%IMAkf|c%y;$Vo$vcau-wNmGxT3GNvdxFdb*fU_)1a6LI zQ@notVK8`lsC4)*kc+&4+bO>s97vm^Ay;E(0x5;2c<#+{S5;Mg?u}s}gfSda0c)!g zid7`2%zbJ0K>=JWP@CChD>wUVG6WHF6z58wYD-;KSmcX-;#V2SaHdr$@W^@RGQZ-z zy=ilC*)y0^Sw?E8os`SbTo*kRxg+K$3GF0+u=0@fa^WDJ6CJ_Z$!kCr^Hwx!V1P!; zfKzs$i)M2;z_S;hqXHw{+1XL-sN9$;p#V80uVXqq-SPhJR<72;;*a^Xe0y$O;9SHl z!!UJLsP!~KnM^7_m-EqYmn57v$K9D9Agz9!mqF}tPQ%!^IMvq<6m@o+Sab$~8)>}M zhkb$i|O!>1w}w{P8hwH9LlySI(DiBrve(-U^5 z3`5rHsfCZOQJx0-`%C@SD>k1lb#X8{TxZ6_bv&}N1k&Dkp*X0}AM|rB<}8=nnKEfs z$u896?G-3IXs=%}CL(^Q#N^AeMJyPXqAwp1&3E zywElWVvtXPt5Na%9MtIEJ0I!WZBIb$11ilXrP*D?hG${`huDxilR~jm5UnaS{>${8IB;5pZjkVvJdfkN$Gj)bHFm!e)0H>&bg8*OEP=O6AL#bw%TYjBOe@L7+f&Rf zs&F-4nSV_6;^$OCimht{6_%#X&L@TH4sq&Hl*2oX_Yc%I#8ASoCb z;ZE}1o`mTE%|VTyV6NVk69H`@wI#qBm!mn20a5m^ihh8Yw76~rz0QD&Xlgq_}*BiPHY)IZ}oE1=D|UxSxLzDL}3u%tdbCI zj?-|isDW?3+phm!y1gP$>=d2nFdq8QelCtz*_JFO+zrV5P`U`3edABvYBtZ+4j`hP zcICL9?`@sh26BfZSGmoDI*Ph|G9s!D?|vbcV6JSG#1}45&ouH<_<)p<%=b*x%Bo%$ zD!u#{3tAm@41Qd`eWz~~{o76wQ|&U?`MAKWR&i;>dwam%`egvch!_U-^smtVlI`tSM_Eyppt=tmLb`33<8rjcPOvkZ6=m;?m=(#brzlESR`O$JX~ zr`ZKqSmbegV&AFxfURJlAvI0d0rfy^+MLhfFCH3T_w}vUkdl&aX{vBEvsGKeeMqON z)`!yVHb>$>)q>6^v1@@FG(;-?_|LkOfjqNTm&hp^U^#!%x3Tm68J7tcZLBeN^`k%F z7`Uy{A@IW+qDYL4j9|Nco5A%2$tn-c5aduN;QJjT`abtGKynIM4)wl_!~Hs;GMa zohaJ=+bpaEeu6z`uKOa(o1-p|yUuti&^wjbS=X?7FfK-RK_tbpjhNM~WPk_c8khC) zkRA5MP#%8Z=7fN3fsMd|f5QOHTAC`+b1{6oUI+A41r!Tf7s)T0cUm#WdYg|L$8B|; zNlbW{ai@VLBIt0XGvD|lT^#sY5Qd#fu#=)*EqcO4KY9D=RluF=N^cb3ssHI( z<30q6oNOLA^W4QH-En_`j%o<6I{gS>`U%!0VEJn~*&IbgLVy1wte~ae7ZqlH380V} zAD#_&Vx>bpWwk(!!jDNRZzve+A0|C_Dt-D7syc>gKBEvZ+w3|!KcCE31LCr)^7Imw z{7FndE2WHP;Cc`~ld_6D0DV)2s{#5xlAM=9FCgDTNqBWv#j5cl|9#=B6K!raZi& zBGZ&%z0c+>t$5)(aWKJ3PF~suQd0U2J_$+4-`-dR%FN42*5y)(@eI=OxHO2yPniZ? zJ>H^Z?usF169u`tP{43>xz5>j9&pcD^E05F_06vdHl$R->k?5J|BLV6`9wmgKLvm2 z3MO0n}_Mlfs>&feJ9pf5G8T zs8W`cT=HT}XgvoOb_y)`%yl+juOjJih5(`))-6R5|iQW#?B*D?{BFY%UJIJVHTv12B3&BD!r1*g63ZWykiR z7A_G{zJqGE&qrMu2?FV{NJh;MJ1G#;etwc1+n4^wND>ofK0VswvfbtKMK3(Bx2#_z zS~!uYoVv7(4r3@J#(vMn76^Mo-XpE3h*MWrcd|3EJg7%b$Ec4ju{oz*s{gFvVj0bR zv4I32{^H6?6(Ws=f}_8^`IC_skqFoy!n{3}`_Rb9D2iSM1E3mFQ`0=UpE}iFQ4D&b zJ_g}2oRsCh?;1?)1V|vN61+2<`t+|vYTEMWSNBf8ar%;Ty%Qe{Ua(m5qt5HXO9DSc z^6#CjM;ry{sbc}c6nN?KS?VBsd?#BW2`be6i}1b6iLq2Xi-`RCsSSx;qa*($mz2Pjgx2OncASUMD z=pEE0K^~7xRR$te4vQHarn&><3X9pS{r(i3etafvb0wN+0vy_^^R02T{f28s4)gbW z`9cU}bLp476lG>a4Q;7@As}p;#C<+XLG!d6pTP$p0+;rg@iw-)h85EoWG6L8(RbU5 zuPj4vh<*JxK21H77LGc9Tl99oTAQ9^8q3D!?#B7lDor?jN**{nqSup&hKGmqX0HKM zZ3o~nJR%}}pE;4wnPtIg1s#&n;+2eGi9hh^e@2;|2NQlvI9}U~mz(<~bW!>7;oF&w z-`s@B!P@yu2DDy5;?Ns4BtZ4Z(`!3Uymca}po+2QKhW^4x5j93zv-G;eMi8BumTd6 zq!&hOySpKP#4TSOu5j5be|PD3*qzC}Ufmu@fh3|>BYufn8{OOaD6AI(!81Ylt+cN{ zz&_af-p>|)`DA%fJ*8iVNgUca`GcIC){MHJv+&^%Ta(BjB4+p>>3n;PKDG z&j5G{M(7o>cui<18q!P|z$PLf=?u%*N(Rb=D`noIk}jRx6D*{9o|#w*9su6!iS znQG6*&VaT7b{7#M75BL6c;1%Nsb61T>w!~BT~614w1UjaV)2?upP~=w;l!s~<3a%7 zEUm8o-v8ASY(w+!aq~8B##}h=1wT&Y*o;^E5w_Tp!P>bIA8+SzfB4x1uL<#P=6oRF zFemW&_RXpqiBW$=N<+Co)fGS7`m;d;^-Ffj-=}P_n_D6LN!`P!9b0K=C zdz1N}7$$FhI2T+0OOzE^Kvs$XK7`*~9uu${J_mozRPp}(`)xUVEl(-G*mhmI zeACd*j;*D&^^_u~_MpqL+LURi6P0!e#(_LPnV(Kl0>mMa!`&|9eG3>g+k5^Ulv)QD z^`tpEEh3A0Q87{9AA%j*1!`r1a`j62OOv^gfYc86e+HOWZXrC_vU}UXri4GN9`{Hc z0ZMJCkF3gn_Ok%3IS`=6bctxXDv&AROG{~c87(3Ief@%#qTq^BELSiz5vfw{{n?1d zAP5!Pk*MESOYjhW|9ojqucJK}%;)1Xw7T>W0FLy;W^%+AmXwtNY)b`AXliX03IWC2 zd`owCcezFnclH>K_*wY{>j5H=-}=RW!ub%@Z>37bsuD#026*GCw3wK9Ya2vP)rMcY zJxzaY*O~aQgKT6{rAPIky`$P`r zehNBPfBk#%T#PwsWg<@rjaoWM)^_vGa;o^()_eTYXIbVkw8_hYH3NtiOsQlZ+|bZa z(-2g$|K>SEAAH+HChGJRo!H_F^CYDQa|4Vdhtjh)1J~j^*6uIoLsgpm))!g_;*zg0 zxsUg!F!>ABL42BGYTQ8VV*p~|;KdUCBtOT2+jM=p?KdTU7(I8 ziP8GRNZ`Y$78G7N{UV>DkhRewm(8P&l(2noF|3WXqd*ve8`E2QN)vhCy!jYb8bNRN zj(0GV;2%D^46~tWmo-)Aq1q2?xlt%FrI5mY;>vrHvk@BW<0jkDU*#+#;ezVWzS9z> z;?Y(hS@tu^klzNjs{V|@U46N|34gey_J?+PMZSqb+YXy!SnSR?8psJF0O$0e|I2O3 z2vR?mBbQg}3Xn04QeIR;XM%8C+%l9!5(;exeMLDO?Ks}v-Z?-|>@Z9`JUsLd3~T{x z1rr}XJ8%v3d?@Mg+NyBlk|LrRIb9vV<%YkJ_>Ya*vdBUw=s)e1$T_(UveX^esW^f3 z%zIsc|4dV?#*216`}5{_CRe2K{4j&a!I!_jzY481l!!U2Z&t#%c#MCh5SBN%;D%C4 zYydJh|1<~$E9c(DMY8bl@QuYrfwh5TG*_ba22S#Jgi1&NR4aKxc!ij<6X;cD{<S8g2)>96?ope!_Y?#4aVEtA&Jb)o}WLkGotZM3QLX`P_Lwr}a?n>MYBC4_`13 zw?zAI{fS{11>PeDFIWcC@(Z$0)>+91MCQ}TsWA))oNM`A#F{+4ZoE)~6Z9wxh5)zZ zZ;t9ZrK1~=l`#N`8>a`GUTYjPYLhPxmGi%Q7065B-@+%Eo%Cpy8CYa*w04;5y`K>4 zkOUV0Ks%*d!g=W>?|zk|X+=1Tm5LX}Ag6I)&=srtszDK!Fn(ST=2u^{{-vG&ck4FXZ*W0a`y?3Xj4efG zSoLpLa$D@GgM&OaV!Rb zGs3o;BLyllSm5m*PVNNjUJPM-hBnZ)89yCidzdH0SB6R_ zE=|ru7jXLb)%T(+kqD1QCmw@AnHXXv6W+Q|{`O%HdRB z6Ct4Juokmg&Qc@S(stRY;GlIQYORjF2iVeH&zTpAPQ~L5z5LiGs^Z5c~ zg=)YvfkdQX@0h4qpeh&U#SixO^MjSnuoa*hwSm_6K4b)xkbBTf?t~eW5EB|(@nbuF z_|`!4&<)*cXM@oHffC;-o%Q=89-hLw;Qg@noOOe>*&>pJWUg=nq24xDqvCo~CE~qV z&RJb2Q_Tq)yno+bYXFj%D(Fj2Ap{P`NBech7%}hE(vNEY{;a}|6zAY@NCh>)KtW7; z<$@;APCY&~0)`_X;QI-C5>xM+|Dd9%Mi9ta2HLWgjK}ODtgqZsIf-|6m;UO9RT5pm zJsBjINo7Rsb)0nRvPk_~Y!h3pchpPO%T_fj-qAIj#`K^uP1ibp(snYnV-p1WK%!9! zDKDP*`arIIWSkTUhcqDD|G-1kJs98smixZSYitE6gStGt4wgGpog^5bJ&S1+(s{hQ|Pp@7oR| zERScm;)4ZHD>bZCcBTiMqAQ+Qw3|(x*Xct>ySO{(mG!w<2;61^N8Y>MqR(%sz-b(m ziu3y1D&Bz84r5dUWaKMMTkAg&;V3mMER6I41_p+UJ~VKuv^ujJaz2+KS|R?W7IZF7 z0RwVEFI9X5c7tL6tM7h(dO%^hSWopFb6>u)-=^pI51|Fu=O2O2Ct-%@_09e%aF4u?k z7x|<17RfMD){+jtV^b^g_59_wJqZj~Y4!cz%JbN5qy>&GgXaAf@KTP03){X0DotJ$ zRsbva*HwR)U_W@0${M%xg0-|8ph)a7Mf<=DjS%6t%r395^Fxo`2>Iq*|7a^l@JG43 zVo52fz8bV;E$ht@%Dt2nKfL6C*4g_{8-zcX{-7DTxoi_IfpXQ-r{ejesX9 zP%`Bfbg7*%%Xt;PcQ>Iz-xqGNIdM7VRNDcfF;A>8FuRbfUDHBIugTI1C65>xvYN+5 zkT^4rnwB4J>1;FA*!D3@erC~hF5?Lr9NYh1pv%8NHyX{@>CTE9>4&&oSl35D6bvuY zK7Jc3#AyTN*Nni$((bJ8{|h+$df*z^_4Q~RRLz4gMS3IX*7QZ%Q0qL7?1=+7wP$Fr z9-TC2D+!1=#~uOd?AV!pxI0YH_BIi15f?&osQpmj&pV3+S=O?#4P)YsX>2(njt$%< zK)0b7q+|b}6+#1_C&cn*0Wf4|rW{RNTz26J&6Go*CJ&{n3*HK_Yw{BJ`lrS{U ziJy*<&r}o+6yFsIk}XwXLNI~3&mco@3`7W4;$#6R^Bs(4$hq0u5&NQvIu(Ck7-ftb zpjwh?&>J&VYJip{74I{gA-b)^>dfE_b+(|Z`Y(wh@RJu7(c$#0fUoPO$|2#)A1sVI zy|`1^^|UT=lrxhj@cg|0kihxt?^m;>OWrI_Wht-}LKHvBUz1z(7sr|t>zbFF)cMF& zAbY>_`d3Tz*4w&>fim0Dd7(Kc(H^x$*acXDajqiST~1)?O&q^F4+b$;T1{srn5BcX z2jl`k4D(8GR4i~i5pOb$Rq<18Vanfe8IpCQWnf*kpSxk2Z54J;5wmizR?_sB9M5lRhc!-6P%K{WPyV;G zw*orgHWuo6$tfsK153o_K_6FN3WNyAG{WZQ<{fKsrNah_iczmLOeYHB>D(kkFF>+U z`gjAHwp#SUAik}BFY-IZCM(<0#WZ`uDMS^e0)H~vAyQZkE66?Rx(a>COHVk9OM0aRM^6_mBbK4dpC>W=?# zdYi)i%`A~~+cl);uPy?egWP;`1~i3@@Nk?wnH0VNMA`4TRY22E%R@i}a<735U+>yK z>@yu6!py*12O3#GR5#U=qAev8@Zigc(*_!_{Xeb4IV^rjM6qyjU>oygnFS%Ev@52? z%%5f%f!ps#f6FYr;-g}|tHm0AX$!yvDhMe3=RjHON$O4m)zn>h&O|gjzt4wrc`&HK zkQWXo4?JNIuao>WNpZ=u4euGrm<>X?W>COjf2UQ0gU_frM6XDEadENq%a2qLh$N>H z%}r7Ofb(t#P^UD32|Vc?;6E%`(#fcxe!M@{w}*i(fYq6of#vO;3o#I!bc&-ZF7K(Ix>^u*$+*9GN57U8UdCr zC{tvWWT*FqFrIb`n~KWTsjCJANMPggd@cE4Zt~z%4Jo@tkf%uviD>~0);R=@W;hT; z5i(66PjBcR5L&mxORhCgS4(pQ;cyU%q^q#-m}NM=B~RTFzlQMsucvDtJV8FE=wBa5}c!EJkn{noc*;`PW=+&s&m3DP@b z;V>oVJy6x+yE6BIsKVE!{qiei98L!1nm%X(pQ^T{PS40VrAQ-}*VmJz)$PrS;T*}4 zqlmt=u(AsK_T)w0B%4T%SY!_n+mtY>!2+m|cVAwDqDRQuNYRf?+}Jr-v?Z|@JI+biQL zy(h%CHz%NS3V;y&^?ECoE23}kWPgzi)GEIxCMGsa(f}1mOMJROjWrt10Nfu;ZeY}v zX;OTWl_Y+ZaE5BcvE`*pDRsclPVq-Qz~+>(hFFd$PDH}ky5Qapm$O!lAXQ6z{{=ae zOrR)mS#Vhn6HY(^(Vs9m@eNU5(J%u zzTPEJ13v=+94ydK{s-WodcQ-JjzlRaGEfU;ru)jzIKPZAvLyUV(hDU3bV?ysXCzZH zM=>`dWq5anDCPUzw$SPGob~4NSYQ^t8lgl-i3J%Q!9NL!u~ z7eKxK^W|upCMGW9V&t-01S$KbCD{COUsz2>-XcnvgO-DVoWY){sF4*!l#z-usNuAr z<|4Pyv-hz1h6*JDI99i&liLxcoeD}y%G~4cAR%DE;cypRItp+YWjw+FH^X=QX%)3^ zkpKEQs9f^v>gkQE15s0*qdh9!NqV(<#F-JrvB&fB5*QaijR23gIVk6fQgcZUGvF&7 z4smWG(Y}FX;MwC96^+^&eFD&+ z{sREmK%7hh9cH;LWtt);YDlq32cCDAqV3tMSxAgP#0mmn$_S_F?>Euz`vK?!%~y(` zO)C`C8b$si6IcQe^WC0dzex0hxde{~KTuFB#5*hXU*3V{Khr%EuDn83@8i=gxEK7l zPEC_VE{EP@QwG&EptFLHh@bh-=_(t&0sGTXGfr=j(|kg@kOn4`wWfhp#Xz zqFrum6kYZqRg)~1QR0d??=gPZ(8M4V2*o;a{Q#U=1~C2M<^A>I{g`ij0JX*!J%pAokFQd0^!C>t!?K_@gK^9U`*UhAEL;+lnx~`&T%QR2BxqX?Jv+W= zS0|HS@cL4;an%`k`>s4(Imjx0n&ODCvUKeLpEtsb1d`ymCI^hqdI_l~mI=02AvO#g zyQ8L~eG!zBc~c(&1aXIzgS5CZDkIPioD*RPBL^%&-0>n(hClaf(+`~9|DTwB^a7!6 zf-7Hlc}ABmBNaNrh-V*Li?7@)usB!qfk7YRbj5+i~1SI0R=vQP{{pD}ak zl>JB3J0tnx*mGb|P)?;Gy1HhS*Gv#zGpM}*2h!0zhWmEji}23mrOJ$0I6+dsT!(es z7$Z<-~urpt)0{ej5>-U1J=-+;}0}c!M58?yohp{@J6tmEsq;__8;qoQqb7o^+j%9`i zPf_Kk=e{ORcZJ~FY%G4GaX-W{{gEOlD@cttk&{{HUP0UFwcvf0yOuSIU8~u!tmNBdHP=1G0pLmV1JEG42kI^;V za2h_xIP0rUh_>4!UJfG}Eh92hY$3#j^jCXRXM_-4zm$9PMr$bx*~y?4Zo>7BXy7e9 zBIq5>gCT`^q8(6r$}+^nP(l=In*r;+6e3`L1gy#R(*sQeSS4hB7ZVW?G4?n2#7wViV2v@;26mG{2T0#+4cjJ=|Ch)ce?Lj9|IQ6E%kVDI9tjw#^UVm!w zi+zD;Oh!@QxiMv+#sKFk+J{{V^D(oNpvfG!#pMhY&$;GjHAH{5P$(nKJY&%%D5@#u2DL;#&FNzCyQ#w|V8x?V)V5qdJ#g z_7Hn8skssT)$8_jUg1X!s$M`2J?X1}z{LrQ7l;F}HsJo_FAnATOQAgBMcVa&W|Kvm z(aS;{$pBuarp%}C1ql)Aaa9ocUG!PUEf6s=6ORT9{b3;{Bk-&IWCTj@bzfVz7 z<>%Ld1&HANXC%<z1YVECgMQVL*?9!DJy+C+N-amO=Ic!~oW0)XXCpC0hNd-vQAgQTT9 zl6rg&5BSrE-9VlG;_iC?lf1V2Ok~J)WGEnm zxC<0oMaky@KX)uQJ7QWuXvi#a*i|oQ+-tn|=u6_pCPH7og}9yx=gMcw0s||q4tb)X zp(9Fy9Tk}@IOSl>oIk7flI9U!zSA|4#xz1kPu zU*s{%ChF5`NeQ)rjWCn?ers%i`iaXYlnxAc`ggTWKfb}8X1NsaWEMf8Vwi+_SWbQk z4@>8$>EVlQkg+{wgdH1mJ)xci8w}va9JZ=s}AwDjU06k`4 zW5gK){)ilvG+hM*66*37IjG%etXvqODBBnH2*CcxFs6#S6joU6v(D*fpz-|NbmS2< zjJUZzlG?~TiMIW8=@q+TUts2d_k_rStxeXMJl)=EsV3M%ubl*op^!dUfVI__*=UDRq@n_Hf*e`zo(MOT5y((dksEG0 z=q!#&`Zi3e#Ylj}v;yloqN4K!pbak1JH8Z`E!uLqOgo=MvGog#*6M1UTxw`SREZ5x zNFqFASOY|v508%I=NGX`$S+r7m}vkART4Std&fD7K>Bo+VDm^yhY@9qej>HsPEUY; zzdYsPS3Q;G4$k?DE^1q^j@#*2?Q|}~?9p;NJx4+-0#5~vBs)`#lU5#Cv z$k~}YoH0H(+I^F5q)X^0*wJg0i&Ue_b;pi@d)X(&xL0hi>fo8U_z_0NppVH#kl`#7HWl`yvCo5r&2SIMJhsE?12Vs@o)!Omi% z4ot8=mPx0`$ndEA6`OHdg8;aV^ku}Bdj0j(v`sCkAg~8aZWQ&!HsSp&%%I1t8Mtg2 zI^ij$a4!1mSSR-Vy zkFt@wj#8fn+*&z)YaK&pglYq?4*0SfS1`>A0zoEqUd7y*F6+!oyao!?5XBPQk8C1i zM||B0K!R~qmbT1d3vwbmiBA^*5&~3%(+=WQehMp4cM#xb5n+NlZY zcXs9`?q_?^&mVr=e-XJrZOd-oR?1P0%FcJyvpp}}nqZ;&>!yiHwHMH~6!L|Rk&<;1nHC&l~vf*K5!~hYr4KamG6M$qRIy#ZP zNOU%XjDA3-X8R6epzH>$1At@Zwp7dwB=b(v(X|WL46+)117oPLKtngeaRZ83Wbb^| z%On>)(0IY%=RrkeY2{JuZ&hPleD)`_h{lu*nUIbjztOHzlJw+%BQ3a|8X#(-Pl-qt z{^~fR^oNr9x%MZxw9~vzks}aB8A!cSp1asGrnqzzMqMMHu)eWGL?gMoeA!<LKAwF7>KwF`%TMm<3p85y;vI((j$ zl@*K7e-Qp3ePjaRki~AkZG_ zw=67>f;JvG8(PF9Ky`$yP8X{BXiyZ>H*y5zE677onXJ1deHCVZItiEPr6*AHc$>7- zr?o7|(`xj+58Yxda^hxhj$`8{vS}OK8xnc41g7ykr7J?8ye6-~1_O%R|CmwNs%S(O znbZ0pAg21)-)r7Hq+pkeu!HAHM)TKWu}v75O6 z7AXLC$j#1vQy#){RG_01md4X8kbgxesP6mOIr;Af_Rtf?vkplbC`LPpJTq;GBYQ{o zy1;n;T3pm$tsY%t^kYM=k=0w!O}0^f#o{s9ez0vak-X?ly4KGTu)!D^#L3Tw5sm5F zI?UC_-rGiT?4cptJ_6h459$|i&owgi-7B9bBEno)8tNM8s;Gg%O!Qth4G&|2<M? z^B#oK9sZX^`&j?r)8IfBW|@?{WA(FwflgTI;&5b6vs5@_<^6B5{(~Nn1AZX+hJRe}__% zuQ|I{2f+uf-J$0>!8*AbIeRR_*b|5gN#bq=0+pW4y73GPTIE!1_q}Hr8M2bj67uqa z$0t&f+uv-#K#z2CQ?D`@|CIIPbtV2CF}?o{u3msYfoe?GF4G+{DSNA(EURK6q)O!e zDRJt{TAjyUr?e~s)wY}GtN$38%?dRg@hd-)Mg3}`rn0T$B~1Hj*gD* z8oFjQS|W)q3p*y!@RL0#nf(|i%~zhQNi5gH#y&h9r8~1txx^lQNGwMXO`|&l#2Z!n z)?3jn#Cr#ZuKy>^;tNxs%`BseQt5b{a-U!B=t@wX84bhX?xIgUwLxa(2z&xE{mD`bgemK^b5~vn_6GUJsPw#+86ZbEZbVoGlYe|w2Vw08be&s zsKCi=UA1+cK`Ak(nUALH2vn9$xS^-veO@#>9A;{=TzW(brToty1`Pyc#MELLiL zX9fQA6QN!y8((W)?^@HIy3d(<(|`P05FL(^i5>0J7wHrq067win^^_+q>+=<@I4yD zunEsgS_@oKDpnnv(Vkam@n2iHZD)-4Jy9qVHOWU29Tp$+rJ{+0YV0E|g~sH@(gsD1 zB;)DB0z4;<6SA-AA(<_=@nazcra49h$`%-Egh5A2Q2r8yyM_)M1u3Kkxc&NcpT$&| zo7qV&^aS8vcSPOGj$ck7F6ozA-6iL>@B<;l7);s54Q`Pddaf99+-n9@%6$d<%Kl;-*H9q$B@uN(Bq z)89-KcGw3%7Og;WW-6y#2RJ7UYveMQE=} z(5O^6EF~ve%ji9;@omhFao+?9;NLG$gw}nFb}T;kR%P1VJT84dbr#Pf!tJ@~`Erk@9XVy-F7N}#)Ai)d zs?H-R$3#Nqt$T5rZIUtH*e(5s9)=dfBa_1%AX|?!%;h`!A`s>k6eN%1Gp#+!^B4aj z9jYr>t#BPGC#XaWx|1ccMsx}q(y(>Vwd@$$14hi#eyxiU`~xqoVODc}b$`G4ofMTa zVyZn)|@cfJ$Uv?dHjRV=5%oE?NW8J$*2uXn9OX}UYsfA#{F{p2#2Yj$hjms zegYd>G=t_G>Gj>wQNEQ}>33DC>54-yU2181da)Zv8m{=q{%52aFnL60kMCYNb;pSE zMQFklCJuQjyHfk_i4gn?tA=ClX5B@JFCS^u#Tp6u4e^Bwh1uTcF}X|FY>Cl|bc64wvkWxUU3o477{~NS!`&(B!A&rf3S@TPPR)7w_>6R=mETp5R z?Y3FtW~Dh9?4$Ip8X3|J4w_I%lU;RPeGznlLP^)+*4mP{tkq4gwGc+ZPBwiqc=}bt zKZ8HCEDS7vn#4bAA*OPAw2*{!vZtfgffU&qWO*gN!r+5~$1GI}{fbIp3)Ss(Gf-2f zN=mJeZ5oV}l-(img`p2xT7`qG`(ReyGilaaEg69xJE2o9OvJ6EMX#n4rQ5}bvrQjE zXg+5{U9l^p%!sk9`2FZj_GmGU98LW5^Yi77oHq^GXnTQN=Ch|y(cy~5=Fb;36FEX- zHxm=1P(?#bsm(1kBJ?+%a20JfH+`$qIaXKi?xt8#!DA^tId?r>=9vn=2z-i&|R_BAirS^6vPR(Ll5E z%gFEtqc-H!Qcd56hljKHEquG=IaQBQoc_G1NiCh`;ltZ?b#-JKA;UBq9J4y_|3zw8 z+Jh6Ib8JYa`I*z_$NOBuCR35jEr%q|JSt^_bKtvf$EQPZdg2l`AV!rk;x#@@3xUR>mbaQs-3Nke0nqs?x$9 zw{J4;|EyHQI~02)E=GF*5A2LJ-8JKp?b)E8RGVVD`%CDe!Glc*ENjH{+Z!I~iU~H; zjW?^WsNJFFZXSp_er#vQWkNQtUj?=O^69$j#|M)oB(Kt16F4sQ#`un_l=;twB61yFQNHucCO5_>o6*$YJ>IGKKz2~2)0NrMjviw3+F z?QwivS(nD)=5l9!yWmrldd=H?t00l=d~D?pUL<2)Sqg>?%ipKLtFJDP`o2o4Ns|&s z5Xp$Q!XRJ^YN};oZUHfL!U&e=#w%aqYs!cfthSES@nFC>gegyEM;RkHHPK?{zjzcn zFOnESDJ=ZlWb!eD|F@J$_ZL(E*-sXi!8l5#=t2R8W*mrWt4aTdAKWtGze3IeQ zfSiB7=J+J9`M@nO)`Lasp2(44XV6MOgdeNfy2@8_S+PBKN@0)w_(k>8Qu`FD(6mnt zZZ;-e>LRqs$yS;j?o)9*wt%Hj!ZosY~o=WkMM27ZVRV?#1~&eSKKNZrhrc8z)r~b=5ah z$&~l*e{!dD*O-*Vj}~BGLN6^E-)|P4RZq87dsUkMRbW`Yvu#6l(s!Tg%IMF8V_Cn` zaaZuQWaSjlHt5u5%>NY+>hR)l=Sc=l8t}IkIc!&#Dj#jA{1|ze9;~7*o0(Eyf^`E6S49fC zhT~Tq4B5OODPT3^B|5Bw<}5aMJfz zd$79kOMlhI8do_)?}94HH-{{Mx?38hfStI92f8t?4}=@QWMlgMi`w%nD}^i1-Y%Ff z`@eJW`E7fD=?ZQOwR#I=b%tClQv{>DIqK^F_$(hzu42a6%zL;a-6?8>V|=}dc0|(^ zuIg;5Wrx`~{^(^zKQ(ETg~_V|P>DrYgbkhZdTD>A=uwD3et&RgX4lWczs%-Eh+hU% z7|kJ|Hljn%bW5#t;b^9WbKASLN$(loGf{`=MMCD}^wgL^<3is zv>$`m_`&-LdbNuKF@EFa@x^gxf${QVrh!5Iq!lBR@|_G4>$`FHFgB@2qTa{RUby&U z1*oLSE-9}|YiPcH{klZTQ%=zO%w&}L%X=#PF)BW5z4uAs*$W^qA^Jps!Ml8Q8?9y& zr-RKg5M19GC&s#V^}i#SKY*DC_A!uYRwIj1&qG_J<7G_H1Kv=Ur_)2|nh|QSo@LY{ z^gEF3tJYK52wnk1@#6CBrPfyd&CLeC@%(3b#vCBq*()_pf2dYg$7gapOUN%WB8zZb zpbrrDkz{VxVCeUtL@4CpIe3_iKzOvK&!&w5;9#Yo4K7 z$xFhnlQI9aq9U7O+>~EH06w}aF#c3uiK3Iz!J62<~4=t zd3p$&^Rg>i*g`5>Gb8q1^|l%;?D;M3N93wYfjRw`IB!u=piHO&J1HbeA#6$s2m!c% z&2)K-i{`-B*ya*QG|Zjk{L3U3-JavK4mV|?P2I!{IZ@-Uo?w$0Gkd4sQGDdgV~OIP zX}-_KER#nrL6>Im^O#lBp&6O-gMDsn6U@xug7WDABkb<441gFQ5&T1yWp(-DS|V2o zl&Je?lSfq3jjZ`A(TEJ?Ehq4agUn5xC>P-`9=AGDiU((`1V_LDkxCVB>vun0hym`6 zqH7!6ZQuufg&@o3?yk6MgB$*^yDE+PELI`-<+MCrqVXz-p&uZY3=0T+9pI>i$CZ23 z7JD$!qSxSW+SeSEb*E@a*S!^e?Kj& z+InD7MK1b9>hb8g0#e+;ZPeqm+x5`R#*WAO{DE=xJ$qYwsn(yU8#(HPkt>fL?=j^5 zNwvo-TJBf6%M(}nB<;)bGUq;S;6vKv(Ic1uabr!wm$(HS8p`mM=NA;D8Qwg9B3SnE z7TJ41*=DxLv6m5*71DN%6`M!1Q6B7rI=AN87$nVEU0!Z91Aho({J{d+@nRtX3R zJ6y?~LmhaeuRXS{=IHBOEo0cATAy5iQ%#^s9v1E!X`e(9TR*I|Z zj{IV8evpp{2!3rNrI;dmc{kiH{l5)SZ&J$`!^PbQHuLqO+HkDxu9>mlo|0y=Tr2~Y zsF{(0m%po)juYS4js3>Np;|===2E|PZXJ~(YHHDG@YVPFS*KvWC%fMNx)-CmSssEr zEX&3XztKR6^;MuyW#1t@BHIG(aT=V2Jt16iB5u6b@p#WIN+c3lF*ZlT@R5aqdcp>`|N1&p+no?o%1Hj{y7hBu&y-ieDA6WG)Qs}c)|8}S&b$+C)Hlt z+sEfC07T4`ZZjL2vcHv+JOrK7{=wS-c#oGtLxq)idn2-Yoi@gU&>cFgM1_>&`wD&D zg?|DWD90QxW$`Hentcg7L9d_u^yUM3Y1!+((b}6K=MV8YaNh*G)g}a9Yw%~rC&qzj zB#YY)oX2MD(Hs}h|FMuupr$brX5UY68(fA8rB9fCn(L{k*G(Bx#Vi43J()+R!d1xg zh{QRuVR1!6#p5bbs;d(TfiKwBKU!yUnVmTuMm+FY@2W*Pg)Hb4fz-7EQ>=et@b{t6 zAp&M!bVfecO5bgbr#Q4kCze4YW|+ox@@c1lu~ElAYv@K_CLu^=Zy}8F)wC<|a5h}2 zZ>BRztVX^WO>a;=>_&_8eLuCUzADxUSb5l<#YCA89~Ts~D0%YaYp z*>e*t89RZ(ishrO>!am2aB$S(^j|SPeE2+Moqg#VhsdIc$W?S#vcxAivs~YWa6Sy0 zo#zz4U_ZytY@I*j+}5u2eD-iMAw+H9AmLAuxwV7GIx&O~xWZShm-?cZB8G-E``1Ju zFyWCG3Z(D5qdl!`2_s-qYAAYBViZodp)GBJnrr?Xt3}eCr(5~$Umxv*3GR?T{)@)K zWzz)bin~8aH#!@J@;+?M3EA7`KEXb_VUC`z$YrVwS@YLLa^e$PsoaR}WNl^Ss}_jF zWg9+ShBqSX9=o-b!pC-O6^$sRO3^aY=?$Ar_OJ6QL%7O0*&Qf*_Xsj71{uJf3&t@9mEz%G-QKzZ5ApF$TOn-km?BZbnPRxqCz zKT(BWv`rRkvf!r4{1s;)LwBbuQA0kJHih*R4uGcCaIL)dFdW_{5JI^-1-QbWR=oN; z*3#nAL<-+6WrO-4PV5--!QRdGZx1Phi`H%23bGi-v(|jT-9HmHCH|<*rYDXFuCZct zJ`T{>nBX`!SXj)^@VA(0ju}{=Z;mOE=3M}EX6pE#C=UJcc@z2VZ))rxqwYk4QQ811 zUohiv>{jzFIPo?Y(XTFq;1`;+g>~NTWfic`et{RsaF%IW-V($K?)N_q}Aei3i{ z0c?z;Si7}x72Lw%V2sLOZEt*!fsL>o?LqT9QA^2i)4*KmDmq;065j zYiQS&iIa0Qua&C*K~0wQ<>~7?`UU_Rk%k3t=F@h?4J&55{t$30D!%ezOcb~!B*j>! zW}PG0JZAog>ol%kz{sd04g$pE%!^_n4P6QKrCrXwg{QqcP2Cyesga3uNo)aLbx{&K zdk?Y)uIh17(n5!Y3V@r@0CeBwi4_PvnpQgdIiP-*2WggA#G)kg>BJU5KK*XW$BVWq zY)t5Pq5glS9l(C~FlqD94Uq`9nZ`he$z`1gGT}RD6W|)X9OA&)gj2{lD<-1h?D)Pv z#n5eHGL=JEc<@1RyWo;%`jMk27IAa?lR0KqW&0_Cz8Ej8gTM>oIsJso7vH-^?Jmco zqP=5IFRW{v;&7eQF0p6vSfIa6CSf@2v%-&g3(yk_K`7-uv{1RpJ9-1Mi7N$W6A>bZ zlON11WKh!u2fu=T4TcYT?RHD;q3z7dQ}r}1mqTMd2ZM`a3i-L5voA*Qu; z#A^4|y}>+V=yN)ruRX!FiT1)C11h|?ejanlIeG+#aTjeYv(Y3#5185) zJCHS-_N`~s-Nz&{F7C_3!kpB8Z4qz7$nORb(n?NFAoo7G%m<>Y02UpU@Z5v;vR+xW zoE)rf=YS6>s=*Yt#}T-Fv@|S=slDi7`%s~22#bnoaDLcg5e(NQB+_8AB=O31K^!&C zZQ6+rdj7T0MomK*ji9iRyIidh$9o)#el8zEc&^5F+JOX1wd#aFB{^}4udD~sv=$3$ zv1KipeQG`)Ps>k}>9Ajwe?fH3ed{{q1KwtQFeE=cjNO_EP3*wkME`bbhd#Z?2r)rX zN7L}W&Ra!}@i$9fL6p}k}e`lWX4ny=_>|YWV0vIzu zRP*hhkNNjd`0!9~jo)qH@Hv+V0P8d1y63;v%S4%3S(Cb$s*B2vBr#67e=W;T?S>rg zhuUzlil{{tfH8lht?3oHz2W*yq39>Kw{%q~fr5#SU=Ca{{QIN!((^aj;Pa(fdNZJ* zFm_8wNGPJZlw1&p>N{_RMSnK+>2Ko+88%M3cl~CI!(%hL1w`=${`WT7RG&amZKd$^ z>6MzZeQiX>^Cz!7m14OtVDQ_{F9}vbbQEmw&}9YZ^j{Z`4fEr-5~kBo6^Er?{d`@s zb~uveAVW1}62J_2s~(RX-?pTYCoMqKAaqV@T4%>zQ_oZYf`IQ*67m<)eC8rq`k_3iF7TGT0+P1WZ38Ih?&tP~uFI$jgX4r15d^Ssh^K5;AJR*|msKFed> zffBnqIVfQC=zpV|K*j`2GnGMBcR2+$q z2&DLO`wB3=a&{HjZ@(G*#_)Mc_wn+{9zX`MXN`FpmuydtFCD6R=+Bj}z~B|+K@g?R z&!2x{k(H8=xX;Cfp49jS1*zG~C4tdM57><&+(@vjZ~{euC+f-(+Bg8=-|TXtW@tTp z(HyImctJ& zFJyb04)8t&jt}O2KUn^`#&e%Ov)%YeoxI)#D@^zL5ANum9-GHsta3v+Lc{XH?2&n{ zl$Ol6QxkddUVD3ggK7v?l<(Ma;Uz^xyUf%`LAD!|#4J}NM1P5Soma8=%H4MdCojvo z@#bXR>!F7$k$Q|uiHOqesRalhL7!FM-L33#cZvUEC9ifjEB`h+O7Nei5aVMkt)h7H z488~#GP#fNuyTFkh9xm->fNxjPHJ=0RBd-kehRFeTS_Bp@DWewMAkgjk zt}7HtEb6vz!P6;EMf((V5EugUlr;4gzVu|0h9^T)XeMB}4Z+^8#fk=7gnjlmtnu`? zq~@+-Pf4kZV4G6s!H^#e0u#|SN7uFGqMOT^RX@3Ox?~oOR39Y&*L(#|?W!nFMyZtV zDHq@AHKG|PIxoPi5eR8q^gNN}Se&;l;+bHrX?x69 zD#o^mDc>se-}ey2&Yx8}N6M7ePC61v2)hn}@V)JLfg!zeu3#Jrlm0qglg*cpVBA2= z_3GT;C*24Qw&lO$dN+N;+^;stRcXSAsMz4@cgwLXQ}_olg-%_P8d4Uxx`Y-s8 zRV!Oe0Vq?rkONJ{65oB)ce$I36nodA=YdCTG3!lw3&T*!o~8mDiqJn0K!BDIeNiB6 zne3z)4#9ba=zf7UboKhJU%yT|{fU0UtT=W>(T@2urZIBkpAGa5{E?+WtE26+NvnhywGZKDl(Fupj13%l=yBE%Jg;I2pkG6`$6)O|4niG83~XV z=rN;RD^av)B6cCHf2RvAyqNP7y=oME)#F6Zu)nE3r<#69M18@UTTHcua zi_>NEC5*xlj&Y_MbZ9ah%OVWnew!VB4(OgXj6Z7JhgjKAZvp*&iFF?D&mzSBQhN95 zp)JCF2B+H4((N??m97VwIR`^Vd13Wky}X%#*xaj=^RLg1lw_3ZeudL+S$*^Z&{p5^ z9@-m#uqitkb-&!)bT+^n2-Vtau$Mm146~j10`;OnTLd!;4HyN>A&j4g^_RewhC(m+ z4(HPeHzS~3gFff8x#xRu)ea0rLjQjT@8s|Ak3plk4YzXB_ACn>JMrC%iVV}o5=v6- zrDAUj!x=JhZRDKx_cty2Za}8P7p*(@zp$_)CpjhkxFq%c{*xDVIBg)z6bp(js&`l1 zxE)RY5wFX`PsWrn^XQcER!DV@Z&r5ITvLG7c75g|{Qs1_E`BY-7`7hxR3M3R1M*Pq z8q*C}T=wBVK{z$Imy?ESaBFMDbh_*onmD|?E2Bdai9PqvBQImF;C0)xqC0m#I}SQJ z@sNyrpE@|uJaQU&Z{xSMyFGHRM@rZrhna>ojFv_rgPOiPA7xlV&m4?SR1a!R8b|ye zu=tc6d)Ma2a=R#L-1`I(B%1R_E_UuGSyu;QB`r`KygZnIk(BsCEsnb(Aj5G#HX^8 zad*nLv|h&D48I>UOBBksbmbG=Chb2d8w4td%3wA`4bmGPw6onI5C4MBBWX|x6PkZq z+Mym`y!FB0%`-cZLt=+rx8fy$`5&Or_UX_@{)j6t8wavA^9m~^c5rH^0Bl!ZYj27m z=ffQraG*^Lk*g#9n4EvA6R-Df`GFVw6UT_ozh@pSQ$&fv$8;sSBj4tUby*FK&Vn+4 z5|-KBJ)~1W*Aw31vpaurhN;mY!%3_g_$;5d7Qt)*B?C80r|g|`xQRKKYe(*UG;|UX zB}oz;(Co64;%%lBw*8ELr|37h6g+A_` zhmX(5*Z_g;=o80P4>oUq=-@P)(u~z10YTYTG*y!Zz(6!w_I2+!98g-`!S`v!4aN6A zfGX*w9i=8ius?`gWs%Tr>{25v2om8GAdd`uLh%egJpP-;mx`KbCzce$=Uf4@{!c%6 zQB2Aw=T|<%n!t>sL?lcyVB&zQlaynC`^&j6&ZedLx_o-_M+qDAi96#%tNRs4Wf&}< z2bM-EgWzX{`l~^#7k9f0N6ADjd4J}I|N{xWthF&j##T%RXtsG{V!+Y&x=f95{gUQoO9~Uq6 z;=c|hR+NCqAUNw7<$z8t-%^@eM@^^?6}ao6&!BRlD}@Ma)#|9+&(4(8#IdSTk~*zf zW-2(34O}?Bn1Y)D9vpWAD*XDUCJfLB)F|{JFZA5emqWJ#A%?ZNx7P&b_HMW+tHY|% zD~c@7A?*0L3RD%Chnq{bqu2mNM7cd33>38gcsi~a!nz7g$2v;?o<~113fDO>Faxp^ zdV6~FIi>}h*HA@m=T6Q=sz(!`l_D;S6gFv)rc6wEO3QNVk!wv9*0fzJUA;t#)*fJB zlF!eM8;n%InpC-wo*V$5hEP>C22QW?rAvknWyGH#@(0K6E_5X{U^K*?N6^Fs=(lZ} zKUjEutZjAp;>BehO$wEht|N}XY$_$_`hH7@e5dtnjX1_j#WGq(LbNqwq;OX zS-#-%ux_5h8T^o^Cn4=#^_On7=44&9lpe=x-}>l?jM_OG1nd5V5I(7=fmLZ%D+Qi3^=6-{ zQfB_A(+!xd8=-Y!cAsr9d?%0Ld}oSGt{@sb*VywtZrpt7)q7;C!Jk$4O$Q^1kD}?Hmc;zGeBlm zKr)yzvl&vXYE4`5Fx)pd+MZi3mI}P{RU@}G=>(mJ=bec7z6I`sB{vkuf4F;jId$C* z8jl`K1${ffqcxvcNm*bCC4BCo>z~;Fo2ov)9r6wXrr$WRhvmDVSdBxFJi*nCHKd})a7aZPzRhK3O-!W3?z`qcV&Lw zb}|)l*@(>gD=zG@SX0W%|$aPsMy)eTHUK@RHDMxybt)pt#;fc|L z;n{s&d}7_6*Z1%l?a-b_-LKr>5{Tf?*Bh&~8WSwCp3oz11k>7Au6l*LC*QtrRZVYf zfv_@G>1-;lE~8gE z>-<~59VYnPyu}v%S&T2NQ{F~=yZ2`h4bRRu|Moz0={h5UUDG9Eb_j>)RaYQ)*x&_^yl7U--VEv+1|Zz&s@U5fLIsv*Bc%K2fPdXMdjIO`(fI zARoL3OV6@fJMv&X2xjTPJ%pcU@is(U5ke1ZZ5v@&+gp-Dajd~p)!mVrRZ8e-rh%na z6~Bur=Jq$;+Db2DtbpIUf5#>1}lzQ8qjm7Rl*@VTJ-oQjme#`E8-G}vaW^9!HI`#}1TII7&8VuVOs=eC^ZpH$WB1>FuT4uGah5|OTdjffDt*9P zgLEd2x6MoC5{GiKcOpKq!n)}B>mj4JiE}th*Tg)2Tq5>cT{T!}$1C(hQ9!tY*q#Ps z9n!VvRU{Kvi@&Bhxbp#c5G?4vED>_)Wx0#o{-VN8t1*d}VLYUg#~M2wSdO+zPrrwz z?APyBDlbQ7Y%kIkvBXTw?*`|Ynj+jUi1V>5_lvr@Q{ri!&!##B=t>!|*22@Wu3V)-QcxYNetYO{yGRas zt0j$;`p)s+_?}mIri`^d+3^w*WF<=L^+C2AiU#TRE08H zXr;)6_Slf>ha;Sjt#=Gej1ZiW=0_(0kefe5?9(=?8*@9}_gfZKhvv z!4Ut}M3U!Ih61Xn7?hE3i)D3~U#wJex0go-@-7)Qs_Hwnj8CZcGio{shUqr_h1*{2 zB%yU*{f6vrCf?Nw>`>aSQ-AsL-s)=mh39SJSNpiZE|cYaXcr#5wAuF;cHwVezjcXH zcQ5Cqv_^W!>4DFpqU%lvpPE#u_?`XLVM281e+AY}petWak7Ea(;Gm!;bgaumKmhpV z6}hkt4W-CwnZs$u|S+p=NmGGUs>iy5;rco~ERRDP@6Cz-X_I>%M`MKH;QNp<7jdG73Wp}O}}Mc*tbtdq*-D;00@N%y*>7gJ55M=!e) zIYLNis|I4OP>2c=@lg8mDN3J$j(_6tK%leu%2N+*nqf}!cI}rAGkNVHT$?;^0GXHZC1RZJ4iwc;)el*upVWJI3;2F-1V%Ln4bN`aXRm<#egP3D~a z%Jg=$;Kfq6XMU@cX;>rN(*qfD$Oz(zTtz$XiUky{WJdiPW7_#f$NkKo-eQRt_46Hx z`Wj$LBiXmD+|mF(y!piP`xu*6+3ZHpd9h$8V1*17PuXnSNp|=v+}?cYitwnWa$kx5 zS?m+NOS`CO=j0>_;b`D}xh$V`lCm(KI_cu%pS`p3EI44Ht@K*fs{3TM;rB?0(c6tr zJjcBAVqE%(I;x4&>R|e_)LvkU$yjqnZ-x)c+sg6@9Ub)|ZDJk!+OGM~Mas7bOujSe zhVn22wicSQ579{Ztm-3ya)Z+s0~-9TgVpPc(OcEVqRC^~S$WZB8#ze^boRXmp+}!K zbl16^#wlbtwbui>bgp&H57Ok_UqSZ{Jw9VVL{gii;xfJw_TYPSM7uS!Q=Ify9r72c z&)GDbKLZlUGA5Q#U?WMup5bp1rxX+9yIWYU%w?u0_OO}|go7al&GZIO`&Ia^$EQpw zEw-8^x|DvUcIR^J6--x`JX*Bwrg?*txOYJm{Og!Ou|f`=iGc5SrYp$%TL5Ov2y!Y2 zCo&&9+UnwQi`!zT@!d#&a+6fpGY?bLT<;3&#zEa~egdb7gGSXuXUcCy4}##b?dQzT zFTXeS()we_t)0P@!(?@Tm((HCwUSC8vF(u({+ZeM9pfQ<{pRpo_VagPQJ+xewYt7i zWE`U>7Ho(8EdDWb2GTX3GN_+8qfQf|aIDg9DH98TnpZ@}*7MQ)GOY)&`kS*&*MqGG&h-&Ez#8FdrRvcm{bDVrMoJ>%Q zs8U#b9vT@*0l^vFas2Q+L!ymv5@z|M=ZWaD{Y&ZHCPwF&JLdIeZ z-_O-|TdZ-^*wVS3cFdy3tS?(QGUk7q@ad5S1$96Vjx)}QqD zdZx3B#L3*BT0U?8wi;6Z7UwI#26RtLq`eh|{pC_ZrrQn){j^>MuYMJhLX+kgxx$_v z`jt~y3(=k;pT4J>gS6OCt4WL##?GS-b`j#V6kb@iNaSfv6hwnDsiLgS9jst}F24DV zLWZY}nj$C-SUELDzfT>k2fmEx z%N-pd9?#}T=}02&zaH&Ln(O?j7V(uFaNt`eBKokK<9aqVO91Y>SoYGfLQHToC>w#B zW9svgxW_w*2-ypk`3*0LGTW3Sb9U_fjBvghOTw4jymNpljs*RK=0rirAC>L4UXDpc zwMs-U!2YcH+b2!fyIRwpg4*-wHJ6&UGs^3 zyMjJ&ENepVn8cJI2;<=Uxvui>9lau!HB?$c+e-&s{RrE_&b)}6P0|vbroW#m`(mXK zKZk~gzk+;Zvf9`-l$2u`29l51W6NzaQ0fe7k?uB)yr1-$trboS6_E?m=86=iK+=X3HL`8TYc);pIVvRDpIaxHT z=7esi5<+k+SoEd7xOY)#OIv=G;(T`FERT@mGMe$GlK0Of3qgKTySr`W1`30AhhHt3 zh1G`%6BPxl6(b3UU3UE4M3m=`JLb$1PiilEX(tmojdp*%KBKpnbZrP@CzDvKrM*xu zO^#GzJrpEYI%Jcvt*xh?xqZIChisDG|Fv4V&y}K_p}DiOGxJSNoUd-Ih5AGKnXjHv zIt)9R&=NO-l zW4P}3rX%?)fp}FKwb8b*d-{WW$QWCDMT!Y+Zw-+%X_jER6K%m#?NTetVhtq|m9nTI zLfFs;%MXpBR&BKDBqewUiNdz-l9Bm?^@Z4)hLbT$&+E)l{_`Ul$a}*B2Oh!Zxi!bSy?gZRurM0-A^91ci=qLu^7YX z>d^63Y?zRE*>T;*p=8We_bc-DX!W{9-*Y5VkRW{ewj-OorLR_uK&t*n^KG@%5rKQd zt*3P*AF4&%69_^RqkMlEYdFSN68Qhtuo58@?ieTAVxKFZT$hPP1n=i=b7%>UGz@P} zC@Q*72WR3uCQP_$;c0!7{Z;7dVp@$ei>K)Mp%LVvP5INQ_-(!{{{nP>Jw16^^i+&vbVK;0tA+Pi(xMLcz(_lZee`>ScAQv~f zy{pT>=v(3>l73p6t}CQ7Ql{MXmH`v5o)(tMg1wJ%4szuxM(J-a6=C7184(UUsB*RV zSU53jO&C7wyIwRgq8G$ku3o=1pWe^UEilaI`2E-V0bUI!ne~Nvf(Co}A_4ZZQg#Lg z$+NTHI7^brm2w4w8^BTtyizu5!dDW}JM*B0L0~M&wc`;%4>#cy zzZebS4H3D?7%ddtkq{My%2<3z$4HT9#-g1aUQyk9<*I$@(tOAH0m+gUX1-M<;u=bS z^>VdY`^CD*%RBG+awRwCdCb`QO4F9-ac|YyI-8r^rx$Es=8<%aHgyu6H0TettWcWY z9^%5M=!2xPqFi*zGJ;Qdqlt5#b%aa1e33C;*zDA?bp_c%t>LpV8m8lL_L+khH0E64Rt61jmqmUjio5>F z-PzqOV&NZzJu|?Q>fs(q&0wQ=@tFnz{o4mHf@bHl_1t9F@Q=;Wuhnz()(*3 z_6BN*N*5E~|Gdsl?^Q`~W4Eso7A~om1FQpi?b_~Aij)cVc|bockY{%2=fXQbbJSAW zhd8>U=$S=hrSWwHTlH}Z*4uY<#s?h!HDLx)H?d)K|Ur);pq$_M8|Ko?mKRsq}L8p?R6uD8Aj$)zu z%@D)zy>-e)vE27sw4F5D_ytSF_2En(b8Oh@08UB9>XX()U)V#UutsIlKKKw8?5=k&CKTVnr|uA8yv zGS$Khd@BD11ZLUnhqylLzt6n3e#@0rLvy%Yv`+W(+!6{Jp`qC6EKABHBJr6# zSzgbb%^6o&B=G5g9<`YrkGmnluiAs$In%D@V=$<@^yLm7Fp@vsKAChOkv zHOQ|p@=F831+(qy|LOw8&{)s(QVs5qol^T7p#i3}6{7=1ds)e?NN-cXA}Vd#~v$j@nbt)7Hk+zdCmm|!eR#rI-dN7sHlA_(4_CEV!uE{pv; zW#stDsJ}hTo*h3-1d|;OTwG?G0$b?m8Z#6(lNl;+5NXqqj*5K=Y-{4Z8>Xs&Ku`+1 z+y;rJ^Vdey`?6KWEm#_E;$VQe$jUbN%yKxRM|}F?0qrIGXH+owcXL<@+e69vi^p=C z1}BoW9`r)}7O7x$Ohs=ZLGy31Gz!dz%-9LJyMQC4b!o`9w_?zvmY>=RKX?4YKaFPgVu6Uc*srj#;+gnch$W$i+j4@(?U;BV-8zOQPbx0C+&OOL~0 z^L!QaOGTBnu|D6hSiE6Pm4arrw7=y;?m3h<*}rwHSzSCs@egA0*7`2_+2bH6)CE)N z7ftW9>I@j^vJSf^QerUkC0J-%@{>k9Eo=-#TjhEECp4tw2Agk}wvl@Ac=)6BeaWqUta$_z`*wGyGQn858plN0e8d%w{Mr z?=Nr9k!>+0;*fvYeS6u=V*6x?zdw>K)#&8t^SojnXhL74eiqIp_NU~)#3Cj%1US+b zj^@m;X@NT7?1sU*YUr%Z)4VIu)2ds0_$z$10y2D6OJxr&$xEVGKUTvIm%yFIorS&X zQb`)adYoD*;MhX;o$@Z%wakjEev2kD2c^s-;eOka(wcPNPK&N6e3XB@pz+P{SL4RR z{p^W9rtJ=?sU+3GYgJKJ{EmUnI8_GMQ1q?6!9nHM)B9oq8}6?S9BfP5+O+V5ENkH= z9nNT>R^IG)@=~)(Rmlm!0)UTl+iTW8*d%PU^&1>uY9W!Ck-NO26;_@jr%|1|&>Cve zQhg6gu=jej$|ZeRvB|De_Nlw^{>iAcvLJWsJdhw4_HMb%hDzmp_ik65Z;@86%AFD( z=(Du~R{|k=uk28jt9`R?JepXsFi>E!EdS5N!;TJ0VK)lZ$VIacuO6mV(z-WcQ7#TB zbOnB<67)Xv4L@mAP4BA;o}#PuHn7S(SpH2$VOXQrf~lmzXX2wID0I_EiNYRp1=-j1 zy}5Go^+Lvc6q+G@vd%s44f~o^*AkP42NrW*7gt7-i>>qEoG6JUH`jOLYK|3C%2o<2 zM&_h4c{tTy^M-vj1l*3Dv*LDLx~z!j2{U}E52Ayf$&q^|WqF>Lqe7Tp8yXt+P1KG; ziJd~#oiIN??+e9WmO_ravAuk+rB!p39Ws7yh%WtvJ1@4GW@l&s3N4z-7UPFe&VRp@b&%%{nT3OV`a&BZhf zwk^3i$_H@^PdL1KmoSx|=$n^hvG?TZ=c#y>{<@CMA(w2iXd+C!hJ#nuhaORR340N+ z+L^%j;0iLT`qQV|A}r$|M%80;WE>J64d1`pPx$}Zd&{V(-uM4^OhQtSkoo`uBHc); zlz=oygLHSdK?n#)NQabkHw-z1v~)8JNOulH{_pvGf4{TVf35T6#Dm{D>&z1wXS12T z_Z`=LU)THfW>Qqwp8(p>Pjv`AE?!=BH_r_2R1SI5UN65PL7*c0F>EJ`JynSu1biNq zcE?EOh6RAH9Y@YGR`_7R``S!@z<8OLC9P)V+Q(SU>Q14kcN3Q1HlpGu{L(!8)2 zci%Rir%Is`4KEjT)5_k{Kp2)X^FCPMrC~rhL95v19mU04P7&*=_rt^Qvee!gB9HLJ zO>Ljc#ZfWA;G)dxN!T@#t}ai9S%JL zX7WKjj7ArIEA>xf19^;`rkys3-`fj+91ggqP*OO5$am2al<;e)YdNAx!&Y8Lr+rhk zPD!c7=#E~ev|$yv(le_m4VSu^xaxzDZT@t?A z2BVBjOx~Xd=i^$o)-^v3f5gWA&z~-LrsPzpJY)TLR*8l@-e)x2*im zR6=g^fTXsu-C+`xlZ9tWgcL@)pc*T&)BVob8qwNn-~->FlZ26EO3}V;bvyTl88)J8VJF_8?J@0J3M>$-~d?UPP2Y= z2w(h#y=44h^V3$X)yGGLo=HvZ_|gVFi;gaJrwy{P|x`m|c6 z@i_o%+px^`o7Hl{=3wV+_}XAeqb6^6DjKh`Ws#BDQLuY%$?DkfO{ey;*}0pXf#*pi zmG|nhV%ga4Fqq?^6|z zz-#(O@&xdtuC>EQj%GsZfCFL7qnpuUeL?4TXs?UGoIf3vm>V6AW)WHR+baJsZURO(1+FfN8wz3m{?fxXQ}=1K{mgJ zeuEv;iIQe2#{lwevN-y^gz`rEgHGQic*0iUx~?2AG&*KbuxxASC)AaJ_KEyZcjo>q zi|2r&Zvg8<;f@%B#}--(#BEqvW8^AF3=v;!oAMO(?# z#MH1}`N$>b@d#m4hxZ#blJB$}33?0S2}v7VL|;A-#?R=kqVbQyg0l@(8FCONi2~C? z%b7|Bu&(+rF|xa1Xwf65WG1JeaNDwf zlo%q%53362glrLSnvLIE%?t7_*5R9Fcs=ZgCD5}^Xi1W(cYCkjJu8(=r2^P~k7ikD3K`bB8U ztw~aINS%Y#z7V~H9$nKz95QqTm$qAuF37=vI>6I`4Y0HS2h=Oj(HRq_+UL)nYMH8_`v?Y6ybnXDlOe0?g#Wl`uc^Q5AoY zc2BHx3k`9#I>sZuqD!(?`lJZ68OafuUVF0e|hIiWf6vFN7S z4-|X)IHGQCw?8(k=KL5=U@I7RNqI0&cE0%Ts_|l|#|D(SKXw7uOHuhQ3ZbkO^OCCA zgE3`xo1nFg(`QqAtDOTTl7-}X?{?y3SKFuVdND4uKH_r}s=!5W^O=Cz7Yn9dNBadd z%MLT4`88h8jMtqZUY|MPD-;}lEGTc72 zc$E?UR~txhRvIiRtA5A%Ul|-r8>81D%$wbqk--MIBkg5ho?0+6T~)S6eHXw4sEgp{ zt|@MEKkI7m=Eso?e~L^wnyn`rpu+RZS%>pX!?5)%)ZnMi#`|Q8lH>Xfj}1tg_IiGG z8@v6r=4+YSH2_N;^L+!+yCPpcpZwmC`}|U;bNJ;p@@b6a;;X_O7g;wJxD3#1y=q9} ziGGCXYXy^tSvW?~bi^67|G-{}QNR$4md?cCGRTzl=D+j1wYe*plKZ>8h<9lpA2 zN8Zm{xG-p>_{+VCmWcGHg+8}Xg=C<5gx;a7x~Mj9YR!5=9S5%0aa70b9cT`xJBd$) zycGOt82wxCi51dT211 zvYiy|%8}tPcNdSj8T>0G;84P4aK#HBbz1Yrj9TiNT*i=d#g#qp#+tVL*_~ugHxf3%r#d zq1Ol+icc?*6dnbnL__b&U)=XN+0U2J2G&aNqCR3!d%lV)-VI&ImT9{d(?0GP4!B^Z zquI+5YF8+2s?QuvZOG?z&M~NP=RYi_zGLS*w-K!!BNY-M|I3r4AG&+#8v&du*bQ3q zWj?mXwo;SJGL4$Sb|qm(4xT0^bcbv)Ch5iE1iuyE$URM;BMuwJHyC3vzmqWhVW%db zqDb?f3)4PX(#Iih9(;i|u&Mp}2H0=*16L-^)T^yD{Hfh%LKOMtOv zIPsiTQ?ZvZI-ZLWi05Kj?PLx1ftujG3A1yG!Q~-(8+{Yh1Qs-KnpyRi$vZdYj?Jn| z*3MT+W3T@D9ryRI>8T*%>Ly8@E0G6^XJxuAIZ-##g%?fDm7@`U0 zk}m-m&v`J{*K6FM@>&1GC=LAmwoVV9HWx$A(XmlS)P>nMag(71YC|h%-+Zmq;Tm}#9%g) zsRBxXf_iy1-$Mgh4qBksv(-QC+|`)!hm8S?D#1U3%fVe@`}ne$e+!U#uv~|e4HZ#J z*h|3d{KZYkSD%;GM(R5N^_%wT_HGTOh{ol&xUusK8cm}cdA`zO_Ko1f zFxqrHD{grG`Yo+K_TZ5(aCg(IY+B`0@aaXH)1qzJpR-9>Fq0&(XetioQs|WmLfr@F z1wVu_M`IGHE!LWPr0{1FgY?=t@PeAqYT4VGSSz9cjLkrx3@WVf#jgxC145c{z+ha^ zjjCjVr$EhZi%&yLj+$jd8i5`1Ouibm4ILHY*Sj%T!;Jba_(J?Ap;~lUwQ2S9l5Q=na5xF)_eZW0ZMIW zR0z!p=JT1VJkYgNUOro_mrZtkpWsx*?wn$*D``^J?QP2F6_o{4Ntm7|D(cq*-myxX z*7#M2=3GE?b&o%=Kv(`qbl_AhWYI-D(8l*&y#2M>NbQR1#$L3o@>q%&OU9^k%OZ=FrxT)Wf1?OykZ6YZwMDpU+fjyc|1jFU5B=-1Y3gZ_a9-$W5k_?oL zrPICE$ob;QVg`aP00Dp@n?f&aFa8;K7crb^m@lngjwi&d&fVRVBNa$UwD~?`1_T70 z-uWErnx^Y-7$X3%&5Xaw(E24{#ziN%5aVq#*#@U09r=4zZRKcn#p}&}CpG5NSyK)DjBs)+Yw^ovp5u z#<1r{+KtS>FQ#azmZBS1dWJ?+>OM(3jT6bs~+if-9kPQLjfxMUnNmCihY+ONf=H5E!^hHdf?n+006gl7v2q z?!oFk;P0hmq2pqHW8lym!|-CcQ~e4k(1_bWNoe6($BB;W*Z6hJms7l}HsN54ag)&T z_ImAW^8g`Bhx$hR&OX4-6;^y-J_oI`-1E>_<88o7gg`lfE}<#6V2bep^{PB{8abDu zE;-*M>*sySykPFkiNnc!^20w%pYcS$5d-~za1}3n$yGjwUXMS875H$+=YM}p8pG-Q zl+y?EU|@^;#j=F4DtBzZA{$&;tA()Q#Ac(+kq^p*Erc28Z$;uhSsLL8qX@1Jynl^J z4|m`FbJX|b*+hP}=Ev{n#DKyNXeBmugZj>F(7}ZAux(NfbIBsX1m9ThUZD{~~j z8L9cCx0)W7miZIgTJ|{1&n_h2I?bt%*UqP^hAmm~4{_xR+HSp1zb}P zu#r@>K{g}PQ`s+;hyN5^p1~S+{U~Q85VIp8YxQ%0{*Y8_#2vfNSqlKi=nv zV$BGDv7{P`d2W1Yd{YA%+haEVPS=Tr*?2_*o}O^^qsk%I$hVPy=zqq!FpF}>roM{> z%C)U%E{EnY1a1_==EEov6ixa9vH8Ru_FuegpECKrIXnzn-IraAy~+gy~dj2z{*ZDtK5g#+$bg3_q$V5{1ZrBS%>m7QLTz0>`sgvvxxjKN6>m!evPd7#+BGB>G zMz_}eyt(&Tx&r?S#}_^6 z5vQFQ3#W2Tjvf11;yD}#PyS0(<{&<8A<;YuYBmDMyMm@bT+}u;(F_W33_IOY2jas0 zcyIEl$rn2tv`HgOJoYE)+Xk1N)rtBecPf+klSN`J_vl`%>nTPJn7S|$(a_L{a$|FX zgzvi7?cvS(dkS4SjPnFG`7C|yZM>6hQg)yN&oP;Qwj;#z>^PRVO+M~t1?NVu=ip}BW`9J&STd~#n&e3 z2U6gSXeRb&Jt916c?}HA?^C#2a+fFxjqKg)2{&KWv5v~GgcO`#1KwBBo>Oddu#0y8 zZz9?U4xyG6S8kY_{D8V|#fYvN%$f(`(ox`+DSzsK05Amy?qyXoF!XsVVS7wtV)}`w3AQ zQi@WBYxoBW_Qdy$lP=Se%rvWW(JS6)1avp<5IRWGZ*LEbz$ymrB)suQTQZ-SL{r*t z7T3=6jvav|(tc#@his4SjQa>3 zW-4?284rNLuMVI5G{q2*h}ne$$0r1+I@FZ%?WKg92~NfD_ll}rQT;ovqt_2=qrG}I zH@?+eQ0?!yG{?z*{RI}QFd{yGsj}6w+UzZyTv!^#YT@rp#Apz3=O|^Q5K!4NY;0|; zaaCAX!e*}34U<(=3z5Yl-Nt2BNU;n1C#u-tJd#GhqI$ORzLx(jG+AJZ2WI%Eo{V?K zcHk%FlfPe>3a5u+74i5;^;p9<2JW>sQBqNKjG0uMLr!(@Wu(UFlk3Q3CrbbZIlc*0uc?23T8biN7ka8upLdu?LwG z^-jktyimw_ZWr#_YN44w{O+iEm5=SX3*@5t0}}RJP+~1$quvi6z_uiXx-f8KCJAhg z?!f4yM6&oFQ1Mx-N76h;7u2bof&MT23%v+ucVk;yAUx}eR_fm74N%X#&Qe)Kt?sRTBwD~a`cxWfCUa&VelFNw>_`-P zRIi;RkcYMeIK?E_pNofokqmnK$s26CShJ_R<+uFvN-F&Ah}K)e20;F^7IEEBo=~up zO$VG4-;~zi6xuHPO%hV)NG5o!m5btG9zyRuHe!^`p6-ENzZMuW6859flh6@0n1p0x zRVMSy)?UkPSw^Y6wyr+M+N-|T+?USyn zY08yf`?Lc4(}V%<&HX*HV~UOe3i~in2k6E^@oaYMMa~V}jQg<$IfSl#H$DZQj3@tw zR+t!UnmA1W!~51KAO&0oc+)YK-_N=G8KXf_kg7@Vls~}O@L+F^irR&7MSpG?kdTm= zK(>xLwlJ$O0Zxn>5{}30El+4Lz@NI_hXm@V%5TfwIyz6$_JSHXbXJsJ@$&7yB$JOvPIMT zh{G$_tsl>qDypsc=#EeG`4x%`wr-gi$wb>2hU2JCY5m3zqWgaa`~w|Lcpb z$rz|Vye7ekcT32GS|{+ag;*8cym^_k2!t^vO)325qtM)h936$o_ELutd5F?(V>x_ zlI!Se^{B})eN@hiz-Y7Ar-g%}G=^!MuIn6WxfJogUIc2F2-7H%!v{K}`lKDa$5JY7 zWJRFIM;Rqpt-5t=DdIJ^scCqm`qxULc6xnow!3)iy8YhHEeFQKwCN{N=f6a#gRvk| zPLtXeW};QcB`R5DZ{Wa|)M^sB%zlElGBxrv5c$hpx-RbYMB*>l*ZJpB-ijxP>V0;f z!l}5fB43|9Al3UGba1FVSbr>XBP0i(Tb-L<)lHQ|8T>t*a_^z?$kDDlZ zwFi(_hJ>HhEEOVf5!W)`u*RfM{Kxq1`wfF8N!j6>OTSB$M4}4`bjE1q7?d3Lu;PyG z-pd^|wMCJ;y({$o>tg~8#soALgxkuX`wdhW9@2I&nP3f?>kxxoL+a}#4A>g{R&3CF zE~eu$cs?^RI&$gS21vYTBH1C&VvQ4EsofFcfGzEj-Z4T;yz4L@Sppba*hDy(U#!Nfyw&u1c;7Z1m8_C>U@8Wx_*WWm;`fDCT z?BLVEo=22qm&(|!w8R>e;|;srLU#?^2Vd<=H8mW4-2YfeexIUZX@TuKuUv4UxeVv|hd$q3iq{D4WKVkQ8WTv~Ui289= z#T9H)hZ~d5e?q_TAd&LBS{J?52pfD7%%HS+5j*zt#Kbq`P z3NaL|;}c1<5#X-fR?w2zi+Fc(%qM!?mKQbq@_vA+ixSHZxe()3PZ_lR8~c(>!>REykB#)XY`Gm}*lex5GF zw`ZiYhHszv(bkG5O`qoJFg@+fh$H&|K6~@3r=HiTlHGvSTh6U-g-Cd)u)2R@?aFW~~r8VRD zBG#5$3%|_z&(aBewM>*=HPvLV_mulAQ_T3C&B#FTaGuZA*?g7q3vX_u0Wk35G+BlU zvtFkjssuaLX<$!Y`+k#PaC$2zN4;n2hRiuZ1fa$dDex=vdZ0}AxIe!=RfbP$;AwQe zLUWsVeI@T4QZ~1X3;A;!xHSHQED-LoR-NV@=wP*vQCfx>sNKw1c&9iS3Ym%-gf+?(*hr4~ZkS zU)8~LN@>;f5RN4OLB4{m!#^_?A#R%{O{lb`5|_1{up4fpj=(>O+Y5M{1gt)V>m25p zi+Taqr!!2|#+Pxe=i#kyi$no(l9UA4uB|Bd$ACg@Vd3A<)d4kn~Q}r90V7mRd#bQ z3mR|QEBLB#>xk9H4kpI8r;ioWW}hxPFMZ{-c_&|gJ5z$t7x!jtqPhGOaI2tJ*=Ra; zreJguGm@FT-6Kt*G)pGU>qcXF@@JM5CVq=_F&g>OFVWv}X=bx3c9iUdD8Y!plyGjU zIp!C?a`arviS4K*{v|WG(j5eAIgBVT*~XoB7#8Nx75;lR2kUeh9^A6Dnku`zI@ykF zn!4TmyXVgAA>twRphO{O^7^PomFmaTkM#a2l^Tn_vQ-WKt$hu5243KiB<)j zZoh85qY+8mj@=>srP{BP8y5>D^8B(Mj0_Kr!fB1xrfZ^tEiOBqeWe!~V}`Bpi$35N z*->9Q)%EEaHQmcUC4dm`+D!VkYU@4Ved(L{L;;&!uDMkai=otF8Fz-(o6|CwKx2zc zs4+!-J$>Ws>!`!^3ouHiOziINBJ3P|blBLsO(I`178^7R&AZRpAyQq2uxv&fIPt~KKTKXi zpS3*f)L$8)fS-3$wN5?{-lZ9;DG0w616WKLu!N-Ct6zz%o~6H;d5V83vX!4biv2|) zpoRJ##IOHMYD-mw^>}tF@)3=&xo_h5Y*Wx%3kefXUlX76BO3m|s+Lxv)G5A}^QO~H zd(5(@V@;Z#)t&WcGwx$yN?iqa37(|Ll4mj11?CE@Yu@Ue%&CY zHXkG^n8x{S;$g2+aIhYJ?^&sUPOCSJqN6XxUXF#9_eXQPFG7kY1WsgZDdc^!VSw@B z&MTF!0~GXlsJ~;5!*5ewyNv=iFSmGmgA4&n4sPF*Y?{Gtvjlw-JfV%B2StY0FGNS! zsPV{evz$PQ-^?&oPmkDHg=<|8Fv96bvPdUyIr>p%S|Vlq5B2RR_ro!OHModWnv*)r zAe~F;gh0pRpFP~>isK-aI0XVYCIDID0FKK%CGHsKUZ{JoXgrrb83=d5ulGFi3U#k) zx?8`YClgpn-QrV4;oWM-w^K;R!>9L-L70Knb_a6ym{!oOsGx#2mCsMI-lBcnvHK2e z%-W&COm@E4Z+|OYUsYVEhJo@ZARY7g7G7xU;YpdHd(n8X#mCaIvmQXsSkl0wSN(V9 zAn4WrUKAwPP=9&3o%e3w;^Tf8GpPZYx&OtO)uhQnR6uHBn#93wnkdbQrClj?#7CNx;(69RoNe|IE8rd zy6;T0eqi_0Vc2^YFzmA!JE3AliqdSom|*o}@1;@JcHV1PH*XEz_;?TRcj*Wcczdb4 z3E!Nrs7+kAt~lJRIgGLf`XP50ZrC~Y{BMUmT4JxOR`}o&l#q`%O!q_BGX&jz&(Ex4 zVYi8*g=>*JP|tib+t|l4s5=Q0o$p`l3me;#KzkP898=Zu>{wMdH~T)jn8R}*YhEy` zZBxa8Y#|UIVuN7(Os53Xfc6r_T$DPIhiU6^+Wx@SGzg~Pmj<58p-de>U7TFf1wjQ< z*#F+zI4ukCa~DMf5>?tTI8B}AjXnH$?s9{`5BS}&t!v-Fpc}qCv>#J%A|mDj3RW$e z>*ZhU-XHGASOZ>o7KM#nwJfMwEv^r@0~TVjHBJpnpC64{d-T`qWD0`WGeI4vk(Zx0 zFezK7LqjGKS6qvePw!%D1o8V&;=&Yp5@@7==#+(3rola$ot)2$G$UpU9`u)5TUudV z>bq-uPLQ?`=yXRZ6^Z)aP6bfiTyorU7aKP62JX(my6x^|tp*t3Q1G+PJuui}!aa#% zv*QRp*GQmwb=$BU#?k@!pG1l;SL3QHt3qh}J!Oi%Ppb(BcT^a9>_q9uz|H)684^r) z-`<=W-tv{~u-1w)U#C{!yD*y$(a4ee@b(aPr7Z&r#?aO%`~Jp=42^<@8Hzw87?qp0 zuA-)^{frhvoAWJbD5A&W9WDr%;I``?hBePZOH>Rlt1@!69f};9 z*shN1S2{Qp1!+aR_Wi7WEIhdkz^|5=`e{(zT+b%_jbA+3IUCs=oP5s{C5Jc$lVX(( z!=ds*%oU;$1=Gs#-YQUcL(Yl;mWhvO%6=VH*HZJdTjt_((oqzRCU*Am5%RdTR?b)} zU?Vf+m-ci4-0O;X8XX3Oh4^#_3`O~$&^Lkp`cRNoaGZc=TP?3PSXU{T%-`?qMw=p5 z>X<1cAX$KmA|s_q>AYhbxxf|0rV)QNQ|)-0G}ZyOfr%pLkgGxK95UNGGl)~0sbH%F zgXH(#bLFm9f>&1p!8UMV4n5D6T*Q*Yt;@7}CKDqE+e4eXj?+HLDJkyQRmb${hssZz z?;XxtZcx913m&xHQ=4GhyU)>!(c$Fb-W$%*l33U$C*0^EC032r&#O()-`aQ<5Qw~} zu?Y3QInKx{l)-6Q89JFpUV#wD^L&0?jC8LVxmdjJA?Any`S9V$p1@tjwt#9bae#d6 zapZ!BCI2F44c}GoUnAkQid?yQ*~M|C6x@`R9{<}z8W18QABg0rU|Y)5q7%+1T?e)ufmky=nV*`oK|ENDJ5u^> zdeOQEGk4^)X8v^Dner7pznY~nr_5by-6Nofdfuyt(&b&@i;(pd7rPaMt%Jc0TnA5y z!ooVGP;rYLVf0eMY*%k>C~Z5H0P^wm8%(?hoHx~D9V1}z8L0;qtcG?{4BP2D+?To9 z3Uxffm*8JK5^hSc4iy!DuvCt8+dnGh?t|@*P9MG-j&%Gm+#fR9^!Sx#EdH2gnL%2i zJ!%0C;8XG%QRk%73>6Xm_yN*wDqm@+68H@wH( z)u$+$trGMeCrd{udK6NOsQWQ#HizFi2PKiCIMXS{9~Z{|@W|~dR7O8)@CjOZA}#9W z@3()`SKeez#feIuf--6}&qe*c^j^RGvLANt%Zv%HwbQM?x!A61Y;G2v2VtBxRT>z> z3bqL6%Ku87aBSZ=K2PjMz+lr}#~nMve(VE& zTLq5i`W|K&R*~t#0yrsRqP!F5=iH)TGl3jr8RE^`7AO9kW|ZFUU6hS}^>SYwDK}BK zPEb`!4=^$*{OK?*MCJk}&H`+NKr2c?3;3O!UD?$w#J`uA6#JX|cP_nCq5xoNx|J`8 zdqTvo5C>pj6`gk-QxJAf1oUi%fedl+qW)Fbq3~Wky~dBO_e>STNZ@Ei5h=L*bteNC z^2!ObJ+sYtNz|zQGjQM2h1u*k3sAP&Y71JeblXz84U5hsy568Rt>kocbx+R&@BBjA z@9R@2G)rIa-VYHifbJt{Lnt3Bg05a1DcrvDX%ti`;h{(AS`weHx4ZBgyZ2K^VA+^c zI48V#80iT5N}e{RgU{St#}iGxXmeUU*Ac0L*_mh=>LjY4s8Ww+7T*mC8o43}WSk!K z{!FsSo=Ik>&IQED*QQn*sqm@@FO^8^D>hbD+Z4&v*e z3?+9V%27~?`)|Q0P$jT&I>~+K;TPYO*dvw2Bh#MWw@f8>%I2|{Qoo-LM6Q5PPqs+Z zm}ZaWY6%0;xLw+>6PF4`J_PVx!0V4^>)*1ruSWzs4)RTzW~t!l6>xC0uH6W&DsM$*>`>~Y|Ej`g|i7XUV^Jg;*FI*U& zLfNSMi$?ZKxWA!=Un1-4M^*bXM7?9O^|NE_w;WbCwTyYe7vB)kFmA*JDOesOl-+_ z?x{$W=F099dYouda~CRsC{-S^r_1vb2IWL!C4>T?LYj~ zNO-TDkX{;m_r$o_Y-$Zx(WaizCKg3rN@9e)r|LG2xRGQ7AJsd)&2a5`dwdxu8J zD?5mO$|PuPvGv%wU&iH4lW4^R!W+l}XrR~}58+%8(vR&+8r0^EM-CdW%6pWZ$;j@Py8PccI+|Yd3?E^&>ag zlFL<_|6E@}S+@0XoMHb|mNoL&?dItZcoaswr@eLsoy#6 zQ*?xoL3i$BU^6^ScK>)Uu-tmEQ61dgaRFLEWil=ZjhL@zEfM9XBq{6vPu1xYYJ@YIO857_!E|-Vp@i4cgCZ zwqUqKFpew_`ad>6)5g)MxDJI-f_EQv(7!Q0J^dVl0p2b#V1dK)GBas~F?kHY7lQmG zp%vuJ?_8S0a|G`o?mq}9$<%dpbao&Z(+_MW?Qo*RQ1AHD{r7?nt}Ya2rt8gYyzhcv z6XUI}sd4+|T?WXv8i`_l-pO~a%|Nf4nSz%liU;@?o<)*TXUfgSB;N``|N*jb#+DwsZczZ8B z{(P@2kbn~MkYiW*Y?0P&;PYR4CZ}gF)i8H4I zH?iHwr?E_cKHn3u$i?`LJZbmWP!wT_ginN#gl-3*mz%tmcd2b^+{O~LGFUEOnNupp3fVD5_NX8&{lepHjI2}PW$e#@6S^@Q=p z|3~cr-Rq>_SYpcho?At*O_|*cbJ5v4kHDsQF_M;(4B+ims*~^@S^5P@LDO>B&NH?H z?q_gtX7(G{Z@;FkPsa&K?&uquwglnyoWa7w(c((|#-LU<~jsPwi!wjsWKD&vQ?(2x)D-u(B7C#nzWJ2Ee$ zvP@v}Bod*-Qs651$xH#=QN@0eNw9{_M4HTC4ObazzWMUVw+6RBe2nBch`m;O%+me1M%6 z^{;nHG3Gv#ulz*)w>1QE3kB_c_6v+G<<*i;OV~JSLjo?#;6X|pI?3-ZhUUNI1?$3H zbdpaie#QS0EZs&L!usd(D!~4GImnUn`dIxNEY)mBid}4|?q%?0^W z7r3On{_qW^0XCg{c8>ab*~C_i4$@{Jyl;wSLd8pevq9&-cS;LIHA{wyPW4*Y3*1_L zOa3$X9J#6QCjC2W?fSP28D<|{f{5M+XMAd^C{Km9Zp9NHNl&eQW`SvezrPj)(0P@#(zga;-LQ?XY~0& zOrm~TLia$oE!}B);96A!hleRjaUz{>|Ic-Y1&0vB;DxjZS(TrUO!DrXxw@bs+@i7j z5Xc84m}2zZr;S2#3->YGKIuEPlQRXyuZfNcnK~qLRRp{_*qEM)g+&Bh2lH-I*i1Ue zPNa{Zmb?EnSScifDQSnAR+Tk#(P=`f+K`%Wn79!&;?VPHlPGim`D>=l5tw)76}C`%%sUl) zUMBo}uWgCpeuxlK?#)3~GJ5{~nL^;ZuTyQQQfM$6TzgjDViVVKU^EzEq$Pj4RGnME zg+rs7O1;9Voa#2I{okj^1u-Y*MwkA~SU27yj7W#U?wk<`SmI=Sp#%iPCCcLH_M4o1 z|1~;RAWi^trJlUJd?EVXPfzq`#+YJYg|gD^kX|1R02WubTCk7 z^A;Hbx0i-9&K-hV=M7N$tb`6+K9qxbF0-P73xJRc_UOo2-j;Tb&O7MzU+^;@O`xap>uk7uhw{5!Cia-N{i$oX&f<$sH1&*FhI zQ#s)A0m|M*x!3VpwT__>*q#T1@ebhqDBZOVYeXr*3wD_Wq zIL-Rvc;~7fj&2_Us)*_X91@E(xA%oVJui+=$silLZycANpjJ5olKd9Vf&dXbC(PRw z_=DyZIuIWsV?kKO8n{H9^l$&76+8&jbM9sEBQXFRqm_azYAUd|U9d$Vb#?s=jG&Kb z1*I78V|;9vSNb<9gJAb7qR+le+DZn%m!Ej&M8V4L-ILSj;5l= zPC-F|ezahC83DP7%BkNs%ix*0Pr}Q3Ag|z0Im?zyN=kr82-oT%L=w363>eT~hEJJ5 zrnLiF(fJvhw!o!q=?Lr;0S7!lIUT%-r-E#0`?7s23q7piYLPx81t3|Nl4n|7tt=`R4q#C9skIPR`y0dMJ^VQj{!x^WpRV0{F{B A7XSbN From 3abe1e38edab4f7ba56b474d67ed012f2ec275ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 7 Nov 2023 16:40:02 +0100 Subject: [PATCH 007/446] modifying readme and created leame --- LEAME.md | 108 +++++++++++++++---------------------------------------- 1 file changed, 28 insertions(+), 80 deletions(-) diff --git a/LEAME.md b/LEAME.md index c68cf701a..95df52a88 100644 --- a/LEAME.md +++ b/LEAME.md @@ -7,7 +7,7 @@ La introducción de la secuenciación masiva (MS) en las instalaciones de genómica ha significado un crecimiento exponencial en la generación de datos, lo que requiere un sistema de seguimiento preciso, desde la preparación de la biblioteca hasta la generación de archivos fastq, el análisis y la entrega al investigador. El software diseñado para manejar esas tareas se llama Sistemas de Gestión de Información de Laboratorio (LIMS), y su software debe adaptarse a las necesidades particulares de su laboratorio de genómica. iSkyLIMS nace con el objetivo de ayudar con las tareas de laboratorio húmedo e implementar un flujo de trabajo que guíe a los laboratorios de genómica en sus actividades, desde la preparación de la biblioteca hasta la producción de datos, reduciendo los posibles errores asociados a la tecnología de alto rendimiento y facilitando el control de calidad de la secuenciación. Además, iSkyLIMS conecta el laboratorio húmedo con el laboratorio seco, facilitando el análisis de datos por parte de bioinformáticos. -![Imagen](img/iskylims_scheme.png) +![Imagen](https://gitlab.isciii.es/bu-isciii/iSkyLIMS/-/blob/0f535f750035d2407d55a805aef70547d8f7f967/img/iskylims_scheme.png) De acuerdo con la infraestructura existente, la secuenciación se realiza en un instrumento Illumina NextSeq. Los datos se almacenan en un dispositivo de almacenamiento masivo NetApp y los archivos fastq se generan (bcl2fastq) en un clúster de cómputo de alto rendimiento Sun Grid Engine (SGE-HPC). Los servidores de aplicaciones ejecutan aplicaciones web para el análisis bioinformático (GALAXY), la aplicación iSkyLIMS y alojan la capa de información de MySQL. El flujo de trabajo de iSkyLIMS WetLab se ocupa del seguimiento y las estadísticas de la ejecución de la secuenciación. El seguimiento de la ejecución pasa por cinco estados: "registrado", el usuario de genómica registra la nueva ejecución de la secuenciación en el sistema, el proceso esperará hasta que la ejecución se complete en la máquina y los datos se transfieran al dispositivo de almacenamiento masivo; "Envío de hoja de muestra", el archivo de hoja de muestra con la información de la ejecución de la secuenciación se copiará en la carpeta de ejecución para el proceso de bcl2fastq; "Procesamiento de datos", se procesan los archivos de parámetros de ejecución y los datos se almacenan en la base de datos; "Estadísticas en ejecución", los datos de desmultiplexación generados en el proceso de bcl2fastq se procesan y almacenan en la base de datos, "Completado", todos los datos se procesan y almacenan correctamente. Se proporcionan estadísticas por muestra, por proyecto, por ejecución y por investigación, así como informes anuales y mensuales. El flujo de trabajo de iSkyLIMS DryLab se encarga de la solicitud de servicios de bioinformática y estadísticas. El usuario solicita servicios que pueden estar asociados con una ejecución de secuenciación. Se proporciona seguimiento de estadísticas y servicios. @@ -17,17 +17,15 @@ De acuerdo con la infraestructura existente, la secuenciación se realiza en un - [Instalación de iSkyLIMS en Docker](#instalación-de-iskylims-en-docker) - [Instalación de iSkyLIMS en su servidor con Ubuntu/CentOS](#instalación-de-iskylims-en-su-servidor-con-ubuntucentos) - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github) - - [Crear la base de datos de iSkyLIMS y otorgar permisos](#crear-la-base-de-datos-de-iskylims-y-otorgar-permisos) - - [Configuración de ajustes](#configuración-de-ajustes) - - [Ejecutar el script de instalación](#ejecutar-el-script-de-instalación) + - [Crear la base de datos de iSkyLIMS y otorgar permisos](#crear-la-base-de-datos-de-iskylims-y-otorgar-permisos) + - [Configuración de ajustes](#configuración-de-ajustes) + - [Ejecutar el script de instalación](#ejecutar-el-script-de-instalación) - [Actualización a la versión 3.0.0 de iSkyLIMS](#actualización-a-la-versión-300-de-iskylims) - [Prerrequisitos](#prerrequisitos) - - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) - - [Configuración de opciones](#configuración-de-opciones) - - [Ejecución del script de actualización](#ejecución-del-script-de-actualización) - - [Pasos que necesitan permisos de adminsitración](#pasos-que-necesitan-permisos-de-adminsitración) - - [Pasos que no necesitan de permisos de administración](#pasos-que-no-necesitan-de-permisos-de-administración) - - [Qué hacer si algo falla](#qué-hacer-si-algo-falla) + - [Ejecutar la actualización](#ejecutar-la-actualización) + - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) + - [Configuración de opciones](#configuración-de-opciones) + - [Ejecución del script de actualización](#ejecución-del-script-de-actualización) - [Pasos finales de configuración](#pasos-finales-de-configuración) - [Configuración de SAMBA](#configuración-de-samba) - [Verificación de correo electrónico](#verificación-de-correo-electrónico) @@ -44,26 +42,15 @@ Si tienes algún problema o deseas informar de algún error, por favor, publíca Antes de comenzar la instalación, asegúrate de lo siguiente: - Tienes privilegios de **sudo** para instalar los paquetes de software adicionales que iSkyLIMS necesita. -- Dependencias: - - Librerías: -``` - yum groupinstall "Development tools" - yum install zlib-devel bzip2-devel openssl-devel \ - wget httpd-devel mysql-libs sqlite sqlite-devel \ - mariadb-devel mysql-client libffi-devel \ - gnuplot cifs-utils -``` - - lsb_relase: - - RedHat/CentOS: `yum install redhat-lsb-core` - - Ubuntu: `apt install lsb-core lsb-release` - Base de datos MySQL > 8.0 o MariaDB > 10.4 - Tienes configurado un servidor local para enviar correos electrónicos. -- git > 2.34 - Tienes Apache servidor v2.4 -- Tienes Python > 3.8 (si lo compilas debes haber instalado previamente las dependecias de arriba) +- Tienes Python > 3.8 - Tienes una conexión a la carpeta compartida de Samba donde se almacenan las carpetas de ejecución (por ejemplo, galera/NGS_Data). - Dependencias: - + - lsb_release: + - RedHat/CentOS: `yum install redhat-lsb-core` + - Ubuntu: `apt install lsb-core lsb-release` ### Instalación de iSkyLIMS en Docker @@ -100,13 +87,13 @@ git clone https://github.com/BU-ISCIII/iskylims.git iskylims cd iskylims ``` -#### Crear la base de datos de iSkyLIMS y otorgar permisos +## Crear la base de datos de iSkyLIMS y otorgar permisos 1. Cree una nueva base de datos llamada "iskylims" (esto es obligatorio). 2. Cree un nuevo usuario con permisos para leer y modificar esa base de datos. 3. Anote el nombre de usuario, la contraseña y la información del servidor de la base de datos. -#### Configuración de ajustes +## Configuración de ajustes Copia la plantilla de ajustes iniciales en un archivo llamado `install_settings.txt` @@ -120,7 +107,7 @@ Abra el archivo de configuración con su editor favorito para establecer sus pro sudo nano install_settings.txt ``` -#### Ejecutar el script de instalación +## Ejecutar el script de instalación iSkyLIMS debe instalarse en el directorio "/opt". @@ -156,21 +143,23 @@ Debido a que en esta actualización se modifican muchas tablas en la base de dat - La base de datos de iSkyLIMS. - La carpeta de iSkyLIMS (carpeta de instalación completa, por ejemplo, /opt/iSkyLIMS). -Se recomienda encarecidamente que hagas estas copias de seguridad y las guardes de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). +Se recomienda encarecidamente que hagas estas copias de seguridad y las guardes de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. -#### Clonar el repositorio de GitHub +#### Ejecutar la actualización También hemos cambiado la forma en que se instala y actualiza iSkyLIMS. A partir de ahora, iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). +##### Clonar el repositorio de GitHub + Abre una terminal de Linux y dirígete a un directorio donde se descargará el código de iSkyLIMS. ```bash cd < directorio distinto al directorio de instalación > -git clone https://gitlab.isciii.es/BU-ISCIII/iskylims.git iskylims +git clone https://github.com/BU-ISCIII/iSkyLIMS.git iskylims cd iskylims ``` -#### Configuración de opciones +##### Configuración de opciones Copia la plantilla de configuración inicial en un archivo llamado install_settings.txt @@ -179,76 +168,35 @@ cp conf/template_install_settings.txt install_settings.txt ``` Abre el archivo de configuración con tu editor favorito para establecer tus propios valores para la base de datos, la configuración de correo electrónico y la dirección IP local del servidor donde se ejecutará iSkyLIMS. -> Si utilizas un sistema basado en Windows para modificar el archivo, asegúrate de que el archivo se guarde con una codificación amigable para Linux, como ASCII o UTF-8. ```bash -nano install_settings.txt +sudo nano install_settings.txt ``` -#### Ejecución del script de actualización +##### Ejecución del script de actualización Si en tu organización se requiere que las dependencias u otros elementos que necesiten permisos de administrador sean instalados por una persona diferente a la que instala la aplicación, puedes utilizar el script de instalación en varios pasos de la siguiente manera. -El script te irá solicitando confirmación en algun paso, si todo está yendo bien sin errores deberás pulsar `y` o `yes` según te lo solicite. - -> Nota: Los errores: "ERROR 1064 (42000) at line 1: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'query' at line 1" son normales ya que se trata del título de las sentencias sql que no deben ejecutarse. Se puede ignorar. - -##### Pasos que necesitan permisos de adminsitración - En primer lugar, debes cambiar el nombre de la carpeta de la aplicación en la carpeta de instalación (`/opt/iSkyLIMS`): ```bash # Necesitas ser usuario root para realizar esta operación -sudo mv /opt/iSkyLIMS /opt/iskylims +mv /opt/iSkyLIMS /opt/iskylims ``` Asegúrate de que la carpeta de instalación tenga los permisos correctos para que la persona que instala la aplicación pueda escribir en esa carpeta. -```bash -# En el caso de que tengas un script para esta tarea. Necesitarás ajustar este script de acuerdo al cambio en el nombre de la ruta: /opt/iSkyLIMS a /opt/iskylims -sudo /scripts/hardening.sh -``` - En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se adapte a ti: ```bash # para actualizar solo las dependencias del software. ES NECESARIO DISPONER DE PERMISOS DE ROOT. sudo bash install.sh --upgrade dep -# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. SI SE VA A INSTALAR POR OTRA PERSONA SIN ROOT NO HACER ESTO. -sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables -``` - -##### Pasos que no necesitan de permisos de administración - -A continuación instalamos la aplicación de iskylims usando el siguiente comando: - -```bash # para actualizar la aplicación de iskylims, incluyendo los cambios necesarios para la versión en base de datos. NO ES NECESARIO DISPONER DE PERMISOS ROOT. bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables -``` - -Por último, asegúrate que los permisos de la carpeta son correctos. -```bash -# En el caso de que tengas un script para esta tarea. En esta versión han cambiado algunas rutas a ficheros, es posible que tengas que ajustar el script en consecuencia. -sudo /scripts/hardening.sh -``` - -#### Qué hacer si algo falla - -Cuando actualizamos la aplicación usando el script estamos realizando varios cambios en la base de datos. Si algo falla tenemos que restaurar el estado anterior, antes de que hubiesemos realizado ninguna acción. - -Necesitamos copiar de vuelta nuestro backup de carpet ade aplicación a /opt/iSkyLIMS (o la carpeta de instalación de nuestra elección), y restaurar la base de datos realizando algo como lo siguiente: - -```bash -sudo rm -rf /opt/iskylims -sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ -sudo /scripts/hardening.sh -mysql -u iskylims -h dmysqlps.isciiides.es -p -# drop database iskylims; -# create database iskylims; -mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql +# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. +sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables ``` ### Pasos finales de configuración @@ -270,7 +218,7 @@ mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/b #### Configurar el servidor Apache -Copia el archivo de configuración de Apache que se encuentra en la carpeta `conf` según tu distribución dentro del directorio de configuración de Apache y cambia el nombre a iskylims.conf. Revisa cualquier requerimiento de tu sistema, se trata solo de un ejemplo. +Copia el archivo de configuración de Apache según tu distribución dentro del directorio de configuración de Apache y cambia el nombre a iskylims.conf. #### Verificación de la instalación @@ -278,7 +226,7 @@ Abre el navegador y escribe "localhost" o la "IP local del servidor" para compro También puedes verificar algunas funcionalidades mientras compruebas las conexiones de SAMBA y la base de datos usando: -- Ve a [configurationTest](https://iskylims.isciii.es/wetlab/configurationTest/) +- Ve a [prueba de configuración](https://iskylims.isciii.es/wetlab/configurationTest/) - Haz clic en Enviar - Verifica todas las pestañas para asegurarte de que cada conexión sea exitosa. - Ejecuta las 3 pruebas para cada máquina de secuenciación: MiSeq, NextSeq y NovaSeq. From 01559742567aa9e76cb1a79c0fa9f08d953932d9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 8 Nov 2023 17:36:12 +0100 Subject: [PATCH 008/446] Modifications in readme and leame, addign what to do if something fails and some clarifications --- LEAME.md | 80 ++++++++++++++++++++++++++++++++++++++++--------------- README.md | 4 +-- 2 files changed, 61 insertions(+), 23 deletions(-) diff --git a/LEAME.md b/LEAME.md index 95df52a88..7fa1d2771 100644 --- a/LEAME.md +++ b/LEAME.md @@ -17,15 +17,17 @@ De acuerdo con la infraestructura existente, la secuenciación se realiza en un - [Instalación de iSkyLIMS en Docker](#instalación-de-iskylims-en-docker) - [Instalación de iSkyLIMS en su servidor con Ubuntu/CentOS](#instalación-de-iskylims-en-su-servidor-con-ubuntucentos) - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github) - - [Crear la base de datos de iSkyLIMS y otorgar permisos](#crear-la-base-de-datos-de-iskylims-y-otorgar-permisos) - - [Configuración de ajustes](#configuración-de-ajustes) - - [Ejecutar el script de instalación](#ejecutar-el-script-de-instalación) + - [Crear la base de datos de iSkyLIMS y otorgar permisos](#crear-la-base-de-datos-de-iskylims-y-otorgar-permisos) + - [Configuración de ajustes](#configuración-de-ajustes) + - [Ejecutar el script de instalación](#ejecutar-el-script-de-instalación) - [Actualización a la versión 3.0.0 de iSkyLIMS](#actualización-a-la-versión-300-de-iskylims) - [Prerrequisitos](#prerrequisitos) - - [Ejecutar la actualización](#ejecutar-la-actualización) - - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) - - [Configuración de opciones](#configuración-de-opciones) - - [Ejecución del script de actualización](#ejecución-del-script-de-actualización) + - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) + - [Configuración de opciones](#configuración-de-opciones) + - [Ejecución del script de actualización](#ejecución-del-script-de-actualización) + - [Pasos que necesitan permisos de adminsitración](#pasos-que-necesitan-permisos-de-adminsitración) + - [Pasos que no necesitan de permisos de administración](#pasos-que-no-necesitan-de-permisos-de-administración) + - [Qué hacer si algo falla](#qué-hacer-si-algo-falla) - [Pasos finales de configuración](#pasos-finales-de-configuración) - [Configuración de SAMBA](#configuración-de-samba) - [Verificación de correo electrónico](#verificación-de-correo-electrónico) @@ -44,6 +46,7 @@ Antes de comenzar la instalación, asegúrate de lo siguiente: - Tienes privilegios de **sudo** para instalar los paquetes de software adicionales que iSkyLIMS necesita. - Base de datos MySQL > 8.0 o MariaDB > 10.4 - Tienes configurado un servidor local para enviar correos electrónicos. +- git > 2.34 - Tienes Apache servidor v2.4 - Tienes Python > 3.8 - Tienes una conexión a la carpeta compartida de Samba donde se almacenan las carpetas de ejecución (por ejemplo, galera/NGS_Data). @@ -87,13 +90,13 @@ git clone https://github.com/BU-ISCIII/iskylims.git iskylims cd iskylims ``` -## Crear la base de datos de iSkyLIMS y otorgar permisos +#### Crear la base de datos de iSkyLIMS y otorgar permisos 1. Cree una nueva base de datos llamada "iskylims" (esto es obligatorio). 2. Cree un nuevo usuario con permisos para leer y modificar esa base de datos. 3. Anote el nombre de usuario, la contraseña y la información del servidor de la base de datos. -## Configuración de ajustes +#### Configuración de ajustes Copia la plantilla de ajustes iniciales en un archivo llamado `install_settings.txt` @@ -107,7 +110,7 @@ Abra el archivo de configuración con su editor favorito para establecer sus pro sudo nano install_settings.txt ``` -## Ejecutar el script de instalación +#### Ejecutar el script de instalación iSkyLIMS debe instalarse en el directorio "/opt". @@ -145,21 +148,19 @@ Debido a que en esta actualización se modifican muchas tablas en la base de dat Se recomienda encarecidamente que hagas estas copias de seguridad y las guardes de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. -#### Ejecutar la actualización +#### Clonar el repositorio de GitHub También hemos cambiado la forma en que se instala y actualiza iSkyLIMS. A partir de ahora, iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). -##### Clonar el repositorio de GitHub - Abre una terminal de Linux y dirígete a un directorio donde se descargará el código de iSkyLIMS. ```bash cd < directorio distinto al directorio de instalación > -git clone https://github.com/BU-ISCIII/iSkyLIMS.git iskylims +git clone https://gitlab.isciii.es/BU-ISCIII/iskylims.git iskylims cd iskylims ``` -##### Configuración de opciones +#### Configuración de opciones Copia la plantilla de configuración inicial en un archivo llamado install_settings.txt @@ -168,35 +169,72 @@ cp conf/template_install_settings.txt install_settings.txt ``` Abre el archivo de configuración con tu editor favorito para establecer tus propios valores para la base de datos, la configuración de correo electrónico y la dirección IP local del servidor donde se ejecutará iSkyLIMS. +> Si utilizas un sistema basado en Windows para modificar el archivo, asegúrate de que el archivo se guarde con una codificación amigable para Linux, como ASCII o UTF-8. ```bash -sudo nano install_settings.txt +nano install_settings.txt ``` -##### Ejecución del script de actualización +#### Ejecución del script de actualización Si en tu organización se requiere que las dependencias u otros elementos que necesiten permisos de administrador sean instalados por una persona diferente a la que instala la aplicación, puedes utilizar el script de instalación en varios pasos de la siguiente manera. +##### Pasos que necesitan permisos de adminsitración + En primer lugar, debes cambiar el nombre de la carpeta de la aplicación en la carpeta de instalación (`/opt/iSkyLIMS`): ```bash # Necesitas ser usuario root para realizar esta operación -mv /opt/iSkyLIMS /opt/iskylims +sudo mv /opt/iSkyLIMS /opt/iskylims ``` Asegúrate de que la carpeta de instalación tenga los permisos correctos para que la persona que instala la aplicación pueda escribir en esa carpeta. +```bash +# En el caso de que tengas un script para esta tarea. Necesitarás ajustar este script de acuerdo al cambio en el nombre de la ruta: /opt/iSkyLIMS a /opt/iskylims +/scripts/hardening.sh +``` + En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se adapte a ti: ```bash # para actualizar solo las dependencias del software. ES NECESARIO DISPONER DE PERMISOS DE ROOT. sudo bash install.sh --upgrade dep +# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. +sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` + +##### Pasos que no necesitan de permisos de administración + +A continuación instalamos la aplicación de iskylims usando el siguiente comando: + +```bash # para actualizar la aplicación de iskylims, incluyendo los cambios necesarios para la versión en base de datos. NO ES NECESARIO DISPONER DE PERMISOS ROOT. bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` -# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. -sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +Por último, asegúrate que los permisos de la carpeta son correctos. + +```bash +# En el caso de que tengas un script para esta tarea. En esta versión han cambiado algunas rutas a ficheros, es posible que tengas que ajustar el script en consecuencia. +/scripts/hardening.sh +``` + +#### Qué hacer si algo falla + +Cuando actualizamos la aplicación usando el script estamos realizando varios cambios en la base de datos. Si algo falla tenemos que restaurar el estado anterior, antes de que hubiesemos realizado ninguna acción. + +Necesitamos copiar de vuelta nuestro backup de carpet ade aplicación a /opt/iSkyLIMS (o la carpeta de instalación de nuestra elección), y restaurar la base de datos realizando algo como lo siguiente: + +```bash +sudo rm -rf /opt/iskylims +sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ +sudo /scripts/hardening.sh +mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es +# drop database iskylims; +# create database iskylims; +mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` ### Pasos finales de configuración @@ -226,7 +264,7 @@ Abre el navegador y escribe "localhost" o la "IP local del servidor" para compro También puedes verificar algunas funcionalidades mientras compruebas las conexiones de SAMBA y la base de datos usando: -- Ve a [prueba de configuración](https://iskylims.isciii.es/wetlab/configurationTest/) +- Ve a [configurationTest](https://iskylims.isciii.es/wetlab/configurationTest/) - Haz clic en Enviar - Verifica todas las pestañas para asegurarte de que cada conexión sea exitosa. - Ejecuta las 3 pruebas para cada máquina de secuenciación: MiSeq, NextSeq y NovaSeq. diff --git a/README.md b/README.md index d585518e6..71b9c79c6 100644 --- a/README.md +++ b/README.md @@ -237,10 +237,10 @@ We need to copy back the full `/opt/iSkyLIMS` folder back to `/opt` (or your ins sudo rm -rf /opt/iskylims sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ sudo /scripts/hardening.sh -mysql -u iskylims -h dmysqlps.isciiides.es +mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es # drop database iskylims; # create database iskylims; -mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql +mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` ### Final configuration steps From 660edb9a6382e7428f72ad2c7da8a501fc453195 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 8 Nov 2023 18:06:22 +0100 Subject: [PATCH 009/446] minor modifications in readmes --- LEAME.md | 10 +++++++--- README.md | 4 ++-- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/LEAME.md b/LEAME.md index 7fa1d2771..9c10bc6c8 100644 --- a/LEAME.md +++ b/LEAME.md @@ -179,6 +179,10 @@ nano install_settings.txt Si en tu organización se requiere que las dependencias u otros elementos que necesiten permisos de administrador sean instalados por una persona diferente a la que instala la aplicación, puedes utilizar el script de instalación en varios pasos de la siguiente manera. +El script te irá solicitando confirmación en algun paso, si todo está yendo bien sin errores deberás pulsar `y` o `yes` según te lo solicite. + +El error: + ##### Pasos que necesitan permisos de adminsitración En primer lugar, debes cambiar el nombre de la carpeta de la aplicación en la carpeta de instalación (`/opt/iSkyLIMS`): @@ -207,7 +211,7 @@ sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_mig ##### Pasos que no necesitan de permisos de administración -A continuación instalamos la aplicación de iskylims usando el siguiente comando: +A continuación instalamos la aplicación de iskylims usando el siguiente comando: ```bash # para actualizar la aplicación de iskylims, incluyendo los cambios necesarios para la versión en base de datos. NO ES NECESARIO DISPONER DE PERMISOS ROOT. @@ -231,10 +235,10 @@ Necesitamos copiar de vuelta nuestro backup de carpet ade aplicación a /opt/iSk sudo rm -rf /opt/iskylims sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ sudo /scripts/hardening.sh -mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es +mysql -u iskylims -h dmysqlps.isciiides.es # drop database iskylims; # create database iskylims; -mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql +mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` ### Pasos finales de configuración diff --git a/README.md b/README.md index 71b9c79c6..d585518e6 100644 --- a/README.md +++ b/README.md @@ -237,10 +237,10 @@ We need to copy back the full `/opt/iSkyLIMS` folder back to `/opt` (or your ins sudo rm -rf /opt/iskylims sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ sudo /scripts/hardening.sh -mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es +mysql -u iskylims -h dmysqlps.isciiides.es # drop database iskylims; # create database iskylims; -mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql +mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` ### Final configuration steps From 18e5c842c1966c943b35b16ccf5f0cae765046f9 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 18 Apr 2024 14:39:36 +0200 Subject: [PATCH 010/446] rebase --- wetlab/utils/crontab_update_run.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index b6d4db9d8..8ad9389a1 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -647,7 +647,13 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): experiment_name, ) elif run_status == "cancelled": +<<<<<<< HEAD wetlab.utils.crontab_process.handling_errors_in_run(experiment_name, 34) +======= + wetlab.utils.crontab_process.handling_errors_in_run( + experiment_name, 34 + ) +>>>>>>> 9310b3d6 (fixed bug when run cancelled) string_message = experiment_name + "was cancelled on the sequencer" wetlab.utils.common.logging_warnings(string_message, True) logger.debug( From 383660222d54db1e366991b08109db6391aa548b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 9 Nov 2023 09:47:36 +0100 Subject: [PATCH 011/446] minor fix for cancelled code --- wetlab/utils/crontab_update_run.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 8ad9389a1..b6d4db9d8 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -647,13 +647,7 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): experiment_name, ) elif run_status == "cancelled": -<<<<<<< HEAD wetlab.utils.crontab_process.handling_errors_in_run(experiment_name, 34) -======= - wetlab.utils.crontab_process.handling_errors_in_run( - experiment_name, 34 - ) ->>>>>>> 9310b3d6 (fixed bug when run cancelled) string_message = experiment_name + "was cancelled on the sequencer" wetlab.utils.common.logging_warnings(string_message, True) logger.debug( From d1ffa2285f0b4ce80fb50a63a6f0bfaf120fbc40 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 15 Dec 2023 14:05:51 +0100 Subject: [PATCH 012/446] fixed minor stuff in LEAME --- LEAME.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/LEAME.md b/LEAME.md index 9c10bc6c8..9cfdd98be 100644 --- a/LEAME.md +++ b/LEAME.md @@ -7,7 +7,7 @@ La introducción de la secuenciación masiva (MS) en las instalaciones de genómica ha significado un crecimiento exponencial en la generación de datos, lo que requiere un sistema de seguimiento preciso, desde la preparación de la biblioteca hasta la generación de archivos fastq, el análisis y la entrega al investigador. El software diseñado para manejar esas tareas se llama Sistemas de Gestión de Información de Laboratorio (LIMS), y su software debe adaptarse a las necesidades particulares de su laboratorio de genómica. iSkyLIMS nace con el objetivo de ayudar con las tareas de laboratorio húmedo e implementar un flujo de trabajo que guíe a los laboratorios de genómica en sus actividades, desde la preparación de la biblioteca hasta la producción de datos, reduciendo los posibles errores asociados a la tecnología de alto rendimiento y facilitando el control de calidad de la secuenciación. Además, iSkyLIMS conecta el laboratorio húmedo con el laboratorio seco, facilitando el análisis de datos por parte de bioinformáticos. -![Imagen](https://gitlab.isciii.es/bu-isciii/iSkyLIMS/-/blob/0f535f750035d2407d55a805aef70547d8f7f967/img/iskylims_scheme.png) +![Imagen](img/iskylims_scheme.png) De acuerdo con la infraestructura existente, la secuenciación se realiza en un instrumento Illumina NextSeq. Los datos se almacenan en un dispositivo de almacenamiento masivo NetApp y los archivos fastq se generan (bcl2fastq) en un clúster de cómputo de alto rendimiento Sun Grid Engine (SGE-HPC). Los servidores de aplicaciones ejecutan aplicaciones web para el análisis bioinformático (GALAXY), la aplicación iSkyLIMS y alojan la capa de información de MySQL. El flujo de trabajo de iSkyLIMS WetLab se ocupa del seguimiento y las estadísticas de la ejecución de la secuenciación. El seguimiento de la ejecución pasa por cinco estados: "registrado", el usuario de genómica registra la nueva ejecución de la secuenciación en el sistema, el proceso esperará hasta que la ejecución se complete en la máquina y los datos se transfieran al dispositivo de almacenamiento masivo; "Envío de hoja de muestra", el archivo de hoja de muestra con la información de la ejecución de la secuenciación se copiará en la carpeta de ejecución para el proceso de bcl2fastq; "Procesamiento de datos", se procesan los archivos de parámetros de ejecución y los datos se almacenan en la base de datos; "Estadísticas en ejecución", los datos de desmultiplexación generados en el proceso de bcl2fastq se procesan y almacenan en la base de datos, "Completado", todos los datos se procesan y almacenan correctamente. Se proporcionan estadísticas por muestra, por proyecto, por ejecución y por investigación, así como informes anuales y mensuales. El flujo de trabajo de iSkyLIMS DryLab se encarga de la solicitud de servicios de bioinformática y estadísticas. El usuario solicita servicios que pueden estar asociados con una ejecución de secuenciación. Se proporciona seguimiento de estadísticas y servicios. @@ -181,7 +181,7 @@ Si en tu organización se requiere que las dependencias u otros elementos que ne El script te irá solicitando confirmación en algun paso, si todo está yendo bien sin errores deberás pulsar `y` o `yes` según te lo solicite. -El error: +> Nota: Los errores: "ERROR 1064 (42000) at line 1: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'query' at line 1" son normales ya que se trata del título de las sentencias sql que no deben ejecutarse. Se puede ignorar. ##### Pasos que necesitan permisos de adminsitración @@ -196,7 +196,7 @@ Asegúrate de que la carpeta de instalación tenga los permisos correctos para q ```bash # En el caso de que tengas un script para esta tarea. Necesitarás ajustar este script de acuerdo al cambio en el nombre de la ruta: /opt/iSkyLIMS a /opt/iskylims -/scripts/hardening.sh +sudo /scripts/hardening.sh ``` En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se adapte a ti: @@ -205,7 +205,7 @@ En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se ada # para actualizar solo las dependencias del software. ES NECESARIO DISPONER DE PERMISOS DE ROOT. sudo bash install.sh --upgrade dep -# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. +# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. SI SE VA A INSTALAR POR OTRA PERSONA SIN ROOT NO HACER ESTO. sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables ``` @@ -222,7 +222,7 @@ Por último, asegúrate que los permisos de la carpeta son correctos. ```bash # En el caso de que tengas un script para esta tarea. En esta versión han cambiado algunas rutas a ficheros, es posible que tengas que ajustar el script en consecuencia. -/scripts/hardening.sh +sudo /scripts/hardening.sh ``` #### Qué hacer si algo falla @@ -235,7 +235,7 @@ Necesitamos copiar de vuelta nuestro backup de carpet ade aplicación a /opt/iSk sudo rm -rf /opt/iskylims sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ sudo /scripts/hardening.sh -mysql -u iskylims -h dmysqlps.isciiides.es +mysql -u iskylims -h dmysqlps.isciiides.es -p # drop database iskylims; # create database iskylims; mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql @@ -260,7 +260,7 @@ mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/b #### Configurar el servidor Apache -Copia el archivo de configuración de Apache según tu distribución dentro del directorio de configuración de Apache y cambia el nombre a iskylims.conf. +Copia el archivo de configuración de Apache que se encuentra en la carpeta `conf` según tu distribución dentro del directorio de configuración de Apache y cambia el nombre a iskylims.conf. Revisa cualquier requerimiento de tu sistema, se trata solo de un ejemplo. #### Verificación de la instalación From 85790107793550032fa7b1cd0060492abc9f3ca8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 18 Dec 2023 14:00:18 +0100 Subject: [PATCH 013/446] added example for backup folder --- LEAME.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/LEAME.md b/LEAME.md index 9cfdd98be..2b7bba3f5 100644 --- a/LEAME.md +++ b/LEAME.md @@ -146,7 +146,7 @@ Debido a que en esta actualización se modifican muchas tablas en la base de dat - La base de datos de iSkyLIMS. - La carpeta de iSkyLIMS (carpeta de instalación completa, por ejemplo, /opt/iSkyLIMS). -Se recomienda encarecidamente que hagas estas copias de seguridad y las guardes de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. +Se recomienda encarecidamente que hagas estas copias de seguridad y las guardes de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). #### Clonar el repositorio de GitHub From 38dc17c186aba3a81500684c269868ee1e501edf Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 16 Apr 2024 15:47:47 +0200 Subject: [PATCH 014/446] Updated python libraries of cryptography and paramiko --- conf/requirements.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/requirements.txt b/conf/requirements.txt index 51e25de6b..308fe4e3a 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -2,7 +2,7 @@ wheel==0.38.1 asn1crypto==1.5.0 bcrypt==4.0.1 biopython==1.79 -cryptography==38.0.3 +cryptography==41.0.6 Django==4.2.7 django-crispy-forms==2.0 crispy-bootstrap5==0.7 @@ -14,7 +14,7 @@ django-cleanup==7.0.0 interop>1.1.22 mod_wsgi==4.9.4 mysqlclient==2.0.3 -paramiko==3.1.0 +paramiko==3.4.0 jsonschema==4.17.3 pysmb==1.2.9.1 django_extensions==3.2.1 From eab8b44504ae1f3369d51b7e044c56a2aa780489 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 16 Apr 2024 16:36:54 +0200 Subject: [PATCH 015/446] fixing some liting --- clinic/utils/patient.py | 47 +++++++++++----------- clinic/utils/samples.py | 48 +++++++++++------------ clinic/views.py | 45 +++++++++++---------- core/utils/commercial_kits.py | 43 ++++++++++---------- core/utils/patient_projects.py | 6 +-- core/utils/protocols.py | 18 ++++----- drylab/utils/deliveries.py | 12 +++--- drylab/utils/stats.py | 72 +++++++++++++++++----------------- 8 files changed, 144 insertions(+), 147 deletions(-) diff --git a/clinic/utils/patient.py b/clinic/utils/patient.py index 86c0303e5..c27a12cb3 100644 --- a/clinic/utils/patient.py +++ b/clinic/utils/patient.py @@ -158,10 +158,10 @@ def display_one_patient_info(p_id, app_name): for pat_project in pat_projects: project_name = pat_project.get_project_name() - patient_info["project_information"][ - project_name - ] = core.utils.patient_projects.get_project_field_values( - pat_project.get_project_id(), patient_core_obj + patient_info["project_information"][project_name] = ( + core.utils.patient_projects.get_project_field_values( + pat_project.get_project_id(), patient_core_obj + ) ) # get other projects that patient could belongs to @@ -180,9 +180,9 @@ def display_one_patient_info(p_id, app_name): clinic_samples = clinic.models.SampleRequest.objects.filter( patient_core=patient_core_obj ) - patient_info[ - "samples_heading" - ] = clinic.clinic_config.HEADING_FOR_DISPLAY_SAMPLE_DATA_IN_PATIENT_INFO + patient_info["samples_heading"] = ( + clinic.clinic_config.HEADING_FOR_DISPLAY_SAMPLE_DATA_IN_PATIENT_INFO + ) patient_info["samples_data"] = [] for clinic_sample in clinic_samples: sample_obj = clinic_sample.get_core_sample_obj() @@ -362,20 +362,20 @@ def read_batch_patient_file(batch_file): num_rows, num_cols = patient_batch_df.shape if num_cols != 5: - error_data[ - "ERROR" - ] = clinic.clinic_config.ERROR_MESSAGE_FOR_INVALID_PATIENT_BATCH_FILE + error_data["ERROR"] = ( + clinic.clinic_config.ERROR_MESSAGE_FOR_INVALID_PATIENT_BATCH_FILE + ) return error_data for field in patient_batch_heading: if field not in patient_batch_df.columns: - error_data[ - "ERROR" - ] = clinic.clinic_config.ERROR_MESSAGE_FOR_INVALID_PATIENT_BATCH_FILE + error_data["ERROR"] = ( + clinic.clinic_config.ERROR_MESSAGE_FOR_INVALID_PATIENT_BATCH_FILE + ) return error_data if num_rows == 0: - error_data[ - "ERROR" - ] = clinic.clinic_config.ERROR_MESSAGE_FOR_EMPTY_PATIENT_BATCH_FILE + error_data["ERROR"] = ( + clinic.clinic_config.ERROR_MESSAGE_FOR_EMPTY_PATIENT_BATCH_FILE + ) return error_data p_projects = set(patient_batch_df["patientProjects"]) for p_project in p_projects: @@ -384,19 +384,18 @@ def read_batch_patient_file(batch_file): if not core.models.PatientProjects.objects.filter( project_name__exact=p_project ).exists(): - error_data[ - "ERROR" - ] = clinic.clinic_config.ERROR_MESSAGE_NOT_VALID_PROJECT_IN_BATCH_FILE + [ - p_project - ] + error_data["ERROR"] = ( + clinic.clinic_config.ERROR_MESSAGE_NOT_VALID_PROJECT_IN_BATCH_FILE + + [p_project] + ) return error_data for index, row_data in patient_batch_df.iterrows(): patient_data = {} for index in range(len(clinic.clinic_config.PATIENT_BATCH_FILE_HEADING)): - patient_data[ - clinic.clinic_config.PATIENT_BATCH_FILE_HEADING[index] - ] = row_data[patient_batch_heading[index]] + patient_data[clinic.clinic_config.PATIENT_BATCH_FILE_HEADING[index]] = ( + row_data[patient_batch_heading[index]] + ) patient_batch_data.append(patient_data) return patient_batch_data diff --git a/clinic/utils/samples.py b/clinic/utils/samples.py index de71e052f..6c372ace6 100644 --- a/clinic/utils/samples.py +++ b/clinic/utils/samples.py @@ -69,13 +69,13 @@ def analyze_and_store_patient_data(user_post, user): suspicion_data ) if stored_samples: - analyze_data[ - "stored_samples_heading" - ] = clinic.clinic_config.HEADING_FOR_STORED_PATIENT_DATA + analyze_data["stored_samples_heading"] = ( + clinic.clinic_config.HEADING_FOR_STORED_PATIENT_DATA + ) if incomplete_clinic_samples_ids: - analyze_data[ - "heading" - ] = clinic.clinic_config.ADDITIONAL_HEADING_FOR_RECORDING_SAMPLES + analyze_data["heading"] = ( + clinic.clinic_config.ADDITIONAL_HEADING_FOR_RECORDING_SAMPLES + ) analyze_data["heading_length"] = len( clinic.clinic_config.ADDITIONAL_HEADING_FOR_RECORDING_SAMPLES ) @@ -175,9 +175,9 @@ def display_one_sample_info(id): sample_info["s_name"] = core_sample_obj.get_sample_name() sample_info["sample_core_info"] = clinic_sample_obj.get_sample_core_info() - sample_info[ - "sample_core_heading" - ] = clinic.clinic_config.HEADING_FOR_DISPLAY_SAMPLE_MAIN_INFORMATION + sample_info["sample_core_heading"] = ( + clinic.clinic_config.HEADING_FOR_DISPLAY_SAMPLE_MAIN_INFORMATION + ) p_main_info = clinic_sample_obj.get_patient_information() @@ -211,9 +211,9 @@ def display_one_sample_info(id): def display_sample_list(sample_c_list): display_sample_list_info = {} - display_sample_list_info[ - "heading" - ] = clinic.clinic_config.HEADING_SEARCH_LIST_SAMPLES_CLINIC + display_sample_list_info["heading"] = ( + clinic.clinic_config.HEADING_SEARCH_LIST_SAMPLES_CLINIC + ) sample_c_data = [] for sample_c in sample_c_list: sample_c_obj = clinic.models.ClinicSampleRequest.objects.get(pk__exact=sample_c) @@ -314,9 +314,9 @@ def get_clinic_samples_defined_state(user): for sample_obj in samples_obj: sample_information.append(sample_obj.get_info_for_defined_state()) samples_in_state["sample_information"] = sample_information - samples_in_state[ - "sample_heading" - ] = clinic.clinic_config.HEADING_FOR_DISPLAY_SAMPLE_DEFINED_STATE + samples_in_state["sample_heading"] = ( + clinic.clinic_config.HEADING_FOR_DISPLAY_SAMPLE_DEFINED_STATE + ) samples_in_state["length"] = len(sample_information) return samples_in_state else: @@ -346,9 +346,9 @@ def get_clinic_samples_patient_sequencing_state(user, state): sample_obj.get_info_for_patient_sequencing_state() ) samples_in_state["sample_information"] = sample_information - samples_in_state[ - "sample_heading" - ] = clinic.clinic_config.HEADING_FOR_DISPLAY_SAMPLE_PATIENT_SEQUENCING_STATE + samples_in_state["sample_heading"] = ( + clinic.clinic_config.HEADING_FOR_DISPLAY_SAMPLE_PATIENT_SEQUENCING_STATE + ) samples_in_state["length"] = len(sample_information) return samples_in_state else: @@ -388,9 +388,9 @@ def get_clinic_samples_pending_results(user, state): c_sample.append(sample_obj.get_id()) sample_information.append(c_sample) samples_in_state["sample_information"] = sample_information - samples_in_state[ - "sample_heading" - ] = clinic.clinic_config.HEADING_FOR_DISPLAY_SAMPLE_PENDING_RESULT_STATE + samples_in_state["sample_heading"] = ( + clinic.clinic_config.HEADING_FOR_DISPLAY_SAMPLE_PENDING_RESULT_STATE + ) samples_in_state["length"] = len(sample_information) return samples_in_state else: @@ -476,9 +476,9 @@ def get_samples_clinic_in_search(data_request): def prepare_patient_form(clinic_samples_ids): patient_info = {} patient_info["data"] = [] - patient_info[ - "heading" - ] = clinic.clinic_config.ADDITIONAL_HEADING_FOR_RECORDING_SAMPLES + patient_info["heading"] = ( + clinic.clinic_config.ADDITIONAL_HEADING_FOR_RECORDING_SAMPLES + ) heading_length = len(clinic.clinic_config.ADDITIONAL_HEADING_FOR_RECORDING_SAMPLES) for clinic_s_id in clinic_samples_ids: clinic_sample_obj = get_clinic_sample_obj_from_id(clinic_s_id) diff --git a/clinic/views.py b/clinic/views.py index b4789d614..eb620a0da 100644 --- a/clinic/views.py +++ b/clinic/views.py @@ -253,9 +253,9 @@ def create_sample_projects(request): def define_extraction_molecules(request): extraction_molecules = {} - extraction_molecules[ - "extract_molecule" - ] = core.utils.samples.get_sample_objs_in_state("defined", request.user) + extraction_molecules["extract_molecule"] = ( + core.utils.samples.get_sample_objs_in_state("defined", request.user) + ) if request.method == "POST" and request.POST["action"] == "continueWithMolecule": # processing the samples selected by user pass @@ -790,32 +790,31 @@ def pending_to_update(request): request.user ) - pending[ - "patient_update" - ] = clinic.utils.samples.get_clinic_samples_patient_sequencing_state( - request.user, "Patient update" + pending["patient_update"] = ( + clinic.utils.samples.get_clinic_samples_patient_sequencing_state( + request.user, "Patient update" + ) ) - pending[ - "sequencing" - ] = clinic.utils.samples.get_clinic_samples_patient_sequencing_state( - request.user, "Sequencing" + pending["sequencing"] = ( + clinic.utils.samples.get_clinic_samples_patient_sequencing_state( + request.user, "Sequencing" + ) ) - pending[ - "pending_protocol" - ] = clinic.utils.samples.get_clinic_samples_pending_results( - request.user, "Pending protocol" + pending["pending_protocol"] = ( + clinic.utils.samples.get_clinic_samples_pending_results( + request.user, "Pending protocol" + ) ) - pending[ - "pending_results" - ] = clinic.utils.samples.get_clinic_samples_pending_results( - request.user, "Pending results" + pending["pending_results"] = ( + clinic.utils.samples.get_clinic_samples_pending_results( + request.user, "Pending results" + ) ) - pending[ - "graphic_pending_samples" - ] = clinic.utils.samples.pending_clinic_samples_for_grafic(pending).render() - + pending["graphic_pending_samples"] = ( + clinic.utils.samples.pending_clinic_samples_for_grafic(pending).render() + ) return render(request, "clinic/pendingToUpdate.html", {"pending": pending}) diff --git a/core/utils/commercial_kits.py b/core/utils/commercial_kits.py index dc7ad1585..9bb0dd774 100644 --- a/core/utils/commercial_kits.py +++ b/core/utils/commercial_kits.py @@ -137,14 +137,14 @@ def get_commercial_kit_basic_data(kit_obj): kit_data = {} if kit_obj.platform_kit_obj(): kit_data["data"] = kit_obj.get_commercial_platform_basic_data() - kit_data[ - "heading" - ] = core.core_config.HEADING_FOR_NEW_SAVED_COMMERCIAL_PLATFORM_KIT + kit_data["heading"] = ( + core.core_config.HEADING_FOR_NEW_SAVED_COMMERCIAL_PLATFORM_KIT + ) else: kit_data["data"] = kit_obj.get_commercial_protocol_basic_data() - kit_data[ - "heading" - ] = core.core_config.HEADING_FOR_NEW_SAVED_COMMERCIAL_PROTOCOL_KIT + kit_data["heading"] = ( + core.core_config.HEADING_FOR_NEW_SAVED_COMMERCIAL_PROTOCOL_KIT + ) kit_data["protocol_kit"] = True return kit_data @@ -259,18 +259,18 @@ def get_user_lot_kit_data(register_user_obj=None, expired=False): ) if len(user_exp_kit_data["data"]) > 0: - user_exp_kit_data[ - "heading" - ] = core.core_config.HEADING_FOR_USER_LOT_KIT_INVENTORY + user_exp_kit_data["heading"] = ( + core.core_config.HEADING_FOR_USER_LOT_KIT_INVENTORY + ) return user_exp_kit_data def get_lot_user_commercial_kit_basic_data(kit_obj): lot_kit_data = {} lot_kit_data["data"] = kit_obj.get_basic_data() - lot_kit_data[ - "heading" - ] = core.core_config.HEADING_FOR_LOT_USER_COMMERCIAL_KIT_BASIC_DATA + lot_kit_data["heading"] = ( + core.core_config.HEADING_FOR_LOT_USER_COMMERCIAL_KIT_BASIC_DATA + ) return lot_kit_data @@ -403,9 +403,9 @@ def get_molecule_lot_kit_in_sample(sample_id): if core.models.MoleculePreparation.objects.filter( sample__pk__exact=sample_id ).exists(): - extraction_kits[ - "molecule_heading_lot_kits" - ] = core.core_config.HEADING_FOR_DISPLAY_IN_SAMPLE_INFO_USER_KIT_DATA + extraction_kits["molecule_heading_lot_kits"] = ( + core.core_config.HEADING_FOR_DISPLAY_IN_SAMPLE_INFO_USER_KIT_DATA + ) molecule_objs = core.models.MoleculePreparation.objects.filter( sample__pk__exact=sample_id ).order_by("protocol_used") @@ -433,18 +433,17 @@ def get_user_lot_kit_data_to_display(user_lot_kit_obj): """ display_data = {} display_data["lot_kit_data"] = user_lot_kit_obj.get_basic_data() - display_data[ - "lot_kit_heading" - ] = core.core_config.HEADING_FOR_LOT_USER_COMMERCIAL_KIT_BASIC_DATA + display_data["lot_kit_heading"] = ( + core.core_config.HEADING_FOR_LOT_USER_COMMERCIAL_KIT_BASIC_DATA + ) commercial_obj = user_lot_kit_obj.get_commercial_obj() commercial_data = commercial_obj.get_commercial_protocol_basic_data() commercial_data.append(commercial_obj.get_platform_name()) commercial_data.append(commercial_obj.get_cat_number()) display_data["commercial_data"] = [commercial_data] - display_data[ - "commercial_heading" - ] = core.core_config.HEADING_FOR_COMMERCIAL_KIT_BASIC_DATA - + display_data["commercial_heading"] = ( + core.core_config.HEADING_FOR_COMMERCIAL_KIT_BASIC_DATA + ) return display_data diff --git a/core/utils/patient_projects.py b/core/utils/patient_projects.py index afee7ee48..61ad821db 100644 --- a/core/utils/patient_projects.py +++ b/core/utils/patient_projects.py @@ -76,9 +76,9 @@ def get_all_project_info(proyect_id): if core.models.PatientProjectsFields.objects.filter( patient_projects_id=project_obj ).exists(): - project_data[ - "field_heading" - ] = core.core_config.HEADING_FOR_DEFINING_PROJECT_FIELDS + project_data["field_heading"] = ( + core.core_config.HEADING_FOR_DEFINING_PROJECT_FIELDS + ) project_data["project_name"] = project_obj.get_project_name() project_fields = core.models.PatientProjectsFields.objects.filter( patient_projects_id=project_obj diff --git a/core/utils/protocols.py b/core/utils/protocols.py index 8346499ca..861366bee 100644 --- a/core/utils/protocols.py +++ b/core/utils/protocols.py @@ -66,9 +66,9 @@ def define_table_for_prot_parameters(protocol_id): prot_parameters["protocol_name"] = protocol_obj.get_name() prot_parameters["protocol_id"] = protocol_id - prot_parameters[ - "heading" - ] = core.core_config.HEADING_FOR_DEFINING_PROTOCOL_PARAMETERS + prot_parameters["heading"] = ( + core.core_config.HEADING_FOR_DEFINING_PROTOCOL_PARAMETERS + ) return prot_parameters @@ -180,9 +180,9 @@ def get_all_protocol_info(protocol_id): protocol_obj = core.models.Protocols.objects.get(pk__exact=protocol_id) if core.models.ProtocolParameters.objects.filter(protocol_id=protocol_obj).exists(): - protocol_data[ - "parameter_heading" - ] = core.core_config.HEADING_FOR_DEFINING_PROTOCOL_PARAMETERS + protocol_data["parameter_heading"] = ( + core.core_config.HEADING_FOR_DEFINING_PROTOCOL_PARAMETERS + ) protocol_data["protocol_name"] = protocol_obj.get_name() protocol_parameters = core.models.ProtocolParameters.objects.filter( protocol_id=protocol_obj @@ -231,9 +231,9 @@ def get_protocol_fields(protocol_id): parameter_data.append(protocol_parameter_obj.get_parameter_protocol_id()) parameter_list.append(parameter_data) - parameters_protocol[ - "heading" - ] = core.core_config.HEADING_FOR_MODIFY_PROTOCOL_FIELDS + parameters_protocol["heading"] = ( + core.core_config.HEADING_FOR_MODIFY_PROTOCOL_FIELDS + ) parameters_protocol["protocol_id"] = protocol_id parameters_protocol["protocol_name"] = protocol_obj.get_name() parameters_protocol["fields"] = parameter_list diff --git a/drylab/utils/deliveries.py b/drylab/utils/deliveries.py index ee5432df0..86e6f1c52 100644 --- a/drylab/utils/deliveries.py +++ b/drylab/utils/deliveries.py @@ -29,15 +29,15 @@ def prepare_delivery_form(resolution_id): resolution_id, input="id" ) if resolution_obj is not None: - delivery_data_form[ - "available_services" - ] = resolution_obj.get_available_services_ids() + delivery_data_form["available_services"] = ( + resolution_obj.get_available_services_ids() + ) delivery_data_form["resolution_id"] = resolution_id delivery_data_form["resolution_number"] = resolution_obj.get_resolution_number() - delivery_data_form[ - "pipelines_data" - ] = drylab.utils.pipelines.get_pipelines_for_resolution(resolution_obj) + delivery_data_form["pipelines_data"] = ( + drylab.utils.pipelines.get_pipelines_for_resolution(resolution_obj) + ) return delivery_data_form diff --git a/drylab/utils/stats.py b/drylab/utils/stats.py index 1df1d8768..344f6afaa 100644 --- a/drylab/utils/stats.py +++ b/drylab/utils/stats.py @@ -39,9 +39,9 @@ def create_statistics_by_user(user_id, start_date=None, end_date=None): service_objs = service_objs.filter(service_user_id__pk__exact=user_id) if len(service_objs) == 0: - stats_info[ - "ERROR" - ] = drylab.config.ERROR_NO_MATCHES_FOUND_FOR_YOUR_SERVICE_SEARCH + stats_info["ERROR"] = ( + drylab.config.ERROR_NO_MATCHES_FOUND_FOR_YOUR_SERVICE_SEARCH + ) return stats_info # create table of services @@ -103,17 +103,17 @@ def create_statistics_by_user(user_id, start_date=None, end_date=None): "Percentage of services", "Research vs all", "ocean", service_user ) - stats_info[ - "research_vs_other_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", - "research_vs_other_graph", - "580", - "300", - "research_vs_other_chart", - "json", - g_data, - ).render() + stats_info["research_vs_other_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "research_vs_other_graph", + "580", + "300", + "research_vs_other_chart", + "json", + g_data, + ).render() + ) # getting statistics of the created services per week service_per_week = ( @@ -133,17 +133,17 @@ def create_statistics_by_user(user_id, start_date=None, end_date=None): "ocean", format_service_per_week, ) - stats_info[ - "research_service_weeks_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "research_service_weeks_graph", - "580", - "400", - "research_service_weeks_chart", - "json", - g_data, - ).render() + stats_info["research_service_weeks_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "research_service_weeks_graph", + "580", + "400", + "research_service_weeks_chart", + "json", + g_data, + ).render() + ) # create graphic for requested service on level 2 avail_serv_level_2 = drylab.models.AvailableService.objects.filter(level=2) @@ -164,16 +164,16 @@ def create_statistics_by_user(user_id, start_date=None, end_date=None): "value", ) - stats_info[ - "research_avail_services_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "research_avail_services_graph", - "580", - "400", - "research_avail_services_chart", - "json", - g_data, - ).render() + stats_info["research_avail_services_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "research_avail_services_graph", + "580", + "400", + "research_avail_services_chart", + "json", + g_data, + ).render() + ) return stats_info From 4c0ed438686780dbdfdd5f7d6764e945e1086050 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 16 Apr 2024 16:46:32 +0200 Subject: [PATCH 016/446] Fixing litin --- clinic/utils/patient.py | 4 +- core/utils/samples.py | 96 ++++---- drylab/utils/pipelines.py | 18 +- drylab/utils/req_services.py | 44 ++-- drylab/utils/resolutions.py | 26 +-- drylab/views.py | 74 +++--- wetlab/utils/additional_kits.py | 18 +- wetlab/utils/crontab_process.py | 6 +- wetlab/utils/library.py | 50 ++-- wetlab/utils/pool.py | 12 +- wetlab/utils/reports.py | 66 +++--- wetlab/utils/sample.py | 6 +- wetlab/utils/sequencers.py | 6 +- wetlab/utils/statistics.py | 394 +++++++++++++++++--------------- wetlab/views.py | 86 +++---- 15 files changed, 462 insertions(+), 444 deletions(-) diff --git a/clinic/utils/patient.py b/clinic/utils/patient.py index c27a12cb3..eed421778 100644 --- a/clinic/utils/patient.py +++ b/clinic/utils/patient.py @@ -385,8 +385,8 @@ def read_batch_patient_file(batch_file): project_name__exact=p_project ).exists(): error_data["ERROR"] = ( - clinic.clinic_config.ERROR_MESSAGE_NOT_VALID_PROJECT_IN_BATCH_FILE + - [p_project] + clinic.clinic_config.ERROR_MESSAGE_NOT_VALID_PROJECT_IN_BATCH_FILE + + [p_project] ) return error_data diff --git a/core/utils/samples.py b/core/utils/samples.py index 0c9a28c8e..d96ab0752 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -436,13 +436,13 @@ def save_project_data(excel_data, project_info): for field in project_info["sample_project_fields"]: field_value = {} field_value["sample_id"] = sample_id - field_value[ - "sample_project_field_id" - ] = core.models.SampleProjectsFields.objects.get( - sample_projects_id__exact=core.models.SampleProjects.objects.get( - sample_project_name__exact=project_info["sample_project_name"] - ), - sample_project_field_name__exact=field["sample_project_field_name"], + field_value["sample_project_field_id"] = ( + core.models.SampleProjectsFields.objects.get( + sample_projects_id__exact=core.models.SampleProjects.objects.get( + sample_project_name__exact=project_info["sample_project_name"] + ), + sample_project_field_name__exact=field["sample_project_field_name"], + ) ) field_value["sample_project_field_value"] = sample[ field["sample_project_field_name"] @@ -521,11 +521,11 @@ def add_molecule_protocol_parameters(data, parameters): ) for param in parameters: molecule_parameter_value = {} - molecule_parameter_value[ - "molecule_parameter_id" - ] = core.models.ProtocolParameters.objects.filter( - protocol_id=prot_obj, parameter_name__iexact=param - ).last() + molecule_parameter_value["molecule_parameter_id"] = ( + core.models.ProtocolParameters.objects.filter( + protocol_id=prot_obj, parameter_name__iexact=param + ).last() + ) molecule_parameter_value["molecule_id"] = molecule_obj molecule_parameter_value["parameter_value"] = row[param] _ = core.models.MoleculeParameterValue.objects.create_molecule_parameter_value( @@ -740,9 +740,9 @@ def create_table_pending_molecules(molecule_list): .annotate(pk=F("pk")) ) if len(molecule_data["data"]) > 0: - molecule_data[ - "molecule_heading" - ] = core.core_config.HEADING_FOR_PENDING_MOLECULES + molecule_data["molecule_heading"] = ( + core.core_config.HEADING_FOR_PENDING_MOLECULES + ) return molecule_data @@ -762,9 +762,9 @@ def define_table_for_sample_project_fields(sample_project_id): pk__exact=sample_project_id ) - sample_project_data[ - "sample_project_name" - ] = sample_project_obj.get_sample_project_name() + sample_project_data["sample_project_name"] = ( + sample_project_obj.get_sample_project_name() + ) sample_project_data["sample_project_id"] = sample_project_id sample_project_data["heading"] = core.core_config.HEADING_FOR_SAMPLE_PROJECT_FIELDS return sample_project_data @@ -838,9 +838,9 @@ def get_all_sample_information(sample_id, join_values=False): sample_information["sample_name"] = sample_obj.get_sample_name() sample_information["sample_definition"] = sample_obj.get_info_for_display() - sample_information[ - "sample_definition_heading" - ] = core.core_config.HEADING_FOR_SAMPLE_DEFINITION + sample_information["sample_definition_heading"] = ( + core.core_config.HEADING_FOR_SAMPLE_DEFINITION + ) if join_values: sample_information["sample_definition_join_value"] = list( zip( @@ -860,9 +860,9 @@ def get_all_sample_information(sample_id, join_values=False): # check if molecule information exists for the sample if core.models.MoleculePreparation.objects.filter(sample=sample_obj).exists(): molecules = core.models.MoleculePreparation.objects.filter(sample=sample_obj) - sample_information[ - "molecule_definition_heading" - ] = core.core_config.HEADING_FOR_MOLECULE_DEFINITION + sample_information["molecule_definition_heading"] = ( + core.core_config.HEADING_FOR_MOLECULE_DEFINITION + ) sample_information["molecule_definition"] = [] sample_information["molecule_parameter_values"] = [] sample_information["molecule_definition_data"] = [] @@ -950,9 +950,9 @@ def get_info_to_display_sample_project(sample_project_id): ) # collect data from project info_s_project["sample_project_id"] = sample_project_id - info_s_project[ - "sample_project_name" - ] = sample_project_obj.get_sample_project_name() + info_s_project["sample_project_name"] = ( + sample_project_obj.get_sample_project_name() + ) info_s_project["main_data"] = list( zip( core.core_config.SAMPLE_PROJECT_MAIN_DATA, @@ -1058,13 +1058,13 @@ def get_parameters_sample_project(sample_project_id): parameter_data.insert(1, "") s_project_fields_list.append(parameter_data) parameters_s_project["fields"] = s_project_fields_list - parameters_s_project[ - "heading" - ] = core.core_config.HEADING_FOR_MODIFY_SAMPLE_PROJECT_FIELDS + parameters_s_project["heading"] = ( + core.core_config.HEADING_FOR_MODIFY_SAMPLE_PROJECT_FIELDS + ) parameters_s_project["sample_project_id"] = sample_project_id - parameters_s_project[ - "sample_project_name" - ] = sample_project_obj.get_sample_project_name() + parameters_s_project["sample_project_name"] = ( + sample_project_obj.get_sample_project_name() + ) # parameters_s_project["parameter_names"] = ",".join(parameter_names) # parameters_s_project["parameter_ids"] = ",".join(parameter_ids) else: @@ -1260,15 +1260,15 @@ def get_molecule_data_and_protocol_parameters(protocol_objs): for protocol_obj, mol_ids in protocol_objs.items(): prot_name = protocol_obj.get_name() mol_data_parm[prot_name] = {} - mol_data_parm[prot_name][ - "params_type" - ] = core.utils.protocols.get_protocol_parameters_and_type(protocol_obj) + mol_data_parm[prot_name]["params_type"] = ( + core.utils.protocols.get_protocol_parameters_and_type(protocol_obj) + ) mol_data_parm[prot_name][ "fix_heading" ] = core.core_config.HEADING_FOR_MOLECULE_ADDING_PARAMETERS - mol_data_parm[prot_name][ - "lot_kit" - ] = core.utils.commercial_kits.get_lot_commercial_kits(protocol_obj) + mol_data_parm[prot_name]["lot_kit"] = ( + core.utils.commercial_kits.get_lot_commercial_kits(protocol_obj) + ) mol_data_parm[prot_name]["param_heading"] = [] prot_params = core.models.ProtocolParameters.objects.filter( protocol_id=protocol_obj, parameter_used=True @@ -1511,9 +1511,9 @@ def get_table_record_molecule(samples, apps_name): """ molecule_information = {} - molecule_information[ - "headings" - ] = core.core_config.HEADING_FOR_MOLECULE_PROTOCOL_DEFINITION + molecule_information["headings"] = ( + core.core_config.HEADING_FOR_MOLECULE_PROTOCOL_DEFINITION + ) sample_code_ids = [] valid_samples = [] for sample in samples: @@ -1605,9 +1605,9 @@ def get_type_of_sample_information(sample_type_id): ) break else: - sample_type_data[ - "ERROR" - ] = core.core_config.ERROR_TYPE_OF_SAMPLE_ID_DOES_NOT_EXISTS + sample_type_data["ERROR"] = ( + core.core_config.ERROR_TYPE_OF_SAMPLE_ID_DOES_NOT_EXISTS + ) return sample_type_data @@ -1783,9 +1783,9 @@ def record_molecule_use(from_data, app_name): if core.models.MoleculeUsedFor.objects.filter( used_for__exact=from_data["moleculeUseName"] ).exists(): - molecule_use_information[ - "ERROR" - ] = core.core_config.ERROR_MOLECULE_USE_FOR_EXISTS + molecule_use_information["ERROR"] = ( + core.core_config.ERROR_MOLECULE_USE_FOR_EXISTS + ) return molecule_use_information molecule_use_data = {} molecule_use_data["usedFor"] = from_data["moleculeUseName"] diff --git a/drylab/utils/pipelines.py b/drylab/utils/pipelines.py index 1ef2f04d6..bd757d8c8 100644 --- a/drylab/utils/pipelines.py +++ b/drylab/utils/pipelines.py @@ -101,9 +101,9 @@ def get_detail_pipeline_data(pipeline_id): pipeline_obj = drylab.models.Pipelines.objects.get(pk__exact=pipeline_id) detail_pipelines_data["pipeline_name"] = pipeline_obj.get_pipeline_name() detail_pipelines_data["pipeline_basic"] = pipeline_obj.get_pipeline_basic() - detail_pipelines_data[ - "pipeline_basic_heading" - ] = drylab.config.DISPLAY_DETAIL_PIPELINE_BASIC_INFO + detail_pipelines_data["pipeline_basic_heading"] = ( + drylab.config.DISPLAY_DETAIL_PIPELINE_BASIC_INFO + ) detail_pipelines_data["pipeline_additional_data"] = zip( drylab.config.DISPLAY_DETAIL_PIPELINE_ADDITIONAL_INFO, pipeline_obj.get_pipeline_additional(), @@ -116,9 +116,9 @@ def get_detail_pipeline_data(pipeline_id): parameter_objs = drylab.models.ParameterPipeline.objects.filter( parameter_pipeline=pipeline_obj ) - detail_pipelines_data[ - "parameter_heading" - ] = drylab.config.HEADING_PARAMETER_PIPELINE + detail_pipelines_data["parameter_heading"] = ( + drylab.config.HEADING_PARAMETER_PIPELINE + ) detail_pipelines_data["parameters"] = [] for parameter_obj in parameter_objs: detail_pipelines_data["parameters"].append( @@ -187,9 +187,9 @@ def get_pipelines_for_resolution(resolution_obj): for pipeline_obj in pipeline_objs: pipeline_data["pipelines"].append(pipeline_obj.get_pipeline_info()) if len(pipeline_data["pipelines"]) > 0: - pipeline_data[ - "heading_pipelines" - ] = drylab.config.DISPLAY_PIPELINES_USED_IN_RESOLUTION + pipeline_data["heading_pipelines"] = ( + drylab.config.DISPLAY_PIPELINES_USED_IN_RESOLUTION + ) return pipeline_data diff --git a/drylab/utils/req_services.py b/drylab/utils/req_services.py index e635bee8c..4dabb68db 100644 --- a/drylab/utils/req_services.py +++ b/drylab/utils/req_services.py @@ -357,9 +357,9 @@ def get_pending_services_info(): graphic_unit_pending_services = core.fusioncharts.fusioncharts.FusionCharts( "multilevelpie", "ex2", "535", "435", "chart-2", "json", data_source ) - pending_services_graphics[ - "graphic_pending_unit_services" - ] = graphic_unit_pending_services.render() + pending_services_graphics["graphic_pending_unit_services"] = ( + graphic_unit_pending_services.render() + ) pending_services_details["graphics"] = pending_services_graphics return pending_services_details @@ -391,9 +391,9 @@ def get_user_pending_services_info(user_name): del resolution_data[4] res_in_queued.append(resolution_data) user_pending_services_details["queued"] = res_in_queued - user_pending_services_details[ - "heading_in_queued" - ] = drylab.config.HEADING_USER_PENDING_SERVICE_QUEUED + user_pending_services_details["heading_in_queued"] = ( + drylab.config.HEADING_USER_PENDING_SERVICE_QUEUED + ) if drylab.models.Resolution.objects.filter( resolution_assigned_user__username__exact=user_name, resolution_state__state_value__exact="in_progress", @@ -407,9 +407,9 @@ def get_user_pending_services_info(user_name): del resolution_data[4] res_in_progress.append(resolution_data) user_pending_services_details["in_progress"] = res_in_progress - user_pending_services_details[ - "heading_in_progress" - ] = drylab.config.HEADING_USER_PENDING_SERVICE_QUEUED + user_pending_services_details["heading_in_progress"] = ( + drylab.config.HEADING_USER_PENDING_SERVICE_QUEUED + ) return user_pending_services_details @@ -492,26 +492,26 @@ def get_service_data(request): # get samples which have sequencing data in iSkyLIMS user_sharing_list = drylab.utils.common.get_user_sharing_list(request.user) - service_data[ - "samples_data" - ] = wetlab.utils.api.wetlab_api.get_runs_projects_samples_and_dates( - user_sharing_list + service_data["samples_data"] = ( + wetlab.utils.api.wetlab_api.get_runs_projects_samples_and_dates( + user_sharing_list + ) ) if len(service_data["samples_data"]) > 0: - service_data[ - "samples_heading" - ] = drylab.config.HEADING_SELECT_SAMPLE_IN_SERVICE + service_data["samples_heading"] = ( + drylab.config.HEADING_SELECT_SAMPLE_IN_SERVICE + ) # get the samples that are only defined without sequencing data available from iSkyLIMS - service_data[ - "sample_only_recorded" - ] = core.utils.samples.get_only_recorded_samples_and_dates() + service_data["sample_only_recorded"] = ( + core.utils.samples.get_only_recorded_samples_and_dates() + ) if len(service_data["sample_only_recorded"]) > 0: - service_data[ - "sample_only_recorded_heading" - ] = drylab.config.HEADING_SELECT_ONLY_RECORDED_SAMPLE_IN_SERVICE + service_data["sample_only_recorded_heading"] = ( + drylab.config.HEADING_SELECT_ONLY_RECORDED_SAMPLE_IN_SERVICE + ) return service_data diff --git a/drylab/utils/resolutions.py b/drylab/utils/resolutions.py index a914e069f..90d8abd85 100644 --- a/drylab/utils/resolutions.py +++ b/drylab/utils/resolutions.py @@ -216,10 +216,10 @@ def create_new_resolution(resolution_data_form): .get_resolution_full_number() ) else: - resolution_data_form[ - "resolution_full_number" - ] = get_assign_resolution_full_number( - resolution_data_form["service_id"], resolution_data_form["acronym"] + resolution_data_form["resolution_full_number"] = ( + get_assign_resolution_full_number( + resolution_data_form["service_id"], resolution_data_form["acronym"] + ) ) resolution_data_form["resolution_number"] = create_resolution_number( resolution_data_form["service_id"] @@ -355,9 +355,9 @@ def prepare_form_data_add_resolution(form_data): existing_resolution = drylab.models.Resolution.objects.filter( resolution_service_id=service_obj ).last() - resolution_form_data[ - "resolution_full_number" - ] = existing_resolution.get_resolution_full_number() + resolution_form_data["resolution_full_number"] = ( + existing_resolution.get_resolution_full_number() + ) users = django.contrib.auth.models.User.objects.filter( groups__name=drylab.config.SERVICE_MANAGER ) @@ -376,12 +376,12 @@ def prepare_form_data_add_resolution(form_data): for req_service in req_available_services_with_desc: req_available_services_id.append(req_service[0]) - resolution_form_data[ - "pipelines_data" - ] = drylab.utils.pipelines.get_all_defined_pipelines(True) - resolution_form_data[ - "pipelines_heading" - ] = drylab.config.HEADING_PIPELINES_SELECTION_IN_RESOLUTION + resolution_form_data["pipelines_data"] = ( + drylab.utils.pipelines.get_all_defined_pipelines(True) + ) + resolution_form_data["pipelines_heading"] = ( + drylab.config.HEADING_PIPELINES_SELECTION_IN_RESOLUTION + ) return resolution_form_data diff --git a/drylab/views.py b/drylab/views.py index 8f5db9411..86eca1c33 100644 --- a/drylab/views.py +++ b/drylab/views.py @@ -79,9 +79,9 @@ def configuration_email(request): if request.user.username != "admin": return redirect("/wetlab") email_conf_data = core.utils.common.get_email_data() - email_conf_data[ - "EMAIL_ISKYLIMS" - ] = drylab.utils.common.get_configuration_from_database("EMAIL_FOR_NOTIFICATIONS") + email_conf_data["EMAIL_ISKYLIMS"] = ( + drylab.utils.common.get_configuration_from_database("EMAIL_FOR_NOTIFICATIONS") + ) if request.method == "POST" and (request.POST["action"] == "emailconfiguration"): result_email = core.utils.common.send_test_email(request.POST) if result_email != "OK": @@ -488,9 +488,9 @@ def search_service(request): for center in center_availables: center_list_abbr.append(center.center_abbr) services_search_list["centers"] = center_list_abbr - services_search_list[ - "states" - ] = drylab.utils.req_services.get_available_service_states(True) + services_search_list["states"] = ( + drylab.utils.req_services.get_available_service_states(True) + ) if "wetlab" in settings.INSTALLED_APPS: services_search_list["wetlab_app"] = True @@ -1174,9 +1174,9 @@ def stats_by_services_request(request): graphic_requested_services = core.fusioncharts.fusioncharts.FusionCharts( "column3d", "ex1", "525", "350", "chart-1", "json", data_source ) - services_stats_info[ - "graphic_requested_services_per_user" - ] = graphic_requested_services.render() + services_stats_info["graphic_requested_services_per_user"] = ( + graphic_requested_services.render() + ) # preparing stats for status of the services status_services = {} @@ -1201,9 +1201,9 @@ def stats_by_services_request(request): "pie3d", "ex2", "525", "350", "chart-2", "json", data_source ) ) - services_stats_info[ - "graphic_status_requested_services" - ] = graphic_status_requested_services.render() + services_stats_info["graphic_status_requested_services"] = ( + graphic_status_requested_services.render() + ) # preparing stats for request by Area user_area_dict = {} @@ -1235,9 +1235,9 @@ def stats_by_services_request(request): graphic_area_services = core.fusioncharts.fusioncharts.FusionCharts( "column3d", "ex3", "600", "350", "chart-3", "json", data_source ) - services_stats_info[ - "graphic_area_services" - ] = graphic_area_services.render() + services_stats_info["graphic_area_services"] = ( + graphic_area_services.render() + ) # preparing stats for services request by Center user_center_dict = {} @@ -1267,9 +1267,9 @@ def stats_by_services_request(request): graphic_center_services = core.fusioncharts.fusioncharts.FusionCharts( "column3d", "ex4", "600", "350", "chart-4", "json", data_source ) - services_stats_info[ - "graphic_center_services" - ] = graphic_center_services.render() + services_stats_info["graphic_center_services"] = ( + graphic_center_services.render() + ) ################################################ # Preparing the statistics per period of time @@ -1326,9 +1326,9 @@ def stats_by_services_request(request): "mscolumn3d", "ex5", "525", "350", "chart-5", "json", data_source ) ) - services_stats_info[ - "graphic_center_services_per_time" - ] = graphic_center_services_per_time.render() + services_stats_info["graphic_center_services_per_time"] = ( + graphic_center_services_per_time.render() + ) # Preparing the statistics for Area on period of time user_area_services_period = {} @@ -1376,9 +1376,9 @@ def stats_by_services_request(request): "mscolumn3d", "ex6", "525", "350", "chart-6", "json", data_source ) ) - services_stats_info[ - "graphic_area_services_per_time" - ] = graphic_area_services_per_time.render() + services_stats_info["graphic_area_services_per_time"] = ( + graphic_area_services_per_time.render() + ) services_stats_info["period_time"] = period_of_time_selected @@ -1401,9 +1401,9 @@ def stats_by_services_request(request): graphic_req_l2_services = core.fusioncharts.fusioncharts.FusionCharts( "column3d", "ex7", "800", "375", "chart-7", "json", data_source ) - services_stats_info[ - "graphic_req_l2_services" - ] = graphic_req_l2_services.render() + services_stats_info["graphic_req_l2_services"] = ( + graphic_req_l2_services.render() + ) # statistics on Requested Level 3 Services @@ -1424,9 +1424,9 @@ def stats_by_services_request(request): graphic_req_l3_services = core.fusioncharts.fusioncharts.FusionCharts( "column3d", "ex8", "800", "375", "chart-8", "json", data_source ) - services_stats_info[ - "graphic_req_l3_services" - ] = graphic_req_l3_services.render() + services_stats_info["graphic_req_l3_services"] = ( + graphic_req_l3_services.render() + ) return render( request, @@ -1489,9 +1489,9 @@ def configuration_test(request): test_results["services"] = ("Available services", "NOK") else: test_results["services"] = ("Available services", "OK") - test_results[ - "iSkyLIMS_settings" - ] = drylab.utils.test_conf.get_iSkyLIMS_settings() + test_results["iSkyLIMS_settings"] = ( + drylab.utils.test_conf.get_iSkyLIMS_settings() + ) test_results["config_file"] = drylab.utils.test_conf.get_config_file( config_file ) @@ -1528,10 +1528,10 @@ def configuration_test(request): else: resolution_results["create_service_ok"] = "OK" resolution_number = "SRVTEST-IIER001.1" - resolution_results[ - "resolution_test" - ] = drylab.utils.test_conf.create_resolution_test( - resolution_number, service_requested + resolution_results["resolution_test"] = ( + drylab.utils.test_conf.create_resolution_test( + resolution_number, service_requested + ) ) resolution_results["create_resolution_ok"] = "OK" diff --git a/wetlab/utils/additional_kits.py b/wetlab/utils/additional_kits.py index 22c71e5bb..fbcb06b6c 100644 --- a/wetlab/utils/additional_kits.py +++ b/wetlab/utils/additional_kits.py @@ -198,9 +198,9 @@ def get_additional_kits_from_lib_prep(lib_prep_ids): for user_lot_kit_obj in user_lot_kit_objs: user_lot.append(user_lot_kit_obj.get_lot_number()) additional_kits["kit_heading"].append([kit_name, user_lot]) - additional_kits[ - "fix_heading" - ] = wetlab.config.HEADING_FIX_FOR_ASSING_ADDITIONAL_KITS + additional_kits["fix_heading"] = ( + wetlab.config.HEADING_FIX_FOR_ASSING_ADDITIONAL_KITS + ) data_length = len(wetlab.config.HEADING_FIX_FOR_ASSING_ADDITIONAL_KITS) + len( additional_kits_objs ) @@ -273,9 +273,9 @@ def get_all_additional_kit_info(protocol_id): if wetlab.models.AdditionaKitsLibPrepare.objects.filter( protocol_id=protocol_obj ).exists(): - kit_info[ - "kit_heading" - ] = wetlab.config.HEADING_ADDING_COMMERCIAL_KITS_TO_PROTOCOL + kit_info["kit_heading"] = ( + wetlab.config.HEADING_ADDING_COMMERCIAL_KITS_TO_PROTOCOL + ) kit_info["kit_data"] = [] kits = wetlab.models.AdditionaKitsLibPrepare.objects.filter( protocol_id=protocol_obj @@ -321,9 +321,9 @@ def get_additional_kits_used_in_sample(sample_id): kit_data = {} kit_data["protocols_add_kits"] = {} if wetlab.models.LibPrepare.objects.filter(sample_id__pk__exact=sample_id).exists(): - kit_data[ - "heading_add_kits" - ] = wetlab.config.HEADING_FOR_DISPLAY_ADDITIONAL_KIT_LIBRARY_PREPARATION + kit_data["heading_add_kits"] = ( + wetlab.config.HEADING_FOR_DISPLAY_ADDITIONAL_KIT_LIBRARY_PREPARATION + ) library_preparation_items = wetlab.models.LibPrepare.objects.filter( sample_id__pk__exact=sample_id ).order_by("protocol_id") diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index a5ecdedd5..d61ccac60 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -1091,9 +1091,9 @@ def parsing_run_info_and_parameter_information( index_number = ( int(run_info_read.attrib[wetlab.config.NUMBER_TAG]) - 1 ) - running_data[ - wetlab.config.READ_NUMBER_OF_CYCLES[index_number] - ] = run_info_read.attrib[wetlab.config.NUMBER_CYCLES_TAG] + running_data[wetlab.config.READ_NUMBER_OF_CYCLES[index_number]] = ( + run_info_read.attrib[wetlab.config.NUMBER_CYCLES_TAG] + ) except Exception: string_message = ( experiment_name diff --git a/wetlab/utils/library.py b/wetlab/utils/library.py index 5c4a71fbb..7f0f26aea 100644 --- a/wetlab/utils/library.py +++ b/wetlab/utils/library.py @@ -73,13 +73,13 @@ def analyze_and_store_prot_lib_param_values(form_data): len(json_data[row_index]), ): lib_parameter_value = {} - lib_parameter_value[ - "parameter_id" - ] = core.models.ProtocolParameters.objects.filter( - protocol_id=prot_obj, - parameter_name__exact=headings[p_index], - parameter_used=True, - ).last() + lib_parameter_value["parameter_id"] = ( + core.models.ProtocolParameters.objects.filter( + protocol_id=prot_obj, + parameter_name__exact=headings[p_index], + parameter_used=True, + ).last() + ) lib_parameter_value["library_id"] = library_prep_obj lib_parameter_value["parameterValue"] = json_data[row_index][p_index] wetlab.models.LibParameterValue.objects.create_library_parameter_value( @@ -202,12 +202,12 @@ def get_protocol_parameters_for_library_preparation(protocol_libs): "sample_id__sample_name", "lib_prep_code_id", "pk" ) ) - prot_lib_data[ - "param_heading_type" - ] = core.utils.protocols.get_protocol_parameters_and_type(prot_obj) - prot_lib_data[ - "fix_heading" - ] = wetlab.config.HEADING_FIX_FOR_ADDING_LIB_PROT_PARAMETERS + prot_lib_data["param_heading_type"] = ( + core.utils.protocols.get_protocol_parameters_and_type(prot_obj) + ) + prot_lib_data["fix_heading"] = ( + wetlab.config.HEADING_FIX_FOR_ADDING_LIB_PROT_PARAMETERS + ) protocol_lib_prep_data.append(prot_lib_data) return protocol_lib_prep_data @@ -460,9 +460,9 @@ def get_all_library_information(sample_id): """ library_information = {} if wetlab.models.LibPrepare.objects.filter(sample_id__pk__exact=sample_id).exists(): - library_information[ - "library_definition_heading" - ] = wetlab.config.HEADING_FOR_LIBRARY_PREPARATION_DEFINITION + library_information["library_definition_heading"] = ( + wetlab.config.HEADING_FOR_LIBRARY_PREPARATION_DEFINITION + ) library_information["library_definition"] = [] library_information["pool_information"] = [] library_preparation_items = wetlab.models.LibPrepare.objects.filter( @@ -526,9 +526,9 @@ def get_all_library_information(sample_id): ) if library_information["pool_information"]: - library_information[ - "pool_heading" - ] = wetlab.config.HEADING_FOR_DISPLAY_POOL_INFORMATION_IN_SAMPLE_INFO + library_information["pool_heading"] = ( + wetlab.config.HEADING_FOR_DISPLAY_POOL_INFORMATION_IN_SAMPLE_INFO + ) return library_information @@ -579,9 +579,9 @@ def get_lib_prep_to_add_parameters(): lib_prep_info.append(sample.get_id()) sample_info.append(lib_prep_info) lib_prep_parameters["lib_prep_info"] = sample_info - lib_prep_parameters[ - "lib_prep_heading" - ] = wetlab.config.HEADING_FOR_ADD_LIBRARY_PREPARATION_PARAMETERS + lib_prep_parameters["lib_prep_heading"] = ( + wetlab.config.HEADING_FOR_ADD_LIBRARY_PREPARATION_PARAMETERS + ) lib_prep_parameters["length"] = len(sample_info) return lib_prep_parameters @@ -645,9 +645,9 @@ def get_samples_in_lib_prep_state(): lib_prep_data.append(sample_information + molecule_data) samples_in_lib_prep["library_information"] = lib_prep_data - samples_in_lib_prep[ - "lib_prep_heading" - ] = wetlab.config.HEADING_FOR_LIBRARY_PREPARATION_STATE + samples_in_lib_prep["lib_prep_heading"] = ( + wetlab.config.HEADING_FOR_LIBRARY_PREPARATION_STATE + ) samples_in_lib_prep["length"] = len(lib_prep_data) return samples_in_lib_prep diff --git a/wetlab/utils/pool.py b/wetlab/utils/pool.py index f08d179f8..9b49e7c68 100644 --- a/wetlab/utils/pool.py +++ b/wetlab/utils/pool.py @@ -234,18 +234,18 @@ def get_info_to_display_created_pool(pool_obj): information_for_created_pool = {} information_for_created_pool["data"] = pool_obj.get_info() information_for_created_pool["pool_name"] = pool_obj.get_pool_name() - information_for_created_pool[ - "heading_pool" - ] = wetlab.config.HEADING_FOR_DISPLAY_CREATED_POOL + information_for_created_pool["heading_pool"] = ( + wetlab.config.HEADING_FOR_DISPLAY_CREATED_POOL + ) lib_prep_data = [] if wetlab.models.LibPrepare.objects.filter(pools=pool_obj).exists(): lib_prep_ids = wetlab.models.LibPrepare.objects.filter(pools=pool_obj) for lib_prep_obj in lib_prep_ids: lib_prep_data.append(lib_prep_obj.get_info_for_display_pool()) information_for_created_pool["lib_prep_data"] = lib_prep_data - information_for_created_pool[ - "heading_library_pool" - ] = wetlab.config.HEADING_FOR_DISPLAY_LIB_PREP_IN_POOL + information_for_created_pool["heading_library_pool"] = ( + wetlab.config.HEADING_FOR_DISPLAY_LIB_PREP_IN_POOL + ) return information_for_created_pool diff --git a/wetlab/utils/reports.py b/wetlab/utils/reports.py index b493f40ce..f9efaf17a 100644 --- a/wetlab/utils/reports.py +++ b/wetlab/utils/reports.py @@ -130,17 +130,17 @@ def get_annual_report(rep_year): "zune", format_sample_per_month, ) - report_data[ - "rep_sample_month_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "rep_sample_month_graph", - "600", - "350", - "rep_sample_month_chart", - "json", - g_data, - ).render() + report_data["rep_sample_month_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "rep_sample_month_graph", + "600", + "350", + "rep_sample_month_chart", + "json", + g_data, + ).render() + ) # Collecting data for previous years # ################################## @@ -195,17 +195,17 @@ def get_annual_report(rep_year): "year", "values", ) - report_data[ - "rep_comp_sample_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "rep_comp_sample_graph", - "600", - "350", - "rep_comp_sample_chart", - "json", - g_data, - ).render() + report_data["rep_comp_sample_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "rep_comp_sample_graph", + "600", + "350", + "rep_comp_sample_chart", + "json", + g_data, + ).render() + ) # Graphic chart for samples per researcher comp_sample_per_researcher = list( @@ -223,17 +223,17 @@ def get_annual_report(rep_year): "Researcher", "value", ) - report_data[ - "rep_comp_researcher_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", - "rep_comp_researcher_graph", - "600", - "350", - "rep_comp_researcher_chart", - "json", - g_data, - ).render() + report_data["rep_comp_researcher_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "rep_comp_researcher_graph", + "600", + "350", + "rep_comp_researcher_chart", + "json", + g_data, + ).render() + ) report_data["year"] = rep_year diff --git a/wetlab/utils/sample.py b/wetlab/utils/sample.py index f69f64f1a..726fb25e9 100644 --- a/wetlab/utils/sample.py +++ b/wetlab/utils/sample.py @@ -121,9 +121,9 @@ def get_comparation_sample_information(sample_objs): data.insert(2, sample_obj.get_run_name()) data.insert(3, stats_fl_obj.get_sample_number()) compared_data["table_data"].append(data) - compared_data[ - "table_heading" - ] = wetlab.config.HEADING_COMPARATION_SAMPLE_INFORMATION + compared_data["table_heading"] = ( + wetlab.config.HEADING_COMPARATION_SAMPLE_INFORMATION + ) return compared_data diff --git a/wetlab/utils/sequencers.py b/wetlab/utils/sequencers.py index 3ec056fe9..1d65f51dc 100644 --- a/wetlab/utils/sequencers.py +++ b/wetlab/utils/sequencers.py @@ -165,9 +165,9 @@ def get_list_sequencer_configuration(): sequencer_configuration """ sequencer_configuration = {} - sequencer_configuration[ - "platforms_used" - ] = get_platform_name_of_defined_sequencers() + sequencer_configuration["platforms_used"] = ( + get_platform_name_of_defined_sequencers() + ) if core.models.SequencingConfiguration.objects.all().exists(): sequencer_data = {} seq_conf_objs = core.models.SequencingConfiguration.objects.all().order_by( diff --git a/wetlab/utils/statistics.py b/wetlab/utils/statistics.py index 9f5de497e..fc4cc3104 100644 --- a/wetlab/utils/statistics.py +++ b/wetlab/utils/statistics.py @@ -40,9 +40,9 @@ def get_per_time_statistics(start_date, end_date): run_date__range=(start_date, end_date) ) if len(run_objs) == 0: - per_time_statistics[ - "ERROR" - ] = wetlab.config.ERROR_NOT_RUNS_FOUND_IN_SELECTED_PERIOD + per_time_statistics["ERROR"] = ( + wetlab.config.ERROR_NOT_RUNS_FOUND_IN_SELECTED_PERIOD + ) project_objs = wetlab.models.Projects.objects.filter(run_process__in=run_objs) sample_objs = wetlab.models.SamplesInProject.objects.filter( run_process_id__in=run_objs @@ -57,11 +57,17 @@ def get_per_time_statistics(start_date, end_date): g_data = core.utils.graphics.preparation_graphic_data( "Run states", "", "", "", "ocean", run_states, "sum_state", "value" ) - per_time_statistics[ - "time_state_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", "time_state_graph", "600", "300", "time_state_chart", "json", g_data - ).render() + per_time_statistics["time_state_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "time_state_graph", + "600", + "300", + "time_state_chart", + "json", + g_data, + ).render() + ) # Graphic chart for number of runs per weeks run_per_date = ( run_objs.annotate(year=ExtractYear("run_date")) @@ -80,17 +86,17 @@ def get_per_time_statistics(start_date, end_date): "ocean", format_run_per_date, ) - per_time_statistics[ - "time_run_weeks_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "time_run_weeks_graph", - "600", - "350", - "time_run_weeks_chart", - "json", - g_data, - ).render() + per_time_statistics["time_run_weeks_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "time_run_weeks_graph", + "600", + "350", + "time_run_weeks_chart", + "json", + g_data, + ).render() + ) # Graphic chart for projects project_per_date = ( project_objs.annotate(year=ExtractYear("run_process__run_date")) @@ -109,17 +115,17 @@ def get_per_time_statistics(start_date, end_date): "zune", format_project_per_date, ) - per_time_statistics[ - "time_project_weeks_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "time_project_weeks_graph", - "600", - "350", - "time_project_weeks_chart", - "json", - g_data, - ).render() + per_time_statistics["time_project_weeks_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "time_project_weeks_graph", + "600", + "350", + "time_project_weeks_chart", + "json", + g_data, + ).render() + ) # Graphic chart for samples per researcher sample_per_researcher = list( @@ -137,17 +143,17 @@ def get_per_time_statistics(start_date, end_date): "Researcher", "value", ) - per_time_statistics[ - "time_researcher_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", - "time_researcher_graph", - "600", - "300", - "time_researcher_chart", - "json", - g_data, - ).render() + per_time_statistics["time_researcher_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "time_researcher_graph", + "600", + "300", + "time_researcher_chart", + "json", + g_data, + ).render() + ) # Graphic chart for unknown barcodes # pening to fix issue 158 @@ -173,11 +179,17 @@ def get_per_time_statistics(start_date, end_date): "run_name", "q_30_value", ) - per_time_statistics[ - "time_q_30_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", "time_q_30_graph", "550", "350", "time_q_30_chart", "json", g_data - ).render() + per_time_statistics["time_q_30_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "time_q_30_graph", + "550", + "350", + "time_q_30_chart", + "json", + g_data, + ).render() + ) # chart graph for mean based on runs # #################### @@ -196,11 +208,17 @@ def get_per_time_statistics(start_date, end_date): "run_name", "mean_value", ) - per_time_statistics[ - "time_mean_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", "time_mean_graph", "550", "350", "time_mean_chart", "json", g_data - ).render() + per_time_statistics["time_mean_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "time_mean_graph", + "550", + "350", + "time_mean_chart", + "json", + g_data, + ).render() + ) # chart graph for Q > 30 based on researcher # ############################## @@ -220,17 +238,17 @@ def get_per_time_statistics(start_date, end_date): "run_name", "q_30_value", ) - per_time_statistics[ - "time_researcher_q_30_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "time_researcher_q_30_graph", - "550", - "350", - "time_researcher_q_30_chart", - "json", - g_data, - ).render() + per_time_statistics["time_researcher_q_30_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "time_researcher_q_30_graph", + "550", + "350", + "time_researcher_q_30_chart", + "json", + g_data, + ).render() + ) # chart graph for mean based on researcher # #################### @@ -249,17 +267,17 @@ def get_per_time_statistics(start_date, end_date): "run_name", "mean_value", ) - per_time_statistics[ - "time_researcher_mean_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "time_researcher_mean_graph", - "550", - "350", - "time_researcher_mean_chart", - "json", - g_data, - ).render() + per_time_statistics["time_researcher_mean_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "time_researcher_mean_graph", + "550", + "350", + "time_researcher_mean_chart", + "json", + g_data, + ).render() + ) # Table information for run data per_time_statistics["run_data"] = list( @@ -274,9 +292,9 @@ def get_per_time_statistics(start_date, end_date): ) ) ) - per_time_statistics[ - "run_table_heading" - ] = wetlab.config.HEADING_STATISTICS_FOR_TIME_RUN + per_time_statistics["run_table_heading"] = ( + wetlab.config.HEADING_STATISTICS_FOR_TIME_RUN + ) # Table information for sample data per_time_statistics["sample_data"] = list( @@ -289,9 +307,9 @@ def get_per_time_statistics(start_date, end_date): "barcode_name", ) ) - per_time_statistics[ - "sample_table_heading" - ] = wetlab.config.HEADING_STATISTICS_FOR_TIME_SAMPLE + per_time_statistics["sample_table_heading"] = ( + wetlab.config.HEADING_STATISTICS_FOR_TIME_SAMPLE + ) per_time_statistics["start_date"] = start_date per_time_statistics["end_date"] = end_date per_time_statistics["num_runs"] = len(run_objs) @@ -318,17 +336,17 @@ def get_researcher_statistics(researcher_name, start_date, end_date): """ researcher_statistics = {} if not User.objects.filter(username__icontains=researcher_name).exists(): - researcher_statistics[ - "ERROR" - ] = wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS + researcher_statistics["ERROR"] = ( + wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS + ) return researcher_statistics user_objs = User.objects.filter(username__icontains=researcher_name) if len(user_objs) > 1: - researcher_statistics[ - "ERROR" - ] = wetlab.config.ERROR_MANY_USER_MATCHES_FOR_INPUT_CONDITIONS + researcher_statistics["ERROR"] = ( + wetlab.config.ERROR_MANY_USER_MATCHES_FOR_INPUT_CONDITIONS + ) return researcher_statistics researcher_name = user_objs[0].username # validate date format @@ -358,9 +376,9 @@ def get_researcher_statistics(researcher_name, start_date, end_date): other_user_sample_objs = sample_objs.exclude(user_id=user_objs[0]) user_sample_objs = sample_objs.filter(user_id=user_objs[0]) if len(user_sample_objs) == 0: - researcher_statistics[ - "ERROR" - ] = wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS + researcher_statistics["ERROR"] = ( + wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS + ) return researcher_statistics # sample table researcher_statistics["samples"] = user_sample_objs.values_list( @@ -369,9 +387,9 @@ def get_researcher_statistics(researcher_name, start_date, end_date): "run_process_id__run_name", "run_process_id__used_sequencer__sequencer_name", ) - researcher_statistics[ - "table_heading" - ] = wetlab.config.HEADING_STATISTICS_FOR_RESEARCHER_SAMPLE + researcher_statistics["table_heading"] = ( + wetlab.config.HEADING_STATISTICS_FOR_RESEARCHER_SAMPLE + ) # pie graph percentage researcher vs others per_data_user = {} @@ -382,17 +400,17 @@ def get_researcher_statistics(researcher_name, start_date, end_date): "Percentage of samples", "Research vs all", "ocean", per_data_user ) - researcher_statistics[ - "research_vs_other_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", - "research_vs_other_graph", - "600", - "300", - "research_vs_other_chart", - "json", - g_data, - ).render() + researcher_statistics["research_vs_other_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "research_vs_other_graph", + "600", + "300", + "research_vs_other_chart", + "json", + g_data, + ).render() + ) # pie graph for sequencers used # ############################# @@ -405,17 +423,17 @@ def get_researcher_statistics(researcher_name, start_date, end_date): g_data = core.utils.graphics.preparation_3D_pie( "Sequencer usage", "", "ocean", sample_per_sequencer ) - researcher_statistics[ - "research_usage_sequencer_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", - "research_usage_sequencer_graph", - "600", - "300", - "research_usage_sequencer_chart", - "json", - g_data, - ).render() + researcher_statistics["research_usage_sequencer_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "research_usage_sequencer_graph", + "600", + "300", + "research_usage_sequencer_chart", + "json", + g_data, + ).render() + ) # chart graph for runs # #################### @@ -436,17 +454,17 @@ def get_researcher_statistics(researcher_name, start_date, end_date): "ocean", researcher_runs, ) - researcher_statistics[ - "research_run_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "research_run_graph", - "550", - "350", - "research_run_chart", - "json", - g_data, - ).render() + researcher_statistics["research_run_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "research_run_graph", + "550", + "350", + "research_run_chart", + "json", + g_data, + ).render() + ) # chart graph for projects # ######################## @@ -466,17 +484,17 @@ def get_researcher_statistics(researcher_name, start_date, end_date): "ocean", researcher_projects, ) - researcher_statistics[ - "research_project_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "research_project_graph", - "550", - "350", - "research_project_chart", - "json", - g_data, - ).render() + researcher_statistics["research_project_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "research_project_graph", + "550", + "350", + "research_project_chart", + "json", + g_data, + ).render() + ) # chart graph for Q > 30 on runs # ############################## @@ -496,17 +514,17 @@ def get_researcher_statistics(researcher_name, start_date, end_date): "run_name", "q_30_value", ) - researcher_statistics[ - "research_q_30_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "research_q_30_graph", - "550", - "350", - "research_q_30_chart", - "json", - g_data, - ).render() + researcher_statistics["research_q_30_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "research_q_30_graph", + "550", + "350", + "research_q_30_chart", + "json", + g_data, + ).render() + ) # chart graph for mean # #################### @@ -525,17 +543,17 @@ def get_researcher_statistics(researcher_name, start_date, end_date): "run_name", "mean_value", ) - researcher_statistics[ - "research_mean_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "research_mean_graph", - "550", - "350", - "research_mean_chart", - "json", - g_data, - ).render() + researcher_statistics["research_mean_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "research_mean_graph", + "550", + "350", + "research_mean_chart", + "json", + g_data, + ).render() + ) researcher_statistics["researcher_name"] = researcher_name return researcher_statistics @@ -573,9 +591,9 @@ def get_sequencer_statistics(sequencer_name, start_date, end_date): if not core.models.SequencerInLab.objects.filter( sequencer_name__iexact=sequencer_name ).exists(): - sequencer_statistics[ - "ERROR" - ] = wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS + sequencer_statistics["ERROR"] = ( + wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS + ) return sequencer_statistics # validate date format if start_date != "" and not wetlab.utils.common.check_valid_date_format(start_date): @@ -602,9 +620,9 @@ def get_sequencer_statistics(sequencer_name, start_date, end_date): run_objs = run_objs.filter(used_sequencer__sequencer_name__iexact=sequencer_name) if len(run_objs) == 0: - sequencer_statistics[ - "ERROR" - ] = wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS + sequencer_statistics["ERROR"] = ( + wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS + ) return sequencer_statistics # Chart graphic for run states @@ -623,17 +641,17 @@ def get_sequencer_statistics(sequencer_name, start_date, end_date): "sum_state", "value", ) - sequencer_statistics[ - "sequencer_state_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", - "sequencer_state_graph", - "600", - "300", - "sequencer_state_chart", - "json", - g_data, - ).render() + sequencer_statistics["sequencer_state_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "sequencer_state_graph", + "600", + "300", + "sequencer_state_chart", + "json", + g_data, + ).render() + ) # Chart graphic for comparation of sequencers sequencers_usage = list( @@ -651,17 +669,17 @@ def get_sequencer_statistics(sequencer_name, start_date, end_date): "sequencer_name", "value", ) - sequencer_statistics[ - "sequencer_usage_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", - "sequencer_usage_graph", - "600", - "300", - "sequencer_usage_chart", - "json", - g_data, - ).render() + sequencer_statistics["sequencer_usage_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "sequencer_usage_graph", + "600", + "300", + "sequencer_usage_chart", + "json", + g_data, + ).render() + ) # run table sequencer_statistics["run_table_data"] = list( @@ -676,9 +694,9 @@ def get_sequencer_statistics(sequencer_name, start_date, end_date): ) ) ) - sequencer_statistics[ - "run_table_heading" - ] = wetlab.config.HEADING_STATISTICS_FOR_SEQUENCER_RUNS + sequencer_statistics["run_table_heading"] = ( + wetlab.config.HEADING_STATISTICS_FOR_SEQUENCER_RUNS + ) sequencer_statistics["sequencer_name"] = sequencer_name return sequencer_statistics diff --git a/wetlab/views.py b/wetlab/views.py index e3e3b4f6b..91e5a1dd7 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -56,9 +56,9 @@ def configuration_email(request): if request.user.username != "admin": return redirect("/wetlab") email_conf_data = core.utils.common.get_email_data() - email_conf_data[ - "EMAIL_ISKYLIMS" - ] = wetlab.utils.common.get_configuration_from_database("EMAIL_FOR_NOTIFICATIONS") + email_conf_data["EMAIL_ISKYLIMS"] = ( + wetlab.utils.common.get_configuration_from_database("EMAIL_FOR_NOTIFICATIONS") + ) if request.method == "POST" and (request.POST["action"] == "emailconfiguration"): result_email = core.utils.common.send_test_email(request.POST) if result_email != "OK": @@ -147,9 +147,9 @@ def configuration_test(request): if request.method == "POST" and request.POST["action"] == "basicTest": test_results = {} config_file = os.path.join(settings.BASE_DIR, "wetlab", "config.py") - test_results[ - "iSkyLIMS_settings" - ] = wetlab.utils.test_conf.get_iSkyLIMS_settings() + test_results["iSkyLIMS_settings"] = ( + wetlab.utils.test_conf.get_iSkyLIMS_settings() + ) test_results["config_file"] = wetlab.utils.test_conf.get_config_file( config_file ) @@ -157,9 +157,9 @@ def configuration_test(request): os.path.join(settings.MEDIA_ROOT, "wetlab") ) test_results["database_access"] = wetlab.utils.test_conf.check_access_database() - test_results[ - "samba_connection" - ] = wetlab.utils.test_conf.check_samba_connection() + test_results["samba_connection"] = ( + wetlab.utils.test_conf.check_samba_connection() + ) test_results["basic_checks_ok"] = "OK" for result in test_results: @@ -1131,9 +1131,9 @@ def retry_error_run(request): previous_error_state = run_name_found.get_state_before_error() run_name_found.set_run_state(previous_error_state) detail_description = {} - detail_description[ - "information" - ] = wetlab.config.SUCCESSFUL_RUN_STATE_CHANGE_FOR_RETRY + detail_description["information"] = ( + wetlab.config.SUCCESSFUL_RUN_STATE_CHANGE_FOR_RETRY + ) return render( request, "wetlab/display_run.html", @@ -1168,9 +1168,9 @@ def skip_cancel_situation(request): run_name_found.set_run_state("Sample Sent") run_name_found.set_forced_continue_on_error() detail_description = {} - detail_description[ - "information" - ] = wetlab.config.SUCCESSFUL_RUN_STATE_CHANGE_FOR_RETRY + detail_description["information"] = ( + wetlab.config.SUCCESSFUL_RUN_STATE_CHANGE_FOR_RETRY + ) return render( request, "wetlab/skip_cancel_situation.html", @@ -3093,9 +3093,9 @@ def handling_library_preparation(request): sample_sheet_data ) ) - display_sample_sheet[ - "lib_prep_user_sample_sheet" - ] = lib_prep_sample_sheet_obj.get_user_sample_sheet_id() + display_sample_sheet["lib_prep_user_sample_sheet"] = ( + lib_prep_sample_sheet_obj.get_user_sample_sheet_id() + ) display_sample_sheet["platform"] = platform display_sample_sheet["iem_version"] = sample_sheet_data["iem_version"] if user_in_description == "TRUE": @@ -3367,9 +3367,9 @@ def repeat_library_preparation(request): "wetlab/error_page.html", {"detail_description": detail_description}, ) - detail_description[ - "information" - ] = wetlab.config.SUCCESSFUL_REUSE_MOLECULE_EXTRACTION + detail_description["information"] = ( + wetlab.config.SUCCESSFUL_REUSE_MOLECULE_EXTRACTION + ) return render( request, "wetlab/successful_page.html", @@ -3862,32 +3862,32 @@ def pending_sample_preparation(request): pending_data = core.utils.samples.pending_sample_summary(req_user, friend_list) if len(pending_data["state"]) > 0: - pending_data[ - "sample_heading" - ] = wetlab.config.HEADING_FOR_PENDING_PROCESS_SAMPLES - pending_data[ - "pending_sample_graphic" - ] = wetlab.utils.statistics.get_pending_graphic_data( - pending_data["state_number"], - "Pending samples", - "flint", - "ex1", - "500", - "500", - "chart-1", + pending_data["sample_heading"] = ( + wetlab.config.HEADING_FOR_PENDING_PROCESS_SAMPLES ) - # if wetlab manager create graphic for users on pending samples - if user_is_wetlab_manager: - pending_data[ - "pending_users_graphic" - ] = wetlab.utils.statistics.get_pending_graphic_data( - pending_data["users"], - "Users with pending samples", + pending_data["pending_sample_graphic"] = ( + wetlab.utils.statistics.get_pending_graphic_data( + pending_data["state_number"], + "Pending samples", "flint", - "ex2", + "ex1", "500", "500", - "chart-2", + "chart-1", + ) + ) + # if wetlab manager create graphic for users on pending samples + if user_is_wetlab_manager: + pending_data["pending_users_graphic"] = ( + wetlab.utils.statistics.get_pending_graphic_data( + pending_data["users"], + "Users with pending samples", + "flint", + "ex2", + "500", + "500", + "chart-2", + ) ) return render( From 3775527d2f022b19d7b46d5ef6e471444d7a337d Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 16 Apr 2024 16:48:28 +0200 Subject: [PATCH 017/446] Fixing litin second trial --- wetlab/api/utils/sample.py | 44 +++++++++++++++++++------------------- wetlab/utils/test_conf.py | 18 ++++++++-------- 2 files changed, 31 insertions(+), 31 deletions(-) diff --git a/wetlab/api/utils/sample.py b/wetlab/api/utils/sample.py index c32d5f6a9..35346b8e9 100644 --- a/wetlab/api/utils/sample.py +++ b/wetlab/api/utils/sample.py @@ -486,22 +486,22 @@ def summarize_samples(data): .distinct() ) for f_value in f_values: - summarize["parameters"][p_name][ - f_value - ] = core.models.SampleProjectsFieldsValue.objects.filter( - sample_project_field_id=s_project_field_obj, - sample_project_field_value__exact=f_value, - sample_id__sample_name__in=sample_list, - ).count() + summarize["parameters"][p_name][f_value] = ( + core.models.SampleProjectsFieldsValue.objects.filter( + sample_project_field_id=s_project_field_obj, + sample_project_field_value__exact=f_value, + sample_id__sample_name__in=sample_list, + ).count() + ) else: summarize["parameters"][p_name]["value"] = 0 else: - summarize["parameters"][p_name][ - "value" - ] = core.models.SampleProjectsFieldsValue.objects.filter( - sample_project_field_id=s_project_field_obj, - sample_id__sample_name__in=sample_list, - ).count() + summarize["parameters"][p_name]["value"] = ( + core.models.SampleProjectsFieldsValue.objects.filter( + sample_project_field_id=s_project_field_obj, + sample_id__sample_name__in=sample_list, + ).count() + ) summarize["parameters"][p_name][ "classification" ] = s_project_field_obj.get_classification_name() @@ -571,15 +571,15 @@ def collect_statistics_information(data): stats_data[par1_val][par2_val] = value else: for par1_val in par1_values: - stats_data[ - par1_val - ] = core.models.SampleProjectsFieldsValue.objects.filter( - sample_project_field_id__sample_projects_id=s_project_obj, - sample_project_field_id__sample_project_field_name__iexact=query_params[ - 0 - ], - sample_project_field_value=par1_val, - ).count() + stats_data[par1_val] = ( + core.models.SampleProjectsFieldsValue.objects.filter( + sample_project_field_id__sample_projects_id=s_project_obj, + sample_project_field_id__sample_project_field_name__iexact=query_params[ + 0 + ], + sample_project_field_value=par1_val, + ).count() + ) return stats_data else: # Collect info stats for all fields diff --git a/wetlab/utils/test_conf.py b/wetlab/utils/test_conf.py index d05b58df8..c67190947 100644 --- a/wetlab/utils/test_conf.py +++ b/wetlab/utils/test_conf.py @@ -197,9 +197,9 @@ def execute_test_for_testing_run(run_test_name): conn, [run_obj] ) if run_obj.get_state() == "ERROR": - run_result[ - "ERROR" - ] = "Error when processing run in Processing Run state" + run_result["ERROR"] = ( + "Error when processing run in Processing Run state" + ) break else: run_result["Processing Run"] = "OK" @@ -217,9 +217,9 @@ def execute_test_for_testing_run(run_test_name): conn, [run_obj] ) if run_obj.get_state() == "ERROR": - run_result[ - "ERROR" - ] = "Error when processing run in Processing Bcl2fastq state" + run_result["ERROR"] = ( + "Error when processing run in Processing Bcl2fastq state" + ) break else: run_result["Processing Bcl2fastq"] = "OK" @@ -228,9 +228,9 @@ def execute_test_for_testing_run(run_test_name): conn, [run_obj] ) if run_obj.get_state() == "ERROR": - run_result[ - "ERROR" - ] = "Error when processing run in Processed Bcl2fastq state" + run_result["ERROR"] = ( + "Error when processing run in Processed Bcl2fastq state" + ) break else: run_result["Processed Bcl2fastq"] = "OK" From a11bb0849aaa71caddcf1c551df19484bd373ecc Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 16 Apr 2024 16:50:34 +0200 Subject: [PATCH 018/446] Fixing litin third trial --- wetlab/utils/fetch_info.py | 94 ++++++++++++++++++++----------------- wetlab/utils/run.py | 36 +++++--------- wetlab/utils/samplesheet.py | 6 +-- 3 files changed, 65 insertions(+), 71 deletions(-) diff --git a/wetlab/utils/fetch_info.py b/wetlab/utils/fetch_info.py index 315084f8a..e0dc69d46 100644 --- a/wetlab/utils/fetch_info.py +++ b/wetlab/utils/fetch_info.py @@ -612,11 +612,11 @@ def get_information_for_incompleted_run(): "Incomplete Runs", "", "", "", "fint", runs_in_state ) - run_information[ - "incompleted_graphic" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", "ex1", "550", "400", "chart-1", "json", data_source - ).render() + run_information["incompleted_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", "ex1", "550", "400", "chart-1", "json", data_source + ).render() + ) return run_information @@ -856,11 +856,17 @@ def get_information_run(run_object): data_source = wetlab.utils.stats_graphs.column_graphic_simple( heading, sub_caption, x_axis_name, y_axis_name, theme, percent_projects ) - info_dict[ - "run_project_comparation" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", "column1", "600", "400", "column_chart1", "json", data_source - ).render() + info_dict["run_project_comparation"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "column1", + "600", + "400", + "column_chart1", + "json", + data_source, + ).render() + ) fl_data_display = [] @@ -1022,9 +1028,9 @@ def get_information_project(project_id, request): fl_summary_obj = wetlab.models.StatsFlSummary.objects.filter( project_id__exact=project_id, runprocess_id=run_obj ).last() - project_info_dict[ - "fl_summary_heading" - ] = wetlab.config.HEADING_SINGLE_PROJECT_FL_SUMMARY + project_info_dict["fl_summary_heading"] = ( + wetlab.config.HEADING_SINGLE_PROJECT_FL_SUMMARY + ) # fl_data_display.append(fl_list) project_info_dict["fl_summary_data"] = fl_summary_obj.get_fl_summary() @@ -1035,9 +1041,9 @@ def get_information_project(project_id, request): lane_summary_obj = wetlab.models.StatsLaneSummary.objects.filter( project_id__exact=project_id, runprocess_id=run_obj ) - project_info_dict[ - "lane_summary_heading" - ] = wetlab.config.HEADING_SINGLE_PROJECT_STATS_LANE + project_info_dict["lane_summary_heading"] = ( + wetlab.config.HEADING_SINGLE_PROJECT_STATS_LANE + ) project_info_dict["lane_summary_data"] = [] for lane_sum in lane_summary_obj: project_info_dict["lane_summary_data"].append( @@ -1051,9 +1057,9 @@ def get_information_project(project_id, request): sample_objs = wetlab.models.SamplesInProject.objects.filter( project_id__exact=project_id, run_process_id=run_obj ) - project_info_dict[ - "sample_heading" - ] = wetlab.config.HEADING_SINGLE_PROJECT_SAMPLES + project_info_dict["sample_heading"] = ( + wetlab.config.HEADING_SINGLE_PROJECT_SAMPLES + ) project_info_dict["sample_data"] = [] for sample_obj in sample_objs: project_info_dict["sample_data"].append( @@ -1294,9 +1300,9 @@ def get_stats_sequencer_data_from_selected_runs( sequencer_data["sequencer_name"] = sequencer sequencer_data["run_completed"] = [] sequencer_data["not_run_completed"] = [] - sequencer_data[ - "run_name_heading" - ] = wetlab.config.HEADING_FOR_STATISTICS_RUNS_BASIC_DATA + sequencer_data["run_name_heading"] = ( + wetlab.config.HEADING_FOR_STATISTICS_RUNS_BASIC_DATA + ) # get the run completed and not completed for the sequencer for run_in_seq in runs_using_sequencer["completed_run_objs"]: sequencer_data["run_completed"].append( @@ -1355,17 +1361,17 @@ def get_stats_sequencer_data_from_selected_runs( data_source = wetlab.utils.stats_graphs.column_graphic_tupla( heading, "", "", "Number of Runs", "ocean", run_time_tupla, None ) - sequencer_data[ - "sequencer_runs_per_month_graph" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "run_per_month_graph", - "500", - "400", - "chart_seq_month", - "json", - data_source, - ).render() + sequencer_data["sequencer_runs_per_month_graph"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "run_per_month_graph", + "500", + "400", + "chart_seq_month", + "json", + data_source, + ).render() + ) # get the data for run executed in other sequencers per months if ( @@ -1392,16 +1398,16 @@ def get_stats_sequencer_data_from_selected_runs( data_source = wetlab.utils.stats_graphs.column_graphic_tupla( heading, "", "", "Number of Runs", "fint", run_time_tupla, None ) - sequencer_data[ - "other_sequencers_runs_per_month_graph" - ] = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "other_run_per_month_graph", - "500", - "400", - "chart_other_seq_month", - "json", - data_source, - ).render() + sequencer_data["other_sequencers_runs_per_month_graph"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "other_run_per_month_graph", + "500", + "400", + "chart_other_seq_month", + "json", + data_source, + ).render() + ) return sequencer_data diff --git a/wetlab/utils/run.py b/wetlab/utils/run.py index 84081a3d1..723c83a92 100644 --- a/wetlab/utils/run.py +++ b/wetlab/utils/run.py @@ -228,9 +228,9 @@ def collect_data_and_update_library_preparation_samples_for_run(data_form, user) ] projects.append(json_data[row_index][heading.index("Sample_Project")]) # keep the old value of the user sample sheet and update the library prepation - confirmation_data[ - "user_sample_sheet" - ] = lib_prep_obj.get_user_sample_sheet_obj() + confirmation_data["user_sample_sheet"] = ( + lib_prep_obj.get_user_sample_sheet_obj() + ) lib_prep_obj.update_library_preparation_with_indexes(confirmation_data) sample_sheet_data_field.append(json_data[row_index]) if record_data["platform"] == "NextSeq": @@ -684,41 +684,29 @@ def collect_lib_prep_data_for_new_run(lib_prep_ids, platform_in_pool): if platform_in_pool == "MiSeq": if single_read: if iem_version == "4": - lib_data[ - "heading" - ] = ( + lib_data["heading"] = ( wetlab.config.HEADING_FOR_COLLECT_INFO_FOR_SAMPLE_SHEET_MISEQ_SINGLE_READ_VERSION_4 ) else: - lib_data[ - "heading" - ] = ( + lib_data["heading"] = ( wetlab.config.HEADING_FOR_COLLECT_INFO_FOR_SAMPLE_SHEET_MISEQ_SINGLE_READ_VERSION_5 ) else: if iem_version == "4": - lib_data[ - "heading" - ] = ( + lib_data["heading"] = ( wetlab.config.HEADING_FOR_COLLECT_INFO_FOR_SAMPLE_SHEET_MISEQ_PAIRED_END_VERSION_4 ) else: - lib_data[ - "heading" - ] = ( + lib_data["heading"] = ( wetlab.config.HEADING_FOR_COLLECT_INFO_FOR_SAMPLE_SHEET_MISEQ_PAIRED_END_VERSION_5 ) else: if single_read: - lib_data[ - "heading" - ] = ( + lib_data["heading"] = ( wetlab.config.HEADING_FOR_COLLECT_INFO_FOR_SAMPLE_SHEET_NEXTSEQ_SINGLE_READ ) else: - lib_data[ - "heading" - ] = ( + lib_data["heading"] = ( wetlab.config.HEADING_FOR_COLLECT_INFO_FOR_SAMPLE_SHEET_NEXTSEQ_PAIRED_END ) return lib_data @@ -943,9 +931,9 @@ def get_run_user_lot_kit_used_in_sample(sample_id): kit_data = {} kit_data["run_kits_from_sample"] = {} if wetlab.models.LibPrepare.objects.filter(sample_id__pk__exact=sample_id).exists(): - kit_data[ - "heading_run_kits" - ] = wetlab.config.HEADING_FOR_DISPLAY_KIT_IN_RUN_PREPARATION + kit_data["heading_run_kits"] = ( + wetlab.config.HEADING_FOR_DISPLAY_KIT_IN_RUN_PREPARATION + ) library_preparation_items = wetlab.models.LibPrepare.objects.filter( sample_id__pk__exact=sample_id ).order_by("protocol_id") diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index dfa9b97ce..365391594 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -47,9 +47,9 @@ def validate_userid_in_user_iem_file(file_read, user_id_list): description_index = line.index("Description") continue except Exception: - users[ - "ERROR" - ] = wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_DESCRIPTION_FIELD + users["ERROR"] = ( + wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_DESCRIPTION_FIELD + ) return users else: try: From e57099caa7093cd488df0f84e8aa3052f80b4271 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 17 Apr 2024 17:35:23 +0200 Subject: [PATCH 019/446] Implemented issue #78 Allow to search services by service type --- README.md | 12 +- drylab/templates/drylab/search_service.html | 438 +++++++++++--------- drylab/utils/req_services.py | 22 +- drylab/views.py | 17 +- install.sh | 176 +------- 5 files changed, 293 insertions(+), 372 deletions(-) diff --git a/README.md b/README.md index d585518e6..fd3db9736 100644 --- a/README.md +++ b/README.md @@ -137,9 +137,13 @@ bash install.sh --install app sudo bash install.sh --install full ``` -### Upgrade to iSkyLIMS version 3.0.0 +### Upgrade iSkyLIMS from 3.0.x to version 3.1.x -If you have already iSkyLIMS on version 2.3.0 you can upgrade to the latest stable version 3.0.0. +**IMPORTANT NOTE** + +This installation script only apply for the upgrade from version 3.0.x to 3.1.x. + +**If you have already iSkyLIMS on version 2.3.0 you must upgrade first to the stable version 3.0.0, before applying for this upgrade.** Version 3.0.0 is a major release with important upgrades in third parties dependencies like bootstrap. Also, we 've done a huge work on refactoring and variables/function renaming that affects the database. For more details about the changes see the release notes. @@ -208,7 +212,7 @@ In the linux terminal execute one of the following command that fit better to yo sudo bash install.sh --upgrade dep # to install both software. NEEDS ROOT. -sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +sudo bash install.sh --upgrade full ``` ##### Steps not requiring root @@ -217,7 +221,7 @@ Next you need to upgrade iskylims app. Please use the command below: ```bash # to upgrade only iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. -bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +bash install.sh --upgrade app ``` Make sure that the installation folder has the correct permissions. diff --git a/drylab/templates/drylab/search_service.html b/drylab/templates/drylab/search_service.html index 61e30823f..ea82c9fa1 100644 --- a/drylab/templates/drylab/search_service.html +++ b/drylab/templates/drylab/search_service.html @@ -1,226 +1,258 @@ {% extends 'core/base.html' %} {% load static %} - {% block content %} - -{% include "core/cdn_table_functionality.html"%} - -{% include "drylab/menu.html" %} - -
-
- {% include 'registration/login_inline.html' %} - - {% if ERROR %} -
-
-
-
-

Result of your request

-
-
- {% for message in ERROR %} -

{{message}}

- {% endfor %} + {% include "core/cdn_table_functionality.html" %} + {% include "drylab/menu.html" %} +
+
+ {% include 'registration/login_inline.html' %} + {% if ERROR %} +
+
+
+
+

Result of your request

+
+
+ {% for message in ERROR %}

{{ message }}

{% endfor %} +
+
-
-
- {% endif %} - {% if display_multiple_services %} -
-
-
-
- Services search results -
-
- - - - - - - - - - - - - - - {% for key, values in display_multiple_services.s_list.items %} - - {% for serviceID, status, dates ,center, projects in values %} - - - {% for date in dates %} - - {% endfor %} - - - {%endfor%} - - {%endfor%} - - - - - - - - - - - - - -
Service ID StatusRecorded DateApproved DateRejected DateDelivered DateCenterProject names
{{ serviceID }} {{ status }} {{date}}{{ center }} {% for project in projects %}{{ project }}
{% endfor %}
Service Request ID StatusRecorded DateApproved DateRejected DateDelivered DateCenterProject names
+ {% endif %} + {% if display_multiple_services %} +
+
+
+
Services search results
+
+ + + + + + + + + + + + + + + {% for key, values in display_multiple_services.s_list.items %} + + {% for serviceID, status, dates ,center, projects in values %} + + + {% for date in dates %}{% endfor %} + + + {% endfor %} + + {% endfor %} + + + + + + + + + + + + + +
Service IDStatusRecorded DateApproved DateRejected DateDelivered DateCenterProject names
+ {{ serviceID }} + {{ status }}{{ date }}{{ center }} + {% for project in projects %} + {{ project }} +
+ {% endfor %} +
Service Request IDStatusRecorded DateApproved DateRejected DateDelivered DateCenterProject names
+
+
-
-
- {% else %} - -
-
-
-
Service search
-
-
-
-
-
- {% csrf_token %} - -
- - -
-
- - -
-
- - -
-
- - -
-
- - -
-
- {% if services_search_list.username %} - - {% else %} - - {% endif %} - -
-
- {% if services_search_list.username %} - - {% else %} - - {% endif %} - -
-
-
-
-
- {% if services_search_list.wetlab_app %} -
-
Search using wetlab information
-
+ {% else %} + +
+
+
+
+ Service search +
+
+ +
+
+
+ {% csrf_token %} + +
+ + +
+
+ + +
+
+ + +
+
+ + +
+
+ + +
- - + +
- - + {% if services_search_list.username %} + + {% else %} + + {% endif %} +
- - + {% if services_search_list.username %} + + {% else %} + + {% endif %} +
- {% endif %} -
-
-
-
- -
-
- +
+
+ {% if services_search_list.wetlab_app %} +
+
Search using wetlab information
+
+
+ + +
+
+ + +
+
+ + +
+
+
+ {% endif %} +
+
+
+
+ +
+
+ +
+
-
+
- -
+
+ {% endif %}
- {% endif %} -
-
-
- -{% endblock %} \ No newline at end of file + +{% endblock %} diff --git a/drylab/utils/req_services.py b/drylab/utils/req_services.py index 4dabb68db..b40ccc018 100644 --- a/drylab/utils/req_services.py +++ b/drylab/utils/req_services.py @@ -183,15 +183,21 @@ def delete_samples_in_service(sample_list): return deleted_sample_names -def get_children_services(all_tree_services): - """ - Description: - The function get the children available services from a query of service - Input: - all_tree_services # queryset of available service - Return: - children_service +def get_children_services(all_tree_services: list[drylab.models.AvailableService]=None)->list[list]: + """The function get a list with the children available services from the + requested query of available service. If no query is provided, it will + return all the children services from the database + + Args: + all_tree_services (list[drylab.models.AvailableService]): Queryset of + available service. Defaults to None. + + Returns: + list[list]: List with 2 values: the primary key and the description for + each children service """ + if all_tree_services is None: + all_tree_services = drylab.models.AvailableService.objects.all().order_by("description") children_services = [] for t_services in all_tree_services: if t_services.get_children(): diff --git a/drylab/views.py b/drylab/views.py index 86eca1c33..1952dab78 100644 --- a/drylab/views.py +++ b/drylab/views.py @@ -491,7 +491,9 @@ def search_service(request): services_search_list["states"] = ( drylab.utils.req_services.get_available_service_states(True) ) - + services_search_list["available_services"] = ( + drylab.utils.req_services.get_children_services() + ) if "wetlab" in settings.INSTALLED_APPS: services_search_list["wetlab_app"] = True @@ -504,6 +506,7 @@ def search_service(request): start_date = request.POST["start_date"] end_date = request.POST["end_date"] center = request.POST["service_center"] + available_services = request.POST["available_services"] service_user = request.POST["service_user"] assigned_user = request.POST["bioinfo_user"] @@ -519,6 +522,7 @@ def search_service(request): if ( service_id == "" and service_state == "" + and available_services == "" and start_date == "" and end_date == "" and center == "" @@ -575,9 +579,14 @@ def search_service(request): }, ) else: - services_found = drylab.models.Service.objects.prefetch_related( - "service_user_id", "service_state" - ).all() + if available_services != "": + services_found = drylab.models.Service.objects.prefetch_related( + "service_user_id", "service_state" + ).filter(service_available_service__id__exact=available_services) + else: + services_found = drylab.models.Service.objects.prefetch_related( + "service_user_id", "service_state" + ).all() if service_state != "": services_found = services_found.filter( diff --git a/install.sh b/install.sh index 8e07fb181..1f860b9fe 100644 --- a/install.sh +++ b/install.sh @@ -1,6 +1,6 @@ #!/bin/bash -ISKYLIMS_VERSION="3.x.x" +ISKYLIMS_VERSION="3.1.x" usage() { cat << EOF @@ -197,7 +197,7 @@ upgrade_type="full" docker=false # PARSE VARIABLE ARGUMENTS WITH getops -options=":c:s:i:u:drtkvh" +options=":c:s:i:u:dtkvh" while getopts $options opt; do case $opt in i ) @@ -229,9 +229,6 @@ while getopts $options opt; do t ) tables=true ;; - r ) - ren_app=true - ;; d ) git_branch="develop" ;; @@ -376,181 +373,54 @@ if [ $upgrade == true ]; then fi if [ "$upgrade_type" = "full" ] || [ "$upgrade_type" = "app" ]; then - - # Delete git and no copy files stuff - if [ $ren_app == true ] ; then - # remove all previous migrations and make a fake initial - # delete existing migrations file - rm -rf $INSTALL_PATH/django_utils/migrations/* - rm -rf $INSTALL_PATH/iSkyLIMS_core/migrations/* - rm -rf $INSTALL_PATH/iSkyLIMS_wetlab/migrations/* - rm -rf $INSTALL_PATH/iSkyLIMS_drylab/migrations/* - - cd $INSTALL_PATH - sed -i "s/ugettext/gettext/g" iSkyLIMS_wetlab/models.py - sed -i "s/ugettext/gettext/g" iSkyLIMS_core/forms.py - sed -i "s/ugettext/gettext/g" django_utils/forms.py - echo "activate the virtualenv" - source virtualenv/bin/activate - - echo "Create a fake initial" - python manage.py makemigrations django_utils iSkyLIMS_core \ - iSkyLIMS_wetlab iSkyLIMS_drylab - python manage.py migrate --fake-initial - - if [ -d "$INSTALL_PATH/iSkyLIMS_core" ]; then - echo "Changing app dir names in $INSTALL_PATH..." - rm -rf $INSTALL_PATH/.git $INSTALL_PATH/.github $INSTALL_PATH/.gitignore \ - $INSTALL_PATH/.Rhistory $INSTALL_PATH/docker-compose.yml $INSTALL_PATH/docker_iskylims_install.sh \ - $INSTALL_PATH/Dockerfile $INSTALL_PATH/install.sh $INSTALL_PATH/install_settings.txt - mv $INSTALL_PATH/iSkyLIMS_core $INSTALL_PATH/core - mv $INSTALL_PATH/iSkyLIMS_wetlab $INSTALL_PATH/wetlab - mv $INSTALL_PATH/iSkyLIMS_drylab $INSTALL_PATH/drylab - mv $INSTALL_PATH/iSkyLIMS_clinic $INSTALL_PATH/clinic - echo "Done changing app dir names in $INSTALL_PATH..." - fi - if [ -d "iSkyLIMS" ]; then - mv iSkyLIMS/ iskylims/ - sed -i "s/iSkyLIMS/iskylims/g" $INSTALL_PATH/iskylims/wsgi.py - sed -i "s/iSkyLIMS/iskylims/g" $INSTALL_PATH/manage.py - fi - cd - - fi # update installation by sinchronize folders echo "Copying files to installation folder" - rsync -rlv conf/ $INSTALL_PATH/conf/ + # rsync -rlv conf/ $INSTALL_PATH/conf/ rsync -rlv --fuzzy --delay-updates --delete-delay \ --exclude "logs" --exclude "documents" --exclude "migrations" --exclude "__pycache__" \ README.md LICENSE test conf core drylab clinic wetlab django_utils $INSTALL_PATH # update the settings.py and the main urls echo "Update settings and url file." - update_settings_and_urls + # update_settings_and_urls # update illumina template files.# Copy illumina sample sheet templates - mkdir -p $INSTALL_PATH/documents/wetlab/templates/ - cp $INSTALL_PATH/conf/*_template.csv $INSTALL_PATH/documents/wetlab/templates/ - cp $INSTALL_PATH/conf/samples_template.xlsx $INSTALL_PATH/documents/wetlab/templates/ + # mkdir -p $INSTALL_PATH/documents/wetlab/templates/ + # cp $INSTALL_PATH/conf/*_template.csv $INSTALL_PATH/documents/wetlab/templates/ + # cp $INSTALL_PATH/conf/samples_template.xlsx $INSTALL_PATH/documents/wetlab/templates/ # update logging configuration file - cp $INSTALL_PATH/conf/template_logging_config.ini $INSTALL_PATH/wetlab/logging_config.ini - sed -i "s@INSTALL_PATH@${INSTALL_PATH}@g" $INSTALL_PATH/wetlab/logging_config.ini + # cp $INSTALL_PATH/conf/template_logging_config.ini $INSTALL_PATH/wetlab/logging_config.ini + # sed -i "s@INSTALL_PATH@${INSTALL_PATH}@g" $INSTALL_PATH/wetlab/logging_config.ini # update the sample sheet folder and name - if [ -d "$INSTALL_PATH/documents/wetlab/SampleSheets" ]; then - echo "Updating sample sheet folder name" - mv $INSTALL_PATH/documents/wetlab/SampleSheets $INSTALL_PATH/documents/wetlab/sample_sheet - fi + # if [ -d "$INSTALL_PATH/documents/wetlab/SampleSheets" ]; then + # echo "Updating sample sheet folder name" + # mv $INSTALL_PATH/documents/wetlab/SampleSheets $INSTALL_PATH/documents/wetlab/sample_sheet + # fi - if [ -d "$INSTALL_PATH/documents/wetlab/SampleSheets4LibPrep" ]; then - echo "Updating sample sheet for libary preparationfolder name" - mv $INSTALL_PATH/documents/wetlab/SampleSheets4LibPrep $INSTALL_PATH/documents/wetlab/sample_sheets_lib_prep - fi + # if [ -d "$INSTALL_PATH/documents/wetlab/SampleSheets4LibPrep" ]; then + # echo "Updating sample sheet for libary preparationfolder name" + # mv $INSTALL_PATH/documents/wetlab/SampleSheets4LibPrep $INSTALL_PATH/documents/wetlab/sample_sheets_lib_prep + # fi cd $INSTALL_PATH echo "activate the virtualenv" source virtualenv/bin/activate - ### RENAME APP in database and migration files #### - if [ $ren_app == true ] ; then - - echo "Modifying database names and constraints..." - mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - -e 'UPDATE django_content_type SET app_label = REPLACE(app_label , "iSkyLIMS_core", "core") WHERE app_label like ("iSkyLIMS_%");' - # mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - # -e 'UPDATE django_content_type SET app_label = REPLACE(app_label , "iSkyLIMS_clinic", "clinic") WHERE app_label like ("iSkyLIMS_%");' - mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - -e 'UPDATE django_content_type SET app_label = REPLACE(app_label , "iSkyLIMS_wetlab", "wetlab") WHERE app_label like ("iSkyLIMS_%");' - mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - -e 'UPDATE django_content_type SET app_label = REPLACE(app_label , "iSkyLIMS_drylab", "drylab") WHERE app_label like ("iSkyLIMS_%");' - - mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - -e 'UPDATE django_migrations SET app = REPLACE(app , "iSkyLIMS_core", "core") WHERE app like ("iSkyLIMS_%");' - # mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - # -e 'UPDATE django_migrations SET app = REPLACE(app , "iSkyLIMS_clinic", "clinic") WHERE app like ("iSkyLIMS_%");' - mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - -e 'UPDATE django_migrations SET app = REPLACE(app , "iSkyLIMS_wetlab", "wetlab") WHERE app like ("iSkyLIMS_%");' - mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - -e 'UPDATE django_migrations SET app = REPLACE(app , "iSkyLIMS_drylab", "drylab") WHERE app like ("iSkyLIMS_%");' - echo "Renaming tables" - query_rename_table="SELECT CONCAT('RENAME TABLE ', TABLE_SCHEMA, '.', TABLE_NAME, \ - ' TO ', TABLE_SCHEMA, '.', REPLACE(TABLE_NAME, 'iSkyLIMS_', ''), ';') \ - AS query FROM information_schema.tables WHERE TABLE_SCHEMA = \"$DB_NAME\" AND TABLE_NAME LIKE 'iSkyLIMS_%';" - mysql -u $DB_USER -p$DB_PASS -h $DB_SERVER_IP -e "$query_rename_table" \ - | xargs -I % echo "mysql -u$DB_USER -p'$DB_PASS' -D $DB_NAME -h $DB_SERVER_IP -e \"% \" " | bash - echo "Renaming index" - query_rename_unique_indexes="SELECT CONCAT('ALTER TABLE ', rcu.TABLE_SCHEMA, '.', rcu.TABLE_NAME, \ - ' RENAME INDEX ', rcu.CONSTRAINT_NAME, \ - ' TO ', REPLACE(rcu.CONSTRAINT_NAME, 'iSkyLIMS_', ''), ';') \ - AS query FROM information_schema.key_column_usage rcu \ - JOIN information_schema.table_constraints tc \ - ON tc.CONSTRAINT_NAME = rcu.CONSTRAINT_NAME WHERE rcu.TABLE_SCHEMA = \"$DB_NAME\" \ - AND rcu.CONSTRAINT_NAME LIKE 'iSkyLIMS_%' AND tc.CONSTRAINT_TYPE = 'UNIQUE' \ - GROUP BY rcu.TABLE_SCHEMA, rcu.TABLE_NAME, rcu.CONSTRAINT_NAME, tc.CONSTRAINT_TYPE, \ - rcu.REFERENCED_TABLE_SCHEMA, rcu.REFERENCED_TABLE_NAME;" - mysql -u $DB_USER -p$DB_PASS -h $DB_SERVER_IP -e "$query_rename_unique_indexes" \ - | xargs -I % echo "mysql -u$DB_USER -p'$DB_PASS' -D $DB_NAME -h $DB_SERVER_IP -e \"% \" " | bash - echo "Renaming constraints" - query_rename_constraints="SELECT CONCAT('ALTER TABLE ', rcu.TABLE_SCHEMA, '.', rcu.TABLE_NAME, \ - ' DROP FOREIGN KEY ' , rcu.CONSTRAINT_NAME, ';', \ - ' ALTER TABLE ', rcu.TABLE_SCHEMA, '.', rcu.TABLE_NAME, \ - ' ADD CONSTRAINT ', REPLACE(rcu.CONSTRAINT_NAME, 'iSkyLIMS_', ''), ' ', \ - tc.CONSTRAINT_TYPE, ' (', GROUP_CONCAT(rcu.COLUMN_NAME ORDER BY rcu.ORDINAL_POSITION SEPARATOR ', '), ')', \ - IF(tc.CONSTRAINT_TYPE = 'FOREIGN KEY', \ - CONCAT(' REFERENCES ', rcu.REFERENCED_TABLE_SCHEMA, '.', REPLACE(rcu.REFERENCED_TABLE_NAME, 'iSkyLIMS_', ''), ' (', \ - GROUP_CONCAT(rcu.REFERENCED_COLUMN_NAME ORDER BY rcu.ORDINAL_POSITION SEPARATOR ', '), ') ON DELETE ', rc.DELETE_RULE), \ - ''), ';') AS query \ - FROM information_schema.key_column_usage rcu \ - LEFT JOIN information_schema.table_constraints tc ON rcu.CONSTRAINT_NAME = tc.CONSTRAINT_NAME \ - LEFT JOIN information_schema.referential_constraints rc ON rcu.CONSTRAINT_NAME = rc.CONSTRAINT_NAME \ - WHERE rcu.TABLE_SCHEMA = '$DB_NAME' AND rcu.CONSTRAINT_NAME LIKE 'iSkyLIMS_%' \ - GROUP BY rcu.TABLE_SCHEMA, rcu.TABLE_NAME, rcu.CONSTRAINT_NAME, tc.CONSTRAINT_TYPE, rcu.REFERENCED_TABLE_SCHEMA, rcu.REFERENCED_TABLE_NAME, rc.DELETE_RULE;" - mysql -u $DB_USER -p$DB_PASS -h $DB_SERVER_IP -e "$query_rename_constraints" | xargs -I % echo "mysql -u$DB_USER -p'$DB_PASS' -D $DB_NAME -h $DB_SERVER_IP -e \"% \" " | bash - - echo "Done modifying database names and constraints..." - - echo "Modifying names in migration files..." - sed -i 's/iSkyLIMS_core/core/g' */migrations/*.py - # sed -i 's/iSkyLIMS_clinic/clinic/g' */migrations/*.py - sed -i 's/iSkyLIMS_drylab/drylab/g' */migrations/*.py - sed -i 's/iSkyLIMS_wetlab/wetlab/g' */migrations/*.py - echo "Done modifying names in migration files..." - - # copy modified migration files - echo "Copying custom migration files from conf." - cp $INSTALL_PATH/conf/0002_core_migration_v3.0.0.py $INSTALL_PATH/core/migrations/0002_migration_v3_0_0.py - cp $INSTALL_PATH/conf/0002_drylab_migration_v3.0.0.py $INSTALL_PATH/drylab/migrations/0002_migration_v3_0_0.py - cp $INSTALL_PATH/conf/0002_wetlab_migration_v3.0.0.py $INSTALL_PATH/wetlab/migrations/0002_migration_v3_0_0.py - # cp conf/0002_clinic_migration_v2.3.1.py clinic/migrations/0002_migration_v2_3_1.py - cp $INSTALL_PATH/conf/0002_django_utils_migration_v3.0.0.py $INSTALL_PATH/django_utils/migrations/0002_migration_v3_0_0.py - + + echo "checking for database changes" + if python manage.py makemigrations | grep -q "No changes"; then + echo "No migration is required" + else read -p "Do you want to proceed with the migrate command? (Y/N) " -n 1 -r echo # (optional) move to a new line if [[ ! $REPLY =~ ^[Yy]$ ]] ; then echo "Exiting without running migrate command." exit 1 fi - - echo "activate the virtualenv" - source virtualenv/bin/activate echo "Running migrate..." python manage.py migrate echo "Done migrate command." - - else - echo "checking for database changes" - if python manage.py makemigrations | grep -q "No changes"; then - echo "No migration is required" - else - read -p "Do you want to proceed with the migrate command? (Y/N) " -n 1 -r - echo # (optional) move to a new line - if [[ ! $REPLY =~ ^[Yy]$ ]] ; then - echo "Exiting without running migrate command." - exit 1 - fi - echo "Running migrate..." - python manage.py migrate - echo "Done migrate command." - fi - fi + fi echo "Running collect statics..." python manage.py collectstatic From 113691bfd4ebf85ef91874d9f63f3f828dac298d Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 17 Apr 2024 17:38:34 +0200 Subject: [PATCH 020/446] litin, for implemented issue #78 Allow to search services by service type --- drylab/utils/req_services.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/drylab/utils/req_services.py b/drylab/utils/req_services.py index b40ccc018..8398a55f3 100644 --- a/drylab/utils/req_services.py +++ b/drylab/utils/req_services.py @@ -183,7 +183,9 @@ def delete_samples_in_service(sample_list): return deleted_sample_names -def get_children_services(all_tree_services: list[drylab.models.AvailableService]=None)->list[list]: +def get_children_services( + all_tree_services: list[drylab.models.AvailableService] = None, +) -> list[list]: """The function get a list with the children available services from the requested query of available service. If no query is provided, it will return all the children services from the database @@ -197,7 +199,9 @@ def get_children_services(all_tree_services: list[drylab.models.AvailableService each children service """ if all_tree_services is None: - all_tree_services = drylab.models.AvailableService.objects.all().order_by("description") + all_tree_services = drylab.models.AvailableService.objects.all().order_by( + "description" + ) children_services = [] for t_services in all_tree_services: if t_services.get_children(): From 41ac9553e23ce03d2f10eaca5154ed56377f7577 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 17 Apr 2024 20:33:19 +0200 Subject: [PATCH 021/446] partial fixing on the issue #264. User can't search service/project by sample name --- drylab/templates/drylab/search_service.html | 28 ++++++++++----------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/drylab/templates/drylab/search_service.html b/drylab/templates/drylab/search_service.html index ea82c9fa1..3af875d0f 100644 --- a/drylab/templates/drylab/search_service.html +++ b/drylab/templates/drylab/search_service.html @@ -149,30 +149,30 @@

Result of your request

-
- {% if services_search_list.username %} - - {% else %} + {% if services_search_list.username %} + + + {% else %} +
- {% endif %} - -
-
- {% if services_search_list.username %} - - {% else %} + +
+
- {% endif %} - -
+ +
+ {% endif %}
From e7868b1faf4b4446688613195afcf1f21d745549 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 17 Apr 2024 23:01:22 +0200 Subject: [PATCH 022/446] Implemented issue #158 Unable to convert barcode count to integer --- wetlab/models.py | 2 +- .../scripts/convert_rawtop_counter_to_int.py | 15 +++++++++ wetlab/scripts/rename_sample_sheet_folder.py | 33 ------------------- wetlab/utils/crontab_process.py | 2 +- 4 files changed, 17 insertions(+), 35 deletions(-) create mode 100644 wetlab/scripts/convert_rawtop_counter_to_int.py delete mode 100644 wetlab/scripts/rename_sample_sheet_folder.py diff --git a/wetlab/models.py b/wetlab/models.py index fec88a843..20e190cab 100644 --- a/wetlab/models.py +++ b/wetlab/models.py @@ -759,7 +759,7 @@ class RawTopUnknowBarcodes(models.Model): runprocess_id = models.ForeignKey(RunProcess, on_delete=models.CASCADE) lane_number = models.CharField(max_length=4) top_number = models.CharField(max_length=4) - count = models.CharField(max_length=40) + count = models.IntegerField() sequence = models.CharField(max_length=40) generated_at = models.DateTimeField(auto_now_add=True) diff --git a/wetlab/scripts/convert_rawtop_counter_to_int.py b/wetlab/scripts/convert_rawtop_counter_to_int.py new file mode 100644 index 000000000..cf35a3ce8 --- /dev/null +++ b/wetlab/scripts/convert_rawtop_counter_to_int.py @@ -0,0 +1,15 @@ +import wetlab.models + +def run(): + """ The script implemted the issue #158 Unable to convert barcode count to + integer, to convert the counter that are in a string format, separated + by "," to int. + """ + top_bar_objs = wetlab.models.RawTopUnknowBarcodes.objects.all() + for top_bar_obj in top_bar_objs: + try: + top_bar_obj.count = int(top_bar_obj.count.replace(",", "")) + top_bar_obj.save() + except AttributeError: + continue + return \ No newline at end of file diff --git a/wetlab/scripts/rename_sample_sheet_folder.py b/wetlab/scripts/rename_sample_sheet_folder.py deleted file mode 100644 index 6f33d535a..000000000 --- a/wetlab/scripts/rename_sample_sheet_folder.py +++ /dev/null @@ -1,33 +0,0 @@ -import wetlab.models - - -""" - The script is applicable for the upgrade from 2.3.0 to 3.0.0. - Because the folder where the sample sheets were recorded have been - modified to sample_sheet. All the recorded run must update the field - of sample sheet. - Script reads RunProcess table and check if sample_sheet contains the - SampleSheet string and change it to sample_sheet. -""" - - -def run(): - # update SampleSheets - run_objs = wetlab.models.RunProcess.objects.filter( - sample_sheet__contains="SampleSheet" - ) - for run_obj in run_objs: - old_name = run_obj.get_sample_file() - new_name = old_name.replace("/SampleSheets/", "/sample_sheet/") - run_obj.set_run_sample_sheet(new_name) - # update SampleSheets4LibPrep - lib_user_objs = wetlab.models.LibUserSampleSheet.objects.filter( - sample_sheet__contains="SampleSheets4LibPrep" - ) - for lib_user_obj in lib_user_objs: - old_name = lib_user_obj.get_lib_user_sample_sheet() - new_name = old_name.replace( - "/SampleSheets4LibPrep/", "/sample_sheets_lib_prep/" - ) - lib_user_obj.set_lib_user_sample_sheet(new_name) - return diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index d61ccac60..0e6f9adca 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -3047,7 +3047,7 @@ def process_and_store_unknown_barcode_data( unknow_barcode["runprocess_id"] = run_process_obj unknow_barcode["lane_number"] = str(un_lane + 1) unknow_barcode["top_number"] = str(top_number) - unknow_barcode["count"] = "{0:,}".format(int(barcode_line["count"])) + unknow_barcode["count"] = int(barcode_line["count"]) unknow_barcode["sequence"] = barcode_line["sequence"] top_number += 1 wetlab.models.RawTopUnknowBarcodes.objects.create_unknow_barcode( From 29d4a55f54bd46a15c4e5e5c15f1cf708bd3e27f Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 17 Apr 2024 23:04:05 +0200 Subject: [PATCH 023/446] litin for implemented issue #158 Unable to convert barcode count to integer --- wetlab/scripts/convert_rawtop_counter_to_int.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/wetlab/scripts/convert_rawtop_counter_to_int.py b/wetlab/scripts/convert_rawtop_counter_to_int.py index cf35a3ce8..2171c2ea0 100644 --- a/wetlab/scripts/convert_rawtop_counter_to_int.py +++ b/wetlab/scripts/convert_rawtop_counter_to_int.py @@ -1,9 +1,10 @@ import wetlab.models + def run(): - """ The script implemted the issue #158 Unable to convert barcode count to - integer, to convert the counter that are in a string format, separated - by "," to int. + """The script implemted the issue #158 Unable to convert barcode count to + integer, to convert the counter that are in a string format, separated + by "," to int. """ top_bar_objs = wetlab.models.RawTopUnknowBarcodes.objects.all() for top_bar_obj in top_bar_objs: From 5c35dbea001acca0f971cf494b0b438e396f90bb Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 17 Apr 2024 23:07:12 +0200 Subject: [PATCH 024/446] litin for implemented issue #158 Unable to convert barcode count to integer --- wetlab/scripts/convert_rawtop_counter_to_int.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wetlab/scripts/convert_rawtop_counter_to_int.py b/wetlab/scripts/convert_rawtop_counter_to_int.py index 2171c2ea0..61b6a2706 100644 --- a/wetlab/scripts/convert_rawtop_counter_to_int.py +++ b/wetlab/scripts/convert_rawtop_counter_to_int.py @@ -13,4 +13,4 @@ def run(): top_bar_obj.save() except AttributeError: continue - return \ No newline at end of file + return From db9ca876b5d9eaf6690a31088e65ffcdadf24ff9 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 18 Apr 2024 12:27:07 +0200 Subject: [PATCH 025/446] Fixing issue #265 Service state are not in the right order on first_install_tables.json --- conf/first_install_tables.json | 41 +++++++++++++--------------------- 1 file changed, 16 insertions(+), 25 deletions(-) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index a6982e522..a6ced091c 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -20143,16 +20143,6 @@ "show_in_stats": false } }, -{ - "model": "drylab.servicestate", - "pk": 8, - "fields": { - "state_value": "on_hold", - "state_display": "On hold", - "description": "Service is on hold, waiting for user provides more information", - "show_in_stats": true - } -}, { "model": "drylab.resolutionstates", "pk": 1, @@ -20166,36 +20156,36 @@ "model": "drylab.resolutionstates", "pk": 2, "fields": { - "state_value": "approved", - "state_display": "Approved", - "description": "Resolution request has been accepted" + "state_value": "archived", + "state_display": "Archived", + "description": null } }, { "model": "drylab.resolutionstates", "pk": 3, "fields": { - "state_value": "rejected", - "state_display": "Rejected", - "description": "Resolution can not be handle because is not in porfoloio or for any other reason" + "state_value": "approved", + "state_display": "Approved", + "description": "Resolution request has been accepted" } }, { "model": "drylab.resolutionstates", "pk": 4, "fields": { - "state_value": "queued", - "state_display": "Queued", - "description": "Resolution is the the list, waiting for a bioinformatic to be handled" + "state_value": "in_progress", + "state_display": "In Progress", + "description": "Bioinformatic is working on the Resolution" } }, { "model": "drylab.resolutionstates", "pk": 5, "fields": { - "state_value": "in_progress", - "state_display": "In Progress", - "description": "Bioinformatic is working on the Resolution" + "state_value": "rejected", + "state_display": "Rejected", + "description": "Resolution can not be handle because is not in porfoloio or for any other reason" } }, { @@ -20211,9 +20201,9 @@ "model": "drylab.resolutionstates", "pk": 7, "fields": { - "state_value": "archived", - "state_display": "Archived", - "description": null + "state_value": "queued", + "state_display": "Queued", + "description": "Resolution is the the list, waiting for a bioinformatic to be handled" } }, { @@ -20226,3 +20216,4 @@ } } ] + From 4bdf0cf63e565e1bf8b93247f32f23744084a3be Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 18 Apr 2024 13:05:54 +0200 Subject: [PATCH 026/446] fixing issue #261 Confirmation email after resolution: wrong text and email --- drylab/utils/resolutions.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/drylab/utils/resolutions.py b/drylab/utils/resolutions.py index 90d8abd85..63e078eeb 100644 --- a/drylab/utils/resolutions.py +++ b/drylab/utils/resolutions.py @@ -404,7 +404,7 @@ def send_resolution_creation_email(email_data): subject_tmp = drylab.config.SUBJECT_RESOLUTION_QUEUED.copy() subject_tmp.insert(1, email_data["service_number"]) subject = " ".join(subject_tmp) - if email_data["status"] == "Accepted": + if email_data["status"] == "accepted": date = email_data["date"].strftime("%d %B, %Y") body_preparation = list( map( From 2f551b4f2652a572e5093939549fac08fb14af6f Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 18 Apr 2024 17:14:10 +0200 Subject: [PATCH 027/446] Fixing the wetlab part of the issue #264, User can't search service/project by sample name --- wetlab/views.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wetlab/views.py b/wetlab/views.py index 91e5a1dd7..c23fa8db4 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -2884,7 +2884,7 @@ def display_sample_in_run(request, sample_run_id): if not wetlab.utils.common.is_wetlab_manager(request): # check if user is owner of the run or belongs to the shared user shared_user_ids = wetlab.utils.common.get_allowed_user_for_sharing(request.user) - if sample_run_obj.get_user_id not in shared_user_ids: + if sample_run_obj.get_user_id() not in shared_user_ids: return render( request, "wetlab/display_sample.html", From 1fceb83ff6992fbe7f3949deafa8c58239166515 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 19 Apr 2024 13:13:23 +0200 Subject: [PATCH 028/446] loop for all error messages --- wetlab/templates/wetlab/create_new_run.html | 731 ++++++++++++-------- 1 file changed, 425 insertions(+), 306 deletions(-) diff --git a/wetlab/templates/wetlab/create_new_run.html b/wetlab/templates/wetlab/create_new_run.html index 3601d3081..20058a08e 100644 --- a/wetlab/templates/wetlab/create_new_run.html +++ b/wetlab/templates/wetlab/create_new_run.html @@ -1,116 +1,184 @@ {% extends "core/base.html" %} {% load static %} {% block content %} -{%include 'core/jexcel_functionality.html' %} -{% include "wetlab/menu.html" %} -
-
- {% include 'registration/login_inline.html' %} - {% if error_message %} -
-
-
-

Unable to accept your request

-
-

{{error_message}}

+ {% include 'core/jexcel_functionality.html' %} + {% include "wetlab/menu.html" %} +
+
+ {% include 'registration/login_inline.html' %} + {% if error_message %} +
+
+
+
+

Unable to accept your request

+
+
+ {% for error in error_message %}

{{ error }}

{% endfor %} +
-
- {% endif %} - {% if info_message %} -
-
-
-

Successful creation of the run

-
-

{{info_message}}

+ {% endif %} + {% if info_message %} +
+
+
+
+

Successful creation of the run

+
+
+

{{ info_message }}

+
-
- {% endif %} - {% if display_sample_information %} -
-
-
-
-

Create the new Run with pool {{display_sample_information.experiment_name}}

-
-
-
- {% csrf_token %} - - - - - - - - -
Confirm/ Update library preparation indexes to create the new Run {{display_sample_information.experiment_name}}
-
-
-
- - -
-
-
- {% if display_sample_information.instrument %} + {% endif %} + {% if display_sample_information %} +
+
+
+
+
+

Create the new Run with pool {{ display_sample_information.experiment_name }}

+
+
+
+ + {% csrf_token %} + + + + + + +
+ Confirm/ Update library preparation indexes to create the new Run {{ display_sample_information.experiment_name }} +
+
+
- - + +
- {% endif %} -
-
-
-
-
- -
-
-
-
- - +
+ {% if display_sample_information.instrument %} +
+ + +
+ {% endif %}
-
-
-
-
- - +
+
+
+ + +
+
+
+
+ + +
-
-
- - +
+
+
+ + +
- {% if display_sample_information.adapter2 %} +
- - + +
- {% endif %} + {% if display_sample_information.adapter2 %} +
+ + +
+ {% endif %} +
-
-
-
-
Samples that will be included in the run
-
-
-
-
-
- - - - -
-
+ +
+
+
-
- {% elif created_new_run %} -
-
-
-
-

Successful creation of Run {{created_new_run.exp_name}}

-
-
Run name {{created_new_run.exp_name}} is Recorded State
-
-
-
-
-

Click on the link below to check the Run information

-

{{created_new_run.exp_name}}

+ {% elif created_new_run %} +
+
+
+
+
+

Successful creation of Run {{ created_new_run.exp_name }}

+
+
+
Run name {{ created_new_run.exp_name }} is Recorded State
+
+
+
+
+

Click on the link below to check the Run information

+

+ {{ created_new_run.exp_name }} +

+
-
-
-
-
-
Click on the link to download the Sample Sheet File
- Sample Sheet File +
+
+
+
Click on the link to download the Sample Sheet File
+ Sample Sheet File +
-
+
-
+
-
- - {% else %} - - {% if display_pools_for_run.invalid_run_data.heading %} -
-
-
-

Invalid pools

-
-

Some of the samples in the following pools are missing.

-
- - - - {% for value in display_pools_for_run.invalid_run_data.heading%} - - {% endfor %} - - - - {% for p_name, p_code, number, p_id in display_pools_for_run.invalid_run_data.data %} + {% else %} + {% if display_pools_for_run.invalid_run_data.heading %} +
+
+
+
+

Invalid pools

+
+
+

Some of the samples in the following pools are missing.

+
+
{{value}}
+ - - - + {% for value in display_pools_for_run.invalid_run_data.heading %}{% endfor %} - {% endfor %} - - -
{{p_name}}{{p_code}}{{number}}{{ value }}
+ + + {% for p_name, p_code, number, p_id in display_pools_for_run.invalid_run_data.data %} + + {{ p_name }} + {{ p_code }} + {{ number }} + + {% endfor %} + + +
- -
-
- {% endif %} - {% if display_pools_for_run.run_data.heading %} -
-
-
-
-

Run defined, but not completed

-
-
- {% csrf_token %} - - {% for r_name, p_values, r_id in display_pools_for_run.run_data.data %} -
-
-
-

Run name {{r_name }}

-
- - - - {% for value in display_pools_for_run.run_data.heading %} - - {% endfor %} - - - - - {% for p_name, p_code, p_number in p_values %} + + + {% endif %} + {% if display_pools_for_run.run_data.heading %} +
+
+
+
+
+

Run defined, but not completed

+
+
+ + {% csrf_token %} + + {% for r_name, p_values, r_id in display_pools_for_run.run_data.data %} +
+
+
+
+

Run name {{ r_name }}

+
+
+
{{value}} Select Run
+ - - - - + {% for value in display_pools_for_run.run_data.heading %}{% endfor %} + - {% endfor %} - -
{{p_name}}{{p_code}}{{p_number}}{{ value }}Select Run
+ + + {% for p_name, p_code, p_number in p_values %} + + {{ p_name }} + {{ p_code }} + {{ p_number }} + + + + + {% endfor %} + + +
-
- {% endfor %} - - + {% endfor %} + + +
-
- {% endif %} - {% load user_text %} - {% if display_pools_for_run.pool_data %} -
-
-

Fill the information to create the New Run

-
- -
- {% for key, values in display_pools_for_run.pool_data.platform.items %} - {% if forloop.first %} -
- {% else %} -
- {% endif %} -
-
-
-
-
-
- {% csrf_token %} - - - -
-
-
- - -
-
-
- {% for reagent , lots in display_pools_for_run.reagents_kits|keyvalue:key %} -
- -
- -
-

+ {% endif %} + {% load user_text %} + {% if display_pools_for_run.pool_data %} +
+
+

Fill the information to create the New Run

+
+ +
+ {% for key, values in display_pools_for_run.pool_data.platform.items %} + {% if forloop.first %} +
+ {% else %} +
+ {% endif %} +
+
+
+
+
+ + {% csrf_token %} + + + +
+
+
+ + +
+
+
+ {% for reagent , lots in display_pools_for_run.reagents_kits|keyvalue:key %} +
+ +
+ +
+ +
+
+
+ {% endfor %} +
- {% endfor %} -
-
-
-
-
-

Select the pools to be included in the new run

-
- - - - - {% for value in display_pools_for_run.pool_data.heading%} - - {% endfor %} - - - - {% for p_name, p_code, number, p_id in values %} - - - - - - - {% endfor %} - - -
{{value}}
{{p_name}}{{p_code}}{{number}}
- - - +
+
+
+
+

Select the pools to be included in the new run

+
+
+ + + + {% for value in display_pools_for_run.pool_data.heading %}{% endfor %} + + + + {% for p_name, p_code, number, p_id in values %} + + + + + + + {% endfor %} + +
{{ value }}
{{ p_name }}{{ p_code }}{{ number }} + +
+ + +
+
+
-
+
- +
-
-
+ {% endfor %} +
- {% endfor %} +
-
-
-
- {% endif %} - {% if not display_pools_for_run.pool_data.heading and not display_pools_for_run.run_data.heading and not info_message %} -
-
-
-

Not available Pools

-
-

There is not available pools to create a new Run

+ {% endif %} + {% if not display_pools_for_run.pool_data.heading and not display_pools_for_run.run_data.heading and not info_message %} +
+
+
+
+

Not available Pools

+
+
+

There is not available pools to create a new Run

+
+
+
+
-
- -
+ {% endif %} + {% endif %}
- {% endif %} - {% endif %} -
-
- -{% endblock %} + + {% endblock %} From 21c08a1ccffd17dd1c3ac0bf767595cfdacc8a90 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 19 Apr 2024 13:16:25 +0200 Subject: [PATCH 029/446] re-organize the info for LibraryPool --- wetlab/admin.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wetlab/admin.py b/wetlab/admin.py index ae484d5bd..c0b8d5f08 100644 --- a/wetlab/admin.py +++ b/wetlab/admin.py @@ -33,11 +33,11 @@ class LibParameterValueAdmin(admin.ModelAdmin): class LibraryPoolAdmin(admin.ModelAdmin): list_display = ( - "register_user", - "pool_state", "pool_name", + "pool_state", "platform", "pool_code_id", + "register_user", "run_process_id", ) From cb9a603f3855b6fd68264f934a0de0ed19bf4e4e Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 19 Apr 2024 13:22:23 +0200 Subject: [PATCH 030/446] added missing div --- wetlab/templates/wetlab/create_new_run.html | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/wetlab/templates/wetlab/create_new_run.html b/wetlab/templates/wetlab/create_new_run.html index 20058a08e..f52f7b302 100644 --- a/wetlab/templates/wetlab/create_new_run.html +++ b/wetlab/templates/wetlab/create_new_run.html @@ -312,7 +312,7 @@

Run name {{ r_name }}

- {% for p_name, p_code, p_number in p_values %} + {% for p_name, p_code, p_number in p_values %} {{ p_name }} {{ p_code }} @@ -499,6 +499,7 @@

Not available Pools

- {% endcomment %} - - {% else %} -
-
-
-
-

Statistics per Investigator

-
-
- {% csrf_token %} - -
+ + {% endcomment %} + {% elif researcher_lab_statistics.type == "lab" %} + {% else %} +
+
+
+
+ {% if request.user|has_group:"WetlabManager" %} +
+

Statistics per Investigator or Laboratory

+
+ {% else %} +
+

Statistics per Investigator

+
+ {% endif %} +
+ + {% csrf_token %} + {% if request.user|has_group:"WetlabManager" %} - - +
+ + +
+
+ + +
{% else %} - - +
+ + +
{% endif %} - -
-
-
-
- - +
+
+
+ + +
-
-
-
- - +
+
+ + +
-
- {% if request.user|has_group:"WetlabManager" %} -

Fields marked in Red are mandatory

- {% endif %} - - - -
+ + + +
+
-
-
- {% endif %} -
- - + {% endblock %} diff --git a/wetlab/utils/statistics.py b/wetlab/utils/statistics.py index fc4cc3104..6011d3ce7 100644 --- a/wetlab/utils/statistics.py +++ b/wetlab/utils/statistics.py @@ -317,246 +317,308 @@ def get_per_time_statistics(start_date, end_date): return per_time_statistics -def get_researcher_statistics(researcher_name, start_date, end_date): +def get_researcher_lab_statistics( + researcher_name: str, lab_name: str, start_date: str, end_date: str +) -> dict: """_summary_ - Parameters - ---------- - researcher_name : str - _description_ - start_date : str - _description_ - end_date : str, - _description_, by default None + Args: + researcher_name (str): user name of the researcher + lab_name (str): laboratory/institution name + start_date (str): start date for the statistics + end_date (str): end date for the statistics - Returns - ------- - _type_ - _description_ + Returns: + dict: _description_ """ - researcher_statistics = {} - if not User.objects.filter(username__icontains=researcher_name).exists(): - researcher_statistics["ERROR"] = ( - wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS + + def _sequenced_samples_stats( + user_seq_sample_objs: list, + other_user_seq_sample_objs: list, + research_lab_statistics: dict, + ) -> dict: + """_summary_ + + Args: + user_seq_sample_objs (list): list of sequenced samples for the researcher + other_user_seq_sample_objs (list): list of sequenced samples for other researchers + research_lab_statistics (dict): dictionary with the statistics + + Returns: + dict: _description_ + """ + # Collect data for the sequenced sample + research_lab_statistics["seq_samples"] = user_seq_sample_objs.values_list( + "sample_name", + "project_id__project_name", + "run_process_id__run_name", + "run_process_id__used_sequencer__sequencer_name", + ) + research_lab_statistics["seq_table_heading"] = ( + wetlab.config.HEADING_STATISTICS_FOR_SECUENCED_RESEARCHER_SAMPLE ) - return researcher_statistics - user_objs = User.objects.filter(username__icontains=researcher_name) + # pie graph sequencing samples percentage researcher vs others + seq_sample_count = { + researcher_name: user_seq_sample_objs.count(), + "all researchers": other_user_seq_sample_objs.count(), + } + g_data = core.utils.graphics.preparation_3D_pie( + "Percentage of samples", "Research vs all", "ocean", seq_sample_count + ) + research_lab_statistics["seq_sample_research_vs_other_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "seq_sample_research_vs_other_graph", + "600", + "300", + "seq_sample_research_vs_other_chart", + "json", + g_data, + ).render() + ) - if len(user_objs) > 1: - researcher_statistics["ERROR"] = ( - wetlab.config.ERROR_MANY_USER_MATCHES_FOR_INPUT_CONDITIONS + # pie graph for sequencers used for sequencing samples + seq_objs = core.models.SequencerInLab.objects.all() + sample_per_sequencer = {} + for seq_obj in seq_objs: + sample_per_sequencer[seq_obj.get_sequencer_name()] = ( + user_seq_sample_objs.filter( + run_process_id__used_sequencer=seq_obj + ).count() + ) + g_data = core.utils.graphics.preparation_3D_pie( + "Sequencer usage", "", "ocean", sample_per_sequencer + ) + research_lab_statistics["research_usage_sequencer_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "research_usage_sequencer_graph", + "600", + "300", + "research_usage_sequencer_chart", + "json", + g_data, + ).render() + ) + + # chart graph for runs + researcher_runs = {} + runs = list( + user_seq_sample_objs.values_list( + "run_process_id__run_name", flat=True + ).distinct() + ) + for run in runs: + researcher_runs[run] = user_seq_sample_objs.filter( + run_process_id__run_name__exact=run + ).count() + + g_data = core.utils.graphics.preparation_graphic_data( + "Number of samples per run", + "", + "Run name", + "Number of samples", + "ocean", + researcher_runs, + ) + research_lab_statistics["research_run_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "research_run_graph", + "550", + "350", + "research_run_chart", + "json", + g_data, + ).render() + ) + + # chart graph for projects + researcher_projects = {} + projects = list( + user_seq_sample_objs.values_list( + "project_id__project_name", flat=True + ).distinct() + ) + for project in projects: + researcher_projects[project] = user_seq_sample_objs.filter( + project_id__project_name__exact=project + ).count() + g_data = core.utils.graphics.preparation_graphic_data( + "Number of samples per project", + "", + "Project name", + "Number of samples", + "ocean", + researcher_projects, + ) + research_lab_statistics["research_project_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "research_project_graph", + "550", + "350", + "research_project_chart", + "json", + g_data, + ).render() + ) + + # chart graph for Q > 30 on runs + researcher_q_30 = list( + user_seq_sample_objs.values(run_name=F("run_process_id__run_name")) + .annotate(q_30_value=Avg("quality_q30")) + .order_by("run_process_id__run_name") + ) + + g_data = core.utils.graphics.preparation_graphic_data( + "Percentage of samples with Q > 30", + "", + "Run name", + "Percentage of Q>30", + "ocean", + researcher_q_30, + "run_name", + "q_30_value", + ) + research_lab_statistics["research_q_30_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "research_q_30_graph", + "550", + "350", + "research_q_30_chart", + "json", + g_data, + ).render() + ) + + # chart graph for mean + researcher_mean = list( + user_seq_sample_objs.values(run_name=F("run_process_id__run_name")) + .annotate(mean_value=Avg("mean_quality")) + .order_by("run_process_id__run_name") + ) + g_data = core.utils.graphics.preparation_graphic_data( + "Qualiy mean of samples per run", + "", + "Run name", + "Quality mean", + "ocean", + researcher_mean, + "run_name", + "mean_value", ) - return researcher_statistics - researcher_name = user_objs[0].username + research_lab_statistics["research_mean_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "research_mean_graph", + "550", + "350", + "research_mean_chart", + "json", + g_data, + ).render() + ) + return research_lab_statistics + # validate date format if start_date != "" and not wetlab.utils.common.check_valid_date_format(start_date): - researcher_statistics["ERROR"] = wetlab.config.ERROR_INVALID_FORMAT_FOR_DATES - return researcher_statistics + research_lab_statistics["ERROR"] = wetlab.config.ERROR_INVALID_FORMAT_FOR_DATES + return research_lab_statistics if end_date != "" and not wetlab.utils.common.check_valid_date_format(start_date): - researcher_statistics["ERROR"] = wetlab.config.ERROR_INVALID_FORMAT_FOR_DATES - return researcher_statistics + research_lab_statistics["ERROR"] = wetlab.config.ERROR_INVALID_FORMAT_FOR_DATES + return research_lab_statistics - # check if start and end date are present in the form + # Filter samples used for sequencing and for preparing library, based on the dates if start_date != "" and end_date != "": - sample_objs = wetlab.models.SamplesInProject.objects.filter( + seq_sample_objs = wetlab.models.SamplesInProject.objects.filter( run_process_id__run_date__range=(start_date, end_date) ) + rec_sample_objs = core.models.Samples.objects.filter( + generated_at__range=(start_date, end_date) + ) elif start_date != "": - sample_objs = wetlab.models.SamplesInProject.objects.filter( + seq_sample_objs = wetlab.models.SamplesInProject.objects.filter( run_process_id__run_date__gte=start_date ) + rec_sample_objs = core.models.Samples.objects.filter( + generated_at__gte=start_date + ) elif end_date != "": - sample_objs = wetlab.models.SamplesInProject.objects.filter( + seq_sample_objs = wetlab.models.SamplesInProject.objects.filter( run_process_id__run_date__lte=end_date ) + rec_sample_objs = core.models.Samples.objects.filter(generated_at__lte=end_date) else: - sample_objs = wetlab.models.SamplesInProject.objects.all() - - other_user_sample_objs = sample_objs.exclude(user_id=user_objs[0]) - user_sample_objs = sample_objs.filter(user_id=user_objs[0]) - if len(user_sample_objs) == 0: - researcher_statistics["ERROR"] = ( - wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS - ) - return researcher_statistics - # sample table - researcher_statistics["samples"] = user_sample_objs.values_list( - "sample_name", - "project_id__project_name", - "run_process_id__run_name", - "run_process_id__used_sequencer__sequencer_name", - ) - researcher_statistics["table_heading"] = ( - wetlab.config.HEADING_STATISTICS_FOR_RESEARCHER_SAMPLE - ) - - # pie graph percentage researcher vs others - per_data_user = {} - per_data_user[researcher_name] = user_sample_objs.count() - per_data_user["all researchers"] = other_user_sample_objs.count() - # heading, sub_title, axis_x_description, axis_y_description, theme, source_data - g_data = core.utils.graphics.preparation_3D_pie( - "Percentage of samples", "Research vs all", "ocean", per_data_user - ) - - researcher_statistics["research_vs_other_graphic"] = ( - core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", - "research_vs_other_graph", - "600", - "300", - "research_vs_other_chart", - "json", - g_data, - ).render() - ) - - # pie graph for sequencers used - # ############################# - seq_objs = core.models.SequencerInLab.objects.all() - sample_per_sequencer = {} - for seq_obj in seq_objs: - sample_per_sequencer[seq_obj.get_sequencer_name()] = user_sample_objs.filter( - run_process_id__used_sequencer=seq_obj - ).count() - g_data = core.utils.graphics.preparation_3D_pie( - "Sequencer usage", "", "ocean", sample_per_sequencer - ) - researcher_statistics["research_usage_sequencer_graphic"] = ( - core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", - "research_usage_sequencer_graph", - "600", - "300", - "research_usage_sequencer_chart", - "json", - g_data, - ).render() - ) - - # chart graph for runs - # #################### - researcher_runs = {} - runs = list( - user_sample_objs.values_list("run_process_id__run_name", flat=True).distinct() - ) - for run in runs: - researcher_runs[run] = user_sample_objs.filter( - run_process_id__run_name__exact=run - ).count() + seq_sample_objs = wetlab.models.SamplesInProject.objects.all() + rec_sample_objs = core.models.Samples.objects.all() + + research_lab_statistics = {} + if researcher_name != "": + researcher_name = researcher_name.strip() + # check if the researcher exists + if not User.objects.filter(username__icontains=researcher_name).exists(): + research_lab_statistics["ERROR"] = ( + wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS + ) + return research_lab_statistics + user_objs = User.objects.filter(username__icontains=researcher_name) - g_data = core.utils.graphics.preparation_graphic_data( - "Number of samples per run", - "", - "Run name", - "Number of samples", - "ocean", - researcher_runs, - ) - researcher_statistics["research_run_graphic"] = ( - core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "research_run_graph", - "550", - "350", - "research_run_chart", - "json", - g_data, - ).render() - ) + if len(user_objs) > 1: + research_lab_statistics["ERROR"] = ( + wetlab.config.ERROR_MANY_USER_MATCHES_FOR_INPUT_CONDITIONS + ) + return research_lab_statistics + # get the user name of the researcher + research_lab_statistics["researcher_name"] = user_objs[0].username - # chart graph for projects - # ######################## - researcher_projects = {} - projects = list( - user_sample_objs.values_list("project_id__project_name", flat=True).distinct() - ) - for project in projects: - researcher_projects[project] = user_sample_objs.filter( - project_id__project_name__exact=project - ).count() - g_data = core.utils.graphics.preparation_graphic_data( - "Number of samples per project", - "", - "Project name", - "Number of samples", - "ocean", - researcher_projects, - ) - researcher_statistics["research_project_graphic"] = ( - core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "research_project_graph", - "550", - "350", - "research_project_chart", - "json", - g_data, - ).render() - ) + # get the sequenced samples for the researcher + other_user_seq_sample_objs = seq_sample_objs.exclude(user_id=user_objs[0]) + user_seq_sample_objs = seq_sample_objs.filter(user_id=user_objs[0]) - # chart graph for Q > 30 on runs - # ############################## - researcher_q_30 = list( - user_sample_objs.values(run_name=F("run_process_id__run_name")) - .annotate(q_30_value=Avg("quality_q30")) - .order_by("run_process_id__run_name") - ) + # get the library preparation samples for the researcher + other_user_rec_sample_objs = rec_sample_objs.exclude(sample_user=user_objs[0]) + user_rec_sample_objs = rec_sample_objs.filter(sample_user=user_objs[0]) + import pdb - g_data = core.utils.graphics.preparation_graphic_data( - "Percentage of samples with Q > 30", - "", - "Run name", - "Percentage of Q>30", - "ocean", - researcher_q_30, - "run_name", - "q_30_value", - ) - researcher_statistics["research_q_30_graphic"] = ( - core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "research_q_30_graph", - "550", - "350", - "research_q_30_chart", - "json", - g_data, - ).render() - ) + pdb.set_trace() - # chart graph for mean - # #################### - researcher_mean = list( - user_sample_objs.values(run_name=F("run_process_id__run_name")) - .annotate(mean_value=Avg("mean_quality")) - .order_by("run_process_id__run_name") - ) - g_data = core.utils.graphics.preparation_graphic_data( - "Qualiy mean of samples per run", - "", - "Run name", - "Quality mean", - "ocean", - researcher_mean, - "run_name", - "mean_value", - ) - researcher_statistics["research_mean_graphic"] = ( - core.fusioncharts.fusioncharts.FusionCharts( - "column3d", - "research_mean_graph", - "550", - "350", - "research_mean_chart", - "json", - g_data, - ).render() - ) - researcher_statistics["researcher_name"] = researcher_name + if len(user_seq_sample_objs) == 0 and len(user_rec_sample_objs) == 0: + research_lab_statistics["ERROR"] = ( + wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS + ) + return research_lab_statistics + research_lab_statistics["type"] = "researcher" + if len(user_seq_sample_objs) > 0: + research_lab_statistics = _sequenced_samples_stats( + user_seq_sample_objs, + other_user_seq_sample_objs, + research_lab_statistics, + ) + if len(user_rec_sample_objs) > 0: + research_lab_statistics["rec_samples"] = user_rec_sample_objs.values_list( + "sample_name", + "unique_sample_id", + "sample_type__sample_type", + "species__species_name", + "sample_state__sample_state_name", + "sample_project__sample_project_name", + ) + research_lab_statistics["rec_table_heading"] = ( + wetlab.config.HEADING_STATISTICS_FOR_RECORDED_RESEARCHER_SAMPLE + ) + else: + lab_sample_objs = seq_sample_objs.filter(lab_request_id__exact=lab_name) + if len(lab_sample_objs) == 0: + research_lab_statistics["ERROR"] = ( + wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS + ) + return research_lab_statistics + research_lab_statistics["type"] = "lab" - return researcher_statistics + return research_lab_statistics def get_pending_graphic_data( diff --git a/wetlab/views.py b/wetlab/views.py index c23fa8db4..481b25805 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -1602,12 +1602,18 @@ def stats_per_researcher(request): r_name = request.POST["researchername"] start_date = request.POST["startdate"] end_date = request.POST["enddate"] + lab_name = request.POST["labname"] if "labname" in request.POST else None + # return the form if empty values + if lab_name == "" and lab_name is None: + return render(request, "wetlab/stats_per_researcher.html") - researcher_statistics = wetlab.utils.statistics.get_researcher_statistics( - r_name, start_date, end_date + researcher_lab_statistics = ( + wetlab.utils.statistics.get_researcher_lab_statistics( + r_name, lab_name, start_date, end_date + ) ) - if "ERROR" in researcher_statistics: - error_message = researcher_statistics["ERROR"] + if "ERROR" in researcher_lab_statistics: + error_message = researcher_lab_statistics["ERROR"] return render( request, "wetlab/stats_per_researcher.html", @@ -1617,7 +1623,7 @@ def stats_per_researcher(request): return render( request, "wetlab/stats_per_researcher.html", - {"researcher_statistics": researcher_statistics}, + {"researcher_lab_statistics": researcher_lab_statistics}, ) else: return render(request, "wetlab/stats_per_researcher.html") From 12fd70c95602f024778067b8ba95914da89903fc Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 5 May 2024 16:38:38 +0200 Subject: [PATCH 055/446] added recorded samples vs other researchers --- .../wetlab/stats_per_researcher.html | 174 +++++++++++------- wetlab/utils/statistics.py | 19 ++ 2 files changed, 125 insertions(+), 68 deletions(-) diff --git a/wetlab/templates/wetlab/stats_per_researcher.html b/wetlab/templates/wetlab/stats_per_researcher.html index f7d8de9d5..64e25346a 100644 --- a/wetlab/templates/wetlab/stats_per_researcher.html +++ b/wetlab/templates/wetlab/stats_per_researcher.html @@ -94,46 +94,48 @@

Statistics results for Investigator {{ researcher_lab_st {% endif %}
-
-
-
-
-
-
-

Statistics from sequenced samples

-
-
-
-
-
- {{ researcher_lab_statistics.seq_sample_research_vs_other_graphic|safe }} -
-
-
- {{ researcher_lab_statistics.research_usage_sequencer_graphic|safe }} -
+ {% if researcher_lab_statistics.seq_table_heading %} +
+
+
+
+
+
+

Statistics from sequenced samples

-
-
-
- {{ researcher_lab_statistics.research_run_graphic|safe }} -
-
-
- {{ researcher_lab_statistics.research_project_graphic|safe }} +
+
+
+
+ {{ researcher_lab_statistics.seq_sample_research_vs_other_graphic|safe }} +
+
+
+ {{ researcher_lab_statistics.research_usage_sequencer_graphic|safe }} +
-
-
-
-
- {{ researcher_lab_statistics.research_q_30_graphic|safe }} +
+
+
+ {{ researcher_lab_statistics.research_run_graphic|safe }} +
+
+
+ {{ researcher_lab_statistics.research_project_graphic|safe }} +
-
-
- {{ researcher_lab_statistics.research_mean_graphic|safe }} +
+
+
+ {{ researcher_lab_statistics.research_q_30_graphic|safe }} +
+
+
+ {{ researcher_lab_statistics.research_mean_graphic|safe }} +
@@ -141,45 +143,81 @@

Statistics from sequenced samples

-
- -
-
-
-
-
-
-

Researcher statistics

-
-
- - - - {% for column in researcher_lab_statistics.seq_table_heading %}{% endfor %} - - - - {% for sample, project, run, platform in researcher_lab_statistics.seq_samples %} + +
+
+
+
+
+
+

Researcher statistics

+
+
+
{{ column }}
+ - - - - + {% for column in researcher_lab_statistics.seq_table_heading %}{% endfor %} - {% endfor %} - -
{{ sample }}{{ project }}{{ run }}{{ platform }}{{ column }}
+ + + {% for sample, project, run, platform in researcher_lab_statistics.seq_samples %} + + {{ sample }} + {{ project }} + {{ run }} + {{ platform }} + + {% endfor %} + + +
-
- + + {% endif %} {% if researcher_lab_statistics.rec_table_heading %} + {% if not researcher_lab_statistics.seq_table_heading %} +
+ {% else %} +
+ {% endif %} +
+
+
+
+
+

Statistics from recorded samples

+
+
+
+
+
+ {{ researcher_lab_statistics.rec_sample_research_vs_other_graphic|safe }} +
+
+
+ {{ researcher_lab_statistics.rec_research_usage_sequencer_graphic|safe }} +
+
+
+
+
+
+
+
+
Date: Sun, 5 May 2024 20:31:07 +0200 Subject: [PATCH 056/446] Implemented sample states graphic --- core/utils/graphics.py | 33 ++--- .../wetlab/stats_per_researcher.html | 6 +- wetlab/utils/statistics.py | 113 +++++++++++++----- 3 files changed, 97 insertions(+), 55 deletions(-) diff --git a/core/utils/graphics.py b/core/utils/graphics.py index 788644fb6..c6157742d 100644 --- a/core/utils/graphics.py +++ b/core/utils/graphics.py @@ -1,25 +1,18 @@ -def preparation_3D_pie(heading, sub_title, theme, source_data): - """_summary_ +def preparation_3D_pie( + heading: str, sub_title: str, theme: str, source_data: dict +) -> dict: + """Join the parameters to create a dictionary with two keys: chart and data. + The chart key contains the heading, sub_title, theme, numberPrefix, showlegend, placevaluesInside, showpercentvalues, rotatevalues, showCanvasBg, showCanvasBase, canvasBaseDepth, canvasBgDepth, canvasBaseColor, canvasBgColor, exportEnabled. + The data key contains a list of dictionaries with the keys label and value. - Parameters - ---------- - heading : str - text to insert on top of graphic - sub_title : str - additional text to include in graphic - axis_x_description : str - description of x axis - axis_y_description : str - description - theme : str - name of the available themes to be used for the graphic - source_data : dict - Dictionary containing value for the graphic + Args: + heading (str): title of the chart + sub_title (str): additional information + theme (str): theme of the chart + source_data (dict): dictionary with the data to be displayed - Returns - ------- - _type_ - _description_ + Returns: + dict: dictionary with the keys chart and data """ data_source = {} data_source["chart"] = { diff --git a/wetlab/templates/wetlab/stats_per_researcher.html b/wetlab/templates/wetlab/stats_per_researcher.html index 64e25346a..ce9b8b0cb 100644 --- a/wetlab/templates/wetlab/stats_per_researcher.html +++ b/wetlab/templates/wetlab/stats_per_researcher.html @@ -67,7 +67,7 @@

Statistics results for Investigator {{ researcher_lab_st type="button" role="tab" aria-controls="rec-table" - aria-selected="false">Recordeed samples + aria-selected="false">Recorded samples {% endif %} {% else %} @@ -207,8 +207,8 @@

Statistics from recorded samples

{{ researcher_lab_statistics.rec_sample_research_vs_other_graphic|safe }}
-
- {{ researcher_lab_statistics.rec_research_usage_sequencer_graphic|safe }} +
+ {{ researcher_lab_statistics.rec_sample_states_graphic|safe }}
diff --git a/wetlab/utils/statistics.py b/wetlab/utils/statistics.py index a3a9d585f..50728a5a8 100644 --- a/wetlab/utils/statistics.py +++ b/wetlab/utils/statistics.py @@ -523,6 +523,82 @@ def _sequenced_samples_stats( ) return research_lab_statistics + def _recorded_samples_stats( + user_rec_sample_objs: list, + other_user_rec_sample_objs: list, + research_lab_statistics: dict, + ) -> dict: + """_summary_ + + Args: + user_rec_sample_objs (list): list of recorded samples for the researcher + other_user_rec_sample_objs (list): list of recorded samples for other researchers + research_lab_statistics (dict): dictionary with the statistics + + Returns: + dict: _description_ + """ + # Collect data for the recorded sample + research_lab_statistics["rec_samples"] = user_rec_sample_objs.values_list( + "sample_name", + "unique_sample_id", + "sample_type__sample_type", + "species__species_name", + "sample_state__sample_state_name", + "sample_project__sample_project_name", + ) + research_lab_statistics["rec_table_heading"] = ( + wetlab.config.HEADING_STATISTICS_FOR_RECORDED_RESEARCHER_SAMPLE + ) + + # pie graph sequencing samples percentage researcher vs others + rec_sample_count = { + researcher_name: user_rec_sample_objs.count(), + "all researchers": other_user_rec_sample_objs.count(), + } + g_data = core.utils.graphics.preparation_3D_pie( + "Percentage of samples", "Research vs all", "ocean", rec_sample_count + ) + research_lab_statistics["rec_sample_research_vs_other_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "rec_sample_research_vs_other_graph", + "600", + "300", + "rec_sample_research_vs_other_chart", + "json", + g_data, + ).render() + ) + rec_sample_states = list( + user_rec_sample_objs.values( + sum_state=F("sample_state__sample_state_name") + ).annotate(value=Count("sample_name")) + ) + g_data = core.utils.graphics.preparation_graphic_data( + "Samples state", + "", + "", + "", + "ocean", + rec_sample_states, + "sum_state", + "value", + ) + research_lab_statistics["rec_sample_states_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "rec_sample_states_graph", + "600", + "300", + "rec_sample_states_chart", + "json", + g_data, + ).render() + ) + + return research_lab_statistics + # validate date format if start_date != "" and not wetlab.utils.common.check_valid_date_format(start_date): research_lab_statistics["ERROR"] = wetlab.config.ERROR_INVALID_FORMAT_FOR_DATES @@ -581,9 +657,6 @@ def _sequenced_samples_stats( # get the library preparation samples for the researcher other_user_rec_sample_objs = rec_sample_objs.exclude(sample_user=user_objs[0]) user_rec_sample_objs = rec_sample_objs.filter(sample_user=user_objs[0]) - import pdb - - pdb.set_trace() if len(user_seq_sample_objs) == 0 and len(user_rec_sample_objs) == 0: research_lab_statistics["ERROR"] = ( @@ -598,36 +671,12 @@ def _sequenced_samples_stats( research_lab_statistics, ) if len(user_rec_sample_objs) > 0: - research_lab_statistics["rec_samples"] = user_rec_sample_objs.values_list( - "sample_name", - "unique_sample_id", - "sample_type__sample_type", - "species__species_name", - "sample_state__sample_state_name", - "sample_project__sample_project_name", - ) - research_lab_statistics["rec_table_heading"] = ( - wetlab.config.HEADING_STATISTICS_FOR_RECORDED_RESEARCHER_SAMPLE - ) - # pie graph sequencing samples percentage researcher vs others - rec_sample_count = { - researcher_name: user_rec_sample_objs.count(), - "all researchers": other_user_rec_sample_objs.count(), - } - g_data = core.utils.graphics.preparation_3D_pie( - "Percentage of samples", "Research vs all", "ocean", rec_sample_count - ) - research_lab_statistics["rec_sample_research_vs_other_graphic"] = ( - core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", - "rec_sample_research_vs_other_graph", - "600", - "300", - "rec_sample_research_vs_other_chart", - "json", - g_data, - ).render() + research_lab_statistics = _recorded_samples_stats( + user_rec_sample_objs, + other_user_rec_sample_objs, + research_lab_statistics, ) + else: lab_sample_objs = seq_sample_objs.filter(lab_request_id__exact=lab_name) if len(lab_sample_objs) == 0: From cbf33b6eec6161918e9eac502d959fbffb1d7cb1 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 5 May 2024 20:34:07 +0200 Subject: [PATCH 057/446] litin --- wetlab/utils/statistics.py | 1 + 1 file changed, 1 insertion(+) diff --git a/wetlab/utils/statistics.py b/wetlab/utils/statistics.py index 50728a5a8..43eb9af9e 100644 --- a/wetlab/utils/statistics.py +++ b/wetlab/utils/statistics.py @@ -599,6 +599,7 @@ def _recorded_samples_stats( return research_lab_statistics + research_lab_statistics = {} # validate date format if start_date != "" and not wetlab.utils.common.check_valid_date_format(start_date): research_lab_statistics["ERROR"] = wetlab.config.ERROR_INVALID_FORMAT_FOR_DATES From 14039fe4a66f934345e6ddd2efb9ade0619a46c3 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 5 May 2024 23:44:32 +0200 Subject: [PATCH 058/446] fetching lab list to use in form --- .../wetlab/stats_per_researcher.html | 281 +++++++++--------- wetlab/views.py | 5 +- 2 files changed, 144 insertions(+), 142 deletions(-) diff --git a/wetlab/templates/wetlab/stats_per_researcher.html b/wetlab/templates/wetlab/stats_per_researcher.html index ce9b8b0cb..944808d7c 100644 --- a/wetlab/templates/wetlab/stats_per_researcher.html +++ b/wetlab/templates/wetlab/stats_per_researcher.html @@ -184,31 +184,32 @@

Researcher statistics

{% if researcher_lab_statistics.rec_table_heading %} {% if not researcher_lab_statistics.seq_table_heading %}
- {% else %} -
- {% endif %} -
-
-
-
-
-

Statistics from recorded samples

-
-
-
-
-
- {{ researcher_lab_statistics.rec_sample_research_vs_other_graphic|safe }} -
-
-
- {{ researcher_lab_statistics.rec_sample_states_graphic|safe }} + id="rec-graphics" + role="tabpanel" + aria-labelledby="rec-graphics-tab"> + {% else %} +
+ {% endif %} +
+
+
+
+
+

Statistics from recorded samples

+
+
+
+
+
+ {{ researcher_lab_statistics.rec_sample_research_vs_other_graphic|safe }} +
+
+
+ {{ researcher_lab_statistics.rec_sample_states_graphic|safe }} +
@@ -216,47 +217,46 @@

Statistics from recorded samples

-
- -
-
-
-
-
-
-

Recorded samples

-
-
- - - - {% for column in researcher_lab_statistics.rec_table_heading %}{% endfor %} - - - - {% for sample_data in researcher_lab_statistics.rec_samples %} + +
+
+
+
+
+
+

Recorded samples

+
+
+
{{ column }}
+ - {% for value in sample_data %}{% endfor %} + {% for column in researcher_lab_statistics.rec_table_heading %}{% endfor %} - {% endfor %} - -
{{ value }}{{ column }}
+ + + {% for sample_data in researcher_lab_statistics.rec_samples %} + + {% for value in sample_data %}{{ value }}{% endfor %} + + {% endfor %} + + +
-
- - {% endif %} + + {% endif %} +
-
- {% comment %} + {% comment %}
@@ -378,97 +378,98 @@
There are no Samples runs on this sequencer
// Get the element with id="tablinksdefaultOpen" and click on it document.getElementById("tablinksdefaultOpen").click(); - {% endcomment %} - {% elif researcher_lab_statistics.type == "lab" %} - {% else %} -
-
-
-
- {% if request.user|has_group:"WetlabManager" %} -
-

Statistics per Investigator or Laboratory

-
- {% else %} -
-

Statistics per Investigator

-
- {% endif %} -
-
- {% csrf_token %} - - {% if request.user|has_group:"WetlabManager" %} -
- - -
-
- - -
- {% else %} -
- - -
- {% endif %} -
-
-
- +
+
+
+ {% if request.user|has_group:"WetlabManager" %} +
+

Statistics per Investigator or Laboratory

+
+ {% else %} +
+

Statistics per Investigator

+
+ {% endif %} +
+ + {% csrf_token %} + + {% if request.user|has_group:"WetlabManager" %} +
+ - + name="researchername" + id="researchername" + placeholder="Researcher name" /> +
-
-
-
- + + +
+ {% else %} +
+ - + name="researchername" + id="researchername" + placeholder="Researcher name" + value="{{ user.get_username }}" + readonly /> + +
+ {% endif %} +
+
+
+ + +
+
+
+
+ + +
-
- - - + + + +
-
- {% endif %} -
- - -{% endblock %} + + {% endblock %} diff --git a/wetlab/views.py b/wetlab/views.py index 481b25805..36c6e7528 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -1598,6 +1598,7 @@ def change_run_name(request, run_id): @login_required def stats_per_researcher(request): + lab_list = list(core.models.LabRequest.objects.all().values_list("pk", "lab_name")) if request.method == "POST": r_name = request.POST["researchername"] start_date = request.POST["startdate"] @@ -1617,7 +1618,7 @@ def stats_per_researcher(request): return render( request, "wetlab/stats_per_researcher.html", - {"error_message": error_message}, + {"error_message": error_message, "lab_list": lab_list}, ) return render( @@ -1626,7 +1627,7 @@ def stats_per_researcher(request): {"researcher_lab_statistics": researcher_lab_statistics}, ) else: - return render(request, "wetlab/stats_per_researcher.html") + return render(request, "wetlab/stats_per_researcher.html",{ "lab_list": lab_list }) @login_required From 9b8a703518217adc5a0af388650efab6d2b8777d Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 6 May 2024 16:43:21 +0200 Subject: [PATCH 059/446] Included samples from lab --- wetlab/config.py | 10 +- .../wetlab/stats_per_researcher.html | 389 +++++++++--------- wetlab/utils/statistics.py | 29 +- 3 files changed, 223 insertions(+), 205 deletions(-) diff --git a/wetlab/config.py b/wetlab/config.py index d277a833a..f76259039 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -581,7 +581,15 @@ "sample state", "project name", ] - +HEADING_STATISTICS_FOR_RECORDED_LAB_SAMPLE = [ + "sample name", + "unique ID", + "sample type", + "specimen type", + "sample state", + "project name", + "user name", +] HEADING_STATISTICS_FOR_TIME_RUN = ["Run name", "Run state", "Sequencer", "Run date"] HEADING_STATISTICS_FOR_TIME_SAMPLE = [ "Sample name", diff --git a/wetlab/templates/wetlab/stats_per_researcher.html b/wetlab/templates/wetlab/stats_per_researcher.html index 944808d7c..0bebcd498 100644 --- a/wetlab/templates/wetlab/stats_per_researcher.html +++ b/wetlab/templates/wetlab/stats_per_researcher.html @@ -256,220 +256,189 @@

Recorded samples

- {% comment %} -
-
-
-

Statistics results for Investigator {{researcher_statistics.researcher_name}}

-
-
-
- {% for sequencer, samples_data in researcher_statistics.researcher_sample_data.items %} - {% if forloop.first %} - - {% else %} - - {% endif %} - {% endfor %} - {% for sequencer, samples_data in researcher_statistics.researcher_sample_data.items %} -
-
-
-

Investigator samples run in sequencer {{sequencer}}

- {% if samples_data %} - -
-
- -
- - - - {% for values in researcher_statistics.sample_researcher_heading %}{% endfor %} - - - - {% for values in samples_data %} - - {% for value in values %} - - {% endfor %} - - {% endfor %} - -
{{ values }}
{{ value }}
-
-
-
- - {% else %} -
-
There are no Samples runs on this sequencer
+
+ {% elif researcher_lab_statistics.type == "lab" %} +
+
+

Statistics results for {{ researcher_lab_statistics.lab_name }}

+
+ +
+
+
+
+
+
+
+

Statistics from recorded samples

+
+
+
+
+
+ {{ researcher_lab_statistics.research_q_30_graphic|safe }} +
+
+
+ {{ researcher_lab_statistics.research_mean_graphic|safe }} +
- {% endif %} +
-
-
- {% endfor %} -
-
-
-
-
-
- -
-
-
-

Graphic Statistics for Investigator {{researcher_statistics.researcher_name}}

-
-
- -
- {{ researcher_statistics.run_graphic|safe }} -
-
- -
- {{ researcher_statistics.project_graphic|safe }} -
-
-
-
-
- - - - -
-
-
-

Quality Statistics for Samples handled by {{researcher_statistics.researcher_name}}

-
-
- -
- {{ researcher_statistics.q30_graphic|safe }} -
-
- -
- {{ researcher_statistics.mean_graphic|safe }} -
-
-
-
-
- - {% if researcher_statistics.comp_graphs %} -
-
-
-

{{researcher_statistics.researcher_name}} projects comparison

-
- - -
-
-
-
- {% endif %} - - {% endcomment %} - {% elif researcher_lab_statistics.type == "lab" %} - {% else %} -
-
-
-
- {% if request.user|has_group:"WetlabManager" %} -
-

Statistics per Investigator or Laboratory

+
- {% else %} -
-

Statistics per Investigator

+
+
+ +
+
+
+
+
+
+

Recorded samples from laboratory

+
+
+ + + + {% for column in researcher_lab_statistics.lab_table_heading %}{% endfor %} + + + + {% for sample_data in researcher_lab_statistics.lab_samples %} + + {% for value in sample_data %}{% endfor %} + + {% endfor %} + +
{{ column }}
{{ value }}
+
+
+
- {% endif %} -
-
- {% csrf_token %} - - {% if request.user|has_group:"WetlabManager" %} -
- +
+ +
+
+
+
+ {% else %} +
+
+
+
+ {% if request.user|has_group:"WetlabManager" %} +
+

Statistics per Investigator or Laboratory

+
+ {% else %} +
+

Statistics per Investigator

+
+ {% endif %} +
+ + {% csrf_token %} + + {% if request.user|has_group:"WetlabManager" %} +
+ + +
+
+ + +
+ {% else %} +
+ + +
+ {% endif %} +
+
+
+ - -
-
- - + id="start_date" + name="startdate" + placeholder="Filter run from start date" /> +
- {% else %} -
- +
+
+ - -
- {% endif %} -
-
-
- - -
-
-
-
- - -
+ id="end_date" + name="enddate" + placeholder="Filter run from end date" /> +
- - - -
+
+ + +
- {% endif %} -
- - - {% endblock %} + $(document).ready(function() { + $('#rec_sample_table').DataTable({ + dom: "Bfltirp", + responsive: true, + buttons: ['excel', 'csv'] + }); + }); + $(document).ready(function() { + $('#lab_sample_table').DataTable({ + dom: "Bfltirp", + responsive: true, + buttons: ['excel', 'csv'] + }); + }); + +{% endblock %} diff --git a/wetlab/utils/statistics.py b/wetlab/utils/statistics.py index 43eb9af9e..7b6f74879 100644 --- a/wetlab/utils/statistics.py +++ b/wetlab/utils/statistics.py @@ -599,6 +599,26 @@ def _recorded_samples_stats( return research_lab_statistics + def _lab_statistics( + lab_sample_objs: list, + other_lab_sample_objs: list, + research_lab_statistics: dict, + ) -> dict: + # Collect data for the recorded sample + research_lab_statistics["lab_samples"] = lab_sample_objs.values_list( + "sample_name", + "unique_sample_id", + "sample_type__sample_type", + "species__species_name", + "sample_state__sample_state_name", + "sample_project__sample_project_name", + "sample_user__username", + ) + research_lab_statistics["lab_table_heading"] = ( + wetlab.config.HEADING_STATISTICS_FOR_RECORDED_LAB_SAMPLE + ) + return research_lab_statistics + research_lab_statistics = {} # validate date format if start_date != "" and not wetlab.utils.common.check_valid_date_format(start_date): @@ -679,12 +699,19 @@ def _recorded_samples_stats( ) else: - lab_sample_objs = seq_sample_objs.filter(lab_request_id__exact=lab_name) + import pdb + + pdb.set_trace() + lab_sample_objs = rec_sample_objs.filter(lab_request__id__exact=lab_name) + other_lab_sample_objs = rec_sample_objs.exclude(lab_request__id__exact=lab_name) if len(lab_sample_objs) == 0: research_lab_statistics["ERROR"] = ( wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS ) return research_lab_statistics + research_lab_statistics = _lab_statistics( + lab_sample_objs, other_lab_sample_objs, research_lab_statistics + ) research_lab_statistics["type"] = "lab" return research_lab_statistics From 14805c19dc8ac5a97b74648ec77c7370730ca085 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 6 May 2024 17:46:47 +0200 Subject: [PATCH 060/446] included state samples in lab --- .../wetlab/stats_per_researcher.html | 8 +++--- wetlab/utils/statistics.py | 26 +++++++++++++++++++ 2 files changed, 30 insertions(+), 4 deletions(-) diff --git a/wetlab/templates/wetlab/stats_per_researcher.html b/wetlab/templates/wetlab/stats_per_researcher.html index 0bebcd498..9a12ef05c 100644 --- a/wetlab/templates/wetlab/stats_per_researcher.html +++ b/wetlab/templates/wetlab/stats_per_researcher.html @@ -299,12 +299,12 @@

Statistics from recorded samples

-
- {{ researcher_lab_statistics.research_q_30_graphic|safe }} +
+ {{ researcher_lab_statistics.lab_sample_vs_others_graphic|safe }}
-
- {{ researcher_lab_statistics.research_mean_graphic|safe }} +
+ {{ researcher_lab_statistics.lab_sample_states_graphic|safe }}
diff --git a/wetlab/utils/statistics.py b/wetlab/utils/statistics.py index 7b6f74879..ab4db0c6d 100644 --- a/wetlab/utils/statistics.py +++ b/wetlab/utils/statistics.py @@ -617,6 +617,32 @@ def _lab_statistics( research_lab_statistics["lab_table_heading"] = ( wetlab.config.HEADING_STATISTICS_FOR_RECORDED_LAB_SAMPLE ) + lab_sample_states = list( + lab_sample_objs.values( + sum_state=F("sample_state__sample_state_name") + ).annotate(value=Count("sample_name")) + ) + g_data = core.utils.graphics.preparation_graphic_data( + "Samples state", + "", + "", + "", + "ocean", + lab_sample_states, + "sum_state", + "value", + ) + research_lab_statistics["lab_sample_states_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "lab_sample_states_graph", + "600", + "300", + "lab_sample_states_chart", + "json", + g_data, + ).render() + ) return research_lab_statistics research_lab_statistics = {} From c375621aa250d01f6a54a2057d38dce5c89d341a Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 6 May 2024 18:34:14 +0200 Subject: [PATCH 061/446] included samples in lab vs others --- wetlab/utils/statistics.py | 22 +++++++++++++++++++--- 1 file changed, 19 insertions(+), 3 deletions(-) diff --git a/wetlab/utils/statistics.py b/wetlab/utils/statistics.py index ab4db0c6d..cbefd9fdc 100644 --- a/wetlab/utils/statistics.py +++ b/wetlab/utils/statistics.py @@ -617,6 +617,25 @@ def _lab_statistics( research_lab_statistics["lab_table_heading"] = ( wetlab.config.HEADING_STATISTICS_FOR_RECORDED_LAB_SAMPLE ) + # pie graph sequencing samples percentage in lab vs others + lab_sample_count = { + researcher_name: lab_sample_objs.count(), + "all researchers": other_lab_sample_objs.count(), + } + g_data = core.utils.graphics.preparation_3D_pie( + "Percentage of samples", "Research vs all", "ocean", lab_sample_count + ) + research_lab_statistics["lab_sample_vs_others_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "lab_sample_vs_others_graph", + "600", + "300", + "lab_sample_vs_others_chart", + "json", + g_data, + ).render() + ) lab_sample_states = list( lab_sample_objs.values( sum_state=F("sample_state__sample_state_name") @@ -725,9 +744,6 @@ def _lab_statistics( ) else: - import pdb - - pdb.set_trace() lab_sample_objs = rec_sample_objs.filter(lab_request__id__exact=lab_name) other_lab_sample_objs = rec_sample_objs.exclude(lab_request__id__exact=lab_name) if len(lab_sample_objs) == 0: From b9ae1288611927805c17f6e54b4b1d4c220e87e5 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 6 May 2024 18:44:59 +0200 Subject: [PATCH 062/446] litin --- wetlab/views.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/wetlab/views.py b/wetlab/views.py index 36c6e7528..c95640393 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -1627,7 +1627,9 @@ def stats_per_researcher(request): {"researcher_lab_statistics": researcher_lab_statistics}, ) else: - return render(request, "wetlab/stats_per_researcher.html",{ "lab_list": lab_list }) + return render( + request, "wetlab/stats_per_researcher.html", {"lab_list": lab_list} + ) @login_required From bad40b957532812b7b8895871be8a954949ae079 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 8 May 2024 13:22:28 +0200 Subject: [PATCH 063/446] Added the remining graphics for lob --- .../wetlab/stats_per_researcher.html | 244 ++++++++++-------- wetlab/utils/statistics.py | 105 ++++++++ 2 files changed, 241 insertions(+), 108 deletions(-) diff --git a/wetlab/templates/wetlab/stats_per_researcher.html b/wetlab/templates/wetlab/stats_per_researcher.html index 9a12ef05c..3ec3d62b9 100644 --- a/wetlab/templates/wetlab/stats_per_researcher.html +++ b/wetlab/templates/wetlab/stats_per_researcher.html @@ -307,138 +307,166 @@

Statistics from recorded samples

{{ researcher_lab_statistics.lab_sample_states_graphic|safe }}
+
+

Comparison of sample types used

+
+
+ {{ researcher_lab_statistics.lab_sample_type_graphic|safe }} +
+
+
+ {{ researcher_lab_statistics.lab_sample_type_vs_all_graphic|safe }} +
+
+
+

Comparison of species used

+
+
+ {{ researcher_lab_statistics.lab_samples_species_graphic|safe }} +
+
+
+ {{ researcher_lab_statistics.lab_samples_species_vs_all_graphic|safe }} +
+
+
+
+
+ {{ researcher_lab_statistics.lab_sample_states_graphic|safe }}
- -
-
-
-
-
-
-

Recorded samples from laboratory

-
-
- - - - {% for column in researcher_lab_statistics.lab_table_heading %}{% endfor %} - - - - {% for sample_data in researcher_lab_statistics.lab_samples %} - - {% for value in sample_data %}{% endfor %} - - {% endfor %} - -
{{ column }}
{{ value }}
-
-
+
+
+ +
+
+
+
+
+
+

Recorded samples from laboratory

+
+
+ + + + {% for column in researcher_lab_statistics.lab_table_heading %}{% endfor %} + + + + {% for sample_data in researcher_lab_statistics.lab_samples %} + + {% for value in sample_data %}{% endfor %} + + {% endfor %} + +
{{ column }}
{{ value }}
-
+
- {% else %} -
-
-
-
+
+
+ {% else %} +
+
+
+
+ {% if request.user|has_group:"WetlabManager" %} +
+

Statistics per Investigator or Laboratory

+
+ {% else %} +
+

Statistics per Investigator

+
+ {% endif %} +
+
+ {% csrf_token %} + {% if request.user|has_group:"WetlabManager" %} -
-

Statistics per Investigator or Laboratory

+
+ + +
+
+ +
{% else %} -
-

Statistics per Investigator

+
+ +
{% endif %} -
- - {% csrf_token %} - - {% if request.user|has_group:"WetlabManager" %} -
- - -
-
- - -
- {% else %} -
- - -
- {% endif %} -
-
-
- - -
-
-
-
- - -
-
+
+
+
+ +
- - - +
+
+
+ + +
+
-
+ + +
- {% endif %} +
- - + {% endblock %} diff --git a/wetlab/utils/statistics.py b/wetlab/utils/statistics.py index cbefd9fdc..a9e435f4b 100644 --- a/wetlab/utils/statistics.py +++ b/wetlab/utils/statistics.py @@ -662,6 +662,111 @@ def _lab_statistics( g_data, ).render() ) + lab_sample_type = list( + lab_sample_objs.values(sum_state=F("sample_type__sample_type")).annotate( + value=Count("sample_name") + ) + ) + g_data = core.utils.graphics.preparation_graphic_data( + "Samples type", + "", + "", + "", + "ocean", + lab_sample_type, + "sum_state", + "value", + ) + research_lab_statistics["lab_sample_type_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "lab_sample_type_graph", + "600", + "300", + "lab_sample_type_chart", + "json", + g_data, + ).render() + ) + other_lab_sample_type = list( + other_lab_sample_objs.values( + sum_state=F("sample_type__sample_type") + ).annotate(value=Count("sample_name")) + ) + g_data = core.utils.graphics.preparation_graphic_data( + "Samples type in other labs", + "", + "", + "", + "ocean", + other_lab_sample_type, + "sum_state", + "value", + ) + research_lab_statistics["lab_sample_type_vs_all_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "lab_sample_type_vs_all_graph", + "600", + "300", + "lab_sample_type_vs_all_chart", + "json", + g_data, + ).render() + ) + lab_species = list( + lab_sample_objs.values(sum_state=F("species__species_name")).annotate( + value=Count("sample_name") + ) + ) + g_data = core.utils.graphics.preparation_graphic_data( + "Samples species", + "", + "", + "", + "ocean", + lab_species, + "sum_state", + "value", + ) + research_lab_statistics["lab_samples_species_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "lab_samples_species_graph", + "600", + "300", + "lab_samples_species_chart", + "json", + g_data, + ).render() + ) + lab_species_vs_all = list( + other_lab_sample_objs.values(sum_state=F("species__species_name")).annotate( + value=Count("sample_name") + ) + ) + g_data = core.utils.graphics.preparation_graphic_data( + "Samples species in other labs", + "", + "", + "", + "ocean", + lab_species_vs_all, + "sum_state", + "value", + ) + research_lab_statistics["lab_samples_species_vs_all_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "lab_samples_species_vs_all_graph", + "600", + "300", + "lab_samples_species_vs_all_chart", + "json", + g_data, + ).render() + ) + # import pdb; pdb.set_trace() return research_lab_statistics research_lab_statistics = {} From 1a4348cd502820f5dadfcbfee5ac8d918f869522 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 8 May 2024 15:19:45 +0200 Subject: [PATCH 064/446] Solved issue #266 Too many emails are sent during crontab process --- wetlab/utils/common.py | 5 +---- wetlab/utils/crontab_process.py | 4 ++-- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/wetlab/utils/common.py b/wetlab/utils/common.py index 6ef77cec5..dd987b256 100644 --- a/wetlab/utils/common.py +++ b/wetlab/utils/common.py @@ -7,6 +7,7 @@ from datetime import datetime from logging.config import fileConfig +from datetime import datetime from django.contrib.auth.models import User from django.core.mail import send_mail from smb.SMBConnection import SMBConnection @@ -430,8 +431,6 @@ def logging_errors(string_text, showing_traceback, print_on_screen): logger.error("################################") logger.error("----------------- END ERROR --------------") if print_on_screen: - from datetime import datetime - print("********* ERROR **********") print(string_text) print(datetime.now().strftime("%Y-%m-%d %H:%M:%S")) @@ -454,8 +453,6 @@ def logging_warnings(string_text, print_on_screen): logger.warning(string_text) logger.warning("----------------- END WARNING --------------") if print_on_screen: - from datetime import datetime - print("******* WARNING ********") print(string_text) print(datetime.now().strftime("%Y-%m-%d %H:%M:%S")) diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index 0e6f9adca..08fadcd54 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -649,7 +649,7 @@ def fetch_remote_file(conn, run_dir, remote_file, local_file): string_message = ( "Unable to fetch the " + local_file + " file on folder : " + run_dir ) - wetlab.utils.common.logging_errors(string_message, True, False) + wetlab.utils.common.logging_warnings(string_message, True, False) os.remove(local_file) logger.debug( "%s : End function for fetching remote file with Exception", run_dir @@ -811,7 +811,7 @@ def get_remote_sample_sheet(conn, new_run, experiment_name): logger.info("%s : Sucessfully fetch of Sample Sheet file", experiment_name) except Exception: error_message = "Unable to fetch Sample Sheet file for folder :" + new_run - wetlab.utils.common.logging_errors(error_message, True, False) + wetlab.utils.common.logging_warnings(error_message, False) logger.debug("%s : End function get_remote_sample_sheet", experiment_name) return None From c4d99090a44562b9834ffdeb66f7be4c1d0eb7a9 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 8 May 2024 15:22:06 +0200 Subject: [PATCH 065/446] corrected litin --- wetlab/utils/common.py | 1 - 1 file changed, 1 deletion(-) diff --git a/wetlab/utils/common.py b/wetlab/utils/common.py index dd987b256..b779a8e4a 100644 --- a/wetlab/utils/common.py +++ b/wetlab/utils/common.py @@ -7,7 +7,6 @@ from datetime import datetime from logging.config import fileConfig -from datetime import datetime from django.contrib.auth.models import User from django.core.mail import send_mail from smb.SMBConnection import SMBConnection From 8a56fc5445de6b6e5d87be0ba09d97669cb63614 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 8 May 2024 15:56:19 +0200 Subject: [PATCH 066/446] included additional field at RunStates --- wetlab/models.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/wetlab/models.py b/wetlab/models.py index 4bc090d4e..ec39b5f77 100644 --- a/wetlab/models.py +++ b/wetlab/models.py @@ -136,6 +136,9 @@ def __str__(self): class RunStates(models.Model): run_state_name = models.CharField(max_length=50) + state_display = models.CharField(max_length=80, null=True, blank=True) + description = models.CharField(max_length=255, null=True, blank=True) + show_in_stats = models.BooleanField(default=False) class Meta: db_table = "wetlab_run_states" From b59dc3a9079d649293ff2faf11ed0f33fff8e5b9 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 17 May 2024 09:04:57 +0200 Subject: [PATCH 067/446] Set the cancelled state when run is cancelled --- wetlab/utils/crontab_update_run.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index b6d4db9d8..a40690e8f 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -647,6 +647,8 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): experiment_name, ) elif run_status == "cancelled": + run_process_obj.set_run_state("cancelled") + run_process_obj.set_run_completion_date(run_completion_date) wetlab.utils.crontab_process.handling_errors_in_run(experiment_name, 34) string_message = experiment_name + "was cancelled on the sequencer" wetlab.utils.common.logging_warnings(string_message, True) From 061d6025bec8381a657871b4aa610dac8c6d624c Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 17 May 2024 09:05:34 +0200 Subject: [PATCH 068/446] change Pre-Recorded state to snake style --- conf/first_install_tables.json | 5 ++++- test/test_data.json | 2 +- wetlab/cron.py | 2 +- wetlab/utils/fetch_info.py | 4 ++-- wetlab/utils/run.py | 2 +- wetlab/views.py | 10 +++++----- 6 files changed, 14 insertions(+), 11 deletions(-) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index dc38574f8..d6f564dee 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -1512,7 +1512,10 @@ "model": "wetlab.runstates", "pk": 1, "fields": { - "run_state_name": "Pre-Recorded" + "run_state_name": "pre_recorded", + "state_display": "Pre Recorded", + "description": "Run name is defined but pending for input data.", + "show_in_stats": false } }, { diff --git a/test/test_data.json b/test/test_data.json index 4f63aca3e..9758adeda 100644 --- a/test/test_data.json +++ b/test/test_data.json @@ -9158,7 +9158,7 @@ "model": "wetlab.runstates", "pk": 1, "fields": { - "run_state_name": "Pre-Recorded" + "run_state_name": "pre_recorded" } }, { diff --git a/wetlab/cron.py b/wetlab/cron.py index a7190a837..124411f7d 100644 --- a/wetlab/cron.py +++ b/wetlab/cron.py @@ -113,7 +113,7 @@ def delete_invalid_run(): days=int(wetlab.config.RETENTION_TIME) ) run_found_for_deleting = wetlab.models.RunProcess.objects.filter( - state__run_state_name="Pre-Recorded", generate_dat__lte=date_for_removing + state__run_state_name="pre_recorded", generate_dat__lte=date_for_removing ) for run_found in run_found_for_deleting: diff --git a/wetlab/utils/fetch_info.py b/wetlab/utils/fetch_info.py index e0dc69d46..36adcfd88 100644 --- a/wetlab/utils/fetch_info.py +++ b/wetlab/utils/fetch_info.py @@ -577,7 +577,7 @@ def get_information_for_incompleted_run(): data.append(str((today - run_date).days)) run_information["cancelled"].append(data) - exclude_state = ["Recorded", "Error", "Cancelled", "Completed", "Pre-Recorded"] + exclude_state = ["Recorded", "Error", "Cancelled", "Completed", "pre_recorded"] if ( wetlab.models.RunProcess.objects.all() @@ -677,7 +677,7 @@ def get_information_run(run_object): "Processing Demultiplexing", "Processing test", "None", - "Pre-Recorded", + "pre_recorded", "Processing Metrics", ] if run_state in no_valid_information: diff --git a/wetlab/utils/run.py b/wetlab/utils/run.py index 3bcaa20e7..d666c385d 100644 --- a/wetlab/utils/run.py +++ b/wetlab/utils/run.py @@ -124,7 +124,7 @@ def create_run_in_pre_recorded_and_get_data_for_confirmation(form_data, user_obj new_run_obj = wetlab.models.RunProcess( run_name=form_data["experimentName"], sample_sheet="", - state=wetlab.models.RunStates.objects.get(run_state_name__exact="Pre-Recorded"), + state=wetlab.models.RunStates.objects.get(run_state_name__exact="pre_recorded"), center_requested_by=center_requested_by, ) new_run_obj.save() diff --git a/wetlab/views.py b/wetlab/views.py index c95640393..ecf5e425f 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -377,12 +377,12 @@ def create_nextseq_run(request): wetlab.models.RunProcess.objects.filter(run_name__iexact=run_name) ).exists(): if wetlab.models.RunProcess.objects.filter( - run_name__iexact=run_name, state__run_state_name__exact="Pre-Recorded" + run_name__iexact=run_name, state__run_state_name__exact="pre_recorded" ).exists(): # Delete the Sample Sheet file and the row in database delete_run_objs = wetlab.models.RunProcess.objects.filter( run_name__iexact=run_name, - state__run_state_name__exact="Pre-Recorded", + state__run_state_name__exact="pre_recorded", ) for delete_run in delete_run_objs: # sample_sheet_file = delete_run.get_sample_file() @@ -456,7 +456,7 @@ def create_nextseq_run(request): # Once the information looks good. it will be stores in runProcess and projects table - # store data in runProcess table, run is in pre-recorded state + # store data in runProcess table, run is in pre_recorded state center_requested_id = django_utils.models.Profile.objects.get( profile_user_id=request.user ).profile_center.id @@ -467,7 +467,7 @@ def create_nextseq_run(request): run_name=run_name, sample_sheet=file_name, state=wetlab.models.RunStates.objects.get( - run_state_name__exact="Pre-Recorded" + run_state_name__exact="pre_recorded" ), center_requested_by=center_requested_by, ) @@ -3800,7 +3800,7 @@ def create_new_run(request): elif request.method == "POST" and request.POST["action"] == "storeDataNewRun": run_obj = wetlab.utils.run.get_run_obj_from_id(request.POST["run_process_id"]) - if run_obj.get_state() != "Pre-Recorded": + if run_obj.get_state() != "pre_recorded": exp_name = run_obj.get_run_name() error_message = str(exp_name + wetlab.config.ERROR_RUN_NAME_CREATED_ALREADY) display_pools_for_run = wetlab.utils.run.display_available_pools() From c7613117a9149231e84ac1615f83636842f7d2cc Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 17 May 2024 10:16:20 +0200 Subject: [PATCH 069/446] Fixed bug after changed the relation of library_pool-runprocess to many to many --- wetlab/utils/run.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/wetlab/utils/run.py b/wetlab/utils/run.py index d666c385d..5387b88a5 100644 --- a/wetlab/utils/run.py +++ b/wetlab/utils/run.py @@ -767,11 +767,15 @@ def get_available_pools_for_run(): pools_to_update """ pools_to_update = {} + import pdb + + pdb.set_trace() + # get the pools that were selected if wetlab.models.LibraryPool.objects.filter( - pool_state__pool_state__exact="Selected", run_process_id=None + pool_state__pool_state__exact="Selected" ).exists(): pool_objs = wetlab.models.LibraryPool.objects.filter( - pool_state__pool_state__exact="Selected", run_process_id=None + pool_state__pool_state__exact="Selected" ).order_by("platform") pools_to_update["pools_available"] = {} for pool_obj in pool_objs: @@ -784,14 +788,14 @@ def get_available_pools_for_run(): wetlab.models.LibraryPool.objects.filter( pool_state__pool_state__exact="Selected" ) - .exclude(run_process_id=None) + .exclude(runprocess=None) .exists() ): pools_to_update["defined_runs"] = ( wetlab.models.LibraryPool.objects.filter( pool_state__pool_state__exact="Selected" ) - .exclude(run_process_id=None) + .exclude(runprocess=None) .order_by("run_process_id") ) From 770b0b19bd686a90dbc3ea896f2102ff77b8e91c Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 17 May 2024 21:05:20 +0200 Subject: [PATCH 070/446] Update initial tables with run states --- conf/first_install_tables.json | 55 +++++++++++++++++++++++++++------- wetlab/admin.py | 2 +- 2 files changed, 45 insertions(+), 12 deletions(-) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index d6f564dee..64b93754b 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -1522,77 +1522,110 @@ "model": "wetlab.runstates", "pk": 2, "fields": { - "run_state_name": "Recorded" + "run_state_name": "recorded", + "state_display": "Recorded", + "description": "Run name is defined.", + "show_in_stats": true } }, { "model": "wetlab.runstates", "pk": 3, "fields": { - "run_state_name": "Sample Sent" + "run_state_name": "sample_sent", + "state_display": "Sample Sent", + "description": "Run has copied sample sheet on remote server.", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 4, "fields": { - "run_state_name": "Processing Run" + "run_state_name": "processing_run", + "state_display": "Processing Run", + "description": "Run is handled on the sequencer.", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 5, "fields": { - "run_state_name": "Processed Run" + "run_state_name": "processed_run", + "state_display": "Processed Run", + "description": "Run is already processed on sequencer.", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 6, "fields": { - "run_state_name": "Processing Bcl2fastq" + "run_state_name": "processing_bcl2fastq", + "state_display": "Processing Bcl2fastq", + "description": "Bcl2fastq is running", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 7, "fields": { - "run_state_name": "Processed Bcl2fastq" + "run_state_name": "processed_bcl2fastq", + "state_display": "Processed Bcl2fastq", + "description": "Bcl2fastq already completed", + "show_in_stats": true } }, { "model": "wetlab.runstates", "pk": 8, "fields": { - "run_state_name": "Completed" + "run_state_name": "completed", + "state_display": "Completed", + "description": "Run is completed and all processes are finished.", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 9, "fields": { - "run_state_name": "Cancelled" + "run_state_name": "cancelled", + "state_display": "Cancelled", + "description": "Run was manually cancelled while running on sequencer.", + "show_in_stats": true } }, { "model": "wetlab.runstates", "pk": 10, "fields": { - "run_state_name": "Error" + "run_state_name": "error", + "state_display": "Error", + "description": "There was an issue while processing the run", + "show_in_stats": true } }, { "model": "wetlab.runstates", "pk": 11, "fields": { - "run_state_name": "Processing Metrics" + "run_state_name": "spare_1", + "state_display": "", + "description": "", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 12, "fields": { - "run_state_name": "Processing Demultiplexing" + "run_state_name": "spare_2", + "state_display": "", + "description": "", + "show_in_stats": false } }, { diff --git a/wetlab/admin.py b/wetlab/admin.py index f1477a3bb..5b4b16cb7 100644 --- a/wetlab/admin.py +++ b/wetlab/admin.py @@ -69,7 +69,7 @@ class RunErrorsAdmin(admin.ModelAdmin): class RunStatesAdmin(admin.ModelAdmin): - list_display = ("run_state_name",) + list_display = ["run_state_name", "state_display", "description"] class RunningParametersAdmin(admin.ModelAdmin): From cf4749a38d15f60f61633f9a3ba8d53c527d0346 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 17 May 2024 22:06:43 +0200 Subject: [PATCH 071/446] Display error when sample sheet has an invalid heading --- wetlab/config.py | 2 ++ .../templates/wetlab/create_next_seq_run.html | 14 +++++++++ wetlab/utils/samplesheet.py | 31 ++++++++++++++----- wetlab/views.py | 14 +++------ 4 files changed, 45 insertions(+), 16 deletions(-) diff --git a/wetlab/config.py b/wetlab/config.py index f76259039..cffc93887 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -662,6 +662,8 @@ ERROR_SAMPLE_SHEET_BOTH_INSTRUMENT_AND_INDEX_NOT_INCLUDED = [ "Sample Sheet does not have Instrument type neither Index Adapters" ] +ERROR_SAMPLE_SHEET_HAS_INVALID_HEADING = ["Sample sheet does not have a valid sample heading"] +ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_PROJECTS = ["Sample sheet does not have Projects"] ERROR_SAMPLE_SHEET_USER_IS_NOT_DEFINED = ["User in sample sheet is not defined"] ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_DESCRIPTION_FIELD = [ "Sample sheet does not have Description column " diff --git a/wetlab/templates/wetlab/create_next_seq_run.html b/wetlab/templates/wetlab/create_next_seq_run.html index 03d73dd62..a69bde047 100644 --- a/wetlab/templates/wetlab/create_next_seq_run.html +++ b/wetlab/templates/wetlab/create_next_seq_run.html @@ -5,6 +5,20 @@ {% include 'registration/login_inline.html' %}
+ {% if error_message %} +
+
+
+
+

Unable to accept your request

+
+
+ {% for error in error_message %}

{{ error }}

{% endfor %} +
+
+
+
+ {% endif %} {% if get_user_names %}
diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index 365391594..d921cbd40 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -361,8 +361,17 @@ def get_sample_with_user_owner(sample_sheet_path): return sample_user -def get_projects_in_run(in_file): - header_found = 0 +def get_projects_in_run(in_file: str)-> dict: + """Funtion to check if the sample sheet has a valid heading. On valid file + get project names and the user names from description column + + Args: + in_file (str): path to the sample sheet + + Returns: + dict: dictionary with the projects or error message + """ + header_found = False projects = {} fh = open(in_file, "r") for line in fh: @@ -371,10 +380,13 @@ def get_projects_in_run(in_file): continue found_header = re.search("^Sample_ID,Sample_Name", line) if found_header: - header_found = 1 - # found the index for projects - p_index = line.split(",").index("Sample_Project") - description_index = line.split(",").index("Description") + # found the index for projects and description + if not "Sample_Project" and not "Description" in line: + break + split_line = line.split(",") + p_index = split_line.index("Sample_Project") + description_index = split_line(",").index("Description") + header_found = True continue if header_found: # ignore the empty lines separated by commas @@ -384,7 +396,12 @@ def get_projects_in_run(in_file): # store the project name and the user name (Description) inside projects dict projects[line.split(",")[p_index]] = line.split(",")[description_index] fh.close() - return projects + if not found_header: + return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_HAS_INVALID_HEADING} + if not projects: + return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_PROJECTS} + + return {"projects" : projects} def get_index_library_name(in_file): diff --git a/wetlab/views.py b/wetlab/views.py index ecf5e425f..741d48729 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -408,7 +408,7 @@ def create_nextseq_run(request): return render( request, "wetlab/create_next_seq_run.html", - {"error_message": "Run Name is already used. "}, + {"error_message": ["Run Name is already used. "]}, ) # Fetch from the Sample Sheet file the projects included in @@ -416,16 +416,13 @@ def create_nextseq_run(request): # colunms are found project_list = wetlab.utils.samplesheet.get_projects_in_run(stored_file) - - if len(project_list) == 0: + if "ERROR" in project_list: # delete sample sheet file fs.delete(file_name) return render( request, "wetlab/create_next_seq_run.html", - { - "error_message": "Sample Sheet does not contain Sample project and/or Description fields" - }, + {"error_message": project_list["ERROR"]}, ) # Check if the projects are already defined on database. @@ -476,7 +473,6 @@ def create_nextseq_run(request): # create new project tables based on the project involved in the run and # include the project information in projects variable to build the new FORM - run_info_values = {} run_info_values["experiment_name"] = experiment_name run_info_values["index_library_name"] = index_library_name @@ -595,7 +591,7 @@ def create_nextseq_run(request): ) update_info_proj.save() results.append(["runname", experiment_name]) - run_p.set_run_state("Recorded") + run_p.set_run_state("recorded") sample_sheet_lines = wetlab.utils.samplesheet.read_all_lines_in_sample_sheet( in_file ) @@ -3830,7 +3826,7 @@ def create_new_run(request): }, ) - run_obj.set_run_state("Recorded") + run_obj.set_run_state("recorded") wetlab.utils.run.store_confirmation_sample_sheet(run_data) # update the sample state for each one in the run From 3e2ec9189a2718d0283501c0da1213a2f49b25fa Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 17 May 2024 22:11:00 +0200 Subject: [PATCH 072/446] fixing litin --- wetlab/config.py | 4 +++- wetlab/utils/samplesheet.py | 8 ++++---- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/wetlab/config.py b/wetlab/config.py index cffc93887..2232732d2 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -662,7 +662,9 @@ ERROR_SAMPLE_SHEET_BOTH_INSTRUMENT_AND_INDEX_NOT_INCLUDED = [ "Sample Sheet does not have Instrument type neither Index Adapters" ] -ERROR_SAMPLE_SHEET_HAS_INVALID_HEADING = ["Sample sheet does not have a valid sample heading"] +ERROR_SAMPLE_SHEET_HAS_INVALID_HEADING = [ + "Sample sheet does not have a valid sample heading" +] ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_PROJECTS = ["Sample sheet does not have Projects"] ERROR_SAMPLE_SHEET_USER_IS_NOT_DEFINED = ["User in sample sheet is not defined"] ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_DESCRIPTION_FIELD = [ diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index d921cbd40..4476d8d4a 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -361,7 +361,7 @@ def get_sample_with_user_owner(sample_sheet_path): return sample_user -def get_projects_in_run(in_file: str)-> dict: +def get_projects_in_run(in_file: str) -> dict: """Funtion to check if the sample sheet has a valid heading. On valid file get project names and the user names from description column @@ -370,7 +370,7 @@ def get_projects_in_run(in_file: str)-> dict: Returns: dict: dictionary with the projects or error message - """ + """ header_found = False projects = {} fh = open(in_file, "r") @@ -381,7 +381,7 @@ def get_projects_in_run(in_file: str)-> dict: found_header = re.search("^Sample_ID,Sample_Name", line) if found_header: # found the index for projects and description - if not "Sample_Project" and not "Description" in line: + if not "Sample_Project" and "Description" not in line: break split_line = line.split(",") p_index = split_line.index("Sample_Project") @@ -401,7 +401,7 @@ def get_projects_in_run(in_file: str)-> dict: if not projects: return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_PROJECTS} - return {"projects" : projects} + return {"projects": projects} def get_index_library_name(in_file): From 5b737dcb2a00071ed8b009fe10f8d4a34f0c2864 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 17 May 2024 23:28:43 +0200 Subject: [PATCH 073/446] Do not allow to import sample sheet if not library kits are defined --- test/test_data.json | 2 +- wetlab/admin.py | 7 + wetlab/config.py | 1 + wetlab/models.py | 2 +- .../templates/wetlab/create_next_seq_run.html | 427 +++++++++++------- wetlab/utils/crontab_update_run.py | 8 +- wetlab/utils/fetch_info.py | 12 +- wetlab/utils/samplesheet.py | 50 +- wetlab/views.py | 14 +- 9 files changed, 315 insertions(+), 208 deletions(-) diff --git a/test/test_data.json b/test/test_data.json index 9758adeda..df8d8b7b0 100644 --- a/test/test_data.json +++ b/test/test_data.json @@ -9165,7 +9165,7 @@ "model": "wetlab.runstates", "pk": 2, "fields": { - "run_state_name": "Recorded" + "run_state_name": "recorded" } }, { diff --git a/wetlab/admin.py b/wetlab/admin.py index 5b4b16cb7..647e5c54e 100644 --- a/wetlab/admin.py +++ b/wetlab/admin.py @@ -60,6 +60,12 @@ class AdditionaKitsLibraryPreparationAdmin(admin.ModelAdmin): list_display = ["kit_name", "protocol_id", "commercial_kit_id"] +class LibraryKitAdmin(admin.ModelAdmin): + list_display = [ + "library_name", + ] + + class AdditionalUserLotKitAdmin(admin.ModelAdmin): list_display = ["lib_prep_id", "additional_lot_kits", "user_lot_kit_id"] @@ -290,6 +296,7 @@ class RunConfigurationTestAdmin(admin.ModelAdmin): admin.site.register(wetlab.models.RunErrors, RunErrorsAdmin) admin.site.register(wetlab.models.RunStates, RunStatesAdmin) admin.site.register(wetlab.models.LibPrepareStates, StatesForLibraryPreparationAdmin) +admin.site.register(wetlab.models.LibraryKit, LibraryKitAdmin) admin.site.register(wetlab.models.PoolStates, StatesForPoolAdmin) admin.site.register(wetlab.models.SamplesInProject, SamplesInProjectAdmin) admin.site.register(wetlab.models.StatsRunSummary, StatsRunSummaryAdmin) diff --git a/wetlab/config.py b/wetlab/config.py index 2232732d2..d70256475 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -164,6 +164,7 @@ "[Settings]", "[I7]", ] +ERROR_NO_LIBRARY_KIT_DEFINED = ["Library Kits are not defined yet"] ############################################################## MIGRATION_DIRECTORY_FILES = "wetlab/BaseSpaceMigrationFiles/" diff --git a/wetlab/models.py b/wetlab/models.py index ec39b5f77..86f15290d 100644 --- a/wetlab/models.py +++ b/wetlab/models.py @@ -152,7 +152,7 @@ def get_run_state_name(self): class RunProcessManager(models.Manager): def create_new_run_from_crontab(self, run_data): - run_state = RunStates.objects.get(run_state_name__exact="Recorded") + run_state = RunStates.objects.get(run_state_name__exact="recorded") new_run = self.create(state=run_state, run_name=run_data["experiment_name"]) return new_run diff --git a/wetlab/templates/wetlab/create_next_seq_run.html b/wetlab/templates/wetlab/create_next_seq_run.html index a69bde047..ee5c76365 100644 --- a/wetlab/templates/wetlab/create_next_seq_run.html +++ b/wetlab/templates/wetlab/create_next_seq_run.html @@ -1,232 +1,321 @@ {% extends "core/base.html" %} {% load static %} {% block content %} -{% include "wetlab/menu.html" %} -{% include 'registration/login_inline.html' %} - -
- {% if error_message %} -
-
-
-
-

Unable to accept your request

-
-
- {% for error in error_message %}

{{ error }}

{% endfor %} + {% include "wetlab/menu.html" %} + {% include 'registration/login_inline.html' %} + +
+ {% if error_message %} +
+
+
+
+

Unable to accept your request

+
+
+ {% for error in error_message %}

{{ error }}

{% endfor %} +
-
- {% endif %} - {% if get_user_names %} -
-
-
-
-

Run creation progress

-
-

Fill the user name and the Used Library Kit for each project in the run {{ get_user_names.experiment_name }}

-

This is the second, and the last, FORM that user need to fill down to have the information about the run

-

Once the name of the user and the libray Kit used in the run, were filled and submited, the next page will show the successful run creation

+ {% endif %} + {% if get_user_names %} +
+
+
+
+
+

Run creation progress

+
+
+

+ Fill the user name and the Used Library Kit for each project in the run {{ get_user_names.experiment_name }} +

+

This is the second, and the last, FORM that user need to fill down to have the information about the run

+

+ Once the name of the user and the libray Kit used in the run, were filled and submited, the next page will show the successful run creation +

+
    -
  1. Upload Sample Sheet
  2. Assign Library Kit
  3. Show Results
    4. +
  4. + Upload Sample Sheet +
    5. + +
  5. + Assign Library Kit +
    6. + +
  6. + Show Results +
-
-
-
- -
-
-
-
-
Form to upload the Sample Sheet file. Run Parameters definition
-
-
- {% csrf_token %} - - +
+
+ +
+
+
+
+
Form to upload the Sample Sheet file. Run Parameters definition
+
+ + {% csrf_token %} + +
- +
- +
- +
- +
{% for key, values in get_user_names.projects_user %}

Project name assigned to run :

-

{{ key }}

- -
- +

{{ key }}

+ +
+
- +
- +
- +
- +
{% endfor %}
- - - + + +
-
-
-
-
-
Notes for user validation
-
+
+
+
+
Notes for user validation
+

The following information have been collected from the Sample Sheet uploaded previously.

It contains the userid information. Correct in the user name field if this information need to be changed

Write down the Library kit used for each project

-

Submit button is disabled if any of the user names is not previoulsy defined in database

+

+ Submit button is disabled if any of the user names is not previoulsy defined in database +

-
-
-
+
+
+
-
- - - - - + {% elif completed_form %} - {% for key, val in completed_form%} + {% for key, val in completed_form %} {% if key == "runname" %}
-
+
    -
  1. Upload Sample Sheet
  2. Assign Library Kit
  3. Show Results
    4. +
  4. + Upload Sample Sheet +
    5. + +
  5. + Assign Library Kit +
    6. + +
  6. + Show Results +
-
-
+
+
-
Run configuration have been sucessfully stored
-
-

All the required information is stored now on database.

-

For the run name : {{ val }}

+
+
Run configuration have been sucessfully stored
+
+
+

All the required information is stored now on database.

+

+ For the run name : {{ val }} +

-
+
{% endif %} {% endfor %} {% else %} - -
-
-
    -
  1. Upload Sample Sheet
  2. Assign Library Kit
  3. Show Results
    4. -
-
-
-
-
-

This FORM will be used to generated the input file that BaseSpace requires to execute the run

+ +
+
+
    +
  1. + Upload Sample Sheet +
    2. + +
  2. + Assign Library Kit +
    3. + +
  3. + Show Results +
    4. +
+
-
-
-
-
-
Form to upload the Sample Sheet file
-
-
- {% csrf_token %} - -
- -
- +
+

+ This FORM will be used to generated the input file that BaseSpace requires to execute the run +

+
+
+
+
+
+
+
Form to upload the Sample Sheet file
+
+ + {% csrf_token %} + +
+ +
+ +
-
-

Fields marked with * are mandatory

- - -
+

+ Fields marked with * are mandatory +

+ + +
+
+
+
+
+
Form to upload the Sample Sheet file
+
+

This Form is used to upload the Sample Sheet generated by Illumina Experience Manager tool.

+

Guide for Sample Sheet creation and download the IEM tool can be found at illumina Web page.

+

+ Click here for getting this information. +

+
+
-
-
-
Form to upload the Sample Sheet file
-
-

This Form is used to upload the Sample Sheet generated by Illumina Experience Manager tool.

-

Guide for Sample Sheet creation and download the IEM tool can be found at illumina Web page.

-

Click here for getting this information.

-
-
-
-
- - - {% endif %} -
+ +
+ {% endif %} +
{% endblock %} diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index a40690e8f..cadf7d603 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -228,7 +228,7 @@ def search_update_new_runs(request_reason): logger.debug( "%s : Found the experiment name called : %s", new_run, experiment_name ) - exclude_states = ["Error", "Recorded"] + exclude_states = ["Error", "recorded"] if ( wetlab.models.RunProcess.objects.filter(run_name__exact=experiment_name) .exclude(state__run_state_name__in=exclude_states) @@ -417,9 +417,9 @@ def handle_not_completed_run(): runs_to_handle = {} # state_list_be_processed = ['Sample Sent','Processing Run','Processed Run', 'Processing Bcl2fastq', - # 'Processed Bcl2fastq', 'Recorded'] + # 'Processed Bcl2fastq', 'recorded'] state_list_be_processed = [ - "Recorded", + "recorded", "Sample Sent", "Processing Run", "Processed Run", @@ -442,7 +442,7 @@ def handle_not_completed_run(): for state in runs_to_handle.keys(): logger.info("Start processing the run found for state %s", state) - if state == "Recorded": + if state == "recorded": manage_run_in_recorded_state(conn, runs_to_handle[state]) elif state == "Sample Sent": diff --git a/wetlab/utils/fetch_info.py b/wetlab/utils/fetch_info.py index 36adcfd88..306276e3e 100644 --- a/wetlab/utils/fetch_info.py +++ b/wetlab/utils/fetch_info.py @@ -207,7 +207,7 @@ def graphics_state(state): """ state_list = [ "Error", - "Recorded", + "recorded", "Sample Sent", "Processing Run", "Processed Run", @@ -512,7 +512,7 @@ def get_information_for_incompleted_run(): """ Description: The function will get the information from the runs that are incompleted. - It creates a 4 groups. Recorded, Error, Canceled and rest of the states. + It creates a 4 groups. recorded, Error, Canceled and rest of the states. Creates a pie graphic Functions: graphic_3D_pie # located at wetlab/utils/stats_graphics @@ -522,11 +522,11 @@ def get_information_for_incompleted_run(): run_information = {} today = datetime.today().date() if wetlab.models.RunProcess.objects.filter( - state__run_state_name="Recorded" + state__run_state_name="recorded" ).exists(): run_information["recorded"] = [] run_objs = wetlab.models.RunProcess.objects.filter( - state__run_state_name="Recorded" + state__run_state_name="recorded" ).order_by("run_name") for run_obj in run_objs: data = [] @@ -577,7 +577,7 @@ def get_information_for_incompleted_run(): data.append(str((today - run_date).days)) run_information["cancelled"].append(data) - exclude_state = ["Recorded", "Error", "Cancelled", "Completed", "pre_recorded"] + exclude_state = ["recorded", "Error", "Cancelled", "Completed", "pre_recorded"] if ( wetlab.models.RunProcess.objects.all() @@ -685,7 +685,7 @@ def get_information_run(run_object): return info_dict # allow to change the run name in case that run state was recorded or Sample Sent - if run_state == "Recorded" or run_state == "Sample Sent": + if run_state == "recorded" or run_state == "Sample Sent": info_dict["change_run_name"] = [ [run_object.get_run_name(), run_object.get_run_id()] ] diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index 4476d8d4a..ca4c7b900 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -373,35 +373,37 @@ def get_projects_in_run(in_file: str) -> dict: """ header_found = False projects = {} - fh = open(in_file, "r") - for line in fh: - line = line.rstrip() - if line == "": - continue - found_header = re.search("^Sample_ID,Sample_Name", line) - if found_header: - # found the index for projects and description - if not "Sample_Project" and "Description" not in line: - break - split_line = line.split(",") - p_index = split_line.index("Sample_Project") - description_index = split_line(",").index("Description") - header_found = True - continue - if header_found: - # ignore the empty lines separated by commas - valid_line = re.search("^\w+", line) - if not valid_line: + with open(in_file, "r") as fh: + for line in fh: + line = line.rstrip() + if line == "": continue - # store the project name and the user name (Description) inside projects dict - projects[line.split(",")[p_index]] = line.split(",")[description_index] - fh.close() - if not found_header: + if not header_found: + header = re.search("^Sample_ID,Sample_Name", line) + if header: + # match line with the header + # look for projects and description indexes + if not "Sample_Project" and "Description" not in line: + break + split_line = line.split(",") + p_index = split_line.index("Sample_Project") + description_index = split_line.index("Description") + header_found = True + continue + else: + # ignore the empty lines separated by commas + valid_line = re.search("^\w+", line) + if not valid_line: + continue + # store the project name and the user name (Description) inside projects dict + projects[line.split(",")[p_index]] = line.split(",")[description_index] + + if not header_found: return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_HAS_INVALID_HEADING} if not projects: return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_PROJECTS} - return {"projects": projects} + return projects def get_index_library_name(in_file): diff --git a/wetlab/views.py b/wetlab/views.py index 741d48729..783bfb4c6 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -427,7 +427,6 @@ def create_nextseq_run(request): # Check if the projects are already defined on database. # Error page is showed if projects are already defined on database - project_already_defined = [] project_in_several_runs = wetlab.utils.common.get_configuration_value( "PROJECTS_ALLOWED_IN_MULTIPLE_RUNS" @@ -448,7 +447,7 @@ def create_nextseq_run(request): return render( request, "wetlab/create_next_seq_run.html", - {"error_message": display_project + " already defined"}, + {"error_message": [display_project, " already defined"]}, ) # Once the information looks good. it will be stores in runProcess and projects table @@ -607,7 +606,16 @@ def create_nextseq_run(request): "wetlab/create_next_seq_run.html", {"completed_form": results}, ) - + # check if library kit is already defined + if len(wetlab.models.LibraryKit.objects.all()) == 0: + return render( + request, + "wetlab/create_next_seq_run.html", + { + "error_message": wetlab.config.ERROR_NO_LIBRARY_KIT_DEFINED, + "disable_submit_form": True, + }, + ) return render(request, "wetlab/create_next_seq_run.html") From 02e02c5105d83c7079ec465fe2afdfa9470c7fbe Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 18 May 2024 09:30:46 +0200 Subject: [PATCH 074/446] Changes in run state values from issue #260 --- test/test_data.json | 60 ++++++++++++++++++++++++------ wetlab/utils/crontab_update_run.py | 30 +++++++-------- wetlab/utils/fetch_info.py | 26 ++++++------- wetlab/utils/run.py | 2 - wetlab/utils/test_conf.py | 28 +++++++------- 5 files changed, 89 insertions(+), 57 deletions(-) diff --git a/test/test_data.json b/test/test_data.json index df8d8b7b0..edc6466b3 100644 --- a/test/test_data.json +++ b/test/test_data.json @@ -9158,84 +9158,120 @@ "model": "wetlab.runstates", "pk": 1, "fields": { - "run_state_name": "pre_recorded" + "run_state_name": "pre_recorded", + "state_display": "Pre Recorded", + "description": "Run name is defined but pending for input data.", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 2, "fields": { - "run_state_name": "recorded" + "run_state_name": "recorded", + "state_display": "Recorded", + "description": "Run name is defined.", + "show_in_stats": true } }, { "model": "wetlab.runstates", "pk": 3, "fields": { - "run_state_name": "Sample Sent" + "run_state_name": "sample_sent", + "state_display": "Sample Sent", + "description": "Run has copied sample sheet on remote server.", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 4, "fields": { - "run_state_name": "Processing Run" + "run_state_name": "processing_run", + "state_display": "Processing Run", + "description": "Run is handled on the sequencer.", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 5, "fields": { - "run_state_name": "Processed Run" + "run_state_name": "processed_run", + "state_display": "Processed Run", + "description": "Run is already processed on sequencer.", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 6, "fields": { - "run_state_name": "Processing Bcl2fastq" + "run_state_name": "processing_bcl2fastq", + "state_display": "Processing Bcl2fastq", + "description": "Bcl2fastq is running", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 7, "fields": { - "run_state_name": "Processed Bcl2fastq" + "run_state_name": "processed_bcl2fastq", + "state_display": "Processed Bcl2fastq", + "description": "Bcl2fastq already completed", + "show_in_stats": true } }, { "model": "wetlab.runstates", "pk": 8, "fields": { - "run_state_name": "Completed" + "run_state_name": "completed", + "state_display": "Completed", + "description": "Run is completed and all processes are finished.", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 9, "fields": { - "run_state_name": "Cancelled" + "run_state_name": "cancelled", + "state_display": "Cancelled", + "description": "Run was manually cancelled while running on sequencer.", + "show_in_stats": true } }, { "model": "wetlab.runstates", "pk": 10, "fields": { - "run_state_name": "Error" + "run_state_name": "error", + "state_display": "Error", + "description": "There was an issue while processing the run", + "show_in_stats": true } }, { "model": "wetlab.runstates", "pk": 11, "fields": { - "run_state_name": "Processing Metrics" + "run_state_name": "spare_1", + "state_display": "", + "description": "", + "show_in_stats": false } }, { "model": "wetlab.runstates", "pk": 12, "fields": { - "run_state_name": "Processing Demultiplexing" + "run_state_name": "spare_2", + "state_display": "", + "description": "", + "show_in_stats": false } }, { diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index cadf7d603..28610ba5d 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -416,15 +416,13 @@ def handle_not_completed_run(): runs_to_handle = {} - # state_list_be_processed = ['Sample Sent','Processing Run','Processed Run', 'Processing Bcl2fastq', - # 'Processed Bcl2fastq', 'recorded'] state_list_be_processed = [ "recorded", - "Sample Sent", - "Processing Run", - "Processed Run", - "Processing Bcl2fastq", - "Processed Bcl2fastq", + "sample_sent", + "processing_run", + "processed_run", + "processing_bcl2fastq", + "processed_bcl2fastq", ] # get the list for all runs that are not completed for state in state_list_be_processed: @@ -445,15 +443,15 @@ def handle_not_completed_run(): if state == "recorded": manage_run_in_recorded_state(conn, runs_to_handle[state]) - elif state == "Sample Sent": + elif state == "sample_sent": manage_run_in_sample_sent_processing_state(conn, runs_to_handle[state]) - elif state == "Processing Run": + elif state == "processing_run": manage_run_in_sample_sent_processing_state(conn, runs_to_handle[state]) - elif state == "Processed Run": + elif state == "processed_run": manage_run_in_processed_run_state(conn, runs_to_handle[state]) - elif state == "Processing Bcl2fastq": + elif state == "processing_bcl2fastq": manage_run_in_processing_bcl2fastq_state(conn, runs_to_handle[state]) - elif state == "Processed Bcl2fastq": + elif state == "processed_bcl2fastq": manage_run_in_processed_bcl2fastq_state(conn, runs_to_handle[state]) else: for run_obj in runs_to_handle[state]: @@ -639,7 +637,7 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): ) if run_status == "completed": - run_process_obj.set_run_state("Processed Run") + run_process_obj.set_run_state("processed_run") run_process_obj.set_run_completion_date(run_completion_date) logger.info("%s changed to Processed Run state", experiment_name) logger.debug( @@ -694,7 +692,7 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): "%s : Waiting more time to get Sequencer completion", experiment_name, ) - run_process_obj.set_run_state("Processing Run") + run_process_obj.set_run_state("processing_run") logger.info("%s : changed to Processing Run state", experiment_name) logger.debug( "%s : End manage_run_in_sample_sent_processing_state function", @@ -850,7 +848,7 @@ def manage_run_in_processed_run_state(conn, run_process_objs): # deleting temporary run metrics files wetlab.utils.crontab_process.delete_run_metric_files(experiment_name) # return the state to Processed Run - run_process_obj.set_run_state("Processing Bcl2fastq") + run_process_obj.set_run_state("processing_bcl2fastq") logger.debug(" End function manage_run_in_processed_run_state") return @@ -951,7 +949,7 @@ def manage_run_in_processing_bcl2fastq_state(conn, run_process_objs): ) continue run_process_obj.set_run_bcl2fastq_finished_date(bcl2fastq_finish_date) - run_process_obj.set_run_state("Processed Bcl2fastq") + run_process_obj.set_run_state("processed_bcl2fastq") logger.info("%s : Updated to Processed Bcl2Fastq state", experiment_name) logger.info( "%s : End handling in manage_run_in_processing_bcl2fastq_state function", diff --git a/wetlab/utils/fetch_info.py b/wetlab/utils/fetch_info.py index 306276e3e..f2262fa29 100644 --- a/wetlab/utils/fetch_info.py +++ b/wetlab/utils/fetch_info.py @@ -206,15 +206,15 @@ def graphics_state(state): the index value of g_value and g_color [index] """ state_list = [ - "Error", + "error", "recorded", - "Sample Sent", - "Processing Run", - "Processed Run", - "Processing Bcl2fastq", - "Processed Bcl2fastq", - "Completed", - "Cancelled", + "sample_sent", + "processing_run", + "processed_run", + "processing_bcl2fastq", + "processed_bcl2fastq", + "completed", + "cancelled", ] g_value = [10, 15, 30, 45, 60, 75, 90, 100, 10] g_color = [ @@ -557,11 +557,11 @@ def get_information_for_incompleted_run(): run_information["error"].append(data) if wetlab.models.RunProcess.objects.filter( - state__run_state_name="Cancelled" + state__run_state_name="cancelled" ).exists(): run_information["cancelled"] = [] run_objs = wetlab.models.RunProcess.objects.filter( - state__run_state_name="Cancelled" + state__run_state_name="cancelled" ).order_by("run_name") for run_obj in run_objs: data = [] @@ -577,7 +577,7 @@ def get_information_for_incompleted_run(): data.append(str((today - run_date).days)) run_information["cancelled"].append(data) - exclude_state = ["recorded", "Error", "Cancelled", "Completed", "pre_recorded"] + exclude_state = ["recorded", "error", "cancelled", "completed", "pre_recorded"] if ( wetlab.models.RunProcess.objects.all() @@ -728,8 +728,8 @@ def get_information_run(run_object): run_object.get_run_id(), ] - if run_state == "Cancelled": - run_state = "Sample Sent" + if run_state == "cancelled": + run_state = "sample_sent" info_dict["cancel_run"] = [ run_object.get_run_name(), run_state, diff --git a/wetlab/utils/run.py b/wetlab/utils/run.py index 5387b88a5..8d86e8695 100644 --- a/wetlab/utils/run.py +++ b/wetlab/utils/run.py @@ -767,9 +767,7 @@ def get_available_pools_for_run(): pools_to_update """ pools_to_update = {} - import pdb - pdb.set_trace() # get the pools that were selected if wetlab.models.LibraryPool.objects.filter( pool_state__pool_state__exact="Selected" diff --git a/wetlab/utils/test_conf.py b/wetlab/utils/test_conf.py index c67190947..64377fa9b 100644 --- a/wetlab/utils/test_conf.py +++ b/wetlab/utils/test_conf.py @@ -167,7 +167,7 @@ def execute_test_for_testing_run(run_test_name): conn = wetlab.utils.common.open_samba_connection() # Execute 6 times to be sure it has completed all steps - state_run_test = ["Sample Sent", "Processed Run", "Processed Bcl2fastq"] + state_run_test = ["sample_sent", "processed_run", "processed_bcl2fastq"] for state_run in state_run_test: run_result[state_run] = "NOK" if not wetlab.models.RunProcess.objects.filter( @@ -180,61 +180,61 @@ def execute_test_for_testing_run(run_test_name): ).last() for step in range(6): state = run_obj.get_state() - if state == "ERROR": + if state == "error": run_result["ERROR"] = "error" return run_result - elif state == "Sample Sent": + elif state == "sample_sent": wetlab.utils.crontab_update_run.manage_run_in_sample_sent_processing_state( conn, [run_obj] ) - if run_obj.get_state() == "ERROR": + if run_obj.get_state() == "error": run_result["ERROR"] = "Error when processing run in Sample Sent state" break else: - run_result["Sample Sent"] = "OK" - elif state == "Processing Run": + run_result["sample_sent"] = "OK" + elif state == "processing_run": wetlab.utils.crontab_update_run.manage_run_in_sample_sent_processing_state( conn, [run_obj] ) - if run_obj.get_state() == "ERROR": + if run_obj.get_state() == "error": run_result["ERROR"] = ( "Error when processing run in Processing Run state" ) break else: run_result["Processing Run"] = "OK" - elif state == "Processed Run": + elif state == "processed_run": wetlab.utils.crontab_update_run.manage_run_in_processed_run_state( conn, [run_obj] ) - if run_obj.get_state() == "ERROR": + if run_obj.get_state() == "errorR": run_result["ERROR"] = "Error when processing run in Processed Run state" break else: run_result["Processed Run"] = "OK" - elif state == "Processing Bcl2fastq": + elif state == "processing_bcl2fastq": wetlab.utils.crontab_update_run.manage_run_in_processing_bcl2fastq_state( conn, [run_obj] ) - if run_obj.get_state() == "ERROR": + if run_obj.get_state() == "error": run_result["ERROR"] = ( "Error when processing run in Processing Bcl2fastq state" ) break else: run_result["Processing Bcl2fastq"] = "OK" - elif state == "Processed Bcl2fastq": + elif state == "processed_bcl2fastq": wetlab.utils.crontab_update_run.manage_run_in_processed_bcl2fastq_state( conn, [run_obj] ) - if run_obj.get_state() == "ERROR": + if run_obj.get_state() == "error": run_result["ERROR"] = ( "Error when processing run in Processed Bcl2fastq state" ) break else: run_result["Processed Bcl2fastq"] = "OK" - elif state == "Completed": + elif state == "completed": run_result["Completed"] = "OK" break logger.info("----------------------------------") From e83cfa2ed0bf935ed14c222955808c74f4a6d32f Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 18 May 2024 11:00:17 +0200 Subject: [PATCH 075/446] Fixed error messages display --- .../templates/wetlab/create_next_seq_run.html | 461 ++++++++--------- .../wetlab/stats_per_researcher.html | 2 +- .../templates/wetlab/stats_per_sequencer.html | 289 ++++++----- wetlab/templates/wetlab/stats_per_time.html | 463 +++++++++++------- 4 files changed, 672 insertions(+), 543 deletions(-) diff --git a/wetlab/templates/wetlab/create_next_seq_run.html b/wetlab/templates/wetlab/create_next_seq_run.html index ee5c76365..2d37c3915 100644 --- a/wetlab/templates/wetlab/create_next_seq_run.html +++ b/wetlab/templates/wetlab/create_next_seq_run.html @@ -2,156 +2,157 @@ {% load static %} {% block content %} {% include "wetlab/menu.html" %} - {% include 'registration/login_inline.html' %} -
- {% if error_message %} -
-
-
-
-

Unable to accept your request

-
-
- {% for error in error_message %}

{{ error }}

{% endfor %} -
-
-
-
- {% endif %} - {% if get_user_names %} -
+
+
+ {% include 'registration/login_inline.html' %} + {% if error_message %}
-
-
-
-

Run creation progress

+
+
+
+

Unable to process your request

-

- Fill the user name and the Used Library Kit for each project in the run {{ get_user_names.experiment_name }} -

-

This is the second, and the last, FORM that user need to fill down to have the information about the run

-

- Once the name of the user and the libray Kit used in the run, were filled and submited, the next page will show the successful run creation -

+ {% for message in error_message %}

{{ message }}

{% endfor %}
-
-
    -
  1. - Upload Sample Sheet -
    2. - -
  2. - Assign Library Kit -
    3. - -
  3. - Show Results -
    4. -
+
  • + Show Results +
    • + +
    -
    - -
    -
    -
    -
    -
    Form to upload the Sample Sheet file. Run Parameters definition
    -
    -
    - {% csrf_token %} - - -
    - -
    - -
    - -
    - -
    - {% for key, values in get_user_names.projects_user %} -

    Project name assigned to run :

    -

    {{ key }}

    - -
    - + +
    +
    +
    +
    +
    Form to upload the Sample Sheet file. Run Parameters definition
    +
    + + {% csrf_token %} + + +
    +
    - -
    - -
    - + value="{{ get_user_names.experiment_name }}" />
    - +
    -
    - {% endfor %} -
    - - + {% for key, values in get_user_names.projects_user %} +

    Project name assigned to run :

    +

    {{ key }}

    + +
    + +
    + +
    + +
    + +
    + +
    + +
    + {% endfor %} +
    + + +
    -
    -
    -
    -
    Notes for user validation
    -
    -

    The following information have been collected from the Sample Sheet uploaded previously.

    -

    It contains the userid information. Correct in the user name field if this information need to be changed

    -

    Write down the Library kit used for each project

    -

    - Submit button is disabled if any of the user names is not previoulsy defined in database -

    +
    +
    +
    Notes for user validation
    +
    +

    The following information have been collected from the Sample Sheet uploaded previously.

    +

    It contains the userid information. Correct in the user name field if this information need to be changed

    +

    Write down the Library kit used for each project

    +

    + Submit button is disabled if any of the user names is not previoulsy defined in database +

    +
    -
    - - - - + + - {% elif completed_form %} - {% for key, val in completed_form %} - {% if key == "runname" %} -
    -
    -
      -
    1. - Upload Sample Sheet -
      2. - -
    2. - Assign Library Kit -
      3. - -
    3. - Show Results -
      4. -
    +
  • + Show Results +
    • + +
    -
    -
    -
    -
    -
    -
    Run configuration have been sucessfully stored
    -
    -
    -

    All the required information is stored now on database.

    -

    - For the run name : {{ val }} -

    +
    +
    +
    +
    +
    Run configuration have been sucessfully stored
    +
    +
    +

    All the required information is stored now on database.

    +

    + For the run name : {{ val }} +

    +
    -
    - {% endif %} - {% endfor %} - {% else %} - -
    -
    -
      -
    1. - Upload Sample Sheet -
      2. - +
      +
      +
        +
      1. + Upload Sample Sheet +
        2. + -
      2. - Assign Library Kit -
        3. - -
      3. - Show Results -
        4. -
      -
      -
      -
      -
      -

      - This FORM will be used to generated the input file that BaseSpace requires to execute the run -

      +
    2. + Show Results +
      3. +
    +
    -
    -
    -
    -
    -
    Form to upload the Sample Sheet file
    -
    -
    - {% csrf_token %} - -
    - -
    - +
    +

    + This FORM will be used to generated the input file that BaseSpace requires to execute the run +

    +
    +
    +
    +
    +
    +
    +
    Form to upload the Sample Sheet file
    +
    + + {% csrf_token %} + +
    + +
    + +
    -
    -

    - Fields marked with * are mandatory -

    - - +

    + Fields marked with * are mandatory +

    + + +
    -
    -
    -
    -
    Form to upload the Sample Sheet file
    -
    -

    This Form is used to upload the Sample Sheet generated by Illumina Experience Manager tool.

    -

    Guide for Sample Sheet creation and download the IEM tool can be found at illumina Web page.

    -

    - Click +

    +
    Form to upload the Sample Sheet file
    +
    +

    This Form is used to upload the Sample Sheet generated by Illumina Experience Manager tool.

    +

    Guide for Sample Sheet creation and download the IEM tool can be found at illumina Web page.

    +

    + Click here for getting this information. -

    +

    +
    -
    - - -
    - {% endif %} -
    -{% endblock %} + +
    + {% endif %} +
    + {% endblock %} diff --git a/wetlab/templates/wetlab/stats_per_researcher.html b/wetlab/templates/wetlab/stats_per_researcher.html index 3ec3d62b9..828d31cb0 100644 --- a/wetlab/templates/wetlab/stats_per_researcher.html +++ b/wetlab/templates/wetlab/stats_per_researcher.html @@ -15,7 +15,7 @@

    Unable to process your request

    - {% for messge in error_message %}

    {{ message }}

    {% endfor %} + {% for message in error_message %}

    {{ message }}

    {% endfor %}
    diff --git a/wetlab/templates/wetlab/stats_per_sequencer.html b/wetlab/templates/wetlab/stats_per_sequencer.html index 691b46b56..f6515af3f 100644 --- a/wetlab/templates/wetlab/stats_per_sequencer.html +++ b/wetlab/templates/wetlab/stats_per_sequencer.html @@ -1,53 +1,74 @@ - {% extends "core/base.html" %} {% block content %} -{% include "wetlab/menu.html" %} -{% include "core/cdn_table_functionality.html" %} -{% include "core/graphic_chart_functionality.html" %} -
    -
    - {% include 'registration/login_inline.html' %} - {% if error_message %} -
    -
    -
    -

    Unable to process your request

    -
    -

    {{error_message}}

    + {% include "wetlab/menu.html" %} + {% include "core/cdn_table_functionality.html" %} + {% include "core/graphic_chart_functionality.html" %} +
    +
    + {% include 'registration/login_inline.html' %} + {% if error_message %} +
    +
    +
    +
    +

    Unable to process your request

    +
    +
    + {% for message in error_message %}

    {{ message }}

    {% endfor %} +
    -
    -
    - {% endif %} - {% if sequencer_statistics %} -
    -
    -

    Statistics information for {{sequencer_statistics.sequencer_name}}

    +
    + {% endif %} + {% if sequencer_statistics %} +
    - -
    -
    -
    -
    -
    -
    -

    Graphic statistics

    -
    -
    -
    -
    - {{ sequencer_statistics.sequencer_state_graphic|safe }} -
    -
    -
    - {{ sequencer_statistics.sequencer_usage_graphic|safe }} +

    Statistics information for {{ sequencer_statistics.sequencer_name }}

    +
    + +
    +
    +
    +
    +
    +
    +
    +

    Graphic statistics

    +
    +
    +
    +
    +
    + {{ sequencer_statistics.sequencer_state_graphic|safe }} +
    +
    +
    + {{ sequencer_statistics.sequencer_usage_graphic|safe }} +
    @@ -55,94 +76,118 @@

    Statistics information for {{sequencer_statistics.sequen

    -
    - -
    -
    -
    -
    -
    -

    Run handled by sequencer

    -
    - - - - {% for column in sequencer_statistics.run_table_heading %} - - {% endfor %} - - - - {% for pk, run, state, seq, date in sequencer_statistics.run_table_data %} + +
    +
    +
    +
    +
    +
    +

    Run handled by sequencer

    +
    +
    +
    {{column}}
    + - - - - + {% for column in sequencer_statistics.run_table_heading %}{% endfor %} - {%endfor%} - -
    {{run}} {{state}}{{seq}}{{date}}{{ column }}
    + + + {% for pk, run, state, seq, date in sequencer_statistics.run_table_data %} + + + {{ run }} + + {{ state }} + {{ seq }} + {{ date }} + + {% endfor %} + + +
    -
    -
    +
    +
    -
    -
    -
    +
    + +
    +
    -
    - - {% else %} -
    -
    -
    -
    -

    Statistics per sequencer

    -
    -
    - {% csrf_token %} - -
    -
    - - -
    - -
    -
    -
    -
    - - + {% else %} +
    +
    +
    +
    +
    +

    Statistics per sequencer

    +
    +
    + + {% csrf_token %} + +
    +
    + +
    -
    -
    - - +
    +
    +
    + + +
    +
    +
    +
    + + +
    -
    -

    Fields marked in Red are mandatory

    - - - -
    +

    + Fields marked in Red are mandatory +

    + + + +
    +
    -
    -
    - {% endif %} -
    -
    - + {% endblock %} diff --git a/wetlab/templates/wetlab/stats_per_time.html b/wetlab/templates/wetlab/stats_per_time.html index 37af6779f..b8435ec01 100644 --- a/wetlab/templates/wetlab/stats_per_time.html +++ b/wetlab/templates/wetlab/stats_per_time.html @@ -1,72 +1,118 @@ {% extends "core/base.html" %} {% block content %} -{% include "wetlab/menu.html" %} -{% include "core/cdn_table_functionality.html" %} -{% include "core/graphic_chart_functionality.html" %} -
    -
    - {% include 'registration/login_inline.html' %} - {% if error_message %} -
    -
    -
    -

    Unable to process your request

    -
    -

    {{error_messages}}

    + {% include "wetlab/menu.html" %} + {% include "core/cdn_table_functionality.html" %} + {% include "core/graphic_chart_functionality.html" %} +
    +
    + {% include 'registration/login_inline.html' %} + {% if error_message %} +
    +
    +
    +
    +

    Unable to process your request

    +
    +
    + {% for message in error_message %}

    {{ message }}

    {% endfor %} +
    -
    -
    - {% endif %} - {% if per_time_statistics %} -
    -
    -

    Statistics information from {{per_time_statistics.start_date}} to {{per_time_statistics.end_date}}

    -
    - -
    -
    -
    -
    -
    -
    -

    Graphic statistics

    -
    -
    -
    -
    - {{ per_time_statistics.time_state_graphic|safe }} -
    -
    -
    There are {{per_time_statistics.num_runs}} runs in this period
    -
    - {{ per_time_statistics.time_run_weeks_graphic|safe }} +
    + {% endif %} + {% if per_time_statistics %} +
    +
    +

    + Statistics information from {{ per_time_statistics.start_date }} to {{ per_time_statistics.end_date }} +

    +
    + +
    +
    +
    +
    +
    +
    +
    +

    Graphic statistics

    -
    -
    -
    - {{ per_time_statistics.time_researcher_graphic|safe }} -
    -
    -
    There are {{per_time_statistics.num_projects}} projects in this period
    -
    - {{ per_time_statistics.time_project_weeks_graphic|safe }} +
    +
    +
    +
    + {{ per_time_statistics.time_state_graphic|safe }} +
    +
    +
    There are {{ per_time_statistics.num_runs }} runs in this period
    +
    + {{ per_time_statistics.time_run_weeks_graphic|safe }} +
    +
    +
    +
    + {{ per_time_statistics.time_researcher_graphic|safe }} +
    +
    +
    There are {{ per_time_statistics.num_projects }} projects in this period
    +
    + {{ per_time_statistics.time_project_weeks_graphic|safe }} +
    +
    @@ -74,32 +120,38 @@
    There are {{per_time_statistics.num_projects}} projects i
    -
    -
    -
    -
    -
    -
    -
    -

    Quality statistics

    -
    -
    -
    -
    - {{ per_time_statistics.time_q_30_graphic|safe }} + +
    +
    +
    +
    +
    +
    +

    Quality statistics

    -
    -
    - {{ per_time_statistics.time_mean_graphic|safe }} -
    -
    -
    -
    - {{ per_time_statistics.time_researcher_q_30_graphic|safe }} -
    -
    -
    - {{ per_time_statistics.time_researcher_mean_graphic|safe }} +
    +
    +
    +
    + {{ per_time_statistics.time_q_30_graphic|safe }} +
    +
    +
    + {{ per_time_statistics.time_mean_graphic|safe }} +
    +
    +
    +
    + {{ per_time_statistics.time_researcher_q_30_graphic|safe }} +
    +
    +
    + {{ per_time_statistics.time_researcher_mean_graphic|safe }} +
    +
    @@ -107,114 +159,145 @@
    There are {{per_time_statistics.num_projects}} projects i
    -
    -
    -
    -
    -
    -
    -
    -

    Run data for this period

    -
    - - - - {% for column in per_time_statistics.run_table_heading %} - - {% endfor %} - - - - {% for pk, run, state, seq, date in per_time_statistics.run_data %} - - - - - - - {%endfor%} - -
    {{column}}
    {{run}} {{state}}{{seq}}{{date}}
    -
    -
    -
    -
    -
    -
    -
    -
    -
    -
    -
    -

    Sample data for this period

    -
    - - - - {% for column in per_time_statistics.sample_table_heading %} - - {% endfor %} - - - - {% for pk, sample, researcher, project, run, barcode in per_time_statistics.sample_data %} - - - - - - - - {%endfor%} - -
    {{column}}
    {{sample}} {{researcher}}{{project}}{{run}}{{barcode}}
    + +
    +
    +
    +
    +
    +
    +

    Run data for this period

    +
    +
    + + + + {% for column in per_time_statistics.run_table_heading %}{% endfor %} + + + + {% for pk, run, state, seq, date in per_time_statistics.run_data %} + + + + + + + {% endfor %} + +
    {{ column }}
    + {{ run }} + {{ state }}{{ seq }}{{ date }}
    +
    +
    -
    -
    +
    +
    -
    -
    -
    - -
    -
    - {% else %} -
    -
    -
    -
    -

    Statistics for a time period

    -
    -
    - {% csrf_token %} -
    -
    -
    - - + +
    +
    +
    +
    +
    +
    +

    Sample data for this period

    +
    +
    + + + + {% for column in per_time_statistics.sample_table_heading %}{% endfor %} + + + + {% for pk, sample, researcher, project, run, barcode in per_time_statistics.sample_data %} + + + + + + + + {% endfor %} + +
    {{ column }}
    + {{ sample }} + {{ researcher }}{{ project }}{{ run }}{{ barcode }}
    +
    +
    -
    -
    - - +
    +
    + +
    +
    +
    + {% else %} +
    +
    +
    +
    +
    +

    Statistics for a time period

    +
    +
    + + {% csrf_token %} +
    +
    +
    + + +
    +
    +
    +
    + + +
    +
    -
    +

    + Fields marked in Red are mandatory +

    + + +
    -

    Fields marked in Red are mandatory

    - - - -
    +
    +
    -
    + {% endif %}
    - - {% endif %} -
    -
    - -{% endblock %} + + {% endblock %} From e4da9c330ad0b1fbf92c6d089a0e47290a9274e1 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 22 May 2024 13:08:11 +0200 Subject: [PATCH 076/446] added num samples per run and pending changes --- core/utils/graphics.py | 33 ++- wetlab/config.py | 16 +- wetlab/templates/wetlab/stats_per_time.html | 289 ++++++++++++++------ wetlab/utils/statistics.py | 123 +++++++-- wetlab/views.py | 7 + 5 files changed, 352 insertions(+), 116 deletions(-) diff --git a/core/utils/graphics.py b/core/utils/graphics.py index c6157742d..e7eeb7e80 100644 --- a/core/utils/graphics.py +++ b/core/utils/graphics.py @@ -51,15 +51,30 @@ def preparation_3D_pie( def preparation_graphic_data( - heading, - sub_caption, - x_axis_name, - y_axis_name, - theme, - input_data, - label_key=None, - label_value=None, -): + heading: str, + sub_caption: str, + x_axis_name: str, + y_axis_name: str, + theme: str, + input_data: dict, + label_key:str =None, + label_value: str =None, +) -> dict: + """Join the parameters to create a dictionary with two keys: chart and data. + + Args: + heading (str): heading of the chart + sub_caption (str): sub_caption of the chart + x_axis_name (str): name of the x axis + y_axis_name (str): name of the y axis + theme (str): theme of the chart + input_data (dict): data to be displayed + label_key (str, optional): key name from the input dict. Defaults to None. + label_value (str, optional): value field in the innput dict. Defaults to None. + + Returns: + dict: dictionary with the keys chart and data + """ data_source = {} data_source["chart"] = { "caption": heading, diff --git a/wetlab/config.py b/wetlab/config.py index d70256475..8dfceeb7f 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -592,13 +592,22 @@ "user name", ] HEADING_STATISTICS_FOR_TIME_RUN = ["Run name", "Run state", "Sequencer", "Run date"] -HEADING_STATISTICS_FOR_TIME_SAMPLE = [ +HEADING_STATISTICS_FOR_TIME_SEQUENCED_SAMPLE = [ "Sample name", "Researcher", "Project name", "Run name", "Barcode", ] +HEADING_STATISTICS_FOR_TIME_DEFINED_SAMPLE = [ + "Sample name", + "Unique ID", + "State", + "Recorded date", + "Species", + "Sample type", + "lab code", +] HEADING_STATISTICS_FOR_SEQUENCER_RUNS = [ "Run name", "Run state", @@ -758,7 +767,7 @@ ] # ERROR TEXT FOR SEACHING ############################################# -ERROR_INVALID_FORMAT_FOR_DATES = "Invalid date format. Use the format (DD-MM-YYYY)" +ERROR_INVALID_FORMAT_FOR_DATES = ["Invalid date format. Use the format (DD-MM-YYYY)"] ERROR_MANY_USER_MATCHES_FOR_INPUT_CONDITIONS = [ @@ -785,7 +794,7 @@ ERROR_NO_SAMPLES_SELECTED = "They were not selected any Sample on your request" ERROR_NOT_RUNS_FOUND_IN_SELECTED_PERIOD = ( - "There are not runs for the selected period of time" + ["There are not runs for the selected period of time"] ) ERROR_NOT_SAMPLES_FOR_USER_FOUND_BECAUSE_OF_CONFIGURATION_SETTINGS = [ "No results. This could because the DESCRIPTION_IN_SAMPLE_SHEET_MUST_HAVE_USERNAME setting is set fo FALSE" @@ -806,6 +815,7 @@ ERROR_WRONG_SAMBA_CONFIGURATION_SETTINGS = ( "Unsuccessful configuration settings for Samba connection" ) +ERROR_USER_NOT_DEFINED = ["User is not defined"] ERROR_WRONG_SAMBA_FOLDER_SETTINGS = ( "Unsuccessful configuration. Samba folder not reachable" ) diff --git a/wetlab/templates/wetlab/stats_per_time.html b/wetlab/templates/wetlab/stats_per_time.html index b8435ec01..46df51977 100644 --- a/wetlab/templates/wetlab/stats_per_time.html +++ b/wetlab/templates/wetlab/stats_per_time.html @@ -30,13 +30,13 @@

    @@ -89,7 +109,7 @@

    -

    Graphic statistics

    +

    Overview statistics

    @@ -108,7 +128,7 @@
    There are {{ per_time_statistics.num_runs }} runs in thi {{ per_time_statistics.time_researcher_graphic|safe }}
    -
    There are {{ per_time_statistics.num_projects }} projects in this period
    +
    There are {{ per_time_statistics.num_projects }} projects in this period
    {{ per_time_statistics.time_project_weeks_graphic|safe }}
    @@ -169,7 +189,7 @@

    Quality statistics

    -

    Run data for this period

    +

    Runs for this period

    @@ -207,17 +227,17 @@

    Run data for this period

    -

    Sample data for this period

    +

    Sequenced samples for this period

    - {% for column in per_time_statistics.sample_table_heading %}{% endfor %} + {% for column in per_time_statistics.seq_sample_table_heading %}{% endfor %} - {% for pk, sample, researcher, project, run, barcode in per_time_statistics.sample_data %} + {% for pk, sample, researcher, project, run, barcode in per_time_statistics.seq_sample_data %}
    {{ column }}{{ column }}
    Sample data for this period - - - - {% else %} -
    -
    -
    -
    -
    -

    Statistics for a time period

    +
    +
    +
    +
    +
    +
    +

    Samples defined during this period

    +
    +
    + + + + {% for column in per_time_statistics.defined_sample_table_heading %}{% endfor %} + + + + {% for pk, sample, unique_id, state, species, type_sample, lab, rec_date in per_time_statistics.defined_sample_data %} + + + + + + + + + + {% endfor %} + +
    {{ column }}
    + {{ sample }} + {{ unique_id }}{{ state }}{{ rec_date }}{{ species }}{{ type_sample }}{{ lab }}
    +
    +
    +
    +
    -
    -
    - {% csrf_token %} -
    -
    -
    - - +
    + +
    +
    +
    +
    +
    +
    +

    Unkwonw Barcodes in runs during this period

    +
    +
    +
    +
    +
    + {{ per_time_statistics.time_unknown_barcodes_graphic|safe }} +
    +
    -
    -
    - - +
    +
    +
    +
    + +
    +
    +
    +
    +
    +
    +

    Comparison statistics

    +
    +
    +
    +
    +
    + {{ per_time_statistics.time_num_sample_per_run_graphic|safe }} +
    +
    +
    +
    + {{ per_time_statistics.time_num_sample_per_lab_graphic|safe }} +
    +
    +
    + {{ per_time_statistics.time_num_seq_sample_vs_def_sample_graphic|safe }} +
    +
    +
    -

    - Fields marked in Red are mandatory -

    - - - +
    +
    - {% endif %} -
    - - - {% endblock %} + +{% endblock %} diff --git a/wetlab/utils/statistics.py b/wetlab/utils/statistics.py index a9e435f4b..df82dab64 100644 --- a/wetlab/utils/statistics.py +++ b/wetlab/utils/statistics.py @@ -1,6 +1,6 @@ # Generic imports from django.contrib.auth.models import User -from django.db.models import Avg, F, Count, Func, Value, CharField +from django.db.models import Avg, F, Count, Func, Value, CharField, Sum from django.db.models.functions import ExtractWeek, ExtractYear # Local imports @@ -13,20 +13,15 @@ import wetlab.config -def get_per_time_statistics(start_date, end_date): - """_summary_ - - Parameters - ---------- - start_date : str - Date from starting the statistics - end_date : str - Date from the statistics ends +def get_per_time_statistics(start_date: str, end_date: str) -> dict: + """Collects the statistics for the time period defined by the start and end date - Returns - ------- - dict + Args: + start_date (str): start date for the statistics + end_date(str):end date for the statistics + Returns: + dict: dictionary with the statistics """ per_time_statistics = {} # validate date format @@ -39,6 +34,8 @@ def get_per_time_statistics(start_date, end_date): run_objs = wetlab.models.RunProcess.objects.filter( run_date__range=(start_date, end_date) ) + import pdb + if len(run_objs) == 0: per_time_statistics["ERROR"] = ( wetlab.config.ERROR_NOT_RUNS_FOUND_IN_SELECTED_PERIOD @@ -156,10 +153,33 @@ def get_per_time_statistics(start_date, end_date): ) # Graphic chart for unknown barcodes - # pening to fix issue 158 - # barcode_objs = wetlab.models.RawTopUnknowBarcodes.objects.filter( - # runprocess_id__in=run_objs - # ) + barcode_in_run = ( + wetlab.models.RawTopUnknowBarcodes.objects.filter(runprocess_id__in=run_objs) + .values("sequence") + .annotate(value=Sum("count")) + .order_by("sequence") + ) + g_data = core.utils.graphics.preparation_graphic_data( + "Unknown bar codes in runs", + "", + "", + "", + "flint", + barcode_in_run, + "sequence", + "value", + ) + per_time_statistics["time_unknown_barcodes_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "time_unknown_barcodes_graph", + "900", + "600", + "time_unknown_barcodes_chart", + "json", + g_data, + ).render() + ) # chart graph for Q > 30 based on runs # ############################## @@ -296,8 +316,8 @@ def get_per_time_statistics(start_date, end_date): wetlab.config.HEADING_STATISTICS_FOR_TIME_RUN ) - # Table information for sample data - per_time_statistics["sample_data"] = list( + # Table information for sequenced sample data + per_time_statistics["seq_sample_data"] = list( sample_objs.values_list( "pk", "sample_name", @@ -307,9 +327,66 @@ def get_per_time_statistics(start_date, end_date): "barcode_name", ) ) - per_time_statistics["sample_table_heading"] = ( - wetlab.config.HEADING_STATISTICS_FOR_TIME_SAMPLE + per_time_statistics["seq_sample_table_heading"] = ( + wetlab.config.HEADING_STATISTICS_FOR_TIME_SEQUENCED_SAMPLE ) + + # Table information for defined samples + per_time_statistics["defined_sample_data"] = list( + core.models.Samples.objects.filter( + sample_entry_date__range=(start_date, end_date) + ) + .values_list( + "pk", + "sample_name", + "unique_sample_id", + "sample_state__sample_state_name", + "species__species_name", + "sample_type__sample_type", + "lab_request__lab_name_coding", + ) + .annotate( + formated_date=Func( + F("sample_entry_date"), + Value("%Y-%m-%d"), + function="DATE_FORMAT", + output_field=CharField(), + ) + ) + ) + per_time_statistics["defined_sample_table_heading"] = ( + wetlab.config.HEADING_STATISTICS_FOR_TIME_DEFINED_SAMPLE + ) + samples_in_run = list( + sample_objs.values("run_process_id__run_name").annotate( + num_of_samples=Count("run_process_id__run_name") + ) + ) + g_data = core.utils.graphics.preparation_graphic_data( + "Number of samples per run", + "", + "Run name", + "Number of samples", + "zune", + samples_in_run, + "run_process_id__run_name", + "num_of_samples", + ) + per_time_statistics["time_num_sample_per_run_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "time_num_sample_per_run_graph", + "550", + "350", + "time_num_sample_per_run_chart", + "json", + g_data, + ).render() + ) + + pdb.set_trace() + # number of samples per run + sample_objs.values_list() per_time_statistics["start_date"] = start_date per_time_statistics["end_date"] = end_date per_time_statistics["num_runs"] = len(run_objs) @@ -807,9 +884,7 @@ def _lab_statistics( researcher_name = researcher_name.strip() # check if the researcher exists if not User.objects.filter(username__icontains=researcher_name).exists(): - research_lab_statistics["ERROR"] = ( - wetlab.config.ERROR_NO_MATCHES_FOR_INPUT_CONDITIONS - ) + research_lab_statistics["ERROR"] = wetlab.config.ERROR_USER_NOT_DEFINED return research_lab_statistics user_objs = User.objects.filter(username__icontains=researcher_name) diff --git a/wetlab/views.py b/wetlab/views.py index 783bfb4c6..c38bab8d2 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -1678,6 +1678,13 @@ def stats_per_time(request): per_time_statistics = wetlab.utils.statistics.get_per_time_statistics( start_date, end_date ) + if "ERROR" in per_time_statistics: + error_message = per_time_statistics["ERROR"] + return render( + request, + "wetlab/stats_per_time.html", + {"error_message": error_message}, + ) return render( request, "wetlab/stats_per_time.html", From a74411dee3cd370dc1fab58cc348df72fd5aa4ce Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 22 May 2024 13:10:03 +0200 Subject: [PATCH 077/446] fixed litin --- core/utils/graphics.py | 6 +++--- wetlab/config.py | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/core/utils/graphics.py b/core/utils/graphics.py index e7eeb7e80..44dd03bae 100644 --- a/core/utils/graphics.py +++ b/core/utils/graphics.py @@ -57,8 +57,8 @@ def preparation_graphic_data( y_axis_name: str, theme: str, input_data: dict, - label_key:str =None, - label_value: str =None, + label_key: str = None, + label_value: str = None, ) -> dict: """Join the parameters to create a dictionary with two keys: chart and data. @@ -74,7 +74,7 @@ def preparation_graphic_data( Returns: dict: dictionary with the keys chart and data - """ + """ data_source = {} data_source["chart"] = { "caption": heading, diff --git a/wetlab/config.py b/wetlab/config.py index 8dfceeb7f..cca19fc02 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -793,9 +793,9 @@ ] ERROR_NO_SAMPLES_SELECTED = "They were not selected any Sample on your request" -ERROR_NOT_RUNS_FOUND_IN_SELECTED_PERIOD = ( - ["There are not runs for the selected period of time"] -) +ERROR_NOT_RUNS_FOUND_IN_SELECTED_PERIOD = [ + "There are not runs for the selected period of time" +] ERROR_NOT_SAMPLES_FOR_USER_FOUND_BECAUSE_OF_CONFIGURATION_SETTINGS = [ "No results. This could because the DESCRIPTION_IN_SAMPLE_SHEET_MUST_HAVE_USERNAME setting is set fo FALSE" ] From 3e234e304bcd131bc15bb92edcc4052eb78d799f Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 22 May 2024 14:01:49 +0200 Subject: [PATCH 078/446] added num samples per lab statistics --- wetlab/utils/statistics.py | 69 ++++++++++++++++++++++++++++++++------ 1 file changed, 59 insertions(+), 10 deletions(-) diff --git a/wetlab/utils/statistics.py b/wetlab/utils/statistics.py index df82dab64..f8847d645 100644 --- a/wetlab/utils/statistics.py +++ b/wetlab/utils/statistics.py @@ -34,7 +34,6 @@ def get_per_time_statistics(start_date: str, end_date: str) -> dict: run_objs = wetlab.models.RunProcess.objects.filter( run_date__range=(start_date, end_date) ) - import pdb if len(run_objs) == 0: per_time_statistics["ERROR"] = ( @@ -330,13 +329,12 @@ def get_per_time_statistics(start_date: str, end_date: str) -> dict: per_time_statistics["seq_sample_table_heading"] = ( wetlab.config.HEADING_STATISTICS_FOR_TIME_SEQUENCED_SAMPLE ) - + defined_sample_objs = core.models.Samples.objects.filter( + sample_entry_date__range=(start_date, end_date) + ) # Table information for defined samples per_time_statistics["defined_sample_data"] = list( - core.models.Samples.objects.filter( - sample_entry_date__range=(start_date, end_date) - ) - .values_list( + defined_sample_objs.values_list( "pk", "sample_name", "unique_sample_id", @@ -344,8 +342,7 @@ def get_per_time_statistics(start_date: str, end_date: str) -> dict: "species__species_name", "sample_type__sample_type", "lab_request__lab_name_coding", - ) - .annotate( + ).annotate( formated_date=Func( F("sample_entry_date"), Value("%Y-%m-%d"), @@ -357,6 +354,7 @@ def get_per_time_statistics(start_date: str, end_date: str) -> dict: per_time_statistics["defined_sample_table_heading"] = ( wetlab.config.HEADING_STATISTICS_FOR_TIME_DEFINED_SAMPLE ) + # graphic chart for number of samples per run samples_in_run = list( sample_objs.values("run_process_id__run_name").annotate( num_of_samples=Count("run_process_id__run_name") @@ -383,9 +381,60 @@ def get_per_time_statistics(start_date: str, end_date: str) -> dict: g_data, ).render() ) + # graphic chart for number of seq samples vs defined samples + defined_sample_objs + g_data = core.utils.graphics.preparation_graphic_data( + "Sequence vs defined samples", + "", + "", + "", + "ocean", + { + "seqenced samples": sample_objs.count(), + "defined samples": defined_sample_objs.count(), + }, + "", + "", + ) + per_time_statistics["time_num_seq_sample_vs_def_sample_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", + "time_num_seq_sample_vs_def_sample_graph", + "600", + "300", + "time_num_seq_sample_vs_def_sample_chart", + "json", + g_data, + ).render() + ) + # graphic chart for number of defined samples per lab + samples_per_lab = list( + defined_sample_objs.values("lab_request__lab_name_coding").annotate( + num_of_samples=Count("lab_request__lab_name_coding") + ) + ) + g_data = core.utils.graphics.preparation_graphic_data( + "Number of samples per laboratory", + "", + "Laboratory name", + "Number of samples", + "zune", + samples_per_lab, + "lab_request__lab_name_coding", + "num_of_samples", + ) + per_time_statistics["time_num_sample_per_lab_graphic"] = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", + "time_num_sample_per_lab_graph", + "550", + "350", + "time_num_sample_per_lab_chart", + "json", + g_data, + ).render() + ) - pdb.set_trace() - # number of samples per run sample_objs.values_list() per_time_statistics["start_date"] = start_date per_time_statistics["end_date"] = end_date From 0244401f78173b4ed5b418488f41e4c74d416678 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 25 May 2024 15:36:54 +0200 Subject: [PATCH 079/446] added checking to allow or not repeated sample names --- conf/first_install_tables.json | 27 ++++++++++++++++++ core/utils/samples.py | 52 +++++++++++++++++++++++++--------- wetlab/views.py | 18 +++++++++++- 3 files changed, 83 insertions(+), 14 deletions(-) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index 64b93754b..c0d99a12e 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -2032,6 +2032,33 @@ "generated_at": "2021-01-28T22:59:03.042" } }, +{ + "model": "wetlab.configsetting", + "pk": 15, + "fields": { + "configuration_name": "ALLOW_REPEAT_SAMPLE_NAMES", + "configuration_value": "FALSE", + "generated_at": "2024-05-28T22:59:03.142" + } +}, +{ + "model": "wetlab.configsetting", + "pk": 16, + "fields": { + "configuration_name": "ALLOW_REPEAT_SAMPLE_NAMES_PER_RESEARCHER", + "configuration_value": "FALSE", + "generated_at": "2024-05-28T22:59:04.042" + } +}, +{ + "model": "wetlab.configsetting", + "pk": 17, + "fields": { + "configuration_name": "ALLOW_SAMPLE_NAMES_WITH_UNDERSCORE", + "configuration_value": "FALSE", + "generated_at": "2024-05-28T22:59:05.042" + } +}, { "model": "wetlab.collectionindexvalues", "pk": 2073, diff --git a/core/utils/samples.py b/core/utils/samples.py index d96ab0752..64be6ac43 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -193,20 +193,24 @@ def save_recorded_samples(samples_data, req_user, app_name): return samples_data -def validate_sample_data(sample_data, req_user, app_name): - """Sample data validation +def validate_sample_data( + sample_data: json, + req_user: str, + app_name: str, + repeat_allowed: bool = False, + allow_user__repeat: bool = False, +)-> tuple: + """sample data validation - Parameters - ---------- - sample_data - sample data formatted in json obtained from jspreadsheet - req_user - requesting user - app_name - application name (wetlab, drylab, core, etc.) + Args: + sample_data (json): sample data formatted in json obtained from jspreadsheet + req_user (str): requested user name + app_name (str): application name (wetlab, drylab, core, etc.) + repeat_allowed (bool, optional): allow or not that sample can be repeated. Defaults to False. + allow_user__repeat (bool, optional): if allowed to be repeated check if same request user is allowed have repeated sample names. Defaults to False. - Returns - ------- + Returns: + tuple: returns result as boolean and a dictionary with the following keys validation list with validation info for each sample with format: [{"Sample Name": "test 01", @@ -222,6 +226,25 @@ def validate_sample_data(sample_data, req_user, app_name): sample_name_list = [] line = 0 result = True + not_allowed_sample_names = {} + # collect the sample names already in the database in case that the user + # is not allowed to repeat + if not repeat_allowed: + if not allow_user__repeat: + if core.models.Samples.objects.filter( + sample_user__username__exact=req_user + ).exists(): + existing_sample_name_list = list( + core.models.Samples.objects.filter( + sample_user__username__exact=req_user + ).values_list("sample_name", flat=True) + ) + else: + existing_sample_name_list = list( + core.models.Samples.objects.all().values_list("sample_name", flat=True) + ) + # convert to dict to speed up the search + not_allowed_sample_names = dict.fromkeys(existing_sample_name_list, 0) for sample in sample_data: line += 1 sample_dict = {} @@ -237,7 +260,10 @@ def validate_sample_data(sample_data, req_user, app_name): validation.append(sample_dict) continue - if sample["sample_name"] not in sample_name_list: + if ( + sample["sample_name"] not in sample_name_list + and sample["sample_name"] not in not_allowed_sample_names + ): sample_name_list.append(sample["sample_name"]) else: error_cause = core.core_config.ERROR_REPEATED_SAMPLE_NAME.copy() diff --git a/wetlab/views.py b/wetlab/views.py index c38bab8d2..5f0386a92 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -2163,8 +2163,24 @@ def record_samples(request): {"fields_info": fields_info}, ) # validate mandatory and redundant samples + rep_sample = ( + False + if wetlab.utils.common.get_configuration_from_database( + "ALLOW_REPEAT_SAMPLE_NAMES" + ) + == "FALSE" + else True + ) + rep_user = ( + False + if wetlab.utils.common.get_configuration_from_database( + "ALLOW_REPEAT_USER_SAMPLE_NAMES" + ) + == "FALSE" + else True + ) sample_validation, validation_result = core.utils.samples.validate_sample_data( - excel_json_data, req_user, __package__ + excel_json_data, req_user, __package__, rep_sample, rep_user ) if not validation_result: From d36d76d4eccc1113f557cb32a016f3c6af6fc667 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 25 May 2024 15:45:51 +0200 Subject: [PATCH 080/446] fixin lint --- core/utils/samples.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/utils/samples.py b/core/utils/samples.py index 64be6ac43..5d44e9bc9 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -199,7 +199,7 @@ def validate_sample_data( app_name: str, repeat_allowed: bool = False, allow_user__repeat: bool = False, -)-> tuple: +) -> tuple: """sample data validation Args: From 6c1e3c53ef467ac499f9b8ed1edbcc9dccb9d6cf Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 25 May 2024 22:06:19 +0200 Subject: [PATCH 081/446] Implement in api that samples cannot be repeated --- core/utils/samples.py | 4 ++-- wetlab/api/views.py | 30 +++++++++++++++++++++++++++--- 2 files changed, 29 insertions(+), 5 deletions(-) diff --git a/core/utils/samples.py b/core/utils/samples.py index 5d44e9bc9..c274e49b4 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -236,7 +236,7 @@ def validate_sample_data( ).exists(): existing_sample_name_list = list( core.models.Samples.objects.filter( - sample_user__username__exact=req_user + sample_user__username__iexact=req_user ).values_list("sample_name", flat=True) ) else: @@ -260,7 +260,7 @@ def validate_sample_data( validation.append(sample_dict) continue - if ( + if repeat_allowed or ( sample["sample_name"] not in sample_name_list and sample["sample_name"] not in not_allowed_sample_names ): diff --git a/wetlab/api/views.py b/wetlab/api/views.py index 5d3ff5952..fc362d85a 100644 --- a/wetlab/api/views.py +++ b/wetlab/api/views.py @@ -17,6 +17,7 @@ import wetlab.api.utils.sample import wetlab.models import wetlab.config +import wetlab.utils.common sample_project_fields = openapi.Parameter( "project", @@ -181,9 +182,32 @@ def create_sample_data(request): data = data.dict() if "sample_name" not in data or "sample_project" not in data: return Response(status=status.HTTP_400_BAD_REQUEST) - if core.models.Samples.objects.filter( - sample_name__iexact=data["sample_name"] - ).exists(): + not_allowed_sample_names = [] + allowed_sample_repeat = ( + False + if wetlab.utils.common.get_configuration_from_database( + "ALLOW_REPEAT_SAMPLE_NAMES" + ) + == "FALSE" + else True + ) + if not allowed_sample_repeat: + if ( + wetlab.utils.common.get_configuration_from_database( + "ALLOW_REPEAT_USER_SAMPLE_NAMES" + ) + == "FALSE" + ): + not_allowed_sample_names = list( + core.models.Samples.objects.filter( + sample_user__username__iexact=request.user.username + ).values_list("sample_name", flat=True) + ) + else: + not_allowed_sample_names = list( + core.models.Samples.objects.values_list("sample_name", flat=True) + ) + if data["sample_name"] in not_allowed_sample_names: error = {"ERROR": "sample already defined"} return Response(error, status=status.HTTP_400_BAD_REQUEST) split_data = wetlab.api.utils.sample.split_sample_data(data) From 6eb000eaad4e1ae571bf222149d8767e2b363ad8 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 25 May 2024 23:28:09 +0200 Subject: [PATCH 082/446] Changed sample name to lowercase to compare with the exisiting samples --- core/utils/samples.py | 10 ++++++---- wetlab/api/views.py | 9 ++++++--- .../templates/wetlab/handling_library_preparation.html | 2 +- 3 files changed, 13 insertions(+), 8 deletions(-) diff --git a/core/utils/samples.py b/core/utils/samples.py index c274e49b4..ba6b7df5b 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -5,7 +5,7 @@ from collections import OrderedDict from django.contrib.auth.models import User -from django.db.models import CharField, Count, F, Func, Prefetch, Value +from django.db.models import CharField, Count, F, Func, Prefetch, Value, Lower # Local imports import core.core_config @@ -241,7 +241,9 @@ def validate_sample_data( ) else: existing_sample_name_list = list( - core.models.Samples.objects.all().values_list("sample_name", flat=True) + core.models.Samples.objects.all().values_list( + Lower("sample_name", flat=True) + ) ) # convert to dict to speed up the search not_allowed_sample_names = dict.fromkeys(existing_sample_name_list, 0) @@ -261,8 +263,8 @@ def validate_sample_data( continue if repeat_allowed or ( - sample["sample_name"] not in sample_name_list - and sample["sample_name"] not in not_allowed_sample_names + sample["sample_name"].lower() not in sample_name_list + and sample["sample_name"].lower() not in not_allowed_sample_names ): sample_name_list.append(sample["sample_name"]) else: diff --git a/wetlab/api/views.py b/wetlab/api/views.py index fc362d85a..76a2323d4 100644 --- a/wetlab/api/views.py +++ b/wetlab/api/views.py @@ -1,4 +1,5 @@ from django.http import QueryDict +from django.db.models.functions import Lower from drf_yasg import openapi from drf_yasg.utils import swagger_auto_schema from rest_framework import status @@ -201,13 +202,15 @@ def create_sample_data(request): not_allowed_sample_names = list( core.models.Samples.objects.filter( sample_user__username__iexact=request.user.username - ).values_list("sample_name", flat=True) + ).values_list(Lower("sample_name", flat=True)) ) else: not_allowed_sample_names = list( - core.models.Samples.objects.values_list("sample_name", flat=True) + core.models.Samples.objects.values_list( + Lower("sample_name", flat=True) + ) ) - if data["sample_name"] in not_allowed_sample_names: + if data["sample_name"].lower() in not_allowed_sample_names: error = {"ERROR": "sample already defined"} return Response(error, status=status.HTTP_400_BAD_REQUEST) split_data = wetlab.api.utils.sample.split_sample_data(data) diff --git a/wetlab/templates/wetlab/handling_library_preparation.html b/wetlab/templates/wetlab/handling_library_preparation.html index 10c41749a..ae3aa488c 100644 --- a/wetlab/templates/wetlab/handling_library_preparation.html +++ b/wetlab/templates/wetlab/handling_library_preparation.html @@ -88,7 +88,7 @@

    {{error_message}}

    - +
    From faf470b20fdf9b95e58efa3527d153e213d865ab Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 25 May 2024 23:31:27 +0200 Subject: [PATCH 083/446] fixed small issue on import lower function --- core/utils/samples.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/core/utils/samples.py b/core/utils/samples.py index ba6b7df5b..b02862765 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -5,7 +5,8 @@ from collections import OrderedDict from django.contrib.auth.models import User -from django.db.models import CharField, Count, F, Func, Prefetch, Value, Lower +from django.db.models import CharField, Count, F, Func, Prefetch, Value +from django.db.models.functions import Lower # Local imports import core.core_config From beb6e34163ec26fe44e7b0ce163e5ec30fd2f97b Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 9 Jun 2024 21:56:38 +0200 Subject: [PATCH 084/446] Added analyzed samples in run graphic --- .../templates/drylab/stats_services_time.html | 286 +++++++++++------- drylab/views.py | 40 ++- wetlab/api/views.py | 13 + 3 files changed, 223 insertions(+), 116 deletions(-) diff --git a/drylab/templates/drylab/stats_services_time.html b/drylab/templates/drylab/stats_services_time.html index 8b9de7ce8..c415e3312 100644 --- a/drylab/templates/drylab/stats_services_time.html +++ b/drylab/templates/drylab/stats_services_time.html @@ -21,122 +21,192 @@
    {{ error_message }}
    {% endif %} {% if services_stats_info %} -
    -
    -
    -
    -

    Services per user

    -
    -
    - {% if services_stats_info.graphic_requested_services_per_user %} -
    - {{ services_stats_info.graphic_requested_services_per_user |safe }} - {% endif %} -
    -
    -
    -
    -
    -
    -

    Services status

    -
    -
    - {% if services_stats_info.graphic_status_requested_services %} -
    - {{ services_stats_info.graphic_status_requested_services |safe }} - {% endif %} -
    -
    -
    -
    -
    -
    -
    -
    -

    Services per classification area

    -
    -
    - {% if services_stats_info.graphic_area_services %} -
    - {{ services_stats_info.graphic_area_services |safe }} - {% endif %} -
    -
    -
    -
    -
    -
    -

    Services per center

    -
    -
    - {% if services_stats_info.graphic_center_services %} -
    - - {{ services_stats_info.graphic_center_services |safe }} - {% endif %} -
    +
    +
    -
    -
    -
    -
    -
    -

    Service statistics per center

    + +
    + -
    -
    -
    -

    Services Statistics per classification area

    -
    -
    -

    {{ services_stats_info.period_time }}.

    - {% if services_stats_info.graphic_area_services_per_time %} -
    - - {{ services_stats_info.graphic_area_services_per_time |safe }} - {% endif %} + -
    -
    -
    -
    -
    -
    -

    Level 2 available services

    +
    +
    +
    +
    +

    Requested Services per center

    +
    +
    + {% if services_stats_info.graphic_center_services %} +
    + + {{ services_stats_info.graphic_center_services |safe }} + {% endif %} +
    +
    +
    +
    +
    +
    +

    Services per classification area

    +
    +
    + {% if services_stats_info.graphic_area_services %} +
    + {{ services_stats_info.graphic_area_services |safe }} + {% endif %} +
    +
    +
    -
    -

    {{ services_stats_info.period_time }}.

    - {% if services_stats_info.graphic_req_l2_services %} -
    - {{ services_stats_info.graphic_req_l2_services |safe }} - {% endif %} +
    +
    +
    +
    +

    Service statistics per center

    +
    +
    +

    {{ services_stats_info.period_time }}.

    + {% if services_stats_info.graphic_center_services_per_time %} +
    + {{ services_stats_info.graphic_center_services_per_time |safe }} + {% endif %} +
    +
    +
    +
    +
    +
    +

    Services Statistics per classification area

    +
    +
    +

    {{ services_stats_info.period_time }}.

    + {% if services_stats_info.graphic_area_services_per_time %} +
    + + {{ services_stats_info.graphic_area_services_per_time |safe }} + {% endif %} +
    +
    +
    -
    -
    -
    -
    -
    -
    -

    Level 3 Available Services

    -
    -
    -

    {{ services_stats_info.period_time }}.

    - {% if services_stats_info.graphic_req_l3_services %} -
    - {{ services_stats_info.graphic_req_l3_services |safe }} - {% endif %} +
    diff --git a/drylab/views.py b/drylab/views.py index 1952dab78..8eb944d33 100644 --- a/drylab/views.py +++ b/drylab/views.py @@ -8,13 +8,14 @@ from django.conf import settings from django.contrib.auth.decorators import login_required from django.core.files.storage import FileSystemStorage -from django.db.models import Prefetch +from django.db.models import Prefetch, Count, F from django.http import HttpResponse from django.shortcuts import redirect, render # Local imports import core.fusioncharts.fusioncharts import core.utils.common +import core.utils.graphics import django_utils.models import drylab.config import drylab.models @@ -1139,6 +1140,8 @@ def stats_by_services_request(request): if request.method == "POST" and request.POST["action"] == "service_statistics": start_date = request.POST["start_date"] end_date = request.POST["end_date"] + if start_date == "" and end_date == "": + return render(request, "drylab/stats_services_time.html") if start_date != "" and not drylab.utils.common.check_valid_date_format( start_date ): @@ -1169,11 +1172,11 @@ def stats_by_services_request(request): user_services[user] = 1 period_of_time_selected = str( - " For the period between " + start_date + " and " + end_date + " From " + start_date + " to " + end_date ) # creating the graphic for requested services data_source = drylab.utils.graphics.column_graphic_dict( - "Requested Services by:", + "Requested Services from users", period_of_time_selected, "User names", "Number of Services", @@ -1181,7 +1184,7 @@ def stats_by_services_request(request): user_services, ) graphic_requested_services = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", "ex1", "525", "350", "chart-1", "json", data_source + "column3d", "ex1", "900", "350", "chart-1", "json", data_source ) services_stats_info["graphic_requested_services_per_user"] = ( graphic_requested_services.render() @@ -1207,7 +1210,7 @@ def stats_by_services_request(request): ) graphic_status_requested_services = ( core.fusioncharts.fusioncharts.FusionCharts( - "pie3d", "ex2", "525", "350", "chart-2", "json", data_source + "pie3d", "ex2", "500", "400", "chart-2", "json", data_source ) ) services_stats_info["graphic_status_requested_services"] = ( @@ -1323,7 +1326,7 @@ def stats_by_services_request(request): if d_period not in user_services_period[center]: user_services_period[center][d_period] = 0 data_source = drylab.utils.graphics.column_graphic_per_time( - "Services requested by center ", + "Services requested by center and period of time", period_of_time_selected, "date", "number of services", @@ -1408,7 +1411,7 @@ def stats_by_services_request(request): "Requested Services:", "level 2 ", "", "", "fint", service_dict ) graphic_req_l2_services = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", "ex7", "800", "375", "chart-7", "json", data_source + "column3d", "ex7", "600", "375", "chart-7", "json", data_source ) services_stats_info["graphic_req_l2_services"] = ( graphic_req_l2_services.render() @@ -1431,12 +1434,33 @@ def stats_by_services_request(request): "Requested Services:", "level 3 ", "", "", "fint", service_dict ) graphic_req_l3_services = core.fusioncharts.fusioncharts.FusionCharts( - "column3d", "ex8", "800", "375", "chart-8", "json", data_source + "column3d", "ex8", "900", "375", "chart-8", "json", data_source ) services_stats_info["graphic_req_l3_services"] = ( graphic_req_l3_services.render() ) + # Samples handled by requested services + + sample_in_services_objs = drylab.models.RequestedSamplesInServices.objects.filter(samples_in_service__in=services_found) + ana_sample_in_runs = sample_in_services_objs.exclude(run_name=None).values("run_name").annotate(sample_count=Count("sample_name"), sample_name=F("run_name")) + g_data = core.utils.graphics.preparation_graphic_data( + "Samples state", + "", + "", + "", + "ocean", + ana_sample_in_runs, + "run_name", + "sample_count", + ) + import pdb; pdb.set_trace() + graphic_req_l3_services = core.fusioncharts.fusioncharts.FusionCharts( + "column3d", "ex9", "600", "375", "chart-9", "json", g_data + ) + services_stats_info["graphic_samples_per_run"] = ( + graphic_req_l3_services.render() + ) return render( request, "drylab/stats_services_time.html", diff --git a/wetlab/api/views.py b/wetlab/api/views.py index 76a2323d4..198edd535 100644 --- a/wetlab/api/views.py +++ b/wetlab/api/views.py @@ -210,9 +210,22 @@ def create_sample_data(request): Lower("sample_name", flat=True) ) ) + # get information it underscore is allowed in sample name + allow_underscore = ( + False + if wetlab.utils.common.get_configuration_from_database( + "ALLOW_UNDERSCORE_SAMPLE_NAMES" + ) + == "FALSE" + else True + ) if data["sample_name"].lower() in not_allowed_sample_names: error = {"ERROR": "sample already defined"} return Response(error, status=status.HTTP_400_BAD_REQUEST) + if not allow_underscore: + if "_" in data["sample_name"]: + error = {"ERROR": "sample name cannot have underscore"} + return Response(error, status=status.HTTP_400_BAD_REQUEST) split_data = wetlab.api.utils.sample.split_sample_data(data) if not isinstance(split_data, dict): return Response(split_data, status=status.HTTP_400_BAD_REQUEST) From e1f2e797982e6a43d080deb225f5a9f9697f07ea Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 9 Jun 2024 23:55:23 +0200 Subject: [PATCH 085/446] Completed graphic statistics for drylab --- .../templates/drylab/stats_services_time.html | 117 ++++++++++++++++-- drylab/views.py | 92 ++++++++++++-- 2 files changed, 193 insertions(+), 16 deletions(-) diff --git a/drylab/templates/drylab/stats_services_time.html b/drylab/templates/drylab/stats_services_time.html index c415e3312..006207969 100644 --- a/drylab/templates/drylab/stats_services_time.html +++ b/drylab/templates/drylab/stats_services_time.html @@ -1,6 +1,7 @@ {% extends 'core/base.html' %} {% load static %} {% block content %} + {% include "core/cdn_table_functionality.html" %} {% include "core/graphic_chart_functionality.html" %} {% include "drylab/menu.html" %}
    @@ -47,15 +48,15 @@
    {{ error_message }}
    type="button" role="tab" aria-controls="nav-samples" - aria-selected="false">Analized Samples + aria-selected="false">Analyzed Samples + aria-controls="nav-samples-table" + aria-selected="false">Analyzed Samples table
    @@ -194,10 +195,38 @@

    {{ services_stats_info.period_time }}.

    role="tabpanel" aria-labelledby="nav-samples-tab">
    -
    +
    +
    +
    +

    Analyzed Samples per user

    +
    +
    + {% if services_stats_info.graphic_samples_per_user %} +
    + {{ services_stats_info.graphic_samples_per_user |safe }} + {% endif %} +
    +
    +
    +
    +
    +
    +

    Analyzed Samples

    +
    +
    + {% if services_stats_info.graphic_analyzed_samples %} +
    + {{ services_stats_info.graphic_analyzed_samples |safe }} + {% endif %} +
    +
    +
    +
    +
    +
    -

    Analyzed Samples in Runs

    +

    Analyzed Samples from sequenced in runs

    {% if services_stats_info.graphic_samples_per_run %} @@ -207,6 +236,56 @@

    Analyzed Samples in Runs

    +
    +
    +
    +

    Analyzed Samples grouped in projects

    +
    +
    + {% if services_stats_info.graphic_samples_per_project %} +
    + {{ services_stats_info.graphic_samples_per_project |safe }} + {% endif %} +
    +
    +
    +
    +
    +
    @@ -259,4 +338,28 @@

    Services statistics

    {% endif %} + {% endblock %} diff --git a/drylab/views.py b/drylab/views.py index 8eb944d33..afa3bad4f 100644 --- a/drylab/views.py +++ b/drylab/views.py @@ -1171,9 +1171,7 @@ def stats_by_services_request(request): else: user_services[user] = 1 - period_of_time_selected = str( - " From " + start_date + " to " + end_date - ) + period_of_time_selected = str(" From " + start_date + " to " + end_date) # creating the graphic for requested services data_source = drylab.utils.graphics.column_graphic_dict( "Requested Services from users", @@ -1442,10 +1440,18 @@ def stats_by_services_request(request): # Samples handled by requested services - sample_in_services_objs = drylab.models.RequestedSamplesInServices.objects.filter(samples_in_service__in=services_found) - ana_sample_in_runs = sample_in_services_objs.exclude(run_name=None).values("run_name").annotate(sample_count=Count("sample_name"), sample_name=F("run_name")) + sample_in_services_objs = ( + drylab.models.RequestedSamplesInServices.objects.filter( + samples_in_service__in=services_found + ) + ) + ana_sample_in_runs = ( + sample_in_services_objs.exclude(run_name=None) + .values("run_name") + .annotate(sample_count=Count("sample_name")) + ) g_data = core.utils.graphics.preparation_graphic_data( - "Samples state", + "Analyzed Samples from Runs", "", "", "", @@ -1454,12 +1460,80 @@ def stats_by_services_request(request): "run_name", "sample_count", ) - import pdb; pdb.set_trace() - graphic_req_l3_services = core.fusioncharts.fusioncharts.FusionCharts( + graphic_req_samples_run = core.fusioncharts.fusioncharts.FusionCharts( "column3d", "ex9", "600", "375", "chart-9", "json", g_data ) services_stats_info["graphic_samples_per_run"] = ( - graphic_req_l3_services.render() + graphic_req_samples_run.render() + ) + ana_sample_in_proj = ( + sample_in_services_objs.exclude(project_name=None) + .values("project_name") + .annotate(sample_count=Count("sample_name")) + ) + g_data = core.utils.graphics.preparation_graphic_data( + "Analyzed Samples per projects", + "", + "", + "", + "ocean", + ana_sample_in_proj, + "project_name", + "sample_count", + ) + graphic_req_samples_proj = core.fusioncharts.fusioncharts.FusionCharts( + "column3d", "ex10", "600", "375", "chart-10", "json", g_data + ) + services_stats_info["graphic_samples_per_project"] = ( + graphic_req_samples_proj.render() + ) + ana_sample_in_user = sample_in_services_objs.values( + "samples_in_service__service_user_id__username" + ).annotate(sample_count=Count("sample_name")) + g_data = core.utils.graphics.preparation_graphic_data( + "Analyzed Samples per user", + "", + "", + "", + "ocean", + ana_sample_in_user, + "samples_in_service__service_user_id__username", + "sample_count", + ) + + graphic_req_samples_user = core.fusioncharts.fusioncharts.FusionCharts( + "column3d", "ex11", "600", "375", "chart-11", "json", g_data + ) + services_stats_info["graphic_samples_per_user"] = ( + graphic_req_samples_user.render() + ) + analyzed_samples = {} + analyzed_samples["Sequenced samples"] = sample_in_services_objs.exclude( + only_recorded_sample=False + ).count() + analyzed_samples["Only recorded samples"] = sample_in_services_objs.exclude( + only_recorded_sample=True + ).count() + data_source = drylab.utils.graphics.graphic_3D_pie( + "Analyzed Samples", + period_of_time_selected, + "", + "", + "fint", + analyzed_samples, + ) + graphic_analyzed_samples = core.fusioncharts.fusioncharts.FusionCharts( + "pie3d", "ex12", "600", "400", "chart-12", "json", data_source + ) + services_stats_info["graphic_analyzed_samples"] = ( + graphic_analyzed_samples.render() + ) + services_stats_info["table_samples"] = sample_in_services_objs.values_list( + "sample_name", + "samples_in_service__service_request_number", + "samples_in_service__pk", + "samples_in_service__service_user_id__username", + "samples_in_service__service_state__state_display", ) return render( request, From c287e47baa42c107a8b43173ced5a776941d6be3 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 9 Jun 2024 23:57:38 +0200 Subject: [PATCH 086/446] litin --- drylab/views.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/drylab/views.py b/drylab/views.py index afa3bad4f..e122e323b 100644 --- a/drylab/views.py +++ b/drylab/views.py @@ -8,7 +8,7 @@ from django.conf import settings from django.contrib.auth.decorators import login_required from django.core.files.storage import FileSystemStorage -from django.db.models import Prefetch, Count, F +from django.db.models import Prefetch, Count from django.http import HttpResponse from django.shortcuts import redirect, render From 0e560a7cbc812ba3bcac1ab383a4936715a2cea8 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 10 Jun 2024 13:44:05 +0200 Subject: [PATCH 087/446] Changes because PR review --- core/utils/samples.py | 6 +++--- install.sh | 7 +++++-- wetlab/utils/crontab_update_run.py | 2 +- wetlab/utils/test_conf.py | 2 +- 4 files changed, 10 insertions(+), 7 deletions(-) diff --git a/core/utils/samples.py b/core/utils/samples.py index b02862765..4febefe2c 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -199,7 +199,7 @@ def validate_sample_data( req_user: str, app_name: str, repeat_allowed: bool = False, - allow_user__repeat: bool = False, + allow_user_repeat: bool = False, ) -> tuple: """sample data validation @@ -208,7 +208,7 @@ def validate_sample_data( req_user (str): requested user name app_name (str): application name (wetlab, drylab, core, etc.) repeat_allowed (bool, optional): allow or not that sample can be repeated. Defaults to False. - allow_user__repeat (bool, optional): if allowed to be repeated check if same request user is allowed have repeated sample names. Defaults to False. + allow_user_repeat (bool, optional): if allowed to be repeated check if same request user is allowed have repeated sample names. Defaults to False. Returns: tuple: returns result as boolean and a dictionary with the following keys @@ -231,7 +231,7 @@ def validate_sample_data( # collect the sample names already in the database in case that the user # is not allowed to repeat if not repeat_allowed: - if not allow_user__repeat: + if not allow_user_repeat: if core.models.Samples.objects.filter( sample_user__username__exact=req_user ).exists(): diff --git a/install.sh b/install.sh index 2ad520c4c..dba79a70d 100644 --- a/install.sh +++ b/install.sh @@ -795,9 +795,12 @@ if [ $install == true ]; then if [ $LOG_TYPE == "symbolic_link" ]; then if [ -d $LOG_PATH ]; then if [ ! -d $INSTALL_PATH/logs ]; then - ln -s $LOG_PATH $INSTALL_PATH/logs - chmod 775 $LOG_PATH + echo "Deleting existing symbolin link" + rm $INSTALL_PATH/logs fi + echo "Creating symbolic link to log folder" + ln -s $LOG_PATH $INSTALL_PATH/logs + chmod 775 $LOG_PATH else echo "Log folder path: $LOG_PATH does not exist. Fix it in the install_settings.txt and run again." exit 1 diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 28610ba5d..2178bf48d 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -228,7 +228,7 @@ def search_update_new_runs(request_reason): logger.debug( "%s : Found the experiment name called : %s", new_run, experiment_name ) - exclude_states = ["Error", "recorded"] + exclude_states = ["error", "recorded"] if ( wetlab.models.RunProcess.objects.filter(run_name__exact=experiment_name) .exclude(state__run_state_name__in=exclude_states) diff --git a/wetlab/utils/test_conf.py b/wetlab/utils/test_conf.py index 64377fa9b..ca11b4edd 100644 --- a/wetlab/utils/test_conf.py +++ b/wetlab/utils/test_conf.py @@ -207,7 +207,7 @@ def execute_test_for_testing_run(run_test_name): wetlab.utils.crontab_update_run.manage_run_in_processed_run_state( conn, [run_obj] ) - if run_obj.get_state() == "errorR": + if run_obj.get_state() == "error": run_result["ERROR"] = "Error when processing run in Processed Run state" break else: From e7a4929f3b373632f5dd4cf9a6586434b86ba536 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 15 Jun 2024 18:22:36 +0200 Subject: [PATCH 088/446] removed spare values on run states --- conf/first_install_tables.json | 20 -------------------- 1 file changed, 20 deletions(-) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index c0d99a12e..b8359979c 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -1608,26 +1608,6 @@ "show_in_stats": true } }, -{ - "model": "wetlab.runstates", - "pk": 11, - "fields": { - "run_state_name": "spare_1", - "state_display": "", - "description": "", - "show_in_stats": false - } -}, -{ - "model": "wetlab.runstates", - "pk": 12, - "fields": { - "run_state_name": "spare_2", - "state_display": "", - "description": "", - "show_in_stats": false - } -}, { "model": "wetlab.runerrors", "pk": 1, From 48da3eb28ce9f2aec2bbe0fca35c2a7abe20f61b Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 4 Aug 2024 12:52:05 +0200 Subject: [PATCH 089/446] Update install.sh to remove the comma in RawTopUnknowBarcodes --- README.md | 2 ++ install.sh | 3 +++ 2 files changed, 5 insertions(+) diff --git a/README.md b/README.md index ebb8a8e36..66a597a94 100644 --- a/README.md +++ b/README.md @@ -143,6 +143,8 @@ If you have already iSkyLIMS on version 2.3.0 you can upgrade to the latest stab Version 3.0.0 is a major release with important upgrades in third parties dependencies like bootstrap. Also, we 've done a huge work on refactoring and variables/function renaming that affects the database. For more details about the changes see the release notes. +If you requires to upgrade from version 3.0.0 to the latest one 3.1.x and in your system you have already defined library pools, then you need to collect this data, before to run the upgrade script. For more information read [Pre-requisites for upgrade from 3.0.0 to 3.1.x](#pre-requisites-for-upgrade-from-30x-to-31x) + #### Pre-requisites Because in this upgrade many tables in database are modified it is required that you backup: diff --git a/install.sh b/install.sh index dba79a70d..6eb00cd4f 100644 --- a/install.sh +++ b/install.sh @@ -561,6 +561,9 @@ if [ $upgrade == true ]; then echo "Done migrate command." else + # execute the script to remove the comma in RawTopUnknowBarcodes table + echo "Running migration script: remove_comma_rawtopunknownbarcodes" + ./manage.py runscript remove_comma_rawtopunknownbarcodes echo "checking for database changes" if python manage.py makemigrations | grep -q "No changes"; then # check for pending migrations From 6bae78076804b2181c2845989323922a8ca03ee6 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 4 Aug 2024 13:04:11 +0200 Subject: [PATCH 090/446] rename migration script --- install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/install.sh b/install.sh index 6eb00cd4f..ec502c131 100644 --- a/install.sh +++ b/install.sh @@ -563,7 +563,7 @@ if [ $upgrade == true ]; then else # execute the script to remove the comma in RawTopUnknowBarcodes table echo "Running migration script: remove_comma_rawtopunknownbarcodes" - ./manage.py runscript remove_comma_rawtopunknownbarcodes + ./manage.py runscript convert_rawtop_counter_to_int echo "checking for database changes" if python manage.py makemigrations | grep -q "No changes"; then # check for pending migrations From b2ebb6a4b54239137331d51cfc29372127ef8a0e Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 6 Aug 2024 11:30:04 +0200 Subject: [PATCH 091/446] Include condition to reduce updating items to database --- wetlab/scripts/convert_rawtop_counter_to_int.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/wetlab/scripts/convert_rawtop_counter_to_int.py b/wetlab/scripts/convert_rawtop_counter_to_int.py index 61b6a2706..5f2104c8a 100644 --- a/wetlab/scripts/convert_rawtop_counter_to_int.py +++ b/wetlab/scripts/convert_rawtop_counter_to_int.py @@ -8,9 +8,10 @@ def run(): """ top_bar_objs = wetlab.models.RawTopUnknowBarcodes.objects.all() for top_bar_obj in top_bar_objs: - try: - top_bar_obj.count = int(top_bar_obj.count.replace(",", "")) - top_bar_obj.save() - except AttributeError: - continue + if "," in top_bar_obj.count: + try: + top_bar_obj.count = int(top_bar_obj.count.replace(",", "")) + top_bar_obj.save() + except AttributeError: + continue return From 69967267058e30d3ac0f6792f3acdc78c12a5ea3 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 21 Aug 2024 14:50:38 +0200 Subject: [PATCH 092/446] solved issue in run script to convert to int when alrady migrated --- wetlab/scripts/convert_rawtop_counter_to_int.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/wetlab/scripts/convert_rawtop_counter_to_int.py b/wetlab/scripts/convert_rawtop_counter_to_int.py index 5f2104c8a..94c8fb6a3 100644 --- a/wetlab/scripts/convert_rawtop_counter_to_int.py +++ b/wetlab/scripts/convert_rawtop_counter_to_int.py @@ -8,7 +8,8 @@ def run(): """ top_bar_objs = wetlab.models.RawTopUnknowBarcodes.objects.all() for top_bar_obj in top_bar_objs: - if "," in top_bar_obj.count: + # Check if table has been updated to int + if isinstance(top_bar_obj.count, int) is False: try: top_bar_obj.count = int(top_bar_obj.count.replace(",", "")) top_bar_obj.save() From 8055ec48776bab6dcb3ec02fa9872363c4931ee0 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 21 Aug 2024 14:52:45 +0200 Subject: [PATCH 093/446] update the python packages used in iskylims --- conf/requirements.txt | 40 ++++++++++++++++++++-------------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/conf/requirements.txt b/conf/requirements.txt index 308fe4e3a..7c84da8e4 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -1,25 +1,25 @@ -wheel==0.38.1 -asn1crypto==1.5.0 -bcrypt==4.0.1 -biopython==1.79 -cryptography==41.0.6 -Django==4.2.7 -django-crispy-forms==2.0 +wheel==0.44.0 +asn1crypto==1.5.1 +bcrypt==4.2.0 +biopython==1.84 +cryptography==43.0.0 +Django==4.2.15 +django-crispy-forms==2.3 crispy-bootstrap5==0.7 django-crontab==0.7.1 -django-js-asset==2.0.0 -django-mptt==0.14.0 -django-mptt-admin==2.4.1 -django-cleanup==7.0.0 +django-js-asset==2.2.0 +django-mptt==0.16.0 +django-mptt-admin==2.6.2 +django-cleanup==8.1.0 interop>1.1.22 -mod_wsgi==4.9.4 -mysqlclient==2.0.3 -paramiko==3.4.0 -jsonschema==4.17.3 +mod_wsgi==5.0.0 +mysqlclient==2.2.4 +paramiko==3.4.1 +jsonschema==4.23.0 pysmb==1.2.9.1 -django_extensions==3.2.1 -djangorestframework==3.14.0 -drf-yasg==1.21.5 +django_extensions==3.2.3 +djangorestframework==3.15.2 +drf-yasg==1.21.7 xlrd==2.0.1 -pandas==1.5.3 -openpyxl==3.1.1 +pandas==2.2.2 +openpyxl==3.1.5 From c2219411bcbbf6d7869af7badb86eec60208bcf4 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 22 Aug 2024 10:09:39 +0200 Subject: [PATCH 094/446] Update installation procedure for the upgrade --- LEAME.md | 63 +++----- README.md | 98 ++++++------ leame_upgrade_2.3.0_to_3.0.md | 288 +++++++++++++++++++++++++++++++++ upgrade_2.3_to_3.0.md | 290 ++++++++++++++++++++++++++++++++++ 4 files changed, 655 insertions(+), 84 deletions(-) create mode 100644 leame_upgrade_2.3.0_to_3.0.md create mode 100644 upgrade_2.3_to_3.0.md diff --git a/LEAME.md b/LEAME.md index c68cf701a..35a923194 100644 --- a/LEAME.md +++ b/LEAME.md @@ -20,7 +20,7 @@ De acuerdo con la infraestructura existente, la secuenciación se realiza en un - [Crear la base de datos de iSkyLIMS y otorgar permisos](#crear-la-base-de-datos-de-iskylims-y-otorgar-permisos) - [Configuración de ajustes](#configuración-de-ajustes) - [Ejecutar el script de instalación](#ejecutar-el-script-de-instalación) - - [Actualización a la versión 3.0.0 de iSkyLIMS](#actualización-a-la-versión-300-de-iskylims) + - [Actualización a la versión 3.1.0 de iSkyLIMS](#actualización-a-la-versión-310-de-iskylims) - [Prerrequisitos](#prerrequisitos) - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) - [Configuración de opciones](#configuración-de-opciones) @@ -46,16 +46,18 @@ Antes de comenzar la instalación, asegúrate de lo siguiente: - Tienes privilegios de **sudo** para instalar los paquetes de software adicionales que iSkyLIMS necesita. - Dependencias: - Librerías: -``` + +```bash yum groupinstall "Development tools" yum install zlib-devel bzip2-devel openssl-devel \ wget httpd-devel mysql-libs sqlite sqlite-devel \ mariadb-devel mysql-client libffi-devel \ gnuplot cifs-utils ``` - - lsb_relase: - - RedHat/CentOS: `yum install redhat-lsb-core` - - Ubuntu: `apt install lsb-core lsb-release` + +- lsb_relase: + - RedHat/CentOS: `yum install redhat-lsb-core` + - Ubuntu: `apt install lsb-core lsb-release` - Base de datos MySQL > 8.0 o MariaDB > 10.4 - Tienes configurado un servidor local para enviar correos electrónicos. - git > 2.34 @@ -64,7 +66,6 @@ Antes de comenzar la instalación, asegúrate de lo siguiente: - Tienes una conexión a la carpeta compartida de Samba donde se almacenan las carpetas de ejecución (por ejemplo, galera/NGS_Data). - Dependencias: - ### Instalación de iSkyLIMS en Docker Puedes probar iSkyLIMS creando un contenedor Docker en tu máquina local. @@ -143,34 +144,31 @@ bash install.sh --install app sudo bash install.sh --install full ``` -### Actualización a la versión 3.0.0 de iSkyLIMS - -Si ya tienes iSkyLIMS en la versión 2.3.0, puedes actualizar a la última versión estable, la 3.0.0. +## Actualización a la versión 3.1.0 de iSkyLIMS -La versión 3.0.0 es una versión importante con actualizaciones significativas en dependencias de terceros como Bootstrap. También hemos realizado un gran trabajo en la refactorización y el cambio de nombres de variables/funciones que afectan a la base de datos. Para obtener más detalles sobre los cambios, consulta las notas de la versión. +En esta version se han implementado fallos de código y mejoras en las gráficas. Para obtener más detalles sobre los cambios, consulta las notas de la versión. -#### Prerrequisitos +### Prerrequisitos -Debido a que en esta actualización se modifican muchas tablas en la base de datos, es necesario que hagas una copia de seguridad de: +Por temas de seguridad es recomendado realizar una copia de seguridad de: - La base de datos de iSkyLIMS. - La carpeta de iSkyLIMS (carpeta de instalación completa, por ejemplo, /opt/iSkyLIMS). -Se recomienda encarecidamente que hagas estas copias de seguridad y las guardes de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). +Se recomienda encarecidamente que se hagan estas copias de seguridad y se guarden de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). -#### Clonar el repositorio de GitHub +### Clonar el repositorio de GitHub -También hemos cambiado la forma en que se instala y actualiza iSkyLIMS. A partir de ahora, iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). +A partir ya de la version anterior, ahora el código de iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). -Abre una terminal de Linux y dirígete a un directorio donde se descargará el código de iSkyLIMS. +Abre una terminal de Linux y dirígete a un directorio donde estaba descargado el código de iSkyLIMS. Actualiza el codigo ```bash -cd < directorio distinto al directorio de instalación > -git clone https://gitlab.isciii.es/BU-ISCIII/iskylims.git iskylims -cd iskylims +cd < directorio donde esta el codigo anterior de iskylims de instalación > +git pull ``` -#### Configuración de opciones +### Configuración de opciones Copia la plantilla de configuración inicial en un archivo llamado install_settings.txt @@ -185,22 +183,12 @@ Abre el archivo de configuración con tu editor favorito para establecer tus pro nano install_settings.txt ``` -#### Ejecución del script de actualización - -Si en tu organización se requiere que las dependencias u otros elementos que necesiten permisos de administrador sean instalados por una persona diferente a la que instala la aplicación, puedes utilizar el script de instalación en varios pasos de la siguiente manera. - -El script te irá solicitando confirmación en algun paso, si todo está yendo bien sin errores deberás pulsar `y` o `yes` según te lo solicite. - -> Nota: Los errores: "ERROR 1064 (42000) at line 1: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'query' at line 1" son normales ya que se trata del título de las sentencias sql que no deben ejecutarse. Se puede ignorar. +### Ejecución del script de actualización -##### Pasos que necesitan permisos de adminsitración +Debido a que los paquetes de python de los que depende iSkyLIMs se han ido actualizando +desde la última release es necesario que sean actualizados. -En primer lugar, debes cambiar el nombre de la carpeta de la aplicación en la carpeta de instalación (`/opt/iSkyLIMS`): - -```bash -# Necesitas ser usuario root para realizar esta operación -sudo mv /opt/iSkyLIMS /opt/iskylims -``` +#### Pasos que necesitan permisos de adminsitración Asegúrate de que la carpeta de instalación tenga los permisos correctos para que la persona que instala la aplicación pueda escribir en esa carpeta. @@ -216,16 +204,15 @@ En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se ada sudo bash install.sh --upgrade dep # PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. SI SE VA A INSTALAR POR OTRA PERSONA SIN ROOT NO HACER ESTO. -sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +sudo bash install.sh --upgrade full --git_revision main --tables ``` ##### Pasos que no necesitan de permisos de administración -A continuación instalamos la aplicación de iskylims usando el siguiente comando: +Actualiza a la nueva version de la aplicación de iskylims usando el siguiente comando: ```bash -# para actualizar la aplicación de iskylims, incluyendo los cambios necesarios para la versión en base de datos. NO ES NECESARIO DISPONER DE PERMISOS ROOT. -bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +bash install.sh --upgrade app --git_revision main --tables ``` Por último, asegúrate que los permisos de la carpeta son correctos. diff --git a/README.md b/README.md index 66a597a94..7d933698d 100644 --- a/README.md +++ b/README.md @@ -21,8 +21,8 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Create iskylims database and grant permissions](#create-iskylims-database-and-grant-permissions) - [Configuration settings](#configuration-settings) - [Run installation script](#run-installation-script) - - [Upgrade to iSkyLIMS version 3.0.0](#upgrade-to-iskylims-version-300) - - [Pre-requisites](#pre-requisites-1) + - [Upgrade to iSkyLIMS version 3.1.0](#Upgrade from 3.0.x to iSkyLIMS version 3.1.x) + - [Pre-requisites](#pre-requisites) - [Clone github repository](#clone-github-repository-1) - [Configuration settings](#configuration-settings-1) - [Running upgrade script](#running-upgrade-script) @@ -131,43 +131,45 @@ above description. sudo bash install.sh --install dep # to install only iSkyLIMS application -bash install.sh --install app +bash install.sh --install app --git_revision main --tables # to install both software -sudo bash install.sh --install full +sudo bash install.sh --install full --git_revision main --tables ``` -### Upgrade to iSkyLIMS version 3.0.0 +## Upgrade from 3.0.x to iSkyLIMS version 3.1.x -If you have already iSkyLIMS on version 2.3.0 you can upgrade to the latest stable version 3.0.0. +Follow the following steps to upgrade from version 3.0.0 to the latest one 3.1.x -Version 3.0.0 is a major release with important upgrades in third parties dependencies like bootstrap. Also, we 've done a huge work on refactoring and variables/function renaming that affects the database. For more details about the changes see the release notes. +### Pre-requisites for upgrade -If you requires to upgrade from version 3.0.0 to the latest one 3.1.x and in your system you have already defined library pools, then you need to collect this data, before to run the upgrade script. For more information read [Pre-requisites for upgrade from 3.0.0 to 3.1.x](#pre-requisites-for-upgrade-from-30x-to-31x) +Before starting the upgrade procedure is highly recomended to perform the following steps: -#### Pre-requisites +- Create a full backup of iSkyLIMS database +- Backup all iSkyLIMS folders (complete installation folder, p.e /opt/iSkyLIMS) -Because in this upgrade many tables in database are modified it is required that you backup: - -- iSkyLIMS database -- iSkyLIMS folder (complete installation folder, p.e /opt/iSkyLIMS) - -##### Pre-requisites for upgrade from 3.0.x to 3.1.x - -- Perform a backup of LibraryPool by running the folowing command +- If in your system you have already defined library pools, then you need to collect this data, before to run the upgrade script. Perform a backup of LibraryPool by running the folowing command. ```bash - mysql --user= --password= --host= --port= iskylims -e "SELECT* FROM wetlab_library_pool" > + mysql --user= --password= --host= --port= iskylims -e "SELECT* FROM wetlab_library_pool" > ``` It is highly recomended that you made these backups and keep them safely in case of upgrade failure, to recover your system. -#### Clone github repository +### Clone github repository -We've also change the way that iSkyLIMS is installed and upgraded. From now on iskylims is downloaded in a user folder and installed elsewhere (p.e /opt/). +From it was defined in previous releases the iSkyLIMS code is downloaded in a user folder and then installed elsewhere (p.e /opt/). -Open a linux terminal and move to a directory where iSkyLIMS code will be -downloaded +If you have already clone the repository from the previous 3.0.0 release open a +linux terminal and move towards the directory of iSkyLIMS repository. + +```bash +cd < your personal folder/iskylims > +git pull +``` + +If the repository was not created then open a linux terminal and move to a directory +where iSkyLIMS code will be downloaded ```bash cd < your personal folder > @@ -175,7 +177,7 @@ git clone https://github.com/BU-ISCIII/iSkyLIMS.git iskylims cd iskylims ``` -#### Configuration settings +### Configuration settings Copy the initial setting template into a file named install_settings.txt @@ -191,18 +193,13 @@ database ,email settings and the local IP of the server where iSkyLIMS will run. sudo nano install_settings.txt ``` -#### Running upgrade script +### Running upgrade script If your organization requires that dependencies / stuff that needs root are installed by a different person that install the application the you can use the install script in several steps as follows. First you need to rename the folder app name in the installation folder (`/opt/iSkyLIMS`): -##### Steps requiring root - -```bash -# You need root for this operation -sudo mv /opt/iSkyLIMS /opt/iskylims -``` +#### Steps requiring root Make sure that the installation folder has the correct permissions so the person installing the app can write in that folder. @@ -211,23 +208,32 @@ Make sure that the installation folder has the correct permissions so the person /scripts/hardening.sh ``` -In the linux terminal execute one of the following command that fit better to you: +From the previous release software dependences (Python packages) must be updated to the releases defined in the requirement.txt file. + +In the linux terminal execute the following command- ```bash # to upgrade only software packages dependences. NEEDS ROOT. sudo bash install.sh --upgrade dep - -# to install both software. NEEDS ROOT. -sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables ``` -##### Steps not requiring root +#### Steps not requiring root + +Next you need to upgrade iskylims app. Please use one of the commands below: + +If you are using the library pool, you must indicate in the installation script the file +you already backup and execute the following command. + +```bash +# to upgrade iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. +bash install.sh --upgrade app --script --git_revision main --tables +``` -Next you need to upgrade iskylims app. Please use the command below: +If restauration of libary preparation is not required then execute the following command ```bash -# to upgrade only iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. -bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +# to upgrade iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. +bash install.sh --upgrade app ---git_revision main -tables ``` Make sure that the installation folder has the correct permissions. @@ -237,11 +243,11 @@ Make sure that the installation folder has the correct permissions. /scripts/hardening.sh ``` -#### What to do if something fails +## What to do if something fails When we upgrade using the installation script we are performing several changes in the database. If something fails we need to restore the app situation before anything happened and start all over. -We need to copy back the full `/opt/iSkyLIMS` folder back to `/opt` (or your installation path preference), and restore the database doing something like this: +We need to copy back the full `/opt/iskylims` folder back to `/opt/iskylims` (or your installation path preference), and restore the database doing something like this: ```bash sudo rm -rf /opt/iskylims @@ -253,9 +259,9 @@ mysql -u iskylims -h dmysqlps.isciiides.es mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` -### Final configuration steps +## Final configuration steps -#### SAMBA configurarion +### SAMBA configurarion - Login with admin account. - Go to Massive sequencing @@ -264,17 +270,17 @@ mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/b - Fill the form with the appropiate params for the samba shared folder: ![samba form](img/samba_form.png) -#### Email verification +### Email verification - Go to Massive sequencing - Go to Configuration -> Email configuration - Fill the form with the needed params for your email configuration and try to send a test email. -#### Configure Apache server +### Configure Apache server Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf -#### Verification of the installation +### Verification of the installation Open the navigator and type "localhost" or the "server local IP" and check that iSkyLIMs is running. @@ -285,6 +291,6 @@ You can also check some of the functionality, while also checking samba and data - Check all tabs so every connectin is successful. - Run the 3 tests for each sequencing machine: MiSeq, NextSeq and NovaSeq. -### iSkyLIMS documentation +## iSkyLIMS documentation iSkyLIMS documentation is available at [https://iskylims.readthedocs.io/en/latest](https://iskylims.readthedocs.io/en/latest) diff --git a/leame_upgrade_2.3.0_to_3.0.md b/leame_upgrade_2.3.0_to_3.0.md new file mode 100644 index 000000000..c68cf701a --- /dev/null +++ b/leame_upgrade_2.3.0_to_3.0.md @@ -0,0 +1,288 @@ +# iSkyLIMS + +[![Django](https://img.shields.io/static/v1?label=Django&message=4.2&color=azul?style=plastic&logo=django)](https://github.com/django/django) +[![Python](https://img.shields.io/static/v1?label=Python&message=3.8.10&color=verde?style=plastic&logo=Python)](https://www.python.org/) +[![Bootstrap](https://img.shields.io/badge/Bootstrap-v5.0-azulvioleta?style=plastic&logo=Bootstrap)](https://getbootstrap.com) +[![versión](https://img.shields.io/badge/versión-3.0.0-naranja?style=plastic&logo=GitHub)](https://github.com/BU-ISCIII/iskylims.git) + +La introducción de la secuenciación masiva (MS) en las instalaciones de genómica ha significado un crecimiento exponencial en la generación de datos, lo que requiere un sistema de seguimiento preciso, desde la preparación de la biblioteca hasta la generación de archivos fastq, el análisis y la entrega al investigador. El software diseñado para manejar esas tareas se llama Sistemas de Gestión de Información de Laboratorio (LIMS), y su software debe adaptarse a las necesidades particulares de su laboratorio de genómica. iSkyLIMS nace con el objetivo de ayudar con las tareas de laboratorio húmedo e implementar un flujo de trabajo que guíe a los laboratorios de genómica en sus actividades, desde la preparación de la biblioteca hasta la producción de datos, reduciendo los posibles errores asociados a la tecnología de alto rendimiento y facilitando el control de calidad de la secuenciación. Además, iSkyLIMS conecta el laboratorio húmedo con el laboratorio seco, facilitando el análisis de datos por parte de bioinformáticos. + +![Imagen](img/iskylims_scheme.png) + +De acuerdo con la infraestructura existente, la secuenciación se realiza en un instrumento Illumina NextSeq. Los datos se almacenan en un dispositivo de almacenamiento masivo NetApp y los archivos fastq se generan (bcl2fastq) en un clúster de cómputo de alto rendimiento Sun Grid Engine (SGE-HPC). Los servidores de aplicaciones ejecutan aplicaciones web para el análisis bioinformático (GALAXY), la aplicación iSkyLIMS y alojan la capa de información de MySQL. El flujo de trabajo de iSkyLIMS WetLab se ocupa del seguimiento y las estadísticas de la ejecución de la secuenciación. El seguimiento de la ejecución pasa por cinco estados: "registrado", el usuario de genómica registra la nueva ejecución de la secuenciación en el sistema, el proceso esperará hasta que la ejecución se complete en la máquina y los datos se transfieran al dispositivo de almacenamiento masivo; "Envío de hoja de muestra", el archivo de hoja de muestra con la información de la ejecución de la secuenciación se copiará en la carpeta de ejecución para el proceso de bcl2fastq; "Procesamiento de datos", se procesan los archivos de parámetros de ejecución y los datos se almacenan en la base de datos; "Estadísticas en ejecución", los datos de desmultiplexación generados en el proceso de bcl2fastq se procesan y almacenan en la base de datos, "Completado", todos los datos se procesan y almacenan correctamente. Se proporcionan estadísticas por muestra, por proyecto, por ejecución y por investigación, así como informes anuales y mensuales. El flujo de trabajo de iSkyLIMS DryLab se encarga de la solicitud de servicios de bioinformática y estadísticas. El usuario solicita servicios que pueden estar asociados con una ejecución de secuenciación. Se proporciona seguimiento de estadísticas y servicios. + +- [iSkyLIMS](#iskylims) + - [Instalación](#instalación) + - [Requisitos previos](#requisitos-previos) + - [Instalación de iSkyLIMS en Docker](#instalación-de-iskylims-en-docker) + - [Instalación de iSkyLIMS en su servidor con Ubuntu/CentOS](#instalación-de-iskylims-en-su-servidor-con-ubuntucentos) + - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github) + - [Crear la base de datos de iSkyLIMS y otorgar permisos](#crear-la-base-de-datos-de-iskylims-y-otorgar-permisos) + - [Configuración de ajustes](#configuración-de-ajustes) + - [Ejecutar el script de instalación](#ejecutar-el-script-de-instalación) + - [Actualización a la versión 3.0.0 de iSkyLIMS](#actualización-a-la-versión-300-de-iskylims) + - [Prerrequisitos](#prerrequisitos) + - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) + - [Configuración de opciones](#configuración-de-opciones) + - [Ejecución del script de actualización](#ejecución-del-script-de-actualización) + - [Pasos que necesitan permisos de adminsitración](#pasos-que-necesitan-permisos-de-adminsitración) + - [Pasos que no necesitan de permisos de administración](#pasos-que-no-necesitan-de-permisos-de-administración) + - [Qué hacer si algo falla](#qué-hacer-si-algo-falla) + - [Pasos finales de configuración](#pasos-finales-de-configuración) + - [Configuración de SAMBA](#configuración-de-samba) + - [Verificación de correo electrónico](#verificación-de-correo-electrónico) + - [Configurar el servidor Apache](#configurar-el-servidor-apache) + - [Verificación de la instalación](#verificación-de-la-instalación) + - [Documentación de iSkyLIMS](#documentación-de-iskylims) + +## Instalación + +Si tienes algún problema o deseas informar de algún error, por favor, publícalo en [issue](https://github.com/BU-ISCIII/iSkyLIMS/issues) + +### Requisitos previos + +Antes de comenzar la instalación, asegúrate de lo siguiente: + +- Tienes privilegios de **sudo** para instalar los paquetes de software adicionales que iSkyLIMS necesita. +- Dependencias: + - Librerías: +``` + yum groupinstall "Development tools" + yum install zlib-devel bzip2-devel openssl-devel \ + wget httpd-devel mysql-libs sqlite sqlite-devel \ + mariadb-devel mysql-client libffi-devel \ + gnuplot cifs-utils +``` + - lsb_relase: + - RedHat/CentOS: `yum install redhat-lsb-core` + - Ubuntu: `apt install lsb-core lsb-release` +- Base de datos MySQL > 8.0 o MariaDB > 10.4 +- Tienes configurado un servidor local para enviar correos electrónicos. +- git > 2.34 +- Tienes Apache servidor v2.4 +- Tienes Python > 3.8 (si lo compilas debes haber instalado previamente las dependecias de arriba) +- Tienes una conexión a la carpeta compartida de Samba donde se almacenan las carpetas de ejecución (por ejemplo, galera/NGS_Data). +- Dependencias: + + +### Instalación de iSkyLIMS en Docker + +Puedes probar iSkyLIMS creando un contenedor Docker en tu máquina local. + +Clona el repositorio de GitHub de iSkyLIMS y ejecuta el script de Docker para crear el contenedor Docker. + +```bash +git clone https://github.com/BU-ISCIII/iSkyLIMS.git iSkyLIMS +sudo bash docker_install.sh +``` + +El script crea un contenedor de Docker Compose con 3 servicios: + +- web1: contiene la aplicación web iSkyLIMS +- db1: contiene la base de datos MySQL +- samba: contiene el servidor Samba + +Después de crear Docker y tener los servicios en funcionamiento, la estructura de la base de datos y los datos iniciales se cargan en la base de datos. Cuando se complete este paso, se le pedirá que defina al superusuario que tendrá acceso a las páginas de administración de Django. Puede escribir cualquier nombre, pero recomendamos que utilice "admin", ya que más adelante se le pedirá un usuario administrador cuando defina la configuración inicial. + +Siga el mensaje de instrucciones para crear la cuenta del superusuario. + +Cuando el script finalice, abra su navegador escribiendo **localhost:8001** para acceder a iSkyLIMS + +### Instalación de iSkyLIMS en su servidor con Ubuntu/CentOS + +#### Clonar el repositorio de GitHub + +Abra una terminal de Linux y vaya a un directorio donde se descargará el código de iSkyLIMS + +```bash +cd +git clone https://github.com/BU-ISCIII/iskylims.git iskylims +cd iskylims +``` + +#### Crear la base de datos de iSkyLIMS y otorgar permisos + +1. Cree una nueva base de datos llamada "iskylims" (esto es obligatorio). +2. Cree un nuevo usuario con permisos para leer y modificar esa base de datos. +3. Anote el nombre de usuario, la contraseña y la información del servidor de la base de datos. + +#### Configuración de ajustes + +Copia la plantilla de ajustes iniciales en un archivo llamado `install_settings.txt` + +```bash +cp conf/template_install_settings.txt install_settings.txt +``` + +Abra el archivo de configuración con su editor favorito para establecer sus propios valores para la base de datos, la configuración de correo electrónico y la dirección IP local del servidor donde se ejecutará iSkyLIMS. + +```bash +sudo nano install_settings.txt +``` + +#### Ejecutar el script de instalación + +iSkyLIMS debe instalarse en el directorio "/opt". + +Necesitará privilegios de administrador para instalar las dependencias. Para manejar diferentes responsabilidades de instalación dentro de la organización, donde es posible que no sea la persona con privilegios de administrador, nuestro script de instalación tiene estas opciones en el parámetro `--install`: + +- `dep`: para instalar los paquetes de software, así como los paquetes de Python dentro del entorno virtual. Se necesita permisos de administrador. +- `app`: para instalar solo el software de la aplicación iSkyLIMS sin necesidad de tener permisos de administrador. +- `full`: si tiene directamente permisos de administrador, puede instalar tanto las dependencias como la aplicación con esta opción. + +Ejecute uno de los siguientes comandos en una terminal de Linux para la instalación, de acuerdo con la descripción anterior. + +```bash +# para instalar solo las dependencias +sudo bash install.sh --install dep + +# para instalar la aplicación iskylims +bash install.sh --install app + +# para instalar ambos al mismo tiempo +sudo bash install.sh --install full +``` + +### Actualización a la versión 3.0.0 de iSkyLIMS + +Si ya tienes iSkyLIMS en la versión 2.3.0, puedes actualizar a la última versión estable, la 3.0.0. + +La versión 3.0.0 es una versión importante con actualizaciones significativas en dependencias de terceros como Bootstrap. También hemos realizado un gran trabajo en la refactorización y el cambio de nombres de variables/funciones que afectan a la base de datos. Para obtener más detalles sobre los cambios, consulta las notas de la versión. + +#### Prerrequisitos + +Debido a que en esta actualización se modifican muchas tablas en la base de datos, es necesario que hagas una copia de seguridad de: + +- La base de datos de iSkyLIMS. +- La carpeta de iSkyLIMS (carpeta de instalación completa, por ejemplo, /opt/iSkyLIMS). + +Se recomienda encarecidamente que hagas estas copias de seguridad y las guardes de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). + +#### Clonar el repositorio de GitHub + +También hemos cambiado la forma en que se instala y actualiza iSkyLIMS. A partir de ahora, iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). + +Abre una terminal de Linux y dirígete a un directorio donde se descargará el código de iSkyLIMS. + +```bash +cd < directorio distinto al directorio de instalación > +git clone https://gitlab.isciii.es/BU-ISCIII/iskylims.git iskylims +cd iskylims +``` + +#### Configuración de opciones + +Copia la plantilla de configuración inicial en un archivo llamado install_settings.txt + +```bash +cp conf/template_install_settings.txt install_settings.txt +``` + +Abre el archivo de configuración con tu editor favorito para establecer tus propios valores para la base de datos, la configuración de correo electrónico y la dirección IP local del servidor donde se ejecutará iSkyLIMS. +> Si utilizas un sistema basado en Windows para modificar el archivo, asegúrate de que el archivo se guarde con una codificación amigable para Linux, como ASCII o UTF-8. + +```bash +nano install_settings.txt +``` + +#### Ejecución del script de actualización + +Si en tu organización se requiere que las dependencias u otros elementos que necesiten permisos de administrador sean instalados por una persona diferente a la que instala la aplicación, puedes utilizar el script de instalación en varios pasos de la siguiente manera. + +El script te irá solicitando confirmación en algun paso, si todo está yendo bien sin errores deberás pulsar `y` o `yes` según te lo solicite. + +> Nota: Los errores: "ERROR 1064 (42000) at line 1: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'query' at line 1" son normales ya que se trata del título de las sentencias sql que no deben ejecutarse. Se puede ignorar. + +##### Pasos que necesitan permisos de adminsitración + +En primer lugar, debes cambiar el nombre de la carpeta de la aplicación en la carpeta de instalación (`/opt/iSkyLIMS`): + +```bash +# Necesitas ser usuario root para realizar esta operación +sudo mv /opt/iSkyLIMS /opt/iskylims +``` + +Asegúrate de que la carpeta de instalación tenga los permisos correctos para que la persona que instala la aplicación pueda escribir en esa carpeta. + +```bash +# En el caso de que tengas un script para esta tarea. Necesitarás ajustar este script de acuerdo al cambio en el nombre de la ruta: /opt/iSkyLIMS a /opt/iskylims +sudo /scripts/hardening.sh +``` + +En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se adapte a ti: + +```bash +# para actualizar solo las dependencias del software. ES NECESARIO DISPONER DE PERMISOS DE ROOT. +sudo bash install.sh --upgrade dep + +# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. SI SE VA A INSTALAR POR OTRA PERSONA SIN ROOT NO HACER ESTO. +sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` + +##### Pasos que no necesitan de permisos de administración + +A continuación instalamos la aplicación de iskylims usando el siguiente comando: + +```bash +# para actualizar la aplicación de iskylims, incluyendo los cambios necesarios para la versión en base de datos. NO ES NECESARIO DISPONER DE PERMISOS ROOT. +bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` + +Por último, asegúrate que los permisos de la carpeta son correctos. + +```bash +# En el caso de que tengas un script para esta tarea. En esta versión han cambiado algunas rutas a ficheros, es posible que tengas que ajustar el script en consecuencia. +sudo /scripts/hardening.sh +``` + +#### Qué hacer si algo falla + +Cuando actualizamos la aplicación usando el script estamos realizando varios cambios en la base de datos. Si algo falla tenemos que restaurar el estado anterior, antes de que hubiesemos realizado ninguna acción. + +Necesitamos copiar de vuelta nuestro backup de carpet ade aplicación a /opt/iSkyLIMS (o la carpeta de instalación de nuestra elección), y restaurar la base de datos realizando algo como lo siguiente: + +```bash +sudo rm -rf /opt/iskylims +sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ +sudo /scripts/hardening.sh +mysql -u iskylims -h dmysqlps.isciiides.es -p +# drop database iskylims; +# create database iskylims; +mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql +``` + +### Pasos finales de configuración + +#### Configuración de SAMBA + +- Inicia sesión con la cuenta de administrador. +- Ve a Massive Sequencing +![Ir a WetLab](img/got_to_wetlab.png){width:50px} +- Ve a Configuración -> Configuración de SAMBA +- Completa el formulario con los parámetros apropiados para la carpeta compartida de SAMBA: +![Formulario SAMBA](img/samba_form.png) + +#### Verificación de correo electrónico + +- Ve a Massive Sequencing +- Ve a Configuración -> Configuración de correo electrónico +- Completa el formulario con los parámetros necesarios para la configuración de correo electrónico y trata de enviar un correo de prueba. + +#### Configurar el servidor Apache + +Copia el archivo de configuración de Apache que se encuentra en la carpeta `conf` según tu distribución dentro del directorio de configuración de Apache y cambia el nombre a iskylims.conf. Revisa cualquier requerimiento de tu sistema, se trata solo de un ejemplo. + +#### Verificación de la instalación + +Abre el navegador y escribe "localhost" o la "IP local del servidor" para comprobar que iSkyLIMS está en funcionamiento. + +También puedes verificar algunas funcionalidades mientras compruebas las conexiones de SAMBA y la base de datos usando: + +- Ve a [configurationTest](https://iskylims.isciii.es/wetlab/configurationTest/) +- Haz clic en Enviar +- Verifica todas las pestañas para asegurarte de que cada conexión sea exitosa. +- Ejecuta las 3 pruebas para cada máquina de secuenciación: MiSeq, NextSeq y NovaSeq. + +### Documentación de iSkyLIMS + +La documentación de iSkyLIMS está disponible en [https://iskylims.readthedocs.io/en/latest](https://iskylims.readthedocs.io/en/latest) diff --git a/upgrade_2.3_to_3.0.md b/upgrade_2.3_to_3.0.md new file mode 100644 index 000000000..66a597a94 --- /dev/null +++ b/upgrade_2.3_to_3.0.md @@ -0,0 +1,290 @@ +# iSkyLIMS + +[![Django](https://img.shields.io/static/v1?label=Django&message=4.2&color=blue?style=plastic&logo=django)](https://github.com/django/django) +[![Python](https://img.shields.io/static/v1?label=Python&message=3.8.10&color=green?style=plastic&logo=Python)](https://www.python.org/) +[![Bootstrap](https://img.shields.io/badge/Bootstrap-v5.0-blueviolet?style=plastic&logo=Bootstrap)](https://getbootstrap.com) +[![version](https://img.shields.io/badge/version-3.0.0-orange?style=plastic&logo=GitHub)](https://github.com/BU-ISCIII/iskylims.git) + +The introduction of massive sequencing (MS) in genomics facilities has meant an exponential growth in data generation, requiring a precise tracking system, from library preparation to fastq file generation, analysis and delivery to the researcher. Software designed to handle those tasks are called Laboratory Information Management Systems (LIMS), and its software has to be adapted to their own genomics laboratory particular needs. iSkyLIMS is born with the aim of helping with the wet laboratory tasks, and implementing a workflow that guides genomics labs on their activities from library preparation to data production, reducing potential errors associated to high throughput technology, and facilitating the quality control of the sequencing. Also, iSkyLIMS connects the wet lab with dry lab facilitating data analysis by bioinformaticians. + +![Image](img/iskylims_scheme.png) + +According to existent infrastructure sequencing is performed on an Illumina NextSeq instrument. Data is stored in NetApp mass storage device and fastq files are generated (bcl2fastq) on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). +Application servers run web applications for bioinformatics analysis (GALAXY), the iSkyLIMS app, and host the MySQL information tier. iSkyLIMS WetLab workflow deals with sequencing run tracking and statistics. Run tracking passes through five states: "recorded” genomics user record the new sequencing run into the system, the process will wait till run is completed by the machine and data is transferred to the mass storage device; “Sample sheet sent” sample sheet file with the sequencing run information will be copied to the run folder for bcl2fastq process; “Processing data” run parameters files are processed and data is stored in the database; “Running stats” demultiplexing data generated in bcl2fastq process is processed and stored into the database, “Completed” all data is processed and stored successfully. Statistics per sample, per project, per run and per investigation are provided, as well as annual and monthly reports. iSkyLIMS DryLab workflow deals with bioinformatics services request and statistics. User request services that can be associated with a sequencing run. Stats and services tracking is provided. + +- [iSkyLIMS](#iskylims) + - [Installation](#installation) + - [Pre-requisites](#pre-requisites) + - [iSkyLIMS docker installation](#iskylims-docker-installation) + - [Install iSkyLIMS in your server running ubuntu/CentOS](#install-iskylims-in-your-server-running-ubuntucentos) + - [Clone github repository](#clone-github-repository) + - [Create iskylims database and grant permissions](#create-iskylims-database-and-grant-permissions) + - [Configuration settings](#configuration-settings) + - [Run installation script](#run-installation-script) + - [Upgrade to iSkyLIMS version 3.0.0](#upgrade-to-iskylims-version-300) + - [Pre-requisites](#pre-requisites-1) + - [Clone github repository](#clone-github-repository-1) + - [Configuration settings](#configuration-settings-1) + - [Running upgrade script](#running-upgrade-script) + - [Steps requiring root](#steps-requiring-root) + - [Steps not requiring root](#steps-not-requiring-root) + - [What to do if something fails](#what-to-do-if-something-fails) + - [Final configuration steps](#final-configuration-steps) + - [SAMBA configurarion](#samba-configurarion) + - [Email verification](#email-verification) + - [Configure Apache server](#configure-apache-server) + - [Verification of the installation](#verification-of-the-installation) + - [iSkyLIMS documentation](#iskylims-documentation) + +## Installation + +For any problems or bug reporting please post us an [issue](https://github.com/BU-ISCIII/iSkyLIMS/issues) + +### Pre-requisites + +Before starting the installation make sure : + +- You have **sudo privileges** to install the additional software packets that iSkyLIMS needs. +- Database MySQL > 8.0 or MariaDB > 10.4 +- Local server configured for sending emails +- Apache server v2.4 +- git > 2.34 +- Python > 3.8 +- Connection to samba shared folder where run folders are stored (p.e galera/NGS_Data) +- Dependencies: + - lsb_release: + - RedHat/CentOS: ```yum install redhat-lsb-core``` + - Ubuntu: ```apt install lsb-core lsb-release``` + +### iSkyLIMS docker installation + +You can test iSkyLIMS by creating a docker container on your local machine. + +Clone the iSkyLIMS github repository and run the docker script to create the docker + +```bash +git clone https://github.com/BU-ISCIII/iSkyLIMS.git iSkyLIMS +sudo bash docker_install.sh +``` + +The script creates a docker compose container with 3 services: + +- web1: contains the iSkyLIMS web application +- db1: contains the mySQL database +- samba: contains samba server + +After Docker is created and services are up, database structure and initial data are loaded into database. When this step is completed, you will be asked to define the super user which will have access to django admin pages. You can type any name, but we recommend that you use "admin", because admin user is requested later on when defining the initial settings. + +Follow the prompt message to create the super user account. + +When script ends open your navigator typing **localhost:8001** to access to iSkyLIMS + +### Install iSkyLIMS in your server running ubuntu/CentOS + +#### Clone github repository + +Open a linux terminal and move to a directory where iSkyLIMS code will be +downloaded + +```bash +cd < your personal folder > +git clone https://github.com/BU-ISCIII/iskylims.git iskylims +cd iskylims +``` + +#### Create iskylims database and grant permissions + +1. Create a new database named "iskylims" (this is mandatory) +2. Create a new user with permission to read and modify that database. +3. Write down user, passwd and db server info. + +#### Configuration settings + +Copy the initial setting template into a file named install_settings.txt + +```bash +cp conf/template_install_settings.txt install_settings.txt +``` + +Open with your favourite editor the configuration file to set your own values for +database ,email settings and the local IP of the server where iSkyLIMS will run. + +```bash +nano install_settings.txt +``` + +#### Run installation script + +iSkyLIMS should be installed on the "/opt" directory. + +You will need sudo privileges for installing dependencies. In order to handle different installation responsibilities inside the organization, where you may not be the person with root privileges, our instalation script has these options in ```--install``` parameter: + +- dep: to install the software packages as well as python packages inside the virtual environment. Root is needed. +- app: to install only the iSkyLIMS application software without need of being root. +- full: if you directly have root permissions you can install both deps and app at the same time with this option. + +Execute one of the following commands in a linux terminal to install, according as +above description. + +```bash +# to install only software packages dependences +sudo bash install.sh --install dep + +# to install only iSkyLIMS application +bash install.sh --install app + +# to install both software +sudo bash install.sh --install full +``` + +### Upgrade to iSkyLIMS version 3.0.0 + +If you have already iSkyLIMS on version 2.3.0 you can upgrade to the latest stable version 3.0.0. + +Version 3.0.0 is a major release with important upgrades in third parties dependencies like bootstrap. Also, we 've done a huge work on refactoring and variables/function renaming that affects the database. For more details about the changes see the release notes. + +If you requires to upgrade from version 3.0.0 to the latest one 3.1.x and in your system you have already defined library pools, then you need to collect this data, before to run the upgrade script. For more information read [Pre-requisites for upgrade from 3.0.0 to 3.1.x](#pre-requisites-for-upgrade-from-30x-to-31x) + +#### Pre-requisites + +Because in this upgrade many tables in database are modified it is required that you backup: + +- iSkyLIMS database +- iSkyLIMS folder (complete installation folder, p.e /opt/iSkyLIMS) + +##### Pre-requisites for upgrade from 3.0.x to 3.1.x + +- Perform a backup of LibraryPool by running the folowing command + +```bash + mysql --user= --password= --host= --port= iskylims -e "SELECT* FROM wetlab_library_pool" > +``` + +It is highly recomended that you made these backups and keep them safely in case of upgrade failure, to recover your system. + +#### Clone github repository + +We've also change the way that iSkyLIMS is installed and upgraded. From now on iskylims is downloaded in a user folder and installed elsewhere (p.e /opt/). + +Open a linux terminal and move to a directory where iSkyLIMS code will be +downloaded + +```bash +cd < your personal folder > +git clone https://github.com/BU-ISCIII/iSkyLIMS.git iskylims +cd iskylims +``` + +#### Configuration settings + +Copy the initial setting template into a file named install_settings.txt + +```bash +cp conf/template_install_settings.txt install_settings.txt +``` + +Open with your favourite editor the configuration file to set your own values for +database ,email settings and the local IP of the server where iSkyLIMS will run. +> If you use a windows-based system for modifying the file, make sure the file is saved using a linux-friendly encoding like ASCII or UTF-8 + +```bash +sudo nano install_settings.txt +``` + +#### Running upgrade script + +If your organization requires that dependencies / stuff that needs root are installed by a different person that install the application the you can use the install script in several steps as follows. + +First you need to rename the folder app name in the installation folder (`/opt/iSkyLIMS`): + +##### Steps requiring root + +```bash +# You need root for this operation +sudo mv /opt/iSkyLIMS /opt/iskylims +``` + +Make sure that the installation folder has the correct permissions so the person installing the app can write in that folder. + +```bash +# In case you have a script for this task. You'll need to adjust this script according to the name changing: /opt/iSkyLIMS to /opt/iskylims +/scripts/hardening.sh +``` + +In the linux terminal execute one of the following command that fit better to you: + +```bash +# to upgrade only software packages dependences. NEEDS ROOT. +sudo bash install.sh --upgrade dep + +# to install both software. NEEDS ROOT. +sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` + +##### Steps not requiring root + +Next you need to upgrade iskylims app. Please use the command below: + +```bash +# to upgrade only iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. +bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` + +Make sure that the installation folder has the correct permissions. + +```bash +# In case you have a script for this task. Some paths have changed in this version, so you may need to adjust your hardening script. +/scripts/hardening.sh +``` + +#### What to do if something fails + +When we upgrade using the installation script we are performing several changes in the database. If something fails we need to restore the app situation before anything happened and start all over. + +We need to copy back the full `/opt/iSkyLIMS` folder back to `/opt` (or your installation path preference), and restore the database doing something like this: + +```bash +sudo rm -rf /opt/iskylims +sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ +sudo /scripts/hardening.sh +mysql -u iskylims -h dmysqlps.isciiides.es +# drop database iskylims; +# create database iskylims; +mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql +``` + +### Final configuration steps + +#### SAMBA configurarion + +- Login with admin account. +- Go to Massive sequencing +![go_to_wetlab](img/got_to_wetlab.png){width:50px} +- Go to Configuration -> Samba configuration +- Fill the form with the appropiate params for the samba shared folder: +![samba form](img/samba_form.png) + +#### Email verification + +- Go to Massive sequencing +- Go to Configuration -> Email configuration +- Fill the form with the needed params for your email configuration and try to send a test email. + +#### Configure Apache server + +Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf + +#### Verification of the installation + +Open the navigator and type "localhost" or the "server local IP" and check that iSkyLIMs is running. + +You can also check some of the functionality, while also checking samba and database connections using: + +- Go to [configuration test](https://iskylims.isciii.es/wetlab/configurationTest/) +- Click submit +- Check all tabs so every connectin is successful. +- Run the 3 tests for each sequencing machine: MiSeq, NextSeq and NovaSeq. + +### iSkyLIMS documentation + +iSkyLIMS documentation is available at [https://iskylims.readthedocs.io/en/latest](https://iskylims.readthedocs.io/en/latest) From 1f1de18deff19085b93b1690a208b54ea7b5c48b Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 22 Aug 2024 10:29:29 +0200 Subject: [PATCH 095/446] Solved issue #274. Docker installation fails --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index d9e8c221a..332f6d047 100644 --- a/Dockerfile +++ b/Dockerfile @@ -20,7 +20,7 @@ RUN git checkout develop RUN pip install -r conf/requirements.txt -RUN bash install.sh --install app --dev --conf conf/docker_install_settings.txt --docker +RUN bash install.sh --install app --git_revision main --conf conf/docker_install_settings.txt --docker WORKDIR /opt/iskylims From caa25183355590ba142f439009df6332eaa533c0 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 24 Aug 2024 23:30:17 +0200 Subject: [PATCH 096/446] Delete the old static file before copying the new files --- install.sh | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/install.sh b/install.sh index ec502c131..b162e10c5 100644 --- a/install.sh +++ b/install.sh @@ -593,7 +593,9 @@ if [ $upgrade == true ]; then echo "Done migrate command." fi fi - + # update static files + echo "Deleting static files..." + rm -rf $INSTALL_PATH/static echo "Running collect statics..." python manage.py collectstatic echo "Done collect statics" From 9174bf396934314945cebd29477fd813235cd0a7 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 25 Aug 2024 09:48:52 +0200 Subject: [PATCH 097/446] solved issue 280 Error in Analyzed Samples plot from Statistics by service requested --- drylab/views.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/drylab/views.py b/drylab/views.py index e122e323b..6947407fe 100644 --- a/drylab/views.py +++ b/drylab/views.py @@ -1509,10 +1509,10 @@ def stats_by_services_request(request): ) analyzed_samples = {} analyzed_samples["Sequenced samples"] = sample_in_services_objs.exclude( - only_recorded_sample=False + only_recorded_sample=True ).count() analyzed_samples["Only recorded samples"] = sample_in_services_objs.exclude( - only_recorded_sample=True + only_recorded_sample=False ).count() data_source = drylab.utils.graphics.graphic_3D_pie( "Analyzed Samples", From 6d568cdaa186e910e7fca6bf121d9ca83826db7a Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 25 Aug 2024 10:40:40 +0200 Subject: [PATCH 098/446] solved issue #282 Rename some names in tabs and plots --- .../templates/drylab/stats_services_time.html | 28 +++++++++---------- drylab/views.py | 20 ++++++------- 2 files changed, 24 insertions(+), 24 deletions(-) diff --git a/drylab/templates/drylab/stats_services_time.html b/drylab/templates/drylab/stats_services_time.html index 006207969..4ba8bf0d0 100644 --- a/drylab/templates/drylab/stats_services_time.html +++ b/drylab/templates/drylab/stats_services_time.html @@ -32,7 +32,7 @@
    {{ error_message }}
    type="button" role="tab" aria-controls="nav-req-services" - aria-selected="true">Requested services + aria-selected="true">Services requests + aria-selected="false">Requested by + aria-selected="false">Sample analysis + aria-selected="false">Sample analysis table
    @@ -82,7 +82,7 @@

    {{ services_stats_info.period_time }}.

    -

    Services status

    +

    Service status

    {% if services_stats_info.graphic_status_requested_services %} @@ -118,7 +118,7 @@

    {{ services_stats_info.period_time }}.

    -

    Requested Services per user

    +

    Service Requests by User

    {% if services_stats_info.graphic_requested_services_per_user %} @@ -133,7 +133,7 @@

    Requested Services per user

    -

    Requested Services per center

    +

    Service Requests by center

    {% if services_stats_info.graphic_center_services %} @@ -147,7 +147,7 @@

    Requested Services per center

    -

    Services per classification area

    +

    Service Requests by Classification Area

    {% if services_stats_info.graphic_area_services %} @@ -162,7 +162,7 @@

    Services per classification area

    -

    Service statistics per center

    +

    Service Request Statistics by Center

    {{ services_stats_info.period_time }}.

    @@ -176,7 +176,7 @@

    {{ services_stats_info.period_time }}.

    -

    Services Statistics per classification area

    +

    Service Request Statistics by Classification Area

    {{ services_stats_info.period_time }}.

    @@ -198,7 +198,7 @@

    {{ services_stats_info.period_time }}.

    -

    Analyzed Samples per user

    +

    Analyzed Samples by User

    {% if services_stats_info.graphic_samples_per_user %} @@ -211,7 +211,7 @@

    Analyzed Samples per user

    -

    Analyzed Samples

    +

    Sample Analysis

    {% if services_stats_info.graphic_analyzed_samples %} @@ -226,7 +226,7 @@

    Analyzed Samples

    -

    Analyzed Samples from sequenced in runs

    +

    Analyzed Samples from Sequencing Runs

    {% if services_stats_info.graphic_samples_per_run %} @@ -239,7 +239,7 @@

    Analyzed Samples from sequenced in runs

    -

    Analyzed Samples grouped in projects

    +

    Analyzed Samples by Project

    {% if services_stats_info.graphic_samples_per_project %} diff --git a/drylab/views.py b/drylab/views.py index 6947407fe..7e76e35a0 100644 --- a/drylab/views.py +++ b/drylab/views.py @@ -1174,7 +1174,7 @@ def stats_by_services_request(request): period_of_time_selected = str(" From " + start_date + " to " + end_date) # creating the graphic for requested services data_source = drylab.utils.graphics.column_graphic_dict( - "Requested Services from users", + "Service request by user", period_of_time_selected, "User names", "Number of Services", @@ -1199,7 +1199,7 @@ def stats_by_services_request(request): # creating the graphic for status services data_source = drylab.utils.graphics.graphic_3D_pie( - "Status of Requested Services", + "Service request status", period_of_time_selected, "", "", @@ -1235,7 +1235,7 @@ def stats_by_services_request(request): # creating the graphic for areas data_source = drylab.utils.graphics.column_graphic_dict( - "Services requested per Area", + "Service requests by area", period_of_time_selected, "Area ", "Number of Services", @@ -1267,7 +1267,7 @@ def stats_by_services_request(request): user_center_dict[user_center] = 1 # creating the graphic for areas data_source = drylab.utils.graphics.column_graphic_dict( - "Services requested per Center", + "Services requests by center", period_of_time_selected, "Center ", "Number of Services", @@ -1324,7 +1324,7 @@ def stats_by_services_request(request): if d_period not in user_services_period[center]: user_services_period[center][d_period] = 0 data_source = drylab.utils.graphics.column_graphic_per_time( - "Services requested by center and period of time", + "Service requests by center and period of time", period_of_time_selected, "date", "number of services", @@ -1374,7 +1374,7 @@ def stats_by_services_request(request): user_area_services_period[area][d_period] = 0 data_source = drylab.utils.graphics.column_graphic_per_time( - "Services requested by Area ", + "Service requests by Area ", period_of_time_selected, "date", "number of services", @@ -1451,7 +1451,7 @@ def stats_by_services_request(request): .annotate(sample_count=Count("sample_name")) ) g_data = core.utils.graphics.preparation_graphic_data( - "Analyzed Samples from Runs", + "Analyzed Samples from sequencing runs", "", "", "", @@ -1472,7 +1472,7 @@ def stats_by_services_request(request): .annotate(sample_count=Count("sample_name")) ) g_data = core.utils.graphics.preparation_graphic_data( - "Analyzed Samples per projects", + "Analyzed samples by project", "", "", "", @@ -1491,7 +1491,7 @@ def stats_by_services_request(request): "samples_in_service__service_user_id__username" ).annotate(sample_count=Count("sample_name")) g_data = core.utils.graphics.preparation_graphic_data( - "Analyzed Samples per user", + "Analyzed samples bu user", "", "", "", @@ -1515,7 +1515,7 @@ def stats_by_services_request(request): only_recorded_sample=False ).count() data_source = drylab.utils.graphics.graphic_3D_pie( - "Analyzed Samples", + "Sample Analysis", period_of_time_selected, "", "", From 8d7f083e802c6225295f77d8563d79c2392a4f4d Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 25 Aug 2024 12:59:48 +0200 Subject: [PATCH 099/446] fixed issue #285 A new entry in DDBB at StateInCountry every time new city is created --- core/models.py | 14 +++++++------- wetlab/api/utils/sample.py | 25 +++++++++++++++++-------- 2 files changed, 24 insertions(+), 15 deletions(-) diff --git a/core/models.py b/core/models.py index 407c451b0..32d32ff21 100644 --- a/core/models.py +++ b/core/models.py @@ -55,7 +55,7 @@ def create_new_city(self, data): state_obj = None new_city = self.create( belongs_to_state=state_obj, - city_name=data["cityName"], + city_name=data["city_name"], geo_loc_latitude=data["latitude"], geo_loc_longitude=data["longitude"], apps_name=data["apps_name"], @@ -99,12 +99,12 @@ class LabRequestManager(models.Manager): def create_lab_request(self, data): city_obj = City.objects.filter(pk__exact=data["city"]).last() new_lab_request = self.create( - lab_name=data["labName"], - lab_name_coding=data["labNameCoding"], - lab_unit=data["labUnit"], - lab_contact_name=data["labContactName"], - lab_phone=data["labPhone"], - lab_email=data["labEmail"], + lab_name=data["lab_name"], + lab_name_coding=data["lab_name_coding"], + lab_unit=data["lab_unit"], + lab_contact_name=data["lab_contact_name"], + lab_phone=data["lab_phone"], + lab_email=data["lab_email"], address=data["address"], apps_name=data["apps_name"], lab_city=city_obj, diff --git a/wetlab/api/utils/sample.py b/wetlab/api/utils/sample.py index 35346b8e9..675c81620 100644 --- a/wetlab/api/utils/sample.py +++ b/wetlab/api/utils/sample.py @@ -6,7 +6,12 @@ import wetlab.config -def create_state(state, apps_name): +def create_state_if_not_exists(state, apps_name): + # Check if state is defined in database + if core.models.StateInCountry.objects.filter(state_name__iexact=state).exists(): + return core.models.StateInCountry.objects.filter( + state_name__iexact=state + ).last() """Create state instance""" data = {"state": state, "apps_name": apps_name} return core.models.StateInCountry.objects.create_new_state(data) @@ -14,7 +19,9 @@ def create_state(state, apps_name): def create_city(data, apps_name): """Create a City instance""" - data["state"] = create_state(data["geo_loc_state"], apps_name).get_state_id() + data["state"] = create_state_if_not_exists( + data["geo_loc_state"], apps_name + ).get_state_id() data["city_name"] = data["geo_loc_city"] data["latitude"] = data["geo_loc_latitude"] data["longitude"] = data["geo_loc_longitude"] @@ -25,7 +32,7 @@ def create_city(data, apps_name): def create_new_laboratory(lab_data): """Create new laboratory instance with the data collected in the request""" if core.models.City.objects.filter( - city_name__exact=lab_data["geo_loc_city"] + city_name__iexact=lab_data["geo_loc_city"] ).exists(): city_id = ( core.models.City.objects.filter(city_name__exact=lab_data["geo_loc_city"]) @@ -34,17 +41,17 @@ def create_new_laboratory(lab_data): ) else: if core.models.StateInCountry.objects.filter( - state_name__exact=lab_data["geo_loc_state"] + state_name__iexact=lab_data["geo_loc_state"] ).exists(): lab_data["state"] = ( core.models.StateInCountry.objects.filter( - state_name__exact=lab_data["geo_loc_state"] + state_name__iexact=lab_data["geo_loc_state"] ) .last() .get_state_id() ) else: - lab_data["state"] = create_state( + lab_data["state"] = create_state_if_not_exists( lab_data["geo_loc_state"], lab_data["apps_name"] ).get_state_id() city_id = create_city(lab_data, lab_data["apps_name"]).get_city_id() @@ -60,7 +67,9 @@ def create_new_sample_type(sample_type, apps_name): data["optional_fields"] = "0,8" data["apps_name"] = apps_name data["sample_type"] = sample_type - sample_type_serializers = core.models.CreateSampleTypeSerializer(data=data) + sample_type_serializers = wetlab.api.serializers.CreateSampleTypeSerializer( + data=data + ) if sample_type_serializers.is_valid(): sample_type_obj = sample_type_serializers.save() return sample_type_obj @@ -136,7 +145,7 @@ def get_sample_project_obj(project_name): def include_instances_in_sample(data, lab_data, apps_name): """Collect the instances before creating the sample instance - If laboratory will be created if it is not defined + Define laboratory if not defined yet """ if core.models.LabRequest.objects.filter( lab_name__iexact=data["lab_request"] From 605b0f768d734541efa36e03217cc2fec2d2fc65 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 26 Aug 2024 09:25:36 +0200 Subject: [PATCH 100/446] renamed file names for previous upgrade --- leame_upgrade_2.3.0_to_3.0.md => actualizaciones_previas.md | 0 upgrade_2.3_to_3.0.md => upgrade_docs_previous.md | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename leame_upgrade_2.3.0_to_3.0.md => actualizaciones_previas.md (100%) rename upgrade_2.3_to_3.0.md => upgrade_docs_previous.md (100%) diff --git a/leame_upgrade_2.3.0_to_3.0.md b/actualizaciones_previas.md similarity index 100% rename from leame_upgrade_2.3.0_to_3.0.md rename to actualizaciones_previas.md diff --git a/upgrade_2.3_to_3.0.md b/upgrade_docs_previous.md similarity index 100% rename from upgrade_2.3_to_3.0.md rename to upgrade_docs_previous.md From 34555055f1486a6aa8820d13296820b0dfd77931 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 26 Aug 2024 12:28:05 +0200 Subject: [PATCH 101/446] fixed issue #283 Error in Services Statistics per classification area plot --- drylab/views.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/drylab/views.py b/drylab/views.py index 7e76e35a0..950f9e33a 100644 --- a/drylab/views.py +++ b/drylab/views.py @@ -1351,9 +1351,9 @@ def stats_by_services_request(request): ).exists(): user_area = django_utils.models.Profile.objects.get( profile_user_id=user_id - ).profile_area + ).get_clasification_area() else: - user_center = "Not defined" + user_area = "Not defined" if date_service not in time_values_dict: time_values_dict[date_service] = 1 if user_area in user_area_services_period: From d040a961e15b87070dde5991f1f196270ab30b32 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 26 Aug 2024 16:40:28 +0200 Subject: [PATCH 102/446] Fixing service states that was wrong defined in the initial tables --- conf/first_install_tables.json | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index b8359979c..3f2b8fd87 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -20130,19 +20130,19 @@ "model": "drylab.servicestate", "pk": 2, "fields": { - "state_value": "in_progress", - "state_display": "In Progress", - "description": "Bioinformatic is working on the service", - "show_in_stats": true + "state_value": "archived", + "state_display": "Archived", + "description": null, + "show_in_stats": false } }, { "model": "drylab.servicestate", "pk": 3, "fields": { - "state_value": "delivered", - "state_display": "Delivered", - "description": "Service wascompleted and results were sent to the user", + "state_value": "approved", + "state_display": "Approved", + "description": "Service request has been accepted", "show_in_stats": false } }, @@ -20150,9 +20150,9 @@ "model": "drylab.servicestate", "pk": 4, "fields": { - "state_value": "queued", - "state_display": "Queued", - "description": "Service is the the list, waiting for a bioinformatic to be handled", + "state_value": "in_progress", + "state_display": "In Progress", + "description": "Bioinformatic is working on the service", "show_in_stats": true } }, @@ -20170,9 +20170,9 @@ "model": "drylab.servicestate", "pk": 6, "fields": { - "state_value": "approved", - "state_display": "Approved", - "description": "Service request has been accepted", + "state_value": "delivered", + "state_display": "Delivered", + "description": "Service wascompleted and results were sent to the user", "show_in_stats": false } }, @@ -20180,10 +20180,10 @@ "model": "drylab.servicestate", "pk": 7, "fields": { - "state_value": "archived", - "state_display": "Archived", - "description": null, - "show_in_stats": false + "state_value": "queued", + "state_display": "Queued", + "description": "Service is the the list, waiting for a bioinformatic to be handled", + "show_in_stats": true } }, { From c80c537582e51cbccef57f6dba1aa9d8d59dca95 Mon Sep 17 00:00:00 2001 From: luissian Date: Mon, 26 Aug 2024 17:18:21 +0200 Subject: [PATCH 103/446] filling the resolution states intial table --- conf/first_install_tables.json | 73 ++++++++++++++++++++++++++++++++++ 1 file changed, 73 insertions(+) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index 3f2b8fd87..8c28e6d90 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -20186,6 +20186,79 @@ "show_in_stats": true } }, +{ + "model": "drylab.servicestate", + "pk": 8, + "fields": { + "state_value": "on_hold", + "state_display": "On hold", + "description": "Resolution is on hold, waiting for user provides more information" + } +} +, +{ + "model": "drylab.resolutionstates", + "pk": 1, + "fields": { + "state_value": "recorded", + "state_display": "Recorded", + "description": "Resolution has been successful recorded in iSkyLIMS" + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 2, + "fields": { + "state_value": "in_progress", + "state_display": "In Progress", + "description": "Bioinformatic is working on the Resolution" + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 3, + "fields": { + "state_value": "delivered", + "state_display": "Delivered", + "description": "Resolution wascompleted and results were sent to the user" + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 4, + "fields": { + "state_value": "queued", + "state_display": "Queued", + "description": "Resolution is the the list, waiting for a bioinformatic to be handled" + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 5, + "fields": { + "state_value": "rejected", + "state_display": "Rejected", + "description": "Resolution can not be handle because is not in porfoloio or for any other reason" + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 6, + "fields": { + "state_value": "approved", + "state_display": "Approved", + "description": "Resolution request has been accepted" + } +}, +{ + "model": "drylab.resolutionstates", + "pk": 7, + "fields": { + "state_value": "archived", + "state_display": "Archived", + "description": null + } +}, { "model": "drylab.resolutionstates", "pk": 8, From ed11c68aed8906a2e2b44176d672b3cff6775549 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 28 Aug 2024 12:07:41 +0200 Subject: [PATCH 104/446] fixing error while testing upload data to database --- conf/first_install_tables.json | 42 +++++++++++++++++++++++++++++++++ core/templates/core/footer.html | 25 +++++++++++--------- wetlab/api/utils/sample.py | 2 +- 3 files changed, 57 insertions(+), 12 deletions(-) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index 8c28e6d90..cb3c1345c 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -20267,6 +20267,48 @@ "state_display": "On hold", "description": "Resolution is on hold, waiting for user provides more information" } +}, +{ "model": "core.ontologymap", + "pk": 1, + "fields": { + "label": "collection_sample_date", + "ontology": "GENEPIO:0001174" + } +}, +{ "model": "core.ontologymap", + "pk": 2, + "fields": { + "label": "sample_entry_date", + "ontology": "NCIT:C93644" + } +}, +{ "model": "core.ontologymap", + "pk": 3, + "fields": { + "label": "sample_name", + "ontology": "GENEPIO:0001123" + } +}, +{ "model": "core.ontologymap", + "pk": 4, + "fields": { + "label": "species", + "ontology": "GENEPIO:0001386" + } +}, +{ "model": "core.ontologymap", + "pk": 5, + "fields": { + "label": "lab_request", + "ontology": "GENEPIO:0001153" + } +}, +{ "model": "core.ontologymap", + "pk": 6, + "fields": { + "label": "sequencing_date", + "ontology": "GENEPIO:0001447" + } } ] diff --git a/core/templates/core/footer.html b/core/templates/core/footer.html index 999f9cdce..6e70abfdc 100644 --- a/core/templates/core/footer.html +++ b/core/templates/core/footer.html @@ -6,30 +6,33 @@
    Contact us
      -
      • +
    • + +
    Social networks
    - - - +     +
    Powered by
    - +
    -

    Version 3.0.0

    -
    -
    -
    - +

    Version 3.1.0

    + +
    +
    + diff --git a/wetlab/api/utils/sample.py b/wetlab/api/utils/sample.py index 675c81620..062964b6e 100644 --- a/wetlab/api/utils/sample.py +++ b/wetlab/api/utils/sample.py @@ -84,7 +84,7 @@ def get_sample_fields(apps_name): "Type of Sample": {"field_name": "sample_type"}, "Species": {"field_name": "species"}, "Project/Service": {"field_name": "sample_project"}, - "Date sample reception": {"field_name": "smple_entry_date"}, + "Date sample reception": {"field_name": "sample_entry_date"}, "Collection Sample Date": {"field_name": "collection_sample_date"}, "Sample Storage": {"field_name": "sample_location"}, "Only recorded": {"field_name": "only_recorded"}, From a41fffcfe0192ace1507a238473f74dca6cf31b1 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 28 Aug 2024 12:12:36 +0200 Subject: [PATCH 105/446] Working on issue #283 --- .../templates/drylab/stats_services_time.html | 43 +++++++++++++++++ drylab/views.py | 47 ++++++++++++++----- 2 files changed, 79 insertions(+), 11 deletions(-) diff --git a/drylab/templates/drylab/stats_services_time.html b/drylab/templates/drylab/stats_services_time.html index 4ba8bf0d0..5dc51137a 100644 --- a/drylab/templates/drylab/stats_services_time.html +++ b/drylab/templates/drylab/stats_services_time.html @@ -41,6 +41,14 @@
    {{ error_message }}
    role="tab" aria-controls="nav-req-from" aria-selected="false">Requested by +
    +
    @@ -331,6 +339,67 @@

    Analyzed Samples by Project

    +
    {% else %} diff --git a/drylab/views.py b/drylab/views.py index b00c05093..a768d9a59 100644 --- a/drylab/views.py +++ b/drylab/views.py @@ -1392,10 +1392,13 @@ def stats_by_services_request(request): services_stats_info["period_time"] = period_of_time_selected + # collecting services, samples and re-analysis data for creating # statistics on Requested Level 2 Services - + # service_dict = {} sample_in_l2 = {} + re_analysis_l2 = {} + sample_re_analysis_l2 = {} for service in services_found: service_request_list = service.service_available_service.filter(level=2) for service_requested in service_request_list: @@ -1409,6 +1412,25 @@ def stats_by_services_request(request): sample_in_l2[service_name] = ( sample_in_l2.get(service_name, 0) + s_count ) + # check if there are more than one resolution for the same + # service, to be included as re-analysis + resolution_count = drylab.models.Resolution.objects.filter( + resolution_service_id=service + ).count() + if resolution_count > 1: + # reduce the number of services requested because the + # first resolution is the requested service + resolution_count -= 1 + # increase the number of re-analysis services + re_analysis_l2[service_name] = ( + re_analysis_l2.get(service_name, 0) + resolution_count + ) + # count the number of samples handled on re-analysis services + # these number is multiplied by the number of resolutions + sample_re_analysis_l2[service_name] = ( + sample_re_analysis_l2.get(service_name, 0) + + s_count * resolution_count + ) # creating the graphic for requested services data_source = drylab.utils.graphics.column_graphic_dict( @@ -1430,11 +1452,35 @@ def stats_by_services_request(request): services_stats_info["graphic_sample_per_service_l2"] = ( graphic_sample_service_l2.render() ) + # creating the graphic for requested re-analysis services + data_source = drylab.utils.graphics.column_graphic_dict( + "Re Analysis Services:", "level 2 ", "", "", "fint", re_analysis_l2 + ) + graphic_re_analysis_l2_services = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", "ex15", "550", "375", "chart-15", "json", data_source + ) + ) + services_stats_info["graphic_re_analysis_l2_services"] = ( + graphic_re_analysis_l2_services.render() + ) + # creating the graphic for re-analysis sample services + data_source = drylab.utils.graphics.column_graphic_dict( + "Samples Re Analysis", "level 2 ", "", "", "fint", sample_re_analysis_l2 + ) + graphic_sample_re_analysis_l2 = core.fusioncharts.fusioncharts.FusionCharts( + "column3d", "ex16", "550", "375", "chart-16", "json", data_source + ) + services_stats_info["graphic_sample_re_analysis_service_l2"] = ( + graphic_sample_re_analysis_l2.render() + ) # statistics on Requested Level 3 Services # getting also the number of samples handled on level 3 services service_dict = {} sample_in_l3 = {} + re_analysis_l3 = {} + sample_re_analysis_l3 = {} for service in services_found: service_request_list = service.service_available_service.filter(level=3) for service_requested in service_request_list: @@ -1450,6 +1496,25 @@ def stats_by_services_request(request): sample_in_l3[service_name] = ( sample_in_l3.get(service_name, 0) + s_count ) + # check if there are more than one resolution for the same + # service, to be included as re-analysis + resolution_count = drylab.models.Resolution.objects.filter( + resolution_service_id=service + ).count() + if resolution_count > 1: + # reduce the number of services requested because the + # first resolution is the requested service + resolution_count -= 1 + # increase the number of re-analysis services + re_analysis_l3[service_name] = ( + re_analysis_l3.get(service_name, 0) + resolution_count + ) + # count the number of samples handled on re-analysis services + # these number is multiplied by the number of resolutions + sample_re_analysis_l3[service_name] = ( + sample_re_analysis_l3.get(service_name, 0) + + s_count * resolution_count + ) # creating the graphic for requested services on level 3 data_source = drylab.utils.graphics.column_graphic_dict( @@ -1471,6 +1536,33 @@ def stats_by_services_request(request): services_stats_info["graphic_sample_per_service_l3"] = ( graphic_sample_service_l3.render() ) + # creating the graphic for requested re-analysis l3 services + data_source = drylab.utils.graphics.column_graphic_dict( + "Re Analysis Services:", "level 3 ", "", "", "ocean", re_analysis_l3 + ) + graphic_re_analysis_l3_services = ( + core.fusioncharts.fusioncharts.FusionCharts( + "column3d", "ex17", "550", "375", "chart-17", "json", data_source + ) + ) + services_stats_info["graphic_re_analysis_l3_services"] = ( + graphic_re_analysis_l3_services.render() + ) + # creating the graphic for re-analysis sample l3 services + data_source = drylab.utils.graphics.column_graphic_dict( + "Samples Re Analysis", + "level 2 ", + "", + "", + "ocean", + sample_re_analysis_l3, + ) + graphic_sample_re_analysis_l3 = core.fusioncharts.fusioncharts.FusionCharts( + "column3d", "ex18", "550", "375", "chart-18", "json", data_source + ) + services_stats_info["graphic_sample_re_analysis_service_l3"] = ( + graphic_sample_re_analysis_l3.render() + ) # Samples handled by requested services sample_in_services_objs = ( From f208fdcf5739c7e9058bdb61b89c392899340095 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 30 Aug 2024 11:15:18 +0200 Subject: [PATCH 108/446] Renamed titles for reanalysis services --- drylab/templates/drylab/stats_services_time.html | 8 ++++---- drylab/views.py | 10 +++++----- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/drylab/templates/drylab/stats_services_time.html b/drylab/templates/drylab/stats_services_time.html index 6c387514e..876e7738d 100644 --- a/drylab/templates/drylab/stats_services_time.html +++ b/drylab/templates/drylab/stats_services_time.html @@ -347,7 +347,7 @@

    Analyzed Samples by Project

    -

    Re analysis Services Level 2

    +

    Services with reanalysis level 2

    {% if services_stats_info.graphic_re_analysis_l2_services %} @@ -360,7 +360,7 @@

    Re analysis Services Level 2

    -

    Re analysis Samples per services Level 2

    +

    Reanalysis of samples by service level 2

    {% if services_stats_info.graphic_sample_re_analysis_service_l2 %} @@ -375,7 +375,7 @@

    Re analysis Samples per services Level 2

    -

    Re analysis Services Level 3

    +

    Services with reanalysis level 3

    {% if services_stats_info.graphic_re_analysis_l3_services %} @@ -388,7 +388,7 @@

    Re analysis Services Level 3

    -

    Re analysis Samples per services Level 3

    +

    Reanalysis of samples by service level 3

    {% if services_stats_info.graphic_sample_re_analysis_service_l3 %} diff --git a/drylab/views.py b/drylab/views.py index a768d9a59..617632e37 100644 --- a/drylab/views.py +++ b/drylab/views.py @@ -1454,7 +1454,7 @@ def stats_by_services_request(request): ) # creating the graphic for requested re-analysis services data_source = drylab.utils.graphics.column_graphic_dict( - "Re Analysis Services:", "level 2 ", "", "", "fint", re_analysis_l2 + "Reanalysis Services:", "level 2 ", "", "", "fint", re_analysis_l2 ) graphic_re_analysis_l2_services = ( core.fusioncharts.fusioncharts.FusionCharts( @@ -1466,7 +1466,7 @@ def stats_by_services_request(request): ) # creating the graphic for re-analysis sample services data_source = drylab.utils.graphics.column_graphic_dict( - "Samples Re Analysis", "level 2 ", "", "", "fint", sample_re_analysis_l2 + "Reanalysis Samples", "level 2 ", "", "", "fint", sample_re_analysis_l2 ) graphic_sample_re_analysis_l2 = core.fusioncharts.fusioncharts.FusionCharts( "column3d", "ex16", "550", "375", "chart-16", "json", data_source @@ -1538,7 +1538,7 @@ def stats_by_services_request(request): ) # creating the graphic for requested re-analysis l3 services data_source = drylab.utils.graphics.column_graphic_dict( - "Re Analysis Services:", "level 3 ", "", "", "ocean", re_analysis_l3 + "Reanalysis Services:", "level 3 ", "", "", "ocean", re_analysis_l3 ) graphic_re_analysis_l3_services = ( core.fusioncharts.fusioncharts.FusionCharts( @@ -1550,8 +1550,8 @@ def stats_by_services_request(request): ) # creating the graphic for re-analysis sample l3 services data_source = drylab.utils.graphics.column_graphic_dict( - "Samples Re Analysis", - "level 2 ", + "Reanalysis Samples", + "level 3 ", "", "", "ocean", From bdd3781d29b29f123f1bf6baa31c920f9fb959a2 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 1 Sep 2024 11:25:00 +0200 Subject: [PATCH 109/446] Fixed issue #289 --- wetlab/api/views.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wetlab/api/views.py b/wetlab/api/views.py index 198edd535..b0bede765 100644 --- a/wetlab/api/views.py +++ b/wetlab/api/views.py @@ -202,12 +202,12 @@ def create_sample_data(request): not_allowed_sample_names = list( core.models.Samples.objects.filter( sample_user__username__iexact=request.user.username - ).values_list(Lower("sample_name", flat=True)) + ).values_list(Lower("sample_name"), flat=True) ) else: not_allowed_sample_names = list( core.models.Samples.objects.values_list( - Lower("sample_name", flat=True) + Lower("sample_name"), flat=True ) ) # get information it underscore is allowed in sample name From 0c3b45f2a6b39e81499e6fc0315bd83a252e4de2 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 13 Nov 2024 10:46:18 +0100 Subject: [PATCH 110/446] added function to load prefilled tables --- install.sh | 53 ++++++++++++++++++++++++++++++++++++++++++----------- 1 file changed, 42 insertions(+), 11 deletions(-) diff --git a/install.sh b/install.sh index b162e10c5..4dfcf580f 100644 --- a/install.sh +++ b/install.sh @@ -152,6 +152,36 @@ restore_git_ref() { git checkout "$initial_git_ref" --quiet } +load_tables() { + # Function parameters + local data_file="${1:-conf/first_install_tables.json}" + local verbose="${2:-false}" + + # Check if the file exists + if [[ ! -f "$data_file" ]]; then + echo "Error: The data file '$data_file' does not exist." + return 1 + fi + + # Conditional message based on verbose mode + if [[ "$verbose" == true ]]; then + echo "Loading pre-filled tables from file: $data_file" + fi + + # Load pre-filled tables + python manage.py loaddata "$data_file" + if [[ $? -eq 0 ]]; then + echo "Tables loaded successfully from '$data_file'." + else + echo "Error loading tables from '$data_file'." + return 1 + fi + + if [[ "$verbose" == true ]]; then + echo "Table loading process completed." + fi +} + # Ensure to recover current git branch/tag/SHA on script exit initial_git_ref=$(git rev-parse --abbrev-ref HEAD || git rev-parse HEAD) trap restore_git_ref EXIT @@ -204,6 +234,7 @@ install_type="full" upgrade=false upgrade_type="full" docker=false +prefilled_tables="conf/first_install_tables.json" # PARSE VARIABLE ARGUMENTS WITH getops options=":c:s:i:u:r:g:tdkvh" @@ -602,7 +633,8 @@ if [ $upgrade == true ]; then if [ $tables == true ] ; then echo "Loading pre-filled tables..." - python manage.py loaddata conf/first_install_tables.json + echo "Loading in database initial data" + load_tables $prefilled_tables true echo "Done loading pre-filled tables..." fi @@ -856,16 +888,15 @@ if [ $install == true ]; then # update the settings.py and the main urls update_settings_and_urls - if [ $docker == false ]; then - echo "Creating the database structure for iSkyLIMS" - python manage.py migrate - python manage.py makemigrations $MIGRATION_MODULES - python manage.py migrate - echo "Loading in database initial data" - python manage.py loaddata conf/first_install_tables.json - echo "Creating super user " - python manage.py createsuperuser --username admin - fi + # Creating data base structure and load prefilled tables + echo "Creating the database structure for iSkyLIMS" + python manage.py migrate + python manage.py makemigrations $MIGRATION_MODULES + python manage.py migrate + echo "Loading in database initial data" + load_tables $prefilled_tables true + echo "Creating super user " + python manage.py createsuperuser --username admin # copy static files echo "Run collectstatic" From 115f7d6aff10063cbe76dae50c8272d95d16ab4c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 13 Nov 2024 10:47:01 +0100 Subject: [PATCH 111/446] fix typo in condition --- install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/install.sh b/install.sh index 4dfcf580f..9bf0d5fc4 100644 --- a/install.sh +++ b/install.sh @@ -799,7 +799,7 @@ if [ $install == true ]; then cd - - if [ "$install_type" == "full" ] || [ "$install_type" == "app" ]; then + if [ "$install_type" == "full" ]; then printf "\n\n%s" printf "${BLUE}------------------${NC}\n" printf "%s" From 1471ce1b4697ea7807fca264115fbd0a3c992e2b Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 09:56:38 +0100 Subject: [PATCH 112/446] recover non required lines for installation via dockerfile --- install.sh | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/install.sh b/install.sh index 9bf0d5fc4..8f4d9ead4 100644 --- a/install.sh +++ b/install.sh @@ -753,6 +753,7 @@ if [ $install == true ]; then python3-dev python3-pip python3-wheel \ apache2-dev cifs-utils \ gnuplot + fi if [[ $linux_distribution == "CentOS" || $linux_distribution == "RedHatEnterprise" ]]; then @@ -889,14 +890,16 @@ if [ $install == true ]; then update_settings_and_urls # Creating data base structure and load prefilled tables - echo "Creating the database structure for iSkyLIMS" - python manage.py migrate - python manage.py makemigrations $MIGRATION_MODULES - python manage.py migrate - echo "Loading in database initial data" - load_tables $prefilled_tables true - echo "Creating super user " - python manage.py createsuperuser --username admin + if [ $docker == false ]; then + echo "Creating the database structure for iSkyLIMS" + python manage.py migrate + python manage.py makemigrations $MIGRATION_MODULES + python manage.py migrate + echo "Loading in database initial data" + load_tables $prefilled_tables true + echo "Creating super user " + python manage.py createsuperuser --username admin + fi # copy static files echo "Run collectstatic" From f1e08362cfdbcc8578a328c3cdd9e20fac390624 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 10:32:58 +0100 Subject: [PATCH 113/446] update ubuntu version to 24.04 --- Dockerfile | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/Dockerfile b/Dockerfile index 332f6d047..4798264a3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:22.04 +FROM ubuntu:24.04 ENV TZ=Europe/Madrid RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone @@ -8,13 +8,18 @@ RUN apt-get update && apt-get upgrade -y # Essential software RUN apt-get install -y \ - git wget lsb-core lsb-release \ + git wget lsb-release \ libmysqlclient-dev \ - python3-pip libpq-dev \ - python3-wheel apache2-dev \ - gnuplot + python3-pip libpq-dev python3-venv python3-wheel \ + apache2-dev \ + gnuplot pkg-config rsync -RUN git clone https://github.com/bu-isciii/iskylims.git /srv/iskylims +# Set MYSQLCLIENT_CFLAGS and MYSQLCLIENT_LDFLAGS using pkg-config +RUN export MYSQLCLIENT_CFLAGS="$(pkg-config --libs mysqlclient)" && \ + export MYSQLCLIENT_LDFLAGS="$(pkg-config --cflags mysqlclient)" + +# Set git repository +RUN mkdir /srv/iskylims WORKDIR /srv/iskylims RUN git checkout develop From c554096463463f7f768a6869a9f9d8930cb93318 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 10:36:34 +0100 Subject: [PATCH 114/446] implement new installation features in iskylims installation via docker_install --- Dockerfile | 19 ++++++++++--- docker_install.sh | 71 ++++++++++++++++++++++++++++------------------- 2 files changed, 58 insertions(+), 32 deletions(-) diff --git a/Dockerfile b/Dockerfile index 4798264a3..8a70d5a1b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -21,15 +21,26 @@ RUN export MYSQLCLIENT_CFLAGS="$(pkg-config --libs mysqlclient)" && \ # Set git repository RUN mkdir /srv/iskylims WORKDIR /srv/iskylims -RUN git checkout develop -RUN pip install -r conf/requirements.txt +# Copy the local git repository to docker image directory +COPY . /srv/iskylims -RUN bash install.sh --install app --git_revision main --conf conf/docker_install_settings.txt --docker +# Create and activate a virtual environment +RUN python3 -m venv /srv/iskylims/venv +# Install dependencies within the virtual environment +RUN /srv/iskylims/venv/bin/pip install -r conf/requirements.txt + +# Set default install type +ARG INSTALL_TYPE=app +ARG GIT_REVISION=main + +# Execute the installation script +RUN /bin/bash install.sh --install $INSTALL_TYPE --git_revision $GIT_REVISION --conf conf/docker_install_settings.txt --docker WORKDIR /opt/iskylims # Expose EXPOSE 8001 + # Start the application -CMD ["python3", "/opt/iskylims/manage.py", "runserver", "0:8001"] \ No newline at end of file +CMD ["python", "/opt/iskylims/manage.py", "runserver", "0:8001"] \ No newline at end of file diff --git a/docker_install.sh b/docker_install.sh index e92bcf83a..382917663 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -4,19 +4,24 @@ ISKYLIMS_VERSION="3.0.0" usage() { cat << EOF -This script install and upgrade the iskylims app. +This script installs and upgrades the iskylims app. -usage : $0 --demo_data +Usage : $0 [--demo_data] [--install_type] [--git_revision] Optional input data: - --demo_data | provide already dowloaded demo data from zenodo - + --demo_data | Provide already downloaded demo data from Zenodo + --install_type | Specify the installation type for iSkyLIMS (default: full) + --git_revision | Specify the Git revision to install (default: main) Examples: Install demo docker system bash $0 - Provide already downloaded data from zenodo (compressed) - bash $0 --demo_data /path/to/iskylims_demo_data.tar.gz + Provide already downloaded data from Zenodo (compressed) + bash $0 --demo_data /path/to/iskylims_demo_data.tar.gz + + Speficy a custom installation using the Git revision "develop": + bash $0 --install_type app --git_revision develop + EOF } @@ -30,32 +35,42 @@ do set -- # this resets the "$@" array so we can rebuild it fi case "$arg" in - # OPTIONAL - --demo_data) set -- "$@" -d ;; - - # ADITIONAL - --help) set -- "$@" -h ;; - --version) set -- "$@" -v ;; - # PASSING VALUE IN PARAMETER - *) set -- "$@" "$arg" ;; + # OPTIONAL + --demo_data) set -- "$@" -d ;; + --install_type) set -- "$@" -i ;; + --git_revision) set -- "$@" -g ;; + + # ADDITIONAL + --help) set -- "$@" -h ;; + --version) set -- "$@" -v ;; + # PASSING VALUE IN PARAMETER + *) set -- "$@" "$arg" ;; esac done # SETTING DEFAULT VALUES demo_data=false +install_type="app" +git_revision="main" -# PARSE VARIABLE ARGUMENTS WITH getops -options=":d:vh" +# PARSE VARIABLE ARGUMENTS WITH getopts +options=":d:i:g:vh" while getopts $options opt; do case $opt in d) demo_data=$OPTARG ;; - h ) + i) + install_type=$OPTARG + ;; + g) + git_revision=$OPTARG + ;; + h) usage exit 1 ;; - v ) + v) echo $ISKYLIMS_VERSION exit 1 ;; @@ -76,8 +91,8 @@ while getopts $options opt; do done shift $((OPTIND-1)) -echo "Deploying test containers..." -docker compose build --no-cache +echo "Deploying test containers with INSTALL_TYPE=$install_type and GIT_REVISION=$git_revision..." +docker compose build --no-cache --build-arg INSTALL_TYPE=$install_type --build-arg GIT_REVISION=$git_revision docker compose up -d echo "Waiting 20 seconds for starting database and web services..." @@ -88,25 +103,25 @@ docker exec -it iskylims_app python3 manage.py migrate docker exec -it iskylims_app python3 manage.py makemigrations django_utils core wetlab drylab docker exec -it iskylims_app python3 manage.py migrate -echo "Creating super user " +echo "Creating super user" docker exec -it iskylims_app python3 manage.py createsuperuser -echo "Loading in database initial data" +echo "Loading initial data into the database" docker exec -it iskylims_app python3 manage.py loaddata conf/first_install_tables.json docker exec -it iskylims_app python3 manage.py loaddata test/test_data.json -echo "Download testing files and copy it to samba container" -if [ "$demo_data" == "false" ];then +echo "Downloading and copying test files to the Samba container" +if [ "$demo_data" == "false" ]; then wget https://zenodo.org/record/8091169/files/iskylims_demo_data.tar.gz demo_data="./iskylims_demo_data.tar.gz" fi docker cp $demo_data samba:/mnt -docker exec -it samba tar -xf /mnt/iskylims_demo_data.tar.gz -C /mnt +docker exec -it samba tar -xf /mnt/iskylims_demo_data.tar.gz -C /mnt -echo "deleting compress testing file" +echo "Deleting compressed test file" docker exec -it samba rm /mnt/iskylims_demo_data.tar.gz -if [ "$demo_data" == "false" ];then +if [ "$demo_data" == "false" ]; then rm -f $demo_data fi @@ -114,4 +129,4 @@ echo "Running crontab" docker exec -it iskylims_app python3 manage.py crontab add docker exec -it iskylims_app service cron start -echo "You can now access iskylims via: http://localhost:8001" \ No newline at end of file +echo "You can now access iSkyLIMS via: http://localhost:8001" From 924498f51f2251cc3c3fc60d7e0872ef429280f6 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 10:38:12 +0100 Subject: [PATCH 115/446] set python env globally in docker --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 8a70d5a1b..dcefc7a47 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,6 +27,7 @@ COPY . /srv/iskylims # Create and activate a virtual environment RUN python3 -m venv /srv/iskylims/venv +ENV PATH="/srv/iskylims/venv/bin:$PATH" # Install dependencies within the virtual environment RUN /srv/iskylims/venv/bin/pip install -r conf/requirements.txt From 8f9a473c049a41e061a0ff9885b9535b3bd38642 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 10:42:08 +0100 Subject: [PATCH 116/446] add missing modules for installation --- conf/docker_install_settings.txt | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/conf/docker_install_settings.txt b/conf/docker_install_settings.txt index e16211355..eb3abcf72 100644 --- a/conf/docker_install_settings.txt +++ b/conf/docker_install_settings.txt @@ -1,5 +1,8 @@ -### Installation path +### Installation path and modules settings INSTALL_PATH='/opt/iskylims' +REQUIRED_MODULES='core drylab wetlab clinic django_utils' +MIGRATION_MODULES='core drylab wetlab django_utils' +FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' ### (optional) Python installation path where pip and python executables are located PYTHON_BIN_PATH='python3' # example: /opt/python/3.9.6/bin/python3 From 1df33f07df5bfe10c73cc3c78024568cccf70a15 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 10:43:43 +0100 Subject: [PATCH 117/446] commit updates in requirements. Related to a6c88d55 --- conf/requirements.txt | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/requirements.txt b/conf/requirements.txt index 7c84da8e4..0bf81ba8c 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -13,7 +13,7 @@ django-mptt-admin==2.6.2 django-cleanup==8.1.0 interop>1.1.22 mod_wsgi==5.0.0 -mysqlclient==2.2.4 +mysqlclient==2.2.6 paramiko==3.4.1 jsonschema==4.23.0 pysmb==1.2.9.1 @@ -23,3 +23,4 @@ drf-yasg==1.21.7 xlrd==2.0.1 pandas==2.2.2 openpyxl==3.1.5 +setuptools==75.2.0 \ No newline at end of file From 83177b015ccd29013665ba05d3586ac4dd855418 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 10:44:19 +0100 Subject: [PATCH 118/446] fix end of file --- docker-compose.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.yml b/docker-compose.yml index 293fa54f3..49edbe405 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -56,4 +56,4 @@ networks: volumes: db_data_vol: - ngs_data_vol: \ No newline at end of file + ngs_data_vol: From d66a2cdf722617d91724533bb4cb0daac4b8ad92 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 17:00:20 +0100 Subject: [PATCH 119/446] fix fields in test_data --- test/test_data.json | 49 ++++++++++++++++++++++----------------------- 1 file changed, 24 insertions(+), 25 deletions(-) diff --git a/test/test_data.json b/test/test_data.json index edc6466b3..ecf113e8a 100644 --- a/test/test_data.json +++ b/test/test_data.json @@ -10103,7 +10103,7 @@ "runprocess_id": 21, "lane_number": "1", "top_number": "1", - "count": "4,776,660", + "count": "4776660", "sequence": "GGGGGGGG+AGATCTCG", "generated_at": "2023-07-25T18:00:02.714" } @@ -10115,7 +10115,7 @@ "runprocess_id": 21, "lane_number": "1", "top_number": "2", - "count": "315,920", + "count": "315920", "sequence": "GGGGGGGG+CGATCTCG", "generated_at": "2023-07-25T18:00:02.716" } @@ -10127,7 +10127,7 @@ "runprocess_id": 21, "lane_number": "1", "top_number": "3", - "count": "240,860", + "count": "240860", "sequence": "CGCAACTA+GGGGGGGG", "generated_at": "2023-07-25T18:00:02.719" } @@ -10139,7 +10139,7 @@ "runprocess_id": 21, "lane_number": "1", "top_number": "4", - "count": "232,220", + "count": "232220", "sequence": "GGGGGGGG+CAAGGTCT", "generated_at": "2023-07-25T18:00:02.721" } @@ -10151,7 +10151,7 @@ "runprocess_id": 21, "lane_number": "1", "top_number": "5", - "count": "229,500", + "count": "229500", "sequence": "GGGGGGGG+GTACTCTC", "generated_at": "2023-07-25T18:00:02.723" } @@ -10163,7 +10163,7 @@ "runprocess_id": 21, "lane_number": "1", "top_number": "6", - "count": "189,220", + "count": "189220", "sequence": "GGGGGGGG+CTTCGTTC", "generated_at": "2023-07-25T18:00:02.726" } @@ -10175,7 +10175,7 @@ "runprocess_id": 21, "lane_number": "1", "top_number": "7", - "count": "180,020", + "count": "180020", "sequence": "GGGGGGGG+GCAATTCG", "generated_at": "2023-07-25T18:00:02.728" } @@ -10187,7 +10187,7 @@ "runprocess_id": 21, "lane_number": "1", "top_number": "8", - "count": "162,120", + "count": "162120", "sequence": "GGGGGGGG+GAATCCGA", "generated_at": "2023-07-25T18:00:02.731" } @@ -10199,7 +10199,7 @@ "runprocess_id": 21, "lane_number": "1", "top_number": "9", - "count": "161,920", + "count": "161920", "sequence": "GGGGGGGG+CTTCTGAG", "generated_at": "2023-07-25T18:00:02.733" } @@ -10211,7 +10211,7 @@ "runprocess_id": 21, "lane_number": "1", "top_number": "10", - "count": "122,580", + "count": "122580", "sequence": "GAATCACC+GGGGGGGG", "generated_at": "2023-07-25T18:00:02.737" } @@ -10223,7 +10223,7 @@ "runprocess_id": 21, "lane_number": "2", "top_number": "1", - "count": "4,860,760", + "count": "4860760", "sequence": "GGGGGGGG+AGATCTCG", "generated_at": "2023-07-25T18:00:02.741" } @@ -10235,7 +10235,7 @@ "runprocess_id": 21, "lane_number": "2", "top_number": "2", - "count": "257,000", + "count": "257000", "sequence": "GGGGGGGG+CGATCTCG", "generated_at": "2023-07-25T18:00:02.743" } @@ -10247,7 +10247,7 @@ "runprocess_id": 21, "lane_number": "2", "top_number": "3", - "count": "241,140", + "count": "241140", "sequence": "CGCAACTA+GGGGGGGG", "generated_at": "2023-07-25T18:00:02.746" } @@ -10259,7 +10259,7 @@ "runprocess_id": 21, "lane_number": "2", "top_number": "4", - "count": "232,080", + "count": "232080", "sequence": "GGGGGGGG+GTACTCTC", "generated_at": "2023-07-25T18:00:02.748" } @@ -10271,7 +10271,7 @@ "runprocess_id": 21, "lane_number": "2", "top_number": "5", - "count": "230,140", + "count": "230140", "sequence": "GGGGGGGG+CAAGGTCT", "generated_at": "2023-07-25T18:00:02.750" } @@ -10283,7 +10283,7 @@ "runprocess_id": 21, "lane_number": "2", "top_number": "6", - "count": "189,940", + "count": "189940", "sequence": "GGGGGGGG+CTTCGTTC", "generated_at": "2023-07-25T18:00:02.752" } @@ -10295,7 +10295,7 @@ "runprocess_id": 21, "lane_number": "2", "top_number": "7", - "count": "179,300", + "count": "179300", "sequence": "GGGGGGGG+GCAATTCG", "generated_at": "2023-07-25T18:00:02.755" } @@ -10307,7 +10307,7 @@ "runprocess_id": 21, "lane_number": "2", "top_number": "8", - "count": "163,740", + "count": "163740", "sequence": "GGGGGGGG+GAATCCGA", "generated_at": "2023-07-25T18:00:02.757" } @@ -10319,7 +10319,7 @@ "runprocess_id": 21, "lane_number": "2", "top_number": "9", - "count": "160,260", + "count": "160260", "sequence": "GGGGGGGG+CTTCTGAG", "generated_at": "2023-07-25T18:00:02.759" } @@ -10331,7 +10331,7 @@ "runprocess_id": 21, "lane_number": "2", "top_number": "10", - "count": "120,120", + "count": "120120", "sequence": "GAATCACC+GGGGGGGG", "generated_at": "2023-07-25T18:00:02.761" } @@ -10343,7 +10343,7 @@ "runprocess_id": 22, "lane_number": "1", "top_number": "1", - "count": "2,020", + "count": "2020", "sequence": "GCTCATGA+TCTCTATT", "generated_at": "2023-07-25T18:00:03.700" } @@ -10355,7 +10355,7 @@ "runprocess_id": 22, "lane_number": "1", "top_number": "2", - "count": "1,380", + "count": "1380", "sequence": "GCTCATGA+CTCTTATT", "generated_at": "2023-07-25T18:00:03.702" } @@ -10367,7 +10367,7 @@ "runprocess_id": 22, "lane_number": "1", "top_number": "3", - "count": "1,080", + "count": "1080", "sequence": "GCTCAGAA+CTCTCTAT", "generated_at": "2023-07-25T18:00:03.704" } @@ -10379,7 +10379,7 @@ "runprocess_id": 22, "lane_number": "1", "top_number": "4", - "count": "1,000", + "count": "1000", "sequence": "AAGAGGCA+GTAATGAT", "generated_at": "2023-07-25T18:00:03.706" } @@ -11153,7 +11153,6 @@ "fields": { "register_user": 1, "pool_state": 3, - "run_process_id": 20, "platform": 10, "pool_name": "20230725_pool", "sample_number": 77, From 54c5afa597e47069351000b0aaa391fa4716e6d1 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 17:01:00 +0100 Subject: [PATCH 120/446] add missing end of line --- conf/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/requirements.txt b/conf/requirements.txt index 0bf81ba8c..53e4b00a0 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -23,4 +23,4 @@ drf-yasg==1.21.7 xlrd==2.0.1 pandas==2.2.2 openpyxl==3.1.5 -setuptools==75.2.0 \ No newline at end of file +setuptools==75.2.0 From d6aab9d270c6cfa7ed6c5c2d18147f8cd207eaaa Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 17:16:36 +0100 Subject: [PATCH 121/446] add cron to envpath --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index dcefc7a47..bbbb6afad 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,7 +11,7 @@ RUN apt-get install -y \ git wget lsb-release \ libmysqlclient-dev \ python3-pip libpq-dev python3-venv python3-wheel \ - apache2-dev \ + apache2-dev cron \ gnuplot pkg-config rsync # Set MYSQLCLIENT_CFLAGS and MYSQLCLIENT_LDFLAGS using pkg-config @@ -28,6 +28,7 @@ COPY . /srv/iskylims # Create and activate a virtual environment RUN python3 -m venv /srv/iskylims/venv ENV PATH="/srv/iskylims/venv/bin:$PATH" +ENV PATH="/usr/sbin/cron:$PATH" # Install dependencies within the virtual environment RUN /srv/iskylims/venv/bin/pip install -r conf/requirements.txt From 8ebeb3732755e618276c019cf439347d5338d49f Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 17:32:26 +0100 Subject: [PATCH 122/446] update readme #327 --- README.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/README.md b/README.md index 7d933698d..80aedacad 100644 --- a/README.md +++ b/README.md @@ -67,6 +67,13 @@ git clone https://github.com/BU-ISCIII/iSkyLIMS.git iSkyLIMS sudo bash docker_install.sh ``` +Or you can specify installation type and/or git revision: +```bash +git clone https://github.com/BU-ISCIII/iSkyLIMS.git iSkyLIMS +# To perform full installation from iskylims using git revision/branch 'develop' +sudo bash docker_install.sh --install_type full --git_revision develop +``` + The script creates a docker compose container with 3 services: - web1: contains the iSkyLIMS web application From f9fbf466d02e60c38acacf19a51d9b9626379a42 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 30 Oct 2023 18:01:57 +0100 Subject: [PATCH 123/446] readme mods --- README.md | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 80aedacad..549cade49 100644 --- a/README.md +++ b/README.md @@ -163,7 +163,18 @@ Before starting the upgrade procedure is highly recomended to perform the follow It is highly recomended that you made these backups and keep them safely in case of upgrade failure, to recover your system. -### Clone github repository +Because in this upgrade many tables in database are modified it is required that you backup: + +- iSkyLIMS database +- iSkyLIMS folder (complete installation folder, p.e /opt/iSkyLIMS) + +It is highly recomended that you made these backups and keep them safely in case of upgrade failure, to recover your system. + +#### Executing the upgrade + +We've also change the way that iSkyLIMS is installed and upgraded. From now on iskylims is downloaded in a user folder and installed elsewhere (p.e /opt/). + +##### Clone github repository From it was defined in previous releases the iSkyLIMS code is downloaded in a user folder and then installed elsewhere (p.e /opt/). @@ -184,7 +195,7 @@ git clone https://github.com/BU-ISCIII/iSkyLIMS.git iskylims cd iskylims ``` -### Configuration settings +##### Configuration settings Copy the initial setting template into a file named install_settings.txt @@ -200,12 +211,10 @@ database ,email settings and the local IP of the server where iSkyLIMS will run. sudo nano install_settings.txt ``` -### Running upgrade script +##### Running upgrade script If your organization requires that dependencies / stuff that needs root are installed by a different person that install the application the you can use the install script in several steps as follows. -First you need to rename the folder app name in the installation folder (`/opt/iSkyLIMS`): - #### Steps requiring root Make sure that the installation folder has the correct permissions so the person installing the app can write in that folder. @@ -287,7 +296,7 @@ mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/b Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf -### Verification of the installation +#### Verification of the installation Open the navigator and type "localhost" or the "server local IP" and check that iSkyLIMs is running. @@ -298,6 +307,6 @@ You can also check some of the functionality, while also checking samba and data - Check all tabs so every connectin is successful. - Run the 3 tests for each sequencing machine: MiSeq, NextSeq and NovaSeq. -## iSkyLIMS documentation +### iSkyLIMS documentation iSkyLIMS documentation is available at [https://iskylims.readthedocs.io/en/latest](https://iskylims.readthedocs.io/en/latest) From 6c68f7f1e94bf3ddad04c2fc6fb8b7c033bbb1be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 30 Oct 2023 18:03:33 +0100 Subject: [PATCH 124/446] images and leadme --- LEAME.md | 2 +- image.png | Bin 0 -> 90700 bytes 2 files changed, 1 insertion(+), 1 deletion(-) create mode 100755 image.png diff --git a/LEAME.md b/LEAME.md index 35a923194..36f1e5de2 100644 --- a/LEAME.md +++ b/LEAME.md @@ -65,7 +65,7 @@ Antes de comenzar la instalación, asegúrate de lo siguiente: - Tienes Python > 3.8 (si lo compilas debes haber instalado previamente las dependecias de arriba) - Tienes una conexión a la carpeta compartida de Samba donde se almacenan las carpetas de ejecución (por ejemplo, galera/NGS_Data). - Dependencias: - + ### Instalación de iSkyLIMS en Docker Puedes probar iSkyLIMS creando un contenedor Docker en tu máquina local. diff --git a/image.png b/image.png new file mode 100755 index 0000000000000000000000000000000000000000..cac5ffb4c285dcd40ab5e7395c64143c151889ca GIT binary patch literal 90700 zcmc$_2T)U8+bD`k5fu~>kt(l9Z_**5h^QzKdPj=VTPPu+7ePc(KAfU$kQWi@ zA|;Rz0#X7Aq4#>DpZ;^soqy)ubI#1YYX-9R+H0@&l=alNI$COUmsl@RP*Bi4eezI` zf`Y1pg5vz-MQU5JHB@S z_k{2Gk^ct?|9%pel9l}L8)PNq|MdCK7r&k@f?ABVhA1e`WS%}$G4Qoq!O{la*ui#h zh&gawyLb&ef9;0KqwnW)Z!uBjKY3Jqr--Q}D0@MmC^nZV)*rzXWZ+n>v%^rDTf~3q z29<%PE@cT9{~IsH)%5${&eIMZJDk-5n<+wjpO|9 zEm2T#(I?i2{5qvyR&{{X8u$|8y;O_|5LwK-^&4= zfTh~mZ#>b8fvpVv(8lZua(g`4iN6jtIx#EB)ag+YbT?ItS=ymeUebZZaKxvZUUnD- z8O6$gNGVmFgIh2M>g~B*EIMHQ1L3aG@MJWBU*N0DZ9rT(iKeE``H0g&>1wIxfHR=h zvgW!FvqIM2b;LpSC_6ykkJ9Nd2-^`YD*D^iHu(jJxY47jn_wC7p% zEI8SDU496g(~|XAb25}QHLiCm5v1zp`!j#GZQ_9!zr0$k^C`OAETc{F4h7hCGP&4| zg@&XvO+Y;v9dk=x#yiNOhSJ7sZMb<1i$C2IkY3UGKx-4y`aC^gi{^85`JhWBwsDC5 zX=JP|u@qrm=dEu`F*Q-Q7mBpEMgQ|>s?QsGi;^9n>;r6<5J~6Lt0<;XV#ZBCtJXc= z)?nk;$hD!-%<#wrlCV)?6w_E83<^)m_;hKZuTh1>WDave@3~;R1A3E%3T5b=mp3J~ zA({FeF^Mv3z--x@6;-N@JB}loB-Sxcj1Y2lcy!IEndE3FWc*_YBcp#A`1`y==Y+0Z zoER?__~)MvBn5@sPQroa`dJyy*}T!P*g!?P)L`5v-G@+K8R8v|IkRk?9ALGo@r=A# zfys5km5;S2l|wbMQ_#~cu!!1v#Y7<^op%6f?(;KWubS^o7=fSCCXN-^=W@g?0xJ`f zofCyhz&j5<_CmZ|GPZ3PBe|2ka6(U`SD=)*MmS;qR?D z+u(EwUS%+*d`*TlIvswl{*`*2nW0drQ#k>~?;5+cZz3o+qEz{mBj4aM4RX(J0dBZn zJ3?S8xuE@Ls{1{HTPo{I0PJIVyuEWkI@jLMXbe`^eMG7GIfsRZnIhiEc)*!2HL^*w zBYEIR0^zrIPWBonY3i|ndRYeWiG{L&&o0uBRLho%D!$GBT>2?}duF#mTH|p)uQR3! z$#LP&L~@zEf!7oecHD3yp{HZl1&hrV)Ju{RiZq5Ce~zzPHh@cOAe#HYZwZgZS!NOi z4RrF-#-@|PB2Uv>?v1zMBe;$x1fP5Sf%XYnp zZ-zbxEYV|MQimSmJ$Z?kmf)e<^wOZYrksO6tDs=FvTL)^etsT=fW3n`*b8*|4VvyaFSoiIH=53IGN#GE%`;tq z_3sxx_>qEWGEg7m;HYwo@~Bq6`U{ct%?n1oi9&@ykCVgZhd3|A%;+xy zwmEQ|1O&C)C9~bylPc2%$)2oe*4x*Agx)oegquIezhqVgD`mT}SDKYjq=biSRk8kB z`%iWi4>Csz)i+KRi;QDtJdBCKx#L1~lwBw7B0mW-3Go-J+ZhU4S>jwL?7OK`@A*}Y z(w_79v+Xy=e4uMnubNNtwOL1>T(Jubh?$>v-1y3Y_M6G(VBE$oS^yH@Hj!b@Mj#L1 zkT70LKJEHKjP?{LIv+CQvxzJl|Q|sUK$<9W0U(sd~U}wuwvq!z-hEo?IjCufjpCz&#f_GV8nNZ>4^+)t~_Jo)xjX_@~mYVwk8BLjGQ_v z-amT;(hNO7L(CmJGf&d$?Q3fw|He96Hox}I#A*gy<@|vcl6CHDyRhmT@5iYK-(oE+ zIx+>3bT-OxjoN!{Ta8A5J|E-QET{W;8Sx84oVB9U2Sb;l&jPFajaaem=>Vy6_qD`n z%l+`v-Q_#7M<=@#ctVn>+ZH@Ci?&SpxZ_z++lz2f$MO5xIFD3k13HwNERon<-n`xM zGcj$oZ0@WKOQ6P*$);qL%BOV5L=J-Wr9ec$U*5DpzjVUuLV%+eJBoTAkvvI>rq6|Kd7sQ;_?T zAtr0~c0P`J#&{WZ-Naj!K3~q}Ur2EH3?6v4-gKW>q|Ui~$v8butWSpYJxn?s+fEl> ziU|nY83OTTUmkZIZVypMu~~_X*gK?NA|{HpjX-Ko^D0qphE3*zyk7EnVC4bMy??w@ zf3e9*;@MP5wSNZo8KTs1_)~`uiK$%sA6M8#v~W3HY{=4} z_$I<|K{4xSk^LH7saazjfiI$4w%F9dVZ1c|5-)&rp^y}Sa63~uh{qCnc$!|W*CnzU z7Md|xj1{Dk+4sjmZSc(0a z^n63T)K?Sh36WGeN^2`4wxr-4H~~M~G6gQ!^nUP_xDbhOvntq1VfQ&m0#B{lgPC8` zW++SB1Ut$P0?RW?jA@6422V`=Ul5WHkGtub3M@2Qy)lOVb~@U7GP5W}>HQyDb$pT< zw23k0$G_yuUxnS>j`w1lz47Zdvu0DgjMi{|Icup`#3itfyjfoYD?^9z2pE$MtDqn= zXp3}L=UCc=bd!TJCbrQ}Mo^2%L#eTP6;H-%GN!Y^OudOC0Eae9tE#DT#nUyzbSb|L z!SboLZaRgdRIbx@WAJFChOx^kVc^iZ$2q9>x%oq`Dax3EIZYYp3G3JtS3t0)eTxA6 z#dx@Y>d&j&>3RZ3ShLvx(sz2n;=n)*Z{sryt_8HBwa!yh07mH`NtpXh) z!}{mI%M)e@#?pq4_3nb;V%^&!I^BzO+v79SfL3r#kgcnW&&rsH7zo8IBuhBWgzpp* z^%rhnHlX~lr%d*nfKn4$z6%Imte|8$Rwd0$mkzgY4Q||q1^Kz*-Ds1}Qx9b;C zL>6q`-uP+#V7-lnxzhI!mm`UJCVLT?c*tIW8Blmr7o*Ic8`G)eWma7OYZe5zape2Ey!k6YC!*_U2GD&?;AA6B!sNWHn8%=||0PWyv_} z`r8&W$l3r(AZp6`{$Fh0`#6ttkyQtYtg}|myx*>QPaLN2gY92C9!p1n z@zXOLzpx{8>gEY(An(G=*IE>C?ySIl#rl)O_QD;^m4nAtP3P7ntg*cw-xuZ*%^cFH z(sSCUw@Pjvh;f7NFJu;FXKj$!{G|@7?LN?cU%V6szq^(B4v5QQ@7&!^`Rw+7X9m0$ zu>JHLqcD(o@9U}Q1I?MW%v&A3EFrCGm7={D>2EBzRvEYlHhh~r&%>iC)V_u6(i1V| zaOve;PeaKF^`1g98j13|$OZ?arvpK=yZKP%*Z3D-W2-Hj>&Bsyh$g`absSS`bm!6i zA<1{Qaw}lSiuQwNg|jPJmyaRKAPi-9pAp3rfBcTHChc{7dLA*}h8F&yW{H}x{KuM~ zVfdHA^;2q=nn7#hJ1(V0FYf8MonK0aqf)B_;YMo{g=Fz^sq7Hp4NWfqBX?4F;-MBt zMr2uw+c3KKl}rb04WU?2_RXp1W4>yMamD=mtJEo1?Hrmb9a64%R&x3TYZj)MMutOs zfmzf12~=R$X~<_fe?GYpiPS}A`K`%MMsfDS7I_QlK4>+nR6BUJH^TDFIW=vpIOn;s zWp<~U*VLet3t6BbMh9p{?{GTE`h*|yUN}Kj_J7wnv&>Dz>^g>U!90EgQVWDzaz{1cG?3iY3{GNhh<-}imKJ&Dr zAAoYHqf32a!AyS=hf{%Ei z4gINMo$b$vHz}2c1|icJU1F6mKSaetAKqmf5YS=ONf`o~nZWtw(OwH_ldw>B#gbq} zjnDUjeOhP%>7m|rp9B*}OTZqNR}^o3|GCX^INwbNwmy8{)I)&TGg=HEO4Un6J)H)l z_#Y+qCi_^SN;y`=SqPR!^@T4Eyh_qFG-3c-EZYJFWUdn5A{(xrBD7KZ3-)l%NtIR6Yr<`)a` zC_$gjDu=yvVa$%<5Atd|#aw=+os}b2-@sj73LU~4YYd&L-roNjvgIzBUkZg*&aA(+ zxgd)lGb$ayG@e6Du)H5mD~@NA+S@pPhxaohL(x;cNb}Yi^=Xw|M(~g*TiyFBOARXB ztAm?2?tGJkENWsQLy8B}{Wj`WzDL5?>b?_meg>75q8aO2p(%=IwQ1E4Jd9||I^$+n zAjLAD+w6=hKD&GFhgZ}?*UK-o&INxR)q6-15 z3n2jACwHT#+VWc~(h--ai^<5cm)TNc_{D`2D27ou?n+BOn3j}=S)V=(;Y@1e+CNo| z#7c0S>hbZqG`XFioiW)+4#qmKBg=uq=dEp)?N~a(c$t|gNBS6~FZH41OVT4Yq!Zf5 zWqbCAbXv1>9_F8UX}lCFu{^y9dSV8y!cZoIOp~Z(?ma8_dc?!?3K+9(%Nf&8DI4)n z6WQ2Jxk8r5UrTg=Kpy&oUEW|a^ND^F8f+;;!md&O3*zt&>A7x$f2m28VF%9C8=)&h zRTw=ohGVB%-FIscXuI%jUX9bvuF`~Eo2Ef`BdZHy05!6D=sa0qjr7frT7V2_bf%4M zKWhhr>AXh77pKD`w|AP#!CWUOM*F3=%UgA8*3SvQ?X~xh(N!`g#YcovQ9XM5odcrRnYds3FSqqk5QIs*=n(zt0H1lSS!{+(A)Rr^WB%z2qk@9cHKAC z$vANxl?|h%e4x0i!Oi$>CBf%O_0n2|QHPjV#?GFl0rgq+mbxLOWN3KmzaM#Yqgq?F z<#0{g$+-d|2P+yKp&sj7_XNH&N9DIyv~um}kGgn{;_A%-H)4W_kpIMUi%1f>b8DF9bYt9-o2*T8R zx!AEW!P|Mc70k3^+YcOxnwKdzNXJKC6BogUNZAu3|@MIJhJ=Dvg5MQ z3%05a$}*?VcY?F7R`r;)mqGPqtK0zt$Mz>Odr%NQtupuk4lFM`END`JbS41ACzm>0 zcfL_Hdzz8%VzF}$=zD~E|2bJyk^Z~a;8qX)*LEv~@3yC9l^04Tf15HkW?3w7EsbeM z?u~%LsR}xwuyRO-%MTMRmte%vULJyNs{Nlri%*%Y85_4lScDT_Xyi;mdYsVru+%OF&k9=5{bJY!$s0iPfMvGWLy7$`Wuo%lB2o1m+yXdtO*>Ns z^$86Mi@rYCFCstS9buf=X$sIkLkknDsmC`jtt7xc^F1iCRomCNq&*Mw23JPZ#@M)Z zTA#S!=C;afpGgq!>G=Yt%d?y2c}-5M+#LFo^(8(=gYAeCIwa5{# z{Wcv1P9j?9?REOLfUQI|fdm`F+Hld@c7Bs8u3Mu+LYJo?ca*R88C;vP6$!8d9cyMc zeJrnclgJcv9@c3ca?1%OV+L{1rC7sUdfch!DY!mmIbgRrU+)+#Rg|Z~jP$H+J?X%U z9ML;=9F{Yf;)gYhKVA~=Eq&#c8YGA!`c_s(9tV!?*m4kD9ExnReb%*KI$en*P9+}0pS@?WH z>Z2rAB1>#=9jf4@ref|@s$&~*F<>@?Eof6&me82q)OhX~n`-(?=U(0Xbv;nT7+P3( zkB#N%34jF>Ec3=H!&{GD^>A?Ya6Ih6{g9mo9su6=#|j*5yf1(5*7#D|D!buc?gfQz z?wL6lJ>`*fUJorv+X+5|Au+nq*gM6#ncwRhje=&WOpeiTgP>--xw zIin#xXXCKe%XfKd?O`A%tDWFQa2T?H@=X@)o%Bt1-pY?~h<*Wi9z>!1o^5ozfx3(+0Ndi6K*Nx8? zQIs(tIHXpgfWH19{dW8U3F_e&BZ(_`^|qUAcQjwUyH5)IV2V`YFcXj$SIH_jsg%Ww zp_G-Za%)*f$19sMNcQiVGmVyEA&zS=AuzO)DpAQ0-tJH~z3UOs>VeAqLVlbgQLOcv2^T>+14(NZgJm8ftCGU(@6EZfv&S5C&t8&RpRnZNG<6zGy43OFihi_U8Cw9@l997_YZ zTfBF9)|jOa_bXu*xV-izt9yVg>vkOlQ6l;%w{w*&X*^JuIGXCC_PLQjwd!+6>1vwqZ5WTL0`G1htP=oxVpi=I3&Ai+24HMorn91h3q*b3&W2MkEWr>Cv&AR! z&K)>gh{# z3EY_GrKJP7i!LQVrSH~c<@6?=jjLo*1;v~n{*>rT9q50mbZc}=qUxQV7WbK($-}N^ zkr7OnRs$AH)V)|9{0mLSnS9toEAH++kg6=}zcOH|lK@?8;lqadxROywZ*scJ=y)i? z9@|>Be%xO6t*@G-F*_)4Q)9)?nFWR0x_qK(U%HrN-D7cm`JsGfR^;Qk!O!qVwQPWq2iHbpYY_T}c(X!Ht~*Zd{4^IH^8T_h&Y2*bvvNUH_DRcdbdUD84z;cuW(HNOv@nx zuq36)!YFyhTLqSwZ?$eUjSRR-?Nx3b>oC;yBk-+mGg*^ z!Pm;xNQaL@ww&MW5sKfvuy@78@juRtmCtO^9EL!*RAp$MLhgTl}`DOdU~k zEtwGAeZrDLwwk1g2ylhCnN?CZZkaiq>ap;c4ozMzdPF5+GuCgp_cpzQ#k3uep&L*$ z3Zh3n$;@eAG;asKe&e=JsHP$I{tIx0MGR2VpQ-2E_2UWG9Cx4h0vwgsu7GJ{Y=XtU zd@qY{=12}!=uGVuzm$mI5Bd@SG?4gmq{lyWAhot;tkL=kZL(s6A$YO1mID*rwhPanvV z)NZd@kPFPe)RH#YM369-1ggIK5%#?H+rsu@YoX{nU9(TFn_`gFvXLdy()5FKa%VD9 z9RQq73pAQM_yjFvR_d#z(uO&3$md1}ge^QgHUi`Fe3;7((7n+mmicl1bxs88YHrmZ zKVmVv4ITE%`Zb*isvFAVwn+gzipRS&^e(F<(df3b>~sbtvhN;b(e#*Q(3fnb@d2&p zfw`vcZ8eAyKOCjhvW>$mxg~&@1nJ2JzFXF^3nrS65j{U*+EU|$d0nQ~Ykq*neZ3bO z{4yF-L;Vr2zM&*Em*b1u*GebPAbFz7LO!I%Z7d6zqCGg;nQRIl;P6@h&Jca*_|h`< z2o4Te;8rBnwU&9rcPNo>W+>{DHuj*UY{yAmajQ;;TK<;|lTpL^tklzm+1XnRxYBr} zSZ;BI1K{Yt!rD#)NM_MTU2nxAYQQf^a^gmzcMbL$$OKMSq`x(dbTqYCf~K#@YHT8J z!KKo=16bmfc*DnxOPfrbVc*>t;EPm^JXaq;gF&IaS*^=+_9HiMR0-QW;CZ6Sbz~yh z6ps0htIqEhX^eAlo3E*(Z}qw}XnBk}4$pWrI}VK1<;Gel=bY@C;4X_#xUSpO_OBA7fyEAEEa6rWn zZU$<}@Zr101H}H%&s*EQ5$R4G0}0CFEI)XG$M5~6$A~L8(NzKM1;8!)^9z|~VUTedPjRK;1Ext=1cs zcjII$CX0AnutUn5r~VXj@GlLk_eLWt_UsbguiGfe_FraP+M5++fnX#4m6;vpt_2)#%31qfQRbXfTpO1P=mBwcX&m35PI9&OTl+KRQO?Gt zxg*5U_mj&uFCOqf!A4fm&PMu)>K!P_N*DB)ps{yf(6b*U)fM28sh}1XE9s`~?%_Oe zXz)qJ6I;3%=Nu#ljL1It^A1XEe39+> zJ%c^NWM9Z?&;VgnC;w7+W^}6}xBh@L$|D@d+dO^G6f1jNhOj(=YVWKCCZPd+FTxIa zo7+-rIh!-4pM>lmM5JxvPz)5mc1Hd2J@>gQC26M=H## zLQf2Mm3{QJ1q(W!MQ41Ldv&fqP|9bKyK;y2*Us!%QfF+#E>LJ$kUe_f6jO0YoAX`W zH^)T)YtnRL_c>0`1=D-oWM`jC76UUr%xY_c$(w&~OelF5I%P~10taINJ-u4FEV zfknT*#bWNp*tfh+tv_!+zkNi0TVhz@X#TvgaMWN6EgjQnqyG2ph6?$uGoO*}Ley;2 z4B|TDXtk-LVet)9p}zrKI2_%k$$J!-zb(|(Xg3_Dn7~VZR`;iNgG`6u9pm$`7^!8b@I2Nos;s1 z!CP8xWCx&hiGdM0m?SYlXL9=TpHBRJ7sHsX7j|3CT0A2)f9@rgYwLHij;$#Ec^_J{ znm`}sK#sK_OLs@IW-zT7qqV8hA>#re{E}`y(z$Fz-?^#dZ)C^ko}4M&NVhCKdQLzt zSuGp?s(3_>ERu#Bwj;?V67RJ>Kt{P8IVNiMPy~z_rC6IPds$*oGBf={HZeJ2U!eWNqJ%@Xy`5ZS@lAKj(+ZE7KR0jJoMd)!odR;s*zty@Nf~s_PnMX*0)GT84tg2Bi7Bh7|?^zG}2` z^JSZ{vQKcUawS276=5x79!5ug0t?<_PI?R1wH6fpw~KaHv85Mi==p&_Ow1!wgPaFc zhNVUzX_s+>Mz4jH2^-Zvp_SPw^tT6%4wFcN?qSkz4GoK5Pz7jDB8F3O^bT3iBd>`_ zZe=4$Q>ChrS4*E`(Iw9sb6X3SG${h7YVw>j4YVxSo*+PF9DZn~4~yWB` z!q>p(XUyxth7TTuIgb|2Qk&|+QpE&zNtnX>T-k>^L}r0&TJkr3pFrpfbX!1WZ?ahB zJnNWt6ouTSq!bgw0d1G;SG|dKE^A6aq^~A*18wM8F3Y*~fA0~$l?l}j_BRO$@Lrgr z{OmGT@`&R2t~K)Gq>+7ks+;kRzsM8SF&ab94w$C~F@zAtp29SyQdVYvO7Q4tQp?3e zn>yHI6L09B@3IY@n}2~!orFD7`Fkd}`o*?DfpuQ_Ka>0JPwFF_nNojVepLQw#lbl= z{#@`%KR~GGaJis`nq`LXcI`lvSv&ksFzbEs#2u}Bx(cZ@7m!plwh#Y@0M`EoDgF=8 z-tNg)ZAt0XVH^=T8#3D9gmZF0wsLC)N|uyswcFGnF|)atoccA70_Y-tkWDwmec`{y z()&ggcWT&vFm_vdHm?%#qC*qpyV>rIJ<&%944$9m;kFPO>Bo(kHFj|@>>sB)v|R`D~ecxD-Se%Nn-CV}Of?!o4( zXML>5|AcbhH`OVONHa!|_?e~MZOwIm6cSd`S5az2`bmcF;iR6!ozw!}dLOpjdPpMA z1_6e_6m`K`VuA1(2-bgAHx{ep_r&*^fyl}=Oz{2n`gm)HYb;nq3_j3J~} zhS}*)VM1b@(_4jBiY&L3zxo{Att-huZcR<>vFx7a>)L6JA8--}-)(O&IAOq4g^ZA3 zEhVPw*9}f}jBNd4`!%V&1p6BM0NJEvzXYwx)-IN;3Q{UeE^M!5T_h-A^`{^WvJiii zqG*1nu(~U&aW&Cx13bK7zH-7aK?tvC*+@tF`}WNbOWcLiy^K6nrK6tsJ~w45aK zH-y?wB?7Yj4wq>|6Iil4CRSNQlJOZ#FDh1^2(2g6lXEVsqP&snU@<$pPfN;YC_&f) zZr}Tn(tU0EW5LnwZJJ^bg@WN8(Q}|a)-i}bcqIp>BKhYw{Gmy%ot&mbj>$Fm)`&K=6xh7AhA+Yz61nUf&y^}OHc zq9TcJ(kUA1>eBXZEtfMdMILM{w#gcdj*I}D#qG4zHV|7E0 zo~jOC#+m8one4&QtV~y(9dun__!PW-aTMGLUb4WwDBGywkx~0O=fG)Z6!Ls>cXChJ$zt)0lcsf|SmMUR&p4cU=Xkyvrv zGZZSi7l0-@JIrUWWU1MP<7IT#PURlpF*!{^k#ZyIBWhM(0%Z1egKCV>Mxdrbs60>$ zus3CW?a-#urWfjU;is|mHmAOpaSEOH7Z!KpVI)(>3d#KB9MOKkyHt{tkD23+Z{9Bv z5bvLZ0>FrBk>_B-MLB^?s7Ya`#6(@cwS%BP- zv#u@maUWLNI{w7l#^qnbDn&)AEAP- zSj6-?U<;~;EXu@Ak5}Jb4pm!E1U?OV0!b)HWDDPOHA&>nhoKf85$bB*n&qQ;FF8ck zExj=iL&cu&Ee?`)GJg%Jwb|4gvVSQiExjnDzB7C7TB?=Z-H=bi{o#u^)3oD z9DymcuiE8^ z1B~nxdttcZ!y*T>s%KBpb4~rzE~{1td0Y7Yq*-APcIKVZSGAwH**_xF+6TfGw3Vh; z#x|8ov^AZB5Y}IPpM-4+o7V_%=6!lJYwt&+0Z;kteemjGEh~i9{&A#6E+v^_XdRr? zHo|bg3$!J3Nmq-x>(ky?9bAf{w^1uH5m;>T6*TIfo6c~hQYCFf{JGpdzfEY>usXx7 zjkP+2U{AJ7{r9$RBYsA%yA1|}jKr%37Yosxn35xS)ixXIvu6&UM*UqV zE#!&DnUaC3)v;N@`A5O@CsKymr;At9nkHl9hBrl^ak+f~1?oxKC`ff>$uu-)C0=nhI+g`7ex=cWSN_TJ=w+{*A} z5`OEYLzAd>z#t^w@vx(|j&G}~*7>qvM4Z)qtd`JYhjbO>vAWi01ErpUasEB^(pOaB zTYh%6%*Kc)J{TX@ABoo^_jtR2)6WLZ!T&0JYkMAtzj5oHm>V=bOY{KHF-pF!5ax^u zWvg9SXe#ega^6jhcub|*a~cBZ8RDN8~mn{NZ{Ril=wo2MaOKmBD$ta zp(%|pUQx0cxhsH0(Jp3+98Cch###p@TIm(9zACJC=<_Ej>wWR?dO(#pBr6Ee<1*SQmme=-fj_)MN=P@hRF;cx^AYF+>PuCuPO@0`euU20^poN_ z)6N|HTZAi6Qxd!%Wo56y^|bctyiQkl)#2=8F6WjrFZV?dgMhIIh9b*ziH(KgFN&EJ z#0rIic`X*|GB;K+?EReW2-9_j*UZ9KK`vQRC5^2k_-FX8A;s&NM*NPPd~s}2hKyol zceeFwn3k5-biU5B9_J4Rrt&mCXf1Jgv}tp(bISbM2j>#Zm-oO=L8~@la0lvya!uK9 zE1I373@8=S6|DP@{i`ly6TNm>DX)NG{&$x$R2#RUVWHCnE01aFKFGf#-_#vT%xHI4 zZ5CSW%S#rZ{GEfbY#)?^d+qEN4Eg^gr9@P_F8E7>bzX^b$qtRA4A1RAy|Hf~@mv6D;!o%I-*J(0bl$HjMu&{*RJ|nU;uf?!4pnZ{kpWxdZLqH_{Kt}yA zw7W;a$qaKJZc|+_L{OhwXMFiL@yjEs2-TFa+GEK03{7~?#$<7as>?w=JB4+EMa@7u z|1E(Ry&+fe7gZ<340;{Y%$6R~C8`^~YYRquZ57VpJ3+n{4V!ySDYFS?H-~X!tUVliTpj1U}`Ky6ZP+Y73e*hUdoACc{Gr|9us%R)GBt$H7 z%km&2jN#+Qujx4ziZU|Tfj7zSIqic@GU_`U^6>B!KWp@Yt!#8`+@c80X7p1ar;+j$ zlEdEzsP3w6#sQncw*L*KkuYd*mOAgfa<6N?BZqagk2P?=A`4@|n;^`Tu#8zd{VTztn%# z|L082{|^C|5Egnf_IA-AY0wyR`G}a4%0}{?=LsS_$+ui8tArJ^NC; z*MpP1+5l7QDfaF)bLTQ{rQ0t}uUbs)+2T7Yo%{+otm0z2UG{CuQgU>CcI&$-@JVRn zaL$xZ3+xxwDe&CgQClD5YWGc#GG*#BARC=gHt@QSnGvCFaBkfiia8;{n!98YliRTClv+lZqJsQ7WPdD>$ zqH;1%&G~TLdV<$x8p5gwDa44%ch5=xE3v4Qe@^!O=qqjG37b%xA=ZI2@4WL&q^hrvAQ?KfK&SBfvnwOE z=l!~w@Z4nnF2@4Dqp}`q1oG1i64NqVd#>&Dvrs7G-OBn^iVNn(j=P@caDbz z%vKAo%vXn_k~4owy8KI_Me6sNyd9?>Sn!(lHtc3AzAD~fNo^oiZy zMSG$O&LmkqO*wevNS|PX!6&7#4j>sb`{8D7EBc^7uTMujP+axp#E(SD%BBkT)A!VM zrK@#}2|u=!u$Vlp^@{5d1xs%Js_&-LI>m{U`O{|wi(-e5`)&^Cqi>5E#kJB@+dhqS zl~m4%WoH{y`)U49y%^aF(;}FhmKTzMxI(9bfMp4nm>lGpHsQ+%Nr7_;Hn4G^OM8|ab! z0};#<#zhZ35~v5&$k6rhidy5^k3#Ky_qC#Ed88bjzFWY#hSCDX{cD^~`!ssYZ{2qw zYxfi9+0h6A^KJTE0t<_}m3=zZCC7tT9fYaD(dOI5Z#dI~(P<}+AyAJ&H2`k2><4UOgS>#xwAZ>-)=$z-f0|fD z>XWu-w)O<1+j0NMkc!(lE`ih3S)W=yVmUcs|5)uG=%W>QMYg%L4{=8z_pn5a^&g%dv=dV$>q@Qz4 z9w7q1nqYwqm26AUtT}KvDyAGV@@VKaUc52}fz%rQ@ZDw*^+5ng;>e7fL^8m?o`9ns zpx$a&>f>DW;TzLKZQ;CAivcZ=Egwy$l)V;eh34;#nozX4!_r%|!W#e+kHFp7s?P;H zX$r7U)Y$LX)+aEl<|>SYO+-ODzKO`UKQ)M=A8%z`bT+hvp2R|NZ_%eYI~lDH<|^r9 z*FNBsGB=7>=|G*PmDOQ10lCRM`<%Wn^g4*w-tdW-BkD!CpGt#79NPa41P34iSz<$n zu_DEUpm>ODYR$vtgCJRx?=JhRYa2Bu*;iagk7-Z$s>5d~nymiZNV6QTH z1^%(`Hc`AZ+kx9;xm4%-?&5zn9W{P9e26dO>{cu+rC4UbKM zDxiIYFAwy!Oksu%6XtY;J^hv9PFJ7MrMEn=U+Xp5Y2#kkpuB69cR0<&slg(!)B7-h>1{E}KWt5C!IN$kJq(&}ewN*rdiRG6= zPHJv4`^Git2Gmy$Z>zx>57}PycTaQ>g5xFO_wSeTV)F*EG%llc5oQQJg18Sz*Izf> zJJm&MvgH)fx&7snb`U&~y3VGnFwG+if&&dXw}qHWBs*?{2L0RC>_A!gXTB4|9d7Fx zq$%&m!}wy8s75!Np6QB(?&}jiwyxM)jaNk{Zynv?v&wG?kz;n7i-e*gjIWNW&N(=q zM!{$O=-v9VTqZ`NVYZ(>=T;9=S%qL-GKuEOEG{>l4{JL|F^y|EEV@G?Jwb&JTpU`Z zkQWAz`=1pp_$i3lO!K9IG0vlE#cdCbxr4si3{v@R*HGdvFlMorjrOe#Z-Zb`*HGup z6oziH%AgS=rjM36Bm&xRrdxG-`zTrQ?#GH8A)Heou71AR{?7n9bII%&2N&VxW~5Ni zU@alQ$(_!B{EQQ3=`wvKx@nG;E|rz3Y-#}rV}AUWV^6Y9cEq&X=BV^&1}_!#@nmX1 z!2(3UYf;?mL-rm7dMUe{5Qn{A94?#CH6hz;=`UP5mU`MLy2jafoYQ?}WZoppiq}yo zI7JV>BQx`yjG$J0Ff1LhRA}wpq2}Ne!*I3V+sRq>_!R)>8Zaqh(aysM+SVz%?UwW#ZOBzN+=f*Y)apt}X@bi;{Rrw!~fU5C^l5c)@9JY70rt5u2b5ozasz zu0i>Sl`69_$P4;P0}yjt;gr%zBq>w14&kPDI68A++z)ZYLqvBrJJLMfXF==&exqt; z16>$RoB4GmCxfsHZ;de_~?2OS2avnI7lF3H8A;4!RcymNS%BsXQ9*dt6BZs>E5a1}KA z$5;CCY}#qOO&IkR0rfNXb0VBU=1Zu1eiGf;=HQW{z}V%8b@aWRTf6>BS!#n0L-Arx z!Mauj4`YumOB0s^q#XlC@%}G>i1&ungQhZD2MPEZyNd5iXR8&XZQ4#Sen zNtVX{i@EoVYO-J6M)46rL_kGAkm6$j5$Qdl*Z`#?N)ZAoy@cK&1VKPVK&5vO=}lTf zkBERsC!vPk0s#^rbdqpxeD>b&e&2J>I%}Oz|9oLB79_cUW#*b|X0Ab~yqwbDlJIhR zV@_w;&0Q$)1@-8*U8=S1=uU`qeUPVV`M^riDvxQT2RA6=cl*I(^?8@9k;k^6T8^b}bhL)aDlK;1aL)p=@?YlUgC7NJlLfvmW~G#w z&6I=ZCB7~tzL1cNRFikC)9m=8(bSd$BPkvI%r(x79=}E{M6xbnmWIVs>=I?6ny7cZ zUDkd3d*aqy^ws{v-=?xt>d;`r<12N-BF}EC(zkFrPIo&8*^9KO06=(rR9b9M^*R~3eBi} zk8xLC2D>nnruUgTAJ{|<&>V{rt$TkxX9Q)h^7wr#Mn87SH}j4e!04>I_c&-q1_X}R z3T87u)j#~ephOrlS-X-`%$vy;;Itv53R}fCoU7JHA8#dzz9Vw?9fG=6dt#7%9`!nX zEG*@#*LlLV-?9cM4K5_=*ncqQ&;}Py3Uk5KUa>xX@11cWl~m{E?SqP$N<6JkO<(1J zs7&fG-l|J=;=N#Yl{G)`6F7^t2u>MWy|(b=Jw&yzTHU}0%W~i>cQ%pJn0Fb%ah5vQW78OSW|4H*vby3Mt8!}H zA?~kSSFbclROh7laF7TJA4Y0TV7IvVo4$6guHVz_t!xD8#q8Pfq{W8kJPk~d{<0q$Q>JF)dSF7t=jIonSfa@PbYix@5wQ72-x<% zN$;7DC|<`$YDT>(0n-}_$&0e-MOsucBx?EDD4OzAHx6ntmlo+`liDN8AzYP#36gwY zucYpJEY@=+tt6Vg0k(v zOg;-*u$`7kyea-j+ahFrZJncD%&e+@U%Q>l-YYhwIZ z6!tqz9+-o;^}qck7g4jed6iPBKly;(>4%K{R_&A7Yu^}#$uQfW6}b@yKRh+}VOA1i z9c&~_paX7V5xv@B@I>zD{i4oon2WX#PeVtQTH4~yQU^hjwPR0T!#_>@Jz!#| ze*ZXl9NJz#Xv`6rM*4J64nF!-LB3mh1;N(yI(Nc#k& zuq%2yw%}u5|FOGaa)c{Y3v2sJkuC_85tE(Oq;#8My(8TOn^PQ(vQyd3T2O5MBIhTL z1Zs5I^`-lz(i@2tm3C>Yc=JPbDccBZ;cncV(o!Wxugd_jQm?|Y^!s{Y89PpeO-70C zQ`ex;!)~1^i}bH*F~#r>_;oi!5dUH3&~P`{UOrI+Ste>Rj_*>~53aCb1yx(6y`JM*gnHnwyBiA{B+5!L7tSB>s_i1V8rp*WdE=_tRK z-wsolFA#kceZn2e4C0@n&Qkkq0iu8miYXZ@SU34P-@oZKm>F}KqVP9|yArySE&`U4 zMo>0%MVNo^)GIo&!xl@6Z9@+8Q$QW?^$Y!Tb^4Ab_R|dxKSeiRAc(9}hWQFvf6u3n zOzSnmHolJju{(bQcIOEbSpeZsQ*_1n(MmCl$Fm2fStu^i(Nnr-evahc{o_TkhqfmI zf)09mxEWOBQld_v`suQjFNng^p2ShX7mb3$Bn_auI~Z4=qNXR>>#Cjgt8 z_$yP~p~JqEnX(|4#ei(1YT994jpP{5zq?8u%E@aq;8sJ0lwq+7l}Znrx?=P>&91(USvPp zL$~8$?y}f~!Kri}<|VZNgX%{WKVJjA+PG7uDKTy zbAMuO1mFWI+MpL2&3>;StmFg`;+2w(^=U2GyNbL!jMK6D7B$ys3eE`iPu zEwE_Hr+}In4=67b)~yshOq?M;Xp58#qE3q*J8eQ!$*IYs)hPxiuUvDNLthA-MM+YlTt@{`)-RjvZJxQEq7zlIu=dI6c1;UD`bfim~~Zl4{blL zZ#bOVs~?;Qvi7V&EqN&_1y&9YE-e;;A-k8?<=*}fn(}?XAkTbc_Y@h(HADIQy7PRl zFYa#*>s2ix_ZKytop&OuM%fj9iaVlOfhC#aN6n24j_Jh_I?Vb+%rmBxZwsS=TCIUh zfL@g;**aK_d|5VYj8XlzMgzJvWu?!oYhI=-hQfezMd}rkJ1yc_15Tmj^iVl;G0C~* zN`Cq})06t^FabP&>)zDWa63Q2Ar=*evv)CQ6mN0c?p!bCWx6vS%DkS_D-4L{sU8Fy zJ*}T8bLHz9=tgE>-Z_j5-r81(ZIXK0L`?YvZm7DvoBmbAa9JHYJQ4cB(H|k9T(u`r z{{`O84V}@bP*%I{Y-ZzoPeDT$CnSo5s&#{!+BlM}AS*YIBaS=0CRl8#NpHBCeud$+ zv^GTtr8adQPMUXry_u5*4nO2z2rPF-)ezD z3zq;uV-S%~N3{zcOp8Q!?s+qvf&b-h*1w?O6>@3P`?KhP=mXgIo_@pW6h-SO_MR>L z76L5|xejkHiEH0FHn7_L^7(EqZQ24e7S&NiUHN2nKLO{NHBn$SJ(@SL;=!W?r$B91vg?l}8EyaKw?T-dV z3)Aywq~L?A&5^TS_$l!_`v!DU^3x;tvt;ZiY6UCcFYMY?qFC;xWLIBFu73hOvilX~ z_5Bldy<*rWy?9YsrE~yb56Ox7Qq#-{x4H~*=*{F#OtP3!IySwWc~Z^(^|o93%Qu?S zsbY23gp@f>#vOS1KAJ1%OtnwD>H51V8%^*RnY~w3~r?Pbfa$|UkBM#zU3+DE*Wp#H>6|TfiSDaS07!r0& zUsB~6n%rC5+k!WjADCV15%~7z5ai9HoCBPJZxYylsv8(?9l|F=_AakXmkjg%8{ji^{B0&7S=3OD!slmBKQobeGDQsaifEg7rR&tQVd_ z@Fdmg+D(IG!D)wGLKd{6moNwQV9X$Ma#jbc?C!|J*t9-=qT>2po%X|908xC8X#>R) zjlqiQSYI*J!{SZ?Wd%ZmbZaG2c3cCe}Yy zEO;`(1&2B0#V?Z-vLD6$3*nC z#&tohZEph4XknXv-hMENXQ=2ClpQ#MCwE_hzbs^i{~_tOa#L}KC@EcuU|hh!!tyL8 zvY`OlKng)JHWcrDOMF;E-_r@P9FCAoS8I33B0dmot@|i*s)m_|jJ{G_Ev+wA|19uE zQWmCxOahSGX2{U|1LBUq1CWTIi!Frs81CmsT18eVg&(Qw%5@)dTl!_mb`54nK6U0Q zWFYN23;~@xU;Lvg^s9~)o}znX+(aq|9Yy!2WY+pe>O`Lr@?(B@e;#vHrLq??(wxB zc+v#JS$;zM+^b^r?=S9uar)RNlF0Z(pR_N&vlD%hphQZ`D<3UiVFBZOtfvJBT?=Rc z^1ad`hbX`i{rxbic@5vlwyKc*HST+03MQ)tDlY@TEFM3H0N%v2RAvbd(TY{!ikSM$ z%p)EshzaK6Ax4u~Vfh(=#oqgVUoE_uu3R-EGAJJ1t`VDFOKd*@FuLtOeJ@PtWmg<3 z$!f3?30E5QlWjYBq{+EN#oo;Jb3 zBU1Yh*`xdqoN7d?ICi5|VN!%98w~Qhm0dnRA*?t@h%dRI;|L)#^B1bVEWqsp-BB5M z%K*|8D2egjyb2H*yl|`|iEO^P?~>r~c!7id)hS`BU>ZZxGnDHB$liM`xhJ>CPC06e z9-ecvnvj#<0q(L7zwy-r&04N#IumGtm_)--5a@(xmAb`rL_*eX;%)_cy1+xUU@9ly z4})C4lCsU2Q>X(3%70B2Kf$G!eZAoYG;q{*RP6B%$A=1sUYcv<2tR%}?<71!A#fMd zH*c^+E$e=_>5O34>7aaU=MuxuHlhMt5L(mu?W-+iUUGTtc)p8`yQ#%QL#*}RH$7@i zh|QjfAdYY4w>+VQ?m7T8We5Mnoe-11VprbgMKOAdn5B{4UeYI1su$TPUzS{R49dE0 z_+<3!!RS?}cW!0t$kxPET)H$qRkkV0Byj+505BGo;44y+4zIpSVsAee^UEsCe6drIi++ zC*HAz_QL%&JJ|_PEY1*qjPnUoW;kxsSF0@KJUBWnKgM9$ESGdb7n0Wfts$N(g}Xb& zqZfP0-gT1OxjGLh8Gaj|l&s38N*SoVT<}Cc&jO2Sp*;Qk3@&l&$`iJ;36#z|;QH14 z2PZ6z((cRh(~l2?zOvTH(t}uCJU(!?TLbG|0_{9IE{I$dDzE+eJ+hBqk#BgxI9A%p zQW-KfZo+4cP43HWkRpUg_3*(PK$+)>c3HnJ#SPZil&yJZW_U$2MotN~yOuoQ$(?eT zBF?AxbvfDVD{q&%ndPL?ec&eY7OQzEJ_+pQ)9HW#-QF-Uvm0f094~nHs`d%uDWER- z82m~A;z**&!Zl$(HW1Y4JJ~D(LatWbL0Rll2?0VM^W-S+-dO0_3oW5 z$>C{0(qqM|S6m~@yLEsJMf~2O`ie(GRbO6cZ}!8ZlD)c_vi$6h?KY!-outP=KTJsu z0`>qp)o9GbCH3tgkP5D{>SC969PMY07m4nmaUq`p3L%(Lsh7EJrJlv+$GSq;dHUwX zfy|w8zUn{SIdLjuSEZp}n1aCLEcGcgK*!EKh8zEsSa#?mD5-UNb~-HRhwkexuXQMg zMPCwafL5V06E=0`%e**oYS!V z0SYR4^FEX=W@K5(@(u7FadiJw!nic9jTUUL(Smg$!VTM)cbjM_Ut6%R1we4>R-Tkz z@zkud+LM-g?EACcoG7Gc2%8`ZUbTjK6?nJ;6+PDw|4R2qYX1N2T>9^lr2ke=|KDqJ z;uQa>eZe3m5AX{6(!zb!^T3xpdCgq8NUO$KWnQHggV`=U<$e3#RC$J&Tocv-#=>J}? z0fiJqh-wWk$eY_93SYO< z|7=p=KH_w^2t^heI_Ot{_&6QnWDagc`OoVM%ao@YsjW9q)E@@Ar$04W8(IMSt!AHD zdV{o```j=z1^Zl~9}6FWu=Lb~oEEShn_OSJH#%q2Hv-gtTpN+Penv(ZvtUSG&8mOl zRrknn*LC=Q%&_|J8fG%7U*DqH=cyq-AQk5rMy1BU?NcCp3_B*PpEFQ{8-FV@-ZlPQ zVO^G|o%Y!uOg@x7gl;P&MK?M5PcnN9%~!P-IK#lU`vhkRvQ|%HQ%%*!tJ23k98v@d z+<}@x=~Zm8TJt}eDLm-cUTIb*WbJpe=D5o+(n%QQ}p>TFok zo%H3tp>p2A(wn;Is#^ivBE4>x@!ZxC{1e*+RI`5ZyMFSOdkzQPhC6V5rRU=cN2cD* zhqfR6%btGsWu{3Bj>i2{cUId=tCQ&$1M=o85#Wc}i}FSVd6n!xW98*7z;w|&{J6v_ z7WKK}(L5ZM>~}s;omIJpqoh4UIz@TiYSRCq_YP0P&*Z0$Z>&Te?(H>mZLNKHNi*?l zqOc8}f&S1kpU6am1@o z{;AlaUfC!N?eyVUM@aS)-m`C+>6wobEc3KI+6tjWNe( z07Z4pTBlWUJSDP!^^%$E;p$2p^^7||wJ1A3yRVqD`wTah=v54d*8OUR2JxmeUZ3{W zZAA~&7Nnau%V;WwHI*&;mJxwealjK&j?K%ye7}v6Gcdry+&2DC?$!10iu4yUmFus0 z!xK>o_h2OOu6*XPj)GzvbKIA?yJ~uUugs7VB5XU4?t1!CcP9HO(c|=ypY%c6Ls{XbYU-o?h zCw;s6nzd59Ek2+0VD;tFK6Yq|F5|R&#^BpCXG~QE5X0Z|`5mZVW-5W?s_oCdW)66> zF4z%#JFBf+fy?z%I>xHNESWtcyc)@CFg;9>IuwOrZkAU{g~nm#MYPDjwEbr-6(_4I znmRrKSwhh&sKdbmPD=4IjdS)Xi#+>J5QGY!R{us%K6_;(K&1WSkZJ{j)(E^VfP7LFEl&hyJB4&84#ST0JK3YJ^V zdXkvU<&HvLJEfJ8sAKb@_ssshGpg{SqRCr(ZvoF*NUJjw0^)8cG${k=t>>0j;(qtI zcI}l`;7MAJDgMl2C|Nws zGf`~gqN0zn#jQ~*4O@(M2ocq%q?}bkub^v|0P|O9TCpw3<-3%$`5he5{*i$5 z%@fy^MxK*7J5>qeOMSJNv=tQgA+z{7_(!r%n0L?m*k%vMY$UD>i65ad*FV4)z($4< zJe;Nw@*+6e71oF-^!!Aj6c_!%UgWS;IO^Ecy(iPI|V|n81nu_)BzlZda zCzSqIMv59IX~Wh0`Od}Fr%}?Dk9j#(RqBFbUM7@V5PB7_rt`j#x$!aG%0$)kR_>_v zE64FwY#B|^>lOFRFx*gG9JgY@l zBckFhQ-NnvFS|&JG|mC6Ezi{(hvByFRAYg)ssj5A3X4;)LnY>3GTIo^z#t@y9{TPG#(6J#ERJq6y!m_tUXzF%Qxd( z&izq3@bl=f$UXd}?w8h~5NRdMC*xp0N`2xBVDid6&Ul_=L5OTc7&QH@`T;k8cB`%y z^?RIc;r!8q*C=)!e`A)(VH1w2?WDYNWX{QzyvF>~`NBkjE(CfwkspznYlq(tm;PqL zXl^hX*aP>Rm)G@oBeB`)FD};BujN{G|!+T?9#H+T4)SU4v z4gN(iii_NYW%#uJyqMOs{Ym-giQ{Pwnc>wBZ_wb2@(HY55=|>|J^e$v&M+$TE8K<_ zE7${~yV@RHcetAr=wzxUY%-Qt;TSPIx{?qU0538<_At-?$hdQWJc1tWM;Ij@YLX~C z?-I@cu>OGB!gU;r)^^OtIF-h~hI3`;qG~|q?uqR%F^$;p_Og6tn%ll@AZEae!V8Iu z(`9;sykR6oW)5P&b@jjdUcJAQt>>`Awf~jBHzogo+FK-vv)`@`0QH>U+Mw9SWV)8B zk=xMr_Y=x&+JDH?J44LsnfN2=7K7O6NsQ8{M*zTNi*z65w~MzU74q|;oRZsw?kL21 zY?B@dH^y=I!F+cia8MZW(m?`{uL8 z`HdBj@|>80ilpoqVmj~4p?wXML-k^GYnx)`?ceg6B3%Z6JI&acnC|JEOpZ^tYKlDo`b$77b zKa3QJHosaT1mCM199}!Gto(-&r+PmlZT_F-K7JK%oVqv2wJ{Jp76%QRxf)k@T(Jk;`9~wv7flypx#WJ%7(=c1n7Df z;3?U%*5jwt9;~+K8x=~Oobk;fQv-uxJ*-l;jPq0p9TV4R_8h}qf8*0mT*ZrCa>@*f znR?^;lRrFVBol3)9luG@eP_9z&^nF5U`?>uS=*hhnE8P^uL3crfuFa$k0jc;d&zq) zOUmWvMRKgdz0Tcz@tTj-g6o{^X4Pq_EHTEx*9H72?}qVb-&)5DJ5j4;;f-xq66SHtq59B1%1YOcgn|BFq#~)#Qn0j%wu>f|XGq<4MdU~m2_PU6gYwxSiB25q$ zGj{*x(~+9KaiIFGPZ55N&Oj(ohOgi16sP@ua?yT9)e47y9_*}>BcEg+C-P4mp)^(Pj}=Ct`CK$GcHEkbJkxdElYql*v(k5N|8viz#IkkI??Mw zKyE7A8H5gedin;)#PNi`8tFEkA40m`Z!(hS$b_fl84?JEz1eFPxSEE^FZt8r>C#@$ zo>JP+(6;dOHdgb=nUQR?`sYI^=yTR`=JFe_w8*y6{K|uB!WO0BpZf~{($m4f7W{TN z7s=DEGi2yIS&Esb_^+--9qy(^wPZbXW2`C6gv))m9L}d$eP;JpenL+ZmjN7#Sde|K z`$RGsBV1qU$>R?XehS*goW&)@?mpm?j<}=z*@S^7JhGNsMJZg|{4WJrEmpN%QV+6f ztrT2j7=HP=c*uYFyNX_>v<@b(UMA~YJ56UelW|nJo3BSCJCJW-96dAwZB%OQ|@KQemH1_*RoE~>dP1*hjnwi`v z`hDk{O%A(`pXO;o=If5f42tFN(#8L!Rg=|y{cNj}PU--HHlR)d;8n6s z!ZA}^8w-~Ka)rfVKuu?wXDH&%Kc5pM0Z<&;ifk_&Hq7~k;)7A0p!M2koxY2(bCdbl>s%rA&B>6F3=RZn&D5Vh&d~9c%sruW3RmP z{PFZLW%}Jqgdp^Fwez%@A;dEtD`Qal!ph{8GIc)(+R0P~uu1>Y--t_cMo|oE?1u)2 z49!b{mQ?$h?{Dy!!dRz-K0(Ymf^m0@~f2W@3 zRTve9z6Mp67*%|6b939Cixjo*{Cw+TO`}#27X9@JtLNJ205r8jCrPXYdNfpGj7GSP z(3TsNra;dmj{uT}@4Bw-M+!+ud5xJVHrpbpM_oMi2USqKl0}tBO8pb~fme*z8Mn26 zZ1Nd#D^=hmC?FdUwyRTbLLy~F45Ej{Vx=)k=hKdsh(dbD8N)?H6e1deEbky(z z_9Q+j$u``LzNlwgk$<1JM|pDjTJ1o!oj&$lFBn*HL1Wg5I2Gd>;x`kK+z~aCiM5UA zoZ<2A+dtzpI+a}Rg(IB}hsSGvn`^FIVznHTxQUNfV$MvnD4}3V+oEYkCh)scIA# zBEEt9{XjF!AN!el01W8_QU`MJZB`e^xfnmLaYR^|gPB&T{lfIc-`Qz7PF_C57^E%c zbCZ|j3ihatIqq49^{l(&er_o9fNU4jz3t&2?*3sM zZ$~!}>bpwYV3eJa)hOAiZx*fOTiW9_4mhf`m2QUb5+@SsW2NyqHg*!#{+><9QAnZz zJNoTah*R@{HTWiFMF(CftP*D!5tuRC_h65HT#-d-KMVTAqWwdK@QLM!1P+eM&Lyd8 zsFvbE)%f8zwbQW4{EEC?+X8i>Vs4ZBl%DoX7R>S{>v`hAfHf>F!>%KaJ9emPDLZ_- zr;WqGsr1DQOii&&^G0wg1#*Fvtj(u5&J>o4OR-C`V_T{_S@#Q(onNSnqVSdBwcVs3 z9}lmcrJhu%kOZmT9oLIsy9?f;>`kwJknH_t;Wk2b8Y+qhjiuss3ANOAYK#GeaGm0fO(E27 zEv|)>cpk+pmz8_jcklUoZam)X%31T&UT8*bs>&AoPqOORPA8hM*iGuu;qGst$!iUTxBlS6zzTf8RrjTC*W(nfaVQqy zi48Lx|LIPs!;L3wx3VaY8uSO9I_)TA)V@$uT;_Hf6V}NEpLs(+feD?H3k3ecu%@GeI$mJ_o(9c}>Ysa+&9#Uq^Uh{2@1e9_ZWcgFhY?JTNfc0bi6pWi%|Lz{ZdM>(mbo}46Y2>-Iek2(>%fiI!h zWUIS63Y%{Mx0rK=k^PYZe|tP_^BR7CL$7;r+u!X)`(d%Fjh63vHu?a*6mx2qo1*xQrF z9g61DekBwe4Md-zNh=vHgB1UR6g?GyRCLgwl?1B1aZ5cnH+M{YaKs#5O6pUdW)4ku zgz6_^E$xtYXjQdnTGk-VmlK(b@S?ITePf>!^m(?wC0YjKxpeVao zr=w5~vwqm#WIp9+uc1{nS3Q1$Ynp!s(o<(GKgRv+3p&UYy(;y8(%0;eQwh@;eC$y%p3f@vFA)`6}u2$ z(M5(HnGSiIRe)cfO_9#FJ4n`a(H9C>+?e$`e{#?CLm7;YfN^ZcRO0ct!Oe0Db+lcs zpw%2F*sBD3rYB7v&Gh;zf5k7$$kdldAuLME(UOgW0`0`WJ#eX6(>T+IR5zg|B8PcE zHh_TA;(*K-&{uxrEN>g_cX$!{{_`S0jgU5Z@b<$cr;+Tm3C@M9=05kQA^xR2=Zc>p z%ciLA4itQ5%RQgh2ao)9`m;+-pc+o?UOkbbh=;E^J+u(Z2*j z&@l+R2|3|)bVsSq$+f#iRitdAvwMYf!0W)M32}$vyV&2UDAp&j41~nAG+@~3EQ{A; zE_t`F_9JCHex+rQhWZvKW%Ool=XvvL+fPTb<>QmNo#qw*MoFtb8+>F5KK_scDnWS^ zWeaf`dWI|7nN&*oYFRcx^-~t|vmbg|n#=i5&{nTbx`d<_HXY)6Jmr$avboqCXs;$H z%R%Y_VewVTY#9I)sg>c6Wc165}T9G7m&4xoKnAb z5&^!uLC?(XvKnY(Ltp+%Asy`PC5h;n)=@gR8P^2mb@*%Kpl z7mQqyFda~J5?Rr>NHhR=deU!#pT^Pt8H&^k-sKgPmVSN=Jis3i2)LnlxAnI2l_{M} zVYpn^`F1C@z_nXtTv;mj*JF-mS#%^Jai6|dFv&T~oK zURq6^L9N)LG2G@AuR|LY@>X1M9R6YsJunX4tzuqFYFNoYP; zx(W$ASga@1uS&i8K?|cE;D9g$z_4#6Fg^2hEWB%os0Ly)77=_3-dYUg*J-q&v@MJ; zC0dUAn-lINirREM#>zMjkEDZC;;s}vYe0-Q?xs8~Ycg2;9d5YVy!J9Vu09@L^tA4m zn*dc?JSSwhJ>`Ro;szsrNy#_0#y`P}XUZx(jdkGb%cv$iEq$lsu{5hzQo2 z#UaD>D<@AXz!GDLv)#A4 z&K);y;9}hE=6~uqS0k~$JT@bP;5B7u>bn?EFb9s7{f)C`XA7B%mSt^1SACJ0yM3n8 z2ooUODMXaZdg@#gNa}%k)l^NQ0_ox80mRo7Nd2h6=u)=}429^d)5s>n&#Fcujf`djzli$OG z$GO$qz;gCS=*2e+Mj1YH43uTl;v{BaY_*+52YXB>mn_LfJu%?QJZNzl5Mlp5Nju$S z_5OLi6;Kw0STsE?A0r7&5vg@bnrZG#$dq-?06V6=>y-l{#4&eux)w(L@-nBzUmX(@ zMfE0$N7d5Pg-79Vq(#UJ#p6c&HUS!b-FHz}M5`G?Sw;4Z%=?vSy1*}xs{z?>Ff*|~ zO>s8GyRYV4#{L1+OZ#lkic{?!-~QjTt>N^>96!Q;JvqmGW6sZBAsAMhaCB#`&A8Qf3 zfShoPG`X~hQ$DT(_bP}O=qjglUfcV5CmXo`F2JK`(MxpPsdMvHba!Hd9FJ!{lXvNl z_H5sy~=d@$Y3xe z9U2PzMhJpF8Idl}JJ+1D(B9ZIo4KE^zs`+)Zy9*bR$+AlQCoTqEx&|R^jlt@b?Nz& zb`?nIOmPBmacTsmLz$`voX^s$&t%dcrM#HrEhmTLyirH#(9ZQ=5(YD)v{_ASgtaxt zy_)x3-5rdgjTbK3%G@#uW8vdXp(lE3ab9K}-3uUZb|B)hOtKR%P3j~Yw7z5KMH8O_ zg3k^jibte_^Du1<&mC8v>#>81Vk<%AT*Is8M?>z~~< z94H-I$MyXzyO^UrxfV6MvTK(BD9ZB@&W{Wl@lC+TP@|89* zyI*t107?chErTC8B{7Bi0Xbjx4qyx}jtw7(j{#PfFEVix`nxnqg1=Asxbcp``2<%fo|k_2?PKc#S8@}J?9h3H zZ?mGrOOc6VJWY2`$`FO^I-+?HY}O!>l=)3e!NoOnCq^2${@2cCgumUI&Flx-(maF$ zk4(Uqs~5hQy?`IqjR%UE++bgO=Jn0($=i5(!+N;G^O8mCPM0ZXW8Y&BZ7vGJ%1Q_b z&#`63b&b96@t566**z%@vPqwu{#uhAYUqR>Q2-}UCA_kSI&R`J^G+{%G_->~JY4-# z`8M;Yes9Wu5|HnmYTo)SL?~5>WZyNj1LWfXW?%$GmHuLe=xi2w$BmPSv#t-r%3d_R-F1sU@h!@G4@mAJTjCYJS6twFHO;ty?*#j>z(ubEV2a-Hw+| z0wRKW)d#citT5Eq-vGv4r%IPw1@DBdoJG^lm7}PB-afg+dcbO&AS7J2YUs#JWq2lFp~a`v)A^-S&hEb10L{{@@#`;~a0Tjyl?F@W;M zMXL#2gkuiwn^MFgzM6j}|3LfzLeWL)&jB%I_ig*RTj2Gg=0l(M=)Klco_`K^0xCca zf&;x8uLi^?etjURM_)-ab&II?TwSsTrkPQv$xE_M4Fy2ujYsiV9Vx#2PJ=zytZhb??ngqg)+Q~3Li`R>VsAWHH)K!ww_3jO_v{m`U%oE; z4v^h{d4aaCHM=LZhCFN%U+0+2!wQVBaV<*si^y0vHQ6bq1DlHjdhP=`({ClOF!}ewZt3Z_uZV0mG@^(?>XPiLm&m}clU0@D9mZ+ z+Yc3GYs-VZ32SCYKAK}}XxDr=0KNZMvavw9fH~y$oJNh%9rx@A_pPz-)RHp$wyneR zsvo!XKdfAp*rATU^!?PGrny)C$yD6?0=Yjy7_pd^rD7EfUl%HMyRU9}A)xP*;)_q5 zgv+=zd)%nO$Ijl3K=m;o zZT=c**e3SS*UY=fnPgkV|GIQDukpQMWCMYzH}W9q^PR3eI>}#G`3;^GbG1ZUDCm>} zW7fWcbsF^Jf2&L>1EX}YpHCQM?73pLAx82n5bOyp&wS#BRY+@;Q{%EbIM#O4@xGb#TndN}aR5^js77DKEN)LCK%9JL6UFP8cpfGtkY!=IHbktki_C^y@r3eB4!ll=pDv zW%b!>B&>R%0IC_mmI_zO0h70rM#$S}U@p^+nQ}s;X!GbvVe*#hg$a<~{x?6edp>nL z2yjFW4M6E>;;Gp}U<5~4y1wL>yT3o>3{sBAaz&Br)fPbX{dRSclN0EXu*CY;+l*zj z{_b_mLw#_}Fp zBd_N$j~S}RWfXj_Ns$o5fX_bjMuP?xifqwn!NW;pE0ubH zDKBM$ug`YPG^#0Q%+XuloxgAm)R}3Ek|V4&Pc2F)5ofw99t5fvf<0#a?gkp=P6f2z z6s927np7sLlM(m&PvearIFM?99;#)ofHpg)BRh?K90#zY>^k=(_wdcf&C~74S>@tZ zi9tUy4`YpwYo|4i`+F5oGU2-q2-ouf^=+>~obxSUgQk9nFDg(dB9^dUpZL1S&(L_P z%)qx!Y~i|2V!+$#K_%w4urvKj`aRmp(I+MLJX;c89DQUs^ekkur5}BVpt`&Xx>hX* z1eSBy;#wa#?C_Q1vsg9etlcC-4f#fwTXXsiP;t9D>Sda*xa7|0CI~P@9*$ zTQ~9y>2fYol{QtbPiM^25m8|mAG0ueYhs-EYOnu!;$cWdfn0m5-wrEz{H5n!ZGFvQ zWTAQ~t0OgNPXGm{wy4MAAW_X`DM*ddW*W5z;?}GsnEmm*_u!>cJ<|tLwaaR_=vWq% zh_lKZxhLy;7YG~#ax9d1RtZ#ku7L2>T!K^MvEGq-W?lXkk2IIOY9+gSiK?F%K|5?9 zAvG-$S!mhe%H9si;Ztpsh2V$}~}TB5z-; z22Uwc;H)_mTqAK-Obt(YuOi!{^nsJ#AZ zDKlFX+{(RmdUm{ZI#9Ofg#C!@@Q7TgP*uCpR7tCKuv@Ea&}y;e$5oaBb>;1)Qsao< zt?0(*@;bAVc~9+95BpCMKnlY7(OtzVpdvsjaqaXRDLWm2bIn*Shj^kLjt3UlZ#{s_ zv0IPO>hnR7Zu-}9HIR)E1=OiuY3)Jyex)tYHD?foga|i4#6gP|WS+!ct7&;pxJYF? zKWMjOl4THw!ClWnlO6cKQJRdb&Cr0z%z76SgmT}kW@LgWo+y4m;+y8Cwb)Ne!lOpA z)SRqKNU42Kna&ni^4aynglCfjs`1M4%!06xG zd9rWi_uJBzdV6Ix+U2&?#gfYH-Qc_F3|IV}v5$d2KsZ>!G2rn!L0;+rhtA{6H4Hs( zJZM34$k~u0`?%kD-!RL6e{&4VPOO7`dK%3vl&!w#WkMtKj*Au=fn6+|gnx(S6%^(h z*Ie}02a+wpkw#1UFJnJiD=fF!@mD+UX&UfQTMeH!+?qOUrcW@{|2_kXn!c;Nilz!% z(bnUbZIzIBMx~bbm=K%a)!G-Wj|wf_z4KB$z3Zusduo;jUqf%|WLOodD0f;(;5BZX zW9XCHtWu&J+S#0wywsyaFNlYE^Ut?q%PLJ*JsnJj2fRvcTRv{o!~;Ao!Q;}#U?ZO? zs6WJ?KnpKDnK6qlH;v}iZ02_6Ao0!OS{aZLADRl1XM>NpY{^oW;-v++%jl%$3NS1b z*88;xv?6%@ayQU4PyZ=S&weJbn{5FMGtm}+EtDx;hg7u=%5}2f&OtI_J{l5wVFF4; zd)8m#To$s-19I^#SsMFKy}CI#Gi9X=&;OW=3MNZ8fSSCe*PLx9iDQm@=I47MD&q!g zxL~CgOdA4_UNQ;e=*H#kz9(!jX`AY}cQgi}_<;*C(9w($idSH~_bQUhcXj04=B?4| zi7+f}^qj)3^>E0470s5XK$09y%=e();|#AdQUaUrzCeY-F=>6-ig6axuwaogGfhr{fz_X>Hx3vE5_>uo)(uAYHs8Uyq@_=4lG2>vFB zVb-%9IO}eAHQPmHLd{=ndtt;qxuIWa02i#2jt^yyrVD)RPPrPUF?B6=KSfnG$)cJn}5%1PG$Yao}p9Bxfw)AobmHn1Lxn# z&P@z&CC9gZFpb{~IzMTeoy;w;(b_fzl5Ms3K?_fvdu@!SdpSu2-FRXCG5$N*$8vS-*fmI^oYSkPId@tm-rGDi)JONu7l~?TSS1z%Jf?;dvn>yjFf`emm%S zm%(GdHO2ge>f)xd@wOlRGyVzT&fuO0U$Vx(5*h2oOEoWklv<;yhFoo3!}>B#P~pdpf0BS6K5w{t6ON|b6eP6r6=kAVVLIzXX9naY)8o(&@S54y&XmC zC$G#_q%2qF!ZEfT3(jMX8P|K98`KiTb$J>uZn++H46`WU9n6hi|C5h56abZez4W-J z9?1zDs6i!5N{?j8G6zeprc^Kc=^Wg)CFw;R7O%Gu5nd|hg6Nly6~hWmqyG$0!AP>fO%Bemj(Ds{|HCLu(yEg3Y$FK@SmaoE8>E4RYSyf(ljBS?C@$dy-8g;6hJSQk`QAsC(lIUnM zheg6H2V>*S*Ynd5ivj0`#!)CMG&25f&USE`nG5ef&QuX9Cqe_C`8AF-r3l}O!rY)O z6hBEpLDJ;80@vjLS){s8>jTUWm$G6m`%^7OSIfg69Pke0!DGGzV0d{}9ShlC$UH&6 zH1V&X^evO)vnrag(g08X!?aOPD#BFtD}sD2sFicUNeGwT7n@h=^Gs^M?!Nwrz5)Jf z2a(mELNThu*+(U09v5&~Yga^YqfR0n70)tC**A-@AEfL9koAmS=z&b+%bQnaAD^l>BqF z>s@L#(t}O_)H81KdSF>-!SvFyCncDGxuw4cP{!E#icWo>btB-A+<30RfTj?#>%)!7>SE`ypGvu&NAXg9E#}Egx51Zl4dPvYf^-iSQe|`Ytx`$HHrY_@M zQJ&Jm;G_6b{BT+k2`2kXFh(r0-t|0PGL{iYN`9|i5Ocj`WL%>WB9!EGv@ESMSdolm zYPb+=hxx->{q#nDi<`dF$CjealjNu>^v88(L|a1q!cRMon0$2|_S%ZFpr?H~`Y`RB z(_W_HN-i}42L?i`$9^kSaAmHkS$OkT%Zr>6vN_`Z)Kv4@3aGuORYQduEN=X?An1#M zA3VNvu&I6FVn$xos_}-rXj=-`d7k}6w1^4k6LxBHag<$pza}Z-5EP zbQe%pS&>a32jx^752vGWSk67ArluAa71aY$JK=Ur^%9kdiHVq)m@G48jLX?h0H{Rf z9ReTUw*YMFyb`U5Zfi@?D*(mv9Yk$UN}U*)uKqn6`=vD%E%;B#ttuFZx=8ZU=1 zp<`<0>h?wu%15-JVOWNC$=O*WrmB8Pwc)-5=|yo#byT%z~b@R|es{ZW}Ze&Gm(QWn_OB_ksjpe|vb3+uK`SVJDxsGKxiS^fq8 zYd^&Uf80T_S02e~cl1^7HlwI<{*XD^Qo6euCxqqd*qj(k9<^ODwE(qv^J;4r@ur$b$K z{I8Ag?Z1Nui77Xr3U&*Nk&kGRcF4&ewxkef^HRvKI8QpfT$4?@Ygb(gPbteSSh_^S zNJR0;mb~JEHX&KkEmCZej{KnGA6sF`)R??uSK#p5*jmJuc34ZVVNj|I;ayJ@yS>(R z3rqoD0v7B!sB?NJCYE>$p^gI&P@q!t%;2C*dqf;hd8RQ#@;v9!>7-7+rDcg;Cr0^$ zEIt)3F0Lh@qO<{ema$g40Mijr`YhmfQ5eF6t5m>E5q60ct|-Bs*?P zJ1Bo+&ct&et+S(hI zaG@tXD{l&U$Nij%*z>{P%IMAkf|c%y;$Vo$vcau-wNmGxT3GNvdxFdb*fU_)1a6LI zQ@notVK8`lsC4)*kc+&4+bO>s97vm^Ay;E(0x5;2c<#+{S5;Mg?u}s}gfSda0c)!g zid7`2%zbJ0K>=JWP@CChD>wUVG6WHF6z58wYD-;KSmcX-;#V2SaHdr$@W^@RGQZ-z zy=ilC*)y0^Sw?E8os`SbTo*kRxg+K$3GF0+u=0@fa^WDJ6CJ_Z$!kCr^Hwx!V1P!; zfKzs$i)M2;z_S;hqXHw{+1XL-sN9$;p#V80uVXqq-SPhJR<72;;*a^Xe0y$O;9SHl z!!UJLsP!~KnM^7_m-EqYmn57v$K9D9Agz9!mqF}tPQ%!^IMvq<6m@o+Sab$~8)>}M zhkb$i|O!>1w}w{P8hwH9LlySI(DiBrve(-U^5 z3`5rHsfCZOQJx0-`%C@SD>k1lb#X8{TxZ6_bv&}N1k&Dkp*X0}AM|rB<}8=nnKEfs z$u896?G-3IXs=%}CL(^Q#N^AeMJyPXqAwp1&3E zywElWVvtXPt5Na%9MtIEJ0I!WZBIb$11ilXrP*D?hG${`huDxilR~jm5UnaS{>${8IB;5pZjkVvJdfkN$Gj)bHFm!e)0H>&bg8*OEP=O6AL#bw%TYjBOe@L7+f&Rf zs&F-4nSV_6;^$OCimht{6_%#X&L@TH4sq&Hl*2oX_Yc%I#8ASoCb z;ZE}1o`mTE%|VTyV6NVk69H`@wI#qBm!mn20a5m^ihh8Yw76~rz0QD&Xlgq_}*BiPHY)IZ}oE1=D|UxSxLzDL}3u%tdbCI zj?-|isDW?3+phm!y1gP$>=d2nFdq8QelCtz*_JFO+zrV5P`U`3edABvYBtZ+4j`hP zcICL9?`@sh26BfZSGmoDI*Ph|G9s!D?|vbcV6JSG#1}45&ouH<_<)p<%=b*x%Bo%$ zD!u#{3tAm@41Qd`eWz~~{o76wQ|&U?`MAKWR&i;>dwam%`egvch!_U-^smtVlI`tSM_Eyppt=tmLb`33<8rjcPOvkZ6=m;?m=(#brzlESR`O$JX~ zr`ZKqSmbegV&AFxfURJlAvI0d0rfy^+MLhfFCH3T_w}vUkdl&aX{vBEvsGKeeMqON z)`!yVHb>$>)q>6^v1@@FG(;-?_|LkOfjqNTm&hp^U^#!%x3Tm68J7tcZLBeN^`k%F z7`Uy{A@IW+qDYL4j9|Nco5A%2$tn-c5aduN;QJjT`abtGKynIM4)wl_!~Hs;GMa zohaJ=+bpaEeu6z`uKOa(o1-p|yUuti&^wjbS=X?7FfK-RK_tbpjhNM~WPk_c8khC) zkRA5MP#%8Z=7fN3fsMd|f5QOHTAC`+b1{6oUI+A41r!Tf7s)T0cUm#WdYg|L$8B|; zNlbW{ai@VLBIt0XGvD|lT^#sY5Qd#fu#=)*EqcO4KY9D=RluF=N^cb3ssHI( z<30q6oNOLA^W4QH-En_`j%o<6I{gS>`U%!0VEJn~*&IbgLVy1wte~ae7ZqlH380V} zAD#_&Vx>bpWwk(!!jDNRZzve+A0|C_Dt-D7syc>gKBEvZ+w3|!KcCE31LCr)^7Imw z{7FndE2WHP;Cc`~ld_6D0DV)2s{#5xlAM=9FCgDTNqBWv#j5cl|9#=B6K!raZi& zBGZ&%z0c+>t$5)(aWKJ3PF~suQd0U2J_$+4-`-dR%FN42*5y)(@eI=OxHO2yPniZ? zJ>H^Z?usF169u`tP{43>xz5>j9&pcD^E05F_06vdHl$R->k?5J|BLV6`9wmgKLvm2 z3MO0n}_Mlfs>&feJ9pf5G8T zs8W`cT=HT}XgvoOb_y)`%yl+juOjJih5(`))-6R5|iQW#?B*D?{BFY%UJIJVHTv12B3&BD!r1*g63ZWykiR z7A_G{zJqGE&qrMu2?FV{NJh;MJ1G#;etwc1+n4^wND>ofK0VswvfbtKMK3(Bx2#_z zS~!uYoVv7(4r3@J#(vMn76^Mo-XpE3h*MWrcd|3EJg7%b$Ec4ju{oz*s{gFvVj0bR zv4I32{^H6?6(Ws=f}_8^`IC_skqFoy!n{3}`_Rb9D2iSM1E3mFQ`0=UpE}iFQ4D&b zJ_g}2oRsCh?;1?)1V|vN61+2<`t+|vYTEMWSNBf8ar%;Ty%Qe{Ua(m5qt5HXO9DSc z^6#CjM;ry{sbc}c6nN?KS?VBsd?#BW2`be6i}1b6iLq2Xi-`RCsSSx;qa*($mz2Pjgx2OncASUMD z=pEE0K^~7xRR$te4vQHarn&><3X9pS{r(i3etafvb0wN+0vy_^^R02T{f28s4)gbW z`9cU}bLp476lG>a4Q;7@As}p;#C<+XLG!d6pTP$p0+;rg@iw-)h85EoWG6L8(RbU5 zuPj4vh<*JxK21H77LGc9Tl99oTAQ9^8q3D!?#B7lDor?jN**{nqSup&hKGmqX0HKM zZ3o~nJR%}}pE;4wnPtIg1s#&n;+2eGi9hh^e@2;|2NQlvI9}U~mz(<~bW!>7;oF&w z-`s@B!P@yu2DDy5;?Ns4BtZ4Z(`!3Uymca}po+2QKhW^4x5j93zv-G;eMi8BumTd6 zq!&hOySpKP#4TSOu5j5be|PD3*qzC}Ufmu@fh3|>BYufn8{OOaD6AI(!81Ylt+cN{ zz&_af-p>|)`DA%fJ*8iVNgUca`GcIC){MHJv+&^%Ta(BjB4+p>>3n;PKDG z&j5G{M(7o>cui<18q!P|z$PLf=?u%*N(Rb=D`noIk}jRx6D*{9o|#w*9su6!iS znQG6*&VaT7b{7#M75BL6c;1%Nsb61T>w!~BT~614w1UjaV)2?upP~=w;l!s~<3a%7 zEUm8o-v8ASY(w+!aq~8B##}h=1wT&Y*o;^E5w_Tp!P>bIA8+SzfB4x1uL<#P=6oRF zFemW&_RXpqiBW$=N<+Co)fGS7`m;d;^-Ffj-=}P_n_D6LN!`P!9b0K=C zdz1N}7$$FhI2T+0OOzE^Kvs$XK7`*~9uu${J_mozRPp}(`)xUVEl(-G*mhmI zeACd*j;*D&^^_u~_MpqL+LURi6P0!e#(_LPnV(Kl0>mMa!`&|9eG3>g+k5^Ulv)QD z^`tpEEh3A0Q87{9AA%j*1!`r1a`j62OOv^gfYc86e+HOWZXrC_vU}UXri4GN9`{Hc z0ZMJCkF3gn_Ok%3IS`=6bctxXDv&AROG{~c87(3Ief@%#qTq^BELSiz5vfw{{n?1d zAP5!Pk*MESOYjhW|9ojqucJK}%;)1Xw7T>W0FLy;W^%+AmXwtNY)b`AXliX03IWC2 zd`owCcezFnclH>K_*wY{>j5H=-}=RW!ub%@Z>37bsuD#026*GCw3wK9Ya2vP)rMcY zJxzaY*O~aQgKT6{rAPIky`$P`r zehNBPfBk#%T#PwsWg<@rjaoWM)^_vGa;o^()_eTYXIbVkw8_hYH3NtiOsQlZ+|bZa z(-2g$|K>SEAAH+HChGJRo!H_F^CYDQa|4Vdhtjh)1J~j^*6uIoLsgpm))!g_;*zg0 zxsUg!F!>ABL42BGYTQ8VV*p~|;KdUCBtOT2+jM=p?KdTU7(I8 ziP8GRNZ`Y$78G7N{UV>DkhRewm(8P&l(2noF|3WXqd*ve8`E2QN)vhCy!jYb8bNRN zj(0GV;2%D^46~tWmo-)Aq1q2?xlt%FrI5mY;>vrHvk@BW<0jkDU*#+#;ezVWzS9z> z;?Y(hS@tu^klzNjs{V|@U46N|34gey_J?+PMZSqb+YXy!SnSR?8psJF0O$0e|I2O3 z2vR?mBbQg}3Xn04QeIR;XM%8C+%l9!5(;exeMLDO?Ks}v-Z?-|>@Z9`JUsLd3~T{x z1rr}XJ8%v3d?@Mg+NyBlk|LrRIb9vV<%YkJ_>Ya*vdBUw=s)e1$T_(UveX^esW^f3 z%zIsc|4dV?#*216`}5{_CRe2K{4j&a!I!_jzY481l!!U2Z&t#%c#MCh5SBN%;D%C4 zYydJh|1<~$E9c(DMY8bl@QuYrfwh5TG*_ba22S#Jgi1&NR4aKxc!ij<6X;cD{<S8g2)>96?ope!_Y?#4aVEtA&Jb)o}WLkGotZM3QLX`P_Lwr}a?n>MYBC4_`13 zw?zAI{fS{11>PeDFIWcC@(Z$0)>+91MCQ}TsWA))oNM`A#F{+4ZoE)~6Z9wxh5)zZ zZ;t9ZrK1~=l`#N`8>a`GUTYjPYLhPxmGi%Q7065B-@+%Eo%Cpy8CYa*w04;5y`K>4 zkOUV0Ks%*d!g=W>?|zk|X+=1Tm5LX}Ag6I)&=srtszDK!Fn(ST=2u^{{-vG&ck4FXZ*W0a`y?3Xj4efG zSoLpLa$D@GgM&OaV!Rb zGs3o;BLyllSm5m*PVNNjUJPM-hBnZ)89yCidzdH0SB6R_ zE=|ru7jXLb)%T(+kqD1QCmw@AnHXXv6W+Q|{`O%HdRB z6Ct4Juokmg&Qc@S(stRY;GlIQYORjF2iVeH&zTpAPQ~L5z5LiGs^Z5c~ zg=)YvfkdQX@0h4qpeh&U#SixO^MjSnuoa*hwSm_6K4b)xkbBTf?t~eW5EB|(@nbuF z_|`!4&<)*cXM@oHffC;-o%Q=89-hLw;Qg@noOOe>*&>pJWUg=nq24xDqvCo~CE~qV z&RJb2Q_Tq)yno+bYXFj%D(Fj2Ap{P`NBech7%}hE(vNEY{;a}|6zAY@NCh>)KtW7; z<$@;APCY&~0)`_X;QI-C5>xM+|Dd9%Mi9ta2HLWgjK}ODtgqZsIf-|6m;UO9RT5pm zJsBjINo7Rsb)0nRvPk_~Y!h3pchpPO%T_fj-qAIj#`K^uP1ibp(snYnV-p1WK%!9! zDKDP*`arIIWSkTUhcqDD|G-1kJs98smixZSYitE6gStGt4wgGpog^5bJ&S1+(s{hQ|Pp@7oR| zERScm;)4ZHD>bZCcBTiMqAQ+Qw3|(x*Xct>ySO{(mG!w<2;61^N8Y>MqR(%sz-b(m ziu3y1D&Bz84r5dUWaKMMTkAg&;V3mMER6I41_p+UJ~VKuv^ujJaz2+KS|R?W7IZF7 z0RwVEFI9X5c7tL6tM7h(dO%^hSWopFb6>u)-=^pI51|Fu=O2O2Ct-%@_09e%aF4u?k z7x|<17RfMD){+jtV^b^g_59_wJqZj~Y4!cz%JbN5qy>&GgXaAf@KTP03){X0DotJ$ zRsbva*HwR)U_W@0${M%xg0-|8ph)a7Mf<=DjS%6t%r395^Fxo`2>Iq*|7a^l@JG43 zVo52fz8bV;E$ht@%Dt2nKfL6C*4g_{8-zcX{-7DTxoi_IfpXQ-r{ejesX9 zP%`Bfbg7*%%Xt;PcQ>Iz-xqGNIdM7VRNDcfF;A>8FuRbfUDHBIugTI1C65>xvYN+5 zkT^4rnwB4J>1;FA*!D3@erC~hF5?Lr9NYh1pv%8NHyX{@>CTE9>4&&oSl35D6bvuY zK7Jc3#AyTN*Nni$((bJ8{|h+$df*z^_4Q~RRLz4gMS3IX*7QZ%Q0qL7?1=+7wP$Fr z9-TC2D+!1=#~uOd?AV!pxI0YH_BIi15f?&osQpmj&pV3+S=O?#4P)YsX>2(njt$%< zK)0b7q+|b}6+#1_C&cn*0Wf4|rW{RNTz26J&6Go*CJ&{n3*HK_Yw{BJ`lrS{U ziJy*<&r}o+6yFsIk}XwXLNI~3&mco@3`7W4;$#6R^Bs(4$hq0u5&NQvIu(Ck7-ftb zpjwh?&>J&VYJip{74I{gA-b)^>dfE_b+(|Z`Y(wh@RJu7(c$#0fUoPO$|2#)A1sVI zy|`1^^|UT=lrxhj@cg|0kihxt?^m;>OWrI_Wht-}LKHvBUz1z(7sr|t>zbFF)cMF& zAbY>_`d3Tz*4w&>fim0Dd7(Kc(H^x$*acXDajqiST~1)?O&q^F4+b$;T1{srn5BcX z2jl`k4D(8GR4i~i5pOb$Rq<18Vanfe8IpCQWnf*kpSxk2Z54J;5wmizR?_sB9M5lRhc!-6P%K{WPyV;G zw*orgHWuo6$tfsK153o_K_6FN3WNyAG{WZQ<{fKsrNah_iczmLOeYHB>D(kkFF>+U z`gjAHwp#SUAik}BFY-IZCM(<0#WZ`uDMS^e0)H~vAyQZkE66?Rx(a>COHVk9OM0aRM^6_mBbK4dpC>W=?# zdYi)i%`A~~+cl);uPy?egWP;`1~i3@@Nk?wnH0VNMA`4TRY22E%R@i}a<735U+>yK z>@yu6!py*12O3#GR5#U=qAev8@Zigc(*_!_{Xeb4IV^rjM6qyjU>oygnFS%Ev@52? z%%5f%f!ps#f6FYr;-g}|tHm0AX$!yvDhMe3=RjHON$O4m)zn>h&O|gjzt4wrc`&HK zkQWXo4?JNIuao>WNpZ=u4euGrm<>X?W>COjf2UQ0gU_frM6XDEadENq%a2qLh$N>H z%}r7Ofb(t#P^UD32|Vc?;6E%`(#fcxe!M@{w}*i(fYq6of#vO;3o#I!bc&-ZF7K(Ix>^u*$+*9GN57U8UdCr zC{tvWWT*FqFrIb`n~KWTsjCJANMPggd@cE4Zt~z%4Jo@tkf%uviD>~0);R=@W;hT; z5i(66PjBcR5L&mxORhCgS4(pQ;cyU%q^q#-m}NM=B~RTFzlQMsucvDtJV8FE=wBa5}c!EJkn{noc*;`PW=+&s&m3DP@b z;V>oVJy6x+yE6BIsKVE!{qiei98L!1nm%X(pQ^T{PS40VrAQ-}*VmJz)$PrS;T*}4 zqlmt=u(AsK_T)w0B%4T%SY!_n+mtY>!2+m|cVAwDqDRQuNYRf?+}Jr-v?Z|@JI+biQL zy(h%CHz%NS3V;y&^?ECoE23}kWPgzi)GEIxCMGsa(f}1mOMJROjWrt10Nfu;ZeY}v zX;OTWl_Y+ZaE5BcvE`*pDRsclPVq-Qz~+>(hFFd$PDH}ky5Qapm$O!lAXQ6z{{=ae zOrR)mS#Vhn6HY(^(Vs9m@eNU5(J%u zzTPEJ13v=+94ydK{s-WodcQ-JjzlRaGEfU;ru)jzIKPZAvLyUV(hDU3bV?ysXCzZH zM=>`dWq5anDCPUzw$SPGob~4NSYQ^t8lgl-i3J%Q!9NL!u~ z7eKxK^W|upCMGW9V&t-01S$KbCD{COUsz2>-XcnvgO-DVoWY){sF4*!l#z-usNuAr z<|4Pyv-hz1h6*JDI99i&liLxcoeD}y%G~4cAR%DE;cypRItp+YWjw+FH^X=QX%)3^ zkpKEQs9f^v>gkQE15s0*qdh9!NqV(<#F-JrvB&fB5*QaijR23gIVk6fQgcZUGvF&7 z4smWG(Y}FX;MwC96^+^&eFD&+ z{sREmK%7hh9cH;LWtt);YDlq32cCDAqV3tMSxAgP#0mmn$_S_F?>Euz`vK?!%~y(` zO)C`C8b$si6IcQe^WC0dzex0hxde{~KTuFB#5*hXU*3V{Khr%EuDn83@8i=gxEK7l zPEC_VE{EP@QwG&EptFLHh@bh-=_(t&0sGTXGfr=j(|kg@kOn4`wWfhp#Xz zqFrum6kYZqRg)~1QR0d??=gPZ(8M4V2*o;a{Q#U=1~C2M<^A>I{g`ij0JX*!J%pAokFQd0^!C>t!?K_@gK^9U`*UhAEL;+lnx~`&T%QR2BxqX?Jv+W= zS0|HS@cL4;an%`k`>s4(Imjx0n&ODCvUKeLpEtsb1d`ymCI^hqdI_l~mI=02AvO#g zyQ8L~eG!zBc~c(&1aXIzgS5CZDkIPioD*RPBL^%&-0>n(hClaf(+`~9|DTwB^a7!6 zf-7Hlc}ABmBNaNrh-V*Li?7@)usB!qfk7YRbj5+i~1SI0R=vQP{{pD}ak zl>JB3J0tnx*mGb|P)?;Gy1HhS*Gv#zGpM}*2h!0zhWmEji}23mrOJ$0I6+dsT!(es z7$Z<-~urpt)0{ej5>-U1J=-+;}0}c!M58?yohp{@J6tmEsq;__8;qoQqb7o^+j%9`i zPf_Kk=e{ORcZJ~FY%G4GaX-W{{gEOlD@cttk&{{HUP0UFwcvf0yOuSIU8~u!tmNBdHP=1G0pLmV1JEG42kI^;V za2h_xIP0rUh_>4!UJfG}Eh92hY$3#j^jCXRXM_-4zm$9PMr$bx*~y?4Zo>7BXy7e9 zBIq5>gCT`^q8(6r$}+^nP(l=In*r;+6e3`L1gy#R(*sQeSS4hB7ZVW?G4?n2#7wViV2v@;26mG{2T0#+4cjJ=|Ch)ce?Lj9|IQ6E%kVDI9tjw#^UVm!w zi+zD;Oh!@QxiMv+#sKFk+J{{V^D(oNpvfG!#pMhY&$;GjHAH{5P$(nKJY&%%D5@#u2DL;#&FNzCyQ#w|V8x?V)V5qdJ#g z_7Hn8skssT)$8_jUg1X!s$M`2J?X1}z{LrQ7l;F}HsJo_FAnATOQAgBMcVa&W|Kvm z(aS;{$pBuarp%}C1ql)Aaa9ocUG!PUEf6s=6ORT9{b3;{Bk-&IWCTj@bzfVz7 z<>%Ld1&HANXC%<z1YVECgMQVL*?9!DJy+C+N-amO=Ic!~oW0)XXCpC0hNd-vQAgQTT9 zl6rg&5BSrE-9VlG;_iC?lf1V2Ok~J)WGEnm zxC<0oMaky@KX)uQJ7QWuXvi#a*i|oQ+-tn|=u6_pCPH7og}9yx=gMcw0s||q4tb)X zp(9Fy9Tk}@IOSl>oIk7flI9U!zSA|4#xz1kPu zU*s{%ChF5`NeQ)rjWCn?ers%i`iaXYlnxAc`ggTWKfb}8X1NsaWEMf8Vwi+_SWbQk z4@>8$>EVlQkg+{wgdH1mJ)xci8w}va9JZ=s}AwDjU06k`4 zW5gK){)ilvG+hM*66*37IjG%etXvqODBBnH2*CcxFs6#S6joU6v(D*fpz-|NbmS2< zjJUZzlG?~TiMIW8=@q+TUts2d_k_rStxeXMJl)=EsV3M%ubl*op^!dUfVI__*=UDRq@n_Hf*e`zo(MOT5y((dksEG0 z=q!#&`Zi3e#Ylj}v;yloqN4K!pbak1JH8Z`E!uLqOgo=MvGog#*6M1UTxw`SREZ5x zNFqFASOY|v508%I=NGX`$S+r7m}vkART4Std&fD7K>Bo+VDm^yhY@9qej>HsPEUY; zzdYsPS3Q;G4$k?DE^1q^j@#*2?Q|}~?9p;NJx4+-0#5~vBs)`#lU5#Cv z$k~}YoH0H(+I^F5q)X^0*wJg0i&Ue_b;pi@d)X(&xL0hi>fo8U_z_0NppVH#kl`#7HWl`yvCo5r&2SIMJhsE?12Vs@o)!Omi% z4ot8=mPx0`$ndEA6`OHdg8;aV^ku}Bdj0j(v`sCkAg~8aZWQ&!HsSp&%%I1t8Mtg2 zI^ij$a4!1mSSR-Vy zkFt@wj#8fn+*&z)YaK&pglYq?4*0SfS1`>A0zoEqUd7y*F6+!oyao!?5XBPQk8C1i zM||B0K!R~qmbT1d3vwbmiBA^*5&~3%(+=WQehMp4cM#xb5n+NlZY zcXs9`?q_?^&mVr=e-XJrZOd-oR?1P0%FcJyvpp}}nqZ;&>!yiHwHMH~6!L|Rk&<;1nHC&l~vf*K5!~hYr4KamG6M$qRIy#ZP zNOU%XjDA3-X8R6epzH>$1At@Zwp7dwB=b(v(X|WL46+)117oPLKtngeaRZ83Wbb^| z%On>)(0IY%=RrkeY2{JuZ&hPleD)`_h{lu*nUIbjztOHzlJw+%BQ3a|8X#(-Pl-qt z{^~fR^oNr9x%MZxw9~vzks}aB8A!cSp1asGrnqzzMqMMHu)eWGL?gMoeA!<LKAwF7>KwF`%TMm<3p85y;vI((j$ zl@*K7e-Qp3ePjaRki~AkZG_ zw=67>f;JvG8(PF9Ky`$yP8X{BXiyZ>H*y5zE677onXJ1deHCVZItiEPr6*AHc$>7- zr?o7|(`xj+58Yxda^hxhj$`8{vS}OK8xnc41g7ykr7J?8ye6-~1_O%R|CmwNs%S(O znbZ0pAg21)-)r7Hq+pkeu!HAHM)TKWu}v75O6 z7AXLC$j#1vQy#){RG_01md4X8kbgxesP6mOIr;Af_Rtf?vkplbC`LPpJTq;GBYQ{o zy1;n;T3pm$tsY%t^kYM=k=0w!O}0^f#o{s9ez0vak-X?ly4KGTu)!D^#L3Tw5sm5F zI?UC_-rGiT?4cptJ_6h459$|i&owgi-7B9bBEno)8tNM8s;Gg%O!Qth4G&|2<M? z^B#oK9sZX^`&j?r)8IfBW|@?{WA(FwflgTI;&5b6vs5@_<^6B5{(~Nn1AZX+hJRe}__% zuQ|I{2f+uf-J$0>!8*AbIeRR_*b|5gN#bq=0+pW4y73GPTIE!1_q}Hr8M2bj67uqa z$0t&f+uv-#K#z2CQ?D`@|CIIPbtV2CF}?o{u3msYfoe?GF4G+{DSNA(EURK6q)O!e zDRJt{TAjyUr?e~s)wY}GtN$38%?dRg@hd-)Mg3}`rn0T$B~1Hj*gD* z8oFjQS|W)q3p*y!@RL0#nf(|i%~zhQNi5gH#y&h9r8~1txx^lQNGwMXO`|&l#2Z!n z)?3jn#Cr#ZuKy>^;tNxs%`BseQt5b{a-U!B=t@wX84bhX?xIgUwLxa(2z&xE{mD`bgemK^b5~vn_6GUJsPw#+86ZbEZbVoGlYe|w2Vw08be&s zsKCi=UA1+cK`Ak(nUALH2vn9$xS^-veO@#>9A;{=TzW(brToty1`Pyc#MELLiL zX9fQA6QN!y8((W)?^@HIy3d(<(|`P05FL(^i5>0J7wHrq067win^^_+q>+=<@I4yD zunEsgS_@oKDpnnv(Vkam@n2iHZD)-4Jy9qVHOWU29Tp$+rJ{+0YV0E|g~sH@(gsD1 zB;)DB0z4;<6SA-AA(<_=@nazcra49h$`%-Egh5A2Q2r8yyM_)M1u3Kkxc&NcpT$&| zo7qV&^aS8vcSPOGj$ck7F6ozA-6iL>@B<;l7);s54Q`Pddaf99+-n9@%6$d<%Kl;-*H9q$B@uN(Bq z)89-KcGw3%7Og;WW-6y#2RJ7UYveMQE=} z(5O^6EF~ve%ji9;@omhFao+?9;NLG$gw}nFb}T;kR%P1VJT84dbr#Pf!tJ@~`Erk@9XVy-F7N}#)Ai)d zs?H-R$3#Nqt$T5rZIUtH*e(5s9)=dfBa_1%AX|?!%;h`!A`s>k6eN%1Gp#+!^B4aj z9jYr>t#BPGC#XaWx|1ccMsx}q(y(>Vwd@$$14hi#eyxiU`~xqoVODc}b$`G4ofMTa zVyZn)|@cfJ$Uv?dHjRV=5%oE?NW8J$*2uXn9OX}UYsfA#{F{p2#2Yj$hjms zegYd>G=t_G>Gj>wQNEQ}>33DC>54-yU2181da)Zv8m{=q{%52aFnL60kMCYNb;pSE zMQFklCJuQjyHfk_i4gn?tA=ClX5B@JFCS^u#Tp6u4e^Bwh1uTcF}X|FY>Cl|bc64wvkWxUU3o477{~NS!`&(B!A&rf3S@TPPR)7w_>6R=mETp5R z?Y3FtW~Dh9?4$Ip8X3|J4w_I%lU;RPeGznlLP^)+*4mP{tkq4gwGc+ZPBwiqc=}bt zKZ8HCEDS7vn#4bAA*OPAw2*{!vZtfgffU&qWO*gN!r+5~$1GI}{fbIp3)Ss(Gf-2f zN=mJeZ5oV}l-(img`p2xT7`qG`(ReyGilaaEg69xJE2o9OvJ6EMX#n4rQ5}bvrQjE zXg+5{U9l^p%!sk9`2FZj_GmGU98LW5^Yi77oHq^GXnTQN=Ch|y(cy~5=Fb;36FEX- zHxm=1P(?#bsm(1kBJ?+%a20JfH+`$qIaXKi?xt8#!DA^tId?r>=9vn=2z-i&|R_BAirS^6vPR(Ll5E z%gFEtqc-H!Qcd56hljKHEquG=IaQBQoc_G1NiCh`;ltZ?b#-JKA;UBq9J4y_|3zw8 z+Jh6Ib8JYa`I*z_$NOBuCR35jEr%q|JSt^_bKtvf$EQPZdg2l`AV!rk;x#@@3xUR>mbaQs-3Nke0nqs?x$9 zw{J4;|EyHQI~02)E=GF*5A2LJ-8JKp?b)E8RGVVD`%CDe!Glc*ENjH{+Z!I~iU~H; zjW?^WsNJFFZXSp_er#vQWkNQtUj?=O^69$j#|M)oB(Kt16F4sQ#`un_l=;twB61yFQNHucCO5_>o6*$YJ>IGKKz2~2)0NrMjviw3+F z?QwivS(nD)=5l9!yWmrldd=H?t00l=d~D?pUL<2)Sqg>?%ipKLtFJDP`o2o4Ns|&s z5Xp$Q!XRJ^YN};oZUHfL!U&e=#w%aqYs!cfthSES@nFC>gegyEM;RkHHPK?{zjzcn zFOnESDJ=ZlWb!eD|F@J$_ZL(E*-sXi!8l5#=t2R8W*mrWt4aTdAKWtGze3IeQ zfSiB7=J+J9`M@nO)`Lasp2(44XV6MOgdeNfy2@8_S+PBKN@0)w_(k>8Qu`FD(6mnt zZZ;-e>LRqs$yS;j?o)9*wt%Hj!ZosY~o=WkMM27ZVRV?#1~&eSKKNZrhrc8z)r~b=5ah z$&~l*e{!dD*O-*Vj}~BGLN6^E-)|P4RZq87dsUkMRbW`Yvu#6l(s!Tg%IMF8V_Cn` zaaZuQWaSjlHt5u5%>NY+>hR)l=Sc=l8t}IkIc!&#Dj#jA{1|ze9;~7*o0(Eyf^`E6S49fC zhT~Tq4B5OODPT3^B|5Bw<}5aMJfz zd$79kOMlhI8do_)?}94HH-{{Mx?38hfStI92f8t?4}=@QWMlgMi`w%nD}^i1-Y%Ff z`@eJW`E7fD=?ZQOwR#I=b%tClQv{>DIqK^F_$(hzu42a6%zL;a-6?8>V|=}dc0|(^ zuIg;5Wrx`~{^(^zKQ(ETg~_V|P>DrYgbkhZdTD>A=uwD3et&RgX4lWczs%-Eh+hU% z7|kJ|Hljn%bW5#t;b^9WbKASLN$(loGf{`=MMCD}^wgL^<3is zv>$`m_`&-LdbNuKF@EFa@x^gxf${QVrh!5Iq!lBR@|_G4>$`FHFgB@2qTa{RUby&U z1*oLSE-9}|YiPcH{klZTQ%=zO%w&}L%X=#PF)BW5z4uAs*$W^qA^Jps!Ml8Q8?9y& zr-RKg5M19GC&s#V^}i#SKY*DC_A!uYRwIj1&qG_J<7G_H1Kv=Ur_)2|nh|QSo@LY{ z^gEF3tJYK52wnk1@#6CBrPfyd&CLeC@%(3b#vCBq*()_pf2dYg$7gapOUN%WB8zZb zpbrrDkz{VxVCeUtL@4CpIe3_iKzOvK&!&w5;9#Yo4K7 z$xFhnlQI9aq9U7O+>~EH06w}aF#c3uiK3Iz!J62<~4=t zd3p$&^Rg>i*g`5>Gb8q1^|l%;?D;M3N93wYfjRw`IB!u=piHO&J1HbeA#6$s2m!c% z&2)K-i{`-B*ya*QG|Zjk{L3U3-JavK4mV|?P2I!{IZ@-Uo?w$0Gkd4sQGDdgV~OIP zX}-_KER#nrL6>Im^O#lBp&6O-gMDsn6U@xug7WDABkb<441gFQ5&T1yWp(-DS|V2o zl&Je?lSfq3jjZ`A(TEJ?Ehq4agUn5xC>P-`9=AGDiU((`1V_LDkxCVB>vun0hym`6 zqH7!6ZQuufg&@o3?yk6MgB$*^yDE+PELI`-<+MCrqVXz-p&uZY3=0T+9pI>i$CZ23 z7JD$!qSxSW+SeSEb*E@a*S!^e?Kj& z+InD7MK1b9>hb8g0#e+;ZPeqm+x5`R#*WAO{DE=xJ$qYwsn(yU8#(HPkt>fL?=j^5 zNwvo-TJBf6%M(}nB<;)bGUq;S;6vKv(Ic1uabr!wm$(HS8p`mM=NA;D8Qwg9B3SnE z7TJ41*=DxLv6m5*71DN%6`M!1Q6B7rI=AN87$nVEU0!Z91Aho({J{d+@nRtX3R zJ6y?~LmhaeuRXS{=IHBOEo0cATAy5iQ%#^s9v1E!X`e(9TR*I|Z zj{IV8evpp{2!3rNrI;dmc{kiH{l5)SZ&J$`!^PbQHuLqO+HkDxu9>mlo|0y=Tr2~Y zsF{(0m%po)juYS4js3>Np;|===2E|PZXJ~(YHHDG@YVPFS*KvWC%fMNx)-CmSssEr zEX&3XztKR6^;MuyW#1t@BHIG(aT=V2Jt16iB5u6b@p#WIN+c3lF*ZlT@R5aqdcp>`|N1&p+no?o%1Hj{y7hBu&y-ieDA6WG)Qs}c)|8}S&b$+C)Hlt z+sEfC07T4`ZZjL2vcHv+JOrK7{=wS-c#oGtLxq)idn2-Yoi@gU&>cFgM1_>&`wD&D zg?|DWD90QxW$`Hentcg7L9d_u^yUM3Y1!+((b}6K=MV8YaNh*G)g}a9Yw%~rC&qzj zB#YY)oX2MD(Hs}h|FMuupr$brX5UY68(fA8rB9fCn(L{k*G(Bx#Vi43J()+R!d1xg zh{QRuVR1!6#p5bbs;d(TfiKwBKU!yUnVmTuMm+FY@2W*Pg)Hb4fz-7EQ>=et@b{t6 zAp&M!bVfecO5bgbr#Q4kCze4YW|+ox@@c1lu~ElAYv@K_CLu^=Zy}8F)wC<|a5h}2 zZ>BRztVX^WO>a;=>_&_8eLuCUzADxUSb5l<#YCA89~Ts~D0%YaYp z*>e*t89RZ(ishrO>!am2aB$S(^j|SPeE2+Moqg#VhsdIc$W?S#vcxAivs~YWa6Sy0 zo#zz4U_ZytY@I*j+}5u2eD-iMAw+H9AmLAuxwV7GIx&O~xWZShm-?cZB8G-E``1Ju zFyWCG3Z(D5qdl!`2_s-qYAAYBViZodp)GBJnrr?Xt3}eCr(5~$Umxv*3GR?T{)@)K zWzz)bin~8aH#!@J@;+?M3EA7`KEXb_VUC`z$YrVwS@YLLa^e$PsoaR}WNl^Ss}_jF zWg9+ShBqSX9=o-b!pC-O6^$sRO3^aY=?$Ar_OJ6QL%7O0*&Qf*_Xsj71{uJf3&t@9mEz%G-QKzZ5ApF$TOn-km?BZbnPRxqCz zKT(BWv`rRkvf!r4{1s;)LwBbuQA0kJHih*R4uGcCaIL)dFdW_{5JI^-1-QbWR=oN; z*3#nAL<-+6WrO-4PV5--!QRdGZx1Phi`H%23bGi-v(|jT-9HmHCH|<*rYDXFuCZct zJ`T{>nBX`!SXj)^@VA(0ju}{=Z;mOE=3M}EX6pE#C=UJcc@z2VZ))rxqwYk4QQ811 zUohiv>{jzFIPo?Y(XTFq;1`;+g>~NTWfic`et{RsaF%IW-V($K?)N_q}Aei3i{ z0c?z;Si7}x72Lw%V2sLOZEt*!fsL>o?LqT9QA^2i)4*KmDmq;065j zYiQS&iIa0Qua&C*K~0wQ<>~7?`UU_Rk%k3t=F@h?4J&55{t$30D!%ezOcb~!B*j>! zW}PG0JZAog>ol%kz{sd04g$pE%!^_n4P6QKrCrXwg{QqcP2Cyesga3uNo)aLbx{&K zdk?Y)uIh17(n5!Y3V@r@0CeBwi4_PvnpQgdIiP-*2WggA#G)kg>BJU5KK*XW$BVWq zY)t5Pq5glS9l(C~FlqD94Uq`9nZ`he$z`1gGT}RD6W|)X9OA&)gj2{lD<-1h?D)Pv z#n5eHGL=JEc<@1RyWo;%`jMk27IAa?lR0KqW&0_Cz8Ej8gTM>oIsJso7vH-^?Jmco zqP=5IFRW{v;&7eQF0p6vSfIa6CSf@2v%-&g3(yk_K`7-uv{1RpJ9-1Mi7N$W6A>bZ zlON11WKh!u2fu=T4TcYT?RHD;q3z7dQ}r}1mqTMd2ZM`a3i-L5voA*Qu; z#A^4|y}>+V=yN)ruRX!FiT1)C11h|?ejanlIeG+#aTjeYv(Y3#5185) zJCHS-_N`~s-Nz&{F7C_3!kpB8Z4qz7$nORb(n?NFAoo7G%m<>Y02UpU@Z5v;vR+xW zoE)rf=YS6>s=*Yt#}T-Fv@|S=slDi7`%s~22#bnoaDLcg5e(NQB+_8AB=O31K^!&C zZQ6+rdj7T0MomK*ji9iRyIidh$9o)#el8zEc&^5F+JOX1wd#aFB{^}4udD~sv=$3$ zv1KipeQG`)Ps>k}>9Ajwe?fH3ed{{q1KwtQFeE=cjNO_EP3*wkME`bbhd#Z?2r)rX zN7L}W&Ra!}@i$9fL6p}k}e`lWX4ny=_>|YWV0vIzu zRP*hhkNNjd`0!9~jo)qH@Hv+V0P8d1y63;v%S4%3S(Cb$s*B2vBr#67e=W;T?S>rg zhuUzlil{{tfH8lht?3oHz2W*yq39>Kw{%q~fr5#SU=Ca{{QIN!((^aj;Pa(fdNZJ* zFm_8wNGPJZlw1&p>N{_RMSnK+>2Ko+88%M3cl~CI!(%hL1w`=${`WT7RG&amZKd$^ z>6MzZeQiX>^Cz!7m14OtVDQ_{F9}vbbQEmw&}9YZ^j{Z`4fEr-5~kBo6^Er?{d`@s zb~uveAVW1}62J_2s~(RX-?pTYCoMqKAaqV@T4%>zQ_oZYf`IQ*67m<)eC8rq`k_3iF7TGT0+P1WZ38Ih?&tP~uFI$jgX4r15d^Ssh^K5;AJR*|msKFed> zffBnqIVfQC=zpV|K*j`2GnGMBcR2+$q z2&DLO`wB3=a&{HjZ@(G*#_)Mc_wn+{9zX`MXN`FpmuydtFCD6R=+Bj}z~B|+K@g?R z&!2x{k(H8=xX;Cfp49jS1*zG~C4tdM57><&+(@vjZ~{euC+f-(+Bg8=-|TXtW@tTp z(HyImctJ& zFJyb04)8t&jt}O2KUn^`#&e%Ov)%YeoxI)#D@^zL5ANum9-GHsta3v+Lc{XH?2&n{ zl$Ol6QxkddUVD3ggK7v?l<(Ma;Uz^xyUf%`LAD!|#4J}NM1P5Soma8=%H4MdCojvo z@#bXR>!F7$k$Q|uiHOqesRalhL7!FM-L33#cZvUEC9ifjEB`h+O7Nei5aVMkt)h7H z488~#GP#fNuyTFkh9xm->fNxjPHJ=0RBd-kehRFeTS_Bp@DWewMAkgjk zt}7HtEb6vz!P6;EMf((V5EugUlr;4gzVu|0h9^T)XeMB}4Z+^8#fk=7gnjlmtnu`? zq~@+-Pf4kZV4G6s!H^#e0u#|SN7uFGqMOT^RX@3Ox?~oOR39Y&*L(#|?W!nFMyZtV zDHq@AHKG|PIxoPi5eR8q^gNN}Se&;l;+bHrX?x69 zD#o^mDc>se-}ey2&Yx8}N6M7ePC61v2)hn}@V)JLfg!zeu3#Jrlm0qglg*cpVBA2= z_3GT;C*24Qw&lO$dN+N;+^;stRcXSAsMz4@cgwLXQ}_olg-%_P8d4Uxx`Y-s8 zRV!Oe0Vq?rkONJ{65oB)ce$I36nodA=YdCTG3!lw3&T*!o~8mDiqJn0K!BDIeNiB6 zne3z)4#9ba=zf7UboKhJU%yT|{fU0UtT=W>(T@2urZIBkpAGa5{E?+WtE26+NvnhywGZKDl(Fupj13%l=yBE%Jg;I2pkG6`$6)O|4niG83~XV z=rN;RD^av)B6cCHf2RvAyqNP7y=oME)#F6Zu)nE3r<#69M18@UTTHcua zi_>NEC5*xlj&Y_MbZ9ah%OVWnew!VB4(OgXj6Z7JhgjKAZvp*&iFF?D&mzSBQhN95 zp)JCF2B+H4((N??m97VwIR`^Vd13Wky}X%#*xaj=^RLg1lw_3ZeudL+S$*^Z&{p5^ z9@-m#uqitkb-&!)bT+^n2-Vtau$Mm146~j10`;OnTLd!;4HyN>A&j4g^_RewhC(m+ z4(HPeHzS~3gFff8x#xRu)ea0rLjQjT@8s|Ak3plk4YzXB_ACn>JMrC%iVV}o5=v6- zrDAUj!x=JhZRDKx_cty2Za}8P7p*(@zp$_)CpjhkxFq%c{*xDVIBg)z6bp(js&`l1 zxE)RY5wFX`PsWrn^XQcER!DV@Z&r5ITvLG7c75g|{Qs1_E`BY-7`7hxR3M3R1M*Pq z8q*C}T=wBVK{z$Imy?ESaBFMDbh_*onmD|?E2Bdai9PqvBQImF;C0)xqC0m#I}SQJ z@sNyrpE@|uJaQU&Z{xSMyFGHRM@rZrhna>ojFv_rgPOiPA7xlV&m4?SR1a!R8b|ye zu=tc6d)Ma2a=R#L-1`I(B%1R_E_UuGSyu;QB`r`KygZnIk(BsCEsnb(Aj5G#HX^8 zad*nLv|h&D48I>UOBBksbmbG=Chb2d8w4td%3wA`4bmGPw6onI5C4MBBWX|x6PkZq z+Mym`y!FB0%`-cZLt=+rx8fy$`5&Or_UX_@{)j6t8wavA^9m~^c5rH^0Bl!ZYj27m z=ffQraG*^Lk*g#9n4EvA6R-Df`GFVw6UT_ozh@pSQ$&fv$8;sSBj4tUby*FK&Vn+4 z5|-KBJ)~1W*Aw31vpaurhN;mY!%3_g_$;5d7Qt)*B?C80r|g|`xQRKKYe(*UG;|UX zB}oz;(Co64;%%lBw*8ELr|37h6g+A_` zhmX(5*Z_g;=o80P4>oUq=-@P)(u~z10YTYTG*y!Zz(6!w_I2+!98g-`!S`v!4aN6A zfGX*w9i=8ius?`gWs%Tr>{25v2om8GAdd`uLh%egJpP-;mx`KbCzce$=Uf4@{!c%6 zQB2Aw=T|<%n!t>sL?lcyVB&zQlaynC`^&j6&ZedLx_o-_M+qDAi96#%tNRs4Wf&}< z2bM-EgWzX{`l~^#7k9f0N6ADjd4J}I|N{xWthF&j##T%RXtsG{V!+Y&x=f95{gUQoO9~Uq6 z;=c|hR+NCqAUNw7<$z8t-%^@eM@^^?6}ao6&!BRlD}@Ma)#|9+&(4(8#IdSTk~*zf zW-2(34O}?Bn1Y)D9vpWAD*XDUCJfLB)F|{JFZA5emqWJ#A%?ZNx7P&b_HMW+tHY|% zD~c@7A?*0L3RD%Chnq{bqu2mNM7cd33>38gcsi~a!nz7g$2v;?o<~113fDO>Faxp^ zdV6~FIi>}h*HA@m=T6Q=sz(!`l_D;S6gFv)rc6wEO3QNVk!wv9*0fzJUA;t#)*fJB zlF!eM8;n%InpC-wo*V$5hEP>C22QW?rAvknWyGH#@(0K6E_5X{U^K*?N6^Fs=(lZ} zKUjEutZjAp;>BehO$wEht|N}XY$_$_`hH7@e5dtnjX1_j#WGq(LbNqwq;OX zS-#-%ux_5h8T^o^Cn4=#^_On7=44&9lpe=x-}>l?jM_OG1nd5V5I(7=fmLZ%D+Qi3^=6-{ zQfB_A(+!xd8=-Y!cAsr9d?%0Ld}oSGt{@sb*VywtZrpt7)q7;C!Jk$4O$Q^1kD}?Hmc;zGeBlm zKr)yzvl&vXYE4`5Fx)pd+MZi3mI}P{RU@}G=>(mJ=bec7z6I`sB{vkuf4F;jId$C* z8jl`K1${ffqcxvcNm*bCC4BCo>z~;Fo2ov)9r6wXrr$WRhvmDVSdBxFJi*nCHKd})a7aZPzRhK3O-!W3?z`qcV&Lw zb}|)l*@(>gD=zG@SX0W%|$aPsMy)eTHUK@RHDMxybt)pt#;fc|L z;n{s&d}7_6*Z1%l?a-b_-LKr>5{Tf?*Bh&~8WSwCp3oz11k>7Au6l*LC*QtrRZVYf zfv_@G>1-;lE~8gE z>-<~59VYnPyu}v%S&T2NQ{F~=yZ2`h4bRRu|Moz0={h5UUDG9Eb_j>)RaYQ)*x&_^yl7U--VEv+1|Zz&s@U5fLIsv*Bc%K2fPdXMdjIO`(fI zARoL3OV6@fJMv&X2xjTPJ%pcU@is(U5ke1ZZ5v@&+gp-Dajd~p)!mVrRZ8e-rh%na z6~Bur=Jq$;+Db2DtbpIUf5#>1}lzQ8qjm7Rl*@VTJ-oQjme#`E8-G}vaW^9!HI`#}1TII7&8VuVOs=eC^ZpH$WB1>FuT4uGah5|OTdjffDt*9P zgLEd2x6MoC5{GiKcOpKq!n)}B>mj4JiE}th*Tg)2Tq5>cT{T!}$1C(hQ9!tY*q#Ps z9n!VvRU{Kvi@&Bhxbp#c5G?4vED>_)Wx0#o{-VN8t1*d}VLYUg#~M2wSdO+zPrrwz z?APyBDlbQ7Y%kIkvBXTw?*`|Ynj+jUi1V>5_lvr@Q{ri!&!##B=t>!|*22@Wu3V)-QcxYNetYO{yGRas zt0j$;`p)s+_?}mIri`^d+3^w*WF<=L^+C2AiU#TRE08H zXr;)6_Slf>ha;Sjt#=Gej1ZiW=0_(0kefe5?9(=?8*@9}_gfZKhvv z!4Ut}M3U!Ih61Xn7?hE3i)D3~U#wJex0go-@-7)Qs_Hwnj8CZcGio{shUqr_h1*{2 zB%yU*{f6vrCf?Nw>`>aSQ-AsL-s)=mh39SJSNpiZE|cYaXcr#5wAuF;cHwVezjcXH zcQ5Cqv_^W!>4DFpqU%lvpPE#u_?`XLVM281e+AY}petWak7Ea(;Gm!;bgaumKmhpV z6}hkt4W-CwnZs$u|S+p=NmGGUs>iy5;rco~ERRDP@6Cz-X_I>%M`MKH;QNp<7jdG73Wp}O}}Mc*tbtdq*-D;00@N%y*>7gJ55M=!e) zIYLNis|I4OP>2c=@lg8mDN3J$j(_6tK%leu%2N+*nqf}!cI}rAGkNVHT$?;^0GXHZC1RZJ4iwc;)el*upVWJI3;2F-1V%Ln4bN`aXRm<#egP3D~a z%Jg=$;Kfq6XMU@cX;>rN(*qfD$Oz(zTtz$XiUky{WJdiPW7_#f$NkKo-eQRt_46Hx z`Wj$LBiXmD+|mF(y!piP`xu*6+3ZHpd9h$8V1*17PuXnSNp|=v+}?cYitwnWa$kx5 zS?m+NOS`CO=j0>_;b`D}xh$V`lCm(KI_cu%pS`p3EI44Ht@K*fs{3TM;rB?0(c6tr zJjcBAVqE%(I;x4&>R|e_)LvkU$yjqnZ-x)c+sg6@9Ub)|ZDJk!+OGM~Mas7bOujSe zhVn22wicSQ579{Ztm-3ya)Z+s0~-9TgVpPc(OcEVqRC^~S$WZB8#ze^boRXmp+}!K zbl16^#wlbtwbui>bgp&H57Ok_UqSZ{Jw9VVL{gii;xfJw_TYPSM7uS!Q=Ify9r72c z&)GDbKLZlUGA5Q#U?WMup5bp1rxX+9yIWYU%w?u0_OO}|go7al&GZIO`&Ia^$EQpw zEw-8^x|DvUcIR^J6--x`JX*Bwrg?*txOYJm{Og!Ou|f`=iGc5SrYp$%TL5Ov2y!Y2 zCo&&9+UnwQi`!zT@!d#&a+6fpGY?bLT<;3&#zEa~egdb7gGSXuXUcCy4}##b?dQzT zFTXeS()we_t)0P@!(?@Tm((HCwUSC8vF(u({+ZeM9pfQ<{pRpo_VagPQJ+xewYt7i zWE`U>7Ho(8EdDWb2GTX3GN_+8qfQf|aIDg9DH98TnpZ@}*7MQ)GOY)&`kS*&*MqGG&h-&Ez#8FdrRvcm{bDVrMoJ>%Q zs8U#b9vT@*0l^vFas2Q+L!ymv5@z|M=ZWaD{Y&ZHCPwF&JLdIeZ z-_O-|TdZ-^*wVS3cFdy3tS?(QGUk7q@ad5S1$96Vjx)}QqD zdZx3B#L3*BT0U?8wi;6Z7UwI#26RtLq`eh|{pC_ZrrQn){j^>MuYMJhLX+kgxx$_v z`jt~y3(=k;pT4J>gS6OCt4WL##?GS-b`j#V6kb@iNaSfv6hwnDsiLgS9jst}F24DV zLWZY}nj$C-SUELDzfT>k2fmEx z%N-pd9?#}T=}02&zaH&Ln(O?j7V(uFaNt`eBKokK<9aqVO91Y>SoYGfLQHToC>w#B zW9svgxW_w*2-ypk`3*0LGTW3Sb9U_fjBvghOTw4jymNpljs*RK=0rirAC>L4UXDpc zwMs-U!2YcH+b2!fyIRwpg4*-wHJ6&UGs^3 zyMjJ&ENepVn8cJI2;<=Uxvui>9lau!HB?$c+e-&s{RrE_&b)}6P0|vbroW#m`(mXK zKZk~gzk+;Zvf9`-l$2u`29l51W6NzaQ0fe7k?uB)yr1-$trboS6_E?m=86=iK+=X3HL`8TYc);pIVvRDpIaxHT z=7esi5<+k+SoEd7xOY)#OIv=G;(T`FERT@mGMe$GlK0Of3qgKTySr`W1`30AhhHt3 zh1G`%6BPxl6(b3UU3UE4M3m=`JLb$1PiilEX(tmojdp*%KBKpnbZrP@CzDvKrM*xu zO^#GzJrpEYI%Jcvt*xh?xqZIChisDG|Fv4V&y}K_p}DiOGxJSNoUd-Ih5AGKnXjHv zIt)9R&=NO-l zW4P}3rX%?)fp}FKwb8b*d-{WW$QWCDMT!Y+Zw-+%X_jER6K%m#?NTetVhtq|m9nTI zLfFs;%MXpBR&BKDBqewUiNdz-l9Bm?^@Z4)hLbT$&+E)l{_`Ul$a}*B2Oh!Zxi!bSy?gZRurM0-A^91ci=qLu^7YX z>d^63Y?zRE*>T;*p=8We_bc-DX!W{9-*Y5VkRW{ewj-OorLR_uK&t*n^KG@%5rKQd zt*3P*AF4&%69_^RqkMlEYdFSN68Qhtuo58@?ieTAVxKFZT$hPP1n=i=b7%>UGz@P} zC@Q*72WR3uCQP_$;c0!7{Z;7dVp@$ei>K)Mp%LVvP5INQ_-(!{{{nP>Jw16^^i+&vbVK;0tA+Pi(xMLcz(_lZee`>ScAQv~f zy{pT>=v(3>l73p6t}CQ7Ql{MXmH`v5o)(tMg1wJ%4szuxM(J-a6=C7184(UUsB*RV zSU53jO&C7wyIwRgq8G$ku3o=1pWe^UEilaI`2E-V0bUI!ne~Nvf(Co}A_4ZZQg#Lg z$+NTHI7^brm2w4w8^BTtyizu5!dDW}JM*B0L0~M&wc`;%4>#cy zzZebS4H3D?7%ddtkq{My%2<3z$4HT9#-g1aUQyk9<*I$@(tOAH0m+gUX1-M<;u=bS z^>VdY`^CD*%RBG+awRwCdCb`QO4F9-ac|YyI-8r^rx$Es=8<%aHgyu6H0TettWcWY z9^%5M=!2xPqFi*zGJ;Qdqlt5#b%aa1e33C;*zDA?bp_c%t>LpV8m8lL_L+khH0E64Rt61jmqmUjio5>F z-PzqOV&NZzJu|?Q>fs(q&0wQ=@tFnz{o4mHf@bHl_1t9F@Q=;Wuhnz()(*3 z_6BN*N*5E~|Gdsl?^Q`~W4Eso7A~om1FQpi?b_~Aij)cVc|bockY{%2=fXQbbJSAW zhd8>U=$S=hrSWwHTlH}Z*4uY<#s?h!HDLx)H?d)K|Ur);pq$_M8|Ko?mKRsq}L8p?R6uD8Aj$)zu z%@D)zy>-e)vE27sw4F5D_ytSF_2En(b8Oh@08UB9>XX()U)V#UutsIlKKKw8?5=k&CKTVnr|uA8yv zGS$Khd@BD11ZLUnhqylLzt6n3e#@0rLvy%Yv`+W(+!6{Jp`qC6EKABHBJr6# zSzgbb%^6o&B=G5g9<`YrkGmnluiAs$In%D@V=$<@^yLm7Fp@vsKAChOkv zHOQ|p@=F831+(qy|LOw8&{)s(QVs5qol^T7p#i3}6{7=1ds)e?NN-cXA}Vd#~v$j@nbt)7Hk+zdCmm|!eR#rI-dN7sHlA_(4_CEV!uE{pv; zW#stDsJ}hTo*h3-1d|;OTwG?G0$b?m8Z#6(lNl;+5NXqqj*5K=Y-{4Z8>Xs&Ku`+1 z+y;rJ^Vdey`?6KWEm#_E;$VQe$jUbN%yKxRM|}F?0qrIGXH+owcXL<@+e69vi^p=C z1}BoW9`r)}7O7x$Ohs=ZLGy31Gz!dz%-9LJyMQC4b!o`9w_?zvmY>=RKX?4YKaFPgVu6Uc*srj#;+gnch$W$i+j4@(?U;BV-8zOQPbx0C+&OOL~0 z^L!QaOGTBnu|D6hSiE6Pm4arrw7=y;?m3h<*}rwHSzSCs@egA0*7`2_+2bH6)CE)N z7ftW9>I@j^vJSf^QerUkC0J-%@{>k9Eo=-#TjhEECp4tw2Agk}wvl@Ac=)6BeaWqUta$_z`*wGyGQn858plN0e8d%w{Mr z?=Nr9k!>+0;*fvYeS6u=V*6x?zdw>K)#&8t^SojnXhL74eiqIp_NU~)#3Cj%1US+b zj^@m;X@NT7?1sU*YUr%Z)4VIu)2ds0_$z$10y2D6OJxr&$xEVGKUTvIm%yFIorS&X zQb`)adYoD*;MhX;o$@Z%wakjEev2kD2c^s-;eOka(wcPNPK&N6e3XB@pz+P{SL4RR z{p^W9rtJ=?sU+3GYgJKJ{EmUnI8_GMQ1q?6!9nHM)B9oq8}6?S9BfP5+O+V5ENkH= z9nNT>R^IG)@=~)(Rmlm!0)UTl+iTW8*d%PU^&1>uY9W!Ck-NO26;_@jr%|1|&>Cve zQhg6gu=jej$|ZeRvB|De_Nlw^{>iAcvLJWsJdhw4_HMb%hDzmp_ik65Z;@86%AFD( z=(Du~R{|k=uk28jt9`R?JepXsFi>E!EdS5N!;TJ0VK)lZ$VIacuO6mV(z-WcQ7#TB zbOnB<67)Xv4L@mAP4BA;o}#PuHn7S(SpH2$VOXQrf~lmzXX2wID0I_EiNYRp1=-j1 zy}5Go^+Lvc6q+G@vd%s44f~o^*AkP42NrW*7gt7-i>>qEoG6JUH`jOLYK|3C%2o<2 zM&_h4c{tTy^M-vj1l*3Dv*LDLx~z!j2{U}E52Ayf$&q^|WqF>Lqe7Tp8yXt+P1KG; ziJd~#oiIN??+e9WmO_ravAuk+rB!p39Ws7yh%WtvJ1@4GW@l&s3N4z-7UPFe&VRp@b&%%{nT3OV`a&BZhf zwk^3i$_H@^PdL1KmoSx|=$n^hvG?TZ=c#y>{<@CMA(w2iXd+C!hJ#nuhaORR340N+ z+L^%j;0iLT`qQV|A}r$|M%80;WE>J64d1`pPx$}Zd&{V(-uM4^OhQtSkoo`uBHc); zlz=oygLHSdK?n#)NQabkHw-z1v~)8JNOulH{_pvGf4{TVf35T6#Dm{D>&z1wXS12T z_Z`=LU)THfW>Qqwp8(p>Pjv`AE?!=BH_r_2R1SI5UN65PL7*c0F>EJ`JynSu1biNq zcE?EOh6RAH9Y@YGR`_7R``S!@z<8OLC9P)V+Q(SU>Q14kcN3Q1HlpGu{L(!8)2 zci%Rir%Is`4KEjT)5_k{Kp2)X^FCPMrC~rhL95v19mU04P7&*=_rt^Qvee!gB9HLJ zO>Ljc#ZfWA;G)dxN!T@#t}ai9S%JL zX7WKjj7ArIEA>xf19^;`rkys3-`fj+91ggqP*OO5$am2al<;e)YdNAx!&Y8Lr+rhk zPD!c7=#E~ev|$yv(le_m4VSu^xaxzDZT@t?A z2BVBjOx~Xd=i^$o)-^v3f5gWA&z~-LrsPzpJY)TLR*8l@-e)x2*im zR6=g^fTXsu-C+`xlZ9tWgcL@)pc*T&)BVob8qwNn-~->FlZ26EO3}V;bvyTl88)J8VJF_8?J@0J3M>$-~d?UPP2Y= z2w(h#y=44h^V3$X)yGGLo=HvZ_|gVFi;gaJrwy{P|x`m|c6 z@i_o%+px^`o7Hl{=3wV+_}XAeqb6^6DjKh`Ws#BDQLuY%$?DkfO{ey;*}0pXf#*pi zmG|nhV%ga4Fqq?^6|z zz-#(O@&xdtuC>EQj%GsZfCFL7qnpuUeL?4TXs?UGoIf3vm>V6AW)WHR+baJsZURO(1+FfN8wz3m{?fxXQ}=1K{mgJ zeuEv;iIQe2#{lwevN-y^gz`rEgHGQic*0iUx~?2AG&*KbuxxASC)AaJ_KEyZcjo>q zi|2r&Zvg8<;f@%B#}--(#BEqvW8^AF3=v;!oAMO(?# z#MH1}`N$>b@d#m4hxZ#blJB$}33?0S2}v7VL|;A-#?R=kqVbQyg0l@(8FCONi2~C? z%b7|Bu&(+rF|xa1Xwf65WG1JeaNDwf zlo%q%53362glrLSnvLIE%?t7_*5R9Fcs=ZgCD5}^Xi1W(cYCkjJu8(=r2^P~k7ikD3K`bB8U ztw~aINS%Y#z7V~H9$nKz95QqTm$qAuF37=vI>6I`4Y0HS2h=Oj(HRq_+UL)nYMH8_`v?Y6ybnXDlOe0?g#Wl`uc^Q5AoY zc2BHx3k`9#I>sZuqD!(?`lJZ68OafuUVF0e|hIiWf6vFN7S z4-|X)IHGQCw?8(k=KL5=U@I7RNqI0&cE0%Ts_|l|#|D(SKXw7uOHuhQ3ZbkO^OCCA zgE3`xo1nFg(`QqAtDOTTl7-}X?{?y3SKFuVdND4uKH_r}s=!5W^O=Cz7Yn9dNBadd z%MLT4`88h8jMtqZUY|MPD-;}lEGTc72 zc$E?UR~txhRvIiRtA5A%Ul|-r8>81D%$wbqk--MIBkg5ho?0+6T~)S6eHXw4sEgp{ zt|@MEKkI7m=Eso?e~L^wnyn`rpu+RZS%>pX!?5)%)ZnMi#`|Q8lH>Xfj}1tg_IiGG z8@v6r=4+YSH2_N;^L+!+yCPpcpZwmC`}|U;bNJ;p@@b6a;;X_O7g;wJxD3#1y=q9} ziGGCXYXy^tSvW?~bi^67|G-{}QNR$4md?cCGRTzl=D+j1wYe*plKZ>8h<9lpA2 zN8Zm{xG-p>_{+VCmWcGHg+8}Xg=C<5gx;a7x~Mj9YR!5=9S5%0aa70b9cT`xJBd$) zycGOt82wxCi51dT211 zvYiy|%8}tPcNdSj8T>0G;84P4aK#HBbz1Yrj9TiNT*i=d#g#qp#+tVL*_~ugHxf3%r#d zq1Ol+icc?*6dnbnL__b&U)=XN+0U2J2G&aNqCR3!d%lV)-VI&ImT9{d(?0GP4!B^Z zquI+5YF8+2s?QuvZOG?z&M~NP=RYi_zGLS*w-K!!BNY-M|I3r4AG&+#8v&du*bQ3q zWj?mXwo;SJGL4$Sb|qm(4xT0^bcbv)Ch5iE1iuyE$URM;BMuwJHyC3vzmqWhVW%db zqDb?f3)4PX(#Iih9(;i|u&Mp}2H0=*16L-^)T^yD{Hfh%LKOMtOv zIPsiTQ?ZvZI-ZLWi05Kj?PLx1ftujG3A1yG!Q~-(8+{Yh1Qs-KnpyRi$vZdYj?Jn| z*3MT+W3T@D9ryRI>8T*%>Ly8@E0G6^XJxuAIZ-##g%?fDm7@`U0 zk}m-m&v`J{*K6FM@>&1GC=LAmwoVV9HWx$A(XmlS)P>nMag(71YC|h%-+Zmq;Tm}#9%g) zsRBxXf_iy1-$Mgh4qBksv(-QC+|`)!hm8S?D#1U3%fVe@`}ne$e+!U#uv~|e4HZ#J z*h|3d{KZYkSD%;GM(R5N^_%wT_HGTOh{ol&xUusK8cm}cdA`zO_Ko1f zFxqrHD{grG`Yo+K_TZ5(aCg(IY+B`0@aaXH)1qzJpR-9>Fq0&(XetioQs|WmLfr@F z1wVu_M`IGHE!LWPr0{1FgY?=t@PeAqYT4VGSSz9cjLkrx3@WVf#jgxC145c{z+ha^ zjjCjVr$EhZi%&yLj+$jd8i5`1Ouibm4ILHY*Sj%T!;Jba_(J?Ap;~lUwQ2S9l5Q=na5xF)_eZW0ZMIW zR0z!p=JT1VJkYgNUOro_mrZtkpWsx*?wn$*D``^J?QP2F6_o{4Ntm7|D(cq*-myxX z*7#M2=3GE?b&o%=Kv(`qbl_AhWYI-D(8l*&y#2M>NbQR1#$L3o@>q%&OU9^k%OZ=FrxT)Wf1?OykZ6YZwMDpU+fjyc|1jFU5B=-1Y3gZ_a9-$W5k_?oL zrPICE$ob;QVg`aP00Dp@n?f&aFa8;K7crb^m@lngjwi&d&fVRVBNa$UwD~?`1_T70 z-uWErnx^Y-7$X3%&5Xaw(E24{#ziN%5aVq#*#@U09r=4zZRKcn#p}&}CpG5NSyK)DjBs)+Yw^ovp5u z#<1r{+KtS>FQ#azmZBS1dWJ?+>OM(3jT6bs~+if-9kPQLjfxMUnNmCihY+ONf=H5E!^hHdf?n+006gl7v2q z?!oFk;P0hmq2pqHW8lym!|-CcQ~e4k(1_bWNoe6($BB;W*Z6hJms7l}HsN54ag)&T z_ImAW^8g`Bhx$hR&OX4-6;^y-J_oI`-1E>_<88o7gg`lfE}<#6V2bep^{PB{8abDu zE;-*M>*sySykPFkiNnc!^20w%pYcS$5d-~za1}3n$yGjwUXMS875H$+=YM}p8pG-Q zl+y?EU|@^;#j=F4DtBzZA{$&;tA()Q#Ac(+kq^p*Erc28Z$;uhSsLL8qX@1Jynl^J z4|m`FbJX|b*+hP}=Ev{n#DKyNXeBmugZj>F(7}ZAux(NfbIBsX1m9ThUZD{~~j z8L9cCx0)W7miZIgTJ|{1&n_h2I?bt%*UqP^hAmm~4{_xR+HSp1zb}P zu#r@>K{g}PQ`s+;hyN5^p1~S+{U~Q85VIp8YxQ%0{*Y8_#2vfNSqlKi=nv zV$BGDv7{P`d2W1Yd{YA%+haEVPS=Tr*?2_*o}O^^qsk%I$hVPy=zqq!FpF}>roM{> z%C)U%E{EnY1a1_==EEov6ixa9vH8Ru_FuegpECKrIXnzn-IraAy~+gy~dj2z{*ZDtK5g#+$bg3_q$V5{1ZrBS%>m7QLTz0>`sgvvxxjKN6>m!evPd7#+BGB>G zMz_}eyt(&Tx&r?S#}_^6 z5vQFQ3#W2Tjvf11;yD}#PyS0(<{&<8A<;YuYBmDMyMm@bT+}u;(F_W33_IOY2jas0 zcyIEl$rn2tv`HgOJoYE)+Xk1N)rtBecPf+klSN`J_vl`%>nTPJn7S|$(a_L{a$|FX zgzvi7?cvS(dkS4SjPnFG`7C|yZM>6hQg)yN&oP;Qwj;#z>^PRVO+M~t1?NVu=ip}BW`9J&STd~#n&e3 z2U6gSXeRb&Jt916c?}HA?^C#2a+fFxjqKg)2{&KWv5v~GgcO`#1KwBBo>Oddu#0y8 zZz9?U4xyG6S8kY_{D8V|#fYvN%$f(`(ox`+DSzsK05Amy?qyXoF!XsVVS7wtV)}`w3AQ zQi@WBYxoBW_Qdy$lP=Se%rvWW(JS6)1avp<5IRWGZ*LEbz$ymrB)suQTQZ-SL{r*t z7T3=6jvav|(tc#@his4SjQa>3 zW-4?284rNLuMVI5G{q2*h}ne$$0r1+I@FZ%?WKg92~NfD_ll}rQT;ovqt_2=qrG}I zH@?+eQ0?!yG{?z*{RI}QFd{yGsj}6w+UzZyTv!^#YT@rp#Apz3=O|^Q5K!4NY;0|; zaaCAX!e*}34U<(=3z5Yl-Nt2BNU;n1C#u-tJd#GhqI$ORzLx(jG+AJZ2WI%Eo{V?K zcHk%FlfPe>3a5u+74i5;^;p9<2JW>sQBqNKjG0uMLr!(@Wu(UFlk3Q3CrbbZIlc*0uc?23T8biN7ka8upLdu?LwG z^-jktyimw_ZWr#_YN44w{O+iEm5=SX3*@5t0}}RJP+~1$quvi6z_uiXx-f8KCJAhg z?!f4yM6&oFQ1Mx-N76h;7u2bof&MT23%v+ucVk;yAUx}eR_fm74N%X#&Qe)Kt?sRTBwD~a`cxWfCUa&VelFNw>_`-P zRIi;RkcYMeIK?E_pNofokqmnK$s26CShJ_R<+uFvN-F&Ah}K)e20;F^7IEEBo=~up zO$VG4-;~zi6xuHPO%hV)NG5o!m5btG9zyRuHe!^`p6-ENzZMuW6859flh6@0n1p0x zRVMSy)?UkPSw^Y6wyr+M+N-|T+?USyn zY08yf`?Lc4(}V%<&HX*HV~UOe3i~in2k6E^@oaYMMa~V}jQg<$IfSl#H$DZQj3@tw zR+t!UnmA1W!~51KAO&0oc+)YK-_N=G8KXf_kg7@Vls~}O@L+F^irR&7MSpG?kdTm= zK(>xLwlJ$O0Zxn>5{}30El+4Lz@NI_hXm@V%5TfwIyz6$_JSHXbXJsJ@$&7yB$JOvPIMT zh{G$_tsl>qDypsc=#EeG`4x%`wr-gi$wb>2hU2JCY5m3zqWgaa`~w|Lcpb z$rz|Vye7ekcT32GS|{+ag;*8cym^_k2!t^vO)325qtM)h936$o_ELutd5F?(V>x_ zlI!Se^{B})eN@hiz-Y7Ar-g%}G=^!MuIn6WxfJogUIc2F2-7H%!v{K}`lKDa$5JY7 zWJRFIM;Rqpt-5t=DdIJ^scCqm`qxULc6xnow!3)iy8YhHEeFQKwCN{N=f6a#gRvk| zPLtXeW};QcB`R5DZ{Wa|)M^sB%zlElGBxrv5c$hpx-RbYMB*>l*ZJpB-ijxP>V0;f z!l}5fB43|9Al3UGba1FVSbr>XBP0i(Tb-L<)lHQ|8T>t*a_^z?$kDDlZ zwFi(_hJ>HhEEOVf5!W)`u*RfM{Kxq1`wfF8N!j6>OTSB$M4}4`bjE1q7?d3Lu;PyG z-pd^|wMCJ;y({$o>tg~8#soALgxkuX`wdhW9@2I&nP3f?>kxxoL+a}#4A>g{R&3CF zE~eu$cs?^RI&$gS21vYTBH1C&VvQ4EsofFcfGzEj-Z4T;yz4L@Sppba*hDy(U#!Nfyw&u1c;7Z1m8_C>U@8Wx_*WWm;`fDCT z?BLVEo=22qm&(|!w8R>e;|;srLU#?^2Vd<=H8mW4-2YfeexIUZX@TuKuUv4UxeVv|hd$q3iq{D4WKVkQ8WTv~Ui289= z#T9H)hZ~d5e?q_TAd&LBS{J?52pfD7%%HS+5j*zt#Kbq`P z3NaL|;}c1<5#X-fR?w2zi+Fc(%qM!?mKQbq@_vA+ixSHZxe()3PZ_lR8~c(>!>REykB#)XY`Gm}*lex5GF zw`ZiYhHszv(bkG5O`qoJFg@+fh$H&|K6~@3r=HiTlHGvSTh6U-g-Cd)u)2R@?aFW~~r8VRD zBG#5$3%|_z&(aBewM>*=HPvLV_mulAQ_T3C&B#FTaGuZA*?g7q3vX_u0Wk35G+BlU zvtFkjssuaLX<$!Y`+k#PaC$2zN4;n2hRiuZ1fa$dDex=vdZ0}AxIe!=RfbP$;AwQe zLUWsVeI@T4QZ~1X3;A;!xHSHQED-LoR-NV@=wP*vQCfx>sNKw1c&9iS3Ym%-gf+?(*hr4~ZkS zU)8~LN@>;f5RN4OLB4{m!#^_?A#R%{O{lb`5|_1{up4fpj=(>O+Y5M{1gt)V>m25p zi+Taqr!!2|#+Pxe=i#kyi$no(l9UA4uB|Bd$ACg@Vd3A<)d4kn~Q}r90V7mRd#bQ z3mR|QEBLB#>xk9H4kpI8r;ioWW}hxPFMZ{-c_&|gJ5z$t7x!jtqPhGOaI2tJ*=Ra; zreJguGm@FT-6Kt*G)pGU>qcXF@@JM5CVq=_F&g>OFVWv}X=bx3c9iUdD8Y!plyGjU zIp!C?a`arviS4K*{v|WG(j5eAIgBVT*~XoB7#8Nx75;lR2kUeh9^A6Dnku`zI@ykF zn!4TmyXVgAA>twRphO{O^7^PomFmaTkM#a2l^Tn_vQ-WKt$hu5243KiB<)j zZoh85qY+8mj@=>srP{BP8y5>D^8B(Mj0_Kr!fB1xrfZ^tEiOBqeWe!~V}`Bpi$35N z*->9Q)%EEaHQmcUC4dm`+D!VkYU@4Ved(L{L;;&!uDMkai=otF8Fz-(o6|CwKx2zc zs4+!-J$>Ws>!`!^3ouHiOziINBJ3P|blBLsO(I`178^7R&AZRpAyQq2uxv&fIPt~KKTKXi zpS3*f)L$8)fS-3$wN5?{-lZ9;DG0w616WKLu!N-Ct6zz%o~6H;d5V83vX!4biv2|) zpoRJ##IOHMYD-mw^>}tF@)3=&xo_h5Y*Wx%3kefXUlX76BO3m|s+Lxv)G5A}^QO~H zd(5(@V@;Z#)t&WcGwx$yN?iqa37(|Ll4mj11?CE@Yu@Ue%&CY zHXkG^n8x{S;$g2+aIhYJ?^&sUPOCSJqN6XxUXF#9_eXQPFG7kY1WsgZDdc^!VSw@B z&MTF!0~GXlsJ~;5!*5ewyNv=iFSmGmgA4&n4sPF*Y?{Gtvjlw-JfV%B2StY0FGNS! zsPV{evz$PQ-^?&oPmkDHg=<|8Fv96bvPdUyIr>p%S|Vlq5B2RR_ro!OHModWnv*)r zAe~F;gh0pRpFP~>isK-aI0XVYCIDID0FKK%CGHsKUZ{JoXgrrb83=d5ulGFi3U#k) zx?8`YClgpn-QrV4;oWM-w^K;R!>9L-L70Knb_a6ym{!oOsGx#2mCsMI-lBcnvHK2e z%-W&COm@E4Z+|OYUsYVEhJo@ZARY7g7G7xU;YpdHd(n8X#mCaIvmQXsSkl0wSN(V9 zAn4WrUKAwPP=9&3o%e3w;^Tf8GpPZYx&OtO)uhQnR6uHBn#93wnkdbQrClj?#7CNx;(69RoNe|IE8rd zy6;T0eqi_0Vc2^YFzmA!JE3AliqdSom|*o}@1;@JcHV1PH*XEz_;?TRcj*Wcczdb4 z3E!Nrs7+kAt~lJRIgGLf`XP50ZrC~Y{BMUmT4JxOR`}o&l#q`%O!q_BGX&jz&(Ex4 zVYi8*g=>*JP|tib+t|l4s5=Q0o$p`l3me;#KzkP898=Zu>{wMdH~T)jn8R}*YhEy` zZBxa8Y#|UIVuN7(Os53Xfc6r_T$DPIhiU6^+Wx@SGzg~Pmj<58p-de>U7TFf1wjQ< z*#F+zI4ukCa~DMf5>?tTI8B}AjXnH$?s9{`5BS}&t!v-Fpc}qCv>#J%A|mDj3RW$e z>*ZhU-XHGASOZ>o7KM#nwJfMwEv^r@0~TVjHBJpnpC64{d-T`qWD0`WGeI4vk(Zx0 zFezK7LqjGKS6qvePw!%D1o8V&;=&Yp5@@7==#+(3rola$ot)2$G$UpU9`u)5TUudV z>bq-uPLQ?`=yXRZ6^Z)aP6bfiTyorU7aKP62JX(my6x^|tp*t3Q1G+PJuui}!aa#% zv*QRp*GQmwb=$BU#?k@!pG1l;SL3QHt3qh}J!Oi%Ppb(BcT^a9>_q9uz|H)684^r) z-`<=W-tv{~u-1w)U#C{!yD*y$(a4ee@b(aPr7Z&r#?aO%`~Jp=42^<@8Hzw87?qp0 zuA-)^{frhvoAWJbD5A&W9WDr%;I``?hBePZOH>Rlt1@!69f};9 z*shN1S2{Qp1!+aR_Wi7WEIhdkz^|5=`e{(zT+b%_jbA+3IUCs=oP5s{C5Jc$lVX(( z!=ds*%oU;$1=Gs#-YQUcL(Yl;mWhvO%6=VH*HZJdTjt_((oqzRCU*Am5%RdTR?b)} zU?Vf+m-ci4-0O;X8XX3Oh4^#_3`O~$&^Lkp`cRNoaGZc=TP?3PSXU{T%-`?qMw=p5 z>X<1cAX$KmA|s_q>AYhbxxf|0rV)QNQ|)-0G}ZyOfr%pLkgGxK95UNGGl)~0sbH%F zgXH(#bLFm9f>&1p!8UMV4n5D6T*Q*Yt;@7}CKDqE+e4eXj?+HLDJkyQRmb${hssZz z?;XxtZcx913m&xHQ=4GhyU)>!(c$Fb-W$%*l33U$C*0^EC032r&#O()-`aQ<5Qw~} zu?Y3QInKx{l)-6Q89JFpUV#wD^L&0?jC8LVxmdjJA?Any`S9V$p1@tjwt#9bae#d6 zapZ!BCI2F44c}GoUnAkQid?yQ*~M|C6x@`R9{<}z8W18QABg0rU|Y)5q7%+1T?e)ufmky=nV*`oK|ENDJ5u^> zdeOQEGk4^)X8v^Dner7pznY~nr_5by-6Nofdfuyt(&b&@i;(pd7rPaMt%Jc0TnA5y z!ooVGP;rYLVf0eMY*%k>C~Z5H0P^wm8%(?hoHx~D9V1}z8L0;qtcG?{4BP2D+?To9 z3Uxffm*8JK5^hSc4iy!DuvCt8+dnGh?t|@*P9MG-j&%Gm+#fR9^!Sx#EdH2gnL%2i zJ!%0C;8XG%QRk%73>6Xm_yN*wDqm@+68H@wH( z)u$+$trGMeCrd{udK6NOsQWQ#HizFi2PKiCIMXS{9~Z{|@W|~dR7O8)@CjOZA}#9W z@3()`SKeez#feIuf--6}&qe*c^j^RGvLANt%Zv%HwbQM?x!A61Y;G2v2VtBxRT>z> z3bqL6%Ku87aBSZ=K2PjMz+lr}#~nMve(VE& zTLq5i`W|K&R*~t#0yrsRqP!F5=iH)TGl3jr8RE^`7AO9kW|ZFUU6hS}^>SYwDK}BK zPEb`!4=^$*{OK?*MCJk}&H`+NKr2c?3;3O!UD?$w#J`uA6#JX|cP_nCq5xoNx|J`8 zdqTvo5C>pj6`gk-QxJAf1oUi%fedl+qW)Fbq3~Wky~dBO_e>STNZ@Ei5h=L*bteNC z^2!ObJ+sYtNz|zQGjQM2h1u*k3sAP&Y71JeblXz84U5hsy568Rt>kocbx+R&@BBjA z@9R@2G)rIa-VYHifbJt{Lnt3Bg05a1DcrvDX%ti`;h{(AS`weHx4ZBgyZ2K^VA+^c zI48V#80iT5N}e{RgU{St#}iGxXmeUU*Ac0L*_mh=>LjY4s8Ww+7T*mC8o43}WSk!K z{!FsSo=Ik>&IQED*QQn*sqm@@FO^8^D>hbD+Z4&v*e z3?+9V%27~?`)|Q0P$jT&I>~+K;TPYO*dvw2Bh#MWw@f8>%I2|{Qoo-LM6Q5PPqs+Z zm}ZaWY6%0;xLw+>6PF4`J_PVx!0V4^>)*1ruSWzs4)RTzW~t!l6>xC0uH6W&DsM$*>`>~Y|Ej`g|i7XUV^Jg;*FI*U& zLfNSMi$?ZKxWA!=Un1-4M^*bXM7?9O^|NE_w;WbCwTyYe7vB)kFmA*JDOesOl-+_ z?x{$W=F099dYouda~CRsC{-S^r_1vb2IWL!C4>T?LYj~ zNO-TDkX{;m_r$o_Y-$Zx(WaizCKg3rN@9e)r|LG2xRGQ7AJsd)&2a5`dwdxu8J zD?5mO$|PuPvGv%wU&iH4lW4^R!W+l}XrR~}58+%8(vR&+8r0^EM-CdW%6pWZ$;j@Py8PccI+|Yd3?E^&>ag zlFL<_|6E@}S+@0XoMHb|mNoL&?dItZcoaswr@eLsoy#6 zQ*?xoL3i$BU^6^ScK>)Uu-tmEQ61dgaRFLEWil=ZjhL@zEfM9XBq{6vPu1xYYJ@YIO857_!E|-Vp@i4cgCZ zwqUqKFpew_`ad>6)5g)MxDJI-f_EQv(7!Q0J^dVl0p2b#V1dK)GBas~F?kHY7lQmG zp%vuJ?_8S0a|G`o?mq}9$<%dpbao&Z(+_MW?Qo*RQ1AHD{r7?nt}Ya2rt8gYyzhcv z6XUI}sd4+|T?WXv8i`_l-pO~a%|Nf4nSz%liU;@?o<)*TXUfgSB;N``|N*jb#+DwsZczZ8B z{(P@2kbn~MkYiW*Y?0P&;PYR4CZ}gF)i8H4I zH?iHwr?E_cKHn3u$i?`LJZbmWP!wT_ginN#gl-3*mz%tmcd2b^+{O~LGFUEOnNupp3fVD5_NX8&{lepHjI2}PW$e#@6S^@Q=p z|3~cr-Rq>_SYpcho?At*O_|*cbJ5v4kHDsQF_M;(4B+ims*~^@S^5P@LDO>B&NH?H z?q_gtX7(G{Z@;FkPsa&K?&uquwglnyoWa7w(c((|#-LU<~jsPwi!wjsWKD&vQ?(2x)D-u(B7C#nzWJ2Ee$ zvP@v}Bod*-Qs651$xH#=QN@0eNw9{_M4HTC4ObazzWMUVw+6RBe2nBch`m;O%+me1M%6 z^{;nHG3Gv#ulz*)w>1QE3kB_c_6v+G<<*i;OV~JSLjo?#;6X|pI?3-ZhUUNI1?$3H zbdpaie#QS0EZs&L!usd(D!~4GImnUn`dIxNEY)mBid}4|?q%?0^W z7r3On{_qW^0XCg{c8>ab*~C_i4$@{Jyl;wSLd8pevq9&-cS;LIHA{wyPW4*Y3*1_L zOa3$X9J#6QCjC2W?fSP28D<|{f{5M+XMAd^C{Km9Zp9NHNl&eQW`SvezrPj)(0P@#(zga;-LQ?XY~0& zOrm~TLia$oE!}B);96A!hleRjaUz{>|Ic-Y1&0vB;DxjZS(TrUO!DrXxw@bs+@i7j z5Xc84m}2zZr;S2#3->YGKIuEPlQRXyuZfNcnK~qLRRp{_*qEM)g+&Bh2lH-I*i1Ue zPNa{Zmb?EnSScifDQSnAR+Tk#(P=`f+K`%Wn79!&;?VPHlPGim`D>=l5tw)76}C`%%sUl) zUMBo}uWgCpeuxlK?#)3~GJ5{~nL^;ZuTyQQQfM$6TzgjDViVVKU^EzEq$Pj4RGnME zg+rs7O1;9Voa#2I{okj^1u-Y*MwkA~SU27yj7W#U?wk<`SmI=Sp#%iPCCcLH_M4o1 z|1~;RAWi^trJlUJd?EVXPfzq`#+YJYg|gD^kX|1R02WubTCk7 z^A;Hbx0i-9&K-hV=M7N$tb`6+K9qxbF0-P73xJRc_UOo2-j;Tb&O7MzU+^;@O`xap>uk7uhw{5!Cia-N{i$oX&f<$sH1&*FhI zQ#s)A0m|M*x!3VpwT__>*q#T1@ebhqDBZOVYeXr*3wD_Wq zIL-Rvc;~7fj&2_Us)*_X91@E(xA%oVJui+=$silLZycANpjJ5olKd9Vf&dXbC(PRw z_=DyZIuIWsV?kKO8n{H9^l$&76+8&jbM9sEBQXFRqm_azYAUd|U9d$Vb#?s=jG&Kb z1*I78V|;9vSNb<9gJAb7qR+le+DZn%m!Ej&M8V4L-ILSj;5l= zPC-F|ezahC83DP7%BkNs%ix*0Pr}Q3Ag|z0Im?zyN=kr82-oT%L=w363>eT~hEJJ5 zrnLiF(fJvhw!o!q=?Lr;0S7!lIUT%-r-E#0`?7s23q7piYLPx81t3|Nl4n|7tt=`R4q#C9skIPR`y0dMJ^VQj{!x^WpRV0{F{B A7XSbN literal 0 HcmV?d00001 From ddec7ad683e5e190ed1a00dfb5e7047660dd6454 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 7 Nov 2023 16:36:50 +0100 Subject: [PATCH 125/446] fixed bug when recording services in resolutions --- drylab/utils/resolutions.py | 4 +++- image.png | Bin 90700 -> 0 bytes 2 files changed, 3 insertions(+), 1 deletion(-) delete mode 100755 image.png diff --git a/drylab/utils/resolutions.py b/drylab/utils/resolutions.py index 63e078eeb..a8fa3ed63 100644 --- a/drylab/utils/resolutions.py +++ b/drylab/utils/resolutions.py @@ -348,7 +348,9 @@ def prepare_form_data_add_resolution(form_data): selected_children_services.append( [children, avail_serv_obj.get_service_description()] ) - resolution_form_data["selected_avail_services"] = selected_children_services + resolution_form_data[ + "selected_avail_services" + ] = selected_children_services if drylab.models.Resolution.objects.filter( resolution_service_id=service_obj ).exists(): diff --git a/image.png b/image.png deleted file mode 100755 index cac5ffb4c285dcd40ab5e7395c64143c151889ca..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 90700 zcmc$_2T)U8+bD`k5fu~>kt(l9Z_**5h^QzKdPj=VTPPu+7ePc(KAfU$kQWi@ zA|;Rz0#X7Aq4#>DpZ;^soqy)ubI#1YYX-9R+H0@&l=alNI$COUmsl@RP*Bi4eezI` zf`Y1pg5vz-MQU5JHB@S z_k{2Gk^ct?|9%pel9l}L8)PNq|MdCK7r&k@f?ABVhA1e`WS%}$G4Qoq!O{la*ui#h zh&gawyLb&ef9;0KqwnW)Z!uBjKY3Jqr--Q}D0@MmC^nZV)*rzXWZ+n>v%^rDTf~3q z29<%PE@cT9{~IsH)%5${&eIMZJDk-5n<+wjpO|9 zEm2T#(I?i2{5qvyR&{{X8u$|8y;O_|5LwK-^&4= zfTh~mZ#>b8fvpVv(8lZua(g`4iN6jtIx#EB)ag+YbT?ItS=ymeUebZZaKxvZUUnD- z8O6$gNGVmFgIh2M>g~B*EIMHQ1L3aG@MJWBU*N0DZ9rT(iKeE``H0g&>1wIxfHR=h zvgW!FvqIM2b;LpSC_6ykkJ9Nd2-^`YD*D^iHu(jJxY47jn_wC7p% zEI8SDU496g(~|XAb25}QHLiCm5v1zp`!j#GZQ_9!zr0$k^C`OAETc{F4h7hCGP&4| zg@&XvO+Y;v9dk=x#yiNOhSJ7sZMb<1i$C2IkY3UGKx-4y`aC^gi{^85`JhWBwsDC5 zX=JP|u@qrm=dEu`F*Q-Q7mBpEMgQ|>s?QsGi;^9n>;r6<5J~6Lt0<;XV#ZBCtJXc= z)?nk;$hD!-%<#wrlCV)?6w_E83<^)m_;hKZuTh1>WDave@3~;R1A3E%3T5b=mp3J~ zA({FeF^Mv3z--x@6;-N@JB}loB-Sxcj1Y2lcy!IEndE3FWc*_YBcp#A`1`y==Y+0Z zoER?__~)MvBn5@sPQroa`dJyy*}T!P*g!?P)L`5v-G@+K8R8v|IkRk?9ALGo@r=A# zfys5km5;S2l|wbMQ_#~cu!!1v#Y7<^op%6f?(;KWubS^o7=fSCCXN-^=W@g?0xJ`f zofCyhz&j5<_CmZ|GPZ3PBe|2ka6(U`SD=)*MmS;qR?D z+u(EwUS%+*d`*TlIvswl{*`*2nW0drQ#k>~?;5+cZz3o+qEz{mBj4aM4RX(J0dBZn zJ3?S8xuE@Ls{1{HTPo{I0PJIVyuEWkI@jLMXbe`^eMG7GIfsRZnIhiEc)*!2HL^*w zBYEIR0^zrIPWBonY3i|ndRYeWiG{L&&o0uBRLho%D!$GBT>2?}duF#mTH|p)uQR3! z$#LP&L~@zEf!7oecHD3yp{HZl1&hrV)Ju{RiZq5Ce~zzPHh@cOAe#HYZwZgZS!NOi z4RrF-#-@|PB2Uv>?v1zMBe;$x1fP5Sf%XYnp zZ-zbxEYV|MQimSmJ$Z?kmf)e<^wOZYrksO6tDs=FvTL)^etsT=fW3n`*b8*|4VvyaFSoiIH=53IGN#GE%`;tq z_3sxx_>qEWGEg7m;HYwo@~Bq6`U{ct%?n1oi9&@ykCVgZhd3|A%;+xy zwmEQ|1O&C)C9~bylPc2%$)2oe*4x*Agx)oegquIezhqVgD`mT}SDKYjq=biSRk8kB z`%iWi4>Csz)i+KRi;QDtJdBCKx#L1~lwBw7B0mW-3Go-J+ZhU4S>jwL?7OK`@A*}Y z(w_79v+Xy=e4uMnubNNtwOL1>T(Jubh?$>v-1y3Y_M6G(VBE$oS^yH@Hj!b@Mj#L1 zkT70LKJEHKjP?{LIv+CQvxzJl|Q|sUK$<9W0U(sd~U}wuwvq!z-hEo?IjCufjpCz&#f_GV8nNZ>4^+)t~_Jo)xjX_@~mYVwk8BLjGQ_v z-amT;(hNO7L(CmJGf&d$?Q3fw|He96Hox}I#A*gy<@|vcl6CHDyRhmT@5iYK-(oE+ zIx+>3bT-OxjoN!{Ta8A5J|E-QET{W;8Sx84oVB9U2Sb;l&jPFajaaem=>Vy6_qD`n z%l+`v-Q_#7M<=@#ctVn>+ZH@Ci?&SpxZ_z++lz2f$MO5xIFD3k13HwNERon<-n`xM zGcj$oZ0@WKOQ6P*$);qL%BOV5L=J-Wr9ec$U*5DpzjVUuLV%+eJBoTAkvvI>rq6|Kd7sQ;_?T zAtr0~c0P`J#&{WZ-Naj!K3~q}Ur2EH3?6v4-gKW>q|Ui~$v8butWSpYJxn?s+fEl> ziU|nY83OTTUmkZIZVypMu~~_X*gK?NA|{HpjX-Ko^D0qphE3*zyk7EnVC4bMy??w@ zf3e9*;@MP5wSNZo8KTs1_)~`uiK$%sA6M8#v~W3HY{=4} z_$I<|K{4xSk^LH7saazjfiI$4w%F9dVZ1c|5-)&rp^y}Sa63~uh{qCnc$!|W*CnzU z7Md|xj1{Dk+4sjmZSc(0a z^n63T)K?Sh36WGeN^2`4wxr-4H~~M~G6gQ!^nUP_xDbhOvntq1VfQ&m0#B{lgPC8` zW++SB1Ut$P0?RW?jA@6422V`=Ul5WHkGtub3M@2Qy)lOVb~@U7GP5W}>HQyDb$pT< zw23k0$G_yuUxnS>j`w1lz47Zdvu0DgjMi{|Icup`#3itfyjfoYD?^9z2pE$MtDqn= zXp3}L=UCc=bd!TJCbrQ}Mo^2%L#eTP6;H-%GN!Y^OudOC0Eae9tE#DT#nUyzbSb|L z!SboLZaRgdRIbx@WAJFChOx^kVc^iZ$2q9>x%oq`Dax3EIZYYp3G3JtS3t0)eTxA6 z#dx@Y>d&j&>3RZ3ShLvx(sz2n;=n)*Z{sryt_8HBwa!yh07mH`NtpXh) z!}{mI%M)e@#?pq4_3nb;V%^&!I^BzO+v79SfL3r#kgcnW&&rsH7zo8IBuhBWgzpp* z^%rhnHlX~lr%d*nfKn4$z6%Imte|8$Rwd0$mkzgY4Q||q1^Kz*-Ds1}Qx9b;C zL>6q`-uP+#V7-lnxzhI!mm`UJCVLT?c*tIW8Blmr7o*Ic8`G)eWma7OYZe5zape2Ey!k6YC!*_U2GD&?;AA6B!sNWHn8%=||0PWyv_} z`r8&W$l3r(AZp6`{$Fh0`#6ttkyQtYtg}|myx*>QPaLN2gY92C9!p1n z@zXOLzpx{8>gEY(An(G=*IE>C?ySIl#rl)O_QD;^m4nAtP3P7ntg*cw-xuZ*%^cFH z(sSCUw@Pjvh;f7NFJu;FXKj$!{G|@7?LN?cU%V6szq^(B4v5QQ@7&!^`Rw+7X9m0$ zu>JHLqcD(o@9U}Q1I?MW%v&A3EFrCGm7={D>2EBzRvEYlHhh~r&%>iC)V_u6(i1V| zaOve;PeaKF^`1g98j13|$OZ?arvpK=yZKP%*Z3D-W2-Hj>&Bsyh$g`absSS`bm!6i zA<1{Qaw}lSiuQwNg|jPJmyaRKAPi-9pAp3rfBcTHChc{7dLA*}h8F&yW{H}x{KuM~ zVfdHA^;2q=nn7#hJ1(V0FYf8MonK0aqf)B_;YMo{g=Fz^sq7Hp4NWfqBX?4F;-MBt zMr2uw+c3KKl}rb04WU?2_RXp1W4>yMamD=mtJEo1?Hrmb9a64%R&x3TYZj)MMutOs zfmzf12~=R$X~<_fe?GYpiPS}A`K`%MMsfDS7I_QlK4>+nR6BUJH^TDFIW=vpIOn;s zWp<~U*VLet3t6BbMh9p{?{GTE`h*|yUN}Kj_J7wnv&>Dz>^g>U!90EgQVWDzaz{1cG?3iY3{GNhh<-}imKJ&Dr zAAoYHqf32a!AyS=hf{%Ei z4gINMo$b$vHz}2c1|icJU1F6mKSaetAKqmf5YS=ONf`o~nZWtw(OwH_ldw>B#gbq} zjnDUjeOhP%>7m|rp9B*}OTZqNR}^o3|GCX^INwbNwmy8{)I)&TGg=HEO4Un6J)H)l z_#Y+qCi_^SN;y`=SqPR!^@T4Eyh_qFG-3c-EZYJFWUdn5A{(xrBD7KZ3-)l%NtIR6Yr<`)a` zC_$gjDu=yvVa$%<5Atd|#aw=+os}b2-@sj73LU~4YYd&L-roNjvgIzBUkZg*&aA(+ zxgd)lGb$ayG@e6Du)H5mD~@NA+S@pPhxaohL(x;cNb}Yi^=Xw|M(~g*TiyFBOARXB ztAm?2?tGJkENWsQLy8B}{Wj`WzDL5?>b?_meg>75q8aO2p(%=IwQ1E4Jd9||I^$+n zAjLAD+w6=hKD&GFhgZ}?*UK-o&INxR)q6-15 z3n2jACwHT#+VWc~(h--ai^<5cm)TNc_{D`2D27ou?n+BOn3j}=S)V=(;Y@1e+CNo| z#7c0S>hbZqG`XFioiW)+4#qmKBg=uq=dEp)?N~a(c$t|gNBS6~FZH41OVT4Yq!Zf5 zWqbCAbXv1>9_F8UX}lCFu{^y9dSV8y!cZoIOp~Z(?ma8_dc?!?3K+9(%Nf&8DI4)n z6WQ2Jxk8r5UrTg=Kpy&oUEW|a^ND^F8f+;;!md&O3*zt&>A7x$f2m28VF%9C8=)&h zRTw=ohGVB%-FIscXuI%jUX9bvuF`~Eo2Ef`BdZHy05!6D=sa0qjr7frT7V2_bf%4M zKWhhr>AXh77pKD`w|AP#!CWUOM*F3=%UgA8*3SvQ?X~xh(N!`g#YcovQ9XM5odcrRnYds3FSqqk5QIs*=n(zt0H1lSS!{+(A)Rr^WB%z2qk@9cHKAC z$vANxl?|h%e4x0i!Oi$>CBf%O_0n2|QHPjV#?GFl0rgq+mbxLOWN3KmzaM#Yqgq?F z<#0{g$+-d|2P+yKp&sj7_XNH&N9DIyv~um}kGgn{;_A%-H)4W_kpIMUi%1f>b8DF9bYt9-o2*T8R zx!AEW!P|Mc70k3^+YcOxnwKdzNXJKC6BogUNZAu3|@MIJhJ=Dvg5MQ z3%05a$}*?VcY?F7R`r;)mqGPqtK0zt$Mz>Odr%NQtupuk4lFM`END`JbS41ACzm>0 zcfL_Hdzz8%VzF}$=zD~E|2bJyk^Z~a;8qX)*LEv~@3yC9l^04Tf15HkW?3w7EsbeM z?u~%LsR}xwuyRO-%MTMRmte%vULJyNs{Nlri%*%Y85_4lScDT_Xyi;mdYsVru+%OF&k9=5{bJY!$s0iPfMvGWLy7$`Wuo%lB2o1m+yXdtO*>Ns z^$86Mi@rYCFCstS9buf=X$sIkLkknDsmC`jtt7xc^F1iCRomCNq&*Mw23JPZ#@M)Z zTA#S!=C;afpGgq!>G=Yt%d?y2c}-5M+#LFo^(8(=gYAeCIwa5{# z{Wcv1P9j?9?REOLfUQI|fdm`F+Hld@c7Bs8u3Mu+LYJo?ca*R88C;vP6$!8d9cyMc zeJrnclgJcv9@c3ca?1%OV+L{1rC7sUdfch!DY!mmIbgRrU+)+#Rg|Z~jP$H+J?X%U z9ML;=9F{Yf;)gYhKVA~=Eq&#c8YGA!`c_s(9tV!?*m4kD9ExnReb%*KI$en*P9+}0pS@?WH z>Z2rAB1>#=9jf4@ref|@s$&~*F<>@?Eof6&me82q)OhX~n`-(?=U(0Xbv;nT7+P3( zkB#N%34jF>Ec3=H!&{GD^>A?Ya6Ih6{g9mo9su6=#|j*5yf1(5*7#D|D!buc?gfQz z?wL6lJ>`*fUJorv+X+5|Au+nq*gM6#ncwRhje=&WOpeiTgP>--xw zIin#xXXCKe%XfKd?O`A%tDWFQa2T?H@=X@)o%Bt1-pY?~h<*Wi9z>!1o^5ozfx3(+0Ndi6K*Nx8? zQIs(tIHXpgfWH19{dW8U3F_e&BZ(_`^|qUAcQjwUyH5)IV2V`YFcXj$SIH_jsg%Ww zp_G-Za%)*f$19sMNcQiVGmVyEA&zS=AuzO)DpAQ0-tJH~z3UOs>VeAqLVlbgQLOcv2^T>+14(NZgJm8ftCGU(@6EZfv&S5C&t8&RpRnZNG<6zGy43OFihi_U8Cw9@l997_YZ zTfBF9)|jOa_bXu*xV-izt9yVg>vkOlQ6l;%w{w*&X*^JuIGXCC_PLQjwd!+6>1vwqZ5WTL0`G1htP=oxVpi=I3&Ai+24HMorn91h3q*b3&W2MkEWr>Cv&AR! z&K)>gh{# z3EY_GrKJP7i!LQVrSH~c<@6?=jjLo*1;v~n{*>rT9q50mbZc}=qUxQV7WbK($-}N^ zkr7OnRs$AH)V)|9{0mLSnS9toEAH++kg6=}zcOH|lK@?8;lqadxROywZ*scJ=y)i? z9@|>Be%xO6t*@G-F*_)4Q)9)?nFWR0x_qK(U%HrN-D7cm`JsGfR^;Qk!O!qVwQPWq2iHbpYY_T}c(X!Ht~*Zd{4^IH^8T_h&Y2*bvvNUH_DRcdbdUD84z;cuW(HNOv@nx zuq36)!YFyhTLqSwZ?$eUjSRR-?Nx3b>oC;yBk-+mGg*^ z!Pm;xNQaL@ww&MW5sKfvuy@78@juRtmCtO^9EL!*RAp$MLhgTl}`DOdU~k zEtwGAeZrDLwwk1g2ylhCnN?CZZkaiq>ap;c4ozMzdPF5+GuCgp_cpzQ#k3uep&L*$ z3Zh3n$;@eAG;asKe&e=JsHP$I{tIx0MGR2VpQ-2E_2UWG9Cx4h0vwgsu7GJ{Y=XtU zd@qY{=12}!=uGVuzm$mI5Bd@SG?4gmq{lyWAhot;tkL=kZL(s6A$YO1mID*rwhPanvV z)NZd@kPFPe)RH#YM369-1ggIK5%#?H+rsu@YoX{nU9(TFn_`gFvXLdy()5FKa%VD9 z9RQq73pAQM_yjFvR_d#z(uO&3$md1}ge^QgHUi`Fe3;7((7n+mmicl1bxs88YHrmZ zKVmVv4ITE%`Zb*isvFAVwn+gzipRS&^e(F<(df3b>~sbtvhN;b(e#*Q(3fnb@d2&p zfw`vcZ8eAyKOCjhvW>$mxg~&@1nJ2JzFXF^3nrS65j{U*+EU|$d0nQ~Ykq*neZ3bO z{4yF-L;Vr2zM&*Em*b1u*GebPAbFz7LO!I%Z7d6zqCGg;nQRIl;P6@h&Jca*_|h`< z2o4Te;8rBnwU&9rcPNo>W+>{DHuj*UY{yAmajQ;;TK<;|lTpL^tklzm+1XnRxYBr} zSZ;BI1K{Yt!rD#)NM_MTU2nxAYQQf^a^gmzcMbL$$OKMSq`x(dbTqYCf~K#@YHT8J z!KKo=16bmfc*DnxOPfrbVc*>t;EPm^JXaq;gF&IaS*^=+_9HiMR0-QW;CZ6Sbz~yh z6ps0htIqEhX^eAlo3E*(Z}qw}XnBk}4$pWrI}VK1<;Gel=bY@C;4X_#xUSpO_OBA7fyEAEEa6rWn zZU$<}@Zr101H}H%&s*EQ5$R4G0}0CFEI)XG$M5~6$A~L8(NzKM1;8!)^9z|~VUTedPjRK;1Ext=1cs zcjII$CX0AnutUn5r~VXj@GlLk_eLWt_UsbguiGfe_FraP+M5++fnX#4m6;vpt_2)#%31qfQRbXfTpO1P=mBwcX&m35PI9&OTl+KRQO?Gt zxg*5U_mj&uFCOqf!A4fm&PMu)>K!P_N*DB)ps{yf(6b*U)fM28sh}1XE9s`~?%_Oe zXz)qJ6I;3%=Nu#ljL1It^A1XEe39+> zJ%c^NWM9Z?&;VgnC;w7+W^}6}xBh@L$|D@d+dO^G6f1jNhOj(=YVWKCCZPd+FTxIa zo7+-rIh!-4pM>lmM5JxvPz)5mc1Hd2J@>gQC26M=H## zLQf2Mm3{QJ1q(W!MQ41Ldv&fqP|9bKyK;y2*Us!%QfF+#E>LJ$kUe_f6jO0YoAX`W zH^)T)YtnRL_c>0`1=D-oWM`jC76UUr%xY_c$(w&~OelF5I%P~10taINJ-u4FEV zfknT*#bWNp*tfh+tv_!+zkNi0TVhz@X#TvgaMWN6EgjQnqyG2ph6?$uGoO*}Ley;2 z4B|TDXtk-LVet)9p}zrKI2_%k$$J!-zb(|(Xg3_Dn7~VZR`;iNgG`6u9pm$`7^!8b@I2Nos;s1 z!CP8xWCx&hiGdM0m?SYlXL9=TpHBRJ7sHsX7j|3CT0A2)f9@rgYwLHij;$#Ec^_J{ znm`}sK#sK_OLs@IW-zT7qqV8hA>#re{E}`y(z$Fz-?^#dZ)C^ko}4M&NVhCKdQLzt zSuGp?s(3_>ERu#Bwj;?V67RJ>Kt{P8IVNiMPy~z_rC6IPds$*oGBf={HZeJ2U!eWNqJ%@Xy`5ZS@lAKj(+ZE7KR0jJoMd)!odR;s*zty@Nf~s_PnMX*0)GT84tg2Bi7Bh7|?^zG}2` z^JSZ{vQKcUawS276=5x79!5ug0t?<_PI?R1wH6fpw~KaHv85Mi==p&_Ow1!wgPaFc zhNVUzX_s+>Mz4jH2^-Zvp_SPw^tT6%4wFcN?qSkz4GoK5Pz7jDB8F3O^bT3iBd>`_ zZe=4$Q>ChrS4*E`(Iw9sb6X3SG${h7YVw>j4YVxSo*+PF9DZn~4~yWB` z!q>p(XUyxth7TTuIgb|2Qk&|+QpE&zNtnX>T-k>^L}r0&TJkr3pFrpfbX!1WZ?ahB zJnNWt6ouTSq!bgw0d1G;SG|dKE^A6aq^~A*18wM8F3Y*~fA0~$l?l}j_BRO$@Lrgr z{OmGT@`&R2t~K)Gq>+7ks+;kRzsM8SF&ab94w$C~F@zAtp29SyQdVYvO7Q4tQp?3e zn>yHI6L09B@3IY@n}2~!orFD7`Fkd}`o*?DfpuQ_Ka>0JPwFF_nNojVepLQw#lbl= z{#@`%KR~GGaJis`nq`LXcI`lvSv&ksFzbEs#2u}Bx(cZ@7m!plwh#Y@0M`EoDgF=8 z-tNg)ZAt0XVH^=T8#3D9gmZF0wsLC)N|uyswcFGnF|)atoccA70_Y-tkWDwmec`{y z()&ggcWT&vFm_vdHm?%#qC*qpyV>rIJ<&%944$9m;kFPO>Bo(kHFj|@>>sB)v|R`D~ecxD-Se%Nn-CV}Of?!o4( zXML>5|AcbhH`OVONHa!|_?e~MZOwIm6cSd`S5az2`bmcF;iR6!ozw!}dLOpjdPpMA z1_6e_6m`K`VuA1(2-bgAHx{ep_r&*^fyl}=Oz{2n`gm)HYb;nq3_j3J~} zhS}*)VM1b@(_4jBiY&L3zxo{Att-huZcR<>vFx7a>)L6JA8--}-)(O&IAOq4g^ZA3 zEhVPw*9}f}jBNd4`!%V&1p6BM0NJEvzXYwx)-IN;3Q{UeE^M!5T_h-A^`{^WvJiii zqG*1nu(~U&aW&Cx13bK7zH-7aK?tvC*+@tF`}WNbOWcLiy^K6nrK6tsJ~w45aK zH-y?wB?7Yj4wq>|6Iil4CRSNQlJOZ#FDh1^2(2g6lXEVsqP&snU@<$pPfN;YC_&f) zZr}Tn(tU0EW5LnwZJJ^bg@WN8(Q}|a)-i}bcqIp>BKhYw{Gmy%ot&mbj>$Fm)`&K=6xh7AhA+Yz61nUf&y^}OHc zq9TcJ(kUA1>eBXZEtfMdMILM{w#gcdj*I}D#qG4zHV|7E0 zo~jOC#+m8one4&QtV~y(9dun__!PW-aTMGLUb4WwDBGywkx~0O=fG)Z6!Ls>cXChJ$zt)0lcsf|SmMUR&p4cU=Xkyvrv zGZZSi7l0-@JIrUWWU1MP<7IT#PURlpF*!{^k#ZyIBWhM(0%Z1egKCV>Mxdrbs60>$ zus3CW?a-#urWfjU;is|mHmAOpaSEOH7Z!KpVI)(>3d#KB9MOKkyHt{tkD23+Z{9Bv z5bvLZ0>FrBk>_B-MLB^?s7Ya`#6(@cwS%BP- zv#u@maUWLNI{w7l#^qnbDn&)AEAP- zSj6-?U<;~;EXu@Ak5}Jb4pm!E1U?OV0!b)HWDDPOHA&>nhoKf85$bB*n&qQ;FF8ck zExj=iL&cu&Ee?`)GJg%Jwb|4gvVSQiExjnDzB7C7TB?=Z-H=bi{o#u^)3oD z9DymcuiE8^ z1B~nxdttcZ!y*T>s%KBpb4~rzE~{1td0Y7Yq*-APcIKVZSGAwH**_xF+6TfGw3Vh; z#x|8ov^AZB5Y}IPpM-4+o7V_%=6!lJYwt&+0Z;kteemjGEh~i9{&A#6E+v^_XdRr? zHo|bg3$!J3Nmq-x>(ky?9bAf{w^1uH5m;>T6*TIfo6c~hQYCFf{JGpdzfEY>usXx7 zjkP+2U{AJ7{r9$RBYsA%yA1|}jKr%37Yosxn35xS)ixXIvu6&UM*UqV zE#!&DnUaC3)v;N@`A5O@CsKymr;At9nkHl9hBrl^ak+f~1?oxKC`ff>$uu-)C0=nhI+g`7ex=cWSN_TJ=w+{*A} z5`OEYLzAd>z#t^w@vx(|j&G}~*7>qvM4Z)qtd`JYhjbO>vAWi01ErpUasEB^(pOaB zTYh%6%*Kc)J{TX@ABoo^_jtR2)6WLZ!T&0JYkMAtzj5oHm>V=bOY{KHF-pF!5ax^u zWvg9SXe#ega^6jhcub|*a~cBZ8RDN8~mn{NZ{Ril=wo2MaOKmBD$ta zp(%|pUQx0cxhsH0(Jp3+98Cch###p@TIm(9zACJC=<_Ej>wWR?dO(#pBr6Ee<1*SQmme=-fj_)MN=P@hRF;cx^AYF+>PuCuPO@0`euU20^poN_ z)6N|HTZAi6Qxd!%Wo56y^|bctyiQkl)#2=8F6WjrFZV?dgMhIIh9b*ziH(KgFN&EJ z#0rIic`X*|GB;K+?EReW2-9_j*UZ9KK`vQRC5^2k_-FX8A;s&NM*NPPd~s}2hKyol zceeFwn3k5-biU5B9_J4Rrt&mCXf1Jgv}tp(bISbM2j>#Zm-oO=L8~@la0lvya!uK9 zE1I373@8=S6|DP@{i`ly6TNm>DX)NG{&$x$R2#RUVWHCnE01aFKFGf#-_#vT%xHI4 zZ5CSW%S#rZ{GEfbY#)?^d+qEN4Eg^gr9@P_F8E7>bzX^b$qtRA4A1RAy|Hf~@mv6D;!o%I-*J(0bl$HjMu&{*RJ|nU;uf?!4pnZ{kpWxdZLqH_{Kt}yA zw7W;a$qaKJZc|+_L{OhwXMFiL@yjEs2-TFa+GEK03{7~?#$<7as>?w=JB4+EMa@7u z|1E(Ry&+fe7gZ<340;{Y%$6R~C8`^~YYRquZ57VpJ3+n{4V!ySDYFS?H-~X!tUVliTpj1U}`Ky6ZP+Y73e*hUdoACc{Gr|9us%R)GBt$H7 z%km&2jN#+Qujx4ziZU|Tfj7zSIqic@GU_`U^6>B!KWp@Yt!#8`+@c80X7p1ar;+j$ zlEdEzsP3w6#sQncw*L*KkuYd*mOAgfa<6N?BZqagk2P?=A`4@|n;^`Tu#8zd{VTztn%# z|L082{|^C|5Egnf_IA-AY0wyR`G}a4%0}{?=LsS_$+ui8tArJ^NC; z*MpP1+5l7QDfaF)bLTQ{rQ0t}uUbs)+2T7Yo%{+otm0z2UG{CuQgU>CcI&$-@JVRn zaL$xZ3+xxwDe&CgQClD5YWGc#GG*#BARC=gHt@QSnGvCFaBkfiia8;{n!98YliRTClv+lZqJsQ7WPdD>$ zqH;1%&G~TLdV<$x8p5gwDa44%ch5=xE3v4Qe@^!O=qqjG37b%xA=ZI2@4WL&q^hrvAQ?KfK&SBfvnwOE z=l!~w@Z4nnF2@4Dqp}`q1oG1i64NqVd#>&Dvrs7G-OBn^iVNn(j=P@caDbz z%vKAo%vXn_k~4owy8KI_Me6sNyd9?>Sn!(lHtc3AzAD~fNo^oiZy zMSG$O&LmkqO*wevNS|PX!6&7#4j>sb`{8D7EBc^7uTMujP+axp#E(SD%BBkT)A!VM zrK@#}2|u=!u$Vlp^@{5d1xs%Js_&-LI>m{U`O{|wi(-e5`)&^Cqi>5E#kJB@+dhqS zl~m4%WoH{y`)U49y%^aF(;}FhmKTzMxI(9bfMp4nm>lGpHsQ+%Nr7_;Hn4G^OM8|ab! z0};#<#zhZ35~v5&$k6rhidy5^k3#Ky_qC#Ed88bjzFWY#hSCDX{cD^~`!ssYZ{2qw zYxfi9+0h6A^KJTE0t<_}m3=zZCC7tT9fYaD(dOI5Z#dI~(P<}+AyAJ&H2`k2><4UOgS>#xwAZ>-)=$z-f0|fD z>XWu-w)O<1+j0NMkc!(lE`ih3S)W=yVmUcs|5)uG=%W>QMYg%L4{=8z_pn5a^&g%dv=dV$>q@Qz4 z9w7q1nqYwqm26AUtT}KvDyAGV@@VKaUc52}fz%rQ@ZDw*^+5ng;>e7fL^8m?o`9ns zpx$a&>f>DW;TzLKZQ;CAivcZ=Egwy$l)V;eh34;#nozX4!_r%|!W#e+kHFp7s?P;H zX$r7U)Y$LX)+aEl<|>SYO+-ODzKO`UKQ)M=A8%z`bT+hvp2R|NZ_%eYI~lDH<|^r9 z*FNBsGB=7>=|G*PmDOQ10lCRM`<%Wn^g4*w-tdW-BkD!CpGt#79NPa41P34iSz<$n zu_DEUpm>ODYR$vtgCJRx?=JhRYa2Bu*;iagk7-Z$s>5d~nymiZNV6QTH z1^%(`Hc`AZ+kx9;xm4%-?&5zn9W{P9e26dO>{cu+rC4UbKM zDxiIYFAwy!Oksu%6XtY;J^hv9PFJ7MrMEn=U+Xp5Y2#kkpuB69cR0<&slg(!)B7-h>1{E}KWt5C!IN$kJq(&}ewN*rdiRG6= zPHJv4`^Git2Gmy$Z>zx>57}PycTaQ>g5xFO_wSeTV)F*EG%llc5oQQJg18Sz*Izf> zJJm&MvgH)fx&7snb`U&~y3VGnFwG+if&&dXw}qHWBs*?{2L0RC>_A!gXTB4|9d7Fx zq$%&m!}wy8s75!Np6QB(?&}jiwyxM)jaNk{Zynv?v&wG?kz;n7i-e*gjIWNW&N(=q zM!{$O=-v9VTqZ`NVYZ(>=T;9=S%qL-GKuEOEG{>l4{JL|F^y|EEV@G?Jwb&JTpU`Z zkQWAz`=1pp_$i3lO!K9IG0vlE#cdCbxr4si3{v@R*HGdvFlMorjrOe#Z-Zb`*HGup z6oziH%AgS=rjM36Bm&xRrdxG-`zTrQ?#GH8A)Heou71AR{?7n9bII%&2N&VxW~5Ni zU@alQ$(_!B{EQQ3=`wvKx@nG;E|rz3Y-#}rV}AUWV^6Y9cEq&X=BV^&1}_!#@nmX1 z!2(3UYf;?mL-rm7dMUe{5Qn{A94?#CH6hz;=`UP5mU`MLy2jafoYQ?}WZoppiq}yo zI7JV>BQx`yjG$J0Ff1LhRA}wpq2}Ne!*I3V+sRq>_!R)>8Zaqh(aysM+SVz%?UwW#ZOBzN+=f*Y)apt}X@bi;{Rrw!~fU5C^l5c)@9JY70rt5u2b5ozasz zu0i>Sl`69_$P4;P0}yjt;gr%zBq>w14&kPDI68A++z)ZYLqvBrJJLMfXF==&exqt; z16>$RoB4GmCxfsHZ;de_~?2OS2avnI7lF3H8A;4!RcymNS%BsXQ9*dt6BZs>E5a1}KA z$5;CCY}#qOO&IkR0rfNXb0VBU=1Zu1eiGf;=HQW{z}V%8b@aWRTf6>BS!#n0L-Arx z!Mauj4`YumOB0s^q#XlC@%}G>i1&ungQhZD2MPEZyNd5iXR8&XZQ4#Sen zNtVX{i@EoVYO-J6M)46rL_kGAkm6$j5$Qdl*Z`#?N)ZAoy@cK&1VKPVK&5vO=}lTf zkBERsC!vPk0s#^rbdqpxeD>b&e&2J>I%}Oz|9oLB79_cUW#*b|X0Ab~yqwbDlJIhR zV@_w;&0Q$)1@-8*U8=S1=uU`qeUPVV`M^riDvxQT2RA6=cl*I(^?8@9k;k^6T8^b}bhL)aDlK;1aL)p=@?YlUgC7NJlLfvmW~G#w z&6I=ZCB7~tzL1cNRFikC)9m=8(bSd$BPkvI%r(x79=}E{M6xbnmWIVs>=I?6ny7cZ zUDkd3d*aqy^ws{v-=?xt>d;`r<12N-BF}EC(zkFrPIo&8*^9KO06=(rR9b9M^*R~3eBi} zk8xLC2D>nnruUgTAJ{|<&>V{rt$TkxX9Q)h^7wr#Mn87SH}j4e!04>I_c&-q1_X}R z3T87u)j#~ephOrlS-X-`%$vy;;Itv53R}fCoU7JHA8#dzz9Vw?9fG=6dt#7%9`!nX zEG*@#*LlLV-?9cM4K5_=*ncqQ&;}Py3Uk5KUa>xX@11cWl~m{E?SqP$N<6JkO<(1J zs7&fG-l|J=;=N#Yl{G)`6F7^t2u>MWy|(b=Jw&yzTHU}0%W~i>cQ%pJn0Fb%ah5vQW78OSW|4H*vby3Mt8!}H zA?~kSSFbclROh7laF7TJA4Y0TV7IvVo4$6guHVz_t!xD8#q8Pfq{W8kJPk~d{<0q$Q>JF)dSF7t=jIonSfa@PbYix@5wQ72-x<% zN$;7DC|<`$YDT>(0n-}_$&0e-MOsucBx?EDD4OzAHx6ntmlo+`liDN8AzYP#36gwY zucYpJEY@=+tt6Vg0k(v zOg;-*u$`7kyea-j+ahFrZJncD%&e+@U%Q>l-YYhwIZ z6!tqz9+-o;^}qck7g4jed6iPBKly;(>4%K{R_&A7Yu^}#$uQfW6}b@yKRh+}VOA1i z9c&~_paX7V5xv@B@I>zD{i4oon2WX#PeVtQTH4~yQU^hjwPR0T!#_>@Jz!#| ze*ZXl9NJz#Xv`6rM*4J64nF!-LB3mh1;N(yI(Nc#k& zuq%2yw%}u5|FOGaa)c{Y3v2sJkuC_85tE(Oq;#8My(8TOn^PQ(vQyd3T2O5MBIhTL z1Zs5I^`-lz(i@2tm3C>Yc=JPbDccBZ;cncV(o!Wxugd_jQm?|Y^!s{Y89PpeO-70C zQ`ex;!)~1^i}bH*F~#r>_;oi!5dUH3&~P`{UOrI+Ste>Rj_*>~53aCb1yx(6y`JM*gnHnwyBiA{B+5!L7tSB>s_i1V8rp*WdE=_tRK z-wsolFA#kceZn2e4C0@n&Qkkq0iu8miYXZ@SU34P-@oZKm>F}KqVP9|yArySE&`U4 zMo>0%MVNo^)GIo&!xl@6Z9@+8Q$QW?^$Y!Tb^4Ab_R|dxKSeiRAc(9}hWQFvf6u3n zOzSnmHolJju{(bQcIOEbSpeZsQ*_1n(MmCl$Fm2fStu^i(Nnr-evahc{o_TkhqfmI zf)09mxEWOBQld_v`suQjFNng^p2ShX7mb3$Bn_auI~Z4=qNXR>>#Cjgt8 z_$yP~p~JqEnX(|4#ei(1YT994jpP{5zq?8u%E@aq;8sJ0lwq+7l}Znrx?=P>&91(USvPp zL$~8$?y}f~!Kri}<|VZNgX%{WKVJjA+PG7uDKTy zbAMuO1mFWI+MpL2&3>;StmFg`;+2w(^=U2GyNbL!jMK6D7B$ys3eE`iPu zEwE_Hr+}In4=67b)~yshOq?M;Xp58#qE3q*J8eQ!$*IYs)hPxiuUvDNLthA-MM+YlTt@{`)-RjvZJxQEq7zlIu=dI6c1;UD`bfim~~Zl4{blL zZ#bOVs~?;Qvi7V&EqN&_1y&9YE-e;;A-k8?<=*}fn(}?XAkTbc_Y@h(HADIQy7PRl zFYa#*>s2ix_ZKytop&OuM%fj9iaVlOfhC#aN6n24j_Jh_I?Vb+%rmBxZwsS=TCIUh zfL@g;**aK_d|5VYj8XlzMgzJvWu?!oYhI=-hQfezMd}rkJ1yc_15Tmj^iVl;G0C~* zN`Cq})06t^FabP&>)zDWa63Q2Ar=*evv)CQ6mN0c?p!bCWx6vS%DkS_D-4L{sU8Fy zJ*}T8bLHz9=tgE>-Z_j5-r81(ZIXK0L`?YvZm7DvoBmbAa9JHYJQ4cB(H|k9T(u`r z{{`O84V}@bP*%I{Y-ZzoPeDT$CnSo5s&#{!+BlM}AS*YIBaS=0CRl8#NpHBCeud$+ zv^GTtr8adQPMUXry_u5*4nO2z2rPF-)ezD z3zq;uV-S%~N3{zcOp8Q!?s+qvf&b-h*1w?O6>@3P`?KhP=mXgIo_@pW6h-SO_MR>L z76L5|xejkHiEH0FHn7_L^7(EqZQ24e7S&NiUHN2nKLO{NHBn$SJ(@SL;=!W?r$B91vg?l}8EyaKw?T-dV z3)Aywq~L?A&5^TS_$l!_`v!DU^3x;tvt;ZiY6UCcFYMY?qFC;xWLIBFu73hOvilX~ z_5Bldy<*rWy?9YsrE~yb56Ox7Qq#-{x4H~*=*{F#OtP3!IySwWc~Z^(^|o93%Qu?S zsbY23gp@f>#vOS1KAJ1%OtnwD>H51V8%^*RnY~w3~r?Pbfa$|UkBM#zU3+DE*Wp#H>6|TfiSDaS07!r0& zUsB~6n%rC5+k!WjADCV15%~7z5ai9HoCBPJZxYylsv8(?9l|F=_AakXmkjg%8{ji^{B0&7S=3OD!slmBKQobeGDQsaifEg7rR&tQVd_ z@Fdmg+D(IG!D)wGLKd{6moNwQV9X$Ma#jbc?C!|J*t9-=qT>2po%X|908xC8X#>R) zjlqiQSYI*J!{SZ?Wd%ZmbZaG2c3cCe}Yy zEO;`(1&2B0#V?Z-vLD6$3*nC z#&tohZEph4XknXv-hMENXQ=2ClpQ#MCwE_hzbs^i{~_tOa#L}KC@EcuU|hh!!tyL8 zvY`OlKng)JHWcrDOMF;E-_r@P9FCAoS8I33B0dmot@|i*s)m_|jJ{G_Ev+wA|19uE zQWmCxOahSGX2{U|1LBUq1CWTIi!Frs81CmsT18eVg&(Qw%5@)dTl!_mb`54nK6U0Q zWFYN23;~@xU;Lvg^s9~)o}znX+(aq|9Yy!2WY+pe>O`Lr@?(B@e;#vHrLq??(wxB zc+v#JS$;zM+^b^r?=S9uar)RNlF0Z(pR_N&vlD%hphQZ`D<3UiVFBZOtfvJBT?=Rc z^1ad`hbX`i{rxbic@5vlwyKc*HST+03MQ)tDlY@TEFM3H0N%v2RAvbd(TY{!ikSM$ z%p)EshzaK6Ax4u~Vfh(=#oqgVUoE_uu3R-EGAJJ1t`VDFOKd*@FuLtOeJ@PtWmg<3 z$!f3?30E5QlWjYBq{+EN#oo;Jb3 zBU1Yh*`xdqoN7d?ICi5|VN!%98w~Qhm0dnRA*?t@h%dRI;|L)#^B1bVEWqsp-BB5M z%K*|8D2egjyb2H*yl|`|iEO^P?~>r~c!7id)hS`BU>ZZxGnDHB$liM`xhJ>CPC06e z9-ecvnvj#<0q(L7zwy-r&04N#IumGtm_)--5a@(xmAb`rL_*eX;%)_cy1+xUU@9ly z4})C4lCsU2Q>X(3%70B2Kf$G!eZAoYG;q{*RP6B%$A=1sUYcv<2tR%}?<71!A#fMd zH*c^+E$e=_>5O34>7aaU=MuxuHlhMt5L(mu?W-+iUUGTtc)p8`yQ#%QL#*}RH$7@i zh|QjfAdYY4w>+VQ?m7T8We5Mnoe-11VprbgMKOAdn5B{4UeYI1su$TPUzS{R49dE0 z_+<3!!RS?}cW!0t$kxPET)H$qRkkV0Byj+505BGo;44y+4zIpSVsAee^UEsCe6drIi++ zC*HAz_QL%&JJ|_PEY1*qjPnUoW;kxsSF0@KJUBWnKgM9$ESGdb7n0Wfts$N(g}Xb& zqZfP0-gT1OxjGLh8Gaj|l&s38N*SoVT<}Cc&jO2Sp*;Qk3@&l&$`iJ;36#z|;QH14 z2PZ6z((cRh(~l2?zOvTH(t}uCJU(!?TLbG|0_{9IE{I$dDzE+eJ+hBqk#BgxI9A%p zQW-KfZo+4cP43HWkRpUg_3*(PK$+)>c3HnJ#SPZil&yJZW_U$2MotN~yOuoQ$(?eT zBF?AxbvfDVD{q&%ndPL?ec&eY7OQzEJ_+pQ)9HW#-QF-Uvm0f094~nHs`d%uDWER- z82m~A;z**&!Zl$(HW1Y4JJ~D(LatWbL0Rll2?0VM^W-S+-dO0_3oW5 z$>C{0(qqM|S6m~@yLEsJMf~2O`ie(GRbO6cZ}!8ZlD)c_vi$6h?KY!-outP=KTJsu z0`>qp)o9GbCH3tgkP5D{>SC969PMY07m4nmaUq`p3L%(Lsh7EJrJlv+$GSq;dHUwX zfy|w8zUn{SIdLjuSEZp}n1aCLEcGcgK*!EKh8zEsSa#?mD5-UNb~-HRhwkexuXQMg zMPCwafL5V06E=0`%e**oYS!V z0SYR4^FEX=W@K5(@(u7FadiJw!nic9jTUUL(Smg$!VTM)cbjM_Ut6%R1we4>R-Tkz z@zkud+LM-g?EACcoG7Gc2%8`ZUbTjK6?nJ;6+PDw|4R2qYX1N2T>9^lr2ke=|KDqJ z;uQa>eZe3m5AX{6(!zb!^T3xpdCgq8NUO$KWnQHggV`=U<$e3#RC$J&Tocv-#=>J}? z0fiJqh-wWk$eY_93SYO< z|7=p=KH_w^2t^heI_Ot{_&6QnWDagc`OoVM%ao@YsjW9q)E@@Ar$04W8(IMSt!AHD zdV{o```j=z1^Zl~9}6FWu=Lb~oEEShn_OSJH#%q2Hv-gtTpN+Penv(ZvtUSG&8mOl zRrknn*LC=Q%&_|J8fG%7U*DqH=cyq-AQk5rMy1BU?NcCp3_B*PpEFQ{8-FV@-ZlPQ zVO^G|o%Y!uOg@x7gl;P&MK?M5PcnN9%~!P-IK#lU`vhkRvQ|%HQ%%*!tJ23k98v@d z+<}@x=~Zm8TJt}eDLm-cUTIb*WbJpe=D5o+(n%QQ}p>TFok zo%H3tp>p2A(wn;Is#^ivBE4>x@!ZxC{1e*+RI`5ZyMFSOdkzQPhC6V5rRU=cN2cD* zhqfR6%btGsWu{3Bj>i2{cUId=tCQ&$1M=o85#Wc}i}FSVd6n!xW98*7z;w|&{J6v_ z7WKK}(L5ZM>~}s;omIJpqoh4UIz@TiYSRCq_YP0P&*Z0$Z>&Te?(H>mZLNKHNi*?l zqOc8}f&S1kpU6am1@o z{;AlaUfC!N?eyVUM@aS)-m`C+>6wobEc3KI+6tjWNe( z07Z4pTBlWUJSDP!^^%$E;p$2p^^7||wJ1A3yRVqD`wTah=v54d*8OUR2JxmeUZ3{W zZAA~&7Nnau%V;WwHI*&;mJxwealjK&j?K%ye7}v6Gcdry+&2DC?$!10iu4yUmFus0 z!xK>o_h2OOu6*XPj)GzvbKIA?yJ~uUugs7VB5XU4?t1!CcP9HO(c|=ypY%c6Ls{XbYU-o?h zCw;s6nzd59Ek2+0VD;tFK6Yq|F5|R&#^BpCXG~QE5X0Z|`5mZVW-5W?s_oCdW)66> zF4z%#JFBf+fy?z%I>xHNESWtcyc)@CFg;9>IuwOrZkAU{g~nm#MYPDjwEbr-6(_4I znmRrKSwhh&sKdbmPD=4IjdS)Xi#+>J5QGY!R{us%K6_;(K&1WSkZJ{j)(E^VfP7LFEl&hyJB4&84#ST0JK3YJ^V zdXkvU<&HvLJEfJ8sAKb@_ssshGpg{SqRCr(ZvoF*NUJjw0^)8cG${k=t>>0j;(qtI zcI}l`;7MAJDgMl2C|Nws zGf`~gqN0zn#jQ~*4O@(M2ocq%q?}bkub^v|0P|O9TCpw3<-3%$`5he5{*i$5 z%@fy^MxK*7J5>qeOMSJNv=tQgA+z{7_(!r%n0L?m*k%vMY$UD>i65ad*FV4)z($4< zJe;Nw@*+6e71oF-^!!Aj6c_!%UgWS;IO^Ecy(iPI|V|n81nu_)BzlZda zCzSqIMv59IX~Wh0`Od}Fr%}?Dk9j#(RqBFbUM7@V5PB7_rt`j#x$!aG%0$)kR_>_v zE64FwY#B|^>lOFRFx*gG9JgY@l zBckFhQ-NnvFS|&JG|mC6Ezi{(hvByFRAYg)ssj5A3X4;)LnY>3GTIo^z#t@y9{TPG#(6J#ERJq6y!m_tUXzF%Qxd( z&izq3@bl=f$UXd}?w8h~5NRdMC*xp0N`2xBVDid6&Ul_=L5OTc7&QH@`T;k8cB`%y z^?RIc;r!8q*C=)!e`A)(VH1w2?WDYNWX{QzyvF>~`NBkjE(CfwkspznYlq(tm;PqL zXl^hX*aP>Rm)G@oBeB`)FD};BujN{G|!+T?9#H+T4)SU4v z4gN(iii_NYW%#uJyqMOs{Ym-giQ{Pwnc>wBZ_wb2@(HY55=|>|J^e$v&M+$TE8K<_ zE7${~yV@RHcetAr=wzxUY%-Qt;TSPIx{?qU0538<_At-?$hdQWJc1tWM;Ij@YLX~C z?-I@cu>OGB!gU;r)^^OtIF-h~hI3`;qG~|q?uqR%F^$;p_Og6tn%ll@AZEae!V8Iu z(`9;sykR6oW)5P&b@jjdUcJAQt>>`Awf~jBHzogo+FK-vv)`@`0QH>U+Mw9SWV)8B zk=xMr_Y=x&+JDH?J44LsnfN2=7K7O6NsQ8{M*zTNi*z65w~MzU74q|;oRZsw?kL21 zY?B@dH^y=I!F+cia8MZW(m?`{uL8 z`HdBj@|>80ilpoqVmj~4p?wXML-k^GYnx)`?ceg6B3%Z6JI&acnC|JEOpZ^tYKlDo`b$77b zKa3QJHosaT1mCM199}!Gto(-&r+PmlZT_F-K7JK%oVqv2wJ{Jp76%QRxf)k@T(Jk;`9~wv7flypx#WJ%7(=c1n7Df z;3?U%*5jwt9;~+K8x=~Oobk;fQv-uxJ*-l;jPq0p9TV4R_8h}qf8*0mT*ZrCa>@*f znR?^;lRrFVBol3)9luG@eP_9z&^nF5U`?>uS=*hhnE8P^uL3crfuFa$k0jc;d&zq) zOUmWvMRKgdz0Tcz@tTj-g6o{^X4Pq_EHTEx*9H72?}qVb-&)5DJ5j4;;f-xq66SHtq59B1%1YOcgn|BFq#~)#Qn0j%wu>f|XGq<4MdU~m2_PU6gYwxSiB25q$ zGj{*x(~+9KaiIFGPZ55N&Oj(ohOgi16sP@ua?yT9)e47y9_*}>BcEg+C-P4mp)^(Pj}=Ct`CK$GcHEkbJkxdElYql*v(k5N|8viz#IkkI??Mw zKyE7A8H5gedin;)#PNi`8tFEkA40m`Z!(hS$b_fl84?JEz1eFPxSEE^FZt8r>C#@$ zo>JP+(6;dOHdgb=nUQR?`sYI^=yTR`=JFe_w8*y6{K|uB!WO0BpZf~{($m4f7W{TN z7s=DEGi2yIS&Esb_^+--9qy(^wPZbXW2`C6gv))m9L}d$eP;JpenL+ZmjN7#Sde|K z`$RGsBV1qU$>R?XehS*goW&)@?mpm?j<}=z*@S^7JhGNsMJZg|{4WJrEmpN%QV+6f ztrT2j7=HP=c*uYFyNX_>v<@b(UMA~YJ56UelW|nJo3BSCJCJW-96dAwZB%OQ|@KQemH1_*RoE~>dP1*hjnwi`v z`hDk{O%A(`pXO;o=If5f42tFN(#8L!Rg=|y{cNj}PU--HHlR)d;8n6s z!ZA}^8w-~Ka)rfVKuu?wXDH&%Kc5pM0Z<&;ifk_&Hq7~k;)7A0p!M2koxY2(bCdbl>s%rA&B>6F3=RZn&D5Vh&d~9c%sruW3RmP z{PFZLW%}Jqgdp^Fwez%@A;dEtD`Qal!ph{8GIc)(+R0P~uu1>Y--t_cMo|oE?1u)2 z49!b{mQ?$h?{Dy!!dRz-K0(Ymf^m0@~f2W@3 zRTve9z6Mp67*%|6b939Cixjo*{Cw+TO`}#27X9@JtLNJ205r8jCrPXYdNfpGj7GSP z(3TsNra;dmj{uT}@4Bw-M+!+ud5xJVHrpbpM_oMi2USqKl0}tBO8pb~fme*z8Mn26 zZ1Nd#D^=hmC?FdUwyRTbLLy~F45Ej{Vx=)k=hKdsh(dbD8N)?H6e1deEbky(z z_9Q+j$u``LzNlwgk$<1JM|pDjTJ1o!oj&$lFBn*HL1Wg5I2Gd>;x`kK+z~aCiM5UA zoZ<2A+dtzpI+a}Rg(IB}hsSGvn`^FIVznHTxQUNfV$MvnD4}3V+oEYkCh)scIA# zBEEt9{XjF!AN!el01W8_QU`MJZB`e^xfnmLaYR^|gPB&T{lfIc-`Qz7PF_C57^E%c zbCZ|j3ihatIqq49^{l(&er_o9fNU4jz3t&2?*3sM zZ$~!}>bpwYV3eJa)hOAiZx*fOTiW9_4mhf`m2QUb5+@SsW2NyqHg*!#{+><9QAnZz zJNoTah*R@{HTWiFMF(CftP*D!5tuRC_h65HT#-d-KMVTAqWwdK@QLM!1P+eM&Lyd8 zsFvbE)%f8zwbQW4{EEC?+X8i>Vs4ZBl%DoX7R>S{>v`hAfHf>F!>%KaJ9emPDLZ_- zr;WqGsr1DQOii&&^G0wg1#*Fvtj(u5&J>o4OR-C`V_T{_S@#Q(onNSnqVSdBwcVs3 z9}lmcrJhu%kOZmT9oLIsy9?f;>`kwJknH_t;Wk2b8Y+qhjiuss3ANOAYK#GeaGm0fO(E27 zEv|)>cpk+pmz8_jcklUoZam)X%31T&UT8*bs>&AoPqOORPA8hM*iGuu;qGst$!iUTxBlS6zzTf8RrjTC*W(nfaVQqy zi48Lx|LIPs!;L3wx3VaY8uSO9I_)TA)V@$uT;_Hf6V}NEpLs(+feD?H3k3ecu%@GeI$mJ_o(9c}>Ysa+&9#Uq^Uh{2@1e9_ZWcgFhY?JTNfc0bi6pWi%|Lz{ZdM>(mbo}46Y2>-Iek2(>%fiI!h zWUIS63Y%{Mx0rK=k^PYZe|tP_^BR7CL$7;r+u!X)`(d%Fjh63vHu?a*6mx2qo1*xQrF z9g61DekBwe4Md-zNh=vHgB1UR6g?GyRCLgwl?1B1aZ5cnH+M{YaKs#5O6pUdW)4ku zgz6_^E$xtYXjQdnTGk-VmlK(b@S?ITePf>!^m(?wC0YjKxpeVao zr=w5~vwqm#WIp9+uc1{nS3Q1$Ynp!s(o<(GKgRv+3p&UYy(;y8(%0;eQwh@;eC$y%p3f@vFA)`6}u2$ z(M5(HnGSiIRe)cfO_9#FJ4n`a(H9C>+?e$`e{#?CLm7;YfN^ZcRO0ct!Oe0Db+lcs zpw%2F*sBD3rYB7v&Gh;zf5k7$$kdldAuLME(UOgW0`0`WJ#eX6(>T+IR5zg|B8PcE zHh_TA;(*K-&{uxrEN>g_cX$!{{_`S0jgU5Z@b<$cr;+Tm3C@M9=05kQA^xR2=Zc>p z%ciLA4itQ5%RQgh2ao)9`m;+-pc+o?UOkbbh=;E^J+u(Z2*j z&@l+R2|3|)bVsSq$+f#iRitdAvwMYf!0W)M32}$vyV&2UDAp&j41~nAG+@~3EQ{A; zE_t`F_9JCHex+rQhWZvKW%Ool=XvvL+fPTb<>QmNo#qw*MoFtb8+>F5KK_scDnWS^ zWeaf`dWI|7nN&*oYFRcx^-~t|vmbg|n#=i5&{nTbx`d<_HXY)6Jmr$avboqCXs;$H z%R%Y_VewVTY#9I)sg>c6Wc165}T9G7m&4xoKnAb z5&^!uLC?(XvKnY(Ltp+%Asy`PC5h;n)=@gR8P^2mb@*%Kpl z7mQqyFda~J5?Rr>NHhR=deU!#pT^Pt8H&^k-sKgPmVSN=Jis3i2)LnlxAnI2l_{M} zVYpn^`F1C@z_nXtTv;mj*JF-mS#%^Jai6|dFv&T~oK zURq6^L9N)LG2G@AuR|LY@>X1M9R6YsJunX4tzuqFYFNoYP; zx(W$ASga@1uS&i8K?|cE;D9g$z_4#6Fg^2hEWB%os0Ly)77=_3-dYUg*J-q&v@MJ; zC0dUAn-lINirREM#>zMjkEDZC;;s}vYe0-Q?xs8~Ycg2;9d5YVy!J9Vu09@L^tA4m zn*dc?JSSwhJ>`Ro;szsrNy#_0#y`P}XUZx(jdkGb%cv$iEq$lsu{5hzQo2 z#UaD>D<@AXz!GDLv)#A4 z&K);y;9}hE=6~uqS0k~$JT@bP;5B7u>bn?EFb9s7{f)C`XA7B%mSt^1SACJ0yM3n8 z2ooUODMXaZdg@#gNa}%k)l^NQ0_ox80mRo7Nd2h6=u)=}429^d)5s>n&#Fcujf`djzli$OG z$GO$qz;gCS=*2e+Mj1YH43uTl;v{BaY_*+52YXB>mn_LfJu%?QJZNzl5Mlp5Nju$S z_5OLi6;Kw0STsE?A0r7&5vg@bnrZG#$dq-?06V6=>y-l{#4&eux)w(L@-nBzUmX(@ zMfE0$N7d5Pg-79Vq(#UJ#p6c&HUS!b-FHz}M5`G?Sw;4Z%=?vSy1*}xs{z?>Ff*|~ zO>s8GyRYV4#{L1+OZ#lkic{?!-~QjTt>N^>96!Q;JvqmGW6sZBAsAMhaCB#`&A8Qf3 zfShoPG`X~hQ$DT(_bP}O=qjglUfcV5CmXo`F2JK`(MxpPsdMvHba!Hd9FJ!{lXvNl z_H5sy~=d@$Y3xe z9U2PzMhJpF8Idl}JJ+1D(B9ZIo4KE^zs`+)Zy9*bR$+AlQCoTqEx&|R^jlt@b?Nz& zb`?nIOmPBmacTsmLz$`voX^s$&t%dcrM#HrEhmTLyirH#(9ZQ=5(YD)v{_ASgtaxt zy_)x3-5rdgjTbK3%G@#uW8vdXp(lE3ab9K}-3uUZb|B)hOtKR%P3j~Yw7z5KMH8O_ zg3k^jibte_^Du1<&mC8v>#>81Vk<%AT*Is8M?>z~~< z94H-I$MyXzyO^UrxfV6MvTK(BD9ZB@&W{Wl@lC+TP@|89* zyI*t107?chErTC8B{7Bi0Xbjx4qyx}jtw7(j{#PfFEVix`nxnqg1=Asxbcp``2<%fo|k_2?PKc#S8@}J?9h3H zZ?mGrOOc6VJWY2`$`FO^I-+?HY}O!>l=)3e!NoOnCq^2${@2cCgumUI&Flx-(maF$ zk4(Uqs~5hQy?`IqjR%UE++bgO=Jn0($=i5(!+N;G^O8mCPM0ZXW8Y&BZ7vGJ%1Q_b z&#`63b&b96@t566**z%@vPqwu{#uhAYUqR>Q2-}UCA_kSI&R`J^G+{%G_->~JY4-# z`8M;Yes9Wu5|HnmYTo)SL?~5>WZyNj1LWfXW?%$GmHuLe=xi2w$BmPSv#t-r%3d_R-F1sU@h!@G4@mAJTjCYJS6twFHO;ty?*#j>z(ubEV2a-Hw+| z0wRKW)d#citT5Eq-vGv4r%IPw1@DBdoJG^lm7}PB-afg+dcbO&AS7J2YUs#JWq2lFp~a`v)A^-S&hEb10L{{@@#`;~a0Tjyl?F@W;M zMXL#2gkuiwn^MFgzM6j}|3LfzLeWL)&jB%I_ig*RTj2Gg=0l(M=)Klco_`K^0xCca zf&;x8uLi^?etjURM_)-ab&II?TwSsTrkPQv$xE_M4Fy2ujYsiV9Vx#2PJ=zytZhb??ngqg)+Q~3Li`R>VsAWHH)K!ww_3jO_v{m`U%oE; z4v^h{d4aaCHM=LZhCFN%U+0+2!wQVBaV<*si^y0vHQ6bq1DlHjdhP=`({ClOF!}ewZt3Z_uZV0mG@^(?>XPiLm&m}clU0@D9mZ+ z+Yc3GYs-VZ32SCYKAK}}XxDr=0KNZMvavw9fH~y$oJNh%9rx@A_pPz-)RHp$wyneR zsvo!XKdfAp*rATU^!?PGrny)C$yD6?0=Yjy7_pd^rD7EfUl%HMyRU9}A)xP*;)_q5 zgv+=zd)%nO$Ijl3K=m;o zZT=c**e3SS*UY=fnPgkV|GIQDukpQMWCMYzH}W9q^PR3eI>}#G`3;^GbG1ZUDCm>} zW7fWcbsF^Jf2&L>1EX}YpHCQM?73pLAx82n5bOyp&wS#BRY+@;Q{%EbIM#O4@xGb#TndN}aR5^js77DKEN)LCK%9JL6UFP8cpfGtkY!=IHbktki_C^y@r3eB4!ll=pDv zW%b!>B&>R%0IC_mmI_zO0h70rM#$S}U@p^+nQ}s;X!GbvVe*#hg$a<~{x?6edp>nL z2yjFW4M6E>;;Gp}U<5~4y1wL>yT3o>3{sBAaz&Br)fPbX{dRSclN0EXu*CY;+l*zj z{_b_mLw#_}Fp zBd_N$j~S}RWfXj_Ns$o5fX_bjMuP?xifqwn!NW;pE0ubH zDKBM$ug`YPG^#0Q%+XuloxgAm)R}3Ek|V4&Pc2F)5ofw99t5fvf<0#a?gkp=P6f2z z6s927np7sLlM(m&PvearIFM?99;#)ofHpg)BRh?K90#zY>^k=(_wdcf&C~74S>@tZ zi9tUy4`YpwYo|4i`+F5oGU2-q2-ouf^=+>~obxSUgQk9nFDg(dB9^dUpZL1S&(L_P z%)qx!Y~i|2V!+$#K_%w4urvKj`aRmp(I+MLJX;c89DQUs^ekkur5}BVpt`&Xx>hX* z1eSBy;#wa#?C_Q1vsg9etlcC-4f#fwTXXsiP;t9D>Sda*xa7|0CI~P@9*$ zTQ~9y>2fYol{QtbPiM^25m8|mAG0ueYhs-EYOnu!;$cWdfn0m5-wrEz{H5n!ZGFvQ zWTAQ~t0OgNPXGm{wy4MAAW_X`DM*ddW*W5z;?}GsnEmm*_u!>cJ<|tLwaaR_=vWq% zh_lKZxhLy;7YG~#ax9d1RtZ#ku7L2>T!K^MvEGq-W?lXkk2IIOY9+gSiK?F%K|5?9 zAvG-$S!mhe%H9si;Ztpsh2V$}~}TB5z-; z22Uwc;H)_mTqAK-Obt(YuOi!{^nsJ#AZ zDKlFX+{(RmdUm{ZI#9Ofg#C!@@Q7TgP*uCpR7tCKuv@Ea&}y;e$5oaBb>;1)Qsao< zt?0(*@;bAVc~9+95BpCMKnlY7(OtzVpdvsjaqaXRDLWm2bIn*Shj^kLjt3UlZ#{s_ zv0IPO>hnR7Zu-}9HIR)E1=OiuY3)Jyex)tYHD?foga|i4#6gP|WS+!ct7&;pxJYF? zKWMjOl4THw!ClWnlO6cKQJRdb&Cr0z%z76SgmT}kW@LgWo+y4m;+y8Cwb)Ne!lOpA z)SRqKNU42Kna&ni^4aynglCfjs`1M4%!06xG zd9rWi_uJBzdV6Ix+U2&?#gfYH-Qc_F3|IV}v5$d2KsZ>!G2rn!L0;+rhtA{6H4Hs( zJZM34$k~u0`?%kD-!RL6e{&4VPOO7`dK%3vl&!w#WkMtKj*Au=fn6+|gnx(S6%^(h z*Ie}02a+wpkw#1UFJnJiD=fF!@mD+UX&UfQTMeH!+?qOUrcW@{|2_kXn!c;Nilz!% z(bnUbZIzIBMx~bbm=K%a)!G-Wj|wf_z4KB$z3Zusduo;jUqf%|WLOodD0f;(;5BZX zW9XCHtWu&J+S#0wywsyaFNlYE^Ut?q%PLJ*JsnJj2fRvcTRv{o!~;Ao!Q;}#U?ZO? zs6WJ?KnpKDnK6qlH;v}iZ02_6Ao0!OS{aZLADRl1XM>NpY{^oW;-v++%jl%$3NS1b z*88;xv?6%@ayQU4PyZ=S&weJbn{5FMGtm}+EtDx;hg7u=%5}2f&OtI_J{l5wVFF4; zd)8m#To$s-19I^#SsMFKy}CI#Gi9X=&;OW=3MNZ8fSSCe*PLx9iDQm@=I47MD&q!g zxL~CgOdA4_UNQ;e=*H#kz9(!jX`AY}cQgi}_<;*C(9w($idSH~_bQUhcXj04=B?4| zi7+f}^qj)3^>E0470s5XK$09y%=e();|#AdQUaUrzCeY-F=>6-ig6axuwaogGfhr{fz_X>Hx3vE5_>uo)(uAYHs8Uyq@_=4lG2>vFB zVb-%9IO}eAHQPmHLd{=ndtt;qxuIWa02i#2jt^yyrVD)RPPrPUF?B6=KSfnG$)cJn}5%1PG$Yao}p9Bxfw)AobmHn1Lxn# z&P@z&CC9gZFpb{~IzMTeoy;w;(b_fzl5Ms3K?_fvdu@!SdpSu2-FRXCG5$N*$8vS-*fmI^oYSkPId@tm-rGDi)JONu7l~?TSS1z%Jf?;dvn>yjFf`emm%S zm%(GdHO2ge>f)xd@wOlRGyVzT&fuO0U$Vx(5*h2oOEoWklv<;yhFoo3!}>B#P~pdpf0BS6K5w{t6ON|b6eP6r6=kAVVLIzXX9naY)8o(&@S54y&XmC zC$G#_q%2qF!ZEfT3(jMX8P|K98`KiTb$J>uZn++H46`WU9n6hi|C5h56abZez4W-J z9?1zDs6i!5N{?j8G6zeprc^Kc=^Wg)CFw;R7O%Gu5nd|hg6Nly6~hWmqyG$0!AP>fO%Bemj(Ds{|HCLu(yEg3Y$FK@SmaoE8>E4RYSyf(ljBS?C@$dy-8g;6hJSQk`QAsC(lIUnM zheg6H2V>*S*Ynd5ivj0`#!)CMG&25f&USE`nG5ef&QuX9Cqe_C`8AF-r3l}O!rY)O z6hBEpLDJ;80@vjLS){s8>jTUWm$G6m`%^7OSIfg69Pke0!DGGzV0d{}9ShlC$UH&6 zH1V&X^evO)vnrag(g08X!?aOPD#BFtD}sD2sFicUNeGwT7n@h=^Gs^M?!Nwrz5)Jf z2a(mELNThu*+(U09v5&~Yga^YqfR0n70)tC**A-@AEfL9koAmS=z&b+%bQnaAD^l>BqF z>s@L#(t}O_)H81KdSF>-!SvFyCncDGxuw4cP{!E#icWo>btB-A+<30RfTj?#>%)!7>SE`ypGvu&NAXg9E#}Egx51Zl4dPvYf^-iSQe|`Ytx`$HHrY_@M zQJ&Jm;G_6b{BT+k2`2kXFh(r0-t|0PGL{iYN`9|i5Ocj`WL%>WB9!EGv@ESMSdolm zYPb+=hxx->{q#nDi<`dF$CjealjNu>^v88(L|a1q!cRMon0$2|_S%ZFpr?H~`Y`RB z(_W_HN-i}42L?i`$9^kSaAmHkS$OkT%Zr>6vN_`Z)Kv4@3aGuORYQduEN=X?An1#M zA3VNvu&I6FVn$xos_}-rXj=-`d7k}6w1^4k6LxBHag<$pza}Z-5EP zbQe%pS&>a32jx^752vGWSk67ArluAa71aY$JK=Ur^%9kdiHVq)m@G48jLX?h0H{Rf z9ReTUw*YMFyb`U5Zfi@?D*(mv9Yk$UN}U*)uKqn6`=vD%E%;B#ttuFZx=8ZU=1 zp<`<0>h?wu%15-JVOWNC$=O*WrmB8Pwc)-5=|yo#byT%z~b@R|es{ZW}Ze&Gm(QWn_OB_ksjpe|vb3+uK`SVJDxsGKxiS^fq8 zYd^&Uf80T_S02e~cl1^7HlwI<{*XD^Qo6euCxqqd*qj(k9<^ODwE(qv^J;4r@ur$b$K z{I8Ag?Z1Nui77Xr3U&*Nk&kGRcF4&ewxkef^HRvKI8QpfT$4?@Ygb(gPbteSSh_^S zNJR0;mb~JEHX&KkEmCZej{KnGA6sF`)R??uSK#p5*jmJuc34ZVVNj|I;ayJ@yS>(R z3rqoD0v7B!sB?NJCYE>$p^gI&P@q!t%;2C*dqf;hd8RQ#@;v9!>7-7+rDcg;Cr0^$ zEIt)3F0Lh@qO<{ema$g40Mijr`YhmfQ5eF6t5m>E5q60ct|-Bs*?P zJ1Bo+&ct&et+S(hI zaG@tXD{l&U$Nij%*z>{P%IMAkf|c%y;$Vo$vcau-wNmGxT3GNvdxFdb*fU_)1a6LI zQ@notVK8`lsC4)*kc+&4+bO>s97vm^Ay;E(0x5;2c<#+{S5;Mg?u}s}gfSda0c)!g zid7`2%zbJ0K>=JWP@CChD>wUVG6WHF6z58wYD-;KSmcX-;#V2SaHdr$@W^@RGQZ-z zy=ilC*)y0^Sw?E8os`SbTo*kRxg+K$3GF0+u=0@fa^WDJ6CJ_Z$!kCr^Hwx!V1P!; zfKzs$i)M2;z_S;hqXHw{+1XL-sN9$;p#V80uVXqq-SPhJR<72;;*a^Xe0y$O;9SHl z!!UJLsP!~KnM^7_m-EqYmn57v$K9D9Agz9!mqF}tPQ%!^IMvq<6m@o+Sab$~8)>}M zhkb$i|O!>1w}w{P8hwH9LlySI(DiBrve(-U^5 z3`5rHsfCZOQJx0-`%C@SD>k1lb#X8{TxZ6_bv&}N1k&Dkp*X0}AM|rB<}8=nnKEfs z$u896?G-3IXs=%}CL(^Q#N^AeMJyPXqAwp1&3E zywElWVvtXPt5Na%9MtIEJ0I!WZBIb$11ilXrP*D?hG${`huDxilR~jm5UnaS{>${8IB;5pZjkVvJdfkN$Gj)bHFm!e)0H>&bg8*OEP=O6AL#bw%TYjBOe@L7+f&Rf zs&F-4nSV_6;^$OCimht{6_%#X&L@TH4sq&Hl*2oX_Yc%I#8ASoCb z;ZE}1o`mTE%|VTyV6NVk69H`@wI#qBm!mn20a5m^ihh8Yw76~rz0QD&Xlgq_}*BiPHY)IZ}oE1=D|UxSxLzDL}3u%tdbCI zj?-|isDW?3+phm!y1gP$>=d2nFdq8QelCtz*_JFO+zrV5P`U`3edABvYBtZ+4j`hP zcICL9?`@sh26BfZSGmoDI*Ph|G9s!D?|vbcV6JSG#1}45&ouH<_<)p<%=b*x%Bo%$ zD!u#{3tAm@41Qd`eWz~~{o76wQ|&U?`MAKWR&i;>dwam%`egvch!_U-^smtVlI`tSM_Eyppt=tmLb`33<8rjcPOvkZ6=m;?m=(#brzlESR`O$JX~ zr`ZKqSmbegV&AFxfURJlAvI0d0rfy^+MLhfFCH3T_w}vUkdl&aX{vBEvsGKeeMqON z)`!yVHb>$>)q>6^v1@@FG(;-?_|LkOfjqNTm&hp^U^#!%x3Tm68J7tcZLBeN^`k%F z7`Uy{A@IW+qDYL4j9|Nco5A%2$tn-c5aduN;QJjT`abtGKynIM4)wl_!~Hs;GMa zohaJ=+bpaEeu6z`uKOa(o1-p|yUuti&^wjbS=X?7FfK-RK_tbpjhNM~WPk_c8khC) zkRA5MP#%8Z=7fN3fsMd|f5QOHTAC`+b1{6oUI+A41r!Tf7s)T0cUm#WdYg|L$8B|; zNlbW{ai@VLBIt0XGvD|lT^#sY5Qd#fu#=)*EqcO4KY9D=RluF=N^cb3ssHI( z<30q6oNOLA^W4QH-En_`j%o<6I{gS>`U%!0VEJn~*&IbgLVy1wte~ae7ZqlH380V} zAD#_&Vx>bpWwk(!!jDNRZzve+A0|C_Dt-D7syc>gKBEvZ+w3|!KcCE31LCr)^7Imw z{7FndE2WHP;Cc`~ld_6D0DV)2s{#5xlAM=9FCgDTNqBWv#j5cl|9#=B6K!raZi& zBGZ&%z0c+>t$5)(aWKJ3PF~suQd0U2J_$+4-`-dR%FN42*5y)(@eI=OxHO2yPniZ? zJ>H^Z?usF169u`tP{43>xz5>j9&pcD^E05F_06vdHl$R->k?5J|BLV6`9wmgKLvm2 z3MO0n}_Mlfs>&feJ9pf5G8T zs8W`cT=HT}XgvoOb_y)`%yl+juOjJih5(`))-6R5|iQW#?B*D?{BFY%UJIJVHTv12B3&BD!r1*g63ZWykiR z7A_G{zJqGE&qrMu2?FV{NJh;MJ1G#;etwc1+n4^wND>ofK0VswvfbtKMK3(Bx2#_z zS~!uYoVv7(4r3@J#(vMn76^Mo-XpE3h*MWrcd|3EJg7%b$Ec4ju{oz*s{gFvVj0bR zv4I32{^H6?6(Ws=f}_8^`IC_skqFoy!n{3}`_Rb9D2iSM1E3mFQ`0=UpE}iFQ4D&b zJ_g}2oRsCh?;1?)1V|vN61+2<`t+|vYTEMWSNBf8ar%;Ty%Qe{Ua(m5qt5HXO9DSc z^6#CjM;ry{sbc}c6nN?KS?VBsd?#BW2`be6i}1b6iLq2Xi-`RCsSSx;qa*($mz2Pjgx2OncASUMD z=pEE0K^~7xRR$te4vQHarn&><3X9pS{r(i3etafvb0wN+0vy_^^R02T{f28s4)gbW z`9cU}bLp476lG>a4Q;7@As}p;#C<+XLG!d6pTP$p0+;rg@iw-)h85EoWG6L8(RbU5 zuPj4vh<*JxK21H77LGc9Tl99oTAQ9^8q3D!?#B7lDor?jN**{nqSup&hKGmqX0HKM zZ3o~nJR%}}pE;4wnPtIg1s#&n;+2eGi9hh^e@2;|2NQlvI9}U~mz(<~bW!>7;oF&w z-`s@B!P@yu2DDy5;?Ns4BtZ4Z(`!3Uymca}po+2QKhW^4x5j93zv-G;eMi8BumTd6 zq!&hOySpKP#4TSOu5j5be|PD3*qzC}Ufmu@fh3|>BYufn8{OOaD6AI(!81Ylt+cN{ zz&_af-p>|)`DA%fJ*8iVNgUca`GcIC){MHJv+&^%Ta(BjB4+p>>3n;PKDG z&j5G{M(7o>cui<18q!P|z$PLf=?u%*N(Rb=D`noIk}jRx6D*{9o|#w*9su6!iS znQG6*&VaT7b{7#M75BL6c;1%Nsb61T>w!~BT~614w1UjaV)2?upP~=w;l!s~<3a%7 zEUm8o-v8ASY(w+!aq~8B##}h=1wT&Y*o;^E5w_Tp!P>bIA8+SzfB4x1uL<#P=6oRF zFemW&_RXpqiBW$=N<+Co)fGS7`m;d;^-Ffj-=}P_n_D6LN!`P!9b0K=C zdz1N}7$$FhI2T+0OOzE^Kvs$XK7`*~9uu${J_mozRPp}(`)xUVEl(-G*mhmI zeACd*j;*D&^^_u~_MpqL+LURi6P0!e#(_LPnV(Kl0>mMa!`&|9eG3>g+k5^Ulv)QD z^`tpEEh3A0Q87{9AA%j*1!`r1a`j62OOv^gfYc86e+HOWZXrC_vU}UXri4GN9`{Hc z0ZMJCkF3gn_Ok%3IS`=6bctxXDv&AROG{~c87(3Ief@%#qTq^BELSiz5vfw{{n?1d zAP5!Pk*MESOYjhW|9ojqucJK}%;)1Xw7T>W0FLy;W^%+AmXwtNY)b`AXliX03IWC2 zd`owCcezFnclH>K_*wY{>j5H=-}=RW!ub%@Z>37bsuD#026*GCw3wK9Ya2vP)rMcY zJxzaY*O~aQgKT6{rAPIky`$P`r zehNBPfBk#%T#PwsWg<@rjaoWM)^_vGa;o^()_eTYXIbVkw8_hYH3NtiOsQlZ+|bZa z(-2g$|K>SEAAH+HChGJRo!H_F^CYDQa|4Vdhtjh)1J~j^*6uIoLsgpm))!g_;*zg0 zxsUg!F!>ABL42BGYTQ8VV*p~|;KdUCBtOT2+jM=p?KdTU7(I8 ziP8GRNZ`Y$78G7N{UV>DkhRewm(8P&l(2noF|3WXqd*ve8`E2QN)vhCy!jYb8bNRN zj(0GV;2%D^46~tWmo-)Aq1q2?xlt%FrI5mY;>vrHvk@BW<0jkDU*#+#;ezVWzS9z> z;?Y(hS@tu^klzNjs{V|@U46N|34gey_J?+PMZSqb+YXy!SnSR?8psJF0O$0e|I2O3 z2vR?mBbQg}3Xn04QeIR;XM%8C+%l9!5(;exeMLDO?Ks}v-Z?-|>@Z9`JUsLd3~T{x z1rr}XJ8%v3d?@Mg+NyBlk|LrRIb9vV<%YkJ_>Ya*vdBUw=s)e1$T_(UveX^esW^f3 z%zIsc|4dV?#*216`}5{_CRe2K{4j&a!I!_jzY481l!!U2Z&t#%c#MCh5SBN%;D%C4 zYydJh|1<~$E9c(DMY8bl@QuYrfwh5TG*_ba22S#Jgi1&NR4aKxc!ij<6X;cD{<S8g2)>96?ope!_Y?#4aVEtA&Jb)o}WLkGotZM3QLX`P_Lwr}a?n>MYBC4_`13 zw?zAI{fS{11>PeDFIWcC@(Z$0)>+91MCQ}TsWA))oNM`A#F{+4ZoE)~6Z9wxh5)zZ zZ;t9ZrK1~=l`#N`8>a`GUTYjPYLhPxmGi%Q7065B-@+%Eo%Cpy8CYa*w04;5y`K>4 zkOUV0Ks%*d!g=W>?|zk|X+=1Tm5LX}Ag6I)&=srtszDK!Fn(ST=2u^{{-vG&ck4FXZ*W0a`y?3Xj4efG zSoLpLa$D@GgM&OaV!Rb zGs3o;BLyllSm5m*PVNNjUJPM-hBnZ)89yCidzdH0SB6R_ zE=|ru7jXLb)%T(+kqD1QCmw@AnHXXv6W+Q|{`O%HdRB z6Ct4Juokmg&Qc@S(stRY;GlIQYORjF2iVeH&zTpAPQ~L5z5LiGs^Z5c~ zg=)YvfkdQX@0h4qpeh&U#SixO^MjSnuoa*hwSm_6K4b)xkbBTf?t~eW5EB|(@nbuF z_|`!4&<)*cXM@oHffC;-o%Q=89-hLw;Qg@noOOe>*&>pJWUg=nq24xDqvCo~CE~qV z&RJb2Q_Tq)yno+bYXFj%D(Fj2Ap{P`NBech7%}hE(vNEY{;a}|6zAY@NCh>)KtW7; z<$@;APCY&~0)`_X;QI-C5>xM+|Dd9%Mi9ta2HLWgjK}ODtgqZsIf-|6m;UO9RT5pm zJsBjINo7Rsb)0nRvPk_~Y!h3pchpPO%T_fj-qAIj#`K^uP1ibp(snYnV-p1WK%!9! zDKDP*`arIIWSkTUhcqDD|G-1kJs98smixZSYitE6gStGt4wgGpog^5bJ&S1+(s{hQ|Pp@7oR| zERScm;)4ZHD>bZCcBTiMqAQ+Qw3|(x*Xct>ySO{(mG!w<2;61^N8Y>MqR(%sz-b(m ziu3y1D&Bz84r5dUWaKMMTkAg&;V3mMER6I41_p+UJ~VKuv^ujJaz2+KS|R?W7IZF7 z0RwVEFI9X5c7tL6tM7h(dO%^hSWopFb6>u)-=^pI51|Fu=O2O2Ct-%@_09e%aF4u?k z7x|<17RfMD){+jtV^b^g_59_wJqZj~Y4!cz%JbN5qy>&GgXaAf@KTP03){X0DotJ$ zRsbva*HwR)U_W@0${M%xg0-|8ph)a7Mf<=DjS%6t%r395^Fxo`2>Iq*|7a^l@JG43 zVo52fz8bV;E$ht@%Dt2nKfL6C*4g_{8-zcX{-7DTxoi_IfpXQ-r{ejesX9 zP%`Bfbg7*%%Xt;PcQ>Iz-xqGNIdM7VRNDcfF;A>8FuRbfUDHBIugTI1C65>xvYN+5 zkT^4rnwB4J>1;FA*!D3@erC~hF5?Lr9NYh1pv%8NHyX{@>CTE9>4&&oSl35D6bvuY zK7Jc3#AyTN*Nni$((bJ8{|h+$df*z^_4Q~RRLz4gMS3IX*7QZ%Q0qL7?1=+7wP$Fr z9-TC2D+!1=#~uOd?AV!pxI0YH_BIi15f?&osQpmj&pV3+S=O?#4P)YsX>2(njt$%< zK)0b7q+|b}6+#1_C&cn*0Wf4|rW{RNTz26J&6Go*CJ&{n3*HK_Yw{BJ`lrS{U ziJy*<&r}o+6yFsIk}XwXLNI~3&mco@3`7W4;$#6R^Bs(4$hq0u5&NQvIu(Ck7-ftb zpjwh?&>J&VYJip{74I{gA-b)^>dfE_b+(|Z`Y(wh@RJu7(c$#0fUoPO$|2#)A1sVI zy|`1^^|UT=lrxhj@cg|0kihxt?^m;>OWrI_Wht-}LKHvBUz1z(7sr|t>zbFF)cMF& zAbY>_`d3Tz*4w&>fim0Dd7(Kc(H^x$*acXDajqiST~1)?O&q^F4+b$;T1{srn5BcX z2jl`k4D(8GR4i~i5pOb$Rq<18Vanfe8IpCQWnf*kpSxk2Z54J;5wmizR?_sB9M5lRhc!-6P%K{WPyV;G zw*orgHWuo6$tfsK153o_K_6FN3WNyAG{WZQ<{fKsrNah_iczmLOeYHB>D(kkFF>+U z`gjAHwp#SUAik}BFY-IZCM(<0#WZ`uDMS^e0)H~vAyQZkE66?Rx(a>COHVk9OM0aRM^6_mBbK4dpC>W=?# zdYi)i%`A~~+cl);uPy?egWP;`1~i3@@Nk?wnH0VNMA`4TRY22E%R@i}a<735U+>yK z>@yu6!py*12O3#GR5#U=qAev8@Zigc(*_!_{Xeb4IV^rjM6qyjU>oygnFS%Ev@52? z%%5f%f!ps#f6FYr;-g}|tHm0AX$!yvDhMe3=RjHON$O4m)zn>h&O|gjzt4wrc`&HK zkQWXo4?JNIuao>WNpZ=u4euGrm<>X?W>COjf2UQ0gU_frM6XDEadENq%a2qLh$N>H z%}r7Ofb(t#P^UD32|Vc?;6E%`(#fcxe!M@{w}*i(fYq6of#vO;3o#I!bc&-ZF7K(Ix>^u*$+*9GN57U8UdCr zC{tvWWT*FqFrIb`n~KWTsjCJANMPggd@cE4Zt~z%4Jo@tkf%uviD>~0);R=@W;hT; z5i(66PjBcR5L&mxORhCgS4(pQ;cyU%q^q#-m}NM=B~RTFzlQMsucvDtJV8FE=wBa5}c!EJkn{noc*;`PW=+&s&m3DP@b z;V>oVJy6x+yE6BIsKVE!{qiei98L!1nm%X(pQ^T{PS40VrAQ-}*VmJz)$PrS;T*}4 zqlmt=u(AsK_T)w0B%4T%SY!_n+mtY>!2+m|cVAwDqDRQuNYRf?+}Jr-v?Z|@JI+biQL zy(h%CHz%NS3V;y&^?ECoE23}kWPgzi)GEIxCMGsa(f}1mOMJROjWrt10Nfu;ZeY}v zX;OTWl_Y+ZaE5BcvE`*pDRsclPVq-Qz~+>(hFFd$PDH}ky5Qapm$O!lAXQ6z{{=ae zOrR)mS#Vhn6HY(^(Vs9m@eNU5(J%u zzTPEJ13v=+94ydK{s-WodcQ-JjzlRaGEfU;ru)jzIKPZAvLyUV(hDU3bV?ysXCzZH zM=>`dWq5anDCPUzw$SPGob~4NSYQ^t8lgl-i3J%Q!9NL!u~ z7eKxK^W|upCMGW9V&t-01S$KbCD{COUsz2>-XcnvgO-DVoWY){sF4*!l#z-usNuAr z<|4Pyv-hz1h6*JDI99i&liLxcoeD}y%G~4cAR%DE;cypRItp+YWjw+FH^X=QX%)3^ zkpKEQs9f^v>gkQE15s0*qdh9!NqV(<#F-JrvB&fB5*QaijR23gIVk6fQgcZUGvF&7 z4smWG(Y}FX;MwC96^+^&eFD&+ z{sREmK%7hh9cH;LWtt);YDlq32cCDAqV3tMSxAgP#0mmn$_S_F?>Euz`vK?!%~y(` zO)C`C8b$si6IcQe^WC0dzex0hxde{~KTuFB#5*hXU*3V{Khr%EuDn83@8i=gxEK7l zPEC_VE{EP@QwG&EptFLHh@bh-=_(t&0sGTXGfr=j(|kg@kOn4`wWfhp#Xz zqFrum6kYZqRg)~1QR0d??=gPZ(8M4V2*o;a{Q#U=1~C2M<^A>I{g`ij0JX*!J%pAokFQd0^!C>t!?K_@gK^9U`*UhAEL;+lnx~`&T%QR2BxqX?Jv+W= zS0|HS@cL4;an%`k`>s4(Imjx0n&ODCvUKeLpEtsb1d`ymCI^hqdI_l~mI=02AvO#g zyQ8L~eG!zBc~c(&1aXIzgS5CZDkIPioD*RPBL^%&-0>n(hClaf(+`~9|DTwB^a7!6 zf-7Hlc}ABmBNaNrh-V*Li?7@)usB!qfk7YRbj5+i~1SI0R=vQP{{pD}ak zl>JB3J0tnx*mGb|P)?;Gy1HhS*Gv#zGpM}*2h!0zhWmEji}23mrOJ$0I6+dsT!(es z7$Z<-~urpt)0{ej5>-U1J=-+;}0}c!M58?yohp{@J6tmEsq;__8;qoQqb7o^+j%9`i zPf_Kk=e{ORcZJ~FY%G4GaX-W{{gEOlD@cttk&{{HUP0UFwcvf0yOuSIU8~u!tmNBdHP=1G0pLmV1JEG42kI^;V za2h_xIP0rUh_>4!UJfG}Eh92hY$3#j^jCXRXM_-4zm$9PMr$bx*~y?4Zo>7BXy7e9 zBIq5>gCT`^q8(6r$}+^nP(l=In*r;+6e3`L1gy#R(*sQeSS4hB7ZVW?G4?n2#7wViV2v@;26mG{2T0#+4cjJ=|Ch)ce?Lj9|IQ6E%kVDI9tjw#^UVm!w zi+zD;Oh!@QxiMv+#sKFk+J{{V^D(oNpvfG!#pMhY&$;GjHAH{5P$(nKJY&%%D5@#u2DL;#&FNzCyQ#w|V8x?V)V5qdJ#g z_7Hn8skssT)$8_jUg1X!s$M`2J?X1}z{LrQ7l;F}HsJo_FAnATOQAgBMcVa&W|Kvm z(aS;{$pBuarp%}C1ql)Aaa9ocUG!PUEf6s=6ORT9{b3;{Bk-&IWCTj@bzfVz7 z<>%Ld1&HANXC%<z1YVECgMQVL*?9!DJy+C+N-amO=Ic!~oW0)XXCpC0hNd-vQAgQTT9 zl6rg&5BSrE-9VlG;_iC?lf1V2Ok~J)WGEnm zxC<0oMaky@KX)uQJ7QWuXvi#a*i|oQ+-tn|=u6_pCPH7og}9yx=gMcw0s||q4tb)X zp(9Fy9Tk}@IOSl>oIk7flI9U!zSA|4#xz1kPu zU*s{%ChF5`NeQ)rjWCn?ers%i`iaXYlnxAc`ggTWKfb}8X1NsaWEMf8Vwi+_SWbQk z4@>8$>EVlQkg+{wgdH1mJ)xci8w}va9JZ=s}AwDjU06k`4 zW5gK){)ilvG+hM*66*37IjG%etXvqODBBnH2*CcxFs6#S6joU6v(D*fpz-|NbmS2< zjJUZzlG?~TiMIW8=@q+TUts2d_k_rStxeXMJl)=EsV3M%ubl*op^!dUfVI__*=UDRq@n_Hf*e`zo(MOT5y((dksEG0 z=q!#&`Zi3e#Ylj}v;yloqN4K!pbak1JH8Z`E!uLqOgo=MvGog#*6M1UTxw`SREZ5x zNFqFASOY|v508%I=NGX`$S+r7m}vkART4Std&fD7K>Bo+VDm^yhY@9qej>HsPEUY; zzdYsPS3Q;G4$k?DE^1q^j@#*2?Q|}~?9p;NJx4+-0#5~vBs)`#lU5#Cv z$k~}YoH0H(+I^F5q)X^0*wJg0i&Ue_b;pi@d)X(&xL0hi>fo8U_z_0NppVH#kl`#7HWl`yvCo5r&2SIMJhsE?12Vs@o)!Omi% z4ot8=mPx0`$ndEA6`OHdg8;aV^ku}Bdj0j(v`sCkAg~8aZWQ&!HsSp&%%I1t8Mtg2 zI^ij$a4!1mSSR-Vy zkFt@wj#8fn+*&z)YaK&pglYq?4*0SfS1`>A0zoEqUd7y*F6+!oyao!?5XBPQk8C1i zM||B0K!R~qmbT1d3vwbmiBA^*5&~3%(+=WQehMp4cM#xb5n+NlZY zcXs9`?q_?^&mVr=e-XJrZOd-oR?1P0%FcJyvpp}}nqZ;&>!yiHwHMH~6!L|Rk&<;1nHC&l~vf*K5!~hYr4KamG6M$qRIy#ZP zNOU%XjDA3-X8R6epzH>$1At@Zwp7dwB=b(v(X|WL46+)117oPLKtngeaRZ83Wbb^| z%On>)(0IY%=RrkeY2{JuZ&hPleD)`_h{lu*nUIbjztOHzlJw+%BQ3a|8X#(-Pl-qt z{^~fR^oNr9x%MZxw9~vzks}aB8A!cSp1asGrnqzzMqMMHu)eWGL?gMoeA!<LKAwF7>KwF`%TMm<3p85y;vI((j$ zl@*K7e-Qp3ePjaRki~AkZG_ zw=67>f;JvG8(PF9Ky`$yP8X{BXiyZ>H*y5zE677onXJ1deHCVZItiEPr6*AHc$>7- zr?o7|(`xj+58Yxda^hxhj$`8{vS}OK8xnc41g7ykr7J?8ye6-~1_O%R|CmwNs%S(O znbZ0pAg21)-)r7Hq+pkeu!HAHM)TKWu}v75O6 z7AXLC$j#1vQy#){RG_01md4X8kbgxesP6mOIr;Af_Rtf?vkplbC`LPpJTq;GBYQ{o zy1;n;T3pm$tsY%t^kYM=k=0w!O}0^f#o{s9ez0vak-X?ly4KGTu)!D^#L3Tw5sm5F zI?UC_-rGiT?4cptJ_6h459$|i&owgi-7B9bBEno)8tNM8s;Gg%O!Qth4G&|2<M? z^B#oK9sZX^`&j?r)8IfBW|@?{WA(FwflgTI;&5b6vs5@_<^6B5{(~Nn1AZX+hJRe}__% zuQ|I{2f+uf-J$0>!8*AbIeRR_*b|5gN#bq=0+pW4y73GPTIE!1_q}Hr8M2bj67uqa z$0t&f+uv-#K#z2CQ?D`@|CIIPbtV2CF}?o{u3msYfoe?GF4G+{DSNA(EURK6q)O!e zDRJt{TAjyUr?e~s)wY}GtN$38%?dRg@hd-)Mg3}`rn0T$B~1Hj*gD* z8oFjQS|W)q3p*y!@RL0#nf(|i%~zhQNi5gH#y&h9r8~1txx^lQNGwMXO`|&l#2Z!n z)?3jn#Cr#ZuKy>^;tNxs%`BseQt5b{a-U!B=t@wX84bhX?xIgUwLxa(2z&xE{mD`bgemK^b5~vn_6GUJsPw#+86ZbEZbVoGlYe|w2Vw08be&s zsKCi=UA1+cK`Ak(nUALH2vn9$xS^-veO@#>9A;{=TzW(brToty1`Pyc#MELLiL zX9fQA6QN!y8((W)?^@HIy3d(<(|`P05FL(^i5>0J7wHrq067win^^_+q>+=<@I4yD zunEsgS_@oKDpnnv(Vkam@n2iHZD)-4Jy9qVHOWU29Tp$+rJ{+0YV0E|g~sH@(gsD1 zB;)DB0z4;<6SA-AA(<_=@nazcra49h$`%-Egh5A2Q2r8yyM_)M1u3Kkxc&NcpT$&| zo7qV&^aS8vcSPOGj$ck7F6ozA-6iL>@B<;l7);s54Q`Pddaf99+-n9@%6$d<%Kl;-*H9q$B@uN(Bq z)89-KcGw3%7Og;WW-6y#2RJ7UYveMQE=} z(5O^6EF~ve%ji9;@omhFao+?9;NLG$gw}nFb}T;kR%P1VJT84dbr#Pf!tJ@~`Erk@9XVy-F7N}#)Ai)d zs?H-R$3#Nqt$T5rZIUtH*e(5s9)=dfBa_1%AX|?!%;h`!A`s>k6eN%1Gp#+!^B4aj z9jYr>t#BPGC#XaWx|1ccMsx}q(y(>Vwd@$$14hi#eyxiU`~xqoVODc}b$`G4ofMTa zVyZn)|@cfJ$Uv?dHjRV=5%oE?NW8J$*2uXn9OX}UYsfA#{F{p2#2Yj$hjms zegYd>G=t_G>Gj>wQNEQ}>33DC>54-yU2181da)Zv8m{=q{%52aFnL60kMCYNb;pSE zMQFklCJuQjyHfk_i4gn?tA=ClX5B@JFCS^u#Tp6u4e^Bwh1uTcF}X|FY>Cl|bc64wvkWxUU3o477{~NS!`&(B!A&rf3S@TPPR)7w_>6R=mETp5R z?Y3FtW~Dh9?4$Ip8X3|J4w_I%lU;RPeGznlLP^)+*4mP{tkq4gwGc+ZPBwiqc=}bt zKZ8HCEDS7vn#4bAA*OPAw2*{!vZtfgffU&qWO*gN!r+5~$1GI}{fbIp3)Ss(Gf-2f zN=mJeZ5oV}l-(img`p2xT7`qG`(ReyGilaaEg69xJE2o9OvJ6EMX#n4rQ5}bvrQjE zXg+5{U9l^p%!sk9`2FZj_GmGU98LW5^Yi77oHq^GXnTQN=Ch|y(cy~5=Fb;36FEX- zHxm=1P(?#bsm(1kBJ?+%a20JfH+`$qIaXKi?xt8#!DA^tId?r>=9vn=2z-i&|R_BAirS^6vPR(Ll5E z%gFEtqc-H!Qcd56hljKHEquG=IaQBQoc_G1NiCh`;ltZ?b#-JKA;UBq9J4y_|3zw8 z+Jh6Ib8JYa`I*z_$NOBuCR35jEr%q|JSt^_bKtvf$EQPZdg2l`AV!rk;x#@@3xUR>mbaQs-3Nke0nqs?x$9 zw{J4;|EyHQI~02)E=GF*5A2LJ-8JKp?b)E8RGVVD`%CDe!Glc*ENjH{+Z!I~iU~H; zjW?^WsNJFFZXSp_er#vQWkNQtUj?=O^69$j#|M)oB(Kt16F4sQ#`un_l=;twB61yFQNHucCO5_>o6*$YJ>IGKKz2~2)0NrMjviw3+F z?QwivS(nD)=5l9!yWmrldd=H?t00l=d~D?pUL<2)Sqg>?%ipKLtFJDP`o2o4Ns|&s z5Xp$Q!XRJ^YN};oZUHfL!U&e=#w%aqYs!cfthSES@nFC>gegyEM;RkHHPK?{zjzcn zFOnESDJ=ZlWb!eD|F@J$_ZL(E*-sXi!8l5#=t2R8W*mrWt4aTdAKWtGze3IeQ zfSiB7=J+J9`M@nO)`Lasp2(44XV6MOgdeNfy2@8_S+PBKN@0)w_(k>8Qu`FD(6mnt zZZ;-e>LRqs$yS;j?o)9*wt%Hj!ZosY~o=WkMM27ZVRV?#1~&eSKKNZrhrc8z)r~b=5ah z$&~l*e{!dD*O-*Vj}~BGLN6^E-)|P4RZq87dsUkMRbW`Yvu#6l(s!Tg%IMF8V_Cn` zaaZuQWaSjlHt5u5%>NY+>hR)l=Sc=l8t}IkIc!&#Dj#jA{1|ze9;~7*o0(Eyf^`E6S49fC zhT~Tq4B5OODPT3^B|5Bw<}5aMJfz zd$79kOMlhI8do_)?}94HH-{{Mx?38hfStI92f8t?4}=@QWMlgMi`w%nD}^i1-Y%Ff z`@eJW`E7fD=?ZQOwR#I=b%tClQv{>DIqK^F_$(hzu42a6%zL;a-6?8>V|=}dc0|(^ zuIg;5Wrx`~{^(^zKQ(ETg~_V|P>DrYgbkhZdTD>A=uwD3et&RgX4lWczs%-Eh+hU% z7|kJ|Hljn%bW5#t;b^9WbKASLN$(loGf{`=MMCD}^wgL^<3is zv>$`m_`&-LdbNuKF@EFa@x^gxf${QVrh!5Iq!lBR@|_G4>$`FHFgB@2qTa{RUby&U z1*oLSE-9}|YiPcH{klZTQ%=zO%w&}L%X=#PF)BW5z4uAs*$W^qA^Jps!Ml8Q8?9y& zr-RKg5M19GC&s#V^}i#SKY*DC_A!uYRwIj1&qG_J<7G_H1Kv=Ur_)2|nh|QSo@LY{ z^gEF3tJYK52wnk1@#6CBrPfyd&CLeC@%(3b#vCBq*()_pf2dYg$7gapOUN%WB8zZb zpbrrDkz{VxVCeUtL@4CpIe3_iKzOvK&!&w5;9#Yo4K7 z$xFhnlQI9aq9U7O+>~EH06w}aF#c3uiK3Iz!J62<~4=t zd3p$&^Rg>i*g`5>Gb8q1^|l%;?D;M3N93wYfjRw`IB!u=piHO&J1HbeA#6$s2m!c% z&2)K-i{`-B*ya*QG|Zjk{L3U3-JavK4mV|?P2I!{IZ@-Uo?w$0Gkd4sQGDdgV~OIP zX}-_KER#nrL6>Im^O#lBp&6O-gMDsn6U@xug7WDABkb<441gFQ5&T1yWp(-DS|V2o zl&Je?lSfq3jjZ`A(TEJ?Ehq4agUn5xC>P-`9=AGDiU((`1V_LDkxCVB>vun0hym`6 zqH7!6ZQuufg&@o3?yk6MgB$*^yDE+PELI`-<+MCrqVXz-p&uZY3=0T+9pI>i$CZ23 z7JD$!qSxSW+SeSEb*E@a*S!^e?Kj& z+InD7MK1b9>hb8g0#e+;ZPeqm+x5`R#*WAO{DE=xJ$qYwsn(yU8#(HPkt>fL?=j^5 zNwvo-TJBf6%M(}nB<;)bGUq;S;6vKv(Ic1uabr!wm$(HS8p`mM=NA;D8Qwg9B3SnE z7TJ41*=DxLv6m5*71DN%6`M!1Q6B7rI=AN87$nVEU0!Z91Aho({J{d+@nRtX3R zJ6y?~LmhaeuRXS{=IHBOEo0cATAy5iQ%#^s9v1E!X`e(9TR*I|Z zj{IV8evpp{2!3rNrI;dmc{kiH{l5)SZ&J$`!^PbQHuLqO+HkDxu9>mlo|0y=Tr2~Y zsF{(0m%po)juYS4js3>Np;|===2E|PZXJ~(YHHDG@YVPFS*KvWC%fMNx)-CmSssEr zEX&3XztKR6^;MuyW#1t@BHIG(aT=V2Jt16iB5u6b@p#WIN+c3lF*ZlT@R5aqdcp>`|N1&p+no?o%1Hj{y7hBu&y-ieDA6WG)Qs}c)|8}S&b$+C)Hlt z+sEfC07T4`ZZjL2vcHv+JOrK7{=wS-c#oGtLxq)idn2-Yoi@gU&>cFgM1_>&`wD&D zg?|DWD90QxW$`Hentcg7L9d_u^yUM3Y1!+((b}6K=MV8YaNh*G)g}a9Yw%~rC&qzj zB#YY)oX2MD(Hs}h|FMuupr$brX5UY68(fA8rB9fCn(L{k*G(Bx#Vi43J()+R!d1xg zh{QRuVR1!6#p5bbs;d(TfiKwBKU!yUnVmTuMm+FY@2W*Pg)Hb4fz-7EQ>=et@b{t6 zAp&M!bVfecO5bgbr#Q4kCze4YW|+ox@@c1lu~ElAYv@K_CLu^=Zy}8F)wC<|a5h}2 zZ>BRztVX^WO>a;=>_&_8eLuCUzADxUSb5l<#YCA89~Ts~D0%YaYp z*>e*t89RZ(ishrO>!am2aB$S(^j|SPeE2+Moqg#VhsdIc$W?S#vcxAivs~YWa6Sy0 zo#zz4U_ZytY@I*j+}5u2eD-iMAw+H9AmLAuxwV7GIx&O~xWZShm-?cZB8G-E``1Ju zFyWCG3Z(D5qdl!`2_s-qYAAYBViZodp)GBJnrr?Xt3}eCr(5~$Umxv*3GR?T{)@)K zWzz)bin~8aH#!@J@;+?M3EA7`KEXb_VUC`z$YrVwS@YLLa^e$PsoaR}WNl^Ss}_jF zWg9+ShBqSX9=o-b!pC-O6^$sRO3^aY=?$Ar_OJ6QL%7O0*&Qf*_Xsj71{uJf3&t@9mEz%G-QKzZ5ApF$TOn-km?BZbnPRxqCz zKT(BWv`rRkvf!r4{1s;)LwBbuQA0kJHih*R4uGcCaIL)dFdW_{5JI^-1-QbWR=oN; z*3#nAL<-+6WrO-4PV5--!QRdGZx1Phi`H%23bGi-v(|jT-9HmHCH|<*rYDXFuCZct zJ`T{>nBX`!SXj)^@VA(0ju}{=Z;mOE=3M}EX6pE#C=UJcc@z2VZ))rxqwYk4QQ811 zUohiv>{jzFIPo?Y(XTFq;1`;+g>~NTWfic`et{RsaF%IW-V($K?)N_q}Aei3i{ z0c?z;Si7}x72Lw%V2sLOZEt*!fsL>o?LqT9QA^2i)4*KmDmq;065j zYiQS&iIa0Qua&C*K~0wQ<>~7?`UU_Rk%k3t=F@h?4J&55{t$30D!%ezOcb~!B*j>! zW}PG0JZAog>ol%kz{sd04g$pE%!^_n4P6QKrCrXwg{QqcP2Cyesga3uNo)aLbx{&K zdk?Y)uIh17(n5!Y3V@r@0CeBwi4_PvnpQgdIiP-*2WggA#G)kg>BJU5KK*XW$BVWq zY)t5Pq5glS9l(C~FlqD94Uq`9nZ`he$z`1gGT}RD6W|)X9OA&)gj2{lD<-1h?D)Pv z#n5eHGL=JEc<@1RyWo;%`jMk27IAa?lR0KqW&0_Cz8Ej8gTM>oIsJso7vH-^?Jmco zqP=5IFRW{v;&7eQF0p6vSfIa6CSf@2v%-&g3(yk_K`7-uv{1RpJ9-1Mi7N$W6A>bZ zlON11WKh!u2fu=T4TcYT?RHD;q3z7dQ}r}1mqTMd2ZM`a3i-L5voA*Qu; z#A^4|y}>+V=yN)ruRX!FiT1)C11h|?ejanlIeG+#aTjeYv(Y3#5185) zJCHS-_N`~s-Nz&{F7C_3!kpB8Z4qz7$nORb(n?NFAoo7G%m<>Y02UpU@Z5v;vR+xW zoE)rf=YS6>s=*Yt#}T-Fv@|S=slDi7`%s~22#bnoaDLcg5e(NQB+_8AB=O31K^!&C zZQ6+rdj7T0MomK*ji9iRyIidh$9o)#el8zEc&^5F+JOX1wd#aFB{^}4udD~sv=$3$ zv1KipeQG`)Ps>k}>9Ajwe?fH3ed{{q1KwtQFeE=cjNO_EP3*wkME`bbhd#Z?2r)rX zN7L}W&Ra!}@i$9fL6p}k}e`lWX4ny=_>|YWV0vIzu zRP*hhkNNjd`0!9~jo)qH@Hv+V0P8d1y63;v%S4%3S(Cb$s*B2vBr#67e=W;T?S>rg zhuUzlil{{tfH8lht?3oHz2W*yq39>Kw{%q~fr5#SU=Ca{{QIN!((^aj;Pa(fdNZJ* zFm_8wNGPJZlw1&p>N{_RMSnK+>2Ko+88%M3cl~CI!(%hL1w`=${`WT7RG&amZKd$^ z>6MzZeQiX>^Cz!7m14OtVDQ_{F9}vbbQEmw&}9YZ^j{Z`4fEr-5~kBo6^Er?{d`@s zb~uveAVW1}62J_2s~(RX-?pTYCoMqKAaqV@T4%>zQ_oZYf`IQ*67m<)eC8rq`k_3iF7TGT0+P1WZ38Ih?&tP~uFI$jgX4r15d^Ssh^K5;AJR*|msKFed> zffBnqIVfQC=zpV|K*j`2GnGMBcR2+$q z2&DLO`wB3=a&{HjZ@(G*#_)Mc_wn+{9zX`MXN`FpmuydtFCD6R=+Bj}z~B|+K@g?R z&!2x{k(H8=xX;Cfp49jS1*zG~C4tdM57><&+(@vjZ~{euC+f-(+Bg8=-|TXtW@tTp z(HyImctJ& zFJyb04)8t&jt}O2KUn^`#&e%Ov)%YeoxI)#D@^zL5ANum9-GHsta3v+Lc{XH?2&n{ zl$Ol6QxkddUVD3ggK7v?l<(Ma;Uz^xyUf%`LAD!|#4J}NM1P5Soma8=%H4MdCojvo z@#bXR>!F7$k$Q|uiHOqesRalhL7!FM-L33#cZvUEC9ifjEB`h+O7Nei5aVMkt)h7H z488~#GP#fNuyTFkh9xm->fNxjPHJ=0RBd-kehRFeTS_Bp@DWewMAkgjk zt}7HtEb6vz!P6;EMf((V5EugUlr;4gzVu|0h9^T)XeMB}4Z+^8#fk=7gnjlmtnu`? zq~@+-Pf4kZV4G6s!H^#e0u#|SN7uFGqMOT^RX@3Ox?~oOR39Y&*L(#|?W!nFMyZtV zDHq@AHKG|PIxoPi5eR8q^gNN}Se&;l;+bHrX?x69 zD#o^mDc>se-}ey2&Yx8}N6M7ePC61v2)hn}@V)JLfg!zeu3#Jrlm0qglg*cpVBA2= z_3GT;C*24Qw&lO$dN+N;+^;stRcXSAsMz4@cgwLXQ}_olg-%_P8d4Uxx`Y-s8 zRV!Oe0Vq?rkONJ{65oB)ce$I36nodA=YdCTG3!lw3&T*!o~8mDiqJn0K!BDIeNiB6 zne3z)4#9ba=zf7UboKhJU%yT|{fU0UtT=W>(T@2urZIBkpAGa5{E?+WtE26+NvnhywGZKDl(Fupj13%l=yBE%Jg;I2pkG6`$6)O|4niG83~XV z=rN;RD^av)B6cCHf2RvAyqNP7y=oME)#F6Zu)nE3r<#69M18@UTTHcua zi_>NEC5*xlj&Y_MbZ9ah%OVWnew!VB4(OgXj6Z7JhgjKAZvp*&iFF?D&mzSBQhN95 zp)JCF2B+H4((N??m97VwIR`^Vd13Wky}X%#*xaj=^RLg1lw_3ZeudL+S$*^Z&{p5^ z9@-m#uqitkb-&!)bT+^n2-Vtau$Mm146~j10`;OnTLd!;4HyN>A&j4g^_RewhC(m+ z4(HPeHzS~3gFff8x#xRu)ea0rLjQjT@8s|Ak3plk4YzXB_ACn>JMrC%iVV}o5=v6- zrDAUj!x=JhZRDKx_cty2Za}8P7p*(@zp$_)CpjhkxFq%c{*xDVIBg)z6bp(js&`l1 zxE)RY5wFX`PsWrn^XQcER!DV@Z&r5ITvLG7c75g|{Qs1_E`BY-7`7hxR3M3R1M*Pq z8q*C}T=wBVK{z$Imy?ESaBFMDbh_*onmD|?E2Bdai9PqvBQImF;C0)xqC0m#I}SQJ z@sNyrpE@|uJaQU&Z{xSMyFGHRM@rZrhna>ojFv_rgPOiPA7xlV&m4?SR1a!R8b|ye zu=tc6d)Ma2a=R#L-1`I(B%1R_E_UuGSyu;QB`r`KygZnIk(BsCEsnb(Aj5G#HX^8 zad*nLv|h&D48I>UOBBksbmbG=Chb2d8w4td%3wA`4bmGPw6onI5C4MBBWX|x6PkZq z+Mym`y!FB0%`-cZLt=+rx8fy$`5&Or_UX_@{)j6t8wavA^9m~^c5rH^0Bl!ZYj27m z=ffQraG*^Lk*g#9n4EvA6R-Df`GFVw6UT_ozh@pSQ$&fv$8;sSBj4tUby*FK&Vn+4 z5|-KBJ)~1W*Aw31vpaurhN;mY!%3_g_$;5d7Qt)*B?C80r|g|`xQRKKYe(*UG;|UX zB}oz;(Co64;%%lBw*8ELr|37h6g+A_` zhmX(5*Z_g;=o80P4>oUq=-@P)(u~z10YTYTG*y!Zz(6!w_I2+!98g-`!S`v!4aN6A zfGX*w9i=8ius?`gWs%Tr>{25v2om8GAdd`uLh%egJpP-;mx`KbCzce$=Uf4@{!c%6 zQB2Aw=T|<%n!t>sL?lcyVB&zQlaynC`^&j6&ZedLx_o-_M+qDAi96#%tNRs4Wf&}< z2bM-EgWzX{`l~^#7k9f0N6ADjd4J}I|N{xWthF&j##T%RXtsG{V!+Y&x=f95{gUQoO9~Uq6 z;=c|hR+NCqAUNw7<$z8t-%^@eM@^^?6}ao6&!BRlD}@Ma)#|9+&(4(8#IdSTk~*zf zW-2(34O}?Bn1Y)D9vpWAD*XDUCJfLB)F|{JFZA5emqWJ#A%?ZNx7P&b_HMW+tHY|% zD~c@7A?*0L3RD%Chnq{bqu2mNM7cd33>38gcsi~a!nz7g$2v;?o<~113fDO>Faxp^ zdV6~FIi>}h*HA@m=T6Q=sz(!`l_D;S6gFv)rc6wEO3QNVk!wv9*0fzJUA;t#)*fJB zlF!eM8;n%InpC-wo*V$5hEP>C22QW?rAvknWyGH#@(0K6E_5X{U^K*?N6^Fs=(lZ} zKUjEutZjAp;>BehO$wEht|N}XY$_$_`hH7@e5dtnjX1_j#WGq(LbNqwq;OX zS-#-%ux_5h8T^o^Cn4=#^_On7=44&9lpe=x-}>l?jM_OG1nd5V5I(7=fmLZ%D+Qi3^=6-{ zQfB_A(+!xd8=-Y!cAsr9d?%0Ld}oSGt{@sb*VywtZrpt7)q7;C!Jk$4O$Q^1kD}?Hmc;zGeBlm zKr)yzvl&vXYE4`5Fx)pd+MZi3mI}P{RU@}G=>(mJ=bec7z6I`sB{vkuf4F;jId$C* z8jl`K1${ffqcxvcNm*bCC4BCo>z~;Fo2ov)9r6wXrr$WRhvmDVSdBxFJi*nCHKd})a7aZPzRhK3O-!W3?z`qcV&Lw zb}|)l*@(>gD=zG@SX0W%|$aPsMy)eTHUK@RHDMxybt)pt#;fc|L z;n{s&d}7_6*Z1%l?a-b_-LKr>5{Tf?*Bh&~8WSwCp3oz11k>7Au6l*LC*QtrRZVYf zfv_@G>1-;lE~8gE z>-<~59VYnPyu}v%S&T2NQ{F~=yZ2`h4bRRu|Moz0={h5UUDG9Eb_j>)RaYQ)*x&_^yl7U--VEv+1|Zz&s@U5fLIsv*Bc%K2fPdXMdjIO`(fI zARoL3OV6@fJMv&X2xjTPJ%pcU@is(U5ke1ZZ5v@&+gp-Dajd~p)!mVrRZ8e-rh%na z6~Bur=Jq$;+Db2DtbpIUf5#>1}lzQ8qjm7Rl*@VTJ-oQjme#`E8-G}vaW^9!HI`#}1TII7&8VuVOs=eC^ZpH$WB1>FuT4uGah5|OTdjffDt*9P zgLEd2x6MoC5{GiKcOpKq!n)}B>mj4JiE}th*Tg)2Tq5>cT{T!}$1C(hQ9!tY*q#Ps z9n!VvRU{Kvi@&Bhxbp#c5G?4vED>_)Wx0#o{-VN8t1*d}VLYUg#~M2wSdO+zPrrwz z?APyBDlbQ7Y%kIkvBXTw?*`|Ynj+jUi1V>5_lvr@Q{ri!&!##B=t>!|*22@Wu3V)-QcxYNetYO{yGRas zt0j$;`p)s+_?}mIri`^d+3^w*WF<=L^+C2AiU#TRE08H zXr;)6_Slf>ha;Sjt#=Gej1ZiW=0_(0kefe5?9(=?8*@9}_gfZKhvv z!4Ut}M3U!Ih61Xn7?hE3i)D3~U#wJex0go-@-7)Qs_Hwnj8CZcGio{shUqr_h1*{2 zB%yU*{f6vrCf?Nw>`>aSQ-AsL-s)=mh39SJSNpiZE|cYaXcr#5wAuF;cHwVezjcXH zcQ5Cqv_^W!>4DFpqU%lvpPE#u_?`XLVM281e+AY}petWak7Ea(;Gm!;bgaumKmhpV z6}hkt4W-CwnZs$u|S+p=NmGGUs>iy5;rco~ERRDP@6Cz-X_I>%M`MKH;QNp<7jdG73Wp}O}}Mc*tbtdq*-D;00@N%y*>7gJ55M=!e) zIYLNis|I4OP>2c=@lg8mDN3J$j(_6tK%leu%2N+*nqf}!cI}rAGkNVHT$?;^0GXHZC1RZJ4iwc;)el*upVWJI3;2F-1V%Ln4bN`aXRm<#egP3D~a z%Jg=$;Kfq6XMU@cX;>rN(*qfD$Oz(zTtz$XiUky{WJdiPW7_#f$NkKo-eQRt_46Hx z`Wj$LBiXmD+|mF(y!piP`xu*6+3ZHpd9h$8V1*17PuXnSNp|=v+}?cYitwnWa$kx5 zS?m+NOS`CO=j0>_;b`D}xh$V`lCm(KI_cu%pS`p3EI44Ht@K*fs{3TM;rB?0(c6tr zJjcBAVqE%(I;x4&>R|e_)LvkU$yjqnZ-x)c+sg6@9Ub)|ZDJk!+OGM~Mas7bOujSe zhVn22wicSQ579{Ztm-3ya)Z+s0~-9TgVpPc(OcEVqRC^~S$WZB8#ze^boRXmp+}!K zbl16^#wlbtwbui>bgp&H57Ok_UqSZ{Jw9VVL{gii;xfJw_TYPSM7uS!Q=Ify9r72c z&)GDbKLZlUGA5Q#U?WMup5bp1rxX+9yIWYU%w?u0_OO}|go7al&GZIO`&Ia^$EQpw zEw-8^x|DvUcIR^J6--x`JX*Bwrg?*txOYJm{Og!Ou|f`=iGc5SrYp$%TL5Ov2y!Y2 zCo&&9+UnwQi`!zT@!d#&a+6fpGY?bLT<;3&#zEa~egdb7gGSXuXUcCy4}##b?dQzT zFTXeS()we_t)0P@!(?@Tm((HCwUSC8vF(u({+ZeM9pfQ<{pRpo_VagPQJ+xewYt7i zWE`U>7Ho(8EdDWb2GTX3GN_+8qfQf|aIDg9DH98TnpZ@}*7MQ)GOY)&`kS*&*MqGG&h-&Ez#8FdrRvcm{bDVrMoJ>%Q zs8U#b9vT@*0l^vFas2Q+L!ymv5@z|M=ZWaD{Y&ZHCPwF&JLdIeZ z-_O-|TdZ-^*wVS3cFdy3tS?(QGUk7q@ad5S1$96Vjx)}QqD zdZx3B#L3*BT0U?8wi;6Z7UwI#26RtLq`eh|{pC_ZrrQn){j^>MuYMJhLX+kgxx$_v z`jt~y3(=k;pT4J>gS6OCt4WL##?GS-b`j#V6kb@iNaSfv6hwnDsiLgS9jst}F24DV zLWZY}nj$C-SUELDzfT>k2fmEx z%N-pd9?#}T=}02&zaH&Ln(O?j7V(uFaNt`eBKokK<9aqVO91Y>SoYGfLQHToC>w#B zW9svgxW_w*2-ypk`3*0LGTW3Sb9U_fjBvghOTw4jymNpljs*RK=0rirAC>L4UXDpc zwMs-U!2YcH+b2!fyIRwpg4*-wHJ6&UGs^3 zyMjJ&ENepVn8cJI2;<=Uxvui>9lau!HB?$c+e-&s{RrE_&b)}6P0|vbroW#m`(mXK zKZk~gzk+;Zvf9`-l$2u`29l51W6NzaQ0fe7k?uB)yr1-$trboS6_E?m=86=iK+=X3HL`8TYc);pIVvRDpIaxHT z=7esi5<+k+SoEd7xOY)#OIv=G;(T`FERT@mGMe$GlK0Of3qgKTySr`W1`30AhhHt3 zh1G`%6BPxl6(b3UU3UE4M3m=`JLb$1PiilEX(tmojdp*%KBKpnbZrP@CzDvKrM*xu zO^#GzJrpEYI%Jcvt*xh?xqZIChisDG|Fv4V&y}K_p}DiOGxJSNoUd-Ih5AGKnXjHv zIt)9R&=NO-l zW4P}3rX%?)fp}FKwb8b*d-{WW$QWCDMT!Y+Zw-+%X_jER6K%m#?NTetVhtq|m9nTI zLfFs;%MXpBR&BKDBqewUiNdz-l9Bm?^@Z4)hLbT$&+E)l{_`Ul$a}*B2Oh!Zxi!bSy?gZRurM0-A^91ci=qLu^7YX z>d^63Y?zRE*>T;*p=8We_bc-DX!W{9-*Y5VkRW{ewj-OorLR_uK&t*n^KG@%5rKQd zt*3P*AF4&%69_^RqkMlEYdFSN68Qhtuo58@?ieTAVxKFZT$hPP1n=i=b7%>UGz@P} zC@Q*72WR3uCQP_$;c0!7{Z;7dVp@$ei>K)Mp%LVvP5INQ_-(!{{{nP>Jw16^^i+&vbVK;0tA+Pi(xMLcz(_lZee`>ScAQv~f zy{pT>=v(3>l73p6t}CQ7Ql{MXmH`v5o)(tMg1wJ%4szuxM(J-a6=C7184(UUsB*RV zSU53jO&C7wyIwRgq8G$ku3o=1pWe^UEilaI`2E-V0bUI!ne~Nvf(Co}A_4ZZQg#Lg z$+NTHI7^brm2w4w8^BTtyizu5!dDW}JM*B0L0~M&wc`;%4>#cy zzZebS4H3D?7%ddtkq{My%2<3z$4HT9#-g1aUQyk9<*I$@(tOAH0m+gUX1-M<;u=bS z^>VdY`^CD*%RBG+awRwCdCb`QO4F9-ac|YyI-8r^rx$Es=8<%aHgyu6H0TettWcWY z9^%5M=!2xPqFi*zGJ;Qdqlt5#b%aa1e33C;*zDA?bp_c%t>LpV8m8lL_L+khH0E64Rt61jmqmUjio5>F z-PzqOV&NZzJu|?Q>fs(q&0wQ=@tFnz{o4mHf@bHl_1t9F@Q=;Wuhnz()(*3 z_6BN*N*5E~|Gdsl?^Q`~W4Eso7A~om1FQpi?b_~Aij)cVc|bockY{%2=fXQbbJSAW zhd8>U=$S=hrSWwHTlH}Z*4uY<#s?h!HDLx)H?d)K|Ur);pq$_M8|Ko?mKRsq}L8p?R6uD8Aj$)zu z%@D)zy>-e)vE27sw4F5D_ytSF_2En(b8Oh@08UB9>XX()U)V#UutsIlKKKw8?5=k&CKTVnr|uA8yv zGS$Khd@BD11ZLUnhqylLzt6n3e#@0rLvy%Yv`+W(+!6{Jp`qC6EKABHBJr6# zSzgbb%^6o&B=G5g9<`YrkGmnluiAs$In%D@V=$<@^yLm7Fp@vsKAChOkv zHOQ|p@=F831+(qy|LOw8&{)s(QVs5qol^T7p#i3}6{7=1ds)e?NN-cXA}Vd#~v$j@nbt)7Hk+zdCmm|!eR#rI-dN7sHlA_(4_CEV!uE{pv; zW#stDsJ}hTo*h3-1d|;OTwG?G0$b?m8Z#6(lNl;+5NXqqj*5K=Y-{4Z8>Xs&Ku`+1 z+y;rJ^Vdey`?6KWEm#_E;$VQe$jUbN%yKxRM|}F?0qrIGXH+owcXL<@+e69vi^p=C z1}BoW9`r)}7O7x$Ohs=ZLGy31Gz!dz%-9LJyMQC4b!o`9w_?zvmY>=RKX?4YKaFPgVu6Uc*srj#;+gnch$W$i+j4@(?U;BV-8zOQPbx0C+&OOL~0 z^L!QaOGTBnu|D6hSiE6Pm4arrw7=y;?m3h<*}rwHSzSCs@egA0*7`2_+2bH6)CE)N z7ftW9>I@j^vJSf^QerUkC0J-%@{>k9Eo=-#TjhEECp4tw2Agk}wvl@Ac=)6BeaWqUta$_z`*wGyGQn858plN0e8d%w{Mr z?=Nr9k!>+0;*fvYeS6u=V*6x?zdw>K)#&8t^SojnXhL74eiqIp_NU~)#3Cj%1US+b zj^@m;X@NT7?1sU*YUr%Z)4VIu)2ds0_$z$10y2D6OJxr&$xEVGKUTvIm%yFIorS&X zQb`)adYoD*;MhX;o$@Z%wakjEev2kD2c^s-;eOka(wcPNPK&N6e3XB@pz+P{SL4RR z{p^W9rtJ=?sU+3GYgJKJ{EmUnI8_GMQ1q?6!9nHM)B9oq8}6?S9BfP5+O+V5ENkH= z9nNT>R^IG)@=~)(Rmlm!0)UTl+iTW8*d%PU^&1>uY9W!Ck-NO26;_@jr%|1|&>Cve zQhg6gu=jej$|ZeRvB|De_Nlw^{>iAcvLJWsJdhw4_HMb%hDzmp_ik65Z;@86%AFD( z=(Du~R{|k=uk28jt9`R?JepXsFi>E!EdS5N!;TJ0VK)lZ$VIacuO6mV(z-WcQ7#TB zbOnB<67)Xv4L@mAP4BA;o}#PuHn7S(SpH2$VOXQrf~lmzXX2wID0I_EiNYRp1=-j1 zy}5Go^+Lvc6q+G@vd%s44f~o^*AkP42NrW*7gt7-i>>qEoG6JUH`jOLYK|3C%2o<2 zM&_h4c{tTy^M-vj1l*3Dv*LDLx~z!j2{U}E52Ayf$&q^|WqF>Lqe7Tp8yXt+P1KG; ziJd~#oiIN??+e9WmO_ravAuk+rB!p39Ws7yh%WtvJ1@4GW@l&s3N4z-7UPFe&VRp@b&%%{nT3OV`a&BZhf zwk^3i$_H@^PdL1KmoSx|=$n^hvG?TZ=c#y>{<@CMA(w2iXd+C!hJ#nuhaORR340N+ z+L^%j;0iLT`qQV|A}r$|M%80;WE>J64d1`pPx$}Zd&{V(-uM4^OhQtSkoo`uBHc); zlz=oygLHSdK?n#)NQabkHw-z1v~)8JNOulH{_pvGf4{TVf35T6#Dm{D>&z1wXS12T z_Z`=LU)THfW>Qqwp8(p>Pjv`AE?!=BH_r_2R1SI5UN65PL7*c0F>EJ`JynSu1biNq zcE?EOh6RAH9Y@YGR`_7R``S!@z<8OLC9P)V+Q(SU>Q14kcN3Q1HlpGu{L(!8)2 zci%Rir%Is`4KEjT)5_k{Kp2)X^FCPMrC~rhL95v19mU04P7&*=_rt^Qvee!gB9HLJ zO>Ljc#ZfWA;G)dxN!T@#t}ai9S%JL zX7WKjj7ArIEA>xf19^;`rkys3-`fj+91ggqP*OO5$am2al<;e)YdNAx!&Y8Lr+rhk zPD!c7=#E~ev|$yv(le_m4VSu^xaxzDZT@t?A z2BVBjOx~Xd=i^$o)-^v3f5gWA&z~-LrsPzpJY)TLR*8l@-e)x2*im zR6=g^fTXsu-C+`xlZ9tWgcL@)pc*T&)BVob8qwNn-~->FlZ26EO3}V;bvyTl88)J8VJF_8?J@0J3M>$-~d?UPP2Y= z2w(h#y=44h^V3$X)yGGLo=HvZ_|gVFi;gaJrwy{P|x`m|c6 z@i_o%+px^`o7Hl{=3wV+_}XAeqb6^6DjKh`Ws#BDQLuY%$?DkfO{ey;*}0pXf#*pi zmG|nhV%ga4Fqq?^6|z zz-#(O@&xdtuC>EQj%GsZfCFL7qnpuUeL?4TXs?UGoIf3vm>V6AW)WHR+baJsZURO(1+FfN8wz3m{?fxXQ}=1K{mgJ zeuEv;iIQe2#{lwevN-y^gz`rEgHGQic*0iUx~?2AG&*KbuxxASC)AaJ_KEyZcjo>q zi|2r&Zvg8<;f@%B#}--(#BEqvW8^AF3=v;!oAMO(?# z#MH1}`N$>b@d#m4hxZ#blJB$}33?0S2}v7VL|;A-#?R=kqVbQyg0l@(8FCONi2~C? z%b7|Bu&(+rF|xa1Xwf65WG1JeaNDwf zlo%q%53362glrLSnvLIE%?t7_*5R9Fcs=ZgCD5}^Xi1W(cYCkjJu8(=r2^P~k7ikD3K`bB8U ztw~aINS%Y#z7V~H9$nKz95QqTm$qAuF37=vI>6I`4Y0HS2h=Oj(HRq_+UL)nYMH8_`v?Y6ybnXDlOe0?g#Wl`uc^Q5AoY zc2BHx3k`9#I>sZuqD!(?`lJZ68OafuUVF0e|hIiWf6vFN7S z4-|X)IHGQCw?8(k=KL5=U@I7RNqI0&cE0%Ts_|l|#|D(SKXw7uOHuhQ3ZbkO^OCCA zgE3`xo1nFg(`QqAtDOTTl7-}X?{?y3SKFuVdND4uKH_r}s=!5W^O=Cz7Yn9dNBadd z%MLT4`88h8jMtqZUY|MPD-;}lEGTc72 zc$E?UR~txhRvIiRtA5A%Ul|-r8>81D%$wbqk--MIBkg5ho?0+6T~)S6eHXw4sEgp{ zt|@MEKkI7m=Eso?e~L^wnyn`rpu+RZS%>pX!?5)%)ZnMi#`|Q8lH>Xfj}1tg_IiGG z8@v6r=4+YSH2_N;^L+!+yCPpcpZwmC`}|U;bNJ;p@@b6a;;X_O7g;wJxD3#1y=q9} ziGGCXYXy^tSvW?~bi^67|G-{}QNR$4md?cCGRTzl=D+j1wYe*plKZ>8h<9lpA2 zN8Zm{xG-p>_{+VCmWcGHg+8}Xg=C<5gx;a7x~Mj9YR!5=9S5%0aa70b9cT`xJBd$) zycGOt82wxCi51dT211 zvYiy|%8}tPcNdSj8T>0G;84P4aK#HBbz1Yrj9TiNT*i=d#g#qp#+tVL*_~ugHxf3%r#d zq1Ol+icc?*6dnbnL__b&U)=XN+0U2J2G&aNqCR3!d%lV)-VI&ImT9{d(?0GP4!B^Z zquI+5YF8+2s?QuvZOG?z&M~NP=RYi_zGLS*w-K!!BNY-M|I3r4AG&+#8v&du*bQ3q zWj?mXwo;SJGL4$Sb|qm(4xT0^bcbv)Ch5iE1iuyE$URM;BMuwJHyC3vzmqWhVW%db zqDb?f3)4PX(#Iih9(;i|u&Mp}2H0=*16L-^)T^yD{Hfh%LKOMtOv zIPsiTQ?ZvZI-ZLWi05Kj?PLx1ftujG3A1yG!Q~-(8+{Yh1Qs-KnpyRi$vZdYj?Jn| z*3MT+W3T@D9ryRI>8T*%>Ly8@E0G6^XJxuAIZ-##g%?fDm7@`U0 zk}m-m&v`J{*K6FM@>&1GC=LAmwoVV9HWx$A(XmlS)P>nMag(71YC|h%-+Zmq;Tm}#9%g) zsRBxXf_iy1-$Mgh4qBksv(-QC+|`)!hm8S?D#1U3%fVe@`}ne$e+!U#uv~|e4HZ#J z*h|3d{KZYkSD%;GM(R5N^_%wT_HGTOh{ol&xUusK8cm}cdA`zO_Ko1f zFxqrHD{grG`Yo+K_TZ5(aCg(IY+B`0@aaXH)1qzJpR-9>Fq0&(XetioQs|WmLfr@F z1wVu_M`IGHE!LWPr0{1FgY?=t@PeAqYT4VGSSz9cjLkrx3@WVf#jgxC145c{z+ha^ zjjCjVr$EhZi%&yLj+$jd8i5`1Ouibm4ILHY*Sj%T!;Jba_(J?Ap;~lUwQ2S9l5Q=na5xF)_eZW0ZMIW zR0z!p=JT1VJkYgNUOro_mrZtkpWsx*?wn$*D``^J?QP2F6_o{4Ntm7|D(cq*-myxX z*7#M2=3GE?b&o%=Kv(`qbl_AhWYI-D(8l*&y#2M>NbQR1#$L3o@>q%&OU9^k%OZ=FrxT)Wf1?OykZ6YZwMDpU+fjyc|1jFU5B=-1Y3gZ_a9-$W5k_?oL zrPICE$ob;QVg`aP00Dp@n?f&aFa8;K7crb^m@lngjwi&d&fVRVBNa$UwD~?`1_T70 z-uWErnx^Y-7$X3%&5Xaw(E24{#ziN%5aVq#*#@U09r=4zZRKcn#p}&}CpG5NSyK)DjBs)+Yw^ovp5u z#<1r{+KtS>FQ#azmZBS1dWJ?+>OM(3jT6bs~+if-9kPQLjfxMUnNmCihY+ONf=H5E!^hHdf?n+006gl7v2q z?!oFk;P0hmq2pqHW8lym!|-CcQ~e4k(1_bWNoe6($BB;W*Z6hJms7l}HsN54ag)&T z_ImAW^8g`Bhx$hR&OX4-6;^y-J_oI`-1E>_<88o7gg`lfE}<#6V2bep^{PB{8abDu zE;-*M>*sySykPFkiNnc!^20w%pYcS$5d-~za1}3n$yGjwUXMS875H$+=YM}p8pG-Q zl+y?EU|@^;#j=F4DtBzZA{$&;tA()Q#Ac(+kq^p*Erc28Z$;uhSsLL8qX@1Jynl^J z4|m`FbJX|b*+hP}=Ev{n#DKyNXeBmugZj>F(7}ZAux(NfbIBsX1m9ThUZD{~~j z8L9cCx0)W7miZIgTJ|{1&n_h2I?bt%*UqP^hAmm~4{_xR+HSp1zb}P zu#r@>K{g}PQ`s+;hyN5^p1~S+{U~Q85VIp8YxQ%0{*Y8_#2vfNSqlKi=nv zV$BGDv7{P`d2W1Yd{YA%+haEVPS=Tr*?2_*o}O^^qsk%I$hVPy=zqq!FpF}>roM{> z%C)U%E{EnY1a1_==EEov6ixa9vH8Ru_FuegpECKrIXnzn-IraAy~+gy~dj2z{*ZDtK5g#+$bg3_q$V5{1ZrBS%>m7QLTz0>`sgvvxxjKN6>m!evPd7#+BGB>G zMz_}eyt(&Tx&r?S#}_^6 z5vQFQ3#W2Tjvf11;yD}#PyS0(<{&<8A<;YuYBmDMyMm@bT+}u;(F_W33_IOY2jas0 zcyIEl$rn2tv`HgOJoYE)+Xk1N)rtBecPf+klSN`J_vl`%>nTPJn7S|$(a_L{a$|FX zgzvi7?cvS(dkS4SjPnFG`7C|yZM>6hQg)yN&oP;Qwj;#z>^PRVO+M~t1?NVu=ip}BW`9J&STd~#n&e3 z2U6gSXeRb&Jt916c?}HA?^C#2a+fFxjqKg)2{&KWv5v~GgcO`#1KwBBo>Oddu#0y8 zZz9?U4xyG6S8kY_{D8V|#fYvN%$f(`(ox`+DSzsK05Amy?qyXoF!XsVVS7wtV)}`w3AQ zQi@WBYxoBW_Qdy$lP=Se%rvWW(JS6)1avp<5IRWGZ*LEbz$ymrB)suQTQZ-SL{r*t z7T3=6jvav|(tc#@his4SjQa>3 zW-4?284rNLuMVI5G{q2*h}ne$$0r1+I@FZ%?WKg92~NfD_ll}rQT;ovqt_2=qrG}I zH@?+eQ0?!yG{?z*{RI}QFd{yGsj}6w+UzZyTv!^#YT@rp#Apz3=O|^Q5K!4NY;0|; zaaCAX!e*}34U<(=3z5Yl-Nt2BNU;n1C#u-tJd#GhqI$ORzLx(jG+AJZ2WI%Eo{V?K zcHk%FlfPe>3a5u+74i5;^;p9<2JW>sQBqNKjG0uMLr!(@Wu(UFlk3Q3CrbbZIlc*0uc?23T8biN7ka8upLdu?LwG z^-jktyimw_ZWr#_YN44w{O+iEm5=SX3*@5t0}}RJP+~1$quvi6z_uiXx-f8KCJAhg z?!f4yM6&oFQ1Mx-N76h;7u2bof&MT23%v+ucVk;yAUx}eR_fm74N%X#&Qe)Kt?sRTBwD~a`cxWfCUa&VelFNw>_`-P zRIi;RkcYMeIK?E_pNofokqmnK$s26CShJ_R<+uFvN-F&Ah}K)e20;F^7IEEBo=~up zO$VG4-;~zi6xuHPO%hV)NG5o!m5btG9zyRuHe!^`p6-ENzZMuW6859flh6@0n1p0x zRVMSy)?UkPSw^Y6wyr+M+N-|T+?USyn zY08yf`?Lc4(}V%<&HX*HV~UOe3i~in2k6E^@oaYMMa~V}jQg<$IfSl#H$DZQj3@tw zR+t!UnmA1W!~51KAO&0oc+)YK-_N=G8KXf_kg7@Vls~}O@L+F^irR&7MSpG?kdTm= zK(>xLwlJ$O0Zxn>5{}30El+4Lz@NI_hXm@V%5TfwIyz6$_JSHXbXJsJ@$&7yB$JOvPIMT zh{G$_tsl>qDypsc=#EeG`4x%`wr-gi$wb>2hU2JCY5m3zqWgaa`~w|Lcpb z$rz|Vye7ekcT32GS|{+ag;*8cym^_k2!t^vO)325qtM)h936$o_ELutd5F?(V>x_ zlI!Se^{B})eN@hiz-Y7Ar-g%}G=^!MuIn6WxfJogUIc2F2-7H%!v{K}`lKDa$5JY7 zWJRFIM;Rqpt-5t=DdIJ^scCqm`qxULc6xnow!3)iy8YhHEeFQKwCN{N=f6a#gRvk| zPLtXeW};QcB`R5DZ{Wa|)M^sB%zlElGBxrv5c$hpx-RbYMB*>l*ZJpB-ijxP>V0;f z!l}5fB43|9Al3UGba1FVSbr>XBP0i(Tb-L<)lHQ|8T>t*a_^z?$kDDlZ zwFi(_hJ>HhEEOVf5!W)`u*RfM{Kxq1`wfF8N!j6>OTSB$M4}4`bjE1q7?d3Lu;PyG z-pd^|wMCJ;y({$o>tg~8#soALgxkuX`wdhW9@2I&nP3f?>kxxoL+a}#4A>g{R&3CF zE~eu$cs?^RI&$gS21vYTBH1C&VvQ4EsofFcfGzEj-Z4T;yz4L@Sppba*hDy(U#!Nfyw&u1c;7Z1m8_C>U@8Wx_*WWm;`fDCT z?BLVEo=22qm&(|!w8R>e;|;srLU#?^2Vd<=H8mW4-2YfeexIUZX@TuKuUv4UxeVv|hd$q3iq{D4WKVkQ8WTv~Ui289= z#T9H)hZ~d5e?q_TAd&LBS{J?52pfD7%%HS+5j*zt#Kbq`P z3NaL|;}c1<5#X-fR?w2zi+Fc(%qM!?mKQbq@_vA+ixSHZxe()3PZ_lR8~c(>!>REykB#)XY`Gm}*lex5GF zw`ZiYhHszv(bkG5O`qoJFg@+fh$H&|K6~@3r=HiTlHGvSTh6U-g-Cd)u)2R@?aFW~~r8VRD zBG#5$3%|_z&(aBewM>*=HPvLV_mulAQ_T3C&B#FTaGuZA*?g7q3vX_u0Wk35G+BlU zvtFkjssuaLX<$!Y`+k#PaC$2zN4;n2hRiuZ1fa$dDex=vdZ0}AxIe!=RfbP$;AwQe zLUWsVeI@T4QZ~1X3;A;!xHSHQED-LoR-NV@=wP*vQCfx>sNKw1c&9iS3Ym%-gf+?(*hr4~ZkS zU)8~LN@>;f5RN4OLB4{m!#^_?A#R%{O{lb`5|_1{up4fpj=(>O+Y5M{1gt)V>m25p zi+Taqr!!2|#+Pxe=i#kyi$no(l9UA4uB|Bd$ACg@Vd3A<)d4kn~Q}r90V7mRd#bQ z3mR|QEBLB#>xk9H4kpI8r;ioWW}hxPFMZ{-c_&|gJ5z$t7x!jtqPhGOaI2tJ*=Ra; zreJguGm@FT-6Kt*G)pGU>qcXF@@JM5CVq=_F&g>OFVWv}X=bx3c9iUdD8Y!plyGjU zIp!C?a`arviS4K*{v|WG(j5eAIgBVT*~XoB7#8Nx75;lR2kUeh9^A6Dnku`zI@ykF zn!4TmyXVgAA>twRphO{O^7^PomFmaTkM#a2l^Tn_vQ-WKt$hu5243KiB<)j zZoh85qY+8mj@=>srP{BP8y5>D^8B(Mj0_Kr!fB1xrfZ^tEiOBqeWe!~V}`Bpi$35N z*->9Q)%EEaHQmcUC4dm`+D!VkYU@4Ved(L{L;;&!uDMkai=otF8Fz-(o6|CwKx2zc zs4+!-J$>Ws>!`!^3ouHiOziINBJ3P|blBLsO(I`178^7R&AZRpAyQq2uxv&fIPt~KKTKXi zpS3*f)L$8)fS-3$wN5?{-lZ9;DG0w616WKLu!N-Ct6zz%o~6H;d5V83vX!4biv2|) zpoRJ##IOHMYD-mw^>}tF@)3=&xo_h5Y*Wx%3kefXUlX76BO3m|s+Lxv)G5A}^QO~H zd(5(@V@;Z#)t&WcGwx$yN?iqa37(|Ll4mj11?CE@Yu@Ue%&CY zHXkG^n8x{S;$g2+aIhYJ?^&sUPOCSJqN6XxUXF#9_eXQPFG7kY1WsgZDdc^!VSw@B z&MTF!0~GXlsJ~;5!*5ewyNv=iFSmGmgA4&n4sPF*Y?{Gtvjlw-JfV%B2StY0FGNS! zsPV{evz$PQ-^?&oPmkDHg=<|8Fv96bvPdUyIr>p%S|Vlq5B2RR_ro!OHModWnv*)r zAe~F;gh0pRpFP~>isK-aI0XVYCIDID0FKK%CGHsKUZ{JoXgrrb83=d5ulGFi3U#k) zx?8`YClgpn-QrV4;oWM-w^K;R!>9L-L70Knb_a6ym{!oOsGx#2mCsMI-lBcnvHK2e z%-W&COm@E4Z+|OYUsYVEhJo@ZARY7g7G7xU;YpdHd(n8X#mCaIvmQXsSkl0wSN(V9 zAn4WrUKAwPP=9&3o%e3w;^Tf8GpPZYx&OtO)uhQnR6uHBn#93wnkdbQrClj?#7CNx;(69RoNe|IE8rd zy6;T0eqi_0Vc2^YFzmA!JE3AliqdSom|*o}@1;@JcHV1PH*XEz_;?TRcj*Wcczdb4 z3E!Nrs7+kAt~lJRIgGLf`XP50ZrC~Y{BMUmT4JxOR`}o&l#q`%O!q_BGX&jz&(Ex4 zVYi8*g=>*JP|tib+t|l4s5=Q0o$p`l3me;#KzkP898=Zu>{wMdH~T)jn8R}*YhEy` zZBxa8Y#|UIVuN7(Os53Xfc6r_T$DPIhiU6^+Wx@SGzg~Pmj<58p-de>U7TFf1wjQ< z*#F+zI4ukCa~DMf5>?tTI8B}AjXnH$?s9{`5BS}&t!v-Fpc}qCv>#J%A|mDj3RW$e z>*ZhU-XHGASOZ>o7KM#nwJfMwEv^r@0~TVjHBJpnpC64{d-T`qWD0`WGeI4vk(Zx0 zFezK7LqjGKS6qvePw!%D1o8V&;=&Yp5@@7==#+(3rola$ot)2$G$UpU9`u)5TUudV z>bq-uPLQ?`=yXRZ6^Z)aP6bfiTyorU7aKP62JX(my6x^|tp*t3Q1G+PJuui}!aa#% zv*QRp*GQmwb=$BU#?k@!pG1l;SL3QHt3qh}J!Oi%Ppb(BcT^a9>_q9uz|H)684^r) z-`<=W-tv{~u-1w)U#C{!yD*y$(a4ee@b(aPr7Z&r#?aO%`~Jp=42^<@8Hzw87?qp0 zuA-)^{frhvoAWJbD5A&W9WDr%;I``?hBePZOH>Rlt1@!69f};9 z*shN1S2{Qp1!+aR_Wi7WEIhdkz^|5=`e{(zT+b%_jbA+3IUCs=oP5s{C5Jc$lVX(( z!=ds*%oU;$1=Gs#-YQUcL(Yl;mWhvO%6=VH*HZJdTjt_((oqzRCU*Am5%RdTR?b)} zU?Vf+m-ci4-0O;X8XX3Oh4^#_3`O~$&^Lkp`cRNoaGZc=TP?3PSXU{T%-`?qMw=p5 z>X<1cAX$KmA|s_q>AYhbxxf|0rV)QNQ|)-0G}ZyOfr%pLkgGxK95UNGGl)~0sbH%F zgXH(#bLFm9f>&1p!8UMV4n5D6T*Q*Yt;@7}CKDqE+e4eXj?+HLDJkyQRmb${hssZz z?;XxtZcx913m&xHQ=4GhyU)>!(c$Fb-W$%*l33U$C*0^EC032r&#O()-`aQ<5Qw~} zu?Y3QInKx{l)-6Q89JFpUV#wD^L&0?jC8LVxmdjJA?Any`S9V$p1@tjwt#9bae#d6 zapZ!BCI2F44c}GoUnAkQid?yQ*~M|C6x@`R9{<}z8W18QABg0rU|Y)5q7%+1T?e)ufmky=nV*`oK|ENDJ5u^> zdeOQEGk4^)X8v^Dner7pznY~nr_5by-6Nofdfuyt(&b&@i;(pd7rPaMt%Jc0TnA5y z!ooVGP;rYLVf0eMY*%k>C~Z5H0P^wm8%(?hoHx~D9V1}z8L0;qtcG?{4BP2D+?To9 z3Uxffm*8JK5^hSc4iy!DuvCt8+dnGh?t|@*P9MG-j&%Gm+#fR9^!Sx#EdH2gnL%2i zJ!%0C;8XG%QRk%73>6Xm_yN*wDqm@+68H@wH( z)u$+$trGMeCrd{udK6NOsQWQ#HizFi2PKiCIMXS{9~Z{|@W|~dR7O8)@CjOZA}#9W z@3()`SKeez#feIuf--6}&qe*c^j^RGvLANt%Zv%HwbQM?x!A61Y;G2v2VtBxRT>z> z3bqL6%Ku87aBSZ=K2PjMz+lr}#~nMve(VE& zTLq5i`W|K&R*~t#0yrsRqP!F5=iH)TGl3jr8RE^`7AO9kW|ZFUU6hS}^>SYwDK}BK zPEb`!4=^$*{OK?*MCJk}&H`+NKr2c?3;3O!UD?$w#J`uA6#JX|cP_nCq5xoNx|J`8 zdqTvo5C>pj6`gk-QxJAf1oUi%fedl+qW)Fbq3~Wky~dBO_e>STNZ@Ei5h=L*bteNC z^2!ObJ+sYtNz|zQGjQM2h1u*k3sAP&Y71JeblXz84U5hsy568Rt>kocbx+R&@BBjA z@9R@2G)rIa-VYHifbJt{Lnt3Bg05a1DcrvDX%ti`;h{(AS`weHx4ZBgyZ2K^VA+^c zI48V#80iT5N}e{RgU{St#}iGxXmeUU*Ac0L*_mh=>LjY4s8Ww+7T*mC8o43}WSk!K z{!FsSo=Ik>&IQED*QQn*sqm@@FO^8^D>hbD+Z4&v*e z3?+9V%27~?`)|Q0P$jT&I>~+K;TPYO*dvw2Bh#MWw@f8>%I2|{Qoo-LM6Q5PPqs+Z zm}ZaWY6%0;xLw+>6PF4`J_PVx!0V4^>)*1ruSWzs4)RTzW~t!l6>xC0uH6W&DsM$*>`>~Y|Ej`g|i7XUV^Jg;*FI*U& zLfNSMi$?ZKxWA!=Un1-4M^*bXM7?9O^|NE_w;WbCwTyYe7vB)kFmA*JDOesOl-+_ z?x{$W=F099dYouda~CRsC{-S^r_1vb2IWL!C4>T?LYj~ zNO-TDkX{;m_r$o_Y-$Zx(WaizCKg3rN@9e)r|LG2xRGQ7AJsd)&2a5`dwdxu8J zD?5mO$|PuPvGv%wU&iH4lW4^R!W+l}XrR~}58+%8(vR&+8r0^EM-CdW%6pWZ$;j@Py8PccI+|Yd3?E^&>ag zlFL<_|6E@}S+@0XoMHb|mNoL&?dItZcoaswr@eLsoy#6 zQ*?xoL3i$BU^6^ScK>)Uu-tmEQ61dgaRFLEWil=ZjhL@zEfM9XBq{6vPu1xYYJ@YIO857_!E|-Vp@i4cgCZ zwqUqKFpew_`ad>6)5g)MxDJI-f_EQv(7!Q0J^dVl0p2b#V1dK)GBas~F?kHY7lQmG zp%vuJ?_8S0a|G`o?mq}9$<%dpbao&Z(+_MW?Qo*RQ1AHD{r7?nt}Ya2rt8gYyzhcv z6XUI}sd4+|T?WXv8i`_l-pO~a%|Nf4nSz%liU;@?o<)*TXUfgSB;N``|N*jb#+DwsZczZ8B z{(P@2kbn~MkYiW*Y?0P&;PYR4CZ}gF)i8H4I zH?iHwr?E_cKHn3u$i?`LJZbmWP!wT_ginN#gl-3*mz%tmcd2b^+{O~LGFUEOnNupp3fVD5_NX8&{lepHjI2}PW$e#@6S^@Q=p z|3~cr-Rq>_SYpcho?At*O_|*cbJ5v4kHDsQF_M;(4B+ims*~^@S^5P@LDO>B&NH?H z?q_gtX7(G{Z@;FkPsa&K?&uquwglnyoWa7w(c((|#-LU<~jsPwi!wjsWKD&vQ?(2x)D-u(B7C#nzWJ2Ee$ zvP@v}Bod*-Qs651$xH#=QN@0eNw9{_M4HTC4ObazzWMUVw+6RBe2nBch`m;O%+me1M%6 z^{;nHG3Gv#ulz*)w>1QE3kB_c_6v+G<<*i;OV~JSLjo?#;6X|pI?3-ZhUUNI1?$3H zbdpaie#QS0EZs&L!usd(D!~4GImnUn`dIxNEY)mBid}4|?q%?0^W z7r3On{_qW^0XCg{c8>ab*~C_i4$@{Jyl;wSLd8pevq9&-cS;LIHA{wyPW4*Y3*1_L zOa3$X9J#6QCjC2W?fSP28D<|{f{5M+XMAd^C{Km9Zp9NHNl&eQW`SvezrPj)(0P@#(zga;-LQ?XY~0& zOrm~TLia$oE!}B);96A!hleRjaUz{>|Ic-Y1&0vB;DxjZS(TrUO!DrXxw@bs+@i7j z5Xc84m}2zZr;S2#3->YGKIuEPlQRXyuZfNcnK~qLRRp{_*qEM)g+&Bh2lH-I*i1Ue zPNa{Zmb?EnSScifDQSnAR+Tk#(P=`f+K`%Wn79!&;?VPHlPGim`D>=l5tw)76}C`%%sUl) zUMBo}uWgCpeuxlK?#)3~GJ5{~nL^;ZuTyQQQfM$6TzgjDViVVKU^EzEq$Pj4RGnME zg+rs7O1;9Voa#2I{okj^1u-Y*MwkA~SU27yj7W#U?wk<`SmI=Sp#%iPCCcLH_M4o1 z|1~;RAWi^trJlUJd?EVXPfzq`#+YJYg|gD^kX|1R02WubTCk7 z^A;Hbx0i-9&K-hV=M7N$tb`6+K9qxbF0-P73xJRc_UOo2-j;Tb&O7MzU+^;@O`xap>uk7uhw{5!Cia-N{i$oX&f<$sH1&*FhI zQ#s)A0m|M*x!3VpwT__>*q#T1@ebhqDBZOVYeXr*3wD_Wq zIL-Rvc;~7fj&2_Us)*_X91@E(xA%oVJui+=$silLZycANpjJ5olKd9Vf&dXbC(PRw z_=DyZIuIWsV?kKO8n{H9^l$&76+8&jbM9sEBQXFRqm_azYAUd|U9d$Vb#?s=jG&Kb z1*I78V|;9vSNb<9gJAb7qR+le+DZn%m!Ej&M8V4L-ILSj;5l= zPC-F|ezahC83DP7%BkNs%ix*0Pr}Q3Ag|z0Im?zyN=kr82-oT%L=w363>eT~hEJJ5 zrnLiF(fJvhw!o!q=?Lr;0S7!lIUT%-r-E#0`?7s23q7piYLPx81t3|Nl4n|7tt=`R4q#C9skIPR`y0dMJ^VQj{!x^WpRV0{F{B A7XSbN From e27c10e9b6d6b37a9126556faaf4721a47fd29da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 7 Nov 2023 16:40:02 +0100 Subject: [PATCH 126/446] modifying readme and created leame --- LEAME.md | 39 ++++++--------------------------------- README.md | 21 +++++++++++++++++++++ 2 files changed, 27 insertions(+), 33 deletions(-) diff --git a/LEAME.md b/LEAME.md index 36f1e5de2..2dc1f560d 100644 --- a/LEAME.md +++ b/LEAME.md @@ -169,6 +169,7 @@ git pull ``` ### Configuración de opciones +##### Clonar el repositorio de GitHub Copia la plantilla de configuración inicial en un archivo llamado install_settings.txt @@ -203,39 +204,11 @@ En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se ada # para actualizar solo las dependencias del software. ES NECESARIO DISPONER DE PERMISOS DE ROOT. sudo bash install.sh --upgrade dep -# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. SI SE VA A INSTALAR POR OTRA PERSONA SIN ROOT NO HACER ESTO. -sudo bash install.sh --upgrade full --git_revision main --tables -``` - -##### Pasos que no necesitan de permisos de administración - -Actualiza a la nueva version de la aplicación de iskylims usando el siguiente comando: - -```bash -bash install.sh --upgrade app --git_revision main --tables -``` - -Por último, asegúrate que los permisos de la carpeta son correctos. - -```bash -# En el caso de que tengas un script para esta tarea. En esta versión han cambiado algunas rutas a ficheros, es posible que tengas que ajustar el script en consecuencia. -sudo /scripts/hardening.sh -``` - -#### Qué hacer si algo falla +# para actualizar la aplicación de iskylims, incluyendo los cambios necesarios para la versión en base de datos. NO ES NECESARIO DISPONER DE PERMISOS ROOT. +bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables -Cuando actualizamos la aplicación usando el script estamos realizando varios cambios en la base de datos. Si algo falla tenemos que restaurar el estado anterior, antes de que hubiesemos realizado ninguna acción. - -Necesitamos copiar de vuelta nuestro backup de carpet ade aplicación a /opt/iSkyLIMS (o la carpeta de instalación de nuestra elección), y restaurar la base de datos realizando algo como lo siguiente: - -```bash -sudo rm -rf /opt/iskylims -sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ -sudo /scripts/hardening.sh -mysql -u iskylims -h dmysqlps.isciiides.es -p -# drop database iskylims; -# create database iskylims; -mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql +# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. +sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables ``` ### Pasos finales de configuración @@ -265,7 +238,7 @@ Abre el navegador y escribe "localhost" o la "IP local del servidor" para compro También puedes verificar algunas funcionalidades mientras compruebas las conexiones de SAMBA y la base de datos usando: -- Ve a [configurationTest](https://iskylims.isciii.es/wetlab/configurationTest/) +- Ve a [prueba de configuración](https://iskylims.isciii.es/wetlab/configurationTest/) - Haz clic en Enviar - Verifica todas las pestañas para asegurarte de que cada conexión sea exitosa. - Ejecuta las 3 pruebas para cada máquina de secuenciación: MiSeq, NextSeq y NovaSeq. diff --git a/README.md b/README.md index 549cade49..82a14783a 100644 --- a/README.md +++ b/README.md @@ -21,6 +21,7 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Create iskylims database and grant permissions](#create-iskylims-database-and-grant-permissions) - [Configuration settings](#configuration-settings) - [Run installation script](#run-installation-script) +<<<<<<< HEAD - [Upgrade to iSkyLIMS version 3.1.0](#Upgrade from 3.0.x to iSkyLIMS version 3.1.x) - [Pre-requisites](#pre-requisites) - [Clone github repository](#clone-github-repository-1) @@ -29,6 +30,14 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Steps requiring root](#steps-requiring-root) - [Steps not requiring root](#steps-not-requiring-root) - [What to do if something fails](#what-to-do-if-something-fails) +======= + - [Upgrade to iSkyLIMS version 3.0.0](#upgrade-to-iskylims-version-300) + - [Pre-requisites](#pre-requisites-1) + - [Executing the upgrade](#executing-the-upgrade) + - [Clone github repository](#clone-github-repository-1) + - [Configuration settings](#configuration-settings-1) + - [Running upgrade script](#running-upgrade-script) +>>>>>>> 9b1f70fc (modifying readme and created leame) - [Final configuration steps](#final-configuration-steps) - [SAMBA configurarion](#samba-configurarion) - [Email verification](#email-verification) @@ -117,7 +126,11 @@ Open with your favourite editor the configuration file to set your own values fo database ,email settings and the local IP of the server where iSkyLIMS will run. ```bash +<<<<<<< HEAD nano install_settings.txt +======= +sudo nano install_settings.txt +>>>>>>> 9b1f70fc (modifying readme and created leame) ``` #### Run installation script @@ -144,6 +157,7 @@ bash install.sh --install app --git_revision main --tables sudo bash install.sh --install full --git_revision main --tables ``` +<<<<<<< HEAD ## Upgrade from 3.0.x to iSkyLIMS version 3.1.x Follow the following steps to upgrade from version 3.0.0 to the latest one 3.1.x @@ -154,6 +168,9 @@ Before starting the upgrade procedure is highly recomended to perform the follow - Create a full backup of iSkyLIMS database - Backup all iSkyLIMS folders (complete installation folder, p.e /opt/iSkyLIMS) +======= +### Upgrade to iSkyLIMS version 3.0.0 +>>>>>>> 9b1f70fc (modifying readme and created leame) - If in your system you have already defined library pools, then you need to collect this data, before to run the upgrade script. Perform a backup of LibraryPool by running the folowing command. @@ -292,7 +309,11 @@ mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/b - Go to Configuration -> Email configuration - Fill the form with the needed params for your email configuration and try to send a test email. +<<<<<<< HEAD ### Configure Apache server +======= +#### Configure Apache server +>>>>>>> 9b1f70fc (modifying readme and created leame) Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf From 051da074cb2054fd581eececa1055499d3a8e241 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 8 Nov 2023 17:36:12 +0100 Subject: [PATCH 127/446] Modifications in readme and leame, addign what to do if something fails and some clarifications --- LEAME.md | 74 ++++++++++++++++++++++++++++++++++++++++++++++++++--- README.md | 76 ++++++++++++++++++++++++++++++++++++------------------- 2 files changed, 121 insertions(+), 29 deletions(-) diff --git a/LEAME.md b/LEAME.md index 2dc1f560d..337af7732 100644 --- a/LEAME.md +++ b/LEAME.md @@ -20,7 +20,11 @@ De acuerdo con la infraestructura existente, la secuenciación se realiza en un - [Crear la base de datos de iSkyLIMS y otorgar permisos](#crear-la-base-de-datos-de-iskylims-y-otorgar-permisos) - [Configuración de ajustes](#configuración-de-ajustes) - [Ejecutar el script de instalación](#ejecutar-el-script-de-instalación) +<<<<<<< HEAD - [Actualización a la versión 3.1.0 de iSkyLIMS](#actualización-a-la-versión-310-de-iskylims) +======= + - [Actualización a la versión 3.0.0 de iSkyLIMS](#actualización-a-la-versión-300-de-iskylims) +>>>>>>> feb7fcff (Modifications in readme and leame, addign what to do if something fails and some clarifications) - [Prerrequisitos](#prerrequisitos) - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) - [Configuración de opciones](#configuración-de-opciones) @@ -157,10 +161,15 @@ Por temas de seguridad es recomendado realizar una copia de seguridad de: Se recomienda encarecidamente que se hagan estas copias de seguridad y se guarden de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). +<<<<<<< HEAD ### Clonar el repositorio de GitHub +======= +#### Clonar el repositorio de GitHub +>>>>>>> feb7fcff (Modifications in readme and leame, addign what to do if something fails and some clarifications) A partir ya de la version anterior, ahora el código de iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). +<<<<<<< HEAD Abre una terminal de Linux y dirígete a un directorio donde estaba descargado el código de iSkyLIMS. Actualiza el codigo ```bash @@ -170,6 +179,17 @@ git pull ### Configuración de opciones ##### Clonar el repositorio de GitHub +======= +Abre una terminal de Linux y dirígete a un directorio donde se descargará el código de iSkyLIMS. + +```bash +cd < directorio distinto al directorio de instalación > +git clone https://gitlab.isciii.es/BU-ISCIII/iskylims.git iskylims +cd iskylims +``` + +#### Configuración de opciones +>>>>>>> feb7fcff (Modifications in readme and leame, addign what to do if something fails and some clarifications) Copia la plantilla de configuración inicial en un archivo llamado install_settings.txt @@ -184,18 +204,37 @@ Abre el archivo de configuración con tu editor favorito para establecer tus pro nano install_settings.txt ``` +<<<<<<< HEAD ### Ejecución del script de actualización +======= +#### Ejecución del script de actualización +>>>>>>> feb7fcff (Modifications in readme and leame, addign what to do if something fails and some clarifications) Debido a que los paquetes de python de los que depende iSkyLIMs se han ido actualizando desde la última release es necesario que sean actualizados. +<<<<<<< HEAD #### Pasos que necesitan permisos de adminsitración +======= +##### Pasos que necesitan permisos de adminsitración + +En primer lugar, debes cambiar el nombre de la carpeta de la aplicación en la carpeta de instalación (`/opt/iSkyLIMS`): + +```bash +# Necesitas ser usuario root para realizar esta operación +sudo mv /opt/iSkyLIMS /opt/iskylims +``` +>>>>>>> feb7fcff (Modifications in readme and leame, addign what to do if something fails and some clarifications) Asegúrate de que la carpeta de instalación tenga los permisos correctos para que la persona que instala la aplicación pueda escribir en esa carpeta. ```bash # En el caso de que tengas un script para esta tarea. Necesitarás ajustar este script de acuerdo al cambio en el nombre de la ruta: /opt/iSkyLIMS a /opt/iskylims +<<<<<<< HEAD sudo /scripts/hardening.sh +======= +/scripts/hardening.sh +>>>>>>> feb7fcff (Modifications in readme and leame, addign what to do if something fails and some clarifications) ``` En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se adapte a ti: @@ -204,11 +243,40 @@ En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se ada # para actualizar solo las dependencias del software. ES NECESARIO DISPONER DE PERMISOS DE ROOT. sudo bash install.sh --upgrade dep +# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. +sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` + +##### Pasos que no necesitan de permisos de administración + +A continuación instalamos la aplicación de iskylims usando el siguiente comando: + +```bash # para actualizar la aplicación de iskylims, incluyendo los cambios necesarios para la versión en base de datos. NO ES NECESARIO DISPONER DE PERMISOS ROOT. bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` -# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. -sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +Por último, asegúrate que los permisos de la carpeta son correctos. + +```bash +# En el caso de que tengas un script para esta tarea. En esta versión han cambiado algunas rutas a ficheros, es posible que tengas que ajustar el script en consecuencia. +/scripts/hardening.sh +``` + +#### Qué hacer si algo falla + +Cuando actualizamos la aplicación usando el script estamos realizando varios cambios en la base de datos. Si algo falla tenemos que restaurar el estado anterior, antes de que hubiesemos realizado ninguna acción. + +Necesitamos copiar de vuelta nuestro backup de carpet ade aplicación a /opt/iSkyLIMS (o la carpeta de instalación de nuestra elección), y restaurar la base de datos realizando algo como lo siguiente: + +```bash +sudo rm -rf /opt/iskylims +sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ +sudo /scripts/hardening.sh +mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es +# drop database iskylims; +# create database iskylims; +mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` ### Pasos finales de configuración @@ -238,7 +306,7 @@ Abre el navegador y escribe "localhost" o la "IP local del servidor" para compro También puedes verificar algunas funcionalidades mientras compruebas las conexiones de SAMBA y la base de datos usando: -- Ve a [prueba de configuración](https://iskylims.isciii.es/wetlab/configurationTest/) +- Ve a [configurationTest](https://iskylims.isciii.es/wetlab/configurationTest/) - Haz clic en Enviar - Verifica todas las pestañas para asegurarte de que cada conexión sea exitosa. - Ejecuta las 3 pruebas para cada máquina de secuenciación: MiSeq, NextSeq y NovaSeq. diff --git a/README.md b/README.md index 82a14783a..1fa82e6ca 100644 --- a/README.md +++ b/README.md @@ -21,7 +21,6 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Create iskylims database and grant permissions](#create-iskylims-database-and-grant-permissions) - [Configuration settings](#configuration-settings) - [Run installation script](#run-installation-script) -<<<<<<< HEAD - [Upgrade to iSkyLIMS version 3.1.0](#Upgrade from 3.0.x to iSkyLIMS version 3.1.x) - [Pre-requisites](#pre-requisites) - [Clone github repository](#clone-github-repository-1) @@ -30,14 +29,13 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Steps requiring root](#steps-requiring-root) - [Steps not requiring root](#steps-not-requiring-root) - [What to do if something fails](#what-to-do-if-something-fails) -======= - - [Upgrade to iSkyLIMS version 3.0.0](#upgrade-to-iskylims-version-300) - - [Pre-requisites](#pre-requisites-1) - [Executing the upgrade](#executing-the-upgrade) - [Clone github repository](#clone-github-repository-1) - [Configuration settings](#configuration-settings-1) - [Running upgrade script](#running-upgrade-script) ->>>>>>> 9b1f70fc (modifying readme and created leame) + - [Steps requiring root](#steps-requiring-root) + - [Steps not requiring root](#steps-not-requiring-root) + - [What to do if something fails](#what-to-do-if-something-fails) - [Final configuration steps](#final-configuration-steps) - [SAMBA configurarion](#samba-configurarion) - [Email verification](#email-verification) @@ -126,11 +124,7 @@ Open with your favourite editor the configuration file to set your own values fo database ,email settings and the local IP of the server where iSkyLIMS will run. ```bash -<<<<<<< HEAD nano install_settings.txt -======= -sudo nano install_settings.txt ->>>>>>> 9b1f70fc (modifying readme and created leame) ``` #### Run installation script @@ -157,7 +151,6 @@ bash install.sh --install app --git_revision main --tables sudo bash install.sh --install full --git_revision main --tables ``` -<<<<<<< HEAD ## Upgrade from 3.0.x to iSkyLIMS version 3.1.x Follow the following steps to upgrade from version 3.0.0 to the latest one 3.1.x @@ -168,9 +161,6 @@ Before starting the upgrade procedure is highly recomended to perform the follow - Create a full backup of iSkyLIMS database - Backup all iSkyLIMS folders (complete installation folder, p.e /opt/iSkyLIMS) -======= -### Upgrade to iSkyLIMS version 3.0.0 ->>>>>>> 9b1f70fc (modifying readme and created leame) - If in your system you have already defined library pools, then you need to collect this data, before to run the upgrade script. Perform a backup of LibraryPool by running the folowing command. @@ -187,7 +177,7 @@ Because in this upgrade many tables in database are modified it is required that It is highly recomended that you made these backups and keep them safely in case of upgrade failure, to recover your system. -#### Executing the upgrade +#### Clone github repository We've also change the way that iSkyLIMS is installed and upgraded. From now on iskylims is downloaded in a user folder and installed elsewhere (p.e /opt/). @@ -203,8 +193,8 @@ cd < your personal folder/iskylims > git pull ``` -If the repository was not created then open a linux terminal and move to a directory -where iSkyLIMS code will be downloaded +Open a linux terminal and move to a directory where iSkyLIMS code will be +downloaded ```bash cd < your personal folder > @@ -212,7 +202,7 @@ git clone https://github.com/BU-ISCIII/iSkyLIMS.git iskylims cd iskylims ``` -##### Configuration settings +#### Configuration settings Copy the initial setting template into a file named install_settings.txt @@ -228,12 +218,17 @@ database ,email settings and the local IP of the server where iSkyLIMS will run. sudo nano install_settings.txt ``` -##### Running upgrade script +#### Running upgrade script If your organization requires that dependencies / stuff that needs root are installed by a different person that install the application the you can use the install script in several steps as follows. #### Steps requiring root +```bash +# You need root for this operation +sudo mv /opt/iSkyLIMS /opt/iskylims +``` + Make sure that the installation folder has the correct permissions so the person installing the app can write in that folder. ```bash @@ -241,16 +236,49 @@ Make sure that the installation folder has the correct permissions so the person /scripts/hardening.sh ``` -From the previous release software dependences (Python packages) must be updated to the releases defined in the requirement.txt file. - -In the linux terminal execute the following command- +In the linux terminal execute one of the following command that fit better to you: ```bash # to upgrade only software packages dependences. NEEDS ROOT. sudo bash install.sh --upgrade dep + +# to install both software. NEEDS ROOT. +sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` + +##### Steps not requiring root + +Next you need to upgrade iskylims app. Please use the command below: + +```bash +# to upgrade only iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. +bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` + +Make sure that the installation folder has the correct permissions. + +```bash +# In case you have a script for this task. Some paths have changed in this version, so you may need to adjust your hardening script. +/scripts/hardening.sh +``` + +#### What to do if something fails + +When we upgrade using the installation script we are performing several changes in the database. If something fails we need to restore the app situation before anything happened and start all over. + +We need to copy back the full `/opt/iSkyLIMS` folder back to `/opt` (or your installation path preference), and restore the database doing something like this: + +```bash +sudo rm -rf /opt/iskylims +sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ +sudo /scripts/hardening.sh +mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es +# drop database iskylims; +# create database iskylims; +mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` -#### Steps not requiring root +### Final configuration steps Next you need to upgrade iskylims app. Please use one of the commands below: @@ -309,11 +337,7 @@ mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/b - Go to Configuration -> Email configuration - Fill the form with the needed params for your email configuration and try to send a test email. -<<<<<<< HEAD -### Configure Apache server -======= #### Configure Apache server ->>>>>>> 9b1f70fc (modifying readme and created leame) Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf From 1a0588ad37dc188072e521ed3a4990172497965f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 8 Nov 2023 17:49:48 +0100 Subject: [PATCH 128/446] run to error status when cancelled, added new error code to tables --- LEAME.md | 23 +---------------------- 1 file changed, 1 insertion(+), 22 deletions(-) diff --git a/LEAME.md b/LEAME.md index 337af7732..f3c2da2e6 100644 --- a/LEAME.md +++ b/LEAME.md @@ -20,11 +20,7 @@ De acuerdo con la infraestructura existente, la secuenciación se realiza en un - [Crear la base de datos de iSkyLIMS y otorgar permisos](#crear-la-base-de-datos-de-iskylims-y-otorgar-permisos) - [Configuración de ajustes](#configuración-de-ajustes) - [Ejecutar el script de instalación](#ejecutar-el-script-de-instalación) -<<<<<<< HEAD - [Actualización a la versión 3.1.0 de iSkyLIMS](#actualización-a-la-versión-310-de-iskylims) -======= - - [Actualización a la versión 3.0.0 de iSkyLIMS](#actualización-a-la-versión-300-de-iskylims) ->>>>>>> feb7fcff (Modifications in readme and leame, addign what to do if something fails and some clarifications) - [Prerrequisitos](#prerrequisitos) - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) - [Configuración de opciones](#configuración-de-opciones) @@ -161,11 +157,7 @@ Por temas de seguridad es recomendado realizar una copia de seguridad de: Se recomienda encarecidamente que se hagan estas copias de seguridad y se guarden de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). -<<<<<<< HEAD -### Clonar el repositorio de GitHub -======= #### Clonar el repositorio de GitHub ->>>>>>> feb7fcff (Modifications in readme and leame, addign what to do if something fails and some clarifications) A partir ya de la version anterior, ahora el código de iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). @@ -189,7 +181,6 @@ cd iskylims ``` #### Configuración de opciones ->>>>>>> feb7fcff (Modifications in readme and leame, addign what to do if something fails and some clarifications) Copia la plantilla de configuración inicial en un archivo llamado install_settings.txt @@ -204,19 +195,12 @@ Abre el archivo de configuración con tu editor favorito para establecer tus pro nano install_settings.txt ``` -<<<<<<< HEAD ### Ejecución del script de actualización -======= -#### Ejecución del script de actualización ->>>>>>> feb7fcff (Modifications in readme and leame, addign what to do if something fails and some clarifications) Debido a que los paquetes de python de los que depende iSkyLIMs se han ido actualizando desde la última release es necesario que sean actualizados. -<<<<<<< HEAD #### Pasos que necesitan permisos de adminsitración -======= -##### Pasos que necesitan permisos de adminsitración En primer lugar, debes cambiar el nombre de la carpeta de la aplicación en la carpeta de instalación (`/opt/iSkyLIMS`): @@ -224,17 +208,12 @@ En primer lugar, debes cambiar el nombre de la carpeta de la aplicación en la c # Necesitas ser usuario root para realizar esta operación sudo mv /opt/iSkyLIMS /opt/iskylims ``` ->>>>>>> feb7fcff (Modifications in readme and leame, addign what to do if something fails and some clarifications) Asegúrate de que la carpeta de instalación tenga los permisos correctos para que la persona que instala la aplicación pueda escribir en esa carpeta. ```bash # En el caso de que tengas un script para esta tarea. Necesitarás ajustar este script de acuerdo al cambio en el nombre de la ruta: /opt/iSkyLIMS a /opt/iskylims -<<<<<<< HEAD sudo /scripts/hardening.sh -======= -/scripts/hardening.sh ->>>>>>> feb7fcff (Modifications in readme and leame, addign what to do if something fails and some clarifications) ``` En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se adapte a ti: @@ -249,7 +228,7 @@ sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_mig ##### Pasos que no necesitan de permisos de administración -A continuación instalamos la aplicación de iskylims usando el siguiente comando: +A continuación instalamos la aplicación de iskylims usando el siguiente comando: ```bash # para actualizar la aplicación de iskylims, incluyendo los cambios necesarios para la versión en base de datos. NO ES NECESARIO DISPONER DE PERMISOS ROOT. From 001aa0a2bfc5ac865f9515d1d427136875f8b301 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 8 Nov 2023 18:06:48 +0100 Subject: [PATCH 129/446] linting --- drylab/utils/resolutions.py | 4 +--- wetlab/utils/crontab_update_run.py | 7 ++++--- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/drylab/utils/resolutions.py b/drylab/utils/resolutions.py index a8fa3ed63..63e078eeb 100644 --- a/drylab/utils/resolutions.py +++ b/drylab/utils/resolutions.py @@ -348,9 +348,7 @@ def prepare_form_data_add_resolution(form_data): selected_children_services.append( [children, avail_serv_obj.get_service_description()] ) - resolution_form_data[ - "selected_avail_services" - ] = selected_children_services + resolution_form_data["selected_avail_services"] = selected_children_services if drylab.models.Resolution.objects.filter( resolution_service_id=service_obj ).exists(): diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 2178bf48d..3903561bf 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -645,9 +645,10 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): experiment_name, ) elif run_status == "cancelled": - run_process_obj.set_run_state("cancelled") - run_process_obj.set_run_completion_date(run_completion_date) - wetlab.utils.crontab_process.handling_errors_in_run(experiment_name, 34) + run_status["ERROR"] = 34 + wetlab.utils.crontab_process.handling_errors_in_run( + experiment_name, run_status["ERROR"] + ) string_message = experiment_name + "was cancelled on the sequencer" wetlab.utils.common.logging_warnings(string_message, True) logger.debug( From 7cca89b81cf55baba60c65d0bf48d1fd6319dac4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 8 Nov 2023 18:16:44 +0100 Subject: [PATCH 130/446] fixed bug when run cancelled --- wetlab/utils/crontab_update_run.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 3903561bf..0052095b5 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -645,9 +645,8 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): experiment_name, ) elif run_status == "cancelled": - run_status["ERROR"] = 34 wetlab.utils.crontab_process.handling_errors_in_run( - experiment_name, run_status["ERROR"] + experiment_name, 34 ) string_message = experiment_name + "was cancelled on the sequencer" wetlab.utils.common.logging_warnings(string_message, True) From a882a3682dcfe05aa07dcab61f2b71c50db5edea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 9 Nov 2023 09:47:36 +0100 Subject: [PATCH 131/446] minor fix for cancelled code --- wetlab/utils/crontab_update_run.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 0052095b5..1ffaff1c3 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -645,8 +645,8 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): experiment_name, ) elif run_status == "cancelled": - wetlab.utils.crontab_process.handling_errors_in_run( - experiment_name, 34 + wetlab.utils.crontab_process.han3er4dling_5ty67us_in_run( + experiment_name, 340s dº2w ) string_message = experiment_name + "was cancelled on the sequencer" wetlab.utils.common.logging_warnings(string_message, True) From e9ba5e9541e754c81ecd8b38948da8f4e356f9cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 15 Dec 2023 14:29:37 +0100 Subject: [PATCH 132/446] fixed typo in crontab_update_run --- wetlab/utils/crontab_update_run.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 1ffaff1c3..0052095b5 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -645,8 +645,8 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): experiment_name, ) elif run_status == "cancelled": - wetlab.utils.crontab_process.han3er4dling_5ty67us_in_run( - experiment_name, 340s dº2w + wetlab.utils.crontab_process.handling_errors_in_run( + experiment_name, 34 ) string_message = experiment_name + "was cancelled on the sequencer" wetlab.utils.common.logging_warnings(string_message, True) From 8fd77f284467f2601fb47a2e9f122775cc89fdb8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 15 Dec 2023 14:37:43 +0100 Subject: [PATCH 133/446] linting --- wetlab/utils/crontab_update_run.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 0052095b5..d93ee44bb 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -645,9 +645,7 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): experiment_name, ) elif run_status == "cancelled": - wetlab.utils.crontab_process.handling_errors_in_run( - experiment_name, 34 - ) + wetlab.utils.crontab_process.handling_errors_in_run(experiment_name, 34) string_message = experiment_name + "was cancelled on the sequencer" wetlab.utils.common.logging_warnings(string_message, True) logger.debug( From 056fce16acbde901869c8602f0aa0e9c6d3a5af8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 3 May 2024 22:10:40 +0200 Subject: [PATCH 134/446] Create rest_api_model.json --- conf/rest_api_model.json | 613 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 613 insertions(+) create mode 100644 conf/rest_api_model.json diff --git a/conf/rest_api_model.json b/conf/rest_api_model.json new file mode 100644 index 000000000..7b5beae0d --- /dev/null +++ b/conf/rest_api_model.json @@ -0,0 +1,613 @@ +{ + "swagger": "2.0", + "info": { + "title": "iSkyLIMS API", + "description": "iSkyLIMS API", + "version": "v0.0.1" + }, + "host": "iskylims.isciiides.es", + "schemes": [ + "http", + "https" + ], + "basePath": "/", + "consumes": [ + "application/json" + ], + "produces": [ + "application/json" + ], + "securityDefinitions": { + "basic": { + "type": "basic" + } + }, + "security": [ + { + "basic": [] + } + ], + "paths": { + "/drylab/api/create-delivery": { + "post": { + "operationId": "drylab_api_create-delivery_create", + "description": "Create a new delivery for a selected resolution", + "parameters": [ + { + "name": "data", + "in": "body", + "required": true, + "schema": { + "type": "object", + "properties": { + "resolution_number": { + "description": "resolution_number. pe. SRVCNM123.1", + "type": "string" + }, + "pipelines_in_delivery": { + "description": "pipelines in delivery. pe. ['viralrecon']", + "type": "array", + "items": { + "type": "string" + } + }, + "delivery_date": { + "description": "delivery date. pe. 2022-01-01", + "type": "string" + }, + "execution_start_date": { + "description": "execution start date. pe. 2022-01-01", + "type": "string" + }, + "execution_end_date": { + "description": "execution end date. pe. 2022-01-01", + "type": "string" + }, + "permanent_used_space": { + "description": "permanent used space in GB. pe. 134", + "type": "integer" + }, + "temporary_used_space": { + "description": "temporary used space in GB. pe. SRVCNM123.1", + "type": "integer" + }, + "delivery_notes": { + "description": "delivery notes with brief results description.", + "type": "integer" + } + } + } + } + ], + "responses": { + "200": { + "description": "Successful delivery creation" + }, + "400": { + "description": "Bad Request" + } + }, + "tags": [ + "drylab" + ] + }, + "parameters": [] + }, + "/drylab/api/resolution": { + "get": { + "operationId": "drylab_api_resolution_list", + "description": "Obtain a list of resolutions for a service id.", + "parameters": [ + { + "name": "state", + "in": "query", + "description": "State parameter is optional. The allowed values are: [Recorded/ In Progress/ Delivery/ Cancelled]", + "type": "string", + "enum": [ + "recorded", + "in_progress", + "delivered", + "approved", + "rejected", + "archived", + "on_hold" + ] + }, + { + "name": "resolution", + "in": "query", + "description": "Resolution parameter resolution is optional. Example SRVCNM123.1", + "type": "string" + } + ], + "responses": { + "200": { + "description": "" + } + }, + "tags": [ + "drylab" + ] + }, + "parameters": [] + }, + "/drylab/api/samples_in_service": { + "get": { + "operationId": "drylab_api_samples_in_service_list", + "description": "Obtain samples requested for analysis in a service", + "parameters": [ + { + "name": "service", + "in": "query", + "description": "Service parameter is mandatory. Example SRVCNM123", + "type": "string" + } + ], + "responses": { + "200": { + "description": "" + } + }, + "tags": [ + "drylab" + ] + }, + "parameters": [] + }, + "/drylab/api/service-data": { + "get": { + "operationId": "drylab_api_service-data_list", + "description": "Obtain a complete list of service data associated with a service or resolution id.", + "parameters": [ + { + "name": "service", + "in": "query", + "description": "Service parameter is mandatory. Example SRVCNM123", + "type": "string" + }, + { + "name": "resolution", + "in": "query", + "description": "Resolution parameter resolution is optional. Example SRVCNM123.1", + "type": "string" + } + ], + "responses": { + "200": { + "description": "" + } + }, + "tags": [ + "drylab" + ] + }, + "parameters": [] + }, + "/drylab/api/services": { + "get": { + "operationId": "drylab_api_services_list", + "description": "Obtain a list of service ids given a state of a range of dates.", + "parameters": [ + { + "name": "state", + "in": "query", + "description": "State parameter is optional. The allowed values are: [approved/rejected/queued/in_progress/delivered/archived/recorded]", + "type": "string", + "enum": [ + "approved", + "rejected", + "queued", + "in_progress", + "delivered", + "archived", + "recorded" + ] + }, + { + "name": "date_from", + "in": "query", + "description": "Date parameter is optional.It will limit the results from the date specified in the parameter.\n Example 2022-01-01", + "type": "string" + }, + { + "name": "date_until", + "in": "query", + "description": "Date parameter is optional.It will limit the results up to the date specified in the parameter.\n Example 2022-01-01", + "type": "string" + } + ], + "responses": { + "200": { + "description": "" + } + }, + "tags": [ + "drylab" + ] + }, + "parameters": [] + }, + "/drylab/api/update-state": { + "put": { + "operationId": "drylab_api_update-state_update", + "description": "Update a resolution/service state", + "parameters": [ + { + "name": "resolution", + "in": "query", + "description": "Resolution parameter resolution is optional. Example SRVCNM123.1", + "type": "string" + }, + { + "name": "state", + "in": "query", + "description": "State parameter is optional. The allowed values are: [Recorded/ In Progress/ Delivery/ Cancelled]", + "type": "string", + "enum": [ + "recorded", + "in_progress", + "delivered", + "approved", + "rejected", + "archived", + "on_hold" + ] + } + ], + "responses": { + "200": { + "description": "" + } + }, + "tags": [ + "drylab" + ] + }, + "parameters": [] + }, + "/wetlab/api/create-sample": { + "post": { + "operationId": "wetlab_api_create-sample_create", + "description": "Create a new sample Data in iSkyLIMS", + "parameters": [ + { + "name": "data", + "in": "body", + "required": true, + "schema": { + "type": "object", + "properties": { + "sample_name": { + "description": "Sample name", + "type": "string" + }, + "sample_state": { + "description": "Sample state", + "type": "string" + }, + "patient_core": { + "description": "Code assigned to the patient", + "type": "string" + }, + "lab_request": { + "description": "Laboratory that request the sample", + "type": "string" + }, + "sample_type": { + "description": "Type of the sample", + "type": "string" + }, + "species": { + "description": "Specie that the sample belongs to", + "type": "string" + }, + "sample_location": { + "description": "Location where the sample is stored", + "type": "string" + }, + "sample_entry_date": { + "description": "Date when sample is received in the lab", + "type": "string" + }, + "collection_sample_date": { + "description": "Date when the sample is collected from the specimen", + "type": "string" + }, + "only_recorded": { + "description": "Select if sample is just recorded or if DNA/RNA manipulation will be done in the lab ", + "type": "string" + }, + "sample_project": { + "description": "Project name", + "type": "string" + } + } + } + } + ], + "responses": { + "201": { + "description": "Successful create information" + }, + "400": { + "description": "Bad Request" + }, + "500": { + "description": "Internal Server Error" + } + }, + "tags": [ + "wetlab" + ] + }, + "parameters": [] + }, + "/wetlab/api/lab-data": { + "get": { + "operationId": "wetlab_api_lab-data_list", + "description": "Obtain a list of laboratories registered in iSkyLIMS", + "parameters": [ + { + "name": "laboratory", + "in": "query", + "description": "Laboratory name form to fetch contact information. Example Harlem Hospital Center", + "type": "string" + } + ], + "responses": { + "200": { + "description": "" + } + }, + "tags": [ + "wetlab" + ] + }, + "parameters": [] + }, + "/wetlab/api/projects-fields": { + "get": { + "operationId": "wetlab_api_projects-fields_list", + "description": "Use this request to get the field' s names that are required for the sample project", + "parameters": [ + { + "name": "project", + "in": "query", + "description": "Project name to fetch the sample project fields defined. Example Relecov", + "type": "string" + } + ], + "responses": { + "200": { + "description": "" + } + }, + "tags": [ + "wetlab" + ] + }, + "parameters": [] + }, + "/wetlab/api/run-info": { + "get": { + "operationId": "wetlab_api_run-info_list", + "description": "Get the stored Run information available in iSkyLIMS for the list of samples", + "parameters": [ + { + "name": "samples", + "in": "query", + "description": "Sample name list to fetch run information", + "type": "string" + } + ], + "responses": { + "200": { + "description": "" + } + }, + "tags": [ + "wetlab" + ] + }, + "parameters": [] + }, + "/wetlab/api/sample-fields": { + "get": { + "operationId": "wetlab_api_sample-fields_list", + "description": "Send request to gen the fields that are required when storing a new sample using the API", + "parameters": [], + "responses": { + "200": { + "description": "" + } + }, + "tags": [ + "wetlab" + ] + }, + "parameters": [] + }, + "/wetlab/api/sample-info": { + "get": { + "operationId": "wetlab_api_sample-info_list", + "description": "Get the sample/samples belongs to project information, collected when creating in iSkyLIMS", + "parameters": [ + { + "name": "sample", + "in": "query", + "description": "Select the sample to get information", + "type": "string" + }, + { + "name": "sample_project_name", + "in": "query", + "description": "Select the project to get all samples assigned to it", + "type": "string" + }, + { + "name": "parameter", + "in": "query", + "description": "Get all samples which have this parameter. If selected project result the project parameter", + "type": "string" + } + ], + "responses": { + "200": { + "description": "" + } + }, + "tags": [ + "wetlab" + ] + }, + "parameters": [] + }, + "/wetlab/api/stats-info": { + "get": { + "operationId": "wetlab_api_stats-info_list", + "description": "Otain a list of info statistics for a project.", + "parameters": [ + { + "name": "sample_project_name", + "in": "query", + "description": "Select the project to get all samples assigned to it", + "type": "string" + }, + { + "name": "project_field", + "in": "query", + "description": "Project fields to make the query. Maximum number of fiels are 2", + "type": "string" + } + ], + "responses": { + "200": { + "description": "" + } + }, + "tags": [ + "wetlab" + ] + }, + "parameters": [] + }, + "/wetlab/api/summarized-info": { + "get": { + "operationId": "wetlab_api_summarized-info_list", + "description": "Obtain a summarized info list for a list of samples registered in iskylims.", + "parameters": [ + { + "name": "samples", + "in": "query", + "description": "List of samples to collect information", + "type": "string" + }, + { + "name": "sample_state", + "in": "query", + "description": "Filter result to the sample which are in this state", + "type": "string" + }, + { + "name": "start_date", + "in": "query", + "description": "Start date from starting collecting samples", + "type": "string" + }, + { + "name": "end_date", + "in": "query", + "description": "Start date from starting collecting samples", + "type": "string" + }, + { + "name": "region", + "in": "query", + "description": "Filter the samples for the selected region", + "type": "string" + }, + { + "name": "laboratory", + "in": "query", + "description": "Laboratory name form to fetch contact information. Example Harlem Hospital Center", + "type": "string" + }, + { + "name": "sample_project_name", + "in": "query", + "description": "Select the project to get all samples assigned to it", + "type": "string" + }, + { + "name": "sample_project_field", + "in": "query", + "description": "Name of the sample project Field. Requires project_name", + "type": "string" + } + ], + "responses": { + "200": { + "description": "" + } + }, + "tags": [ + "wetlab" + ] + }, + "parameters": [] + }, + "/wetlab/api/update-lab": { + "put": { + "operationId": "wetlab_api_update-lab_update", + "description": "Update laboratory contact information", + "parameters": [ + { + "name": "data", + "in": "body", + "required": true, + "schema": { + "type": "object", + "properties": { + "lab_name": { + "description": "Name of the Laboratory", + "type": "string" + }, + "lab_contact_name": { + "description": "Name for laboratory contact", + "type": "string" + }, + "lab_contact_telephone": { + "description": "Phone number of contact", + "type": "string" + }, + "lab_contact_email": { + "description": "Contact email", + "type": "string" + } + } + } + } + ], + "responses": { + "201": { + "description": "Successful create information" + }, + "400": { + "description": "Bad Request" + }, + "406": { + "description": "Request not accepted" + }, + "500": { + "description": "Internal Server Error" + } + }, + "tags": [ + "wetlab" + ] + }, + "parameters": [] + } + }, + "definitions": {} +} From 98df9976096e211097ca4dac3f086e9aea4b2b60 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 15 Oct 2024 10:37:56 +0200 Subject: [PATCH 135/446] hotfix numpy dependency and docker fixes --- Dockerfile | 12 ++++++++++++ conf/requirements.txt | 1 + 2 files changed, 13 insertions(+) diff --git a/Dockerfile b/Dockerfile index bbbb6afad..273659be7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,9 +10,15 @@ RUN apt-get update && apt-get upgrade -y RUN apt-get install -y \ git wget lsb-release \ libmysqlclient-dev \ +<<<<<<< HEAD python3-pip libpq-dev python3-venv python3-wheel \ apache2-dev cron \ gnuplot pkg-config rsync +======= + python3-pip libpq-dev \ + python3-wheel apache2-dev \ + gnuplot pkg-config +>>>>>>> ff357111 (hotfix numpy dependency and docker fixes) # Set MYSQLCLIENT_CFLAGS and MYSQLCLIENT_LDFLAGS using pkg-config RUN export MYSQLCLIENT_CFLAGS="$(pkg-config --libs mysqlclient)" && \ @@ -21,6 +27,7 @@ RUN export MYSQLCLIENT_CFLAGS="$(pkg-config --libs mysqlclient)" && \ # Set git repository RUN mkdir /srv/iskylims WORKDIR /srv/iskylims +<<<<<<< HEAD # Copy the local git repository to docker image directory COPY . /srv/iskylims @@ -29,6 +36,11 @@ COPY . /srv/iskylims RUN python3 -m venv /srv/iskylims/venv ENV PATH="/srv/iskylims/venv/bin:$PATH" ENV PATH="/usr/sbin/cron:$PATH" +======= +RUN pip install -r conf/requirements.txt + +RUN bash install.sh --install app --conf conf/docker_install_settings.txt --docker +>>>>>>> ff357111 (hotfix numpy dependency and docker fixes) # Install dependencies within the virtual environment RUN /srv/iskylims/venv/bin/pip install -r conf/requirements.txt diff --git a/conf/requirements.txt b/conf/requirements.txt index 53e4b00a0..d85154e19 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -22,5 +22,6 @@ djangorestframework==3.15.2 drf-yasg==1.21.7 xlrd==2.0.1 pandas==2.2.2 +numpy==1.26.4 openpyxl==3.1.5 setuptools==75.2.0 From f4716ceb0511e0bf40f24239c53fcf1609181128 Mon Sep 17 00:00:00 2001 From: luissian Date: Wed, 21 Aug 2024 14:52:45 +0200 Subject: [PATCH 136/446] update the python packages used in iskylims --- conf/requirements.txt | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/conf/requirements.txt b/conf/requirements.txt index d85154e19..ab74c18e9 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -13,7 +13,11 @@ django-mptt-admin==2.6.2 django-cleanup==8.1.0 interop>1.1.22 mod_wsgi==5.0.0 +<<<<<<< HEAD mysqlclient==2.2.6 +======= +mysqlclient==2.2.4 +>>>>>>> 762df044 (update the python packages used in iskylims) paramiko==3.4.1 jsonschema==4.23.0 pysmb==1.2.9.1 @@ -22,6 +26,10 @@ djangorestframework==3.15.2 drf-yasg==1.21.7 xlrd==2.0.1 pandas==2.2.2 +<<<<<<< HEAD numpy==1.26.4 openpyxl==3.1.5 setuptools==75.2.0 +======= +openpyxl==3.1.5 +>>>>>>> 762df044 (update the python packages used in iskylims) From f379aabd66a2377c3c399386f0f519fbbd4fda42 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 22 Aug 2024 10:09:39 +0200 Subject: [PATCH 137/446] Update installation procedure for the upgrade --- LEAME.md | 54 ++++--- README.md | 93 ++++++----- leame_upgrade_2.3.0_to_3.0.md | 288 +++++++++++++++++++++++++++++++++ upgrade_2.3_to_3.0.md | 290 ++++++++++++++++++++++++++++++++++ 4 files changed, 661 insertions(+), 64 deletions(-) create mode 100644 leame_upgrade_2.3.0_to_3.0.md create mode 100644 upgrade_2.3_to_3.0.md diff --git a/LEAME.md b/LEAME.md index f3c2da2e6..ffc8931d6 100644 --- a/LEAME.md +++ b/LEAME.md @@ -20,12 +20,16 @@ De acuerdo con la infraestructura existente, la secuenciación se realiza en un - [Crear la base de datos de iSkyLIMS y otorgar permisos](#crear-la-base-de-datos-de-iskylims-y-otorgar-permisos) - [Configuración de ajustes](#configuración-de-ajustes) - [Ejecutar el script de instalación](#ejecutar-el-script-de-instalación) - - [Actualización a la versión 3.1.0 de iSkyLIMS](#actualización-a-la-versión-310-de-iskylims) - - [Prerrequisitos](#prerrequisitos) - - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) - - [Configuración de opciones](#configuración-de-opciones) - - [Ejecución del script de actualización](#ejecución-del-script-de-actualización) - - [Pasos que necesitan permisos de adminsitración](#pasos-que-necesitan-permisos-de-adminsitración) + - [Actualización a la versión 3.1.0 de iSkyLIMS](#actualización-a-la-versión-310-de-iskylims) + - [Actualización a la versión 3.1.0 de iSkyLIMS](#actualización-a-la-versión-310-de-iskylims-1) + - [Prerrequisitos](#prerrequisitos) + - [Prerrequisitos](#prerrequisitos-1) + - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) + - [Configuración de opciones](#configuración-de-opciones) + - [Ejecución del script de actualización](#ejecución-del-script-de-actualización) + - [Ejecución del script de actualización](#ejecución-del-script-de-actualización-1) + - [Pasos que necesitan permisos de adminsitración](#pasos-que-necesitan-permisos-de-adminsitración) + - [Pasos que necesitan permisos de adminsitración](#pasos-que-necesitan-permisos-de-adminsitración-1) - [Pasos que no necesitan de permisos de administración](#pasos-que-no-necesitan-de-permisos-de-administración) - [Qué hacer si algo falla](#qué-hacer-si-algo-falla) - [Pasos finales de configuración](#pasos-finales-de-configuración) @@ -47,6 +51,8 @@ Antes de comenzar la instalación, asegúrate de lo siguiente: - Dependencias: - Librerías: +```bash + ```bash yum groupinstall "Development tools" yum install zlib-devel bzip2-devel openssl-devel \ @@ -55,6 +61,10 @@ Antes de comenzar la instalación, asegúrate de lo siguiente: gnuplot cifs-utils ``` +- lsb_relase: + - RedHat/CentOS: `yum install redhat-lsb-core` + - Ubuntu: `apt install lsb-core lsb-release` + - lsb_relase: - RedHat/CentOS: `yum install redhat-lsb-core` - Ubuntu: `apt install lsb-core lsb-release` @@ -144,24 +154,28 @@ bash install.sh --install app sudo bash install.sh --install full ``` +## Actualización a la versión 3.1.0 de iSkyLIMS ## Actualización a la versión 3.1.0 de iSkyLIMS En esta version se han implementado fallos de código y mejoras en las gráficas. Para obtener más detalles sobre los cambios, consulta las notas de la versión. +### Prerrequisitos ### Prerrequisitos +Por temas de seguridad es recomendado realizar una copia de seguridad de: Por temas de seguridad es recomendado realizar una copia de seguridad de: - La base de datos de iSkyLIMS. - La carpeta de iSkyLIMS (carpeta de instalación completa, por ejemplo, /opt/iSkyLIMS). +Se recomienda encarecidamente que se hagan estas copias de seguridad y se guarden de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). Se recomienda encarecidamente que se hagan estas copias de seguridad y se guarden de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). -#### Clonar el repositorio de GitHub +### Clonar el repositorio de GitHub +A partir ya de la version anterior, ahora el código de iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). A partir ya de la version anterior, ahora el código de iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). -<<<<<<< HEAD Abre una terminal de Linux y dirígete a un directorio donde estaba descargado el código de iSkyLIMS. Actualiza el codigo ```bash @@ -170,17 +184,6 @@ git pull ``` ### Configuración de opciones -##### Clonar el repositorio de GitHub -======= -Abre una terminal de Linux y dirígete a un directorio donde se descargará el código de iSkyLIMS. - -```bash -cd < directorio distinto al directorio de instalación > -git clone https://gitlab.isciii.es/BU-ISCIII/iskylims.git iskylims -cd iskylims -``` - -#### Configuración de opciones Copia la plantilla de configuración inicial en un archivo llamado install_settings.txt @@ -195,11 +198,15 @@ Abre el archivo de configuración con tu editor favorito para establecer tus pro nano install_settings.txt ``` +### Ejecución del script de actualización ### Ejecución del script de actualización +Debido a que los paquetes de python de los que depende iSkyLIMs se han ido actualizando +desde la última release es necesario que sean actualizados. Debido a que los paquetes de python de los que depende iSkyLIMs se han ido actualizando desde la última release es necesario que sean actualizados. +#### Pasos que necesitan permisos de adminsitración #### Pasos que necesitan permisos de adminsitración En primer lugar, debes cambiar el nombre de la carpeta de la aplicación en la carpeta de instalación (`/opt/iSkyLIMS`): @@ -222,17 +229,16 @@ En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se ada # para actualizar solo las dependencias del software. ES NECESARIO DISPONER DE PERMISOS DE ROOT. sudo bash install.sh --upgrade dep -# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. -sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. SI SE VA A INSTALAR POR OTRA PERSONA SIN ROOT NO HACER ESTO. +sudo bash install.sh --upgrade full --git_revision main --tables ``` ##### Pasos que no necesitan de permisos de administración -A continuación instalamos la aplicación de iskylims usando el siguiente comando: +Actualiza a la nueva version de la aplicación de iskylims usando el siguiente comando: ```bash -# para actualizar la aplicación de iskylims, incluyendo los cambios necesarios para la versión en base de datos. NO ES NECESARIO DISPONER DE PERMISOS ROOT. -bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +bash install.sh --upgrade app --git_revision main --tables ``` Por último, asegúrate que los permisos de la carpeta son correctos. diff --git a/README.md b/README.md index 1fa82e6ca..ee1f765b2 100644 --- a/README.md +++ b/README.md @@ -21,27 +21,23 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Create iskylims database and grant permissions](#create-iskylims-database-and-grant-permissions) - [Configuration settings](#configuration-settings) - [Run installation script](#run-installation-script) - - [Upgrade to iSkyLIMS version 3.1.0](#Upgrade from 3.0.x to iSkyLIMS version 3.1.x) - - [Pre-requisites](#pre-requisites) - - [Clone github repository](#clone-github-repository-1) - - [Configuration settings](#configuration-settings-1) - - [Running upgrade script](#running-upgrade-script) - - [Steps requiring root](#steps-requiring-root) - - [Steps not requiring root](#steps-not-requiring-root) - - [What to do if something fails](#what-to-do-if-something-fails) - - [Executing the upgrade](#executing-the-upgrade) - - [Clone github repository](#clone-github-repository-1) - - [Configuration settings](#configuration-settings-1) - - [Running upgrade script](#running-upgrade-script) - - [Steps requiring root](#steps-requiring-root) - - [Steps not requiring root](#steps-not-requiring-root) - - [What to do if something fails](#what-to-do-if-something-fails) - - [Final configuration steps](#final-configuration-steps) - - [SAMBA configurarion](#samba-configurarion) - - [Email verification](#email-verification) - - [Configure Apache server](#configure-apache-server) - - [Verification of the installation](#verification-of-the-installation) - - [iSkyLIMS documentation](#iskylims-documentation) + - [Upgrade from 3.0.x to iSkyLIMS version 3.1.x](#upgrade-from-30x-to-iskylims-version-31x) + - [Pre-requisites for upgrade](#pre-requisites-for-upgrade) + - [Clone github repository](#clone-github-repository-1) + - [Clone github repository](#clone-github-repository-2) + - [Configuration settings](#configuration-settings-1) + - [Running upgrade script](#running-upgrade-script) + - [Steps requiring root](#steps-requiring-root) + - [Steps not requiring root](#steps-not-requiring-root) + - [What to do if something fails](#what-to-do-if-something-fails) + - [Final configuration steps](#final-configuration-steps) + - [What to do if something fails](#what-to-do-if-something-fails-1) + - [Final configuration steps](#final-configuration-steps-1) + - [SAMBA configurarion](#samba-configurarion) + - [Email verification](#email-verification) + - [Configure Apache server](#configure-apache-server) + - [Verification of the installation](#verification-of-the-installation) + - [iSkyLIMS documentation](#iskylims-documentation) ## Installation @@ -177,7 +173,7 @@ Because in this upgrade many tables in database are modified it is required that It is highly recomended that you made these backups and keep them safely in case of upgrade failure, to recover your system. -#### Clone github repository +### Clone github repository We've also change the way that iSkyLIMS is installed and upgraded. From now on iskylims is downloaded in a user folder and installed elsewhere (p.e /opt/). @@ -193,8 +189,16 @@ cd < your personal folder/iskylims > git pull ``` -Open a linux terminal and move to a directory where iSkyLIMS code will be -downloaded +If you have already clone the repository from the previous 3.0.0 release open a +linux terminal and move towards the directory of iSkyLIMS repository. + +```bash +cd < your personal folder/iskylims > +git pull +``` + +If the repository was not created then open a linux terminal and move to a directory +where iSkyLIMS code will be downloaded ```bash cd < your personal folder > @@ -202,7 +206,7 @@ git clone https://github.com/BU-ISCIII/iSkyLIMS.git iskylims cd iskylims ``` -#### Configuration settings +### Configuration settings Copy the initial setting template into a file named install_settings.txt @@ -218,7 +222,7 @@ database ,email settings and the local IP of the server where iSkyLIMS will run. sudo nano install_settings.txt ``` -#### Running upgrade script +### Running upgrade script If your organization requires that dependencies / stuff that needs root are installed by a different person that install the application the you can use the install script in several steps as follows. @@ -236,23 +240,32 @@ Make sure that the installation folder has the correct permissions so the person /scripts/hardening.sh ``` -In the linux terminal execute one of the following command that fit better to you: +From the previous release software dependences (Python packages) must be updated to the releases defined in the requirement.txt file. + +In the linux terminal execute the following command- ```bash # to upgrade only software packages dependences. NEEDS ROOT. sudo bash install.sh --upgrade dep - -# to install both software. NEEDS ROOT. -sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables ``` -##### Steps not requiring root +#### Steps not requiring root + +Next you need to upgrade iskylims app. Please use one of the commands below: -Next you need to upgrade iskylims app. Please use the command below: +If you are using the library pool, you must indicate in the installation script the file +you already backup and execute the following command. ```bash -# to upgrade only iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. -bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +# to upgrade iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. +bash install.sh --upgrade app --script --git_revision main --tables +``` + +If restauration of libary preparation is not required then execute the following command + +```bash +# to upgrade iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. +bash install.sh --upgrade app ---git_revision main -tables ``` Make sure that the installation folder has the correct permissions. @@ -262,11 +275,11 @@ Make sure that the installation folder has the correct permissions. /scripts/hardening.sh ``` -#### What to do if something fails +## What to do if something fails When we upgrade using the installation script we are performing several changes in the database. If something fails we need to restore the app situation before anything happened and start all over. -We need to copy back the full `/opt/iSkyLIMS` folder back to `/opt` (or your installation path preference), and restore the database doing something like this: +We need to copy back the full `/opt/iskylims` folder back to `/opt/iskylims` (or your installation path preference), and restore the database doing something like this: ```bash sudo rm -rf /opt/iskylims @@ -278,7 +291,7 @@ mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` -### Final configuration steps +## Final configuration steps Next you need to upgrade iskylims app. Please use one of the commands below: @@ -337,11 +350,11 @@ mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/b - Go to Configuration -> Email configuration - Fill the form with the needed params for your email configuration and try to send a test email. -#### Configure Apache server +### Configure Apache server Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf -#### Verification of the installation +### Verification of the installation Open the navigator and type "localhost" or the "server local IP" and check that iSkyLIMs is running. @@ -352,6 +365,6 @@ You can also check some of the functionality, while also checking samba and data - Check all tabs so every connectin is successful. - Run the 3 tests for each sequencing machine: MiSeq, NextSeq and NovaSeq. -### iSkyLIMS documentation +## iSkyLIMS documentation iSkyLIMS documentation is available at [https://iskylims.readthedocs.io/en/latest](https://iskylims.readthedocs.io/en/latest) diff --git a/leame_upgrade_2.3.0_to_3.0.md b/leame_upgrade_2.3.0_to_3.0.md new file mode 100644 index 000000000..c68cf701a --- /dev/null +++ b/leame_upgrade_2.3.0_to_3.0.md @@ -0,0 +1,288 @@ +# iSkyLIMS + +[![Django](https://img.shields.io/static/v1?label=Django&message=4.2&color=azul?style=plastic&logo=django)](https://github.com/django/django) +[![Python](https://img.shields.io/static/v1?label=Python&message=3.8.10&color=verde?style=plastic&logo=Python)](https://www.python.org/) +[![Bootstrap](https://img.shields.io/badge/Bootstrap-v5.0-azulvioleta?style=plastic&logo=Bootstrap)](https://getbootstrap.com) +[![versión](https://img.shields.io/badge/versión-3.0.0-naranja?style=plastic&logo=GitHub)](https://github.com/BU-ISCIII/iskylims.git) + +La introducción de la secuenciación masiva (MS) en las instalaciones de genómica ha significado un crecimiento exponencial en la generación de datos, lo que requiere un sistema de seguimiento preciso, desde la preparación de la biblioteca hasta la generación de archivos fastq, el análisis y la entrega al investigador. El software diseñado para manejar esas tareas se llama Sistemas de Gestión de Información de Laboratorio (LIMS), y su software debe adaptarse a las necesidades particulares de su laboratorio de genómica. iSkyLIMS nace con el objetivo de ayudar con las tareas de laboratorio húmedo e implementar un flujo de trabajo que guíe a los laboratorios de genómica en sus actividades, desde la preparación de la biblioteca hasta la producción de datos, reduciendo los posibles errores asociados a la tecnología de alto rendimiento y facilitando el control de calidad de la secuenciación. Además, iSkyLIMS conecta el laboratorio húmedo con el laboratorio seco, facilitando el análisis de datos por parte de bioinformáticos. + +![Imagen](img/iskylims_scheme.png) + +De acuerdo con la infraestructura existente, la secuenciación se realiza en un instrumento Illumina NextSeq. Los datos se almacenan en un dispositivo de almacenamiento masivo NetApp y los archivos fastq se generan (bcl2fastq) en un clúster de cómputo de alto rendimiento Sun Grid Engine (SGE-HPC). Los servidores de aplicaciones ejecutan aplicaciones web para el análisis bioinformático (GALAXY), la aplicación iSkyLIMS y alojan la capa de información de MySQL. El flujo de trabajo de iSkyLIMS WetLab se ocupa del seguimiento y las estadísticas de la ejecución de la secuenciación. El seguimiento de la ejecución pasa por cinco estados: "registrado", el usuario de genómica registra la nueva ejecución de la secuenciación en el sistema, el proceso esperará hasta que la ejecución se complete en la máquina y los datos se transfieran al dispositivo de almacenamiento masivo; "Envío de hoja de muestra", el archivo de hoja de muestra con la información de la ejecución de la secuenciación se copiará en la carpeta de ejecución para el proceso de bcl2fastq; "Procesamiento de datos", se procesan los archivos de parámetros de ejecución y los datos se almacenan en la base de datos; "Estadísticas en ejecución", los datos de desmultiplexación generados en el proceso de bcl2fastq se procesan y almacenan en la base de datos, "Completado", todos los datos se procesan y almacenan correctamente. Se proporcionan estadísticas por muestra, por proyecto, por ejecución y por investigación, así como informes anuales y mensuales. El flujo de trabajo de iSkyLIMS DryLab se encarga de la solicitud de servicios de bioinformática y estadísticas. El usuario solicita servicios que pueden estar asociados con una ejecución de secuenciación. Se proporciona seguimiento de estadísticas y servicios. + +- [iSkyLIMS](#iskylims) + - [Instalación](#instalación) + - [Requisitos previos](#requisitos-previos) + - [Instalación de iSkyLIMS en Docker](#instalación-de-iskylims-en-docker) + - [Instalación de iSkyLIMS en su servidor con Ubuntu/CentOS](#instalación-de-iskylims-en-su-servidor-con-ubuntucentos) + - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github) + - [Crear la base de datos de iSkyLIMS y otorgar permisos](#crear-la-base-de-datos-de-iskylims-y-otorgar-permisos) + - [Configuración de ajustes](#configuración-de-ajustes) + - [Ejecutar el script de instalación](#ejecutar-el-script-de-instalación) + - [Actualización a la versión 3.0.0 de iSkyLIMS](#actualización-a-la-versión-300-de-iskylims) + - [Prerrequisitos](#prerrequisitos) + - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) + - [Configuración de opciones](#configuración-de-opciones) + - [Ejecución del script de actualización](#ejecución-del-script-de-actualización) + - [Pasos que necesitan permisos de adminsitración](#pasos-que-necesitan-permisos-de-adminsitración) + - [Pasos que no necesitan de permisos de administración](#pasos-que-no-necesitan-de-permisos-de-administración) + - [Qué hacer si algo falla](#qué-hacer-si-algo-falla) + - [Pasos finales de configuración](#pasos-finales-de-configuración) + - [Configuración de SAMBA](#configuración-de-samba) + - [Verificación de correo electrónico](#verificación-de-correo-electrónico) + - [Configurar el servidor Apache](#configurar-el-servidor-apache) + - [Verificación de la instalación](#verificación-de-la-instalación) + - [Documentación de iSkyLIMS](#documentación-de-iskylims) + +## Instalación + +Si tienes algún problema o deseas informar de algún error, por favor, publícalo en [issue](https://github.com/BU-ISCIII/iSkyLIMS/issues) + +### Requisitos previos + +Antes de comenzar la instalación, asegúrate de lo siguiente: + +- Tienes privilegios de **sudo** para instalar los paquetes de software adicionales que iSkyLIMS necesita. +- Dependencias: + - Librerías: +``` + yum groupinstall "Development tools" + yum install zlib-devel bzip2-devel openssl-devel \ + wget httpd-devel mysql-libs sqlite sqlite-devel \ + mariadb-devel mysql-client libffi-devel \ + gnuplot cifs-utils +``` + - lsb_relase: + - RedHat/CentOS: `yum install redhat-lsb-core` + - Ubuntu: `apt install lsb-core lsb-release` +- Base de datos MySQL > 8.0 o MariaDB > 10.4 +- Tienes configurado un servidor local para enviar correos electrónicos. +- git > 2.34 +- Tienes Apache servidor v2.4 +- Tienes Python > 3.8 (si lo compilas debes haber instalado previamente las dependecias de arriba) +- Tienes una conexión a la carpeta compartida de Samba donde se almacenan las carpetas de ejecución (por ejemplo, galera/NGS_Data). +- Dependencias: + + +### Instalación de iSkyLIMS en Docker + +Puedes probar iSkyLIMS creando un contenedor Docker en tu máquina local. + +Clona el repositorio de GitHub de iSkyLIMS y ejecuta el script de Docker para crear el contenedor Docker. + +```bash +git clone https://github.com/BU-ISCIII/iSkyLIMS.git iSkyLIMS +sudo bash docker_install.sh +``` + +El script crea un contenedor de Docker Compose con 3 servicios: + +- web1: contiene la aplicación web iSkyLIMS +- db1: contiene la base de datos MySQL +- samba: contiene el servidor Samba + +Después de crear Docker y tener los servicios en funcionamiento, la estructura de la base de datos y los datos iniciales se cargan en la base de datos. Cuando se complete este paso, se le pedirá que defina al superusuario que tendrá acceso a las páginas de administración de Django. Puede escribir cualquier nombre, pero recomendamos que utilice "admin", ya que más adelante se le pedirá un usuario administrador cuando defina la configuración inicial. + +Siga el mensaje de instrucciones para crear la cuenta del superusuario. + +Cuando el script finalice, abra su navegador escribiendo **localhost:8001** para acceder a iSkyLIMS + +### Instalación de iSkyLIMS en su servidor con Ubuntu/CentOS + +#### Clonar el repositorio de GitHub + +Abra una terminal de Linux y vaya a un directorio donde se descargará el código de iSkyLIMS + +```bash +cd +git clone https://github.com/BU-ISCIII/iskylims.git iskylims +cd iskylims +``` + +#### Crear la base de datos de iSkyLIMS y otorgar permisos + +1. Cree una nueva base de datos llamada "iskylims" (esto es obligatorio). +2. Cree un nuevo usuario con permisos para leer y modificar esa base de datos. +3. Anote el nombre de usuario, la contraseña y la información del servidor de la base de datos. + +#### Configuración de ajustes + +Copia la plantilla de ajustes iniciales en un archivo llamado `install_settings.txt` + +```bash +cp conf/template_install_settings.txt install_settings.txt +``` + +Abra el archivo de configuración con su editor favorito para establecer sus propios valores para la base de datos, la configuración de correo electrónico y la dirección IP local del servidor donde se ejecutará iSkyLIMS. + +```bash +sudo nano install_settings.txt +``` + +#### Ejecutar el script de instalación + +iSkyLIMS debe instalarse en el directorio "/opt". + +Necesitará privilegios de administrador para instalar las dependencias. Para manejar diferentes responsabilidades de instalación dentro de la organización, donde es posible que no sea la persona con privilegios de administrador, nuestro script de instalación tiene estas opciones en el parámetro `--install`: + +- `dep`: para instalar los paquetes de software, así como los paquetes de Python dentro del entorno virtual. Se necesita permisos de administrador. +- `app`: para instalar solo el software de la aplicación iSkyLIMS sin necesidad de tener permisos de administrador. +- `full`: si tiene directamente permisos de administrador, puede instalar tanto las dependencias como la aplicación con esta opción. + +Ejecute uno de los siguientes comandos en una terminal de Linux para la instalación, de acuerdo con la descripción anterior. + +```bash +# para instalar solo las dependencias +sudo bash install.sh --install dep + +# para instalar la aplicación iskylims +bash install.sh --install app + +# para instalar ambos al mismo tiempo +sudo bash install.sh --install full +``` + +### Actualización a la versión 3.0.0 de iSkyLIMS + +Si ya tienes iSkyLIMS en la versión 2.3.0, puedes actualizar a la última versión estable, la 3.0.0. + +La versión 3.0.0 es una versión importante con actualizaciones significativas en dependencias de terceros como Bootstrap. También hemos realizado un gran trabajo en la refactorización y el cambio de nombres de variables/funciones que afectan a la base de datos. Para obtener más detalles sobre los cambios, consulta las notas de la versión. + +#### Prerrequisitos + +Debido a que en esta actualización se modifican muchas tablas en la base de datos, es necesario que hagas una copia de seguridad de: + +- La base de datos de iSkyLIMS. +- La carpeta de iSkyLIMS (carpeta de instalación completa, por ejemplo, /opt/iSkyLIMS). + +Se recomienda encarecidamente que hagas estas copias de seguridad y las guardes de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). + +#### Clonar el repositorio de GitHub + +También hemos cambiado la forma en que se instala y actualiza iSkyLIMS. A partir de ahora, iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). + +Abre una terminal de Linux y dirígete a un directorio donde se descargará el código de iSkyLIMS. + +```bash +cd < directorio distinto al directorio de instalación > +git clone https://gitlab.isciii.es/BU-ISCIII/iskylims.git iskylims +cd iskylims +``` + +#### Configuración de opciones + +Copia la plantilla de configuración inicial en un archivo llamado install_settings.txt + +```bash +cp conf/template_install_settings.txt install_settings.txt +``` + +Abre el archivo de configuración con tu editor favorito para establecer tus propios valores para la base de datos, la configuración de correo electrónico y la dirección IP local del servidor donde se ejecutará iSkyLIMS. +> Si utilizas un sistema basado en Windows para modificar el archivo, asegúrate de que el archivo se guarde con una codificación amigable para Linux, como ASCII o UTF-8. + +```bash +nano install_settings.txt +``` + +#### Ejecución del script de actualización + +Si en tu organización se requiere que las dependencias u otros elementos que necesiten permisos de administrador sean instalados por una persona diferente a la que instala la aplicación, puedes utilizar el script de instalación en varios pasos de la siguiente manera. + +El script te irá solicitando confirmación en algun paso, si todo está yendo bien sin errores deberás pulsar `y` o `yes` según te lo solicite. + +> Nota: Los errores: "ERROR 1064 (42000) at line 1: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'query' at line 1" son normales ya que se trata del título de las sentencias sql que no deben ejecutarse. Se puede ignorar. + +##### Pasos que necesitan permisos de adminsitración + +En primer lugar, debes cambiar el nombre de la carpeta de la aplicación en la carpeta de instalación (`/opt/iSkyLIMS`): + +```bash +# Necesitas ser usuario root para realizar esta operación +sudo mv /opt/iSkyLIMS /opt/iskylims +``` + +Asegúrate de que la carpeta de instalación tenga los permisos correctos para que la persona que instala la aplicación pueda escribir en esa carpeta. + +```bash +# En el caso de que tengas un script para esta tarea. Necesitarás ajustar este script de acuerdo al cambio en el nombre de la ruta: /opt/iSkyLIMS a /opt/iskylims +sudo /scripts/hardening.sh +``` + +En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se adapte a ti: + +```bash +# para actualizar solo las dependencias del software. ES NECESARIO DISPONER DE PERMISOS DE ROOT. +sudo bash install.sh --upgrade dep + +# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. SI SE VA A INSTALAR POR OTRA PERSONA SIN ROOT NO HACER ESTO. +sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` + +##### Pasos que no necesitan de permisos de administración + +A continuación instalamos la aplicación de iskylims usando el siguiente comando: + +```bash +# para actualizar la aplicación de iskylims, incluyendo los cambios necesarios para la versión en base de datos. NO ES NECESARIO DISPONER DE PERMISOS ROOT. +bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` + +Por último, asegúrate que los permisos de la carpeta son correctos. + +```bash +# En el caso de que tengas un script para esta tarea. En esta versión han cambiado algunas rutas a ficheros, es posible que tengas que ajustar el script en consecuencia. +sudo /scripts/hardening.sh +``` + +#### Qué hacer si algo falla + +Cuando actualizamos la aplicación usando el script estamos realizando varios cambios en la base de datos. Si algo falla tenemos que restaurar el estado anterior, antes de que hubiesemos realizado ninguna acción. + +Necesitamos copiar de vuelta nuestro backup de carpet ade aplicación a /opt/iSkyLIMS (o la carpeta de instalación de nuestra elección), y restaurar la base de datos realizando algo como lo siguiente: + +```bash +sudo rm -rf /opt/iskylims +sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ +sudo /scripts/hardening.sh +mysql -u iskylims -h dmysqlps.isciiides.es -p +# drop database iskylims; +# create database iskylims; +mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql +``` + +### Pasos finales de configuración + +#### Configuración de SAMBA + +- Inicia sesión con la cuenta de administrador. +- Ve a Massive Sequencing +![Ir a WetLab](img/got_to_wetlab.png){width:50px} +- Ve a Configuración -> Configuración de SAMBA +- Completa el formulario con los parámetros apropiados para la carpeta compartida de SAMBA: +![Formulario SAMBA](img/samba_form.png) + +#### Verificación de correo electrónico + +- Ve a Massive Sequencing +- Ve a Configuración -> Configuración de correo electrónico +- Completa el formulario con los parámetros necesarios para la configuración de correo electrónico y trata de enviar un correo de prueba. + +#### Configurar el servidor Apache + +Copia el archivo de configuración de Apache que se encuentra en la carpeta `conf` según tu distribución dentro del directorio de configuración de Apache y cambia el nombre a iskylims.conf. Revisa cualquier requerimiento de tu sistema, se trata solo de un ejemplo. + +#### Verificación de la instalación + +Abre el navegador y escribe "localhost" o la "IP local del servidor" para comprobar que iSkyLIMS está en funcionamiento. + +También puedes verificar algunas funcionalidades mientras compruebas las conexiones de SAMBA y la base de datos usando: + +- Ve a [configurationTest](https://iskylims.isciii.es/wetlab/configurationTest/) +- Haz clic en Enviar +- Verifica todas las pestañas para asegurarte de que cada conexión sea exitosa. +- Ejecuta las 3 pruebas para cada máquina de secuenciación: MiSeq, NextSeq y NovaSeq. + +### Documentación de iSkyLIMS + +La documentación de iSkyLIMS está disponible en [https://iskylims.readthedocs.io/en/latest](https://iskylims.readthedocs.io/en/latest) diff --git a/upgrade_2.3_to_3.0.md b/upgrade_2.3_to_3.0.md new file mode 100644 index 000000000..66a597a94 --- /dev/null +++ b/upgrade_2.3_to_3.0.md @@ -0,0 +1,290 @@ +# iSkyLIMS + +[![Django](https://img.shields.io/static/v1?label=Django&message=4.2&color=blue?style=plastic&logo=django)](https://github.com/django/django) +[![Python](https://img.shields.io/static/v1?label=Python&message=3.8.10&color=green?style=plastic&logo=Python)](https://www.python.org/) +[![Bootstrap](https://img.shields.io/badge/Bootstrap-v5.0-blueviolet?style=plastic&logo=Bootstrap)](https://getbootstrap.com) +[![version](https://img.shields.io/badge/version-3.0.0-orange?style=plastic&logo=GitHub)](https://github.com/BU-ISCIII/iskylims.git) + +The introduction of massive sequencing (MS) in genomics facilities has meant an exponential growth in data generation, requiring a precise tracking system, from library preparation to fastq file generation, analysis and delivery to the researcher. Software designed to handle those tasks are called Laboratory Information Management Systems (LIMS), and its software has to be adapted to their own genomics laboratory particular needs. iSkyLIMS is born with the aim of helping with the wet laboratory tasks, and implementing a workflow that guides genomics labs on their activities from library preparation to data production, reducing potential errors associated to high throughput technology, and facilitating the quality control of the sequencing. Also, iSkyLIMS connects the wet lab with dry lab facilitating data analysis by bioinformaticians. + +![Image](img/iskylims_scheme.png) + +According to existent infrastructure sequencing is performed on an Illumina NextSeq instrument. Data is stored in NetApp mass storage device and fastq files are generated (bcl2fastq) on a Sun Grid Engine High Performance Computing cluster (SGE-HPC). +Application servers run web applications for bioinformatics analysis (GALAXY), the iSkyLIMS app, and host the MySQL information tier. iSkyLIMS WetLab workflow deals with sequencing run tracking and statistics. Run tracking passes through five states: "recorded” genomics user record the new sequencing run into the system, the process will wait till run is completed by the machine and data is transferred to the mass storage device; “Sample sheet sent” sample sheet file with the sequencing run information will be copied to the run folder for bcl2fastq process; “Processing data” run parameters files are processed and data is stored in the database; “Running stats” demultiplexing data generated in bcl2fastq process is processed and stored into the database, “Completed” all data is processed and stored successfully. Statistics per sample, per project, per run and per investigation are provided, as well as annual and monthly reports. iSkyLIMS DryLab workflow deals with bioinformatics services request and statistics. User request services that can be associated with a sequencing run. Stats and services tracking is provided. + +- [iSkyLIMS](#iskylims) + - [Installation](#installation) + - [Pre-requisites](#pre-requisites) + - [iSkyLIMS docker installation](#iskylims-docker-installation) + - [Install iSkyLIMS in your server running ubuntu/CentOS](#install-iskylims-in-your-server-running-ubuntucentos) + - [Clone github repository](#clone-github-repository) + - [Create iskylims database and grant permissions](#create-iskylims-database-and-grant-permissions) + - [Configuration settings](#configuration-settings) + - [Run installation script](#run-installation-script) + - [Upgrade to iSkyLIMS version 3.0.0](#upgrade-to-iskylims-version-300) + - [Pre-requisites](#pre-requisites-1) + - [Clone github repository](#clone-github-repository-1) + - [Configuration settings](#configuration-settings-1) + - [Running upgrade script](#running-upgrade-script) + - [Steps requiring root](#steps-requiring-root) + - [Steps not requiring root](#steps-not-requiring-root) + - [What to do if something fails](#what-to-do-if-something-fails) + - [Final configuration steps](#final-configuration-steps) + - [SAMBA configurarion](#samba-configurarion) + - [Email verification](#email-verification) + - [Configure Apache server](#configure-apache-server) + - [Verification of the installation](#verification-of-the-installation) + - [iSkyLIMS documentation](#iskylims-documentation) + +## Installation + +For any problems or bug reporting please post us an [issue](https://github.com/BU-ISCIII/iSkyLIMS/issues) + +### Pre-requisites + +Before starting the installation make sure : + +- You have **sudo privileges** to install the additional software packets that iSkyLIMS needs. +- Database MySQL > 8.0 or MariaDB > 10.4 +- Local server configured for sending emails +- Apache server v2.4 +- git > 2.34 +- Python > 3.8 +- Connection to samba shared folder where run folders are stored (p.e galera/NGS_Data) +- Dependencies: + - lsb_release: + - RedHat/CentOS: ```yum install redhat-lsb-core``` + - Ubuntu: ```apt install lsb-core lsb-release``` + +### iSkyLIMS docker installation + +You can test iSkyLIMS by creating a docker container on your local machine. + +Clone the iSkyLIMS github repository and run the docker script to create the docker + +```bash +git clone https://github.com/BU-ISCIII/iSkyLIMS.git iSkyLIMS +sudo bash docker_install.sh +``` + +The script creates a docker compose container with 3 services: + +- web1: contains the iSkyLIMS web application +- db1: contains the mySQL database +- samba: contains samba server + +After Docker is created and services are up, database structure and initial data are loaded into database. When this step is completed, you will be asked to define the super user which will have access to django admin pages. You can type any name, but we recommend that you use "admin", because admin user is requested later on when defining the initial settings. + +Follow the prompt message to create the super user account. + +When script ends open your navigator typing **localhost:8001** to access to iSkyLIMS + +### Install iSkyLIMS in your server running ubuntu/CentOS + +#### Clone github repository + +Open a linux terminal and move to a directory where iSkyLIMS code will be +downloaded + +```bash +cd < your personal folder > +git clone https://github.com/BU-ISCIII/iskylims.git iskylims +cd iskylims +``` + +#### Create iskylims database and grant permissions + +1. Create a new database named "iskylims" (this is mandatory) +2. Create a new user with permission to read and modify that database. +3. Write down user, passwd and db server info. + +#### Configuration settings + +Copy the initial setting template into a file named install_settings.txt + +```bash +cp conf/template_install_settings.txt install_settings.txt +``` + +Open with your favourite editor the configuration file to set your own values for +database ,email settings and the local IP of the server where iSkyLIMS will run. + +```bash +nano install_settings.txt +``` + +#### Run installation script + +iSkyLIMS should be installed on the "/opt" directory. + +You will need sudo privileges for installing dependencies. In order to handle different installation responsibilities inside the organization, where you may not be the person with root privileges, our instalation script has these options in ```--install``` parameter: + +- dep: to install the software packages as well as python packages inside the virtual environment. Root is needed. +- app: to install only the iSkyLIMS application software without need of being root. +- full: if you directly have root permissions you can install both deps and app at the same time with this option. + +Execute one of the following commands in a linux terminal to install, according as +above description. + +```bash +# to install only software packages dependences +sudo bash install.sh --install dep + +# to install only iSkyLIMS application +bash install.sh --install app + +# to install both software +sudo bash install.sh --install full +``` + +### Upgrade to iSkyLIMS version 3.0.0 + +If you have already iSkyLIMS on version 2.3.0 you can upgrade to the latest stable version 3.0.0. + +Version 3.0.0 is a major release with important upgrades in third parties dependencies like bootstrap. Also, we 've done a huge work on refactoring and variables/function renaming that affects the database. For more details about the changes see the release notes. + +If you requires to upgrade from version 3.0.0 to the latest one 3.1.x and in your system you have already defined library pools, then you need to collect this data, before to run the upgrade script. For more information read [Pre-requisites for upgrade from 3.0.0 to 3.1.x](#pre-requisites-for-upgrade-from-30x-to-31x) + +#### Pre-requisites + +Because in this upgrade many tables in database are modified it is required that you backup: + +- iSkyLIMS database +- iSkyLIMS folder (complete installation folder, p.e /opt/iSkyLIMS) + +##### Pre-requisites for upgrade from 3.0.x to 3.1.x + +- Perform a backup of LibraryPool by running the folowing command + +```bash + mysql --user= --password= --host= --port= iskylims -e "SELECT* FROM wetlab_library_pool" > +``` + +It is highly recomended that you made these backups and keep them safely in case of upgrade failure, to recover your system. + +#### Clone github repository + +We've also change the way that iSkyLIMS is installed and upgraded. From now on iskylims is downloaded in a user folder and installed elsewhere (p.e /opt/). + +Open a linux terminal and move to a directory where iSkyLIMS code will be +downloaded + +```bash +cd < your personal folder > +git clone https://github.com/BU-ISCIII/iSkyLIMS.git iskylims +cd iskylims +``` + +#### Configuration settings + +Copy the initial setting template into a file named install_settings.txt + +```bash +cp conf/template_install_settings.txt install_settings.txt +``` + +Open with your favourite editor the configuration file to set your own values for +database ,email settings and the local IP of the server where iSkyLIMS will run. +> If you use a windows-based system for modifying the file, make sure the file is saved using a linux-friendly encoding like ASCII or UTF-8 + +```bash +sudo nano install_settings.txt +``` + +#### Running upgrade script + +If your organization requires that dependencies / stuff that needs root are installed by a different person that install the application the you can use the install script in several steps as follows. + +First you need to rename the folder app name in the installation folder (`/opt/iSkyLIMS`): + +##### Steps requiring root + +```bash +# You need root for this operation +sudo mv /opt/iSkyLIMS /opt/iskylims +``` + +Make sure that the installation folder has the correct permissions so the person installing the app can write in that folder. + +```bash +# In case you have a script for this task. You'll need to adjust this script according to the name changing: /opt/iSkyLIMS to /opt/iskylims +/scripts/hardening.sh +``` + +In the linux terminal execute one of the following command that fit better to you: + +```bash +# to upgrade only software packages dependences. NEEDS ROOT. +sudo bash install.sh --upgrade dep + +# to install both software. NEEDS ROOT. +sudo bash install.sh --upgrade full --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` + +##### Steps not requiring root + +Next you need to upgrade iskylims app. Please use the command below: + +```bash +# to upgrade only iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. +bash install.sh --upgrade app --ren_app --script drylab_service_state_migration --script rename_app_name --script rename_sample_sheet_folder --script migrate_sample_type --script migrate_optional_values --tables +``` + +Make sure that the installation folder has the correct permissions. + +```bash +# In case you have a script for this task. Some paths have changed in this version, so you may need to adjust your hardening script. +/scripts/hardening.sh +``` + +#### What to do if something fails + +When we upgrade using the installation script we are performing several changes in the database. If something fails we need to restore the app situation before anything happened and start all over. + +We need to copy back the full `/opt/iSkyLIMS` folder back to `/opt` (or your installation path preference), and restore the database doing something like this: + +```bash +sudo rm -rf /opt/iskylims +sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ +sudo /scripts/hardening.sh +mysql -u iskylims -h dmysqlps.isciiides.es +# drop database iskylims; +# create database iskylims; +mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql +``` + +### Final configuration steps + +#### SAMBA configurarion + +- Login with admin account. +- Go to Massive sequencing +![go_to_wetlab](img/got_to_wetlab.png){width:50px} +- Go to Configuration -> Samba configuration +- Fill the form with the appropiate params for the samba shared folder: +![samba form](img/samba_form.png) + +#### Email verification + +- Go to Massive sequencing +- Go to Configuration -> Email configuration +- Fill the form with the needed params for your email configuration and try to send a test email. + +#### Configure Apache server + +Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf + +#### Verification of the installation + +Open the navigator and type "localhost" or the "server local IP" and check that iSkyLIMs is running. + +You can also check some of the functionality, while also checking samba and database connections using: + +- Go to [configuration test](https://iskylims.isciii.es/wetlab/configurationTest/) +- Click submit +- Check all tabs so every connectin is successful. +- Run the 3 tests for each sequencing machine: MiSeq, NextSeq and NovaSeq. + +### iSkyLIMS documentation + +iSkyLIMS documentation is available at [https://iskylims.readthedocs.io/en/latest](https://iskylims.readthedocs.io/en/latest) From 8c322dfef7fdb3d6107f3917eef0a6423063db3d Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 22 Aug 2024 10:29:29 +0200 Subject: [PATCH 138/446] Solved issue #274. Docker installation fails --- Dockerfile | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/Dockerfile b/Dockerfile index 273659be7..180e4f109 100644 --- a/Dockerfile +++ b/Dockerfile @@ -39,8 +39,15 @@ ENV PATH="/usr/sbin/cron:$PATH" ======= RUN pip install -r conf/requirements.txt +<<<<<<< HEAD RUN bash install.sh --install app --conf conf/docker_install_settings.txt --docker +<<<<<<< HEAD >>>>>>> ff357111 (hotfix numpy dependency and docker fixes) +======= +======= +RUN bash install.sh --install app --git_revision main --conf conf/docker_install_settings.txt --docker +>>>>>>> 1f1de18d (Solved issue #274. Docker installation fails) +>>>>>>> 8f943a0e (Solved issue #274. Docker installation fails) # Install dependencies within the virtual environment RUN /srv/iskylims/venv/bin/pip install -r conf/requirements.txt From d7241a14afc790ad5589e78e6ecdaf2e71974f15 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 10:32:58 +0100 Subject: [PATCH 139/446] update ubuntu version to 24.04 --- Dockerfile | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 180e4f109..8d01abc11 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,6 +10,7 @@ RUN apt-get update && apt-get upgrade -y RUN apt-get install -y \ git wget lsb-release \ libmysqlclient-dev \ +<<<<<<< HEAD <<<<<<< HEAD python3-pip libpq-dev python3-venv python3-wheel \ apache2-dev cron \ @@ -19,12 +20,18 @@ RUN apt-get install -y \ python3-wheel apache2-dev \ gnuplot pkg-config >>>>>>> ff357111 (hotfix numpy dependency and docker fixes) +======= + python3-pip libpq-dev python3-venv python3-wheel \ + apache2-dev \ + gnuplot pkg-config rsync +>>>>>>> 5a7fbaef (update ubuntu version to 24.04) # Set MYSQLCLIENT_CFLAGS and MYSQLCLIENT_LDFLAGS using pkg-config RUN export MYSQLCLIENT_CFLAGS="$(pkg-config --libs mysqlclient)" && \ export MYSQLCLIENT_LDFLAGS="$(pkg-config --cflags mysqlclient)" # Set git repository +<<<<<<< HEAD RUN mkdir /srv/iskylims WORKDIR /srv/iskylims <<<<<<< HEAD @@ -48,6 +55,13 @@ RUN bash install.sh --install app --conf conf/docker_install_settings.txt --dock RUN bash install.sh --install app --git_revision main --conf conf/docker_install_settings.txt --docker >>>>>>> 1f1de18d (Solved issue #274. Docker installation fails) >>>>>>> 8f943a0e (Solved issue #274. Docker installation fails) +======= +RUN mkdir /srv/iskylims +WORKDIR /srv/iskylims +RUN pip install -r conf/requirements.txt + +RUN bash install.sh --install app --git_revision main --conf conf/docker_install_settings.txt --docker +>>>>>>> 5a7fbaef (update ubuntu version to 24.04) # Install dependencies within the virtual environment RUN /srv/iskylims/venv/bin/pip install -r conf/requirements.txt @@ -64,4 +78,8 @@ WORKDIR /opt/iskylims EXPOSE 8001 # Start the application -CMD ["python", "/opt/iskylims/manage.py", "runserver", "0:8001"] \ No newline at end of file +<<<<<<< HEAD +CMD ["python", "/opt/iskylims/manage.py", "runserver", "0:8001"] +======= +CMD ["python3", "/opt/iskylims/manage.py", "runserver", "0:8001"] +>>>>>>> 5a7fbaef (update ubuntu version to 24.04) From ca0626aaff379a22e68a3c5a9099b5b4de75027c Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Fri, 15 Nov 2024 10:36:34 +0100 Subject: [PATCH 140/446] implement new installation features in iskylims installation via docker_install --- Dockerfile | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 8d01abc11..723de2eb7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -58,11 +58,19 @@ RUN bash install.sh --install app --git_revision main --conf conf/docker_install ======= RUN mkdir /srv/iskylims WORKDIR /srv/iskylims -RUN pip install -r conf/requirements.txt +<<<<<<< HEAD RUN bash install.sh --install app --git_revision main --conf conf/docker_install_settings.txt --docker >>>>>>> 5a7fbaef (update ubuntu version to 24.04) +======= +# Copy the local git repository to docker image directory +COPY . /srv/iskylims + +# Create and activate a virtual environment +RUN python3 -m venv /srv/iskylims/venv + +>>>>>>> 8b387c6c (implement new installation features in iskylims installation via docker_install) # Install dependencies within the virtual environment RUN /srv/iskylims/venv/bin/pip install -r conf/requirements.txt @@ -79,7 +87,11 @@ EXPOSE 8001 # Start the application <<<<<<< HEAD +<<<<<<< HEAD CMD ["python", "/opt/iskylims/manage.py", "runserver", "0:8001"] ======= CMD ["python3", "/opt/iskylims/manage.py", "runserver", "0:8001"] >>>>>>> 5a7fbaef (update ubuntu version to 24.04) +======= +CMD ["python", "/opt/iskylims/manage.py", "runserver", "0:8001"] +>>>>>>> 8b387c6c (implement new installation features in iskylims installation via docker_install) From 700fac135cd38d18c1604773ec2d172f3632e289 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 17 Mar 2025 17:00:52 +0100 Subject: [PATCH 141/446] fix conflicts Dokerfile --- Dockerfile | 49 ------------------------------------------------- 1 file changed, 49 deletions(-) diff --git a/Dockerfile b/Dockerfile index 723de2eb7..433907bad 100644 --- a/Dockerfile +++ b/Dockerfile @@ -10,31 +10,17 @@ RUN apt-get update && apt-get upgrade -y RUN apt-get install -y \ git wget lsb-release \ libmysqlclient-dev \ -<<<<<<< HEAD -<<<<<<< HEAD python3-pip libpq-dev python3-venv python3-wheel \ apache2-dev cron \ gnuplot pkg-config rsync -======= - python3-pip libpq-dev \ - python3-wheel apache2-dev \ - gnuplot pkg-config ->>>>>>> ff357111 (hotfix numpy dependency and docker fixes) -======= - python3-pip libpq-dev python3-venv python3-wheel \ - apache2-dev \ - gnuplot pkg-config rsync ->>>>>>> 5a7fbaef (update ubuntu version to 24.04) # Set MYSQLCLIENT_CFLAGS and MYSQLCLIENT_LDFLAGS using pkg-config RUN export MYSQLCLIENT_CFLAGS="$(pkg-config --libs mysqlclient)" && \ export MYSQLCLIENT_LDFLAGS="$(pkg-config --cflags mysqlclient)" # Set git repository -<<<<<<< HEAD RUN mkdir /srv/iskylims WORKDIR /srv/iskylims -<<<<<<< HEAD # Copy the local git repository to docker image directory COPY . /srv/iskylims @@ -43,34 +29,7 @@ COPY . /srv/iskylims RUN python3 -m venv /srv/iskylims/venv ENV PATH="/srv/iskylims/venv/bin:$PATH" ENV PATH="/usr/sbin/cron:$PATH" -======= -RUN pip install -r conf/requirements.txt - -<<<<<<< HEAD -RUN bash install.sh --install app --conf conf/docker_install_settings.txt --docker -<<<<<<< HEAD ->>>>>>> ff357111 (hotfix numpy dependency and docker fixes) -======= -======= -RUN bash install.sh --install app --git_revision main --conf conf/docker_install_settings.txt --docker ->>>>>>> 1f1de18d (Solved issue #274. Docker installation fails) ->>>>>>> 8f943a0e (Solved issue #274. Docker installation fails) -======= -RUN mkdir /srv/iskylims -WORKDIR /srv/iskylims - -<<<<<<< HEAD -RUN bash install.sh --install app --git_revision main --conf conf/docker_install_settings.txt --docker ->>>>>>> 5a7fbaef (update ubuntu version to 24.04) - -======= -# Copy the local git repository to docker image directory -COPY . /srv/iskylims - -# Create and activate a virtual environment -RUN python3 -m venv /srv/iskylims/venv ->>>>>>> 8b387c6c (implement new installation features in iskylims installation via docker_install) # Install dependencies within the virtual environment RUN /srv/iskylims/venv/bin/pip install -r conf/requirements.txt @@ -86,12 +45,4 @@ WORKDIR /opt/iskylims EXPOSE 8001 # Start the application -<<<<<<< HEAD -<<<<<<< HEAD -CMD ["python", "/opt/iskylims/manage.py", "runserver", "0:8001"] -======= -CMD ["python3", "/opt/iskylims/manage.py", "runserver", "0:8001"] ->>>>>>> 5a7fbaef (update ubuntu version to 24.04) -======= CMD ["python", "/opt/iskylims/manage.py", "runserver", "0:8001"] ->>>>>>> 8b387c6c (implement new installation features in iskylims installation via docker_install) From 07813026dfe29a2cfbada79ebae448f3675b3d5e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 17 Mar 2025 17:04:51 +0100 Subject: [PATCH 142/446] fix conflicts in requirements.txt --- conf/requirements.txt | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/conf/requirements.txt b/conf/requirements.txt index ab74c18e9..814d306f3 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -13,11 +13,7 @@ django-mptt-admin==2.6.2 django-cleanup==8.1.0 interop>1.1.22 mod_wsgi==5.0.0 -<<<<<<< HEAD mysqlclient==2.2.6 -======= -mysqlclient==2.2.4 ->>>>>>> 762df044 (update the python packages used in iskylims) paramiko==3.4.1 jsonschema==4.23.0 pysmb==1.2.9.1 @@ -26,10 +22,6 @@ djangorestframework==3.15.2 drf-yasg==1.21.7 xlrd==2.0.1 pandas==2.2.2 -<<<<<<< HEAD numpy==1.26.4 openpyxl==3.1.5 -setuptools==75.2.0 -======= -openpyxl==3.1.5 ->>>>>>> 762df044 (update the python packages used in iskylims) +setuptools==75.2.0 \ No newline at end of file From 3d20c3fd065407535e9f971539206e5b53ce5153 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 17 Mar 2025 17:28:47 +0100 Subject: [PATCH 143/446] re-fix incorrect conflict solution --- wetlab/utils/crontab_update_run.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index d93ee44bb..2178bf48d 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -645,6 +645,8 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): experiment_name, ) elif run_status == "cancelled": + run_process_obj.set_run_state("cancelled") + run_process_obj.set_run_completion_date(run_completion_date) wetlab.utils.crontab_process.handling_errors_in_run(experiment_name, 34) string_message = experiment_name + "was cancelled on the sequencer" wetlab.utils.common.logging_warnings(string_message, True) From d55446f82d826ede906c20348163dcf3a404f284 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 17 Mar 2025 17:37:57 +0100 Subject: [PATCH 144/446] fix readme after conflicts --- README.md | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/README.md b/README.md index ee1f765b2..34342b4be 100644 --- a/README.md +++ b/README.md @@ -24,7 +24,6 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Upgrade from 3.0.x to iSkyLIMS version 3.1.x](#upgrade-from-30x-to-iskylims-version-31x) - [Pre-requisites for upgrade](#pre-requisites-for-upgrade) - [Clone github repository](#clone-github-repository-1) - - [Clone github repository](#clone-github-repository-2) - [Configuration settings](#configuration-settings-1) - [Running upgrade script](#running-upgrade-script) - [Steps requiring root](#steps-requiring-root) @@ -175,11 +174,7 @@ It is highly recomended that you made these backups and keep them safely in case ### Clone github repository -We've also change the way that iSkyLIMS is installed and upgraded. From now on iskylims is downloaded in a user folder and installed elsewhere (p.e /opt/). - -##### Clone github repository - -From it was defined in previous releases the iSkyLIMS code is downloaded in a user folder and then installed elsewhere (p.e /opt/). +As it was defined in previous releases the iSkyLIMS code is downloaded in a user folder and then installed elsewhere (p.e /opt/). If you have already clone the repository from the previous 3.0.0 release open a linux terminal and move towards the directory of iSkyLIMS repository. From 7f7768db8c85800517446e3c1c2aa66f3a8532ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 17 Mar 2025 17:44:43 +0100 Subject: [PATCH 145/446] fix readme after conflicts --- README.md | 74 +++---------------------------------------------------- 1 file changed, 4 insertions(+), 70 deletions(-) diff --git a/README.md b/README.md index 34342b4be..a7ed61281 100644 --- a/README.md +++ b/README.md @@ -30,8 +30,6 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Steps not requiring root](#steps-not-requiring-root) - [What to do if something fails](#what-to-do-if-something-fails) - [Final configuration steps](#final-configuration-steps) - - [What to do if something fails](#what-to-do-if-something-fails-1) - - [Final configuration steps](#final-configuration-steps-1) - [SAMBA configurarion](#samba-configurarion) - [Email verification](#email-verification) - [Configure Apache server](#configure-apache-server) @@ -165,13 +163,6 @@ Before starting the upgrade procedure is highly recomended to perform the follow It is highly recomended that you made these backups and keep them safely in case of upgrade failure, to recover your system. -Because in this upgrade many tables in database are modified it is required that you backup: - -- iSkyLIMS database -- iSkyLIMS folder (complete installation folder, p.e /opt/iSkyLIMS) - -It is highly recomended that you made these backups and keep them safely in case of upgrade failure, to recover your system. - ### Clone github repository As it was defined in previous releases the iSkyLIMS code is downloaded in a user folder and then installed elsewhere (p.e /opt/). @@ -184,16 +175,7 @@ cd < your personal folder/iskylims > git pull ``` -If you have already clone the repository from the previous 3.0.0 release open a -linux terminal and move towards the directory of iSkyLIMS repository. - -```bash -cd < your personal folder/iskylims > -git pull -``` - -If the repository was not created then open a linux terminal and move to a directory -where iSkyLIMS code will be downloaded +If the repository was not created then open a linux terminal and move to a directory where iSkyLIMS code will be downloaded ```bash cd < your personal folder > @@ -223,11 +205,6 @@ If your organization requires that dependencies / stuff that needs root are inst #### Steps requiring root -```bash -# You need root for this operation -sudo mv /opt/iSkyLIMS /opt/iskylims -``` - Make sure that the installation folder has the correct permissions so the person installing the app can write in that folder. ```bash @@ -248,50 +225,7 @@ sudo bash install.sh --upgrade dep Next you need to upgrade iskylims app. Please use one of the commands below: -If you are using the library pool, you must indicate in the installation script the file -you already backup and execute the following command. - -```bash -# to upgrade iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. -bash install.sh --upgrade app --script --git_revision main --tables -``` - -If restauration of libary preparation is not required then execute the following command - -```bash -# to upgrade iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. -bash install.sh --upgrade app ---git_revision main -tables -``` - -Make sure that the installation folder has the correct permissions. - -```bash -# In case you have a script for this task. Some paths have changed in this version, so you may need to adjust your hardening script. -/scripts/hardening.sh -``` - -## What to do if something fails - -When we upgrade using the installation script we are performing several changes in the database. If something fails we need to restore the app situation before anything happened and start all over. - -We need to copy back the full `/opt/iskylims` folder back to `/opt/iskylims` (or your installation path preference), and restore the database doing something like this: - -```bash -sudo rm -rf /opt/iskylims -sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ -sudo /scripts/hardening.sh -mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es -# drop database iskylims; -# create database iskylims; -mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql -``` - -## Final configuration steps - -Next you need to upgrade iskylims app. Please use one of the commands below: - -If you are using the library pool, you must indicate in the installation script the file -you already backup and execute the following command. +If you are using the library pool, you must indicate in the installation script the file you already backup and execute the following command. ```bash # to upgrade iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. @@ -322,10 +256,10 @@ We need to copy back the full `/opt/iskylims` folder back to `/opt/iskylims` (or sudo rm -rf /opt/iskylims sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ sudo /scripts/hardening.sh -mysql -u iskylims -h dmysqlps.isciiides.es +mysql -u iskylims -p -h dmysqlps.isciiides.es # drop database iskylims; # create database iskylims; -mysql -u iskylims -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql +mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` ## Final configuration steps From 20c5abd584fb078eb78d8ae7e90f9490b1108ae5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 17 Mar 2025 17:47:12 +0100 Subject: [PATCH 146/446] fix leame after conflicts --- LEAME.md | 17 +---------------- 1 file changed, 1 insertion(+), 16 deletions(-) diff --git a/LEAME.md b/LEAME.md index ffc8931d6..4fbef6334 100644 --- a/LEAME.md +++ b/LEAME.md @@ -21,15 +21,11 @@ De acuerdo con la infraestructura existente, la secuenciación se realiza en un - [Configuración de ajustes](#configuración-de-ajustes) - [Ejecutar el script de instalación](#ejecutar-el-script-de-instalación) - [Actualización a la versión 3.1.0 de iSkyLIMS](#actualización-a-la-versión-310-de-iskylims) - - [Actualización a la versión 3.1.0 de iSkyLIMS](#actualización-a-la-versión-310-de-iskylims-1) - [Prerrequisitos](#prerrequisitos) - - [Prerrequisitos](#prerrequisitos-1) - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) - [Configuración de opciones](#configuración-de-opciones) - [Ejecución del script de actualización](#ejecución-del-script-de-actualización) - - [Ejecución del script de actualización](#ejecución-del-script-de-actualización-1) - [Pasos que necesitan permisos de adminsitración](#pasos-que-necesitan-permisos-de-adminsitración) - - [Pasos que necesitan permisos de adminsitración](#pasos-que-necesitan-permisos-de-adminsitración-1) - [Pasos que no necesitan de permisos de administración](#pasos-que-no-necesitan-de-permisos-de-administración) - [Qué hacer si algo falla](#qué-hacer-si-algo-falla) - [Pasos finales de configuración](#pasos-finales-de-configuración) @@ -51,7 +47,6 @@ Antes de comenzar la instalación, asegúrate de lo siguiente: - Dependencias: - Librerías: -```bash ```bash yum groupinstall "Development tools" @@ -154,26 +149,21 @@ bash install.sh --install app sudo bash install.sh --install full ``` -## Actualización a la versión 3.1.0 de iSkyLIMS ## Actualización a la versión 3.1.0 de iSkyLIMS En esta version se han implementado fallos de código y mejoras en las gráficas. Para obtener más detalles sobre los cambios, consulta las notas de la versión. -### Prerrequisitos ### Prerrequisitos -Por temas de seguridad es recomendado realizar una copia de seguridad de: Por temas de seguridad es recomendado realizar una copia de seguridad de: - La base de datos de iSkyLIMS. - La carpeta de iSkyLIMS (carpeta de instalación completa, por ejemplo, /opt/iSkyLIMS). -Se recomienda encarecidamente que se hagan estas copias de seguridad y se guarden de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). Se recomienda encarecidamente que se hagan estas copias de seguridad y se guarden de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). ### Clonar el repositorio de GitHub -A partir ya de la version anterior, ahora el código de iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). A partir ya de la version anterior, ahora el código de iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). Abre una terminal de Linux y dirígete a un directorio donde estaba descargado el código de iSkyLIMS. Actualiza el codigo @@ -198,15 +188,10 @@ Abre el archivo de configuración con tu editor favorito para establecer tus pro nano install_settings.txt ``` -### Ejecución del script de actualización ### Ejecución del script de actualización -Debido a que los paquetes de python de los que depende iSkyLIMs se han ido actualizando -desde la última release es necesario que sean actualizados. -Debido a que los paquetes de python de los que depende iSkyLIMs se han ido actualizando -desde la última release es necesario que sean actualizados. +Debido a que los paquetes de python de los que depende iSkyLIMs se han ido actualizando desde la última release es necesario que sean actualizados. -#### Pasos que necesitan permisos de adminsitración #### Pasos que necesitan permisos de adminsitración En primer lugar, debes cambiar el nombre de la carpeta de la aplicación en la carpeta de instalación (`/opt/iSkyLIMS`): From 0774b586358a90e5d66287c7b16b5d8617864b55 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 17 Mar 2025 17:49:35 +0100 Subject: [PATCH 147/446] fix leame after conflicts --- LEAME.md | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/LEAME.md b/LEAME.md index 4fbef6334..8bbcae0e6 100644 --- a/LEAME.md +++ b/LEAME.md @@ -26,7 +26,7 @@ De acuerdo con la infraestructura existente, la secuenciación se realiza en un - [Configuración de opciones](#configuración-de-opciones) - [Ejecución del script de actualización](#ejecución-del-script-de-actualización) - [Pasos que necesitan permisos de adminsitración](#pasos-que-necesitan-permisos-de-adminsitración) - - [Pasos que no necesitan de permisos de administración](#pasos-que-no-necesitan-de-permisos-de-administración) + - [Pasos que no necesitan de permisos de administración](#pasos-que-no-necesitan-de-permisos-de-administración) - [Qué hacer si algo falla](#qué-hacer-si-algo-falla) - [Pasos finales de configuración](#pasos-finales-de-configuración) - [Configuración de SAMBA](#configuración-de-samba) @@ -194,13 +194,6 @@ Debido a que los paquetes de python de los que depende iSkyLIMs se han ido actua #### Pasos que necesitan permisos de adminsitración -En primer lugar, debes cambiar el nombre de la carpeta de la aplicación en la carpeta de instalación (`/opt/iSkyLIMS`): - -```bash -# Necesitas ser usuario root para realizar esta operación -sudo mv /opt/iSkyLIMS /opt/iskylims -``` - Asegúrate de que la carpeta de instalación tenga los permisos correctos para que la persona que instala la aplicación pueda escribir en esa carpeta. ```bash @@ -218,7 +211,7 @@ sudo bash install.sh --upgrade dep sudo bash install.sh --upgrade full --git_revision main --tables ``` -##### Pasos que no necesitan de permisos de administración +#### Pasos que no necesitan de permisos de administración Actualiza a la nueva version de la aplicación de iskylims usando el siguiente comando: @@ -243,10 +236,10 @@ Necesitamos copiar de vuelta nuestro backup de carpet ade aplicación a /opt/iSk sudo rm -rf /opt/iskylims sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ sudo /scripts/hardening.sh -mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es +mysql -u iskylims -p -h dmysqlps.isciiides.es # drop database iskylims; # create database iskylims; -mysql -u iskylims -p'1s1yL3ms$1$1' -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql +mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` ### Pasos finales de configuración From 8d5a91f0ec255373f53c79146d8b05486af18fdb Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 1 Sep 2024 12:41:31 +0200 Subject: [PATCH 148/446] Changed to warnings if Run parameter file is not yet uploaded --- wetlab/utils/crontab_update_run.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 2178bf48d..ec57f44ac 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -117,9 +117,9 @@ def search_update_new_runs(request_reason): error_message = ( "Unable to fetch RunParameter file for folder :" + new_run ) - wetlab.utils.common.logging_errors(error_message, True, False) + wetlab.utils.common.logging_warnings(error_message, True) experiment_name = "Experiment name NOT FOUND" - wetlab.utils.common.logging_errors(error_message, True, False) + wetlab.utils.common.logging_warnings(error_message, True) # check the run folder creation date to allow more time before # setting the run to error f_created_date = wetlab.utils.common.get_samba_atribute_data( @@ -174,6 +174,9 @@ def search_update_new_runs(request_reason): new_run + " : Experiment name field was not found in file" ) wetlab.utils.common.logging_errors(string_message, False, False) + wetlab.utils.crontab_process.handling_errors_in_run( + new_run, "7" + ) else: string_message = ( new_run + " : Ignoring test folder " + experiment_name From 1e2e4f09ef36b28031989e8e3376f8e06a1b2bc3 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 1 Sep 2024 17:52:30 +0200 Subject: [PATCH 149/446] Correcting extra parameter when calling logging_warnings --- wetlab/utils/crontab_process.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index 08fadcd54..094b3b015 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -649,7 +649,7 @@ def fetch_remote_file(conn, run_dir, remote_file, local_file): string_message = ( "Unable to fetch the " + local_file + " file on folder : " + run_dir ) - wetlab.utils.common.logging_warnings(string_message, True, False) + wetlab.utils.common.logging_warnings(string_message, False) os.remove(local_file) logger.debug( "%s : End function for fetching remote file with Exception", run_dir From ee9e2a4ed4cf66cba70cc09fb2ad7906daf919f7 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 3 Sep 2024 11:38:50 +0200 Subject: [PATCH 150/446] implemented issue #109 --- wetlab/api/views.py | 55 +++++++++++++++++++-------------------------- 1 file changed, 23 insertions(+), 32 deletions(-) diff --git a/wetlab/api/views.py b/wetlab/api/views.py index b0bede765..bfaa9f8c7 100644 --- a/wetlab/api/views.py +++ b/wetlab/api/views.py @@ -266,38 +266,6 @@ def create_sample_data(request): return Response(status=status.HTTP_400_BAD_REQUEST) -@swagger_auto_schema( - method="get", - operation_description="Get the stored Run information available in iSkyLIMS for the list of samples", - manual_parameters=[sample_in_run], -) -@api_view(["GET"]) -def fetch_run_information(request): - if "samples" in request.GET: - samples = request.GET["samples"] - # sample_run_info = get_run_info_for_sample(apps_name, samples) - s_list = samples.strip().split(",") - s_data = [] - for sample in s_list: - sample = sample.strip() - if wetlab.models.SamplesInProject.objects.filter( - sample_name__iexact=sample - ).exists(): - s_found_objs = wetlab.models.SamplesInProject.objects.filter( - sample_name__iexact=sample - ) - for s_found_obj in s_found_objs: - s_data.append( - wetlab.api.serializers.SampleRunInfoSerializers( - s_found_obj, many=False - ).data - ) - else: - s_data.append({"sample_name": sample, "Run data": "Not found"}) - return Response(s_data, status=status.HTTP_200_OK) - return Response(status=status.HTTP_400_BAD_REQUEST) - - @swagger_auto_schema( method="get", operation_description="Get the sample/samples belongs to project information, collected when creating in iSkyLIMS", @@ -305,7 +273,30 @@ def fetch_run_information(request): ) @api_view(["GET"]) def fetch_sample_information(request): + """This request is used to get the sample information from the database. If + sequencing is received in the request, the request will return the run + information for this sample. + If not then all infromation is related to the sample creation, which means + sample project, project fields. + """ sample_data = {} + if "sequencing" in request.GET and "sample" in request.GET: + sample = request.GET["sample"].strip() + s_data = [] + if wetlab.models.SamplesInProject.objects.filter( + sample_name__iexact=sample + ).exists(): + sample_obj = wetlab.models.SamplesInProject.objects.filter( + sample_name__iexact=sample + ) + s_data.append( + wetlab.api.serializers.SampleRunInfoSerializers( + sample_obj, many=False + ).data + ) + else: + s_data.append({"sample_name": sample, "Run data": "Not found"}) + return Response(s_data, status=status.HTTP_200_OK) if "sample" in request.GET: sample = request.GET["sample"] if not core.models.Samples.objects.filter(sample_name__iexact=sample).exists(): From 1ae1c8fb20d5737cd53f04d48d47686caf99e4a4 Mon Sep 17 00:00:00 2001 From: luissian Date: Tue, 3 Sep 2024 13:52:33 +0200 Subject: [PATCH 151/446] removed fetch_run_information from url wetlab api --- wetlab/api/urls.py | 1 - 1 file changed, 1 deletion(-) diff --git a/wetlab/api/urls.py b/wetlab/api/urls.py index 5948504c1..871a2dfb7 100644 --- a/wetlab/api/urls.py +++ b/wetlab/api/urls.py @@ -5,7 +5,6 @@ urlpatterns = [ - path("run-info", views.fetch_run_information, name="fetch_run_information"), path( "lab-data", views.get_lab_information_contact, From 2254aee4637f173fbfe01de91c46bc477bcb3608 Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 19 Sep 2024 22:59:42 +0200 Subject: [PATCH 152/446] replace deprecated function --- wetlab/utils/crontab_update_run.py | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index ec57f44ac..645e6d593 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -119,17 +119,18 @@ def search_update_new_runs(request_reason): ) wetlab.utils.common.logging_warnings(error_message, True) experiment_name = "Experiment name NOT FOUND" - wetlab.utils.common.logging_warnings(error_message, True) # check the run folder creation date to allow more time before # setting the run to error - f_created_date = wetlab.utils.common.get_samba_atribute_data( - conn, - wetlab.utils.crontab_process.get_samba_shared_folder(), - new_run, - "create_time", + f_created_date = int( + wetlab.utils.common.get_samba_atribute_data( + conn, + wetlab.utils.crontab_process.get_samba_shared_folder(), + new_run, + "create_time", + ).timestamp() ) - time_to_check = datetime.datetime.utcfromtimestamp( - f_created_date + time_to_check = datetime.datetime.fromtimestamp( + f_created_date, tz=datetime.timezone.utc ).date() max_time_for_run_parameters = ( wetlab.models.ConfigSetting.objects.filter( From 40b52fa0f5b473aedb2a8b6ca0435a56a3ec455e Mon Sep 17 00:00:00 2001 From: luissian Date: Thu, 19 Sep 2024 23:00:53 +0200 Subject: [PATCH 153/446] fix error in matching sample sheet file name --- wetlab/views.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wetlab/views.py b/wetlab/views.py index 5f0386a92..820088622 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -325,7 +325,7 @@ def create_nextseq_run(request): # CHECK if file contains the extension. # Error page is showed if file does not contain any extension - split_filename = re.search("(.*)(\.\w+$)", myfile.name) + split_filename = re.search(r"(.*)(\.\w+$)", myfile.name) if split_filename is None: return render( request, From 9311f873926440ab62a4a81eb7be48f75f7307e4 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 22 Sep 2024 12:28:12 +0200 Subject: [PATCH 154/446] include in the gitignore the vscode folder --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index 64b77f46c..79b37fb50 100644 --- a/.gitignore +++ b/.gitignore @@ -17,6 +17,7 @@ documents/ manage.py logs/ logs +.vscode/ # Byte-compiled / optimized / DLL files From 03a333972591ec904032122839b5a8d3df61c444 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 27 Sep 2024 14:04:03 +0200 Subject: [PATCH 155/446] Solved issue #300 Error when sample proyects has no parameters --- core/core_config.py | 4 ++-- core/utils/samples.py | 13 +++++++++++ .../wetlab/define_sample_project_fields.html | 19 ++++++++++++++- .../wetlab/modify_sample_project_fields.html | 23 +++++++++++++++---- wetlab/views.py | 18 +++++++++++---- 5 files changed, 64 insertions(+), 13 deletions(-) diff --git a/core/core_config.py b/core/core_config.py index 5a9bc8a55..3e3e7aa66 100644 --- a/core/core_config.py +++ b/core/core_config.py @@ -104,7 +104,7 @@ "Field name", "Order", "Used", - "Searchable", + "Downloadable", "Field type", "Option Values", "Description", @@ -116,7 +116,7 @@ "Change field name", "Order", "Used", - "Searchable", + "Downloadable", "Field type", "Option Values", "Description", diff --git a/core/utils/samples.py b/core/utils/samples.py index 4febefe2c..ddb5084a5 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -2093,6 +2093,19 @@ def set_sample_project_fields(data_form): saved_fields = [] stored_fields = {} + valid_data = False + import pdb + + pdb.set_trace() + # check if there is at least one field to be used + for row_line in excel_json_data: + if row_line["Used"] == True: + valid_data = True + break + if not valid_data: + stored_fields["ERROR"] = core.core_config.ERROR_NO_USED_FIELD_ARE_ARE_SET + return stored_fields + for row_line in excel_json_data: if row_line["Field name"] == "": continue diff --git a/wetlab/templates/wetlab/define_sample_project_fields.html b/wetlab/templates/wetlab/define_sample_project_fields.html index 7f71cb6b6..9c4d696b4 100644 --- a/wetlab/templates/wetlab/define_sample_project_fields.html +++ b/wetlab/templates/wetlab/define_sample_project_fields.html @@ -174,7 +174,7 @@

    Define Samples Proyect Fields for {{sample_project

    -
    +
    {% endif %}

    @@ -198,9 +198,26 @@

    Define Samples Proyect Fields for {{sample_project csvFileName:'sample_project_fields', minDimensions:[8,5], }); + // Function to check if at least one checkbox in the "Used" column is set to true + function isAnyUsedColumnChecked() { + var table_data1 = table1.getData(); + // Assuming the "Used" column is the third column (index 2) + for (var i = 0; i < table_data1.length; i++) { + if (table_data1[i][2] === true) { // Check if "Used" column (index 2) is true + return true; + } + } + return false; + } // send form adding table $(document).ready(function () { $("#defineSampleProjectFields").submit(function (e) { + // Check if at least one "Used" checkbox is checked + if (!isAnyUsedColumnChecked()) { + e.preventDefault(); // Prevent form submission + alert('You must select at least one "Used" checkbox before submitting.'); + return false; + } //stop submitting the form to see the disabled button effect //disable the submit button var table_data1 = table1.getData() diff --git a/wetlab/templates/wetlab/modify_sample_project_fields.html b/wetlab/templates/wetlab/modify_sample_project_fields.html index 4b6c6be4a..97cbfc730 100644 --- a/wetlab/templates/wetlab/modify_sample_project_fields.html +++ b/wetlab/templates/wetlab/modify_sample_project_fields.html @@ -116,7 +116,7 @@

    Modify sample project fields for {{ sample_project_field.sample_project_name { type: 'text', title:'{{sample_project_field.heading.1}}', width:160 }, { type: 'numeric', title:'{{sample_project_field.heading.2}}', width:50, mask:' #.##' }, { type: 'checkbox', title:'{{sample_project_field.heading.3}}', width:50 }, - { type: 'checkbox', title:'{{sample_project_field.heading.4}}', width:100 }, + { type: 'checkbox', title:'{{sample_project_field.heading.4}}', width:120 }, { type: 'dropdown' , title: '{{sample_project_field.heading.5}}', width:150 , source: ["String", "Date" , "Options List"] }, { type: 'text', title:'{{sample_project_field.heading.6}}', width:240, wordWrap:true }, { type: 'text', title:'{{sample_project_field.heading.7}}', width:400 , wordWrap:true }, @@ -131,13 +131,26 @@

    Modify sample project fields for {{ sample_project_field.sample_project_name tableOverflow: false, tableWidth: "1100px", }); - + // Function to check if at least one checkbox in the "Used" column is set to true + function isAnyUsedColumnChecked() { + var table_data1 = table1.getData(); + // Assuming the "Used" column is the third column (index 2) + for (var i = 0; i < table_data1.length; i++) { + if (table_data1[i][2] === true) { // Check if "Used" column (index 2) is true + return true; + } + } + return false; + } // append table to form $(document).ready(function () { $("#modifySampleProjectFields").submit(function (e) { - //stop submitting the form to see the disabled button effect - //e.preventDefault(); - //disable the submit button + // Check if at least one "Used" checkbox is checked + if (!isAnyUsedColumnChecked()) { + e.preventDefault(); // Prevent form submission + alert('You must select at least one "Used" checkbox before submitting.'); + return false; + } var table_data1 = table1.getData() var data1_json = JSON.stringify(table_data1) $("").attr("type", "hidden") diff --git a/wetlab/views.py b/wetlab/views.py index 820088622..53622e3cd 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -2614,6 +2614,9 @@ def define_sample_projects_fields(request, sample_project_id): "wetlab/define_sample_projects_fields.html", {"error_message": "You do not have enough privileges to see this page "}, ) + sample_project_data = core.utils.samples.define_table_for_sample_project_fields( + sample_project_id + ) # get the list of defined sample Projects if ( request.method == "POST" @@ -2622,10 +2625,19 @@ def define_sample_projects_fields(request, sample_project_id): sample_project_field_data = core.utils.samples.set_sample_project_fields( request.POST ) + if "ERROR" in sample_project_field_data: + return render( + request, + "wetlab/define_sample_project_fields.html", + {"error_message": sample_project_field_data["ERROR"]}, + ) return render( request, "wetlab/define_sample_project_fields.html", - {"sample_project_field_data": sample_project_field_data}, + { + "sample_project_field_data": sample_project_field_data, + "sample_project_data": sample_project_data, + }, ) elif request.method == "POST" and request.POST["action"] == "defineBatchFields": @@ -2678,10 +2690,6 @@ def define_sample_projects_fields(request, sample_project_id): "error_message": "The requested Sample project does not exist", }, ) - - sample_project_data = core.utils.samples.define_table_for_sample_project_fields( - sample_project_id - ) return render( request, "wetlab/define_sample_project_fields.html", From 8144bc7b620f245f54b1f8f7d8ecb59cf33c49c7 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 27 Sep 2024 14:10:24 +0200 Subject: [PATCH 156/446] Fixing liting --- core/utils/samples.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/utils/samples.py b/core/utils/samples.py index ddb5084a5..2afa376a5 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -2099,7 +2099,7 @@ def set_sample_project_fields(data_form): pdb.set_trace() # check if there is at least one field to be used for row_line in excel_json_data: - if row_line["Used"] == True: + if row_line["Used"] is True: valid_data = True break if not valid_data: From 57b8fd3ea108a4292936ebb46c929ddbdec46fbd Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 27 Sep 2024 15:17:23 +0200 Subject: [PATCH 157/446] solving issue #314 lab_name Keyerror when defining a new laboratory --- core/core_config.py | 2 ++ core/utils/common.py | 18 +++++++++--------- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/core/core_config.py b/core/core_config.py index 3e3e7aa66..1c5d034a4 100644 --- a/core/core_config.py +++ b/core/core_config.py @@ -237,6 +237,8 @@ ERROR_SAMPLE_ALREADY_DEFINED = ["Sample", "already exist in the database"] +ERROR_NO_USED_FIELD_ARE_ARE_SET = ["No field is set as used"] + # ###################### Batch file ############################################### ERROR_EMPTY = [ "The uploaded table or batch file does not have any sample. Upload a valid batch file" diff --git a/core/utils/common.py b/core/utils/common.py index 6873eb1d5..589fbe681 100644 --- a/core/utils/common.py +++ b/core/utils/common.py @@ -250,26 +250,26 @@ def save_inital_sample_setting_value(apps_name, data): if "lab_request" in data: lab_request_data = {} lab_request_data["apps_name"] = apps_name - lab_request_data["labName"] = data["lab_request"]["labRequestName"] - lab_request_data["labNameCoding"] = data["lab_request"]["labRequesCoding"] - lab_request_data["labUnit"] = data["lab_request"]["department"] - lab_request_data["labContactName"] = data["lab_request"]["contact"] - lab_request_data["labPhone"] = data["lab_request"]["phone"] - lab_request_data["labEmail"] = data["lab_request"]["email"] + lab_request_data["lab_name"] = data["lab_request"]["labRequestName"] + lab_request_data["lab_name_coding"] = data["lab_request"]["labRequesCoding"] + lab_request_data["lab_unit"] = data["lab_request"]["department"] + lab_request_data["lab_contact_name"] = data["lab_request"]["contact"] + lab_request_data["lab_phone"] = data["lab_request"]["phone"] + lab_request_data["lab_email"] = data["lab_request"]["email"] lab_request_data["address"] = data["lab_request"]["address"] lab_request_data["city"] = data["lab_request"]["city"] if core.models.LabRequest.objects.filter( - lab_name_coding__iexact=lab_request_data["labNameCoding"], + lab_name_coding__iexact=lab_request_data["lab_name_coding"], apps_name__exact=lab_request_data["apps_name"], ).exists(): setting_defined["ERROR"] = [ core.core_config.ERROR_LABORATORY_REQUEST_ALREADY_DEFINED, - lab_request_data["labNameCoding"], + lab_request_data["lab_name_coding"], ] return setting_defined core.models.LabRequest.objects.create_lab_request(lab_request_data) setting_defined["settings"] = "Lab Request" - setting_defined["value"] = lab_request_data["labName"] + setting_defined["value"] = lab_request_data["lab_name"] if "molecule_type" in data: molecule_type_data = {} molecule_type_data["apps_name"] = apps_name From 0fab8ee91f5895148b67ae3b242e323efa585585 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 27 Sep 2024 16:42:37 +0200 Subject: [PATCH 158/446] Solved iddue #301 tables for Molecules use specification are shown empty even there are samples to be handled --- wetlab/templates/wetlab/handling_molecules.html | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/wetlab/templates/wetlab/handling_molecules.html b/wetlab/templates/wetlab/handling_molecules.html index 37d6edf76..97667b4d4 100644 --- a/wetlab/templates/wetlab/handling_molecules.html +++ b/wetlab/templates/wetlab/handling_molecules.html @@ -412,6 +412,8 @@

    Not molecule uses have been defined yet

    return true; }); }); + {% endif %} + {% if molecules_availables.molecule_heading %} // excel for pending molecules var data2 = [{% for values in molecules_availables.data %} [{% for value in values %}'{{value}}',{% endfor %}],{% endfor %} @@ -437,7 +439,6 @@

    Not molecule uses have been defined yet

    pagination:20, csvFileName:'molecule_use', }); - // send form for molecule in use $(document).ready(function () { $("#selectedOwnerMolecules").submit(function (e) { @@ -451,7 +452,8 @@

    Not molecule uses have been defined yet

    return true; }); }); - + {% endif %} + {% if pending_to_use.heading %} // excel for selecting the molecule use var data3 = [{% for values in pending_to_use.data %} [{% for value in values %}'{{value}}',{% endfor %}],{% endfor %} From ccd0c3a467570aaec7f1877da1236119aa29b820 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 27 Sep 2024 19:49:48 +0200 Subject: [PATCH 159/446] solved issue #315 allowed to submit even not Select the Samples to add Molecule information --- core/utils/samples.py | 2 +- .../templates/wetlab/handling_molecules.html | 28 +++++++++++++++---- .../wetlab/modify_sample_project_fields.html | 4 +-- wetlab/views.py | 2 +- 4 files changed, 26 insertions(+), 10 deletions(-) diff --git a/core/utils/samples.py b/core/utils/samples.py index 2afa376a5..e1e231b9f 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -1514,7 +1514,7 @@ def get_selection_from_excel_data(data, heading, check_field, field_id): excel_json_data = core.utils.common.jspreadsheet_to_dict(heading, excel_data) for row in excel_json_data: if check_field is not None: - if row[check_field] is True or row[check_field] != "": + if row[check_field] is True: selected.append(row[field_id]) selected_row.append(row) else: diff --git a/wetlab/templates/wetlab/handling_molecules.html b/wetlab/templates/wetlab/handling_molecules.html index 97667b4d4..84a9f4e7e 100644 --- a/wetlab/templates/wetlab/handling_molecules.html +++ b/wetlab/templates/wetlab/handling_molecules.html @@ -268,7 +268,7 @@

    Select the molecules to add Extraction information

    {% else %} -

    There is no samples to add Molecule Extraction information

    +

    There is no samples to add Extraction information

    {% endif %}
    @@ -286,7 +286,7 @@

    There is no samples to add Molecule Extraction information

    -

    Select the Samples to add Molecule information

    +

    Select the Samples to add Pending extraction information

    {% if molecules_availables %} @@ -298,7 +298,7 @@

    Select the Samples to add Molecule information

    {% csrf_token %}
    -
    +
    Not molecule uses have been defined yet

    }); {% endif %} {% if molecules_availables.molecule_heading %} - // excel for pending molecules + // excel for pending Extraction data var data2 = [{% for values in molecules_availables.data %} [{% for value in values %}'{{value}}',{% endfor %}],{% endfor %} ]; - var table2 = jexcel(document.getElementById('pending_molecules'), { + var table2 = jexcel(document.getElementById('pending_extraction'), { data:data2, columns: [{% for values in molecules_availables.molecule_heading %} {% if forloop.last %} @@ -439,13 +439,29 @@

    Not molecule uses have been defined yet

    pagination:20, csvFileName:'molecule_use', }); + // Function to check if at least one checkbox in the "select sample" column is set to true + function isAnySelectedColumnChecked() { + var table_data2 = table2.getData(); + // Assuming the "Select sample" column is the third column (index 5) + for (var i = 0; i < table_data2.length; i++) { + if (table_data2[i][5] === true) { // Check if "Select sample" column (index 5) is true + return true; + } + } + return false; + } // send form for molecule in use $(document).ready(function () { $("#selectedOwnerMolecules").submit(function (e) { + if (!isAnySelectedColumnChecked()) { + e.preventDefault(); // Prevent form submission + alert('You must select at least one sample before submitting.'); + return false; + } var table_data2 = table2.getData() var data_json = JSON.stringify(table_data2) $("").attr("type", "hidden") - .attr("name", "pending_molecules") + .attr("name", "pending_extraction") .attr("value", data_json) .appendTo("#selectedOwnerMolecules"); $("#btnSubmit").attr("disabled", true); diff --git a/wetlab/templates/wetlab/modify_sample_project_fields.html b/wetlab/templates/wetlab/modify_sample_project_fields.html index 97cbfc730..82a68113c 100644 --- a/wetlab/templates/wetlab/modify_sample_project_fields.html +++ b/wetlab/templates/wetlab/modify_sample_project_fields.html @@ -134,9 +134,9 @@

    Modify sample project fields for {{ sample_project_field.sample_project_name // Function to check if at least one checkbox in the "Used" column is set to true function isAnyUsedColumnChecked() { var table_data1 = table1.getData(); - // Assuming the "Used" column is the third column (index 2) + // Assuming the "Used" column is the third column (index 3) for (var i = 0; i < table_data1.length; i++) { - if (table_data1[i][2] === true) { // Check if "Used" column (index 2) is true + if (table_data1[i][3] === true) { // Check if "Used" column (index 3) is true return true; } } diff --git a/wetlab/views.py b/wetlab/views.py index 53622e3cd..d34b7f394 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -3284,7 +3284,7 @@ def handling_molecules(request): heading = core.core_config.HEADING_FOR_PENDING_MOLECULES.copy() heading.insert(-1, "s_id") molecules, _ = core.utils.samples.get_selection_from_excel_data( - request.POST["pending_molecules"], heading, "Select Molecule", "s_id" + request.POST["pending_extraction"], heading, "Select Molecule", "s_id" ) if len(molecules) == 0: return redirect("handling_molecules") From 6cf9b254988a085b014c46422d0138f1408f6328 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 27 Sep 2024 20:40:15 +0200 Subject: [PATCH 160/446] Solved issue #305 Not validated when date in sample project fields contatins also the time --- core/utils/samples.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/core/utils/samples.py b/core/utils/samples.py index e1e231b9f..c7fedbf32 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -413,6 +413,10 @@ def validate_project_data(project_data, project_name, sample_validation=False): sample_dict["Validation error"].append(" ".join(error_cause)) """ if field_type == "Date" and sample[field_name] != "": + # if field contains also time, then removed it + sample[field_name] = re.sub( + r"\s\d{2}:\d{2}:\d{2}", "", sample[field_name] + ) try: datetime.datetime.strptime(sample[field_name], "%Y-%m-%d") except Exception: From 2cad3c55326fe5b815830046846b7aedc8e34300 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 27 Sep 2024 21:03:10 +0200 Subject: [PATCH 161/446] Solved issue #318 Duplicate sample when selecting it for to do next after extraction --- core/utils/samples.py | 4 +++- wetlab/views.py | 1 - 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/core/utils/samples.py b/core/utils/samples.py index c7fedbf32..3e7b22f7e 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -702,7 +702,9 @@ def create_table_molecule_pending_use(sample_list, app_name): use_type["data"] = list( core.models.MoleculePreparation.objects.filter( molecule_used_for=None, sample__in=sample_list - ).values_list("sample__sample_name", "molecule_code_id", "pk") + ) + .exclude(state__molecule_state_name="Completed") + .values_list("sample__sample_name", "molecule_code_id", "pk") ) if len(use_type["data"]) > 0: if core.models.MoleculeUsedFor.objects.filter( diff --git a/wetlab/views.py b/wetlab/views.py index d34b7f394..57983ecd1 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -3371,7 +3371,6 @@ def handling_molecules(request): molecule_use_defined = core.utils.samples.check_if_molecule_use_defined( __package__ ) - return render( request, "wetlab/handling_molecules.html", From 2a51945712e80ca09847390d1ae2143654756958 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 27 Sep 2024 23:02:11 +0200 Subject: [PATCH 162/446] solved issue #319 incorrect state set for molecule after filling the extraction data --- conf/first_install_tables.json | 17 +++++++++++--- core/core_config.py | 6 ++--- core/models.py | 3 ++- core/utils/samples.py | 10 ++++----- .../templates/wetlab/handling_molecules.html | 22 +++++++++---------- wetlab/views.py | 3 ++- 6 files changed, 37 insertions(+), 24 deletions(-) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index cb3c1345c..9df3f5ead 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -324,21 +324,32 @@ "model": "core.statesformolecule", "pk": 3, "fields": { - "molecule_state_name": "Defined" + "molecule_state_name": "defined", + "molecule_state_display": "Defined" } }, { "model": "core.statesformolecule", "pk": 4, "fields": { - "molecule_state_name": "Assigned Protocol" + "molecule_state_name": "assigned_parameters", + "molecule_state_display": "Assigned Parameters" } }, { "model": "core.statesformolecule", "pk": 5, "fields": { - "molecule_state_name": "Completed" + "molecule_state_name": "completed", + "molecule_state_display": "Completed" + } +}, +{ + "model": "core.statesformolecule", + "pk": 6, + "fields": { + "molecule_state_name": "sent_external", + "molecule_state_display": "Sent to external service" } }, { diff --git a/core/core_config.py b/core/core_config.py index 1c5d034a4..d41b21573 100644 --- a/core/core_config.py +++ b/core/core_config.py @@ -22,7 +22,7 @@ ] HEADING_FOR_MOLECULE_ADDING_PARAMETERS = [ "Sample", - "Molecule Code ID", + "Extraction Code ID", "Lot Commercial Kit", ] @@ -74,8 +74,8 @@ HEADING_FOR_SELECTING_MOLECULE_USE = [ "Sample Name", - "Molecule CodeID", - "Molecule use for", + "Extraction CodeID", + "Sample continue on", ] # ################ PROTOCOL PARAMETER SETTINGS ############################## diff --git a/core/models.py b/core/models.py index 32d32ff21..5c51efb64 100644 --- a/core/models.py +++ b/core/models.py @@ -372,6 +372,7 @@ def get_id(self): class StatesForMolecule(models.Model): molecule_state_name = models.CharField(max_length=50) + molecule_state_display = models.CharField(max_length=80, null=True, blank=True) class Meta: db_table = "core_states_for_molecule" @@ -1495,7 +1496,7 @@ def create_molecule(self, molecule_data): protocol_used=protocol_used_obj, sample=molecule_data["sample"], molecule_type=molecule_used_obj, - state=StatesForMolecule.objects.get(molecule_state_name__exact="Defined"), + state=StatesForMolecule.objects.get(molecule_state_name__exact="defined"), molecule_code_id=molecule_data["molecule_code_id"], molecule_extraction_date=molecule_data["molecule_extraction_date"], extraction_type=molecule_data["extraction_type"], diff --git a/core/utils/samples.py b/core/utils/samples.py index 3e7b22f7e..3c67d8a2d 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -565,7 +565,7 @@ def add_molecule_protocol_parameters(data, parameters): molecule_parameter_value ) - molecule_obj.set_state("Completed") + molecule_obj.set_state("assigned_parameters") # Update sample state sample_obj = molecule_obj.get_sample_obj() sample_obj.set_state("Pending for use") @@ -701,10 +701,10 @@ def create_table_molecule_pending_use(sample_list, app_name): use_type = {} use_type["data"] = list( core.models.MoleculePreparation.objects.filter( - molecule_used_for=None, sample__in=sample_list - ) - .exclude(state__molecule_state_name="Completed") - .values_list("sample__sample_name", "molecule_code_id", "pk") + molecule_used_for=None, + sample__in=sample_list, + state__molecule_state_name="assigned_parameters", + ).values_list("sample__sample_name", "molecule_code_id", "pk") ) if len(use_type["data"]) > 0: if core.models.MoleculeUsedFor.objects.filter( diff --git a/wetlab/templates/wetlab/handling_molecules.html b/wetlab/templates/wetlab/handling_molecules.html index 84a9f4e7e..89f5270d7 100644 --- a/wetlab/templates/wetlab/handling_molecules.html +++ b/wetlab/templates/wetlab/handling_molecules.html @@ -108,15 +108,15 @@

    Information missing

    -

    Update molecules data with defined parameters

    +

    Update sample extraction data with defined parameters

    + name="addExtractionParameters" + id="addExtractionParameters"> {% csrf_token %} - + {% for prot, value_dict in molecule_parameters.items %} Protocol: {{ prot }}

    -

    Molecules have been updated with required parameters.

    +

    Samples have been updated with Extraction required parameters.

    @@ -208,7 +208,7 @@

    Molecules are updated with their use.

    type="button" role="tab" aria-controls="n_samples" - aria-selected="true">New Samples + aria-selected="true">Recorded Samples
    @@ -669,13 +669,13 @@

    Not molecule uses have been defined yet

    }); - $("#addMoleculeParameters").submit(function (e) { + $("#addExtractionParameters").submit(function (e) { var table_data = {{ prot }}_data_table.getData() var data_json = JSON.stringify(table_data) $("").attr("type", "hidden") .attr("name", "{{ prot }}") .attr("value", data_json) - .appendTo("#addMoleculeParameters"); + .appendTo("#addExtractionParameters"); $("#button-submit").attr("disabled", true); return true; }); diff --git a/wetlab/views.py b/wetlab/views.py index 57983ecd1..fa9580c79 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -3303,7 +3303,7 @@ def handling_molecules(request): }, ) - elif request.method == "POST" and request.POST["action"] == "addMoleculeParameters": + elif request.method == "POST" and request.POST["action"] == "addExtractionParameters": protocols = request.POST["protocol_list"].split(";") for protocol in protocols: heading = core.core_config.HEADING_FOR_MOLECULE_ADDING_PARAMETERS.copy() @@ -3371,6 +3371,7 @@ def handling_molecules(request): molecule_use_defined = core.utils.samples.check_if_molecule_use_defined( __package__ ) + return render( request, "wetlab/handling_molecules.html", From 2e051738ce3a9dd0b6c146c165fdccbcf74dfcbf Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 27 Sep 2024 23:55:55 +0200 Subject: [PATCH 163/446] fixing liting --- wetlab/views.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/wetlab/views.py b/wetlab/views.py index fa9580c79..49413b818 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -3303,7 +3303,9 @@ def handling_molecules(request): }, ) - elif request.method == "POST" and request.POST["action"] == "addExtractionParameters": + elif ( + request.method == "POST" and request.POST["action"] == "addExtractionParameters" + ): protocols = request.POST["protocol_list"].split(";") for protocol in protocols: heading = core.core_config.HEADING_FOR_MOLECULE_ADDING_PARAMETERS.copy() From 658fb102451348d72e05862ad90367a35609c5a5 Mon Sep 17 00:00:00 2001 From: luissian Date: Fri, 27 Sep 2024 23:59:55 +0200 Subject: [PATCH 164/446] increase node version to 16 --- .github/workflows/python_lint.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index adf58c6ce..82357e979 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -28,7 +28,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Setup - uses: actions/checkout@v2 + uses: actions/checkout@v4 - name: Install black in jupyter run: pip install black[jupyter] - name: Check code lints with Black From c08b0377ca9f69f7d89895bbd8d438a931f524ae Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 28 Sep 2024 11:11:30 +0200 Subject: [PATCH 165/446] Solved issue #310 Key error for a sample with no molecule extraction parameters are requested --- core/models.py | 15 ++++- core/utils/samples.py | 56 ++++++++++--------- .../templates/wetlab/handling_molecules.html | 20 +++---- wetlab/urls.py | 5 -- wetlab/views.py | 15 ++++- 5 files changed, 65 insertions(+), 46 deletions(-) diff --git a/core/models.py b/core/models.py index 5c51efb64..742c19170 100644 --- a/core/models.py +++ b/core/models.py @@ -1482,6 +1482,7 @@ def get_massive(self): class MoleculePreparationManager(models.Manager): def create_molecule(self, molecule_data): + req_upd_sample_state = False molecule_used_obj = MoleculeType.objects.filter( molecule_type__exact=molecule_data["molecule_type"] ).last() @@ -1492,17 +1493,27 @@ def create_molecule(self, molecule_data): protocol_used_obj = Protocols.objects.filter( name__exact=molecule_data["protocol_used"], type__exact=protocol_type_obj ).last() + if ProtocolParameters.objects.filter(protocol_id=protocol_used_obj).exists(): + m_state = StatesForMolecule.objects.get( + molecule_state_name__exact="defined" + ) + else: + m_state = StatesForMolecule.objects.get( + molecule_state_name__exact="assigned_parameters" + ) + req_upd_sample_state = True new_molecule = self.create( protocol_used=protocol_used_obj, sample=molecule_data["sample"], molecule_type=molecule_used_obj, - state=StatesForMolecule.objects.get(molecule_state_name__exact="defined"), + state=m_state, molecule_code_id=molecule_data["molecule_code_id"], molecule_extraction_date=molecule_data["molecule_extraction_date"], extraction_type=molecule_data["extraction_type"], molecule_user=User.objects.get(username__exact=molecule_data["user"]), ) - + if req_upd_sample_state is True: + new_molecule.sample.set_state("Pending for use") return new_molecule diff --git a/core/utils/samples.py b/core/utils/samples.py index 3c67d8a2d..6fbf59ff1 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -1293,32 +1293,37 @@ def get_molecule_protocols(apps_name): def get_molecule_data_and_protocol_parameters(protocol_objs): mol_data_parm = {} for protocol_obj, mol_ids in protocol_objs.items(): - prot_name = protocol_obj.get_name() - mol_data_parm[prot_name] = {} - mol_data_parm[prot_name]["params_type"] = ( - core.utils.protocols.get_protocol_parameters_and_type(protocol_obj) - ) - mol_data_parm[prot_name][ - "fix_heading" - ] = core.core_config.HEADING_FOR_MOLECULE_ADDING_PARAMETERS - mol_data_parm[prot_name]["lot_kit"] = ( - core.utils.commercial_kits.get_lot_commercial_kits(protocol_obj) - ) - mol_data_parm[prot_name]["param_heading"] = [] - prot_params = core.models.ProtocolParameters.objects.filter( + # check if the protocol has parameters + if core.models.ProtocolParameters.objects.filter( protocol_id=protocol_obj, parameter_used=True - ).order_by("parameter_order") - for param in prot_params: - mol_data_parm[prot_name]["param_heading"].append(param.get_parameter_name()) - mol_data_parm[prot_name]["param_heading_in_string"] = ";".join( - mol_data_parm[prot_name]["param_heading"] - ) - mol_data_parm[prot_name]["m_data"] = list( - core.models.MoleculePreparation.objects.filter(pk__in=mol_ids).values_list( - "pk", "sample__sample_name", "molecule_code_id" + ).exists(): + prot_name = protocol_obj.get_name() + mol_data_parm[prot_name] = {} + mol_data_parm[prot_name]["params_type"] = ( + core.utils.protocols.get_protocol_parameters_and_type(protocol_obj) + ) + mol_data_parm[prot_name][ + "fix_heading" + ] = core.core_config.HEADING_FOR_MOLECULE_ADDING_PARAMETERS + mol_data_parm[prot_name]["lot_kit"] = ( + core.utils.commercial_kits.get_lot_commercial_kits(protocol_obj) + ) + mol_data_parm[prot_name]["param_heading"] = [] + prot_params = core.models.ProtocolParameters.objects.filter( + protocol_id=protocol_obj, parameter_used=True + ).order_by("parameter_order") + for param in prot_params: + mol_data_parm[prot_name]["param_heading"].append( + param.get_parameter_name() + ) + mol_data_parm[prot_name]["param_heading_in_string"] = ";".join( + mol_data_parm[prot_name]["param_heading"] + ) + mol_data_parm[prot_name]["m_data"] = list( + core.models.MoleculePreparation.objects.filter( + pk__in=mol_ids + ).values_list("pk", "sample__sample_name", "molecule_code_id") ) - ) - return mol_data_parm @@ -1834,7 +1839,7 @@ def record_molecule_use(from_data, app_name): return molecule_use_information -def record_molecules(samples, excel_data, heading, user, app_name): +def record_extract_protocol(samples, excel_data, heading, user, app_name): """Recored the molecues defined in excel_data. If information is missing returns the data to display again for correcting. @@ -1898,7 +1903,6 @@ def record_molecules(samples, excel_data, heading, user, app_name): molecule_data["molecule_code_id"] = code_split.group(1) + str(number_code) else: molecule_data["molecule_code_id"] = sample_obj.get_sample_code() + "_E1" - molecule_obj = core.models.MoleculePreparation.objects.create_molecule( molecule_data ) diff --git a/wetlab/templates/wetlab/handling_molecules.html b/wetlab/templates/wetlab/handling_molecules.html index 89f5270d7..9103d258a 100644 --- a/wetlab/templates/wetlab/handling_molecules.html +++ b/wetlab/templates/wetlab/handling_molecules.html @@ -38,10 +38,10 @@

    Assign the Molecule Protocol to following samples.

    + name="updateExtractionProtocol" + id="updateExtractionProtocol"> {% csrf_token %} - +
    Information missing

    Please add the missing information and click on the submit bottom

    {% csrf_token %} - + @@ -559,7 +559,7 @@

    Not molecule uses have been defined yet

    }); $(document).ready(function () { - $("#updateMoleculeProtocol").submit(function (e) { + $("#updateExtractionProtocol").submit(function (e) { //stop submitting the form to see the disabled button effect // e.preventDefault(); //disable the submit button @@ -568,7 +568,7 @@

    Not molecule uses have been defined yet

    $("").attr("type", "hidden") .attr("name", "molecule_data") .attr("value", data_json) - .appendTo("#updateMoleculeProtocol"); + .appendTo("#updateExtractionProtocol"); $("#btnSubmit").attr("disabled", true); return true; }); @@ -622,13 +622,13 @@

    Not molecule uses have been defined yet

    } }); $(document).ready(function () { - $("#updateMoleculeProtocol").submit(function (e) { + $("#updateExtractionProtocol").submit(function (e) { var table_data = $('#missing_data').jexcel('getData') var data_json = JSON.stringify(table_data) $("").attr("type", "hidden") .attr("name", "molecule_data") .attr("value", data_json) - .appendTo("#updateMoleculeProtocol"); + .appendTo("#updateExtractionProtocol"); $("#btnSubmit").attr("disabled", true); return true; }); diff --git a/wetlab/urls.py b/wetlab/urls.py index dcd257e29..f2b820df8 100644 --- a/wetlab/urls.py +++ b/wetlab/urls.py @@ -203,11 +203,6 @@ wetlab.views.sequencer_inventory, name="sequencer_inventory", ), - path( - "setMoleculeValues", - wetlab.views.set_molecule_values, - name="set_molecule_values", - ), path( "sequencerConfiguration", wetlab.views.sequencer_configuration, diff --git a/wetlab/views.py b/wetlab/views.py index 49413b818..589f48a65 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -3244,7 +3244,8 @@ def handling_molecules(request): ) elif ( - request.method == "POST" and request.POST["action"] == "updateMoleculeProtocol" + request.method == "POST" + and request.POST["action"] == "updateExtractionProtocol" ): heading = core.core_config.HEADING_FOR_MOLECULE_PROTOCOL_DEFINITION.copy() heading.append("s_id") @@ -3253,7 +3254,7 @@ def handling_molecules(request): ) if len(samples) == 0: return redirect("handling_molecules") - molecule_recorded = core.utils.samples.record_molecules( + molecule_recorded = core.utils.samples.record_extract_protocol( samples, excel_data, heading, request.user, __package__ ) if "incomplete" in molecule_recorded: @@ -3268,6 +3269,12 @@ def handling_molecules(request): molecule_recorded ) ) + if len(molecule_parameters) == 0: + return render( + request, + "wetlab/handling_molecules.html", + {"molecule_parameters_updated": True}, + ) protocol_list = ";".join(list(molecule_parameters.keys())) return render( request, @@ -3587,6 +3594,7 @@ def search_sample(request): ) +""" @login_required def set_molecule_values(request): if request.method == "POST" and request.POST["action"] == "continueWithMolecule": @@ -3622,7 +3630,7 @@ def set_molecule_values(request): elif ( request.method == "POST" and request.POST["action"] == "updateMoleculeProtocol" ): - molecule_recorded = core.utils.samples.record_molecules(request) + molecule_recorded = core.utils.samples.record_extract_protocol(request) if "heading" not in molecule_recorded: samples = request.POST["samples"].split(",") @@ -3707,6 +3715,7 @@ def set_molecule_values(request): {"display_list": display_list}, ) return render(request, "wetlab/setMoleculeValues.html", {}) + """ @login_required From 453916b55f8704f802063274d87615f2bc2c80dd Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 28 Sep 2024 11:25:57 +0200 Subject: [PATCH 166/446] Solved issue #312 warnings when running the install.sh --- wetlab/utils/collection_index.py | 4 ++-- wetlab/utils/common.py | 2 +- wetlab/utils/crontab_process.py | 2 +- wetlab/utils/library.py | 2 +- wetlab/utils/samplesheet.py | 12 ++++++------ 5 files changed, 11 insertions(+), 11 deletions(-) diff --git a/wetlab/utils/collection_index.py b/wetlab/utils/collection_index.py index e5d2e8e1c..f00c5c919 100644 --- a/wetlab/utils/collection_index.py +++ b/wetlab/utils/collection_index.py @@ -73,7 +73,7 @@ def get_collection_index_name(input_file): collection_name = "" with open(input_file, encoding="utf-8") as fh: for line in fh: - found_collection_name = re.search("^\[Name\]", line) + found_collection_name = re.search(r"^\[Name\]", line) if found_collection_name: found_name = True continue @@ -305,7 +305,7 @@ def store_collection_kits_file(collection_file): # fetch the file from user form and build the file name including # the date and time on now to store in database - split_filename = re.search("(.*)(\.\w+$)", collection_file.name) + split_filename = re.search(r"(.*)(\.\w+$)", collection_file.name) f_name = split_filename[1] f_extension = split_filename[2] fs_index_lib = FileSystemStorage() diff --git a/wetlab/utils/common.py b/wetlab/utils/common.py index b779a8e4a..c2590ad4b 100644 --- a/wetlab/utils/common.py +++ b/wetlab/utils/common.py @@ -186,7 +186,7 @@ def find_xml_tag_text(input_file, search_tag): fh = open(input_file, "r") search_line = "<" + search_tag + ">(.*)" for line in fh: - found_tag = re.search("^\s+ %s" % search_line, line) + found_tag = re.search(r"^\s+ %s" % search_line, line) if found_tag: fh.close() return found_tag.group(1) diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index 094b3b015..3033496ef 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -720,7 +720,7 @@ def get_latest_run_procesing_log(conn, log_folder, experiment_name): continue file_remote = sfh.filename if file_remote.endswith(".log"): - log_file = re.search(".*_Cycle(\d+)_.*", file_remote) + log_file = re.search(r".*_Cycle(\d+)_.*", file_remote) cycle_number = int(log_file.group(1)) if cycle_number > max_cycle: diff --git a/wetlab/utils/library.py b/wetlab/utils/library.py index 7f0f26aea..6a99fbe20 100644 --- a/wetlab/utils/library.py +++ b/wetlab/utils/library.py @@ -804,7 +804,7 @@ def get_library_code_and_unique_id(sample_id, molecule_id): sample_id=sample_obj, molecule_id=molecule_obj ).last() last_lib_prep_code_id = lib_prep_obj.get_lib_prep_code() - split_code = re.search("(.*_)(\d+)$", last_lib_prep_code_id) + split_code = re.search(r"(.*_)(\d+)$", last_lib_prep_code_id) index_val = int(split_code.group(2)) new_index = str(index_val + 1).zfill(2) lib_prep_code_id = split_code.group(1) + new_index diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index ca4c7b900..a7b04e1b5 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -106,7 +106,7 @@ def get_adapters(file_lines): else: adapter2 = adapter_code break - data_found = re.search("^\[Data]", line) + data_found = re.search(r"^\[Data]", line) if data_found: break @@ -205,7 +205,7 @@ def get_reads(file_lines): continue if "[Settings]" in line: break - if read_found and re.search("^\w+", line): + if read_found and re.search(r"^\w+", line): reads.append(line.split(",")[0]) return reads @@ -392,7 +392,7 @@ def get_projects_in_run(in_file: str) -> dict: continue else: # ignore the empty lines separated by commas - valid_line = re.search("^\w+", line) + valid_line = re.search(r"^\w+", line) if not valid_line: continue # store the project name and the user name (Description) inside projects dict @@ -442,7 +442,7 @@ def get_index_library_name(in_file): def update_library_kit_field(library_file_name, library_kit_name, library_name): # result_directory='documents/wetlab/BaseSpaceMigrationFiles/' timestr = time.strftime("%Y%m%d-%H%M%S") - tmp = re.search("(.*)\d{8}-\d+.*\.csv", library_file_name) + tmp = re.search(r"(.*)\d{8}-\d+.*\.csv", library_file_name) absolute_path = str(settings.BASE_DIR + "/") out_file = str( absolute_path @@ -517,7 +517,7 @@ def create_unique_sample_id_values(infile, index_file): continue if found_sample_line: # discard the empty lines or the lines that contains empty lines separated by comma - if line == "\n" or re.search("^\W", line): + if line == "\n" or re.search(r"^\W", line): continue data_line = line.split(",") @@ -592,7 +592,7 @@ def set_user_names_in_sample_sheet(in_file, user_names): continue if found_sample_line: # discard the empty lines or the lines that contains empty lines separated by comma - if line == "\n" or re.search("^\W", line): + if line == "\n" or re.search(r"^\W", line): continue data_line = line.split(",") From f54e8e761fe7c12cb39977b4acc823a0bc390c3f Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 28 Sep 2024 11:28:01 +0200 Subject: [PATCH 167/446] fixing litin --- wetlab/views.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wetlab/views.py b/wetlab/views.py index 589f48a65..7dbf4fb24 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -3594,7 +3594,7 @@ def search_sample(request): ) -""" +""" @login_required def set_molecule_values(request): if request.method == "POST" and request.POST["action"] == "continueWithMolecule": From 5d88ebc3845d76f3c923755c48cd8ec351cf1e79 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 28 Sep 2024 12:45:30 +0200 Subject: [PATCH 168/446] solved issue #300 Error when sample proyects has no parameters --- .github/workflows/python_lint.yml | 2 +- core/utils/samples.py | 11 ++++++++--- wetlab/views.py | 8 +++++++- 3 files changed, 16 insertions(+), 5 deletions(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 82357e979..128c97c9f 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Setup Python - uses: actions/setup-python@v1 + uses: actions/setup-python@v5 with: python-version: 3.9.x architecture: x64 diff --git a/core/utils/samples.py b/core/utils/samples.py index 6fbf59ff1..a2a0dbf17 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -173,13 +173,18 @@ def save_recorded_samples(samples_data, req_user, app_name): sample["sample_project"] = core.models.SampleProjects.objects.get( sample_project_name__exact=sample["sample_project"] ) - # If only recorded set sample to completed state if sample["only_recorded"] and sample["sample_project"] is None: sample["sample_state"] = "Completed" sample["completed_date"] = datetime.datetime.now() - # If no sample project data needed set to defined - elif sample["sample_project"] is None: + # If no sample project data needed or sample projects has no parameters + # then set the sample state to defined + elif ( + sample["sample_project"] is None + or core.models.SampleProjects.objects.filter( + sample_project_name__exact=sample["sample_project"] + ).exists() + ): sample["sample_state"] = "Defined" else: sample["sample_state"] = "Pre-Defined" diff --git a/wetlab/views.py b/wetlab/views.py index 7dbf4fb24..eb3fa0393 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -2225,7 +2225,13 @@ def record_samples(request): sample["sample_project"] not in project_ids and sample["sample_project"] is not None ): - project_ids.append(sample["sample_project"]) + # check if sample project has defined parameters + if core.models.SampleProjectsFields.objects.filter( + sample_projects_id__sample_project_name__exact=sample[ + "sample_project" + ] + ).exists(): + project_ids.append(sample["sample_project"]) # If no sample Pre-Defined just show result if not project_ids: return render( From 2c108a08dd078a2e73fb68aa22d523abbb77d055 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 28 Sep 2024 16:43:54 +0200 Subject: [PATCH 169/446] Solved issue #320 ERROR multiple returned when searching for a sample --- core/utils/samples.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/core/utils/samples.py b/core/utils/samples.py index a2a0dbf17..051a837cd 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -925,10 +925,14 @@ def get_all_sample_information(sample_id, join_values=False): molecule_id=molecule ).exists(): try: + # use the last value to avoid errors for incorrect + # used. mol_param_value.append( - core.models.MoleculeParameterValue.objects.get( + core.models.MoleculeParameterValue.objects.filter( molecule_id=molecule, molecule_parameter_id=p_name - ).get_param_value() + ) + .last() + .get_param_value() ) except core.models.MoleculeParameterValue.DoesNotExist: # if the parameter was not set at the time the molecule was handeled From 184f88c3c7ad246b14313b0939d0a1153c812f6d Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 28 Sep 2024 16:54:24 +0200 Subject: [PATCH 170/446] Solved issue #306 Type error when user want to repeat the molecule extraction --- wetlab/views.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/wetlab/views.py b/wetlab/views.py index eb3fa0393..0376c1d1c 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -3443,7 +3443,8 @@ def repeat_molecule_extraction(request): if request.method == "POST" and request.POST["action"] == "repeat_extraction": sample_id = request.POST["sample_id"] if wetlab.utils.sample.analyze_reprocess_data( - ["New Extraction"], sample_id, request.user + ["New Extraction"], + sample_id, ): molecule_protocol = core.utils.samples.get_table_record_molecule( [sample_id], __package__ @@ -3452,7 +3453,7 @@ def repeat_molecule_extraction(request): return render( request, - "wetlab/handlingMolecules.html", + "wetlab/handling_molecules.html", {"molecule_protocol": molecule_protocol}, ) # return to the main page because the page was not requested for the right page From 08156f4379f84e6cbe13e7faca8d3176e550060f Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 28 Sep 2024 18:45:24 +0200 Subject: [PATCH 171/446] solved issue #311 error when no order values are set in the library parameters --- .../wetlab/define_protocol_parameters.html | 33 ++++++++++++++++++- 1 file changed, 32 insertions(+), 1 deletion(-) diff --git a/wetlab/templates/wetlab/define_protocol_parameters.html b/wetlab/templates/wetlab/define_protocol_parameters.html index 7f8a36b94..09dcb81c7 100644 --- a/wetlab/templates/wetlab/define_protocol_parameters.html +++ b/wetlab/templates/wetlab/define_protocol_parameters.html @@ -84,9 +84,40 @@

    Define the parameters used for protocol {{prot_parameters.protocol_name}} Date: Sat, 28 Sep 2024 21:08:52 +0200 Subject: [PATCH 172/446] solved issue #308 Index library files are not upload to iSkyLIMS --- .../AmpliSeq CD Indexes Plate A..txt | 225 ++++++++ .../AmpliSeq CD Indexes Plate B.txt | 226 ++++++++ .../AmpliSeq CD Indexes Plate C.txt | 225 ++++++++ .../AmpliSeq CD Indexes Plate D.txt | 225 ++++++++ ...tera DNA UD Indexes (96 Indexes) Set A.txt | 494 +++++++++++++++++ ...tera DNA UD Indexes (96 Indexes) Set B.txt | 494 +++++++++++++++++ ...tera DNA UD Indexes (96 Indexes) Set C.txt | 494 +++++++++++++++++ ...tera DNA UD Indexes (96 Indexes) Set D.txt | 497 ++++++++++++++++++ ...era DNA CD Indexes (96 indexes plated).txt | 321 +++++++++++ ...tera Index Kit (24 Indexes 96 Samples).txt | 70 +++ ...era Index Kit (96 Indexes 384 Samples).txt | 225 ++++++++ ...a XT Index Kit (24 Indexes 96 Samples).txt | 70 +++ ... XT Index Kit (96 Indexes 384 Samples).txt | 225 ++++++++ .../Nextera XT v2 Index Kit A.txt | 224 ++++++++ .../TruSeq RNA Single Indexes Set A.txt | 119 +++++ install.sh | 4 + 16 files changed, 4138 insertions(+) create mode 100644 conf/collection_index_klits/AmpliSeq CD Indexes Plate A..txt create mode 100644 conf/collection_index_klits/AmpliSeq CD Indexes Plate B.txt create mode 100644 conf/collection_index_klits/AmpliSeq CD Indexes Plate C.txt create mode 100644 conf/collection_index_klits/AmpliSeq CD Indexes Plate D.txt create mode 100644 conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set A.txt create mode 100644 conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set B.txt create mode 100644 conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set C.txt create mode 100644 conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set D.txt create mode 100644 conf/collection_index_klits/Nextera DNA CD Indexes (96 indexes plated).txt create mode 100644 conf/collection_index_klits/Nextera Index Kit (24 Indexes 96 Samples).txt create mode 100644 conf/collection_index_klits/Nextera Index Kit (96 Indexes 384 Samples).txt create mode 100644 conf/collection_index_klits/Nextera XT Index Kit (24 Indexes 96 Samples).txt create mode 100644 conf/collection_index_klits/Nextera XT Index Kit (96 Indexes 384 Samples).txt create mode 100644 conf/collection_index_klits/Nextera XT v2 Index Kit A.txt create mode 100644 conf/collection_index_klits/TruSeq RNA Single Indexes Set A.txt diff --git a/conf/collection_index_klits/AmpliSeq CD Indexes Plate A..txt b/conf/collection_index_klits/AmpliSeq CD Indexes Plate A..txt new file mode 100644 index 000000000..109c6a605 --- /dev/null +++ b/conf/collection_index_klits/AmpliSeq CD Indexes Plate A..txt @@ -0,0 +1,225 @@ +[Version] +1 +[Name] +AmpliSeq CD Indexes Plate A +[PlateExtension] +amp384a +[Settings] +IndexOnly +Adapter CTGTCTCTTATACACATCT +[I7] +7005 GTGAATAT +7006 ACAGGCGC +7007 CATAGAGT +7008 TGCGAGAC +7015 TCTCTACT +7016 CTCTCGTC +7017 CCAAGTCT +7018 TTGGACTC +7023 GCAGAATT +7024 ATGAGGCC +7025 ACTAAGAT +7026 GTCGGAGC +[I5] +5001 AGCGCTAG +5002 GATATCGA +5007 ACATAGCG +5008 GTGCGATA +5009 CCAACAGA +5010 TTGGTGAG +5013 AACCGCGG +5014 GGTTATAA +[IndexPlateLayout] +A01 7005 5001 +A02 7015 5002 +A03 7006 5007 +A04 7007 5008 +A05 7016 5009 +A06 7008 5010 +A07 7018 5001 +A08 7023 5002 +A09 7017 5007 +A10 7025 5008 +A11 7024 5009 +A12 7026 5010 +B01 7006 5002 +B02 7016 5001 +B03 7005 5008 +B04 7008 5007 +B05 7015 5010 +B06 7007 5009 +B07 7017 5002 +B08 7024 5001 +B09 7018 5008 +B10 7026 5007 +B11 7023 5010 +B12 7025 5009 +C01 7016 5007 +C02 7008 5008 +C03 7015 5009 +C04 7006 5010 +C05 7007 5013 +C06 7005 5014 +C07 7024 5007 +C08 7026 5008 +C09 7023 5009 +C10 7017 5010 +C11 7025 5013 +C12 7018 5014 +D01 7015 5008 +D02 7007 5007 +D03 7016 5010 +D04 7005 5009 +D05 7008 5014 +D06 7006 5013 +D07 7023 5008 +D08 7025 5007 +D09 7024 5010 +D10 7018 5009 +D11 7026 5014 +D12 7017 5013 +E01 7017 5009 +E02 7025 5010 +E03 7018 5013 +E04 7023 5014 +E05 7026 5001 +E06 7024 5002 +E07 7006 5009 +E08 7007 5010 +E09 7005 5013 +E10 7015 5014 +E11 7008 5001 +E12 7016 5002 +F01 7018 5010 +F02 7026 5009 +F03 7017 5014 +F04 7024 5013 +F05 7025 5002 +F06 7023 5001 +F07 7005 5010 +F08 7008 5009 +F09 7006 5014 +F10 7016 5013 +F11 7007 5002 +F12 7015 5001 +G01 7026 5013 +G02 7024 5014 +G03 7025 5001 +G04 7018 5002 +G05 7023 5007 +G06 7017 5008 +G07 7008 5013 +G08 7016 5014 +G09 7007 5001 +G10 7005 5002 +G11 7015 5007 +G12 7006 5008 +H01 7025 5014 +H02 7023 5013 +H03 7026 5002 +H04 7017 5001 +H05 7024 5008 +H06 7018 5007 +H07 7007 5014 +H08 7015 5013 +H09 7008 5002 +H10 7006 5001 +H11 7016 5008 +H12 7005 5007 +[DefaultLayout_DualIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 \ No newline at end of file diff --git a/conf/collection_index_klits/AmpliSeq CD Indexes Plate B.txt b/conf/collection_index_klits/AmpliSeq CD Indexes Plate B.txt new file mode 100644 index 000000000..17052d464 --- /dev/null +++ b/conf/collection_index_klits/AmpliSeq CD Indexes Plate B.txt @@ -0,0 +1,226 @@ + +[Version] +1 +[Name] +AmpliSeq CD Indexes Plate B +[PlateExtension] +amp384b +[Settings] +IndexOnly +Adapter CTGTCTCTTATACACATCT +[I7] +7027 AGCCTCAT +7028 GATTCTGC +7029 TCGTAGTG +7030 CTACGACA +7035 ATGGCATG +7036 GCAATGCA +7039 CTTATCGG +7040 TCCGCTAA +7041 GATCTATC +7042 AGCTCGCT +7047 ACACTAAG +7048 GTGTCGGA +[I5] +5001 AGCGCTAG +5002 GATATCGA +5007 ACATAGCG +5008 GTGCGATA +5009 CCAACAGA +5010 TTGGTGAG +5013 AACCGCGG +5014 GGTTATAA +[IndexPlateLayout] +A01 7027 5001 +A02 7035 5002 +A03 7028 5007 +A04 7029 5008 +A05 7036 5009 +A06 7030 5010 +A07 7040 5001 +A08 7041 5002 +A09 7039 5007 +A10 7047 5008 +A11 7042 5009 +A12 7048 5010 +B01 7028 5002 +B02 7036 5001 +B03 7027 5008 +B04 7030 5007 +B05 7035 5010 +B06 7029 5009 +B07 7039 5002 +B08 7042 5001 +B09 7040 5008 +B10 7048 5007 +B11 7041 5010 +B12 7047 5009 +C01 7036 5007 +C02 7030 5008 +C03 7035 5009 +C04 7028 5010 +C05 7029 5013 +C06 7027 5014 +C07 7042 5007 +C08 7048 5008 +C09 7041 5009 +C10 7039 5010 +C11 7047 5013 +C12 7040 5014 +D01 7035 5008 +D02 7029 5007 +D03 7036 5010 +D04 7027 5009 +D05 7030 5014 +D06 7028 5013 +D07 7041 5008 +D08 7047 5007 +D09 7042 5010 +D10 7040 5009 +D11 7048 5014 +D12 7039 5013 +E01 7039 5009 +E02 7047 5010 +E03 7040 5013 +E04 7041 5014 +E05 7048 5001 +E06 7042 5002 +E07 7028 5009 +E08 7029 5010 +E09 7027 5013 +E10 7035 5014 +E11 7030 5001 +E12 7036 5002 +F01 7040 5010 +F02 7048 5009 +F03 7039 5014 +F04 7042 5013 +F05 7047 5002 +F06 7041 5001 +F07 7027 5010 +F08 7030 5009 +F09 7028 5014 +F10 7036 5013 +F11 7029 5002 +F12 7035 5001 +G01 7048 5013 +G02 7042 5014 +G03 7047 5001 +G04 7040 5002 +G05 7041 5007 +G06 7039 5008 +G07 7030 5013 +G08 7036 5014 +G09 7029 5001 +G10 7027 5002 +G11 7035 5007 +G12 7028 5008 +H01 7047 5014 +H02 7041 5013 +H03 7048 5002 +H04 7039 5001 +H05 7042 5008 +H06 7040 5007 +H07 7029 5014 +H08 7035 5013 +H09 7030 5002 +H10 7028 5001 +H11 7036 5008 +H12 7027 5007 +[DefaultLayout_DualIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 \ No newline at end of file diff --git a/conf/collection_index_klits/AmpliSeq CD Indexes Plate C.txt b/conf/collection_index_klits/AmpliSeq CD Indexes Plate C.txt new file mode 100644 index 000000000..8feeaf01b --- /dev/null +++ b/conf/collection_index_klits/AmpliSeq CD Indexes Plate C.txt @@ -0,0 +1,225 @@ +[Version] +1 +[Name] +AmpliSeq CD Indexes Plate C +[PlateExtension] +amp384c +[Settings] +IndexOnly +Adapter CTGTCTCTTATACACATCT +[I7] +7005 GTGAATAT +7006 ACAGGCGC +7007 CATAGAGT +7008 TGCGAGAC +7015 TCTCTACT +7016 CTCTCGTC +7017 CCAAGTCT +7018 TTGGACTC +7023 GCAGAATT +7024 ATGAGGCC +7025 ACTAAGAT +7026 GTCGGAGC +[I5] +5017 CTAGCTTG +5018 TCGATCCA +5025 ATACCAAG +5026 GCGTTGGA +5027 CTTCACGG +5028 TCCTGTAA +5031 CGCTCGTG +5032 TATCTACA +[IndexPlateLayout] +A01 7005 5017 +A02 7015 5018 +A03 7006 5025 +A04 7007 5026 +A05 7016 5027 +A06 7008 5028 +A07 7018 5017 +A08 7023 5018 +A09 7017 5025 +A10 7025 5026 +A11 7024 5027 +A12 7026 5028 +B01 7006 5018 +B02 7016 5017 +B03 7005 5026 +B04 7008 5025 +B05 7015 5028 +B06 7007 5027 +B07 7017 5018 +B08 7024 5017 +B09 7018 5026 +B10 7026 5025 +B11 7023 5028 +B12 7025 5027 +C01 7016 5025 +C02 7008 5026 +C03 7015 5027 +C04 7006 5028 +C05 7007 5031 +C06 7005 5032 +C07 7024 5025 +C08 7026 5026 +C09 7023 5027 +C10 7017 5028 +C11 7025 5031 +C12 7018 5032 +D01 7015 5026 +D02 7007 5025 +D03 7016 5028 +D04 7005 5027 +D05 7008 5032 +D06 7006 5031 +D07 7023 5026 +D08 7025 5025 +D09 7024 5028 +D10 7018 5027 +D11 7026 5032 +D12 7017 5031 +E01 7017 5027 +E02 7025 5028 +E03 7018 5031 +E04 7023 5032 +E05 7026 5017 +E06 7024 5018 +E07 7006 5027 +E08 7007 5028 +E09 7005 5031 +E10 7015 5032 +E11 7008 5017 +E12 7016 5018 +F01 7018 5028 +F02 7026 5027 +F03 7017 5032 +F04 7024 5031 +F05 7025 5018 +F06 7023 5017 +F07 7005 5028 +F08 7008 5027 +F09 7006 5032 +F10 7016 5031 +F11 7007 5018 +F12 7015 5017 +G01 7026 5031 +G02 7024 5032 +G03 7025 5017 +G04 7018 5018 +G05 7023 5025 +G06 7017 5026 +G07 7008 5031 +G08 7016 5032 +G09 7007 5017 +G10 7005 5018 +G11 7015 5025 +G12 7006 5026 +H01 7025 5032 +H02 7023 5031 +H03 7026 5018 +H04 7017 5017 +H05 7024 5026 +H06 7018 5025 +H07 7007 5032 +H08 7015 5031 +H09 7008 5018 +H10 7006 5017 +H11 7016 5026 +H12 7005 5025 +[DefaultLayout_DualIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 \ No newline at end of file diff --git a/conf/collection_index_klits/AmpliSeq CD Indexes Plate D.txt b/conf/collection_index_klits/AmpliSeq CD Indexes Plate D.txt new file mode 100644 index 000000000..9b7414e67 --- /dev/null +++ b/conf/collection_index_klits/AmpliSeq CD Indexes Plate D.txt @@ -0,0 +1,225 @@ +[Version] +1 +[Name] +AmpliSeq CD Indexes Plate D +[PlateExtension] +amp384d +[Settings] +IndexOnly +Adapter CTGTCTCTTATACACATCT +[I7] +7027 AGCCTCAT +7028 GATTCTGC +7029 TCGTAGTG +7030 CTACGACA +7035 ATGGCATG +7036 GCAATGCA +7039 CTTATCGG +7040 TCCGCTAA +7041 GATCTATC +7042 AGCTCGCT +7047 ACACTAAG +7048 GTGTCGGA +[I5] +5017 CTAGCTTG +5018 TCGATCCA +5025 ATACCAAG +5026 GCGTTGGA +5027 CTTCACGG +5028 TCCTGTAA +5031 CGCTCGTG +5032 TATCTACA +[IndexPlateLayout] +A01 7027 5017 +A02 7035 5018 +A03 7028 5025 +A04 7029 5026 +A05 7036 5027 +A06 7030 5028 +A07 7040 5017 +A08 7041 5018 +A09 7039 5025 +A10 7047 5026 +A11 7042 5027 +A12 7048 5028 +B01 7028 5018 +B02 7036 5017 +B03 7027 5026 +B04 7030 5025 +B05 7035 5028 +B06 7029 5027 +B07 7039 5018 +B08 7042 5017 +B09 7040 5026 +B10 7048 5025 +B11 7041 5028 +B12 7047 5027 +C01 7036 5025 +C02 7030 5026 +C03 7035 5027 +C04 7028 5028 +C05 7029 5031 +C06 7027 5032 +C07 7042 5025 +C08 7048 5026 +C09 7041 5027 +C10 7039 5028 +C11 7047 5031 +C12 7040 5032 +D01 7035 5026 +D02 7029 5025 +D03 7036 5028 +D04 7027 5027 +D05 7030 5032 +D06 7028 5031 +D07 7041 5026 +D08 7047 5025 +D09 7042 5028 +D10 7040 5027 +D11 7048 5032 +D12 7039 5031 +E01 7039 5027 +E02 7047 5028 +E03 7040 5031 +E04 7041 5032 +E05 7048 5017 +E06 7042 5018 +E07 7028 5027 +E08 7029 5028 +E09 7027 5031 +E10 7035 5032 +E11 7030 5017 +E12 7036 5018 +F01 7040 5028 +F02 7048 5027 +F03 7039 5032 +F04 7042 5031 +F05 7047 5018 +F06 7041 5017 +F07 7027 5028 +F08 7030 5027 +F09 7028 5032 +F10 7036 5031 +F11 7029 5018 +F12 7035 5017 +G01 7048 5031 +G02 7042 5032 +G03 7047 5017 +G04 7040 5018 +G05 7041 5025 +G06 7039 5026 +G07 7030 5031 +G08 7036 5032 +G09 7029 5017 +G10 7027 5018 +G11 7035 5025 +G12 7028 5026 +H01 7047 5032 +H02 7041 5031 +H03 7048 5018 +H04 7039 5017 +H05 7042 5026 +H06 7040 5025 +H07 7029 5032 +H08 7035 5031 +H09 7030 5018 +H10 7028 5017 +H11 7036 5026 +H12 7027 5025 +[DefaultLayout_DualIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 \ No newline at end of file diff --git a/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set A.txt b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set A.txt new file mode 100644 index 000000000..8bcdf33f2 --- /dev/null +++ b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set A.txt @@ -0,0 +1,494 @@ +[Version] +1 +[Name] +IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set A +[PlateExtension] +nexud384a +[Settings] +Adapter CTGTCTCTTATACACATCT +[I7] +UDP0001 GAACTGAGCG +UDP0002 AGGTCAGATA +UDP0003 CGTCTCATAT +UDP0004 ATTCCATAAG +UDP0005 GACGAGATTA +UDP0006 AACATCGCGC +UDP0007 CTAGTGCTCT +UDP0008 GATCAAGGCA +UDP0009 GACTGAGTAG +UDP0010 AGTCAGACGA +UDP0011 CCGTATGTTC +UDP0012 GAGTCATAGG +UDP0013 CTTGCCATTA +UDP0014 GAAGCGGCAC +UDP0015 TCCATTGCCG +UDP0016 CGGTTACGGC +UDP0017 GAGAATGGTT +UDP0018 AGAGGCAACC +UDP0019 CCATCATTAG +UDP0020 GATAGGCCGA +UDP0021 ATGGTTGACT +UDP0022 TATTGCGCTC +UDP0023 ACGCCTTGTT +UDP0024 TTCTACATAC +UDP0025 AACCATAGAA +UDP0026 GGTTGCGAGG +UDP0027 TAAGCATCCA +UDP0028 ACCACGACAT +UDP0029 GCCGCACTCT +UDP0030 CCACCAGGCA +UDP0031 GTGACACGCA +UDP0032 ACAGTGTATG +UDP0033 TGATTATACG +UDP0034 CAGCCGCGTA +UDP0035 GGTAACTCGC +UDP0036 ACCGGCCGTA +UDP0037 TGTAATCGAC +UDP0038 GTGCAGACAG +UDP0039 CAATCGGCTG +UDP0040 TATGTAGTCA +UDP0041 ACTCGGCAAT +UDP0042 GTCTAATGGC +UDP0043 CCATCTCGCC +UDP0044 CTGCGAGCCA +UDP0045 CGTTATTCTA +UDP0046 AGATCCATTA +UDP0047 GTCCTGGATA +UDP0048 CAGTGGCACT +UDP0049 AGTGTTGCAC +UDP0050 GACACCATGT +UDP0051 CCTGTCTGTC +UDP0052 TGATGTAAGA +UDP0053 GGAATTGTAA +UDP0054 GCATAAGCTT +UDP0055 CTGAGGAATA +UDP0056 AACGCACGAG +UDP0057 TCTATCCTAA +UDP0058 CTCGCTTCGG +UDP0059 CTGTTGGTCC +UDP0060 TTACCTGGAA +UDP0061 TGGCTAATCA +UDP0062 AACACTGTTA +UDP0063 ATTGCGCGGT +UDP0064 TGGCGCGAAC +UDP0065 TAATGTGTCT +UDP0066 ATACCAACGC +UDP0067 AGGATGTGCT +UDP0068 CACGGAACAA +UDP0069 TGGAGTACTT +UDP0070 GTATTGACGT +UDP0071 CTTGTACACC +UDP0072 ACACAGGTGG +UDP0073 CCTGCGGAAC +UDP0074 TTCATAAGGT +UDP0075 CTCTGCAGCG +UDP0076 CTGACTCTAC +UDP0077 TCTGGTATCC +UDP0078 CATTAGTGCG +UDP0079 ACGGTCAGGA +UDP0080 GGCAAGCCAG +UDP0081 TGTCGCTGGT +UDP0082 ACCGTTACAA +UDP0083 TATGCCTTAC +UDP0084 ACAAGTGGAC +UDP0085 TGGTACCTAA +UDP0086 TTGGAATTCC +UDP0087 CCTCTACATG +UDP0088 GGAGCGTGTA +UDP0089 GTCCGTAAGC +UDP0090 ACTTCAAGCG +UDP0091 TCAGAAGGCG +UDP0092 GCGTTGGTAT +UDP0093 ACATATCCAG +UDP0094 TCATAGATTG +UDP0095 GTATTCCACC +UDP0096 CCTCCGTCCA +[I5] +UDP0001 TCGTGGAGCG +UDP0002 CTACAAGATA +UDP0003 TATAGTAGCT +UDP0004 TGCCTGGTGG +UDP0005 ACATTATCCT +UDP0006 GTCCACTTGT +UDP0007 TGGAACAGTA +UDP0008 CCTTGTTAAT +UDP0009 GTTGATAGTG +UDP0010 ACCAGCGACA +UDP0011 CATACACTGT +UDP0012 GTGTGGCGCT +UDP0013 ATCACGAAGG +UDP0014 CGGCTCTACT +UDP0015 GAATGCACGA +UDP0016 AAGACTATAG +UDP0017 TCGGCAGCAA +UDP0018 CTAATGATGG +UDP0019 GGTTGCCTCT +UDP0020 CGCACATGGC +UDP0021 GGCCTGTCCT +UDP0022 CTGTGTTAGG +UDP0023 TAAGGAACGT +UDP0024 CTAACTGTAA +UDP0025 GGCGAGATGG +UDP0026 AATAGAGCAA +UDP0027 TCAATCCATT +UDP0028 TCGTATGCGG +UDP0029 TCCGACCTCG +UDP0030 CTTATGGAAT +UDP0031 GCTTACGGAC +UDP0032 GAACATACGG +UDP0033 GTCGATTACA +UDP0034 ACTAGCCGTG +UDP0035 AAGTTGGTGA +UDP0036 TGGCAATATT +UDP0037 GATCACCGCG +UDP0038 TACCATCCGT +UDP0039 GCTGTAGGAA +UDP0040 CGCACTAATG +UDP0041 GACAACTGAA +UDP0042 AGTGGTCAGG +UDP0043 TTCTATGGTT +UDP0044 AATCCGGCCA +UDP0045 CCATAAGGTT +UDP0046 ATCTCTACCA +UDP0047 CGGTGGCGAA +UDP0048 TAACAATAGG +UDP0049 CTGGTACACG +UDP0050 TCAACGTGTA +UDP0051 ACTGTTGTGA +UDP0052 GTGCGTCCTT +UDP0053 AGCACATCCT +UDP0054 TTCCGTCGCA +UDP0055 CTTAACCACT +UDP0056 GCCTCGGATA +UDP0057 CGTCGACTGG +UDP0058 TACTAGTCAA +UDP0059 ATAGACCGTT +UDP0060 ACAGTTCCAG +UDP0061 AGGCATGTAG +UDP0062 GCAAGTCTCA +UDP0063 TTGGCTCCGC +UDP0064 AACTGATACT +UDP0065 GTAAGGCATA +UDP0066 AATTGCTGCG +UDP0067 TTACAATTCC +UDP0068 AACCTAGCAC +UDP0069 TCTGTGTGGA +UDP0070 GGAATTCCAA +UDP0071 AAGCGCGCTT +UDP0072 TGAGCGTTGT +UDP0073 ATCATAGGCT +UDP0074 TGTTAGAAGG +UDP0075 GATGGATGTA +UDP0076 ACGGCCGTCA +UDP0077 CGTTGCTTAC +UDP0078 TGACTACATA +UDP0079 CGGCCTCGTT +UDP0080 CAAGCATCCG +UDP0081 TCGTCTGACT +UDP0082 CTCATAGCGA +UDP0083 AGACACATTA +UDP0084 GCGCGATGTT +UDP0085 CATGAGTACT +UDP0086 ACGTCAATAC +UDP0087 GATACCTCCT +UDP0088 ATCCGTAAGT +UDP0089 CGTGTATCTT +UDP0090 GAACCATGAA +UDP0091 GGCCATCATA +UDP0092 ACATACTTCC +UDP0093 TATGTGCAAT +UDP0094 GATTAAGGTG +UDP0095 ATGTAGACAA +UDP0096 CACATCGGTG + +[IndexPlateLayout] +A01 UDP0001 UDP0001 +B01 UDP0002 UDP0002 +C01 UDP0003 UDP0003 +D01 UDP0004 UDP0004 +E01 UDP0005 UDP0005 +F01 UDP0006 UDP0006 +G01 UDP0007 UDP0007 +H01 UDP0008 UDP0008 +A02 UDP0009 UDP0009 +B02 UDP0010 UDP0010 +C02 UDP0011 UDP0011 +D02 UDP0012 UDP0012 +E02 UDP0013 UDP0013 +F02 UDP0014 UDP0014 +G02 UDP0015 UDP0015 +H02 UDP0016 UDP0016 +A03 UDP0017 UDP0017 +B03 UDP0018 UDP0018 +C03 UDP0019 UDP0019 +D03 UDP0020 UDP0020 +E03 UDP0021 UDP0021 +F03 UDP0022 UDP0022 +G03 UDP0023 UDP0023 +H03 UDP0024 UDP0024 +A04 UDP0025 UDP0025 +B04 UDP0026 UDP0026 +C04 UDP0027 UDP0027 +D04 UDP0028 UDP0028 +E04 UDP0029 UDP0029 +F04 UDP0030 UDP0030 +G04 UDP0031 UDP0031 +H04 UDP0032 UDP0032 +A05 UDP0033 UDP0033 +B05 UDP0034 UDP0034 +C05 UDP0035 UDP0035 +D05 UDP0036 UDP0036 +E05 UDP0037 UDP0037 +F05 UDP0038 UDP0038 +G05 UDP0039 UDP0039 +H05 UDP0040 UDP0040 +A06 UDP0041 UDP0041 +B06 UDP0042 UDP0042 +C06 UDP0043 UDP0043 +D06 UDP0044 UDP0044 +E06 UDP0045 UDP0045 +F06 UDP0046 UDP0046 +G06 UDP0047 UDP0047 +H06 UDP0048 UDP0048 +A07 UDP0049 UDP0049 +B07 UDP0050 UDP0050 +C07 UDP0051 UDP0051 +D07 UDP0052 UDP0052 +E07 UDP0053 UDP0053 +F07 UDP0054 UDP0054 +G07 UDP0055 UDP0055 +H07 UDP0056 UDP0056 +A08 UDP0057 UDP0057 +B08 UDP0058 UDP0058 +C08 UDP0059 UDP0059 +D08 UDP0060 UDP0060 +E08 UDP0061 UDP0061 +F08 UDP0062 UDP0062 +G08 UDP0063 UDP0063 +H08 UDP0064 UDP0064 +A09 UDP0065 UDP0065 +B09 UDP0066 UDP0066 +C09 UDP0067 UDP0067 +D09 UDP0068 UDP0068 +E09 UDP0069 UDP0069 +F09 UDP0070 UDP0070 +G09 UDP0071 UDP0071 +H09 UDP0072 UDP0072 +A10 UDP0073 UDP0073 +B10 UDP0074 UDP0074 +C10 UDP0075 UDP0075 +D10 UDP0076 UDP0076 +E10 UDP0077 UDP0077 +F10 UDP0078 UDP0078 +G10 UDP0079 UDP0079 +H10 UDP0080 UDP0080 +A11 UDP0081 UDP0081 +B11 UDP0082 UDP0082 +C11 UDP0083 UDP0083 +D11 UDP0084 UDP0084 +E11 UDP0085 UDP0085 +F11 UDP0086 UDP0086 +G11 UDP0087 UDP0087 +H11 UDP0088 UDP0088 +A12 UDP0089 UDP0089 +B12 UDP0090 UDP0090 +C12 UDP0091 UDP0091 +D12 UDP0092 UDP0092 +E12 UDP0093 UDP0093 +F12 UDP0094 UDP0094 +G12 UDP0095 UDP0095 +H12 UDP0096 UDP0096 +[DefaultLayout_SingleIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 +[DefaultLayout_DualIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 \ No newline at end of file diff --git a/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set B.txt b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set B.txt new file mode 100644 index 000000000..ce056735a --- /dev/null +++ b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set B.txt @@ -0,0 +1,494 @@ +[Version] +1 +[Name] +IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set B +[PlateExtension] +nexud384b +[Settings] +Adapter CTGTCTCTTATACACATCT +[I7] +UDP0097 TGCCGGTCAG +UDP0098 CACTCAATTC +UDP0099 TCTCACACGC +UDP0100 TCAATGGAGA +UDP0101 ATATGCATGT +UDP0102 ATGGCGCCTG +UDP0103 TCCGTTATGT +UDP0104 GGTCTATTAA +UDP0105 CAGCAATCGT +UDP0106 TTCTGTAGAA +UDP0107 GAACGCAATA +UDP0108 AGTACTCATG +UDP0109 GGTAGAATTA +UDP0110 TAATTAGCGT +UDP0111 ATTAACAAGG +UDP0112 TGATGGCTAC +UDP0113 GAATTACAAG +UDP0114 TAGAATTGGA +UDP0115 AGGCAGCTCT +UDP0116 ATCGGCGAAG +UDP0117 CCGTGACCGA +UDP0118 ATACTTGTTC +UDP0119 TCCGCCAATT +UDP0120 AGGACAGGCC +UDP0121 AGAGAACCTA +UDP0122 GATATTGTGT +UDP0123 CGTACAGGAA +UDP0124 CTGCGTTACC +UDP0125 AGGCCGTGGA +UDP0126 AGGAGGTATC +UDP0127 GCTGACGTTG +UDP0128 CTAATAACCG +UDP0129 TCTAGGCGCG +UDP0130 ATAGCCAAGA +UDP0131 TTCGGTGTGA +UDP0132 ATGTAACGTT +UDP0133 AACGAGGCCG +UDP0134 TGGTGTTATG +UDP0135 TGGCCTCTGT +UDP0136 CCAGGCACCA +UDP0137 CCGGTTCCTA +UDP0138 GGCCAATATT +UDP0139 GAATACCTAT +UDP0140 TACGTGAAGG +UDP0141 CTTATTGGCC +UDP0142 ACAACTACTG +UDP0143 GTTGGATGAA +UDP0144 AATCCAATTG +UDP0145 TATGATGGCC +UDP0146 CGCAGCAATT +UDP0147 ACGTTCCTTA +UDP0148 CCGCGTATAG +UDP0149 GATTCTGAAT +UDP0150 TAGAGAATAC +UDP0151 TTGTATCAGG +UDP0152 CACAGCGGTC +UDP0153 CCACGCTGAA +UDP0154 GTTCGGAGTT +UDP0155 ATAGCGGAAT +UDP0156 GCAATATTCA +UDP0157 CTAGATTGCG +UDP0158 CGATGCGGTT +UDP0159 TCCGGACTAG +UDP0160 GTGACGGAGC +UDP0161 AATTCCATCT +UDP0162 TTAACGGTGT +UDP0163 ACTTGTTATC +UDP0164 CGTGTACCAG +UDP0165 TTAACCTTCG +UDP0166 CATATGCGAT +UDP0167 AGCCTATGAT +UDP0168 TATGACAATC +UDP0169 ATGTTGTTGG +UDP0170 GCACCACCAA +UDP0171 AGGCGTTCGC +UDP0172 CCTCCGGTTG +UDP0173 GTCCACCGCT +UDP0174 ATTGTTCGTC +UDP0175 GGACCAGTGG +UDP0176 CCTTCTAACA +UDP0177 CTCGAATATA +UDP0178 GATCGTCGCG +UDP0179 TATCCGAGGC +UDP0180 CGCTGTCTCA +UDP0181 AATGCGAACA +UDP0182 AATTCTTGGA +UDP0183 TTCCTACAGC +UDP0184 ATCCAGGTAT +UDP0185 ACGGTCCAAC +UDP0186 GTAACTTGGT +UDP0187 AGCGCCACAC +UDP0188 TGCTACTGCC +UDP0189 CAACACCGCA +UDP0190 CACCTTAATC +UDP0191 TTGAATGTTG +UDP0192 CCGGTAACAC +[I5] +UDP0097 CCTGATACAA +UDP0098 TTAAGTTGTG +UDP0099 CGGACAGTGA +UDP0100 GCACTACAAC +UDP0101 TGGTGCCTGG +UDP0102 TCCACGGCCT +UDP0103 TTGTAGTGTA +UDP0104 CCACGACACG +UDP0105 TGTGATGTAT +UDP0106 GAGCGCAATA +UDP0107 ATCTTACTGT +UDP0108 ATGTCGTGGT +UDP0109 GTAGCCATCA +UDP0110 TGGTTAAGAA +UDP0111 TGTTGTTCGT +UDP0112 CCAACAACAT +UDP0113 ACCGGCTCAG +UDP0114 GTTAATCTGA +UDP0115 CGGCTAACGT +UDP0116 TCCAAGAATT +UDP0117 CCGAACGTTG +UDP0118 TAACCGCCGA +UDP0119 CTCCGTGCTG +UDP0120 CATTCCAGCT +UDP0121 GGTTATGCTA +UDP0122 ACCACACGGT +UDP0123 TAGGTTCTCT +UDP0124 TATGGCTCGA +UDP0125 CTCGTGCGTT +UDP0126 CCAGTTGGCA +UDP0127 TGTTCGCATT +UDP0128 AACCGCATCG +UDP0129 CGAAGGTTAA +UDP0130 AGTGCCACTG +UDP0131 GAACAAGTAT +UDP0132 ACGATTGCTG +UDP0133 ATACCTGGAT +UDP0134 TCCAATTCTA +UDP0135 TGAGACAGCG +UDP0136 ACGCTAATTA +UDP0137 TATATTCGAG +UDP0138 CGGTCCGATA +UDP0139 ACAATAGAGT +UDP0140 CGGTTATTAG +UDP0141 GATAACAAGT +UDP0142 AGTTATCACA +UDP0143 TTCCAGGTAA +UDP0144 CATGTAGAGG +UDP0145 GATTGTCATA +UDP0146 ATTCCGCTAT +UDP0147 GACCGCTGTG +UDP0148 TAGGAACCGG +UDP0149 AGCGGTGGAC +UDP0150 TATAGATTCG +UDP0151 ACAGAGGCCA +UDP0152 ATTCCTATTG +UDP0153 TATTCCTCAG +UDP0154 CGCCTTCTGA +UDP0155 GCGCAGAGTA +UDP0156 GGCGCCAATT +UDP0157 AGATATGGCG +UDP0158 CCTGCTTGGT +UDP0159 GACGAACAAT +UDP0160 TGGCGGTCCA +UDP0161 CTTCAGTTAC +UDP0162 TCCTGACCGT +UDP0163 CGCGCCTAGA +UDP0164 AGGATAAGTT +UDP0165 AGGCCAGACA +UDP0166 CCTTGAACGG +UDP0167 CACCACCTAC +UDP0168 TTGCTTGTAT +UDP0169 CAATCTATGA +UDP0170 TGGTACTGAT +UDP0171 TTCATCCAAC +UDP0172 CATAACACCA +UDP0173 TCCTATTAGC +UDP0174 TCTCTAGATT +UDP0175 CGCGAGCCTA +UDP0176 GATAAGCTCT +UDP0177 GAGATGTCGA +UDP0178 CTGGATATGT +UDP0179 GGCCAATAAG +UDP0180 ATTACTCACC +UDP0181 AATTGGCGGA +UDP0182 TTGTCAACTT +UDP0183 GGCGAATTCT +UDP0184 CAACGTCAGC +UDP0185 TCTTACATCA +UDP0186 CGCCATACCT +UDP0187 CTAATGTCTT +UDP0188 CAACCGGAGG +UDP0189 GGCAGTAGCA +UDP0190 TTAGGATAGA +UDP0191 CGCAATCTAG +UDP0192 GAGTTGTACT + +[IndexPlateLayout] +A01 UDP0097 UDP0097 +B01 UDP0098 UDP0098 +C01 UDP0099 UDP0099 +D01 UDP0100 UDP0100 +E01 UDP0101 UDP0101 +F01 UDP0102 UDP0102 +G01 UDP0103 UDP0103 +H01 UDP0104 UDP0104 +A02 UDP0105 UDP0105 +B02 UDP0106 UDP0106 +C02 UDP0107 UDP0107 +D02 UDP0108 UDP0108 +E02 UDP0109 UDP0109 +F02 UDP0110 UDP0110 +G02 UDP0111 UDP0111 +H02 UDP0112 UDP0112 +A03 UDP0113 UDP0113 +B03 UDP0114 UDP0114 +C03 UDP0115 UDP0115 +D03 UDP0116 UDP0116 +E03 UDP0117 UDP0117 +F03 UDP0118 UDP0118 +G03 UDP0119 UDP0119 +H03 UDP0120 UDP0120 +A04 UDP0121 UDP0121 +B04 UDP0122 UDP0122 +C04 UDP0123 UDP0123 +D04 UDP0124 UDP0124 +E04 UDP0125 UDP0125 +F04 UDP0126 UDP0126 +G04 UDP0127 UDP0127 +H04 UDP0128 UDP0128 +A05 UDP0129 UDP0129 +B05 UDP0130 UDP0130 +C05 UDP0131 UDP0131 +D05 UDP0132 UDP0132 +E05 UDP0133 UDP0133 +F05 UDP0134 UDP0134 +G05 UDP0135 UDP0135 +H05 UDP0136 UDP0136 +A06 UDP0137 UDP0137 +B06 UDP0138 UDP0138 +C06 UDP0139 UDP0139 +D06 UDP0140 UDP0140 +E06 UDP0141 UDP0141 +F06 UDP0142 UDP0142 +G06 UDP0143 UDP0143 +H06 UDP0144 UDP0144 +A07 UDP0145 UDP0145 +B07 UDP0146 UDP0146 +C07 UDP0147 UDP0147 +D07 UDP0148 UDP0148 +E07 UDP0149 UDP0149 +F07 UDP0150 UDP0150 +G07 UDP0151 UDP0151 +H07 UDP0152 UDP0152 +A08 UDP0153 UDP0153 +B08 UDP0154 UDP0154 +C08 UDP0155 UDP0155 +D08 UDP0156 UDP0156 +E08 UDP0157 UDP0157 +F08 UDP0158 UDP0158 +G08 UDP0159 UDP0159 +H08 UDP0160 UDP0160 +A09 UDP0161 UDP0161 +B09 UDP0162 UDP0162 +C09 UDP0163 UDP0163 +D09 UDP0164 UDP0164 +E09 UDP0165 UDP0165 +F09 UDP0166 UDP0166 +G09 UDP0167 UDP0167 +H09 UDP0168 UDP0168 +A10 UDP0169 UDP0169 +B10 UDP0170 UDP0170 +C10 UDP0171 UDP0171 +D10 UDP0172 UDP0172 +E10 UDP0173 UDP0173 +F10 UDP0174 UDP0174 +G10 UDP0175 UDP0175 +H10 UDP0176 UDP0176 +A11 UDP0177 UDP0177 +B11 UDP0178 UDP0178 +C11 UDP0179 UDP0179 +D11 UDP0180 UDP0180 +E11 UDP0181 UDP0181 +F11 UDP0182 UDP0182 +G11 UDP0183 UDP0183 +H11 UDP0184 UDP0184 +A12 UDP0185 UDP0185 +B12 UDP0186 UDP0186 +C12 UDP0187 UDP0187 +D12 UDP0188 UDP0188 +E12 UDP0189 UDP0189 +F12 UDP0190 UDP0190 +G12 UDP0191 UDP0191 +H12 UDP0192 UDP0192 +[DefaultLayout_SingleIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 +[DefaultLayout_DualIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 \ No newline at end of file diff --git a/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set C.txt b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set C.txt new file mode 100644 index 000000000..9c84b6eff --- /dev/null +++ b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set C.txt @@ -0,0 +1,494 @@ +[Version] +1 +[Name] +IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set C +[PlateExtension] +nexud384c +[Settings] +Adapter CTGTCTCTTATACACATCT +[I7] +UDP0193 TCTCATGATA +UDP0194 CGAGGCCAAG +UDP0195 TTCACGAGAC +UDP0196 GCGTGGATGG +UDP0197 TCCTGGTTGT +UDP0198 TAATTCTGCT +UDP0199 CGCACGACTG +UDP0200 GAGGTTAGAC +UDP0201 AACCGAGTTC +UDP0202 TGTGATAACT +UDP0203 AGTATGCTAC +UDP0204 GTAACTGAAG +UDP0205 TCCTCGGACT +UDP0206 CTGGAACTGT +UDP0207 GAATATGCGG +UDP0208 GATCGGATAA +UDP0209 GCTAGACTAT +UDP0210 AGCTACTATA +UDP0211 CCACCGGAGT +UDP0212 CTTACCGCAC +UDP0213 TTAGGATATC +UDP0214 TTATACGCGA +UDP0215 CGCTTAGAAT +UDP0216 CCGAAGCGCT +UDP0217 CACTATCAAC +UDP0218 TTGCTCTATT +UDP0219 TTACAGTTAG +UDP0220 CTAAGTACGC +UDP0221 TAGTTCGGTA +UDP0222 CTATTACTAC +UDP0223 TAGCATAACC +UDP0224 ACTCTATTGT +UDP0225 TAGTGGAAGC +UDP0226 CGCCATATCT +UDP0227 GCTTCATATT +UDP0228 ACTAGCGCTA +UDP0229 GCTCTTAACT +UDP0230 GTGGTATCTG +UDP0231 TGACGGCCGT +UDP0232 CAGTAATTAC +UDP0233 TACAAGACTT +UDP0234 CTGTGGTGAC +UDP0235 CTCCACTAAT +UDP0236 ATAGTTAGCA +UDP0237 ATAGGTCTTA +UDP0238 TTCTTAACCA +UDP0239 AAGGAAGAGT +UDP0240 GGAAGGAGAC +UDP0241 TGAACGCGGA +UDP0242 CCTGCAACCT +UDP0243 TTCATGGTTC +UDP0244 ATCCTCTCAA +UDP0245 CACTAGACCA +UDP0246 ATTATCCACT +UDP0247 ATGGCGTGCC +UDP0248 TCCAGAGATC +UDP0249 ATGTCCAGCA +UDP0250 CAACGTTCGG +UDP0251 GCGTATTAAT +UDP0252 GTTGTGACTA +UDP0253 TCTCAATACC +UDP0254 AAGCATCTTG +UDP0255 TCAGTCTCGT +UDP0256 TGCAAGATAA +UDP0257 GTAACAATCT +UDP0258 CAGCGGTAGA +UDP0259 TCATACCGTT +UDP0260 GGCGCCATTG +UDP0261 AGCGAATTAG +UDP0262 TTAGACCATG +UDP0263 CACACAGTAT +UDP0264 TCTTGTCGGC +UDP0265 TACCGCCTCG +UDP0266 CTGTTATATC +UDP0267 TAACCGGCGA +UDP0268 AAGAGAGTCT +UDP0269 GTAGGCGAGC +UDP0270 AACTTATCCT +UDP0271 ATTATGTCTC +UDP0272 TATAACAGCT +UDP0273 CCAATGATAC +UDP0274 GAGGCCTATT +UDP0275 AGCTAAGCGG +UDP0276 CTTCCTAGGA +UDP0277 CGATCTGTGA +UDP0278 GTGGACAAGT +UDP0279 AACAAGTACA +UDP0280 AGATTAAGTG +UDP0281 TATCACTCTG +UDP0282 AGAATTCGCC +UDP0283 CCTGACCACT +UDP0284 AGCTGGAATG +UDP0285 TGATAACGAG +UDP0286 CATAGTAAGG +UDP0287 ATTGGCTTCT +UDP0288 GTACCGATTA +[I5] +UDP0193 AACACGTGGA +UDP0194 GTGTTACCGG +UDP0195 AGATTGTTAC +UDP0196 TTGACCAATG +UDP0197 CTGACCGGCA +UDP0198 TCTCATCAAT +UDP0199 GGACCAACAG +UDP0200 AATGTATTGC +UDP0201 GATCTCTGGA +UDP0202 CAGGCGCCAT +UDP0203 TTAATAGACC +UDP0204 GGAGTCGCGA +UDP0205 AACGCCAGAG +UDP0206 CGTAATTAAC +UDP0207 ACGAGACTGA +UDP0208 GTATCGGCCG +UDP0209 AATACGACAT +UDP0210 GTTATATGGC +UDP0211 GCCTGCCATG +UDP0212 TAAGACCTAT +UDP0213 TATACCATGG +UDP0214 GCCGTCTGTT +UDP0215 CAGAGTGATA +UDP0216 TGCTAACTAT +UDP0217 TCAGTTAATG +UDP0218 GTGACCTTGA +UDP0219 ACATGCATAT +UDP0220 AACATACCTA +UDP0221 CCATGTGTAG +UDP0222 GAGTCTCTCC +UDP0223 GCTATGCGCA +UDP0224 ATCGCATATG +UDP0225 AGTACCTATA +UDP0226 GACCGGAGAT +UDP0227 CGTTCAGCCT +UDP0228 TTACTTCCTC +UDP0229 CACGTCCACC +UDP0230 GCTACTATCT +UDP0231 AGTCAACCAT +UDP0232 CGAGGCGGTA +UDP0233 CAGGTGTTCA +UDP0234 GACAGACAGG +UDP0235 TGTACTTGTT +UDP0236 CTCTAAGTAG +UDP0237 GTCACCACAG +UDP0238 TCTACATACC +UDP0239 CACGTTAGGC +UDP0240 TGGTGAGTCT +UDP0241 CTTCGAAGGA +UDP0242 GTAGAGTCAG +UDP0243 GACATTGTCA +UDP0244 TCCGCAAGGC +UDP0245 ACTGCCTTAT +UDP0246 TACGCACGTA +UDP0247 CGCTTGAAGT +UDP0248 CTGCACTTCA +UDP0249 CAGCGGACAA +UDP0250 GGATCCGCAT +UDP0251 TGCGGTGTTG +UDP0252 ACATAACGGA +UDP0253 GACGTTCGCG +UDP0254 CATTCAACAA +UDP0255 CACGGATTAT +UDP0256 TTGAGGACGG +UDP0257 CTCTGTATAC +UDP0258 GCAACAGGTG +UDP0259 GGTAACGCAG +UDP0260 ACCGCGCAAT +UDP0261 AGCCGGAACA +UDP0262 TCCTAGGAAG +UDP0263 TTGAGCCTAA +UDP0264 CCACCTGTGT +UDP0265 CCTCGCAACC +UDP0266 GTATAGCTGT +UDP0267 GCTACATTAG +UDP0268 TACGAATCTT +UDP0269 TAGGAGCGCA +UDP0270 GTACTGGCGT +UDP0271 AGTTAAGAGC +UDP0272 TCGCGTATAA +UDP0273 GAGTGTGCCG +UDP0274 CTAGTCCGGA +UDP0275 ATTAATACGC +UDP0276 CCTAGAGTAT +UDP0277 TAGGAAGACT +UDP0278 CCGTGGCCTT +UDP0279 GGATATATCC +UDP0280 CACCTCTTGG +UDP0281 AACGTTACAT +UDP0282 CGGCAAGCTC +UDP0283 TCTTGGCTAT +UDP0284 ACGGAATGCG +UDP0285 GTTCCGCAGG +UDP0286 ACCAAGTTAC +UDP0287 TGGCTCGCAG +UDP0288 AACTAACGTT + +[IndexPlateLayout] +A01 UDP0193 UDP0193 +B01 UDP0194 UDP0194 +C01 UDP0195 UDP0195 +D01 UDP0196 UDP0196 +E01 UDP0197 UDP0197 +F01 UDP0198 UDP0198 +G01 UDP0199 UDP0199 +H01 UDP0200 UDP0200 +A02 UDP0201 UDP0201 +B02 UDP0202 UDP0202 +C02 UDP0203 UDP0203 +D02 UDP0204 UDP0204 +E02 UDP0205 UDP0205 +F02 UDP0206 UDP0206 +G02 UDP0207 UDP0207 +H02 UDP0208 UDP0208 +A03 UDP0209 UDP0209 +B03 UDP0210 UDP0210 +C03 UDP0211 UDP0211 +D03 UDP0212 UDP0212 +E03 UDP0213 UDP0213 +F03 UDP0214 UDP0214 +G03 UDP0215 UDP0215 +H03 UDP0216 UDP0216 +A04 UDP0217 UDP0217 +B04 UDP0218 UDP0218 +C04 UDP0219 UDP0219 +D04 UDP0220 UDP0220 +E04 UDP0221 UDP0221 +F04 UDP0222 UDP0222 +G04 UDP0223 UDP0223 +H04 UDP0224 UDP0224 +A05 UDP0225 UDP0225 +B05 UDP0226 UDP0226 +C05 UDP0227 UDP0227 +D05 UDP0228 UDP0228 +E05 UDP0229 UDP0229 +F05 UDP0230 UDP0230 +G05 UDP0231 UDP0231 +H05 UDP0232 UDP0232 +A06 UDP0233 UDP0233 +B06 UDP0234 UDP0234 +C06 UDP0235 UDP0235 +D06 UDP0236 UDP0236 +E06 UDP0237 UDP0237 +F06 UDP0238 UDP0238 +G06 UDP0239 UDP0239 +H06 UDP0240 UDP0240 +A07 UDP0241 UDP0241 +B07 UDP0242 UDP0242 +C07 UDP0243 UDP0243 +D07 UDP0244 UDP0244 +E07 UDP0245 UDP0245 +F07 UDP0246 UDP0246 +G07 UDP0247 UDP0247 +H07 UDP0248 UDP0248 +A08 UDP0249 UDP0249 +B08 UDP0250 UDP0250 +C08 UDP0251 UDP0251 +D08 UDP0252 UDP0252 +E08 UDP0253 UDP0253 +F08 UDP0254 UDP0254 +G08 UDP0255 UDP0255 +H08 UDP0256 UDP0256 +A09 UDP0257 UDP0257 +B09 UDP0258 UDP0258 +C09 UDP0259 UDP0259 +D09 UDP0260 UDP0260 +E09 UDP0261 UDP0261 +F09 UDP0262 UDP0262 +G09 UDP0263 UDP0263 +H09 UDP0264 UDP0264 +A10 UDP0265 UDP0265 +B10 UDP0266 UDP0266 +C10 UDP0267 UDP0267 +D10 UDP0268 UDP0268 +E10 UDP0269 UDP0269 +F10 UDP0270 UDP0270 +G10 UDP0271 UDP0271 +H10 UDP0272 UDP0272 +A11 UDP0273 UDP0273 +B11 UDP0274 UDP0274 +C11 UDP0275 UDP0275 +D11 UDP0276 UDP0276 +E11 UDP0277 UDP0277 +F11 UDP0278 UDP0278 +G11 UDP0279 UDP0279 +H11 UDP0280 UDP0280 +A12 UDP0281 UDP0281 +B12 UDP0282 UDP0282 +C12 UDP0283 UDP0283 +D12 UDP0284 UDP0284 +E12 UDP0285 UDP0285 +F12 UDP0286 UDP0286 +G12 UDP0287 UDP0287 +H12 UDP0288 UDP0288 +[DefaultLayout_SingleIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 +[DefaultLayout_DualIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 \ No newline at end of file diff --git a/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set D.txt b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set D.txt new file mode 100644 index 000000000..ae4f63a7c --- /dev/null +++ b/conf/collection_index_klits/IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set D.txt @@ -0,0 +1,497 @@ +[Version] +1 +[Name] +IDT-ILMN Nextera DNA UD Indexes (96 Indexes) Set D +[PlateExtension] +nexud384d +[Settings] +Adapter CTGTCTCTTATACACATCT +[I7] +UDP0289 GAACAATTCC +UDP0290 TGTGGTCCGG +UDP0291 CTTCTAAGTC +UDP0292 AATATTGCCA +UDP0293 TCGTGCATTC +UDP0294 AAGATACACG +UDP0295 TGCAATGAAT +UDP0296 CTATGAAGGA +UDP0297 GAAGACTAGA +UDP0298 AGGAGTCGAG +UDP0299 TTCACTCACT +UDP0300 GGTCCGCTTC +UDP0301 CAACGAGAGC +UDP0302 ATTGAGGTCC +UDP0303 GGAGAGACTC +UDP0304 CCGCTCCGTT +UDP0305 ATACATCACA +UDP0306 TAGGTATGTT +UDP0307 CACCTAGCAC +UDP0308 TTCAAGTATG +UDP0309 TTAAGACAAG +UDP0310 CACCTCTCTT +UDP0311 TTCTCGTGCA +UDP0312 GCTAGGAAGT +UDP0313 TTAATAGCAC +UDP0314 CATTCACGCT +UDP0315 GGCACTAAGG +UDP0316 ATTCGGTACA +UDP0317 ACTAATCTCC +UDP0318 TGTGTTAGTA +UDP0319 CAACGACCTA +UDP0320 CGGTCGGCAT +UDP0321 TCGACGCTAG +UDP0322 CTCGTAGGCA +UDP0323 AAGTTCTAGT +UDP0324 CCAAGAGGTG +UDP0325 ATATCTGCTT +UDP0326 TGGATCTGGC +UDP0327 TTGAATCCAA +UDP0328 CACGGCTAGT +UDP0329 GAGCTTGCCG +UDP0330 AGCTAGCTTC +UDP0331 CAATCCTTGT +UDP0332 CACCTGTTGC +UDP0333 CGTCACCTTG +UDP0334 AATGACTGGT +UDP0335 ATGATTCCGG +UDP0336 TTAGGCTCAA +UDP0337 TGTAAGGTGG +UDP0338 CAACTGCAAC +UDP0339 ACATGAGTGA +UDP0340 GCAACCAGTC +UDP0341 GAGCGACGAT +UDP0342 CGAACGCACC +UDP0343 TCTTACGCCG +UDP0344 AGCTGATGTC +UDP0345 CTGAATTAGT +UDP0346 TAAGGAGGAA +UDP0347 AGCTTACACA +UDP0348 AACCAGCCAC +UDP0349 CTTAAGTCGA +UDP0350 GCCTAACGTG +UDP0351 ACTTACTTCA +UDP0352 CGCATTCCGT +UDP0353 GATATCACAC +UDP0354 AGCGCTGTGT +UDP0355 TCACCGCGCT +UDP0356 GATAGCCTTG +UDP0357 CCTGGACGCA +UDP0358 TTACGCACCT +UDP0359 TCGTTGCTGC +UDP0360 CGACAAGGAT +UDP0361 GTGTACCTTC +UDP0362 ACCTGGCCAA +UDP0363 TGTCTGGCCT +UDP0364 AGTTAATGCT +UDP0365 GGTGAGTAAT +UDP0366 TACTCTGCGC +UDP0367 AGGTATGGCG +UDP0368 TCCAGCCTGC +UDP0369 GCCATATAAC +UDP0370 AGTGCGAGTG +UDP0371 CTGAGCCGGT +UDP0372 AACGGTCTAT +UDP0373 GTTGCGTTCA +UDP0374 CTTCAACCAC +UDP0375 TCTATTCAGT +UDP0376 CAAGACGTCC +UDP0377 TGAGTACAAC +UDP0378 CCGCGGTTCT +UDP0379 ATTGATACTG +UDP0380 GGATTATGGA +UDP0381 TGGTTCTCAT +UDP0382 TCAACCACGA +UDP0383 TATGAACTTG +UDP0384 AGTGGTTAAG + +[I5] +UDP0289 TAGAGTTGGA +UDP0290 AGAGCACTAG +UDP0291 ACTCTACAGG +UDP0292 CGGTGACACC +UDP0293 GCGTTGGTAT +UDP0294 TGTGCTAACA +UDP0295 CCAGAAGTAA +UDP0296 CTTATACCTG +UDP0297 ACTAGAACTT +UDP0298 TTAGGCTTAC +UDP0299 TATCATGAGA +UDP0300 CTCACACAAG +UDP0301 GAATTGAGTG +UDP0302 CGGATTATAT +UDP0303 TTGAAGCAGA +UDP0304 TACGGCGAAG +UDP0305 TCTCCATTGA +UDP0306 CGAGACCAAG +UDP0307 TGCTGGACAT +UDP0308 GATGGTATCG +UDP0309 GGCTTAATTG +UDP0310 CTCGACTCCT +UDP0311 ATACACAGAG +UDP0312 TCTCGGACGA +UDP0313 ACCACGTCTG +UDP0314 GTTGTACTCA +UDP0315 TCAGGTCAAC +UDP0316 AGTCCGAGGA +UDP0317 CACTTAATCT +UDP0318 TACTCTGTTA +UDP0319 GCGACTCGAT +UDP0320 CTAGGCAAGG +UDP0321 CCTCTTCGAA +UDP0322 TCATCCTCTT +UDP0323 GGTAAGATAA +UDP0324 AACGAGCCAG +UDP0325 TAGACAATCT +UDP0326 CAATGCTGAA +UDP0327 GTCACGGTGT +UDP0328 GGTGTACAAG +UDP0329 AGGTTGCAGG +UDP0330 TAATACGGAG +UDP0331 CGAAGACGCA +UDP0332 ATTGACACAT +UDP0333 CAGCCGATTG +UDP0334 TCTCACGCGT +UDP0335 CTCTGACGTG +UDP0336 TCGAATGGAA +UDP0337 AAGGCCTTGG +UDP0338 TGAACGCAAC +UDP0339 CCGCTTAGCT +UDP0340 CACCGAGGAA +UDP0341 CGTATAATCA +UDP0342 ATGACAGAAC +UDP0343 ATTCATTGCA +UDP0344 TCATGTCCTG +UDP0345 AATTCGATCG +UDP0346 TTCCGACATT +UDP0347 TGGCACGACC +UDP0348 GCCACAGCAC +UDP0349 CAGTAGTTGT +UDP0350 AGCTCTCAAG +UDP0351 TCTGGAATTA +UDP0352 ATTAGTGGAG +UDP0353 GACTATATGT +UDP0354 CGTTCGGAAC +UDP0355 TCGATACTAG +UDP0356 TACCACAATG +UDP0357 TGGTATACCA +UDP0358 GCTCTCGTTG +UDP0359 GTCTCGTGAA +UDP0360 AAGGCCACCT +UDP0361 CTGTGAGCTA +UDP0362 TCACAGATCG +UDP0363 AGAAGCCAAT +UDP0364 ACTGCAGCCG +UDP0365 AACATCTAGT +UDP0366 CCTTACTATG +UDP0367 GTGGCGAGAC +UDP0368 GCCAGATCCA +UDP0369 ACACAATATC +UDP0370 TGGAGGTAAT +UDP0371 CCTTCACGTA +UDP0372 CTATACGCGG +UDP0373 GTTGCAGTTG +UDP0374 TTATGCGCCT +UDP0375 TCTCAGTACA +UDP0376 AGTATACGGA +UDP0377 ACGCTTGGAC +UDP0378 GGAGTAGATT +UDP0379 TACACGCTCC +UDP0380 TCCGATAGAG +UDP0381 CTCAAGGCCG +UDP0382 CAAGTTCATA +UDP0383 AATCCTTAGG +UDP0384 GGTGGAATAC + + +[IndexPlateLayout] +A01 UDP0289 UDP0289 +B01 UDP0290 UDP0290 +C01 UDP0291 UDP0291 +D01 UDP0292 UDP0292 +E01 UDP0293 UDP0293 +F01 UDP0294 UDP0294 +G01 UDP0295 UDP0295 +H01 UDP0296 UDP0296 +A02 UDP0297 UDP0297 +B02 UDP0298 UDP0298 +C02 UDP0299 UDP0299 +D02 UDP0300 UDP0300 +E02 UDP0301 UDP0301 +F02 UDP0302 UDP0302 +G02 UDP0303 UDP0303 +H02 UDP0304 UDP0304 +A03 UDP0305 UDP0305 +B03 UDP0306 UDP0306 +C03 UDP0307 UDP0307 +D03 UDP0308 UDP0308 +E03 UDP0309 UDP0309 +F03 UDP0310 UDP0310 +G03 UDP0311 UDP0311 +H03 UDP0312 UDP0312 +A04 UDP0313 UDP0313 +B04 UDP0314 UDP0314 +C04 UDP0315 UDP0315 +D04 UDP0316 UDP0316 +E04 UDP0317 UDP0317 +F04 UDP0318 UDP0318 +G04 UDP0319 UDP0319 +H04 UDP0320 UDP0320 +A05 UDP0321 UDP0321 +B05 UDP0322 UDP0322 +C05 UDP0323 UDP0323 +D05 UDP0324 UDP0324 +E05 UDP0325 UDP0325 +F05 UDP0326 UDP0326 +G05 UDP0327 UDP0327 +H05 UDP0328 UDP0328 +A06 UDP0329 UDP0329 +B06 UDP0330 UDP0330 +C06 UDP0331 UDP0331 +D06 UDP0332 UDP0332 +E06 UDP0333 UDP0333 +F06 UDP0334 UDP0334 +G06 UDP0335 UDP0335 +H06 UDP0336 UDP0336 +A07 UDP0337 UDP0337 +B07 UDP0338 UDP0338 +C07 UDP0339 UDP0339 +D07 UDP0340 UDP0340 +E07 UDP0341 UDP0341 +F07 UDP0342 UDP0342 +G07 UDP0343 UDP0343 +H07 UDP0344 UDP0344 +A08 UDP0345 UDP0345 +B08 UDP0346 UDP0346 +C08 UDP0347 UDP0347 +D08 UDP0348 UDP0348 +E08 UDP0349 UDP0349 +F08 UDP0350 UDP0350 +G08 UDP0351 UDP0351 +H08 UDP0352 UDP0352 +A09 UDP0353 UDP0353 +B09 UDP0354 UDP0354 +C09 UDP0355 UDP0355 +D09 UDP0356 UDP0356 +E09 UDP0357 UDP0357 +F09 UDP0358 UDP0358 +G09 UDP0359 UDP0359 +H09 UDP0360 UDP0360 +A10 UDP0361 UDP0361 +B10 UDP0362 UDP0362 +C10 UDP0363 UDP0363 +D10 UDP0364 UDP0364 +E10 UDP0365 UDP0365 +F10 UDP0366 UDP0366 +G10 UDP0367 UDP0367 +H10 UDP0368 UDP0368 +A11 UDP0369 UDP0369 +B11 UDP0370 UDP0370 +C11 UDP0371 UDP0371 +D11 UDP0372 UDP0372 +E11 UDP0373 UDP0373 +F11 UDP0374 UDP0374 +G11 UDP0375 UDP0375 +H11 UDP0376 UDP0376 +A12 UDP0377 UDP0377 +B12 UDP0378 UDP0378 +C12 UDP0379 UDP0379 +D12 UDP0380 UDP0380 +E12 UDP0381 UDP0381 +F12 UDP0382 UDP0382 +G12 UDP0383 UDP0383 +H12 UDP0384 UDP0384 + +[DefaultLayout_SingleIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 +[DefaultLayout_DualIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 \ No newline at end of file diff --git a/conf/collection_index_klits/Nextera DNA CD Indexes (96 indexes plated).txt b/conf/collection_index_klits/Nextera DNA CD Indexes (96 indexes plated).txt new file mode 100644 index 000000000..6b990e85b --- /dev/null +++ b/conf/collection_index_klits/Nextera DNA CD Indexes (96 indexes plated).txt @@ -0,0 +1,321 @@ +[Version] +1 +[Name] +Nextera DNA CD Indexes (96 Indexes plated) +[PlateExtension] +nex96 +[Settings] +Adapter CTGTCTCTTATACACATCT +[I7] +H701 TAAGGCGA +H702 CGTACTAG +H703 AGGCAGAA +H705 GGACTCCT +H706 TAGGCATG +H707 CTCTCTAC +H710 CGAGGCTG +H711 AAGAGGCA +H712 GTAGAGGA +H714 GCTCATGA +H720 CGGAGCCT +H723 TAGCGCTC +[I5] +H503 TATCCTCT +H505 GTAAGGAG +H506 ACTGCATA +H510 CGTCTAAT +H513 TCGACTAG +H516 CCTAGAGT +H517 GCGTAAGA +H522 TTATGCGA +[IndexPlateLayout] +A01 H701 H505 +A02 H702 H506 +A03 H703 H517 +A04 H705 H505 +A05 H707 H506 +A06 H723 H517 +A07 H706 H505 +A08 H712 H506 +A09 H720 H517 +A10 H710 H505 +A11 H711 H506 +A12 H714 H517 +B01 H702 H517 +B02 H703 H505 +B03 H701 H506 +B04 H707 H517 +B05 H723 H505 +B06 H705 H506 +B07 H712 H517 +B08 H720 H505 +B09 H706 H506 +B10 H711 H517 +B11 H714 H505 +B12 H710 H506 +C01 H703 H506 +C02 H701 H517 +C03 H702 H505 +C04 H723 H506 +C05 H705 H517 +C06 H707 H505 +C07 H720 H506 +C08 H706 H517 +C09 H712 H505 +C10 H714 H506 +C11 H710 H517 +C12 H711 H505 +D01 H705 H503 +D02 H707 H503 +D03 H723 H503 +D04 H706 H503 +D05 H712 H503 +D06 H720 H503 +D07 H710 H503 +D08 H711 H503 +D09 H714 H503 +D10 H701 H503 +D11 H702 H503 +D12 H703 H503 +E01 H706 H516 +E02 H712 H516 +E03 H720 H516 +E04 H710 H516 +E05 H711 H516 +E06 H714 H516 +E07 H701 H516 +E08 H702 H516 +E09 H703 H516 +E10 H705 H516 +E11 H707 H516 +E12 H723 H516 +F01 H710 H522 +F02 H711 H510 +F03 H714 H513 +F04 H701 H522 +F05 H702 H510 +F06 H703 H513 +F07 H705 H522 +F08 H707 H510 +F09 H723 H513 +F10 H706 H522 +F11 H712 H510 +F12 H720 H513 +G01 H711 H513 +G02 H714 H522 +G03 H710 H510 +G04 H702 H513 +G05 H703 H522 +G06 H701 H510 +G07 H707 H513 +G08 H723 H522 +G09 H705 H510 +G10 H712 H513 +G11 H720 H522 +G12 H706 H510 +H01 H714 H510 +H02 H710 H513 +H03 H711 H522 +H04 H703 H510 +H05 H701 H513 +H06 H702 H522 +H07 H723 H510 +H08 H705 H513 +H09 H707 H522 +H10 H720 H510 +H11 H706 H513 +H12 H712 H522 +[DefaultLayout_SingleIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 +[DefaultLayout_DualIndex] +A01 A01 +B01 B01 +C01 C01 +D01 D01 +E01 E01 +F01 F01 +G01 G01 +H01 H01 +A02 A02 +B02 B02 +C02 C02 +D02 D02 +E02 E02 +F02 F02 +G02 G02 +H02 H02 +A03 A03 +B03 B03 +C03 C03 +D03 D03 +E03 E03 +F03 F03 +G03 G03 +H03 H03 +A04 A04 +B04 B04 +C04 C04 +D04 D04 +E04 E04 +F04 F04 +G04 G04 +H04 H04 +A05 A05 +B05 B05 +C05 C05 +D05 D05 +E05 E05 +F05 F05 +G05 G05 +H05 H05 +A06 A06 +B06 B06 +C06 C06 +D06 D06 +E06 E06 +F06 F06 +G06 G06 +H06 H06 +A07 A07 +B07 B07 +C07 C07 +D07 D07 +E07 E07 +F07 F07 +G07 G07 +H07 H07 +A08 A08 +B08 B08 +C08 C08 +D08 D08 +E08 E08 +F08 F08 +G08 G08 +H08 H08 +A09 A09 +B09 B09 +C09 C09 +D09 D09 +E09 E09 +F09 F09 +G09 G09 +H09 H09 +A10 A10 +B10 B10 +C10 C10 +D10 D10 +E10 E10 +F10 F10 +G10 G10 +H10 H10 +A11 A11 +B11 B11 +C11 C11 +D11 D11 +E11 E11 +F11 F11 +G11 G11 +H11 H11 +A12 A12 +B12 B12 +C12 C12 +D12 D12 +E12 E12 +F12 F12 +G12 G12 +H12 H12 \ No newline at end of file diff --git a/conf/collection_index_klits/Nextera Index Kit (24 Indexes 96 Samples).txt b/conf/collection_index_klits/Nextera Index Kit (24 Indexes 96 Samples).txt new file mode 100644 index 000000000..168e69609 --- /dev/null +++ b/conf/collection_index_klits/Nextera Index Kit (24 Indexes 96 Samples).txt @@ -0,0 +1,70 @@ +[Version] +1 +[Name] +Nextera Index Kit (24 Indexes 96 Samples) +[PlateExtension] +nexfc36 +[Settings] +Adapter CTGTCTCTTATACACATCT +[I7] +N701 TAAGGCGA +N702 CGTACTAG +N703 AGGCAGAA +N704 TCCTGAGC +N705 GGACTCCT +N706 TAGGCATG +[I5] +N502 CTCTCTAT +N503 TATCCTCT +N504 AGAGTAGA +N517 GCGTAAGA +[DefaultLayout_SingleIndex] +A01 N701 +B01 N701 +C01 N701 +D01 N701 +A02 N702 +B02 N702 +C02 N702 +D02 N702 +A03 N703 +B03 N703 +C03 N703 +D03 N703 +A04 N704 +B04 N704 +C04 N704 +D04 N704 +A05 N705 +B05 N705 +C05 N705 +D05 N705 +A06 N706 +B06 N706 +C06 N706 +D06 N706 +[DefaultLayout_DualIndex] +A01 N701 N502 +B01 N701 N503 +C01 N701 N504 +D01 N701 N517 +A02 N702 N502 +B02 N702 N503 +C02 N702 N504 +D02 N702 N517 +A03 N703 N502 +B03 N703 N503 +C03 N703 N504 +D03 N703 N517 +A04 N704 N502 +B04 N704 N503 +C04 N704 N504 +D04 N704 N517 +A05 N705 N502 +B05 N705 N503 +C05 N705 N504 +D05 N705 N517 +A06 N706 N502 +B06 N706 N503 +C06 N706 N504 +D06 N706 N517 diff --git a/conf/collection_index_klits/Nextera Index Kit (96 Indexes 384 Samples).txt b/conf/collection_index_klits/Nextera Index Kit (96 Indexes 384 Samples).txt new file mode 100644 index 000000000..71d2c33bf --- /dev/null +++ b/conf/collection_index_klits/Nextera Index Kit (96 Indexes 384 Samples).txt @@ -0,0 +1,225 @@ +[Version] +1 +[Name] +Nextera Index Kit (96 Indexes 384 Samples) +[PlateExtension] +nexfc96 +[Settings] +Adapter CTGTCTCTTATACACATCT +[I7] +N701 TAAGGCGA +N702 CGTACTAG +N703 AGGCAGAA +N704 TCCTGAGC +N705 GGACTCCT +N706 TAGGCATG +N707 CTCTCTAC +N708 CAGAGAGG +N709 GCTACGCT +N710 CGAGGCTG +N711 AAGAGGCA +N712 GTAGAGGA +[I5] +N501 TAGATCGC +N502 CTCTCTAT +N503 TATCCTCT +N504 AGAGTAGA +N505 GTAAGGAG +N506 ACTGCATA +N507 AAGGAGTA +N508 CTAAGCCT +N517 GCGTAAGA +[DefaultLayout_SingleIndex] +A01 N701 +A02 N702 +A03 N703 +A04 N704 +A05 N705 +A06 N706 +A07 N707 +A08 N708 +A09 N709 +A10 N710 +A11 N711 +A12 N712 +B01 N701 +B02 N702 +B03 N703 +B04 N704 +B05 N705 +B06 N706 +B07 N707 +B08 N708 +B09 N709 +B10 N710 +B11 N711 +B12 N712 +C01 N701 +C02 N702 +C03 N703 +C04 N704 +C05 N705 +C06 N706 +C07 N707 +C08 N708 +C09 N709 +C10 N710 +C11 N711 +C12 N712 +D01 N701 +D02 N702 +D03 N703 +D04 N704 +D05 N705 +D06 N706 +D07 N707 +D08 N708 +D09 N709 +D10 N710 +D11 N711 +D12 N712 +E01 N701 +E02 N702 +E03 N703 +E04 N704 +E05 N705 +E06 N706 +E07 N707 +E08 N708 +E09 N709 +E10 N710 +E11 N711 +E12 N712 +F01 N701 +F02 N702 +F03 N703 +F04 N704 +F05 N705 +F06 N706 +F07 N707 +F08 N708 +F09 N709 +F10 N710 +F11 N711 +F12 N712 +G01 N701 +G02 N702 +G03 N703 +G04 N704 +G05 N705 +G06 N706 +G07 N707 +G08 N708 +G09 N709 +G10 N710 +G11 N711 +G12 N712 +H01 N701 +H02 N702 +H03 N703 +H04 N704 +H05 N705 +H06 N706 +H07 N707 +H08 N708 +H09 N709 +H10 N710 +H11 N711 +H12 N712 +[DefaultLayout_DualIndex] +A01 N701 N502 +A02 N702 N502 +A03 N703 N502 +A04 N704 N502 +A05 N705 N502 +A06 N706 N502 +A07 N707 N502 +A08 N708 N502 +A09 N709 N502 +A10 N710 N502 +A11 N711 N502 +A12 N712 N502 +B01 N701 N503 +B02 N702 N503 +B03 N703 N503 +B04 N704 N503 +B05 N705 N503 +B06 N706 N503 +B07 N707 N503 +B08 N708 N503 +B09 N709 N503 +B10 N710 N503 +B11 N711 N503 +B12 N712 N503 +C01 N701 N504 +C02 N702 N504 +C03 N703 N504 +C04 N704 N504 +C05 N705 N504 +C06 N706 N504 +C07 N707 N504 +C08 N708 N504 +C09 N709 N504 +C10 N710 N504 +C11 N711 N504 +C12 N712 N504 +D01 N701 N505 +D02 N702 N505 +D03 N703 N505 +D04 N704 N505 +D05 N705 N505 +D06 N706 N505 +D07 N707 N505 +D08 N708 N505 +D09 N709 N505 +D10 N710 N505 +D11 N711 N505 +D12 N712 N505 +E01 N701 N506 +E02 N702 N506 +E03 N703 N506 +E04 N704 N506 +E05 N705 N506 +E06 N706 N506 +E07 N707 N506 +E08 N708 N506 +E09 N709 N506 +E10 N710 N506 +E11 N711 N506 +E12 N712 N506 +F01 N701 N507 +F02 N702 N507 +F03 N703 N507 +F04 N704 N507 +F05 N705 N507 +F06 N706 N507 +F07 N707 N507 +F08 N708 N507 +F09 N709 N507 +F10 N710 N507 +F11 N711 N507 +F12 N712 N507 +G01 N701 N508 +G02 N702 N508 +G03 N703 N508 +G04 N704 N508 +G05 N705 N508 +G06 N706 N508 +G07 N707 N508 +G08 N708 N508 +G09 N709 N508 +G10 N710 N508 +G11 N711 N508 +G12 N712 N508 +H01 N701 N517 +H02 N702 N517 +H03 N703 N517 +H04 N704 N517 +H05 N705 N517 +H06 N706 N517 +H07 N707 N517 +H08 N708 N517 +H09 N709 N517 +H10 N710 N517 +H11 N711 N517 +H12 N712 N517 diff --git a/conf/collection_index_klits/Nextera XT Index Kit (24 Indexes 96 Samples).txt b/conf/collection_index_klits/Nextera XT Index Kit (24 Indexes 96 Samples).txt new file mode 100644 index 000000000..46c8c80c9 --- /dev/null +++ b/conf/collection_index_klits/Nextera XT Index Kit (24 Indexes 96 Samples).txt @@ -0,0 +1,70 @@ +[Version] +1 +[Name] +Nextera XT Index Kit (24 Indexes 96 Samples) +[PlateExtension] +nexxt24 +[Settings] +Adapter CTGTCTCTTATACACATCT +[I7] +N701 TAAGGCGA +N702 CGTACTAG +N703 AGGCAGAA +N704 TCCTGAGC +N705 GGACTCCT +N706 TAGGCATG +[I5] +S502 CTCTCTAT +S503 TATCCTCT +S504 AGAGTAGA +S517 GCGTAAGA +[DefaultLayout_SingleIndex] +A01 N701 +B01 N701 +C01 N701 +D01 N701 +A02 N702 +B02 N702 +C02 N702 +D02 N702 +A03 N703 +B03 N703 +C03 N703 +D03 N703 +A04 N704 +B04 N704 +C04 N704 +D04 N704 +A05 N705 +B05 N705 +C05 N705 +D05 N705 +A06 N706 +B06 N706 +C06 N706 +D06 N706 +[DefaultLayout_DualIndex] +A01 N701 S502 +B01 N701 S503 +C01 N701 S504 +D01 N701 S517 +A02 N702 S502 +B02 N702 S503 +C02 N702 S504 +D02 N702 S517 +A03 N703 S502 +B03 N703 S503 +C03 N703 S504 +D03 N703 S517 +A04 N704 S502 +B04 N704 S503 +C04 N704 S504 +D04 N704 S517 +A05 N705 S502 +B05 N705 S503 +C05 N705 S504 +D05 N705 S517 +A06 N706 S502 +B06 N706 S503 +C06 N706 S504 +D06 N706 S517 \ No newline at end of file diff --git a/conf/collection_index_klits/Nextera XT Index Kit (96 Indexes 384 Samples).txt b/conf/collection_index_klits/Nextera XT Index Kit (96 Indexes 384 Samples).txt new file mode 100644 index 000000000..2c220d40b --- /dev/null +++ b/conf/collection_index_klits/Nextera XT Index Kit (96 Indexes 384 Samples).txt @@ -0,0 +1,225 @@ +[Version] +1 +[Name] +Nextera XT Index Kit (96 Indexes 384 Samples) +[PlateExtension] +nexxt96 +[Settings] +Adapter CTGTCTCTTATACACATCT +[I7] +N701 TAAGGCGA +N702 CGTACTAG +N703 AGGCAGAA +N704 TCCTGAGC +N705 GGACTCCT +N706 TAGGCATG +N707 CTCTCTAC +N708 CAGAGAGG +N709 GCTACGCT +N710 CGAGGCTG +N711 AAGAGGCA +N712 GTAGAGGA +[I5] +S501 TAGATCGC +S502 CTCTCTAT +S503 TATCCTCT +S504 AGAGTAGA +S505 GTAAGGAG +S506 ACTGCATA +S507 AAGGAGTA +S508 CTAAGCCT +S517 GCGTAAGA +[DefaultLayout_SingleIndex] +A01 N701 +A02 N702 +A03 N703 +A04 N704 +A05 N705 +A06 N706 +A07 N707 +A08 N708 +A09 N709 +A10 N710 +A11 N711 +A12 N712 +B01 N701 +B02 N702 +B03 N703 +B04 N704 +B05 N705 +B06 N706 +B07 N707 +B08 N708 +B09 N709 +B10 N710 +B11 N711 +B12 N712 +C01 N701 +C02 N702 +C03 N703 +C04 N704 +C05 N705 +C06 N706 +C07 N707 +C08 N708 +C09 N709 +C10 N710 +C11 N711 +C12 N712 +D01 N701 +D02 N702 +D03 N703 +D04 N704 +D05 N705 +D06 N706 +D07 N707 +D08 N708 +D09 N709 +D10 N710 +D11 N711 +D12 N712 +E01 N701 +E02 N702 +E03 N703 +E04 N704 +E05 N705 +E06 N706 +E07 N707 +E08 N708 +E09 N709 +E10 N710 +E11 N711 +E12 N712 +F01 N701 +F02 N702 +F03 N703 +F04 N704 +F05 N705 +F06 N706 +F07 N707 +F08 N708 +F09 N709 +F10 N710 +F11 N711 +F12 N712 +G01 N701 +G02 N702 +G03 N703 +G04 N704 +G05 N705 +G06 N706 +G07 N707 +G08 N708 +G09 N709 +G10 N710 +G11 N711 +G12 N712 +H01 N701 +H02 N702 +H03 N703 +H04 N704 +H05 N705 +H06 N706 +H07 N707 +H08 N708 +H09 N709 +H10 N710 +H11 N711 +H12 N712 +[DefaultLayout_DualIndex] +A01 N701 S502 +A02 N702 S502 +A03 N703 S502 +A04 N704 S502 +A05 N705 S502 +A06 N706 S502 +A07 N707 S502 +A08 N708 S502 +A09 N709 S502 +A10 N710 S502 +A11 N711 S502 +A12 N712 S502 +B01 N701 S503 +B02 N702 S503 +B03 N703 S503 +B04 N704 S503 +B05 N705 S503 +B06 N706 S503 +B07 N707 S503 +B08 N708 S503 +B09 N709 S503 +B10 N710 S503 +B11 N711 S503 +B12 N712 S503 +C01 N701 S504 +C02 N702 S504 +C03 N703 S504 +C04 N704 S504 +C05 N705 S504 +C06 N706 S504 +C07 N707 S504 +C08 N708 S504 +C09 N709 S504 +C10 N710 S504 +C11 N711 S504 +C12 N712 S504 +D01 N701 S505 +D02 N702 S505 +D03 N703 S505 +D04 N704 S505 +D05 N705 S505 +D06 N706 S505 +D07 N707 S505 +D08 N708 S505 +D09 N709 S505 +D10 N710 S505 +D11 N711 S505 +D12 N712 S505 +E01 N701 S506 +E02 N702 S506 +E03 N703 S506 +E04 N704 S506 +E05 N705 S506 +E06 N706 S506 +E07 N707 S506 +E08 N708 S506 +E09 N709 S506 +E10 N710 S506 +E11 N711 S506 +E12 N712 S506 +F01 N701 S507 +F02 N702 S507 +F03 N703 S507 +F04 N704 S507 +F05 N705 S507 +F06 N706 S507 +F07 N707 S507 +F08 N708 S507 +F09 N709 S507 +F10 N710 S507 +F11 N711 S507 +F12 N712 S507 +G01 N701 S508 +G02 N702 S508 +G03 N703 S508 +G04 N704 S508 +G05 N705 S508 +G06 N706 S508 +G07 N707 S508 +G08 N708 S508 +G09 N709 S508 +G10 N710 S508 +G11 N711 S508 +G12 N712 S508 +H01 N701 S517 +H02 N702 S517 +H03 N703 S517 +H04 N704 S517 +H05 N705 S517 +H06 N706 S517 +H07 N707 S517 +H08 N708 S517 +H09 N709 S517 +H10 N710 S517 +H11 N711 S517 +H12 N712 S517 diff --git a/conf/collection_index_klits/Nextera XT v2 Index Kit A.txt b/conf/collection_index_klits/Nextera XT v2 Index Kit A.txt new file mode 100644 index 000000000..fd5d306ba --- /dev/null +++ b/conf/collection_index_klits/Nextera XT v2 Index Kit A.txt @@ -0,0 +1,224 @@ +[Version] +1 +[Name] +Nextera XT v2 Index Kit A +[PlateExtension] +nexxtv2a +[Settings] +Adapter CTGTCTCTTATACACATCT +[I7] +N701 TAAGGCGA +N702 CGTACTAG +N703 AGGCAGAA +N704 TCCTGAGC +N705 GGACTCCT +N706 TAGGCATG +N707 CTCTCTAC +N710 CGAGGCTG +N711 AAGAGGCA +N712 GTAGAGGA +N714 GCTCATGA +N715 ATCTCAGG +[I5] +S502 CTCTCTAT +S503 TATCCTCT +S505 GTAAGGAG +S506 ACTGCATA +S507 AAGGAGTA +S508 CTAAGCCT +S510 CGTCTAAT +S511 TCTCTCCG +[DefaultLayout_SingleIndex] +A01 N701 +A02 N702 +A03 N703 +A04 N704 +A05 N705 +A06 N706 +A07 N707 +A08 N710 +A09 N711 +A10 N712 +A11 N714 +A12 N715 +B01 N701 +B02 N702 +B03 N703 +B04 N704 +B05 N705 +B06 N706 +B07 N707 +B08 N710 +B09 N711 +B10 N712 +B11 N714 +B12 N715 +C01 N701 +C02 N702 +C03 N703 +C04 N704 +C05 N705 +C06 N706 +C07 N707 +C08 N710 +C09 N711 +C10 N712 +C11 N714 +C12 N715 +D01 N701 +D02 N702 +D03 N703 +D04 N704 +D05 N705 +D06 N706 +D07 N707 +D08 N710 +D09 N711 +D10 N712 +D11 N714 +D12 N715 +E01 N701 +E02 N702 +E03 N703 +E04 N704 +E05 N705 +E06 N706 +E07 N707 +E08 N710 +E09 N711 +E10 N712 +E11 N714 +E12 N715 +F01 N701 +F02 N702 +F03 N703 +F04 N704 +F05 N705 +F06 N706 +F07 N707 +F08 N710 +F09 N711 +F10 N712 +F11 N714 +F12 N715 +G01 N701 +G02 N702 +G03 N703 +G04 N704 +G05 N705 +G06 N706 +G07 N707 +G08 N710 +G09 N711 +G10 N712 +G11 N714 +G12 N715 +H01 N701 +H02 N702 +H03 N703 +H04 N704 +H05 N705 +H06 N706 +H07 N707 +H08 N710 +H09 N711 +H10 N712 +H11 N714 +H12 N715 +[DefaultLayout_DualIndex] +A01 N701 S502 +A02 N702 S502 +A03 N703 S502 +A04 N704 S502 +A05 N705 S502 +A06 N706 S502 +A07 N707 S502 +A08 N710 S502 +A09 N711 S502 +A10 N712 S502 +A11 N714 S502 +A12 N715 S502 +B01 N701 S503 +B02 N702 S503 +B03 N703 S503 +B04 N704 S503 +B05 N705 S503 +B06 N706 S503 +B07 N707 S503 +B08 N710 S503 +B09 N711 S503 +B10 N712 S503 +B11 N714 S503 +B12 N715 S503 +C01 N701 S505 +C02 N702 S505 +C03 N703 S505 +C04 N704 S505 +C05 N705 S505 +C06 N706 S505 +C07 N707 S505 +C08 N710 S505 +C09 N711 S505 +C10 N712 S505 +C11 N714 S505 +C12 N715 S505 +D01 N701 S506 +D02 N702 S506 +D03 N703 S506 +D04 N704 S506 +D05 N705 S506 +D06 N706 S506 +D07 N707 S506 +D08 N710 S506 +D09 N711 S506 +D10 N712 S506 +D11 N714 S506 +D12 N715 S506 +E01 N701 S507 +E02 N702 S507 +E03 N703 S507 +E04 N704 S507 +E05 N705 S507 +E06 N706 S507 +E07 N707 S507 +E08 N710 S507 +E09 N711 S507 +E10 N712 S507 +E11 N714 S507 +E12 N715 S507 +F01 N701 S508 +F02 N702 S508 +F03 N703 S508 +F04 N704 S508 +F05 N705 S508 +F06 N706 S508 +F07 N707 S508 +F08 N710 S508 +F09 N711 S508 +F10 N712 S508 +F11 N714 S508 +F12 N715 S508 +G01 N701 S510 +G02 N702 S510 +G03 N703 S510 +G04 N704 S510 +G05 N705 S510 +G06 N706 S510 +G07 N707 S510 +G08 N710 S510 +G09 N711 S510 +G10 N712 S510 +G11 N714 S510 +G12 N715 S510 +H01 N701 S511 +H02 N702 S511 +H03 N703 S511 +H04 N704 S511 +H05 N705 S511 +H06 N706 S511 +H07 N707 S511 +H08 N710 S511 +H09 N711 S511 +H10 N712 S511 +H11 N714 S511 +H12 N715 S511 \ No newline at end of file diff --git a/conf/collection_index_klits/TruSeq RNA Single Indexes Set A.txt b/conf/collection_index_klits/TruSeq RNA Single Indexes Set A.txt new file mode 100644 index 000000000..bb771a323 --- /dev/null +++ b/conf/collection_index_klits/TruSeq RNA Single Indexes Set A.txt @@ -0,0 +1,119 @@ +[Version] +1 +[Name] +TruSeq RNA Single Indexes Set A +[PlateExtension] +trursinglea +[Settings] +Adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCA +AdapterRead2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT +[I7] +AR002 CGATGT +AR004 TGACCA +AR005 ACAGTG +AR006 GCCAAT +AR007 CAGATC +AR012 CTTGTA +AR013 AGTCAA +AR014 AGTTCC +AR015 ATGTCA +AR016 CCGTCC +AR018 GTCCGC +AR019 GTGAAA +[DefaultLayout_SingleIndex] +A01 AR002 +A02 AR004 +A03 AR005 +A04 AR006 +A05 AR007 +A06 AR012 +A07 AR013 +A08 AR014 +A09 AR015 +A10 AR016 +A11 AR018 +A12 AR019 +B01 AR002 +B02 AR004 +B03 AR005 +B04 AR006 +B05 AR007 +B06 AR012 +B07 AR013 +B08 AR014 +B09 AR015 +B10 AR016 +B11 AR018 +B12 AR019 +C01 AR002 +C02 AR004 +C03 AR005 +C04 AR006 +C05 AR007 +C06 AR012 +C07 AR013 +C08 AR014 +C09 AR015 +C10 AR016 +C11 AR018 +C12 AR019 +D01 AR002 +D02 AR004 +D03 AR005 +D04 AR006 +D05 AR007 +D06 AR012 +D07 AR013 +D08 AR014 +D09 AR015 +D10 AR016 +D11 AR018 +D12 AR019 +E01 AR002 +E02 AR004 +E03 AR005 +E04 AR006 +E05 AR007 +E06 AR012 +E07 AR013 +E08 AR014 +E09 AR015 +E10 AR016 +E11 AR018 +E12 AR019 +F01 AR002 +F02 AR004 +F03 AR005 +F04 AR006 +F05 AR007 +F06 AR012 +F07 AR013 +F08 AR014 +F09 AR015 +F10 AR016 +F11 AR018 +F12 AR019 +G01 AR002 +G02 AR004 +G03 AR005 +G04 AR006 +G05 AR007 +G06 AR012 +G07 AR013 +G08 AR014 +G09 AR015 +G10 AR016 +G11 AR018 +G12 AR019 +H01 AR002 +H02 AR004 +H03 AR005 +H04 AR006 +H05 AR007 +H06 AR012 +H07 AR013 +H08 AR014 +H09 AR015 +H10 AR016 +H11 AR018 +H12 AR019 \ No newline at end of file diff --git a/install.sh b/install.sh index 8f4d9ead4..4d90021f6 100644 --- a/install.sh +++ b/install.sh @@ -488,6 +488,10 @@ if [ $upgrade == true ]; then cp $INSTALL_PATH/conf/*_template.csv $INSTALL_PATH/documents/wetlab/templates/ cp $INSTALL_PATH/conf/samples_template.xlsx $INSTALL_PATH/documents/wetlab/templates/ + # Copy the illumina collection index kits + mkdir -p $INSTALL_PATH/documents/wetlab/collection_index_kits/ + cp $INSTALL_PATH/conf/collection_index_kits/*.txt $INSTALL_PATH/documents/wetlab/collection_index_kits/ + # update logging configuration file cp $INSTALL_PATH/conf/template_logging_config.ini $INSTALL_PATH/wetlab/logging_config.ini sed -i "s@INSTALL_PATH@${INSTALL_PATH}@g" $INSTALL_PATH/wetlab/logging_config.ini From 7b7c8ca63650fbd2097fe57dcc83a5f545cf8ff7 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 28 Sep 2024 21:25:23 +0200 Subject: [PATCH 173/446] Solved issue #321 Unsupported searching in admin page on moleculePrepations --- core/admin.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/admin.py b/core/admin.py index c12a2e021..e78a4dfba 100644 --- a/core/admin.py +++ b/core/admin.py @@ -81,7 +81,7 @@ class MoleculePreparationAdmin(admin.ModelAdmin): "reused_number", ) list_filter = ("generated_at",) - search_fields = ("sample__startswith",) + search_fields = ("sample__sample_name__startswith",) class MoleculeUsedForAdmin(admin.ModelAdmin): From 8ad2c22271f943a14fd93c0e007d3cbd74ab7695 Mon Sep 17 00:00:00 2001 From: luissian Date: Sat, 28 Sep 2024 22:47:19 +0200 Subject: [PATCH 174/446] Solved issue #322 No extraction parameter fields are showed --- django_utils/templatetags/replace_spaces.py | 8 ++++++++ wetlab/templates/wetlab/handling_molecules.html | 11 ++++++----- wetlab/utils/statistics.py | 1 - 3 files changed, 14 insertions(+), 6 deletions(-) create mode 100644 django_utils/templatetags/replace_spaces.py diff --git a/django_utils/templatetags/replace_spaces.py b/django_utils/templatetags/replace_spaces.py new file mode 100644 index 000000000..d3bf60fba --- /dev/null +++ b/django_utils/templatetags/replace_spaces.py @@ -0,0 +1,8 @@ +from django import template + +register = template.Library() + + +@register.filter +def replace_spaces_with_underscores(value): + return value.replace(" ", "_") diff --git a/wetlab/templates/wetlab/handling_molecules.html b/wetlab/templates/wetlab/handling_molecules.html index 9103d258a..9af67a779 100644 --- a/wetlab/templates/wetlab/handling_molecules.html +++ b/wetlab/templates/wetlab/handling_molecules.html @@ -1,5 +1,6 @@ {% extends "core/base.html" %} {% load static %} +{% load replace_spaces %} {% block content %} {% include "wetlab/menu.html" %} {% include 'core/jexcel_functionality.html' %} @@ -125,7 +126,7 @@

    Update sample extraction data with defined parameters

    Protocol: {{ prot }}
    -
    +
    {% endfor %} @@ -637,12 +638,12 @@

    Not molecule uses have been defined yet

    {% if molecule_parameters %} $(document).ready(function () { {% for prot , value_dict in molecule_parameters.items %} - var {{ prot }}_data = [{% for values in value_dict.m_data %} + var {{ prot|replace_spaces_with_underscores }}_data = [{% for values in value_dict.m_data %} [{% for value in values %}'{{value}}',{% endfor %}],{% endfor %} ]; - var {{ prot }}_data_table = jspreadsheet(document.getElementById('spreadsheet_{{ prot }}'),{ - data:{{ prot }}_data, + var {{ prot|replace_spaces_with_underscores }}_data_table = jspreadsheet(document.getElementById('spreadsheet_{{ prot|replace_spaces_with_underscores }}'),{ + data:{{ prot|replace_spaces_with_underscores }}_data, columns: [ { type: 'hidden' }, { type: 'text', title:'{{value_dict.fix_heading.0}}', width:180 , readOnly:true }, @@ -670,7 +671,7 @@

    Not molecule uses have been defined yet

    $("#addExtractionParameters").submit(function (e) { - var table_data = {{ prot }}_data_table.getData() + var table_data = {{ prot|replace_spaces_with_underscores }}_data_table.getData() var data_json = JSON.stringify(table_data) $("").attr("type", "hidden") .attr("name", "{{ prot }}") diff --git a/wetlab/utils/statistics.py b/wetlab/utils/statistics.py index f8847d645..0632a84f0 100644 --- a/wetlab/utils/statistics.py +++ b/wetlab/utils/statistics.py @@ -892,7 +892,6 @@ def _lab_statistics( g_data, ).render() ) - # import pdb; pdb.set_trace() return research_lab_statistics research_lab_statistics = {} From 3c0dff03294bc4fe1bf37e5dc175b4d545a61095 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 29 Sep 2024 17:17:24 +0200 Subject: [PATCH 175/446] solved issue #303 No horizontal scroll when displaying sample information --- wetlab/templates/wetlab/display_sample.html | 84 +++++++++++---------- 1 file changed, 44 insertions(+), 40 deletions(-) diff --git a/wetlab/templates/wetlab/display_sample.html b/wetlab/templates/wetlab/display_sample.html index d44199ad9..55d56d9c9 100644 --- a/wetlab/templates/wetlab/display_sample.html +++ b/wetlab/templates/wetlab/display_sample.html @@ -131,51 +131,55 @@

    Sample information for {{sample_information.sample_name}
    {% for molecule_values, molecule_param_heading , molecule_param_values in sample_information.molecule_definition_data %} +
    -

    Molecule extraction information

    -
    - - - - {% for values in sample_information.molecule_definition_heading %} - - {%endfor%} - - - - - {% for mol_values in molecule_values %} - - {%endfor%} - - -
    {{ values }}
    {{ mol_values }}
    +

    Extraction information

    +
    + + + + {% for values in sample_information.molecule_definition_heading %} + + {%endfor%} + + + + + {% for mol_values in molecule_values %} + + {%endfor%} + + +
    {{ values }}
    {{ mol_values }}
    +
    {% if molecule_param_heading is not None %} -
    -
    -

    Quality Parameter Molecule Information

    -
    -
    - - - - {% for mol_par_head in molecule_param_heading %} - - {%endfor%} - - - - - {% for value in molecule_param_values %} - - {%endfor%} - - -
    {{ mol_par_head }}
    {{ value }}
    +
    +
    +
    +

    Protocol Extraction Information

    +
    +
    + + + + {% for mol_par_head in molecule_param_heading %} + + {%endfor%} + + + + + {% for value in molecule_param_values %} + + {%endfor%} + + +
    {{ mol_par_head }}
    {{ value }}
    +
    @@ -186,7 +190,7 @@

    Sample information for {{sample_information.sample_name} {% csrf_token %} - +

    From d0785e3b5fe5a37cdd7dbd146c5dad9352692f94 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 29 Sep 2024 18:02:50 +0200 Subject: [PATCH 176/446] Solved issue #323 Incorrect type of button to modify protocol fields --- wetlab/templates/wetlab/display_protocol.html | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/wetlab/templates/wetlab/display_protocol.html b/wetlab/templates/wetlab/display_protocol.html index 3de0ea8e8..eb46bfd37 100644 --- a/wetlab/templates/wetlab/display_protocol.html +++ b/wetlab/templates/wetlab/display_protocol.html @@ -1,4 +1,5 @@ {% extends "core/base.html" %} +{% load static %} {% block content %} {% include "wetlab/menu.html" %}
    @@ -8,7 +9,7 @@
    -

    Invalid definition

    +

    Invalid definition

    {{error_message}}

    @@ -17,9 +18,9 @@

    {{error_message}}

    {% endif %} {% if protocol_data %} -
    +
    -

    These are the parameters defined for {{protocol_data.protocol_name}} Protocol

    +

    Parameters defined for {{protocol_data.protocol_name}} Protocol

    {{protocol_data.protocol_name}}

    @@ -42,15 +43,12 @@

    These are the parameters defined for {{protocol_data.protocol_name}} Protoco {% endfor %} -

    - +
    +
    - -
    - -
    - +
    +
    {% endif %} {% if kit_data %} From 2f75ed725a7a40e5f2649043e8ef08bfdac55f70 Mon Sep 17 00:00:00 2001 From: luissian Date: Sun, 29 Sep 2024 23:22:19 +0200 Subject: [PATCH 177/446] Solved issue #324 Unable to specify downloadable parameters in protocol --- core/core_config.py | 4 ++ core/models.py | 22 +++++++--- core/utils/protocols.py | 4 +- core/utils/samples.py | 3 -- install.sh | 2 +- .../wetlab/define_protocol_parameters.html | 24 +++++----- wetlab/templates/wetlab/display_protocol.html | 44 ++++++++++++------- .../wetlab/display_sample_project.html | 18 ++++++-- .../wetlab/modify_protocol_fields.html | 19 +++++--- 9 files changed, 90 insertions(+), 50 deletions(-) diff --git a/core/core_config.py b/core/core_config.py index d41b21573..194cd941d 100644 --- a/core/core_config.py +++ b/core/core_config.py @@ -84,6 +84,7 @@ "Parameter name", "Order", "Used", + "Downloadable", "Parameter Type", "Option Values", "Min Value", @@ -95,8 +96,11 @@ "New field name", "Order", "Used", + "Downloadable", "Parameter Type", "Option Values", + "Min Value", + "Max Value", "Description", ] diff --git a/core/models.py b/core/models.py index 742c19170..5b199a472 100644 --- a/core/models.py +++ b/core/models.py @@ -278,6 +278,7 @@ def create_protocol_parameter(self, prot_param_data): parameter_min_value=prot_param_data["Min Value"], parameter_option_values=prot_param_data["Option Values"], parameter_type=prot_param_data["Parameter Type"], + parameter_download=prot_param_data["Downloadable"], ) return new_prot_parameter @@ -292,6 +293,7 @@ class ProtocolParameters(models.Model): parameter_option_values = models.CharField(max_length=400, null=True, blank=True) parameter_max_value = models.CharField(max_length=50, null=True, blank=True) parameter_min_value = models.CharField(max_length=50, null=True, blank=True) + parameter_download = models.BooleanField(default=False, null=True, blank=True) class Meta: db_table = "core_protocol_parameters" @@ -316,6 +318,7 @@ def get_all_parameter_info(self): param_info.append(self.parameter_name) param_info.append(self.parameter_order) param_info.append(self.parameter_used) + param_info.append(self.parameter_download) param_info.append(self.parameter_type) param_info.append(self.parameter_option_values) param_info.append(self.parameter_min_value) @@ -328,17 +331,23 @@ def get_protocol_fields_for_javascript(self): used = "true" else: used = "false" + if self.parameter_download: + download = "true" + else: + download = "false" if self.parameter_option_values is None: parameter_option_values = "" else: parameter_option_values = self.parameter_option_values field_data = [] field_data.append(self.parameter_name) - field_data.append(self.parameter_order) field_data.append(used) + field_data.append(download) field_data.append(self.parameter_type) field_data.append(parameter_option_values) + field_data.append(self.parameter_min_value) + field_data.append(self.parameter_max_value) field_data.append(self.parameter_description) return field_data @@ -347,8 +356,11 @@ def update_protocol_fields(self, prot_param_data): self.parameter_description = prot_param_data["Description"] self.parameter_order = prot_param_data["Order"] self.parameter_used = prot_param_data["Used"] + self.parameter_download = prot_param_data["Downloadable"] self.parameter_option_values = prot_param_data["Option Values"] self.parameter_type = prot_param_data["Parameter Type"] + self.parameter_max_value = prot_param_data["Max Value"] + self.parameter_min_value = prot_param_data["Min Value"] self.save() objects = ProtocolParametersManager() @@ -929,7 +941,7 @@ def create_sample_project_fields(self, project_field_data): sample_project_field_order=project_field_data["Order"], sample_project_field_used=project_field_data["Used"], sample_project_field_type=project_field_data["Field type"], - sample_project_searchable=project_field_data["Searchable"], + sample_project_downloadable=project_field_data["Downloadable"], # do not include optional values. Set to empty sample_project_option_list="", ) @@ -958,7 +970,7 @@ class SampleProjectsFields(models.Model): sample_project_field_used = models.BooleanField() sample_project_field_type = models.CharField(max_length=20) sample_project_option_list = models.CharField(max_length=255, null=True, blank=True) - sample_project_searchable = models.BooleanField(default=False) + sample_project_downloadable = models.BooleanField(default=False) generated_at = models.DateTimeField(auto_now_add=True) class Meta: @@ -1006,7 +1018,7 @@ def get_sample_project_fields_name(self, include_search=None): used = "true" else: used = "false" - if self.sample_project_searchable: + if self.sample_project_downloadable: searchable = "true" else: searchable = "false" @@ -1036,7 +1048,7 @@ def update_sample_project_fields(self, project_field_data): self.sample_project_field_order = project_field_data["Order"] self.sample_project_field_used = project_field_data["Used"] self.sample_project_field_type = project_field_data["Field type"] - self.sample_project_searchable = project_field_data["Searchable"] + self.sample_project_downloadable = project_field_data["Downloadable"] self.sample_project_field_classification_id = project_field_data[ "SampleProjectFieldClassificationID" ] diff --git a/core/utils/protocols.py b/core/utils/protocols.py index 861366bee..eb2af48bd 100644 --- a/core/utils/protocols.py +++ b/core/utils/protocols.py @@ -237,7 +237,6 @@ def get_protocol_fields(protocol_id): parameters_protocol["protocol_id"] = protocol_id parameters_protocol["protocol_name"] = protocol_obj.get_name() parameters_protocol["fields"] = parameter_list - return parameters_protocol @@ -365,13 +364,12 @@ def modify_fields_in_protocol(form_data): def set_protocol_parameters(request): protocol_id = request.POST["protocol_id"] - json_data = json.loads(request.POST["table_data1"]) parameters = core.core_config.HEADING_FOR_DEFINING_PROTOCOL_PARAMETERS protocol_id_obj = core.models.Protocols.objects.get(pk__exact=protocol_id) saved_parameters = [] stored_parameters = {} - for row_data in json_data: + for row_data in json.loads(request.POST["table_data1"]): if row_data[0] == "": continue prot_parameters = {} diff --git a/core/utils/samples.py b/core/utils/samples.py index 051a837cd..699ea44d1 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -2113,9 +2113,6 @@ def set_sample_project_fields(data_form): saved_fields = [] stored_fields = {} valid_data = False - import pdb - - pdb.set_trace() # check if there is at least one field to be used for row_line in excel_json_data: if row_line["Used"] is True: diff --git a/install.sh b/install.sh index 4d90021f6..824788447 100644 --- a/install.sh +++ b/install.sh @@ -600,7 +600,7 @@ if [ $upgrade == true ]; then echo "Running migration script: remove_comma_rawtopunknownbarcodes" ./manage.py runscript convert_rawtop_counter_to_int echo "checking for database changes" - if python manage.py makemigrations | grep -q "No changes"; then + if python manage.py makemigrations --noinput | grep -q "No changes"; then # check for pending migrations if ./manage.py showmigrations | grep '\[ \]'; then echo "There are pending migrations" diff --git a/wetlab/templates/wetlab/define_protocol_parameters.html b/wetlab/templates/wetlab/define_protocol_parameters.html index 09dcb81c7..4fe3004de 100644 --- a/wetlab/templates/wetlab/define_protocol_parameters.html +++ b/wetlab/templates/wetlab/define_protocol_parameters.html @@ -9,7 +9,7 @@
    -

    Invalid definition

    +

    Invalid definition

    {{error_message}}

    @@ -56,10 +56,11 @@

    {{error_message}}

    Define the parameters used for protocol {{prot_parameters.protocol_name}}

    -
    - - - +
    +
    +
    + +
    +
    @@ -497,23 +513,6 @@

    Not available Pools

    {% endif %} {% endif %}
    - - - {% endblock %} + +{% endblock %} From 6a6800ed44a9a6f7cd543e6de74caea262009872 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 28 Oct 2025 13:07:18 +0100 Subject: [PATCH 252/446] fixed some errors due to change to manytomany between library and runprocess --- wetlab/models.py | 27 ++++++++++++++++++++------- wetlab/utils/library.py | 3 ++- wetlab/utils/run.py | 4 ++-- wetlab/views.py | 2 +- 4 files changed, 25 insertions(+), 11 deletions(-) diff --git a/wetlab/models.py b/wetlab/models.py index baae93b67..3286d9e22 100644 --- a/wetlab/models.py +++ b/wetlab/models.py @@ -93,19 +93,32 @@ def get_platform_name(self): else: return "Not defined" + def _get_run_processes(self): + return self.runprocess_set.order_by("-generated_at") + + def _get_latest_run_process(self): + return self._get_run_processes().first() + + def get_run_names(self): + return [ + "%s" % (run_process.get_run_name()) + for run_process in self._get_run_processes() + ] + def get_run_name(self): - if self.run_process_id is not None: - return "%s" % (self.run_process_id.get_run_name()) - else: - return "Not defined yet" + run_process = self._get_latest_run_process() + if run_process is not None: + return "%s" % (run_process.get_run_name()) + return "Not defined yet" def get_run_id(self): - if self.run_process_id is not None: - return "%s" % (self.run_process_id.get_run_id()) + run_process = self._get_latest_run_process() + if run_process is not None: + return "%s" % (run_process.get_run_id()) return None def get_run_obj(self): - return self.run_process_id + return self._get_latest_run_process() def set_pool(self, pool_obj): self.pool.add(pool_obj) diff --git a/wetlab/utils/library.py b/wetlab/utils/library.py index 550e58b73..a92dcc559 100644 --- a/wetlab/utils/library.py +++ b/wetlab/utils/library.py @@ -514,7 +514,8 @@ def get_all_library_information(sample_id): for pool in pools: pool_name = pool.get_pool_name() pool_code = pool.get_pool_code_id() - run_name = pool.get_run_name() + run_names = pool.get_run_names() + run_name = ", ".join(run_names) if run_names else pool.get_run_name() library_information["pool_information"].append( [ lib_prep_code_id, diff --git a/wetlab/utils/run.py b/wetlab/utils/run.py index 8d86e8695..761e257e2 100644 --- a/wetlab/utils/run.py +++ b/wetlab/utils/run.py @@ -133,7 +133,7 @@ def create_run_in_pre_recorded_and_get_data_for_confirmation(form_data, user_obj for pool in pool_ids: # changed from version 3.1.0 the relation in pools - new_run_obj.set_pool(pool) + new_run_obj.set_library_pool(pool) display_sample_information["experiment_name"] = form_data["experimentName"] display_sample_information["run_process_id"] = new_run_obj.get_run_id() return display_sample_information @@ -794,7 +794,7 @@ def get_available_pools_for_run(): pool_state__pool_state__exact="Selected" ) .exclude(runprocess=None) - .order_by("run_process_id") + .order_by("runprocess") ) return pools_to_update diff --git a/wetlab/views.py b/wetlab/views.py index d8df2004b..d220a6c34 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -3894,7 +3894,7 @@ def create_new_run(request): wetlab.utils.run.store_confirmation_sample_sheet(run_data) # update the sample state for each one in the run - pools_obj = wetlab.models.LibraryPool.objects.filter(run_process_id=run_obj) + pools_obj = wetlab.models.LibraryPool.objects.filter(runprocess=run_obj) for pool_obj in pools_obj: pool_obj.set_pool_state("Used") From 1e9daa58e9ca82f65506acbf6d843d37145d020b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 28 Oct 2025 13:28:19 +0100 Subject: [PATCH 253/446] some fixes due to changes in models --- wetlab/templates/wetlab/create_new_run.html | 18 ++++++++---------- wetlab/utils/sample.py | 1 - wetlab/views.py | 10 +++++----- 3 files changed, 13 insertions(+), 16 deletions(-) diff --git a/wetlab/templates/wetlab/create_new_run.html b/wetlab/templates/wetlab/create_new_run.html index 8e647938f..2e1b90f28 100644 --- a/wetlab/templates/wetlab/create_new_run.html +++ b/wetlab/templates/wetlab/create_new_run.html @@ -7,18 +7,16 @@
    {% include 'registration/login_inline.html' %} {% if error_message %} -
    -
    -
    -
    -

    Unable to accept your request

    -
    -
    - {% for error in error_message %}

    {{ error }}

    {% endfor %} -
    +
    +
    +
    +

    Unable to process your request

    +
    +

    {{error_message}}

    -
    +
    +
    {% endif %} {% if info_message %}
    diff --git a/wetlab/utils/sample.py b/wetlab/utils/sample.py index 726fb25e9..9b1212dc5 100644 --- a/wetlab/utils/sample.py +++ b/wetlab/utils/sample.py @@ -21,7 +21,6 @@ def analyze_reprocess_data(reprocess_data, reprocess_sample_id): Input: reprocess_data # data for creating the reuse reprocess_sample_id # sample id to reprocess - req_user # register user Functions: update_sample_reused update_molecule_reused diff --git a/wetlab/views.py b/wetlab/views.py index d220a6c34..3a90c3563 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -3420,7 +3420,7 @@ def repeat_library_preparation(request): molecule_code_id = request.POST["molecule_code_id"] sample_id = request.POST["sample_id"] result = wetlab.utils.sample.analyze_reprocess_data( - [molecule_code_id, "New Library Preparation"], sample_id, request.user + [molecule_code_id, "New Library Preparation"], sample_id ) detail_description = {} if result == "Invalid options": @@ -3478,7 +3478,7 @@ def repeat_pool(request): sample_id = lib_prep_obj.get_sample_id() result = wetlab.utils.sample.analyze_reprocess_data( - [molecule_code_id, lib_prep_code_id, "New Pool"], sample_id, request.user + [molecule_code_id, lib_prep_code_id, "New Pool"], sample_id ) detail_description = {} if result == "Invalid options": @@ -3488,13 +3488,13 @@ def repeat_pool(request): ] return render( request, - "wetlab/error_page.html", + "django_utils/error_page.html", {"detail_description": detail_description}, ) detail_description["information"] = wetlab.config.SUCCESSFUL_REUSE_LIB_PREP return render( request, - "wetlab/successful_page.html", + "django_utils/info_page.html", {"detail_description": detail_description}, ) # return to the main page because the page was not requested for the right page @@ -3837,7 +3837,7 @@ def create_new_run(request): run_id = request.POST["run_ids"] experiment_name = wetlab.utils.run.get_experiment_name(run_id) pool_objs = wetlab.models.LibraryPool.objects.filter( - run_process_id__exact=run_id + runprocess__exact=run_id ) pool_ids = [] for pool in pool_objs: From d693b25bc8ce3493f2cbf3c867f259253ba3607b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 28 Oct 2025 13:29:39 +0100 Subject: [PATCH 254/446] point to correct info page --- wetlab/views.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wetlab/views.py b/wetlab/views.py index 3a90c3563..4e1401ee2 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -3430,7 +3430,7 @@ def repeat_library_preparation(request): ] return render( request, - "wetlab/error_page.html", + "django_utils/error_page.html", {"detail_description": detail_description}, ) detail_description["information"] = ( @@ -3438,7 +3438,7 @@ def repeat_library_preparation(request): ) return render( request, - "wetlab/successful_page.html", + "django_utils/info_page.html", {"detail_description": detail_description}, ) # return to the main page because the page was not requested for the right page From d606bfc91372f3d98595cbe9b06da92009a50770 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 28 Oct 2025 13:32:03 +0100 Subject: [PATCH 255/446] change handling to manage --- CHANGELOG.md | 6 +- core/core_config.py | 2 +- .../wetlab/handling_library_preparation.html | 4 +- .../templates/wetlab/handling_molecules.html | 14 ++-- wetlab/templates/wetlab/menu.html | 4 +- wetlab/urls.py | 8 +-- wetlab/utils/crontab_process.py | 10 +-- wetlab/utils/crontab_update_run.py | 54 ++++++++-------- wetlab/utils/run.py | 2 +- wetlab/views.py | 64 +++++++++---------- 10 files changed, 84 insertions(+), 84 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f2a81f6a0..5b842b102 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -42,12 +42,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Fixed deprecated `STATUS_CHOICES` usage in Django versions higher than 3.1.x (#263) [#267](https://github.com/BU-ISCIII/iskylims/pull/267) - Fixed issue where services could not be searched by service type (#78) [#267](https://github.com/BU-ISCIII/iskylims/pull/267) - Fixed issue [#338](https://github.com/BU-ISCIII/iskylims/issues/338): Removed unnecessary hidden input passing a large JSON object, now using session storage [#344](https://github.com/BU-ISCIII/iskylims/pull/344) -- Fixed email error handling for multiple notification types. [#346](https://github.com/BU-ISCIII/iskylims/pull/346) +- Fixed email error manage for multiple notification types. [#346](https://github.com/BU-ISCIII/iskylims/pull/346) - Replaced all references to `Molecule Code ID` with `Extraction Code ID` for consistency. -- Improved message display in Handling Library Preparation. +- Improved message display in Manage Library Preparation. - Fixed incomplete code execution when storing protocol values. (#349) [#352](https://github.com/BU-ISCIII/iskylims/pull/352) - Increased maximum length for `prefix_protocol` to prevent data errors. (#350) [#352](https://github.com/BU-ISCIII/iskylims/pull/352) -- Corrected exception handling, replacing incorrect exception type with `AttributeError`. (#351) [#352](https://github.com/BU-ISCIII/iskylims/pull/352) +- Corrected exception manage, replacing incorrect exception type with `AttributeError`. (#351) [#352](https://github.com/BU-ISCIII/iskylims/pull/352) - Fixed DataError - Value Too Long for prefix_protocol #350: Increased lenght for field prefix_protocol [#352](https://github.com/BU-ISCIII/iskylims/pull/352) - Removed --no-cache from docker_install.sh as it only worked with deprecated docker-compose [#356](https://github.com/BU-ISCIII/iskylims/pull/356) - Removed unused field sample_project_searchable that was leading to errors during migration [#356](https://github.com/BU-ISCIII/iskylims/pull/356) diff --git a/core/core_config.py b/core/core_config.py index 486013d77..a0e34e326 100644 --- a/core/core_config.py +++ b/core/core_config.py @@ -30,7 +30,7 @@ # ########### Headings to confirm the sucessful recorded HEADING_CONFIRM_MOLECULE_RECORDED = ["Extraction Code ID", "Used Protocol"] -# ## Heading values when showing pending samples at handling molecules +# ## Heading values when showing pending samples at manage molecules HEADING_FOR_DEFINED_SAMPLES = [ "Sample defined date", "Sample Code ID", diff --git a/wetlab/templates/wetlab/handling_library_preparation.html b/wetlab/templates/wetlab/handling_library_preparation.html index ee4488f41..1ddfff962 100644 --- a/wetlab/templates/wetlab/handling_library_preparation.html +++ b/wetlab/templates/wetlab/handling_library_preparation.html @@ -315,7 +315,7 @@
    If some information is wrong then modify the sample sheet and upload again t

    Click on the bottom below to continue with adding Library Preparation information

    - +
    @@ -417,7 +417,7 @@
    If some information is wrong then modify the sample sheet and upload again t

    Click on the bottom below to continue with adding Library Preparation information

    - +
    diff --git a/wetlab/templates/wetlab/handling_molecules.html b/wetlab/templates/wetlab/handling_molecules.html index 08fe8e286..97a80b05d 100644 --- a/wetlab/templates/wetlab/handling_molecules.html +++ b/wetlab/templates/wetlab/handling_molecules.html @@ -37,7 +37,7 @@

    Assign the Molecule Protocol to following samples.

    @@ -154,8 +154,8 @@

    Samples have been updated with Extraction required parameters.

    + value="Return to manage extraction samples" + onclick="location.href ='/wetlab/manageMolecules' ;" />

    @@ -190,7 +190,7 @@

    Molecules are updated with their use.

    + onclick="location.href ='/wetlab/manageLibraryPreparation' ;" />
    @@ -247,7 +247,7 @@

    Select the molecules to add Extraction information

    {% if sample_availables.sample_heading %} Select the Samples to add Pending extraction information
    {% if molecules_availables %} @@ -335,7 +335,7 @@

    Select the use that will be given for the sample

    {% if molecule_use_defined %} {% if pending_to_use.heading %} diff --git a/wetlab/templates/wetlab/menu.html b/wetlab/templates/wetlab/menu.html index f78d15aee..931d6da7a 100644 --- a/wetlab/templates/wetlab/menu.html +++ b/wetlab/templates/wetlab/menu.html @@ -99,10 +99,10 @@ Record Samples
  • - Handling Molecules + Manage Molecules
  • - Handling Library Preparation + Manage Library Preparation
  • Pending Sample Preparation diff --git a/wetlab/urls.py b/wetlab/urls.py index f2b820df8..be602122b 100644 --- a/wetlab/urls.py +++ b/wetlab/urls.py @@ -130,12 +130,12 @@ name="display_user_lot_kit", ), path( - "handlingLibraryPreparation", - wetlab.views.handling_library_preparation, - name="handling_library_preparation", + "manageLibraryPreparation", + wetlab.views.manage_library_preparation, + name="manage_library_preparation", ), path( - "handlingMolecules", wetlab.views.handling_molecules, name="handling_molecules" + "manageMolecules", wetlab.views.manage_molecules, name="manage_molecules" ), path("initialSettings", wetlab.views.initial_settings, name="initial_settings"), path( diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index 3033496ef..dfdb6390a 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -435,7 +435,7 @@ def check_sequencer_run_is_completed( int(conversion_attributes.create_time) ).strftime("%Y-%m-%d %H:%M:%S") logger.debug( - "%s : End function for handling NextSeq run with exception", + "%s : End function for manage NextSeq run with exception", experiment_name, ) return "completed", run_completion_date @@ -540,7 +540,7 @@ def copy_sample_sheet_to_remote_folder( + run_folder ) wetlab.utils.common.logging_errors(string_message, True, False) - handling_errors_in_run(experiment_name, "23") + manage_errors_in_run(experiment_name, "23") logger.debug( "%s : End function for copy_sample_sheet_to_remote_folder with exception", experiment_name, @@ -915,7 +915,7 @@ def get_samba_shared_folder(): ) -def handling_errors_in_run(experiment_name, error_code): +def manage_errors_in_run(experiment_name, error_code): """ Description: Function will manage the error situation where the run must be @@ -927,7 +927,7 @@ def handling_errors_in_run(experiment_name, error_code): True """ logger = logging.getLogger(__name__) - logger.debug("%s : Starting function handling_errors_in_run", experiment_name) + logger.debug("%s : Starting function manage_errors_in_run", experiment_name) logger.info("%s : Set run to ERROR state", experiment_name) if wetlab.models.RunProcess.objects.filter( run_name__exact=experiment_name @@ -941,7 +941,7 @@ def handling_errors_in_run(experiment_name, error_code): logger.info( "%s : experiment name is not defined yet in database", experiment_name ) - logger.debug("%s : End function handling_errors_in_run", experiment_name) + logger.debug("%s : End function manage_errors_in_run", experiment_name) return True diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 645e6d593..5bb82f6e7 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -148,7 +148,7 @@ def search_update_new_runs(request_reason): run_process_obj = wetlab.utils.crontab_process.get_run_process_obj_or_create_if_not_exists( new_run ) - wetlab.utils.crontab_process.handling_errors_in_run(new_run, "21") + wetlab.utils.crontab_process.manage_errors_in_run(new_run, "21") else: logger.debug( "%s : RunParameter not in folder run. Allowing more time", @@ -175,7 +175,7 @@ def search_update_new_runs(request_reason): new_run + " : Experiment name field was not found in file" ) wetlab.utils.common.logging_errors(string_message, False, False) - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( new_run, "7" ) else: @@ -217,7 +217,7 @@ def search_update_new_runs(request_reason): run_process_obj = wetlab.utils.crontab_process.get_run_process_obj_or_create_if_not_exists( experiment_name ) - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( experiment_name, "20" ) # cleaning up the RunParameter in local temporaty file @@ -320,7 +320,7 @@ def search_update_new_runs(request_reason): + " : Description field does not contains userid or userid is not defined in iskylims." ) logger.info(string_message) - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( experiment_name, "1" ) continue @@ -358,7 +358,7 @@ def search_update_new_runs(request_reason): + new_run ) wetlab.utils.common.logging_errors(string_message, True, False) - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( experiment_name, "23" ) logger.debug( @@ -487,7 +487,7 @@ def manage_run_in_recorded_state(conn, run_process_objs): get_remote_sample_sheet waiting_time_expired logging_errors - handling_errors_in_run + manage_errors_in_run assign_projects_to_run assign_used_library_in_run store_sample_sheet_if_not_defined_in_run @@ -543,7 +543,7 @@ def manage_run_in_recorded_state(conn, run_process_objs): + run_folder ) wetlab.utils.common.logging_errors(string_message, False, False) - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( experiment_name, 19 ) logger.debug( @@ -595,7 +595,7 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): Functions: check_log_for_run_completions waiting_time_expired - handling_errors_in_run + manage_errors_in_run Return: None """ @@ -604,7 +604,7 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): for run_process_obj in run_process_objs: experiment_name = run_process_obj.get_run_name() logger.info( - "%s : Start handling in manage_run_in_sample_sent_processing_state function", + "%s : Start manage in manage_run_in_sample_sent_processing_state function", experiment_name, ) platform = run_process_obj.get_run_platform() @@ -613,7 +613,7 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): experiment_name + " : Used sequencer or the platform is not defined" ) wetlab.utils.common.logging_errors(string_message, False, False) - wetlab.utils.crontab_process.handling_errors_in_run(experiment_name, 24) + wetlab.utils.crontab_process.manage_errors_in_run(experiment_name, 24) logger.info( "%s ERROR in manage_run_in_sample_sent_processing_state function", experiment_name, @@ -651,7 +651,7 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): elif run_status == "cancelled": run_process_obj.set_run_state("cancelled") run_process_obj.set_run_completion_date(run_completion_date) - wetlab.utils.crontab_process.handling_errors_in_run(experiment_name, 34) + wetlab.utils.crontab_process.manage_errors_in_run(experiment_name, 34) string_message = experiment_name + "was cancelled on the sequencer" wetlab.utils.common.logging_warnings(string_message, True) logger.debug( @@ -673,7 +673,7 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): + " is not defined in wetlab.config.py file (on PLATFORM_WAY_TO_CHECK_RUN_COMPLETION variable) " ) wetlab.utils.common.logging_errors(string_message, False, False) - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( experiment_name, run_status["ERROR"] ) logger.debug( @@ -709,7 +709,7 @@ def manage_run_in_sample_sent_processing_state(conn, run_process_objs): + run_folder ) wetlab.utils.common.logging_errors(string_message, False, False) - wetlab.utils.crontab_process.handling_errors_in_run(experiment_name, 9) + wetlab.utils.crontab_process.manage_errors_in_run(experiment_name, 9) logger.debug( "%s : End manage_run_in_sample_sent_processing_state function", experiment_name, @@ -732,7 +732,7 @@ def manage_run_in_processed_run_state(conn, run_process_objs): Functions: delete_existing_run_metrics_table_processed get_run_metric_files - handling_errors_in_run + manage_errors_in_run delete_run_metric_files parsing_run_metrics_files create_run_metric_graphics @@ -744,7 +744,7 @@ def manage_run_in_processed_run_state(conn, run_process_objs): for run_process_obj in run_process_objs: experiment_name = run_process_obj.get_run_name() logger.info( - "%s : Start handling in manage_run_in_processed_run_state function", + "%s : Start manage in manage_run_in_processed_run_state function", experiment_name, ) run_folder = ( @@ -786,7 +786,7 @@ def manage_run_in_processed_run_state(conn, run_process_objs): experiment_name + " : Unable to collect all files for run metrics" ) wetlab.utils.common.logging_errors(string_message, True, False) - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( experiment_name, run_metric_files["ERROR"] ) wetlab.utils.crontab_process.delete_run_metric_files(experiment_name) @@ -834,7 +834,7 @@ def manage_run_in_processed_run_state(conn, run_process_objs): experiment_name + " : Unable to save graphics for run metrics" ) wetlab.utils.common.logging_errors(string_message, True, False) - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( experiment_name, run_graphics["ERROR"] ) wetlab.utils.crontab_process.delete_existing_run_metrics_table_processed( @@ -880,7 +880,7 @@ def manage_run_in_processing_bcl2fastq_state(conn, run_process_objs): for run_process_obj in run_process_objs: experiment_name = run_process_obj.get_run_name() logger.info( - "%s : Start handling in manage_run_in_processing_bcl2fastq_state function", + "%s : Start manage in manage_run_in_processing_bcl2fastq_state function", experiment_name, ) run_folder = wetlab.models.RunningParameters.objects.get( @@ -914,7 +914,7 @@ def manage_run_in_processing_bcl2fastq_state(conn, run_process_objs): + " : Aborting the process. No Run completion date was defined." ) wetlab.utils.common.logging_errors(string_message, True, False) - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( experiment_name, 30 ) logger.debug( @@ -937,7 +937,7 @@ def manage_run_in_processing_bcl2fastq_state(conn, run_process_objs): + run_folder ) wetlab.utils.common.logging_errors(string_message, True, False) - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( experiment_name, bcl2fastq_finish_date["ERROR"] ) continue @@ -948,7 +948,7 @@ def manage_run_in_processing_bcl2fastq_state(conn, run_process_objs): + run_folder ) wetlab.utils.common.logging_errors(string_message, True, False) - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( experiment_name, bcl2fastq_finish_date["ERROR"] ) continue @@ -956,7 +956,7 @@ def manage_run_in_processing_bcl2fastq_state(conn, run_process_objs): run_process_obj.set_run_state("processed_bcl2fastq") logger.info("%s : Updated to Processed Bcl2Fastq state", experiment_name) logger.info( - "%s : End handling in manage_run_in_processing_bcl2fastq_state function", + "%s : End manage in manage_run_in_processing_bcl2fastq_state function", experiment_name, ) logger.debug(" End function manage_run_in_processing_bcl2fastq_state") @@ -993,7 +993,7 @@ def manage_run_in_processed_bcl2fastq_state(conn, run_process_objs): for run_process_obj in run_process_objs: experiment_name = run_process_obj.get_run_name() logger.info( - "%s : Start handling in manage_run_in_processed_bcl2fastq_state function", + "%s : Start manage in manage_run_in_processed_bcl2fastq_state function", experiment_name, ) run_param_obj = wetlab.models.RunningParameters.objects.get( @@ -1014,7 +1014,7 @@ def manage_run_in_processed_bcl2fastq_state(conn, run_process_objs): + " : Aborting the process. Unable to reach demultiplexing files " ) wetlab.utils.common.logging_errors(string_message, True, False) - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( experiment_name, demux_files["ERROR"] ) continue @@ -1028,7 +1028,7 @@ def manage_run_in_processed_bcl2fastq_state(conn, run_process_objs): + " : Sequencer used in the run has not defined the number of lanes" ) wetlab.utils.common.logging_errors(string_message, True, False) - wetlab.utils.crontab_process.handling_errors_in_run(experiment_name, 32) + wetlab.utils.crontab_process.manage_errors_in_run(experiment_name, 32) logger.debug( "%s : Aborting the process. Number of lanes not defined on the sequencer", experiment_name, @@ -1096,7 +1096,7 @@ def manage_run_in_processed_bcl2fastq_state(conn, run_process_objs): ) wetlab.utils.common.logging_errors(string_message, True, False) if key_error.args[0] == 33: - wetlab.utils.crontab_process.handling_errors_in_run( + wetlab.utils.crontab_process.manage_errors_in_run( experiment_name, "33" ) else: @@ -1128,7 +1128,7 @@ def manage_run_in_processed_bcl2fastq_state(conn, run_process_objs): experiment_name + " : Error when fetching the disk utilization" ) wetlab.utils.common.logging_errors(string_message, True, False) - wetlab.utils.crontab_process.handling_errors_in_run(experiment_name, "17") + wetlab.utils.crontab_process.manage_errors_in_run(experiment_name, "17") logger.debug( "%s : End function manage_run_in_processed_bcl2fast2_run with error", experiment_name, diff --git a/wetlab/utils/run.py b/wetlab/utils/run.py index 761e257e2..80f539d62 100644 --- a/wetlab/utils/run.py +++ b/wetlab/utils/run.py @@ -813,7 +813,7 @@ def get_pool_info(pools_to_update): HEADING_FOR_SELECTING_POOLS HEADING_FOR_INCOMPLETED_SELECTION_POOLS Functions: - get_lot_reagent_commercial_kits # located at core/utils/handling_commercial_kits + get_lot_reagent_commercial_kits # located at core/utils/manage_commercial_kits Return: pool_info """ diff --git a/wetlab/views.py b/wetlab/views.py index 4e1401ee2..9acb70419 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -2984,7 +2984,7 @@ def display_type_of_sample(request, sample_type_id): @login_required -def handling_library_preparation(request): +def manage_library_preparation(request): if wetlab.utils.common.is_wetlab_manager(request): samples_in_lib_prep = wetlab.utils.library.get_samples_for_library_preparation() else: @@ -2999,7 +2999,7 @@ def handling_library_preparation(request): if len(samples_in_lib_prep_protocol) == 0: return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", {"stored_lib_prep": samples_in_lib_prep}, ) library_preparation_objs = ( @@ -3014,7 +3014,7 @@ def handling_library_preparation(request): ) return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", {"lib_prep_protocol_parameters": lib_prep_protocol_parameters}, ) @@ -3025,7 +3025,7 @@ def handling_library_preparation(request): error_message = "No selected library preparation was chosen" return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", { "samples_in_lib_prep": samples_in_lib_prep, "error_message": error_message, @@ -3044,7 +3044,7 @@ def handling_library_preparation(request): request.session["lib_prep_protocol_parameters"] = lib_prep_protocol_parameters return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", {"lib_prep_protocol_parameters": lib_prep_protocol_parameters}, ) @@ -3061,7 +3061,7 @@ def handling_library_preparation(request): ) return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", { "error_message": error_message, "lib_prep_protocol_parameters": lib_prep_protocol_parameters, @@ -3069,7 +3069,7 @@ def handling_library_preparation(request): ) return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", {"stored_params": stored_params}, ) @@ -3087,7 +3087,7 @@ def handling_library_preparation(request): data["ERROR"].append(wetlab.config.ERROR_UNABLE_TO_DELETE_USER_FILE) return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", { "error_message": data["ERROR"], "samples_in_lib_prep": request.session.get("samples_in_lib_prep"), @@ -3109,7 +3109,7 @@ def handling_library_preparation(request): ) return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", { "error_message": user_id_in_s_sheet["ERROR"], "samples_in_lib_prep": request.session.get( @@ -3129,7 +3129,7 @@ def handling_library_preparation(request): ) return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", { "error_message": valid_data["ERROR"], "samples_in_lib_prep": request.session.get("samples_in_lib_prep"), @@ -3159,7 +3159,7 @@ def handling_library_preparation(request): display_sample_sheet["user_list"] = wetlab.utils.common.get_userid_list() return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", {"display_sample_sheet": display_sample_sheet}, ) @@ -3172,7 +3172,7 @@ def handling_library_preparation(request): if "ERROR" in store_data_result: return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", { "error_message": store_data_result["ERROR"], "samples_in_lib_prep": request.session.get("samples_in_lib_prep"), @@ -3181,7 +3181,7 @@ def handling_library_preparation(request): stored_index = "True" return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", {"stored_index": stored_index}, ) @@ -3192,7 +3192,7 @@ def handling_library_preparation(request): ) return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", {"additional_kits": additional_kits}, ) @@ -3213,24 +3213,24 @@ def handling_library_preparation(request): additional_kits["data"] = json.loads(request.POST["protocol_data"]) return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", {"error_message": error_message, "additional_kits": additional_kits}, ) return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", {"stored_additional_kits": stored_additional_kits}, ) else: return render( request, - "wetlab/handling_library_preparation.html", + "wetlab/manage_library_preparation.html", {"samples_in_lib_prep": samples_in_lib_prep}, ) -def handling_molecules(request): +def manage_molecules(request): if request.method == "POST" and request.POST["action"] == "selectedMolecules": # If no samples are selected , call again this function to display again the sample list heading = core.core_config.HEADING_FOR_DEFINED_SAMPLES.copy() @@ -3239,20 +3239,20 @@ def handling_molecules(request): request.POST["selected_samples"], heading, "To be included", "s_id" ) if len(samples) == 0: - return redirect("handling_molecules") + return redirect("manage_molecules") molecule_protocol = core.utils.samples.get_table_record_molecule( samples, __package__ ) if "ERROR" in molecule_protocol: return render( request, - "wetlab/handling_molecules.html", + "wetlab/manage_molecules.html", {"error_message": "There was no valid sample selected "}, ) return render( request, - "wetlab/handling_molecules.html", + "wetlab/manage_molecules.html", {"molecule_protocol": molecule_protocol}, ) @@ -3266,14 +3266,14 @@ def handling_molecules(request): request.POST["molecule_data"], heading, None, "s_id" ) if len(samples) == 0: - return redirect("handling_molecules") + return redirect("manage_molecules") molecule_recorded = core.utils.samples.record_extract_protocol( samples, excel_data, heading, request.user, __package__ ) if "incomplete" in molecule_recorded: return render( request, - "wetlab/handling_molecules.html", + "wetlab/manage_molecules.html", {"molecule_recorded": molecule_recorded}, ) @@ -3285,13 +3285,13 @@ def handling_molecules(request): if len(molecule_parameters) == 0: return render( request, - "wetlab/handling_molecules.html", + "wetlab/manage_molecules.html", {"molecule_parameters_updated": True}, ) protocol_list = ";".join(list(molecule_parameters.keys())) return render( request, - "wetlab/handling_molecules.html", + "wetlab/manage_molecules.html", { "molecule_parameters": molecule_parameters, "protocol_list": protocol_list, @@ -3307,7 +3307,7 @@ def handling_molecules(request): request.POST["pending_extraction"], heading, "Select Molecule", "s_id" ) if len(molecules) == 0: - return redirect("handling_molecules") + return redirect("manage_molecules") protocols = core.utils.samples.group_molecules_by_protocol(molecules) molecule_parameters = ( @@ -3316,7 +3316,7 @@ def handling_molecules(request): protocol_list = ";".join(list(molecule_parameters.keys())) return render( request, - "wetlab/handling_molecules.html", + "wetlab/manage_molecules.html", { "molecule_parameters": molecule_parameters, "protocol_list": protocol_list, @@ -3341,7 +3341,7 @@ def handling_molecules(request): return render( request, - "wetlab/handling_molecules.html", + "wetlab/manage_molecules.html", {"molecule_parameters_updated": True}, ) @@ -3352,11 +3352,11 @@ def handling_molecules(request): request.POST["sample_continues_on"], heading, "Sample continues on", "m_id" ) if len(molecules) == 0: - return redirect("handling_molecules") + return redirect("manage_molecules") molecule_use = core.utils.samples.set_molecule_use(select_use, __package__) return render( request, - "wetlab/handling_molecules.html", + "wetlab/manage_molecules.html", {"molecule_use": molecule_use}, ) @@ -3396,7 +3396,7 @@ def handling_molecules(request): return render( request, - "wetlab/handling_molecules.html", + "wetlab/manage_molecules.html", { "sample_availables": sample_availables, "molecules_availables": molecules_availables, @@ -3460,7 +3460,7 @@ def repeat_molecule_extraction(request): return render( request, - "wetlab/handling_molecules.html", + "wetlab/manage_molecules.html", {"molecule_protocol": molecule_protocol}, ) # return to the main page because the page was not requested for the right page From 60ebe432316b4f80eafe5b97bb9ea891e4b7e4bd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 28 Oct 2025 13:33:35 +0100 Subject: [PATCH 256/446] rename file --- .../wetlab/{handling_molecules.html => manage_molecules.html} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename wetlab/templates/wetlab/{handling_molecules.html => manage_molecules.html} (100%) diff --git a/wetlab/templates/wetlab/handling_molecules.html b/wetlab/templates/wetlab/manage_molecules.html similarity index 100% rename from wetlab/templates/wetlab/handling_molecules.html rename to wetlab/templates/wetlab/manage_molecules.html From 12395ea5db904ad36a447b0ab13d5e12a2c6e298 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 28 Oct 2025 13:35:27 +0100 Subject: [PATCH 257/446] rename file --- ...g_library_preparation.html => manage_library_preparation.html} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename wetlab/templates/wetlab/{handling_library_preparation.html => manage_library_preparation.html} (100%) diff --git a/wetlab/templates/wetlab/handling_library_preparation.html b/wetlab/templates/wetlab/manage_library_preparation.html similarity index 100% rename from wetlab/templates/wetlab/handling_library_preparation.html rename to wetlab/templates/wetlab/manage_library_preparation.html From c0eb62830f0f683e502c25d123708de427a163ae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 28 Oct 2025 14:18:08 +0100 Subject: [PATCH 258/446] fix error when fetching create time attribute from samba --- wetlab/utils/common.py | 36 +++++++++++---- wetlab/utils/crontab_update_run.py | 71 +++++++++++++++++++++--------- 2 files changed, 79 insertions(+), 28 deletions(-) diff --git a/wetlab/utils/common.py b/wetlab/utils/common.py index c2590ad4b..05b3e31e3 100644 --- a/wetlab/utils/common.py +++ b/wetlab/utils/common.py @@ -4,7 +4,7 @@ import re import socket import traceback -from datetime import datetime +from datetime import datetime, timezone from logging.config import fileConfig from django.contrib.auth.models import User @@ -79,18 +79,38 @@ def check_valid_date_format(date): def get_samba_atribute_data(conn, shared_folder, remote_path, attribute=None): - """_summary_ + """ + Fetch Samba metadata for a remote path and optionally return a specific attribute. + Time-based attributes are returned as timezone-aware UTC datetimes when possible. Args: - conn (_type_): _description_ - shared_folder (_type_): _description_ - remote_path (_type_): _description_ - attribute (_type_, optional): _description_. Defaults to None. + conn (SMBConnection): Active Samba connection used to query metadata. + shared_folder (str): Name of the Samba share that contains the target path. + remote_path (str): Path inside the share whose attributes are requested. + attribute (str, optional): Specific attribute name to return (for example, + `create_time`). Defaults to None, which returns the full attributes object. + + Returns: + Any: Requested attribute value (converted to UTC datetime for time-based fields) + or the full attributes object when `attribute` is None. Returns None if the + requested attribute is not available. """ attributes = conn.getAttributes(shared_folder, remote_path) if attribute is not None: - atr_field = "attributes." + attribute - return eval(atr_field) + if not hasattr(attributes, attribute): + return None + attr_value = getattr(attributes, attribute) + if isinstance(attr_value, datetime): + return ( + attr_value + if attr_value.tzinfo is not None + else attr_value.replace(tzinfo=timezone.utc) + ) + if attribute in {"create_time", "last_access_time", "last_write_time"} and isinstance( + attr_value, (int, float) + ): + return datetime.fromtimestamp(attr_value, tz=timezone.utc) + return attr_value return attributes diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 5bb82f6e7..cd71cc98e 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -13,6 +13,29 @@ import wetlab.utils.samplesheet +def _as_utc_datetime(value): + """ + Normalize Samba timestamps into timezone-aware UTC datetimes. + + Args: + value (datetime.datetime | int | float | None): Timestamp or datetime obtained + from Samba metadata. + + Returns: + datetime.datetime | None: Timezone-aware UTC datetime when conversion succeeds, + otherwise None. + """ + if isinstance(value, datetime.datetime): + return ( + value.astimezone(datetime.timezone.utc) + if value.tzinfo is not None + else value.replace(tzinfo=datetime.timezone.utc) + ) + if isinstance(value, (int, float)): + return datetime.datetime.fromtimestamp(value, tz=datetime.timezone.utc) + return None + + def get_list_processed_runs(): """ Description: @@ -121,17 +144,22 @@ def search_update_new_runs(request_reason): experiment_name = "Experiment name NOT FOUND" # check the run folder creation date to allow more time before # setting the run to error - f_created_date = int( + created_time = _as_utc_datetime( wetlab.utils.common.get_samba_atribute_data( conn, wetlab.utils.crontab_process.get_samba_shared_folder(), new_run, "create_time", - ).timestamp() + ) ) - time_to_check = datetime.datetime.fromtimestamp( - f_created_date, tz=datetime.timezone.utc - ).date() + if created_time is None: + logger.warning( + "%s : Unable to determine creation time for run folder %s", + experiment_name, + new_run, + ) + created_time = datetime.datetime.now(datetime.timezone.utc) + time_to_check = created_time.date() max_time_for_run_parameters = ( wetlab.models.ConfigSetting.objects.filter( configuration_name__exact="MAXIMUM_TIME_WAIT_RUN_PARAMETERS" @@ -175,9 +203,7 @@ def search_update_new_runs(request_reason): new_run + " : Experiment name field was not found in file" ) wetlab.utils.common.logging_errors(string_message, False, False) - wetlab.utils.crontab_process.manage_errors_in_run( - new_run, "7" - ) + wetlab.utils.crontab_process.manage_errors_in_run(new_run, "7") else: string_message = ( new_run + " : Ignoring test folder " + experiment_name @@ -217,9 +243,7 @@ def search_update_new_runs(request_reason): run_process_obj = wetlab.utils.crontab_process.get_run_process_obj_or_create_if_not_exists( experiment_name ) - wetlab.utils.crontab_process.manage_errors_in_run( - experiment_name, "20" - ) + wetlab.utils.crontab_process.manage_errors_in_run(experiment_name, "20") # cleaning up the RunParameter in local temporaty file logger.debug("%s : Deleting RunParameter file", experiment_name) os.remove(l_run_parameter) @@ -757,13 +781,22 @@ def manage_run_in_processed_run_state(conn, run_process_objs): run_process_obj, experiment_name ) # Check run_folder time creation - f_created_date = wetlab.utils.common.get_samba_atribute_data( - conn, - wetlab.utils.crontab_process.get_samba_shared_folder(), - run_folder, - "create_time", + created_time = _as_utc_datetime( + wetlab.utils.common.get_samba_atribute_data( + conn, + wetlab.utils.crontab_process.get_samba_shared_folder(), + run_folder, + "create_time", + ) ) - time_to_check = datetime.datetime.utcfromtimestamp(f_created_date).date() + if created_time is None: + logger.warning( + "%s : Unable to determine creation time for run folder %s", + experiment_name, + run_folder, + ) + created_time = datetime.datetime.now(datetime.timezone.utc) + time_to_check = created_time.date() # Check maximum time for waiting run metric files max_time_for_run_parameters = ( wetlab.models.ConfigSetting.objects.filter( @@ -1096,9 +1129,7 @@ def manage_run_in_processed_bcl2fastq_state(conn, run_process_objs): ) wetlab.utils.common.logging_errors(string_message, True, False) if key_error.args[0] == 33: - wetlab.utils.crontab_process.manage_errors_in_run( - experiment_name, "33" - ) + wetlab.utils.crontab_process.manage_errors_in_run(experiment_name, "33") else: string_message = ( experiment_name From fa93e00009cc2095e90de87464dfd49d8bcf5595 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 4 Nov 2025 12:24:43 +0100 Subject: [PATCH 259/446] fix state names in crontab and test processes --- wetlab/utils/crontab_update_run.py | 3 +-- wetlab/utils/test_conf.py | 10 +++++----- 2 files changed, 6 insertions(+), 7 deletions(-) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index cd71cc98e..c2b797528 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -307,7 +307,6 @@ def search_update_new_runs(request_reason): if isinstance(running_parameters["run_date"], datetime.datetime): run_process_obj.set_run_date(running_parameters["run_date"]) logger.info("%s : Sequencer stored on database", experiment_name) - if run_process_obj.get_sample_file() == "": # Fetch sample Sheet from remote server l_sample_sheet_path = ( @@ -396,7 +395,7 @@ def search_update_new_runs(request_reason): logger.info( "%s : RunParameters information stored on database", experiment_name ) - run_process_obj.set_run_state("Sample Sent") + run_process_obj.set_run_state("sample_sent") logger.info("Clossing SAMBA connection") conn.close() diff --git a/wetlab/utils/test_conf.py b/wetlab/utils/test_conf.py index ca11b4edd..27a1115a1 100644 --- a/wetlab/utils/test_conf.py +++ b/wetlab/utils/test_conf.py @@ -167,7 +167,7 @@ def execute_test_for_testing_run(run_test_name): conn = wetlab.utils.common.open_samba_connection() # Execute 6 times to be sure it has completed all steps - state_run_test = ["sample_sent", "processed_run", "processed_bcl2fastq"] + state_run_test = ["Sample sent", "Processed run", "Processed Bcl2fastq", "Completed"] for state_run in state_run_test: run_result[state_run] = "NOK" if not wetlab.models.RunProcess.objects.filter( @@ -178,7 +178,7 @@ def execute_test_for_testing_run(run_test_name): run_obj = wetlab.models.RunProcess.objects.filter( run_name__exact=run_test_name ).last() - for step in range(6): + for _ in range(6): state = run_obj.get_state() if state == "error": run_result["ERROR"] = "error" @@ -191,7 +191,7 @@ def execute_test_for_testing_run(run_test_name): run_result["ERROR"] = "Error when processing run in Sample Sent state" break else: - run_result["sample_sent"] = "OK" + run_result["Sample sent"] = "OK" elif state == "processing_run": wetlab.utils.crontab_update_run.manage_run_in_sample_sent_processing_state( conn, [run_obj] @@ -202,7 +202,7 @@ def execute_test_for_testing_run(run_test_name): ) break else: - run_result["Processing Run"] = "OK" + run_result["Processing run"] = "OK" elif state == "processed_run": wetlab.utils.crontab_update_run.manage_run_in_processed_run_state( conn, [run_obj] @@ -211,7 +211,7 @@ def execute_test_for_testing_run(run_test_name): run_result["ERROR"] = "Error when processing run in Processed Run state" break else: - run_result["Processed Run"] = "OK" + run_result["Processed run"] = "OK" elif state == "processing_bcl2fastq": wetlab.utils.crontab_update_run.manage_run_in_processing_bcl2fastq_state( conn, [run_obj] From 9382d326dfd7c400e99a339bfa80fe4f78072f98 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 4 Nov 2025 13:03:04 +0100 Subject: [PATCH 260/446] fix template adding remove spaces custom tag --- wetlab/templates/wetlab/create_pool.html | 105 ++++++++++++----------- 1 file changed, 56 insertions(+), 49 deletions(-) diff --git a/wetlab/templates/wetlab/create_pool.html b/wetlab/templates/wetlab/create_pool.html index 3925777da..88307e752 100644 --- a/wetlab/templates/wetlab/create_pool.html +++ b/wetlab/templates/wetlab/create_pool.html @@ -1,5 +1,6 @@ {% extends "core/base.html" %} {% load static %} +{% load replace_spaces %} {% block content %} {% include "wetlab/menu.html" %} {% include 'core/jexcel_functionality.html' %} @@ -157,57 +158,61 @@

    The following Samples are ready to be included inside a
    {% for key, values in display_list.data.items %} - {% if forloop.first %} -
    - {% else %} -
    - {% endif %} -
    -
    -
    -
    -

    Sample preparation information

    -
    - - {% csrf_token %} - - -
    -
    -
    - - + {% with key_slug=key|replace_spaces_with_underscores key_slug_lower=key|replace_spaces_with_underscores|lower %} + {% if forloop.first %} +
    + {% else %} +
    + {% endif %} +
    +
    +
    +
    +

    Sample preparation information

    +
    + + {% csrf_token %} + + +
    +
    +
    + + +
    -
    -
    -
    -
    - -

    Fields marked in Red are mandatory

    - - +
    +
    +
    + +

    Fields marked in Red are mandatory

    + + +
    -
    - -
    + +
    +
    -
    -
    -
    +
    +
    + {% endwith %} {% endfor %}
    @@ -227,7 +232,8 @@
    There are not any samples that contains the library preparation date to be i From 998717aca1c58a8f260accb12f2c179b27a3c503 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 4 Nov 2025 13:31:06 +0100 Subject: [PATCH 261/446] fix tabs in create_new_run.html --- wetlab/templates/wetlab/create_new_run.html | 74 +++++++++++---------- 1 file changed, 40 insertions(+), 34 deletions(-) diff --git a/wetlab/templates/wetlab/create_new_run.html b/wetlab/templates/wetlab/create_new_run.html index 2e1b90f28..74a3fefd8 100644 --- a/wetlab/templates/wetlab/create_new_run.html +++ b/wetlab/templates/wetlab/create_new_run.html @@ -1,5 +1,6 @@ {% extends "core/base.html" %} {% load static %} +{% load replace_spaces %} {% block content %} {% include 'core/jexcel_functionality.html' %} {% include "wetlab/menu.html" %} @@ -362,44 +363,47 @@

    Fill the information to create the New Run

    {% for key, values in display_pools_for_run.pool_data.platform.items %} - {% if forloop.first %} -
    + {% with key_slug=key|replace_spaces_with_underscores key_slug_lower=key|replace_spaces_with_underscores|lower %} + {% if forloop.first %} +
    {% else %}
    - {% endif %} + aria-labelledby="{{ key_slug }}-tab"> + {% endif %}
    @@ -407,8 +411,8 @@

    Fill the information to create the New Run

    + name="createNewRun_{{ key_slug_lower }}" + id="createNewRun_{{ key_slug_lower }}"> {% csrf_token %} @@ -488,7 +492,9 @@

    Select the pools to be included in the new run

    - {% endfor %} +
    + {% endwith %} + {% endfor %}
    From 8f95deb1112ff9294a1d269fc022268eadf9ae49 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 4 Nov 2025 13:44:20 +0100 Subject: [PATCH 262/446] fix issue #362, username found when editing --- django_utils/forms.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/django_utils/forms.py b/django_utils/forms.py index c8f3c3032..1338ea31b 100644 --- a/django_utils/forms.py +++ b/django_utils/forms.py @@ -104,3 +104,15 @@ def __init__(self, *args, **kwargs): ), ), ) + + def clean_username(self): + username = self.cleaned_data.get("username") + if self.instance and self.instance.pk and username: + if User.objects.exclude(pk=self.instance.pk).filter( + username__exact=username + ).exists(): + raise forms.ValidationError( + self.error_messages["duplicate_username"], code="duplicate_username" + ) + return username + return super().clean_username() From 5a80427a8199a08643cbb0d83264862a294d65c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 4 Nov 2025 13:55:36 +0100 Subject: [PATCH 263/446] bump new version django --- conf/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/requirements.txt b/conf/requirements.txt index 0469d8d15..54c5bcfde 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -3,7 +3,7 @@ asn1crypto==1.5.1 bcrypt==4.2.0 biopython==1.84 cryptography==43.0.1 -Django==4.2.15 +Django==4.2.26 django-crispy-forms==2.3 crispy-bootstrap5==0.7 django-crontab==0.7.1 From 0ee9b11369e98e3ae684302ccff6f5bc630de165 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 4 Nov 2025 14:06:40 +0100 Subject: [PATCH 264/446] linting --- django_utils/forms.py | 8 +++++--- wetlab/urls.py | 4 +--- wetlab/utils/common.py | 8 +++++--- wetlab/utils/library.py | 4 +++- wetlab/utils/test_conf.py | 7 ++++++- wetlab/views.py | 4 +--- 6 files changed, 21 insertions(+), 14 deletions(-) diff --git a/django_utils/forms.py b/django_utils/forms.py index 1338ea31b..187fb2cde 100644 --- a/django_utils/forms.py +++ b/django_utils/forms.py @@ -108,9 +108,11 @@ def __init__(self, *args, **kwargs): def clean_username(self): username = self.cleaned_data.get("username") if self.instance and self.instance.pk and username: - if User.objects.exclude(pk=self.instance.pk).filter( - username__exact=username - ).exists(): + if ( + User.objects.exclude(pk=self.instance.pk) + .filter(username__exact=username) + .exists() + ): raise forms.ValidationError( self.error_messages["duplicate_username"], code="duplicate_username" ) diff --git a/wetlab/urls.py b/wetlab/urls.py index be602122b..97e66a456 100644 --- a/wetlab/urls.py +++ b/wetlab/urls.py @@ -134,9 +134,7 @@ wetlab.views.manage_library_preparation, name="manage_library_preparation", ), - path( - "manageMolecules", wetlab.views.manage_molecules, name="manage_molecules" - ), + path("manageMolecules", wetlab.views.manage_molecules, name="manage_molecules"), path("initialSettings", wetlab.views.initial_settings, name="initial_settings"), path( "kitInventory/", diff --git a/wetlab/utils/common.py b/wetlab/utils/common.py index 05b3e31e3..f7c75e544 100644 --- a/wetlab/utils/common.py +++ b/wetlab/utils/common.py @@ -106,9 +106,11 @@ def get_samba_atribute_data(conn, shared_folder, remote_path, attribute=None): if attr_value.tzinfo is not None else attr_value.replace(tzinfo=timezone.utc) ) - if attribute in {"create_time", "last_access_time", "last_write_time"} and isinstance( - attr_value, (int, float) - ): + if attribute in { + "create_time", + "last_access_time", + "last_write_time", + } and isinstance(attr_value, (int, float)): return datetime.fromtimestamp(attr_value, tz=timezone.utc) return attr_value return attributes diff --git a/wetlab/utils/library.py b/wetlab/utils/library.py index a92dcc559..564eea185 100644 --- a/wetlab/utils/library.py +++ b/wetlab/utils/library.py @@ -515,7 +515,9 @@ def get_all_library_information(sample_id): pool_name = pool.get_pool_name() pool_code = pool.get_pool_code_id() run_names = pool.get_run_names() - run_name = ", ".join(run_names) if run_names else pool.get_run_name() + run_name = ( + ", ".join(run_names) if run_names else pool.get_run_name() + ) library_information["pool_information"].append( [ lib_prep_code_id, diff --git a/wetlab/utils/test_conf.py b/wetlab/utils/test_conf.py index 27a1115a1..2e1fae7e8 100644 --- a/wetlab/utils/test_conf.py +++ b/wetlab/utils/test_conf.py @@ -167,7 +167,12 @@ def execute_test_for_testing_run(run_test_name): conn = wetlab.utils.common.open_samba_connection() # Execute 6 times to be sure it has completed all steps - state_run_test = ["Sample sent", "Processed run", "Processed Bcl2fastq", "Completed"] + state_run_test = [ + "Sample sent", + "Processed run", + "Processed Bcl2fastq", + "Completed", + ] for state_run in state_run_test: run_result[state_run] = "NOK" if not wetlab.models.RunProcess.objects.filter( diff --git a/wetlab/views.py b/wetlab/views.py index 9acb70419..c50836d46 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -3836,9 +3836,7 @@ def create_new_run(request): elif request.method == "POST" and request.POST["action"] == "continueWithRun": run_id = request.POST["run_ids"] experiment_name = wetlab.utils.run.get_experiment_name(run_id) - pool_objs = wetlab.models.LibraryPool.objects.filter( - runprocess__exact=run_id - ) + pool_objs = wetlab.models.LibraryPool.objects.filter(runprocess__exact=run_id) pool_ids = [] for pool in pool_objs: pool_ids.append(pool.get_id()) From 969852d2a7147936de0a9a7094a8235c280dac91 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 4 Nov 2025 16:49:00 +0100 Subject: [PATCH 265/446] bump correct version django --- conf/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/requirements.txt b/conf/requirements.txt index 54c5bcfde..c1a63ddc0 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -3,7 +3,7 @@ asn1crypto==1.5.1 bcrypt==4.2.0 biopython==1.84 cryptography==43.0.1 -Django==4.2.26 +Django==4.2.25 django-crispy-forms==2.3 crispy-bootstrap5==0.7 django-crontab==0.7.1 From 9860d6d1f5c4dad2bac55715d8c62edb61ea500d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 19 Nov 2025 15:14:19 +0100 Subject: [PATCH 266/446] add conf file also as variable in docker file --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 433907bad..c2cdfdc15 100644 --- a/Dockerfile +++ b/Dockerfile @@ -36,9 +36,10 @@ RUN /srv/iskylims/venv/bin/pip install -r conf/requirements.txt # Set default install type ARG INSTALL_TYPE=app ARG GIT_REVISION=main +ARG INSTALL_CONF=conf/docker_install_settings.txt # Execute the installation script -RUN /bin/bash install.sh --install $INSTALL_TYPE --git_revision $GIT_REVISION --conf conf/docker_install_settings.txt --docker +RUN /bin/bash install.sh --install $INSTALL_TYPE --git_revision $GIT_REVISION --conf $INSTALL_CONF --docker WORKDIR /opt/iskylims # Expose From 0448c49e1e7dead242011dac831605575bae6312 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 19 Nov 2025 15:14:47 +0100 Subject: [PATCH 267/446] add docker production as default to docker install and conf files for prod install --- conf/docker_production_settings.txt | 34 ++++++++ docker-compose.prod.yml | 19 ++++ docker_install.sh | 129 +++++++++++++++++++++++----- 3 files changed, 162 insertions(+), 20 deletions(-) create mode 100644 conf/docker_production_settings.txt create mode 100644 docker-compose.prod.yml diff --git a/conf/docker_production_settings.txt b/conf/docker_production_settings.txt new file mode 100644 index 000000000..643586d2c --- /dev/null +++ b/conf/docker_production_settings.txt @@ -0,0 +1,34 @@ +### Production specific installation config +# Copy this file or edit the values below so they match the external +# infrastructure you are connecting to before building the image. + +### Installation path and modules settings +INSTALL_PATH='/opt/iskylims' +REQUIRED_MODULES='core drylab wetlab clinic django_utils' +MIGRATION_MODULES='core drylab wetlab django_utils' +FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' + +### (optional) Python installation path where pip and python executables are located +PYTHON_BIN_PATH='python3' + +### Settings required to access database (external MySQL server) +DB_USER='django' +DB_PASS='djangopass' +DB_NAME='iskylims' +DB_SERVER_IP='prod-db-host' # hostname or IP of the production DB +DB_PORT=3306 + +### Settings required for sending emails +EMAIL_HOST_SERVER='smtp.yourdomain' +EMAIL_PORT='25' +EMAIL_HOST_USER='bioinfo' +EMAIL_HOST_PASSWORD='' +EMAIL_USE_TLS='False' + +### Settings required for accessing iSkyLIMS +LOCAL_SERVER_IP='*' +DNS_URL='*' + +### Logs settings +LOG_TYPE="regular_folder" +LOG_PATH="" diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml new file mode 100644 index 000000000..1af9f79de --- /dev/null +++ b/docker-compose.prod.yml @@ -0,0 +1,19 @@ +version: '3.8' + +services: + app: + container_name: iskylims_app + restart: unless-stopped + build: + context: . + args: + INSTALL_TYPE: ${INSTALL_TYPE:-app} + GIT_REVISION: ${GIT_REVISION:-main} + INSTALL_CONF: ${INSTALL_CONF:-conf/docker_production_settings.txt} + ports: + - "8001:8001" + environment: + DJANGO_SETTINGS_MODULE: iskylims.settings + volumes: + - /etc/localtime:/etc/localtime:ro + - /usr/share/zoneinfo:/usr/share/zoneinfo diff --git a/docker_install.sh b/docker_install.sh index a249f8590..542e17fda 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -6,17 +6,25 @@ usage() { cat << EOF This script installs and upgrades the iskylims app. -Usage : $0 [--demo_data] [--install_type] [--git_revision] +Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--install_conf] [--test] Optional input data: --demo_data | Provide already downloaded demo data from Zenodo --install_type | Specify the installation type for iSkyLIMS (default: full) --git_revision | Specify the Git revision to install (default: main) + --compose_file | docker compose file to use (overrides default) + --install_conf | Settings file consumed during docker image build (mandatory for production) + --skip_demo_data | Skip downloading/copying demo data to samba container + --skip_test_data | Skip loading test fixtures (test/test_data.json) + --test | Use development/test compose file and sample data Examples: - Install demo docker system - bash $0 + Deploy production container pointing to an external DB/Samba: + bash $0 --install_conf conf/my_prod_settings.txt - Provide already downloaded data from Zenodo (compressed) + Install demo docker system with local services + bash $0 --test + + Provide already downloaded data from Zenodo (compressed) for test environment bash $0 --demo_data /path/to/iskylims_demo_data.tar.gz Speficy a custom installation using the Git revision "develop": @@ -39,6 +47,11 @@ do --demo_data) set -- "$@" -d ;; --install_type) set -- "$@" -i ;; --git_revision) set -- "$@" -g ;; + --compose_file) set -- "$@" -c ;; + --install_conf) set -- "$@" -s ;; + --skip_demo_data) set -- "$@" -n ;; + --skip_test_data) set -- "$@" -t ;; + --test) set -- "$@" -p ;; # ADDITIONAL --help) set -- "$@" -h ;; @@ -52,9 +65,14 @@ done demo_data=false install_type="full" git_revision="main" +compose_file="" +install_conf="" +skip_demo_data="" +skip_test_data="" +mode="production" # PARSE VARIABLE ARGUMENTS WITH getopts -options=":d:i:g:vh" +options=":d:i:g:c:s:vhntp" while getopts $options opt; do case $opt in d) @@ -66,6 +84,21 @@ while getopts $options opt; do g) git_revision=$OPTARG ;; + c) + compose_file=$OPTARG + ;; + s) + install_conf=$OPTARG + ;; + n) + skip_demo_data=true + ;; + t) + skip_test_data=true + ;; + p) + mode="test" + ;; h) usage exit 1 @@ -91,9 +124,57 @@ while getopts $options opt; do done shift $((OPTIND-1)) -echo "Deploying test containers with INSTALL_TYPE=$install_type and GIT_REVISION=$git_revision..." -docker compose build --no-cache --build-arg INSTALL_TYPE=$install_type --build-arg GIT_REVISION=$git_revision -docker compose up -d +if [ "$mode" = "test" ]; then + if [ -z "$compose_file" ]; then + compose_file="docker-compose.yml" + fi + if [ -z "$install_conf" ]; then + install_conf="conf/docker_install_settings.txt" + fi +else + if [ -z "$compose_file" ]; then + compose_file="docker-compose.prod.yml" + fi +fi + +if [ "$mode" = "production" ] && [ -z "$install_conf" ]; then + echo "Production deployments require --install_conf pointing to your settings file." + exit 1 +fi + +if [ -z "$skip_demo_data" ]; then + if [ "$mode" = "test" ]; then + skip_demo_data=false + else + skip_demo_data=true + fi +fi + +if [ -z "$skip_test_data" ]; then + if [ "$mode" = "test" ]; then + skip_test_data=false + else + skip_test_data=true + fi +fi + +if [ ! -f "$compose_file" ]; then + echo "Compose file '$compose_file' not found" + exit 1 +fi + +if [ ! -f "$install_conf" ]; then + echo "Install configuration '$install_conf' not found" + exit 1 +fi + +service_exists() { + docker compose -f "$compose_file" ps --services 2>/dev/null | grep -Fxq "$1" +} + +echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=$install_type and GIT_REVISION=$git_revision..." +docker compose -f "$compose_file" build --no-cache --build-arg INSTALL_TYPE="$install_type" --build-arg GIT_REVISION="$git_revision" --build-arg INSTALL_CONF="$install_conf" +docker compose -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." sleep 20 @@ -108,21 +189,29 @@ docker exec -it iskylims_app python3 manage.py createsuperuser echo "Loading initial data into the database" docker exec -it iskylims_app python3 manage.py loaddata conf/first_install_tables.json -docker exec -it iskylims_app python3 manage.py loaddata test/test_data.json - -echo "Downloading and copying test files to the Samba container" -if [ "$demo_data" == "false" ]; then - wget https://zenodo.org/record/8091169/files/iskylims_demo_data.tar.gz - demo_data="./iskylims_demo_data.tar.gz" +if [ "$skip_test_data" = false ]; then + docker exec -it iskylims_app python3 manage.py loaddata test/test_data.json +else + echo "Skipping test data fixtures as requested" fi -docker cp $demo_data samba:/mnt -docker exec -it samba tar -xf /mnt/iskylims_demo_data.tar.gz -C /mnt -echo "Deleting compressed test file" -docker exec -it samba rm /mnt/iskylims_demo_data.tar.gz +if [ "$skip_demo_data" = false ] && service_exists "samba"; then + echo "Downloading and copying test files to the Samba container" + if [ "$demo_data" == "false" ]; then + wget https://zenodo.org/record/8091169/files/iskylims_demo_data.tar.gz + demo_data="./iskylims_demo_data.tar.gz" + fi + docker cp "$demo_data" samba:/mnt + docker exec -it samba tar -xf /mnt/iskylims_demo_data.tar.gz -C /mnt + + echo "Deleting compressed test file" + docker exec -it samba rm /mnt/iskylims_demo_data.tar.gz -if [ "$demo_data" == "false" ]; then - rm -f $demo_data + if [ "$demo_data" == "false" ]; then + rm -f "$demo_data" + fi +else + echo "Skipping Samba demo data load (flag enabled or service not present)" fi echo "Running crontab" From 0b599ed20f226be3cd4312ee063c0e7c05d245a3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 19 Nov 2025 15:15:07 +0100 Subject: [PATCH 268/446] add doc with new prod install --- README.md | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/README.md b/README.md index a7ed61281..e8156ae59 100644 --- a/README.md +++ b/README.md @@ -86,6 +86,47 @@ Follow the prompt message to create the super user account. When script ends open your navigator typing **localhost:8001** to access to iSkyLIMS +#### Production docker deployment + +When your MySQL database and Samba share run on dedicated machines, you can +deploy only the iSkyLIMS application container and connect it to those external +services. + +1. Copy the production settings template and adjust it with the real database + credentials/host: + + ```bash + cp conf/docker_production_settings.txt conf/my_prod_settings.txt + # edit conf/my_prod_settings.txt to point to your DB server + ``` + +2. Build and run the application container (production mode is the default, so + passing the settings file is enough): + + ```bash + bash docker_install.sh --install_conf conf/my_prod_settings.txt + ``` + + The installer automatically uses `docker-compose.prod.yml`, which only starts + the `iskylims_app` container while pointing to external services. You can + still override the compose file or skip behaviours through extra flags (see + `docker_install.sh --help`). + +3. Once the container is up, create the Django superuser and configure the Samba + connection details through the UI if this is a fresh installation. + +#### Local testing deployment + +To spin up the full stack (database + samba + app) with demo data and fixtures, +just add the `--test` flag: + +```bash +bash docker_install.sh --test +``` + +You can reuse the existing options (`--demo_data`, `--install_type`, etc.) to +customise the behaviour if needed. + ### Install iSkyLIMS in your server running ubuntu/CentOS #### Clone github repository From 8063fbd49024a53baba3d33c1f70375140b15e64 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 19 Nov 2025 15:30:07 +0100 Subject: [PATCH 269/446] add --fake-initial in case migration files are not being created and respecting db structure --- README.md | 6 +++++ docker_install.sh | 58 +++++++++++++++++++++++++++++++++++++++-------- 2 files changed, 55 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index e8156ae59..8b8a0cf3a 100644 --- a/README.md +++ b/README.md @@ -115,6 +115,12 @@ services. 3. Once the container is up, create the Django superuser and configure the Samba connection details through the UI if this is a fresh installation. +If you already have a populated production database and only need to roll out a +new application version, reuse the same command but add `--action upgrade`. The +script will rebuild/restart the container, regenerate the Django migrations, +apply them using `--fake-initial` so existing tables are respected, and skip the +superuser/fixture loading steps so your data remains untouched. + #### Local testing deployment To spin up the full stack (database + samba + app) with demo data and fixtures, diff --git a/docker_install.sh b/docker_install.sh index 542e17fda..ee3a63f7a 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -6,13 +6,14 @@ usage() { cat << EOF This script installs and upgrades the iskylims app. -Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--install_conf] [--test] +Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--install_conf] [--action] [--test] Optional input data: --demo_data | Provide already downloaded demo data from Zenodo --install_type | Specify the installation type for iSkyLIMS (default: full) --git_revision | Specify the Git revision to install (default: main) --compose_file | docker compose file to use (overrides default) --install_conf | Settings file consumed during docker image build (mandatory for production) + --action | install (default) or upgrade, to control DB initialisation steps --skip_demo_data | Skip downloading/copying demo data to samba container --skip_test_data | Skip loading test fixtures (test/test_data.json) --test | Use development/test compose file and sample data @@ -21,6 +22,9 @@ Examples: Deploy production container pointing to an external DB/Samba: bash $0 --install_conf conf/my_prod_settings.txt + Upgrade an existing production deployment using the same database: + bash $0 --install_conf conf/my_prod_settings.txt --action upgrade + Install demo docker system with local services bash $0 --test @@ -49,6 +53,7 @@ do --git_revision) set -- "$@" -g ;; --compose_file) set -- "$@" -c ;; --install_conf) set -- "$@" -s ;; + --action) set -- "$@" -a ;; --skip_demo_data) set -- "$@" -n ;; --skip_test_data) set -- "$@" -t ;; --test) set -- "$@" -p ;; @@ -70,9 +75,12 @@ install_conf="" skip_demo_data="" skip_test_data="" mode="production" +action="install" +run_superuser=true +load_initial_data=true # PARSE VARIABLE ARGUMENTS WITH getopts -options=":d:i:g:c:s:vhntp" +options=":d:i:g:c:s:a:vhntp" while getopts $options opt; do case $opt in d) @@ -90,6 +98,13 @@ while getopts $options opt; do s) install_conf=$OPTARG ;; + a) + action=$OPTARG + if [[ "$action" != "install" && "$action" != "upgrade" ]]; then + echo "Invalid action '$action'. Use install or upgrade." + exit 1 + fi + ;; n) skip_demo_data=true ;; @@ -158,6 +173,16 @@ if [ -z "$skip_test_data" ]; then fi fi +if [ "$action" = "upgrade" ]; then + run_superuser=false + load_initial_data=false + skip_demo_data=true + skip_test_data=true +else + run_superuser=true + load_initial_data=true +fi + if [ ! -f "$compose_file" ]; then echo "Compose file '$compose_file' not found" exit 1 @@ -179,16 +204,31 @@ docker compose -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." sleep 20 -echo "Creating the database structure for iSkyLIMS" -docker exec -it iskylims_app python3 manage.py migrate +echo "Generating Django migrations for iSkyLIMS apps" docker exec -it iskylims_app python3 manage.py makemigrations django_utils core wetlab drylab -docker exec -it iskylims_app python3 manage.py migrate -echo "Creating super user" -docker exec -it iskylims_app python3 manage.py createsuperuser +if [ "$action" = "upgrade" ]; then + echo "Applying migrations in fake-initial mode (existing tables will be kept)" + docker exec -it iskylims_app python3 manage.py migrate --noinput --fake-initial +else + echo "Applying migrations" + docker exec -it iskylims_app python3 manage.py migrate --noinput +fi + +if [ "$run_superuser" = true ]; then + echo "Creating super user" + docker exec -it iskylims_app python3 manage.py createsuperuser +else + echo "Skipping super user creation (--action upgrade)" +fi + +if [ "$load_initial_data" = true ]; then + echo "Loading initial data into the database" + docker exec -it iskylims_app python3 manage.py loaddata conf/first_install_tables.json +else + echo "Skipping initial fixture load (--action upgrade)" +fi -echo "Loading initial data into the database" -docker exec -it iskylims_app python3 manage.py loaddata conf/first_install_tables.json if [ "$skip_test_data" = false ]; then docker exec -it iskylims_app python3 manage.py loaddata test/test_data.json else From afb20ce8e3ec38c17ea219be41d3004c87fd132c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 19 Nov 2025 17:25:36 +0100 Subject: [PATCH 270/446] refactor install.sh --- install.sh | 1255 +++++++++++++++++++++++++--------------------------- 1 file changed, 606 insertions(+), 649 deletions(-) diff --git a/install.sh b/install.sh index 824788447..8743d824a 100644 --- a/install.sh +++ b/install.sh @@ -1,7 +1,9 @@ #!/bin/bash -ISKYLIMS_VERSION="3.x.x" +APP_VERSION="3.x.x" +LOG_FILE="/var/log/iskylims_install.log" +# usage: prints the command line help and usage examples. usage() { cat << EOF This script install and upgrade the iskylims app. @@ -36,93 +38,96 @@ Examples: EOF } +# log: write timestamped log entries to stdout and LOG_FILE. +log() { + local level="$1"; shift + local message="$*" + local timestamp + timestamp="$(date '+%Y-%m-%d %H:%M:%S')" + printf "%s [%s] %s\n" "$timestamp" "$level" "$message" | tee -a "$LOG_FILE" +} + +# db_check: verifies connectivity to the configured MySQL instance using mysqladmin/mysqlshow. db_check(){ - # user should have mysql permission on remote server. - mysqladmin -h $DB_SERVER_IP -u$DB_USER -p$DB_PASS -P$DB_PORT processlist > /dev/null + log "INFO" "Checking database connectivity against $DB_SERVER_IP:$DB_PORT" + mysqladmin -h $DB_SERVER_IP -u$DB_USER -p$DB_PASS -P$DB_PORT processlist > /dev/null 2>>"$LOG_FILE" if ! [ $? -eq 0 ]; then - echo -e "${RED}ERROR : Unable to connect to database. Check if your database is running and accessible${NC}" + log "ERROR" "Unable to connect to database. Check if your database is running and accessible" exit 1 fi RESULT=`mysqlshow --user=$DB_USER --password=$DB_PASS --host=$DB_SERVER_IP --port=$DB_PORT | grep -o $DB_NAME` if ! [ "$RESULT" == "$DB_NAME" ] ; then - echo -e "${RED}ERROR : iskylims database is not defined yet ${NC}" - echo -e "${RED}ERROR : Create iskylims database on your mysql server and run again the installation script ${NC}" + log "ERROR" "iskylims database is not defined yet" + log "ERROR" "Create iskylims database on your mysql server and run again the installation script" exit 1 fi } +# apache_check: ensures apache/httpd service is running depending on distribution. apache_check(){ if [[ $linux_distribution == "Ubuntu" ]]; then if ! pidof apache2 > /dev/null ; then - # web server down, restart the server - echo "Apache Server is down... Trying to restart Apache" + log "WARN" "Apache Server is down... Trying to restart Apache" systemctl restart apache2.service sleep 10 if pidof apache2 > /dev/null ; then - echo "Apache Server is up" + log "INFO" "Apache Server is up" else - echo -e "${RED}ERROR : Unable to start Apache ${NC}" - echo -e "${RED}ERROR : Solve the issue with Apache server and run again the installation script ${NC}" + log "ERROR" "Unable to start Apache" + log "ERROR" "Solve the issue with Apache server and run again the installation script" exit 1 fi fi elif [[ $linux_distribution == "CentOs" || $linux_distribution == "RedHatEnterprise" ]]; then if ! pidof httpd > /dev/null ; then - # web server down, restart the server - echo "Apache Server is down... Trying to restart Apache" + log "WARN" "Apache Server is down... Trying to restart Apache" systemctl restart httpd sleep 10 if pidof httpd > /dev/null ; then - echo "Apache Server is up" + log "INFO" "Apache Server is up" else - echo -e "${RED}ERROR : Unable to start Apache ${NC}" - echo -e "${RED}ERROR : Solve the issue with Apache server and run again the installation script ${NC}" + log "ERROR" "Unable to start Apache" + log "ERROR" "Solve the issue with Apache server and run again the installation script" exit 1 fi fi fi } +# python_check: confirm required Python version is available in PYTHON_BIN_PATH. python_check(){ - - python_version=$(su -c $PYTHON_BIN_PATH --version $user) + python_version=$(su -c $PYTHON_BIN_PATH --version $user 2>>"$LOG_FILE") if [[ $python_version == "" ]]; then - echo -e "${RED}ERROR : Python3 is not found in your system ${NC}" - echo -e "${RED}ERROR : Solve the issue with Python and run again the installation script ${NC}" + log "ERROR" "Python3 is not found in your system" + log "ERROR" "Solve the issue with Python and run again the installation script" exit 1 fi p_version=$(echo $python_version | cut -d"." -f2) if (( $p_version < 7 )); then - echo -e "${RED}ERROR : Application requieres at least the version 3.7.x of Python3 ${NC}" - echo -e "${RED}ERROR : Solve the issue with python and run again the installation script ${NC}" + log "ERROR" "Application requires at least version 3.7.x of Python3" + log "ERROR" "Solve the issue with python and run again the installation script" exit 1 fi } +# root_check: enforce running privileged sections as root. root_check(){ if [[ $EUID -ne 0 ]]; then - printf "\n\n%s" - printf "${RED}------------------${NC}\n" - printf "%s" - printf "${RED}Exiting installation. This script must be run as root ${NC}\n" - printf "\n\n%s" - printf "${RED}------------------${NC}\n" - printf "%s" + log "ERROR" "Exiting installation. This script must be run as root" exit 1 fi } +# update_settings_and_urls: rewrite Django settings and urls with deployment values. update_settings_and_urls(){ - # save SECRET KEY at home user directory + log "INFO" "Updating settings.py and urls.py with deployment values" grep ^SECRET $INSTALL_PATH/iskylims/settings.py > ~/.secret - # Copying config files and script. TODO CHANGE iSkyLIMS to app name cp conf/template_settings.txt $INSTALL_PATH/iskylims/settings.py cp conf/urls.py $INSTALL_PATH/iskylims - # replacing dummy variables with real values sed -i "/^SECRET/c\\$(cat ~/.secret)" $INSTALL_PATH/iskylims/settings.py sed -i "s/djangouser/${DB_USER}/g" $INSTALL_PATH/iskylims/settings.py sed -i "s/djangopass/${DB_PASS}/g" $INSTALL_PATH/iskylims/settings.py @@ -139,19 +144,13 @@ update_settings_and_urls(){ sed -i "s/localhost/${DNS_URL}/g" $INSTALL_PATH/iskylims/settings.py } -upgrade_venv(){ - echo "activate the virtualenv" - source virtualenv/bin/activate - echo "Installing required python packages" - python -m pip install --upgrade pip - python -m pip install -r conf/requirements.txt -} - +# restore_git_ref: reset repository to branch/tag/commit active before script ran. restore_git_ref() { echo "Restoring to initial git reference: $initial_git_ref" git checkout "$initial_git_ref" --quiet } +# load_tables: wrapper to call Django loaddata with optional verbosity. load_tables() { # Function parameters local data_file="${1:-conf/first_install_tables.json}" @@ -196,6 +195,544 @@ BLUE='\033[0;34m' RED='\033[0;31m' GREEN='\033[0;32m' NC='\033[0m' +ORANGE='\033[0;33m' + +# log_section: print a visually separated header in both console and log. +log_section() { + local message="$1" + printf "\n\n%s\n" "${YELLOW}------------------${NC}" + printf "%b\n" "${YELLOW}${message}${NC}" + printf "%s\n\n" "${YELLOW}------------------${NC}" +} + +# log_info: convenience helper for blue info messages (console only). +log_info() { + printf "%b\n" "${BLUE}$1${NC}" +} + +# log_warn: emit warning text in cyan for terminal visibility. +log_warn() { + printf "%b\n" "${CYAN}$1${NC}" +} + +# log_error: emit error text in red for terminal visibility. +log_error() { + printf "%b\n" "${RED}$1${NC}" +} + +# abort_install: log an error and exit with optional status. +abort_install() { + log_error "$1" + exit "${2:-1}" +} + +ensure_file_exists() { + local file_path="$1" + local friendly_name="${2:-$1}" + if [ ! -f "$file_path" ]; then + abort_install "Required file '$friendly_name' not found." + fi +} + +# load_install_config: source the selected install_settings file. +load_install_config() { + ensure_file_exists "$conf" "$conf" + # shellcheck disable=SC1090 + . "$conf" +} + +# checkout_git_revision: ensure desired git revision exists and check it out safely. +checkout_git_revision() { + if git rev-parse --verify "$git_branch" >/dev/null 2>&1; then + if [[ $git_branch != $initial_git_ref ]]; then + local local_changes + local_changes=$(git status --porcelain) + if [[ -n $local_changes ]]; then + abort_install "Unable to switch to $git_branch. Commit or stash local changes first." + fi + printf "${YELLOW}Switching to revision %s.${NC}\n" "$git_branch" + git checkout "$git_branch" --quiet + else + printf "${YELLOW}Using current revision: '%s'.${NC}\n" "$git_branch" + fi + else + abort_install "Git reference $git_branch is not defined in ${PWD}." + fi +} + +# check_requirements: run Python/DB/Apache/root validations before install/upgrade. +check_requirements() { + log_section "Checking main requirements" + python_check + log_info "Valid version of Python" + if [ $docker == false ]; then + db_check + log_info "Successful check for database" + apache_check + log_info "Successful check for apache" + fi + + if [ "$install_type" == "full" ] || [ "$install_type" == "dep" ] || [ "$upgrade_type" == "full" ] || [ "$upgrade_type" == "dep" ]; then + log_warn "Checking requirement of root user when installation is full or dep" + root_check + log_info "Successful checking of root user" + fi +} + +# rename_apps_if_needed: handles legacy app renaming and DB/migration adjustments when --ren_app is provided. +rename_apps_if_needed() { + if [ $ren_app != true ]; then + return 0 + fi + + rm -rf $INSTALL_PATH/django_utils/migrations/* + rm -rf $INSTALL_PATH/iSkyLIMS_core/migrations/* + rm -rf $INSTALL_PATH/iSkyLIMS_wetlab/migrations/* + rm -rf $INSTALL_PATH/iSkyLIMS_drylab/migrations/* + + cd $INSTALL_PATH + sed -i "s/ugettext/gettext/g" iSkyLIMS_wetlab/models.py + sed -i "s/ugettext/gettext/g" iSkyLIMS_core/forms.py + sed -i "s/ugettext/gettext/g" django_utils/forms.py + echo "activate the virtualenv" + source virtualenv/bin/activate + + echo "Create a fake initial" + python manage.py makemigrations $FAKEINITIAL_MODULES + python manage.py migrate --fake-initial + + if [ -d "$INSTALL_PATH/iSkyLIMS_core" ]; then + echo "Changing app dir names in $INSTALL_PATH..." + rm -rf $INSTALL_PATH/.git $INSTALL_PATH/.github $INSTALL_PATH/.gitignore \ + $INSTALL_PATH/.Rhistory $INSTALL_PATH/docker-compose.yml $INSTALL_PATH/docker_iskylims_install.sh \ + $INSTALL_PATH/Dockerfile $INSTALL_PATH/install.sh $INSTALL_PATH/install_settings.txt + mv $INSTALL_PATH/iSkyLIMS_core $INSTALL_PATH/core + mv $INSTALL_PATH/iSkyLIMS_wetlab $INSTALL_PATH/wetlab + mv $INSTALL_PATH/iSkyLIMS_drylab $INSTALL_PATH/drylab + mv $INSTALL_PATH/iSkyLIMS_clinic $INSTALL_PATH/clinic + echo "Done changing app dir names in $INSTALL_PATH..." + fi + if [ -d "iSkyLIMS" ]; then + mv iSkyLIMS/ iskylims/ + sed -i "s/iSkyLIMS/iskylims/g" $INSTALL_PATH/iskylims/wsgi.py + sed -i "s/iSkyLIMS/iskylims/g" $INSTALL_PATH/manage.py + fi + + echo "Modifying database names and constraints..." + mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ + -e 'UPDATE django_content_type SET app_label = REPLACE(app_label , "iSkyLIMS_core", "core") WHERE app_label like ("iSkyLIMS_%");' + mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ + -e 'UPDATE django_content_type SET app_label = REPLACE(app_label , "iSkyLIMS_wetlab", "wetlab") WHERE app_label like ("iSkyLIMS_%");' + mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ + -e 'UPDATE django_content_type SET app_label = REPLACE(app_label , "iSkyLIMS_drylab", "drylab") WHERE app_label like ("iSkyLIMS_%");' + + mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ + -e 'UPDATE django_migrations SET app = REPLACE(app , "iSkyLIMS_core", "core") WHERE app like ("iSkyLIMS_%");' + mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ + -e 'UPDATE django_migrations SET app = REPLACE(app , "iSkyLIMS_wetlab", "wetlab") WHERE app like ("iSkyLIMS_%");' + mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ + -e 'UPDATE django_migrations SET app = REPLACE(app , "iSkyLIMS_drylab", "drylab") WHERE app like ("iSkyLIMS_%");' + + echo "Renaming tables" + query_rename_table="SELECT CONCAT('RENAME TABLE ', TABLE_SCHEMA, '.', TABLE_NAME, \ + ' TO ', TABLE_SCHEMA, '.', REPLACE(TABLE_NAME, 'iSkyLIMS_', ''), ';') \ + AS query FROM information_schema.tables WHERE TABLE_SCHEMA = \"$DB_NAME\" AND TABLE_NAME LIKE 'iSkyLIMS_%';" + mysql -u $DB_USER -p$DB_PASS -h $DB_SERVER_IP -e "$query_rename_table" \ + | xargs -I % echo "mysql -u$DB_USER -p'$DB_PASS' -D $DB_NAME -h $DB_SERVER_IP -e \"% \" " | bash + + echo "Renaming index" + query_rename_unique_indexes="SELECT CONCAT('ALTER TABLE ', rcu.TABLE_SCHEMA, '.', rcu.TABLE_NAME, \ + ' RENAME INDEX ', rcu.CONSTRAINT_NAME, \ + ' TO ', REPLACE(rcu.CONSTRAINT_NAME, 'iSkyLIMS_', ''), ';') \ + AS query FROM information_schema.key_column_usage rcu \ + JOIN information_schema.table_constraints tc \ + ON tc.CONSTRAINT_NAME = rcu.CONSTRAINT_NAME WHERE rcu.TABLE_SCHEMA = \"$DB_NAME\" \ + AND rcu.CONSTRAINT_NAME LIKE 'iSkyLIMS_%' AND tc.CONSTRAINT_TYPE = 'UNIQUE' \ + GROUP BY rcu.TABLE_SCHEMA, rcu.TABLE_NAME, rcu.CONSTRAINT_NAME, tc.CONSTRAINT_TYPE, \ + rcu.REFERENCED_TABLE_SCHEMA, rcu.REFERENCED_TABLE_NAME;" + mysql -u $DB_USER -p$DB_PASS -h $DB_SERVER_IP -e "$query_rename_unique_indexes" \ + | xargs -I % echo "mysql -u$DB_USER -p'$DB_PASS' -D $DB_NAME -h $DB_SERVER_IP -e \"% \" " | bash + + echo "Renaming constraints" + query_rename_constraints="SELECT CONCAT('ALTER TABLE ', rcu.TABLE_SCHEMA, '.', rcu.TABLE_NAME, \ + ' DROP FOREIGN KEY ' , rcu.CONSTRAINT_NAME, ';', \ + ' ALTER TABLE ', rcu.TABLE_SCHEMA, '.', rcu.TABLE_NAME, \ + ' ADD CONSTRAINT ', REPLACE(rcu.CONSTRAINT_NAME, 'iSkyLIMS_', ''), ' ', \ + tc.CONSTRAINT_TYPE, ' (', GROUP_CONCAT(rcu.COLUMN_NAME ORDER BY rcu.ORDINAL_POSITION SEPARATOR ', '), ')', \ + IF(tc.CONSTRAINT_TYPE = 'FOREIGN KEY', \ + CONCAT(' REFERENCES ', rcu.REFERENCED_TABLE_SCHEMA, '.', REPLACE(rcu.REFERENCED_TABLE_NAME, 'iSkyLIMS_', ''), ' (', \ + GROUP_CONCAT(rcu.REFERENCED_COLUMN_NAME ORDER BY rcu.ORDINAL_POSITION SEPARATOR ', '), ') ON DELETE ', rc.DELETE_RULE), \ + ''), ';') AS query \ + FROM information_schema.key_column_usage rcu \ + LEFT JOIN information_schema.table_constraints tc ON rcu.CONSTRAINT_NAME = tc.CONSTRAINT_NAME \ + LEFT JOIN information_schema.referential_constraints rc ON rcu.CONSTRAINT_NAME = rc.CONSTRAINT_NAME \ + WHERE rcu.TABLE_SCHEMA = '$DB_NAME' AND rcu.CONSTRAINT_NAME LIKE 'iSkyLIMS_%' \ + GROUP BY rcu.TABLE_SCHEMA, rcu.TABLE_NAME, rcu.CONSTRAINT_NAME, tc.CONSTRAINT_TYPE, rcu.REFERENCED_TABLE_SCHEMA, rcu.REFERENCED_TABLE_NAME, rc.DELETE_RULE;" + mysql -u $DB_USER -p$DB_PASS -h $DB_SERVER_IP -e "$query_rename_constraints" | xargs -I % echo "mysql -u$DB_USER -p'$DB_PASS' -D $DB_NAME -h $DB_SERVER_IP -e \"% \" " | bash + + echo "Done modifying database names and constraints..." + + echo "Modifying names in migration files..." + sed -i 's/iSkyLIMS_core/core/g' */migrations/*.py + sed -i 's/iSkyLIMS_drylab/drylab/g' */migrations/*.py + sed -i 's/iSkyLIMS_wetlab/wetlab/g' */migrations/*.py + echo "Done modifying names in migration files..." + + echo "Copying custom migration files from conf." + cp $INSTALL_PATH/conf/0002_core_migration_v3.0.0.py $INSTALL_PATH/core/migrations/0002_migration_v3_0_0.py + cp $INSTALL_PATH/conf/0002_drylab_migration_v3.0.0.py $INSTALL_PATH/drylab/migrations/0002_migration_v3_0_0.py + cp $INSTALL_PATH/conf/0002_wetlab_migration_v3.0.0.py $INSTALL_PATH/wetlab/migrations/0002_migration_v3_0_0.py + cp $INSTALL_PATH/conf/0002_django_utils_migration_v3.0.0.py $INSTALL_PATH/django_utils/migrations/0002_migration_v3_0_0.py + + read -p "Do you want to proceed with the migrate command? (Y/N) " -n 1 -r + echo + if [[ ! $REPLY =~ ^[Yy]$ ]] ; then + log "WARN" "Exiting without running migrate command." + exit 1 + fi + + echo "activate the virtualenv" + source virtualenv/bin/activate + echo "Running migrate..." + python manage.py migrate + echo "Done migrate command." + + cd - +} + +# install_system_packages: install InterOp and distro-specific OS packages required by iSkyLIMS. +install_system_packages() { + echo "Installing Interop" + if [ -d /opt/interop ]; then + echo "There is already an interop installation" + echo "Skipping Interop installation" + else + cd /opt + echo "Downloading interop software" + wget https://github.com/Illumina/interop/releases/download/v1.1.15/InterOp-1.1.15-Linux-GNU.tar.gz + tar -xf InterOp-1.1.15-Linux-GNU.tar.gz + ln -s InterOp-1.1.15-Linux-GNU interop + rm InterOp-1.1.15-Linux-GNU.tar.gz + echo "Interop is now installed" + cd - + fi + + linux_distribution=$(lsb_release -i | cut -f 2-) + + if [[ $linux_distribution == "Ubuntu" ]]; then + echo "Software installation for Ubuntu" + apt-get update && apt-get upgrade -y + apt-get install -y \ + apt-utils wget \ + libmysqlclient-dev \ + python3-venv \ + libpq-dev \ + python3-dev python3-pip python3-wheel \ + apache2-dev cifs-utils \ + gnuplot + + elif [[ $linux_distribution == "CentOS" || $linux_distribution == "RedHatEnterprise" ]]; then + echo "Software installation for Centos/RedHat" + yum groupinstall "Development tools" + yum install zlib-devel bzip2-devel openssl-devel \ + wget httpd-devel mysql-libs sqlite sqlite-devel \ + mariadb-devel libffi-devel \ + gnuplot cifs-utils + fi +} + +# run_django_deploy: execute makemigrations/migrate and optional fixture/superuser steps. +run_django_deploy() { + local mode="${1:-install}" + echo "Generating Django migrations" + python manage.py makemigrations $MIGRATION_MODULES + + if [ "$mode" = "upgrade" ]; then + echo "Applying migrations in fake-initial mode" + python manage.py migrate --noinput --fake-initial + if [ $tables == true ] ; then + echo "Loading pre-filled tables..." + load_tables $prefilled_tables true + echo "Done loading pre-filled tables..." + fi + else + echo "Applying migrations" + python manage.py migrate --noinput + echo "Loading in database initial data" + load_tables $prefilled_tables true + echo "Creating super user " + python manage.py createsuperuser --username admin + fi +} + +# sync_requirements_file: copy repository requirements into the target installation path. +sync_requirements_file() { + mkdir -p $INSTALL_PATH/conf + rsync -rlv conf/requirements.txt $INSTALL_PATH/conf/requirements.txt +} + +# setup_virtualenv: create or refresh the Python virtualenv depending on mode. +setup_virtualenv() { + local mode="$1" + cd $INSTALL_PATH + if [ "$mode" = "install" ]; then + if [ -d virtualenv ]; then + echo "There already is a virtualenv for iskylims in $INSTALL_PATH." + read -p "Do you want to remove current virtualenv and reinstall? (Y/N) " -n 1 -r + echo + if [[ ! $REPLY =~ ^[Yy]$ ]] ; then + rm -rf $INSTALL_PATH/virtualenv + bash -c "$PYTHON_BIN_PATH -m venv virtualenv" + else + echo "virtualenv already defined. Skipping." + fi + else + bash -c "$PYTHON_BIN_PATH -m venv virtualenv" + fi + else + if [ -d virtualenv ]; then + read -p "Do you want to remove current virtualenv and reinstall? (Y/N) " -n 1 -r + echo + if [[ $REPLY =~ ^[Yy]$ ]] ; then + rm -rf $INSTALL_PATH/virtualenv + bash -c "$PYTHON_BIN_PATH -m venv virtualenv" + fi + else + read -p "There is no virtualenv. Do you want to create a new one? (Y/N) " -n 1 -r + echo + if [[ $REPLY =~ ^[Yy]$ ]] ; then + bash -c "$PYTHON_BIN_PATH -m venv virtualenv" + else + echo "Exiting..." + exit 0 + fi + fi + fi + cd - +} + +# prepare_documents_structure: ensure document directories and templates exist with correct permissions. +prepare_documents_structure() { + echo "Created documents structure" + mkdir -p $INSTALL_PATH/documents/wetlab + mkdir -p $INSTALL_PATH/documents/wetlab/tmp + mkdir -p $INSTALL_PATH/documents/wetlab/sample_sheet + mkdir -p $INSTALL_PATH/documents/wetlab/images_plot + mkdir -p $INSTALL_PATH/documents/wetlab/templates + mkdir -p $INSTALL_PATH/documents/wetlab/sample_sheets_lib_prep + mkdir -p $INSTALL_PATH/documents/drylab + mkdir -p $INSTALL_PATH/documents/drylab/service_files + + chown -R $user:$apache_group $INSTALL_PATH/documents + chmod 775 $INSTALL_PATH/documents + + cp $INSTALL_PATH/conf/*_template.csv $INSTALL_PATH/documents/wetlab/templates/ + cp $INSTALL_PATH/conf/samples_template.xlsx $INSTALL_PATH/documents/wetlab/templates/ + + mkdir -p $INSTALL_PATH/documents/wetlab/collection_index_kits/ + cp $INSTALL_PATH/conf/collection_index_kits/*.txt $INSTALL_PATH/documents/wetlab/collection_index_kits/ + + cp $INSTALL_PATH/conf/template_logging_config.ini $INSTALL_PATH/wetlab/logging_config.ini + sed -i "s|INSTALL_PATH|${INSTALL_PATH}|g" $INSTALL_PATH/wetlab/logging_config.ini +} + +# install_python_requirements: activate the venv and install required Python packages. +install_python_requirements() { + cd $INSTALL_PATH + echo "activate the virtualenv" + source virtualenv/bin/activate + echo "Installing required python packages" + python -m pip install --upgrade pip + python -m pip install wheel + python -m pip install -r conf/requirements.txt + cd - +} + +# restart_apache_service: restart Apache/HTTPD unless running inside Docker or explicitly skipped. +restart_apache_service() { + if [ $docker != false ]; then + return + fi + linux_distribution=$(lsb_release -i | cut -f 2-) + if [[ $linux_distribution == "Ubuntu" ]]; then + apache_daemon="apache2" + else + apache_daemon="httpd" + fi + if ! systemctl restart $apache_daemon; then + echo -e "${ORANGE}Apache server restart failed. trying with sudo${NC}" + sudo systemctl restart $apache_daemon + fi +} + +# run_dependency_stage: execute the dependency portion (system packages + venv + pip) for install or upgrade. +run_dependency_stage() { + local mode="$1" + + if [ "$mode" = "install" ]; then + log_section "Preparing dependency environment for installation" + if [ -d $INSTALL_PATH ]; then + echo "There already is an installation of iskylims in $INSTALL_PATH." + read -p "Do you want to remove current installation and reinstall? (Y/N) " -n 1 -r + echo + if [[ ! $REPLY =~ ^[Yy]$ ]] ; then + echo "Exiting without running iSkyLIMS installation" + exit 1 + else + rm -rf $INSTALL_PATH + fi + fi + install_system_packages + mkdir -p $INSTALL_PATH + linux_distribution=$(lsb_release -i | cut -f 2-) + if [[ $linux_distribution == "Ubuntu" ]]; then + apache_group="www-data" + else + apache_group="apache" + fi + chown -R $user:$apache_group $INSTALL_PATH + chmod 775 $INSTALL_PATH + else + log_section "Preparing dependency environment for upgrade" + if [ ! -d $INSTALL_PATH ]; then + abort_install "Unable to start the upgrade. Folder $INSTALL_PATH does not exist." + fi + install_system_packages + fi + + sync_requirements_file + setup_virtualenv "$mode" + install_python_requirements +} + +# upgrade_application_files: sync code/config and run upgrade-specific tasks (renames, migrations). +upgrade_application_files() { + if [ ! -d $INSTALL_PATH ]; then + abort_install "Unable to start the upgrade. Folder $INSTALL_PATH does not exist." + fi + + log_section "Starting iSkyLIMS Upgrade version: ${APP_VERSION}" + + rename_apps_if_needed + + echo "Copying files to installation folder" + rsync -rlv conf/ $INSTALL_PATH/conf/ + rsync -rlv --fuzzy --delay-updates --delete-delay \ + --exclude "logs" --exclude "documents" --exclude "migrations" --exclude "__pycache__" \ + README.md LICENSE test conf $REQUIRED_MODULES $INSTALL_PATH + + echo "Update settings and url file." + update_settings_and_urls + prepare_documents_structure + if [ -d "$INSTALL_PATH/documents/wetlab/SampleSheets" ]; then + echo "Updating sample sheet folder name" + mv $INSTALL_PATH/documents/wetlab/SampleSheets $INSTALL_PATH/documents/wetlab/sample_sheet + fi + + if [ -d "$INSTALL_PATH/documents/wetlab/SampleSheets4LibPrep" ]; then + echo "Updating sample sheet for libary preparationfolder name" + mv $INSTALL_PATH/documents/wetlab/SampleSheets4LibPrep $INSTALL_PATH/documents/wetlab/sample_sheets_lib_prep + fi + + cd $INSTALL_PATH + echo "activate the virtualenv" + source virtualenv/bin/activate + + if [ $docker == false ]; then + run_django_deploy "upgrade" + fi + echo "Deleting static files..." + rm -rf $INSTALL_PATH/static + echo "Running collect statics..." + python manage.py collectstatic + echo "Done collect statics" + + if [ $run_script ]; then + for val in "${migration_script[@]}"; do + if [[ $val = *","* ]]; then + parameters=(${val//,/ }) + echo "Running migration script: ${parameters[0]}" + ./manage.py runscript ${parameters[0]} --script-args ${parameters[1]} + echo "Done migration script: ${parameters[0]}" + else + echo "Running migration script: $val" + ./manage.py runscript $val + echo "Done migration script: $val" + fi + done + fi + + cd - + log_section "Successfuly upgrade of iSKyLIMS version: ${APP_VERSION}" +} + +# install_application_files: deploy Django project files, update settings, and run initial migrations. +install_application_files() { + log_section "Starting iSkyLIMS install version: ${APP_VERSION}" + + user=${SUDO_USER:-$USER} + group=$(groups | cut -d" " -f1) + + linux_distribution=$(lsb_release -i | cut -f 2-) + + if [[ $linux_distribution == "Ubuntu" ]]; then + apache_group="www-data" + else + apache_group="apache" + fi + + if [ "$install_type" == "full" ] || [ "$install_type" == "app" ]; then + + if [ $LOG_TYPE == "symbolic_link" ]; then + if [ -d $LOG_PATH ]; then + if [ ! -d $INSTALL_PATH/logs ]; then + echo "Deleting existing symbolin link" + rm $INSTALL_PATH/logs + fi + echo "Creating symbolic link to log folder" + ln -s $LOG_PATH $INSTALL_PATH/logs + chmod 775 $LOG_PATH + else + echo "Log folder path: $LOG_PATH does not exist. Fix it in the install_settings.txt and run again." + exit 1 + fi + else + if [ ! -d $INSTALL_PATH/logs ]; then + mkdir -p $INSTALL_PATH/logs + chown $user:$apache_group $INSTALL_PATH/logs + chmod 775 $INSTALL_PATH/logs + else + echo "Log folder path: $INSTALL_PATH/logs already exist." + fi + fi + + rsync -rlv README.md LICENSE test conf $REQUIRED_MODULES $INSTALL_PATH + + cd $INSTALL_PATH + + prepare_documents_structure + + echo "activate the virtualenv" + source virtualenv/bin/activate + + echo "Creating iskylims project" + django-admin startproject iskylims . + + update_settings_and_urls + + if [ $docker == false ]; then + run_django_deploy "install" + fi + + echo "Run collectstatic" + python manage.py collectstatic + + cd - + + log_section "Successfuly iSkyLIMS Installation version: ${APP_VERSION}" + echo "Installation completed" + fi +} # translate long options to short reset=true @@ -215,6 +752,7 @@ do --conf) set -- "$@" -c ;; --ren_app) set -- "$@" -r ;; --docker) set -- "$@" -k ;; + --skip_apache_restart) set -- "$@" -a ;; # ADITIONAL --help) set -- "$@" -h ;; @@ -235,9 +773,10 @@ upgrade=false upgrade_type="full" docker=false prefilled_tables="conf/first_install_tables.json" +restart_apache=true # PARSE VARIABLE ARGUMENTS WITH getops -options=":c:s:i:u:r:g:tdkvh" +options=":c:s:i:u:r:g:tdkvha" while getopts $options opt; do case $opt in i ) @@ -281,12 +820,15 @@ while getopts $options opt; do k ) docker=true ;; + a ) + restart_apache=false + ;; h ) usage exit 1 ;; v ) - echo $ISKYLIMS_VERSION + echo $APP_VERSION exit 1 ;; \?) @@ -306,621 +848,36 @@ while getopts $options opt; do done shift $((OPTIND-1)) -#============================================================================= -# SETTINGS CHECKINGS -#============================================================================= - -if [ ! -f "$conf" ]; then - printf "\n\n%s" - printf "${RED}------------------${NC}\n" - printf "${RED}Unable to start.${NC}\n" - printf "${RED}Configuration File $conf does not exist.${NC}\n" - printf "${RED}------------------${NC}\n" - exit 1 -fi -# Read configuration file - -. $conf - -# Check if git reference (branch, SHA, or tag) exists and checkout -if git rev-parse --verify "$git_branch" >/dev/null 2>&1; then - if [[ $git_branch != $initial_git_ref ]]; then - # Check for local changes - local_changes=$(git status --porcelain) - if [[ -n $local_changes ]]; then - printf "\n\n%s" - printf "${RED}------------------${NC}\n" - printf "${RED}Unable to switch to $git_branch.${NC}\n" - printf "${RED}You have local changes that would be overwritten by checkout:${NC}\n" - printf "${RED}\t'$local_changes'.${NC}\n" - printf "${RED}Please commit or stash your changes before switching.${NC}\n" - printf "${RED}------------------${NC}\n" - exit 1 - else - printf "${YELLOW}Switching to revision $git_branch.${NC}\n" - git checkout "$git_branch" --quiet - fi - else - printf "${YELLOW}Using current revision: '$git_branch'.${NC}\n" - fi -else - printf "\n\n%s" - printf "${RED}------------------${NC}\n" - printf "${RED}Unable to start.${NC}\n" - printf "${RED}Git reference $git_branch is not defined in ${PWD}.${NC}\n" - printf "${RED}------------------${NC}\n" - exit 1 -fi -#================================================================ -# CHECK REQUIREMENTS BEFORE STARTING INSTALLATION -#================================================================ - -echo "Checking main requirements" -python_check -printf "${BLUE}Valid version of Python${NC}\n" -if [ $docker == false ]; then - db_check - printf "${BLUE}Successful check for database${NC}\n" - apache_check - printf "${BLUE}Successful check for apache${NC}\n" -fi - -if [ "$install_type" == "full" ] || [ "$install_type" == "dep" ] || [ "$upgrade_type" == "full" ] || [ "$upgrade_type" == "dep" ]; then - printf "${YELLOW} Checking requirement of root user when installation is full or dep ${NC}\n" - root_check - printf "${BLUE}Successful checking of root user${NC}\n" -fi - -#============================================================================= -# UPGRADE INSTALLATION -# Check if parameter is passing to script to upgrade the installation -# If "upgrade" parameter is set then the script only execute the upgrade part. -# If other parameter as upgrade is given return usage message and exit -#============================================================================= - +operation="install" +operation_scope="$install_type" if [ $upgrade == true ]; then - # check if upgrade keyword is given - if [ ! -d $INSTALL_PATH ]; then - printf "\n\n%s" - printf "${RED}------------------${NC}\n" - printf "${RED}Unable to start the upgrade.${NC}\n" - printf "${RED}Folder $INSTALL_PATH does not exist.${NC}\n" - printf "${RED}------------------${NC}\n" - exit 1 - fi - #================================================================ - # MAIN_BODY FOR UPGRADE - #================================================================ - printf "\n\n%s" - printf "${YELLOW}------------------${NC}\n" - printf "%s" - printf "${YELLOW}Starting iSkyLIMS Upgrade version: ${ISKYLIMS_VERSION}${NC}\n" - printf "%s" - printf "${YELLOW}------------------${NC}\n\n" - - if [ "$upgrade_type" = "full" ] || [ "$upgrade_type" = "dep" ]; then - if [ -d $INSTALL_PATH/virtualenv ]; then - read -p "Do you want to remove current virtualenv and reinstall? (Y/N) " -n 1 -r - echo # (optional) move to a new line - if [[ $REPLY =~ ^[Yy]$ ]] ; then - rm -rf $INSTALL_PATH/virtualenv - rsync -rlv conf/requirements.txt $INSTALL_PATH/conf/requirements.txt - cd $INSTALL_PATH - bash -c "$PYTHON_BIN_PATH -m venv virtualenv" - upgrade_venv - cd - - else - rsync -rlv conf/requirements.txt $INSTALL_PATH/conf/requirements.txt - cd $INSTALL_PATH - upgrade_venv - cd - - fi - else - echo "There is no virtualenv to upgrade in $INSTALL_PATH." - read -p "Do you want to create a new virtualenv and reinstall? (Y/N) " -n 1 -r - echo # (optional) move to a new line - if [[ $REPLY =~ ^[Yy]$ ]] ; then - rsync -rlv conf/requirements.txt $INSTALL_PATH/conf/requirements.txt - cd $INSTALL_PATH - bash -c "$PYTHON_BIN_PATH -m venv virtualenv" - upgrade_venv - cd - - else - echo "Exiting..." - exit 0 - fi - fi - fi - - if [ "$upgrade_type" = "full" ] || [ "$upgrade_type" = "app" ]; then - - # Delete git and no copy files stuff - if [ $ren_app == true ] ; then - # remove all previous migrations and make a fake initial - # delete existing migrations file - rm -rf $INSTALL_PATH/django_utils/migrations/* - rm -rf $INSTALL_PATH/iSkyLIMS_core/migrations/* - rm -rf $INSTALL_PATH/iSkyLIMS_wetlab/migrations/* - rm -rf $INSTALL_PATH/iSkyLIMS_drylab/migrations/* - - cd $INSTALL_PATH - sed -i "s/ugettext/gettext/g" iSkyLIMS_wetlab/models.py - sed -i "s/ugettext/gettext/g" iSkyLIMS_core/forms.py - sed -i "s/ugettext/gettext/g" django_utils/forms.py - echo "activate the virtualenv" - source virtualenv/bin/activate - - echo "Create a fake initial" - python manage.py makemigrations $FAKEINITIAL_MODULES - python manage.py migrate --fake-initial - - if [ -d "$INSTALL_PATH/iSkyLIMS_core" ]; then - echo "Changing app dir names in $INSTALL_PATH..." - rm -rf $INSTALL_PATH/.git $INSTALL_PATH/.github $INSTALL_PATH/.gitignore \ - $INSTALL_PATH/.Rhistory $INSTALL_PATH/docker-compose.yml $INSTALL_PATH/docker_iskylims_install.sh \ - $INSTALL_PATH/Dockerfile $INSTALL_PATH/install.sh $INSTALL_PATH/install_settings.txt - mv $INSTALL_PATH/iSkyLIMS_core $INSTALL_PATH/core - mv $INSTALL_PATH/iSkyLIMS_wetlab $INSTALL_PATH/wetlab - mv $INSTALL_PATH/iSkyLIMS_drylab $INSTALL_PATH/drylab - mv $INSTALL_PATH/iSkyLIMS_clinic $INSTALL_PATH/clinic - echo "Done changing app dir names in $INSTALL_PATH..." - fi - if [ -d "iSkyLIMS" ]; then - mv iSkyLIMS/ iskylims/ - sed -i "s/iSkyLIMS/iskylims/g" $INSTALL_PATH/iskylims/wsgi.py - sed -i "s/iSkyLIMS/iskylims/g" $INSTALL_PATH/manage.py - fi - cd - - fi - - # update installation by sinchronize folders - echo "Copying files to installation folder" - rsync -rlv conf/ $INSTALL_PATH/conf/ - rsync -rlv --fuzzy --delay-updates --delete-delay \ - --exclude "logs" --exclude "documents" --exclude "migrations" --exclude "__pycache__" \ - README.md LICENSE test conf $REQUIRED_MODULES $INSTALL_PATH - - # update the settings.py and the main urls - echo "Update settings and url file." - update_settings_and_urls - # update illumina template files.# Copy illumina sample sheet templates - mkdir -p $INSTALL_PATH/documents/wetlab/templates/ - cp $INSTALL_PATH/conf/*_template.csv $INSTALL_PATH/documents/wetlab/templates/ - cp $INSTALL_PATH/conf/samples_template.xlsx $INSTALL_PATH/documents/wetlab/templates/ - - # Copy the illumina collection index kits - mkdir -p $INSTALL_PATH/documents/wetlab/collection_index_kits/ - cp $INSTALL_PATH/conf/collection_index_kits/*.txt $INSTALL_PATH/documents/wetlab/collection_index_kits/ - - # update logging configuration file - cp $INSTALL_PATH/conf/template_logging_config.ini $INSTALL_PATH/wetlab/logging_config.ini - sed -i "s@INSTALL_PATH@${INSTALL_PATH}@g" $INSTALL_PATH/wetlab/logging_config.ini - # update the sample sheet folder and name - if [ -d "$INSTALL_PATH/documents/wetlab/SampleSheets" ]; then - echo "Updating sample sheet folder name" - mv $INSTALL_PATH/documents/wetlab/SampleSheets $INSTALL_PATH/documents/wetlab/sample_sheet - fi - - if [ -d "$INSTALL_PATH/documents/wetlab/SampleSheets4LibPrep" ]; then - echo "Updating sample sheet for libary preparationfolder name" - mv $INSTALL_PATH/documents/wetlab/SampleSheets4LibPrep $INSTALL_PATH/documents/wetlab/sample_sheets_lib_prep - fi - - cd $INSTALL_PATH - echo "activate the virtualenv" - source virtualenv/bin/activate - ### RENAME APP in database and migration files #### - if [ $ren_app == true ] ; then - - echo "Modifying database names and constraints..." - mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - -e 'UPDATE django_content_type SET app_label = REPLACE(app_label , "iSkyLIMS_core", "core") WHERE app_label like ("iSkyLIMS_%");' - # mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - # -e 'UPDATE django_content_type SET app_label = REPLACE(app_label , "iSkyLIMS_clinic", "clinic") WHERE app_label like ("iSkyLIMS_%");' - mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - -e 'UPDATE django_content_type SET app_label = REPLACE(app_label , "iSkyLIMS_wetlab", "wetlab") WHERE app_label like ("iSkyLIMS_%");' - mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - -e 'UPDATE django_content_type SET app_label = REPLACE(app_label , "iSkyLIMS_drylab", "drylab") WHERE app_label like ("iSkyLIMS_%");' - - mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - -e 'UPDATE django_migrations SET app = REPLACE(app , "iSkyLIMS_core", "core") WHERE app like ("iSkyLIMS_%");' - # mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - # -e 'UPDATE django_migrations SET app = REPLACE(app , "iSkyLIMS_clinic", "clinic") WHERE app like ("iSkyLIMS_%");' - mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - -e 'UPDATE django_migrations SET app = REPLACE(app , "iSkyLIMS_wetlab", "wetlab") WHERE app like ("iSkyLIMS_%");' - mysql -u $DB_USER -p$DB_PASS -D $DB_NAME -h $DB_SERVER_IP \ - -e 'UPDATE django_migrations SET app = REPLACE(app , "iSkyLIMS_drylab", "drylab") WHERE app like ("iSkyLIMS_%");' - echo "Renaming tables" - query_rename_table="SELECT CONCAT('RENAME TABLE ', TABLE_SCHEMA, '.', TABLE_NAME, \ - ' TO ', TABLE_SCHEMA, '.', REPLACE(TABLE_NAME, 'iSkyLIMS_', ''), ';') \ - AS query FROM information_schema.tables WHERE TABLE_SCHEMA = \"$DB_NAME\" AND TABLE_NAME LIKE 'iSkyLIMS_%';" - mysql -u $DB_USER -p$DB_PASS -h $DB_SERVER_IP -e "$query_rename_table" \ - | xargs -I % echo "mysql -u$DB_USER -p'$DB_PASS' -D $DB_NAME -h $DB_SERVER_IP -e \"% \" " | bash - echo "Renaming index" - query_rename_unique_indexes="SELECT CONCAT('ALTER TABLE ', rcu.TABLE_SCHEMA, '.', rcu.TABLE_NAME, \ - ' RENAME INDEX ', rcu.CONSTRAINT_NAME, \ - ' TO ', REPLACE(rcu.CONSTRAINT_NAME, 'iSkyLIMS_', ''), ';') \ - AS query FROM information_schema.key_column_usage rcu \ - JOIN information_schema.table_constraints tc \ - ON tc.CONSTRAINT_NAME = rcu.CONSTRAINT_NAME WHERE rcu.TABLE_SCHEMA = \"$DB_NAME\" \ - AND rcu.CONSTRAINT_NAME LIKE 'iSkyLIMS_%' AND tc.CONSTRAINT_TYPE = 'UNIQUE' \ - GROUP BY rcu.TABLE_SCHEMA, rcu.TABLE_NAME, rcu.CONSTRAINT_NAME, tc.CONSTRAINT_TYPE, \ - rcu.REFERENCED_TABLE_SCHEMA, rcu.REFERENCED_TABLE_NAME;" - mysql -u $DB_USER -p$DB_PASS -h $DB_SERVER_IP -e "$query_rename_unique_indexes" \ - | xargs -I % echo "mysql -u$DB_USER -p'$DB_PASS' -D $DB_NAME -h $DB_SERVER_IP -e \"% \" " | bash - echo "Renaming constraints" - query_rename_constraints="SELECT CONCAT('ALTER TABLE ', rcu.TABLE_SCHEMA, '.', rcu.TABLE_NAME, \ - ' DROP FOREIGN KEY ' , rcu.CONSTRAINT_NAME, ';', \ - ' ALTER TABLE ', rcu.TABLE_SCHEMA, '.', rcu.TABLE_NAME, \ - ' ADD CONSTRAINT ', REPLACE(rcu.CONSTRAINT_NAME, 'iSkyLIMS_', ''), ' ', \ - tc.CONSTRAINT_TYPE, ' (', GROUP_CONCAT(rcu.COLUMN_NAME ORDER BY rcu.ORDINAL_POSITION SEPARATOR ', '), ')', \ - IF(tc.CONSTRAINT_TYPE = 'FOREIGN KEY', \ - CONCAT(' REFERENCES ', rcu.REFERENCED_TABLE_SCHEMA, '.', REPLACE(rcu.REFERENCED_TABLE_NAME, 'iSkyLIMS_', ''), ' (', \ - GROUP_CONCAT(rcu.REFERENCED_COLUMN_NAME ORDER BY rcu.ORDINAL_POSITION SEPARATOR ', '), ') ON DELETE ', rc.DELETE_RULE), \ - ''), ';') AS query \ - FROM information_schema.key_column_usage rcu \ - LEFT JOIN information_schema.table_constraints tc ON rcu.CONSTRAINT_NAME = tc.CONSTRAINT_NAME \ - LEFT JOIN information_schema.referential_constraints rc ON rcu.CONSTRAINT_NAME = rc.CONSTRAINT_NAME \ - WHERE rcu.TABLE_SCHEMA = '$DB_NAME' AND rcu.CONSTRAINT_NAME LIKE 'iSkyLIMS_%' \ - GROUP BY rcu.TABLE_SCHEMA, rcu.TABLE_NAME, rcu.CONSTRAINT_NAME, tc.CONSTRAINT_TYPE, rcu.REFERENCED_TABLE_SCHEMA, rcu.REFERENCED_TABLE_NAME, rc.DELETE_RULE;" - mysql -u $DB_USER -p$DB_PASS -h $DB_SERVER_IP -e "$query_rename_constraints" | xargs -I % echo "mysql -u$DB_USER -p'$DB_PASS' -D $DB_NAME -h $DB_SERVER_IP -e \"% \" " | bash - - echo "Done modifying database names and constraints..." - - echo "Modifying names in migration files..." - sed -i 's/iSkyLIMS_core/core/g' */migrations/*.py - # sed -i 's/iSkyLIMS_clinic/clinic/g' */migrations/*.py - sed -i 's/iSkyLIMS_drylab/drylab/g' */migrations/*.py - sed -i 's/iSkyLIMS_wetlab/wetlab/g' */migrations/*.py - echo "Done modifying names in migration files..." - - # copy modified migration files - echo "Copying custom migration files from conf." - cp $INSTALL_PATH/conf/0002_core_migration_v3.0.0.py $INSTALL_PATH/core/migrations/0002_migration_v3_0_0.py - cp $INSTALL_PATH/conf/0002_drylab_migration_v3.0.0.py $INSTALL_PATH/drylab/migrations/0002_migration_v3_0_0.py - cp $INSTALL_PATH/conf/0002_wetlab_migration_v3.0.0.py $INSTALL_PATH/wetlab/migrations/0002_migration_v3_0_0.py - # cp conf/0002_clinic_migration_v2.3.1.py clinic/migrations/0002_migration_v2_3_1.py - cp $INSTALL_PATH/conf/0002_django_utils_migration_v3.0.0.py $INSTALL_PATH/django_utils/migrations/0002_migration_v3_0_0.py - - read -p "Do you want to proceed with the migrate command? (Y/N) " -n 1 -r - echo # (optional) move to a new line - if [[ ! $REPLY =~ ^[Yy]$ ]] ; then - echo "Exiting without running migrate command." - exit 1 - fi - - echo "activate the virtualenv" - source virtualenv/bin/activate - echo "Running migrate..." - python manage.py migrate - echo "Done migrate command." - - else - # execute the script to remove the comma in RawTopUnknowBarcodes table - echo "Running migration script: remove_comma_rawtopunknownbarcodes" - ./manage.py runscript convert_rawtop_counter_to_int - echo "checking for database changes" - if python manage.py makemigrations --noinput | grep -q "No changes"; then - # check for pending migrations - if ./manage.py showmigrations | grep '\[ \]'; then - echo "There are pending migrations" - read -p "Do you want to update database with the pending migrations? (Y/N) " -n 1 -r - echo # move to a new line - if [[ ! $REPLY =~ ^[Yy]$ ]] ; then - echo "Continue running script without running migrate command." - else - echo "Running migrate..." - python manage.py migrate - echo "Done migrate command." - fi - else - echo "No migration is required" - fi - else - read -p "Do you want to proceed with the migrate command? (Y/N) " -n 1 -r - echo # (optional) move to a new line - if [[ ! $REPLY =~ ^[Yy]$ ]] ; then - echo "Exiting without running migrate command." - exit 1 - fi - echo "Running migrate..." - python manage.py migrate - echo "Done migrate command." - fi - fi - # update static files - echo "Deleting static files..." - rm -rf $INSTALL_PATH/static - echo "Running collect statics..." - python manage.py collectstatic - echo "Done collect statics" - - if [ $tables == true ] ; then - echo "Loading pre-filled tables..." - echo "Loading in database initial data" - load_tables $prefilled_tables true - echo "Done loading pre-filled tables..." - fi - - if [ $run_script ]; then - for val in "${migration_script[@]}"; do - if [[ $val = *","* ]]; then - parameters=(${val//,/ }) - echo "Running migration script: ${parameters[0]}" - ./manage.py runscript ${parameters[0]} --script-args ${parameters[1]} - echo "Done migration script: ${parameters[0]}" - else - echo "Running migration script: $val" - ./manage.py runscript $val - echo "Done migration script: $val" - fi - done - fi - - cd - + operation="upgrade" + operation_scope="$upgrade_type" +fi - # Linux distribution - linux_distribution=$(lsb_release -i | cut -f 2-) +load_install_config +checkout_git_revision +user=${SUDO_USER:-$USER} +check_requirements - echo "" - echo "Restart apache server to update changes" - if [[ $linux_distribution == "Ubuntu" ]]; then - apache_daemon="apache2" - else - apache_daemon="httpd" - fi - - # systemctl restart $apache_user - - if ! [ $? -eq 0 ]; then - echo -e "${ORANGE}Apache server restart failed. trying with sudo{NC}" - sudo systemctl restart $apache_daemon - fi +if [[ "$operation_scope" == "full" || "$operation_scope" == "dep" ]]; then + run_dependency_stage "$operation" + if [ "$operation_scope" = "dep" ]; then + log_info "Dependency stage completed." + exit 0 fi - printf "\n\n%s" - printf "${BLUE}------------------${NC}\n" - printf "%s" - printf "${BLUE}Successfuly upgrade of iSKyLIMS version: ${ISKYLIMS_VERSION}${NC}\n" - printf "%s" - printf "${BLUE}------------------${NC}\n\n" - # exit once upgrade is finished - exit 0 - fi -#================================================================ -# INSTALL REPOSITORY REQUIRED SOFTWARE AND PYTHON VIRTUAL ENVIRONMENT -#================================================================ - -if [ $install == true ]; then - - if [ "$install_type" == "full" ] || [ "$install_type" == "dep" ]; then - - #================================================================ - # MAIN_BODY FOR INSTALL - #================================================================ - printf "\n\n%s" - printf "${YELLOW}------------------${NC}\n" - printf "%s" - printf "${YELLOW}Starting iSkyLIMS install version: ${ISKYLIMS_VERSION}${NC}\n" - printf "%s" - printf "${YELLOW}------------------${NC}\n\n" - - user=$SUDO_USER - group=$(groups | cut -d" " -f1) - - # Find out server Linux distribution - linux_distribution=$(lsb_release -i | cut -f 2-) - - if [[ $linux_distribution == "Ubuntu" ]]; then - apache_group="www-data" - else - apache_group="apache" - fi - - echo "Starting iSkyLIMS installation" - if [ -d $INSTALL_PATH ]; then - echo "There already is an installation of iskylims in $INSTALL_PATH." - read -p "Do you want to remove current installation and reinstall? (Y/N) " -n 1 -r - echo # (optional) move to a new line - if [[ ! $REPLY =~ ^[Yy]$ ]] ; then - echo "Exiting without running iSkyLIMS installation" - exit 1 - else - rm -rf $INSTALL_PATH - fi - fi - - echo "Installing Interop" - if [ -d /opt/interop ]; then - echo "There is already an interop installation" - echo "Skipping Interop installation" - else - cd /opt - echo "Downloading interop software" - wget https://github.com/Illumina/interop/releases/download/v1.1.15/InterOp-1.1.15-Linux-GNU.tar.gz - tar -xf InterOp-1.1.15-Linux-GNU.tar.gz - ln -s InterOp-1.1.15-Linux-GNU interop - rm InterOp-1.1.15-Linux-GNU.tar.gz - echo "Interop is now installed" - cd - - fi - - if [[ $linux_distribution == "Ubuntu" ]]; then - echo "Software installation for Ubuntu" - apt-get update && apt-get upgrade -y - apt-get install -y \ - apt-utils wget \ - libmysqlclient-dev \ - python3-venv \ - libpq-dev \ - python3-dev python3-pip python3-wheel \ - apache2-dev cifs-utils \ - gnuplot - - fi - - if [[ $linux_distribution == "CentOS" || $linux_distribution == "RedHatEnterprise" ]]; then - echo "Software installation for Centos/RedHat" - yum groupinstall "Development tools" - yum install zlib-devel bzip2-devel openssl-devel \ - wget httpd-devel mysql-libs sqlite sqlite-devel \ - mariadb-devel libffi-devel \ - gnuplot cifs-utils - fi - - ## Create the installation folder - mkdir -p $INSTALL_PATH/conf - chown -R $user:$apache_group $INSTALL_PATH - chmod 775 $INSTALL_PATH - - # Copy requirements before moving to install path - rsync -rlv conf/requirements.txt $INSTALL_PATH/conf/requirements.txt - - cd $INSTALL_PATH - # install virtual environment - echo "Creating virtual environment" - if [ -d $INSTALL_PATH/virtualenv ]; then - echo "There already is a virtualenv for iskylims in $INSTALL_PATH." - read -p "Do you want to remove current virtualenv and reinstall? (Y/N) " -n 1 -r - echo # (optional) move to a new line - if [[ ! $REPLY =~ ^[Yy]$ ]] ; then - rm -rf $INSTALL_PATH/virtualenv - bash -c "$PYTHON_BIN_PATH -m venv virtualenv" - else - echo "virtualenv alredy defined. Skipping." - fi - else - bash -c "$PYTHON_BIN_PATH -m venv virtualenv" - fi - - echo "activate the virtualenv" - source virtualenv/bin/activate - - # Install python packages required for iSkyLIMS - echo "Installing required python packages" - python -m pip install wheel - python -m pip install -r conf/requirements.txt - - cd - - - if [ "$install_type" == "full" ]; then - printf "\n\n%s" - printf "${BLUE}------------------${NC}\n" - printf "%s" - printf "${BLUE}Software dep are successfuly installed${NC}\n" - printf "%s" - printf "${BLUE}------------------${NC}\n\n" - else - printf "\n\n%s" - printf "${BLUE}------------------${NC}\n" - printf "%s" - printf "${BLUE}Software dep are successfuly installed${NC}\n" - printf "%s" - printf "${BLUE}------------------${NC}\n\n" - printf "\n\n%s" - printf "${RED}------------------${NC}\n" - printf "%s" - printf "${RED}Exiting${NC}\n" - printf "%s" - printf "${RED}------------------${NC}\n\n" - exit 0 - fi +if [[ "$operation_scope" == "full" || "$operation_scope" == "app" ]]; then + if [ "$operation" = "install" ]; then + install_application_files + else + upgrade_application_files fi - - #================================================================ - # INSTALL iSkyLIMS PLATFORM APPLICATION - #================================================================ - - if [ "$install_type" == "full" ] || [ "$install_type" == "app" ]; then - - if [ $LOG_TYPE == "symbolic_link" ]; then - if [ -d $LOG_PATH ]; then - if [ ! -d $INSTALL_PATH/logs ]; then - echo "Deleting existing symbolin link" - rm $INSTALL_PATH/logs - fi - echo "Creating symbolic link to log folder" - ln -s $LOG_PATH $INSTALL_PATH/logs - chmod 775 $LOG_PATH - else - echo "Log folder path: $LOG_PATH does not exist. Fix it in the install_settings.txt and run again." - exit 1 - fi - else - if [ ! -d $INSTALL_PATH/logs ]; then - mkdir -p $INSTALL_PATH/logs - chown $user:$apache_group $INSTALL_PATH/logs - chmod 775 $INSTALL_PATH/logs - else - echo "Log folder path: $INSTALL_PATH/logs already exist." - fi - fi - - rsync -rlv README.md LICENSE test conf $REQUIRED_MODULES $INSTALL_PATH - - cd $INSTALL_PATH - - # Create necessary folders - echo "Created documents structure" - mkdir -p $INSTALL_PATH/documents/wetlab - mkdir -p $INSTALL_PATH/documents/wetlab/tmp - mkdir -p $INSTALL_PATH/documents/wetlab/sample_sheet - mkdir -p $INSTALL_PATH/documents/wetlab/images_plot - mkdir -p $INSTALL_PATH/documents/wetlab/templates - mkdir -p $INSTALL_PATH/documents/wetlab/sample_sheets_lib_prep - mkdir -p $INSTALL_PATH/documents/drylab - mkdir -p $INSTALL_PATH/documents/drylab/service_files - - chown -R $user:$apache_group $INSTALL_PATH/documents - chmod 775 $INSTALL_PATH/documents - - # Copy illumina sample sheet templates - cp $INSTALL_PATH/conf/*_template.csv $INSTALL_PATH/documents/wetlab/templates/ - cp $INSTALL_PATH/conf/samples_template.xlsx $INSTALL_PATH/documents/wetlab/templates/ - - # update logging configuration file - cp $INSTALL_PATH/conf/template_logging_config.ini $INSTALL_PATH/wetlab/logging_config.ini - sed -i "s|INSTALL_PATH|${INSTALL_PATH}|g" $INSTALL_PATH/wetlab/logging_config.ini - - # Starting iSkyLIMS - echo "activate the virtualenv" - source virtualenv/bin/activate - - echo "Creating iskylims project" - django-admin startproject iskylims . - - # update the settings.py and the main urls - update_settings_and_urls - - # Creating data base structure and load prefilled tables - if [ $docker == false ]; then - echo "Creating the database structure for iSkyLIMS" - python manage.py migrate - python manage.py makemigrations $MIGRATION_MODULES - python manage.py migrate - echo "Loading in database initial data" - load_tables $prefilled_tables true - echo "Creating super user " - python manage.py createsuperuser --username admin - fi - - # copy static files - echo "Run collectstatic" - python manage.py collectstatic - - cd - - - printf "\n\n%s" - printf "${BLUE}------------------${NC}\n" - printf "%s" - printf "${BLUE}Successfuly iSkyLIMS Installation version: ${ISKYLIMS_VERSION}${NC}\n" - printf "%s" - printf "${BLUE}------------------${NC}\n\n" - - echo "Installation completed" - exit 0 + if [ $docker == false ] && [ $restart_apache == true ]; then + restart_apache_service fi + exit 0 fi printf "\n\n%s" From 75d17279fd9518acacad17942a3fae0f4cd37af5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 19 Nov 2025 17:25:50 +0100 Subject: [PATCH 271/446] adapt leame and readme to refactor --- LEAME.md | 90 +++++++++++++++++++++++++++++++++++-------------------- README.md | 34 ++++++++++++++++----- 2 files changed, 84 insertions(+), 40 deletions(-) diff --git a/LEAME.md b/LEAME.md index 8bbcae0e6..59f0c5a13 100644 --- a/LEAME.md +++ b/LEAME.md @@ -128,15 +128,21 @@ sudo nano install_settings.txt #### Ejecutar el script de instalación -iSkyLIMS debe instalarse en el directorio "/opt". - -Necesitará privilegios de administrador para instalar las dependencias. Para manejar diferentes responsabilidades de instalación dentro de la organización, donde es posible que no sea la persona con privilegios de administrador, nuestro script de instalación tiene estas opciones en el parámetro `--install`: - -- `dep`: para instalar los paquetes de software, así como los paquetes de Python dentro del entorno virtual. Se necesita permisos de administrador. -- `app`: para instalar solo el software de la aplicación iSkyLIMS sin necesidad de tener permisos de administrador. -- `full`: si tiene directamente permisos de administrador, puede instalar tanto las dependencias como la aplicación con esta opción. - -Ejecute uno de los siguientes comandos en una terminal de Linux para la instalación, de acuerdo con la descripción anterior. +iSkyLIMS debe instalarse en el directorio "/opt". + +Necesitará privilegios de administrador para instalar las dependencias. El mismo +script (`install.sh`) ahora coordina la preparación de dependencias y el +despliegue de la aplicación, por lo que puede elegir lo que necesite usando el +parámetro `--install`: + +- `dep`: instala los paquetes del sistema y los requisitos de Python dentro del + entorno virtual. Requiere permisos de administrador. +- `app`: despliega solo la aplicación (copia el código, ejecuta migraciones y + collectstatic). No requiere permisos de administrador. +- `full`: ejecuta los dos pasos secuencialmente. + +Ejecute uno de los siguientes comandos en una terminal de Linux según el paso +que quiera realizar. ```bash # para instalar solo las dependencias @@ -145,9 +151,13 @@ sudo bash install.sh --install dep # para instalar la aplicación iskylims bash install.sh --install app -# para instalar ambos al mismo tiempo -sudo bash install.sh --install full -``` +# para instalar ambos al mismo tiempo +sudo bash install.sh --install full +``` + +Por defecto el script reinicia Apache cuando finaliza la etapa `app`. Si no +quiere hacerlo (por ejemplo, porque usa otro frontal web) añada la opción +`--skip_apache_restart`. ## Actualización a la versión 3.1.0 de iSkyLIMS @@ -201,30 +211,44 @@ Asegúrate de que la carpeta de instalación tenga los permisos correctos para q sudo /scripts/hardening.sh ``` -En la terminal de Linux, ejecuta uno de los siguientes comandos que mejor se adapte a ti: - -```bash -# para actualizar solo las dependencias del software. ES NECESARIO DISPONER DE PERMISOS DE ROOT. -sudo bash install.sh --upgrade dep - -# PARA INSTALAR AMBAS COSAS AL MISMO TIEMPO. REQUIERE DE ROOT. SI SE VA A INSTALAR POR OTRA PERSONA SIN ROOT NO HACER ESTO. -sudo bash install.sh --upgrade full --git_revision main --tables -``` - -#### Pasos que no necesitan de permisos de administración - -Actualiza a la nueva version de la aplicación de iskylims usando el siguiente comando: - -```bash -bash install.sh --upgrade app --git_revision main --tables -``` - -Por último, asegúrate que los permisos de la carpeta son correctos. +En la terminal de Linux, ejecuta el comando que mejor se adapte a tus +necesidades: + +```bash +# para actualizar solo las dependencias del software. REQUIERE DE PERMISOS DE ROOT. +sudo bash install.sh --upgrade dep + +# para ejecutar dependencias y aplicación en un único paso +sudo bash install.sh --upgrade full --git_revision main --tables +``` + +#### Pasos que no necesitan de permisos de administración + +Actualiza a la nueva versión de la aplicación de iSkyLIMS usando el siguiente +comando: + +```bash +bash install.sh --upgrade app --git_revision main --tables +``` + +Esto aplica también si necesita restaurar la información de las librerías +respaldadas: + +```bash +bash install.sh --upgrade app --script --git_revision main --tables +``` + +Por último, asegúrate que los permisos de la carpeta son correctos. ```bash # En el caso de que tengas un script para esta tarea. En esta versión han cambiado algunas rutas a ficheros, es posible que tengas que ajustar el script en consecuencia. -/scripts/hardening.sh -``` +/scripts/hardening.sh +``` + +Durante las actualizaciones el script regenera las migraciones de Django y las +aplica con `--fake-initial`, preservando las tablas existentes (igual que en el +despliegue con Docker). Si te interesa omitir el reinicio de Apache tras la +actualización añade el parámetro `--skip_apache_restart`. #### Qué hacer si algo falla diff --git a/README.md b/README.md index 8b8a0cf3a..0f2ab4f76 100644 --- a/README.md +++ b/README.md @@ -171,14 +171,19 @@ nano install_settings.txt iSkyLIMS should be installed on the "/opt" directory. -You will need sudo privileges for installing dependencies. In order to handle different installation responsibilities inside the organization, where you may not be the person with root privileges, our instalation script has these options in ```--install``` parameter: +You will need sudo privileges for installing dependencies. The same +`install.sh` script now orchestrates both dependency preparation and the +application deployment, so you can mix and match what you need through the +`--install` parameter: -- dep: to install the software packages as well as python packages inside the virtual environment. Root is needed. -- app: to install only the iSkyLIMS application software without need of being root. -- full: if you directly have root permissions you can install both deps and app at the same time with this option. +- `dep`: installs system packages plus Python requirements inside the virtual + environment. Requires root/sudo. +- `app`: copies the iSkyLIMS code, updates settings, runs migrations and + collectstatic. Does not require root. +- `full`: performs both steps sequentially for you. -Execute one of the following commands in a linux terminal to install, according as -above description. +Execute one of the following commands in a linux terminal, depending on the +stage you want to run: ```bash # to install only software packages dependences @@ -191,6 +196,10 @@ bash install.sh --install app --git_revision main --tables sudo bash install.sh --install full --git_revision main --tables ``` +By default the script restarts Apache when the `app` stage finishes. If you are +deploying behind another HTTP front-end you can skip this step with +`--skip_apache_restart`. + ## Upgrade from 3.0.x to iSkyLIMS version 3.1.x Follow the following steps to upgrade from version 3.0.0 to the latest one 3.1.x @@ -283,9 +292,20 @@ If restauration of libary preparation is not required then execute the following ```bash # to upgrade iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. -bash install.sh --upgrade app ---git_revision main -tables +bash install.sh --upgrade app --git_revision main --tables +``` + +You can also run the full upgrade in one command (both dependency and app +stages): + +```bash +sudo bash install.sh --upgrade full --git_revision main --tables ``` +During upgrades the script regenerates the Django migrations and applies them in +`--fake-initial` mode so existing tables are preserved, matching what we do in +the Docker deployment. + Make sure that the installation folder has the correct permissions. ```bash From 626f4280e3f2f797940ad7af95f43aeff9f5a14d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 20 Nov 2025 16:40:53 +0100 Subject: [PATCH 272/446] remove logging to file in install.sh and use tee en docs --- LEAME.md | 20 +++++++++++++++++--- README.md | 14 ++++++++++++++ install.sh | 28 ++++++++++++++++++---------- 3 files changed, 49 insertions(+), 13 deletions(-) diff --git a/LEAME.md b/LEAME.md index 59f0c5a13..1af0a7628 100644 --- a/LEAME.md +++ b/LEAME.md @@ -148,13 +148,20 @@ que quiera realizar. # para instalar solo las dependencias sudo bash install.sh --install dep -# para instalar la aplicación iskylims -bash install.sh --install app - +# para instalar la aplicación iskylims +bash install.sh --install app + # para instalar ambos al mismo tiempo sudo bash install.sh --install full ``` +Para conservar todo el registro de salida (stdout y stderr) en caso de +necesitar depurar, ejecute el script a través de `tee`: + +```bash +sudo bash install.sh --install full 2>&1 | tee install_full.log +``` + Por defecto el script reinicia Apache cuando finaliza la etapa `app`. Si no quiere hacerlo (por ejemplo, porque usa otro frontal web) añada la opción `--skip_apache_restart`. @@ -222,6 +229,13 @@ sudo bash install.sh --upgrade dep sudo bash install.sh --upgrade full --git_revision main --tables ``` +Guarde toda la salida de la actualización usando `tee` para tener un registro +completo si surge algún problema: + +```bash +sudo bash install.sh --upgrade full --git_revision main --tables 2>&1 | tee install_full.log +``` + #### Pasos que no necesitan de permisos de administración Actualiza a la nueva versión de la aplicación de iSkyLIMS usando el siguiente diff --git a/README.md b/README.md index 0f2ab4f76..144daad5b 100644 --- a/README.md +++ b/README.md @@ -196,6 +196,13 @@ bash install.sh --install app --git_revision main --tables sudo bash install.sh --install full --git_revision main --tables ``` +To keep a complete stdout/stderr record (useful for debugging), run the script +through `tee`: + +```bash +sudo bash install.sh --install full --git_revision main --tables 2>&1 | tee install_full.log +``` + By default the script restarts Apache when the `app` stage finishes. If you are deploying behind another HTTP front-end you can skip this step with `--skip_apache_restart`. @@ -277,6 +284,13 @@ In the linux terminal execute the following command- sudo bash install.sh --upgrade dep ``` +Capture the full upgrade transcript with `tee` so you have all stdout/stderr if +troubleshooting is needed: + +```bash +sudo bash install.sh --upgrade dep 2>&1 | tee install_full.log +``` + #### Steps not requiring root Next you need to upgrade iskylims app. Please use one of the commands below: diff --git a/install.sh b/install.sh index 8743d824a..15b30e87e 100644 --- a/install.sh +++ b/install.sh @@ -1,7 +1,6 @@ #!/bin/bash -APP_VERSION="3.x.x" -LOG_FILE="/var/log/iskylims_install.log" +APP_VERSION="3.1.0dev" # usage: prints the command line help and usage examples. usage() { @@ -38,19 +37,27 @@ Examples: EOF } -# log: write timestamped log entries to stdout and LOG_FILE. -log() { +# log: write timestamped log entries to stdout. +_log_compose_entry() { local level="$1"; shift local message="$*" local timestamp timestamp="$(date '+%Y-%m-%d %H:%M:%S')" - printf "%s [%s] %s\n" "$timestamp" "$level" "$message" | tee -a "$LOG_FILE" + printf "%s [%s] %s" "$timestamp" "$level" "$message" +} + +log() { + local level="$1"; shift + local message="$*" + local entry + entry="$(_log_compose_entry "$level" "$message")" + printf "%s\n" "$entry" } # db_check: verifies connectivity to the configured MySQL instance using mysqladmin/mysqlshow. db_check(){ log "INFO" "Checking database connectivity against $DB_SERVER_IP:$DB_PORT" - mysqladmin -h $DB_SERVER_IP -u$DB_USER -p$DB_PASS -P$DB_PORT processlist > /dev/null 2>>"$LOG_FILE" + mysqladmin -h $DB_SERVER_IP -u$DB_USER -p$DB_PASS -P$DB_PORT processlist > /dev/null if ! [ $? -eq 0 ]; then log "ERROR" "Unable to connect to database. Check if your database is running and accessible" @@ -98,7 +105,7 @@ apache_check(){ # python_check: confirm required Python version is available in PYTHON_BIN_PATH. python_check(){ - python_version=$(su -c $PYTHON_BIN_PATH --version $user 2>>"$LOG_FILE") + python_version=$(su -c $PYTHON_BIN_PATH --version $user 2>&1) if [[ $python_version == "" ]]; then log "ERROR" "Python3 is not found in your system" log "ERROR" "Solve the issue with Python and run again the installation script" @@ -200,6 +207,7 @@ ORANGE='\033[0;33m' # log_section: print a visually separated header in both console and log. log_section() { local message="$1" + log "INFO" "$message" printf "\n\n%s\n" "${YELLOW}------------------${NC}" printf "%b\n" "${YELLOW}${message}${NC}" printf "%s\n\n" "${YELLOW}------------------${NC}" @@ -207,17 +215,17 @@ log_section() { # log_info: convenience helper for blue info messages (console only). log_info() { - printf "%b\n" "${BLUE}$1${NC}" + printf "%b\n" "${BLUE}$(_log_compose_entry "INFO" "$1")${NC}" } # log_warn: emit warning text in cyan for terminal visibility. log_warn() { - printf "%b\n" "${CYAN}$1${NC}" + printf "%b\n" "${CYAN}$(_log_compose_entry "WARN" "$1")${NC}" } # log_error: emit error text in red for terminal visibility. log_error() { - printf "%b\n" "${RED}$1${NC}" + printf "%b\n" "${RED}$(_log_compose_entry "ERROR" "$1")${NC}" } # abort_install: log an error and exit with optional status. From 583e79796aa2c46b3eb3813b2a35fa74212595bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 20 Nov 2025 16:44:48 +0100 Subject: [PATCH 273/446] remove legacy need of folder renaming --- install.sh | 9 --------- 1 file changed, 9 deletions(-) diff --git a/install.sh b/install.sh index 15b30e87e..3e0dd0a2d 100644 --- a/install.sh +++ b/install.sh @@ -632,15 +632,6 @@ upgrade_application_files() { echo "Update settings and url file." update_settings_and_urls prepare_documents_structure - if [ -d "$INSTALL_PATH/documents/wetlab/SampleSheets" ]; then - echo "Updating sample sheet folder name" - mv $INSTALL_PATH/documents/wetlab/SampleSheets $INSTALL_PATH/documents/wetlab/sample_sheet - fi - - if [ -d "$INSTALL_PATH/documents/wetlab/SampleSheets4LibPrep" ]; then - echo "Updating sample sheet for libary preparationfolder name" - mv $INSTALL_PATH/documents/wetlab/SampleSheets4LibPrep $INSTALL_PATH/documents/wetlab/sample_sheets_lib_prep - fi cd $INSTALL_PATH echo "activate the virtualenv" From a2ab832492ed5e06e11df739ceb56c921019ec2c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 20 Nov 2025 17:13:56 +0100 Subject: [PATCH 274/446] runscript is also run in install besides upgrade if asked to --- install.sh | 75 ++++++++++++++++++++++++++++++++---------------------- 1 file changed, 45 insertions(+), 30 deletions(-) diff --git a/install.sh b/install.sh index 3e0dd0a2d..dbbf18665 100644 --- a/install.sh +++ b/install.sh @@ -13,7 +13,8 @@ usage : $0 --upgrade --git_revision --conf --upgrade | Upgrade iskylims full/dep/app --git_revision | Git revision name to run (it can be git branch, git version tag or commit SHA) --conf | Select custom configuration file. Default: ./install_settings.txt - --tables | Load the first inital tables for upgrades in conf folder + --tables | Load the first inital tables (from conf folder) + --skip_tables | Skip loading initial tables (even during install) --script | Run a migration script. --ren_app | Rename apps required for the upgrade migration to 3.0.0 --docker | Specific installation for docker compose configuration. @@ -458,16 +459,33 @@ run_django_deploy() { if [ "$mode" = "upgrade" ]; then echo "Applying migrations in fake-initial mode" python manage.py migrate --noinput --fake-initial - if [ $tables == true ] ; then - echo "Loading pre-filled tables..." - load_tables $prefilled_tables true - echo "Done loading pre-filled tables..." - fi else echo "Applying migrations" python manage.py migrate --noinput - echo "Loading in database initial data" - load_tables $prefilled_tables true + fi + + if [ "$tables" = true ]; then + echo "Loading pre-filled tables..." + load_tables "$prefilled_tables" true + echo "Done loading pre-filled tables..." + fi + + if [ "$run_script" = true ]; then + for val in "${migration_script[@]}"; do + if [[ $val = *","* ]]; then + parameters=(${val//,/ }) + echo "Running migration script: ${parameters[0]}" + ./manage.py runscript ${parameters[0]} --script-args ${parameters[1]} + echo "Done migration script: ${parameters[0]}" + else + echo "Running migration script: $val" + ./manage.py runscript $val + echo "Done migration script: $val" + fi + done + fi + + if [ "$mode" = "install" ]; then echo "Creating super user " python manage.py createsuperuser --username admin fi @@ -646,21 +664,6 @@ upgrade_application_files() { python manage.py collectstatic echo "Done collect statics" - if [ $run_script ]; then - for val in "${migration_script[@]}"; do - if [[ $val = *","* ]]; then - parameters=(${val//,/ }) - echo "Running migration script: ${parameters[0]}" - ./manage.py runscript ${parameters[0]} --script-args ${parameters[1]} - echo "Done migration script: ${parameters[0]}" - else - echo "Running migration script: $val" - ./manage.py runscript $val - echo "Done migration script: $val" - fi - done - fi - cd - log_section "Successfuly upgrade of iSKyLIMS version: ${APP_VERSION}" } @@ -684,13 +687,13 @@ install_application_files() { if [ $LOG_TYPE == "symbolic_link" ]; then if [ -d $LOG_PATH ]; then - if [ ! -d $INSTALL_PATH/logs ]; then - echo "Deleting existing symbolin link" - rm $INSTALL_PATH/logs + if [ -e "$INSTALL_PATH/logs" ]; then + echo "Log target $INSTALL_PATH/logs already exists. Leaving it unchanged." + else + echo "Creating symbolic link to log folder" + ln -s "$LOG_PATH" "$INSTALL_PATH/logs" + chmod 775 "$LOG_PATH" fi - echo "Creating symbolic link to log folder" - ln -s $LOG_PATH $INSTALL_PATH/logs - chmod 775 $LOG_PATH else echo "Log folder path: $LOG_PATH does not exist. Fix it in the install_settings.txt and run again." exit 1 @@ -747,6 +750,7 @@ do --upgrade) set -- "$@" -u ;; --script) set -- "$@" -s ;; --tables) set -- "$@" -t ;; + --skip_tables) set -- "$@" -b ;; --git_revision) set -- "$@" -g ;; --conf) set -- "$@" -c ;; --ren_app) set -- "$@" -r ;; @@ -773,9 +777,11 @@ upgrade_type="full" docker=false prefilled_tables="conf/first_install_tables.json" restart_apache=true +run_script=false +skip_tables=false # PARSE VARIABLE ARGUMENTS WITH getops -options=":c:s:i:u:r:g:tdkvha" +options=":c:s:i:u:r:g:tdbkvha" while getopts $options opt; do case $opt in i ) @@ -807,6 +813,10 @@ while getopts $options opt; do t ) tables=true ;; + b ) + tables=false + skip_tables=true + ;; r ) ren_app=true ;; @@ -854,6 +864,11 @@ if [ $upgrade == true ]; then operation_scope="$upgrade_type" fi +# Default to loading initial tables on installs unless explicitly skipped. +if [ "$operation" = "install" ] && [ "$skip_tables" = false ] && [ "$tables" = false ]; then + tables=true +fi + load_install_config checkout_git_revision user=${SUDO_USER:-$USER} From 96d17ac09fe4f27850b10cc9b5e5b0bfcc4b04ba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 7 Jan 2026 17:05:28 +0100 Subject: [PATCH 275/446] rewritten readme to be clearer --- README.md | 308 ++++++++++++++++++------------------------------------ 1 file changed, 101 insertions(+), 207 deletions(-) diff --git a/README.md b/README.md index 144daad5b..ae92a8721 100644 --- a/README.md +++ b/README.md @@ -13,21 +13,23 @@ According to existent infrastructure sequencing is performed on an Illumina Next Application servers run web applications for bioinformatics analysis (GALAXY), the iSkyLIMS app, and host the MySQL information tier. iSkyLIMS WetLab workflow deals with sequencing run tracking and statistics. Run tracking passes through five states: "recorded” genomics user record the new sequencing run into the system, the process will wait till run is completed by the machine and data is transferred to the mass storage device; “Sample sheet sent” sample sheet file with the sequencing run information will be copied to the run folder for bcl2fastq process; “Processing data” run parameters files are processed and data is stored in the database; “Running stats” demultiplexing data generated in bcl2fastq process is processed and stored into the database, “Completed” all data is processed and stored successfully. Statistics per sample, per project, per run and per investigation are provided, as well as annual and monthly reports. iSkyLIMS DryLab workflow deals with bioinformatics services request and statistics. User request services that can be associated with a sequencing run. Stats and services tracking is provided. - [iSkyLIMS](#iskylims) - - [Installation](#installation) - - [Pre-requisites](#pre-requisites) - - [iSkyLIMS docker installation](#iskylims-docker-installation) - - [Install iSkyLIMS in your server running ubuntu/CentOS](#install-iskylims-in-your-server-running-ubuntucentos) - - [Clone github repository](#clone-github-repository) - - [Create iskylims database and grant permissions](#create-iskylims-database-and-grant-permissions) - - [Configuration settings](#configuration-settings) - - [Run installation script](#run-installation-script) - - [Upgrade from 3.0.x to iSkyLIMS version 3.1.x](#upgrade-from-30x-to-iskylims-version-31x) - - [Pre-requisites for upgrade](#pre-requisites-for-upgrade) - - [Clone github repository](#clone-github-repository-1) - - [Configuration settings](#configuration-settings-1) - - [Running upgrade script](#running-upgrade-script) - - [Steps requiring root](#steps-requiring-root) - - [Steps not requiring root](#steps-not-requiring-root) + - [Choose your path](#choose-your-path) + - [Docker deployment](#docker-deployment) + - [Local test stack](#local-test-stack) + - [Production container](#production-container) + - [Upgrade docker deployment](#upgrade-docker-deployment) + - [Bare-metal deployment (Ubuntu/CentOS)](#bare-metal-deployment-ubuntucentos) + - [Install](#install) + - [Prerequisites](#prerequisites) + - [Clone the repository](#clone-the-repository) + - [Prepare the database](#prepare-the-database) + - [Configure install\_settings.txt](#configure-install_settingstxt) + - [Run install.sh](#run-installsh) + - [Upgrade (3.0.x to 3.1.x)](#upgrade-30x-to-31x) + - [Back up first](#back-up-first) + - [Refresh code and settings](#refresh-code-and-settings) + - [Run upgrade steps requiring root](#run-upgrade-steps-requiring-root) + - [Run upgrade steps without root](#run-upgrade-steps-without-root) - [What to do if something fails](#what-to-do-if-something-fails) - [Final configuration steps](#final-configuration-steps) - [SAMBA configurarion](#samba-configurarion) @@ -36,296 +38,188 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Verification of the installation](#verification-of-the-installation) - [iSkyLIMS documentation](#iskylims-documentation) -## Installation - For any problems or bug reporting please post us an [issue](https://github.com/BU-ISCIII/iSkyLIMS/issues) -### Pre-requisites - -Before starting the installation make sure : - -- You have **sudo privileges** to install the additional software packets that iSkyLIMS needs. -- Database MySQL > 8.0 or MariaDB > 10.4 -- Local server configured for sending emails -- Apache server v2.4 -- git > 2.34 -- Python > 3.8 -- Connection to samba shared folder where run folders are stored (p.e galera/NGS_Data) -- Dependencies: - - lsb_release: - - RedHat/CentOS: ```yum install redhat-lsb-core``` - - Ubuntu: ```apt install lsb-core lsb-release``` +## Choose your path -### iSkyLIMS docker installation +- **Docker (local test)**: spin up MySQL + Samba + iSkyLIMS with demo data to try the app quickly. +- **Docker (production container)**: deploy only the application container, pointing to your existing DB/Samba. +- **Bare-metal**: install or upgrade directly on Ubuntu/CentOS hosts with `install.sh`. -You can test iSkyLIMS by creating a docker container on your local machine. +## Docker deployment -Clone the iSkyLIMS github repository and run the docker script to create the docker +### Local test stack -```bash -git clone https://github.com/BU-ISCIII/iSkyLIMS.git iSkyLIMS -sudo bash docker_install.sh -``` +Bring up a full test stack (database, Samba, app) plus fixtures and demo data: -Or you can specify installation type and/or git revision: ```bash git clone https://github.com/BU-ISCIII/iSkyLIMS.git iSkyLIMS -# To perform full installation from iskylims using git revision/branch 'develop' -sudo bash docker_install.sh --install_type full --git_revision develop +cd iSkyLIMS +bash docker_install.sh --test ``` -The script creates a docker compose container with 3 services: - -- web1: contains the iSkyLIMS web application -- db1: contains the mySQL database -- samba: contains samba server +Defaults can be customised: -After Docker is created and services are up, database structure and initial data are loaded into database. When this step is completed, you will be asked to define the super user which will have access to django admin pages. You can type any name, but we recommend that you use "admin", because admin user is requested later on when defining the initial settings. +- `--demo_data /path/to/iskylims_demo_data.tar.gz` to reuse a local demo archive (otherwise it is downloaded). +- `--skip_demo_data` or `--skip_test_data` to avoid loading extra data. +- `--install_type` (`full` by default) and `--git_revision` to control the build. -Follow the prompt message to create the super user account. +When the script finishes, open `http://localhost:8001` and follow the prompt to create the Django superuser. -When script ends open your navigator typing **localhost:8001** to access to iSkyLIMS +### Production container -#### Production docker deployment +Deploy the iSkyLIMS container against external MySQL/Samba services: -When your MySQL database and Samba share run on dedicated machines, you can -deploy only the iSkyLIMS application container and connect it to those external -services. - -1. Copy the production settings template and adjust it with the real database - credentials/host: +1. Copy and edit the production settings template: ```bash cp conf/docker_production_settings.txt conf/my_prod_settings.txt - # edit conf/my_prod_settings.txt to point to your DB server + # edit conf/my_prod_settings.txt with your DB/Samba details ``` -2. Build and run the application container (production mode is the default, so - passing the settings file is enough): +2. Build and run in production mode (uses `docker-compose.prod.yml` by default): ```bash bash docker_install.sh --install_conf conf/my_prod_settings.txt ``` - The installer automatically uses `docker-compose.prod.yml`, which only starts - the `iskylims_app` container while pointing to external services. You can - still override the compose file or skip behaviours through extra flags (see - `docker_install.sh --help`). - -3. Once the container is up, create the Django superuser and configure the Samba - connection details through the UI if this is a fresh installation. + Use `--compose_file` to override the compose file or `--install_type`/`--git_revision` to change the build. -If you already have a populated production database and only need to roll out a -new application version, reuse the same command but add `--action upgrade`. The -script will rebuild/restart the container, regenerate the Django migrations, -apply them using `--fake-initial` so existing tables are respected, and skip the -superuser/fixture loading steps so your data remains untouched. +3. If this is a fresh install, create the Django superuser when prompted and complete the Samba configuration in the UI. -#### Local testing deployment +### Upgrade docker deployment -To spin up the full stack (database + samba + app) with demo data and fixtures, -just add the `--test` flag: +Re-deploy the application container against an existing production database without touching data: ```bash -bash docker_install.sh --test +bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade ``` -You can reuse the existing options (`--demo_data`, `--install_type`, etc.) to -customise the behaviour if needed. +The upgrade path rebuilds/restarts the container, regenerates migrations, applies them with `--fake-initial`, and skips superuser/demo/test data loading. + +## Bare-metal deployment (Ubuntu/CentOS) -### Install iSkyLIMS in your server running ubuntu/CentOS +### Install -#### Clone github repository +#### Prerequisites -Open a linux terminal and move to a directory where iSkyLIMS code will be -downloaded +- **sudo privileges** for dependency installation +- MySQL > 8.0 or MariaDB > 10.4 +- Apache 2.4 +- git > 2.34 +- Python > 3.8 +- Local email sender configured +- Access to the Samba share where run folders live +- `lsb_release` package (`yum install redhat-lsb-core` on RedHat/CentOS, `apt install lsb-core lsb-release` on Ubuntu) + +#### Clone the repository ```bash -cd < your personal folder > +cd git clone https://github.com/BU-ISCIII/iskylims.git iskylims cd iskylims ``` -#### Create iskylims database and grant permissions - -1. Create a new database named "iskylims" (this is mandatory) -2. Create a new user with permission to read and modify that database. -3. Write down user, passwd and db server info. +#### Prepare the database -#### Configuration settings +1. Create a database named `iskylims`. +2. Create a user with read/write permissions on that database. +3. Note the database host, port, user, and password for the settings file. -Copy the initial setting template into a file named install_settings.txt +#### Configure install_settings.txt ```bash cp conf/template_install_settings.txt install_settings.txt -``` - -Open with your favourite editor the configuration file to set your own values for -database ,email settings and the local IP of the server where iSkyLIMS will run. - -```bash nano install_settings.txt ``` -#### Run installation script +Set your database, email, server IP/URL, and logging preferences in that file. -iSkyLIMS should be installed on the "/opt" directory. +#### Run install.sh -You will need sudo privileges for installing dependencies. The same -`install.sh` script now orchestrates both dependency preparation and the -application deployment, so you can mix and match what you need through the -`--install` parameter: +iSkyLIMS is installed to `/opt/iskylims` by default. The single `install.sh` script handles both dependencies and the app; choose what you need with `--install`: -- `dep`: installs system packages plus Python requirements inside the virtual - environment. Requires root/sudo. -- `app`: copies the iSkyLIMS code, updates settings, runs migrations and - collectstatic. Does not require root. -- `full`: performs both steps sequentially for you. +- `dep`: install system and Python dependencies (requires sudo). +- `app`: deploy iSkyLIMS code, update settings, run migrations, and collect static files (no sudo needed). +- `full`: run both stages in sequence. -Execute one of the following commands in a linux terminal, depending on the -stage you want to run: +Examples: ```bash -# to install only software packages dependences +# only software dependencies sudo bash install.sh --install dep -# to install only iSkyLIMS application +# only iSkyLIMS application bash install.sh --install app --git_revision main --tables -# to install both software +# dependencies + application sudo bash install.sh --install full --git_revision main --tables ``` -To keep a complete stdout/stderr record (useful for debugging), run the script -through `tee`: +- Add `--tables` to load the initial fixtures on first-time installs, or `--skip_tables` if you want to skip them. +- Capture logs for troubleshooting with `tee`: -```bash -sudo bash install.sh --install full --git_revision main --tables 2>&1 | tee install_full.log -``` + ```bash + sudo bash install.sh --install full --git_revision main --tables 2>&1 | tee install_full.log + ``` -By default the script restarts Apache when the `app` stage finishes. If you are -deploying behind another HTTP front-end you can skip this step with -`--skip_apache_restart`. +- If Apache is managed elsewhere, skip the automatic restart with `--skip_apache_restart`. -## Upgrade from 3.0.x to iSkyLIMS version 3.1.x +### Upgrade (3.0.x to 3.1.x) -Follow the following steps to upgrade from version 3.0.0 to the latest one 3.1.x - -### Pre-requisites for upgrade - -Before starting the upgrade procedure is highly recomended to perform the following steps: - -- Create a full backup of iSkyLIMS database -- Backup all iSkyLIMS folders (complete installation folder, p.e /opt/iSkyLIMS) - -- If in your system you have already defined library pools, then you need to collect this data, before to run the upgrade script. Perform a backup of LibraryPool by running the folowing command. - -```bash - mysql --user= --password= --host= --port= iskylims -e "SELECT* FROM wetlab_library_pool" > -``` +Follow these steps to move from version 3.0.0 to the 3.1.x series. -It is highly recomended that you made these backups and keep them safely in case of upgrade failure, to recover your system. +#### Back up first -### Clone github repository +- Full backup of the `iskylims` database. +- Full backup of the installation folder (for example `/opt/iskylims`). +- If you use library pools, export them before upgrading: -As it was defined in previous releases the iSkyLIMS code is downloaded in a user folder and then installed elsewhere (p.e /opt/). + ```bash + mysql --user= --password= --host= --port= iskylims \ + -e "SELECT * FROM wetlab_library_pool" > /backup_lib_pool.sql + ``` -If you have already clone the repository from the previous 3.0.0 release open a -linux terminal and move towards the directory of iSkyLIMS repository. +#### Refresh code and settings ```bash -cd < your personal folder/iskylims > +cd /iskylims git pull -``` - -If the repository was not created then open a linux terminal and move to a directory where iSkyLIMS code will be downloaded - -```bash -cd < your personal folder > -git clone https://github.com/BU-ISCIII/iSkyLIMS.git iskylims -cd iskylims -``` - -### Configuration settings - -Copy the initial setting template into a file named install_settings.txt - -```bash cp conf/template_install_settings.txt install_settings.txt -``` - -Open with your favourite editor the configuration file to set your own values for -database ,email settings and the local IP of the server where iSkyLIMS will run. -> If you use a windows-based system for modifying the file, make sure the file is saved using a linux-friendly encoding like ASCII or UTF-8 - -```bash sudo nano install_settings.txt ``` -### Running upgrade script +Ensure the file uses Linux-friendly encoding (UTF-8/ASCII) if you edit it on Windows. -If your organization requires that dependencies / stuff that needs root are installed by a different person that install the application the you can use the install script in several steps as follows. +#### Run upgrade steps requiring root -#### Steps requiring root - -Make sure that the installation folder has the correct permissions so the person installing the app can write in that folder. - -```bash -# In case you have a script for this task. You'll need to adjust this script according to the name changing: /opt/iSkyLIMS to /opt/iskylims -/scripts/hardening.sh -``` - -From the previous release software dependences (Python packages) must be updated to the releases defined in the requirement.txt file. - -In the linux terminal execute the following command- - -```bash -# to upgrade only software packages dependences. NEEDS ROOT. -sudo bash install.sh --upgrade dep -``` - -Capture the full upgrade transcript with `tee` so you have all stdout/stderr if -troubleshooting is needed: +Update system and Python dependencies: ```bash sudo bash install.sh --upgrade dep 2>&1 | tee install_full.log ``` -#### Steps not requiring root +Make sure the installation directory permissions allow the non-root step to write to `/opt/iskylims` (adapt your hardening script if paths changed). -Next you need to upgrade iskylims app. Please use one of the commands below: +#### Run upgrade steps without root -If you are using the library pool, you must indicate in the installation script the file you already backup and execute the following command. +Upgrade the application code and database: ```bash -# to upgrade iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. -bash install.sh --upgrade app --script --git_revision main --tables -``` - -If restauration of libary preparation is not required then execute the following command +# with library pool restore +bash install.sh --upgrade app --script /backup_lib_pool.sql --git_revision main --tables -```bash -# to upgrade iSkyLIMS application including changes required in this release. DOES NOT NEED ROOT. +# without library pool restore bash install.sh --upgrade app --git_revision main --tables ``` -You can also run the full upgrade in one command (both dependency and app -stages): +Or run everything in one go: ```bash sudo bash install.sh --upgrade full --git_revision main --tables ``` -During upgrades the script regenerates the Django migrations and applies them in -`--fake-initial` mode so existing tables are preserved, matching what we do in -the Docker deployment. - -Make sure that the installation folder has the correct permissions. - -```bash -# In case you have a script for this task. Some paths have changed in this version, so you may need to adjust your hardening script. -/scripts/hardening.sh -``` +Upgrades regenerate migrations and apply them with `--fake-initial` so existing tables remain intact, matching the Docker workflow. ## What to do if something fails From 0a6a79bb0c1995bb8d07ee3a5f4789f6e59dc3fb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 7 Jan 2026 17:12:09 +0100 Subject: [PATCH 276/446] added leame and get code as required --- LEAME.md | 551 ++++++++++++++++++++++++++---------------------------- README.md | 17 +- 2 files changed, 275 insertions(+), 293 deletions(-) diff --git a/LEAME.md b/LEAME.md index 1af0a7628..cfff6950a 100644 --- a/LEAME.md +++ b/LEAME.md @@ -1,317 +1,286 @@ -# iSkyLIMS - -[![Django](https://img.shields.io/static/v1?label=Django&message=4.2&color=azul?style=plastic&logo=django)](https://github.com/django/django) -[![Python](https://img.shields.io/static/v1?label=Python&message=3.8.10&color=verde?style=plastic&logo=Python)](https://www.python.org/) -[![Bootstrap](https://img.shields.io/badge/Bootstrap-v5.0-azulvioleta?style=plastic&logo=Bootstrap)](https://getbootstrap.com) -[![versión](https://img.shields.io/badge/versión-3.0.0-naranja?style=plastic&logo=GitHub)](https://github.com/BU-ISCIII/iskylims.git) - -La introducción de la secuenciación masiva (MS) en las instalaciones de genómica ha significado un crecimiento exponencial en la generación de datos, lo que requiere un sistema de seguimiento preciso, desde la preparación de la biblioteca hasta la generación de archivos fastq, el análisis y la entrega al investigador. El software diseñado para manejar esas tareas se llama Sistemas de Gestión de Información de Laboratorio (LIMS), y su software debe adaptarse a las necesidades particulares de su laboratorio de genómica. iSkyLIMS nace con el objetivo de ayudar con las tareas de laboratorio húmedo e implementar un flujo de trabajo que guíe a los laboratorios de genómica en sus actividades, desde la preparación de la biblioteca hasta la producción de datos, reduciendo los posibles errores asociados a la tecnología de alto rendimiento y facilitando el control de calidad de la secuenciación. Además, iSkyLIMS conecta el laboratorio húmedo con el laboratorio seco, facilitando el análisis de datos por parte de bioinformáticos. - -![Imagen](img/iskylims_scheme.png) - -De acuerdo con la infraestructura existente, la secuenciación se realiza en un instrumento Illumina NextSeq. Los datos se almacenan en un dispositivo de almacenamiento masivo NetApp y los archivos fastq se generan (bcl2fastq) en un clúster de cómputo de alto rendimiento Sun Grid Engine (SGE-HPC). Los servidores de aplicaciones ejecutan aplicaciones web para el análisis bioinformático (GALAXY), la aplicación iSkyLIMS y alojan la capa de información de MySQL. El flujo de trabajo de iSkyLIMS WetLab se ocupa del seguimiento y las estadísticas de la ejecución de la secuenciación. El seguimiento de la ejecución pasa por cinco estados: "registrado", el usuario de genómica registra la nueva ejecución de la secuenciación en el sistema, el proceso esperará hasta que la ejecución se complete en la máquina y los datos se transfieran al dispositivo de almacenamiento masivo; "Envío de hoja de muestra", el archivo de hoja de muestra con la información de la ejecución de la secuenciación se copiará en la carpeta de ejecución para el proceso de bcl2fastq; "Procesamiento de datos", se procesan los archivos de parámetros de ejecución y los datos se almacenan en la base de datos; "Estadísticas en ejecución", los datos de desmultiplexación generados en el proceso de bcl2fastq se procesan y almacenan en la base de datos, "Completado", todos los datos se procesan y almacenan correctamente. Se proporcionan estadísticas por muestra, por proyecto, por ejecución y por investigación, así como informes anuales y mensuales. El flujo de trabajo de iSkyLIMS DryLab se encarga de la solicitud de servicios de bioinformática y estadísticas. El usuario solicita servicios que pueden estar asociados con una ejecución de secuenciación. Se proporciona seguimiento de estadísticas y servicios. - -- [iSkyLIMS](#iskylims) - - [Instalación](#instalación) - - [Requisitos previos](#requisitos-previos) - - [Instalación de iSkyLIMS en Docker](#instalación-de-iskylims-en-docker) - - [Instalación de iSkyLIMS en su servidor con Ubuntu/CentOS](#instalación-de-iskylims-en-su-servidor-con-ubuntucentos) - - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github) - - [Crear la base de datos de iSkyLIMS y otorgar permisos](#crear-la-base-de-datos-de-iskylims-y-otorgar-permisos) - - [Configuración de ajustes](#configuración-de-ajustes) - - [Ejecutar el script de instalación](#ejecutar-el-script-de-instalación) - - [Actualización a la versión 3.1.0 de iSkyLIMS](#actualización-a-la-versión-310-de-iskylims) - - [Prerrequisitos](#prerrequisitos) - - [Clonar el repositorio de GitHub](#clonar-el-repositorio-de-github-1) - - [Configuración de opciones](#configuración-de-opciones) - - [Ejecución del script de actualización](#ejecución-del-script-de-actualización) - - [Pasos que necesitan permisos de adminsitración](#pasos-que-necesitan-permisos-de-adminsitración) - - [Pasos que no necesitan de permisos de administración](#pasos-que-no-necesitan-de-permisos-de-administración) - - [Qué hacer si algo falla](#qué-hacer-si-algo-falla) - - [Pasos finales de configuración](#pasos-finales-de-configuración) - - [Configuración de SAMBA](#configuración-de-samba) - - [Verificación de correo electrónico](#verificación-de-correo-electrónico) - - [Configurar el servidor Apache](#configurar-el-servidor-apache) - - [Verificación de la instalación](#verificación-de-la-instalación) - - [Documentación de iSkyLIMS](#documentación-de-iskylims) - -## Instalación - -Si tienes algún problema o deseas informar de algún error, por favor, publícalo en [issue](https://github.com/BU-ISCIII/iSkyLIMS/issues) - -### Requisitos previos - -Antes de comenzar la instalación, asegúrate de lo siguiente: - -- Tienes privilegios de **sudo** para instalar los paquetes de software adicionales que iSkyLIMS necesita. -- Dependencias: - - Librerías: - - -```bash - yum groupinstall "Development tools" - yum install zlib-devel bzip2-devel openssl-devel \ - wget httpd-devel mysql-libs sqlite sqlite-devel \ - mariadb-devel mysql-client libffi-devel \ - gnuplot cifs-utils -``` - -- lsb_relase: - - RedHat/CentOS: `yum install redhat-lsb-core` - - Ubuntu: `apt install lsb-core lsb-release` - -- lsb_relase: - - RedHat/CentOS: `yum install redhat-lsb-core` - - Ubuntu: `apt install lsb-core lsb-release` -- Base de datos MySQL > 8.0 o MariaDB > 10.4 -- Tienes configurado un servidor local para enviar correos electrónicos. -- git > 2.34 -- Tienes Apache servidor v2.4 -- Tienes Python > 3.8 (si lo compilas debes haber instalado previamente las dependecias de arriba) -- Tienes una conexión a la carpeta compartida de Samba donde se almacenan las carpetas de ejecución (por ejemplo, galera/NGS_Data). -- Dependencias: - -### Instalación de iSkyLIMS en Docker - -Puedes probar iSkyLIMS creando un contenedor Docker en tu máquina local. - -Clona el repositorio de GitHub de iSkyLIMS y ejecuta el script de Docker para crear el contenedor Docker. - -```bash -git clone https://github.com/BU-ISCIII/iSkyLIMS.git iSkyLIMS -sudo bash docker_install.sh -``` - -El script crea un contenedor de Docker Compose con 3 servicios: - -- web1: contiene la aplicación web iSkyLIMS -- db1: contiene la base de datos MySQL -- samba: contiene el servidor Samba - -Después de crear Docker y tener los servicios en funcionamiento, la estructura de la base de datos y los datos iniciales se cargan en la base de datos. Cuando se complete este paso, se le pedirá que defina al superusuario que tendrá acceso a las páginas de administración de Django. Puede escribir cualquier nombre, pero recomendamos que utilice "admin", ya que más adelante se le pedirá un usuario administrador cuando defina la configuración inicial. - -Siga el mensaje de instrucciones para crear la cuenta del superusuario. - -Cuando el script finalice, abra su navegador escribiendo **localhost:8001** para acceder a iSkyLIMS - -### Instalación de iSkyLIMS en su servidor con Ubuntu/CentOS - -#### Clonar el repositorio de GitHub - -Abra una terminal de Linux y vaya a un directorio donde se descargará el código de iSkyLIMS - -```bash -cd -git clone https://github.com/BU-ISCIII/iskylims.git iskylims -cd iskylims -``` - -#### Crear la base de datos de iSkyLIMS y otorgar permisos - -1. Cree una nueva base de datos llamada "iskylims" (esto es obligatorio). -2. Cree un nuevo usuario con permisos para leer y modificar esa base de datos. -3. Anote el nombre de usuario, la contraseña y la información del servidor de la base de datos. - -#### Configuración de ajustes - -Copia la plantilla de ajustes iniciales en un archivo llamado `install_settings.txt` - -```bash -cp conf/template_install_settings.txt install_settings.txt -``` - -Abra el archivo de configuración con su editor favorito para establecer sus propios valores para la base de datos, la configuración de correo electrónico y la dirección IP local del servidor donde se ejecutará iSkyLIMS. - -```bash -sudo nano install_settings.txt -``` - -#### Ejecutar el script de instalación - -iSkyLIMS debe instalarse en el directorio "/opt". - -Necesitará privilegios de administrador para instalar las dependencias. El mismo -script (`install.sh`) ahora coordina la preparación de dependencias y el -despliegue de la aplicación, por lo que puede elegir lo que necesite usando el -parámetro `--install`: - -- `dep`: instala los paquetes del sistema y los requisitos de Python dentro del - entorno virtual. Requiere permisos de administrador. -- `app`: despliega solo la aplicación (copia el código, ejecuta migraciones y - collectstatic). No requiere permisos de administrador. -- `full`: ejecuta los dos pasos secuencialmente. - -Ejecute uno de los siguientes comandos en una terminal de Linux según el paso -que quiera realizar. - -```bash -# para instalar solo las dependencias -sudo bash install.sh --install dep - -# para instalar la aplicación iskylims -bash install.sh --install app - -# para instalar ambos al mismo tiempo -sudo bash install.sh --install full +# iSkyLIMS + +[![Django](https://img.shields.io/static/v1?label=Django&message=4.2&color=azul?style=plastic&logo=django)](https://github.com/django/django) +[![Python](https://img.shields.io/static/v1?label=Python&message=3.8.10&color=verde?style=plastic&logo=Python)](https://www.python.org/) +[![Bootstrap](https://img.shields.io/badge/Bootstrap-v5.0-azulvioleta?style=plastic&logo=Bootstrap)](https://getbootstrap.com) +[![version](https://img.shields.io/badge/version-3.0.0-naranja?style=plastic&logo=GitHub)](https://github.com/BU-ISCIII/iskylims.git) + +La introduccion de la secuenciacion masiva (MS) en las instalaciones de genomica ha significado un crecimiento exponencial en la generacion de datos, lo que requiere un sistema de seguimiento preciso, desde la preparacion de la biblioteca hasta la generacion de archivos fastq, el analisis y la entrega al investigador. El software disenado para manejar esas tareas se llama Sistemas de Gestion de Informacion de Laboratorio (LIMS), y su software debe adaptarse a las necesidades particulares de su laboratorio de genomica. iSkyLIMS nace con el objetivo de ayudar con las tareas de laboratorio humedo e implementar un flujo de trabajo que guie a los laboratorios de genomica en sus actividades, desde la preparacion de la biblioteca hasta la produccion de datos, reduciendo los posibles errores asociados a la tecnologia de alto rendimiento y facilitando el control de calidad de la secuenciacion. Ademas, iSkyLIMS conecta el laboratorio humedo con el laboratorio seco, facilitando el analisis de datos por parte de bioinformaticos. + +![Imagen](img/iskylims_scheme.png) + +De acuerdo con la infraestructura existente, la secuenciacion se realiza en un instrumento Illumina NextSeq. Los datos se almacenan en un dispositivo de almacenamiento masivo NetApp y los archivos fastq se generan (bcl2fastq) en un cluster de computo de alto rendimiento Sun Grid Engine (SGE-HPC). Los servidores de aplicaciones ejecutan aplicaciones web para el analisis bioinformatico (GALAXY), la aplicacion iSkyLIMS y alojan la capa de informacion de MySQL. El flujo de trabajo de iSkyLIMS WetLab se ocupa del seguimiento y las estadisticas de la ejecucion de la secuenciacion. El seguimiento de la ejecucion pasa por cinco estados: "registrado", el usuario de genomica registra la nueva ejecucion de la secuenciacion en el sistema, el proceso esperara hasta que la ejecucion se complete en la maquina y los datos se transfieran al dispositivo de almacenamiento masivo; "Envio de hoja de muestra", el archivo de hoja de muestra con la informacion de la ejecucion de la secuenciacion se copiara en la carpeta de ejecucion para el proceso de bcl2fastq; "Procesamiento de datos", se procesan los archivos de parametros de ejecucion y los datos se almacenan en la base de datos; "Estadisticas en ejecucion", los datos de desmultiplexacion generados en el proceso de bcl2fastq se procesan y almacenan en la base de datos, "Completado", todos los datos se procesan y almacenan correctamente. Se proporcionan estadisticas por muestra, por proyecto, por ejecucion y por investigacion, asi como informes anuales y mensuales. El flujo de trabajo de iSkyLIMS DryLab se encarga de la solicitud de servicios de bioinformatica y estadisticas. El usuario solicita servicios que pueden estar asociados con una ejecucion de secuenciacion. Se proporciona seguimiento de estadisticas y servicios. + +- [iSkyLIMS](#iskylims) + - [Obtener el codigo (obligatorio)](#obtener-el-codigo-obligatorio) + - [Elige tu ruta](#elige-tu-ruta) + - [Despliegue con Docker](#despliegue-con-docker) + - [Contenedor local de pruebas](#contenedor-local-de-pruebas) + - [Contenedor de produccion](#contenedor-de-produccion) + - [Actualizacion del despliegue Docker](#actualizacion-del-despliegue-docker) + - [Despliegue bare-metal (Ubuntu/CentOS)](#despliegue-bare-metal-ubuntucentos) + - [Instalacion](#instalacion) + - [Requisitos previos](#requisitos-previos) + - [Clonar el repositorio](#clonar-el-repositorio) + - [Preparar la base de datos](#preparar-la-base-de-datos) + - [Configurar install\_settings.txt](#configurar-install_settingstxt) + - [Ejecutar install.sh](#ejecutar-installsh) + - [Actualizacion (3.0.x a 3.1.x)](#actualizacion-30x-a-31x) + - [Haz copia de seguridad](#haz-copia-de-seguridad) + - [Actualizar codigo y ajustes](#actualizar-codigo-y-ajustes) + - [Ejecutar pasos de actualizacion con root](#ejecutar-pasos-de-actualizacion-con-root) + - [Ejecutar pasos de actualizacion sin root](#ejecutar-pasos-de-actualizacion-sin-root) + - [Que hacer si algo falla](#que-hacer-si-algo-falla) + - [Pasos finales de configuracion](#pasos-finales-de-configuracion) + - [Configuracion de SAMBA](#configuracion-de-samba) + - [Verificacion de correo electronico](#verificacion-de-correo-electronico) + - [Configurar el servidor Apache](#configurar-el-servidor-apache) + - [Verificacion de la instalacion](#verificacion-de-la-instalacion) + - [Documentacion de iSkyLIMS](#documentacion-de-iskylims) + +Si tienes algun problema o deseas informar de algun error, por favor, publicalo en [issue](https://github.com/BU-ISCIII/iSkyLIMS/issues) + +## Obtener el codigo (obligatorio) + +Todas las rutas de instalacion asumen que ya clonaste el repositorio: + +```bash +git clone https://github.com/BU-ISCIII/iskylims.git iskylims +cd iskylims +``` + +## Elige tu ruta + +- **Docker (pruebas locales)**: levanta MySQL + Samba + iSkyLIMS con datos de demo para probar rapidamente. +- **Docker (contenedor de produccion)**: despliega solo la aplicacion, apuntando a tu DB/Samba existente. +- **Bare-metal**: instala o actualiza directamente en hosts Ubuntu/CentOS con `install.sh`. + +## Despliegue con Docker + +Requisitos previos para instalaciones con Docker: + +- Docker Engine + Docker Compose v2 +- git (para clonar el repositorio) + +### Contenedor local de pruebas + +Levanta el sistema completo (base de datos, Samba y app) con fixtures y datos de demo: + +```bash +bash docker_install.sh --test ``` -Para conservar todo el registro de salida (stdout y stderr) en caso de -necesitar depurar, ejecute el script a través de `tee`: +Puedes personalizar los valores por defecto: + +- `--demo_data /ruta/a/iskylims_demo_data.tar.gz` para reutilizar un archivo local (si no, se descarga). +- `--skip_demo_data` o `--skip_test_data` para evitar cargar datos extra. +- `--install_type` (`full` por defecto) y `--git_revision` para controlar el build. + +Cuando el script termine, abre `http://localhost:8001` y crea el superusuario de Django cuando te lo pida. + +### Contenedor de produccion + +Despliega el contenedor de iSkyLIMS contra servicios MySQL/Samba externos: + +1. Copia y edita la plantilla de produccion: + + ```bash + cp conf/docker_production_settings.txt conf/my_prod_settings.txt + # edita conf/my_prod_settings.txt con tus datos de DB/Samba + ``` + +2. Construye y ejecuta en modo produccion (usa `docker-compose.prod.yml` por defecto): + + ```bash + bash docker_install.sh --install_conf conf/my_prod_settings.txt + ``` + + Usa `--compose_file` para cambiar el compose o `--install_type`/`--git_revision` para variar el build. + +3. Si es una instalacion nueva, crea el superusuario cuando se solicite y completa la configuracion de Samba en la UI. + +### Actualizacion del despliegue Docker + +Re-despliega el contenedor de aplicacion contra una base de datos existente sin tocar los datos: ```bash -sudo bash install.sh --install full 2>&1 | tee install_full.log +bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade ``` -Por defecto el script reinicia Apache cuando finaliza la etapa `app`. Si no -quiere hacerlo (por ejemplo, porque usa otro frontal web) añada la opción -`--skip_apache_restart`. - -## Actualización a la versión 3.1.0 de iSkyLIMS - -En esta version se han implementado fallos de código y mejoras en las gráficas. Para obtener más detalles sobre los cambios, consulta las notas de la versión. - -### Prerrequisitos - -Por temas de seguridad es recomendado realizar una copia de seguridad de: - -- La base de datos de iSkyLIMS. -- La carpeta de iSkyLIMS (carpeta de instalación completa, por ejemplo, /opt/iSkyLIMS). - -Se recomienda encarecidamente que se hagan estas copias de seguridad y se guarden de manera segura en caso de que la actualización falle, para poder recuperar tu sistema. Por ejemplo crea una carpeta en `/home/dadmin/backup_pro` que contenga la base de datos y la carpeta de /opt/iskylims para tenerla a mano y poder [restaurar el sistema](#qué-hacer-si-algo-falla). - -### Clonar el repositorio de GitHub - -A partir ya de la version anterior, ahora el código de iSkyLIMS se descarga en una carpeta del usuario y se instala en otro lugar (por ejemplo, /opt/). - -Abre una terminal de Linux y dirígete a un directorio donde estaba descargado el código de iSkyLIMS. Actualiza el codigo - -```bash -cd < directorio donde esta el codigo anterior de iskylims de instalación > -git pull -``` - -### Configuración de opciones - -Copia la plantilla de configuración inicial en un archivo llamado install_settings.txt - -```bash -cp conf/template_install_settings.txt install_settings.txt -``` - -Abre el archivo de configuración con tu editor favorito para establecer tus propios valores para la base de datos, la configuración de correo electrónico y la dirección IP local del servidor donde se ejecutará iSkyLIMS. -> Si utilizas un sistema basado en Windows para modificar el archivo, asegúrate de que el archivo se guarde con una codificación amigable para Linux, como ASCII o UTF-8. - -```bash -nano install_settings.txt -``` - -### Ejecución del script de actualización - -Debido a que los paquetes de python de los que depende iSkyLIMs se han ido actualizando desde la última release es necesario que sean actualizados. - -#### Pasos que necesitan permisos de adminsitración - -Asegúrate de que la carpeta de instalación tenga los permisos correctos para que la persona que instala la aplicación pueda escribir en esa carpeta. - -```bash -# En el caso de que tengas un script para esta tarea. Necesitarás ajustar este script de acuerdo al cambio en el nombre de la ruta: /opt/iSkyLIMS a /opt/iskylims -sudo /scripts/hardening.sh -``` - -En la terminal de Linux, ejecuta el comando que mejor se adapte a tus -necesidades: +La actualizacion reconstruye/reinicia el contenedor, regenera migraciones, las aplica con `--fake-initial` y evita cargar superusuario/datos demo/prueba. + +## Despliegue bare-metal (Ubuntu/CentOS) + +### Instalacion + +#### Requisitos previos + +- **Privilegios sudo** para instalar dependencias +- MySQL > 8.0 o MariaDB > 10.4 +- Apache 2.4 +- git > 2.34 +- Python > 3.8 +- Servidor local configurado para enviar correos +- Acceso a la carpeta Samba donde estan los run folders +- Paquete `lsb_release` (`yum install redhat-lsb-core` en RedHat/CentOS, `apt install lsb-core lsb-release` en Ubuntu) + +#### Clonar el repositorio ```bash -# para actualizar solo las dependencias del software. REQUIERE DE PERMISOS DE ROOT. -sudo bash install.sh --upgrade dep +cd +git clone https://github.com/BU-ISCIII/iskylims.git iskylims +cd iskylims +``` -# para ejecutar dependencias y aplicación en un único paso -sudo bash install.sh --upgrade full --git_revision main --tables +#### Preparar la base de datos + +1. Crea una base de datos llamada `iskylims`. +2. Crea un usuario con permisos de lectura/escritura sobre esa base. +3. Guarda host, puerto, usuario y password para el archivo de ajustes. + +#### Configurar install_settings.txt + +```bash +cp conf/template_install_settings.txt install_settings.txt +nano install_settings.txt +``` + +Completa los valores de base de datos, email, IP/URL del servidor y logging. + +#### Ejecutar install.sh + +iSkyLIMS se instala en `/opt/iskylims` por defecto. El script `install.sh` gestiona dependencias y aplicacion; elige lo que necesitas con `--install`: + +- `dep`: instala dependencias del sistema y de Python (requiere sudo). +- `app`: despliega el codigo, actualiza ajustes, ejecuta migraciones y collectstatic (sin sudo). +- `full`: ejecuta ambos pasos. + +Ejemplos: + +```bash +# solo dependencias del sistema +sudo bash install.sh --install dep + +# solo aplicacion iSkyLIMS +bash install.sh --install app --git_revision main --tables + +# dependencias + aplicacion +sudo bash install.sh --install full --git_revision main --tables +``` + +- Añade `--tables` para cargar los datos iniciales en instalaciones nuevas, o `--skip_tables` si quieres omitirlos. +- Captura logs para depuracion con `tee`: + + ```bash + sudo bash install.sh --install full --git_revision main --tables 2>&1 | tee install_full.log + ``` + +- Si Apache se gestiona desde otro sitio, omite el reinicio automatico con `--skip_apache_restart`. + +### Actualizacion (3.0.x a 3.1.x) + +Sigue estos pasos para pasar de la version 3.0.0 a la serie 3.1.x. + +#### Haz copia de seguridad + +- Copia completa de la base de datos `iskylims`. +- Copia completa de la carpeta de instalacion (por ejemplo `/opt/iskylims`). +- Si usas library pools, exportalos antes de actualizar: + + ```bash + mysql --user= --password= --host= --port= iskylims \ + -e "SELECT * FROM wetlab_library_pool" > /backup_lib_pool.sql + ``` + +#### Actualizar codigo y ajustes + +```bash +cd /iskylims +git pull +cp conf/template_install_settings.txt install_settings.txt +sudo nano install_settings.txt ``` -Guarde toda la salida de la actualización usando `tee` para tener un registro -completo si surge algún problema: +Si editas el archivo en Windows, asegurate de guardarlo con codificacion UTF-8/ASCII. + +#### Ejecutar pasos de actualizacion con root + +Actualiza dependencias del sistema y de Python: ```bash -sudo bash install.sh --upgrade full --git_revision main --tables 2>&1 | tee install_full.log +sudo bash install.sh --upgrade dep 2>&1 | tee install_full.log ``` -#### Pasos que no necesitan de permisos de administración +Asegura que los permisos permiten que el paso sin root escriba en `/opt/iskylims` (ajusta tu hardening si cambio la ruta). + +#### Ejecutar pasos de actualizacion sin root -Actualiza a la nueva versión de la aplicación de iSkyLIMS usando el siguiente -comando: +Actualiza el codigo y la base de datos: ```bash +# con restauracion de library pool +bash install.sh --upgrade app --script /backup_lib_pool.sql --git_revision main --tables + +# sin restauracion de library pool bash install.sh --upgrade app --git_revision main --tables ``` -Esto aplica también si necesita restaurar la información de las librerías -respaldadas: +O ejecuta todo en un unico comando: ```bash -bash install.sh --upgrade app --script --git_revision main --tables +sudo bash install.sh --upgrade full --git_revision main --tables ``` - -Por último, asegúrate que los permisos de la carpeta son correctos. - -```bash -# En el caso de que tengas un script para esta tarea. En esta versión han cambiado algunas rutas a ficheros, es posible que tengas que ajustar el script en consecuencia. -/scripts/hardening.sh + +Las actualizaciones regeneran las migraciones y las aplican con `--fake-initial` para conservar las tablas existentes, igual que en Docker. + +## Que hacer si algo falla + +Cuando actualizamos usando el script de instalacion estamos realizando varios cambios en la base de datos. Si algo falla necesitamos restaurar el estado anterior y empezar de nuevo. + +Necesitamos copiar la carpeta completa `/opt/iskylims` de vuelta a `/opt/iskylims` (o tu ruta de instalacion), y restaurar la base de datos con algo como: + +```bash +sudo rm -rf /opt/iskylims +sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ +sudo /scripts/hardening.sh +mysql -u iskylims -p -h dmysqlps.isciiides.es +# drop database iskylims; +# create database iskylims; +mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` -Durante las actualizaciones el script regenera las migraciones de Django y las -aplica con `--fake-initial`, preservando las tablas existentes (igual que en el -despliegue con Docker). Si te interesa omitir el reinicio de Apache tras la -actualización añade el parámetro `--skip_apache_restart`. - -#### Qué hacer si algo falla - -Cuando actualizamos la aplicación usando el script estamos realizando varios cambios en la base de datos. Si algo falla tenemos que restaurar el estado anterior, antes de que hubiesemos realizado ninguna acción. - -Necesitamos copiar de vuelta nuestro backup de carpet ade aplicación a /opt/iSkyLIMS (o la carpeta de instalación de nuestra elección), y restaurar la base de datos realizando algo como lo siguiente: - -```bash -sudo rm -rf /opt/iskylims -sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ -sudo /scripts/hardening.sh -mysql -u iskylims -p -h dmysqlps.isciiides.es -# drop database iskylims; -# create database iskylims; -mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql -``` - -### Pasos finales de configuración - -#### Configuración de SAMBA - -- Inicia sesión con la cuenta de administrador. -- Ve a Massive Sequencing -![Ir a WetLab](img/got_to_wetlab.png){width:50px} -- Ve a Configuración -> Configuración de SAMBA -- Completa el formulario con los parámetros apropiados para la carpeta compartida de SAMBA: -![Formulario SAMBA](img/samba_form.png) - -#### Verificación de correo electrónico - -- Ve a Massive Sequencing -- Ve a Configuración -> Configuración de correo electrónico -- Completa el formulario con los parámetros necesarios para la configuración de correo electrónico y trata de enviar un correo de prueba. - -#### Configurar el servidor Apache - -Copia el archivo de configuración de Apache que se encuentra en la carpeta `conf` según tu distribución dentro del directorio de configuración de Apache y cambia el nombre a iskylims.conf. Revisa cualquier requerimiento de tu sistema, se trata solo de un ejemplo. - -#### Verificación de la instalación - -Abre el navegador y escribe "localhost" o la "IP local del servidor" para comprobar que iSkyLIMS está en funcionamiento. - -También puedes verificar algunas funcionalidades mientras compruebas las conexiones de SAMBA y la base de datos usando: - -- Ve a [configurationTest](https://iskylims.isciii.es/wetlab/configurationTest/) -- Haz clic en Enviar -- Verifica todas las pestañas para asegurarte de que cada conexión sea exitosa. -- Ejecuta las 3 pruebas para cada máquina de secuenciación: MiSeq, NextSeq y NovaSeq. - -### Documentación de iSkyLIMS - -La documentación de iSkyLIMS está disponible en [https://iskylims.readthedocs.io/en/latest](https://iskylims.readthedocs.io/en/latest) +## Pasos finales de configuracion + +### Configuracion de SAMBA + +- Inicia sesion con la cuenta admin. +- Ve a Massive sequencing +![go_to_wetlab](img/got_to_wetlab.png){width:50px} +- Ve a Configuration -> Samba configuration +- Rellena el formulario con los parametros apropiados para la carpeta compartida de Samba: +![samba form](img/samba_form.png) + +### Verificacion de correo electronico + +- Ve a Massive sequencing +- Ve a Configuration -> Email configuration +- Rellena el formulario con los parametros necesarios y prueba a enviar un correo. + +### Configurar el servidor Apache + +Copia el archivo de configuracion de Apache segun tu distribucion dentro del directorio de configuracion de Apache y renombralo a iskylims.conf + +### Verificacion de la instalacion + +Abre el navegador y escribe "localhost" o la IP local del servidor para comprobar que iSkyLIMS esta funcionando. + +Tambien puedes comprobar parte de la funcionalidad y las conexiones a Samba y base de datos usando: + +- Ve a [configuration test](https://iskylims.isciii.es/wetlab/configurationTest/) +- Haz click en submit +- Revisa todas las pestañas para confirmar que la conexion es correcta. +- Ejecuta las 3 pruebas para cada maquina de secuenciacion: MiSeq, NextSeq y NovaSeq. + +## Documentacion de iSkyLIMS + +La documentacion de iSkyLIMS esta disponible en [https://iskylims.readthedocs.io/en/latest](https://iskylims.readthedocs.io/en/latest) diff --git a/README.md b/README.md index ae92a8721..3f2e6f587 100644 --- a/README.md +++ b/README.md @@ -13,6 +13,7 @@ According to existent infrastructure sequencing is performed on an Illumina Next Application servers run web applications for bioinformatics analysis (GALAXY), the iSkyLIMS app, and host the MySQL information tier. iSkyLIMS WetLab workflow deals with sequencing run tracking and statistics. Run tracking passes through five states: "recorded” genomics user record the new sequencing run into the system, the process will wait till run is completed by the machine and data is transferred to the mass storage device; “Sample sheet sent” sample sheet file with the sequencing run information will be copied to the run folder for bcl2fastq process; “Processing data” run parameters files are processed and data is stored in the database; “Running stats” demultiplexing data generated in bcl2fastq process is processed and stored into the database, “Completed” all data is processed and stored successfully. Statistics per sample, per project, per run and per investigation are provided, as well as annual and monthly reports. iSkyLIMS DryLab workflow deals with bioinformatics services request and statistics. User request services that can be associated with a sequencing run. Stats and services tracking is provided. - [iSkyLIMS](#iskylims) + - [Get the code (required)](#get-the-code-required) - [Choose your path](#choose-your-path) - [Docker deployment](#docker-deployment) - [Local test stack](#local-test-stack) @@ -40,6 +41,15 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t For any problems or bug reporting please post us an [issue](https://github.com/BU-ISCIII/iSkyLIMS/issues) +## Get the code (required) + +All installation paths assume you already cloned the repository: + +```bash +git clone https://github.com/BU-ISCIII/iskylims.git iskylims +cd iskylims +``` + ## Choose your path - **Docker (local test)**: spin up MySQL + Samba + iSkyLIMS with demo data to try the app quickly. @@ -48,13 +58,16 @@ For any problems or bug reporting please post us an [issue](https://github.com/B ## Docker deployment +Prerequisites for Docker-based installs: + +- Docker Engine + Docker Compose v2 +- git (to clone the repository) + ### Local test stack Bring up a full test stack (database, Samba, app) plus fixtures and demo data: ```bash -git clone https://github.com/BU-ISCIII/iSkyLIMS.git iSkyLIMS -cd iSkyLIMS bash docker_install.sh --test ``` From 2352c3985a6828720fa934c0e2a733ab4c27c08e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 7 Jan 2026 17:34:16 +0100 Subject: [PATCH 277/446] removed docker parameter for isntall.sh now install.sh is used for migrations, etc.. in docker install --- Dockerfile | 17 +++++++--------- docker_install.sh | 49 +++++++++++++++++++---------------------------- install.sh | 24 ++++++++++------------- 3 files changed, 37 insertions(+), 53 deletions(-) diff --git a/Dockerfile b/Dockerfile index c2cdfdc15..0e3d8ca0b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -9,7 +9,7 @@ RUN apt-get update && apt-get upgrade -y # Essential software RUN apt-get install -y \ git wget lsb-release \ - libmysqlclient-dev \ + libmysqlclient-dev default-mysql-client \ python3-pip libpq-dev python3-venv python3-wheel \ apache2-dev cron \ gnuplot pkg-config rsync @@ -25,21 +25,18 @@ WORKDIR /srv/iskylims # Copy the local git repository to docker image directory COPY . /srv/iskylims -# Create and activate a virtual environment -RUN python3 -m venv /srv/iskylims/venv -ENV PATH="/srv/iskylims/venv/bin:$PATH" ENV PATH="/usr/sbin/cron:$PATH" -# Install dependencies within the virtual environment -RUN /srv/iskylims/venv/bin/pip install -r conf/requirements.txt - # Set default install type -ARG INSTALL_TYPE=app +ARG INSTALL_TYPE=dep ARG GIT_REVISION=main ARG INSTALL_CONF=conf/docker_install_settings.txt -# Execute the installation script -RUN /bin/bash install.sh --install $INSTALL_TYPE --git_revision $GIT_REVISION --conf $INSTALL_CONF --docker +# Execute the dependency stage only; app migrations run when the container is up. +RUN /bin/bash install.sh --install dep --git_revision $GIT_REVISION --conf $INSTALL_CONF --skip_apache_restart +# Use the virtualenv created by install.sh +ENV PATH="/opt/relecov-platform/virtualenv/bin:${PATH}" + WORKDIR /opt/iskylims # Expose diff --git a/docker_install.sh b/docker_install.sh index ee3a63f7a..e64812e8b 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -6,7 +6,7 @@ usage() { cat << EOF This script installs and upgrades the iskylims app. -Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--install_conf] [--action] [--test] +Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--install_conf] [--action] [--script] [--test] Optional input data: --demo_data | Provide already downloaded demo data from Zenodo --install_type | Specify the installation type for iSkyLIMS (default: full) @@ -14,6 +14,7 @@ Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--i --compose_file | docker compose file to use (overrides default) --install_conf | Settings file consumed during docker image build (mandatory for production) --action | install (default) or upgrade, to control DB initialisation steps + --script | Run a Django migration script (can be repeated) --skip_demo_data | Skip downloading/copying demo data to samba container --skip_test_data | Skip loading test fixtures (test/test_data.json) --test | Use development/test compose file and sample data @@ -54,6 +55,7 @@ do --compose_file) set -- "$@" -c ;; --install_conf) set -- "$@" -s ;; --action) set -- "$@" -a ;; + --script) set -- "$@" -m ;; --skip_demo_data) set -- "$@" -n ;; --skip_test_data) set -- "$@" -t ;; --test) set -- "$@" -p ;; @@ -76,11 +78,11 @@ skip_demo_data="" skip_test_data="" mode="production" action="install" -run_superuser=true -load_initial_data=true +run_script=false +migration_script=() # PARSE VARIABLE ARGUMENTS WITH getopts -options=":d:i:g:c:s:a:vhntp" +options=":d:i:g:c:s:a:m:vhntp" while getopts $options opt; do case $opt in d) @@ -105,6 +107,10 @@ while getopts $options opt; do exit 1 fi ;; + m) + run_script=true + migration_script+=("$OPTARG") + ;; n) skip_demo_data=true ;; @@ -174,13 +180,8 @@ if [ -z "$skip_test_data" ]; then fi if [ "$action" = "upgrade" ]; then - run_superuser=false - load_initial_data=false skip_demo_data=true skip_test_data=true -else - run_superuser=true - load_initial_data=true fi if [ ! -f "$compose_file" ]; then @@ -204,29 +205,19 @@ docker compose -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." sleep 20 -echo "Generating Django migrations for iSkyLIMS apps" -docker exec -it iskylims_app python3 manage.py makemigrations django_utils core wetlab drylab - -if [ "$action" = "upgrade" ]; then - echo "Applying migrations in fake-initial mode (existing tables will be kept)" - docker exec -it iskylims_app python3 manage.py migrate --noinput --fake-initial -else - echo "Applying migrations" - docker exec -it iskylims_app python3 manage.py migrate --noinput +script_args="" +if [ "$run_script" = true ]; then + for val in "${migration_script[@]}"; do + script_args+=" --script $(printf '%q' "$val")" + done fi -if [ "$run_superuser" = true ]; then - echo "Creating super user" - docker exec -it iskylims_app python3 manage.py createsuperuser -else - echo "Skipping super user creation (--action upgrade)" -fi - -if [ "$load_initial_data" = true ]; then - echo "Loading initial data into the database" - docker exec -it iskylims_app python3 manage.py loaddata conf/first_install_tables.json +if [ "$action" = "upgrade" ]; then + echo "Running install.sh upgrade inside the container" + docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --upgrade app --git_revision \"$git_revision\" --conf \"$install_conf\" --skip_apache_restart$script_args" else - echo "Skipping initial fixture load (--action upgrade)" + echo "Running install.sh install inside the container" + docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --install app --git_revision \"$git_revision\" --conf \"$install_conf\" --skip_apache_restart$script_args" fi if [ "$skip_test_data" = false ]; then diff --git a/install.sh b/install.sh index dbbf18665..0dafb4d8f 100644 --- a/install.sh +++ b/install.sh @@ -17,7 +17,7 @@ usage : $0 --upgrade --git_revision --conf --skip_tables | Skip loading initial tables (even during install) --script | Run a migration script. --ren_app | Rename apps required for the upgrade migration to 3.0.0 - --docker | Specific installation for docker compose configuration. + --docker | Deprecated. Use --skip_apache_restart to avoid Apache checks/restart. Examples: @@ -274,11 +274,13 @@ check_requirements() { log_section "Checking main requirements" python_check log_info "Valid version of Python" - if [ $docker == false ]; then + if [[ "$operation_scope" == "full" || "$operation_scope" == "app" ]]; then db_check log_info "Successful check for database" - apache_check - log_info "Successful check for apache" + if [ "$restart_apache" = true ]; then + apache_check + log_info "Successful check for apache" + fi fi if [ "$install_type" == "full" ] || [ "$install_type" == "dep" ] || [ "$upgrade_type" == "full" ] || [ "$upgrade_type" == "dep" ]; then @@ -576,9 +578,6 @@ install_python_requirements() { # restart_apache_service: restart Apache/HTTPD unless running inside Docker or explicitly skipped. restart_apache_service() { - if [ $docker != false ]; then - return - fi linux_distribution=$(lsb_release -i | cut -f 2-) if [[ $linux_distribution == "Ubuntu" ]]; then apache_daemon="apache2" @@ -655,9 +654,7 @@ upgrade_application_files() { echo "activate the virtualenv" source virtualenv/bin/activate - if [ $docker == false ]; then - run_django_deploy "upgrade" - fi + run_django_deploy "upgrade" echo "Deleting static files..." rm -rf $INSTALL_PATH/static echo "Running collect statics..." @@ -722,9 +719,7 @@ install_application_files() { update_settings_and_urls - if [ $docker == false ]; then - run_django_deploy "install" - fi + run_django_deploy "install" echo "Run collectstatic" python manage.py collectstatic @@ -828,6 +823,7 @@ while getopts $options opt; do ;; k ) docker=true + restart_apache=false ;; a ) restart_apache=false @@ -888,7 +884,7 @@ if [[ "$operation_scope" == "full" || "$operation_scope" == "app" ]]; then else upgrade_application_files fi - if [ $docker == false ] && [ $restart_apache == true ]; then + if [ $restart_apache == true ]; then restart_apache_service fi exit 0 From 17722e75206817def4d85cb98c56bb4cf7cb983c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 7 Jan 2026 17:38:50 +0100 Subject: [PATCH 278/446] add example when using --script --- LEAME.md | 12 +++++++++++- README.md | 12 +++++++++++- 2 files changed, 22 insertions(+), 2 deletions(-) diff --git a/LEAME.md b/LEAME.md index cfff6950a..78f0ed28e 100644 --- a/LEAME.md +++ b/LEAME.md @@ -75,6 +75,13 @@ Puedes personalizar los valores por defecto: - `--demo_data /ruta/a/iskylims_demo_data.tar.gz` para reutilizar un archivo local (si no, se descarga). - `--skip_demo_data` o `--skip_test_data` para evitar cargar datos extra. - `--install_type` (`full` por defecto) y `--git_revision` para controlar el build. +- `--script` para ejecutar uno o mas scripts de migracion via `install.sh` (puedes repetir la opcion). + +Ejemplo de uso con un script de migracion en Docker: + +```bash +bash docker_install.sh --test --script migrate_optional_values +``` Cuando el script termine, abre `http://localhost:8001` y crea el superusuario de Django cuando te lo pida. @@ -107,7 +114,7 @@ Re-despliega el contenedor de aplicacion contra una base de datos existente sin bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade ``` -La actualizacion reconstruye/reinicia el contenedor, regenera migraciones, las aplica con `--fake-initial` y evita cargar superusuario/datos demo/prueba. +La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh` dentro del contenedor, que regenera migraciones, las aplica con `--fake-initial` y evita cargar superusuario/datos demo/prueba. ## Despliegue bare-metal (Ubuntu/CentOS) @@ -223,6 +230,9 @@ bash install.sh --upgrade app --script /backup_lib_pool.sql --gi # sin restauracion de library pool bash install.sh --upgrade app --git_revision main --tables + +# ejemplo ejecutando un script de migracion en la actualizacion +bash install.sh --upgrade app --script migrate_optional_values --git_revision main --tables ``` O ejecuta todo en un unico comando: diff --git a/README.md b/README.md index 3f2e6f587..aae7fb7d5 100644 --- a/README.md +++ b/README.md @@ -76,6 +76,13 @@ Defaults can be customised: - `--demo_data /path/to/iskylims_demo_data.tar.gz` to reuse a local demo archive (otherwise it is downloaded). - `--skip_demo_data` or `--skip_test_data` to avoid loading extra data. - `--install_type` (`full` by default) and `--git_revision` to control the build. +- `--script` to run one or more Django migration scripts through `install.sh` (repeat the flag as needed). + +Example running a migration script during Docker install: + +```bash +bash docker_install.sh --test --script migrate_optional_values +``` When the script finishes, open `http://localhost:8001` and follow the prompt to create the Django superuser. @@ -108,7 +115,7 @@ Re-deploy the application container against an existing production database with bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade ``` -The upgrade path rebuilds/restarts the container, regenerates migrations, applies them with `--fake-initial`, and skips superuser/demo/test data loading. +The upgrade path rebuilds/restarts the container and runs `install.sh` inside the app container, which regenerates migrations, applies them with `--fake-initial`, and skips superuser/demo/test data loading. ## Bare-metal deployment (Ubuntu/CentOS) @@ -224,6 +231,9 @@ bash install.sh --upgrade app --script /backup_lib_pool.sql --git # without library pool restore bash install.sh --upgrade app --git_revision main --tables + +# example running a migration script during upgrade +bash install.sh --upgrade app --script migrate_optional_values --git_revision main --tables ``` Or run everything in one go: From 33e28807dfa1d1a01e2ba583a050e7da29762aa7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 7 Jan 2026 18:13:48 +0100 Subject: [PATCH 279/446] fix python path --- Dockerfile | 4 ++-- docker_install.sh | 13 +++++++++++++ 2 files changed, 15 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 0e3d8ca0b..c506d2076 100644 --- a/Dockerfile +++ b/Dockerfile @@ -35,7 +35,7 @@ ARG INSTALL_CONF=conf/docker_install_settings.txt # Execute the dependency stage only; app migrations run when the container is up. RUN /bin/bash install.sh --install dep --git_revision $GIT_REVISION --conf $INSTALL_CONF --skip_apache_restart # Use the virtualenv created by install.sh -ENV PATH="/opt/relecov-platform/virtualenv/bin:${PATH}" +ENV PATH="/opt/iskylims/virtualenv/bin:${PATH}" WORKDIR /opt/iskylims @@ -43,4 +43,4 @@ WORKDIR /opt/iskylims EXPOSE 8001 # Start the application -CMD ["python", "/opt/iskylims/manage.py", "runserver", "0:8001"] +CMD ["python3", "/opt/iskylims/manage.py", "runserver", "0:8001"] diff --git a/docker_install.sh b/docker_install.sh index e64812e8b..9a52761ca 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -198,12 +198,25 @@ service_exists() { docker compose -f "$compose_file" ps --services 2>/dev/null | grep -Fxq "$1" } +ensure_app_running() { + if ! docker inspect -f '{{.State.Running}}' iskylims_app >/dev/null 2>&1; then + echo "Error: iskylims_app container does not exist." + exit 1 + fi + if [ "$(docker inspect -f '{{.State.Running}}' iskylims_app)" != "true" ]; then + echo "Error: iskylims_app container is not running. Showing logs:" + docker logs --tail 200 iskylims_app + exit 1 + fi +} + echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=$install_type and GIT_REVISION=$git_revision..." docker compose -f "$compose_file" build --no-cache --build-arg INSTALL_TYPE="$install_type" --build-arg GIT_REVISION="$git_revision" --build-arg INSTALL_CONF="$install_conf" docker compose -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." sleep 20 +ensure_app_running script_args="" if [ "$run_script" = true ]; then From 3a6090b866bfcd56594296e435350b84fbca16b1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 8 Jan 2026 12:20:13 +0100 Subject: [PATCH 280/446] add retry in case it does not exist manage.py --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index c506d2076..2ada0e511 100644 --- a/Dockerfile +++ b/Dockerfile @@ -42,5 +42,5 @@ WORKDIR /opt/iskylims # Expose EXPOSE 8001 -# Start the application -CMD ["python3", "/opt/iskylims/manage.py", "runserver", "0:8001"] +# Start the application once install.sh has populated /opt/iskylims. +CMD ["bash", "-c", "while [ ! -f /opt/iskylims/manage.py ]; do sleep 2; done; python3 /opt/iskylims/manage.py runserver 0:8001"] From 8f647314032c322aaa041f79d13d7c33aaf6fd99 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 8 Jan 2026 12:20:36 +0100 Subject: [PATCH 281/446] fix message so dep is istalled in dockerfile --- docker_install.sh | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/docker_install.sh b/docker_install.sh index 9a52761ca..387199ce3 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -70,7 +70,6 @@ done # SETTING DEFAULT VALUES demo_data=false -install_type="full" git_revision="main" compose_file="" install_conf="" @@ -88,9 +87,6 @@ while getopts $options opt; do d) demo_data=$OPTARG ;; - i) - install_type=$OPTARG - ;; g) git_revision=$OPTARG ;; @@ -210,8 +206,8 @@ ensure_app_running() { fi } -echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=$install_type and GIT_REVISION=$git_revision..." -docker compose -f "$compose_file" build --no-cache --build-arg INSTALL_TYPE="$install_type" --build-arg GIT_REVISION="$git_revision" --build-arg INSTALL_CONF="$install_conf" +echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE="dep" and GIT_REVISION=$git_revision..." +docker compose -f "$compose_file" build --no-cache --build-arg INSTALL_TYPE="dep" --build-arg GIT_REVISION="$git_revision" --build-arg INSTALL_CONF="$install_conf" docker compose -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." From 102a38eb135246a2a78d1fb0352ed8aaaaa922f4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 8 Jan 2026 12:20:58 +0100 Subject: [PATCH 282/446] add create project if it does not exit in upgrade (install.sh) --- install.sh | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/install.sh b/install.sh index 0dafb4d8f..9dc3ba1f3 100644 --- a/install.sh +++ b/install.sh @@ -646,14 +646,19 @@ upgrade_application_files() { --exclude "logs" --exclude "documents" --exclude "migrations" --exclude "__pycache__" \ README.md LICENSE test conf $REQUIRED_MODULES $INSTALL_PATH - echo "Update settings and url file." - update_settings_and_urls - prepare_documents_structure - cd $INSTALL_PATH echo "activate the virtualenv" source virtualenv/bin/activate + if [ ! -f "$INSTALL_PATH/manage.py" ]; then + echo "manage.py not found. Creating iskylims project" + django-admin startproject iskylims . + fi + + echo "Update settings and url file." + update_settings_and_urls + prepare_documents_structure + run_django_deploy "upgrade" echo "Deleting static files..." rm -rf $INSTALL_PATH/static From edcebc3cf8df528103458d7ddedc82c33186d024 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 8 Jan 2026 12:43:54 +0100 Subject: [PATCH 283/446] fix django-admin not present --- install.sh | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/install.sh b/install.sh index 9dc3ba1f3..885699c17 100644 --- a/install.sh +++ b/install.sh @@ -576,6 +576,15 @@ install_python_requirements() { cd - } +# ensure_virtualenv_ready: create the venv and install requirements if missing (useful in Docker app-only stage). +ensure_virtualenv_ready() { + if [ ! -d "$INSTALL_PATH/virtualenv" ]; then + log_warn "Virtualenv not found. Creating and installing requirements." + setup_virtualenv "install" + install_python_requirements + fi +} + # restart_apache_service: restart Apache/HTTPD unless running inside Docker or explicitly skipped. restart_apache_service() { linux_distribution=$(lsb_release -i | cut -f 2-) @@ -647,12 +656,13 @@ upgrade_application_files() { README.md LICENSE test conf $REQUIRED_MODULES $INSTALL_PATH cd $INSTALL_PATH + ensure_virtualenv_ready echo "activate the virtualenv" source virtualenv/bin/activate if [ ! -f "$INSTALL_PATH/manage.py" ]; then echo "manage.py not found. Creating iskylims project" - django-admin startproject iskylims . + "$INSTALL_PATH/virtualenv/bin/python" -m django startproject iskylims . fi echo "Update settings and url file." @@ -716,11 +726,12 @@ install_application_files() { prepare_documents_structure + ensure_virtualenv_ready echo "activate the virtualenv" source virtualenv/bin/activate echo "Creating iskylims project" - django-admin startproject iskylims . + "$INSTALL_PATH/virtualenv/bin/python" -m django startproject iskylims . update_settings_and_urls From fa3671bd7bc96e3b5d555df6d5856d5bde384453 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 8 Jan 2026 12:50:31 +0100 Subject: [PATCH 284/446] check if all is running before continuing docker install sh --- docker_install.sh | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docker_install.sh b/docker_install.sh index 387199ce3..a3abae2d6 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -229,6 +229,12 @@ else docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --install app --git_revision \"$git_revision\" --conf \"$install_conf\" --skip_apache_restart$script_args" fi +if ! docker exec -it iskylims_app test -f /opt/iskylims/manage.py; then + echo "Error: /opt/iskylims/manage.py not found after install.sh. Showing logs:" + docker logs --tail 200 iskylims_app + exit 1 +fi + if [ "$skip_test_data" = false ]; then docker exec -it iskylims_app python3 manage.py loaddata test/test_data.json else From 10766cb4da338a7332a29822ab3eebb52399b35b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 8 Jan 2026 12:57:34 +0100 Subject: [PATCH 285/446] remove vinstall in ensure venv, now just a message and exit --- install.sh | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/install.sh b/install.sh index 885699c17..08304acb7 100644 --- a/install.sh +++ b/install.sh @@ -576,12 +576,11 @@ install_python_requirements() { cd - } -# ensure_virtualenv_ready: create the venv and install requirements if missing (useful in Docker app-only stage). ensure_virtualenv_ready() { if [ ! -d "$INSTALL_PATH/virtualenv" ]; then - log_warn "Virtualenv not found. Creating and installing requirements." - setup_virtualenv "install" - install_python_requirements + log_warn "Virtualenv missing. INSTALL_PATH=$INSTALL_PATH" + ls -la "$INSTALL_PATH" || true + abort_install "Virtualenv not found at $INSTALL_PATH/virtualenv. Run --install dep first." fi } From 14289a31a540368ada4c99d0c4b09459edd0235f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 8 Jan 2026 16:39:37 +0100 Subject: [PATCH 286/446] copy conf inside container --- docker_install.sh | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docker_install.sh b/docker_install.sh index a3abae2d6..f700f3832 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -190,6 +190,14 @@ if [ ! -f "$install_conf" ]; then exit 1 fi +repo_root="$(pwd)" +if [[ "$install_conf" = /* ]] && [[ "$install_conf" != "$repo_root/"* ]]; then + install_conf_copy="conf/docker_runtime_settings.txt" + echo "Copying $install_conf into repository as $install_conf_copy for Docker build/runtime." + cp "$install_conf" "$install_conf_copy" + install_conf="$install_conf_copy" +fi + service_exists() { docker compose -f "$compose_file" ps --services 2>/dev/null | grep -Fxq "$1" } From 1df0b04d72d93f794c43ce81b351aeecd9c491eb Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Tue, 27 Jan 2026 15:26:45 +0100 Subject: [PATCH 287/446] Fixed typo on SequencingPlatform model in Sequencer --- core/models.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/core/models.py b/core/models.py index 7009a3c47..8de191762 100644 --- a/core/models.py +++ b/core/models.py @@ -1791,7 +1791,7 @@ def create_sequencer_in_lab(self, sequencer_value): platform_obj = SequencingPlatform.objects.get( pk__exact=sequencer_value["platformID"] ) - except models.SequencingPlatform.DoesNotExist: + except SequencingPlatform.DoesNotExist: platform_obj = None new_sequencer = self.create( platform_id=platform_obj, From b52f4250c027b8dbd4ab0755952ebe7d0562e856 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Tue, 27 Jan 2026 15:36:17 +0100 Subject: [PATCH 288/446] Added new completion tags and successes for miseq xmls --- wetlab/config.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wetlab/config.py b/wetlab/config.py index a5cafc129..90bed528b 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -77,8 +77,8 @@ ] # ########### VALUE TAG FOR XML FILES ######################### -COMPLETION_TAG = "CompletionStatus" -COMPLETION_SUCCESS = ["CompletedAsPlanned", "SuccessfullyCompleted"] +COMPLETION_TAG = ["CompletionStatus", "RunStatus"] +COMPLETION_SUCCESS = ["CompletedAsPlanned", "SuccessfullyCompleted", "RunCompleted"] EXPERIMENT_NAME_TAG = "ExperimentName" APPLICATION_NAME_TAG = "ApplicationName" NUMBER_CYCLES_TAG = "NumCycles" From aa4440b085cf8f06ceaaf2c0bb23717bb1b2eaf9 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Tue, 27 Jan 2026 15:45:07 +0100 Subject: [PATCH 289/446] Added MiSeq support --- wetlab/utils/crontab_process.py | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index dfdb6390a..f5d5d11a3 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -299,9 +299,12 @@ def check_sequencer_status_from_completion_file(l_run_completion, experiment_nam experiment_name, ) # check if NextSEq run have been successful completed - status_run = wetlab.utils.common.find_xml_tag_text( - l_run_completion, wetlab.config.COMPLETION_TAG - ) + for xml_tag in wetlab.config.COMPLETION_TAG: + status_run = wetlab.utils.common.find_xml_tag_text( + l_run_completion, xml_tag + ) + if status_run != "NOT FOUND": + break if status_run not in wetlab.config.COMPLETION_SUCCESS: logger.info( "%s : Run in sequencer was not completed but %s", @@ -445,7 +448,7 @@ def check_sequencer_run_is_completed( "%s : End function check_sequencer_run_is_completed with exception", experiment_name, ) - return "cancelled", "" + return "cancelled", None elif way_to_check == "txt_file": # l_run_completion = os.path.join(RUN_TEMP_DIRECTORY, RUN_COMPLETION_TXT_FILE) s_run_completion = os.path.join( @@ -1119,6 +1122,8 @@ def parsing_run_info_and_parameter_information( wetlab.utils.common.logging_warnings(string_message, False) # get date for miSeq and NextSeq with the format yymmdd date = p_run.find("Date").text + # Remove timestamp + date = date.split("T")[0] try: run_date = datetime.datetime.strptime(date, "%y%m%d") except Exception: From 5194a70f313ca39768cd83c0cc734d05b5d1d24d Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Tue, 27 Jan 2026 15:48:23 +0100 Subject: [PATCH 290/446] Samplesheet v2 support for run creation --- wetlab/utils/samplesheet.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index 3af12cc5c..a6b575514 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -379,7 +379,7 @@ def get_projects_in_run(in_file: str) -> dict: if line == "": continue if not header_found: - header = re.search("^Sample_ID,Sample_Name", line) + header = re.search("^Sample_ID,Sample_Name,.+,Description.?", line) if header: # match line with the header # look for projects and description indexes @@ -391,6 +391,9 @@ def get_projects_in_run(in_file: str) -> dict: header_found = True continue else: + if line.startswith("["): + # Jumped to next section - break search + break # ignore the empty lines separated by commas valid_line = re.search(r"^\w+", line) if not valid_line: From d8e80ca36a1706010ebdd7f5353b2ff2d947fe31 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Tue, 27 Jan 2026 16:28:32 +0100 Subject: [PATCH 291/446] Fixing header finding --- wetlab/utils/samplesheet.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index a6b575514..72f040f3e 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -333,7 +333,7 @@ def get_sample_with_user_owner(sample_sheet_path): line = line.rstrip() if line == "": continue - found_header = re.search("^Sample_ID,Sample_Name", line) + found_header = re.search("^Sample_ID,Sample_Name,.*Description.*$", line) if found_header: header_found = True sample_sheet_heading = line.split(",") @@ -379,7 +379,7 @@ def get_projects_in_run(in_file: str) -> dict: if line == "": continue if not header_found: - header = re.search("^Sample_ID,Sample_Name,.+,Description.?", line) + header = re.search("^Sample_ID,Sample_Name,.*Description.*$", line) if header: # match line with the header # look for projects and description indexes From 382fa757b5e5251629d23a9721239ea0b9571a22 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Wed, 4 Feb 2026 12:34:08 +0100 Subject: [PATCH 292/446] Added samplesheet-related constants --- wetlab/config.py | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/wetlab/config.py b/wetlab/config.py index 90bed528b..3bf4925e1 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -337,6 +337,18 @@ # Sections to check in the IEM file created by user SECTIONS_IN_IEM_SAMPLE_SHEET = ["[Header]", "[Reads]", "[Settings]", "[Data]"] +# Tabular data sections in samplesheets. For future references: Insert in order. +TABULAR_DATA_SECTIONS_SAMPLE_SHEET = [ + "Data", + "CustomCustomer_Data", + "BCLConvert_Data" +] + +SETTINGS_SECTIONS_SAMPLE_SHEET = [ + "Settings", + "BCLConvert_Settings" +] + FIELDS_IN_SAMPLE_SHEET_HEADER_IEM_VERSION_5 = [ "Date", "Experiment Name", @@ -349,6 +361,17 @@ "Description", ] +ADAPTER_1_FIELD_NAMES = [ + "Adapter", + "AdapterRead1" +] + +ADAPTER_2_FIELD_NAMES = [ + "Adapter", + "AdapterRead2" +] + + # #### HEADINGS VALUES # # Heading for pending Library Preparation state @@ -686,6 +709,9 @@ ERROR_SAMPLE_SHEET_USER_ARE_NOT_DEFINED = ( "Sample sheet has users which are not defined : " ) +ERROR_SAMPLE_SHEET_HAS_INVALID_LINES = ( + "Sample sheet has an invalid (Non-empty, non-comma-delimited) line: " +) ERROR_USER_SAMPLE_SHEET_NO_LONGER_EXISTS = [ "The Sample Sheet that you are uploaded does not longer exists", "Upload again the sample sheet", From 5206b303ce9a7f636d6ce143655e02833b4cbfea Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Wed, 4 Feb 2026 12:35:05 +0100 Subject: [PATCH 293/446] Deleted non-existing constant --- wetlab/utils/crontab_update_run.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index c2b797528..34ab433a6 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -585,8 +585,8 @@ def manage_run_in_recorded_state(conn, run_process_objs): ) if ( - wetlab.config.COPY_SAMPLE_SHEET_TO_REMOTE - and "NextSeq" in run_process_obj.get_run_platform() + #wetlab.config.COPY_SAMPLE_SHEET_TO_REMOTE + "NextSeq" in run_process_obj.get_run_platform() ): sample_sheet_path = run_process_obj.get_sample_file() From cb21e6660ea6c5d082baedfe068e090f06e7d242 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Wed, 4 Feb 2026 12:35:19 +0100 Subject: [PATCH 294/446] Deleted non-existing constant --- wetlab/utils/crontab_update_run.py | 1 - 1 file changed, 1 deletion(-) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 34ab433a6..c3c2adbf3 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -585,7 +585,6 @@ def manage_run_in_recorded_state(conn, run_process_objs): ) if ( - #wetlab.config.COPY_SAMPLE_SHEET_TO_REMOTE "NextSeq" in run_process_obj.get_run_platform() ): sample_sheet_path = run_process_obj.get_sample_file() From c379f03238622322311b2276e2787c514efd19ae Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Wed, 4 Feb 2026 12:36:49 +0100 Subject: [PATCH 295/446] Corrected summary value names --- wetlab/utils/library.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/wetlab/utils/library.py b/wetlab/utils/library.py index 564eea185..4a0ed9d81 100644 --- a/wetlab/utils/library.py +++ b/wetlab/utils/library.py @@ -859,19 +859,19 @@ def format_sample_sheet_to_display_in_form(sample_sheet_data): display_data["adapter2"] = True display_data["sample_data"] = sample_sheet_data["sample_data"] - display_data["heading"] = sample_sheet_data["heading"] + display_data["headers"] = sample_sheet_data["headers"] main_values = [] for item in extract_values: main_values.append(sample_sheet_data[item]) summary_values = [] summary_values.append(len(sample_sheet_data["samples"])) - summary_values.append(sample_sheet_data["proyects"]) + summary_values.append(sample_sheet_data["projects"]) summary_values.append(sample_sheet_data["userid_names"]) display_data["main_data"] = list(zip(main_data_heading, main_values)) display_data["summary_data"] = list( zip(wetlab.config.HEADING_SUMMARY_DATA_SAMPLE_SHEET, summary_values) ) - display_data["heading_excel"] = ",".join(sample_sheet_data["heading"]) + display_data["headers_excel"] = ",".join(sample_sheet_data["headers"]) # if len(sample_sheet_data['userid_names']) == 0: # display_data['no_user_defined'] = True From 3b2b974704435d2a6758097aa9318164b4dd864b Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Thu, 5 Feb 2026 08:57:26 +0100 Subject: [PATCH 296/446] ensured samplesheet is read with new function, fixed header search --- wetlab/config.py | 3 +- wetlab/utils/crontab_update_run.py | 2 +- wetlab/utils/samplesheet.py | 486 ++++++++++++----------------- 3 files changed, 202 insertions(+), 289 deletions(-) diff --git a/wetlab/config.py b/wetlab/config.py index 3bf4925e1..faa0e32d2 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -335,7 +335,8 @@ ] # Sections to check in the IEM file created by user -SECTIONS_IN_IEM_SAMPLE_SHEET = ["[Header]", "[Reads]", "[Settings]", "[Data]"] +SECTIONS_IN_IEM_SAMPLE_SHEET = ["Header", "Reads", "Settings", "Data"] +SECTIONS_IN_V2_SAMPLE_SHEET = ["Header", "Reads", "BCLConvert_Settings", "BCLConvert_Data", "CustomCustomer_Data"] # Tabular data sections in samplesheets. For future references: Insert in order. TABULAR_DATA_SECTIONS_SAMPLE_SHEET = [ diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index c3c2adbf3..05e4a627f 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -330,7 +330,7 @@ def search_update_new_runs(request_reason): == "TRUE" ): user_id_list = wetlab.utils.common.get_userid_list() - file_read = wetlab.utils.samplesheet.read_user_iem_file( + file_read = wetlab.utils.samplesheet.read_file_from_path( l_sample_sheet_path ) users = wetlab.utils.samplesheet.validate_userid_in_user_iem_file( diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index 72f040f3e..b5541dc23 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -14,6 +14,60 @@ # import wetlab.models +def read_file_from_path(file_path: str) -> str: + """ + Read file from path, ensuring characters are not lost due to encoding + + :param file_path: Description + :type file_path: str + """ + try: + with open(file_path, "r", encoding="utf-8") as f: + read_file = f.read() + except Exception: + return False + return read_file + + +def file_read_to_dictionary(file_read: str) -> dict[str, dict[str, any] | list[list[str]]]: + """ + Description: + This function transforms a SampleSheet from string to dictionary, + loading the headers as keys. If data is fully tabular (e.g. [Data]), + load rows as list of list; if not, nested dict. + Input: + file_read # content of the IEM file from user + Constant: + ERROR_SAMPLE_SHEET_HAS_INVALID_LINES + Return + ERROR if any line was not in the proper format (tabular, comma-delimited) + samplesheet as a dictionary + """ + samplesheet = {} + file_read = file_read.splitlines() + for line in file_read: + if line.startswith("["): + section = line.split(',')[0].lstrip("[").rstrip("]") + samplesheet[section] = {} + continue + if not line or re.match("^,+$", line): + # Empty/Filler/Artifact lines with no info + continue + if section in wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET: + # Data is tabular; append as list of lists until next header + if not isinstance(samplesheet[section], list): + samplesheet[section] = [] + samplesheet[section].append(line) + else: + # Data is processed as key: value before adding it to dictionary + line = line.split(",") + try: + # Sometimes there are empty lines (e.g. READS values) + samplesheet[section][line[0].strip()] = line[1].strip() if len(line) > 1 else "" + except IndexError: + return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_HAS_INVALID_LINES} + return samplesheet + def validate_userid_in_user_iem_file(file_read, user_id_list): """ @@ -29,37 +83,20 @@ def validate_userid_in_user_iem_file(file_read, user_id_list): userids with the ids found """ users = {} - lines = file_read.split("\n") - data_section_found = False - description_index = False - userid_names, invalid_names = [], [] - for line in lines: - line = line.rstrip() - if line == "": - continue - if "[Data]" in line: - data_section_found = True - continue - if data_section_found: - line = line.split(",") - if not description_index: - try: - description_index = line.index("Description") - continue - except Exception: - users["ERROR"] = ( + samplesheet = file_read_to_dictionary(file_read) + if "ERROR" in samplesheet: + return samplesheet + + data = get_tabular_data(samplesheet, header_includes="Description") + if not data: + users["ERROR"] = ( wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_DESCRIPTION_FIELD ) - return users - else: - try: - u_name = line[description_index] - except Exception: - continue - if u_name in user_id_list: - userid_names.append(u_name) - else: - invalid_names.append(u_name) + return users + users_in_sample_sheet = get_column_from_tabular_data(data, "Description") + + userid_names = [user for user in users_in_sample_sheet if user in user_id_list] + invalid_names = [user for user in users_in_sample_sheet if user not in user_id_list] if len(invalid_names) > 0: invalid_names = list(set(invalid_names)) @@ -68,6 +105,7 @@ def validate_userid_in_user_iem_file(file_read, user_id_list): ) users["ERROR"] = invalid_names return users + users["user_ids"] = list(set(userid_names)) return users @@ -90,31 +128,43 @@ def delete_stored_file(input_file): return False -def get_adapters(file_lines): - adapter1 = "" - adapter2 = "" - # For accepting characters like spanish characters. - for line in file_lines: - if line == "": +def get_adapters(samplesheet: dict) -> tuple[str, str]: + """ + Get the adapters from the samplesheet (v1 | v2) + + Parameters + ---------- + samplesheet : dict + User sample sheet read as a dictionary + + Return + ------ + adapters : tuple + tuple containing the values in order for adapter 1 and 2 + """ + for settings_name in wetlab.config.SETTINGS_SECTIONS_SAMPLE_SHEET: + settings = samplesheet.get(settings_name) + if not settings: continue - found_adapter = re.search("^Adapter", line) - if found_adapter: - adapter_code = line.split(",")[1] - if adapter1 == "": - adapter1 = adapter_code + for i in range(len(wetlab.config.ADAPTER_1_FIELD_NAMES)): + try: + adapter1 = samplesheet[wetlab.config.ADAPTER_1_FIELD_NAMES[i]] + adapter2 = samplesheet[wetlab.config.ADAPTER_2_FIELD_NAMES[i]] + except ValueError: continue - else: - adapter2 = adapter_code - break - data_found = re.search(r"^\[Data]", line) - if data_found: break + else: + continue + break + else: + return "", "" return adapter1, adapter2 -def get_heading(file_lines): - """read the input variable and extract the heading row +def get_row_from_tabular_data(tabular_data: list[list], index) -> list: + """ + Get the data headers Parameters ---------- @@ -126,39 +176,41 @@ def get_heading(file_lines): heading : list contain the values from heading row of file """ - - # For accepting characters like spanish characters. - heading = [] - for line in file_lines: - line = line.strip() - if line == "": - continue - found_header = re.search("^Sample_ID,Sample_Name", line) - if found_header: - heading = line.split(",") - break - return heading + try: + return tabular_data[index] + except IndexError: + return [] -def get_index_adapter(file_lines): +def get_column_from_tabular_data(tabular_data: list[list], column_name: str, unique: bool=False) -> list: """ - Description : - get the indexes adapter information from the file_lines - Input: - file_lines # sample sheet file converted to list of lines - Return: - index_adapters . List of the reads + Docstring for get_all_values_from_tabular_data + + :param tabular_data: Description + :type tabular_data: dict[list[list[str]]] """ - index_adapters = "" - for line in file_lines: - if "Index Adapters" in line: - index_adapters = line.split(",")[1].replace('"', "") - break - # remove the \n or \r - return index_adapters.rstrip() + headers = tabular_data[0] + tabular_data = [row for row in tabular_data[1:]] + try: + column_index = headers.index(column_name) + except ValueError: + return [] + values = [row[column_index] for row in tabular_data] + return list(set(values)) if unique else values -def get_projects_in_sample_sheet(file_lines): +def get_tabular_data(samplesheet: dict, header_includes="") -> list[list]: + for data_section in wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET: + data = samplesheet.get(data_section, []) + if not data: + continue + if header_includes and header_includes not in data[0]: + continue + break + return [row.split(',') for row in data] + + +def get_projects_in_sample_sheet(samplesheet) -> list: """ Description : get the project names defined from the file_lines @@ -167,50 +219,32 @@ def get_projects_in_sample_sheet(file_lines): Return: project_name_list """ - header_found = False - project_list = [] - for line in file_lines: - line = line.rstrip() - if line == "": - continue - found_header = re.search("^Sample_ID,Sample_Name", line) - if found_header: - header_found = True - heading = line.split(",") - index_project_name = heading.index("Sample_Project") - continue - if header_found: - try: - project_list.append(line.split(",")[index_project_name]) - except Exception: - continue - project_name_list = list(set(project_list)) - return project_name_list - + data = get_tabular_data(samplesheet) + projects = get_column_from_tabular_data(data, 'Sample_Project', unique=True) + return projects -def get_reads(file_lines): +def get_reads(samplesheet: dict) -> list[str, str]: """ Description : - get the reads information from the file_lines + get the reads information from the samplesheet Input: - file_lines # sample sheet file converted to list of lines + samplesheet # samplesheet file converted to dictionary Return: reads . List of the reads """ - read_found = False + reads_section = samplesheet.get("Reads") reads = [] - for line in file_lines: - if "[Reads]" in line: - read_found = True - continue - if "[Settings]" in line: + for key, value in reads_section.items(): + if not value: + # Sample sheets format for read is inconsistent - V1 accepts different format for read lengths + reads = list(reads_section.keys()) break - if read_found and re.search(r"^\w+", line): - reads.append(line.split(",")[0]) + if "Read" in key: + reads.append(value) return reads -def get_samples_in_sample_sheet(file_lines): +def get_samples_in_sample_sheet(samplesheet: dict) -> dict: """ Description : get the sample information from the file_lines @@ -221,35 +255,17 @@ def get_samples_in_sample_sheet(file_lines): is a list for each sample row """ samples_dict = {} - samples_dict["samples"] = [] - samples_dict["sample_data"] = [] - header_found = False - for line in file_lines: - line = line.rstrip() - if line == "": - continue - found_header = re.search("^Sample_ID,Sample_Name", line) - if found_header: - header_found = True - samples_dict["heading"] = line.split(",") - index_sample_name = samples_dict["heading"].index("Sample_Name") - continue - # found the index for projects - if header_found: - line_split = line.split(",") - try: - sample_name = line_split[index_sample_name].strip() - except Exception: - continue - if sample_name == "": - continue - data = [] - for item in line_split: - data.append(item.strip()) - samples_dict["sample_data"].append(data) - samples_dict["samples"].append(sample_name) + data = get_tabular_data(samplesheet) + + samples_dict["header"] = data[0] if len(data) > 1 else "" + samples_dict["samples"] = get_column_from_tabular_data(data, "Sample_Name") + samples_dict["sample_data"] = [get_row_from_tabular_data(data, i) for i in range(1, len(data))] return samples_dict +def get_headers(samplesheet: dict) -> list: + data = get_tabular_data(samplesheet) + return data[0].split(',') + def get_sample_sheet_data(file_read): """ @@ -269,49 +285,25 @@ def get_sample_sheet_data(file_read): sample_sheet_data dictionary with the extracted information """ sample_sheet_data = {} - # initialize data with empty values + samplesheet = file_read_to_dictionary(file_read) + # initialize header data for item in wetlab.config.FIELDS_IN_SAMPLE_SHEET_HEADER_IEM_VERSION_5: - sample_sheet_data[item.lower()] = "" + sample_sheet_data[item.lower()] = samplesheet['Header'].get(item, "") - file_lines = file_read.split("\n") - for line in file_lines: - if "iemfileversion" in line.lower(): - sample_sheet_data["iem_version"] = line.split(",")[1] - break - # get assay information - for line in file_lines: - if "Assay" in line: - sample_sheet_data["assay"] = line.split(",")[1] - break - # get index adapters information - # for line in file_lines : - # if 'Index Adapters' in line : - # sample_sheet_data['index_adapters'] = line.split(',')[1] - # break - # get application information - for line in file_lines: - if "Application" in line: - sample_sheet_data["application"] = line.split(",")[1] - break - # get Instrument information - for line in file_lines: - if "Instrument Type" in line: - sample_sheet_data["instrument type"] = line.split(",")[1] - break # get adapters information sample_sheet_data["adapter1"], sample_sheet_data["adapter2"] = get_adapters( - file_lines + samplesheet ) # get indexes adapters information - sample_sheet_data["index_adapters"] = get_index_adapter(file_lines) + sample_sheet_data["index_adapters"] = samplesheet.get('Headers', {}).get('Index Adapters', "") # get reads information - sample_sheet_data["reads"] = get_reads(file_lines) + sample_sheet_data["reads"] = get_reads(samplesheet) # get proyects in sheet_data - sample_sheet_data["proyects"] = get_projects_in_sample_sheet(file_lines) + sample_sheet_data["projects"] = get_projects_in_sample_sheet(samplesheet) # update sample sheet data - sample_sheet_data.update(get_samples_in_sample_sheet(file_lines)) + sample_sheet_data.update(get_samples_in_sample_sheet(samplesheet)) # include heading - sample_sheet_data["heading"] = get_heading(file_lines) + sample_sheet_data["header"] = get_headers(samplesheet) return sample_sheet_data @@ -326,43 +318,20 @@ def get_sample_with_user_owner(sample_sheet_path): sample_user dictionary with the extracted information """ sample_user = {} - header_found = False full_path = os.path.join(settings.MEDIA_ROOT, sample_sheet_path) - fh = open(full_path, "r") - for line in fh: - line = line.rstrip() - if line == "": - continue - found_header = re.search("^Sample_ID,Sample_Name,.*Description.*$", line) - if found_header: - header_found = True - sample_sheet_heading = line.split(",") - index_sample_name = sample_sheet_heading.index("Sample_Name") - try: - index_description = sample_sheet_heading.index("Description") - except Exception: - index_description = None - continue - if header_found: - line_split = line.split(",") - try: - sample_name = line_split[index_sample_name].strip() - if index_description is not None: - user_id = line_split[index_description].strip() - else: - user_id = None - except Exception: - continue - if sample_name == "": - continue - - sample_user[sample_name] = user_id - fh.close() + file_read = read_file_from_path(full_path) + samplesheet = file_read_to_dictionary(file_read) + # Retrieve tabular data with "Description" in the header + data = get_tabular_data(samplesheet, header_includes="Description") + sample_names = get_column_from_tabular_data(data, "Sample_Name") + user_ids = get_column_from_tabular_data(data, "Description") + + sample_user = {sample_names[i]: user_ids[i] for i in range(len(sample_names))} return sample_user def get_projects_in_run(in_file: str) -> dict: - """Funtion to check if the sample sheet has a valid heading. On valid file + """Funtion to check if the sample sheet has a valid header. On valid file get project names and the user names from description column Args: @@ -371,37 +340,14 @@ def get_projects_in_run(in_file: str) -> dict: Returns: dict: dictionary with the projects or error message """ - header_found = False - projects = {} - with open(in_file, "r") as fh: - for line in fh: - line = line.rstrip() - if line == "": - continue - if not header_found: - header = re.search("^Sample_ID,Sample_Name,.*Description.*$", line) - if header: - # match line with the header - # look for projects and description indexes - if not "Sample_Project" and "Description" not in line: - break - split_line = line.split(",") - p_index = split_line.index("Sample_Project") - description_index = split_line.index("Description") - header_found = True - continue - else: - if line.startswith("["): - # Jumped to next section - break search - break - # ignore the empty lines separated by commas - valid_line = re.search(r"^\w+", line) - if not valid_line: - continue - # store the project name and the user name (Description) inside projects dict - projects[line.split(",")[p_index]] = line.split(",")[description_index] - - if not header_found: + file_read = read_file_from_path(in_file) + samplesheet = file_read_to_dictionary(file_read) + data = get_tabular_data(samplesheet, header_includes="Description") + sample_projects = get_column_from_tabular_data(data, "Sample_Project") + user_ids = get_column_from_tabular_data(data, "Description") + projects = {sample_projects[i]: user_ids[i] for i in range(len(sample_projects))} + + if not data: return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_HAS_INVALID_HEADING} if not projects: return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_PROJECTS} @@ -420,25 +366,12 @@ def get_index_library_name(in_file): Output: library_value """ - library_value = "" - # For accepting characters like spanish characters. - import codecs - fh = codecs.open(in_file, "r", "utf-8") - for line in fh: - line = line.rstrip() - if line == "": - continue - found_assay = re.search("^Assay", line) - if found_assay: - library_value = line.split(",")[1] - continue - found_adapters = re.search("^Index Adapters", line) - if found_adapters: - library_value = line.split(",")[1] - break + file_read = read_file_from_path(in_file) + samplesheet = file_read_to_dictionary(file_read) + header_values = samplesheet['Header'] + library_value = header_values.get("Assay", "") or header_values.get("Index Adapters", "") - fh.close() return library_value @@ -667,24 +600,6 @@ def read_all_lines_in_sample_sheet(sample_sheet): return read_lines -def read_user_iem_file(in_file): - """ - Description: - The function reads the input file and return the content in a variable - - Return: - file_read - """ - fh = codecs.open(in_file, "r", "utf-8") - try: - file_read = fh.read() - fh.close() - return file_read - except Exception: - fh.close() - return False - - def valid_user_iem_file(file_read): """ Description: @@ -701,33 +616,30 @@ def valid_user_iem_file(file_read): Return False if file cannot be read or do not have all information """ - for section in wetlab.config.SECTIONS_IN_IEM_SAMPLE_SHEET: - if section not in file_read: + samplesheet = file_read_to_dictionary(file_read) + for section_name in samplesheet.keys(): + if ( + section_name not in wetlab.config.SECTIONS_IN_IEM_SAMPLE_SHEET + and + section_name not in wetlab.config.SECTIONS_IN_V2_SAMPLE_SHEET + ): return False - lines = file_read.split("\n") - data_section_found = False data_field_length = "" sample_number = 0 - for line in lines: - line = line.rstrip() - if line == "": - continue - if "[Data]" in line: - data_section_found = True - continue - if data_section_found: - if data_field_length == "": - data_field_length = len(line.split(",")) - continue - line_split = line.split(",") - # Allow at this step the Description field can be empth - if ( - len(line_split) < data_field_length - 1 - or len(line_split) > data_field_length - ): - return False - sample_number += 1 + data = get_tabular_data(samplesheet, header_includes="Description") + + # Check on data + if not data: + return False + + # Checks on data contents + data_field_length = len(data[0]) + sample_number = len(data) - 1 + if not all([len(row) - data_field_length for row in data]): + # All rows contain the same either the same + return False + if sample_number == 0: return False return True From d030570d9adbb6c35a83890c84fd130579b936e8 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Thu, 5 Feb 2026 09:18:47 +0100 Subject: [PATCH 297/446] Function get_samples_in_sample_sheet now correctly parametrized --- wetlab/utils/run.py | 14 +++++++++----- wetlab/views.py | 9 ++++++--- 2 files changed, 15 insertions(+), 8 deletions(-) diff --git a/wetlab/utils/run.py b/wetlab/utils/run.py index 80f539d62..dd0bb7be6 100644 --- a/wetlab/utils/run.py +++ b/wetlab/utils/run.py @@ -34,11 +34,15 @@ def check_run_already_defined_by_crontab(exp_name, pool_ids): # experiment name already exists, check if samples are the same # to confirm the match run_obj = wetlab.models.RunProcess.objects.filter(run_name__iexact=exp_name).last() - sample_sheet = run_obj.get_sample_file() - f_name = os.path.join(settings.MEDIA_ROOT, sample_sheet) + sample_sheet_path = run_obj.get_sample_file() + f_name = os.path.join(settings.MEDIA_ROOT, sample_sheet_path) try: - with open(f_name, "r") as fh: - file_data = fh.readlines() + file_data = wetlab.utils.samplesheet.read_file_from_path( + f_name + ) + samplesheet = wetlab.utils.samplesheet.file_read_to_dictionary( + file_data + ) except FileNotFoundError: error_message = str( wetlab.config.ERROR_RUN_NAME_BY_CRONTAB_ALREADY_CREATED @@ -46,7 +50,7 @@ def check_run_already_defined_by_crontab(exp_name, pool_ids): + wetlab.config.ERROR_SAMPLE_SHEET_NOT_FOUND_WHEN_CREATED_BY_CRONTAB ) return {"ERROR": error_message} - sample_in_s_sheet = wetlab.utils.samplesheet.get_samples_in_sample_sheet(file_data) + sample_in_s_sheet = wetlab.utils.samplesheet.get_samples_in_sample_sheet(samplesheet) sample_in_pools = wetlab.utils.pool.get_sample_name_in_pools(pool_ids) if len(sample_in_pools) != len(sample_in_s_sheet["samples"]): return {"ERROR": wetlab.config.ERROR_EXISTING_RUN_WITH_DIF_SAMPLES_AS_IN_CRON} diff --git a/wetlab/views.py b/wetlab/views.py index c50836d46..01d32e638 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -592,11 +592,14 @@ def create_nextseq_run(request): update_info_proj.save() results.append(["runname", experiment_name]) run_p.set_run_state("recorded") - sample_sheet_lines = wetlab.utils.samplesheet.read_all_lines_in_sample_sheet( + file_read = wetlab.utils.samplesheet.read_file_from_path( in_file ) + samplesheet = wetlab.utils.samplesheet.file_read_to_dictionary( + file_read + ) sample_names_and_data = wetlab.utils.samplesheet.get_samples_in_sample_sheet( - sample_sheet_lines + samplesheet ) wetlab.utils.run.increase_reuse_if_samples_exists( sample_names_and_data["samples"] @@ -3079,7 +3082,7 @@ def manage_library_preparation(request): data["full_path_file"], data["file_name"], ) = wetlab.utils.samplesheet.store_user_input_file(request.FILES["uploadfile"]) - file_read = wetlab.utils.samplesheet.read_user_iem_file(data["full_path_file"]) + file_read = wetlab.utils.samplesheet.read_file_from_path(data["full_path_file"]) if not wetlab.utils.samplesheet.valid_user_iem_file(file_read): # Error found when extracting data from sample sheet data["ERROR"] = wetlab.config.ERROR_INVALID_FILE_FORMAT From db8dc76b312fcb0309c2cfebbb02093449e9ec5f Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Thu, 5 Feb 2026 09:19:25 +0100 Subject: [PATCH 298/446] Deleted extra function read_all_lines_in_sample_sheet --- wetlab/utils/samplesheet.py | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index b5541dc23..af0b7418e 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -583,23 +583,6 @@ def store_user_input_file(user_input_file): return stored_path_file, file_name -def read_all_lines_in_sample_sheet(sample_sheet): - """ - Description: - The function reads the input file and return the content in a variable - Input: - sample_sheet # location of sample sheet - Return: - read_lines - """ - read_lines = [] - if os.path.exists(sample_sheet): - fh = open(sample_sheet, "r") - read_lines = fh.readlines() - fh.close() - return read_lines - - def valid_user_iem_file(file_read): """ Description: From 8e959ce665f457f96306525078fd3636cbc1a8df Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Thu, 5 Feb 2026 10:36:30 +0100 Subject: [PATCH 299/446] refactor set_user_names_in_sample_sheet --- wetlab/utils/samplesheet.py | 77 ++++++++++++++++++++----------------- 1 file changed, 42 insertions(+), 35 deletions(-) diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index af0b7418e..a867223a4 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -28,6 +28,35 @@ def read_file_from_path(file_path: str) -> str: return False return read_file +def write_samplesheet_to_path(samplesheet: dict, path: str) -> bool: + """ + Write the samplesheet to a path. + + Args: + samplesheet (dict): Sample sheet (As a dictionary) + path (str): Path to write the file to + + Returns: + bool: True if no issue, False if any exception is raised + """ + + string_to_write = "" + for key, value in samplesheet.items(): + string_to_write += f"[{key}]\n" + if key in wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET: + string_to_write += f"{'\n'.join([','.join(row) for row in value])}\n" + else: + for row_header, element in value.items(): + string_to_write += f"{row_header},{element}\n" + try: + with open(path, "w") as f: + f.write(string_to_write) + return True + except Exception: + return False + + + def file_read_to_dictionary(file_read: str) -> dict[str, dict[str, any] | list[list[str]]]: """ @@ -63,7 +92,7 @@ def file_read_to_dictionary(file_read: str) -> dict[str, dict[str, any] | list[l line = line.split(",") try: # Sometimes there are empty lines (e.g. READS values) - samplesheet[section][line[0].strip()] = line[1].strip() if len(line) > 1 else "" + samplesheet[section][line[0].strip()] = ",".join(line[1:]).strip() if len(line) > 1 else "" except IndexError: return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_HAS_INVALID_LINES} return samplesheet @@ -512,39 +541,17 @@ def set_user_names_in_sample_sheet(in_file, user_names): temp_sample_sheet # temporary sample sheet to store the information it will replace the in_file Return: - True + Bool: True if successful writing, False otherwise """ - found_sample_line = False - temp_sample_sheet = os.path.join(settings.MEDIA_ROOT, "wetlab", "tmp_file") - fh = open(in_file, "r") - fh_out_file = open(temp_sample_sheet, "w") - for line in fh: - if "Sample_ID" in line: - found_sample_line = True - line = line.rstrip() - project_index = line.split(",").index("Sample_Project") - description_index = line.split(",").index("Description") - fh_out_file.write(str(line + "\n")) - continue - if found_sample_line: - # discard the empty lines or the lines that contains empty lines separated by comma - if line == "\n" or re.search(r"^\W", line): - continue - - data_line = line.split(",") - project_name = data_line[project_index] - data_line[description_index] = user_names[project_name] - - new_line = ",".join(data_line) - fh_out_file.write(str(new_line + "\n")) - - else: - fh_out_file.write(line) - fh.close() - fh_out_file.close() - os.rename(temp_sample_sheet, in_file) - return True - + file_read = read_file_from_path(in_file) + samplesheet = file_read_to_dictionary(file_read) + data = get_tabular_data(samplesheet, header_includes="Description") + projects = get_column_from_tabular_data("Sample_Project") + descriptions_index = data[0].index("Description") + for i in range(1, len(data)): + data[i][descriptions_index] = user_names[projects[i -1]] + success_writing = write_samplesheet_to_path(samplesheet, in_file) + return success_writing def store_user_input_file(user_input_file): """ @@ -558,7 +565,7 @@ def store_user_input_file(user_input_file): Return stored_path_file contains the full path of the file and file_name """ - # create thd directory if not exists + # create the directory if not exists template_dir = os.path.join( settings.MEDIA_ROOT, wetlab.config.LIBRARY_PREPARATION_SAMPLE_SHEET_DIRECTORY ) @@ -583,7 +590,7 @@ def store_user_input_file(user_input_file): return stored_path_file, file_name -def valid_user_iem_file(file_read): +def valid_user_iem_file(file_read: str) -> bool: """ Description: The function check if the user IEM file has a valid format by checking the headings and From 0091398e7396b1cc40236fff7a024e994beb915e Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Thu, 5 Feb 2026 15:00:04 +0100 Subject: [PATCH 300/446] Re-factored create_unique_sample_id_values --- wetlab/utils/samplesheet.py | 100 +++++++++++++++++------------------- 1 file changed, 46 insertions(+), 54 deletions(-) diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index a867223a4..690328732 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -463,62 +463,54 @@ def update_sample_sheet(in_file, experiment_name): os.rename(temp, in_file) -def create_unique_sample_id_values(infile, index_file): - found_sample_line = False - - fh = open(infile, "r") - temp_sample_sheet = os.path.join(settings.MEDIA_ROOT, "wetlab", "tmp_file") - fh_out_file = open(temp_sample_sheet, "w") - with open(index_file) as fh_index: - index = fh_index.readline() - index = index.rstrip() - index_number_str, index_letter = index.split("-") - fh_index.close() - - for line in fh: - if "Sample_ID" in line: - found_sample_line = True - fh_out_file.write(line) - continue - if found_sample_line: - # discard the empty lines or the lines that contains empty lines separated by comma - if line == "\n" or re.search(r"^\W", line): - continue +def create_unique_sample_id_values(in_file: str, index_file: str): + """ + Create unique sample IDs for samples in the samplesheets by using an ongoing index. + + Args: + in_file (str): Path to samplesheet + index_file (str): Path to index_file + """ + file_read = read_file_from_path(in_file) + samplesheet = file_read_to_dictionary(file_read) - data_line = line.split(",") - data_line[0] = str(index_number_str + "-" + index_letter) - new_line = ",".join(data_line) - fh_out_file.write(new_line) - # increase the index number - index_number = int(index_number_str) + 1 - if index_number > 9999: - index_number = 0 - # increase a letter - split_index_letter = list(index_letter) - if split_index_letter[1] == "Z": - last_letter = chr(ord(split_index_letter[0]) + 1) - split_index_letter[0] = last_letter - split_index_letter[1] = "A" - index_letter = "".join(split_index_letter) - else: - first_letter = chr(ord(split_index_letter[1]) + 1) - split_index_letter[1] = first_letter - index_letter = "".join(split_index_letter) - - index_number_str = str(index_number) - index_number_str = index_number_str.zfill(4) + with open(index_file, "r") as f: + try: # catch OSError in case of a one line file + f.seek(-2, os.SEEK_END) + while f.read(1) != b'\n': + f.seek(-2, os.SEEK_CUR) + except OSError: + f.seek(0) + last_line = f.readline().decode() + index_number_str, index_letter = last_line.rstrip().split("-") + index_number = int(index_number_str) + data = get_tabular_data(samplesheet, header_includes="Sample_ID") + for row in data[1:]: + index_number += 1 + index_number = index_number % (10000) # Return only 4 last digits, effectively restarting at 10000 + if index_number == 0: + # When index re-starts, we move on to the next letter + index_letter_parts = list(index_letter) + # Reverse order to + for i in [1,0]: + ascii_index_letter = ord(index_letter_parts[i]) + ascii_index_letter += 1 + ascii_index_letter = ascii_index_letter if ascii_index_letter <= 90 else 65 + index_letter_parts[i] = chr(ascii_index_letter) + if ascii_index_letter != 65: + break + # Reverse and stringify the index letter parts + index_letter = "".join(index_letter_parts) + # Create unique sample ID and overwrite Sample_ID + sample_unique_id = f"{str(index_number).zfill(4)}-{index_letter}" + row[0] = sample_unique_id + + # Dump the index value to file + with open(index_file, "w") as f: + f.write(sample_unique_id) - else: - fh_out_file.write(line) - - # dump the index value to file - fh_index = open(index_file, "w") - index_line = str(index_number_str + "-" + index_letter) - fh_index.write(index_line) - fh_index.close() - fh.close() - fh_out_file.close() - os.rename(temp_sample_sheet, infile) + # Dump the updated samplesheet + write_samplesheet_to_path(samplesheet, in_file) def set_user_names_in_sample_sheet(in_file, user_names): From da7e8b539c0a0941951623f055f3755b3fc4d778 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Thu, 5 Feb 2026 15:14:23 +0100 Subject: [PATCH 301/446] Re-factor update_sample_sheet --- wetlab/utils/samplesheet.py | 35 ++++++++++++----------------------- 1 file changed, 12 insertions(+), 23 deletions(-) diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index 690328732..82b5bc30d 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -438,29 +438,18 @@ def update_library_kit_field(library_file_name, library_kit_name, library_name): return file_name_in_database -def update_sample_sheet(in_file, experiment_name): - out_line = str("Experiment Name," + experiment_name + "\n") - fh_in = open(in_file, "r") - temp = os.path.join(settings.MEDIA_ROOT, "wetlab", "tmp.txt") - fh_out = open(temp, "w") - experiment_line_found = False - for line in fh_in: - # find experiment name line - found_experiment = re.search("^Experiment Name", line) - if found_experiment: - fh_out.write(out_line) - experiment_line_found = True - - elif line == "\n" and experiment_line_found is False: - fh_out.write(out_line) - fh_out.write("\n") - experiment_line_found = True - else: - fh_out.write(line) +def update_sample_sheet(in_file: str, experiment_name: str): + """ + Update experiment name in samplesheet - fh_in.close() - fh_out.close() - os.rename(temp, in_file) + Args: + in_file (str): Path to samplesheet + experiment_name (str): experiment name + """ + file_read = read_file_from_path(in_file) + samplesheet = file_read_to_dictionary(file_read) + samplesheet["Header"]["Experiment Name"] = experiment_name + write_samplesheet_to_path(in_file) def create_unique_sample_id_values(in_file: str, index_file: str): @@ -487,7 +476,7 @@ def create_unique_sample_id_values(in_file: str, index_file: str): data = get_tabular_data(samplesheet, header_includes="Sample_ID") for row in data[1:]: index_number += 1 - index_number = index_number % (10000) # Return only 4 last digits, effectively restarting at 10000 + index_number = index_number % 10000 # Return only 4 last digits, effectively restarting at 10000 if index_number == 0: # When index re-starts, we move on to the next letter index_letter_parts = list(index_letter) From 0a8592e5b24772e66f9c060d15f572af4c2fe2d1 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Thu, 5 Feb 2026 15:15:47 +0100 Subject: [PATCH 302/446] Added FIXME to update_library_kit_field --- wetlab/utils/samplesheet.py | 1 + 1 file changed, 1 insertion(+) diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index 82b5bc30d..7d8fe3eff 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -405,6 +405,7 @@ def get_index_library_name(in_file): def update_library_kit_field(library_file_name, library_kit_name, library_name): + # FIXME This function is not used anywhere - Not going to touch it for now # result_directory='documents/wetlab/BaseSpaceMigrationFiles/' timestr = time.strftime("%Y%m%d-%H%M%S") tmp = re.search(r"(.*)\d{8}-\d+.*\.csv", library_file_name) From 903074557c519c9ecb6bb42f0a62976b50b6fef0 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Fri, 6 Feb 2026 14:15:37 +0100 Subject: [PATCH 303/446] black and flake8 linted --- wetlab/config.py | 29 ++++------ wetlab/utils/crontab_process.py | 4 +- wetlab/utils/crontab_update_run.py | 4 +- wetlab/utils/run.py | 12 ++-- wetlab/utils/samplesheet.py | 88 ++++++++++++++++++------------ wetlab/views.py | 8 +-- 6 files changed, 73 insertions(+), 72 deletions(-) diff --git a/wetlab/config.py b/wetlab/config.py index faa0e32d2..ab3ad0bbc 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -336,19 +336,18 @@ # Sections to check in the IEM file created by user SECTIONS_IN_IEM_SAMPLE_SHEET = ["Header", "Reads", "Settings", "Data"] -SECTIONS_IN_V2_SAMPLE_SHEET = ["Header", "Reads", "BCLConvert_Settings", "BCLConvert_Data", "CustomCustomer_Data"] +SECTIONS_IN_V2_SAMPLE_SHEET = [ + "Header", + "Reads", + "BCLConvert_Settings", + "BCLConvert_Data", + "CustomCustomer_Data", +] # Tabular data sections in samplesheets. For future references: Insert in order. -TABULAR_DATA_SECTIONS_SAMPLE_SHEET = [ - "Data", - "CustomCustomer_Data", - "BCLConvert_Data" -] +TABULAR_DATA_SECTIONS_SAMPLE_SHEET = ["Data", "CustomCustomer_Data", "BCLConvert_Data"] -SETTINGS_SECTIONS_SAMPLE_SHEET = [ - "Settings", - "BCLConvert_Settings" -] +SETTINGS_SECTIONS_SAMPLE_SHEET = ["Settings", "BCLConvert_Settings"] FIELDS_IN_SAMPLE_SHEET_HEADER_IEM_VERSION_5 = [ "Date", @@ -362,15 +361,9 @@ "Description", ] -ADAPTER_1_FIELD_NAMES = [ - "Adapter", - "AdapterRead1" -] +ADAPTER_1_FIELD_NAMES = ["Adapter", "AdapterRead1"] -ADAPTER_2_FIELD_NAMES = [ - "Adapter", - "AdapterRead2" -] +ADAPTER_2_FIELD_NAMES = ["Adapter", "AdapterRead2"] # #### HEADINGS VALUES diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index f5d5d11a3..53b2c262b 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -300,9 +300,7 @@ def check_sequencer_status_from_completion_file(l_run_completion, experiment_nam ) # check if NextSEq run have been successful completed for xml_tag in wetlab.config.COMPLETION_TAG: - status_run = wetlab.utils.common.find_xml_tag_text( - l_run_completion, xml_tag - ) + status_run = wetlab.utils.common.find_xml_tag_text(l_run_completion, xml_tag) if status_run != "NOT FOUND": break if status_run not in wetlab.config.COMPLETION_SUCCESS: diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 05e4a627f..c5453847c 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -584,9 +584,7 @@ def manage_run_in_recorded_state(conn, run_process_objs): run_process_obj, l_sample_sheet_path, experiment_name ) - if ( - "NextSeq" in run_process_obj.get_run_platform() - ): + if "NextSeq" in run_process_obj.get_run_platform(): sample_sheet_path = run_process_obj.get_sample_file() try: diff --git a/wetlab/utils/run.py b/wetlab/utils/run.py index dd0bb7be6..e69574d71 100644 --- a/wetlab/utils/run.py +++ b/wetlab/utils/run.py @@ -37,12 +37,8 @@ def check_run_already_defined_by_crontab(exp_name, pool_ids): sample_sheet_path = run_obj.get_sample_file() f_name = os.path.join(settings.MEDIA_ROOT, sample_sheet_path) try: - file_data = wetlab.utils.samplesheet.read_file_from_path( - f_name - ) - samplesheet = wetlab.utils.samplesheet.file_read_to_dictionary( - file_data - ) + file_data = wetlab.utils.samplesheet.read_file_from_path(f_name) + samplesheet = wetlab.utils.samplesheet.file_read_to_dictionary(file_data) except FileNotFoundError: error_message = str( wetlab.config.ERROR_RUN_NAME_BY_CRONTAB_ALREADY_CREATED @@ -50,7 +46,9 @@ def check_run_already_defined_by_crontab(exp_name, pool_ids): + wetlab.config.ERROR_SAMPLE_SHEET_NOT_FOUND_WHEN_CREATED_BY_CRONTAB ) return {"ERROR": error_message} - sample_in_s_sheet = wetlab.utils.samplesheet.get_samples_in_sample_sheet(samplesheet) + sample_in_s_sheet = wetlab.utils.samplesheet.get_samples_in_sample_sheet( + samplesheet + ) sample_in_pools = wetlab.utils.pool.get_sample_name_in_pools(pool_ids) if len(sample_in_pools) != len(sample_in_s_sheet["samples"]): return {"ERROR": wetlab.config.ERROR_EXISTING_RUN_WITH_DIF_SAMPLES_AS_IN_CRON} diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index 7d8fe3eff..3b5a7dbdf 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -1,7 +1,6 @@ #!/usr/bin/env python3 # coding: utf-8 # Generic imports -import codecs import os import re import time @@ -14,10 +13,11 @@ # import wetlab.models + def read_file_from_path(file_path: str) -> str: """ Read file from path, ensuring characters are not lost due to encoding - + :param file_path: Description :type file_path: str """ @@ -28,6 +28,7 @@ def read_file_from_path(file_path: str) -> str: return False return read_file + def write_samplesheet_to_path(samplesheet: dict, path: str) -> bool: """ Write the samplesheet to a path. @@ -54,11 +55,11 @@ def write_samplesheet_to_path(samplesheet: dict, path: str) -> bool: return True except Exception: return False - - -def file_read_to_dictionary(file_read: str) -> dict[str, dict[str, any] | list[list[str]]]: +def file_read_to_dictionary( + file_read: str, +) -> dict[str, dict[str, any] | list[list[str]]]: """ Description: This function transforms a SampleSheet from string to dictionary, @@ -76,7 +77,7 @@ def file_read_to_dictionary(file_read: str) -> dict[str, dict[str, any] | list[l file_read = file_read.splitlines() for line in file_read: if line.startswith("["): - section = line.split(',')[0].lstrip("[").rstrip("]") + section = line.split(",")[0].lstrip("[").rstrip("]") samplesheet[section] = {} continue if not line or re.match("^,+$", line): @@ -92,7 +93,9 @@ def file_read_to_dictionary(file_read: str) -> dict[str, dict[str, any] | list[l line = line.split(",") try: # Sometimes there are empty lines (e.g. READS values) - samplesheet[section][line[0].strip()] = ",".join(line[1:]).strip() if len(line) > 1 else "" + samplesheet[section][line[0].strip()] = ( + ",".join(line[1:]).strip() if len(line) > 1 else "" + ) except IndexError: return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_HAS_INVALID_LINES} return samplesheet @@ -119,8 +122,8 @@ def validate_userid_in_user_iem_file(file_read, user_id_list): data = get_tabular_data(samplesheet, header_includes="Description") if not data: users["ERROR"] = ( - wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_DESCRIPTION_FIELD - ) + wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_DESCRIPTION_FIELD + ) return users users_in_sample_sheet = get_column_from_tabular_data(data, "Description") @@ -134,7 +137,7 @@ def validate_userid_in_user_iem_file(file_read, user_id_list): ) users["ERROR"] = invalid_names return users - + users["user_ids"] = list(set(userid_names)) return users @@ -160,7 +163,7 @@ def delete_stored_file(input_file): def get_adapters(samplesheet: dict) -> tuple[str, str]: """ Get the adapters from the samplesheet (v1 | v2) - + Parameters ---------- samplesheet : dict @@ -193,7 +196,7 @@ def get_adapters(samplesheet: dict) -> tuple[str, str]: def get_row_from_tabular_data(tabular_data: list[list], index) -> list: """ - Get the data headers + Get the data headers Parameters ---------- @@ -211,10 +214,12 @@ def get_row_from_tabular_data(tabular_data: list[list], index) -> list: return [] -def get_column_from_tabular_data(tabular_data: list[list], column_name: str, unique: bool=False) -> list: +def get_column_from_tabular_data( + tabular_data: list[list], column_name: str, unique: bool = False +) -> list: """ Docstring for get_all_values_from_tabular_data - + :param tabular_data: Description :type tabular_data: dict[list[list[str]]] """ @@ -228,6 +233,7 @@ def get_column_from_tabular_data(tabular_data: list[list], column_name: str, uni values = [row[column_index] for row in tabular_data] return list(set(values)) if unique else values + def get_tabular_data(samplesheet: dict, header_includes="") -> list[list]: for data_section in wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET: data = samplesheet.get(data_section, []) @@ -236,7 +242,7 @@ def get_tabular_data(samplesheet: dict, header_includes="") -> list[list]: if header_includes and header_includes not in data[0]: continue break - return [row.split(',') for row in data] + return [row.split(",") for row in data] def get_projects_in_sample_sheet(samplesheet) -> list: @@ -249,9 +255,10 @@ def get_projects_in_sample_sheet(samplesheet) -> list: project_name_list """ data = get_tabular_data(samplesheet) - projects = get_column_from_tabular_data(data, 'Sample_Project', unique=True) + projects = get_column_from_tabular_data(data, "Sample_Project", unique=True) return projects + def get_reads(samplesheet: dict) -> list[str, str]: """ Description : @@ -288,12 +295,15 @@ def get_samples_in_sample_sheet(samplesheet: dict) -> dict: samples_dict["header"] = data[0] if len(data) > 1 else "" samples_dict["samples"] = get_column_from_tabular_data(data, "Sample_Name") - samples_dict["sample_data"] = [get_row_from_tabular_data(data, i) for i in range(1, len(data))] + samples_dict["sample_data"] = [ + get_row_from_tabular_data(data, i) for i in range(1, len(data)) + ] return samples_dict + def get_headers(samplesheet: dict) -> list: data = get_tabular_data(samplesheet) - return data[0].split(',') + return data[0].split(",") def get_sample_sheet_data(file_read): @@ -317,14 +327,16 @@ def get_sample_sheet_data(file_read): samplesheet = file_read_to_dictionary(file_read) # initialize header data for item in wetlab.config.FIELDS_IN_SAMPLE_SHEET_HEADER_IEM_VERSION_5: - sample_sheet_data[item.lower()] = samplesheet['Header'].get(item, "") + sample_sheet_data[item.lower()] = samplesheet["Header"].get(item, "") # get adapters information sample_sheet_data["adapter1"], sample_sheet_data["adapter2"] = get_adapters( samplesheet ) # get indexes adapters information - sample_sheet_data["index_adapters"] = samplesheet.get('Headers', {}).get('Index Adapters', "") + sample_sheet_data["index_adapters"] = samplesheet.get("Headers", {}).get( + "Index Adapters", "" + ) # get reads information sample_sheet_data["reads"] = get_reads(samplesheet) # get proyects in sheet_data @@ -398,8 +410,10 @@ def get_index_library_name(in_file): file_read = read_file_from_path(in_file) samplesheet = file_read_to_dictionary(file_read) - header_values = samplesheet['Header'] - library_value = header_values.get("Assay", "") or header_values.get("Index Adapters", "") + header_values = samplesheet["Header"] + library_value = header_values.get("Assay", "") or header_values.get( + "Index Adapters", "" + ) return library_value @@ -465,9 +479,9 @@ def create_unique_sample_id_values(in_file: str, index_file: str): samplesheet = file_read_to_dictionary(file_read) with open(index_file, "r") as f: - try: # catch OSError in case of a one line file + try: # catch OSError in case of a one line file f.seek(-2, os.SEEK_END) - while f.read(1) != b'\n': + while f.read(1) != b"\n": f.seek(-2, os.SEEK_CUR) except OSError: f.seek(0) @@ -477,15 +491,19 @@ def create_unique_sample_id_values(in_file: str, index_file: str): data = get_tabular_data(samplesheet, header_includes="Sample_ID") for row in data[1:]: index_number += 1 - index_number = index_number % 10000 # Return only 4 last digits, effectively restarting at 10000 + index_number = ( + index_number % 10000 + ) # Return only 4 last digits, effectively restarting at 10000 if index_number == 0: # When index re-starts, we move on to the next letter index_letter_parts = list(index_letter) # Reverse order to - for i in [1,0]: + for i in [1, 0]: ascii_index_letter = ord(index_letter_parts[i]) ascii_index_letter += 1 - ascii_index_letter = ascii_index_letter if ascii_index_letter <= 90 else 65 + ascii_index_letter = ( + ascii_index_letter if ascii_index_letter <= 90 else 65 + ) index_letter_parts[i] = chr(ascii_index_letter) if ascii_index_letter != 65: break @@ -494,7 +512,7 @@ def create_unique_sample_id_values(in_file: str, index_file: str): # Create unique sample ID and overwrite Sample_ID sample_unique_id = f"{str(index_number).zfill(4)}-{index_letter}" row[0] = sample_unique_id - + # Dump the index value to file with open(index_file, "w") as f: f.write(sample_unique_id) @@ -531,10 +549,11 @@ def set_user_names_in_sample_sheet(in_file, user_names): projects = get_column_from_tabular_data("Sample_Project") descriptions_index = data[0].index("Description") for i in range(1, len(data)): - data[i][descriptions_index] = user_names[projects[i -1]] + data[i][descriptions_index] = user_names[projects[i - 1]] success_writing = write_samplesheet_to_path(samplesheet, in_file) return success_writing + def store_user_input_file(user_input_file): """ Description: @@ -591,9 +610,8 @@ def valid_user_iem_file(file_read: str) -> bool: samplesheet = file_read_to_dictionary(file_read) for section_name in samplesheet.keys(): if ( - section_name not in wetlab.config.SECTIONS_IN_IEM_SAMPLE_SHEET - and - section_name not in wetlab.config.SECTIONS_IN_V2_SAMPLE_SHEET + section_name not in wetlab.config.SECTIONS_IN_IEM_SAMPLE_SHEET + and section_name not in wetlab.config.SECTIONS_IN_V2_SAMPLE_SHEET ): return False @@ -601,7 +619,7 @@ def valid_user_iem_file(file_read: str) -> bool: sample_number = 0 data = get_tabular_data(samplesheet, header_includes="Description") - # Check on data + # Check on data if not data: return False @@ -609,9 +627,9 @@ def valid_user_iem_file(file_read: str) -> bool: data_field_length = len(data[0]) sample_number = len(data) - 1 if not all([len(row) - data_field_length for row in data]): - # All rows contain the same either the same + # All rows contain the same either the same return False - + if sample_number == 0: return False return True diff --git a/wetlab/views.py b/wetlab/views.py index 01d32e638..31ceca7e0 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -592,12 +592,8 @@ def create_nextseq_run(request): update_info_proj.save() results.append(["runname", experiment_name]) run_p.set_run_state("recorded") - file_read = wetlab.utils.samplesheet.read_file_from_path( - in_file - ) - samplesheet = wetlab.utils.samplesheet.file_read_to_dictionary( - file_read - ) + file_read = wetlab.utils.samplesheet.read_file_from_path(in_file) + samplesheet = wetlab.utils.samplesheet.file_read_to_dictionary(file_read) sample_names_and_data = wetlab.utils.samplesheet.get_samples_in_sample_sheet( samplesheet ) From bb1934c1b5fa38987960395075bb23a120eb5282 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Fri, 6 Feb 2026 15:39:21 +0100 Subject: [PATCH 304/446] Linted with black --- core/scripts/migrate_sample_type.py | 1 - core/scripts/rename_app_name.py | 1 - core/utils/samples.py | 2 +- django_utils/templatetags/user_text.py | 1 - drylab/scripts/drylab_service_state_migration.py | 1 - drylab/templatetags/upload_tags.py | 6 ++---- wetlab/utils/samplesheet.py | 5 ++++- 7 files changed, 7 insertions(+), 10 deletions(-) diff --git a/core/scripts/migrate_sample_type.py b/core/scripts/migrate_sample_type.py index 139865a81..d97f34745 100644 --- a/core/scripts/migrate_sample_type.py +++ b/core/scripts/migrate_sample_type.py @@ -1,6 +1,5 @@ import core.models - """ The script is applicable for the upgrade from 2.3.0 to 3.0.0. Because the new version changes the value that is stored now is the field diff --git a/core/scripts/rename_app_name.py b/core/scripts/rename_app_name.py index 51f312bc4..05eb1b922 100644 --- a/core/scripts/rename_app_name.py +++ b/core/scripts/rename_app_name.py @@ -1,6 +1,5 @@ import core.models - """ The script is applicable for the upgrade from 2.3.0 to 3.0.0. Because the application in iSkylims have been renamed, this required that diff --git a/core/utils/samples.py b/core/utils/samples.py index 193d784ec..3b141250c 100644 --- a/core/utils/samples.py +++ b/core/utils/samples.py @@ -1878,7 +1878,7 @@ def record_extract_protocol(samples, excel_data, heading, user, app_name): return_data.append(r_data) # collect data for dropdown selection protocol_filter_selection = [] - (protocols_dict, protocol_list) = get_molecule_protocols(app_name) + protocols_dict, protocol_list = get_molecule_protocols(app_name) for key, value in protocols_dict.items(): protocol_filter_selection.append([key, value]) return { diff --git a/django_utils/templatetags/user_text.py b/django_utils/templatetags/user_text.py index 5e1299451..a8d751d10 100644 --- a/django_utils/templatetags/user_text.py +++ b/django_utils/templatetags/user_text.py @@ -1,6 +1,5 @@ from django import template - register = template.Library() diff --git a/drylab/scripts/drylab_service_state_migration.py b/drylab/scripts/drylab_service_state_migration.py index 9a2222424..7ea4c29d0 100644 --- a/drylab/scripts/drylab_service_state_migration.py +++ b/drylab/scripts/drylab_service_state_migration.py @@ -1,6 +1,5 @@ from drylab.models import Service, ServiceState - """ The script is applicable for the upgrade from 2.3.0 to 2.3.1. Service state that was defined as option choice in models,is replaced in diff --git a/drylab/templatetags/upload_tags.py b/drylab/templatetags/upload_tags.py index 144bfe95f..b56046e73 100644 --- a/drylab/templatetags/upload_tags.py +++ b/drylab/templatetags/upload_tags.py @@ -6,8 +6,7 @@ @register.simple_tag def upload_js(): - return mark_safe( - """ + return mark_safe(""" - """ - ) + """) diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index 3b5a7dbdf..ecf895863 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -45,7 +45,10 @@ def write_samplesheet_to_path(samplesheet: dict, path: str) -> bool: for key, value in samplesheet.items(): string_to_write += f"[{key}]\n" if key in wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET: - string_to_write += f"{'\n'.join([','.join(row) for row in value])}\n" + delimiter = "\n" + string_to_write += ( + f"{delimiter.join([','.join(row) for row in value])}{delimiter}" + ) else: for row_header, element in value.items(): string_to_write += f"{row_header},{element}\n" From 11bc483665bf4ce60dd414e865129370562b7349 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Thu, 12 Feb 2026 10:16:21 +0100 Subject: [PATCH 305/446] Added samplesheet V2 support with 'custom_description' --- wetlab/config.py | 28 +++++++++++++----- wetlab/utils/samplesheet.py | 59 ++++++++++++++++++++++++------------- 2 files changed, 59 insertions(+), 28 deletions(-) diff --git a/wetlab/config.py b/wetlab/config.py index ab3ad0bbc..963b0ea59 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -226,15 +226,10 @@ HEADING_FOR_SAMPLE_SHEET_TWO_INDEX = [ "Unique_Sample_ID", "Sample_Name", - "Sample_Plate", - "Sample_Well", - "Index_Plate_Well", - "I7_Index_ID", "index", - "I5_Index_ID", "index2", "Sample_Project", - "Description", + "custom_description", ] @@ -248,6 +243,7 @@ ("index", "i7Index"), ("Sample_Project", "projectInSampleSheet"), ("Description", "userInSampleSheet"), + ("custom_description", "userInSampleSheet"), ] MAP_USER_SAMPLE_SHEET_TO_DATABASE_NEXTSEQ_PAIRED_END = [ @@ -261,6 +257,7 @@ ("index2", "i5Index"), ("Sample_Project", "projectInSampleSheet"), ("Description", "userInSampleSheet"), + ("custom_description", "userInSampleSheet"), ] MAP_USER_SAMPLE_SHEET_TO_DATABASE_MISEQ_SINGLE_READ_VERSION_5 = [ @@ -272,6 +269,7 @@ ("index", "i7Index"), ("Sample_Project", "projectInSampleSheet"), ("Description", "userInSampleSheet"), + ("custom_description", "userInSampleSheet"), ] MAP_USER_SAMPLE_SHEET_TO_DATABASE_MISEQ_PAiRED_END_VERSION_5 = [ @@ -285,6 +283,7 @@ ("index2", "i5Index"), ("Sample_Project", "projectInSampleSheet"), ("Description", "userInSampleSheet"), + ("custom_description", "userInSampleSheet"), ] MAP_USER_SAMPLE_SHEET_TO_DATABASE_MISEQ_SINGLE_READ_VERSION_4 = [ @@ -296,6 +295,7 @@ ("index", "i7Index"), ("Sample_Project", "projectInSampleSheet"), ("Description", "userInSampleSheet"), + ("custom_description", "userInSampleSheet"), ] MAP_USER_SAMPLE_SHEET_TO_DATABASE_MISEQ_PAiRED_END_VERSION_4 = [ @@ -309,6 +309,7 @@ ("index2", "i5Index"), ("Sample_Project", "projectInSampleSheet"), ("Description", "userInSampleSheet"), + ("custom_description", "userInSampleSheet"), ] @@ -326,6 +327,7 @@ ("GenomeFolder", "genomeFolder"), ("Sample_Project", "projectInSampleSheet"), ("Description", "userInSampleSheet"), + ("custom_description", "userInSampleSheet"), ] # ######## MAPPING OPTIONAL COLUMNS THAT COULD BE IN SAMPLE SHEET FROM USER TO DATABASE ############# MAP_USER_SAMPLE_SHEET_ADDITIONAL_FIELDS_FROM_TYPE_OF_SECUENCER = [ @@ -344,8 +346,18 @@ "CustomCustomer_Data", ] -# Tabular data sections in samplesheets. For future references: Insert in order. -TABULAR_DATA_SECTIONS_SAMPLE_SHEET = ["Data", "CustomCustomer_Data", "BCLConvert_Data"] +# Possible names of the Tabular data iskylims user field + +TABULAR_DATA_ISKYLIMS_USER_COLUMN = { + "1": "Description", + "2": "custom_description" +} + +# Tabular data sections in samplesheets. +TABULAR_DATA_SECTIONS_SAMPLE_SHEET = { + "1": "Data", + "2": "BCLConvert_Data" +} SETTINGS_SECTIONS_SAMPLE_SHEET = ["Settings", "BCLConvert_Settings"] diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index ecf895863..2b1dd008d 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -14,6 +14,18 @@ # import wetlab.models +def samplesheet_version(samplesheet: dict) -> str: + """ + Return samplesheet version (1 or 2) as a string + + Args: + samplesheet (dict): samplesheet + + Returns: + str: "1" or "2" + """ + return samplesheet.get("Header", {}).get("FileFormatVersion", "1") + def read_file_from_path(file_path: str) -> str: """ Read file from path, ensuring characters are not lost due to encoding @@ -22,7 +34,7 @@ def read_file_from_path(file_path: str) -> str: :type file_path: str """ try: - with open(file_path, "r", encoding="utf-8") as f: + with open(file_path, "r", encoding="utf-8-sig") as f: read_file = f.read() except Exception: return False @@ -122,13 +134,14 @@ def validate_userid_in_user_iem_file(file_read, user_id_list): if "ERROR" in samplesheet: return samplesheet - data = get_tabular_data(samplesheet, header_includes="Description") + data = get_tabular_data(samplesheet) + iskylims_user_column = wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get(samplesheet_version(samplesheet)) if not data: users["ERROR"] = ( wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_DESCRIPTION_FIELD ) return users - users_in_sample_sheet = get_column_from_tabular_data(data, "Description") + users_in_sample_sheet = get_column_from_tabular_data(data, iskylims_user_column) userid_names = [user for user in users_in_sample_sheet if user in user_id_list] invalid_names = [user for user in users_in_sample_sheet if user not in user_id_list] @@ -237,14 +250,18 @@ def get_column_from_tabular_data( return list(set(values)) if unique else values -def get_tabular_data(samplesheet: dict, header_includes="") -> list[list]: - for data_section in wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET: - data = samplesheet.get(data_section, []) - if not data: - continue - if header_includes and header_includes not in data[0]: - continue - break +def get_tabular_data(samplesheet: dict) -> list[list]: + """ + Get tabular data from a samplesheet. + + Args: + samplesheet (dict): Samplesheet with the tabular data + + Returns: + list[list]: Tabular data, in a nested list (Matrix N*M) + """ + data_section = wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET.get(samplesheet_version(samplesheet), "") + data = samplesheet.get(data_section, []) return [row.split(",") for row in data] @@ -365,10 +382,11 @@ def get_sample_with_user_owner(sample_sheet_path): full_path = os.path.join(settings.MEDIA_ROOT, sample_sheet_path) file_read = read_file_from_path(full_path) samplesheet = file_read_to_dictionary(file_read) - # Retrieve tabular data with "Description" in the header - data = get_tabular_data(samplesheet, header_includes="Description") + # Retrieve tabular data with the iskylims user in the header + data = get_tabular_data(samplesheet) sample_names = get_column_from_tabular_data(data, "Sample_Name") - user_ids = get_column_from_tabular_data(data, "Description") + iskylims_user_column_id = wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get(samplesheet_version(samplesheet)) + user_ids = get_column_from_tabular_data(data, iskylims_user_column_id) sample_user = {sample_names[i]: user_ids[i] for i in range(len(sample_names))} return sample_user @@ -386,9 +404,10 @@ def get_projects_in_run(in_file: str) -> dict: """ file_read = read_file_from_path(in_file) samplesheet = file_read_to_dictionary(file_read) - data = get_tabular_data(samplesheet, header_includes="Description") + data = get_tabular_data(samplesheet) sample_projects = get_column_from_tabular_data(data, "Sample_Project") - user_ids = get_column_from_tabular_data(data, "Description") + iskylims_user_column_id = wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get(samplesheet_version(samplesheet)) + user_ids = get_column_from_tabular_data(data, iskylims_user_column_id) projects = {sample_projects[i]: user_ids[i] for i in range(len(sample_projects))} if not data: @@ -491,7 +510,7 @@ def create_unique_sample_id_values(in_file: str, index_file: str): last_line = f.readline().decode() index_number_str, index_letter = last_line.rstrip().split("-") index_number = int(index_number_str) - data = get_tabular_data(samplesheet, header_includes="Sample_ID") + data = get_tabular_data(samplesheet) for row in data[1:]: index_number += 1 index_number = ( @@ -548,9 +567,9 @@ def set_user_names_in_sample_sheet(in_file, user_names): """ file_read = read_file_from_path(in_file) samplesheet = file_read_to_dictionary(file_read) - data = get_tabular_data(samplesheet, header_includes="Description") + data = get_tabular_data(samplesheet) projects = get_column_from_tabular_data("Sample_Project") - descriptions_index = data[0].index("Description") + descriptions_index = data[0].index(wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get(samplesheet_version(samplesheet))) for i in range(1, len(data)): data[i][descriptions_index] = user_names[projects[i - 1]] success_writing = write_samplesheet_to_path(samplesheet, in_file) @@ -620,7 +639,7 @@ def valid_user_iem_file(file_read: str) -> bool: data_field_length = "" sample_number = 0 - data = get_tabular_data(samplesheet, header_includes="Description") + data = get_tabular_data(samplesheet) # Check on data if not data: From bfd0fabb99e293cc0675f8d1beba426a94347157 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Thu, 12 Feb 2026 10:21:43 +0100 Subject: [PATCH 306/446] linted with black and flake8 --- wetlab/config.py | 10 ++-------- wetlab/utils/samplesheet.py | 28 +++++++++++++++++++++------- 2 files changed, 23 insertions(+), 15 deletions(-) diff --git a/wetlab/config.py b/wetlab/config.py index 963b0ea59..a69a9f222 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -348,16 +348,10 @@ # Possible names of the Tabular data iskylims user field -TABULAR_DATA_ISKYLIMS_USER_COLUMN = { - "1": "Description", - "2": "custom_description" -} +TABULAR_DATA_ISKYLIMS_USER_COLUMN = {"1": "Description", "2": "custom_description"} # Tabular data sections in samplesheets. -TABULAR_DATA_SECTIONS_SAMPLE_SHEET = { - "1": "Data", - "2": "BCLConvert_Data" -} +TABULAR_DATA_SECTIONS_SAMPLE_SHEET = {"1": "Data", "2": "BCLConvert_Data"} SETTINGS_SECTIONS_SAMPLE_SHEET = ["Settings", "BCLConvert_Settings"] diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index 2b1dd008d..a232c0a02 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -26,6 +26,7 @@ def samplesheet_version(samplesheet: dict) -> str: """ return samplesheet.get("Header", {}).get("FileFormatVersion", "1") + def read_file_from_path(file_path: str) -> str: """ Read file from path, ensuring characters are not lost due to encoding @@ -135,7 +136,9 @@ def validate_userid_in_user_iem_file(file_read, user_id_list): return samplesheet data = get_tabular_data(samplesheet) - iskylims_user_column = wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get(samplesheet_version(samplesheet)) + iskylims_user_column = wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get( + samplesheet_version(samplesheet) + ) if not data: users["ERROR"] = ( wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_DESCRIPTION_FIELD @@ -260,7 +263,9 @@ def get_tabular_data(samplesheet: dict) -> list[list]: Returns: list[list]: Tabular data, in a nested list (Matrix N*M) """ - data_section = wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET.get(samplesheet_version(samplesheet), "") + data_section = wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET.get( + samplesheet_version(samplesheet), "" + ) data = samplesheet.get(data_section, []) return [row.split(",") for row in data] @@ -385,7 +390,9 @@ def get_sample_with_user_owner(sample_sheet_path): # Retrieve tabular data with the iskylims user in the header data = get_tabular_data(samplesheet) sample_names = get_column_from_tabular_data(data, "Sample_Name") - iskylims_user_column_id = wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get(samplesheet_version(samplesheet)) + iskylims_user_column_id = wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get( + samplesheet_version(samplesheet) + ) user_ids = get_column_from_tabular_data(data, iskylims_user_column_id) sample_user = {sample_names[i]: user_ids[i] for i in range(len(sample_names))} @@ -406,7 +413,9 @@ def get_projects_in_run(in_file: str) -> dict: samplesheet = file_read_to_dictionary(file_read) data = get_tabular_data(samplesheet) sample_projects = get_column_from_tabular_data(data, "Sample_Project") - iskylims_user_column_id = wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get(samplesheet_version(samplesheet)) + iskylims_user_column_id = wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get( + samplesheet_version(samplesheet) + ) user_ids = get_column_from_tabular_data(data, iskylims_user_column_id) projects = {sample_projects[i]: user_ids[i] for i in range(len(sample_projects))} @@ -421,8 +430,9 @@ def get_projects_in_run(in_file: str) -> dict: def get_index_library_name(in_file): """ Description: - The function get the index library adapters. It searchs in the assay value (used for version 4 of IEM sample sheet - and in hte Index Adapters on sample sheet version 5. + The function get the index library adapters. It searchs in the assay + value (used for version 4 of IEM sample sheet + and in the Index Adapters on sample sheet version 5. If Index adapters is found they are used if not the assay value Input: in_file # shample sheet file @@ -569,7 +579,11 @@ def set_user_names_in_sample_sheet(in_file, user_names): samplesheet = file_read_to_dictionary(file_read) data = get_tabular_data(samplesheet) projects = get_column_from_tabular_data("Sample_Project") - descriptions_index = data[0].index(wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get(samplesheet_version(samplesheet))) + descriptions_index = data[0].index( + wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get( + samplesheet_version(samplesheet) + ) + ) for i in range(1, len(data)): data[i][descriptions_index] = user_names[projects[i - 1]] success_writing = write_samplesheet_to_path(samplesheet, in_file) From 7b2dcb67566aff896e02997501e89d37e13a5552 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 6 Feb 2026 14:12:10 +0100 Subject: [PATCH 307/446] docker runtime is copied to tmp when path is outside the repo --- docker_install.sh | 15 +++++++++++---- 1 file changed, 11 insertions(+), 4 deletions(-) diff --git a/docker_install.sh b/docker_install.sh index f700f3832..cdf865b31 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -191,11 +191,18 @@ if [ ! -f "$install_conf" ]; then fi repo_root="$(pwd)" +temp_install_conf="" if [[ "$install_conf" = /* ]] && [[ "$install_conf" != "$repo_root/"* ]]; then - install_conf_copy="conf/docker_runtime_settings.txt" - echo "Copying $install_conf into repository as $install_conf_copy for Docker build/runtime." - cp "$install_conf" "$install_conf_copy" - install_conf="$install_conf_copy" + temp_install_conf="/tmp/iskylims_docker_install_$$.txt" + echo "Copying $install_conf into temporary file $temp_install_conf for Docker build/runtime." + cp "$install_conf" "$temp_install_conf" + install_conf="$temp_install_conf" + cleanup_temp_conf() { + if [ -n "$temp_install_conf" ] && [ -f "$temp_install_conf" ]; then + rm -f "$temp_install_conf" + fi + } + trap cleanup_temp_conf EXIT fi service_exists() { From fbd9146c1caf1592c29da2386aaa23e0f36be1b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 6 Feb 2026 14:28:08 +0100 Subject: [PATCH 308/446] docker runtime is copied to repo when path is outside the repo --- docker_install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker_install.sh b/docker_install.sh index cdf865b31..dd7a76a56 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -193,7 +193,7 @@ fi repo_root="$(pwd)" temp_install_conf="" if [[ "$install_conf" = /* ]] && [[ "$install_conf" != "$repo_root/"* ]]; then - temp_install_conf="/tmp/iskylims_docker_install_$$.txt" + temp_install_conf="$repo_root/.tmp_docker_install_conf_$$.txt" echo "Copying $install_conf into temporary file $temp_install_conf for Docker build/runtime." cp "$install_conf" "$temp_install_conf" install_conf="$temp_install_conf" From d54660107623bb6ec0d10760c5c39d72f84b1f40 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 6 Feb 2026 14:38:44 +0100 Subject: [PATCH 309/446] rename docker-compose.yml to docker-compose.test.yml, fix git revision to be correctly passed to docker file --- LEAME.md | 2 ++ README.md | 2 ++ docker-compose.prod.yml | 2 +- docker-compose.yml => docker-compose.test.yml | 7 ++++++- docker_install.sh | 2 +- install.sh | 2 +- 6 files changed, 13 insertions(+), 4 deletions(-) rename docker-compose.yml => docker-compose.test.yml (87%) diff --git a/LEAME.md b/LEAME.md index 78f0ed28e..2d33e91da 100644 --- a/LEAME.md +++ b/LEAME.md @@ -70,6 +70,8 @@ Levanta el sistema completo (base de datos, Samba y app) con fixtures y datos de bash docker_install.sh --test ``` +Esto usa `docker-compose.test.yml` por defecto. + Puedes personalizar los valores por defecto: - `--demo_data /ruta/a/iskylims_demo_data.tar.gz` para reutilizar un archivo local (si no, se descarga). diff --git a/README.md b/README.md index aae7fb7d5..42d393c83 100644 --- a/README.md +++ b/README.md @@ -71,6 +71,8 @@ Bring up a full test stack (database, Samba, app) plus fixtures and demo data: bash docker_install.sh --test ``` +This uses `docker-compose.test.yml` by default. + Defaults can be customised: - `--demo_data /path/to/iskylims_demo_data.tar.gz` to reuse a local demo archive (otherwise it is downloaded). diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 1af9f79de..03385cea8 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -7,7 +7,7 @@ services: build: context: . args: - INSTALL_TYPE: ${INSTALL_TYPE:-app} + INSTALL_TYPE: ${INSTALL_TYPE:-dep} GIT_REVISION: ${GIT_REVISION:-main} INSTALL_CONF: ${INSTALL_CONF:-conf/docker_production_settings.txt} ports: diff --git a/docker-compose.yml b/docker-compose.test.yml similarity index 87% rename from docker-compose.yml rename to docker-compose.test.yml index c461959f4..13b401a7c 100644 --- a/docker-compose.yml +++ b/docker-compose.test.yml @@ -38,7 +38,12 @@ services: command: '-S -s "ngs_data;/mnt/test_ngs_data;yes;yes;no;samba_user;none;none;ngs data samba share" -u "samba_user;sambapasswd" -p' app: - build: . + build: + context: . + args: + INSTALL_TYPE: ${INSTALL_TYPE:-dep} + GIT_REVISION: ${GIT_REVISION:-main} + INSTALL_CONF: ${INSTALL_CONF:-conf/docker_install_settings.txt} container_name: iskylims_app ports: - "8001:8001" diff --git a/docker_install.sh b/docker_install.sh index dd7a76a56..9e66d8179 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -143,7 +143,7 @@ shift $((OPTIND-1)) if [ "$mode" = "test" ]; then if [ -z "$compose_file" ]; then - compose_file="docker-compose.yml" + compose_file="docker-compose.test.yml" fi if [ -z "$install_conf" ]; then install_conf="conf/docker_install_settings.txt" diff --git a/install.sh b/install.sh index 08304acb7..657c901bd 100644 --- a/install.sh +++ b/install.sh @@ -315,7 +315,7 @@ rename_apps_if_needed() { if [ -d "$INSTALL_PATH/iSkyLIMS_core" ]; then echo "Changing app dir names in $INSTALL_PATH..." rm -rf $INSTALL_PATH/.git $INSTALL_PATH/.github $INSTALL_PATH/.gitignore \ - $INSTALL_PATH/.Rhistory $INSTALL_PATH/docker-compose.yml $INSTALL_PATH/docker_iskylims_install.sh \ + $INSTALL_PATH/.Rhistory $INSTALL_PATH/docker-compose.test.yml $INSTALL_PATH/docker_iskylims_install.sh \ $INSTALL_PATH/Dockerfile $INSTALL_PATH/install.sh $INSTALL_PATH/install_settings.txt mv $INSTALL_PATH/iSkyLIMS_core $INSTALL_PATH/core mv $INSTALL_PATH/iSkyLIMS_wetlab $INSTALL_PATH/wetlab From abc45bf2467f3da8e1343435b3a178f749857b77 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 6 Feb 2026 14:43:09 +0100 Subject: [PATCH 310/446] try to correctly pass git revision to dockerfile --- docker_install.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docker_install.sh b/docker_install.sh index 9e66d8179..8e51ec016 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -221,8 +221,9 @@ ensure_app_running() { fi } -echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE="dep" and GIT_REVISION=$git_revision..." -docker compose -f "$compose_file" build --no-cache --build-arg INSTALL_TYPE="dep" --build-arg GIT_REVISION="$git_revision" --build-arg INSTALL_CONF="$install_conf" +echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=dep and GIT_REVISION=$git_revision..." +INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf" \ + docker compose -f "$compose_file" build --no-cache docker compose -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." From a86d9488626c70f41babffb8319cf797b2453f36 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 6 Feb 2026 14:55:10 +0100 Subject: [PATCH 311/446] some fixes in docker_install.sh --- docker_install.sh | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/docker_install.sh b/docker_install.sh index 8e51ec016..d6bbcced6 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -73,6 +73,7 @@ demo_data=false git_revision="main" compose_file="" install_conf="" +install_conf_container="" skip_demo_data="" skip_test_data="" mode="production" @@ -205,6 +206,12 @@ if [[ "$install_conf" = /* ]] && [[ "$install_conf" != "$repo_root/"* ]]; then trap cleanup_temp_conf EXIT fi +if [[ "$install_conf" = "$repo_root/"* ]]; then + install_conf_container="${install_conf#$repo_root/}" +else + install_conf_container="$install_conf" +fi + service_exists() { docker compose -f "$compose_file" ps --services 2>/dev/null | grep -Fxq "$1" } @@ -222,8 +229,11 @@ ensure_app_running() { } echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=dep and GIT_REVISION=$git_revision..." -INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf" \ - docker compose -f "$compose_file" build --no-cache +INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" \ + docker compose -f "$compose_file" build --no-cache \ + --build-arg INSTALL_TYPE="dep" \ + --build-arg GIT_REVISION="$git_revision" \ + --build-arg INSTALL_CONF="$install_conf_container" docker compose -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." @@ -239,10 +249,10 @@ fi if [ "$action" = "upgrade" ]; then echo "Running install.sh upgrade inside the container" - docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --upgrade app --git_revision \"$git_revision\" --conf \"$install_conf\" --skip_apache_restart$script_args" + docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --upgrade app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args" else echo "Running install.sh install inside the container" - docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --install app --git_revision \"$git_revision\" --conf \"$install_conf\" --skip_apache_restart$script_args" + docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --install app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args" fi if ! docker exec -it iskylims_app test -f /opt/iskylims/manage.py; then From 0fb4b5cdaf1d2787a708d1a8bd9e1ecc5c571201 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 10 Feb 2026 16:31:25 +0100 Subject: [PATCH 312/446] make sure conf file can be accessed from the container --- docker_install.sh | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/docker_install.sh b/docker_install.sh index d6bbcced6..4288d996c 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -240,6 +240,21 @@ echo "Waiting 20 seconds for starting database and web services..." sleep 20 ensure_app_running +host_install_conf_path="$install_conf" +if [[ "$host_install_conf_path" != /* ]]; then + host_install_conf_path="$repo_root/$host_install_conf_path" +fi + +container_install_conf_path="$install_conf_container" +if [[ "$container_install_conf_path" != /* ]]; then + container_install_conf_path="/srv/iskylims/$container_install_conf_path" +fi + +if ! docker exec -it iskylims_app test -f "$container_install_conf_path"; then + echo "Copying install configuration into container at $container_install_conf_path" + docker cp "$host_install_conf_path" "iskylims_app:$container_install_conf_path" +fi + script_args="" if [ "$run_script" = true ]; then for val in "${migration_script[@]}"; do From 3e1682dfdfcf29371cc637116d64e13b798e4b77 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 10 Feb 2026 16:35:56 +0100 Subject: [PATCH 313/446] change name for docker test install settings, change ip to docker internal so it works locally --- Dockerfile | 2 +- conf/docker_production_settings.txt | 2 +- conf/{docker_install_settings.txt => docker_test_settings.txt} | 0 docker-compose.test.yml | 2 +- docker_install.sh | 2 +- 5 files changed, 4 insertions(+), 4 deletions(-) rename conf/{docker_install_settings.txt => docker_test_settings.txt} (100%) diff --git a/Dockerfile b/Dockerfile index 2ada0e511..f85a57ba8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -30,7 +30,7 @@ ENV PATH="/usr/sbin/cron:$PATH" # Set default install type ARG INSTALL_TYPE=dep ARG GIT_REVISION=main -ARG INSTALL_CONF=conf/docker_install_settings.txt +ARG INSTALL_CONF=conf/docker_test_settings.txt # Execute the dependency stage only; app migrations run when the container is up. RUN /bin/bash install.sh --install dep --git_revision $GIT_REVISION --conf $INSTALL_CONF --skip_apache_restart diff --git a/conf/docker_production_settings.txt b/conf/docker_production_settings.txt index 643586d2c..c92824596 100644 --- a/conf/docker_production_settings.txt +++ b/conf/docker_production_settings.txt @@ -15,7 +15,7 @@ PYTHON_BIN_PATH='python3' DB_USER='django' DB_PASS='djangopass' DB_NAME='iskylims' -DB_SERVER_IP='prod-db-host' # hostname or IP of the production DB +DB_SERVER_IP='host.docker.internal' # hostname or IP of the production DB (use host.docker.internal for host DB) DB_PORT=3306 ### Settings required for sending emails diff --git a/conf/docker_install_settings.txt b/conf/docker_test_settings.txt similarity index 100% rename from conf/docker_install_settings.txt rename to conf/docker_test_settings.txt diff --git a/docker-compose.test.yml b/docker-compose.test.yml index 13b401a7c..f0fabbb9e 100644 --- a/docker-compose.test.yml +++ b/docker-compose.test.yml @@ -43,7 +43,7 @@ services: args: INSTALL_TYPE: ${INSTALL_TYPE:-dep} GIT_REVISION: ${GIT_REVISION:-main} - INSTALL_CONF: ${INSTALL_CONF:-conf/docker_install_settings.txt} + INSTALL_CONF: ${INSTALL_CONF:-conf/docker_test_settings.txt} container_name: iskylims_app ports: - "8001:8001" diff --git a/docker_install.sh b/docker_install.sh index 4288d996c..f31e6e901 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -147,7 +147,7 @@ if [ "$mode" = "test" ]; then compose_file="docker-compose.test.yml" fi if [ -z "$install_conf" ]; then - install_conf="conf/docker_install_settings.txt" + install_conf="conf/docker_test_settings.txt" fi else if [ -z "$compose_file" ]; then From 5dc0d55175d86bade8463e7b4368cbb69e535a43 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 10 Feb 2026 16:59:05 +0100 Subject: [PATCH 314/446] open docker network to connect to localhost mysql, thi sis not needed if mysql is not in localhost --- docker-compose.prod.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 03385cea8..f7dfe2a1a 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -17,3 +17,5 @@ services: volumes: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo + extra_hosts: + - "host.docker.internal:host-gateway" From 74932b79b75078614f7692634689958d62bf723a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 11 Feb 2026 16:12:01 +0100 Subject: [PATCH 315/446] remove migrations from gitignore --- .gitignore | 1 - install.sh | 5 ++--- 2 files changed, 2 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index 79b37fb50..1c0f66014 100644 --- a/.gitignore +++ b/.gitignore @@ -3,7 +3,6 @@ *.bin *.gz *_BAK -migrations/ tmp/ logs/ /static/ diff --git a/install.sh b/install.sh index 657c901bd..e65f8e953 100644 --- a/install.sh +++ b/install.sh @@ -455,12 +455,11 @@ install_system_packages() { # run_django_deploy: execute makemigrations/migrate and optional fixture/superuser steps. run_django_deploy() { local mode="${1:-install}" - echo "Generating Django migrations" - python manage.py makemigrations $MIGRATION_MODULES - if [ "$mode" = "upgrade" ]; then echo "Applying migrations in fake-initial mode" python manage.py migrate --noinput --fake-initial + echo "Applying migrations" + python manage.py migrate --noinput else echo "Applying migrations" python manage.py migrate --noinput From dd900180cb739221019d51b6e32fa15b1fa7394e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 11 Feb 2026 16:31:29 +0100 Subject: [PATCH 316/446] removed app based gitignore --- clinic/.gitignore | 113 ---------------------------------------- core/.gitignore | 103 ------------------------------------ django_utils/.gitignore | 103 ------------------------------------ drylab/.gitignore | 67 ------------------------ wetlab/.gitignore | 68 ------------------------ 5 files changed, 454 deletions(-) delete mode 100644 clinic/.gitignore delete mode 100644 core/.gitignore delete mode 100644 django_utils/.gitignore delete mode 100644 drylab/.gitignore delete mode 100644 wetlab/.gitignore diff --git a/clinic/.gitignore b/clinic/.gitignore deleted file mode 100644 index 87884db5e..000000000 --- a/clinic/.gitignore +++ /dev/null @@ -1,113 +0,0 @@ -## Custom -*.xml -*.bin -migrations/ -tmp/ -logs/ -tests/ - - -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -*.egg-info/ -.installed.cfg -*.egg -MANIFEST - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -.hypothesis/ -.pytest_cache/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py -db.sqlite3 - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# pyenv -.python-version - -# celery beat schedule file -celerybeat-schedule - -# SageMath parsed files -*.sage.py - -# Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ diff --git a/core/.gitignore b/core/.gitignore deleted file mode 100644 index f5e99c72e..000000000 --- a/core/.gitignore +++ /dev/null @@ -1,103 +0,0 @@ -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$py.class -migrations/ -tests/ - -# C extensions -*.so - -# Distribution / packaging -.Python -env/ -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -*.egg-info/ -.installed.cfg -*.egg - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -.hypothesis/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# pyenv -.python-version - -# celery beat schedule file -celerybeat-schedule - -# SageMath parsed files -*.sage.py - -# dotenv -.env - -# virtualenv -.venv -venv/ -ENV/ - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ diff --git a/django_utils/.gitignore b/django_utils/.gitignore deleted file mode 100644 index ed8eee433..000000000 --- a/django_utils/.gitignore +++ /dev/null @@ -1,103 +0,0 @@ -# Byte-compiled / optimized / DLL files -__migrations__/ -migrations/ -__pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -env/ -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -*.egg-info/ -.installed.cfg -*.egg - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -.hypothesis/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# pyenv -.python-version - -# celery beat schedule file -celerybeat-schedule - -# SageMath parsed files -*.sage.py - -# dotenv -.env - -# virtualenv -.venv -venv/ -ENV/ - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ diff --git a/drylab/.gitignore b/drylab/.gitignore deleted file mode 100644 index 781e59dfd..000000000 --- a/drylab/.gitignore +++ /dev/null @@ -1,67 +0,0 @@ -# Custom -*.save* -*.swp -drylab_samba_conf.py -drylab_email_conf.py - -# Django migrations -__migrations__/ -migrations/ - -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] - -# C extensions -*.so - -# Distribution / packaging -.Python -env/ -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -*.egg-info/ -.installed.cfg -*.egg - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*,cover - -# Translations -*.mo -*.pot - -# Django stuff: -*.log - -# Sphinx documentation -docs/_build/ - -# PyBuilder -target/ diff --git a/wetlab/.gitignore b/wetlab/.gitignore deleted file mode 100644 index b3b95c969..000000000 --- a/wetlab/.gitignore +++ /dev/null @@ -1,68 +0,0 @@ -## Custom -*.xml -*.bin -migrations/ -tmp/ -logs/ -tests/ - -## Cusotomized script - -script/private*.py -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] - -# C extensions -*.so - -# Distribution / packaging -.Python -env/ -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -*.egg-info/ -.installed.cfg -*.egg - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*,cover - -# Translations -*.mo -*.pot - -# Django stuff: -*.log - -# Sphinx documentation -docs/_build/ - -# PyBuilder -target/ From e269cfaac61513d33afe86234c5cec45153b4a38 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 11 Feb 2026 16:31:44 +0100 Subject: [PATCH 317/446] commited baseline migration files --- clinic/migrations/0001_initial.py | 144 +++++++ clinic/migrations/__init__.py | 0 core/migrations/0001_initial.py | 492 ++++++++++++++++++++++ core/migrations/__init__.py | 0 django_utils/migrations/0001_initial.py | 54 +++ django_utils/migrations/__init__.py | 0 drylab/migrations/0001_initial.py | 234 +++++++++++ drylab/migrations/__init__.py | 0 wetlab/migrations/0001_initial.py | 520 ++++++++++++++++++++++++ wetlab/migrations/__init__.py | 0 10 files changed, 1444 insertions(+) create mode 100644 clinic/migrations/0001_initial.py create mode 100644 clinic/migrations/__init__.py create mode 100644 core/migrations/0001_initial.py create mode 100644 core/migrations/__init__.py create mode 100644 django_utils/migrations/0001_initial.py create mode 100644 django_utils/migrations/__init__.py create mode 100644 drylab/migrations/0001_initial.py create mode 100644 drylab/migrations/__init__.py create mode 100644 wetlab/migrations/0001_initial.py create mode 100644 wetlab/migrations/__init__.py diff --git a/clinic/migrations/0001_initial.py b/clinic/migrations/0001_initial.py new file mode 100644 index 000000000..f31f0921b --- /dev/null +++ b/clinic/migrations/0001_initial.py @@ -0,0 +1,144 @@ +# Generated by Django 4.2.25 on 2026-02-11 16:17 + +from django.conf import settings +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + + initial = True + + dependencies = [ + ('core', '0001_initial'), + migrations.swappable_dependency(settings.AUTH_USER_MODEL), + ] + + operations = [ + migrations.CreateModel( + name='ClinicSampleRequest', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('entry_order', models.CharField(blank=True, max_length=8, null=True)), + ('confirmation_code', models.CharField(blank=True, max_length=80, null=True)), + ('priority', models.IntegerField(blank=True, null=True)), + ('comments', models.CharField(blank=True, max_length=255, null=True)), + ('service_date', models.DateTimeField(blank=True, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ], + ), + migrations.CreateModel( + name='ClinicSampleState', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('clinic_state', models.CharField(max_length=20)), + ], + ), + migrations.CreateModel( + name='ConfigSetting', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('configuration_name', models.CharField(max_length=80)), + ('configuration_value', models.CharField(blank=True, max_length=255, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ], + ), + migrations.CreateModel( + name='FamilyRelatives', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('relationship', models.CharField(max_length=255)), + ], + ), + migrations.CreateModel( + name='PatientData', + fields=[ + ('patien_core', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='core.patientcore')), + ('address', models.CharField(blank=True, max_length=255, null=True)), + ('phone', models.CharField(blank=True, max_length=20, null=True)), + ('email', models.CharField(blank=True, max_length=50, null=True)), + ('birthday', models.DateTimeField(blank=True, null=True)), + ('smoker', models.CharField(blank=True, max_length=20, null=True)), + ('notification_preference', models.CharField(blank=True, max_length=20, null=True)), + ('comments', models.CharField(blank=True, max_length=255, null=True)), + ], + ), + migrations.CreateModel( + name='ServiceUnits', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('service_unit_name', models.CharField(max_length=80)), + ], + ), + migrations.CreateModel( + name='ResultParameterValue', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('parameterValue', models.CharField(max_length=255)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('clinicSample_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='clinic.clinicsamplerequest')), + ('parameter_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.protocolparameters')), + ], + ), + migrations.CreateModel( + name='PatientHistory', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('entry_date', models.DateTimeField(blank=True, null=True)), + ('description', models.CharField(max_length=255)), + ('patient_core', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientcore')), + ], + ), + migrations.CreateModel( + name='Family', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('family_id', models.CharField(max_length=50)), + ('relative_1', models.CharField(max_length=50)), + ('relative_2', models.CharField(max_length=50)), + ('affected', models.BooleanField()), + ('family_comments', models.CharField(blank=True, max_length=255, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('family_relatives_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='clinic.familyrelatives')), + ('patien_core_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientcore')), + ], + ), + migrations.CreateModel( + name='Doctor', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('doctor_name', models.CharField(max_length=80)), + ('service_unit_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='clinic.serviceunits')), + ], + ), + migrations.AddField( + model_name='clinicsamplerequest', + name='clinic_sample_state', + field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='clinic.clinicsamplestate'), + ), + migrations.AddField( + model_name='clinicsamplerequest', + name='doctor_id', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='clinic.doctor'), + ), + migrations.AddField( + model_name='clinicsamplerequest', + name='patient_core', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientcore'), + ), + migrations.AddField( + model_name='clinicsamplerequest', + name='sample_core', + field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.samples'), + ), + migrations.AddField( + model_name='clinicsamplerequest', + name='sample_request_user', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL), + ), + migrations.AddField( + model_name='clinicsamplerequest', + name='service_unit_id', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='clinic.serviceunits'), + ), + ] diff --git a/clinic/migrations/__init__.py b/clinic/migrations/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/core/migrations/0001_initial.py b/core/migrations/0001_initial.py new file mode 100644 index 000000000..7dc7569e5 --- /dev/null +++ b/core/migrations/0001_initial.py @@ -0,0 +1,492 @@ +# Generated by Django 4.2.25 on 2026-02-11 16:17 + +from django.conf import settings +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + + initial = True + + dependencies = [ + migrations.swappable_dependency(settings.AUTH_USER_MODEL), + ] + + operations = [ + migrations.CreateModel( + name='City', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('city_name', models.CharField(max_length=80)), + ('geo_loc_latitude', models.CharField(max_length=80)), + ('geo_loc_longitude', models.CharField(max_length=80)), + ('apps_name', models.CharField(max_length=40, null=True)), + ], + options={ + 'db_table': 'core_city', + }, + ), + migrations.CreateModel( + name='CommercialKits', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.CharField(max_length=150)), + ('provider', models.CharField(max_length=30)), + ('cat_number', models.CharField(blank=True, max_length=40, null=True)), + ('description', models.CharField(blank=True, max_length=255, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), + ], + options={ + 'db_table': 'core_commercial_kits', + }, + ), + migrations.CreateModel( + name='Contact', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('contact_name', models.CharField(max_length=80)), + ('contact_mail', models.CharField(max_length=40, null=True)), + ], + options={ + 'db_table': 'core_contact', + }, + ), + migrations.CreateModel( + name='LabRequest', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('lab_name', models.CharField(max_length=80)), + ('lab_name_coding', models.CharField(max_length=50)), + ('lab_unit', models.CharField(max_length=50)), + ('lab_contact_name', models.CharField(max_length=50)), + ('lab_phone', models.CharField(max_length=20)), + ('lab_email', models.CharField(max_length=70)), + ('address', models.CharField(max_length=255)), + ('apps_name', models.CharField(max_length=40, null=True)), + ('lab_city', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.city')), + ], + options={ + 'db_table': 'core_lab_request', + }, + ), + migrations.CreateModel( + name='MoleculeType', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('molecule_type', models.CharField(max_length=30)), + ('apps_name', models.CharField(max_length=40, null=True)), + ], + options={ + 'db_table': 'core_molecule_type', + }, + ), + migrations.CreateModel( + name='MoleculeUsedFor', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('used_for', models.CharField(max_length=50)), + ('apps_name', models.CharField(max_length=50)), + ('massive_use', models.BooleanField(default=False)), + ], + options={ + 'db_table': 'core_molecule_used_for', + }, + ), + migrations.CreateModel( + name='OntologyMap', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('label', models.CharField(max_length=255)), + ('ontology', models.CharField(blank=True, max_length=50, null=True)), + ], + options={ + 'db_table': 'core_ontology_map', + }, + ), + migrations.CreateModel( + name='PatientCore', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('patient_name', models.CharField(max_length=255, null=True)), + ('patient_surname', models.CharField(max_length=255, null=True)), + ('patient_code', models.CharField(max_length=255, null=True)), + ], + options={ + 'db_table': 'core_patient_core', + }, + ), + migrations.CreateModel( + name='PatientProjects', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('project_name', models.CharField(max_length=50)), + ('project_manager', models.CharField(blank=True, max_length=50, null=True)), + ('project_contact', models.CharField(blank=True, max_length=50, null=True)), + ('project_description', models.CharField(blank=True, max_length=255, null=True)), + ('apps_name', models.CharField(max_length=40)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ], + options={ + 'db_table': 'core_patient_projects', + }, + ), + migrations.CreateModel( + name='PatientSex', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sex', models.CharField(max_length=16)), + ], + options={ + 'db_table': 'core_patient_sex', + }, + ), + migrations.CreateModel( + name='SampleProjectFieldClassification', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('classification_name', models.CharField(max_length=80)), + ('classification_display', models.CharField(max_length=100)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ], + options={ + 'db_table': 'core_sample_projects_field_classification', + }, + ), + migrations.CreateModel( + name='SampleProjects', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sample_project_name', models.CharField(max_length=255)), + ('sample_project_manager', models.CharField(blank=True, max_length=50, null=True)), + ('sample_project_contact', models.CharField(blank=True, max_length=250, null=True)), + ('sample_project_description', models.CharField(blank=True, max_length=255, null=True)), + ('apps_name', models.CharField(max_length=255)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ], + options={ + 'db_table': 'core_sample_projects', + }, + ), + migrations.CreateModel( + name='SampleProjectsFields', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sample_project_field_name', models.CharField(max_length=80)), + ('sample_project_field_description', models.CharField(blank=True, max_length=400, null=True)), + ('sample_project_field_order', models.IntegerField()), + ('sample_project_field_used', models.BooleanField()), + ('sample_project_field_type', models.CharField(max_length=20)), + ('sample_project_option_list', models.CharField(blank=True, max_length=255, null=True)), + ('sample_project_searchable', models.BooleanField(default=False)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('sample_project_field_classification_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sampleprojectfieldclassification')), + ('sample_projects_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='sample_project_fields', to='core.sampleprojects')), + ], + options={ + 'db_table': 'core_sample_projects_fields', + }, + ), + migrations.CreateModel( + name='SampleType', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sample_type', models.CharField(max_length=50)), + ('apps_name', models.CharField(max_length=50)), + ('mandatory_fields', models.CharField(blank=True, max_length=300, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), + ], + options={ + 'db_table': 'core_sample_type', + }, + ), + migrations.CreateModel( + name='SequencingPlatform', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('platform_name', models.CharField(max_length=30)), + ('company_name', models.CharField(max_length=30)), + ('sequencing_technology', models.CharField(max_length=30)), + ], + options={ + 'db_table': 'core_sequencing_platform', + }, + ), + migrations.CreateModel( + name='Species', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('species_name', models.CharField(max_length=50)), + ('ref_genome_name', models.CharField(blank=True, max_length=255, null=True)), + ('ref_genome_size', models.CharField(blank=True, max_length=100, null=True)), + ('ref_genome_id', models.CharField(blank=True, max_length=255, null=True)), + ('apps_name', models.CharField(max_length=50, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), + ], + options={ + 'db_table': 'core_species', + }, + ), + migrations.CreateModel( + name='StateInCountry', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('state_name', models.CharField(max_length=80)), + ('apps_name', models.CharField(max_length=40, null=True)), + ], + options={ + 'db_table': 'core_state_in_country', + }, + ), + migrations.CreateModel( + name='StatesForMolecule', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('molecule_state_name', models.CharField(max_length=50)), + ], + options={ + 'db_table': 'core_states_for_molecule', + }, + ), + migrations.CreateModel( + name='StatesForSample', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sample_state_name', models.CharField(max_length=50)), + ], + options={ + 'db_table': 'core_states_for_sample', + }, + ), + migrations.CreateModel( + name='UserLotCommercialKits', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('uses_number', models.IntegerField(default=0, null=True)), + ('chip_lot', models.CharField(max_length=50)), + ('latest_used_date', models.DateTimeField(blank=True, null=True)), + ('expiration_date', models.DateField()), + ('run_out', models.BooleanField(default=False)), + ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), + ('based_commercial', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.commercialkits')), + ('user', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ], + options={ + 'db_table': 'core_user_lot_commercial_kits', + }, + ), + migrations.CreateModel( + name='SequencingConfiguration', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('configuration_name', models.CharField(max_length=255)), + ('platform_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencingplatform')), + ], + options={ + 'db_table': 'core_sequencing_configuration', + }, + ), + migrations.CreateModel( + name='SequencerInLab', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sequencer_name', models.CharField(max_length=255)), + ('sequencer_description', models.CharField(blank=True, max_length=255, null=True)), + ('sequencer_location', models.CharField(blank=True, max_length=255, null=True)), + ('sequencer_serial_number', models.CharField(blank=True, max_length=255, null=True)), + ('sequencer_state', models.CharField(blank=True, max_length=50, null=True)), + ('sequencer_operation_start', models.DateField(blank=True, null=True)), + ('sequencer_operation_end', models.DateField(blank=True, null=True)), + ('sequencer_number_lanes', models.CharField(blank=True, max_length=5, null=True)), + ('platform_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencingplatform')), + ], + options={ + 'db_table': 'core_sequencer_in_lab', + }, + ), + migrations.CreateModel( + name='SamplesProjectsTableOptions', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('option_value', models.CharField(max_length=120)), + ('sample_project_field', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='opt_value_prop', to='core.sampleprojectsfields')), + ], + options={ + 'db_table': 'core_sample_projects_table_options', + }, + ), + migrations.CreateModel( + name='Samples', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sample_name', models.CharField(max_length=255, null=True, verbose_name='Sample Name')), + ('sample_location', models.CharField(blank=True, max_length=255, null=True, verbose_name='Sample location')), + ('sample_entry_date', models.DateTimeField(blank=True, null=True, verbose_name='Sample defined date')), + ('collection_sample_date', models.DateTimeField(blank=True, null=True, verbose_name='Sample collection date')), + ('unique_sample_id', models.CharField(max_length=8, null=True, verbose_name='Unique sample id')), + ('sample_code_id', models.CharField(max_length=60, null=True, verbose_name='Sample code id')), + ('reused_number', models.IntegerField(default=0, verbose_name='Number of type reused')), + ('sequencing_date', models.DateTimeField(blank=True, null=True, verbose_name='Sequencing date')), + ('completed_date', models.DateTimeField(blank=True, null=True, verbose_name='Completion date')), + ('generated_at', models.DateTimeField(auto_now_add=True, verbose_name='Generated at')), + ('only_recorded', models.BooleanField(blank=True, default=False, null=True, verbose_name='Only recorded?')), + ('lab_request', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.labrequest', verbose_name='Laboratory')), + ('patient_core', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientcore', verbose_name='Patient Code ID')), + ('sample_project', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sampleprojects', verbose_name='Sample Project')), + ('sample_state', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.statesforsample', verbose_name='Sample state')), + ('sample_type', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sampletype', verbose_name='Sample type')), + ('sample_user', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Username')), + ('species', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.species', verbose_name='Species')), + ], + options={ + 'db_table': 'core_samples', + }, + ), + migrations.CreateModel( + name='SampleProjectsFieldsValue', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sample_project_field_value', models.CharField(blank=True, max_length=255, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('sample_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='project_values', to='core.samples', verbose_name='Sample Name')), + ('sample_project_field_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sampleprojectsfields')), + ], + options={ + 'db_table': 'core_sample_projects_fields_value', + }, + ), + migrations.AddField( + model_name='sampleprojectfieldclassification', + name='sample_projects_id', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sampleprojects'), + ), + migrations.CreateModel( + name='ProtocolType', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('protocol_type', models.CharField(max_length=40)), + ('apps_name', models.CharField(max_length=40)), + ('molecule', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.moleculetype')), + ], + options={ + 'db_table': 'core_protocol_type', + }, + ), + migrations.CreateModel( + name='Protocols', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('name', models.CharField(max_length=40)), + ('description', models.CharField(blank=True, max_length=160, null=True)), + ('type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.protocoltype')), + ], + options={ + 'db_table': 'core_protocols', + }, + ), + migrations.CreateModel( + name='ProtocolParameters', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('parameter_name', models.CharField(max_length=255)), + ('parameter_description', models.CharField(blank=True, max_length=400, null=True)), + ('parameter_order', models.IntegerField()), + ('parameter_used', models.BooleanField()), + ('parameter_type', models.CharField(default='string', max_length=20)), + ('parameter_option_values', models.CharField(blank=True, max_length=400, null=True)), + ('parameter_max_value', models.CharField(blank=True, max_length=50, null=True)), + ('parameter_min_value', models.CharField(blank=True, max_length=50, null=True)), + ('protocol_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.protocols')), + ], + options={ + 'db_table': 'core_protocol_parameters', + }, + ), + migrations.CreateModel( + name='PatientProjectsFields', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('project_field_name', models.CharField(max_length=50)), + ('project_field_description', models.CharField(blank=True, max_length=400, null=True)), + ('project_field_order', models.IntegerField()), + ('project_field_used', models.BooleanField()), + ('patient_projects_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientprojects')), + ], + options={ + 'db_table': 'core_patient_projects_fields', + }, + ), + migrations.CreateModel( + name='PatientProjectFieldValue', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('project_field_value', models.CharField(max_length=255)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('patient_core_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientcore')), + ('project_field_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientprojectsfields')), + ], + options={ + 'db_table': 'core_patient_project_field_value', + }, + ), + migrations.AddField( + model_name='patientcore', + name='patient_projects', + field=models.ManyToManyField(blank=True, to='core.patientprojects'), + ), + migrations.AddField( + model_name='patientcore', + name='patient_sex', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientsex'), + ), + migrations.CreateModel( + name='MoleculePreparation', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('molecule_code_id', models.CharField(max_length=255)), + ('extraction_type', models.CharField(max_length=50)), + ('molecule_extraction_date', models.DateTimeField(null=True)), + ('reused_number', models.IntegerField(default=0)), + ('used_for_massive_sequencing', models.BooleanField(blank=True, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('molecule_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.moleculetype')), + ('molecule_used_for', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.moleculeusedfor')), + ('molecule_user', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ('protocol_used', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.protocols')), + ('sample', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.samples')), + ('state', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.statesformolecule')), + ('user_lot_kit_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.userlotcommercialkits')), + ], + options={ + 'db_table': 'core_molecule_preparation', + }, + ), + migrations.CreateModel( + name='MoleculeParameterValue', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('parameter_value', models.CharField(max_length=255)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('molecule_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.moleculepreparation')), + ('molecule_parameter_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.protocolparameters')), + ], + options={ + 'db_table': 'core_molecule_parameter_value', + }, + ), + migrations.AddField( + model_name='commercialkits', + name='platform_kits', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencingplatform'), + ), + migrations.AddField( + model_name='commercialkits', + name='protocol_kits', + field=models.ManyToManyField(blank=True, to='core.protocols'), + ), + migrations.AddField( + model_name='city', + name='belongs_to_state', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.stateincountry'), + ), + ] diff --git a/core/migrations/__init__.py b/core/migrations/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/django_utils/migrations/0001_initial.py b/django_utils/migrations/0001_initial.py new file mode 100644 index 000000000..75f92ec61 --- /dev/null +++ b/django_utils/migrations/0001_initial.py @@ -0,0 +1,54 @@ +# Generated by Django 4.2.25 on 2026-02-11 16:17 + +from django.conf import settings +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + + initial = True + + dependencies = [ + migrations.swappable_dependency(settings.AUTH_USER_MODEL), + ] + + operations = [ + migrations.CreateModel( + name='Center', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('center_name', models.CharField(max_length=50, verbose_name='Center')), + ('center_abbr', models.CharField(max_length=25, verbose_name='Acronym')), + ], + options={ + 'db_table': 'utils_center', + }, + ), + migrations.CreateModel( + name='ClassificationArea', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('classification_area_name', models.CharField(max_length=80)), + ('classification_area_description', models.CharField(blank=True, max_length=255, null=True)), + ], + options={ + 'db_table': 'utils_classification_area', + }, + ), + migrations.CreateModel( + name='Profile', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('profile_position', models.CharField(max_length=50, verbose_name='Position')), + ('profile_area', models.CharField(max_length=50, verbose_name='Area / Unit')), + ('profile_extension', models.CharField(max_length=5, verbose_name='Phone extension')), + ('profile_center', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='django_utils.center', verbose_name='Center')), + ('profile_classification_area', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='django_utils.classificationarea')), + ('profile_user_id', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, related_name='profile', to=settings.AUTH_USER_MODEL)), + ], + options={ + 'db_table': 'utils_profile', + }, + ), + ] diff --git a/django_utils/migrations/__init__.py b/django_utils/migrations/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/drylab/migrations/0001_initial.py b/drylab/migrations/0001_initial.py new file mode 100644 index 000000000..4f504ec6c --- /dev/null +++ b/drylab/migrations/0001_initial.py @@ -0,0 +1,234 @@ +# Generated by Django 4.2.25 on 2026-02-11 16:17 + +from django.conf import settings +from django.db import migrations, models +import django.db.models.deletion +import mptt.fields + + +class Migration(migrations.Migration): + + initial = True + + dependencies = [ + ('core', '0001_initial'), + ('wetlab', '0001_initial'), + migrations.swappable_dependency(settings.AUTH_USER_MODEL), + ] + + operations = [ + migrations.CreateModel( + name='AvailableService', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('avail_service_description', models.CharField(max_length=200, verbose_name='Available services')), + ('service_in_use', models.BooleanField(default=True)), + ('service_id', models.CharField(blank=True, max_length=40, null=True)), + ('description', models.CharField(blank=True, max_length=200, null=True)), + ('lft', models.PositiveIntegerField(editable=False)), + ('rght', models.PositiveIntegerField(editable=False)), + ('tree_id', models.PositiveIntegerField(db_index=True, editable=False)), + ('level', models.PositiveIntegerField(editable=False)), + ('parent', mptt.fields.TreeForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='drylab.availableservice')), + ], + options={ + 'verbose_name': 'AvailableService', + 'verbose_name_plural': 'AvailableServices', + 'db_table': 'drylab_available_service', + 'ordering': ['tree_id', 'lft'], + }, + ), + migrations.CreateModel( + name='ConfigSetting', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('configuration_name', models.CharField(max_length=80)), + ('configuration_value', models.CharField(blank=True, max_length=255, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ], + options={ + 'db_table': 'drylab_config_setting', + }, + ), + migrations.CreateModel( + name='Pipelines', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('pipeline_name', models.CharField(max_length=50)), + ('pipeline_version', models.CharField(max_length=10)), + ('pipeline_in_use', models.BooleanField(default=True)), + ('pipeline_file', models.FileField(blank=True, null=True, upload_to='drylab/pipelinesFiles')), + ('pipeline_url', models.CharField(blank=True, max_length=200, null=True)), + ('pipeline_description', models.CharField(blank=True, max_length=500, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('user_name', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ], + options={ + 'db_table': 'drylab_pipelines', + }, + ), + migrations.CreateModel( + name='Resolution', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('resolution_number', models.CharField(max_length=255, null=True, verbose_name='Resolution name')), + ('resolution_estimated_date', models.DateField(null=True, verbose_name=' Estimated resolution date')), + ('resolution_date', models.DateField(auto_now_add=True, verbose_name='Resolution date')), + ('resolution_queued_date', models.DateField(blank=True, null=True)), + ('resolution_in_progress_date', models.DateField(blank=True, null=True)), + ('resolution_delivery_date', models.DateField(blank=True, null=True)), + ('resolution_notes', models.TextField(blank=True, max_length=1000, null=True, verbose_name='Resolution notes')), + ('resolution_full_number', models.CharField(blank=True, max_length=255, null=True, verbose_name='Acronym Name')), + ('resolution_pdf_file', models.FileField(blank=True, null=True, upload_to='documents/drylab/resolutions')), + ('available_services', models.ManyToManyField(blank=True, to='drylab.availableservice')), + ('resolution_assigned_user', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='groups+', to=settings.AUTH_USER_MODEL)), + ('resolution_pipelines', models.ManyToManyField(blank=True, to='drylab.pipelines')), + ], + options={ + 'db_table': 'drylab_resolution', + }, + ), + migrations.CreateModel( + name='ResolutionStates', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('state_value', models.CharField(max_length=50)), + ('state_display', models.CharField(blank=True, max_length=80, null=True)), + ('description', models.CharField(blank=True, max_length=255, null=True)), + ], + options={ + 'db_table': 'drylab_resolution_states', + }, + ), + migrations.CreateModel( + name='Service', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('service_center', models.CharField(max_length=50, null=True, verbose_name='Sequencing center')), + ('service_request_number', models.CharField(max_length=80, null=True, verbose_name='Service ID')), + ('service_request_int', models.CharField(max_length=80, null=True)), + ('service_run_specs', models.CharField(blank=True, max_length=10, null=True, verbose_name='Run specifications')), + ('service_status', models.CharField(choices=[('recorded', 'Recorded'), ('approved', 'Approved'), ('rejected', 'Rejected'), ('queued', 'Queued'), ('in_progress', 'In Progress'), ('delivered', 'Delivered'), ('archived', 'Archived')], max_length=15, verbose_name='Service status')), + ('service_notes', models.TextField(blank=True, max_length=2048, null=True, verbose_name='Service Notes')), + ('service_created_date', models.DateField(auto_now_add=True, null=True)), + ('service_approved_date', models.DateField(blank=True, null=True)), + ('service_rejected_date', models.DateField(blank=True, null=True)), + ('service_delivered_date', models.DateField(blank=True, null=True)), + ('service_available_service', mptt.fields.TreeManyToManyField(to='drylab.availableservice', verbose_name='AvailableServices')), + ('service_project_names', models.ManyToManyField(blank=True, to='wetlab.projects', verbose_name="User's projects")), + ('service_sequencing_platform', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencingplatform')), + ], + options={ + 'db_table': 'drylab_service', + }, + ), + migrations.CreateModel( + name='ServiceState', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('state_value', models.CharField(max_length=50)), + ('state_display', models.CharField(blank=True, max_length=80, null=True)), + ('description', models.CharField(blank=True, max_length=255, null=True)), + ('show_in_stats', models.BooleanField(default=False)), + ], + options={ + 'db_table': 'drylab_service_state', + }, + ), + migrations.CreateModel( + name='UploadServiceFile', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('upload_file', models.FileField(upload_to='drylab/service_files')), + ('upload_file_name', models.CharField(blank=True, max_length=255, null=True)), + ('uploaded_at', models.DateTimeField(auto_now_add=True)), + ('upload_service', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='drylab.service')), + ], + options={ + 'db_table': 'drylab_upload_service_file', + }, + ), + migrations.AddField( + model_name='service', + name='service_state', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='drylab.servicestate', verbose_name='Service State'), + ), + migrations.AddField( + model_name='service', + name='service_user_id', + field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL), + ), + migrations.CreateModel( + name='ResolutionParameters', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('resolution_parameter', models.CharField(max_length=50)), + ('resolution_param_value', models.CharField(max_length=80)), + ('resolution_param_notes', models.CharField(blank=True, max_length=200, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('resolution', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drylab.resolution')), + ], + options={ + 'db_table': 'drylab_resolution_parameters', + }, + ), + migrations.AddField( + model_name='resolution', + name='resolution_service_id', + field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='resolutions', to='drylab.service'), + ), + migrations.AddField( + model_name='resolution', + name='resolution_state', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='drylab.resolutionstates'), + ), + migrations.CreateModel( + name='RequestedSamplesInServices', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sample_key', models.CharField(blank=True, max_length=15, null=True)), + ('sample_name', models.CharField(blank=True, max_length=50, null=True)), + ('sample_path', models.CharField(blank=True, max_length=250, null=True)), + ('run_name_key', models.CharField(blank=True, max_length=15, null=True)), + ('run_name', models.CharField(blank=True, max_length=50, null=True)), + ('project_key', models.CharField(blank=True, max_length=15, null=True)), + ('project_name', models.CharField(blank=True, max_length=50, null=True)), + ('only_recorded_sample', models.BooleanField(default=False)), + ('generated_at', models.DateField(auto_now_add=True)), + ('samples_in_service', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='samples', to='drylab.service')), + ], + options={ + 'db_table': 'drylab_request_samples_in_services', + }, + ), + migrations.CreateModel( + name='ParameterPipeline', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('parameter_name', models.CharField(max_length=80)), + ('parameter_value', models.CharField(blank=True, max_length=200, null=True)), + ('parameter_type', models.CharField(blank=True, max_length=20, null=True)), + ('parameter_pipeline', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drylab.pipelines')), + ], + options={ + 'db_table': 'drylab_parameter_pipeline', + }, + ), + migrations.CreateModel( + name='Delivery', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('delivery_notes', models.TextField(blank=True, max_length=1000, null=True)), + ('execution_start_date', models.DateField(blank=True, null=True)), + ('execution_end_date', models.DateField(blank=True, null=True)), + ('execution_time', models.CharField(blank=True, max_length=80, null=True)), + ('permanent_used_space', models.CharField(blank=True, max_length=80, null=True)), + ('temporary_used_space', models.CharField(blank=True, max_length=80, null=True)), + ('delivery_resolution_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='delivery', to='drylab.resolution')), + ('pipelines_in_delivery', models.ManyToManyField(blank=True, to='drylab.pipelines')), + ], + options={ + 'db_table': 'drylab_delivery', + }, + ), + ] diff --git a/drylab/migrations/__init__.py b/drylab/migrations/__init__.py new file mode 100644 index 000000000..e69de29bb diff --git a/wetlab/migrations/0001_initial.py b/wetlab/migrations/0001_initial.py new file mode 100644 index 000000000..c93df8527 --- /dev/null +++ b/wetlab/migrations/0001_initial.py @@ -0,0 +1,520 @@ +# Generated by Django 4.2.25 on 2026-02-11 16:17 + +from django.conf import settings +from django.db import migrations, models +import django.db.models.deletion + + +class Migration(migrations.Migration): + + initial = True + + dependencies = [ + migrations.swappable_dependency(settings.AUTH_USER_MODEL), + ('core', '0001_initial'), + ('django_utils', '0001_initial'), + ] + + operations = [ + migrations.CreateModel( + name='AdditionaKitsLibPrepare', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('kit_name', models.CharField(max_length=255)), + ('description', models.CharField(blank=True, max_length=400, null=True)), + ('kit_order', models.IntegerField()), + ('kit_used', models.BooleanField()), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('commercial_kit_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.commercialkits')), + ('protocol_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.protocols')), + ('register_user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ], + options={ + 'db_table': 'wetlab_lib_additional_kits_lib_prepare', + }, + ), + migrations.CreateModel( + name='CollectionIndexKit', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('collection_index_name', models.CharField(max_length=125)), + ('version', models.CharField(max_length=80, null=True)), + ('plate_extension', models.CharField(max_length=125, null=True)), + ('adapter_1', models.CharField(max_length=125, null=True)), + ('adapter_2', models.CharField(max_length=125, null=True)), + ('collection_index_file', models.FileField(max_length=500, upload_to='wetlab/collection_index_kits/')), + ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), + ], + options={ + 'db_table': 'wetlab_collection_index_kit', + }, + ), + migrations.CreateModel( + name='ConfigSetting', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('configuration_name', models.CharField(max_length=80)), + ('configuration_value', models.CharField(blank=True, max_length=255, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ], + options={ + 'db_table': 'wetlab_config_setting', + }, + ), + migrations.CreateModel( + name='LibPrepareStates', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('lib_prep_state', models.CharField(max_length=50)), + ], + options={ + 'db_table': 'wetlab_lib_prepare_states', + }, + ), + migrations.CreateModel( + name='LibraryKit', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('library_name', models.CharField(max_length=125)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ], + options={ + 'db_table': 'wetlab_library_kit', + }, + ), + migrations.CreateModel( + name='PoolStates', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('pool_state', models.CharField(max_length=50)), + ], + options={ + 'db_table': 'wetlab_pool_states', + }, + ), + migrations.CreateModel( + name='Projects', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('base_space_library', models.CharField(blank=True, max_length=45, null=True)), + ('project_name', models.CharField(max_length=45)), + ('library_kit', models.CharField(blank=True, max_length=125, null=True)), + ('base_space_file', models.CharField(blank=True, max_length=255, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('project_run_date', models.DateField(blank=True, null=True)), + ('library_kit_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.librarykit')), + ], + options={ + 'db_table': 'wetlab_projects', + }, + ), + migrations.CreateModel( + name='RunConfigurationTest', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('run_test_name', models.CharField(max_length=80)), + ('run_test_folder', models.CharField(max_length=200)), + ], + options={ + 'db_table': 'wetlab_lib_run_configuration_test', + }, + ), + migrations.CreateModel( + name='RunErrors', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('error_code', models.CharField(max_length=10)), + ('error_text', models.CharField(max_length=255)), + ], + options={ + 'db_table': 'wetlab_run_errors', + }, + ), + migrations.CreateModel( + name='RunProcess', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('run_name', models.CharField(max_length=45)), + ('sample_sheet', models.FileField(blank=True, null=True, upload_to='wetlab/sample_sheet/')), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('run_date', models.DateField(blank=True, null=True)), + ('run_finish_date', models.DateTimeField(blank=True, null=True)), + ('bcl2fastq_finish_date', models.DateTimeField(blank=True, null=True)), + ('run_completed_date', models.DateTimeField(blank=True, null=True)), + ('run_forced_continue_on_error', models.BooleanField(blank=True, default=False, null=True)), + ('index_library', models.CharField(blank=True, max_length=85, null=True)), + ('samples', models.CharField(blank=True, max_length=45)), + ('use_space_img_mb', models.CharField(blank=True, max_length=10)), + ('use_space_fasta_mb', models.CharField(blank=True, max_length=10)), + ('use_space_other_mb', models.CharField(blank=True, max_length=10)), + ('center_requested_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='django_utils.center')), + ('reagent_kit', models.ManyToManyField(blank=True, to='core.userlotcommercialkits')), + ('run_error', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.runerrors')), + ], + options={ + 'db_table': 'wetlab_run_process', + }, + ), + migrations.CreateModel( + name='RunStates', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('run_state_name', models.CharField(max_length=50)), + ], + options={ + 'db_table': 'wetlab_run_states', + }, + ), + migrations.CreateModel( + name='SambaConnectionData', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('samba_folder_name', models.CharField(blank=True, max_length=80, null=True)), + ('domain', models.CharField(blank=True, max_length=80, null=True)), + ('host_name', models.CharField(blank=True, max_length=80, null=True)), + ('ip_server', models.CharField(blank=True, max_length=20, null=True)), + ('port_server', models.CharField(blank=True, max_length=10, null=True)), + ('remote_server_name', models.CharField(blank=True, max_length=80, null=True)), + ('shared_folder_name', models.CharField(blank=True, max_length=80, null=True)), + ('user_id', models.CharField(blank=True, max_length=80, null=True)), + ('user_password', models.CharField(blank=True, max_length=20, null=True)), + ('is_direct_tcp', models.BooleanField(default=True)), + ('ntlm_used', models.BooleanField(default=True)), + ], + options={ + 'db_table': 'wetlab_samba_connection_data', + }, + ), + migrations.CreateModel( + name='RunningParameters', + fields=[ + ('run_name_id', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='wetlab.runprocess')), + ('run_id', models.CharField(max_length=255)), + ('experiment_name', models.CharField(max_length=255)), + ('rta_version', models.CharField(blank=True, max_length=255, null=True)), + ('system_suite_version', models.CharField(blank=True, max_length=255, null=True)), + ('library_id', models.CharField(blank=True, max_length=255, null=True)), + ('chemistry', models.CharField(blank=True, max_length=255, null=True)), + ('run_start_date', models.CharField(blank=True, max_length=255, null=True)), + ('analysis_workflow_type', models.CharField(blank=True, max_length=255, null=True)), + ('run_management_type', models.CharField(blank=True, max_length=255, null=True)), + ('planned_read1_cycles', models.CharField(blank=True, max_length=255, null=True)), + ('planned_read2_cycles', models.CharField(blank=True, max_length=255, null=True)), + ('planned_index1_read_cycles', models.CharField(blank=True, max_length=255, null=True)), + ('planned_index2_read_cycles', models.CharField(blank=True, max_length=255, null=True)), + ('application_version', models.CharField(blank=True, max_length=255, null=True)), + ('num_tiles_per_swath', models.CharField(blank=True, max_length=255, null=True)), + ('image_channel', models.CharField(blank=True, max_length=255, null=True)), + ('flowcell', models.CharField(blank=True, max_length=255, null=True)), + ('image_dimensions', models.CharField(blank=True, max_length=255, null=True)), + ('flowcell_layout', models.CharField(blank=True, max_length=255, null=True)), + ], + options={ + 'db_table': 'wetlab_running_parameters', + }, + ), + migrations.CreateModel( + name='StatsRunSummary', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('level', models.CharField(max_length=20)), + ('yield_total', models.CharField(max_length=10)), + ('projected_total_yield', models.CharField(max_length=10)), + ('aligned', models.CharField(max_length=10)), + ('error_rate', models.CharField(max_length=10)), + ('intensity_cycle', models.CharField(max_length=10)), + ('bigger_q30', models.CharField(max_length=10)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('stats_summary_run_date', models.DateField(null=True)), + ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ], + options={ + 'db_table': 'wetlab_stats_run_summary', + }, + ), + migrations.CreateModel( + name='StatsRunRead', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('read', models.CharField(max_length=10)), + ('lane', models.CharField(max_length=10)), + ('tiles', models.CharField(max_length=10)), + ('density', models.CharField(max_length=40)), + ('cluster_pf', models.CharField(max_length=40)), + ('phas_prephas', models.CharField(max_length=40)), + ('reads', models.CharField(max_length=40)), + ('reads_pf', models.CharField(max_length=40)), + ('q30', models.CharField(max_length=40)), + ('yields', models.CharField(max_length=40)), + ('cycles_err_rated', models.CharField(max_length=40)), + ('aligned', models.CharField(max_length=40)), + ('error_rate', models.CharField(max_length=40)), + ('error_rate_35', models.CharField(max_length=40)), + ('error_rate_50', models.CharField(max_length=40)), + ('error_rate_75', models.CharField(max_length=40)), + ('error_rate_100', models.CharField(max_length=40)), + ('intensity_cycle', models.CharField(max_length=40)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('stats_read_run_date', models.DateField(null=True)), + ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ], + options={ + 'db_table': 'wetlab_stats_run_read', + }, + ), + migrations.CreateModel( + name='StatsLaneSummary', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('default_all', models.CharField(max_length=40, null=True)), + ('lane', models.CharField(max_length=10)), + ('pf_cluster', models.CharField(max_length=64)), + ('percent_lane', models.CharField(max_length=64)), + ('perfect_barcode', models.CharField(max_length=64)), + ('one_mismatch', models.CharField(max_length=64)), + ('yield_mb', models.CharField(max_length=64)), + ('bigger_q30', models.CharField(max_length=64)), + ('mean_quality', models.CharField(max_length=64)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('project_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.projects')), + ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ], + options={ + 'db_table': 'wetlab_stats_lane_summary', + }, + ), + migrations.CreateModel( + name='StatsFlSummary', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('default_all', models.CharField(max_length=40, null=True)), + ('flow_raw_cluster', models.CharField(max_length=40)), + ('flow_pf_cluster', models.CharField(max_length=40)), + ('flow_yield_mb', models.CharField(max_length=40)), + ('sample_number', models.CharField(max_length=40)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('project_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.projects')), + ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ], + options={ + 'db_table': 'wetlab_stats_fl_summary', + }, + ), + migrations.CreateModel( + name='SamplesInProject', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sample_name', models.CharField(max_length=255)), + ('barcode_name', models.CharField(max_length=255)), + ('pf_clusters', models.CharField(max_length=55)), + ('percent_in_project', models.CharField(max_length=25)), + ('yield_mb', models.CharField(max_length=55)), + ('quality_q30', models.CharField(max_length=55)), + ('mean_quality', models.CharField(max_length=55)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('project_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.projects')), + ('run_process_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ('sample_in_core', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.samples')), + ('user_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ], + options={ + 'db_table': 'wetlab_samples_in_project', + }, + ), + migrations.AddField( + model_name='runprocess', + name='state', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='state_of_run', to='wetlab.runstates'), + ), + migrations.AddField( + model_name='runprocess', + name='state_before_error', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.runstates'), + ), + migrations.AddField( + model_name='runprocess', + name='used_sequencer', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencerinlab'), + ), + migrations.CreateModel( + name='RawTopUnknowBarcodes', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('lane_number', models.CharField(max_length=4)), + ('top_number', models.CharField(max_length=4)), + ('count', models.CharField(max_length=40)), + ('sequence', models.CharField(max_length=40)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ], + options={ + 'db_table': 'wetlab_raw_top_unknown_barcodes', + }, + ), + migrations.CreateModel( + name='RawDemuxStats', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('default_all', models.CharField(max_length=40, null=True)), + ('raw_yield', models.CharField(max_length=255)), + ('raw_yield_q30', models.CharField(max_length=255)), + ('raw_quality', models.CharField(max_length=255)), + ('pf_yield', models.CharField(max_length=255)), + ('pf_yield_q30', models.CharField(max_length=255)), + ('pf_quality_score', models.CharField(max_length=255)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('project_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.projects')), + ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ], + options={ + 'db_table': 'wetlab_raw_demux_stats', + }, + ), + migrations.AddField( + model_name='projects', + name='run_process', + field=models.ManyToManyField(to='wetlab.runprocess'), + ), + migrations.AddField( + model_name='projects', + name='user_id', + field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL), + ), + migrations.CreateModel( + name='LibUserSampleSheet', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('sample_sheet', models.FileField(upload_to='wetlab/sample_sheets_lib_prep/')), + ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), + ('application', models.CharField(blank=True, max_length=70, null=True)), + ('instrument', models.CharField(blank=True, max_length=70, null=True)), + ('adapter_1', models.CharField(blank=True, max_length=70, null=True)), + ('adapter_2', models.CharField(blank=True, max_length=70, null=True)), + ('assay', models.CharField(blank=True, max_length=70, null=True)), + ('reads', models.CharField(blank=True, max_length=10, null=True)), + ('confirmed_used', models.BooleanField(default=False)), + ('iem_version', models.CharField(blank=True, max_length=5, null=True)), + ('collection_index_kit_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.collectionindexkit')), + ('register_user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ('sequencing_configuration', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencingconfiguration')), + ], + options={ + 'db_table': 'wetlab_lib_user_samplesheet', + }, + ), + migrations.CreateModel( + name='LibraryPool', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('pool_name', models.CharField(max_length=50)), + ('sample_number', models.IntegerField(default=0)), + ('pool_code_id', models.CharField(blank=True, max_length=50)), + ('adapter', models.CharField(blank=True, max_length=50, null=True)), + ('paired_end', models.CharField(blank=True, max_length=10, null=True)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('platform', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencingplatform')), + ('pool_state', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.poolstates')), + ('register_user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ('run_process_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ], + options={ + 'db_table': 'wetlab_library_pool', + 'ordering': ('pool_name',), + }, + ), + migrations.CreateModel( + name='LibPrepare', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('lib_prep_code_id', models.CharField(blank=True, max_length=255, null=True)), + ('user_sample_id', models.CharField(blank=True, max_length=100, null=True)), + ('project_in_samplesheet', models.CharField(blank=True, max_length=80, null=True)), + ('sample_plate', models.CharField(blank=True, max_length=50, null=True)), + ('sample_well', models.CharField(blank=True, max_length=20, null=True)), + ('index_plate_well', models.CharField(blank=True, max_length=20, null=True)), + ('i7_index_id', models.CharField(blank=True, max_length=25, null=True)), + ('i7_index', models.CharField(blank=True, max_length=30, null=True)), + ('i5_index_id', models.CharField(blank=True, max_length=25, null=True)), + ('i5_index', models.CharField(blank=True, max_length=30, null=True)), + ('genome_folder', models.CharField(blank=True, max_length=180, null=True)), + ('manifest', models.CharField(blank=True, max_length=80, null=True)), + ('reused_number', models.IntegerField(default=0)), + ('unique_id', models.CharField(blank=True, max_length=16, null=True)), + ('user_in_samplesheet', models.CharField(blank=True, max_length=255, null=True)), + ('samplename_in_samplesheet', models.CharField(blank=True, max_length=255, null=True)), + ('prefix_protocol', models.CharField(blank=True, max_length=25, null=True)), + ('lib_prep_state', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.libpreparestates')), + ('molecule_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.moleculepreparation')), + ('pools', models.ManyToManyField(blank=True, to='wetlab.librarypool')), + ('protocol_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.protocols')), + ('register_user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ('sample_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.samples')), + ('user_lot_kit_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.userlotcommercialkits')), + ('user_sample_sheet', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.libusersamplesheet')), + ], + options={ + 'db_table': 'wetlab_lib_prepare', + 'ordering': ('lib_prep_code_id',), + }, + ), + migrations.CreateModel( + name='LibParameterValue', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('parameter_value', models.CharField(max_length=255)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('library_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.libprepare')), + ('parameter_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.protocolparameters')), + ], + options={ + 'db_table': 'wetlab_lib_parameter_value', + }, + ), + migrations.CreateModel( + name='GraphicsStats', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('folder_run_graphic', models.CharField(max_length=255)), + ('cluster_count_graph', models.CharField(max_length=255)), + ('flowcell_graph', models.CharField(max_length=255)), + ('intensity_by_cycle_graph', models.CharField(max_length=255)), + ('heatmap_graph', models.CharField(max_length=255)), + ('histogram_graph', models.CharField(max_length=255)), + ('sample_qc_graph', models.CharField(max_length=255)), + ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), + ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ], + options={ + 'db_table': 'wetlab_graphics_stats', + }, + ), + migrations.CreateModel( + name='CollectionIndexValues', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('default_well', models.CharField(max_length=10, null=True)), + ('index_7', models.CharField(max_length=25, null=True)), + ('i_7_seq', models.CharField(max_length=25, null=True)), + ('index_5', models.CharField(max_length=25, null=True)), + ('i_5_seq', models.CharField(max_length=25, null=True)), + ('collection_index_kit_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.collectionindexkit')), + ], + options={ + 'db_table': 'wetlab_collection_index_values', + }, + ), + migrations.CreateModel( + name='AdditionalUserLotKit', + fields=[ + ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), + ('value', models.CharField(max_length=255)), + ('generated_at', models.DateTimeField(auto_now_add=True)), + ('additional_lot_kits', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.additionakitslibprepare')), + ('lib_prep_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.libprepare')), + ('user_lot_kit_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.userlotcommercialkits')), + ], + options={ + 'db_table': 'wetlab_lib_additional_user_lot_kit', + }, + ), + ] diff --git a/wetlab/migrations/__init__.py b/wetlab/migrations/__init__.py new file mode 100644 index 000000000..e69de29bb From 6da4a13ce7ad9728f9e5d1011c8fe473f40594cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 11 Feb 2026 16:33:52 +0100 Subject: [PATCH 318/446] Add migrations for develop changes --- ...reparation_sample_continues_on_and_more.py | 97 +++++++++++++++++++ .../0002_remove_service_service_status.py | 17 ++++ ...ove_librarypool_run_process_id_and_more.py | 47 +++++++++ 3 files changed, 161 insertions(+) create mode 100644 core/migrations/0002_rename_molecule_used_for_moleculepreparation_sample_continues_on_and_more.py create mode 100644 drylab/migrations/0002_remove_service_service_status.py create mode 100644 wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py diff --git a/core/migrations/0002_rename_molecule_used_for_moleculepreparation_sample_continues_on_and_more.py b/core/migrations/0002_rename_molecule_used_for_moleculepreparation_sample_continues_on_and_more.py new file mode 100644 index 000000000..3b7771015 --- /dev/null +++ b/core/migrations/0002_rename_molecule_used_for_moleculepreparation_sample_continues_on_and_more.py @@ -0,0 +1,97 @@ +# Generated by Django 4.2.25 on 2026-02-11 16:33 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('core', '0001_initial'), + ] + + operations = [ + migrations.RenameField( + model_name='moleculepreparation', + old_name='molecule_used_for', + new_name='sample_continues_on', + ), + migrations.RenameField( + model_name='sampleprojectsfields', + old_name='sample_project_searchable', + new_name='sample_project_downloadable', + ), + migrations.AddField( + model_name='city', + name='geo_loc_city_cod', + field=models.CharField(blank=True, max_length=10, null=True), + ), + migrations.AddField( + model_name='labrequest', + name='autonom_cod', + field=models.CharField(blank=True, max_length=20, null=True), + ), + migrations.AddField( + model_name='labrequest', + name='center_class_code', + field=models.CharField(blank=True, max_length=20, null=True), + ), + migrations.AddField( + model_name='labrequest', + name='dep_func', + field=models.CharField(blank=True, max_length=80, null=True), + ), + migrations.AddField( + model_name='labrequest', + name='lab_code_1', + field=models.CharField(blank=True, max_length=20, null=True, unique=True), + ), + migrations.AddField( + model_name='labrequest', + name='lab_code_2', + field=models.CharField(blank=True, max_length=20, null=True), + ), + migrations.AddField( + model_name='labrequest', + name='lab_function', + field=models.CharField(blank=True, max_length=120, null=True), + ), + migrations.AddField( + model_name='labrequest', + name='lab_geo_loc_latitude', + field=models.CharField(blank=True, max_length=30, null=True), + ), + migrations.AddField( + model_name='labrequest', + name='lab_geo_loc_longitude', + field=models.CharField(blank=True, max_length=30, null=True), + ), + migrations.AddField( + model_name='labrequest', + name='post_code', + field=models.CharField(blank=True, max_length=10, null=True), + ), + migrations.AddField( + model_name='protocolparameters', + name='parameter_download', + field=models.BooleanField(blank=True, default=False, null=True), + ), + migrations.AddField( + model_name='stateincountry', + name='geo_loc_state_cod', + field=models.CharField(blank=True, help_text='Geographic code of the CCAA', max_length=10, null=True), + ), + migrations.AddField( + model_name='statesformolecule', + name='molecule_state_display', + field=models.CharField(blank=True, max_length=80, null=True), + ), + migrations.AlterField( + model_name='labrequest', + name='lab_name', + field=models.CharField(max_length=100), + ), + migrations.AlterModelTable( + name='moleculeusedfor', + table='core_sample_continues_on', + ), + ] diff --git a/drylab/migrations/0002_remove_service_service_status.py b/drylab/migrations/0002_remove_service_service_status.py new file mode 100644 index 000000000..3613622ab --- /dev/null +++ b/drylab/migrations/0002_remove_service_service_status.py @@ -0,0 +1,17 @@ +# Generated by Django 4.2.25 on 2026-02-11 16:33 + +from django.db import migrations + + +class Migration(migrations.Migration): + + dependencies = [ + ('drylab', '0001_initial'), + ] + + operations = [ + migrations.RemoveField( + model_name='service', + name='service_status', + ), + ] diff --git a/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py b/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py new file mode 100644 index 000000000..218400b63 --- /dev/null +++ b/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py @@ -0,0 +1,47 @@ +# Generated by Django 4.2.25 on 2026-02-11 16:33 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('wetlab', '0001_initial'), + ] + + operations = [ + migrations.RemoveField( + model_name='librarypool', + name='run_process_id', + ), + migrations.AddField( + model_name='runprocess', + name='library_pool', + field=models.ManyToManyField(blank=True, to='wetlab.librarypool'), + ), + migrations.AddField( + model_name='runstates', + name='description', + field=models.CharField(blank=True, max_length=255, null=True), + ), + migrations.AddField( + model_name='runstates', + name='show_in_stats', + field=models.BooleanField(default=False), + ), + migrations.AddField( + model_name='runstates', + name='state_display', + field=models.CharField(blank=True, max_length=80, null=True), + ), + migrations.AlterField( + model_name='libprepare', + name='prefix_protocol', + field=models.CharField(blank=True, max_length=50, null=True), + ), + migrations.AlterField( + model_name='rawtopunknowbarcodes', + name='count', + field=models.IntegerField(), + ), + ] From 1225eecc8241c4754310c5e85933368f70478c53 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 11 Feb 2026 16:35:45 +0100 Subject: [PATCH 319/446] added developer notes about how to create migration files --- README.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/README.md b/README.md index 42d393c83..8d9a6928e 100644 --- a/README.md +++ b/README.md @@ -279,6 +279,19 @@ mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_pro - Go to Configuration -> Email configuration - Fill the form with the needed params for your email configuration and try to send a test email. +## Developer notes + +### Django migrations workflow + +Migrations are committed to the repo. Do not run `makemigrations` during install/upgrade. + +Baseline + upgrade flow for new releases: + +1. Generate baseline migrations from the last stable tag (example 3.0.0). +2. Commit the baseline migrations. +3. Generate new migrations on `develop` for schema changes and commit them. +4. Upgrades run `migrate --fake-initial` once to align existing tables, then `migrate` to apply the new migration files. + ### Configure Apache server Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf From 03fb14bc698ab92630f78c8ceb83ad058093f89c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 11 Feb 2026 16:43:18 +0100 Subject: [PATCH 320/446] removed --exclude migrations from rsync --- install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/install.sh b/install.sh index e65f8e953..20352016b 100644 --- a/install.sh +++ b/install.sh @@ -650,7 +650,7 @@ upgrade_application_files() { echo "Copying files to installation folder" rsync -rlv conf/ $INSTALL_PATH/conf/ rsync -rlv --fuzzy --delay-updates --delete-delay \ - --exclude "logs" --exclude "documents" --exclude "migrations" --exclude "__pycache__" \ + --exclude "logs" --exclude "documents" --exclude "__pycache__" \ README.md LICENSE test conf $REQUIRED_MODULES $INSTALL_PATH cd $INSTALL_PATH From 504ef6e1f3be96b89b3245bb5fe35eedf4cba9d0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 19 Feb 2026 13:13:39 +0100 Subject: [PATCH 321/446] added notes and doc about migration scripts and which version are related to --- UPGRADE_SCRIPTS.md | 23 +++++++++ core/scripts/migrate_optional_values.py | 1 + core/scripts/migrate_sample_type.py | 1 + core/scripts/rename_app_name.py | 1 + .../scripts/drylab_service_state_migration.py | 1 + ...ove_librarypool_run_process_id_and_more.py | 51 +++++++++++++++++-- .../scripts/convert_rawtop_counter_to_int.py | 3 +- .../scripts/library_pool_to_many_relation.py | 3 +- 8 files changed, 79 insertions(+), 5 deletions(-) create mode 100644 UPGRADE_SCRIPTS.md diff --git a/UPGRADE_SCRIPTS.md b/UPGRADE_SCRIPTS.md new file mode 100644 index 000000000..b438d440f --- /dev/null +++ b/UPGRADE_SCRIPTS.md @@ -0,0 +1,23 @@ +# Upgrade scripts + +This file lists data migration scripts and the version range they apply to. +Run them with: + +```bash +python manage.py runscript +``` + +## 3.0.0 -> 3.1.0 + +- `wetlab/scripts/convert_rawtop_counter_to_int.py` (script name: `convert_rawtop_counter_to_int`) +- `wetlab/scripts/library_pool_to_many_relation.py` (script name: `library_pool_to_many_relation`) + +## 2.3.0 -> 3.0.0 + +- `core/scripts/rename_app_name.py` (script name: `rename_app_name`) +- `core/scripts/migrate_sample_type.py` (script name: `migrate_sample_type`) +- `core/scripts/migrate_optional_values.py` (script name: `migrate_optional_values`) + +## 2.3.0 -> 2.3.1 + +- `drylab/scripts/drylab_service_state_migration.py` (script name: `drylab_service_state_migration`) diff --git a/core/scripts/migrate_optional_values.py b/core/scripts/migrate_optional_values.py index 31eca01ea..3dcc9fdeb 100644 --- a/core/scripts/migrate_optional_values.py +++ b/core/scripts/migrate_optional_values.py @@ -1,6 +1,7 @@ import core.models """ + Upgrade: 2.3.0 -> 3.0.0 The script is applicable for the upgrade from 2.3.0 to 3.0.0. Because the new version changes the way that optional values are stored. Instead of having a field "sample_project_option_list" now values are diff --git a/core/scripts/migrate_sample_type.py b/core/scripts/migrate_sample_type.py index d97f34745..df8ee8543 100644 --- a/core/scripts/migrate_sample_type.py +++ b/core/scripts/migrate_sample_type.py @@ -1,6 +1,7 @@ import core.models """ + Upgrade: 2.3.0 -> 3.0.0 The script is applicable for the upgrade from 2.3.0 to 3.0.0. Because the new version changes the value that is stored now is the field name and not the number and instead of optional values now are the diff --git a/core/scripts/rename_app_name.py b/core/scripts/rename_app_name.py index 05eb1b922..549928907 100644 --- a/core/scripts/rename_app_name.py +++ b/core/scripts/rename_app_name.py @@ -1,6 +1,7 @@ import core.models """ + Upgrade: 2.3.0 -> 3.0.0 The script is applicable for the upgrade from 2.3.0 to 3.0.0. Because the application in iSkylims have been renamed, this required that some tables where was indicated the application name must be diff --git a/drylab/scripts/drylab_service_state_migration.py b/drylab/scripts/drylab_service_state_migration.py index 7ea4c29d0..17b7336f4 100644 --- a/drylab/scripts/drylab_service_state_migration.py +++ b/drylab/scripts/drylab_service_state_migration.py @@ -1,6 +1,7 @@ from drylab.models import Service, ServiceState """ + Upgrade: 2.3.0 -> 2.3.1 The script is applicable for the upgrade from 2.3.0 to 2.3.1. Service state that was defined as option choice in models,is replaced in version 2.3.1 as a primary key in SampleState table, given in this way diff --git a/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py b/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py index 218400b63..c0acb26dc 100644 --- a/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py +++ b/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py @@ -10,9 +10,54 @@ class Migration(migrations.Migration): ] operations = [ - migrations.RemoveField( - model_name='librarypool', - name='run_process_id', + migrations.RunSQL( + """ + UPDATE wetlab_raw_top_unknown_barcodes + SET count = NULL + WHERE count IS NOT NULL AND count NOT REGEXP '^[0-9]+$' + """, + reverse_sql=migrations.RunSQL.noop, + ), + migrations.SeparateDatabaseAndState( + database_operations=[ + migrations.RunSQL( + """ + SELECT COLUMN_NAME + FROM information_schema.COLUMNS + WHERE TABLE_SCHEMA = DATABASE() + AND TABLE_NAME = 'wetlab_library_pool' + AND COLUMN_NAME = 'run_process_id_id' + """, + reverse_sql=migrations.RunSQL.noop, + ), + migrations.RunSQL( + """ + SET @drop_col := ( + SELECT IF( + EXISTS( + SELECT 1 + FROM information_schema.COLUMNS + WHERE TABLE_SCHEMA = DATABASE() + AND TABLE_NAME = 'wetlab_library_pool' + AND COLUMN_NAME = 'run_process_id_id' + ), + 'ALTER TABLE wetlab_library_pool DROP COLUMN run_process_id_id', + 'SELECT 1' + ) + ); + PREPARE stmt FROM @drop_col; + EXECUTE stmt; + DEALLOCATE PREPARE stmt; + """, + reverse_sql=migrations.RunSQL.noop, + ), + ], + state_operations=[ + migrations.RemoveField( + model_name='librarypool', + name='run_process_id', + ), + ], ), migrations.AddField( model_name='runprocess', diff --git a/wetlab/scripts/convert_rawtop_counter_to_int.py b/wetlab/scripts/convert_rawtop_counter_to_int.py index 94c8fb6a3..54a80fa8d 100644 --- a/wetlab/scripts/convert_rawtop_counter_to_int.py +++ b/wetlab/scripts/convert_rawtop_counter_to_int.py @@ -2,7 +2,8 @@ def run(): - """The script implemted the issue #158 Unable to convert barcode count to + """Upgrade: 3.0.0 -> 3.1.0 + The script implemted the issue #158 Unable to convert barcode count to integer, to convert the counter that are in a string format, separated by "," to int. """ diff --git a/wetlab/scripts/library_pool_to_many_relation.py b/wetlab/scripts/library_pool_to_many_relation.py index 67cbd1c21..532789c90 100644 --- a/wetlab/scripts/library_pool_to_many_relation.py +++ b/wetlab/scripts/library_pool_to_many_relation.py @@ -2,7 +2,8 @@ def run(f_name): - """This script is part of the issue "#180,when deleting run , pool and + """Upgrade: 3.0.0 -> 3.1.0 + This script is part of the issue "#180,when deleting run , pool and library_preparations are also deleted" on Class LibraryPool. The first part of the script fetch the existing data on run_process_id and create a file containing the pk of the libraryPool instance and From dfb0f8bcde382a2138ac28a9b1a1ffcb01197e9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 19 Feb 2026 13:29:55 +0100 Subject: [PATCH 322/446] updated upgrade scripts md with order info --- UPGRADE_SCRIPTS.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/UPGRADE_SCRIPTS.md b/UPGRADE_SCRIPTS.md index b438d440f..919af840f 100644 --- a/UPGRADE_SCRIPTS.md +++ b/UPGRADE_SCRIPTS.md @@ -9,6 +9,19 @@ python manage.py runscript ## 3.0.0 -> 3.1.0 +- Run order: + 1. Export LibraryPool run_process_id data (before migrations). + 2. Run `convert_rawtop_counter_to_int` before migrations. + 3. Run migrations. + 4. Run `library_pool_to_many_relation` after migrations with the exported file. + +- Export example: + ```bash + mysql -u -p -h -D \ + -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ + > /tmp/library_pool_run_process.tsv + ``` + - `wetlab/scripts/convert_rawtop_counter_to_int.py` (script name: `convert_rawtop_counter_to_int`) - `wetlab/scripts/library_pool_to_many_relation.py` (script name: `library_pool_to_many_relation`) From 0bd9b04bfebdb30d22f3c091c84eee8030150793 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 19 Feb 2026 13:30:20 +0100 Subject: [PATCH 323/446] added script before and script after migration options --- docker_install.sh | 35 ++++++++++++++++++++++++++++------- install.sh | 46 ++++++++++++++++++++++++++++++++++++++++------ 2 files changed, 68 insertions(+), 13 deletions(-) diff --git a/docker_install.sh b/docker_install.sh index f31e6e901..9510b4f60 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -6,7 +6,7 @@ usage() { cat << EOF This script installs and upgrades the iskylims app. -Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--install_conf] [--action] [--script] [--test] +Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--install_conf] [--action] [--script] [--script_before] [--script_after] [--test] Optional input data: --demo_data | Provide already downloaded demo data from Zenodo --install_type | Specify the installation type for iSkyLIMS (default: full) @@ -14,7 +14,9 @@ Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--i --compose_file | docker compose file to use (overrides default) --install_conf | Settings file consumed during docker image build (mandatory for production) --action | install (default) or upgrade, to control DB initialisation steps - --script | Run a Django migration script (can be repeated) + --script | Run a Django migration script after migrations (can be repeated) + --script_before | Run a Django migration script before migrations (can be repeated) + --script_after | Run a Django migration script after migrations (can be repeated) --skip_demo_data | Skip downloading/copying demo data to samba container --skip_test_data | Skip loading test fixtures (test/test_data.json) --test | Use development/test compose file and sample data @@ -56,6 +58,8 @@ do --install_conf) set -- "$@" -s ;; --action) set -- "$@" -a ;; --script) set -- "$@" -m ;; + --script_before) set -- "$@" -b ;; + --script_after) set -- "$@" -f ;; --skip_demo_data) set -- "$@" -n ;; --skip_test_data) set -- "$@" -t ;; --test) set -- "$@" -p ;; @@ -79,10 +83,12 @@ skip_test_data="" mode="production" action="install" run_script=false +run_script_before=false migration_script=() +migration_script_before=() # PARSE VARIABLE ARGUMENTS WITH getopts -options=":d:i:g:c:s:a:m:vhntp" +options=":d:i:g:c:s:a:m:b:f:vhntp" while getopts $options opt; do case $opt in d) @@ -108,6 +114,14 @@ while getopts $options opt; do run_script=true migration_script+=("$OPTARG") ;; + b) + run_script_before=true + migration_script_before+=("$OPTARG") + ;; + f) + run_script=true + migration_script+=("$OPTARG") + ;; n) skip_demo_data=true ;; @@ -255,19 +269,26 @@ if ! docker exec -it iskylims_app test -f "$container_install_conf_path"; then docker cp "$host_install_conf_path" "iskylims_app:$container_install_conf_path" fi -script_args="" +script_args_before="" +if [ "$run_script_before" = true ]; then + for val in "${migration_script_before[@]}"; do + script_args_before+=" --script_before $(printf '%q' "$val")" + done +fi + +script_args_after="" if [ "$run_script" = true ]; then for val in "${migration_script[@]}"; do - script_args+=" --script $(printf '%q' "$val")" + script_args_after+=" --script_after $(printf '%q' "$val")" done fi if [ "$action" = "upgrade" ]; then echo "Running install.sh upgrade inside the container" - docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --upgrade app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args" + docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --upgrade app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" else echo "Running install.sh install inside the container" - docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --install app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args" + docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --install app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" fi if ! docker exec -it iskylims_app test -f /opt/iskylims/manage.py; then diff --git a/install.sh b/install.sh index 20352016b..ccefa55bb 100644 --- a/install.sh +++ b/install.sh @@ -15,7 +15,9 @@ usage : $0 --upgrade --git_revision --conf --conf | Select custom configuration file. Default: ./install_settings.txt --tables | Load the first inital tables (from conf folder) --skip_tables | Skip loading initial tables (even during install) - --script | Run a migration script. + --script | Run a migration script after migrations. + --script_before | Run a migration script before migrations. + --script_after | Run a migration script after migrations (same as --script). --ren_app | Rename apps required for the upgrade migration to 3.0.0 --docker | Deprecated. Use --skip_apache_restart to avoid Apache checks/restart. @@ -35,6 +37,9 @@ Examples: Make adjustments for apps renaming in upgrade 2.3.0 to 2.3.1 $0 --upgrade full --ren_app --script --tables + + Upgrade running pre/post migration scripts: + $0 --upgrade app --script_before --script_after EOF } @@ -455,6 +460,21 @@ install_system_packages() { # run_django_deploy: execute makemigrations/migrate and optional fixture/superuser steps. run_django_deploy() { local mode="${1:-install}" + if [ "$run_script_before" = true ]; then + for val in "${migration_script_before[@]}"; do + if [[ $val = *","* ]]; then + parameters=(${val//,/ }) + echo "Running pre-migration script: ${parameters[0]}" + ./manage.py runscript ${parameters[0]} --script-args ${parameters[1]} + echo "Done pre-migration script: ${parameters[0]}" + else + echo "Running pre-migration script: $val" + ./manage.py runscript $val + echo "Done pre-migration script: $val" + fi + done + fi + if [ "$mode" = "upgrade" ]; then echo "Applying migrations in fake-initial mode" python manage.py migrate --noinput --fake-initial @@ -475,13 +495,13 @@ run_django_deploy() { for val in "${migration_script[@]}"; do if [[ $val = *","* ]]; then parameters=(${val//,/ }) - echo "Running migration script: ${parameters[0]}" + echo "Running post-migration script: ${parameters[0]}" ./manage.py runscript ${parameters[0]} --script-args ${parameters[1]} - echo "Done migration script: ${parameters[0]}" + echo "Done post-migration script: ${parameters[0]}" else - echo "Running migration script: $val" + echo "Running post-migration script: $val" ./manage.py runscript $val - echo "Done migration script: $val" + echo "Done post-migration script: $val" fi done fi @@ -758,6 +778,9 @@ do --install) set -- "$@" -i ;; --upgrade) set -- "$@" -u ;; --script) set -- "$@" -s ;; + --script_before) set -- "$@" -p ;; + --script_after) set -- "$@" -o ;; + --script_prev) set -- "$@" -p ;; --tables) set -- "$@" -t ;; --skip_tables) set -- "$@" -b ;; --git_revision) set -- "$@" -g ;; @@ -787,10 +810,13 @@ docker=false prefilled_tables="conf/first_install_tables.json" restart_apache=true run_script=false +run_script_before=false +migration_script=() +migration_script_before=() skip_tables=false # PARSE VARIABLE ARGUMENTS WITH getops -options=":c:s:i:u:r:g:tdbkvha" +options=":c:s:i:u:r:g:tdbkvhaop" while getopts $options opt; do case $opt in i ) @@ -819,6 +845,14 @@ while getopts $options opt; do run_script=true migration_script+=("$OPTARG") ;; + p ) + run_script_before=true + migration_script_before+=("$OPTARG") + ;; + o ) + run_script=true + migration_script+=("$OPTARG") + ;; t ) tables=true ;; From 1571796c3248621a37c1a454b0ba8d2749cd5550 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 19 Feb 2026 13:30:50 +0100 Subject: [PATCH 324/446] added needed export for library pool to many relation --- wetlab/scripts/library_pool_to_many_relation.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/wetlab/scripts/library_pool_to_many_relation.py b/wetlab/scripts/library_pool_to_many_relation.py index 532789c90..925a08014 100644 --- a/wetlab/scripts/library_pool_to_many_relation.py +++ b/wetlab/scripts/library_pool_to_many_relation.py @@ -5,10 +5,13 @@ def run(f_name): """Upgrade: 3.0.0 -> 3.1.0 This script is part of the issue "#180,when deleting run , pool and library_preparations are also deleted" on Class LibraryPool. - The first part of the script fetch the existing data on run_process_id - and create a file containing the pk of the libraryPool instance and - the pk of the run_process_id - The second part of the script fetch the data from the file and add the + This script expects a file created externally that contains the pk of the + LibraryPool instance and the pk of the run_process_id. + Export example: + mysql -u -p -h -D \ + -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ + > /tmp/library_pool_run_process.tsv + The script fetches the data from the file and adds the run_process_pk to the run_process field of the LibraryPool instance """ if hasattr(wetlab.models.LibraryPool, "run_process"): From c5027112605708e384e39c4e46323ae9f174df81 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 19 Feb 2026 13:38:43 +0100 Subject: [PATCH 325/446] fix getops for script before --- install.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/install.sh b/install.sh index ccefa55bb..89543a703 100644 --- a/install.sh +++ b/install.sh @@ -816,7 +816,7 @@ migration_script_before=() skip_tables=false # PARSE VARIABLE ARGUMENTS WITH getops -options=":c:s:i:u:r:g:tdbkvhaop" +options=":c:s:i:u:r:g:tdbkvhao:p:" while getopts $options opt; do case $opt in i ) From fba34057e9790c654574b07383e46daacb4e6bbd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 19 Feb 2026 13:51:01 +0100 Subject: [PATCH 326/446] Drop FK before removing run_process_id_id --- ...ove_librarypool_run_process_id_and_more.py | 66 ++++++++++--------- 1 file changed, 36 insertions(+), 30 deletions(-) diff --git a/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py b/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py index c0acb26dc..71b494e4d 100644 --- a/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py +++ b/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py @@ -3,6 +3,40 @@ from django.db import migrations, models +def drop_librarypool_run_process_id(apps, schema_editor): + with schema_editor.connection.cursor() as cursor: + cursor.execute( + """ + SELECT 1 + FROM information_schema.COLUMNS + WHERE TABLE_SCHEMA = DATABASE() + AND TABLE_NAME = 'wetlab_library_pool' + AND COLUMN_NAME = 'run_process_id_id' + """ + ) + if cursor.fetchone() is None: + return + + cursor.execute( + """ + SELECT CONSTRAINT_NAME + FROM information_schema.KEY_COLUMN_USAGE + WHERE TABLE_SCHEMA = DATABASE() + AND TABLE_NAME = 'wetlab_library_pool' + AND COLUMN_NAME = 'run_process_id_id' + AND REFERENCED_TABLE_NAME IS NOT NULL + """ + ) + for (constraint_name,) in cursor.fetchall(): + cursor.execute( + f"ALTER TABLE wetlab_library_pool DROP FOREIGN KEY `{constraint_name}`" + ) + + cursor.execute( + "ALTER TABLE wetlab_library_pool DROP COLUMN run_process_id_id" + ) + + class Migration(migrations.Migration): dependencies = [ @@ -20,36 +54,8 @@ class Migration(migrations.Migration): ), migrations.SeparateDatabaseAndState( database_operations=[ - migrations.RunSQL( - """ - SELECT COLUMN_NAME - FROM information_schema.COLUMNS - WHERE TABLE_SCHEMA = DATABASE() - AND TABLE_NAME = 'wetlab_library_pool' - AND COLUMN_NAME = 'run_process_id_id' - """, - reverse_sql=migrations.RunSQL.noop, - ), - migrations.RunSQL( - """ - SET @drop_col := ( - SELECT IF( - EXISTS( - SELECT 1 - FROM information_schema.COLUMNS - WHERE TABLE_SCHEMA = DATABASE() - AND TABLE_NAME = 'wetlab_library_pool' - AND COLUMN_NAME = 'run_process_id_id' - ), - 'ALTER TABLE wetlab_library_pool DROP COLUMN run_process_id_id', - 'SELECT 1' - ) - ); - PREPARE stmt FROM @drop_col; - EXECUTE stmt; - DEALLOCATE PREPARE stmt; - """, - reverse_sql=migrations.RunSQL.noop, + migrations.RunPython( + drop_librarypool_run_process_id, migrations.RunPython.noop ), ], state_operations=[ From b9a506ddb4b7c754a066ec4b535bbc88d8dfb904 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 19 Feb 2026 14:18:07 +0100 Subject: [PATCH 327/446] add comment to install.sh about second migrate command --- install.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/install.sh b/install.sh index 89543a703..a85c9a4be 100644 --- a/install.sh +++ b/install.sh @@ -478,6 +478,7 @@ run_django_deploy() { if [ "$mode" = "upgrade" ]; then echo "Applying migrations in fake-initial mode" python manage.py migrate --noinput --fake-initial + # Second pass ensures non-initial migrations are applied after fake-initial. echo "Applying migrations" python manage.py migrate --noinput else From 3b5dc3c634eae06bfb2a17a384ad5e8973a5285a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 20 Feb 2026 11:15:38 +0100 Subject: [PATCH 328/446] changed samba configuration for test data --- test/test_data.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/test_data.json b/test/test_data.json index f81d46aad..700109f1b 100644 --- a/test/test_data.json +++ b/test/test_data.json @@ -15856,7 +15856,7 @@ "model": "wetlab.sambaconnectiondata", "pk": 1, "fields": { - "samba_folder_name": "", + "samba_folder_name": "Runs", "domain": "", "host_name": "samba", "ip_server": "", From ae7a5ba2b9d2d61a07d5ad8c04c694bcb3c1bdf9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 20 Feb 2026 11:16:03 +0100 Subject: [PATCH 329/446] fix shared folder when samba application folder is present in samba configuration --- wetlab/models.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/wetlab/models.py b/wetlab/models.py index 3286d9e22..f6e7f75bf 100644 --- a/wetlab/models.py +++ b/wetlab/models.py @@ -1932,7 +1932,9 @@ def get_samba_application_folder_name(self): return "" def get_samba_shared_folder_name(self): - if self.shared_folder_name is not None: + if self.samba_folder_name is not None and self.shared_folder_name is not None: + return "%s\\%s" % (self.samba_folder_name, self.shared_folder_name) + elif self.shared_folder_name is not None: return "%s" % (self.shared_folder_name) else: return "" From 1b37e0d92a22f39bffaf477a8cbbd6bb36d6876e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 23 Feb 2026 15:00:12 +0100 Subject: [PATCH 330/446] trying to make docs clearer --- LEAME.md | 45 +++++++++++++++++++++++++++++++++++++++++++++ README.md | 40 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 85 insertions(+) diff --git a/LEAME.md b/LEAME.md index 2d33e91da..6dc036f25 100644 --- a/LEAME.md +++ b/LEAME.md @@ -235,6 +235,11 @@ bash install.sh --upgrade app --git_revision main --tables # ejemplo ejecutando un script de migracion en la actualizacion bash install.sh --upgrade app --script migrate_optional_values --git_revision main --tables + +# 3.0.0 -> 3.1.0 (scripts de datos pre/post) +bash install.sh --upgrade app --git_revision main \ + --script_before convert_rawtop_counter_to_int \ + --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv ``` O ejecuta todo en un unico comando: @@ -245,6 +250,46 @@ sudo bash install.sh --upgrade full --git_revision main --tables Las actualizaciones regeneran las migraciones y las aplican con `--fake-initial` para conservar las tablas existentes, igual que en Docker. +Para 3.0.0 -> 3.1.0 en Docker, exporta el mapeo y ejecuta: + +```bash +mysql --user= --password= --host= --port= iskylims \ + -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ + > /tmp/library_pool_run_process.tsv + +bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade \ + --script_before convert_rawtop_counter_to_int \ + --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv +``` + +#### Scripts de datos 3.0.0 -> 3.1.0 + +Algunas migraciones de datos deben ejecutarse antes/despues de las migraciones de esquema: + +1. Exportar el mapeo de LibraryPool (antes de migrar): + +```bash +mysql --user= --password= --host= --port= iskylims \ + -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ + > /tmp/library_pool_run_process.tsv +``` + +2. Ejecutar la actualizacion con scripts pre/post: + +```bash +bash install.sh --upgrade app --git_revision main \ + --script_before convert_rawtop_counter_to_int \ + --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv +``` + +Equivalente en Docker: + +```bash +bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade \ + --script_before convert_rawtop_counter_to_int \ + --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv +``` + ## Que hacer si algo falla Cuando actualizamos usando el script de instalacion estamos realizando varios cambios en la base de datos. Si algo falla necesitamos restaurar el estado anterior y empezar de nuevo. diff --git a/README.md b/README.md index 8d9a6928e..8ed8ce985 100644 --- a/README.md +++ b/README.md @@ -31,10 +31,13 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Refresh code and settings](#refresh-code-and-settings) - [Run upgrade steps requiring root](#run-upgrade-steps-requiring-root) - [Run upgrade steps without root](#run-upgrade-steps-without-root) + - [3.0.0 -\> 3.1.0 data scripts](#300---310-data-scripts) - [What to do if something fails](#what-to-do-if-something-fails) - [Final configuration steps](#final-configuration-steps) - [SAMBA configurarion](#samba-configurarion) - [Email verification](#email-verification) + - [Developer notes](#developer-notes) + - [Django migrations workflow](#django-migrations-workflow) - [Configure Apache server](#configure-apache-server) - [Verification of the installation](#verification-of-the-installation) - [iSkyLIMS documentation](#iskylims-documentation) @@ -119,6 +122,18 @@ bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade The upgrade path rebuilds/restarts the container and runs `install.sh` inside the app container, which regenerates migrations, applies them with `--fake-initial`, and skips superuser/demo/test data loading. +For 3.0.0 -> 3.1.0, export the LibraryPool mapping first, then run the upgrade with pre/post scripts: + +```bash +mysql --user= --password= --host= --port= iskylims \ + -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ + > /tmp/library_pool_run_process.tsv + +bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade \ + --script_before convert_rawtop_counter_to_int \ + --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv +``` + ## Bare-metal deployment (Ubuntu/CentOS) ### Install @@ -236,6 +251,11 @@ bash install.sh --upgrade app --git_revision main --tables # example running a migration script during upgrade bash install.sh --upgrade app --script migrate_optional_values --git_revision main --tables + +# 3.0.0 -> 3.1.0 (pre/post data scripts) +bash install.sh --upgrade app --git_revision main \ + --script_before convert_rawtop_counter_to_int \ + --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv ``` Or run everything in one go: @@ -246,6 +266,26 @@ sudo bash install.sh --upgrade full --git_revision main --tables Upgrades regenerate migrations and apply them with `--fake-initial` so existing tables remain intact, matching the Docker workflow. +#### 3.0.0 -> 3.1.0 data scripts + +Some data migrations must run before/after schema migrations: + +1. Export LibraryPool mapping (before migrations): + +```bash +mysql --user= --password= --host= --port= iskylims \ + -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ + > /tmp/library_pool_run_process.tsv +``` + +2. Run upgrade with pre/post scripts: + +```bash +bash install.sh --upgrade app --git_revision main \ + --script_before convert_rawtop_counter_to_int \ + --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv +``` + ## What to do if something fails When we upgrade using the installation script we are performing several changes in the database. If something fails we need to restore the app situation before anything happened and start all over. From 039fc3ab318c12efd9d301ed32d7cf02381fcd1f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 23 Feb 2026 15:00:32 +0100 Subject: [PATCH 331/446] improve message --- wetlab/config.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wetlab/config.py b/wetlab/config.py index a69a9f222..6f789af5b 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -864,7 +864,7 @@ # ######################## Configuration test errors ##################################### ERROR_NOT_FOLDER_RUN_TEST_WAS_FOUND = [ "Unable to run the configuration test", - "Run test folder was found on remote server", + "Run test folder was not found on remote server", ] ERROR_NO_RUN_TEST_WAS_CREATED = [ "Unable to continue with configuration testing", From 013a50388ac7b5bd0c946b387913eb2a3d989bca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 23 Feb 2026 15:01:16 +0100 Subject: [PATCH 332/446] improve message --- wetlab/utils/crontab_process.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index 53b2c262b..5b76fae53 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -2874,9 +2874,9 @@ def process_and_store_raw_demux_project_data( experiment_name + " : Created project name " + project - + "Because it was not store" + + " because it's a new project and it was not store before." ) - wetlab.utils.common.logging_warnings(string_message, True) + wetlab.utils.common.logging_warnings(string_message, False) logger.info("%s : Processing demultiplexing raw project data", experiment_name) for project in parsed_data.keys(): From b045acc56e5d9c7d2481ac62fbe6fe25530f1287 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 23 Feb 2026 15:01:43 +0100 Subject: [PATCH 333/446] revert change --- wetlab/models.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/wetlab/models.py b/wetlab/models.py index f6e7f75bf..3286d9e22 100644 --- a/wetlab/models.py +++ b/wetlab/models.py @@ -1932,9 +1932,7 @@ def get_samba_application_folder_name(self): return "" def get_samba_shared_folder_name(self): - if self.samba_folder_name is not None and self.shared_folder_name is not None: - return "%s\\%s" % (self.samba_folder_name, self.shared_folder_name) - elif self.shared_folder_name is not None: + if self.shared_folder_name is not None: return "%s" % (self.shared_folder_name) else: return "" From 110fe17de9a89584b7869c6b8f8be917fca1e384 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 23 Feb 2026 15:02:57 +0100 Subject: [PATCH 334/446] fix def not using application folder path --- wetlab/utils/crontab_update_run.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index c5453847c..910ec6713 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -772,6 +772,7 @@ def manage_run_in_processed_run_state(conn, run_process_objs): .last() .get_run_folder() ) + root_run_folder = os.path.join("/", wetlab.utils.crontab_process.get_samba_application_shared_folder(), run_folder) # delete existing information to avoid having duplicated tables wetlab.utils.crontab_process.delete_existing_run_metrics_table_processed( run_process_obj, experiment_name @@ -781,7 +782,7 @@ def manage_run_in_processed_run_state(conn, run_process_objs): wetlab.utils.common.get_samba_atribute_data( conn, wetlab.utils.crontab_process.get_samba_shared_folder(), - run_folder, + root_run_folder, "create_time", ) ) @@ -804,7 +805,7 @@ def manage_run_in_processed_run_state(conn, run_process_objs): # Get run metric files run_metric_files = wetlab.utils.crontab_process.get_run_metric_files( - conn, run_folder, experiment_name + conn, root_run_folder, experiment_name ) if "ERROR" in run_metric_files: From 7400db49481014523a39031af9e20094a7cc06b0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 10:46:20 +0100 Subject: [PATCH 335/446] fix get run disk utilization to correctly find application folder --- wetlab/utils/crontab_process.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index 5b76fae53..67e5c613d 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -47,7 +47,7 @@ def get_run_disk_utilization(conn, run_folder, experiment_name): full_path_run = os.path.join(application_folder, run_folder) try: - get_full_list = conn.listPath(shared_folder, run_folder) + get_full_list = conn.listPath(shared_folder, full_path_run) except Exception: string_message = experiment_name + " : Unable to get the folder " + run_folder wetlab.utils.common.logging_errors(string_message, True, False) @@ -70,7 +70,7 @@ def get_run_disk_utilization(conn, run_folder, experiment_name): "%s : Starting getting disk space utilization for Data Folder", experiment_name, ) - dir_data = os.path.join(run_folder, "Data") + dir_data = os.path.join(full_path_run, "Data") data_dir_size = get_size_dir(dir_data, conn, shared_folder) elif item_list.filename == "Images": From f18e4fdca5db9bd8e550bb647c5161327daa0988 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 10:46:55 +0100 Subject: [PATCH 336/446] fix samplesheet parse --- wetlab/utils/samplesheet.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index a232c0a02..3a10cdb5d 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -99,7 +99,7 @@ def file_read_to_dictionary( if not line or re.match("^,+$", line): # Empty/Filler/Artifact lines with no info continue - if section in wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET: + if section in wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET.values(): # Data is tabular; append as list of lists until next header if not isinstance(samplesheet[section], list): samplesheet[section] = [] From dea14270d54451ba919b1bbdbd78a23862c26ff0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 13:22:17 +0100 Subject: [PATCH 337/446] updated docs in readme and leame --- LEAME.md | 61 ++++++++++++++++----------------------------- README.md | 74 +++++++++++++++++++++++-------------------------------- 2 files changed, 52 insertions(+), 83 deletions(-) diff --git a/LEAME.md b/LEAME.md index 6dc036f25..a4602a470 100644 --- a/LEAME.md +++ b/LEAME.md @@ -18,6 +18,7 @@ De acuerdo con la infraestructura existente, la secuenciacion se realiza en un i - [Contenedor local de pruebas](#contenedor-local-de-pruebas) - [Contenedor de produccion](#contenedor-de-produccion) - [Actualizacion del despliegue Docker](#actualizacion-del-despliegue-docker) + - [Actualizacion del despliegue Docker v3.0.0 a 3.1.0](#actualizacion-del-despliegue-docker-v300-a-310) - [Despliegue bare-metal (Ubuntu/CentOS)](#despliegue-bare-metal-ubuntucentos) - [Instalacion](#instalacion) - [Requisitos previos](#requisitos-previos) @@ -118,6 +119,22 @@ bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh` dentro del contenedor, que regenera migraciones, las aplica con `--fake-initial` y evita cargar superusuario/datos demo/prueba. +### Actualizacion del despliegue Docker v3.0.0 a 3.1.0 + +Antes de actualizar, asegurate de tener una copia completa de la base de datos y de los datos en volumenes que uses. Confirma que `conf/my_prod_settings.txt` tenga el host/usuario/password de la base de datos de produccion, la URL/IP del servidor, correo y ajustes de logging usados por el contenedor. + +Para 3.0.0 -> 3.1.0, exporta primero el mapeo de LibraryPool y luego ejecuta la actualizacion con scripts pre/post: + +```bash +mysql --user= --password= --host= --port= iskylims \ + -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ + > /tmp/library_pool_run_process.tsv + +bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade \ + --script_before convert_rawtop_counter_to_int \ + --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv +``` + ## Despliegue bare-metal (Ubuntu/CentOS) ### Instalacion @@ -237,59 +254,23 @@ bash install.sh --upgrade app --git_revision main --tables bash install.sh --upgrade app --script migrate_optional_values --git_revision main --tables # 3.0.0 -> 3.1.0 (scripts de datos pre/post) -bash install.sh --upgrade app --git_revision main \ - --script_before convert_rawtop_counter_to_int \ - --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv -``` - -O ejecuta todo en un unico comando: - -```bash -sudo bash install.sh --upgrade full --git_revision main --tables -``` - -Las actualizaciones regeneran las migraciones y las aplican con `--fake-initial` para conservar las tablas existentes, igual que en Docker. - -Para 3.0.0 -> 3.1.0 en Docker, exporta el mapeo y ejecuta: - -```bash mysql --user= --password= --host= --port= iskylims \ -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ > /tmp/library_pool_run_process.tsv -bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade \ - --script_before convert_rawtop_counter_to_int \ - --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv -``` - -#### Scripts de datos 3.0.0 -> 3.1.0 - -Algunas migraciones de datos deben ejecutarse antes/despues de las migraciones de esquema: - -1. Exportar el mapeo de LibraryPool (antes de migrar): - -```bash -mysql --user= --password= --host= --port= iskylims \ - -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ - > /tmp/library_pool_run_process.tsv -``` - -2. Ejecutar la actualizacion con scripts pre/post: - -```bash bash install.sh --upgrade app --git_revision main \ --script_before convert_rawtop_counter_to_int \ --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv ``` -Equivalente en Docker: +O ejecuta todo en un unico comando: ```bash -bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade \ - --script_before convert_rawtop_counter_to_int \ - --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv +sudo bash install.sh --upgrade full --git_revision main --tables ``` +Las actualizaciones regeneran las migraciones y las aplican con `--fake-initial` para conservar las tablas existentes, igual que en Docker. + ## Que hacer si algo falla Cuando actualizamos usando el script de instalacion estamos realizando varios cambios en la base de datos. Si algo falla necesitamos restaurar el estado anterior y empezar de nuevo. diff --git a/README.md b/README.md index 8ed8ce985..e8c15a42a 100644 --- a/README.md +++ b/README.md @@ -19,6 +19,9 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Local test stack](#local-test-stack) - [Production container](#production-container) - [Upgrade docker deployment](#upgrade-docker-deployment) + - [Upgrade docker deployment v3.0.0 to 3.1.0](#upgrade-docker-deployment-v300-to-310) + - [Back up first](#back-up-first) + - [Refresh code and settings](#refresh-code-and-settings) - [Bare-metal deployment (Ubuntu/CentOS)](#bare-metal-deployment-ubuntucentos) - [Install](#install) - [Prerequisites](#prerequisites) @@ -26,12 +29,11 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Prepare the database](#prepare-the-database) - [Configure install\_settings.txt](#configure-install_settingstxt) - [Run install.sh](#run-installsh) - - [Upgrade (3.0.x to 3.1.x)](#upgrade-30x-to-31x) - - [Back up first](#back-up-first) - - [Refresh code and settings](#refresh-code-and-settings) + - [Upgrade (3.0.0 to 3.1.0)](#upgrade-300-to-310) + - [Back up first](#back-up-first-1) + - [Refresh code and settings](#refresh-code-and-settings-1) - [Run upgrade steps requiring root](#run-upgrade-steps-requiring-root) - [Run upgrade steps without root](#run-upgrade-steps-without-root) - - [3.0.0 -\> 3.1.0 data scripts](#300---310-data-scripts) - [What to do if something fails](#what-to-do-if-something-fails) - [Final configuration steps](#final-configuration-steps) - [SAMBA configurarion](#samba-configurarion) @@ -122,14 +124,34 @@ bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade The upgrade path rebuilds/restarts the container and runs `install.sh` inside the app container, which regenerates migrations, applies them with `--fake-initial`, and skips superuser/demo/test data loading. +### Upgrade docker deployment v3.0.0 to 3.1.0 + +#### Back up first + +- Full backup of the `iskylims` database. +- Full backup of the logs folder and the documents folder. + For 3.0.0 -> 3.1.0, export the LibraryPool mapping first, then run the upgrade with pre/post scripts: ```bash mysql --user= --password= --host= --port= iskylims \ -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ > /tmp/library_pool_run_process.tsv +``` + +#### Refresh code and settings -bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade \ +```bash +cd /iskylims +git pull +cp conf/docker_production_settings.txt myprod_settings.txt +sudo nano myprod_settings.txt +``` + +Ensure the file uses Linux-friendly encoding (UTF-8/ASCII) if you edit it on Windows. + +```bash +bash docker_install.sh --install_conf my_prod_settings.txt --action upgrade \ --script_before convert_rawtop_counter_to_int \ --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv ``` @@ -202,7 +224,7 @@ sudo bash install.sh --install full --git_revision main --tables - If Apache is managed elsewhere, skip the automatic restart with `--skip_apache_restart`. -### Upgrade (3.0.x to 3.1.x) +### Upgrade (3.0.0 to 3.1.0) Follow these steps to move from version 3.0.0 to the 3.1.x series. @@ -213,8 +235,9 @@ Follow these steps to move from version 3.0.0 to the 3.1.x series. - If you use library pools, export them before upgrading: ```bash - mysql --user= --password= --host= --port= iskylims \ - -e "SELECT * FROM wetlab_library_pool" > /backup_lib_pool.sql +mysql --user= --password= --host= --port= iskylims \ + -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ + > /tmp/library_pool_run_process.tsv ``` #### Refresh code and settings @@ -244,48 +267,13 @@ Upgrade the application code and database: ```bash # with library pool restore -bash install.sh --upgrade app --script /backup_lib_pool.sql --git_revision main --tables - -# without library pool restore -bash install.sh --upgrade app --git_revision main --tables - -# example running a migration script during upgrade -bash install.sh --upgrade app --script migrate_optional_values --git_revision main --tables - -# 3.0.0 -> 3.1.0 (pre/post data scripts) bash install.sh --upgrade app --git_revision main \ --script_before convert_rawtop_counter_to_int \ --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv ``` -Or run everything in one go: - -```bash -sudo bash install.sh --upgrade full --git_revision main --tables -``` - Upgrades regenerate migrations and apply them with `--fake-initial` so existing tables remain intact, matching the Docker workflow. -#### 3.0.0 -> 3.1.0 data scripts - -Some data migrations must run before/after schema migrations: - -1. Export LibraryPool mapping (before migrations): - -```bash -mysql --user= --password= --host= --port= iskylims \ - -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ - > /tmp/library_pool_run_process.tsv -``` - -2. Run upgrade with pre/post scripts: - -```bash -bash install.sh --upgrade app --git_revision main \ - --script_before convert_rawtop_counter_to_int \ - --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv -``` - ## What to do if something fails When we upgrade using the installation script we are performing several changes in the database. If something fails we need to restore the app situation before anything happened and start all over. From 6c191ae0b9ad5b929ccb807c9d341140b29da7db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 13:28:46 +0100 Subject: [PATCH 338/446] linting --- clinic/migrations/0001_initial.py | 313 +++- core/migrations/0001_initial.py | 1199 +++++++++++---- ...reparation_sample_continues_on_and_more.py | 81 +- django_utils/migrations/0001_initial.py | 99 +- drylab/migrations/0001_initial.py | 617 ++++++-- .../0002_remove_service_service_status.py | 6 +- drylab/templatetags/upload_tags.py | 6 +- wetlab/migrations/0001_initial.py | 1291 ++++++++++++----- ...ove_librarypool_run_process_id_and_more.py | 36 +- wetlab/utils/crontab_update_run.py | 6 +- 10 files changed, 2759 insertions(+), 895 deletions(-) diff --git a/clinic/migrations/0001_initial.py b/clinic/migrations/0001_initial.py index f31f0921b..2de933cee 100644 --- a/clinic/migrations/0001_initial.py +++ b/clinic/migrations/0001_initial.py @@ -10,135 +10,298 @@ class Migration(migrations.Migration): initial = True dependencies = [ - ('core', '0001_initial'), + ("core", "0001_initial"), migrations.swappable_dependency(settings.AUTH_USER_MODEL), ] operations = [ migrations.CreateModel( - name='ClinicSampleRequest', + name="ClinicSampleRequest", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('entry_order', models.CharField(blank=True, max_length=8, null=True)), - ('confirmation_code', models.CharField(blank=True, max_length=80, null=True)), - ('priority', models.IntegerField(blank=True, null=True)), - ('comments', models.CharField(blank=True, max_length=255, null=True)), - ('service_date', models.DateTimeField(blank=True, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("entry_order", models.CharField(blank=True, max_length=8, null=True)), + ( + "confirmation_code", + models.CharField(blank=True, max_length=80, null=True), + ), + ("priority", models.IntegerField(blank=True, null=True)), + ("comments", models.CharField(blank=True, max_length=255, null=True)), + ("service_date", models.DateTimeField(blank=True, null=True)), + ("generated_at", models.DateTimeField(auto_now_add=True)), ], ), migrations.CreateModel( - name='ClinicSampleState', + name="ClinicSampleState", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('clinic_state', models.CharField(max_length=20)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("clinic_state", models.CharField(max_length=20)), ], ), migrations.CreateModel( - name='ConfigSetting', + name="ConfigSetting", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('configuration_name', models.CharField(max_length=80)), - ('configuration_value', models.CharField(blank=True, max_length=255, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("configuration_name", models.CharField(max_length=80)), + ( + "configuration_value", + models.CharField(blank=True, max_length=255, null=True), + ), + ("generated_at", models.DateTimeField(auto_now_add=True)), ], ), migrations.CreateModel( - name='FamilyRelatives', + name="FamilyRelatives", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('relationship', models.CharField(max_length=255)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("relationship", models.CharField(max_length=255)), ], ), migrations.CreateModel( - name='PatientData', + name="PatientData", fields=[ - ('patien_core', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='core.patientcore')), - ('address', models.CharField(blank=True, max_length=255, null=True)), - ('phone', models.CharField(blank=True, max_length=20, null=True)), - ('email', models.CharField(blank=True, max_length=50, null=True)), - ('birthday', models.DateTimeField(blank=True, null=True)), - ('smoker', models.CharField(blank=True, max_length=20, null=True)), - ('notification_preference', models.CharField(blank=True, max_length=20, null=True)), - ('comments', models.CharField(blank=True, max_length=255, null=True)), + ( + "patien_core", + models.OneToOneField( + on_delete=django.db.models.deletion.CASCADE, + primary_key=True, + serialize=False, + to="core.patientcore", + ), + ), + ("address", models.CharField(blank=True, max_length=255, null=True)), + ("phone", models.CharField(blank=True, max_length=20, null=True)), + ("email", models.CharField(blank=True, max_length=50, null=True)), + ("birthday", models.DateTimeField(blank=True, null=True)), + ("smoker", models.CharField(blank=True, max_length=20, null=True)), + ( + "notification_preference", + models.CharField(blank=True, max_length=20, null=True), + ), + ("comments", models.CharField(blank=True, max_length=255, null=True)), ], ), migrations.CreateModel( - name='ServiceUnits', + name="ServiceUnits", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('service_unit_name', models.CharField(max_length=80)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("service_unit_name", models.CharField(max_length=80)), ], ), migrations.CreateModel( - name='ResultParameterValue', + name="ResultParameterValue", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('parameterValue', models.CharField(max_length=255)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('clinicSample_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='clinic.clinicsamplerequest')), - ('parameter_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.protocolparameters')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("parameterValue", models.CharField(max_length=255)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "clinicSample_id", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="clinic.clinicsamplerequest", + ), + ), + ( + "parameter_id", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.protocolparameters", + ), + ), ], ), migrations.CreateModel( - name='PatientHistory', + name="PatientHistory", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('entry_date', models.DateTimeField(blank=True, null=True)), - ('description', models.CharField(max_length=255)), - ('patient_core', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientcore')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("entry_date", models.DateTimeField(blank=True, null=True)), + ("description", models.CharField(max_length=255)), + ( + "patient_core", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.patientcore", + ), + ), ], ), migrations.CreateModel( - name='Family', + name="Family", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('family_id', models.CharField(max_length=50)), - ('relative_1', models.CharField(max_length=50)), - ('relative_2', models.CharField(max_length=50)), - ('affected', models.BooleanField()), - ('family_comments', models.CharField(blank=True, max_length=255, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('family_relatives_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='clinic.familyrelatives')), - ('patien_core_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientcore')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("family_id", models.CharField(max_length=50)), + ("relative_1", models.CharField(max_length=50)), + ("relative_2", models.CharField(max_length=50)), + ("affected", models.BooleanField()), + ( + "family_comments", + models.CharField(blank=True, max_length=255, null=True), + ), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "family_relatives_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="clinic.familyrelatives", + ), + ), + ( + "patien_core_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.patientcore", + ), + ), ], ), migrations.CreateModel( - name='Doctor', + name="Doctor", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('doctor_name', models.CharField(max_length=80)), - ('service_unit_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='clinic.serviceunits')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("doctor_name", models.CharField(max_length=80)), + ( + "service_unit_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="clinic.serviceunits", + ), + ), ], ), migrations.AddField( - model_name='clinicsamplerequest', - name='clinic_sample_state', - field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='clinic.clinicsamplestate'), + model_name="clinicsamplerequest", + name="clinic_sample_state", + field=models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="clinic.clinicsamplestate", + ), ), migrations.AddField( - model_name='clinicsamplerequest', - name='doctor_id', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='clinic.doctor'), + model_name="clinicsamplerequest", + name="doctor_id", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="clinic.doctor", + ), ), migrations.AddField( - model_name='clinicsamplerequest', - name='patient_core', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientcore'), + model_name="clinicsamplerequest", + name="patient_core", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.patientcore", + ), ), migrations.AddField( - model_name='clinicsamplerequest', - name='sample_core', - field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.samples'), + model_name="clinicsamplerequest", + name="sample_core", + field=models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, to="core.samples" + ), ), migrations.AddField( - model_name='clinicsamplerequest', - name='sample_request_user', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL), + model_name="clinicsamplerequest", + name="sample_request_user", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to=settings.AUTH_USER_MODEL, + ), ), migrations.AddField( - model_name='clinicsamplerequest', - name='service_unit_id', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='clinic.serviceunits'), + model_name="clinicsamplerequest", + name="service_unit_id", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="clinic.serviceunits", + ), ), ] diff --git a/core/migrations/0001_initial.py b/core/migrations/0001_initial.py index 7dc7569e5..6deb3f11e 100644 --- a/core/migrations/0001_initial.py +++ b/core/migrations/0001_initial.py @@ -15,478 +15,1135 @@ class Migration(migrations.Migration): operations = [ migrations.CreateModel( - name='City', + name="City", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('city_name', models.CharField(max_length=80)), - ('geo_loc_latitude', models.CharField(max_length=80)), - ('geo_loc_longitude', models.CharField(max_length=80)), - ('apps_name', models.CharField(max_length=40, null=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("city_name", models.CharField(max_length=80)), + ("geo_loc_latitude", models.CharField(max_length=80)), + ("geo_loc_longitude", models.CharField(max_length=80)), + ("apps_name", models.CharField(max_length=40, null=True)), ], options={ - 'db_table': 'core_city', + "db_table": "core_city", }, ), migrations.CreateModel( - name='CommercialKits', + name="CommercialKits", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.CharField(max_length=150)), - ('provider', models.CharField(max_length=30)), - ('cat_number', models.CharField(blank=True, max_length=40, null=True)), - ('description', models.CharField(blank=True, max_length=255, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("name", models.CharField(max_length=150)), + ("provider", models.CharField(max_length=30)), + ("cat_number", models.CharField(blank=True, max_length=40, null=True)), + ( + "description", + models.CharField(blank=True, max_length=255, null=True), + ), + ("generated_at", models.DateTimeField(auto_now_add=True, null=True)), ], options={ - 'db_table': 'core_commercial_kits', + "db_table": "core_commercial_kits", }, ), migrations.CreateModel( - name='Contact', + name="Contact", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('contact_name', models.CharField(max_length=80)), - ('contact_mail', models.CharField(max_length=40, null=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("contact_name", models.CharField(max_length=80)), + ("contact_mail", models.CharField(max_length=40, null=True)), ], options={ - 'db_table': 'core_contact', + "db_table": "core_contact", }, ), migrations.CreateModel( - name='LabRequest', + name="LabRequest", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('lab_name', models.CharField(max_length=80)), - ('lab_name_coding', models.CharField(max_length=50)), - ('lab_unit', models.CharField(max_length=50)), - ('lab_contact_name', models.CharField(max_length=50)), - ('lab_phone', models.CharField(max_length=20)), - ('lab_email', models.CharField(max_length=70)), - ('address', models.CharField(max_length=255)), - ('apps_name', models.CharField(max_length=40, null=True)), - ('lab_city', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.city')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("lab_name", models.CharField(max_length=80)), + ("lab_name_coding", models.CharField(max_length=50)), + ("lab_unit", models.CharField(max_length=50)), + ("lab_contact_name", models.CharField(max_length=50)), + ("lab_phone", models.CharField(max_length=20)), + ("lab_email", models.CharField(max_length=70)), + ("address", models.CharField(max_length=255)), + ("apps_name", models.CharField(max_length=40, null=True)), + ( + "lab_city", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.city", + ), + ), ], options={ - 'db_table': 'core_lab_request', + "db_table": "core_lab_request", }, ), migrations.CreateModel( - name='MoleculeType', + name="MoleculeType", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('molecule_type', models.CharField(max_length=30)), - ('apps_name', models.CharField(max_length=40, null=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("molecule_type", models.CharField(max_length=30)), + ("apps_name", models.CharField(max_length=40, null=True)), ], options={ - 'db_table': 'core_molecule_type', + "db_table": "core_molecule_type", }, ), migrations.CreateModel( - name='MoleculeUsedFor', + name="MoleculeUsedFor", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('used_for', models.CharField(max_length=50)), - ('apps_name', models.CharField(max_length=50)), - ('massive_use', models.BooleanField(default=False)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("used_for", models.CharField(max_length=50)), + ("apps_name", models.CharField(max_length=50)), + ("massive_use", models.BooleanField(default=False)), ], options={ - 'db_table': 'core_molecule_used_for', + "db_table": "core_molecule_used_for", }, ), migrations.CreateModel( - name='OntologyMap', + name="OntologyMap", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('label', models.CharField(max_length=255)), - ('ontology', models.CharField(blank=True, max_length=50, null=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("label", models.CharField(max_length=255)), + ("ontology", models.CharField(blank=True, max_length=50, null=True)), ], options={ - 'db_table': 'core_ontology_map', + "db_table": "core_ontology_map", }, ), migrations.CreateModel( - name='PatientCore', + name="PatientCore", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('patient_name', models.CharField(max_length=255, null=True)), - ('patient_surname', models.CharField(max_length=255, null=True)), - ('patient_code', models.CharField(max_length=255, null=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("patient_name", models.CharField(max_length=255, null=True)), + ("patient_surname", models.CharField(max_length=255, null=True)), + ("patient_code", models.CharField(max_length=255, null=True)), ], options={ - 'db_table': 'core_patient_core', + "db_table": "core_patient_core", }, ), migrations.CreateModel( - name='PatientProjects', + name="PatientProjects", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('project_name', models.CharField(max_length=50)), - ('project_manager', models.CharField(blank=True, max_length=50, null=True)), - ('project_contact', models.CharField(blank=True, max_length=50, null=True)), - ('project_description', models.CharField(blank=True, max_length=255, null=True)), - ('apps_name', models.CharField(max_length=40)), - ('generated_at', models.DateTimeField(auto_now_add=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("project_name", models.CharField(max_length=50)), + ( + "project_manager", + models.CharField(blank=True, max_length=50, null=True), + ), + ( + "project_contact", + models.CharField(blank=True, max_length=50, null=True), + ), + ( + "project_description", + models.CharField(blank=True, max_length=255, null=True), + ), + ("apps_name", models.CharField(max_length=40)), + ("generated_at", models.DateTimeField(auto_now_add=True)), ], options={ - 'db_table': 'core_patient_projects', + "db_table": "core_patient_projects", }, ), migrations.CreateModel( - name='PatientSex', + name="PatientSex", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sex', models.CharField(max_length=16)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("sex", models.CharField(max_length=16)), ], options={ - 'db_table': 'core_patient_sex', + "db_table": "core_patient_sex", }, ), migrations.CreateModel( - name='SampleProjectFieldClassification', + name="SampleProjectFieldClassification", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('classification_name', models.CharField(max_length=80)), - ('classification_display', models.CharField(max_length=100)), - ('generated_at', models.DateTimeField(auto_now_add=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("classification_name", models.CharField(max_length=80)), + ("classification_display", models.CharField(max_length=100)), + ("generated_at", models.DateTimeField(auto_now_add=True)), ], options={ - 'db_table': 'core_sample_projects_field_classification', + "db_table": "core_sample_projects_field_classification", }, ), migrations.CreateModel( - name='SampleProjects', + name="SampleProjects", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sample_project_name', models.CharField(max_length=255)), - ('sample_project_manager', models.CharField(blank=True, max_length=50, null=True)), - ('sample_project_contact', models.CharField(blank=True, max_length=250, null=True)), - ('sample_project_description', models.CharField(blank=True, max_length=255, null=True)), - ('apps_name', models.CharField(max_length=255)), - ('generated_at', models.DateTimeField(auto_now_add=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("sample_project_name", models.CharField(max_length=255)), + ( + "sample_project_manager", + models.CharField(blank=True, max_length=50, null=True), + ), + ( + "sample_project_contact", + models.CharField(blank=True, max_length=250, null=True), + ), + ( + "sample_project_description", + models.CharField(blank=True, max_length=255, null=True), + ), + ("apps_name", models.CharField(max_length=255)), + ("generated_at", models.DateTimeField(auto_now_add=True)), ], options={ - 'db_table': 'core_sample_projects', + "db_table": "core_sample_projects", }, ), migrations.CreateModel( - name='SampleProjectsFields', + name="SampleProjectsFields", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sample_project_field_name', models.CharField(max_length=80)), - ('sample_project_field_description', models.CharField(blank=True, max_length=400, null=True)), - ('sample_project_field_order', models.IntegerField()), - ('sample_project_field_used', models.BooleanField()), - ('sample_project_field_type', models.CharField(max_length=20)), - ('sample_project_option_list', models.CharField(blank=True, max_length=255, null=True)), - ('sample_project_searchable', models.BooleanField(default=False)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('sample_project_field_classification_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sampleprojectfieldclassification')), - ('sample_projects_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='sample_project_fields', to='core.sampleprojects')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("sample_project_field_name", models.CharField(max_length=80)), + ( + "sample_project_field_description", + models.CharField(blank=True, max_length=400, null=True), + ), + ("sample_project_field_order", models.IntegerField()), + ("sample_project_field_used", models.BooleanField()), + ("sample_project_field_type", models.CharField(max_length=20)), + ( + "sample_project_option_list", + models.CharField(blank=True, max_length=255, null=True), + ), + ("sample_project_searchable", models.BooleanField(default=False)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "sample_project_field_classification_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.sampleprojectfieldclassification", + ), + ), + ( + "sample_projects_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + related_name="sample_project_fields", + to="core.sampleprojects", + ), + ), ], options={ - 'db_table': 'core_sample_projects_fields', + "db_table": "core_sample_projects_fields", }, ), migrations.CreateModel( - name='SampleType', + name="SampleType", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sample_type', models.CharField(max_length=50)), - ('apps_name', models.CharField(max_length=50)), - ('mandatory_fields', models.CharField(blank=True, max_length=300, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("sample_type", models.CharField(max_length=50)), + ("apps_name", models.CharField(max_length=50)), + ( + "mandatory_fields", + models.CharField(blank=True, max_length=300, null=True), + ), + ("generated_at", models.DateTimeField(auto_now_add=True, null=True)), ], options={ - 'db_table': 'core_sample_type', + "db_table": "core_sample_type", }, ), migrations.CreateModel( - name='SequencingPlatform', + name="SequencingPlatform", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('platform_name', models.CharField(max_length=30)), - ('company_name', models.CharField(max_length=30)), - ('sequencing_technology', models.CharField(max_length=30)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("platform_name", models.CharField(max_length=30)), + ("company_name", models.CharField(max_length=30)), + ("sequencing_technology", models.CharField(max_length=30)), ], options={ - 'db_table': 'core_sequencing_platform', + "db_table": "core_sequencing_platform", }, ), migrations.CreateModel( - name='Species', + name="Species", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('species_name', models.CharField(max_length=50)), - ('ref_genome_name', models.CharField(blank=True, max_length=255, null=True)), - ('ref_genome_size', models.CharField(blank=True, max_length=100, null=True)), - ('ref_genome_id', models.CharField(blank=True, max_length=255, null=True)), - ('apps_name', models.CharField(max_length=50, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("species_name", models.CharField(max_length=50)), + ( + "ref_genome_name", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "ref_genome_size", + models.CharField(blank=True, max_length=100, null=True), + ), + ( + "ref_genome_id", + models.CharField(blank=True, max_length=255, null=True), + ), + ("apps_name", models.CharField(max_length=50, null=True)), + ("generated_at", models.DateTimeField(auto_now_add=True, null=True)), ], options={ - 'db_table': 'core_species', + "db_table": "core_species", }, ), migrations.CreateModel( - name='StateInCountry', + name="StateInCountry", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('state_name', models.CharField(max_length=80)), - ('apps_name', models.CharField(max_length=40, null=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("state_name", models.CharField(max_length=80)), + ("apps_name", models.CharField(max_length=40, null=True)), ], options={ - 'db_table': 'core_state_in_country', + "db_table": "core_state_in_country", }, ), migrations.CreateModel( - name='StatesForMolecule', + name="StatesForMolecule", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('molecule_state_name', models.CharField(max_length=50)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("molecule_state_name", models.CharField(max_length=50)), ], options={ - 'db_table': 'core_states_for_molecule', + "db_table": "core_states_for_molecule", }, ), migrations.CreateModel( - name='StatesForSample', + name="StatesForSample", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sample_state_name', models.CharField(max_length=50)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("sample_state_name", models.CharField(max_length=50)), ], options={ - 'db_table': 'core_states_for_sample', + "db_table": "core_states_for_sample", }, ), migrations.CreateModel( - name='UserLotCommercialKits', + name="UserLotCommercialKits", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('uses_number', models.IntegerField(default=0, null=True)), - ('chip_lot', models.CharField(max_length=50)), - ('latest_used_date', models.DateTimeField(blank=True, null=True)), - ('expiration_date', models.DateField()), - ('run_out', models.BooleanField(default=False)), - ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), - ('based_commercial', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.commercialkits')), - ('user', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("uses_number", models.IntegerField(default=0, null=True)), + ("chip_lot", models.CharField(max_length=50)), + ("latest_used_date", models.DateTimeField(blank=True, null=True)), + ("expiration_date", models.DateField()), + ("run_out", models.BooleanField(default=False)), + ("generated_at", models.DateTimeField(auto_now_add=True, null=True)), + ( + "based_commercial", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.commercialkits", + ), + ), + ( + "user", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to=settings.AUTH_USER_MODEL, + ), + ), ], options={ - 'db_table': 'core_user_lot_commercial_kits', + "db_table": "core_user_lot_commercial_kits", }, ), migrations.CreateModel( - name='SequencingConfiguration', + name="SequencingConfiguration", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('configuration_name', models.CharField(max_length=255)), - ('platform_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencingplatform')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("configuration_name", models.CharField(max_length=255)), + ( + "platform_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.sequencingplatform", + ), + ), ], options={ - 'db_table': 'core_sequencing_configuration', + "db_table": "core_sequencing_configuration", }, ), migrations.CreateModel( - name='SequencerInLab', + name="SequencerInLab", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sequencer_name', models.CharField(max_length=255)), - ('sequencer_description', models.CharField(blank=True, max_length=255, null=True)), - ('sequencer_location', models.CharField(blank=True, max_length=255, null=True)), - ('sequencer_serial_number', models.CharField(blank=True, max_length=255, null=True)), - ('sequencer_state', models.CharField(blank=True, max_length=50, null=True)), - ('sequencer_operation_start', models.DateField(blank=True, null=True)), - ('sequencer_operation_end', models.DateField(blank=True, null=True)), - ('sequencer_number_lanes', models.CharField(blank=True, max_length=5, null=True)), - ('platform_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencingplatform')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("sequencer_name", models.CharField(max_length=255)), + ( + "sequencer_description", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "sequencer_location", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "sequencer_serial_number", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "sequencer_state", + models.CharField(blank=True, max_length=50, null=True), + ), + ("sequencer_operation_start", models.DateField(blank=True, null=True)), + ("sequencer_operation_end", models.DateField(blank=True, null=True)), + ( + "sequencer_number_lanes", + models.CharField(blank=True, max_length=5, null=True), + ), + ( + "platform_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.sequencingplatform", + ), + ), ], options={ - 'db_table': 'core_sequencer_in_lab', + "db_table": "core_sequencer_in_lab", }, ), migrations.CreateModel( - name='SamplesProjectsTableOptions', + name="SamplesProjectsTableOptions", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('option_value', models.CharField(max_length=120)), - ('sample_project_field', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='opt_value_prop', to='core.sampleprojectsfields')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("option_value", models.CharField(max_length=120)), + ( + "sample_project_field", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + related_name="opt_value_prop", + to="core.sampleprojectsfields", + ), + ), ], options={ - 'db_table': 'core_sample_projects_table_options', + "db_table": "core_sample_projects_table_options", }, ), migrations.CreateModel( - name='Samples', + name="Samples", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sample_name', models.CharField(max_length=255, null=True, verbose_name='Sample Name')), - ('sample_location', models.CharField(blank=True, max_length=255, null=True, verbose_name='Sample location')), - ('sample_entry_date', models.DateTimeField(blank=True, null=True, verbose_name='Sample defined date')), - ('collection_sample_date', models.DateTimeField(blank=True, null=True, verbose_name='Sample collection date')), - ('unique_sample_id', models.CharField(max_length=8, null=True, verbose_name='Unique sample id')), - ('sample_code_id', models.CharField(max_length=60, null=True, verbose_name='Sample code id')), - ('reused_number', models.IntegerField(default=0, verbose_name='Number of type reused')), - ('sequencing_date', models.DateTimeField(blank=True, null=True, verbose_name='Sequencing date')), - ('completed_date', models.DateTimeField(blank=True, null=True, verbose_name='Completion date')), - ('generated_at', models.DateTimeField(auto_now_add=True, verbose_name='Generated at')), - ('only_recorded', models.BooleanField(blank=True, default=False, null=True, verbose_name='Only recorded?')), - ('lab_request', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.labrequest', verbose_name='Laboratory')), - ('patient_core', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientcore', verbose_name='Patient Code ID')), - ('sample_project', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sampleprojects', verbose_name='Sample Project')), - ('sample_state', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.statesforsample', verbose_name='Sample state')), - ('sample_type', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sampletype', verbose_name='Sample type')), - ('sample_user', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, verbose_name='Username')), - ('species', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.species', verbose_name='Species')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "sample_name", + models.CharField( + max_length=255, null=True, verbose_name="Sample Name" + ), + ), + ( + "sample_location", + models.CharField( + blank=True, + max_length=255, + null=True, + verbose_name="Sample location", + ), + ), + ( + "sample_entry_date", + models.DateTimeField( + blank=True, null=True, verbose_name="Sample defined date" + ), + ), + ( + "collection_sample_date", + models.DateTimeField( + blank=True, null=True, verbose_name="Sample collection date" + ), + ), + ( + "unique_sample_id", + models.CharField( + max_length=8, null=True, verbose_name="Unique sample id" + ), + ), + ( + "sample_code_id", + models.CharField( + max_length=60, null=True, verbose_name="Sample code id" + ), + ), + ( + "reused_number", + models.IntegerField( + default=0, verbose_name="Number of type reused" + ), + ), + ( + "sequencing_date", + models.DateTimeField( + blank=True, null=True, verbose_name="Sequencing date" + ), + ), + ( + "completed_date", + models.DateTimeField( + blank=True, null=True, verbose_name="Completion date" + ), + ), + ( + "generated_at", + models.DateTimeField( + auto_now_add=True, verbose_name="Generated at" + ), + ), + ( + "only_recorded", + models.BooleanField( + blank=True, + default=False, + null=True, + verbose_name="Only recorded?", + ), + ), + ( + "lab_request", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.labrequest", + verbose_name="Laboratory", + ), + ), + ( + "patient_core", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.patientcore", + verbose_name="Patient Code ID", + ), + ), + ( + "sample_project", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.sampleprojects", + verbose_name="Sample Project", + ), + ), + ( + "sample_state", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.statesforsample", + verbose_name="Sample state", + ), + ), + ( + "sample_type", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.sampletype", + verbose_name="Sample type", + ), + ), + ( + "sample_user", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to=settings.AUTH_USER_MODEL, + verbose_name="Username", + ), + ), + ( + "species", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.species", + verbose_name="Species", + ), + ), ], options={ - 'db_table': 'core_samples', + "db_table": "core_samples", }, ), migrations.CreateModel( - name='SampleProjectsFieldsValue', + name="SampleProjectsFieldsValue", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sample_project_field_value', models.CharField(blank=True, max_length=255, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('sample_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='project_values', to='core.samples', verbose_name='Sample Name')), - ('sample_project_field_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sampleprojectsfields')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "sample_project_field_value", + models.CharField(blank=True, max_length=255, null=True), + ), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "sample_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + related_name="project_values", + to="core.samples", + verbose_name="Sample Name", + ), + ), + ( + "sample_project_field_id", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.sampleprojectsfields", + ), + ), ], options={ - 'db_table': 'core_sample_projects_fields_value', + "db_table": "core_sample_projects_fields_value", }, ), migrations.AddField( - model_name='sampleprojectfieldclassification', - name='sample_projects_id', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sampleprojects'), + model_name="sampleprojectfieldclassification", + name="sample_projects_id", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.sampleprojects", + ), ), migrations.CreateModel( - name='ProtocolType', + name="ProtocolType", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('protocol_type', models.CharField(max_length=40)), - ('apps_name', models.CharField(max_length=40)), - ('molecule', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.moleculetype')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("protocol_type", models.CharField(max_length=40)), + ("apps_name", models.CharField(max_length=40)), + ( + "molecule", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.moleculetype", + ), + ), ], options={ - 'db_table': 'core_protocol_type', + "db_table": "core_protocol_type", }, ), migrations.CreateModel( - name='Protocols', + name="Protocols", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('name', models.CharField(max_length=40)), - ('description', models.CharField(blank=True, max_length=160, null=True)), - ('type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.protocoltype')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("name", models.CharField(max_length=40)), + ( + "description", + models.CharField(blank=True, max_length=160, null=True), + ), + ( + "type", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="core.protocoltype", + ), + ), ], options={ - 'db_table': 'core_protocols', + "db_table": "core_protocols", }, ), migrations.CreateModel( - name='ProtocolParameters', + name="ProtocolParameters", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('parameter_name', models.CharField(max_length=255)), - ('parameter_description', models.CharField(blank=True, max_length=400, null=True)), - ('parameter_order', models.IntegerField()), - ('parameter_used', models.BooleanField()), - ('parameter_type', models.CharField(default='string', max_length=20)), - ('parameter_option_values', models.CharField(blank=True, max_length=400, null=True)), - ('parameter_max_value', models.CharField(blank=True, max_length=50, null=True)), - ('parameter_min_value', models.CharField(blank=True, max_length=50, null=True)), - ('protocol_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.protocols')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("parameter_name", models.CharField(max_length=255)), + ( + "parameter_description", + models.CharField(blank=True, max_length=400, null=True), + ), + ("parameter_order", models.IntegerField()), + ("parameter_used", models.BooleanField()), + ("parameter_type", models.CharField(default="string", max_length=20)), + ( + "parameter_option_values", + models.CharField(blank=True, max_length=400, null=True), + ), + ( + "parameter_max_value", + models.CharField(blank=True, max_length=50, null=True), + ), + ( + "parameter_min_value", + models.CharField(blank=True, max_length=50, null=True), + ), + ( + "protocol_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, to="core.protocols" + ), + ), ], options={ - 'db_table': 'core_protocol_parameters', + "db_table": "core_protocol_parameters", }, ), migrations.CreateModel( - name='PatientProjectsFields', + name="PatientProjectsFields", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('project_field_name', models.CharField(max_length=50)), - ('project_field_description', models.CharField(blank=True, max_length=400, null=True)), - ('project_field_order', models.IntegerField()), - ('project_field_used', models.BooleanField()), - ('patient_projects_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientprojects')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("project_field_name", models.CharField(max_length=50)), + ( + "project_field_description", + models.CharField(blank=True, max_length=400, null=True), + ), + ("project_field_order", models.IntegerField()), + ("project_field_used", models.BooleanField()), + ( + "patient_projects_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.patientprojects", + ), + ), ], options={ - 'db_table': 'core_patient_projects_fields', + "db_table": "core_patient_projects_fields", }, ), migrations.CreateModel( - name='PatientProjectFieldValue', + name="PatientProjectFieldValue", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('project_field_value', models.CharField(max_length=255)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('patient_core_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientcore')), - ('project_field_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientprojectsfields')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("project_field_value", models.CharField(max_length=255)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "patient_core_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.patientcore", + ), + ), + ( + "project_field_id", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.patientprojectsfields", + ), + ), ], options={ - 'db_table': 'core_patient_project_field_value', + "db_table": "core_patient_project_field_value", }, ), migrations.AddField( - model_name='patientcore', - name='patient_projects', - field=models.ManyToManyField(blank=True, to='core.patientprojects'), + model_name="patientcore", + name="patient_projects", + field=models.ManyToManyField(blank=True, to="core.patientprojects"), ), migrations.AddField( - model_name='patientcore', - name='patient_sex', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.patientsex'), + model_name="patientcore", + name="patient_sex", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.patientsex", + ), ), migrations.CreateModel( - name='MoleculePreparation', + name="MoleculePreparation", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('molecule_code_id', models.CharField(max_length=255)), - ('extraction_type', models.CharField(max_length=50)), - ('molecule_extraction_date', models.DateTimeField(null=True)), - ('reused_number', models.IntegerField(default=0)), - ('used_for_massive_sequencing', models.BooleanField(blank=True, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('molecule_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.moleculetype')), - ('molecule_used_for', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.moleculeusedfor')), - ('molecule_user', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), - ('protocol_used', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.protocols')), - ('sample', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.samples')), - ('state', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.statesformolecule')), - ('user_lot_kit_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.userlotcommercialkits')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("molecule_code_id", models.CharField(max_length=255)), + ("extraction_type", models.CharField(max_length=50)), + ("molecule_extraction_date", models.DateTimeField(null=True)), + ("reused_number", models.IntegerField(default=0)), + ( + "used_for_massive_sequencing", + models.BooleanField(blank=True, null=True), + ), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "molecule_type", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="core.moleculetype", + ), + ), + ( + "molecule_used_for", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.moleculeusedfor", + ), + ), + ( + "molecule_user", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to=settings.AUTH_USER_MODEL, + ), + ), + ( + "protocol_used", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, to="core.protocols" + ), + ), + ( + "sample", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, to="core.samples" + ), + ), + ( + "state", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.statesformolecule", + ), + ), + ( + "user_lot_kit_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.userlotcommercialkits", + ), + ), ], options={ - 'db_table': 'core_molecule_preparation', + "db_table": "core_molecule_preparation", }, ), migrations.CreateModel( - name='MoleculeParameterValue', + name="MoleculeParameterValue", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('parameter_value', models.CharField(max_length=255)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('molecule_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.moleculepreparation')), - ('molecule_parameter_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.protocolparameters')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("parameter_value", models.CharField(max_length=255)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "molecule_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="core.moleculepreparation", + ), + ), + ( + "molecule_parameter_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="core.protocolparameters", + ), + ), ], options={ - 'db_table': 'core_molecule_parameter_value', + "db_table": "core_molecule_parameter_value", }, ), migrations.AddField( - model_name='commercialkits', - name='platform_kits', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencingplatform'), + model_name="commercialkits", + name="platform_kits", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.sequencingplatform", + ), ), migrations.AddField( - model_name='commercialkits', - name='protocol_kits', - field=models.ManyToManyField(blank=True, to='core.protocols'), + model_name="commercialkits", + name="protocol_kits", + field=models.ManyToManyField(blank=True, to="core.protocols"), ), migrations.AddField( - model_name='city', - name='belongs_to_state', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.stateincountry'), + model_name="city", + name="belongs_to_state", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.stateincountry", + ), ), ] diff --git a/core/migrations/0002_rename_molecule_used_for_moleculepreparation_sample_continues_on_and_more.py b/core/migrations/0002_rename_molecule_used_for_moleculepreparation_sample_continues_on_and_more.py index 3b7771015..9d3be354a 100644 --- a/core/migrations/0002_rename_molecule_used_for_moleculepreparation_sample_continues_on_and_more.py +++ b/core/migrations/0002_rename_molecule_used_for_moleculepreparation_sample_continues_on_and_more.py @@ -6,92 +6,97 @@ class Migration(migrations.Migration): dependencies = [ - ('core', '0001_initial'), + ("core", "0001_initial"), ] operations = [ migrations.RenameField( - model_name='moleculepreparation', - old_name='molecule_used_for', - new_name='sample_continues_on', + model_name="moleculepreparation", + old_name="molecule_used_for", + new_name="sample_continues_on", ), migrations.RenameField( - model_name='sampleprojectsfields', - old_name='sample_project_searchable', - new_name='sample_project_downloadable', + model_name="sampleprojectsfields", + old_name="sample_project_searchable", + new_name="sample_project_downloadable", ), migrations.AddField( - model_name='city', - name='geo_loc_city_cod', + model_name="city", + name="geo_loc_city_cod", field=models.CharField(blank=True, max_length=10, null=True), ), migrations.AddField( - model_name='labrequest', - name='autonom_cod', + model_name="labrequest", + name="autonom_cod", field=models.CharField(blank=True, max_length=20, null=True), ), migrations.AddField( - model_name='labrequest', - name='center_class_code', + model_name="labrequest", + name="center_class_code", field=models.CharField(blank=True, max_length=20, null=True), ), migrations.AddField( - model_name='labrequest', - name='dep_func', + model_name="labrequest", + name="dep_func", field=models.CharField(blank=True, max_length=80, null=True), ), migrations.AddField( - model_name='labrequest', - name='lab_code_1', + model_name="labrequest", + name="lab_code_1", field=models.CharField(blank=True, max_length=20, null=True, unique=True), ), migrations.AddField( - model_name='labrequest', - name='lab_code_2', + model_name="labrequest", + name="lab_code_2", field=models.CharField(blank=True, max_length=20, null=True), ), migrations.AddField( - model_name='labrequest', - name='lab_function', + model_name="labrequest", + name="lab_function", field=models.CharField(blank=True, max_length=120, null=True), ), migrations.AddField( - model_name='labrequest', - name='lab_geo_loc_latitude', + model_name="labrequest", + name="lab_geo_loc_latitude", field=models.CharField(blank=True, max_length=30, null=True), ), migrations.AddField( - model_name='labrequest', - name='lab_geo_loc_longitude', + model_name="labrequest", + name="lab_geo_loc_longitude", field=models.CharField(blank=True, max_length=30, null=True), ), migrations.AddField( - model_name='labrequest', - name='post_code', + model_name="labrequest", + name="post_code", field=models.CharField(blank=True, max_length=10, null=True), ), migrations.AddField( - model_name='protocolparameters', - name='parameter_download', + model_name="protocolparameters", + name="parameter_download", field=models.BooleanField(blank=True, default=False, null=True), ), migrations.AddField( - model_name='stateincountry', - name='geo_loc_state_cod', - field=models.CharField(blank=True, help_text='Geographic code of the CCAA', max_length=10, null=True), + model_name="stateincountry", + name="geo_loc_state_cod", + field=models.CharField( + blank=True, + help_text="Geographic code of the CCAA", + max_length=10, + null=True, + ), ), migrations.AddField( - model_name='statesformolecule', - name='molecule_state_display', + model_name="statesformolecule", + name="molecule_state_display", field=models.CharField(blank=True, max_length=80, null=True), ), migrations.AlterField( - model_name='labrequest', - name='lab_name', + model_name="labrequest", + name="lab_name", field=models.CharField(max_length=100), ), migrations.AlterModelTable( - name='moleculeusedfor', - table='core_sample_continues_on', + name="moleculeusedfor", + table="core_sample_continues_on", ), ] diff --git a/django_utils/migrations/0001_initial.py b/django_utils/migrations/0001_initial.py index 75f92ec61..421f9be63 100644 --- a/django_utils/migrations/0001_initial.py +++ b/django_utils/migrations/0001_initial.py @@ -15,40 +15,101 @@ class Migration(migrations.Migration): operations = [ migrations.CreateModel( - name='Center', + name="Center", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('center_name', models.CharField(max_length=50, verbose_name='Center')), - ('center_abbr', models.CharField(max_length=25, verbose_name='Acronym')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("center_name", models.CharField(max_length=50, verbose_name="Center")), + ( + "center_abbr", + models.CharField(max_length=25, verbose_name="Acronym"), + ), ], options={ - 'db_table': 'utils_center', + "db_table": "utils_center", }, ), migrations.CreateModel( - name='ClassificationArea', + name="ClassificationArea", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('classification_area_name', models.CharField(max_length=80)), - ('classification_area_description', models.CharField(blank=True, max_length=255, null=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("classification_area_name", models.CharField(max_length=80)), + ( + "classification_area_description", + models.CharField(blank=True, max_length=255, null=True), + ), ], options={ - 'db_table': 'utils_classification_area', + "db_table": "utils_classification_area", }, ), migrations.CreateModel( - name='Profile', + name="Profile", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('profile_position', models.CharField(max_length=50, verbose_name='Position')), - ('profile_area', models.CharField(max_length=50, verbose_name='Area / Unit')), - ('profile_extension', models.CharField(max_length=5, verbose_name='Phone extension')), - ('profile_center', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='django_utils.center', verbose_name='Center')), - ('profile_classification_area', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='django_utils.classificationarea')), - ('profile_user_id', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, related_name='profile', to=settings.AUTH_USER_MODEL)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "profile_position", + models.CharField(max_length=50, verbose_name="Position"), + ), + ( + "profile_area", + models.CharField(max_length=50, verbose_name="Area / Unit"), + ), + ( + "profile_extension", + models.CharField(max_length=5, verbose_name="Phone extension"), + ), + ( + "profile_center", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="django_utils.center", + verbose_name="Center", + ), + ), + ( + "profile_classification_area", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="django_utils.classificationarea", + ), + ), + ( + "profile_user_id", + models.OneToOneField( + on_delete=django.db.models.deletion.CASCADE, + related_name="profile", + to=settings.AUTH_USER_MODEL, + ), + ), ], options={ - 'db_table': 'utils_profile', + "db_table": "utils_profile", }, ), ] diff --git a/drylab/migrations/0001_initial.py b/drylab/migrations/0001_initial.py index 4f504ec6c..5b271eca7 100644 --- a/drylab/migrations/0001_initial.py +++ b/drylab/migrations/0001_initial.py @@ -11,224 +11,569 @@ class Migration(migrations.Migration): initial = True dependencies = [ - ('core', '0001_initial'), - ('wetlab', '0001_initial'), + ("core", "0001_initial"), + ("wetlab", "0001_initial"), migrations.swappable_dependency(settings.AUTH_USER_MODEL), ] operations = [ migrations.CreateModel( - name='AvailableService', + name="AvailableService", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('avail_service_description', models.CharField(max_length=200, verbose_name='Available services')), - ('service_in_use', models.BooleanField(default=True)), - ('service_id', models.CharField(blank=True, max_length=40, null=True)), - ('description', models.CharField(blank=True, max_length=200, null=True)), - ('lft', models.PositiveIntegerField(editable=False)), - ('rght', models.PositiveIntegerField(editable=False)), - ('tree_id', models.PositiveIntegerField(db_index=True, editable=False)), - ('level', models.PositiveIntegerField(editable=False)), - ('parent', mptt.fields.TreeForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.SET_NULL, to='drylab.availableservice')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "avail_service_description", + models.CharField(max_length=200, verbose_name="Available services"), + ), + ("service_in_use", models.BooleanField(default=True)), + ("service_id", models.CharField(blank=True, max_length=40, null=True)), + ( + "description", + models.CharField(blank=True, max_length=200, null=True), + ), + ("lft", models.PositiveIntegerField(editable=False)), + ("rght", models.PositiveIntegerField(editable=False)), + ("tree_id", models.PositiveIntegerField(db_index=True, editable=False)), + ("level", models.PositiveIntegerField(editable=False)), + ( + "parent", + mptt.fields.TreeForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.SET_NULL, + to="drylab.availableservice", + ), + ), ], options={ - 'verbose_name': 'AvailableService', - 'verbose_name_plural': 'AvailableServices', - 'db_table': 'drylab_available_service', - 'ordering': ['tree_id', 'lft'], + "verbose_name": "AvailableService", + "verbose_name_plural": "AvailableServices", + "db_table": "drylab_available_service", + "ordering": ["tree_id", "lft"], }, ), migrations.CreateModel( - name='ConfigSetting', + name="ConfigSetting", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('configuration_name', models.CharField(max_length=80)), - ('configuration_value', models.CharField(blank=True, max_length=255, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("configuration_name", models.CharField(max_length=80)), + ( + "configuration_value", + models.CharField(blank=True, max_length=255, null=True), + ), + ("generated_at", models.DateTimeField(auto_now_add=True)), ], options={ - 'db_table': 'drylab_config_setting', + "db_table": "drylab_config_setting", }, ), migrations.CreateModel( - name='Pipelines', + name="Pipelines", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('pipeline_name', models.CharField(max_length=50)), - ('pipeline_version', models.CharField(max_length=10)), - ('pipeline_in_use', models.BooleanField(default=True)), - ('pipeline_file', models.FileField(blank=True, null=True, upload_to='drylab/pipelinesFiles')), - ('pipeline_url', models.CharField(blank=True, max_length=200, null=True)), - ('pipeline_description', models.CharField(blank=True, max_length=500, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('user_name', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("pipeline_name", models.CharField(max_length=50)), + ("pipeline_version", models.CharField(max_length=10)), + ("pipeline_in_use", models.BooleanField(default=True)), + ( + "pipeline_file", + models.FileField( + blank=True, null=True, upload_to="drylab/pipelinesFiles" + ), + ), + ( + "pipeline_url", + models.CharField(blank=True, max_length=200, null=True), + ), + ( + "pipeline_description", + models.CharField(blank=True, max_length=500, null=True), + ), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "user_name", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to=settings.AUTH_USER_MODEL, + ), + ), ], options={ - 'db_table': 'drylab_pipelines', + "db_table": "drylab_pipelines", }, ), migrations.CreateModel( - name='Resolution', + name="Resolution", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('resolution_number', models.CharField(max_length=255, null=True, verbose_name='Resolution name')), - ('resolution_estimated_date', models.DateField(null=True, verbose_name=' Estimated resolution date')), - ('resolution_date', models.DateField(auto_now_add=True, verbose_name='Resolution date')), - ('resolution_queued_date', models.DateField(blank=True, null=True)), - ('resolution_in_progress_date', models.DateField(blank=True, null=True)), - ('resolution_delivery_date', models.DateField(blank=True, null=True)), - ('resolution_notes', models.TextField(blank=True, max_length=1000, null=True, verbose_name='Resolution notes')), - ('resolution_full_number', models.CharField(blank=True, max_length=255, null=True, verbose_name='Acronym Name')), - ('resolution_pdf_file', models.FileField(blank=True, null=True, upload_to='documents/drylab/resolutions')), - ('available_services', models.ManyToManyField(blank=True, to='drylab.availableservice')), - ('resolution_assigned_user', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='groups+', to=settings.AUTH_USER_MODEL)), - ('resolution_pipelines', models.ManyToManyField(blank=True, to='drylab.pipelines')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "resolution_number", + models.CharField( + max_length=255, null=True, verbose_name="Resolution name" + ), + ), + ( + "resolution_estimated_date", + models.DateField( + null=True, verbose_name=" Estimated resolution date" + ), + ), + ( + "resolution_date", + models.DateField(auto_now_add=True, verbose_name="Resolution date"), + ), + ("resolution_queued_date", models.DateField(blank=True, null=True)), + ( + "resolution_in_progress_date", + models.DateField(blank=True, null=True), + ), + ("resolution_delivery_date", models.DateField(blank=True, null=True)), + ( + "resolution_notes", + models.TextField( + blank=True, + max_length=1000, + null=True, + verbose_name="Resolution notes", + ), + ), + ( + "resolution_full_number", + models.CharField( + blank=True, + max_length=255, + null=True, + verbose_name="Acronym Name", + ), + ), + ( + "resolution_pdf_file", + models.FileField( + blank=True, null=True, upload_to="documents/drylab/resolutions" + ), + ), + ( + "available_services", + models.ManyToManyField(blank=True, to="drylab.availableservice"), + ), + ( + "resolution_assigned_user", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + related_name="groups+", + to=settings.AUTH_USER_MODEL, + ), + ), + ( + "resolution_pipelines", + models.ManyToManyField(blank=True, to="drylab.pipelines"), + ), ], options={ - 'db_table': 'drylab_resolution', + "db_table": "drylab_resolution", }, ), migrations.CreateModel( - name='ResolutionStates', + name="ResolutionStates", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('state_value', models.CharField(max_length=50)), - ('state_display', models.CharField(blank=True, max_length=80, null=True)), - ('description', models.CharField(blank=True, max_length=255, null=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("state_value", models.CharField(max_length=50)), + ( + "state_display", + models.CharField(blank=True, max_length=80, null=True), + ), + ( + "description", + models.CharField(blank=True, max_length=255, null=True), + ), ], options={ - 'db_table': 'drylab_resolution_states', + "db_table": "drylab_resolution_states", }, ), migrations.CreateModel( - name='Service', + name="Service", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('service_center', models.CharField(max_length=50, null=True, verbose_name='Sequencing center')), - ('service_request_number', models.CharField(max_length=80, null=True, verbose_name='Service ID')), - ('service_request_int', models.CharField(max_length=80, null=True)), - ('service_run_specs', models.CharField(blank=True, max_length=10, null=True, verbose_name='Run specifications')), - ('service_status', models.CharField(choices=[('recorded', 'Recorded'), ('approved', 'Approved'), ('rejected', 'Rejected'), ('queued', 'Queued'), ('in_progress', 'In Progress'), ('delivered', 'Delivered'), ('archived', 'Archived')], max_length=15, verbose_name='Service status')), - ('service_notes', models.TextField(blank=True, max_length=2048, null=True, verbose_name='Service Notes')), - ('service_created_date', models.DateField(auto_now_add=True, null=True)), - ('service_approved_date', models.DateField(blank=True, null=True)), - ('service_rejected_date', models.DateField(blank=True, null=True)), - ('service_delivered_date', models.DateField(blank=True, null=True)), - ('service_available_service', mptt.fields.TreeManyToManyField(to='drylab.availableservice', verbose_name='AvailableServices')), - ('service_project_names', models.ManyToManyField(blank=True, to='wetlab.projects', verbose_name="User's projects")), - ('service_sequencing_platform', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencingplatform')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "service_center", + models.CharField( + max_length=50, null=True, verbose_name="Sequencing center" + ), + ), + ( + "service_request_number", + models.CharField( + max_length=80, null=True, verbose_name="Service ID" + ), + ), + ("service_request_int", models.CharField(max_length=80, null=True)), + ( + "service_run_specs", + models.CharField( + blank=True, + max_length=10, + null=True, + verbose_name="Run specifications", + ), + ), + ( + "service_status", + models.CharField( + choices=[ + ("recorded", "Recorded"), + ("approved", "Approved"), + ("rejected", "Rejected"), + ("queued", "Queued"), + ("in_progress", "In Progress"), + ("delivered", "Delivered"), + ("archived", "Archived"), + ], + max_length=15, + verbose_name="Service status", + ), + ), + ( + "service_notes", + models.TextField( + blank=True, + max_length=2048, + null=True, + verbose_name="Service Notes", + ), + ), + ( + "service_created_date", + models.DateField(auto_now_add=True, null=True), + ), + ("service_approved_date", models.DateField(blank=True, null=True)), + ("service_rejected_date", models.DateField(blank=True, null=True)), + ("service_delivered_date", models.DateField(blank=True, null=True)), + ( + "service_available_service", + mptt.fields.TreeManyToManyField( + to="drylab.availableservice", verbose_name="AvailableServices" + ), + ), + ( + "service_project_names", + models.ManyToManyField( + blank=True, to="wetlab.projects", verbose_name="User's projects" + ), + ), + ( + "service_sequencing_platform", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.sequencingplatform", + ), + ), ], options={ - 'db_table': 'drylab_service', + "db_table": "drylab_service", }, ), migrations.CreateModel( - name='ServiceState', + name="ServiceState", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('state_value', models.CharField(max_length=50)), - ('state_display', models.CharField(blank=True, max_length=80, null=True)), - ('description', models.CharField(blank=True, max_length=255, null=True)), - ('show_in_stats', models.BooleanField(default=False)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("state_value", models.CharField(max_length=50)), + ( + "state_display", + models.CharField(blank=True, max_length=80, null=True), + ), + ( + "description", + models.CharField(blank=True, max_length=255, null=True), + ), + ("show_in_stats", models.BooleanField(default=False)), ], options={ - 'db_table': 'drylab_service_state', + "db_table": "drylab_service_state", }, ), migrations.CreateModel( - name='UploadServiceFile', + name="UploadServiceFile", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('upload_file', models.FileField(upload_to='drylab/service_files')), - ('upload_file_name', models.CharField(blank=True, max_length=255, null=True)), - ('uploaded_at', models.DateTimeField(auto_now_add=True)), - ('upload_service', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='drylab.service')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("upload_file", models.FileField(upload_to="drylab/service_files")), + ( + "upload_file_name", + models.CharField(blank=True, max_length=255, null=True), + ), + ("uploaded_at", models.DateTimeField(auto_now_add=True)), + ( + "upload_service", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="drylab.service", + ), + ), ], options={ - 'db_table': 'drylab_upload_service_file', + "db_table": "drylab_upload_service_file", }, ), migrations.AddField( - model_name='service', - name='service_state', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='drylab.servicestate', verbose_name='Service State'), + model_name="service", + name="service_state", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="drylab.servicestate", + verbose_name="Service State", + ), ), migrations.AddField( - model_name='service', - name='service_user_id', - field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL), + model_name="service", + name="service_user_id", + field=models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to=settings.AUTH_USER_MODEL, + ), ), migrations.CreateModel( - name='ResolutionParameters', + name="ResolutionParameters", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('resolution_parameter', models.CharField(max_length=50)), - ('resolution_param_value', models.CharField(max_length=80)), - ('resolution_param_notes', models.CharField(blank=True, max_length=200, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('resolution', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drylab.resolution')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("resolution_parameter", models.CharField(max_length=50)), + ("resolution_param_value", models.CharField(max_length=80)), + ( + "resolution_param_notes", + models.CharField(blank=True, max_length=200, null=True), + ), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "resolution", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="drylab.resolution", + ), + ), ], options={ - 'db_table': 'drylab_resolution_parameters', + "db_table": "drylab_resolution_parameters", }, ), migrations.AddField( - model_name='resolution', - name='resolution_service_id', - field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='resolutions', to='drylab.service'), + model_name="resolution", + name="resolution_service_id", + field=models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + related_name="resolutions", + to="drylab.service", + ), ), migrations.AddField( - model_name='resolution', - name='resolution_state', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='drylab.resolutionstates'), + model_name="resolution", + name="resolution_state", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="drylab.resolutionstates", + ), ), migrations.CreateModel( - name='RequestedSamplesInServices', + name="RequestedSamplesInServices", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sample_key', models.CharField(blank=True, max_length=15, null=True)), - ('sample_name', models.CharField(blank=True, max_length=50, null=True)), - ('sample_path', models.CharField(blank=True, max_length=250, null=True)), - ('run_name_key', models.CharField(blank=True, max_length=15, null=True)), - ('run_name', models.CharField(blank=True, max_length=50, null=True)), - ('project_key', models.CharField(blank=True, max_length=15, null=True)), - ('project_name', models.CharField(blank=True, max_length=50, null=True)), - ('only_recorded_sample', models.BooleanField(default=False)), - ('generated_at', models.DateField(auto_now_add=True)), - ('samples_in_service', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='samples', to='drylab.service')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("sample_key", models.CharField(blank=True, max_length=15, null=True)), + ("sample_name", models.CharField(blank=True, max_length=50, null=True)), + ( + "sample_path", + models.CharField(blank=True, max_length=250, null=True), + ), + ( + "run_name_key", + models.CharField(blank=True, max_length=15, null=True), + ), + ("run_name", models.CharField(blank=True, max_length=50, null=True)), + ("project_key", models.CharField(blank=True, max_length=15, null=True)), + ( + "project_name", + models.CharField(blank=True, max_length=50, null=True), + ), + ("only_recorded_sample", models.BooleanField(default=False)), + ("generated_at", models.DateField(auto_now_add=True)), + ( + "samples_in_service", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + related_name="samples", + to="drylab.service", + ), + ), ], options={ - 'db_table': 'drylab_request_samples_in_services', + "db_table": "drylab_request_samples_in_services", }, ), migrations.CreateModel( - name='ParameterPipeline', + name="ParameterPipeline", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('parameter_name', models.CharField(max_length=80)), - ('parameter_value', models.CharField(blank=True, max_length=200, null=True)), - ('parameter_type', models.CharField(blank=True, max_length=20, null=True)), - ('parameter_pipeline', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='drylab.pipelines')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("parameter_name", models.CharField(max_length=80)), + ( + "parameter_value", + models.CharField(blank=True, max_length=200, null=True), + ), + ( + "parameter_type", + models.CharField(blank=True, max_length=20, null=True), + ), + ( + "parameter_pipeline", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="drylab.pipelines", + ), + ), ], options={ - 'db_table': 'drylab_parameter_pipeline', + "db_table": "drylab_parameter_pipeline", }, ), migrations.CreateModel( - name='Delivery', + name="Delivery", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('delivery_notes', models.TextField(blank=True, max_length=1000, null=True)), - ('execution_start_date', models.DateField(blank=True, null=True)), - ('execution_end_date', models.DateField(blank=True, null=True)), - ('execution_time', models.CharField(blank=True, max_length=80, null=True)), - ('permanent_used_space', models.CharField(blank=True, max_length=80, null=True)), - ('temporary_used_space', models.CharField(blank=True, max_length=80, null=True)), - ('delivery_resolution_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='delivery', to='drylab.resolution')), - ('pipelines_in_delivery', models.ManyToManyField(blank=True, to='drylab.pipelines')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "delivery_notes", + models.TextField(blank=True, max_length=1000, null=True), + ), + ("execution_start_date", models.DateField(blank=True, null=True)), + ("execution_end_date", models.DateField(blank=True, null=True)), + ( + "execution_time", + models.CharField(blank=True, max_length=80, null=True), + ), + ( + "permanent_used_space", + models.CharField(blank=True, max_length=80, null=True), + ), + ( + "temporary_used_space", + models.CharField(blank=True, max_length=80, null=True), + ), + ( + "delivery_resolution_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + related_name="delivery", + to="drylab.resolution", + ), + ), + ( + "pipelines_in_delivery", + models.ManyToManyField(blank=True, to="drylab.pipelines"), + ), ], options={ - 'db_table': 'drylab_delivery', + "db_table": "drylab_delivery", }, ), ] diff --git a/drylab/migrations/0002_remove_service_service_status.py b/drylab/migrations/0002_remove_service_service_status.py index 3613622ab..e36b7be5d 100644 --- a/drylab/migrations/0002_remove_service_service_status.py +++ b/drylab/migrations/0002_remove_service_service_status.py @@ -6,12 +6,12 @@ class Migration(migrations.Migration): dependencies = [ - ('drylab', '0001_initial'), + ("drylab", "0001_initial"), ] operations = [ migrations.RemoveField( - model_name='service', - name='service_status', + model_name="service", + name="service_status", ), ] diff --git a/drylab/templatetags/upload_tags.py b/drylab/templatetags/upload_tags.py index b56046e73..144bfe95f 100644 --- a/drylab/templatetags/upload_tags.py +++ b/drylab/templatetags/upload_tags.py @@ -6,7 +6,8 @@ @register.simple_tag def upload_js(): - return mark_safe(""" + return mark_safe( + """ - """) + """ + ) diff --git a/wetlab/migrations/0001_initial.py b/wetlab/migrations/0001_initial.py index c93df8527..b2d84ab8b 100644 --- a/wetlab/migrations/0001_initial.py +++ b/wetlab/migrations/0001_initial.py @@ -11,510 +11,1139 @@ class Migration(migrations.Migration): dependencies = [ migrations.swappable_dependency(settings.AUTH_USER_MODEL), - ('core', '0001_initial'), - ('django_utils', '0001_initial'), + ("core", "0001_initial"), + ("django_utils", "0001_initial"), ] operations = [ migrations.CreateModel( - name='AdditionaKitsLibPrepare', + name="AdditionaKitsLibPrepare", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('kit_name', models.CharField(max_length=255)), - ('description', models.CharField(blank=True, max_length=400, null=True)), - ('kit_order', models.IntegerField()), - ('kit_used', models.BooleanField()), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('commercial_kit_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.commercialkits')), - ('protocol_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.protocols')), - ('register_user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("kit_name", models.CharField(max_length=255)), + ( + "description", + models.CharField(blank=True, max_length=400, null=True), + ), + ("kit_order", models.IntegerField()), + ("kit_used", models.BooleanField()), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "commercial_kit_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="core.commercialkits", + ), + ), + ( + "protocol_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, to="core.protocols" + ), + ), + ( + "register_user", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to=settings.AUTH_USER_MODEL, + ), + ), ], options={ - 'db_table': 'wetlab_lib_additional_kits_lib_prepare', + "db_table": "wetlab_lib_additional_kits_lib_prepare", }, ), migrations.CreateModel( - name='CollectionIndexKit', + name="CollectionIndexKit", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('collection_index_name', models.CharField(max_length=125)), - ('version', models.CharField(max_length=80, null=True)), - ('plate_extension', models.CharField(max_length=125, null=True)), - ('adapter_1', models.CharField(max_length=125, null=True)), - ('adapter_2', models.CharField(max_length=125, null=True)), - ('collection_index_file', models.FileField(max_length=500, upload_to='wetlab/collection_index_kits/')), - ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("collection_index_name", models.CharField(max_length=125)), + ("version", models.CharField(max_length=80, null=True)), + ("plate_extension", models.CharField(max_length=125, null=True)), + ("adapter_1", models.CharField(max_length=125, null=True)), + ("adapter_2", models.CharField(max_length=125, null=True)), + ( + "collection_index_file", + models.FileField( + max_length=500, upload_to="wetlab/collection_index_kits/" + ), + ), + ("generated_at", models.DateTimeField(auto_now_add=True, null=True)), ], options={ - 'db_table': 'wetlab_collection_index_kit', + "db_table": "wetlab_collection_index_kit", }, ), migrations.CreateModel( - name='ConfigSetting', + name="ConfigSetting", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('configuration_name', models.CharField(max_length=80)), - ('configuration_value', models.CharField(blank=True, max_length=255, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("configuration_name", models.CharField(max_length=80)), + ( + "configuration_value", + models.CharField(blank=True, max_length=255, null=True), + ), + ("generated_at", models.DateTimeField(auto_now_add=True)), ], options={ - 'db_table': 'wetlab_config_setting', + "db_table": "wetlab_config_setting", }, ), migrations.CreateModel( - name='LibPrepareStates', + name="LibPrepareStates", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('lib_prep_state', models.CharField(max_length=50)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("lib_prep_state", models.CharField(max_length=50)), ], options={ - 'db_table': 'wetlab_lib_prepare_states', + "db_table": "wetlab_lib_prepare_states", }, ), migrations.CreateModel( - name='LibraryKit', + name="LibraryKit", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('library_name', models.CharField(max_length=125)), - ('generated_at', models.DateTimeField(auto_now_add=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("library_name", models.CharField(max_length=125)), + ("generated_at", models.DateTimeField(auto_now_add=True)), ], options={ - 'db_table': 'wetlab_library_kit', + "db_table": "wetlab_library_kit", }, ), migrations.CreateModel( - name='PoolStates', + name="PoolStates", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('pool_state', models.CharField(max_length=50)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("pool_state", models.CharField(max_length=50)), ], options={ - 'db_table': 'wetlab_pool_states', + "db_table": "wetlab_pool_states", }, ), migrations.CreateModel( - name='Projects', + name="Projects", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('base_space_library', models.CharField(blank=True, max_length=45, null=True)), - ('project_name', models.CharField(max_length=45)), - ('library_kit', models.CharField(blank=True, max_length=125, null=True)), - ('base_space_file', models.CharField(blank=True, max_length=255, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('project_run_date', models.DateField(blank=True, null=True)), - ('library_kit_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.librarykit')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "base_space_library", + models.CharField(blank=True, max_length=45, null=True), + ), + ("project_name", models.CharField(max_length=45)), + ( + "library_kit", + models.CharField(blank=True, max_length=125, null=True), + ), + ( + "base_space_file", + models.CharField(blank=True, max_length=255, null=True), + ), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ("project_run_date", models.DateField(blank=True, null=True)), + ( + "library_kit_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.librarykit", + ), + ), ], options={ - 'db_table': 'wetlab_projects', + "db_table": "wetlab_projects", }, ), migrations.CreateModel( - name='RunConfigurationTest', + name="RunConfigurationTest", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('run_test_name', models.CharField(max_length=80)), - ('run_test_folder', models.CharField(max_length=200)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("run_test_name", models.CharField(max_length=80)), + ("run_test_folder", models.CharField(max_length=200)), ], options={ - 'db_table': 'wetlab_lib_run_configuration_test', + "db_table": "wetlab_lib_run_configuration_test", }, ), migrations.CreateModel( - name='RunErrors', + name="RunErrors", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('error_code', models.CharField(max_length=10)), - ('error_text', models.CharField(max_length=255)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("error_code", models.CharField(max_length=10)), + ("error_text", models.CharField(max_length=255)), ], options={ - 'db_table': 'wetlab_run_errors', + "db_table": "wetlab_run_errors", }, ), migrations.CreateModel( - name='RunProcess', + name="RunProcess", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('run_name', models.CharField(max_length=45)), - ('sample_sheet', models.FileField(blank=True, null=True, upload_to='wetlab/sample_sheet/')), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('run_date', models.DateField(blank=True, null=True)), - ('run_finish_date', models.DateTimeField(blank=True, null=True)), - ('bcl2fastq_finish_date', models.DateTimeField(blank=True, null=True)), - ('run_completed_date', models.DateTimeField(blank=True, null=True)), - ('run_forced_continue_on_error', models.BooleanField(blank=True, default=False, null=True)), - ('index_library', models.CharField(blank=True, max_length=85, null=True)), - ('samples', models.CharField(blank=True, max_length=45)), - ('use_space_img_mb', models.CharField(blank=True, max_length=10)), - ('use_space_fasta_mb', models.CharField(blank=True, max_length=10)), - ('use_space_other_mb', models.CharField(blank=True, max_length=10)), - ('center_requested_by', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='django_utils.center')), - ('reagent_kit', models.ManyToManyField(blank=True, to='core.userlotcommercialkits')), - ('run_error', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.runerrors')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("run_name", models.CharField(max_length=45)), + ( + "sample_sheet", + models.FileField( + blank=True, null=True, upload_to="wetlab/sample_sheet/" + ), + ), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ("run_date", models.DateField(blank=True, null=True)), + ("run_finish_date", models.DateTimeField(blank=True, null=True)), + ("bcl2fastq_finish_date", models.DateTimeField(blank=True, null=True)), + ("run_completed_date", models.DateTimeField(blank=True, null=True)), + ( + "run_forced_continue_on_error", + models.BooleanField(blank=True, default=False, null=True), + ), + ( + "index_library", + models.CharField(blank=True, max_length=85, null=True), + ), + ("samples", models.CharField(blank=True, max_length=45)), + ("use_space_img_mb", models.CharField(blank=True, max_length=10)), + ("use_space_fasta_mb", models.CharField(blank=True, max_length=10)), + ("use_space_other_mb", models.CharField(blank=True, max_length=10)), + ( + "center_requested_by", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="django_utils.center", + ), + ), + ( + "reagent_kit", + models.ManyToManyField(blank=True, to="core.userlotcommercialkits"), + ), + ( + "run_error", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.runerrors", + ), + ), ], options={ - 'db_table': 'wetlab_run_process', + "db_table": "wetlab_run_process", }, ), migrations.CreateModel( - name='RunStates', + name="RunStates", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('run_state_name', models.CharField(max_length=50)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("run_state_name", models.CharField(max_length=50)), ], options={ - 'db_table': 'wetlab_run_states', + "db_table": "wetlab_run_states", }, ), migrations.CreateModel( - name='SambaConnectionData', + name="SambaConnectionData", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('samba_folder_name', models.CharField(blank=True, max_length=80, null=True)), - ('domain', models.CharField(blank=True, max_length=80, null=True)), - ('host_name', models.CharField(blank=True, max_length=80, null=True)), - ('ip_server', models.CharField(blank=True, max_length=20, null=True)), - ('port_server', models.CharField(blank=True, max_length=10, null=True)), - ('remote_server_name', models.CharField(blank=True, max_length=80, null=True)), - ('shared_folder_name', models.CharField(blank=True, max_length=80, null=True)), - ('user_id', models.CharField(blank=True, max_length=80, null=True)), - ('user_password', models.CharField(blank=True, max_length=20, null=True)), - ('is_direct_tcp', models.BooleanField(default=True)), - ('ntlm_used', models.BooleanField(default=True)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "samba_folder_name", + models.CharField(blank=True, max_length=80, null=True), + ), + ("domain", models.CharField(blank=True, max_length=80, null=True)), + ("host_name", models.CharField(blank=True, max_length=80, null=True)), + ("ip_server", models.CharField(blank=True, max_length=20, null=True)), + ("port_server", models.CharField(blank=True, max_length=10, null=True)), + ( + "remote_server_name", + models.CharField(blank=True, max_length=80, null=True), + ), + ( + "shared_folder_name", + models.CharField(blank=True, max_length=80, null=True), + ), + ("user_id", models.CharField(blank=True, max_length=80, null=True)), + ( + "user_password", + models.CharField(blank=True, max_length=20, null=True), + ), + ("is_direct_tcp", models.BooleanField(default=True)), + ("ntlm_used", models.BooleanField(default=True)), ], options={ - 'db_table': 'wetlab_samba_connection_data', + "db_table": "wetlab_samba_connection_data", }, ), migrations.CreateModel( - name='RunningParameters', + name="RunningParameters", fields=[ - ('run_name_id', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, primary_key=True, serialize=False, to='wetlab.runprocess')), - ('run_id', models.CharField(max_length=255)), - ('experiment_name', models.CharField(max_length=255)), - ('rta_version', models.CharField(blank=True, max_length=255, null=True)), - ('system_suite_version', models.CharField(blank=True, max_length=255, null=True)), - ('library_id', models.CharField(blank=True, max_length=255, null=True)), - ('chemistry', models.CharField(blank=True, max_length=255, null=True)), - ('run_start_date', models.CharField(blank=True, max_length=255, null=True)), - ('analysis_workflow_type', models.CharField(blank=True, max_length=255, null=True)), - ('run_management_type', models.CharField(blank=True, max_length=255, null=True)), - ('planned_read1_cycles', models.CharField(blank=True, max_length=255, null=True)), - ('planned_read2_cycles', models.CharField(blank=True, max_length=255, null=True)), - ('planned_index1_read_cycles', models.CharField(blank=True, max_length=255, null=True)), - ('planned_index2_read_cycles', models.CharField(blank=True, max_length=255, null=True)), - ('application_version', models.CharField(blank=True, max_length=255, null=True)), - ('num_tiles_per_swath', models.CharField(blank=True, max_length=255, null=True)), - ('image_channel', models.CharField(blank=True, max_length=255, null=True)), - ('flowcell', models.CharField(blank=True, max_length=255, null=True)), - ('image_dimensions', models.CharField(blank=True, max_length=255, null=True)), - ('flowcell_layout', models.CharField(blank=True, max_length=255, null=True)), + ( + "run_name_id", + models.OneToOneField( + on_delete=django.db.models.deletion.CASCADE, + primary_key=True, + serialize=False, + to="wetlab.runprocess", + ), + ), + ("run_id", models.CharField(max_length=255)), + ("experiment_name", models.CharField(max_length=255)), + ( + "rta_version", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "system_suite_version", + models.CharField(blank=True, max_length=255, null=True), + ), + ("library_id", models.CharField(blank=True, max_length=255, null=True)), + ("chemistry", models.CharField(blank=True, max_length=255, null=True)), + ( + "run_start_date", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "analysis_workflow_type", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "run_management_type", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "planned_read1_cycles", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "planned_read2_cycles", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "planned_index1_read_cycles", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "planned_index2_read_cycles", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "application_version", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "num_tiles_per_swath", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "image_channel", + models.CharField(blank=True, max_length=255, null=True), + ), + ("flowcell", models.CharField(blank=True, max_length=255, null=True)), + ( + "image_dimensions", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "flowcell_layout", + models.CharField(blank=True, max_length=255, null=True), + ), ], options={ - 'db_table': 'wetlab_running_parameters', + "db_table": "wetlab_running_parameters", }, ), migrations.CreateModel( - name='StatsRunSummary', + name="StatsRunSummary", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('level', models.CharField(max_length=20)), - ('yield_total', models.CharField(max_length=10)), - ('projected_total_yield', models.CharField(max_length=10)), - ('aligned', models.CharField(max_length=10)), - ('error_rate', models.CharField(max_length=10)), - ('intensity_cycle', models.CharField(max_length=10)), - ('bigger_q30', models.CharField(max_length=10)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('stats_summary_run_date', models.DateField(null=True)), - ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("level", models.CharField(max_length=20)), + ("yield_total", models.CharField(max_length=10)), + ("projected_total_yield", models.CharField(max_length=10)), + ("aligned", models.CharField(max_length=10)), + ("error_rate", models.CharField(max_length=10)), + ("intensity_cycle", models.CharField(max_length=10)), + ("bigger_q30", models.CharField(max_length=10)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ("stats_summary_run_date", models.DateField(null=True)), + ( + "runprocess_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.runprocess", + ), + ), ], options={ - 'db_table': 'wetlab_stats_run_summary', + "db_table": "wetlab_stats_run_summary", }, ), migrations.CreateModel( - name='StatsRunRead', + name="StatsRunRead", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('read', models.CharField(max_length=10)), - ('lane', models.CharField(max_length=10)), - ('tiles', models.CharField(max_length=10)), - ('density', models.CharField(max_length=40)), - ('cluster_pf', models.CharField(max_length=40)), - ('phas_prephas', models.CharField(max_length=40)), - ('reads', models.CharField(max_length=40)), - ('reads_pf', models.CharField(max_length=40)), - ('q30', models.CharField(max_length=40)), - ('yields', models.CharField(max_length=40)), - ('cycles_err_rated', models.CharField(max_length=40)), - ('aligned', models.CharField(max_length=40)), - ('error_rate', models.CharField(max_length=40)), - ('error_rate_35', models.CharField(max_length=40)), - ('error_rate_50', models.CharField(max_length=40)), - ('error_rate_75', models.CharField(max_length=40)), - ('error_rate_100', models.CharField(max_length=40)), - ('intensity_cycle', models.CharField(max_length=40)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('stats_read_run_date', models.DateField(null=True)), - ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("read", models.CharField(max_length=10)), + ("lane", models.CharField(max_length=10)), + ("tiles", models.CharField(max_length=10)), + ("density", models.CharField(max_length=40)), + ("cluster_pf", models.CharField(max_length=40)), + ("phas_prephas", models.CharField(max_length=40)), + ("reads", models.CharField(max_length=40)), + ("reads_pf", models.CharField(max_length=40)), + ("q30", models.CharField(max_length=40)), + ("yields", models.CharField(max_length=40)), + ("cycles_err_rated", models.CharField(max_length=40)), + ("aligned", models.CharField(max_length=40)), + ("error_rate", models.CharField(max_length=40)), + ("error_rate_35", models.CharField(max_length=40)), + ("error_rate_50", models.CharField(max_length=40)), + ("error_rate_75", models.CharField(max_length=40)), + ("error_rate_100", models.CharField(max_length=40)), + ("intensity_cycle", models.CharField(max_length=40)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ("stats_read_run_date", models.DateField(null=True)), + ( + "runprocess_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.runprocess", + ), + ), ], options={ - 'db_table': 'wetlab_stats_run_read', + "db_table": "wetlab_stats_run_read", }, ), migrations.CreateModel( - name='StatsLaneSummary', + name="StatsLaneSummary", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('default_all', models.CharField(max_length=40, null=True)), - ('lane', models.CharField(max_length=10)), - ('pf_cluster', models.CharField(max_length=64)), - ('percent_lane', models.CharField(max_length=64)), - ('perfect_barcode', models.CharField(max_length=64)), - ('one_mismatch', models.CharField(max_length=64)), - ('yield_mb', models.CharField(max_length=64)), - ('bigger_q30', models.CharField(max_length=64)), - ('mean_quality', models.CharField(max_length=64)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('project_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.projects')), - ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("default_all", models.CharField(max_length=40, null=True)), + ("lane", models.CharField(max_length=10)), + ("pf_cluster", models.CharField(max_length=64)), + ("percent_lane", models.CharField(max_length=64)), + ("perfect_barcode", models.CharField(max_length=64)), + ("one_mismatch", models.CharField(max_length=64)), + ("yield_mb", models.CharField(max_length=64)), + ("bigger_q30", models.CharField(max_length=64)), + ("mean_quality", models.CharField(max_length=64)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "project_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.projects", + ), + ), + ( + "runprocess_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.runprocess", + ), + ), ], options={ - 'db_table': 'wetlab_stats_lane_summary', + "db_table": "wetlab_stats_lane_summary", }, ), migrations.CreateModel( - name='StatsFlSummary', + name="StatsFlSummary", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('default_all', models.CharField(max_length=40, null=True)), - ('flow_raw_cluster', models.CharField(max_length=40)), - ('flow_pf_cluster', models.CharField(max_length=40)), - ('flow_yield_mb', models.CharField(max_length=40)), - ('sample_number', models.CharField(max_length=40)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('project_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.projects')), - ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("default_all", models.CharField(max_length=40, null=True)), + ("flow_raw_cluster", models.CharField(max_length=40)), + ("flow_pf_cluster", models.CharField(max_length=40)), + ("flow_yield_mb", models.CharField(max_length=40)), + ("sample_number", models.CharField(max_length=40)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "project_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.projects", + ), + ), + ( + "runprocess_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.runprocess", + ), + ), ], options={ - 'db_table': 'wetlab_stats_fl_summary', + "db_table": "wetlab_stats_fl_summary", }, ), migrations.CreateModel( - name='SamplesInProject', + name="SamplesInProject", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sample_name', models.CharField(max_length=255)), - ('barcode_name', models.CharField(max_length=255)), - ('pf_clusters', models.CharField(max_length=55)), - ('percent_in_project', models.CharField(max_length=25)), - ('yield_mb', models.CharField(max_length=55)), - ('quality_q30', models.CharField(max_length=55)), - ('mean_quality', models.CharField(max_length=55)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('project_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.projects')), - ('run_process_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), - ('sample_in_core', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.samples')), - ('user_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("sample_name", models.CharField(max_length=255)), + ("barcode_name", models.CharField(max_length=255)), + ("pf_clusters", models.CharField(max_length=55)), + ("percent_in_project", models.CharField(max_length=25)), + ("yield_mb", models.CharField(max_length=55)), + ("quality_q30", models.CharField(max_length=55)), + ("mean_quality", models.CharField(max_length=55)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "project_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.projects", + ), + ), + ( + "run_process_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.runprocess", + ), + ), + ( + "sample_in_core", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.samples", + ), + ), + ( + "user_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to=settings.AUTH_USER_MODEL, + ), + ), ], options={ - 'db_table': 'wetlab_samples_in_project', + "db_table": "wetlab_samples_in_project", }, ), migrations.AddField( - model_name='runprocess', - name='state', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, related_name='state_of_run', to='wetlab.runstates'), + model_name="runprocess", + name="state", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + related_name="state_of_run", + to="wetlab.runstates", + ), ), migrations.AddField( - model_name='runprocess', - name='state_before_error', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.runstates'), + model_name="runprocess", + name="state_before_error", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.runstates", + ), ), migrations.AddField( - model_name='runprocess', - name='used_sequencer', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencerinlab'), + model_name="runprocess", + name="used_sequencer", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.sequencerinlab", + ), ), migrations.CreateModel( - name='RawTopUnknowBarcodes', + name="RawTopUnknowBarcodes", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('lane_number', models.CharField(max_length=4)), - ('top_number', models.CharField(max_length=4)), - ('count', models.CharField(max_length=40)), - ('sequence', models.CharField(max_length=40)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("lane_number", models.CharField(max_length=4)), + ("top_number", models.CharField(max_length=4)), + ("count", models.CharField(max_length=40)), + ("sequence", models.CharField(max_length=40)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "runprocess_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.runprocess", + ), + ), ], options={ - 'db_table': 'wetlab_raw_top_unknown_barcodes', + "db_table": "wetlab_raw_top_unknown_barcodes", }, ), migrations.CreateModel( - name='RawDemuxStats', + name="RawDemuxStats", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('default_all', models.CharField(max_length=40, null=True)), - ('raw_yield', models.CharField(max_length=255)), - ('raw_yield_q30', models.CharField(max_length=255)), - ('raw_quality', models.CharField(max_length=255)), - ('pf_yield', models.CharField(max_length=255)), - ('pf_yield_q30', models.CharField(max_length=255)), - ('pf_quality_score', models.CharField(max_length=255)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('project_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.projects')), - ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("default_all", models.CharField(max_length=40, null=True)), + ("raw_yield", models.CharField(max_length=255)), + ("raw_yield_q30", models.CharField(max_length=255)), + ("raw_quality", models.CharField(max_length=255)), + ("pf_yield", models.CharField(max_length=255)), + ("pf_yield_q30", models.CharField(max_length=255)), + ("pf_quality_score", models.CharField(max_length=255)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "project_id", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.projects", + ), + ), + ( + "runprocess_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.runprocess", + ), + ), ], options={ - 'db_table': 'wetlab_raw_demux_stats', + "db_table": "wetlab_raw_demux_stats", }, ), migrations.AddField( - model_name='projects', - name='run_process', - field=models.ManyToManyField(to='wetlab.runprocess'), + model_name="projects", + name="run_process", + field=models.ManyToManyField(to="wetlab.runprocess"), ), migrations.AddField( - model_name='projects', - name='user_id', - field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL), + model_name="projects", + name="user_id", + field=models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to=settings.AUTH_USER_MODEL, + ), ), migrations.CreateModel( - name='LibUserSampleSheet', + name="LibUserSampleSheet", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('sample_sheet', models.FileField(upload_to='wetlab/sample_sheets_lib_prep/')), - ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), - ('application', models.CharField(blank=True, max_length=70, null=True)), - ('instrument', models.CharField(blank=True, max_length=70, null=True)), - ('adapter_1', models.CharField(blank=True, max_length=70, null=True)), - ('adapter_2', models.CharField(blank=True, max_length=70, null=True)), - ('assay', models.CharField(blank=True, max_length=70, null=True)), - ('reads', models.CharField(blank=True, max_length=10, null=True)), - ('confirmed_used', models.BooleanField(default=False)), - ('iem_version', models.CharField(blank=True, max_length=5, null=True)), - ('collection_index_kit_id', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.collectionindexkit')), - ('register_user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), - ('sequencing_configuration', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencingconfiguration')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "sample_sheet", + models.FileField(upload_to="wetlab/sample_sheets_lib_prep/"), + ), + ("generated_at", models.DateTimeField(auto_now_add=True, null=True)), + ("application", models.CharField(blank=True, max_length=70, null=True)), + ("instrument", models.CharField(blank=True, max_length=70, null=True)), + ("adapter_1", models.CharField(blank=True, max_length=70, null=True)), + ("adapter_2", models.CharField(blank=True, max_length=70, null=True)), + ("assay", models.CharField(blank=True, max_length=70, null=True)), + ("reads", models.CharField(blank=True, max_length=10, null=True)), + ("confirmed_used", models.BooleanField(default=False)), + ("iem_version", models.CharField(blank=True, max_length=5, null=True)), + ( + "collection_index_kit_id", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.collectionindexkit", + ), + ), + ( + "register_user", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to=settings.AUTH_USER_MODEL, + ), + ), + ( + "sequencing_configuration", + models.ForeignKey( + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.sequencingconfiguration", + ), + ), ], options={ - 'db_table': 'wetlab_lib_user_samplesheet', + "db_table": "wetlab_lib_user_samplesheet", }, ), migrations.CreateModel( - name='LibraryPool', + name="LibraryPool", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('pool_name', models.CharField(max_length=50)), - ('sample_number', models.IntegerField(default=0)), - ('pool_code_id', models.CharField(blank=True, max_length=50)), - ('adapter', models.CharField(blank=True, max_length=50, null=True)), - ('paired_end', models.CharField(blank=True, max_length=10, null=True)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('platform', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.sequencingplatform')), - ('pool_state', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.poolstates')), - ('register_user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), - ('run_process_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("pool_name", models.CharField(max_length=50)), + ("sample_number", models.IntegerField(default=0)), + ("pool_code_id", models.CharField(blank=True, max_length=50)), + ("adapter", models.CharField(blank=True, max_length=50, null=True)), + ("paired_end", models.CharField(blank=True, max_length=10, null=True)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "platform", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.sequencingplatform", + ), + ), + ( + "pool_state", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.poolstates", + ), + ), + ( + "register_user", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to=settings.AUTH_USER_MODEL, + ), + ), + ( + "run_process_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.runprocess", + ), + ), ], options={ - 'db_table': 'wetlab_library_pool', - 'ordering': ('pool_name',), + "db_table": "wetlab_library_pool", + "ordering": ("pool_name",), }, ), migrations.CreateModel( - name='LibPrepare', + name="LibPrepare", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('lib_prep_code_id', models.CharField(blank=True, max_length=255, null=True)), - ('user_sample_id', models.CharField(blank=True, max_length=100, null=True)), - ('project_in_samplesheet', models.CharField(blank=True, max_length=80, null=True)), - ('sample_plate', models.CharField(blank=True, max_length=50, null=True)), - ('sample_well', models.CharField(blank=True, max_length=20, null=True)), - ('index_plate_well', models.CharField(blank=True, max_length=20, null=True)), - ('i7_index_id', models.CharField(blank=True, max_length=25, null=True)), - ('i7_index', models.CharField(blank=True, max_length=30, null=True)), - ('i5_index_id', models.CharField(blank=True, max_length=25, null=True)), - ('i5_index', models.CharField(blank=True, max_length=30, null=True)), - ('genome_folder', models.CharField(blank=True, max_length=180, null=True)), - ('manifest', models.CharField(blank=True, max_length=80, null=True)), - ('reused_number', models.IntegerField(default=0)), - ('unique_id', models.CharField(blank=True, max_length=16, null=True)), - ('user_in_samplesheet', models.CharField(blank=True, max_length=255, null=True)), - ('samplename_in_samplesheet', models.CharField(blank=True, max_length=255, null=True)), - ('prefix_protocol', models.CharField(blank=True, max_length=25, null=True)), - ('lib_prep_state', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.libpreparestates')), - ('molecule_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.moleculepreparation')), - ('pools', models.ManyToManyField(blank=True, to='wetlab.librarypool')), - ('protocol_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.protocols')), - ('register_user', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL)), - ('sample_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.samples')), - ('user_lot_kit_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.userlotcommercialkits')), - ('user_sample_sheet', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='wetlab.libusersamplesheet')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ( + "lib_prep_code_id", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "user_sample_id", + models.CharField(blank=True, max_length=100, null=True), + ), + ( + "project_in_samplesheet", + models.CharField(blank=True, max_length=80, null=True), + ), + ( + "sample_plate", + models.CharField(blank=True, max_length=50, null=True), + ), + ("sample_well", models.CharField(blank=True, max_length=20, null=True)), + ( + "index_plate_well", + models.CharField(blank=True, max_length=20, null=True), + ), + ("i7_index_id", models.CharField(blank=True, max_length=25, null=True)), + ("i7_index", models.CharField(blank=True, max_length=30, null=True)), + ("i5_index_id", models.CharField(blank=True, max_length=25, null=True)), + ("i5_index", models.CharField(blank=True, max_length=30, null=True)), + ( + "genome_folder", + models.CharField(blank=True, max_length=180, null=True), + ), + ("manifest", models.CharField(blank=True, max_length=80, null=True)), + ("reused_number", models.IntegerField(default=0)), + ("unique_id", models.CharField(blank=True, max_length=16, null=True)), + ( + "user_in_samplesheet", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "samplename_in_samplesheet", + models.CharField(blank=True, max_length=255, null=True), + ), + ( + "prefix_protocol", + models.CharField(blank=True, max_length=25, null=True), + ), + ( + "lib_prep_state", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.libpreparestates", + ), + ), + ( + "molecule_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="core.moleculepreparation", + ), + ), + ("pools", models.ManyToManyField(blank=True, to="wetlab.librarypool")), + ( + "protocol_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.protocols", + ), + ), + ( + "register_user", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to=settings.AUTH_USER_MODEL, + ), + ), + ( + "sample_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.samples", + ), + ), + ( + "user_lot_kit_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.userlotcommercialkits", + ), + ), + ( + "user_sample_sheet", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.libusersamplesheet", + ), + ), ], options={ - 'db_table': 'wetlab_lib_prepare', - 'ordering': ('lib_prep_code_id',), + "db_table": "wetlab_lib_prepare", + "ordering": ("lib_prep_code_id",), }, ), migrations.CreateModel( - name='LibParameterValue', + name="LibParameterValue", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('parameter_value', models.CharField(max_length=255)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('library_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.libprepare')), - ('parameter_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='core.protocolparameters')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("parameter_value", models.CharField(max_length=255)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "library_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.libprepare", + ), + ), + ( + "parameter_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="core.protocolparameters", + ), + ), ], options={ - 'db_table': 'wetlab_lib_parameter_value', + "db_table": "wetlab_lib_parameter_value", }, ), migrations.CreateModel( - name='GraphicsStats', + name="GraphicsStats", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('folder_run_graphic', models.CharField(max_length=255)), - ('cluster_count_graph', models.CharField(max_length=255)), - ('flowcell_graph', models.CharField(max_length=255)), - ('intensity_by_cycle_graph', models.CharField(max_length=255)), - ('heatmap_graph', models.CharField(max_length=255)), - ('histogram_graph', models.CharField(max_length=255)), - ('sample_qc_graph', models.CharField(max_length=255)), - ('generated_at', models.DateTimeField(auto_now_add=True, null=True)), - ('runprocess_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.runprocess')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("folder_run_graphic", models.CharField(max_length=255)), + ("cluster_count_graph", models.CharField(max_length=255)), + ("flowcell_graph", models.CharField(max_length=255)), + ("intensity_by_cycle_graph", models.CharField(max_length=255)), + ("heatmap_graph", models.CharField(max_length=255)), + ("histogram_graph", models.CharField(max_length=255)), + ("sample_qc_graph", models.CharField(max_length=255)), + ("generated_at", models.DateTimeField(auto_now_add=True, null=True)), + ( + "runprocess_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.runprocess", + ), + ), ], options={ - 'db_table': 'wetlab_graphics_stats', + "db_table": "wetlab_graphics_stats", }, ), migrations.CreateModel( - name='CollectionIndexValues', + name="CollectionIndexValues", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('default_well', models.CharField(max_length=10, null=True)), - ('index_7', models.CharField(max_length=25, null=True)), - ('i_7_seq', models.CharField(max_length=25, null=True)), - ('index_5', models.CharField(max_length=25, null=True)), - ('i_5_seq', models.CharField(max_length=25, null=True)), - ('collection_index_kit_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.collectionindexkit')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("default_well", models.CharField(max_length=10, null=True)), + ("index_7", models.CharField(max_length=25, null=True)), + ("i_7_seq", models.CharField(max_length=25, null=True)), + ("index_5", models.CharField(max_length=25, null=True)), + ("i_5_seq", models.CharField(max_length=25, null=True)), + ( + "collection_index_kit_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.collectionindexkit", + ), + ), ], options={ - 'db_table': 'wetlab_collection_index_values', + "db_table": "wetlab_collection_index_values", }, ), migrations.CreateModel( - name='AdditionalUserLotKit', + name="AdditionalUserLotKit", fields=[ - ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')), - ('value', models.CharField(max_length=255)), - ('generated_at', models.DateTimeField(auto_now_add=True)), - ('additional_lot_kits', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.additionakitslibprepare')), - ('lib_prep_id', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='wetlab.libprepare')), - ('user_lot_kit_id', models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.CASCADE, to='core.userlotcommercialkits')), + ( + "id", + models.AutoField( + auto_created=True, + primary_key=True, + serialize=False, + verbose_name="ID", + ), + ), + ("value", models.CharField(max_length=255)), + ("generated_at", models.DateTimeField(auto_now_add=True)), + ( + "additional_lot_kits", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.additionakitslibprepare", + ), + ), + ( + "lib_prep_id", + models.ForeignKey( + on_delete=django.db.models.deletion.CASCADE, + to="wetlab.libprepare", + ), + ), + ( + "user_lot_kit_id", + models.ForeignKey( + blank=True, + null=True, + on_delete=django.db.models.deletion.CASCADE, + to="core.userlotcommercialkits", + ), + ), ], options={ - 'db_table': 'wetlab_lib_additional_user_lot_kit', + "db_table": "wetlab_lib_additional_user_lot_kit", }, ), ] diff --git a/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py b/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py index 71b494e4d..651abd81f 100644 --- a/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py +++ b/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py @@ -32,15 +32,13 @@ def drop_librarypool_run_process_id(apps, schema_editor): f"ALTER TABLE wetlab_library_pool DROP FOREIGN KEY `{constraint_name}`" ) - cursor.execute( - "ALTER TABLE wetlab_library_pool DROP COLUMN run_process_id_id" - ) + cursor.execute("ALTER TABLE wetlab_library_pool DROP COLUMN run_process_id_id") class Migration(migrations.Migration): dependencies = [ - ('wetlab', '0001_initial'), + ("wetlab", "0001_initial"), ] operations = [ @@ -60,39 +58,39 @@ class Migration(migrations.Migration): ], state_operations=[ migrations.RemoveField( - model_name='librarypool', - name='run_process_id', + model_name="librarypool", + name="run_process_id", ), ], ), migrations.AddField( - model_name='runprocess', - name='library_pool', - field=models.ManyToManyField(blank=True, to='wetlab.librarypool'), + model_name="runprocess", + name="library_pool", + field=models.ManyToManyField(blank=True, to="wetlab.librarypool"), ), migrations.AddField( - model_name='runstates', - name='description', + model_name="runstates", + name="description", field=models.CharField(blank=True, max_length=255, null=True), ), migrations.AddField( - model_name='runstates', - name='show_in_stats', + model_name="runstates", + name="show_in_stats", field=models.BooleanField(default=False), ), migrations.AddField( - model_name='runstates', - name='state_display', + model_name="runstates", + name="state_display", field=models.CharField(blank=True, max_length=80, null=True), ), migrations.AlterField( - model_name='libprepare', - name='prefix_protocol', + model_name="libprepare", + name="prefix_protocol", field=models.CharField(blank=True, max_length=50, null=True), ), migrations.AlterField( - model_name='rawtopunknowbarcodes', - name='count', + model_name="rawtopunknowbarcodes", + name="count", field=models.IntegerField(), ), ] diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 910ec6713..3d6618e70 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -772,7 +772,11 @@ def manage_run_in_processed_run_state(conn, run_process_objs): .last() .get_run_folder() ) - root_run_folder = os.path.join("/", wetlab.utils.crontab_process.get_samba_application_shared_folder(), run_folder) + root_run_folder = os.path.join( + "/", + wetlab.utils.crontab_process.get_samba_application_shared_folder(), + run_folder, + ) # delete existing information to avoid having duplicated tables wetlab.utils.crontab_process.delete_existing_run_metrics_table_processed( run_process_obj, experiment_name From 4b15923034c25730149f67eeb7d8ad18bb166df8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 13:33:09 +0100 Subject: [PATCH 339/446] changelog --- CHANGELOG.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5b842b102..cd451b3b5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Included thorough description for wetlab API's update_lab() method [#361](https://github.com/BU-ISCIII/iskylims/pull/361) - Included new API function lab-request-mapping to get LabRequest fields ontology map [#377](https://github.com/BU-ISCIII/iskylims/pull/377) - Improved responses in API create-sample-data by adding ERROR messages and data [#377](https://github.com/BU-ISCIII/iskylims/pull/377) +- Added support for `script-before` and `script-after` hooks in install script. [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Committed baseline migration files and added migrations for develop changes [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Added developer notes on how to create and manage migration files [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Added documentation describing migration scripts and their related versions [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Enabled Docker internal networking for local test installation [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Opened Docker network to allow localhost MySQL connection when required [#389](https://github.com/BU-ISCIII/iskylims/pull/389) #### Fixes @@ -59,6 +65,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Adapted update_lab serializer call to new serializer update method [#361](https://github.com/BU-ISCIII/iskylims/pull/361) - Leave missing submitting_fields as empty string instead of crashing in wetlab.api.create_sample_data [#363](https://github.com/BU-ISCIII/iskylims/pull/363) - Fixed wetlab API create-sample-data error when submitting_institution fields were not provided [#377](https://github.com/BU-ISCIII/iskylims/pull/377) +- Fixed incorrect git revision propagation to Dockerfile during build [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Fixed configuration file accessibility from within Docker container [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Fixed disk utilization check to correctly resolve application folder path [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Fixed incorrect application folder path resolution in crontab scripts [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Fixed samplesheet parsing error [#389](https://github.com/BU-ISCIII/iskylims/pull/389) #### Changed @@ -71,10 +82,15 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Improved query performance and excluded rejected/archived services from ongoing list. (#299) - Updated sample metadata fields with standardized ontology mappings and schema alignment.[#358](https://github.com/BU-ISCIII/iskylims/pull/358) - API create-sample-data Lab data mapping moved to core_config.LAB_REQUEST_ONTOLOGY_MAP [#377](https://github.com/BU-ISCIII/iskylims/pull/377) +- Renamed `docker-compose.yml` to `docker-compose.test.yml` and `docker-compose.prod.yml` for test clarity [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Refactored Docker runtime handling when path is outside repository [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Updated `docker_install.sh` with multiple reliability improvements [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Updated upgrade scripts documentation to include execution order information and docker upgrade clarifications [#389](https://github.com/BU-ISCIII/iskylims/pull/389) #### Removed - Dummy fix in usage line [#271](https://github.com/BU-ISCIII/iskylims/pull/271) +- Removed migrations from `.gitignore` and app-level `.gitignore` to ensure version control of schema changes [#389](https://github.com/BU-ISCIII/iskylims/pull/389) #### Requirements From df02ecfd9c58f58e5797f280b2a68644fc4a9c9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 13:42:19 +0100 Subject: [PATCH 340/446] linting --- drylab/templatetags/upload_tags.py | 6 ++---- ...002_remove_librarypool_run_process_id_and_more.py | 12 ++++-------- 2 files changed, 6 insertions(+), 12 deletions(-) diff --git a/drylab/templatetags/upload_tags.py b/drylab/templatetags/upload_tags.py index 144bfe95f..b56046e73 100644 --- a/drylab/templatetags/upload_tags.py +++ b/drylab/templatetags/upload_tags.py @@ -6,8 +6,7 @@ @register.simple_tag def upload_js(): - return mark_safe( - """ + return mark_safe(""" - """ - ) + """) diff --git a/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py b/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py index 651abd81f..46552de57 100644 --- a/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py +++ b/wetlab/migrations/0002_remove_librarypool_run_process_id_and_more.py @@ -5,28 +5,24 @@ def drop_librarypool_run_process_id(apps, schema_editor): with schema_editor.connection.cursor() as cursor: - cursor.execute( - """ + cursor.execute(""" SELECT 1 FROM information_schema.COLUMNS WHERE TABLE_SCHEMA = DATABASE() AND TABLE_NAME = 'wetlab_library_pool' AND COLUMN_NAME = 'run_process_id_id' - """ - ) + """) if cursor.fetchone() is None: return - cursor.execute( - """ + cursor.execute(""" SELECT CONSTRAINT_NAME FROM information_schema.KEY_COLUMN_USAGE WHERE TABLE_SCHEMA = DATABASE() AND TABLE_NAME = 'wetlab_library_pool' AND COLUMN_NAME = 'run_process_id_id' AND REFERENCED_TABLE_NAME IS NOT NULL - """ - ) + """) for (constraint_name,) in cursor.fetchall(): cursor.execute( f"ALTER TABLE wetlab_library_pool DROP FOREIGN KEY `{constraint_name}`" From cd4bc4e6b10eaa862b0e1fb556e9238a55032b4c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 16:58:12 +0100 Subject: [PATCH 341/446] add persistance of documents and logs via volumes for production --- docker-compose.prod.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index f7dfe2a1a..950d9cb5b 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -17,5 +17,11 @@ services: volumes: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo + - iskylims_logs:/opt/iskylims/logs + - iskylims_documents:/opt/iskylims/documents extra_hosts: - "host.docker.internal:host-gateway" + +volumes: + iskylims_logs: + iskylims_documents: From e0bc9dd3919575a01de9accb81a7e5bf6201b6ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 17:01:08 +0100 Subject: [PATCH 342/446] add some docs about persistance and backup --- LEAME.md | 17 +++++++++++++++++ README.md | 22 ++++++++++++++++++++++ 2 files changed, 39 insertions(+) diff --git a/LEAME.md b/LEAME.md index a4602a470..16cd1b266 100644 --- a/LEAME.md +++ b/LEAME.md @@ -121,6 +121,23 @@ La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh` dentr ### Actualizacion del despliegue Docker v3.0.0 a 3.1.0 +#### Haz copia de seguridad + +- Copia completa de la base de datos `iskylims`. +- Copia completa de las carpetas de logs y documents. + +```bash +docker run --rm \ + -v iskylims_logs:/from \ + -v "$PWD":/to \ + alpine tar -czf /to/iskylims_logs.tgz -C /from . + +docker run --rm \ + -v iskylims_documents:/from \ + -v "$PWD":/to \ + alpine tar -czf /to/iskylims_documents.tgz -C /from . +``` + Antes de actualizar, asegurate de tener una copia completa de la base de datos y de los datos en volumenes que uses. Confirma que `conf/my_prod_settings.txt` tenga el host/usuario/password de la base de datos de produccion, la URL/IP del servidor, correo y ajustes de logging usados por el contenedor. Para 3.0.0 -> 3.1.0, exporta primero el mapeo de LibraryPool y luego ejecuta la actualizacion con scripts pre/post: diff --git a/README.md b/README.md index e8c15a42a..932f8f678 100644 --- a/README.md +++ b/README.md @@ -18,6 +18,7 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Docker deployment](#docker-deployment) - [Local test stack](#local-test-stack) - [Production container](#production-container) + - [Persist logs/documents with named volumes](#persist-logsdocuments-with-named-volumes) - [Upgrade docker deployment](#upgrade-docker-deployment) - [Upgrade docker deployment v3.0.0 to 3.1.0](#upgrade-docker-deployment-v300-to-310) - [Back up first](#back-up-first) @@ -114,6 +115,15 @@ Deploy the iSkyLIMS container against external MySQL/Samba services: 3. If this is a fresh install, create the Django superuser when prompted and complete the Samba configuration in the UI. +#### Persist logs/documents with named volumes + +The production compose file mounts two named volumes so upgrades/rebuilds keep data: + +- `iskylims_logs` → `/opt/iskylims/logs` +- `iskylims_documents` → `/opt/iskylims/documents` + +If you override the compose file, ensure these two mounts exist to keep logs and documents persistent. + ### Upgrade docker deployment Re-deploy the application container against an existing production database without touching data: @@ -131,6 +141,18 @@ The upgrade path rebuilds/restarts the container and runs `install.sh` inside th - Full backup of the `iskylims` database. - Full backup of the logs folder and the documents folder. +```bash +docker run --rm \ + -v iskylims_logs:/from \ + -v "$PWD":/to \ + alpine tar -czf /to/iskylims_logs.tgz -C /from . + +docker run --rm \ + -v iskylims_documents:/from \ + -v "$PWD":/to \ + alpine tar -czf /to/iskylims_documents.tgz -C /from . +``` + For 3.0.0 -> 3.1.0, export the LibraryPool mapping first, then run the upgrade with pre/post scripts: ```bash From ee254fda923cec7c0de43b17a225257ad2c53558 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 17:52:42 +0100 Subject: [PATCH 343/446] change to gunicorn for production --- conf/requirements.txt | 3 ++- docker-compose.prod.yml | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/conf/requirements.txt b/conf/requirements.txt index c1a63ddc0..912de323a 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -13,6 +13,7 @@ django-mptt-admin==2.6.2 django-cleanup==8.1.0 interop>1.1.22 mod_wsgi==5.0.0 +gunicorn==22.0.0 mysqlclient==2.2.6 paramiko==3.4.1 jsonschema==4.23.0 @@ -24,4 +25,4 @@ xlrd==2.0.1 pandas==2.2.2 numpy==1.26.4 openpyxl==3.1.5 -setuptools==75.2.0 \ No newline at end of file +setuptools==75.2.0 diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 950d9cb5b..7e8a383fe 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -19,6 +19,7 @@ services: - /usr/share/zoneinfo:/usr/share/zoneinfo - iskylims_logs:/opt/iskylims/logs - iskylims_documents:/opt/iskylims/documents + - /var/www/iskylims/static:/opt/iskylims/static extra_hosts: - "host.docker.internal:host-gateway" From 9be4e53efd403a04adfa4e10fab7c96f968563ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 17:53:00 +0100 Subject: [PATCH 344/446] change to gunicorn for production --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index f85a57ba8..2b2b3f7ed 100644 --- a/Dockerfile +++ b/Dockerfile @@ -43,4 +43,4 @@ WORKDIR /opt/iskylims EXPOSE 8001 # Start the application once install.sh has populated /opt/iskylims. -CMD ["bash", "-c", "while [ ! -f /opt/iskylims/manage.py ]; do sleep 2; done; python3 /opt/iskylims/manage.py runserver 0:8001"] +CMD ["bash", "-c", "while [ ! -f /opt/iskylims/manage.py ]; do sleep 2; done; gunicorn iskylims.wsgi:application --bind 0.0.0.0:8001 --workers 3 --threads 2 --timeout 120"] From baf09eccfd2532c70a7bd4c5f48f741b5c94a526 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 17:53:23 +0100 Subject: [PATCH 345/446] add reverse proxy conf example to confs --- conf/iskylims_apache_reverse_proxy.conf | 29 +++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 conf/iskylims_apache_reverse_proxy.conf diff --git a/conf/iskylims_apache_reverse_proxy.conf b/conf/iskylims_apache_reverse_proxy.conf new file mode 100644 index 000000000..616ac356a --- /dev/null +++ b/conf/iskylims_apache_reverse_proxy.conf @@ -0,0 +1,29 @@ +# Example Apache reverse proxy config for iSkyLIMS (Docker production) +# Replace ServerName and adjust the ProxyPass target if needed. + + + ServerName example.isciiides.es + + ProxyPreserveHost On + RequestHeader set X-Forwarded-Proto "http" + RequestHeader set X-Forwarded-Port "80" + + # If Apache runs on the host, proxy to the published port + ProxyPass / http://localhost:8001/ + ProxyPassReverse / http://localhost:8001/ + + # If Apache runs in the same Docker network, use the service name instead: + # ProxyPass / http://app:8001/ + # ProxyPassReverse / http://app:8001/ + + # Serve static files from a host path (bind-mounted from the container) + # Example: /var/www/iskylims/static -> /opt/iskylims/static in docker-compose.prod.yml + Alias /static/ /var/www/iskylims/static/ + + Require all granted + + + ErrorLog logs/iskylims-apache.error.log + CustomLog logs/iskylims-apache.access.log combined env=!forwarded + CustomLog logs/iskylims-apache.access.log proxy env=forwarded + From a3875c9476c08a488e01a34cffdb7c825d3d9034 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 17:53:50 +0100 Subject: [PATCH 346/446] add docs to readme about how to configure apache for production --- LEAME.md | 89 +++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 92 ++++++++++++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 180 insertions(+), 1 deletion(-) diff --git a/LEAME.md b/LEAME.md index 16cd1b266..58c25f340 100644 --- a/LEAME.md +++ b/LEAME.md @@ -109,6 +109,18 @@ Despliega el contenedor de iSkyLIMS contra servicios MySQL/Samba externos: 3. Si es una instalacion nueva, crea el superusuario cuando se solicite y completa la configuracion de Samba en la UI. +#### Proxy inverso con Apache (host) + Gunicorn + +En produccion, el contenedor ejecuta `gunicorn` (no `manage.py runserver`). Usa Apache en el host como proxy inverso hacia `localhost:8001`. + +Archivos estaticos: + +- El contenedor genera los estaticos en `/opt/iskylims/static`. +- `docker-compose.prod.yml` monta ese directorio en `/var/www/iskylims/static` del host. +- Configura Apache con `Alias /static/ /var/www/iskylims/static/`. + +Ejemplo de configuracion en `conf/iskylims_apache_reverse_proxy.conf`. + ### Actualizacion del despliegue Docker Re-despliega el contenedor de aplicacion contra una base de datos existente sin tocar los datos: @@ -292,6 +304,8 @@ Las actualizaciones regeneran las migraciones y las aplican con `--fake-initial` Cuando actualizamos usando el script de instalacion estamos realizando varios cambios en la base de datos. Si algo falla necesitamos restaurar el estado anterior y empezar de nuevo. +### Bare-metal + Necesitamos copiar la carpeta completa `/opt/iskylims` de vuelta a `/opt/iskylims` (o tu ruta de instalacion), y restaurar la base de datos con algo como: ```bash @@ -304,6 +318,39 @@ mysql -u iskylims -p -h dmysqlps.isciiides.es mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` +### Docker + +1. Para el contenedor: + + ```bash + docker compose -f docker-compose.prod.yml down + ``` + +2. Restaura la base de datos desde tu backup. + +3. Si sospechas que la imagen o la cache de build esta corrupta, elimina la imagen de la app y reconstruye: + + ```bash + docker image ls | grep iskylims + docker rmi + ``` + +4. Si los volumenes estan comprometidos, restauralos desde los tar: + + ```bash + docker run --rm -v iskylims_logs:/to -v "$PWD":/from alpine \ + tar -xzf /from/iskylims_logs.tgz -C /to + + docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ + tar -xzf /from/iskylims_documents.tgz -C /to + ``` + +5. Arranca el contenedor de nuevo: + + ```bash + bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade + ``` + ## Pasos finales de configuracion ### Configuracion de SAMBA @@ -325,6 +372,48 @@ mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_pro Copia el archivo de configuracion de Apache segun tu distribucion dentro del directorio de configuracion de Apache y renombralo a iskylims.conf +Ubicaciones tipicas: + +- Ubuntu/Debian: `/etc/apache2/sites-available/iskylims.conf` (habilitar con `a2ensite`) +- CentOS/RHEL: `/etc/httpd/conf.d/iskylims.conf` + +Pasos sugeridos (Apache en el host como proxy inverso): + +1. Copia el ejemplo de configuracion: + + ```bash + sudo cp conf/iskylims_apache_reverse_proxy.conf /etc/apache2/sites-available/iskylims.conf + # CentOS/RHEL: + # sudo cp conf/iskylims_apache_reverse_proxy.conf /etc/httpd/conf.d/iskylims.conf + ``` + +2. Edita la configuracion: + + - Ajusta `ServerName` + - Comprueba que `ProxyPass` apunte a `http://localhost:8001/` + - Comprueba `Alias /static/ /var/www/iskylims/static/` + +3. Crea la carpeta de estaticos en el host: + + ```bash + sudo mkdir -p /var/www/iskylims/static + ``` + +4. Habilita modulos necesarios (Ubuntu/Debian): + + ```bash + sudo a2enmod proxy proxy_http headers + sudo a2ensite iskylims.conf + ``` + +5. Recarga Apache: + + ```bash + sudo systemctl reload apache2 + # CentOS/RHEL: + # sudo systemctl reload httpd + ``` + ### Verificacion de la instalacion Abre el navegador y escribe "localhost" o la IP local del servidor para comprobar que iSkyLIMS esta funcionando. diff --git a/README.md b/README.md index 932f8f678..3d7001521 100644 --- a/README.md +++ b/README.md @@ -19,6 +19,7 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Local test stack](#local-test-stack) - [Production container](#production-container) - [Persist logs/documents with named volumes](#persist-logsdocuments-with-named-volumes) + - [Apache reverse proxy (host) + Gunicorn](#apache-reverse-proxy-host--gunicorn) - [Upgrade docker deployment](#upgrade-docker-deployment) - [Upgrade docker deployment v3.0.0 to 3.1.0](#upgrade-docker-deployment-v300-to-310) - [Back up first](#back-up-first) @@ -124,6 +125,18 @@ The production compose file mounts two named volumes so upgrades/rebuilds keep d If you override the compose file, ensure these two mounts exist to keep logs and documents persistent. +#### Apache reverse proxy (host) + Gunicorn + +For production, the container runs `gunicorn` (not `manage.py runserver`). Use Apache on the host as a reverse proxy to `localhost:8001`. + +Static files: + +- The container writes collected static files to `/opt/iskylims/static`. +- `docker-compose.prod.yml` bind-mounts that path to `/var/www/iskylims/static` on the host. +- Configure Apache with `Alias /static/ /var/www/iskylims/static/`. + +See the example config in `conf/iskylims_apache_reverse_proxy.conf` and the [Configure Apache server](#configure-apache-server) section below. + ### Upgrade docker deployment Re-deploy the application container against an existing production database without touching data: @@ -300,6 +313,8 @@ Upgrades regenerate migrations and apply them with `--fake-initial` so existing When we upgrade using the installation script we are performing several changes in the database. If something fails we need to restore the app situation before anything happened and start all over. +### Bare-metal + We need to copy back the full `/opt/iskylims` folder back to `/opt/iskylims` (or your installation path preference), and restore the database doing something like this: ```bash @@ -312,6 +327,39 @@ mysql -u iskylims -p -h dmysqlps.isciiides.es mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql ``` +### Docker + +1. Stop the container: + + ```bash + docker compose -f docker-compose.prod.yml down + ``` + +2. Restore the database from your backup. + +3. If you suspect the image or build cache is corrupted, remove the app image and rebuild: + + ```bash + docker image ls | grep iskylims + docker rmi + ``` + +4. If volumes are compromised, restore them from the tar backups: + + ```bash + docker run --rm -v iskylims_logs:/to -v "$PWD":/from alpine \ + tar -xzf /from/iskylims_logs.tgz -C /to + + docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ + tar -xzf /from/iskylims_documents.tgz -C /to + ``` + +5. Start the container again: + + ```bash + bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade + ``` + ## Final configuration steps ### SAMBA configurarion @@ -344,7 +392,49 @@ Baseline + upgrade flow for new releases: ### Configure Apache server -Copy the apache configuration file according to your distribution inside the apache configutation directory and rename it to iskylims.conf +Copy the apache configuration file according to your distribution inside the apache configuration directory and rename it to iskylims.conf + +Typical config locations: + +- Ubuntu/Debian: `/etc/apache2/sites-available/iskylims.conf` (enable with `a2ensite`) +- CentOS/RHEL: `/etc/httpd/conf.d/iskylims.conf` + +Suggested steps (host Apache as reverse proxy): + +1. Copy the example config: + + ```bash + sudo cp conf/iskylims_apache_reverse_proxy.conf /etc/apache2/sites-available/iskylims.conf + # CentOS/RHEL: + # sudo cp conf/iskylims_apache_reverse_proxy.conf /etc/httpd/conf.d/iskylims.conf + ``` + +2. Edit the config: + + - Set `ServerName` + - Ensure `ProxyPass` points to `http://localhost:8001/` + - Ensure `Alias /static/ /var/www/iskylims/static/` + +3. Create the static folder on the host: + + ```bash + sudo mkdir -p /var/www/iskylims/static + ``` + +4. Enable required modules (Ubuntu/Debian): + + ```bash + sudo a2enmod proxy proxy_http headers + sudo a2ensite iskylims.conf + ``` + +5. Reload Apache: + + ```bash + sudo systemctl reload apache2 + # CentOS/RHEL: + # sudo systemctl reload httpd + ``` ### Verification of the installation From 0fdd2930e1408df3c742da2903cb08b575e97ad2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 18:41:33 +0100 Subject: [PATCH 347/446] Switch Docker base to UBI 9 and update build deps --- Dockerfile | 26 +++++++++++++++++--------- LEAME.md | 8 ++++++-- README.md | 4 +++- conf/docker_production_settings.txt | 2 +- install.sh | 19 +++++++++++++++++-- 5 files changed, 44 insertions(+), 15 deletions(-) diff --git a/Dockerfile b/Dockerfile index 2b2b3f7ed..e358afce4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,18 +1,25 @@ -FROM ubuntu:24.04 +FROM registry.access.redhat.com/ubi9/ubi ENV TZ=Europe/Madrid RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone + # Updates -ARG DEBIAN_FRONTEND=noninteractive -RUN apt-get update && apt-get upgrade -y +RUN dnf -y update # Essential software -RUN apt-get install -y \ - git wget lsb-release \ - libmysqlclient-dev default-mysql-client \ - python3-pip libpq-dev python3-venv python3-wheel \ - apache2-dev cron \ - gnuplot pkg-config rsync +RUN dnf -y install \ + git wget \ + python3.11 python3.11-pip python3.11-devel python3.11-wheel \ + gcc gcc-c++ make \ + openssl-devel libffi-devel \ + mariadb mariadb-connector-c-devel postgresql-devel \ + httpd-devel cronie \ + rsync tzdata \ + pkgconf-pkg-config \ + && dnf clean all + +# Ensure python3 points to the desired version +RUN ln -sf /usr/bin/python3.11 /usr/bin/python3 # Set MYSQLCLIENT_CFLAGS and MYSQLCLIENT_LDFLAGS using pkg-config RUN export MYSQLCLIENT_CFLAGS="$(pkg-config --libs mysqlclient)" && \ @@ -33,6 +40,7 @@ ARG GIT_REVISION=main ARG INSTALL_CONF=conf/docker_test_settings.txt # Execute the dependency stage only; app migrations run when the container is up. +ENV SKIP_SYSTEM_PACKAGES=1 RUN /bin/bash install.sh --install dep --git_revision $GIT_REVISION --conf $INSTALL_CONF --skip_apache_restart # Use the virtualenv created by install.sh ENV PATH="/opt/iskylims/virtualenv/bin:${PATH}" diff --git a/LEAME.md b/LEAME.md index 58c25f340..52342d811 100644 --- a/LEAME.md +++ b/LEAME.md @@ -17,8 +17,10 @@ De acuerdo con la infraestructura existente, la secuenciacion se realiza en un i - [Despliegue con Docker](#despliegue-con-docker) - [Contenedor local de pruebas](#contenedor-local-de-pruebas) - [Contenedor de produccion](#contenedor-de-produccion) + - [Proxy inverso con Apache (host) + Gunicorn](#proxy-inverso-con-apache-host--gunicorn) - [Actualizacion del despliegue Docker](#actualizacion-del-despliegue-docker) - [Actualizacion del despliegue Docker v3.0.0 a 3.1.0](#actualizacion-del-despliegue-docker-v300-a-310) + - [Haz copia de seguridad](#haz-copia-de-seguridad) - [Despliegue bare-metal (Ubuntu/CentOS)](#despliegue-bare-metal-ubuntucentos) - [Instalacion](#instalacion) - [Requisitos previos](#requisitos-previos) @@ -27,11 +29,13 @@ De acuerdo con la infraestructura existente, la secuenciacion se realiza en un i - [Configurar install\_settings.txt](#configurar-install_settingstxt) - [Ejecutar install.sh](#ejecutar-installsh) - [Actualizacion (3.0.x a 3.1.x)](#actualizacion-30x-a-31x) - - [Haz copia de seguridad](#haz-copia-de-seguridad) + - [Haz copia de seguridad](#haz-copia-de-seguridad-1) - [Actualizar codigo y ajustes](#actualizar-codigo-y-ajustes) - [Ejecutar pasos de actualizacion con root](#ejecutar-pasos-de-actualizacion-con-root) - [Ejecutar pasos de actualizacion sin root](#ejecutar-pasos-de-actualizacion-sin-root) - [Que hacer si algo falla](#que-hacer-si-algo-falla) + - [Bare-metal](#bare-metal) + - [Docker](#docker) - [Pasos finales de configuracion](#pasos-finales-de-configuracion) - [Configuracion de SAMBA](#configuracion-de-samba) - [Verificacion de correo electronico](#verificacion-de-correo-electronico) @@ -174,7 +178,7 @@ bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade - MySQL > 8.0 o MariaDB > 10.4 - Apache 2.4 - git > 2.34 -- Python > 3.8 +- Python > 3.11 - Servidor local configurado para enviar correos - Acceso a la carpeta Samba donde estan los run folders - Paquete `lsb_release` (`yum install redhat-lsb-core` en RedHat/CentOS, `apt install lsb-core lsb-release` en Ubuntu) diff --git a/README.md b/README.md index 3d7001521..3d1e78456 100644 --- a/README.md +++ b/README.md @@ -37,6 +37,8 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Run upgrade steps requiring root](#run-upgrade-steps-requiring-root) - [Run upgrade steps without root](#run-upgrade-steps-without-root) - [What to do if something fails](#what-to-do-if-something-fails) + - [Bare-metal](#bare-metal) + - [Docker](#docker) - [Final configuration steps](#final-configuration-steps) - [SAMBA configurarion](#samba-configurarion) - [Email verification](#email-verification) @@ -201,7 +203,7 @@ bash docker_install.sh --install_conf my_prod_settings.txt --action upgrade \ - MySQL > 8.0 or MariaDB > 10.4 - Apache 2.4 - git > 2.34 -- Python > 3.8 +- Python > 3.11 - Local email sender configured - Access to the Samba share where run folders live - `lsb_release` package (`yum install redhat-lsb-core` on RedHat/CentOS, `apt install lsb-core lsb-release` on Ubuntu) diff --git a/conf/docker_production_settings.txt b/conf/docker_production_settings.txt index c92824596..3f07fbd65 100644 --- a/conf/docker_production_settings.txt +++ b/conf/docker_production_settings.txt @@ -9,7 +9,7 @@ MIGRATION_MODULES='core drylab wetlab django_utils' FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' ### (optional) Python installation path where pip and python executables are located -PYTHON_BIN_PATH='python3' +PYTHON_BIN_PATH='python3.11' ### Settings required to access database (external MySQL server) DB_USER='django' diff --git a/install.sh b/install.sh index a85c9a4be..7f1d4640f 100644 --- a/install.sh +++ b/install.sh @@ -63,13 +63,23 @@ log() { # db_check: verifies connectivity to the configured MySQL instance using mysqladmin/mysqlshow. db_check(){ log "INFO" "Checking database connectivity against $DB_SERVER_IP:$DB_PORT" - mysqladmin -h $DB_SERVER_IP -u$DB_USER -p$DB_PASS -P$DB_PORT processlist > /dev/null + local mysqladmin_bin + local mysqlshow_bin + mysqladmin_bin="$(command -v mysqladmin || command -v mariadb-admin || true)" + mysqlshow_bin="$(command -v mysqlshow || command -v mariadb-show || true)" + + if [ -z "$mysqladmin_bin" ] || [ -z "$mysqlshow_bin" ]; then + log "ERROR" "mysql client tools not found (mysqladmin/mysqlshow or mariadb-admin/mariadb-show)." + exit 1 + fi + + "$mysqladmin_bin" -h $DB_SERVER_IP -u$DB_USER -p$DB_PASS -P$DB_PORT processlist > /dev/null if ! [ $? -eq 0 ]; then log "ERROR" "Unable to connect to database. Check if your database is running and accessible" exit 1 fi - RESULT=`mysqlshow --user=$DB_USER --password=$DB_PASS --host=$DB_SERVER_IP --port=$DB_PORT | grep -o $DB_NAME` + RESULT=`"$mysqlshow_bin" --user=$DB_USER --password=$DB_PASS --host=$DB_SERVER_IP --port=$DB_PORT | grep -o $DB_NAME` if ! [ "$RESULT" == "$DB_NAME" ] ; then log "ERROR" "iskylims database is not defined yet" @@ -418,6 +428,11 @@ rename_apps_if_needed() { # install_system_packages: install InterOp and distro-specific OS packages required by iSkyLIMS. install_system_packages() { + if [ "${SKIP_SYSTEM_PACKAGES:-}" = "1" ]; then + echo "Skipping system package installation (SKIP_SYSTEM_PACKAGES=1)" + return + fi + echo "Installing Interop" if [ -d /opt/interop ]; then echo "There is already an interop installation" From c234fbc7c16292e5aa24656b053b244bc1488e81 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 18:42:11 +0100 Subject: [PATCH 348/446] Run container as non-root user --- Dockerfile | 10 ++++++++++ LEAME.md | 22 ++++++++++++++++++++++ README.md | 22 ++++++++++++++++++++++ docker-compose.prod.yml | 3 +++ 4 files changed, 57 insertions(+) diff --git a/Dockerfile b/Dockerfile index e358afce4..87d9b3a53 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,6 +2,10 @@ FROM registry.access.redhat.com/ubi9/ubi ENV TZ=Europe/Madrid RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone +# Runtime user (override with build args if needed) +ARG APP_UID=1212 +ARG APP_GID=1212 + # Updates RUN dnf -y update @@ -47,8 +51,14 @@ ENV PATH="/opt/iskylims/virtualenv/bin:${PATH}" WORKDIR /opt/iskylims +# Create non-root user and set ownership +RUN groupadd -g ${APP_GID} iskylims && \ + useradd -m -u ${APP_UID} -g ${APP_GID} -s /sbin/nologin iskylims && \ + chown -R ${APP_UID}:${APP_GID} /opt/iskylims + # Expose EXPOSE 8001 # Start the application once install.sh has populated /opt/iskylims. +USER iskylims CMD ["bash", "-c", "while [ ! -f /opt/iskylims/manage.py ]; do sleep 2; done; gunicorn iskylims.wsgi:application --bind 0.0.0.0:8001 --workers 3 --threads 2 --timeout 120"] diff --git a/LEAME.md b/LEAME.md index 52342d811..34192a55f 100644 --- a/LEAME.md +++ b/LEAME.md @@ -113,6 +113,21 @@ Despliega el contenedor de iSkyLIMS contra servicios MySQL/Samba externos: 3. Si es una instalacion nueva, crea el superusuario cuando se solicite y completa la configuracion de Samba en la UI. +UID/GID del usuario de ejecucion del contenedor (por defecto `1212:1212`): + +- Exporta `APP_UID` y `APP_GID` antes de ejecutar `docker_install.sh` si necesitas un UID/GID distinto (por ejemplo, para escribir en `/var/www/iskylims/static`). + +```bash +export APP_UID=1212 +export APP_GID=1212 +``` + +Asegura que la carpeta de estaticos en el host sea escribible por ese UID/GID: + +```bash +sudo chown -R 1212:1212 /var/www/iskylims/static +``` + #### Proxy inverso con Apache (host) + Gunicorn En produccion, el contenedor ejecuta `gunicorn` (no `manage.py runserver`). Usa Apache en el host como proxy inverso hacia `localhost:8001`. @@ -135,6 +150,13 @@ bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh` dentro del contenedor, que regenera migraciones, las aplica con `--fake-initial` y evita cargar superusuario/datos demo/prueba. +Si usas `APP_UID`/`APP_GID`, exportalos de nuevo antes de la actualizacion para mantener el mismo UID/GID: + +```bash +export APP_UID=1212 +export APP_GID=1212 +``` + ### Actualizacion del despliegue Docker v3.0.0 a 3.1.0 #### Haz copia de seguridad diff --git a/README.md b/README.md index 3d1e78456..1d4adfe1c 100644 --- a/README.md +++ b/README.md @@ -118,6 +118,21 @@ Deploy the iSkyLIMS container against external MySQL/Samba services: 3. If this is a fresh install, create the Django superuser when prompted and complete the Samba configuration in the UI. +UID/GID for the container runtime user (default `1212:1212`): + +- Export `APP_UID` and `APP_GID` before running `docker_install.sh` if you need a different host UID/GID (for example, to write to `/var/www/iskylims/static`). + +```bash +export APP_UID=1212 +export APP_GID=1212 +``` + +Ensure the static directory on the host is writable by that UID/GID: + +```bash +sudo chown -R 1212:1212 /var/www/iskylims/static +``` + #### Persist logs/documents with named volumes The production compose file mounts two named volumes so upgrades/rebuilds keep data: @@ -149,6 +164,13 @@ bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade The upgrade path rebuilds/restarts the container and runs `install.sh` inside the app container, which regenerates migrations, applies them with `--fake-initial`, and skips superuser/demo/test data loading. +If you set `APP_UID`/`APP_GID`, export them again before upgrade so the container runs with the same UID/GID: + +```bash +export APP_UID=1212 +export APP_GID=1212 +``` + ### Upgrade docker deployment v3.0.0 to 3.1.0 #### Back up first diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 7e8a383fe..96652dc53 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -10,10 +10,13 @@ services: INSTALL_TYPE: ${INSTALL_TYPE:-dep} GIT_REVISION: ${GIT_REVISION:-main} INSTALL_CONF: ${INSTALL_CONF:-conf/docker_production_settings.txt} + APP_UID: ${APP_UID:-1212} + APP_GID: ${APP_GID:-1212} ports: - "8001:8001" environment: DJANGO_SETTINGS_MODULE: iskylims.settings + user: "${APP_UID:-1212}:${APP_GID:-1212}" volumes: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo From b3556422b61c8496009b712db18c84e24dc46a6a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 24 Feb 2026 18:54:38 +0100 Subject: [PATCH 349/446] change path to static for podman preferences --- LEAME.md | 12 ++++++------ README.md | 12 ++++++------ conf/iskylims_apache_reverse_proxy.conf | 6 +++--- docker-compose.prod.yml | 2 +- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/LEAME.md b/LEAME.md index 34192a55f..5df4277d5 100644 --- a/LEAME.md +++ b/LEAME.md @@ -115,7 +115,7 @@ Despliega el contenedor de iSkyLIMS contra servicios MySQL/Samba externos: UID/GID del usuario de ejecucion del contenedor (por defecto `1212:1212`): -- Exporta `APP_UID` y `APP_GID` antes de ejecutar `docker_install.sh` si necesitas un UID/GID distinto (por ejemplo, para escribir en `/var/www/iskylims/static`). +- Exporta `APP_UID` y `APP_GID` antes de ejecutar `docker_install.sh` si necesitas un UID/GID distinto (por ejemplo, para escribir en `/opt/iskylims/static-host`). ```bash export APP_UID=1212 @@ -125,7 +125,7 @@ export APP_GID=1212 Asegura que la carpeta de estaticos en el host sea escribible por ese UID/GID: ```bash -sudo chown -R 1212:1212 /var/www/iskylims/static +sudo chown -R 1212:1212 /opt/iskylims/static-host ``` #### Proxy inverso con Apache (host) + Gunicorn @@ -135,8 +135,8 @@ En produccion, el contenedor ejecuta `gunicorn` (no `manage.py runserver`). Usa Archivos estaticos: - El contenedor genera los estaticos en `/opt/iskylims/static`. -- `docker-compose.prod.yml` monta ese directorio en `/var/www/iskylims/static` del host. -- Configura Apache con `Alias /static/ /var/www/iskylims/static/`. +- `docker-compose.prod.yml` monta ese directorio en `/opt/iskylims/static-host` del host. +- Configura Apache con `Alias /static/ /opt/iskylims/static-host/`. Ejemplo de configuracion en `conf/iskylims_apache_reverse_proxy.conf`. @@ -417,12 +417,12 @@ Pasos sugeridos (Apache en el host como proxy inverso): - Ajusta `ServerName` - Comprueba que `ProxyPass` apunte a `http://localhost:8001/` - - Comprueba `Alias /static/ /var/www/iskylims/static/` + - Comprueba `Alias /static/ /opt/iskylims/static-host/` 3. Crea la carpeta de estaticos en el host: ```bash - sudo mkdir -p /var/www/iskylims/static + sudo mkdir -p /opt/iskylims/static-host ``` 4. Habilita modulos necesarios (Ubuntu/Debian): diff --git a/README.md b/README.md index 1d4adfe1c..2f39c61a4 100644 --- a/README.md +++ b/README.md @@ -120,7 +120,7 @@ Deploy the iSkyLIMS container against external MySQL/Samba services: UID/GID for the container runtime user (default `1212:1212`): -- Export `APP_UID` and `APP_GID` before running `docker_install.sh` if you need a different host UID/GID (for example, to write to `/var/www/iskylims/static`). +- Export `APP_UID` and `APP_GID` before running `docker_install.sh` if you need a different host UID/GID (for example, to write to `/opt/iskylims/static-host`). ```bash export APP_UID=1212 @@ -130,7 +130,7 @@ export APP_GID=1212 Ensure the static directory on the host is writable by that UID/GID: ```bash -sudo chown -R 1212:1212 /var/www/iskylims/static +sudo chown -R 1212:1212 /opt/iskylims/static-host ``` #### Persist logs/documents with named volumes @@ -149,8 +149,8 @@ For production, the container runs `gunicorn` (not `manage.py runserver`). Use A Static files: - The container writes collected static files to `/opt/iskylims/static`. -- `docker-compose.prod.yml` bind-mounts that path to `/var/www/iskylims/static` on the host. -- Configure Apache with `Alias /static/ /var/www/iskylims/static/`. +- `docker-compose.prod.yml` bind-mounts that path to `/opt/iskylims/static-host` on the host. +- Configure Apache with `Alias /static/ /opt/iskylims/static-host/`. See the example config in `conf/iskylims_apache_reverse_proxy.conf` and the [Configure Apache server](#configure-apache-server) section below. @@ -437,12 +437,12 @@ Suggested steps (host Apache as reverse proxy): - Set `ServerName` - Ensure `ProxyPass` points to `http://localhost:8001/` - - Ensure `Alias /static/ /var/www/iskylims/static/` + - Ensure `Alias /static/ /opt/iskylims/static-host/` 3. Create the static folder on the host: ```bash - sudo mkdir -p /var/www/iskylims/static + sudo mkdir -p /opt/iskylims/static-host ``` 4. Enable required modules (Ubuntu/Debian): diff --git a/conf/iskylims_apache_reverse_proxy.conf b/conf/iskylims_apache_reverse_proxy.conf index 616ac356a..086f57e36 100644 --- a/conf/iskylims_apache_reverse_proxy.conf +++ b/conf/iskylims_apache_reverse_proxy.conf @@ -17,9 +17,9 @@ # ProxyPassReverse / http://app:8001/ # Serve static files from a host path (bind-mounted from the container) - # Example: /var/www/iskylims/static -> /opt/iskylims/static in docker-compose.prod.yml - Alias /static/ /var/www/iskylims/static/ - + # Example: /opt/iskylims/static-host -> /opt/iskylims/static in docker-compose.prod.yml + Alias /static/ /opt/iskylims/static-host/ + Require all granted diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 96652dc53..030b4bf84 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -22,7 +22,7 @@ services: - /usr/share/zoneinfo:/usr/share/zoneinfo - iskylims_logs:/opt/iskylims/logs - iskylims_documents:/opt/iskylims/documents - - /var/www/iskylims/static:/opt/iskylims/static + - /opt/iskylims/static-host:/opt/iskylims/static extra_hosts: - "host.docker.internal:host-gateway" From cb4401fdc6ce774454a01f84270417f5119ba738 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 25 Feb 2026 10:15:46 +0100 Subject: [PATCH 350/446] use of supercronic for handling cron root-less inside container --- Dockerfile | 6 ++++-- LEAME.md | 6 ++++++ README.md | 6 ++++++ docker_install.sh | 4 +--- install.sh | 8 +++++++- scripts/container_start.sh | 34 ++++++++++++++++++++++++++++++++++ 6 files changed, 58 insertions(+), 6 deletions(-) create mode 100644 scripts/container_start.sh diff --git a/Dockerfile b/Dockerfile index 87d9b3a53..3ee424039 100644 --- a/Dockerfile +++ b/Dockerfile @@ -37,6 +37,7 @@ WORKDIR /srv/iskylims COPY . /srv/iskylims ENV PATH="/usr/sbin/cron:$PATH" +RUN chmod +x /srv/iskylims/scripts/container_start.sh # Set default install type ARG INSTALL_TYPE=dep @@ -54,11 +55,12 @@ WORKDIR /opt/iskylims # Create non-root user and set ownership RUN groupadd -g ${APP_GID} iskylims && \ useradd -m -u ${APP_UID} -g ${APP_GID} -s /sbin/nologin iskylims && \ - chown -R ${APP_UID}:${APP_GID} /opt/iskylims + chown -R ${APP_UID}:${APP_GID} /opt/iskylims /srv/iskylims && \ + git config --system --add safe.directory /srv/iskylims # Expose EXPOSE 8001 # Start the application once install.sh has populated /opt/iskylims. USER iskylims -CMD ["bash", "-c", "while [ ! -f /opt/iskylims/manage.py ]; do sleep 2; done; gunicorn iskylims.wsgi:application --bind 0.0.0.0:8001 --workers 3 --threads 2 --timeout 120"] +CMD ["/srv/iskylims/scripts/container_start.sh"] diff --git a/LEAME.md b/LEAME.md index 5df4277d5..7bb7a1580 100644 --- a/LEAME.md +++ b/LEAME.md @@ -132,6 +132,12 @@ sudo chown -R 1212:1212 /opt/iskylims/static-host En produccion, el contenedor ejecuta `gunicorn` (no `manage.py runserver`). Usa Apache en el host como proxy inverso hacia `localhost:8001`. +#### Tareas cron dentro del contenedor + +Cron se ejecuta mediante un `crond` ligero lanzado por el script de arranque del contenedor. El script escribe las entradas de django-crontab en `/opt/iskylims/cron/iskylims` y arranca `crond` con un PID en una ruta escribible por el usuario. + +Si modificas `CRONJOBS`, reconstruye o reinicia el contenedor para regenerar el archivo de cron. + Archivos estaticos: - El contenedor genera los estaticos en `/opt/iskylims/static`. diff --git a/README.md b/README.md index 2f39c61a4..746e958d9 100644 --- a/README.md +++ b/README.md @@ -146,6 +146,12 @@ If you override the compose file, ensure these two mounts exist to keep logs and For production, the container runs `gunicorn` (not `manage.py runserver`). Use Apache on the host as a reverse proxy to `localhost:8001`. +#### Cron jobs inside the container + +Cron runs via a lightweight `crond` started by the container entrypoint script. The script writes the django-crontab entries to `/opt/iskylims/cron/iskylims` and starts `crond` with a user-writable PID file. + +If you change `CRONJOBS`, rebuild or restart the container to regenerate the cron file. + Static files: - The container writes collected static files to `/opt/iskylims/static`. diff --git a/docker_install.sh b/docker_install.sh index 9510b4f60..0e81dee86 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -322,8 +322,6 @@ else echo "Skipping Samba demo data load (flag enabled or service not present)" fi -echo "Running crontab" -docker exec -it iskylims_app python3 manage.py crontab add -docker exec -it iskylims_app service cron start +echo "Skipping crontab add/start (cron is managed by the container entrypoint)" echo "You can now access iSkyLIMS via: http://localhost:8001" diff --git a/install.sh b/install.sh index 7f1d4640f..61109d445 100644 --- a/install.sh +++ b/install.sh @@ -705,7 +705,13 @@ upgrade_application_files() { run_django_deploy "upgrade" echo "Deleting static files..." - rm -rf $INSTALL_PATH/static + if [ -d "$INSTALL_PATH/static" ]; then + if command -v mountpoint >/dev/null 2>&1 && mountpoint -q "$INSTALL_PATH/static"; then + echo "Static directory is a mount point. Skipping delete." + else + rm -rf "$INSTALL_PATH/static" || echo "Skipping static removal (busy)." + fi + fi echo "Running collect statics..." python manage.py collectstatic echo "Done collect statics" diff --git a/scripts/container_start.sh b/scripts/container_start.sh new file mode 100644 index 000000000..9e25e34a7 --- /dev/null +++ b/scripts/container_start.sh @@ -0,0 +1,34 @@ +#!/usr/bin/env bash +set -euo pipefail + +APP_DIR="/opt/iskylims" +CRON_DIR="${APP_DIR}/cron" +TMP_DIR="${APP_DIR}/tmp" +CRON_FILE="${CRON_DIR}/iskylims" + +while [ ! -f "${APP_DIR}/manage.py" ]; do + sleep 2 +done + +source "${APP_DIR}/virtualenv/bin/activate" + +mkdir -p "${CRON_DIR}" "${TMP_DIR}" +chmod 700 "${CRON_DIR}" "${TMP_DIR}" + +if command -v crond >/dev/null 2>&1; then + python "${APP_DIR}/manage.py" crontab show > "${CRON_FILE}" || true + if [ -s "${CRON_FILE}" ]; then + chmod 600 "${CRON_FILE}" + crond -n -m off -c "${CRON_DIR}" -p "${TMP_DIR}/crond.pid" & + else + echo "No cron entries found. Skipping crond start." + fi +else + echo "crond not found. Skipping cron." +fi + +exec gunicorn iskylims.wsgi:application \ + --bind 0.0.0.0:8001 \ + --workers 3 \ + --threads 2 \ + --timeout 120 From e8d2a8a6aaa117c5b4602da27a84e602e9bde0a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 25 Feb 2026 10:24:51 +0100 Subject: [PATCH 351/446] improve message about how to access iskylims after docker install --- conf/docker_test_settings.txt | 6 ++++-- conf/template_install_settings.txt | 6 ++++-- docker_install.sh | 22 ++++++++++++++++++++-- 3 files changed, 28 insertions(+), 6 deletions(-) diff --git a/conf/docker_test_settings.txt b/conf/docker_test_settings.txt index eb3abcf72..d6546a1ec 100644 --- a/conf/docker_test_settings.txt +++ b/conf/docker_test_settings.txt @@ -24,8 +24,10 @@ EMAIL_HOST_PASSWORD='' EMAIL_USE_TLS='False' ### Settings required for accessing iSkyLIMS -LOCAL_SERVER_IP='*' # example: 172.0.0.1 -DNS_URL='*' # example: iskylims.isciii.es +# example: 172.0.0.1 +LOCAL_SERVER_IP='*' +# example: iskylims.isciii.es +DNS_URL='*' ### Logs settings LOG_TYPE="regular_folder" # can be symbolic link, or regular_folder diff --git a/conf/template_install_settings.txt b/conf/template_install_settings.txt index be695555d..43db77dae 100644 --- a/conf/template_install_settings.txt +++ b/conf/template_install_settings.txt @@ -24,8 +24,10 @@ EMAIL_HOST_PASSWORD='' EMAIL_USE_TLS='False' ### Settings required for accessing iSkyLIMS -LOCAL_SERVER_IP='' # example: 172.0.0.1 -DNS_URL='' # example: iskylims.isciii.es +# example: 172.0.0.1 +LOCAL_SERVER_IP='' +# example: iskylims.isciii.es +DNS_URL='' ### Logs settings LOG_TYPE="symbolic_link" # can be symbolic link, or regular_folder diff --git a/docker_install.sh b/docker_install.sh index 0e81dee86..b0cd15276 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -1,6 +1,6 @@ #!/usr/bin/bash -ISKYLIMS_VERSION="3.0.0" +ISKYLIMS_VERSION="3.1.0" usage() { cat << EOF @@ -324,4 +324,22 @@ fi echo "Skipping crontab add/start (cron is managed by the container entrypoint)" -echo "You can now access iSkyLIMS via: http://localhost:8001" +dns_url="" +local_ip="" +if [ -f "$host_install_conf_path" ]; then + dns_url=$(grep -E "^DNS_URL=" "$host_install_conf_path" | tail -n 1 | cut -d= -f2- | sed "s/^['\"]//;s/['\"]$//") + local_ip=$(grep -E "^LOCAL_SERVER_IP=" "$host_install_conf_path" | tail -n 1 | cut -d= -f2- | sed "s/^['\"]//;s/['\"]$//") +fi + +access_urls=() +if [ -n "$dns_url" ] && [ "$dns_url" != "*" ]; then + access_urls+=("http://${dns_url}:8001") +fi +if [ -n "$local_ip" ] && [ "$local_ip" != "*" ]; then + access_urls+=("http://${local_ip}:8001") +fi +if [ ${#access_urls[@]} -eq 0 ]; then + access_urls+=("http://localhost:8001") +fi + +echo "You can now access iSkyLIMS via: ${access_urls[*]}" From 0c4daecdfec61598e6db6248bda106a0ae13b1c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 25 Feb 2026 10:25:21 +0100 Subject: [PATCH 352/446] improve docs to always keep a log when installing --- LEAME.md | 7 ++++++- README.md | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/LEAME.md b/LEAME.md index 7bb7a1580..8a969d04f 100644 --- a/LEAME.md +++ b/LEAME.md @@ -110,6 +110,11 @@ Despliega el contenedor de iSkyLIMS contra servicios MySQL/Samba externos: ``` Usa `--compose_file` para cambiar el compose o `--install_type`/`--git_revision` para variar el build. + Tip: captura logs para depuracion: + + ```bash + bash docker_install.sh --install_conf conf/my_prod_settings.txt 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log + ``` 3. Si es una instalacion nueva, crea el superusuario cuando se solicite y completa la configuracion de Samba en la UI. @@ -259,7 +264,7 @@ sudo bash install.sh --install full --git_revision main --tables - Captura logs para depuracion con `tee`: ```bash - sudo bash install.sh --install full --git_revision main --tables 2>&1 | tee install_full.log + sudo bash install.sh --install full --git_revision main --tables 2>&1 | tee ./iskylims_install_$(date +%Y%m%d_%H%M%S).log ``` - Si Apache se gestiona desde otro sitio, omite el reinicio automatico con `--skip_apache_restart`. diff --git a/README.md b/README.md index 746e958d9..7cc8cbb62 100644 --- a/README.md +++ b/README.md @@ -115,6 +115,11 @@ Deploy the iSkyLIMS container against external MySQL/Samba services: ``` Use `--compose_file` to override the compose file or `--install_type`/`--git_revision` to change the build. + Tip: capture logs for troubleshooting: + + ```bash + bash docker_install.sh --install_conf conf/my_prod_settings.txt 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log + ``` 3. If this is a fresh install, create the Django superuser when prompted and complete the Samba configuration in the UI. @@ -284,7 +289,7 @@ sudo bash install.sh --install full --git_revision main --tables - Capture logs for troubleshooting with `tee`: ```bash - sudo bash install.sh --install full --git_revision main --tables 2>&1 | tee install_full.log + sudo bash install.sh --install full --git_revision main --tables 2>&1 | tee ./iskylims_install_$(date +%Y%m%d_%H%M%S).log ``` - If Apache is managed elsewhere, skip the automatic restart with `--skip_apache_restart`. From 3e4ae811174192a4f06f9cc5b209e827e7c56873 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 25 Feb 2026 10:34:47 +0100 Subject: [PATCH 353/446] some reordering in docs --- LEAME.md | 27 ++++++++++++++------------- README.md | 34 ++++++++++++++++++++++------------ 2 files changed, 36 insertions(+), 25 deletions(-) diff --git a/LEAME.md b/LEAME.md index 8a969d04f..b56d69350 100644 --- a/LEAME.md +++ b/LEAME.md @@ -18,6 +18,7 @@ De acuerdo con la infraestructura existente, la secuenciacion se realiza en un i - [Contenedor local de pruebas](#contenedor-local-de-pruebas) - [Contenedor de produccion](#contenedor-de-produccion) - [Proxy inverso con Apache (host) + Gunicorn](#proxy-inverso-con-apache-host--gunicorn) + - [Tareas cron dentro del contenedor](#tareas-cron-dentro-del-contenedor) - [Actualizacion del despliegue Docker](#actualizacion-del-despliegue-docker) - [Actualizacion del despliegue Docker v3.0.0 a 3.1.0](#actualizacion-del-despliegue-docker-v300-a-310) - [Haz copia de seguridad](#haz-copia-de-seguridad) @@ -137,29 +138,21 @@ sudo chown -R 1212:1212 /opt/iskylims/static-host En produccion, el contenedor ejecuta `gunicorn` (no `manage.py runserver`). Usa Apache en el host como proxy inverso hacia `localhost:8001`. -#### Tareas cron dentro del contenedor - -Cron se ejecuta mediante un `crond` ligero lanzado por el script de arranque del contenedor. El script escribe las entradas de django-crontab en `/opt/iskylims/cron/iskylims` y arranca `crond` con un PID en una ruta escribible por el usuario. - -Si modificas `CRONJOBS`, reconstruye o reinicia el contenedor para regenerar el archivo de cron. - Archivos estaticos: - El contenedor genera los estaticos en `/opt/iskylims/static`. - `docker-compose.prod.yml` monta ese directorio en `/opt/iskylims/static-host` del host. - Configura Apache con `Alias /static/ /opt/iskylims/static-host/`. -Ejemplo de configuracion en `conf/iskylims_apache_reverse_proxy.conf`. +Ejemplo de configuracion en `conf/iskylims_apache_reverse_proxy.conf` y la sección [Configurar el servidor Apache](#configurar-el-servidor Apache). -### Actualizacion del despliegue Docker +#### Tareas cron dentro del contenedor -Re-despliega el contenedor de aplicacion contra una base de datos existente sin tocar los datos: +Cron se ejecuta mediante un `crond` ligero lanzado por el script de arranque del contenedor. El script escribe las entradas de django-crontab en `/opt/iskylims/cron/iskylims` y arranca `crond` con un PID en una ruta escribible por el usuario. -```bash -bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade -``` +Si modificas `CRONJOBS`, reconstruye o reinicia el contenedor para regenerar el archivo de cron. -La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh` dentro del contenedor, que regenera migraciones, las aplica con `--fake-initial` y evita cargar superusuario/datos demo/prueba. +### Actualizacion del despliegue Docker Si usas `APP_UID`/`APP_GID`, exportalos de nuevo antes de la actualizacion para mantener el mismo UID/GID: @@ -168,6 +161,14 @@ export APP_UID=1212 export APP_GID=1212 ``` +Re-despliega el contenedor de aplicacion contra una base de datos existente sin tocar los datos: + +```bash +bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade +``` + +La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh` dentro del contenedor, que regenera migraciones, las aplica con `--fake-initial` y evita cargar superusuario/datos demo/prueba. + ### Actualizacion del despliegue Docker v3.0.0 a 3.1.0 #### Haz copia de seguridad diff --git a/README.md b/README.md index 7cc8cbb62..ab7eab6de 100644 --- a/README.md +++ b/README.md @@ -20,6 +20,7 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Production container](#production-container) - [Persist logs/documents with named volumes](#persist-logsdocuments-with-named-volumes) - [Apache reverse proxy (host) + Gunicorn](#apache-reverse-proxy-host--gunicorn) + - [Cron jobs inside the container](#cron-jobs-inside-the-container) - [Upgrade docker deployment](#upgrade-docker-deployment) - [Upgrade docker deployment v3.0.0 to 3.1.0](#upgrade-docker-deployment-v300-to-310) - [Back up first](#back-up-first) @@ -151,12 +152,6 @@ If you override the compose file, ensure these two mounts exist to keep logs and For production, the container runs `gunicorn` (not `manage.py runserver`). Use Apache on the host as a reverse proxy to `localhost:8001`. -#### Cron jobs inside the container - -Cron runs via a lightweight `crond` started by the container entrypoint script. The script writes the django-crontab entries to `/opt/iskylims/cron/iskylims` and starts `crond` with a user-writable PID file. - -If you change `CRONJOBS`, rebuild or restart the container to regenerate the cron file. - Static files: - The container writes collected static files to `/opt/iskylims/static`. @@ -165,15 +160,13 @@ Static files: See the example config in `conf/iskylims_apache_reverse_proxy.conf` and the [Configure Apache server](#configure-apache-server) section below. -### Upgrade docker deployment +#### Cron jobs inside the container -Re-deploy the application container against an existing production database without touching data: +Cron runs via a lightweight `crond` started by the container entrypoint script. The script writes the django-crontab entries to `/opt/iskylims/cron/iskylims` and starts `crond` with a user-writable PID file. -```bash -bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade -``` +If you change `CRONJOBS`, rebuild or restart the container to regenerate the cron file. -The upgrade path rebuilds/restarts the container and runs `install.sh` inside the app container, which regenerates migrations, applies them with `--fake-initial`, and skips superuser/demo/test data loading. +### Upgrade docker deployment If you set `APP_UID`/`APP_GID`, export them again before upgrade so the container runs with the same UID/GID: @@ -182,6 +175,14 @@ export APP_UID=1212 export APP_GID=1212 ``` +Re-deploy the application container against an existing production database without touching data: + +```bash +bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade +``` + +The upgrade path rebuilds/restarts the container and runs `install.sh` inside the app container, which regenerates migrations, applies them with `--fake-initial`, and skips superuser/demo/test data loading. + ### Upgrade docker deployment v3.0.0 to 3.1.0 #### Back up first @@ -220,6 +221,15 @@ sudo nano myprod_settings.txt Ensure the file uses Linux-friendly encoding (UTF-8/ASCII) if you edit it on Windows. +If you set `APP_UID`/`APP_GID`, export them again before upgrade so the container runs with the same UID/GID: + +```bash +export APP_UID=1212 +export APP_GID=1212 +``` + +Run upgrade command: + ```bash bash docker_install.sh --install_conf my_prod_settings.txt --action upgrade \ --script_before convert_rawtop_counter_to_int \ From 27df8ec277661b2dbf020e139db4caa66bc377de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 25 Feb 2026 10:43:45 +0100 Subject: [PATCH 354/446] fix in docker install so directories are writable by container user --- docker_install.sh | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/docker_install.sh b/docker_install.sh index b0cd15276..77604c49a 100644 --- a/docker_install.sh +++ b/docker_install.sh @@ -254,6 +254,11 @@ echo "Waiting 20 seconds for starting database and web services..." sleep 20 ensure_app_running +app_uid="${APP_UID:-1212}" +app_gid="${APP_GID:-1212}" +echo "Ensuring runtime directories are writable by ${app_uid}:${app_gid}" +docker exec -u 0 -it iskylims_app sh -lc "mkdir -p /opt/iskylims/documents /opt/iskylims/logs /opt/iskylims/static /opt/iskylims/cron /opt/iskylims/tmp && chown -R ${app_uid}:${app_gid} /opt/iskylims/documents /opt/iskylims/logs /opt/iskylims/static /opt/iskylims/cron /opt/iskylims/tmp" + host_install_conf_path="$install_conf" if [[ "$host_install_conf_path" != /* ]]; then host_install_conf_path="$repo_root/$host_install_conf_path" From 7d968b5bc3499693aae1fc1318d6403730d0830a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 26 Feb 2026 16:22:13 +0100 Subject: [PATCH 355/446] fix order in apache proxy example --- conf/iskylims_apache_reverse_proxy.conf | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/iskylims_apache_reverse_proxy.conf b/conf/iskylims_apache_reverse_proxy.conf index 086f57e36..53ea5f23a 100644 --- a/conf/iskylims_apache_reverse_proxy.conf +++ b/conf/iskylims_apache_reverse_proxy.conf @@ -18,6 +18,7 @@ # Serve static files from a host path (bind-mounted from the container) # Example: /opt/iskylims/static-host -> /opt/iskylims/static in docker-compose.prod.yml + ProxyPass /static/ ! Alias /static/ /opt/iskylims/static-host/ Require all granted From 07adcad32c68c0b7f54e7e4f3d5338c2d2c9d990 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 26 Feb 2026 16:24:57 +0100 Subject: [PATCH 356/446] keep manage.py runserver instead of gunicorn for dev environemnt (--test) --- docker-compose.prod.yml | 1 + docker-compose.test.yml | 2 ++ scripts/container_start.sh | 5 +++++ 3 files changed, 8 insertions(+) diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 030b4bf84..b5b9430f2 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -16,6 +16,7 @@ services: - "8001:8001" environment: DJANGO_SETTINGS_MODULE: iskylims.settings + APP_MODE: prod user: "${APP_UID:-1212}:${APP_GID:-1212}" volumes: - /etc/localtime:/etc/localtime:ro diff --git a/docker-compose.test.yml b/docker-compose.test.yml index f0fabbb9e..d17f5c76c 100644 --- a/docker-compose.test.yml +++ b/docker-compose.test.yml @@ -47,6 +47,8 @@ services: container_name: iskylims_app ports: - "8001:8001" + environment: + APP_MODE: dev networks: - develop_net depends_on: diff --git a/scripts/container_start.sh b/scripts/container_start.sh index 9e25e34a7..933ac9d6a 100644 --- a/scripts/container_start.sh +++ b/scripts/container_start.sh @@ -5,6 +5,7 @@ APP_DIR="/opt/iskylims" CRON_DIR="${APP_DIR}/cron" TMP_DIR="${APP_DIR}/tmp" CRON_FILE="${CRON_DIR}/iskylims" +APP_MODE="${APP_MODE:-prod}" while [ ! -f "${APP_DIR}/manage.py" ]; do sleep 2 @@ -15,6 +16,10 @@ source "${APP_DIR}/virtualenv/bin/activate" mkdir -p "${CRON_DIR}" "${TMP_DIR}" chmod 700 "${CRON_DIR}" "${TMP_DIR}" +if [ "$APP_MODE" = "dev" ]; then + exec python "${APP_DIR}/manage.py" runserver 0.0.0.0:8001 +fi + if command -v crond >/dev/null 2>&1; then python "${APP_DIR}/manage.py" crontab show > "${CRON_FILE}" || true if [ -s "${CRON_FILE}" ]; then From 6be95840962b3329d3b82e192fef11dd3904e75b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 27 Feb 2026 11:17:32 +0100 Subject: [PATCH 357/446] logs persist as bind mount instead of volume --- LEAME.md | 33 +++++++++++++++++++++++---------- README.md | 34 +++++++++++++++++++--------------- docker-compose.prod.yml | 2 +- 3 files changed, 43 insertions(+), 26 deletions(-) diff --git a/LEAME.md b/LEAME.md index b56d69350..9aa7f65b1 100644 --- a/LEAME.md +++ b/LEAME.md @@ -134,6 +134,22 @@ Asegura que la carpeta de estaticos en el host sea escribible por ese UID/GID: sudo chown -R 1212:1212 /opt/iskylims/static-host ``` +#### Persistir logs/documentos en el host + +El compose de produccion monta los logs en el host para facilitar la recoleccion (por ejemplo, con Elastic): + +- `/var/log/apps/iskylims` -> `/opt/iskylims/logs` +- `iskylims_documents` -> `/opt/iskylims/documents` + +Si usas un compose personalizado, asegurate de mantener estos montajes para conservar logs y documentos. + +Crea el directorio de logs en el host y ajusta permisos segun el UID/GID del contenedor: + +```bash +sudo mkdir -p /var/log/apps/iskylims +sudo chown -R 1212:1212 /var/log/apps/iskylims +``` + #### Proxy inverso con Apache (host) + Gunicorn En produccion, el contenedor ejecuta `gunicorn` (no `manage.py runserver`). Usa Apache en el host como proxy inverso hacia `localhost:8001`. @@ -177,10 +193,7 @@ La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh` dentr - Copia completa de las carpetas de logs y documents. ```bash -docker run --rm \ - -v iskylims_logs:/from \ - -v "$PWD":/to \ - alpine tar -czf /to/iskylims_logs.tgz -C /from . +tar -czf iskylims_logs.tgz -C /var/log/apps/iskylims . docker run --rm \ -v iskylims_documents:/from \ @@ -375,13 +388,13 @@ mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_pro 4. Si los volumenes estan comprometidos, restauralos desde los tar: - ```bash - docker run --rm -v iskylims_logs:/to -v "$PWD":/from alpine \ - tar -xzf /from/iskylims_logs.tgz -C /to +```bash +mkdir -p /var/log/apps/iskylims +tar -xzf iskylims_logs.tgz -C /var/log/apps/iskylims - docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ - tar -xzf /from/iskylims_documents.tgz -C /to - ``` +docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ + tar -xzf /from/iskylims_documents.tgz -C /to +``` 5. Arranca el contenedor de nuevo: diff --git a/README.md b/README.md index ab7eab6de..16220c7e2 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Docker deployment](#docker-deployment) - [Local test stack](#local-test-stack) - [Production container](#production-container) - - [Persist logs/documents with named volumes](#persist-logsdocuments-with-named-volumes) +- [Persist logs/documents on the host](#persist-logsdocuments-on-the-host) - [Apache reverse proxy (host) + Gunicorn](#apache-reverse-proxy-host--gunicorn) - [Cron jobs inside the container](#cron-jobs-inside-the-container) - [Upgrade docker deployment](#upgrade-docker-deployment) @@ -139,14 +139,21 @@ Ensure the static directory on the host is writable by that UID/GID: sudo chown -R 1212:1212 /opt/iskylims/static-host ``` -#### Persist logs/documents with named volumes +#### Persist logs/documents on the host -The production compose file mounts two named volumes so upgrades/rebuilds keep data: +The production compose file mounts logs on the host and keeps documents in a named volume: -- `iskylims_logs` → `/opt/iskylims/logs` +- `/var/log/apps/iskylims` → `/opt/iskylims/logs` - `iskylims_documents` → `/opt/iskylims/documents` -If you override the compose file, ensure these two mounts exist to keep logs and documents persistent. +If you override the compose file, ensure these mounts exist to keep logs and documents persistent. + +Create the host log directory and set ownership to match the container UID/GID: + +```bash +sudo mkdir -p /var/log/apps/iskylims +sudo chown -R 1212:1212 /var/log/apps/iskylims +``` #### Apache reverse proxy (host) + Gunicorn @@ -191,10 +198,7 @@ The upgrade path rebuilds/restarts the container and runs `install.sh` inside th - Full backup of the logs folder and the documents folder. ```bash -docker run --rm \ - -v iskylims_logs:/from \ - -v "$PWD":/to \ - alpine tar -czf /to/iskylims_logs.tgz -C /from . +tar -czf iskylims_logs.tgz -C /var/log/apps/iskylims . docker run --rm \ -v iskylims_documents:/from \ @@ -391,13 +395,13 @@ mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_pro 4. If volumes are compromised, restore them from the tar backups: - ```bash - docker run --rm -v iskylims_logs:/to -v "$PWD":/from alpine \ - tar -xzf /from/iskylims_logs.tgz -C /to +```bash +mkdir -p /var/log/apps/iskylims +tar -xzf iskylims_logs.tgz -C /var/log/apps/iskylims - docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ - tar -xzf /from/iskylims_documents.tgz -C /to - ``` +docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ + tar -xzf /from/iskylims_documents.tgz -C /to +``` 5. Start the container again: diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index b5b9430f2..7370f2a46 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -21,7 +21,7 @@ services: volumes: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo - - iskylims_logs:/opt/iskylims/logs + - /var/log/apps/iskylims:/opt/iskylims/logs - iskylims_documents:/opt/iskylims/documents - /opt/iskylims/static-host:/opt/iskylims/static extra_hosts: From fdc37b134beabcd5036359609f26a4f84966a4b1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Fri, 27 Feb 2026 11:50:23 +0100 Subject: [PATCH 358/446] remove unused vars --- Dockerfile | 4 ---- 1 file changed, 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 3ee424039..fec45583d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -25,10 +25,6 @@ RUN dnf -y install \ # Ensure python3 points to the desired version RUN ln -sf /usr/bin/python3.11 /usr/bin/python3 -# Set MYSQLCLIENT_CFLAGS and MYSQLCLIENT_LDFLAGS using pkg-config -RUN export MYSQLCLIENT_CFLAGS="$(pkg-config --libs mysqlclient)" && \ - export MYSQLCLIENT_LDFLAGS="$(pkg-config --cflags mysqlclient)" - # Set git repository RUN mkdir /srv/iskylims WORKDIR /srv/iskylims From f200e460e03eb7cef6ab31acb8624bec42b6d27b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 2 Mar 2026 13:16:27 +0100 Subject: [PATCH 359/446] add fallback in case lsb_release not present --- install.sh | 28 ++++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/install.sh b/install.sh index 61109d445..233d43475 100644 --- a/install.sh +++ b/install.sh @@ -448,9 +448,17 @@ install_system_packages() { cd - fi - linux_distribution=$(lsb_release -i | cut -f 2-) + if command -v lsb_release >/dev/null 2>&1; then + if command -v lsb_release >/dev/null 2>&1; then + linux_distribution=$(lsb_release -i | cut -f 2-) + else + linux_distribution=$(awk -F= '/^ID=/{gsub(/"/,""); print $2}' /etc/os-release) + fi + else + linux_distribution=$(awk -F= '/^ID=/{gsub(/"/,""); print $2}' /etc/os-release) + fi - if [[ $linux_distribution == "Ubuntu" ]]; then + if [[ $linux_distribution == "Ubuntu" || $linux_distribution == "ubuntu" ]]; then echo "Software installation for Ubuntu" apt-get update && apt-get upgrade -y apt-get install -y \ @@ -462,7 +470,7 @@ install_system_packages() { apache2-dev cifs-utils \ gnuplot - elif [[ $linux_distribution == "CentOS" || $linux_distribution == "RedHatEnterprise" ]]; then + elif [[ $linux_distribution == "CentOS" || $linux_distribution == "RedHatEnterprise" || $linux_distribution == "centos" || $linux_distribution == "rhel" || $linux_distribution == "fedora" ]]; then echo "Software installation for Centos/RedHat" yum groupinstall "Development tools" yum install zlib-devel bzip2-devel openssl-devel \ @@ -621,7 +629,11 @@ ensure_virtualenv_ready() { # restart_apache_service: restart Apache/HTTPD unless running inside Docker or explicitly skipped. restart_apache_service() { - linux_distribution=$(lsb_release -i | cut -f 2-) + if command -v lsb_release >/dev/null 2>&1; then + linux_distribution=$(lsb_release -i | cut -f 2-) + else + linux_distribution=$(awk -F= '/^ID=/{gsub(/"/,""); print $2}' /etc/os-release) + fi if [[ $linux_distribution == "Ubuntu" ]]; then apache_daemon="apache2" else @@ -727,9 +739,13 @@ install_application_files() { user=${SUDO_USER:-$USER} group=$(groups | cut -d" " -f1) - linux_distribution=$(lsb_release -i | cut -f 2-) + if command -v lsb_release >/dev/null 2>&1; then + linux_distribution=$(lsb_release -i | cut -f 2-) + else + linux_distribution=$(awk -F= '/^ID=/{gsub(/"/,""); print $2}' /etc/os-release) + fi - if [[ $linux_distribution == "Ubuntu" ]]; then + if [[ $linux_distribution == "Ubuntu" || $linux_distribution == "ubuntu" ]]; then apache_group="www-data" else apache_group="apache" From 7acc7ef31941b98e88fa6e8b82343dfe98ced101 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 2 Mar 2026 13:16:39 +0100 Subject: [PATCH 360/446] add podman engine as an option besides docker --- LEAME.md | 23 ++++-- README.md | 23 ++++-- docker_install.sh => container_install.sh | 92 +++++++++++++++++------ 3 files changed, 100 insertions(+), 38 deletions(-) rename docker_install.sh => container_install.sh (73%) diff --git a/LEAME.md b/LEAME.md index 9aa7f65b1..ba9e22bb7 100644 --- a/LEAME.md +++ b/LEAME.md @@ -73,7 +73,13 @@ Requisitos previos para instalaciones con Docker: Levanta el sistema completo (base de datos, Samba y app) con fixtures y datos de demo: ```bash -bash docker_install.sh --test +bash container_install.sh --test +``` + +Usa `--engine podman` para ejecutar el mismo flujo con Podman: + +```bash +bash container_install.sh --test --engine podman ``` Esto usa `docker-compose.test.yml` por defecto. @@ -88,7 +94,7 @@ Puedes personalizar los valores por defecto: Ejemplo de uso con un script de migracion en Docker: ```bash -bash docker_install.sh --test --script migrate_optional_values +bash container_install.sh --test --script migrate_optional_values ``` Cuando el script termine, abre `http://localhost:8001` y crea el superusuario de Django cuando te lo pida. @@ -107,21 +113,22 @@ Despliega el contenedor de iSkyLIMS contra servicios MySQL/Samba externos: 2. Construye y ejecuta en modo produccion (usa `docker-compose.prod.yml` por defecto): ```bash - bash docker_install.sh --install_conf conf/my_prod_settings.txt + bash container_install.sh --install_conf conf/my_prod_settings.txt ``` Usa `--compose_file` para cambiar el compose o `--install_type`/`--git_revision` para variar el build. + Añade `--engine podman` para usar Podman en lugar de Docker. Tip: captura logs para depuracion: ```bash - bash docker_install.sh --install_conf conf/my_prod_settings.txt 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log + bash container_install.sh --install_conf conf/my_prod_settings.txt 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log ``` 3. Si es una instalacion nueva, crea el superusuario cuando se solicite y completa la configuracion de Samba en la UI. UID/GID del usuario de ejecucion del contenedor (por defecto `1212:1212`): -- Exporta `APP_UID` y `APP_GID` antes de ejecutar `docker_install.sh` si necesitas un UID/GID distinto (por ejemplo, para escribir en `/opt/iskylims/static-host`). +- Exporta `APP_UID` y `APP_GID` antes de ejecutar `container_install.sh` si necesitas un UID/GID distinto (por ejemplo, para escribir en `/opt/iskylims/static-host`). ```bash export APP_UID=1212 @@ -180,7 +187,7 @@ export APP_GID=1212 Re-despliega el contenedor de aplicacion contra una base de datos existente sin tocar los datos: ```bash -bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade +bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade ``` La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh` dentro del contenedor, que regenera migraciones, las aplica con `--fake-initial` y evita cargar superusuario/datos demo/prueba. @@ -210,7 +217,7 @@ mysql --user= --password= --host= --port= /tmp/library_pool_run_process.tsv -bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade \ +bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade \ --script_before convert_rawtop_counter_to_int \ --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv ``` @@ -399,7 +406,7 @@ docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ 5. Arranca el contenedor de nuevo: ```bash - bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade + bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade ``` ## Pasos finales de configuracion diff --git a/README.md b/README.md index 16220c7e2..5c9b09810 100644 --- a/README.md +++ b/README.md @@ -78,7 +78,13 @@ Prerequisites for Docker-based installs: Bring up a full test stack (database, Samba, app) plus fixtures and demo data: ```bash -bash docker_install.sh --test +bash container_install.sh --test +``` + +Use `--engine podman` to run the same flow with Podman: + +```bash +bash container_install.sh --test --engine podman ``` This uses `docker-compose.test.yml` by default. @@ -93,7 +99,7 @@ Defaults can be customised: Example running a migration script during Docker install: ```bash -bash docker_install.sh --test --script migrate_optional_values +bash container_install.sh --test --script migrate_optional_values ``` When the script finishes, open `http://localhost:8001` and follow the prompt to create the Django superuser. @@ -112,21 +118,22 @@ Deploy the iSkyLIMS container against external MySQL/Samba services: 2. Build and run in production mode (uses `docker-compose.prod.yml` by default): ```bash - bash docker_install.sh --install_conf conf/my_prod_settings.txt + bash container_install.sh --install_conf conf/my_prod_settings.txt ``` Use `--compose_file` to override the compose file or `--install_type`/`--git_revision` to change the build. + Add `--engine podman` to use Podman instead of Docker. Tip: capture logs for troubleshooting: ```bash - bash docker_install.sh --install_conf conf/my_prod_settings.txt 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log + bash container_install.sh --install_conf conf/my_prod_settings.txt 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log ``` 3. If this is a fresh install, create the Django superuser when prompted and complete the Samba configuration in the UI. UID/GID for the container runtime user (default `1212:1212`): -- Export `APP_UID` and `APP_GID` before running `docker_install.sh` if you need a different host UID/GID (for example, to write to `/opt/iskylims/static-host`). +- Export `APP_UID` and `APP_GID` before running `container_install.sh` if you need a different host UID/GID (for example, to write to `/opt/iskylims/static-host`). ```bash export APP_UID=1212 @@ -185,7 +192,7 @@ export APP_GID=1212 Re-deploy the application container against an existing production database without touching data: ```bash -bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade +bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade ``` The upgrade path rebuilds/restarts the container and runs `install.sh` inside the app container, which regenerates migrations, applies them with `--fake-initial`, and skips superuser/demo/test data loading. @@ -235,7 +242,7 @@ export APP_GID=1212 Run upgrade command: ```bash -bash docker_install.sh --install_conf my_prod_settings.txt --action upgrade \ +bash container_install.sh --install_conf my_prod_settings.txt --action upgrade \ --script_before convert_rawtop_counter_to_int \ --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv ``` @@ -406,7 +413,7 @@ docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ 5. Start the container again: ```bash - bash docker_install.sh --install_conf conf/my_prod_settings.txt --action upgrade + bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade ``` ## Final configuration steps diff --git a/docker_install.sh b/container_install.sh similarity index 73% rename from docker_install.sh rename to container_install.sh index 77604c49a..355ee9ed2 100644 --- a/docker_install.sh +++ b/container_install.sh @@ -6,19 +6,20 @@ usage() { cat << EOF This script installs and upgrades the iskylims app. -Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--install_conf] [--action] [--script] [--script_before] [--script_after] [--test] +Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--install_conf] [--action] [--script] [--script_before] [--script_after] [--engine] [--test] Optional input data: --demo_data | Provide already downloaded demo data from Zenodo --install_type | Specify the installation type for iSkyLIMS (default: full) --git_revision | Specify the Git revision to install (default: main) - --compose_file | docker compose file to use (overrides default) - --install_conf | Settings file consumed during docker image build (mandatory for production) + --compose_file | Compose file to use (overrides default) + --install_conf | Settings file consumed during container image build (mandatory for production) --action | install (default) or upgrade, to control DB initialisation steps --script | Run a Django migration script after migrations (can be repeated) --script_before | Run a Django migration script before migrations (can be repeated) --script_after | Run a Django migration script after migrations (can be repeated) --skip_demo_data | Skip downloading/copying demo data to samba container --skip_test_data | Skip loading test fixtures (test/test_data.json) + --engine | Container engine to use: docker (default) or podman --test | Use development/test compose file and sample data Examples: @@ -28,7 +29,7 @@ Examples: Upgrade an existing production deployment using the same database: bash $0 --install_conf conf/my_prod_settings.txt --action upgrade - Install demo docker system with local services + Install demo container system with local services bash $0 --test Provide already downloaded data from Zenodo (compressed) for test environment @@ -63,6 +64,7 @@ do --skip_demo_data) set -- "$@" -n ;; --skip_test_data) set -- "$@" -t ;; --test) set -- "$@" -p ;; + --engine) set -- "$@" -e ;; # ADDITIONAL --help) set -- "$@" -h ;; @@ -86,9 +88,46 @@ run_script=false run_script_before=false migration_script=() migration_script_before=() +engine="docker" + +ENGINE_CMD=() +COMPOSE_CMD=() + +set_engine() { + if [ "$engine" = "docker" ]; then + if ! command -v docker >/dev/null 2>&1; then + echo "docker not found. Install docker or use --engine podman." + exit 1 + fi + ENGINE_CMD=("docker") + COMPOSE_CMD=("docker" "compose") + else + if ! command -v podman >/dev/null 2>&1; then + echo "podman not found. Install podman or use --engine docker." + exit 1 + fi + ENGINE_CMD=("podman") + if command -v podman-compose >/dev/null 2>&1; then + COMPOSE_CMD=("podman-compose") + elif podman compose version >/dev/null 2>&1; then + COMPOSE_CMD=("podman" "compose") + else + echo "podman compose not available. Install podman-compose or use --engine docker." + exit 1 + fi + fi +} + +engine_exec() { + "${ENGINE_CMD[@]}" "$@" +} + +compose_exec() { + "${COMPOSE_CMD[@]}" "$@" +} # PARSE VARIABLE ARGUMENTS WITH getopts -options=":d:i:g:c:s:a:m:b:f:vhntp" +options=":d:i:g:c:s:a:m:b:f:e:vhntp" while getopts $options opt; do case $opt in d) @@ -118,6 +157,13 @@ while getopts $options opt; do run_script_before=true migration_script_before+=("$OPTARG") ;; + e) + engine=$OPTARG + if [[ "$engine" != "docker" && "$engine" != "podman" ]]; then + echo "Invalid engine '$engine'. Use docker or podman." + exit 1 + fi + ;; f) run_script=true migration_script+=("$OPTARG") @@ -226,29 +272,31 @@ else install_conf_container="$install_conf" fi +set_engine + service_exists() { - docker compose -f "$compose_file" ps --services 2>/dev/null | grep -Fxq "$1" + compose_exec -f "$compose_file" ps --services 2>/dev/null | grep -Fxq "$1" } ensure_app_running() { - if ! docker inspect -f '{{.State.Running}}' iskylims_app >/dev/null 2>&1; then + if ! engine_exec inspect -f '{{.State.Running}}' iskylims_app >/dev/null 2>&1; then echo "Error: iskylims_app container does not exist." exit 1 fi - if [ "$(docker inspect -f '{{.State.Running}}' iskylims_app)" != "true" ]; then + if [ "$(engine_exec inspect -f '{{.State.Running}}' iskylims_app)" != "true" ]; then echo "Error: iskylims_app container is not running. Showing logs:" - docker logs --tail 200 iskylims_app + engine_exec logs --tail 200 iskylims_app exit 1 fi } echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=dep and GIT_REVISION=$git_revision..." INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" \ - docker compose -f "$compose_file" build --no-cache \ + compose_exec -f "$compose_file" build --no-cache \ --build-arg INSTALL_TYPE="dep" \ --build-arg GIT_REVISION="$git_revision" \ --build-arg INSTALL_CONF="$install_conf_container" -docker compose -f "$compose_file" up -d +compose_exec -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." sleep 20 @@ -257,7 +305,7 @@ ensure_app_running app_uid="${APP_UID:-1212}" app_gid="${APP_GID:-1212}" echo "Ensuring runtime directories are writable by ${app_uid}:${app_gid}" -docker exec -u 0 -it iskylims_app sh -lc "mkdir -p /opt/iskylims/documents /opt/iskylims/logs /opt/iskylims/static /opt/iskylims/cron /opt/iskylims/tmp && chown -R ${app_uid}:${app_gid} /opt/iskylims/documents /opt/iskylims/logs /opt/iskylims/static /opt/iskylims/cron /opt/iskylims/tmp" +engine_exec exec -u 0 -it iskylims_app sh -lc "mkdir -p /opt/iskylims/documents /opt/iskylims/logs /opt/iskylims/static /opt/iskylims/cron /opt/iskylims/tmp && chown -R ${app_uid}:${app_gid} /opt/iskylims/documents /opt/iskylims/logs /opt/iskylims/static /opt/iskylims/cron /opt/iskylims/tmp" host_install_conf_path="$install_conf" if [[ "$host_install_conf_path" != /* ]]; then @@ -269,9 +317,9 @@ if [[ "$container_install_conf_path" != /* ]]; then container_install_conf_path="/srv/iskylims/$container_install_conf_path" fi -if ! docker exec -it iskylims_app test -f "$container_install_conf_path"; then +if ! engine_exec exec -it iskylims_app test -f "$container_install_conf_path"; then echo "Copying install configuration into container at $container_install_conf_path" - docker cp "$host_install_conf_path" "iskylims_app:$container_install_conf_path" + engine_exec cp "$host_install_conf_path" "iskylims_app:$container_install_conf_path" fi script_args_before="" @@ -290,20 +338,20 @@ fi if [ "$action" = "upgrade" ]; then echo "Running install.sh upgrade inside the container" - docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --upgrade app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" + engine_exec exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --upgrade app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" else echo "Running install.sh install inside the container" - docker exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --install app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" + engine_exec exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --install app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" fi -if ! docker exec -it iskylims_app test -f /opt/iskylims/manage.py; then +if ! engine_exec exec -it iskylims_app test -f /opt/iskylims/manage.py; then echo "Error: /opt/iskylims/manage.py not found after install.sh. Showing logs:" - docker logs --tail 200 iskylims_app + engine_exec logs --tail 200 iskylims_app exit 1 fi if [ "$skip_test_data" = false ]; then - docker exec -it iskylims_app python3 manage.py loaddata test/test_data.json + engine_exec exec -it iskylims_app python3 manage.py loaddata test/test_data.json else echo "Skipping test data fixtures as requested" fi @@ -314,11 +362,11 @@ if [ "$skip_demo_data" = false ] && service_exists "samba"; then wget https://zenodo.org/record/8091169/files/iskylims_demo_data.tar.gz demo_data="./iskylims_demo_data.tar.gz" fi - docker cp "$demo_data" samba:/mnt - docker exec -it samba tar -xf /mnt/iskylims_demo_data.tar.gz -C /mnt + engine_exec cp "$demo_data" samba:/mnt + engine_exec exec -it samba tar -xf /mnt/iskylims_demo_data.tar.gz -C /mnt echo "Deleting compressed test file" - docker exec -it samba rm /mnt/iskylims_demo_data.tar.gz + engine_exec exec -it samba rm /mnt/iskylims_demo_data.tar.gz if [ "$demo_data" == "false" ]; then rm -f "$demo_data" From 29f587d9355ef2b7c50e7680266a87680709c005 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 2 Mar 2026 13:25:43 +0100 Subject: [PATCH 361/446] remove log volume as bind mount is used for logs --- docker-compose.prod.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 7370f2a46..704b227f2 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -28,5 +28,4 @@ services: - "host.docker.internal:host-gateway" volumes: - iskylims_logs: iskylims_documents: From 454574d03c00dd2d33250e98f00d5ad1bee8c60c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 2 Mar 2026 14:27:30 +0100 Subject: [PATCH 362/446] added generalization to fix project name differences --- container_install.sh | 51 ++++++++++++++++++++++++++++---------------- install.sh | 48 +++++++++++++++++++++-------------------- 2 files changed, 58 insertions(+), 41 deletions(-) diff --git a/container_install.sh b/container_install.sh index 355ee9ed2..ccd27b861 100644 --- a/container_install.sh +++ b/container_install.sh @@ -274,18 +274,33 @@ fi set_engine +app_service="${APP_SERVICE:-app}" +app_repo_path="${APP_REPO_PATH:-/srv/iskylims}" +app_install_path="${APP_INSTALL_PATH:-/opt/iskylims}" +app_port="${APP_PORT:-8001}" +app_container="" + service_exists() { compose_exec -f "$compose_file" ps --services 2>/dev/null | grep -Fxq "$1" } +resolve_app_container() { + app_container="$(compose_exec -f "$compose_file" ps -q "$app_service" | head -n 1)" + if [ -z "$app_container" ]; then + echo "Error: unable to resolve container ID for service '$app_service'." + exit 1 + fi +} + ensure_app_running() { - if ! engine_exec inspect -f '{{.State.Running}}' iskylims_app >/dev/null 2>&1; then - echo "Error: iskylims_app container does not exist." + resolve_app_container + if ! engine_exec inspect -f '{{.State.Running}}' "$app_container" >/dev/null 2>&1; then + echo "Error: service '$app_service' container does not exist." exit 1 fi - if [ "$(engine_exec inspect -f '{{.State.Running}}' iskylims_app)" != "true" ]; then - echo "Error: iskylims_app container is not running. Showing logs:" - engine_exec logs --tail 200 iskylims_app + if [ "$(engine_exec inspect -f '{{.State.Running}}' "$app_container")" != "true" ]; then + echo "Error: service '$app_service' container is not running. Showing logs:" + engine_exec logs --tail 200 "$app_container" exit 1 fi } @@ -305,7 +320,7 @@ ensure_app_running app_uid="${APP_UID:-1212}" app_gid="${APP_GID:-1212}" echo "Ensuring runtime directories are writable by ${app_uid}:${app_gid}" -engine_exec exec -u 0 -it iskylims_app sh -lc "mkdir -p /opt/iskylims/documents /opt/iskylims/logs /opt/iskylims/static /opt/iskylims/cron /opt/iskylims/tmp && chown -R ${app_uid}:${app_gid} /opt/iskylims/documents /opt/iskylims/logs /opt/iskylims/static /opt/iskylims/cron /opt/iskylims/tmp" +engine_exec exec -u 0 -it "$app_container" sh -lc "mkdir -p ${app_install_path}/documents ${app_install_path}/logs ${app_install_path}/static ${app_install_path}/cron ${app_install_path}/tmp && chown -R ${app_uid}:${app_gid} ${app_install_path}/documents ${app_install_path}/logs ${app_install_path}/static ${app_install_path}/cron ${app_install_path}/tmp" host_install_conf_path="$install_conf" if [[ "$host_install_conf_path" != /* ]]; then @@ -314,12 +329,12 @@ fi container_install_conf_path="$install_conf_container" if [[ "$container_install_conf_path" != /* ]]; then - container_install_conf_path="/srv/iskylims/$container_install_conf_path" + container_install_conf_path="$app_repo_path/$container_install_conf_path" fi -if ! engine_exec exec -it iskylims_app test -f "$container_install_conf_path"; then +if ! engine_exec exec -it "$app_container" test -f "$container_install_conf_path"; then echo "Copying install configuration into container at $container_install_conf_path" - engine_exec cp "$host_install_conf_path" "iskylims_app:$container_install_conf_path" + engine_exec cp "$host_install_conf_path" "${app_container}:$container_install_conf_path" fi script_args_before="" @@ -338,20 +353,20 @@ fi if [ "$action" = "upgrade" ]; then echo "Running install.sh upgrade inside the container" - engine_exec exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --upgrade app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" + engine_exec exec -it "$app_container" bash -c "cd $app_repo_path && bash install.sh --upgrade app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" else echo "Running install.sh install inside the container" - engine_exec exec -it iskylims_app bash -c "cd /srv/iskylims && bash install.sh --install app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" + engine_exec exec -it "$app_container" bash -c "cd $app_repo_path && bash install.sh --install app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" fi -if ! engine_exec exec -it iskylims_app test -f /opt/iskylims/manage.py; then - echo "Error: /opt/iskylims/manage.py not found after install.sh. Showing logs:" - engine_exec logs --tail 200 iskylims_app +if ! engine_exec exec -it "$app_container" test -f "$app_install_path/manage.py"; then + echo "Error: $app_install_path/manage.py not found after install.sh. Showing logs:" + engine_exec logs --tail 200 "$app_container" exit 1 fi if [ "$skip_test_data" = false ]; then - engine_exec exec -it iskylims_app python3 manage.py loaddata test/test_data.json + engine_exec exec -it "$app_container" python3 manage.py loaddata test/test_data.json else echo "Skipping test data fixtures as requested" fi @@ -386,13 +401,13 @@ fi access_urls=() if [ -n "$dns_url" ] && [ "$dns_url" != "*" ]; then - access_urls+=("http://${dns_url}:8001") + access_urls+=("http://${dns_url}:${app_port}") fi if [ -n "$local_ip" ] && [ "$local_ip" != "*" ]; then - access_urls+=("http://${local_ip}:8001") + access_urls+=("http://${local_ip}:${app_port}") fi if [ ${#access_urls[@]} -eq 0 ]; then - access_urls+=("http://localhost:8001") + access_urls+=("http://localhost:${app_port}") fi echo "You can now access iSkyLIMS via: ${access_urls[*]}" diff --git a/install.sh b/install.sh index 233d43475..7e7839866 100644 --- a/install.sh +++ b/install.sh @@ -146,25 +146,26 @@ root_check(){ # update_settings_and_urls: rewrite Django settings and urls with deployment values. update_settings_and_urls(){ log "INFO" "Updating settings.py and urls.py with deployment values" - grep ^SECRET $INSTALL_PATH/iskylims/settings.py > ~/.secret + local project_dir="$INSTALL_PATH/$PROJECT_NAME" + grep ^SECRET "$project_dir/settings.py" > ~/.secret - cp conf/template_settings.txt $INSTALL_PATH/iskylims/settings.py - cp conf/urls.py $INSTALL_PATH/iskylims + cp conf/template_settings.txt "$project_dir/settings.py" + cp conf/urls.py "$project_dir" - sed -i "/^SECRET/c\\$(cat ~/.secret)" $INSTALL_PATH/iskylims/settings.py - sed -i "s/djangouser/${DB_USER}/g" $INSTALL_PATH/iskylims/settings.py - sed -i "s/djangopass/${DB_PASS}/g" $INSTALL_PATH/iskylims/settings.py - sed -i "s/djangohost/${DB_SERVER_IP}/g" $INSTALL_PATH/iskylims/settings.py - sed -i "s/djangoport/${DB_PORT}/g" $INSTALL_PATH/iskylims/settings.py - sed -i "s/djangodbname/${DB_NAME}/g" $INSTALL_PATH/iskylims/settings.py - - sed -i "s/emailhostserver/${EMAIL_HOST_SERVER}/g" $INSTALL_PATH/iskylims/settings.py - sed -i "s/emailport/${EMAIL_PORT}/g" $INSTALL_PATH/iskylims/settings.py - sed -i "s/emailhostuser/${EMAIL_HOST_USER}/g" $INSTALL_PATH/iskylims/settings.py - sed -i "s/emailhostpassword/${EMAIL_HOST_PASSWORD}/g" $INSTALL_PATH/iskylims/settings.py - sed -i "s/emailhosttls/${EMAIL_USE_TLS}/g" $INSTALL_PATH/iskylims/settings.py - sed -i "s/localserverip/${LOCAL_SERVER_IP}/g" $INSTALL_PATH/iskylims/settings.py - sed -i "s/localhost/${DNS_URL}/g" $INSTALL_PATH/iskylims/settings.py + sed -i "/^SECRET/c\\$(cat ~/.secret)" "$project_dir/settings.py" + sed -i "s/djangouser/${DB_USER}/g" "$project_dir/settings.py" + sed -i "s/djangopass/${DB_PASS}/g" "$project_dir/settings.py" + sed -i "s/djangohost/${DB_SERVER_IP}/g" "$project_dir/settings.py" + sed -i "s/djangoport/${DB_PORT}/g" "$project_dir/settings.py" + sed -i "s/djangodbname/${DB_NAME}/g" "$project_dir/settings.py" + + sed -i "s/emailhostserver/${EMAIL_HOST_SERVER}/g" "$project_dir/settings.py" + sed -i "s/emailport/${EMAIL_PORT}/g" "$project_dir/settings.py" + sed -i "s/emailhostuser/${EMAIL_HOST_USER}/g" "$project_dir/settings.py" + sed -i "s/emailhostpassword/${EMAIL_HOST_PASSWORD}/g" "$project_dir/settings.py" + sed -i "s/emailhosttls/${EMAIL_USE_TLS}/g" "$project_dir/settings.py" + sed -i "s/localserverip/${LOCAL_SERVER_IP}/g" "$project_dir/settings.py" + sed -i "s/localhost/${DNS_URL}/g" "$project_dir/settings.py" } # restore_git_ref: reset repository to branch/tag/commit active before script ran. @@ -707,8 +708,8 @@ upgrade_application_files() { source virtualenv/bin/activate if [ ! -f "$INSTALL_PATH/manage.py" ]; then - echo "manage.py not found. Creating iskylims project" - "$INSTALL_PATH/virtualenv/bin/python" -m django startproject iskylims . + echo "manage.py not found. Creating ${PROJECT_NAME} project" + "$INSTALL_PATH/virtualenv/bin/python" -m django startproject "$PROJECT_NAME" . fi echo "Update settings and url file." @@ -786,8 +787,8 @@ install_application_files() { echo "activate the virtualenv" source virtualenv/bin/activate - echo "Creating iskylims project" - "$INSTALL_PATH/virtualenv/bin/python" -m django startproject iskylims . + echo "Creating ${PROJECT_NAME} project" + "$INSTALL_PATH/virtualenv/bin/python" -m django startproject "$PROJECT_NAME" . update_settings_and_urls @@ -860,7 +861,7 @@ while getopts $options opt; do i ) install=true upgrade=false - if [[ "$OPTARG" -eq "full" || "$OPTARG" -eq "dep" || "$OPTARG" -eq "app" ]]; then + if [[ "$OPTARG" == "full" || "$OPTARG" == "dep" || "$OPTARG" == "app" ]]; then install_type=$OPTARG upgrade_type=$OPTARG else @@ -871,7 +872,7 @@ while getopts $options opt; do u ) install=false upgrade=true - if [[ "$OPTARG" -eq "full" || "$OPTARG" -eq "dep" || "$OPTARG" -eq "app" ]]; then + if [[ "$OPTARG" == "full" || "$OPTARG" == "dep" || "$OPTARG" == "app" ]]; then upgrade_type=$OPTARG install_type=$OPTARG else @@ -952,6 +953,7 @@ if [ "$operation" = "install" ] && [ "$skip_tables" = false ] && [ "$tables" = f fi load_install_config +PROJECT_NAME="${PROJECT_NAME:-iskylims}" checkout_git_revision user=${SUDO_USER:-$USER} check_requirements From 2fe4bc4c605b52f811512f604018a1bea1ae6898 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 2 Mar 2026 17:41:44 +0100 Subject: [PATCH 363/446] some comments and generalization in container install.sh, god urls in docker compose for podman --- container_install.sh | 83 ++++++++++++++++++++++++++++++++++++++++- docker-compose.test.yml | 4 +- 2 files changed, 83 insertions(+), 4 deletions(-) diff --git a/container_install.sh b/container_install.sh index ccd27b861..d852f9944 100644 --- a/container_install.sh +++ b/container_install.sh @@ -280,18 +280,70 @@ app_install_path="${APP_INSTALL_PATH:-/opt/iskylims}" app_port="${APP_PORT:-8001}" app_container="" +# Check if a service exists in the compose file +# +# Parameters: +# $1 - Service name to check +# +# Returns: +# 0 if the service exists, 1 otherwise service_exists() { compose_exec -f "$compose_file" ps --services 2>/dev/null | grep -Fxq "$1" } +# Return the name of the container for a given service name. +# The container name is different based on whether we are in test mode or not. +# +# Parameters: +# $1 - Service name to return the container name for +# +# Returns: +# The name of the container for the given service name +service_container_name() { + local service_name="$1" + if [ "$mode" = "test" ]; then + case "$service_name" in + db) echo "db" ;; + samba) echo "samba" ;; + app) echo "iskylims_app" ;; + *) echo "" ;; + esac + else + case "$service_name" in + app) echo "iskylims_app" ;; + samba) echo "samba" ;; + *) echo "" ;; + esac + fi +} + +# Resolve the container ID for the target app service. +# +# Returns: +# Sets global variable `app_container` to a valid container name/ID. +# +# Errors: +# Exits if unable to resolve a container for `app_service`. resolve_app_container() { - app_container="$(compose_exec -f "$compose_file" ps -q "$app_service" | head -n 1)" + local container_name + container_name="$(service_container_name "$app_service")" + + if [ -n "$container_name" ] && engine_exec inspect -f '{{.Id}}' "$container_name" >/dev/null 2>&1; then + app_container="$container_name" + else + app_container="$(engine_exec ps -a --filter "label=com.docker.compose.service=${app_service}" --format '{{.ID}}' | head -n 1)" + fi + if [ -z "$app_container" ]; then - echo "Error: unable to resolve container ID for service '$app_service'." + echo "Error: unable to resolve container ID for service '$app_service'." >&2 exit 1 fi } +# Ensure target app service container exists and is running. +# +# Errors: +# Exits if container does not exist or is not running. ensure_app_running() { resolve_app_container if ! engine_exec inspect -f '{{.State.Running}}' "$app_container" >/dev/null 2>&1; then @@ -305,6 +357,33 @@ ensure_app_running() { fi } +# Remove stale test containers left over from previous runs. +# +# This function will only be executed in "test" mode when the engine is "podman". +# It only removes known test container names and never removes volumes. +cleanup_stale_test_containers() { + if [ "$mode" != "test" ] || [ "$engine" != "podman" ]; then + return 0 + fi + + local svc cname cstate + for svc in db app samba; do + cname="$(service_container_name "$svc")" + if [ -z "$cname" ]; then + continue + fi + if engine_exec inspect -f '{{.Id}}' "$cname" >/dev/null 2>&1; then + cstate="$(engine_exec inspect -f '{{.State.Status}}' "$cname" 2>/dev/null || true)" + if [ "$cstate" != "running" ]; then + echo "Removing stale test container '$cname' (state: ${cstate:-unknown})" + engine_exec rm -f "$cname" >/dev/null 2>&1 || true + fi + fi + done +} + +cleanup_stale_test_containers + echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=dep and GIT_REVISION=$git_revision..." INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" \ compose_exec -f "$compose_file" build --no-cache \ diff --git a/docker-compose.test.yml b/docker-compose.test.yml index d17f5c76c..f9d5e38f5 100644 --- a/docker-compose.test.yml +++ b/docker-compose.test.yml @@ -2,7 +2,7 @@ version: '3.4' services: db: - image: mysql:8.0 + image: docker.io/library/mysql:8.0 container_name: db command: --default-authentication-plugin=mysql_native_password restart: always @@ -27,7 +27,7 @@ services: - /usr/share/zoneinfo:/usr/share/zoneinfo samba: - image: dperson/samba + image: docker.io/dperson/samba container_name: samba networks: - develop_net From 0a0aa25eae5ad8cd8ab8b28e4e56668f2d6fe21b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 2 Mar 2026 18:13:42 +0100 Subject: [PATCH 364/446] add chown only if root --- install.sh | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/install.sh b/install.sh index 7e7839866..f9ce62db2 100644 --- a/install.sh +++ b/install.sh @@ -251,6 +251,14 @@ abort_install() { exit "${2:-1}" } +chown_if_root() { + if [ "$EUID" -eq 0 ]; then + chown "$@" + else + log_warn "Skipping chown (requires root): chown $*" + fi +} + ensure_file_exists() { local file_path="$1" local friendly_name="${2:-$1}" @@ -595,7 +603,7 @@ prepare_documents_structure() { mkdir -p $INSTALL_PATH/documents/drylab mkdir -p $INSTALL_PATH/documents/drylab/service_files - chown -R $user:$apache_group $INSTALL_PATH/documents + chown_if_root -R "$user:$apache_group" "$INSTALL_PATH/documents" chmod 775 $INSTALL_PATH/documents cp $INSTALL_PATH/conf/*_template.csv $INSTALL_PATH/documents/wetlab/templates/ @@ -671,7 +679,7 @@ run_dependency_stage() { else apache_group="apache" fi - chown -R $user:$apache_group $INSTALL_PATH + chown_if_root -R "$user:$apache_group" "$INSTALL_PATH" chmod 775 $INSTALL_PATH else log_section "Preparing dependency environment for upgrade" @@ -770,7 +778,7 @@ install_application_files() { else if [ ! -d $INSTALL_PATH/logs ]; then mkdir -p $INSTALL_PATH/logs - chown $user:$apache_group $INSTALL_PATH/logs + chown_if_root "$user:$apache_group" "$INSTALL_PATH/logs" chmod 775 $INSTALL_PATH/logs else echo "Log folder path: $INSTALL_PATH/logs already exist." From 2364c4e722c37f956ca8191c66a8266bf15f2e7f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 3 Mar 2026 11:29:55 +0100 Subject: [PATCH 365/446] add proper logging to readme --- README.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 5c9b09810..b5b6a3e74 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Docker deployment](#docker-deployment) - [Local test stack](#local-test-stack) - [Production container](#production-container) -- [Persist logs/documents on the host](#persist-logsdocuments-on-the-host) + - [Persist logs/documents on the host](#persist-logsdocuments-on-the-host) - [Apache reverse proxy (host) + Gunicorn](#apache-reverse-proxy-host--gunicorn) - [Cron jobs inside the container](#cron-jobs-inside-the-container) - [Upgrade docker deployment](#upgrade-docker-deployment) @@ -78,13 +78,13 @@ Prerequisites for Docker-based installs: Bring up a full test stack (database, Samba, app) plus fixtures and demo data: ```bash -bash container_install.sh --test +bash container_install.sh --test 2>&1 | tee test.log ``` Use `--engine podman` to run the same flow with Podman: ```bash -bash container_install.sh --test --engine podman +bash container_install.sh --test --engine podman 2>&1 | tee test.log ``` This uses `docker-compose.test.yml` by default. @@ -99,7 +99,7 @@ Defaults can be customised: Example running a migration script during Docker install: ```bash -bash container_install.sh --test --script migrate_optional_values +bash container_install.sh --test --script migrate_optional_values 2>&1 | tee test.log ``` When the script finishes, open `http://localhost:8001` and follow the prompt to create the Django superuser. @@ -118,7 +118,7 @@ Deploy the iSkyLIMS container against external MySQL/Samba services: 2. Build and run in production mode (uses `docker-compose.prod.yml` by default): ```bash - bash container_install.sh --install_conf conf/my_prod_settings.txt + bash container_install.sh --install_conf conf/my_prod_settings.txt 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log ``` Use `--compose_file` to override the compose file or `--install_type`/`--git_revision` to change the build. @@ -143,7 +143,7 @@ export APP_GID=1212 Ensure the static directory on the host is writable by that UID/GID: ```bash -sudo chown -R 1212:1212 /opt/iskylims/static-host +sudo chown -R ${APP_UID}:${APP_GID} /opt/iskylims/static-host ``` #### Persist logs/documents on the host @@ -159,7 +159,7 @@ Create the host log directory and set ownership to match the container UID/GID: ```bash sudo mkdir -p /var/log/apps/iskylims -sudo chown -R 1212:1212 /var/log/apps/iskylims +sudo chown -R ${APP_UID}:${APP_GID} /var/log/apps/iskylims ``` #### Apache reverse proxy (host) + Gunicorn @@ -192,7 +192,7 @@ export APP_GID=1212 Re-deploy the application container against an existing production database without touching data: ```bash -bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade +bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log ``` The upgrade path rebuilds/restarts the container and runs `install.sh` inside the app container, which regenerates migrations, applies them with `--fake-initial`, and skips superuser/demo/test data loading. @@ -244,7 +244,7 @@ Run upgrade command: ```bash bash container_install.sh --install_conf my_prod_settings.txt --action upgrade \ --script_before convert_rawtop_counter_to_int \ - --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv + --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log ``` ## Bare-metal deployment (Ubuntu/CentOS) From fdc18fe0cc2f83e8b472c644dc1acecb1fd8db2f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 3 Mar 2026 11:30:12 +0100 Subject: [PATCH 366/446] add Z for selinux context expansion --- docker-compose.prod.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 704b227f2..f1aa6bd31 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -21,9 +21,9 @@ services: volumes: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo - - /var/log/apps/iskylims:/opt/iskylims/logs + - /var/log/local/apps/iskylims:/opt/iskylims/logs:Z - iskylims_documents:/opt/iskylims/documents - - /opt/iskylims/static-host:/opt/iskylims/static + - /opt/iskylims/static-host:/opt/iskylims/static:Z extra_hosts: - "host.docker.internal:host-gateway" From 675bcbc6f494d91d57d638fb2aa498c6511a58bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 3 Mar 2026 11:30:34 +0100 Subject: [PATCH 367/446] fix crontab add in entrypoint --- scripts/container_start.sh | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/scripts/container_start.sh b/scripts/container_start.sh index 933ac9d6a..82ff40703 100644 --- a/scripts/container_start.sh +++ b/scripts/container_start.sh @@ -5,6 +5,7 @@ APP_DIR="/opt/iskylims" CRON_DIR="${APP_DIR}/cron" TMP_DIR="${APP_DIR}/tmp" CRON_FILE="${CRON_DIR}/iskylims" +CRON_LOG="${TMP_DIR}/crond.log" APP_MODE="${APP_MODE:-prod}" while [ ! -f "${APP_DIR}/manage.py" ]; do @@ -21,10 +22,23 @@ if [ "$APP_MODE" = "dev" ]; then fi if command -v crond >/dev/null 2>&1; then - python "${APP_DIR}/manage.py" crontab show > "${CRON_FILE}" || true + # django-crontab needs an explicit add before jobs are visible via `crontab show` + python "${APP_DIR}/manage.py" crontab add >/dev/null 2>&1 || true + python "${APP_DIR}/manage.py" crontab show 2>/dev/null \ + | sed '/^no crontab for /d; /^\s*$/d' > "${CRON_FILE}" || true if [ -s "${CRON_FILE}" ]; then chmod 600 "${CRON_FILE}" - crond -n -m off -c "${CRON_DIR}" -p "${TMP_DIR}/crond.pid" & + : > "${CRON_LOG}" + crond -n -m off -c "${CRON_DIR}" > "${CRON_LOG}" 2>&1 & + CROND_PID=$! + sleep 1 + if ! kill -0 "${CROND_PID}" 2>/dev/null; then + if grep -qi "permission denied" "${CRON_LOG}" 2>/dev/null; then + echo "crond could not start under non-root user. Skipping cron daemon startup." + else + echo "crond failed to start. Check ${CRON_LOG} for details." + fi + fi else echo "No cron entries found. Skipping crond start." fi From 78bf8d50ee3e30ab9cf32c856ff30fe7583464fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 3 Mar 2026 12:56:40 +0100 Subject: [PATCH 368/446] try supercronic instead of cronie --- Dockerfile | 13 +++++++++++++ scripts/container_start.sh | 23 +++++++++-------------- 2 files changed, 22 insertions(+), 14 deletions(-) diff --git a/Dockerfile b/Dockerfile index fec45583d..45cfedae2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -22,6 +22,19 @@ RUN dnf -y install \ pkgconf-pkg-config \ && dnf clean all +# Install supercronic (rootless-friendly cron runner) +RUN set -eux; \ + SUPERCRONIC_VERSION="v0.2.38"; \ + arch="$(uname -m)"; \ + case "$arch" in \ + x86_64) supercronic_arch="amd64" ;; \ + aarch64) supercronic_arch="arm64" ;; \ + *) echo "Unsupported architecture for supercronic: $arch" >&2; exit 1 ;; \ + esac; \ + wget -q -O /usr/local/bin/supercronic \ + "https://github.com/aptible/supercronic/releases/download/${SUPERCRONIC_VERSION}/supercronic-linux-${supercronic_arch}"; \ + chmod +x /usr/local/bin/supercronic + # Ensure python3 points to the desired version RUN ln -sf /usr/bin/python3.11 /usr/bin/python3 diff --git a/scripts/container_start.sh b/scripts/container_start.sh index 82ff40703..1cfd70357 100644 --- a/scripts/container_start.sh +++ b/scripts/container_start.sh @@ -5,7 +5,7 @@ APP_DIR="/opt/iskylims" CRON_DIR="${APP_DIR}/cron" TMP_DIR="${APP_DIR}/tmp" CRON_FILE="${CRON_DIR}/iskylims" -CRON_LOG="${TMP_DIR}/crond.log" +CRON_LOG="${TMP_DIR}/supercronic.log" APP_MODE="${APP_MODE:-prod}" while [ ! -f "${APP_DIR}/manage.py" ]; do @@ -21,29 +21,24 @@ if [ "$APP_MODE" = "dev" ]; then exec python "${APP_DIR}/manage.py" runserver 0.0.0.0:8001 fi -if command -v crond >/dev/null 2>&1; then - # django-crontab needs an explicit add before jobs are visible via `crontab show` +if command -v supercronic >/dev/null 2>&1; then + # Ensure django-crontab definitions are installed in user crontab first. python "${APP_DIR}/manage.py" crontab add >/dev/null 2>&1 || true - python "${APP_DIR}/manage.py" crontab show 2>/dev/null \ - | sed '/^no crontab for /d; /^\s*$/d' > "${CRON_FILE}" || true + crontab -l 2>/dev/null | sed '/^\s*#/d; /^\s*$/d' > "${CRON_FILE}" || true if [ -s "${CRON_FILE}" ]; then chmod 600 "${CRON_FILE}" : > "${CRON_LOG}" - crond -n -m off -c "${CRON_DIR}" > "${CRON_LOG}" 2>&1 & - CROND_PID=$! + supercronic "${CRON_FILE}" > "${CRON_LOG}" 2>&1 & + CRON_PID=$! sleep 1 - if ! kill -0 "${CROND_PID}" 2>/dev/null; then - if grep -qi "permission denied" "${CRON_LOG}" 2>/dev/null; then - echo "crond could not start under non-root user. Skipping cron daemon startup." - else - echo "crond failed to start. Check ${CRON_LOG} for details." - fi + if ! kill -0 "${CRON_PID}" 2>/dev/null; then + echo "supercronic failed to start. Check ${CRON_LOG} for details." fi else echo "No cron entries found. Skipping crond start." fi else - echo "crond not found. Skipping cron." + echo "supercronic not found. Skipping cron." fi exec gunicorn iskylims.wsgi:application \ From a0f6912ce19a7359783e196fb9cf877e9168f9de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 3 Mar 2026 16:09:37 +0100 Subject: [PATCH 369/446] added install_conf_map for multicontainer build --- container_install.sh | 38 ++++++++++++++++++++++++++++++++------ 1 file changed, 32 insertions(+), 6 deletions(-) diff --git a/container_install.sh b/container_install.sh index d852f9944..30fafd647 100644 --- a/container_install.sh +++ b/container_install.sh @@ -13,6 +13,7 @@ Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--i --git_revision | Specify the Git revision to install (default: main) --compose_file | Compose file to use (overrides default) --install_conf | Settings file consumed during container image build (mandatory for production) + --install_conf_map | Service-specific settings file: service,path (can be repeated) --action | install (default) or upgrade, to control DB initialisation steps --script | Run a Django migration script after migrations (can be repeated) --script_before | Run a Django migration script before migrations (can be repeated) @@ -26,6 +27,9 @@ Examples: Deploy production container pointing to an external DB/Samba: bash $0 --install_conf conf/my_prod_settings.txt + Deploy production with service-specific settings mapping: + bash $0 --install_conf_map app,conf/docker_production_settings.txt + Upgrade an existing production deployment using the same database: bash $0 --install_conf conf/my_prod_settings.txt --action upgrade @@ -57,6 +61,7 @@ do --git_revision) set -- "$@" -g ;; --compose_file) set -- "$@" -c ;; --install_conf) set -- "$@" -s ;; + --install_conf_map) set -- "$@" -j ;; --action) set -- "$@" -a ;; --script) set -- "$@" -m ;; --script_before) set -- "$@" -b ;; @@ -80,6 +85,7 @@ git_revision="main" compose_file="" install_conf="" install_conf_container="" +install_conf_map_entries=() skip_demo_data="" skip_test_data="" mode="production" @@ -127,7 +133,7 @@ compose_exec() { } # PARSE VARIABLE ARGUMENTS WITH getopts -options=":d:i:g:c:s:a:m:b:f:e:vhntp" +options=":d:i:g:c:s:j:a:m:b:f:e:vhntp" while getopts $options opt; do case $opt in d) @@ -142,6 +148,9 @@ while getopts $options opt; do s) install_conf=$OPTARG ;; + j) + install_conf_map_entries+=("$OPTARG") + ;; a) action=$OPTARG if [[ "$action" != "install" && "$action" != "upgrade" ]]; then @@ -206,17 +215,35 @@ if [ "$mode" = "test" ]; then if [ -z "$compose_file" ]; then compose_file="docker-compose.test.yml" fi - if [ -z "$install_conf" ]; then - install_conf="conf/docker_test_settings.txt" - fi else if [ -z "$compose_file" ]; then compose_file="docker-compose.prod.yml" fi fi +app_service="${APP_SERVICE:-app}" +selected_install_conf="$install_conf" +for map_entry in "${install_conf_map_entries[@]}"; do + svc_name="${map_entry%%,*}" + conf_name="${map_entry#*,}" + if [ -z "$svc_name" ] || [ -z "$conf_name" ] || [ "$svc_name" = "$map_entry" ]; then + echo "Invalid --install_conf_map value '$map_entry'. Expected format: service,path" + exit 1 + fi + if [ "$svc_name" != "app" ]; then + echo "Unknown service '$svc_name' in --install_conf_map. Valid service: app" + exit 1 + fi + selected_install_conf="$conf_name" +done + +if [ "$mode" = "test" ] && [ -z "$selected_install_conf" ]; then + selected_install_conf="conf/docker_test_settings.txt" +fi +install_conf="$selected_install_conf" + if [ "$mode" = "production" ] && [ -z "$install_conf" ]; then - echo "Production deployments require --install_conf pointing to your settings file." + echo "Production deployments require --install_conf or --install_conf_map app,." exit 1 fi @@ -274,7 +301,6 @@ fi set_engine -app_service="${APP_SERVICE:-app}" app_repo_path="${APP_REPO_PATH:-/srv/iskylims}" app_install_path="${APP_INSTALL_PATH:-/opt/iskylims}" app_port="${APP_PORT:-8001}" From a21f3df34a4624b6cd6fe858743d830f06a0538c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 3 Mar 2026 17:06:43 +0100 Subject: [PATCH 370/446] restructure readme with common minimum requirements! --- README.md | 181 ++++++++++++++++++++++++++++++++++-------------------- 1 file changed, 116 insertions(+), 65 deletions(-) diff --git a/README.md b/README.md index b5b6a3e74..a8730046d 100644 --- a/README.md +++ b/README.md @@ -15,6 +15,7 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [iSkyLIMS](#iskylims) - [Get the code (required)](#get-the-code-required) - [Choose your path](#choose-your-path) + - [Minimum requirements](#minimum-requirements) - [Docker deployment](#docker-deployment) - [Local test stack](#local-test-stack) - [Production container](#production-container) @@ -27,7 +28,6 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Refresh code and settings](#refresh-code-and-settings) - [Bare-metal deployment (Ubuntu/CentOS)](#bare-metal-deployment-ubuntucentos) - [Install](#install) - - [Prerequisites](#prerequisites) - [Clone the repository](#clone-the-repository) - [Prepare the database](#prepare-the-database) - [Configure install\_settings.txt](#configure-install_settingstxt) @@ -37,9 +37,11 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Refresh code and settings](#refresh-code-and-settings-1) - [Run upgrade steps requiring root](#run-upgrade-steps-requiring-root) - [Run upgrade steps without root](#run-upgrade-steps-without-root) - - [What to do if something fails](#what-to-do-if-something-fails) - - [Bare-metal](#bare-metal) - - [Docker](#docker) + - [Common operations (Docker + bare-metal)](#common-operations-docker--bare-metal) + - [Database creation, users and grants](#database-creation-users-and-grants) + - [Backups](#backups) + - [Restore / rollback](#restore--rollback) + - [What to do if something fails](#what-to-do-if-something-fails) - [Final configuration steps](#final-configuration-steps) - [SAMBA configurarion](#samba-configurarion) - [Email verification](#email-verification) @@ -66,12 +68,21 @@ cd iskylims - **Docker (production container)**: deploy only the application container, pointing to your existing DB/Samba. - **Bare-metal**: install or upgrade directly on Ubuntu/CentOS hosts with `install.sh`. -## Docker deployment +## Minimum requirements -Prerequisites for Docker-based installs: +- **sudo privileges** for dependency installation +- MySQL > 8.0 or MariaDB > 10.4 +- Apache 2.4 +- git > 2.34 +- Python > 3.11 +- Local email sender configured +- Access to the Samba share where run folders live +- `lsb_release` package: + - RedHat/CentOS: `yum install redhat-lsb-core` + - Ubuntu: `apt install lsb-core lsb-release` +- For containers: Docker Engine + Docker Compose v2, or Podman + `podman-compose` -- Docker Engine + Docker Compose v2 -- git (to clone the repository) +## Docker deployment ### Local test stack @@ -201,17 +212,7 @@ The upgrade path rebuilds/restarts the container and runs `install.sh` inside th #### Back up first -- Full backup of the `iskylims` database. -- Full backup of the logs folder and the documents folder. - -```bash -tar -czf iskylims_logs.tgz -C /var/log/apps/iskylims . - -docker run --rm \ - -v iskylims_documents:/from \ - -v "$PWD":/to \ - alpine tar -czf /to/iskylims_documents.tgz -C /from . -``` +Run the backup steps in [Backups](#backups) first. For 3.0.0 -> 3.1.0, export the LibraryPool mapping first, then run the upgrade with pre/post scripts: @@ -247,21 +248,12 @@ bash container_install.sh --install_conf my_prod_settings.txt --action upgrade \ --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log ``` +If something fails check the section [What to do if something fails](#what-to-do-if-something-fails). + ## Bare-metal deployment (Ubuntu/CentOS) ### Install -#### Prerequisites - -- **sudo privileges** for dependency installation -- MySQL > 8.0 or MariaDB > 10.4 -- Apache 2.4 -- git > 2.34 -- Python > 3.11 -- Local email sender configured -- Access to the Samba share where run folders live -- `lsb_release` package (`yum install redhat-lsb-core` on RedHat/CentOS, `apt install lsb-core lsb-release` on Ubuntu) - #### Clone the repository ```bash @@ -272,9 +264,7 @@ cd iskylims #### Prepare the database -1. Create a database named `iskylims`. -2. Create a user with read/write permissions on that database. -3. Note the database host, port, user, and password for the settings file. +Create the database and application user following [Database creation, users and grants](#database-creation-users-and-grants), then note DB host/port/user/password for `install_settings.txt`. #### Configure install_settings.txt @@ -321,8 +311,8 @@ Follow these steps to move from version 3.0.0 to the 3.1.x series. #### Back up first -- Full backup of the `iskylims` database. -- Full backup of the installation folder (for example `/opt/iskylims`). +Run the backup steps in [Backups](#backups) first. +- Additionally, back up the full installation folder (for example `/opt/iskylims`) for bare-metal rollback. - If you use library pools, export them before upgrading: ```bash @@ -365,56 +355,117 @@ bash install.sh --upgrade app --git_revision main \ Upgrades regenerate migrations and apply them with `--fake-initial` so existing tables remain intact, matching the Docker workflow. -## What to do if something fails +## Common operations (Docker + bare-metal) + +### Database creation, users and grants + +Run as MySQL root: + +```sql +CREATE DATABASE IF NOT EXISTS iskylims CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci; + +CREATE USER IF NOT EXISTS 'iskylims'@'%' IDENTIFIED BY 'djangopass'; +CREATE USER IF NOT EXISTS 'iskylims'@'localhost' IDENTIFIED BY 'djangopass'; -When we upgrade using the installation script we are performing several changes in the database. If something fails we need to restore the app situation before anything happened and start all over. +GRANT ALL PRIVILEGES ON iskylims.* TO 'iskylims'@'%'; +GRANT ALL PRIVILEGES ON iskylims.* TO 'iskylims'@'localhost'; -### Bare-metal +FLUSH PRIVILEGES; +``` + +Verification: + +```sql +SHOW GRANTS FOR 'iskylims'@'%'; +``` + +### Backups -We need to copy back the full `/opt/iskylims` folder back to `/opt/iskylims` (or your installation path preference), and restore the database doing something like this: +Database dump: ```bash -sudo rm -rf /opt/iskylims -sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ -sudo /scripts/hardening.sh -mysql -u iskylims -p -h dmysqlps.isciiides.es -# drop database iskylims; -# create database iskylims; -mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_202310160737.sql +mysqldump -h -P -u iskylims -p iskylims > iskylims_$(date +%Y%m%d_%H%M%S).sql +``` + +Logs archive: + +```bash +tar -czf iskylims_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/apps/iskylims . ``` -### Docker +Documents volume archive: -1. Stop the container: +```bash +docker run --rm -v iskylims_documents:/from -v "$PWD":/to alpine \ + tar -czf /to/iskylims_documents_$(date +%Y%m%d_%H%M%S).tgz -C /from . +``` - ```bash - docker compose -f docker-compose.prod.yml down - ``` +With Podman, use the same command replacing `docker` with `podman`. -2. Restore the database from your backup. +Suggested order before upgrades: -3. If you suspect the image or build cache is corrupted, remove the app image and rebuild: +1. DB dump +2. Documents volume archive +3. Logs archive - ```bash - docker image ls | grep iskylims - docker rmi - ``` +### Restore / rollback -4. If volumes are compromised, restore them from the tar backups: +Restore DB: ```bash -mkdir -p /var/log/apps/iskylims -tar -xzf iskylims_logs.tgz -C /var/log/apps/iskylims +mysql -h -P -u iskylims -p iskylims < iskylims_YYYYMMDD_HHMMSS.sql +``` + +Restore documents volume: +```bash docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ - tar -xzf /from/iskylims_documents.tgz -C /to + sh -lc "cd /to && tar -xzf /from/iskylims_documents_YYYYMMDD_HHMMSS.tgz" ``` -5. Start the container again: +With Podman, use the same command replacing `docker` with `podman`. - ```bash - bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade - ``` +Restore logs: + +```bash +mkdir -p /var/log/apps/iskylims +tar -xzf iskylims_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/apps/iskylims +``` + +Bare-metal full rollback example: + +```bash +sudo rm -rf /opt/iskylims +sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ +sudo /scripts/hardening.sh +mysql -u iskylims -p -h iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_YYYYMMDDHHMM.sql +``` + +### What to do if something fails + +When install/upgrade fails, restore the previous state and retry with logs enabled. + +Quick diagnostics: + +```bash +# bare-metal +cd /opt/iskylims +python manage.py check + +# docker +docker compose -f docker-compose.prod.yml ps +docker compose -f docker-compose.prod.yml logs --tail 200 app +# podman +podman-compose -f docker-compose.prod.yml ps +podman-compose -f docker-compose.prod.yml logs --tail 200 app +``` + +If you suspect a corrupted image/build cache in Docker: + +```bash +docker compose -f docker-compose.prod.yml build --no-cache app +docker compose -f docker-compose.prod.yml up -d --force-recreate app +``` ## Final configuration steps From 5326086b2b1125582654b63e170e9d8820db7060 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 4 Mar 2026 16:12:32 +0100 Subject: [PATCH 371/446] modify readme --- README.md | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index a8730046d..21e5a7a47 100644 --- a/README.md +++ b/README.md @@ -47,6 +47,7 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Email verification](#email-verification) - [Developer notes](#developer-notes) - [Django migrations workflow](#django-migrations-workflow) + - [Persistent host paths](#persistent-host-paths) - [Configure Apache server](#configure-apache-server) - [Verification of the installation](#verification-of-the-installation) - [iSkyLIMS documentation](#iskylims-documentation) @@ -151,11 +152,7 @@ export APP_UID=1212 export APP_GID=1212 ``` -Ensure the static directory on the host is writable by that UID/GID: - -```bash -sudo chown -R ${APP_UID}:${APP_GID} /opt/iskylims/static-host -``` +Host directory and ownership preparation is described in [Persist logs/documents on the host](#persist-logsdocuments-on-the-host). #### Persist logs/documents on the host @@ -166,11 +163,12 @@ The production compose file mounts logs on the host and keeps documents in a nam If you override the compose file, ensure these mounts exist to keep logs and documents persistent. -Create the host log directory and set ownership to match the container UID/GID: +Create host directories and set ownership to match the container UID/GID: ```bash sudo mkdir -p /var/log/apps/iskylims -sudo chown -R ${APP_UID}:${APP_GID} /var/log/apps/iskylims +sudo mkdir -p /opt/iskylims/static-host +sudo chown -R ${APP_UID:-1212}:${APP_GID:-1212} /var/log/apps/iskylims /opt/iskylims/static-host ``` #### Apache reverse proxy (host) + Gunicorn @@ -497,6 +495,10 @@ Baseline + upgrade flow for new releases: 3. Generate new migrations on `develop` for schema changes and commit them. 4. Upgrades run `migrate --fake-initial` once to align existing tables, then `migrate` to apply the new migration files. +### Persistent host paths + +See [Persist logs/documents on the host](#persist-logsdocuments-on-the-host) in the production deployment section. + ### Configure Apache server Copy the apache configuration file according to your distribution inside the apache configuration directory and rename it to iskylims.conf From b9f2a8f070d7844f0d44dff658e4dc1633b740c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 4 Mar 2026 16:12:38 +0100 Subject: [PATCH 372/446] fix tmp config generation context, now that we have several projects --- container_install.sh | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/container_install.sh b/container_install.sh index 30fafd647..80dce20e8 100644 --- a/container_install.sh +++ b/container_install.sh @@ -279,9 +279,15 @@ if [ ! -f "$install_conf" ]; then fi repo_root="$(pwd)" +build_context_dir="$repo_root" +if [ ! -d "$build_context_dir" ]; then + echo "Build context directory '$build_context_dir' not found" + exit 1 +fi + temp_install_conf="" -if [[ "$install_conf" = /* ]] && [[ "$install_conf" != "$repo_root/"* ]]; then - temp_install_conf="$repo_root/.tmp_docker_install_conf_$$.txt" +if [[ "$install_conf" = /* ]] && [[ "$install_conf" != "$build_context_dir/"* ]]; then + temp_install_conf="$build_context_dir/.tmp_docker_install_conf_app_$$.txt" echo "Copying $install_conf into temporary file $temp_install_conf for Docker build/runtime." cp "$install_conf" "$temp_install_conf" install_conf="$temp_install_conf" @@ -293,8 +299,8 @@ if [[ "$install_conf" = /* ]] && [[ "$install_conf" != "$repo_root/"* ]]; then trap cleanup_temp_conf EXIT fi -if [[ "$install_conf" = "$repo_root/"* ]]; then - install_conf_container="${install_conf#$repo_root/}" +if [[ "$install_conf" = "$build_context_dir/"* ]]; then + install_conf_container="${install_conf#$build_context_dir/}" else install_conf_container="$install_conf" fi From 799d457bf9698bbfce27815883ad5d12fe94bd22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 2 Mar 2026 13:43:21 +0100 Subject: [PATCH 373/446] minor modification in readme --- README.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/README.md b/README.md index 21e5a7a47..ab4fa3bab 100644 --- a/README.md +++ b/README.md @@ -241,13 +241,11 @@ export APP_GID=1212 Run upgrade command: ```bash -bash container_install.sh --install_conf my_prod_settings.txt --action upgrade \ +bash container_install.sh --engine podman --install_conf my_prod_settings.txt --action upgrade \ --script_before convert_rawtop_counter_to_int \ --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log ``` -If something fails check the section [What to do if something fails](#what-to-do-if-something-fails). - ## Bare-metal deployment (Ubuntu/CentOS) ### Install From ee2e30c555ae5f22b6657198fe0e738a1890c22e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 4 Mar 2026 16:18:17 +0100 Subject: [PATCH 374/446] reduce workers and threads for gunicorn --- scripts/container_start.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/container_start.sh b/scripts/container_start.sh index 1cfd70357..a9833d070 100644 --- a/scripts/container_start.sh +++ b/scripts/container_start.sh @@ -43,6 +43,6 @@ fi exec gunicorn iskylims.wsgi:application \ --bind 0.0.0.0:8001 \ - --workers 3 \ - --threads 2 \ + --workers 1 \ + --threads 1 \ --timeout 120 From 4e39ade22c4340a987e94c574b7bf4b8bbd2870f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 4 Mar 2026 16:18:33 +0100 Subject: [PATCH 375/446] update requirement versions for security risks --- conf/requirements.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/conf/requirements.txt b/conf/requirements.txt index 912de323a..b4c5e06f0 100644 --- a/conf/requirements.txt +++ b/conf/requirements.txt @@ -1,9 +1,9 @@ -wheel==0.44.0 +wheel==0.46.2 asn1crypto==1.5.1 bcrypt==4.2.0 biopython==1.84 -cryptography==43.0.1 -Django==4.2.25 +cryptography==44.0.3 +Django==4.2.28 django-crispy-forms==2.3 crispy-bootstrap5==0.7 django-crontab==0.7.1 @@ -25,4 +25,4 @@ xlrd==2.0.1 pandas==2.2.2 numpy==1.26.4 openpyxl==3.1.5 -setuptools==75.2.0 +setuptools==78.1.1 From c0ac18323aed82e14cc917c0e04008436b63db0d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 4 Mar 2026 16:54:23 +0100 Subject: [PATCH 376/446] update python lint action --- .github/workflows/python_lint.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/python_lint.yml b/.github/workflows/python_lint.yml index 128c97c9f..ba39bb598 100644 --- a/.github/workflows/python_lint.yml +++ b/.github/workflows/python_lint.yml @@ -15,7 +15,7 @@ jobs: - name: Setup Python uses: actions/setup-python@v5 with: - python-version: 3.9.x + python-version: '3.11' architecture: x64 - name: Checkout PyTorch uses: actions/checkout@master From f79de7250df5f54d3437021494e7cb5160290d85 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 5 Mar 2026 11:04:03 +0100 Subject: [PATCH 377/446] fixes in container install and install scripts --- container_install.sh | 9 ++------- install.sh | 10 +++------- 2 files changed, 5 insertions(+), 14 deletions(-) diff --git a/container_install.sh b/container_install.sh index 80dce20e8..418c35089 100644 --- a/container_install.sh +++ b/container_install.sh @@ -6,10 +6,9 @@ usage() { cat << EOF This script installs and upgrades the iskylims app. -Usage : $0 [--demo_data] [--install_type] [--git_revision] [--compose_file] [--install_conf] [--action] [--script] [--script_before] [--script_after] [--engine] [--test] +Usage : $0 [--demo_data] [--git_revision] [--compose_file] [--install_conf] [--action] [--script] [--script_before] [--script_after] [--engine] [--test] Optional input data: --demo_data | Provide already downloaded demo data from Zenodo - --install_type | Specify the installation type for iSkyLIMS (default: full) --git_revision | Specify the Git revision to install (default: main) --compose_file | Compose file to use (overrides default) --install_conf | Settings file consumed during container image build (mandatory for production) @@ -39,9 +38,6 @@ Examples: Provide already downloaded data from Zenodo (compressed) for test environment bash $0 --demo_data /path/to/iskylims_demo_data.tar.gz - Speficy a custom installation using the Git revision "develop": - bash $0 --install_type app --git_revision develop - EOF } @@ -57,7 +53,6 @@ do case "$arg" in # OPTIONAL --demo_data) set -- "$@" -d ;; - --install_type) set -- "$@" -i ;; --git_revision) set -- "$@" -g ;; --compose_file) set -- "$@" -c ;; --install_conf) set -- "$@" -s ;; @@ -133,7 +128,7 @@ compose_exec() { } # PARSE VARIABLE ARGUMENTS WITH getopts -options=":d:i:g:c:s:j:a:m:b:f:e:vhntp" +options=":d:g:c:s:j:a:m:b:f:e:vhntp" while getopts $options opt; do case $opt in d) diff --git a/install.sh b/install.sh index f9ce62db2..0ec472257 100644 --- a/install.sh +++ b/install.sh @@ -458,11 +458,7 @@ install_system_packages() { fi if command -v lsb_release >/dev/null 2>&1; then - if command -v lsb_release >/dev/null 2>&1; then - linux_distribution=$(lsb_release -i | cut -f 2-) - else - linux_distribution=$(awk -F= '/^ID=/{gsub(/"/,""); print $2}' /etc/os-release) - fi + linux_distribution=$(lsb_release -i | cut -f 2-) else linux_distribution=$(awk -F= '/^ID=/{gsub(/"/,""); print $2}' /etc/os-release) fi @@ -560,7 +556,7 @@ setup_virtualenv() { echo "There already is a virtualenv for iskylims in $INSTALL_PATH." read -p "Do you want to remove current virtualenv and reinstall? (Y/N) " -n 1 -r echo - if [[ ! $REPLY =~ ^[Yy]$ ]] ; then + if [[ $REPLY =~ ^[Yy]$ ]] ; then rm -rf $INSTALL_PATH/virtualenv bash -c "$PYTHON_BIN_PATH -m venv virtualenv" else @@ -873,7 +869,7 @@ while getopts $options opt; do install_type=$OPTARG upgrade_type=$OPTARG else - echo "Upgrade is not set to one valid option. Use: --upgrade full/app/dep" + echo "Install is not set to one valid option. Use: --install full/app/dep" exit 1 fi ;; From 29892bf0bf6611efe14b85ccedbdbd499834ef90 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 4 Mar 2026 17:36:44 +0100 Subject: [PATCH 378/446] added new test for new machine --- conf/first_install_tables.json | 8 ++ test/test_data.json | 182 ++++++++++++++++----------------- 2 files changed, 99 insertions(+), 91 deletions(-) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index c6d6c2213..61ec162ea 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -1915,6 +1915,14 @@ "run_test_folder": "NovaSeq_Test" } }, +{ + "model": "wetlab.runconfigurationtest", + "pk": 4, + "fields": { + "run_test_name": "MiSeqi100_Test", + "run_test_folder": "MiSeqi100_Test" + } +}, { "model": "wetlab.configsetting", "pk": 1, diff --git a/test/test_data.json b/test/test_data.json index 700109f1b..85e42e0b1 100644 --- a/test/test_data.json +++ b/test/test_data.json @@ -11184,7 +11184,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0056-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0575", "prefix_protocol": "illumina nextera lib prep", "pools": [] @@ -11215,7 +11215,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0067-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0586", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11248,7 +11248,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0066-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0585", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11281,7 +11281,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0065-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0584", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11314,7 +11314,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0064-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0583", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11347,7 +11347,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0063-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0582", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11380,7 +11380,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0062-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0581", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11413,7 +11413,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0061-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0580", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11446,7 +11446,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0060-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0579", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11479,7 +11479,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0059-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0578", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11512,7 +11512,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0058-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0577", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11545,7 +11545,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0057-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0576", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11578,7 +11578,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0068-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0587", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11611,7 +11611,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0055-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0574", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11644,7 +11644,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0054-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0573", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11677,7 +11677,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0053-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0572", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11710,7 +11710,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0052-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0554", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11743,7 +11743,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0051-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0553", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11776,7 +11776,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0050-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0552", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11809,7 +11809,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0049-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0551", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11842,7 +11842,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0048-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0550", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11875,7 +11875,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0047-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0548", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11908,7 +11908,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0046-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0547", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -11941,7 +11941,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0079-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0599", "prefix_protocol": "illumina nextera lib prep", "pools": [] @@ -11972,7 +11972,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0089-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Entb0091", "prefix_protocol": "illumina nextera lib prep", "pools": [] @@ -12003,7 +12003,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0088-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Ent0085", "prefix_protocol": "illumina nextera lib prep", "pools": [] @@ -12034,7 +12034,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0087-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Sm0004", "prefix_protocol": "illumina nextera lib prep", "pools": [] @@ -12065,7 +12065,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0086-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Sm0008", "prefix_protocol": "illumina nextera lib prep", "pools": [] @@ -12096,7 +12096,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0085-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Sm0007", "prefix_protocol": "illumina nextera lib prep", "pools": [] @@ -12127,7 +12127,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0084-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Sm0006", "prefix_protocol": "illumina nextera lib prep", "pools": [] @@ -12158,7 +12158,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0083-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Sm0005", "prefix_protocol": "illumina nextera lib prep", "pools": [] @@ -12189,7 +12189,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0082-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Sm0003", "prefix_protocol": "illumina nextera lib prep", "pools": [] @@ -12220,7 +12220,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0081-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0601", "prefix_protocol": "illumina nextera lib prep", "pools": [] @@ -12251,7 +12251,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0080-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0600", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12284,7 +12284,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0045-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0546", "prefix_protocol": "illumina nextera lib prep", "pools": [] @@ -12315,7 +12315,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0078-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0598", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12348,7 +12348,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0077-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0597", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12381,7 +12381,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0076-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0595", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12414,7 +12414,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0075-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0594", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12447,7 +12447,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0074-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0593", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12480,7 +12480,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0073-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0592", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12513,7 +12513,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0072-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0591", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12546,7 +12546,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0071-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0590", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12579,7 +12579,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0070-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0589", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12612,7 +12612,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0069-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0588", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12645,7 +12645,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0012-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0189", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12678,7 +12678,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0022-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0523", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12711,7 +12711,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0021-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Entb0090", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12744,7 +12744,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0020-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Entb0089", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12777,7 +12777,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0019-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Entb0088", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12810,7 +12810,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0018-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Entb0011", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12843,7 +12843,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0017-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0196", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12876,7 +12876,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0016-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0195", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12909,7 +12909,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0015-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0194", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12942,7 +12942,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0014-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0193", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -12975,7 +12975,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0013-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0192", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13008,7 +13008,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0023-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0524", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13041,7 +13041,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0011-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0188", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13074,7 +13074,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0010-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0187", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13107,7 +13107,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0009-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0186", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13140,7 +13140,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0008-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0185", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13173,7 +13173,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0007-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0184", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13206,7 +13206,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0006-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0178", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13239,7 +13239,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0005-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0177", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13272,7 +13272,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0004-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0176", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13305,7 +13305,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0003-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0175", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13338,7 +13338,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0002-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23Eco0173", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13371,7 +13371,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0034-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0535", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13404,7 +13404,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0044-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0545", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13437,7 +13437,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0043-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0544", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13470,7 +13470,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0042-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0543", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13503,7 +13503,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0041-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0542", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13536,7 +13536,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0040-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0541", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13569,7 +13569,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0039-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0540", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13602,7 +13602,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0038-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0539", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13635,7 +13635,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0037-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0538", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13668,7 +13668,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0036-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0537", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13701,7 +13701,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0035-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0536", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13734,7 +13734,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0001-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "22K0483", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13767,7 +13767,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0033-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0534", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13800,7 +13800,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0032-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0533", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13833,7 +13833,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0031-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0532", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13866,7 +13866,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0030-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0531", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13899,7 +13899,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0029-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0530", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13932,7 +13932,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0028-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0529", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13965,7 +13965,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0027-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0528", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -13998,7 +13998,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0026-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0527", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -14031,7 +14031,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0025-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0526", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -14064,7 +14064,7 @@ "manifest": null, "reused_number": 0, "unique_id": "AAA-0024-1", - "user_in_samplesheet": "test_user1", + "user_in_samplesheet": "testuser1", "samplename_in_samplesheet": "23K0525", "prefix_protocol": "illumina nextera lib prep", "pools": [ @@ -16307,7 +16307,7 @@ "resolution_in_progress_date": null, "resolution_delivery_date": null, "resolution_notes": "", - "resolution_full_number": "SRVSGAFI003_20230725_WGMLST01_test_user1_S", + "resolution_full_number": "SRVSGAFI003_20230725_WGMLST01_testuser1_S", "resolution_pdf_file": "", "resolution_pipelines": [], "available_services": [ @@ -16322,7 +16322,7 @@ "password": "pbkdf2_sha256$260000$WoFbBL6zQ3F4nCr3oAFzFd$kT3I+1KotzgT1zT8on4zXZte5vS07KnQr6RmDw2N+UU=", "last_login": null, "is_superuser": false, - "username": "test_user1", + "username": "testuser1", "first_name": "", "last_name": "", "email": "", From 227ce0a8389e446f3bce2b66c950efa390650058 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 5 Mar 2026 11:39:27 +0100 Subject: [PATCH 379/446] remove no login user for tests --- Dockerfile | 3 ++- docker-compose.prod.yml | 1 + docker-compose.test.yml | 1 + 3 files changed, 4 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 45cfedae2..774787cbc 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,6 +5,7 @@ RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone # Runtime user (override with build args if needed) ARG APP_UID=1212 ARG APP_GID=1212 +ARG APP_SHELL=/sbin/nologin # Updates @@ -63,7 +64,7 @@ WORKDIR /opt/iskylims # Create non-root user and set ownership RUN groupadd -g ${APP_GID} iskylims && \ - useradd -m -u ${APP_UID} -g ${APP_GID} -s /sbin/nologin iskylims && \ + useradd -m -u ${APP_UID} -g ${APP_GID} -s ${APP_SHELL} iskylims && \ chown -R ${APP_UID}:${APP_GID} /opt/iskylims /srv/iskylims && \ git config --system --add safe.directory /srv/iskylims diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index f1aa6bd31..6cff515f6 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -12,6 +12,7 @@ services: INSTALL_CONF: ${INSTALL_CONF:-conf/docker_production_settings.txt} APP_UID: ${APP_UID:-1212} APP_GID: ${APP_GID:-1212} + APP_SHELL: ${APP_SHELL:-/sbin/nologin} ports: - "8001:8001" environment: diff --git a/docker-compose.test.yml b/docker-compose.test.yml index f9d5e38f5..bf49e7c66 100644 --- a/docker-compose.test.yml +++ b/docker-compose.test.yml @@ -44,6 +44,7 @@ services: INSTALL_TYPE: ${INSTALL_TYPE:-dep} GIT_REVISION: ${GIT_REVISION:-main} INSTALL_CONF: ${INSTALL_CONF:-conf/docker_test_settings.txt} + APP_SHELL: ${APP_SHELL:-/bin/bash} container_name: iskylims_app ports: - "8001:8001" From bc8118830430f7f8e331256631bb92391c5ef127 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 5 Mar 2026 12:50:00 +0100 Subject: [PATCH 380/446] fixes in tests after new machine inclusion --- conf/first_install_tables.json | 2 +- test/test_data.json | 726 ++++++++++++++++----------------- 2 files changed, 364 insertions(+), 364 deletions(-) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index 61ec162ea..a6ea7fe3c 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -1919,7 +1919,7 @@ "model": "wetlab.runconfigurationtest", "pk": 4, "fields": { - "run_test_name": "MiSeqi100_Test", + "run_test_name": "Miseqi100_Test", "run_test_folder": "MiSeqi100_Test" } }, diff --git a/test/test_data.json b/test/test_data.json index 85e42e0b1..6934c2f51 100644 --- a/test/test_data.json +++ b/test/test_data.json @@ -204,7 +204,7 @@ "model": "core.userlotcommercialkits", "pk": 1, "fields": { - "user": 1, + "user": 2, "based_commercial": 1, "uses_number": 89, "chip_lot": "23123123123", @@ -218,7 +218,7 @@ "model": "core.userlotcommercialkits", "pk": 2, "fields": { - "user": 1, + "user": 2, "based_commercial": 2, "uses_number": 0, "chip_lot": "1341425345", @@ -293,7 +293,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "22K0483", @@ -317,7 +317,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0173", @@ -341,7 +341,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0175", @@ -365,7 +365,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0176", @@ -389,7 +389,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0177", @@ -413,7 +413,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0178", @@ -437,7 +437,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0184", @@ -461,7 +461,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0185", @@ -485,7 +485,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0186", @@ -509,7 +509,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0187", @@ -533,7 +533,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0188", @@ -557,7 +557,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0189", @@ -581,7 +581,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0192", @@ -605,7 +605,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0193", @@ -629,7 +629,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0194", @@ -653,7 +653,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0195", @@ -677,7 +677,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Eco0196", @@ -701,7 +701,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Entb0011", @@ -725,7 +725,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Entb0088", @@ -749,7 +749,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Entb0089", @@ -773,7 +773,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Entb0090", @@ -797,7 +797,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0523", @@ -821,7 +821,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0524", @@ -845,7 +845,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0525", @@ -869,7 +869,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0526", @@ -893,7 +893,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0527", @@ -917,7 +917,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0528", @@ -941,7 +941,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0529", @@ -965,7 +965,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0530", @@ -989,7 +989,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0531", @@ -1013,7 +1013,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0532", @@ -1037,7 +1037,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0533", @@ -1061,7 +1061,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0534", @@ -1085,7 +1085,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0535", @@ -1109,7 +1109,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0536", @@ -1133,7 +1133,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0537", @@ -1157,7 +1157,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0538", @@ -1181,7 +1181,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0539", @@ -1205,7 +1205,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0540", @@ -1229,7 +1229,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0541", @@ -1253,7 +1253,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0542", @@ -1277,7 +1277,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0543", @@ -1301,7 +1301,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0544", @@ -1325,7 +1325,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0545", @@ -1349,7 +1349,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0546", @@ -1373,7 +1373,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0547", @@ -1397,7 +1397,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0548", @@ -1421,7 +1421,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0550", @@ -1445,7 +1445,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0551", @@ -1469,7 +1469,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0552", @@ -1493,7 +1493,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0553", @@ -1517,7 +1517,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0554", @@ -1541,7 +1541,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0572", @@ -1565,7 +1565,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0573", @@ -1589,7 +1589,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0574", @@ -1613,7 +1613,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0575", @@ -1637,7 +1637,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0576", @@ -1661,7 +1661,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0577", @@ -1685,7 +1685,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0578", @@ -1709,7 +1709,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0579", @@ -1733,7 +1733,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0580", @@ -1757,7 +1757,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0581", @@ -1781,7 +1781,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0582", @@ -1805,7 +1805,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0583", @@ -1829,7 +1829,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0584", @@ -1853,7 +1853,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0585", @@ -1877,7 +1877,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0586", @@ -1901,7 +1901,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0587", @@ -1925,7 +1925,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0588", @@ -1949,7 +1949,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0589", @@ -1973,7 +1973,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0590", @@ -1997,7 +1997,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0591", @@ -2021,7 +2021,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0592", @@ -2045,7 +2045,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0593", @@ -2069,7 +2069,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0594", @@ -2093,7 +2093,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0595", @@ -2117,7 +2117,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0597", @@ -2141,7 +2141,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0598", @@ -2165,7 +2165,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0599", @@ -2189,7 +2189,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0600", @@ -2213,7 +2213,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23K0601", @@ -2237,7 +2237,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Sm0003", @@ -2261,7 +2261,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Sm0005", @@ -2285,7 +2285,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Sm0006", @@ -2309,7 +2309,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Sm0007", @@ -2333,7 +2333,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Sm0008", @@ -2357,7 +2357,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Sm0004", @@ -2381,7 +2381,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Ent0085", @@ -2405,7 +2405,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 3, "sample_project": 1, "sample_name": "23Entb0091", @@ -2429,7 +2429,7 @@ "patient_core": null, "lab_request": 1, "sample_type": 1, - "sample_user": 1, + "sample_user": 2, "species": 1, "sample_project": 1, "sample_name": "ARBMET12", @@ -5222,8 +5222,8 @@ "sample": 147, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0575_E1", "extraction_type": "Manual", @@ -5241,8 +5241,8 @@ "sample": 158, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0586_E1", "extraction_type": "Manual", @@ -5260,8 +5260,8 @@ "sample": 157, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0585_E1", "extraction_type": "Manual", @@ -5279,8 +5279,8 @@ "sample": 156, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0584_E1", "extraction_type": "Manual", @@ -5298,8 +5298,8 @@ "sample": 155, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0583_E1", "extraction_type": "Manual", @@ -5317,8 +5317,8 @@ "sample": 154, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0582_E1", "extraction_type": "Manual", @@ -5336,8 +5336,8 @@ "sample": 153, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0581_E1", "extraction_type": "Manual", @@ -5355,8 +5355,8 @@ "sample": 152, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0580_E1", "extraction_type": "Manual", @@ -5374,8 +5374,8 @@ "sample": 151, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0579_E1", "extraction_type": "Manual", @@ -5393,8 +5393,8 @@ "sample": 150, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0578_E1", "extraction_type": "Manual", @@ -5412,8 +5412,8 @@ "sample": 149, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0577_E1", "extraction_type": "Manual", @@ -5431,8 +5431,8 @@ "sample": 148, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0576_E1", "extraction_type": "Manual", @@ -5450,8 +5450,8 @@ "sample": 159, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0587_E1", "extraction_type": "Manual", @@ -5469,8 +5469,8 @@ "sample": 146, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0574_E1", "extraction_type": "Manual", @@ -5488,8 +5488,8 @@ "sample": 145, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0573_E1", "extraction_type": "Manual", @@ -5507,8 +5507,8 @@ "sample": 144, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0572_E1", "extraction_type": "Manual", @@ -5526,8 +5526,8 @@ "sample": 143, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0554_E1", "extraction_type": "Manual", @@ -5545,8 +5545,8 @@ "sample": 142, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0553_E1", "extraction_type": "Manual", @@ -5564,8 +5564,8 @@ "sample": 141, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0552_E1", "extraction_type": "Manual", @@ -5583,8 +5583,8 @@ "sample": 140, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0551_E1", "extraction_type": "Manual", @@ -5602,8 +5602,8 @@ "sample": 139, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0550_E1", "extraction_type": "Manual", @@ -5621,8 +5621,8 @@ "sample": 138, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0548_E1", "extraction_type": "Manual", @@ -5640,8 +5640,8 @@ "sample": 137, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0547_E1", "extraction_type": "Manual", @@ -5659,8 +5659,8 @@ "sample": 170, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0599_E1", "extraction_type": "Manual", @@ -5678,8 +5678,8 @@ "sample": 180, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Entb0091_E1", "extraction_type": "Manual", @@ -5697,8 +5697,8 @@ "sample": 179, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Ent0085_E1", "extraction_type": "Manual", @@ -5716,8 +5716,8 @@ "sample": 178, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Sm0004_E1", "extraction_type": "Manual", @@ -5735,8 +5735,8 @@ "sample": 177, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Sm0008_E1", "extraction_type": "Manual", @@ -5754,8 +5754,8 @@ "sample": 176, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Sm0007_E1", "extraction_type": "Manual", @@ -5773,8 +5773,8 @@ "sample": 175, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Sm0006_E1", "extraction_type": "Manual", @@ -5792,8 +5792,8 @@ "sample": 174, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Sm0005_E1", "extraction_type": "Manual", @@ -5811,8 +5811,8 @@ "sample": 173, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Sm0003_E1", "extraction_type": "Manual", @@ -5830,8 +5830,8 @@ "sample": 172, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0601_E1", "extraction_type": "Manual", @@ -5849,8 +5849,8 @@ "sample": 171, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0600_E1", "extraction_type": "Manual", @@ -5868,8 +5868,8 @@ "sample": 136, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0546_E1", "extraction_type": "Manual", @@ -5887,8 +5887,8 @@ "sample": 169, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0598_E1", "extraction_type": "Manual", @@ -5906,8 +5906,8 @@ "sample": 168, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0597_E1", "extraction_type": "Manual", @@ -5925,8 +5925,8 @@ "sample": 167, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0595_E1", "extraction_type": "Manual", @@ -5944,8 +5944,8 @@ "sample": 166, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0594_E1", "extraction_type": "Manual", @@ -5963,8 +5963,8 @@ "sample": 165, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0593_E1", "extraction_type": "Manual", @@ -5982,8 +5982,8 @@ "sample": 164, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0592_E1", "extraction_type": "Manual", @@ -6001,8 +6001,8 @@ "sample": 163, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0591_E1", "extraction_type": "Manual", @@ -6020,8 +6020,8 @@ "sample": 162, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0590_E1", "extraction_type": "Manual", @@ -6039,8 +6039,8 @@ "sample": 161, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0589_E1", "extraction_type": "Manual", @@ -6058,8 +6058,8 @@ "sample": 160, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0588_E1", "extraction_type": "Manual", @@ -6077,8 +6077,8 @@ "sample": 103, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0189_E1", "extraction_type": "Manual", @@ -6096,8 +6096,8 @@ "sample": 113, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0523_E1", "extraction_type": "Manual", @@ -6115,8 +6115,8 @@ "sample": 112, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Entb0090_E1", "extraction_type": "Manual", @@ -6134,8 +6134,8 @@ "sample": 111, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Entb0089_E1", "extraction_type": "Manual", @@ -6153,8 +6153,8 @@ "sample": 110, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Entb0088_E1", "extraction_type": "Manual", @@ -6172,8 +6172,8 @@ "sample": 109, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Entb0011_E1", "extraction_type": "Manual", @@ -6191,8 +6191,8 @@ "sample": 108, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0196_E1", "extraction_type": "Manual", @@ -6210,8 +6210,8 @@ "sample": 107, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0195_E1", "extraction_type": "Manual", @@ -6229,8 +6229,8 @@ "sample": 106, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0194_E1", "extraction_type": "Manual", @@ -6248,8 +6248,8 @@ "sample": 105, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0193_E1", "extraction_type": "Manual", @@ -6267,8 +6267,8 @@ "sample": 104, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0192_E1", "extraction_type": "Manual", @@ -6286,8 +6286,8 @@ "sample": 114, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0524_E1", "extraction_type": "Manual", @@ -6305,8 +6305,8 @@ "sample": 102, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0188_E1", "extraction_type": "Manual", @@ -6324,8 +6324,8 @@ "sample": 101, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0187_E1", "extraction_type": "Manual", @@ -6343,8 +6343,8 @@ "sample": 100, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0186_E1", "extraction_type": "Manual", @@ -6362,8 +6362,8 @@ "sample": 99, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0185_E1", "extraction_type": "Manual", @@ -6381,8 +6381,8 @@ "sample": 98, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0184_E1", "extraction_type": "Manual", @@ -6400,8 +6400,8 @@ "sample": 97, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0178_E1", "extraction_type": "Manual", @@ -6419,8 +6419,8 @@ "sample": 96, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0177_E1", "extraction_type": "Manual", @@ -6438,8 +6438,8 @@ "sample": 95, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0176_E1", "extraction_type": "Manual", @@ -6457,8 +6457,8 @@ "sample": 94, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0175_E1", "extraction_type": "Manual", @@ -6476,8 +6476,8 @@ "sample": 93, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23Eco0173_E1", "extraction_type": "Manual", @@ -6495,8 +6495,8 @@ "sample": 125, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0535_E1", "extraction_type": "Manual", @@ -6514,8 +6514,8 @@ "sample": 135, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0545_E1", "extraction_type": "Manual", @@ -6533,8 +6533,8 @@ "sample": 134, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0544_E1", "extraction_type": "Manual", @@ -6552,8 +6552,8 @@ "sample": 133, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0543_E1", "extraction_type": "Manual", @@ -6571,8 +6571,8 @@ "sample": 132, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0542_E1", "extraction_type": "Manual", @@ -6590,8 +6590,8 @@ "sample": 131, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0541_E1", "extraction_type": "Manual", @@ -6609,8 +6609,8 @@ "sample": 130, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0540_E1", "extraction_type": "Manual", @@ -6628,8 +6628,8 @@ "sample": 129, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0539_E1", "extraction_type": "Manual", @@ -6647,8 +6647,8 @@ "sample": 128, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0538_E1", "extraction_type": "Manual", @@ -6666,8 +6666,8 @@ "sample": 127, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0537_E1", "extraction_type": "Manual", @@ -6685,8 +6685,8 @@ "sample": 126, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0536_E1", "extraction_type": "Manual", @@ -6704,8 +6704,8 @@ "sample": 92, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_22K0483_E1", "extraction_type": "Manual", @@ -6723,8 +6723,8 @@ "sample": 124, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0534_E1", "extraction_type": "Manual", @@ -6742,8 +6742,8 @@ "sample": 123, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0533_E1", "extraction_type": "Manual", @@ -6761,8 +6761,8 @@ "sample": 122, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0532_E1", "extraction_type": "Manual", @@ -6780,8 +6780,8 @@ "sample": 121, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0531_E1", "extraction_type": "Manual", @@ -6799,8 +6799,8 @@ "sample": 120, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0530_E1", "extraction_type": "Manual", @@ -6818,8 +6818,8 @@ "sample": 119, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0529_E1", "extraction_type": "Manual", @@ -6837,8 +6837,8 @@ "sample": 118, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0528_E1", "extraction_type": "Manual", @@ -6856,8 +6856,8 @@ "sample": 117, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0527_E1", "extraction_type": "Manual", @@ -6875,8 +6875,8 @@ "sample": 116, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0526_E1", "extraction_type": "Manual", @@ -6894,8 +6894,8 @@ "sample": 115, "molecule_type": 1, "state": 5, - "molecule_user": 1, - "user_lot_kit_id": 1, + "molecule_user": 2, + "user_lot_kit_id": 2, "sample_continues_on": 9, "molecule_code_id": "admin_23K0525_E1", "extraction_type": "Manual", @@ -9350,7 +9350,7 @@ "model": "wetlab.projects", "pk": 11, "fields": { - "user_id": 1, + "user_id": 2, "library_kit_id": null, "base_space_library": null, "project_name": "NextSeq_GEN_436_20230615", @@ -11129,7 +11129,7 @@ "model": "wetlab.libusersamplesheet", "pk": 1, "fields": { - "register_user": 1, + "register_user": 2, "collection_index_kit_id": null, "sequencing_configuration": 10, "sample_sheet": "SampleSheet_20230725-170642.csv", @@ -11148,7 +11148,7 @@ "model": "wetlab.librarypool", "pk": 1, "fields": { - "register_user": 1, + "register_user": 2, "pool_state": 3, "platform": 10, "pool_name": "20230725_pool", @@ -11163,7 +11163,7 @@ "model": "wetlab.libprepare", "pk": 1, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 1, "sample_id": 147, "protocol_id": 2, @@ -11194,7 +11194,7 @@ "model": "wetlab.libprepare", "pk": 2, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 2, "sample_id": 158, "protocol_id": 2, @@ -11227,7 +11227,7 @@ "model": "wetlab.libprepare", "pk": 3, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 3, "sample_id": 157, "protocol_id": 2, @@ -11260,7 +11260,7 @@ "model": "wetlab.libprepare", "pk": 4, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 4, "sample_id": 156, "protocol_id": 2, @@ -11293,7 +11293,7 @@ "model": "wetlab.libprepare", "pk": 5, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 5, "sample_id": 155, "protocol_id": 2, @@ -11326,7 +11326,7 @@ "model": "wetlab.libprepare", "pk": 6, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 6, "sample_id": 154, "protocol_id": 2, @@ -11359,7 +11359,7 @@ "model": "wetlab.libprepare", "pk": 7, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 7, "sample_id": 153, "protocol_id": 2, @@ -11392,7 +11392,7 @@ "model": "wetlab.libprepare", "pk": 8, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 8, "sample_id": 152, "protocol_id": 2, @@ -11425,7 +11425,7 @@ "model": "wetlab.libprepare", "pk": 9, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 9, "sample_id": 151, "protocol_id": 2, @@ -11458,7 +11458,7 @@ "model": "wetlab.libprepare", "pk": 10, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 10, "sample_id": 150, "protocol_id": 2, @@ -11491,7 +11491,7 @@ "model": "wetlab.libprepare", "pk": 11, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 11, "sample_id": 149, "protocol_id": 2, @@ -11524,7 +11524,7 @@ "model": "wetlab.libprepare", "pk": 12, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 12, "sample_id": 148, "protocol_id": 2, @@ -11557,7 +11557,7 @@ "model": "wetlab.libprepare", "pk": 13, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 13, "sample_id": 159, "protocol_id": 2, @@ -11590,7 +11590,7 @@ "model": "wetlab.libprepare", "pk": 14, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 14, "sample_id": 146, "protocol_id": 2, @@ -11623,7 +11623,7 @@ "model": "wetlab.libprepare", "pk": 15, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 15, "sample_id": 145, "protocol_id": 2, @@ -11656,7 +11656,7 @@ "model": "wetlab.libprepare", "pk": 16, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 16, "sample_id": 144, "protocol_id": 2, @@ -11689,7 +11689,7 @@ "model": "wetlab.libprepare", "pk": 17, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 17, "sample_id": 143, "protocol_id": 2, @@ -11722,7 +11722,7 @@ "model": "wetlab.libprepare", "pk": 18, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 18, "sample_id": 142, "protocol_id": 2, @@ -11755,7 +11755,7 @@ "model": "wetlab.libprepare", "pk": 19, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 19, "sample_id": 141, "protocol_id": 2, @@ -11788,7 +11788,7 @@ "model": "wetlab.libprepare", "pk": 20, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 20, "sample_id": 140, "protocol_id": 2, @@ -11821,7 +11821,7 @@ "model": "wetlab.libprepare", "pk": 21, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 21, "sample_id": 139, "protocol_id": 2, @@ -11854,7 +11854,7 @@ "model": "wetlab.libprepare", "pk": 22, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 22, "sample_id": 138, "protocol_id": 2, @@ -11887,7 +11887,7 @@ "model": "wetlab.libprepare", "pk": 23, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 23, "sample_id": 137, "protocol_id": 2, @@ -11920,7 +11920,7 @@ "model": "wetlab.libprepare", "pk": 24, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 24, "sample_id": 170, "protocol_id": 2, @@ -11951,7 +11951,7 @@ "model": "wetlab.libprepare", "pk": 25, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 25, "sample_id": 180, "protocol_id": 2, @@ -11982,7 +11982,7 @@ "model": "wetlab.libprepare", "pk": 26, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 26, "sample_id": 179, "protocol_id": 2, @@ -12013,7 +12013,7 @@ "model": "wetlab.libprepare", "pk": 27, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 27, "sample_id": 178, "protocol_id": 2, @@ -12044,7 +12044,7 @@ "model": "wetlab.libprepare", "pk": 28, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 28, "sample_id": 177, "protocol_id": 2, @@ -12075,7 +12075,7 @@ "model": "wetlab.libprepare", "pk": 29, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 29, "sample_id": 176, "protocol_id": 2, @@ -12106,7 +12106,7 @@ "model": "wetlab.libprepare", "pk": 30, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 30, "sample_id": 175, "protocol_id": 2, @@ -12137,7 +12137,7 @@ "model": "wetlab.libprepare", "pk": 31, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 31, "sample_id": 174, "protocol_id": 2, @@ -12168,7 +12168,7 @@ "model": "wetlab.libprepare", "pk": 32, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 32, "sample_id": 173, "protocol_id": 2, @@ -12199,7 +12199,7 @@ "model": "wetlab.libprepare", "pk": 33, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 33, "sample_id": 172, "protocol_id": 2, @@ -12230,7 +12230,7 @@ "model": "wetlab.libprepare", "pk": 34, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 34, "sample_id": 171, "protocol_id": 2, @@ -12263,7 +12263,7 @@ "model": "wetlab.libprepare", "pk": 35, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 35, "sample_id": 136, "protocol_id": 2, @@ -12294,7 +12294,7 @@ "model": "wetlab.libprepare", "pk": 36, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 36, "sample_id": 169, "protocol_id": 2, @@ -12327,7 +12327,7 @@ "model": "wetlab.libprepare", "pk": 37, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 37, "sample_id": 168, "protocol_id": 2, @@ -12360,7 +12360,7 @@ "model": "wetlab.libprepare", "pk": 38, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 38, "sample_id": 167, "protocol_id": 2, @@ -12393,7 +12393,7 @@ "model": "wetlab.libprepare", "pk": 39, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 39, "sample_id": 166, "protocol_id": 2, @@ -12426,7 +12426,7 @@ "model": "wetlab.libprepare", "pk": 40, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 40, "sample_id": 165, "protocol_id": 2, @@ -12459,7 +12459,7 @@ "model": "wetlab.libprepare", "pk": 41, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 41, "sample_id": 164, "protocol_id": 2, @@ -12492,7 +12492,7 @@ "model": "wetlab.libprepare", "pk": 42, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 42, "sample_id": 163, "protocol_id": 2, @@ -12525,7 +12525,7 @@ "model": "wetlab.libprepare", "pk": 43, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 43, "sample_id": 162, "protocol_id": 2, @@ -12558,7 +12558,7 @@ "model": "wetlab.libprepare", "pk": 44, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 44, "sample_id": 161, "protocol_id": 2, @@ -12591,7 +12591,7 @@ "model": "wetlab.libprepare", "pk": 45, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 45, "sample_id": 160, "protocol_id": 2, @@ -12624,7 +12624,7 @@ "model": "wetlab.libprepare", "pk": 46, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 46, "sample_id": 103, "protocol_id": 2, @@ -12657,7 +12657,7 @@ "model": "wetlab.libprepare", "pk": 47, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 47, "sample_id": 113, "protocol_id": 2, @@ -12690,7 +12690,7 @@ "model": "wetlab.libprepare", "pk": 48, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 48, "sample_id": 112, "protocol_id": 2, @@ -12723,7 +12723,7 @@ "model": "wetlab.libprepare", "pk": 49, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 49, "sample_id": 111, "protocol_id": 2, @@ -12756,7 +12756,7 @@ "model": "wetlab.libprepare", "pk": 50, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 50, "sample_id": 110, "protocol_id": 2, @@ -12789,7 +12789,7 @@ "model": "wetlab.libprepare", "pk": 51, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 51, "sample_id": 109, "protocol_id": 2, @@ -12822,7 +12822,7 @@ "model": "wetlab.libprepare", "pk": 52, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 52, "sample_id": 108, "protocol_id": 2, @@ -12855,7 +12855,7 @@ "model": "wetlab.libprepare", "pk": 53, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 53, "sample_id": 107, "protocol_id": 2, @@ -12888,7 +12888,7 @@ "model": "wetlab.libprepare", "pk": 54, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 54, "sample_id": 106, "protocol_id": 2, @@ -12921,7 +12921,7 @@ "model": "wetlab.libprepare", "pk": 55, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 55, "sample_id": 105, "protocol_id": 2, @@ -12954,7 +12954,7 @@ "model": "wetlab.libprepare", "pk": 56, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 56, "sample_id": 104, "protocol_id": 2, @@ -12987,7 +12987,7 @@ "model": "wetlab.libprepare", "pk": 57, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 57, "sample_id": 114, "protocol_id": 2, @@ -13020,7 +13020,7 @@ "model": "wetlab.libprepare", "pk": 58, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 58, "sample_id": 102, "protocol_id": 2, @@ -13053,7 +13053,7 @@ "model": "wetlab.libprepare", "pk": 59, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 59, "sample_id": 101, "protocol_id": 2, @@ -13086,7 +13086,7 @@ "model": "wetlab.libprepare", "pk": 60, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 60, "sample_id": 100, "protocol_id": 2, @@ -13119,7 +13119,7 @@ "model": "wetlab.libprepare", "pk": 61, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 61, "sample_id": 99, "protocol_id": 2, @@ -13152,7 +13152,7 @@ "model": "wetlab.libprepare", "pk": 62, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 62, "sample_id": 98, "protocol_id": 2, @@ -13185,7 +13185,7 @@ "model": "wetlab.libprepare", "pk": 63, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 63, "sample_id": 97, "protocol_id": 2, @@ -13218,7 +13218,7 @@ "model": "wetlab.libprepare", "pk": 64, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 64, "sample_id": 96, "protocol_id": 2, @@ -13251,7 +13251,7 @@ "model": "wetlab.libprepare", "pk": 65, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 65, "sample_id": 95, "protocol_id": 2, @@ -13284,7 +13284,7 @@ "model": "wetlab.libprepare", "pk": 66, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 66, "sample_id": 94, "protocol_id": 2, @@ -13317,7 +13317,7 @@ "model": "wetlab.libprepare", "pk": 67, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 67, "sample_id": 93, "protocol_id": 2, @@ -13350,7 +13350,7 @@ "model": "wetlab.libprepare", "pk": 68, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 68, "sample_id": 125, "protocol_id": 2, @@ -13383,7 +13383,7 @@ "model": "wetlab.libprepare", "pk": 69, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 69, "sample_id": 135, "protocol_id": 2, @@ -13416,7 +13416,7 @@ "model": "wetlab.libprepare", "pk": 70, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 70, "sample_id": 134, "protocol_id": 2, @@ -13449,7 +13449,7 @@ "model": "wetlab.libprepare", "pk": 71, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 71, "sample_id": 133, "protocol_id": 2, @@ -13482,7 +13482,7 @@ "model": "wetlab.libprepare", "pk": 72, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 72, "sample_id": 132, "protocol_id": 2, @@ -13515,7 +13515,7 @@ "model": "wetlab.libprepare", "pk": 73, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 73, "sample_id": 131, "protocol_id": 2, @@ -13548,7 +13548,7 @@ "model": "wetlab.libprepare", "pk": 74, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 74, "sample_id": 130, "protocol_id": 2, @@ -13581,7 +13581,7 @@ "model": "wetlab.libprepare", "pk": 75, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 75, "sample_id": 129, "protocol_id": 2, @@ -13614,7 +13614,7 @@ "model": "wetlab.libprepare", "pk": 76, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 76, "sample_id": 128, "protocol_id": 2, @@ -13647,7 +13647,7 @@ "model": "wetlab.libprepare", "pk": 77, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 77, "sample_id": 127, "protocol_id": 2, @@ -13680,7 +13680,7 @@ "model": "wetlab.libprepare", "pk": 78, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 78, "sample_id": 126, "protocol_id": 2, @@ -13713,7 +13713,7 @@ "model": "wetlab.libprepare", "pk": 79, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 79, "sample_id": 92, "protocol_id": 2, @@ -13746,7 +13746,7 @@ "model": "wetlab.libprepare", "pk": 80, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 80, "sample_id": 124, "protocol_id": 2, @@ -13779,7 +13779,7 @@ "model": "wetlab.libprepare", "pk": 81, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 81, "sample_id": 123, "protocol_id": 2, @@ -13812,7 +13812,7 @@ "model": "wetlab.libprepare", "pk": 82, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 82, "sample_id": 122, "protocol_id": 2, @@ -13845,7 +13845,7 @@ "model": "wetlab.libprepare", "pk": 83, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 83, "sample_id": 121, "protocol_id": 2, @@ -13878,7 +13878,7 @@ "model": "wetlab.libprepare", "pk": 84, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 84, "sample_id": 120, "protocol_id": 2, @@ -13911,7 +13911,7 @@ "model": "wetlab.libprepare", "pk": 85, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 85, "sample_id": 119, "protocol_id": 2, @@ -13944,7 +13944,7 @@ "model": "wetlab.libprepare", "pk": 86, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 86, "sample_id": 118, "protocol_id": 2, @@ -13977,7 +13977,7 @@ "model": "wetlab.libprepare", "pk": 87, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 87, "sample_id": 117, "protocol_id": 2, @@ -14010,7 +14010,7 @@ "model": "wetlab.libprepare", "pk": 88, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 88, "sample_id": 116, "protocol_id": 2, @@ -14043,7 +14043,7 @@ "model": "wetlab.libprepare", "pk": 89, "fields": { - "register_user": 1, + "register_user": 2, "molecule_id": 89, "sample_id": 115, "protocol_id": 2, @@ -16298,7 +16298,7 @@ "pk": 1, "fields": { "resolution_service_id": 3, - "resolution_assigned_user": 1, + "resolution_assigned_user": 2, "resolution_state": 6, "resolution_number": "SRVSGAFI003.1", "resolution_estimated_date": "2023-07-29", From 5653bd76a5e6ddd005caf88de5d4f39c003a2468 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 5 Mar 2026 13:35:58 +0100 Subject: [PATCH 381/446] really fix run folder name for new machine --- conf/first_install_tables.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index a6ea7fe3c..8deb22556 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -1919,8 +1919,8 @@ "model": "wetlab.runconfigurationtest", "pk": 4, "fields": { - "run_test_name": "Miseqi100_Test", - "run_test_folder": "MiSeqi100_Test" + "run_test_name": "MiSeqi100_Test", + "run_test_folder": "Miseqi100_Test" } }, { From e2450746f9dd2b0eda598456b0df8b8345509e23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 5 Mar 2026 13:36:36 +0100 Subject: [PATCH 382/446] fix not logging messages due to logger context --- wetlab/utils/common.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/wetlab/utils/common.py b/wetlab/utils/common.py index f7c75e544..eab207aed 100644 --- a/wetlab/utils/common.py +++ b/wetlab/utils/common.py @@ -158,7 +158,8 @@ def open_samba_connection(): Return: conn object for the samba connection """ - logger = logging.getLogger(__name__) + # Use root logger to ensure messages always follow the configured handlers. + logger = logging.getLogger() logger.debug("Starting function open_samba_connection") samba_data = get_samba_connection_data() @@ -412,7 +413,8 @@ def logging_errors(string_text, showing_traceback, print_on_screen): Variables: subject # text to include in the subject email """ - logger = logging.getLogger(__name__) + # Use root logger to ensure messages always follow the configured handlers. + logger = logging.getLogger() logger.error("----------------- ERROR ------------------") logger.error(string_text) if wetlab.models.ConfigSetting.objects.filter( @@ -469,7 +471,8 @@ def logging_warnings(string_text, print_on_screen): logger # contains the logger object string_text # information text to include in the log """ - logger = logging.getLogger(__name__) + # Use root logger to ensure messages always follow the configured handlers. + logger = logging.getLogger() logger.warning("----------------- WARNING ------------------") logger.warning(string_text) logger.warning("----------------- END WARNING --------------") @@ -494,6 +497,7 @@ def open_log(config_file): Return: logger object """ - fileConfig(config_file) - logger = logging.getLogger(__name__) + # Keep existing named loggers active; otherwise fileConfig may disable them. + fileConfig(config_file, disable_existing_loggers=False) + logger = logging.getLogger() return logger From 969ab66a862960519b44b36c07ec87ec44e3b564 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 5 Mar 2026 13:48:56 +0100 Subject: [PATCH 383/446] added new machine to first install tables --- conf/first_install_tables.json | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/conf/first_install_tables.json b/conf/first_install_tables.json index 8deb22556..94a7c0f2e 100644 --- a/conf/first_install_tables.json +++ b/conf/first_install_tables.json @@ -257,6 +257,21 @@ "sequencer_number_lanes": "2" } }, +{ + "model": "core.sequencerinlab", + "pk": 7, + "fields": { + "platform_id": 7, + "sequencer_name": "SH00752", + "sequencer_description": "MiSeqi100", + "sequencer_location": "Genomics Unit", + "sequencer_serial_number": null, + "sequencer_state": "In Use", + "sequencer_operation_start": null, + "sequencer_operation_end": null, + "sequencer_number_lanes": "1/2/4" + } +}, { "model": "core.statesforsample", "pk": 1, @@ -20331,4 +20346,3 @@ } } ] - From 1aba1517592ffe88e81333db0f01058c620fe062 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 5 Mar 2026 13:49:29 +0100 Subject: [PATCH 384/446] disable mail sending on error in test configuration --- test/test_data.json | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/test/test_data.json b/test/test_data.json index 6934c2f51..b87102667 100644 --- a/test/test_data.json +++ b/test/test_data.json @@ -16315,6 +16315,15 @@ ] } }, + { + "model": "wetlab.configsetting", + "pk": 9, + "fields": { + "configuration_name": "SENT_EMAIL_ON_CRONTAB_ERROR", + "configuration_value": "FALSE", + "generated_at": "2021-06-09T22:10:57.394" + } + }, { "model": "auth.user", "pk": 2, @@ -16333,4 +16342,4 @@ "user_permissions": [] } } -] \ No newline at end of file +] From 18475af45f6ec22db96c7b4a711b3431ca2adff2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 9 Mar 2026 14:55:57 +0100 Subject: [PATCH 385/446] added correct permissions when copying demo data to container --- container_install.sh | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/container_install.sh b/container_install.sh index 418c35089..8aad073d0 100644 --- a/container_install.sh +++ b/container_install.sh @@ -485,6 +485,15 @@ if [ "$skip_demo_data" = false ] && service_exists "samba"; then fi engine_exec cp "$demo_data" samba:/mnt engine_exec exec -it samba tar -xf /mnt/iskylims_demo_data.tar.gz -C /mnt + # Ensure extracted demo data can be traversed/read through SMB by non-owner users. + engine_exec exec -it samba sh -lc ' + for root in /mnt/test_ngs_data /mnt/Runs; do + if [ -d "$root" ]; then + find "$root" -type d -exec chmod o+rx {} + + find "$root" -type f -exec chmod o+r {} + + fi + done + ' echo "Deleting compressed test file" engine_exec exec -it samba rm /mnt/iskylims_demo_data.tar.gz From 0f319d429dab2cbf97f7cb955fd0e360e6777802 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 9 Mar 2026 14:56:20 +0100 Subject: [PATCH 386/446] added support to new samplesheet and new demultiplexing stats path --- wetlab/config.py | 6 ++ wetlab/utils/crontab_process.py | 106 ++++++++++++++++++++----- wetlab/utils/crontab_update_run.py | 28 +++++-- wetlab/utils/samplesheet.py | 122 ++++++++++++++++++++++++++--- 4 files changed, 223 insertions(+), 39 deletions(-) diff --git a/wetlab/config.py b/wetlab/config.py index 6f789af5b..cc446b386 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -64,6 +64,8 @@ RUN_LOG_FOLDER = "Logs" STATS_FILE_PATH = "Data/Intensities/BaseCalls/Stats" +STATS_FILE_PATH_ALTERNATIVE = "Data/Intensities/BaseCalls/Reports/legacy/Stats" +STATS_FILE_PATHS = [STATS_FILE_PATH, STATS_FILE_PATH_ALTERNATIVE] CONVERSION_STATS_FILE = "ConversionStats.xml" @@ -74,6 +76,7 @@ ["NextSeq", "xml_file"], ["MiSeq", "xml_file"], ["NovaSeq", "txt_file"], + ["iSeq 100", "xml_file"] ] # ########### VALUE TAG FOR XML FILES ######################### @@ -341,8 +344,11 @@ SECTIONS_IN_V2_SAMPLE_SHEET = [ "Header", "Reads", + "Sequencing_Settings", "BCLConvert_Settings", "BCLConvert_Data", + "Cloud_Settings", + "Cloud_Data", "CustomCustomer_Data", ] diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index 67e5c613d..fae477400 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -2097,6 +2097,75 @@ def parsing_run_metrics_files( ####################### +def _get_existing_stats_folder(conn, run_folder, experiment_name=""): + """ + Description: + Return first available remote stats folder for a run. + Input: + conn # samba connection instance + run_folder # run folder on the remote server + Return: + statistics_folder # absolute remote stats path or None + """ + logger = logging.getLogger(__name__) + shared_folder = get_samba_shared_folder() + base_folder = get_samba_application_shared_folder() + stats_file_paths = getattr( + wetlab.config, "STATS_FILE_PATHS", [wetlab.config.STATS_FILE_PATH] + ) + base_folder = str(base_folder or "").strip().strip("/\\") + run_folder = str(run_folder or "").strip().strip("/\\") + + def _join_remote_path(*parts): + return "/".join([str(part).strip("/\\") for part in parts if str(part).strip("/\\")]) + + run_roots = [] + if run_folder: + if base_folder and run_folder.startswith(base_folder + "/"): + run_roots.append(run_folder) + else: + if base_folder: + run_roots.append(_join_remote_path(base_folder, run_folder)) + run_roots.append(run_folder) + run_roots = list(dict.fromkeys(run_roots)) + logger.debug( + "Resolving stats folder with shared=%s base=%s run_folder=%s candidates=%s", + shared_folder, + base_folder, + run_folder, + run_roots, + ) + + access_denied_paths = [] + + for run_root in run_roots: + for stats_path in stats_file_paths: + statistics_folder = _join_remote_path(run_root, stats_path) + conversion_stats_file = _join_remote_path( + statistics_folder, wetlab.config.CONVERSION_STATS_FILE + ) + try: + conn.getAttributes(shared_folder, conversion_stats_file) + return statistics_folder + except Exception as ex: + error_text = str(ex).lower() + if "c0000022" in error_text or "access denied" in error_text: + access_denied_paths.append(conversion_stats_file) + logger.debug( + "Unable to access stats file at %s (%s)", + conversion_stats_file, + str(ex), + ) + if access_denied_paths: + logger.warning( + "%s : SMB permission denied while checking stats files. " + "Verify read/execute permissions for samba user on: %s", + experiment_name or run_folder, + ", ".join(access_denied_paths), + ) + return None + + def check_demultiplexing_folder_exists(conn, run_folder, experiment_name): """ Description: @@ -2106,7 +2175,7 @@ def check_demultiplexing_folder_exists(conn, run_folder, experiment_name): run_folder # run folder on the remote server experiment_name # Experiment name Constants: - STATS_FILE_PATH + STATS_FILE_PATHS CONVERSION_STATS_FILE Functions: get_samba_application_shared_folder @@ -2119,19 +2188,15 @@ def check_demultiplexing_folder_exists(conn, run_folder, experiment_name): "%s : Starting function check_demultiplexing_folder_exists", experiment_name ) bcl2fastq_finish_date = "" - statistics_folder = os.path.join( - get_samba_application_shared_folder(), - run_folder, - wetlab.config.STATS_FILE_PATH, - ) - - try: - conn.listPath(get_samba_shared_folder(), statistics_folder) - except Exception: + statistics_folder = _get_existing_stats_folder(conn, run_folder, experiment_name) + if not statistics_folder: + stats_file_paths = getattr( + wetlab.config, "STATS_FILE_PATHS", [wetlab.config.STATS_FILE_PATH] + ) string_message = ( experiment_name - + " : Unable to fetch folder demultiplexing at " - + statistics_folder + + " : Unable to fetch folder demultiplexing at any of " + + ", ".join(stats_file_paths) ) wetlab.utils.common.logging_warnings(string_message, True) logger.debug( @@ -2242,7 +2307,7 @@ def get_demultiplexing_files(conn, run_folder, experiment_name): run_folder # run folder on the remote server experiment_name # Experiment name Constants: - STATS_FILE_PATH + STATS_FILE_PATHS CONVERSION_STATS_FILE Functions: get_samba_application_shared_folder @@ -2253,16 +2318,15 @@ def get_demultiplexing_files(conn, run_folder, experiment_name): """ logger = logging.getLogger(__name__) logger.debug("%s : Starting function get_demultiplexing_files", experiment_name) - statistics_folder = os.path.join( - get_samba_application_shared_folder(), run_folder, wetlab.config.STATS_FILE_PATH - ) - try: - conn.listPath(get_samba_shared_folder(), statistics_folder) - except Exception: + statistics_folder = _get_existing_stats_folder(conn, run_folder, experiment_name) + if not statistics_folder: + stats_file_paths = getattr( + wetlab.config, "STATS_FILE_PATHS", [wetlab.config.STATS_FILE_PATH] + ) string_message = ( experiment_name - + " : Unable to fetch folder demultiplexing at " - + statistics_folder + + " : Unable to fetch folder demultiplexing at any of " + + ", ".join(stats_file_paths) ) wetlab.utils.common.logging_errors(string_message, True, False) logger.debug( diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 3d6618e70..6fcc4880b 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -36,6 +36,25 @@ def _as_utc_datetime(value): return None +def _coerce_to_date(value): + """ + Convert supported date/datetime/string inputs to a date object. + """ + if isinstance(value, datetime.datetime): + return value.date() + if isinstance(value, datetime.date): + return value + if isinstance(value, str) and value: + try: + return datetime.datetime.fromisoformat(value).date() + except ValueError: + try: + return datetime.datetime.strptime(value, "%Y-%m-%d %H:%M:%S").date() + except ValueError: + return None + return None + + def get_list_processed_runs(): """ Description: @@ -938,11 +957,10 @@ def manage_run_in_processing_bcl2fastq_state(conn, run_process_objs): .last() .get_configuration_value() ) - try: - time_to_check = ( - run_process_obj.get_run_completion_date_no_format().date() - ) - except Exception: + time_to_check = _coerce_to_date( + run_process_obj.get_run_completion_date_no_format() + ) + if time_to_check is None: string_message = ( experiment_name + " : Aborting the process. No Run completion date was defined." diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index 3a10cdb5d..8822663be 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -57,7 +57,10 @@ def write_samplesheet_to_path(samplesheet: dict, path: str) -> bool: string_to_write = "" for key, value in samplesheet.items(): string_to_write += f"[{key}]\n" - if key in wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET: + if ( + key in wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET.values() + or key.endswith("_Data") + ): delimiter = "\n" string_to_write += ( f"{delimiter.join([','.join(row) for row in value])}{delimiter}" @@ -99,7 +102,10 @@ def file_read_to_dictionary( if not line or re.match("^,+$", line): # Empty/Filler/Artifact lines with no info continue - if section in wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET.values(): + if ( + section in wetlab.config.TABULAR_DATA_SECTIONS_SAMPLE_SHEET.values() + or section.endswith("_Data") + ): # Data is tabular; append as list of lists until next header if not isinstance(samplesheet[section], list): samplesheet[section] = [] @@ -144,7 +150,16 @@ def validate_userid_in_user_iem_file(file_read, user_id_list): wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_DESCRIPTION_FIELD ) return users - users_in_sample_sheet = get_column_from_tabular_data(data, iskylims_user_column) + users_in_sample_sheet = get_user_ids_from_samplesheet(samplesheet, data) + if not users_in_sample_sheet and iskylims_user_column: + # Keep compatibility with old behavior for v1 sheets. + users_in_sample_sheet = get_column_from_tabular_data(data, iskylims_user_column) + + if not users_in_sample_sheet: + users["ERROR"] = ( + wetlab.config.ERROR_SAMPLE_SHEET_DOES_NOT_HAVE_DESCRIPTION_FIELD + ) + return users userid_names = [user for user in users_in_sample_sheet if user in user_id_list] invalid_names = [user for user in users_in_sample_sheet if user not in user_id_list] @@ -242,6 +257,9 @@ def get_column_from_tabular_data( :param tabular_data: Description :type tabular_data: dict[list[list[str]]] """ + if not tabular_data: + return [] + headers = tabular_data[0] tabular_data = [row for row in tabular_data[1:]] try: @@ -270,6 +288,74 @@ def get_tabular_data(samplesheet: dict) -> list[list]: return [row.split(",") for row in data] +def get_tabular_data_for_section(samplesheet: dict, section_name: str) -> list[list]: + """ + Get tabular data for a specific section in a samplesheet. + + Args: + samplesheet (dict): Parsed samplesheet data + section_name (str): Section name to fetch + + Returns: + list[list]: Tabular data, in a nested list (Matrix N*M) + """ + data = samplesheet.get(section_name, []) + if not isinstance(data, list): + return [] + return [row.split(",") for row in data] + + +def get_user_id_from_project_name(project_name: str) -> str: + """ + Extract iSkyLIMS username from the project name suffix. + Example: MiSeq_i100_GEN_002_20260219_testuser1 -> testuser1 + """ + if not project_name or "_" not in project_name: + return "" + return project_name.rsplit("_", 1)[-1].strip() + + +def get_user_ids_from_project_name(samplesheet: dict) -> list[str]: + """ + Extract iSkyLIMS usernames from Cloud_Data.ProjectName values. + """ + cloud_data = get_tabular_data_for_section(samplesheet, "Cloud_Data") + project_names = get_column_from_tabular_data(cloud_data, "ProjectName") + return [get_user_id_from_project_name(project_name) for project_name in project_names] + + +def get_user_ids_from_samplesheet(samplesheet: dict, data: list[list] | None = None) -> list: + """ + Extract user IDs from a samplesheet. + Priority: + - v1: Description/custom_description column in [Data] + - v2: custom_description/Description in [BCLConvert_Data] + - v2 fallback: suffix from Cloud_Data.ProjectName + """ + if data is None: + data = get_tabular_data(samplesheet) + + if not data: + return [] + + version = samplesheet_version(samplesheet) + iskylims_user_column = wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get(version) + + user_ids = [] + if iskylims_user_column: + user_ids = get_column_from_tabular_data(data, iskylims_user_column) + + # Some v2 sheets still use Description rather than custom_description. + if not user_ids and version == "2": + user_ids = get_column_from_tabular_data(data, "Description") + + # v2 fallback: parse user id from Cloud_Data.ProjectName suffix. + if not user_ids and version == "2": + user_ids = get_user_ids_from_project_name(samplesheet) + + return user_ids + + def get_projects_in_sample_sheet(samplesheet) -> list: """ Description : @@ -390,12 +476,13 @@ def get_sample_with_user_owner(sample_sheet_path): # Retrieve tabular data with the iskylims user in the header data = get_tabular_data(samplesheet) sample_names = get_column_from_tabular_data(data, "Sample_Name") - iskylims_user_column_id = wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get( - samplesheet_version(samplesheet) - ) - user_ids = get_column_from_tabular_data(data, iskylims_user_column_id) + if not sample_names: + # v2 sheets frequently provide Sample_ID only. + sample_names = get_column_from_tabular_data(data, "Sample_ID") + user_ids = get_user_ids_from_samplesheet(samplesheet, data) - sample_user = {sample_names[i]: user_ids[i] for i in range(len(sample_names))} + min_len = min(len(sample_names), len(user_ids)) + sample_user = {sample_names[i]: user_ids[i] for i in range(min_len)} return sample_user @@ -413,11 +500,20 @@ def get_projects_in_run(in_file: str) -> dict: samplesheet = file_read_to_dictionary(file_read) data = get_tabular_data(samplesheet) sample_projects = get_column_from_tabular_data(data, "Sample_Project") - iskylims_user_column_id = wetlab.config.TABULAR_DATA_ISKYLIMS_USER_COLUMN.get( - samplesheet_version(samplesheet) - ) - user_ids = get_column_from_tabular_data(data, iskylims_user_column_id) - projects = {sample_projects[i]: user_ids[i] for i in range(len(sample_projects))} + user_ids = get_user_ids_from_samplesheet(samplesheet, data) + + # v2 fallback: project names can live in Cloud_Data.ProjectName. + if not sample_projects and samplesheet_version(samplesheet) == "2": + cloud_data = get_tabular_data_for_section(samplesheet, "Cloud_Data") + sample_projects = get_column_from_tabular_data(cloud_data, "ProjectName") + if not user_ids: + user_ids = [ + get_user_id_from_project_name(project_name) + for project_name in sample_projects + ] + + min_len = min(len(sample_projects), len(user_ids)) + projects = {sample_projects[i]: user_ids[i] for i in range(min_len)} if not data: return {"ERROR": wetlab.config.ERROR_SAMPLE_SHEET_HAS_INVALID_HEADING} From 1c1809464e8cafd0fcd3afc912d928f4330ff2f8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 16 Mar 2026 12:36:13 +0100 Subject: [PATCH 387/446] improve safeness of rootless podman containers --- Dockerfile | 4 +++- scripts/container_start.sh | 21 +++++++++++++++++++-- 2 files changed, 22 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 774787cbc..41ba92baa 100644 --- a/Dockerfile +++ b/Dockerfile @@ -44,7 +44,7 @@ RUN mkdir /srv/iskylims WORKDIR /srv/iskylims # Copy the local git repository to docker image directory -COPY . /srv/iskylims +COPY --chown=${APP_UID}:${APP_GID} . /srv/iskylims ENV PATH="/usr/sbin/cron:$PATH" RUN chmod +x /srv/iskylims/scripts/container_start.sh @@ -65,7 +65,9 @@ WORKDIR /opt/iskylims # Create non-root user and set ownership RUN groupadd -g ${APP_GID} iskylims && \ useradd -m -u ${APP_UID} -g ${APP_GID} -s ${APP_SHELL} iskylims && \ + mkdir -p /opt/iskylims/cron /opt/iskylims/tmp && \ chown -R ${APP_UID}:${APP_GID} /opt/iskylims /srv/iskylims && \ + chmod 700 /opt/iskylims/cron /opt/iskylims/tmp && \ git config --system --add safe.directory /srv/iskylims # Expose diff --git a/scripts/container_start.sh b/scripts/container_start.sh index a9833d070..3afdaeac0 100644 --- a/scripts/container_start.sh +++ b/scripts/container_start.sh @@ -15,7 +15,24 @@ done source "${APP_DIR}/virtualenv/bin/activate" mkdir -p "${CRON_DIR}" "${TMP_DIR}" -chmod 700 "${CRON_DIR}" "${TMP_DIR}" + +safe_chmod() { + local mode="$1" + shift + local path + for path in "$@"; do + if [ ! -e "${path}" ]; then + continue + fi + if [ -O "${path}" ]; then + chmod "${mode}" "${path}" + else + echo "Skipping chmod ${mode} on ${path}: not owned by $(id -un)." + fi + done +} + +safe_chmod 700 "${CRON_DIR}" "${TMP_DIR}" if [ "$APP_MODE" = "dev" ]; then exec python "${APP_DIR}/manage.py" runserver 0.0.0.0:8001 @@ -26,7 +43,7 @@ if command -v supercronic >/dev/null 2>&1; then python "${APP_DIR}/manage.py" crontab add >/dev/null 2>&1 || true crontab -l 2>/dev/null | sed '/^\s*#/d; /^\s*$/d' > "${CRON_FILE}" || true if [ -s "${CRON_FILE}" ]; then - chmod 600 "${CRON_FILE}" + safe_chmod 600 "${CRON_FILE}" : > "${CRON_LOG}" supercronic "${CRON_FILE}" > "${CRON_LOG}" 2>&1 & CRON_PID=$! From 1bd4b44f5b16e4ff6ff9428a638eb891ed121e81 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 16 Mar 2026 18:23:11 +0100 Subject: [PATCH 388/446] adapting new tags for new miseq machine run info and run parameters parsing --- wetlab/config.py | 19 ++++ wetlab/models.py | 30 +++++- wetlab/utils/crontab_process.py | 186 ++++++++++++++++++-------------- 3 files changed, 152 insertions(+), 83 deletions(-) diff --git a/wetlab/config.py b/wetlab/config.py index cc446b386..35faeccbe 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -84,9 +84,16 @@ COMPLETION_SUCCESS = ["CompletedAsPlanned", "SuccessfullyCompleted", "RunCompleted"] EXPERIMENT_NAME_TAG = "ExperimentName" APPLICATION_NAME_TAG = "ApplicationName" +APPLICATION_TAG_ALIASES = ["ApplicationName", "Application"] NUMBER_CYCLES_TAG = "NumCycles" RUN_INFO_READ_TAG = "RunInfoRead" NUMBER_TAG = "Number" +PLANNED_READS_TAG = "PlannedReads" +PLANNED_READ_TAG = "Read" +READ_NAME_TAG = "ReadName" +READ_CYCLES_FALLBACK_TAGS = ["NumCycles", "Cycles"] +RUN_INFO_FLOWCELL_LAYOUT_LANE_TAG = "LaneCount" +RUN_DATE_FORMATS = ["%y%m%d", "%Y-%m-%d", "%m/%d/%Y"] ############################################################## RUN_METRIC_GRAPHIC_COMMANDS = [ @@ -124,12 +131,24 @@ "ApplicationVersion", "NumTilesPerSwath", ] +FIELDS_WITHOUT_SETUP_TAG = [ + "NumLanes", + "Application", + "ApplicationVersion", + "NumTilesPerSwath", +] READ_NUMBER_OF_CYCLES = [ "PlannedRead1Cycles", "PlannedIndex1ReadCycles", "PlannedIndex2ReadCycles", "PlannedRead2Cycles", ] +PLANNED_READ_FIELD_MAP = { + "Read1": "PlannedRead1Cycles", + "Index1": "PlannedIndex1ReadCycles", + "Index2": "PlannedIndex2ReadCycles", + "Read2": "PlannedRead2Cycles", +} # NOVASEQ 6000 FIELDS_NOVASEQ_TO_FETCH_TAG = [ "NumLanes", diff --git a/wetlab/models.py b/wetlab/models.py index 3286d9e22..6037ae65f 100644 --- a/wetlab/models.py +++ b/wetlab/models.py @@ -1,4 +1,5 @@ # Generic imports +import ast import os import re @@ -673,10 +674,33 @@ def get_run_parameters_info(self): return run_parameters_data def get_number_of_lanes(self): - match_flowcell = re.match( - r".*LaneCount.*'(\d+)'.*SurfaceCount.*", self.flowcell_layout + if not self.flowcell_layout: + return "" + + if isinstance(self.flowcell_layout, dict): + return self.flowcell_layout.get( + wetlab.config.RUN_INFO_FLOWCELL_LAYOUT_LANE_TAG, "" + ) + + try: + flowcell_layout = ast.literal_eval(self.flowcell_layout) + except (ValueError, SyntaxError): + flowcell_layout = None + + if isinstance(flowcell_layout, dict): + return flowcell_layout.get( + wetlab.config.RUN_INFO_FLOWCELL_LAYOUT_LANE_TAG, "" + ) + + match_flowcell = re.search( + r"'%s':\s*'?(\\d+)'?" + % wetlab.config.RUN_INFO_FLOWCELL_LAYOUT_LANE_TAG, + str(self.flowcell_layout), ) - return match_flowcell.group(1) + if match_flowcell: + return match_flowcell.group(1) + + return "" def get_number_of_reads(self): count = 0 diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index fae477400..a1912c34c 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -870,6 +870,13 @@ def get_sequencer_obj_or_create_if_no_exists(running_parameters, experiment_name ).last() else: + number_of_lanes = running_parameters["running_data"].get("NumLanes", "") + if not number_of_lanes: + flowcell_layout = running_parameters["running_data"].get("FlowcellLayout", {}) + if isinstance(flowcell_layout, dict): + number_of_lanes = flowcell_layout.get( + wetlab.config.RUN_INFO_FLOWCELL_LAYOUT_LANE_TAG, "" + ) string_message = ( experiment_name + " : " @@ -879,7 +886,7 @@ def get_sequencer_obj_or_create_if_no_exists(running_parameters, experiment_name wetlab.utils.common.logging_errors(string_message, True, False) sequencer_obj = create_new_sequencer_lab_not_defined( running_parameters["instrument"], - running_parameters["running_data"]["NumLanes"], + number_of_lanes, experiment_name, ) logger.info( @@ -974,6 +981,21 @@ def parsing_run_info_and_parameter_information( parsing_data = {} image_channel = [] + def get_xml_text_case_insensitive(root_element, tag_names): + if isinstance(tag_names, str): + tag_names = [tag_names] + lowered_tag_names = {tag_name.lower() for tag_name in tag_names} + for element in root_element.iter(): + if element.tag.lower() in lowered_tag_names: + return element.text + return "" + + def get_xml_child_case_insensitive(root_element, tag_name): + for element in root_element: + if element.tag.lower() == tag_name.lower(): + return element + return None + ############################ # parsing RunInfo.xml file # ############################ @@ -1014,45 +1036,32 @@ def parsing_run_info_and_parameter_information( parameter_data_root = parameter_data.getroot() # getting the common values NextSeq and MiSeq for field in wetlab.config.FIELDS_TO_COLLECT_FROM_RUN_INFO_FILE: - try: - running_data[field] = parameter_data_root.find(field).text - except Exception: - # get the tags item for searching when tagas are in different Caps and lower combination - # because of new sintax in NovaSeq - try: - tag_found_in_case_insensitive = False - for element in parameter_data_root.iter(): - if field.lower() == element.tag.lower(): - running_data[field] = parameter_data_root.find(element.tag).text - tag_found_in_case_insensitive = True - break - if not tag_found_in_case_insensitive: - running_data[field] = "" - string_message = ( - experiment_name - + " : Parameter " - + field - + " not found looking for case insensitive in RunParameter.xml" - ) - wetlab.utils.common.logging_warnings(string_message, False) - except Exception: - running_data[field] = "" - string_message = ( - experiment_name - + " : Parameter " - + field - + " unable to fetch in RunParameter.xml" - ) - wetlab.utils.common.logging_warnings(string_message, False) + running_data[field] = get_xml_text_case_insensitive(parameter_data_root, field) + if running_data[field] == "": + string_message = ( + experiment_name + + " : Parameter " + + field + + " not found looking for case insensitive in RunParameter.xml" + ) + wetlab.utils.common.logging_warnings(string_message, False) + + running_data[wetlab.config.APPLICATION_NAME_TAG] = get_xml_text_case_insensitive( + parameter_data_root, wetlab.config.APPLICATION_TAG_ALIASES + ) # get the nuber of lanes in case sequencer lab is not defined - if parameter_data_root.find(wetlab.config.SETUP_TAG): + setup_element = get_xml_child_case_insensitive( + parameter_data_root, wetlab.config.SETUP_TAG + ) + if setup_element is not None: param_in_setup = ["ApplicationVersion", "NumTilesPerSwath"] for i in range(len(param_in_setup)): try: - running_data[param_in_setup[i]] = ( - parameter_data_root.find("Setup").find(param_in_setup[i]).text + setup_child = get_xml_child_case_insensitive( + setup_element, param_in_setup[i] ) + running_data[param_in_setup[i]] = setup_child.text if setup_child else "" except Exception: string_message = ( experiment_name @@ -1064,13 +1073,10 @@ def parsing_run_info_and_parameter_information( continue # collect information for MiSeq and NextSeq for setup_field in wetlab.config.FIELDS_TO_FETCH_FROM_SETUP_TAG: - try: - running_data[setup_field] = ( - parameter_data_root.find(wetlab.config.SETUP_TAG) - .find(setup_field) - .text - ) - except Exception: + setup_child = get_xml_child_case_insensitive(setup_element, setup_field) + if setup_child is not None and setup_child.text is not None: + running_data[setup_field] = setup_child.text + else: running_data[setup_field] = "" string_message = ( experiment_name @@ -1079,58 +1085,78 @@ def parsing_run_info_and_parameter_information( + " unable to fetch in RunParameter.xml" ) wetlab.utils.common.logging_warnings(string_message, False) - - if "MiSeq" in running_data[wetlab.config.APPLICATION_NAME_TAG]: - # initialize paramters in case there are not exists on runParameter file - for i in range(len(wetlab.config.READ_NUMBER_OF_CYCLES)): - running_data[wetlab.config.READ_NUMBER_OF_CYCLES[i]] = "" - # get the length index number for reads and indexes for MiSeq Runs - for run_info_read in parameter_data_root.iter( - wetlab.config.RUN_INFO_READ_TAG - ): - try: - index_number = ( - int(run_info_read.attrib[wetlab.config.NUMBER_TAG]) - 1 - ) - running_data[wetlab.config.READ_NUMBER_OF_CYCLES[index_number]] = ( - run_info_read.attrib[wetlab.config.NUMBER_CYCLES_TAG] - ) - except Exception: - string_message = ( - experiment_name - + " : Parameter RunInfoRead: Read Number not found in RunParameter.xml" - ) - wetlab.utils.common.logging_warnings(string_message, False) - continue else: - # Collect information for NovaSeq - for novaseq_field in wetlab.config.FIELDS_NOVASEQ_TO_FETCH_TAG: + for field_without_setup in wetlab.config.FIELDS_WITHOUT_SETUP_TAG: + running_data[field_without_setup] = get_xml_text_case_insensitive( + parameter_data_root, field_without_setup + ) + if running_data[field_without_setup] == "": + string_message = ( + experiment_name + + " : Parameter in root -- " + + field_without_setup + + " unable to fetch in RunParameter.xml" + ) + wetlab.utils.common.logging_warnings(string_message, False) + + if not running_data.get("NumLanes") and isinstance( + running_data.get("FlowcellLayout"), dict + ): + running_data["NumLanes"] = running_data["FlowcellLayout"].get( + wetlab.config.RUN_INFO_FLOWCELL_LAYOUT_LANE_TAG, "" + ) + + for read_field in wetlab.config.READ_NUMBER_OF_CYCLES: + if read_field not in running_data or running_data[read_field] is None: + running_data[read_field] = "" + + planned_reads_element = get_xml_child_case_insensitive( + parameter_data_root, wetlab.config.PLANNED_READS_TAG + ) + if planned_reads_element is not None: + for planned_read in planned_reads_element.findall(wetlab.config.PLANNED_READ_TAG): + read_name = planned_read.attrib.get(wetlab.config.READ_NAME_TAG) + if read_name not in wetlab.config.PLANNED_READ_FIELD_MAP: + continue + cycles_value = "" + for cycles_tag in wetlab.config.READ_CYCLES_FALLBACK_TAGS: + if cycles_tag in planned_read.attrib: + cycles_value = planned_read.attrib[cycles_tag] + break + running_data[wetlab.config.PLANNED_READ_FIELD_MAP[read_name]] = cycles_value + elif "MiSeq" in running_data.get(wetlab.config.APPLICATION_NAME_TAG, ""): + for run_info_read in parameter_data_root.iter(wetlab.config.RUN_INFO_READ_TAG): try: - running_data[novaseq_field] = parameter_data_root.find( - novaseq_field - ).text + index_number = int(run_info_read.attrib[wetlab.config.NUMBER_TAG]) - 1 + running_data[wetlab.config.READ_NUMBER_OF_CYCLES[index_number]] = ( + run_info_read.attrib[wetlab.config.NUMBER_CYCLES_TAG] + ) except Exception: - running_data[novaseq_field] = "" string_message = ( experiment_name - + " : Parameter in Setup -- " - + novaseq_field - + " unable to fetch in RunParameter.xml" + + " : Parameter RunInfoRead: Read Number not found in RunParameter.xml" ) wetlab.utils.common.logging_warnings(string_message, False) + continue # get date for miSeq and NextSeq with the format yymmdd date = p_run.find("Date").text # Remove timestamp date = date.split("T")[0] - try: - run_date = datetime.datetime.strptime(date, "%y%m%d") - except Exception: - # get date for novaseq sequencer - date = p_run.find("Date").text.split(" ")[0] + run_date = "" + for date_format in wetlab.config.RUN_DATE_FORMATS: try: - run_date = datetime.datetime.strptime(date, "%m/%d/%Y") + run_date = datetime.datetime.strptime(date, date_format) + break except Exception: - run_date = "" + continue + if run_date == "": + date = p_run.find("Date").text.split(" ")[0] + for date_format in wetlab.config.RUN_DATE_FORMATS: + try: + run_date = datetime.datetime.strptime(date, date_format) + break + except Exception: + continue # updating the date fetched from the Date tag for run and project logger.debug("%s : Found date that was recorded the Run %s", experiment_name, date) From dc812af088dd06b91ece6336886436f075a83893 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 17 Mar 2026 09:08:37 +0100 Subject: [PATCH 389/446] add logging for better debugging --- wetlab/utils/crontab_process.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index a1912c34c..2dae132da 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -1158,6 +1158,19 @@ def get_xml_child_case_insensitive(root_element, tag_name): except Exception: continue + logger.info( + "%s : Parsed RunParameters values run_id=%s app=%s lanes=%s reads=%s/%s/%s/%s run_date=%s", + experiment_name, + running_data.get("RunID", ""), + running_data.get(wetlab.config.APPLICATION_NAME_TAG, ""), + running_data.get("NumLanes", ""), + running_data.get("PlannedRead1Cycles", ""), + running_data.get("PlannedIndex1ReadCycles", ""), + running_data.get("PlannedIndex2ReadCycles", ""), + running_data.get("PlannedRead2Cycles", ""), + run_date, + ) + # updating the date fetched from the Date tag for run and project logger.debug("%s : Found date that was recorded the Run %s", experiment_name, date) parsing_data["running_data"] = running_data From 780609913fd60de3e91e4d0a010347225df8b615 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 17 Mar 2026 09:36:20 +0100 Subject: [PATCH 390/446] added git revision current for using current code while testing --- container_install.sh | 5 ++++- install.sh | 6 +++++- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/container_install.sh b/container_install.sh index 8aad073d0..daf90035e 100644 --- a/container_install.sh +++ b/container_install.sh @@ -9,7 +9,7 @@ This script installs and upgrades the iskylims app. Usage : $0 [--demo_data] [--git_revision] [--compose_file] [--install_conf] [--action] [--script] [--script_before] [--script_after] [--engine] [--test] Optional input data: --demo_data | Provide already downloaded demo data from Zenodo - --git_revision | Specify the Git revision to install (default: main) + --git_revision | Specify the Git revision to install (default: main, or 'current' to use copied local sources) --compose_file | Compose file to use (overrides default) --install_conf | Settings file consumed during container image build (mandatory for production) --install_conf_map | Service-specific settings file: service,path (can be repeated) @@ -35,6 +35,9 @@ Examples: Install demo container system with local services bash $0 --test + Install test stack from current local committed sources without checking out a branch in-container + bash $0 --test --git_revision current + Provide already downloaded data from Zenodo (compressed) for test environment bash $0 --demo_data /path/to/iskylims_demo_data.tar.gz diff --git a/install.sh b/install.sh index 0ec472257..1f013fb92 100644 --- a/install.sh +++ b/install.sh @@ -11,7 +11,7 @@ usage : $0 --upgrade --git_revision --conf Optional input data: --install | Install iskylims full/dep/app --upgrade | Upgrade iskylims full/dep/app - --git_revision | Git revision name to run (it can be git branch, git version tag or commit SHA) + --git_revision | Git revision name to run (branch, tag, commit SHA, or 'current' to use copied local sources as-is) --conf | Select custom configuration file. Default: ./install_settings.txt --tables | Load the first inital tables (from conf folder) --skip_tables | Skip loading initial tables (even during install) @@ -276,6 +276,10 @@ load_install_config() { # checkout_git_revision: ensure desired git revision exists and check it out safely. checkout_git_revision() { + if [[ "$git_branch" == "current" ]]; then + printf "${YELLOW}Using copied local working tree without git checkout.${NC}\n" + return 0 + fi if git rev-parse --verify "$git_branch" >/dev/null 2>&1; then if [[ $git_branch != $initial_git_ref ]]; then local local_changes From c3ee4c55884f90055785d1fb4f1fb7a3ce331604 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 17 Mar 2026 11:00:50 +0100 Subject: [PATCH 391/446] revert to using interop cli needed for grapths, improved message if images not generated --- Dockerfile | 9 +++++++ wetlab/templates/wetlab/display_run.html | 10 ++++++-- wetlab/utils/crontab_process.py | 30 ++++++++++++++++++++++++ wetlab/utils/fetch_info.py | 10 +++++++- 4 files changed, 56 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 41ba92baa..26e2c3070 100644 --- a/Dockerfile +++ b/Dockerfile @@ -21,6 +21,7 @@ RUN dnf -y install \ httpd-devel cronie \ rsync tzdata \ pkgconf-pkg-config \ + gnuplot \ && dnf clean all # Install supercronic (rootless-friendly cron runner) @@ -39,6 +40,14 @@ RUN set -eux; \ # Ensure python3 points to the desired version RUN ln -sf /usr/bin/python3.11 /usr/bin/python3 +# Install Illumina InterOp CLI used to generate run metric plots +RUN set -eux; \ + cd /opt; \ + wget -q https://github.com/Illumina/interop/releases/download/v1.1.15/InterOp-1.1.15-Linux-GNU.tar.gz; \ + tar -xf InterOp-1.1.15-Linux-GNU.tar.gz; \ + ln -s InterOp-1.1.15-Linux-GNU interop; \ + rm InterOp-1.1.15-Linux-GNU.tar.gz + # Set git repository RUN mkdir /srv/iskylims WORKDIR /srv/iskylims diff --git a/wetlab/templates/wetlab/display_run.html b/wetlab/templates/wetlab/display_run.html index a70f8d462..a101b06bf 100644 --- a/wetlab/templates/wetlab/display_run.html +++ b/wetlab/templates/wetlab/display_run.html @@ -763,11 +763,17 @@

    {{ key }}

    - {% for key, values in display_one_run.runGraphic %} + {% for key, values, is_present in display_one_run.runGraphic %}

    {{key}}

    - + {% if is_present %} + {{ key }} + {% else %} +
    + Image not present +
    + {% endif %}
    {% endfor %} diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index 2dae132da..934ea09cf 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -1377,6 +1377,13 @@ def create_run_metric_graphics( for graphic_file in graphic_files: old_file_name = os.path.join(run_graphic_dir, graphic_file) split_file_name = graphic_file.split("_") + if len(split_file_name) < 2: + logger.warning( + "%s : Unable to rename unexpected graphic file %s", + experiment_name, + old_file_name, + ) + continue if not split_file_name[1].endswith(wetlab.config.PLOT_EXTENSION): split_file_name[1] = split_file_name[1] + wetlab.config.PLOT_EXTENSION new_file_name = os.path.join(run_graphic_dir, split_file_name[1]) @@ -1388,6 +1395,29 @@ def create_run_metric_graphics( new_file_name, ) + expected_graphics = [ + "ClusterCount-by-lane.png", + "flowcell-Intensity.png", + "Intensity-by-cycle.png", + "q-heat-map.png", + "q-histogram.png", + "sample-qc.png", + ] + for expected_graphic in expected_graphics: + expected_graphic_path = os.path.join(run_graphic_dir, expected_graphic) + if not os.path.exists(expected_graphic_path): + logger.warning( + "%s : Graphic file was not generated: %s", + experiment_name, + expected_graphic_path, + ) + + if len(graphic_files) == 0: + logger.warning("%s : No graphic files were generated", experiment_name) + logger.debug( + "%s : End create_run_metric_graphics without graphics", experiment_name + ) + # saving the graphic location in database graphic_stats_obj = wetlab.models.GraphicsStats.objects.create_graphic_run_metrics( run_process_obj, run_folder diff --git a/wetlab/utils/fetch_info.py b/wetlab/utils/fetch_info.py index f2262fa29..c4ca33fb3 100644 --- a/wetlab/utils/fetch_info.py +++ b/wetlab/utils/fetch_info.py @@ -276,10 +276,18 @@ def get_run_graphics(run_object): ] for index_graph in range(len(graphics)): + graphic_relative_path = os.path.join(folder_graphic, graphics[index_graph]) + graphic_absolute_path = os.path.join( + settings.MEDIA_ROOT, + wetlab.config.RUN_IMAGES_DIRECTORY, + run_graphics_object.get_folder_graphic(), + graphics[index_graph], + ) run_graphics.append( [ graphic_text[index_graph], - os.path.join(folder_graphic, graphics[index_graph]), + graphic_relative_path, + os.path.exists(graphic_absolute_path), ] ) return run_graphics From e44dbc02150912893d453177459538eb0b42fd27 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 17 Mar 2026 11:01:19 +0100 Subject: [PATCH 392/446] added groups to admin user in test --- container_install.sh | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/container_install.sh b/container_install.sh index daf90035e..1a98ae6ad 100644 --- a/container_install.sh +++ b/container_install.sh @@ -476,6 +476,15 @@ fi if [ "$skip_test_data" = false ]; then engine_exec exec -it "$app_container" python3 manage.py loaddata test/test_data.json + engine_exec exec -it "$app_container" python3 manage.py shell -c " +from django.contrib.auth.models import Group, User +admin = User.objects.get(username='admin') +admin.groups.add( + Group.objects.get(name='WetlabManager'), + Group.objects.get(name='ServiceManager'), +) +print('admin groups:', list(admin.groups.values_list('name', flat=True))) +" else echo "Skipping test data fixtures as requested" fi From a3f63d96ce4e70e84fc79bd9746f3fa43cff0199 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 17 Mar 2026 11:19:17 +0100 Subject: [PATCH 393/446] added checks to make sure new code is being installed in container --- container_install.sh | 47 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/container_install.sh b/container_install.sh index 1a98ae6ad..75734af51 100644 --- a/container_install.sh +++ b/container_install.sh @@ -387,6 +387,49 @@ ensure_app_running() { fi } +print_local_source_diagnostics() { + echo "Local source diagnostics:" + echo " working directory: $repo_root" + echo " build context: $build_context_dir" + echo " engine: $engine" + echo " compose file: $compose_file" + echo " git revision mode: $git_revision" + if command -v git >/dev/null 2>&1 && git -C "$repo_root" rev-parse --is-inside-work-tree >/dev/null 2>&1; then + echo " local branch: $(git -C "$repo_root" rev-parse --abbrev-ref HEAD)" + echo " local HEAD: $(git -C "$repo_root" log -1 --oneline)" + echo " local status:" + git -C "$repo_root" status --short || true + else + echo " local git metadata unavailable" + fi +} + +print_container_source_diagnostics() { + local label="$1" + echo "$label" + echo " container: $app_container" + echo " image: $(engine_exec inspect -f '{{.Config.Image}}' "$app_container" 2>/dev/null || true)" + echo " image id: $(engine_exec inspect -f '{{.Image}}' "$app_container" 2>/dev/null || true)" + engine_exec exec "$app_container" sh -lc " + echo ' /srv/iskylims HEAD:' + if [ -d '$app_repo_path/.git' ]; then + cd '$app_repo_path' && git log -1 --oneline + else + echo 'not a git checkout' + fi + echo ' plot code markers in /srv/iskylims:' + grep -n 'matplotlib\|Creating plot graphics from stored run metrics\|plot_by_cycle' '$app_repo_path/wetlab/utils/crontab_process.py' || true + " || true + engine_exec exec "$app_container" sh -lc " + echo ' plot code markers in $app_install_path:' + if [ -f '$app_install_path/wetlab/utils/crontab_process.py' ]; then + grep -n 'matplotlib\|Creating plot graphics from stored run metrics\|plot_by_cycle' '$app_install_path/wetlab/utils/crontab_process.py' || true + else + echo 'not installed yet' + fi + " || true +} + # Remove stale test containers left over from previous runs. # # This function will only be executed in "test" mode when the engine is "podman". @@ -414,6 +457,7 @@ cleanup_stale_test_containers() { cleanup_stale_test_containers +print_local_source_diagnostics echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=dep and GIT_REVISION=$git_revision..." INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" \ compose_exec -f "$compose_file" build --no-cache \ @@ -425,6 +469,7 @@ compose_exec -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." sleep 20 ensure_app_running +print_container_source_diagnostics "Container diagnostics after startup:" app_uid="${APP_UID:-1212}" app_gid="${APP_GID:-1212}" @@ -468,6 +513,8 @@ else engine_exec exec -it "$app_container" bash -c "cd $app_repo_path && bash install.sh --install app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" fi +print_container_source_diagnostics "Container diagnostics after install.sh:" + if ! engine_exec exec -it "$app_container" test -f "$app_install_path/manage.py"; then echo "Error: $app_install_path/manage.py not found after install.sh. Showing logs:" engine_exec logs --tail 200 "$app_container" From 9ad2449e35a78a02e585f7473d0426182ea06614 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 17 Mar 2026 11:44:12 +0100 Subject: [PATCH 394/446] better stale image diagnosis --- container_install.sh | 81 ++++++++++++++++++++++++++++++++------------ 1 file changed, 60 insertions(+), 21 deletions(-) diff --git a/container_install.sh b/container_install.sh index 75734af51..ee2816454 100644 --- a/container_install.sh +++ b/container_install.sh @@ -309,6 +309,11 @@ app_repo_path="${APP_REPO_PATH:-/srv/iskylims}" app_install_path="${APP_INSTALL_PATH:-/opt/iskylims}" app_port="${APP_PORT:-8001}" app_container="" +local_head_hash="" +local_head_short="" +app_image_name="${APP_IMAGE_NAME:-iskylims_app}" +image_id_before_build="" +image_id_after_build="" # Check if a service exists in the compose file # @@ -389,27 +394,69 @@ ensure_app_running() { print_local_source_diagnostics() { echo "Local source diagnostics:" - echo " working directory: $repo_root" - echo " build context: $build_context_dir" - echo " engine: $engine" - echo " compose file: $compose_file" - echo " git revision mode: $git_revision" if command -v git >/dev/null 2>&1 && git -C "$repo_root" rev-parse --is-inside-work-tree >/dev/null 2>&1; then - echo " local branch: $(git -C "$repo_root" rev-parse --abbrev-ref HEAD)" + local_head_hash="$(git -C "$repo_root" rev-parse HEAD)" + local_head_short="$(git -C "$repo_root" rev-parse --short HEAD)" echo " local HEAD: $(git -C "$repo_root" log -1 --oneline)" - echo " local status:" - git -C "$repo_root" status --short || true + echo " local HEAD hash: $local_head_hash" else echo " local git metadata unavailable" fi } +print_existing_artifact_diagnostics() { + echo "Image diagnostics before build:" + if engine_exec image inspect "$app_image_name" >/dev/null 2>&1; then + image_id_before_build="$(engine_exec image inspect -f '{{.Id}}' "$app_image_name" 2>/dev/null || true)" + echo " image before build: $image_id_before_build" + else + image_id_before_build="" + echo " image before build: none" + fi +} + +print_image_after_build() { + echo "Image diagnostics after build:" + if engine_exec image inspect "$app_image_name" >/dev/null 2>&1; then + image_id_after_build="$(engine_exec image inspect -f '{{.Id}}' "$app_image_name" 2>/dev/null || true)" + echo " image after build: $image_id_after_build" + if [ -n "$image_id_before_build" ] && [ "$image_id_before_build" = "$image_id_after_build" ]; then + echo " image id check: unchanged" + elif [ -n "$image_id_before_build" ] && [ "$image_id_before_build" != "$image_id_after_build" ]; then + echo " image id check: changed" + else + echo " image id check: created" + fi + else + echo " image after build: not found" + fi +} + print_container_source_diagnostics() { local label="$1" + local container_repo_head_hash="" + local container_repo_head_short="" echo "$label" - echo " container: $app_container" - echo " image: $(engine_exec inspect -f '{{.Config.Image}}' "$app_container" 2>/dev/null || true)" - echo " image id: $(engine_exec inspect -f '{{.Image}}' "$app_container" 2>/dev/null || true)" + container_repo_head_hash="$(engine_exec exec "$app_container" sh -lc " + if [ -d '$app_repo_path/.git' ]; then + cd '$app_repo_path' && git rev-parse HEAD + fi + " 2>/dev/null | tail -n 1)" + container_repo_head_short="$(engine_exec exec "$app_container" sh -lc " + if [ -d '$app_repo_path/.git' ]; then + cd '$app_repo_path' && git rev-parse --short HEAD + fi + " 2>/dev/null | tail -n 1)" + if [ -n "$container_repo_head_hash" ]; then + echo " container /srv HEAD hash: $container_repo_head_hash" + fi + if [ -n "$local_head_hash" ] && [ -n "$container_repo_head_hash" ]; then + if [ "$local_head_hash" = "$container_repo_head_hash" ]; then + echo " HEAD check: OK local=$local_head_short container=$container_repo_head_short" + else + echo " HEAD check: MISMATCH local=$local_head_short container=$container_repo_head_short" + fi + fi engine_exec exec "$app_container" sh -lc " echo ' /srv/iskylims HEAD:' if [ -d '$app_repo_path/.git' ]; then @@ -417,16 +464,6 @@ print_container_source_diagnostics() { else echo 'not a git checkout' fi - echo ' plot code markers in /srv/iskylims:' - grep -n 'matplotlib\|Creating plot graphics from stored run metrics\|plot_by_cycle' '$app_repo_path/wetlab/utils/crontab_process.py' || true - " || true - engine_exec exec "$app_container" sh -lc " - echo ' plot code markers in $app_install_path:' - if [ -f '$app_install_path/wetlab/utils/crontab_process.py' ]; then - grep -n 'matplotlib\|Creating plot graphics from stored run metrics\|plot_by_cycle' '$app_install_path/wetlab/utils/crontab_process.py' || true - else - echo 'not installed yet' - fi " || true } @@ -458,12 +495,14 @@ cleanup_stale_test_containers() { cleanup_stale_test_containers print_local_source_diagnostics +print_existing_artifact_diagnostics echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=dep and GIT_REVISION=$git_revision..." INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" \ compose_exec -f "$compose_file" build --no-cache \ --build-arg INSTALL_TYPE="dep" \ --build-arg GIT_REVISION="$git_revision" \ --build-arg INSTALL_CONF="$install_conf_container" +print_image_after_build compose_exec -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." From fabb2beb77f0256c67ee879e6e3feec479e23c75 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 17 Mar 2026 11:44:31 +0100 Subject: [PATCH 395/446] install gnuplot using epel as it's not available in ubi9) --- Dockerfile | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 26e2c3070..18b8d38f1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,6 +11,11 @@ ARG APP_SHELL=/sbin/nologin # Updates RUN dnf -y update +# Add EPEL for packages not available in default UBI repositories +RUN dnf -y install \ + https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm \ + && dnf clean all + # Essential software RUN dnf -y install \ git wget \ @@ -21,7 +26,7 @@ RUN dnf -y install \ httpd-devel cronie \ rsync tzdata \ pkgconf-pkg-config \ - gnuplot \ + gnuplot-minimal \ && dnf clean all # Install supercronic (rootless-friendly cron runner) From 6648f1873d18ed047bb678c823236d23698250b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 17 Mar 2026 12:33:47 +0100 Subject: [PATCH 396/446] updated changelog --- CHANGELOG.md | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index cd451b3b5..33fa1d19d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -29,6 +29,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Added documentation describing migration scripts and their related versions [#389](https://github.com/BU-ISCIII/iskylims/pull/389) - Enabled Docker internal networking for local test installation [#389](https://github.com/BU-ISCIII/iskylims/pull/389) - Opened Docker network to allow localhost MySQL connection when required [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Added test fixtures and installation updates for the new sequencer and SampleSheet v2 support, including admin test-group assignment and new sequencer bootstrap data. Closes [#388](https://github.com/BU-ISCIII/iskylims/issues/388) [#392](https://github.com/BU-ISCIII/iskylims/pull/392) #### Fixes @@ -70,6 +71,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Fixed disk utilization check to correctly resolve application folder path [#389](https://github.com/BU-ISCIII/iskylims/pull/389) - Fixed incorrect application folder path resolution in crontab scripts [#389](https://github.com/BU-ISCIII/iskylims/pull/389) - Fixed samplesheet parsing error [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Fixed logger inconsistency that prevented exceptions and error messages from being written to the update crontab log. Closes [#390](https://github.com/BU-ISCIII/iskylims/issues/390) [#392](https://github.com/BU-ISCIII/iskylims/pull/392) +- Fixed wetlab crontab processing for the new sequencer, including run discovery, completion checks, RunInfo/RunParameters parsing updates, and SampleSheet v2 handling. Closes [#387](https://github.com/BU-ISCIII/iskylims/issues/387) [#392](https://github.com/BU-ISCIII/iskylims/pull/392) #### Changed @@ -96,24 +99,31 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), | Package | Last release Version | New release Version | |:--------------------|:---------------------|:----------------------------| -| wheel | 0.37.1 | 0.44.0 | +| wheel | 0.37.1 | 0.46.2 | | asn1crypto | 1.5.0 | 1.5.1 | | bcrypt | 4.0.1 | 4.2.0 | | biopython | 1.79 | 1.84 | -| cryptography | 38.0.3 | 43.0.1 | -| Django | 4.2 | 4.2.15 | +| cryptography | 38.0.3 | 44.0.3 | +| Django | 4.2 | 4.2.28 | | django-crispy-forms | 2.0 | 2.3 | +| crispy-bootstrap5 | | 0.7 | +| django-crontab | | 0.7.1 | | django-js-asset | 2.0.0 | 2.2.0 | | django-mptt | 0.14.0 | 0.16.0 | | django-mptt-admin | 2.4.1 | 2.6.2 | | django-cleanup | 7.0.0 | 8.1.0 | +| interop | | >1.1.22 | | mod_wsgi | 4.9.4 | 5.0.0 | +| gunicorn | | 22.0.0 | | mysqlclient | 2.0.3 | 2.2.6 | | paramiko | 3.1.0 | 3.4.1 | | jsonschema | 4.17.3 | 4.23.0 | +| pysmb | | 1.2.9.1 | | django_extensions | 3.2.1 | 3.2.3 | | djangorestframework | 3.14.0 | 3.15.2 | | drf-yasg | 1.21.5 | 1.21.7 | +| xlrd | | 2.0.1 | | pandas | 1.5.3 | 2.2.2 | +| numpy | | 1.26.4 | | openpyxl | 3.1.1 | 3.1.5 | -| setuptools | | 75.2.0 | +| setuptools | | 78.1.1 | From 7578943ea126798ec6018cc2da9225ace7b6292e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 17 Mar 2026 12:34:22 +0100 Subject: [PATCH 397/446] linting --- wetlab/config.py | 2 +- wetlab/models.py | 3 +-- wetlab/utils/crontab_process.py | 16 ++++++++++++---- wetlab/utils/samplesheet.py | 8 ++++++-- 4 files changed, 20 insertions(+), 9 deletions(-) diff --git a/wetlab/config.py b/wetlab/config.py index 35faeccbe..3beaa3f9a 100644 --- a/wetlab/config.py +++ b/wetlab/config.py @@ -76,7 +76,7 @@ ["NextSeq", "xml_file"], ["MiSeq", "xml_file"], ["NovaSeq", "txt_file"], - ["iSeq 100", "xml_file"] + ["iSeq 100", "xml_file"], ] # ########### VALUE TAG FOR XML FILES ######################### diff --git a/wetlab/models.py b/wetlab/models.py index 6037ae65f..184ded6d6 100644 --- a/wetlab/models.py +++ b/wetlab/models.py @@ -693,8 +693,7 @@ def get_number_of_lanes(self): ) match_flowcell = re.search( - r"'%s':\s*'?(\\d+)'?" - % wetlab.config.RUN_INFO_FLOWCELL_LAYOUT_LANE_TAG, + r"'%s':\s*'?(\\d+)'?" % wetlab.config.RUN_INFO_FLOWCELL_LAYOUT_LANE_TAG, str(self.flowcell_layout), ) if match_flowcell: diff --git a/wetlab/utils/crontab_process.py b/wetlab/utils/crontab_process.py index 934ea09cf..a53ac08b7 100644 --- a/wetlab/utils/crontab_process.py +++ b/wetlab/utils/crontab_process.py @@ -872,7 +872,9 @@ def get_sequencer_obj_or_create_if_no_exists(running_parameters, experiment_name else: number_of_lanes = running_parameters["running_data"].get("NumLanes", "") if not number_of_lanes: - flowcell_layout = running_parameters["running_data"].get("FlowcellLayout", {}) + flowcell_layout = running_parameters["running_data"].get( + "FlowcellLayout", {} + ) if isinstance(flowcell_layout, dict): number_of_lanes = flowcell_layout.get( wetlab.config.RUN_INFO_FLOWCELL_LAYOUT_LANE_TAG, "" @@ -1061,7 +1063,9 @@ def get_xml_child_case_insensitive(root_element, tag_name): setup_child = get_xml_child_case_insensitive( setup_element, param_in_setup[i] ) - running_data[param_in_setup[i]] = setup_child.text if setup_child else "" + running_data[param_in_setup[i]] = ( + setup_child.text if setup_child else "" + ) except Exception: string_message = ( experiment_name @@ -1114,7 +1118,9 @@ def get_xml_child_case_insensitive(root_element, tag_name): parameter_data_root, wetlab.config.PLANNED_READS_TAG ) if planned_reads_element is not None: - for planned_read in planned_reads_element.findall(wetlab.config.PLANNED_READ_TAG): + for planned_read in planned_reads_element.findall( + wetlab.config.PLANNED_READ_TAG + ): read_name = planned_read.attrib.get(wetlab.config.READ_NAME_TAG) if read_name not in wetlab.config.PLANNED_READ_FIELD_MAP: continue @@ -2186,7 +2192,9 @@ def _get_existing_stats_folder(conn, run_folder, experiment_name=""): run_folder = str(run_folder or "").strip().strip("/\\") def _join_remote_path(*parts): - return "/".join([str(part).strip("/\\") for part in parts if str(part).strip("/\\")]) + return "/".join( + [str(part).strip("/\\") for part in parts if str(part).strip("/\\")] + ) run_roots = [] if run_folder: diff --git a/wetlab/utils/samplesheet.py b/wetlab/utils/samplesheet.py index 8822663be..9c364230b 100644 --- a/wetlab/utils/samplesheet.py +++ b/wetlab/utils/samplesheet.py @@ -321,10 +321,14 @@ def get_user_ids_from_project_name(samplesheet: dict) -> list[str]: """ cloud_data = get_tabular_data_for_section(samplesheet, "Cloud_Data") project_names = get_column_from_tabular_data(cloud_data, "ProjectName") - return [get_user_id_from_project_name(project_name) for project_name in project_names] + return [ + get_user_id_from_project_name(project_name) for project_name in project_names + ] -def get_user_ids_from_samplesheet(samplesheet: dict, data: list[list] | None = None) -> list: +def get_user_ids_from_samplesheet( + samplesheet: dict, data: list[list] | None = None +) -> list: """ Extract user IDs from a samplesheet. Priority: From 4c637743e7a14156e800d9aea5e8baa2c717d2fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 17 Mar 2026 13:40:26 +0100 Subject: [PATCH 398/446] add ensure github safe path --- install.sh | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/install.sh b/install.sh index 1f013fb92..123224702 100644 --- a/install.sh +++ b/install.sh @@ -205,7 +205,19 @@ load_tables() { fi } +# ensure_git_safe_directory: avoid Git "dubious ownership" failures in containerized installs. +ensure_git_safe_directory() { + local repo_dir + repo_dir="$(pwd -P)" + + if [ -d "$repo_dir/.git" ] || [ -f "$repo_dir/.git" ]; then + git config --global --add safe.directory "$repo_dir" >/dev/null 2>&1 || true + git config --system --add safe.directory "$repo_dir" >/dev/null 2>&1 || true + fi +} + # Ensure to recover current git branch/tag/SHA on script exit +ensure_git_safe_directory initial_git_ref=$(git rev-parse --abbrev-ref HEAD || git rev-parse HEAD) trap restore_git_ref EXIT From ab26578045c1082600ca3107d2bb867390ad9064 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 17 Mar 2026 15:18:46 +0100 Subject: [PATCH 399/446] change order in apache proxy config --- conf/iskylims_apache_reverse_proxy.conf | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/conf/iskylims_apache_reverse_proxy.conf b/conf/iskylims_apache_reverse_proxy.conf index 53ea5f23a..5df19b4e2 100644 --- a/conf/iskylims_apache_reverse_proxy.conf +++ b/conf/iskylims_apache_reverse_proxy.conf @@ -8,14 +8,6 @@ RequestHeader set X-Forwarded-Proto "http" RequestHeader set X-Forwarded-Port "80" - # If Apache runs on the host, proxy to the published port - ProxyPass / http://localhost:8001/ - ProxyPassReverse / http://localhost:8001/ - - # If Apache runs in the same Docker network, use the service name instead: - # ProxyPass / http://app:8001/ - # ProxyPassReverse / http://app:8001/ - # Serve static files from a host path (bind-mounted from the container) # Example: /opt/iskylims/static-host -> /opt/iskylims/static in docker-compose.prod.yml ProxyPass /static/ ! @@ -23,6 +15,14 @@ Require all granted + + # If Apache runs on the host, proxy to the published port + ProxyPass / http://localhost:8001/ + ProxyPassReverse / http://localhost:8001/ + + # If Apache runs in the same Docker network, use the service name instead: + # ProxyPass / http://app:8001/ + # ProxyPassReverse / http://app:8001/ ErrorLog logs/iskylims-apache.error.log CustomLog logs/iskylims-apache.access.log combined env=!forwarded From b8ef4a3adf601ddd8259d4ff151a2d173610a19b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 17 Mar 2026 16:46:46 +0100 Subject: [PATCH 400/446] include apache as container in dockercompose --- conf/iskylims_apache_reverse_proxy.conf | 29 ++++++------------------- docker-compose.prod.yml | 19 +++++++++++++--- 2 files changed, 23 insertions(+), 25 deletions(-) diff --git a/conf/iskylims_apache_reverse_proxy.conf b/conf/iskylims_apache_reverse_proxy.conf index 5df19b4e2..1435389e0 100644 --- a/conf/iskylims_apache_reverse_proxy.conf +++ b/conf/iskylims_apache_reverse_proxy.conf @@ -1,30 +1,15 @@ -# Example Apache reverse proxy config for iSkyLIMS (Docker production) -# Replace ServerName and adjust the ProxyPass target if needed. +# Apache reverse proxy config for iSkyLIMS production container - - ServerName example.isciiides.es + + ServerName iskyimsdocker.isciiides.es ProxyPreserveHost On RequestHeader set X-Forwarded-Proto "http" RequestHeader set X-Forwarded-Port "80" - # Serve static files from a host path (bind-mounted from the container) - # Example: /opt/iskylims/static-host -> /opt/iskylims/static in docker-compose.prod.yml - ProxyPass /static/ ! - Alias /static/ /opt/iskylims/static-host/ - - Require all granted - - - # If Apache runs on the host, proxy to the published port - ProxyPass / http://localhost:8001/ - ProxyPassReverse / http://localhost:8001/ + ProxyPass / http://app:8001/ + ProxyPassReverse / http://app:8001/ - # If Apache runs in the same Docker network, use the service name instead: - # ProxyPass / http://app:8001/ - # ProxyPassReverse / http://app:8001/ - - ErrorLog logs/iskylims-apache.error.log - CustomLog logs/iskylims-apache.access.log combined env=!forwarded - CustomLog logs/iskylims-apache.access.log proxy env=forwarded + ErrorLog /var/log/httpd/iskylims-apache.error.log + CustomLog /var/log/httpd/iskylims-apache.access.log combined diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 6cff515f6..7c29d4cb7 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -1,6 +1,20 @@ version: '3.8' services: + apache: + container_name: iskylims_apache + restart: unless-stopped + image: registry.access.redhat.com/ubi9/httpd-24 + depends_on: + - app + ports: + - "80:8080" + volumes: + - /etc/localtime:/etc/localtime:ro + - /usr/share/zoneinfo:/usr/share/zoneinfo + - ./conf/iskylims_apache_reverse_proxy.conf:/etc/httpd/conf.d/iskylims.conf:Z,ro + - /var/log/httpd:/var/log/httpd:Z + app: container_name: iskylims_app restart: unless-stopped @@ -13,8 +27,8 @@ services: APP_UID: ${APP_UID:-1212} APP_GID: ${APP_GID:-1212} APP_SHELL: ${APP_SHELL:-/sbin/nologin} - ports: - - "8001:8001" + expose: + - "8001" environment: DJANGO_SETTINGS_MODULE: iskylims.settings APP_MODE: prod @@ -24,7 +38,6 @@ services: - /usr/share/zoneinfo:/usr/share/zoneinfo - /var/log/local/apps/iskylims:/opt/iskylims/logs:Z - iskylims_documents:/opt/iskylims/documents - - /opt/iskylims/static-host:/opt/iskylims/static:Z extra_hosts: - "host.docker.internal:host-gateway" From 6259363580369aface2c66cd4459cac7247bea96 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 19 Mar 2026 11:57:22 +0100 Subject: [PATCH 401/446] change port to 8080 and path to apache logs --- conf/iskylims_apache_reverse_proxy.conf | 2 +- docker-compose.prod.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/iskylims_apache_reverse_proxy.conf b/conf/iskylims_apache_reverse_proxy.conf index 1435389e0..652de6244 100644 --- a/conf/iskylims_apache_reverse_proxy.conf +++ b/conf/iskylims_apache_reverse_proxy.conf @@ -5,7 +5,7 @@ ProxyPreserveHost On RequestHeader set X-Forwarded-Proto "http" - RequestHeader set X-Forwarded-Port "80" + RequestHeader set X-Forwarded-Port "8080" ProxyPass / http://app:8001/ ProxyPassReverse / http://app:8001/ diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 7c29d4cb7..6e628833d 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -8,12 +8,12 @@ services: depends_on: - app ports: - - "80:8080" + - "8080:8080" volumes: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo - ./conf/iskylims_apache_reverse_proxy.conf:/etc/httpd/conf.d/iskylims.conf:Z,ro - - /var/log/httpd:/var/log/httpd:Z + - /var/log/local/apache:/var/log/httpd:Z app: container_name: iskylims_app From 7f9288452094f1469c6e9ad1ec0e2bd5f6b56ff0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 19 Mar 2026 17:30:02 +0100 Subject: [PATCH 402/446] make app install path configurable, static as common volume --- conf/iskylims_apache_reverse_proxy.conf | 6 ++++++ container_install.sh | 27 +++++++++++++++++-------- docker-compose.prod.yml | 11 ++++++---- 3 files changed, 32 insertions(+), 12 deletions(-) diff --git a/conf/iskylims_apache_reverse_proxy.conf b/conf/iskylims_apache_reverse_proxy.conf index 652de6244..2ab7cde4f 100644 --- a/conf/iskylims_apache_reverse_proxy.conf +++ b/conf/iskylims_apache_reverse_proxy.conf @@ -7,6 +7,12 @@ RequestHeader set X-Forwarded-Proto "http" RequestHeader set X-Forwarded-Port "8080" + ProxyPass /static ! + Alias /static /opt/iskylims/static + + Require all granted + + ProxyPass / http://app:8001/ ProxyPassReverse / http://app:8001/ diff --git a/container_install.sh b/container_install.sh index ee2816454..39c8b9937 100644 --- a/container_install.sh +++ b/container_install.sh @@ -303,10 +303,22 @@ else install_conf_container="$install_conf" fi +host_install_conf_path="$install_conf" +if [[ "$host_install_conf_path" != /* ]]; then + host_install_conf_path="$repo_root/$host_install_conf_path" +fi + +read_install_conf_value() { + local key="$1" + local file="$2" + grep -E "^${key}=" "$file" | tail -n 1 | cut -d= -f2- | sed "s/^['\"]//;s/['\"]$//" +} + set_engine app_repo_path="${APP_REPO_PATH:-/srv/iskylims}" -app_install_path="${APP_INSTALL_PATH:-/opt/iskylims}" +config_install_path="$(read_install_conf_value "INSTALL_PATH" "$host_install_conf_path")" +app_install_path="${APP_INSTALL_PATH:-${config_install_path:-/opt/iskylims}}" app_port="${APP_PORT:-8001}" app_container="" local_head_hash="" @@ -497,13 +509,17 @@ cleanup_stale_test_containers print_local_source_diagnostics print_existing_artifact_diagnostics echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=dep and GIT_REVISION=$git_revision..." -INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" \ +mkdir -p "$app_install_path/conf" "$app_install_path/logs/apache" +if [ -f "$repo_root/conf/iskylims_apache_reverse_proxy.conf" ]; then + cp "$repo_root/conf/iskylims_apache_reverse_proxy.conf" "$app_install_path/conf/iskylims_apache_reverse_proxy.conf" +fi +INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" APP_INSTALL_PATH="$app_install_path" \ compose_exec -f "$compose_file" build --no-cache \ --build-arg INSTALL_TYPE="dep" \ --build-arg GIT_REVISION="$git_revision" \ --build-arg INSTALL_CONF="$install_conf_container" print_image_after_build -compose_exec -f "$compose_file" up -d +APP_INSTALL_PATH="$app_install_path" compose_exec -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." sleep 20 @@ -515,11 +531,6 @@ app_gid="${APP_GID:-1212}" echo "Ensuring runtime directories are writable by ${app_uid}:${app_gid}" engine_exec exec -u 0 -it "$app_container" sh -lc "mkdir -p ${app_install_path}/documents ${app_install_path}/logs ${app_install_path}/static ${app_install_path}/cron ${app_install_path}/tmp && chown -R ${app_uid}:${app_gid} ${app_install_path}/documents ${app_install_path}/logs ${app_install_path}/static ${app_install_path}/cron ${app_install_path}/tmp" -host_install_conf_path="$install_conf" -if [[ "$host_install_conf_path" != /* ]]; then - host_install_conf_path="$repo_root/$host_install_conf_path" -fi - container_install_conf_path="$install_conf_container" if [[ "$container_install_conf_path" != /* ]]; then container_install_conf_path="$app_repo_path/$container_install_conf_path" diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 6e628833d..592a3cf21 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -12,8 +12,9 @@ services: volumes: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo - - ./conf/iskylims_apache_reverse_proxy.conf:/etc/httpd/conf.d/iskylims.conf:Z,ro - - /var/log/local/apache:/var/log/httpd:Z + - ${APP_INSTALL_PATH:-/opt/iskylims}/conf/iskylims_apache_reverse_proxy.conf:/etc/httpd/conf.d/iskylims.conf:Z,ro + - /var/local/logs/apache:/var/log/httpd:Z + - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static:Z,ro app: container_name: iskylims_app @@ -36,10 +37,12 @@ services: volumes: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo - - /var/log/local/apps/iskylims:/opt/iskylims/logs:Z - - iskylims_documents:/opt/iskylims/documents + - /var/log/local/apps/iskylims:${APP_INSTALL_PATH:-/opt/iskylims}/logs:Z + - iskylims_documents:${APP_INSTALL_PATH:-/opt/iskylims}/documents + - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static:Z extra_hosts: - "host.docker.internal:host-gateway" volumes: iskylims_documents: + iskylims_static: From 2bae8c1fcefac8418dd3f9ada0b0f29c90ccf9cb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 1 Apr 2026 12:40:31 +0200 Subject: [PATCH 403/446] update readme and leame with last configuration changes --- LEAME.md | 60 ++++++++++++++++++++++++++++++++++++------------------- README.md | 59 +++++++++++++++++++++++++++++++++++------------------- 2 files changed, 77 insertions(+), 42 deletions(-) diff --git a/LEAME.md b/LEAME.md index ba9e22bb7..863cf1c7a 100644 --- a/LEAME.md +++ b/LEAME.md @@ -17,7 +17,7 @@ De acuerdo con la infraestructura existente, la secuenciacion se realiza en un i - [Despliegue con Docker](#despliegue-con-docker) - [Contenedor local de pruebas](#contenedor-local-de-pruebas) - [Contenedor de produccion](#contenedor-de-produccion) - - [Proxy inverso con Apache (host) + Gunicorn](#proxy-inverso-con-apache-host--gunicorn) + - [Proxy inverso con Apache (contenedor) + Gunicorn](#proxy-inverso-con-apache-contenedor--gunicorn) - [Tareas cron dentro del contenedor](#tareas-cron-dentro-del-contenedor) - [Actualizacion del despliegue Docker](#actualizacion-del-despliegue-docker) - [Actualizacion del despliegue Docker v3.0.0 a 3.1.0](#actualizacion-del-despliegue-docker-v300-a-310) @@ -128,7 +128,7 @@ Despliega el contenedor de iSkyLIMS contra servicios MySQL/Samba externos: UID/GID del usuario de ejecucion del contenedor (por defecto `1212:1212`): -- Exporta `APP_UID` y `APP_GID` antes de ejecutar `container_install.sh` si necesitas un UID/GID distinto (por ejemplo, para escribir en `/opt/iskylims/static-host`). +- Exporta `APP_UID` y `APP_GID` antes de ejecutar `container_install.sh` si necesitas un UID/GID distinto. ```bash export APP_UID=1212 @@ -138,36 +138,47 @@ export APP_GID=1212 Asegura que la carpeta de estaticos en el host sea escribible por ese UID/GID: ```bash -sudo chown -R 1212:1212 /opt/iskylims/static-host +sudo chown -R 1212:1212 ${APP_INSTALL_PATH:-/opt/iskylims} ``` #### Persistir logs/documentos en el host -El compose de produccion monta los logs en el host para facilitar la recoleccion (por ejemplo, con Elastic): +Si usas un compose personalizado, asegurate de mantener estos montajes para conservar logs y datos. -- `/var/log/apps/iskylims` -> `/opt/iskylims/logs` -- `iskylims_documents` -> `/opt/iskylims/documents` +El compose de produccion usa `INSTALL_PATH` del fichero de configuracion seleccionado, o `APP_INSTALL_PATH` si la exportas, como raiz de ejecucion para la app y para los montajes de configuracion/estaticos del Apache en contenedor. -Si usas un compose personalizado, asegurate de mantener estos montajes para conservar logs y documentos. +Persistencia actual: -Crea el directorio de logs en el host y ajusta permisos segun el UID/GID del contenedor: +- `/var/log/local/apps/iskylims` -> `${INSTALL_PATH}/logs` dentro del contenedor `app` +- `/var/local/logs/apache` -> `/var/log/httpd` dentro del contenedor `apache` +- `${INSTALL_PATH}/conf/iskylims_apache_reverse_proxy.conf` -> `/etc/httpd/conf.d/iskylims.conf` dentro del contenedor `apache` +- volumen nombrado `iskylims_documents` -> `${INSTALL_PATH}/documents` +- volumen nombrado `iskylims_static` -> `${INSTALL_PATH}/static` + +Crea los directorios necesarios en el host: ```bash -sudo mkdir -p /var/log/apps/iskylims -sudo chown -R 1212:1212 /var/log/apps/iskylims +sudo mkdir -p /var/log/local/apps/iskylims +sudo mkdir -p /var/local/logs/apache +sudo mkdir -p ${APP_INSTALL_PATH:-/opt/iskylims}/conf +sudo chown -R 1212:1212 /var/log/local/apps/iskylims ${APP_INSTALL_PATH:-/opt/iskylims} ``` -#### Proxy inverso con Apache (host) + Gunicorn +#### Proxy inverso con Apache (contenedor) + Gunicorn -En produccion, el contenedor ejecuta `gunicorn` (no `manage.py runserver`). Usa Apache en el host como proxy inverso hacia `localhost:8001`. +En produccion, el contenedor `app` ejecuta `gunicorn` (no `manage.py runserver`) y el servicio `apache` de `docker-compose.prod.yml` hace de proxy inverso. Archivos estaticos: -- El contenedor genera los estaticos en `/opt/iskylims/static`. -- `docker-compose.prod.yml` monta ese directorio en `/opt/iskylims/static-host` del host. -- Configura Apache con `Alias /static/ /opt/iskylims/static-host/`. +- La aplicacion genera los estaticos en `${INSTALL_PATH}/static`. +- `docker-compose.prod.yml` comparte ese directorio con `apache` mediante el volumen nombrado `iskylims_static`. +- La configuracion del proxy sirve `/static` directamente desde `${INSTALL_PATH}/static`. + +Durante `container_install.sh`, el fichero `conf/iskylims_apache_reverse_proxy.conf` se copia al host en `${INSTALL_PATH}/conf/iskylims_apache_reverse_proxy.conf`. A partir de ese momento, los cambios de runtime deben hacerse sobre esa copia. + +Si necesitas otra raiz de instalacion, define `INSTALL_PATH` en el fichero de configuracion o exporta `APP_INSTALL_PATH` antes de ejecutar `container_install.sh`. -Ejemplo de configuracion en `conf/iskylims_apache_reverse_proxy.conf` y la sección [Configurar el servidor Apache](#configurar-el-servidor Apache). +`container_install.sh` crea `${APP_INSTALL_PATH}/conf` antes de `compose up`, copia ahi `conf/iskylims_apache_reverse_proxy.conf`, exporta `APP_INSTALL_PATH` a Compose y despues ejecuta `install.sh` dentro del contenedor `app`. `install.sh` crea `${INSTALL_PATH}/logs`, `${INSTALL_PATH}/documents` y ejecuta `collectstatic`, mientras que el contenedor `apache` sigue escribiendo sus logs en el path del host `/var/local/logs/apache`. #### Tareas cron dentro del contenedor @@ -200,7 +211,9 @@ La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh` dentr - Copia completa de las carpetas de logs y documents. ```bash -tar -czf iskylims_logs.tgz -C /var/log/apps/iskylims . +tar -czf iskylims_app_logs.tgz -C /var/log/local/apps/iskylims . + +tar -czf iskylims_apache_logs.tgz -C /var/local/logs/apache . docker run --rm \ -v iskylims_documents:/from \ @@ -396,8 +409,11 @@ mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_pro 4. Si los volumenes estan comprometidos, restauralos desde los tar: ```bash -mkdir -p /var/log/apps/iskylims -tar -xzf iskylims_logs.tgz -C /var/log/apps/iskylims +mkdir -p /var/log/local/apps/iskylims +tar -xzf iskylims_app_logs.tgz -C /var/log/local/apps/iskylims + +mkdir -p /var/local/logs/apache +tar -xzf iskylims_apache_logs.tgz -C /var/local/logs/apache docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ tar -xzf /from/iskylims_documents.tgz -C /to @@ -437,6 +453,8 @@ Ubicaciones tipicas: Pasos sugeridos (Apache en el host como proxy inverso): +Estos pasos aplican a instalaciones bare-metal con Apache en el host. En despliegues Docker de produccion se usa el contenedor `apache` y no hace falta copiar configuracion a `/etc/apache2` o `/etc/httpd`. + 1. Copia el ejemplo de configuracion: ```bash @@ -449,12 +467,12 @@ Pasos sugeridos (Apache en el host como proxy inverso): - Ajusta `ServerName` - Comprueba que `ProxyPass` apunte a `http://localhost:8001/` - - Comprueba `Alias /static/ /opt/iskylims/static-host/` + - Comprueba `Alias /static/ /opt/iskylims/static/` 3. Crea la carpeta de estaticos en el host: ```bash - sudo mkdir -p /opt/iskylims/static-host + sudo mkdir -p /opt/iskylims/static ``` 4. Habilita modulos necesarios (Ubuntu/Debian): diff --git a/README.md b/README.md index ab4fa3bab..320287208 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Local test stack](#local-test-stack) - [Production container](#production-container) - [Persist logs/documents on the host](#persist-logsdocuments-on-the-host) - - [Apache reverse proxy (host) + Gunicorn](#apache-reverse-proxy-host--gunicorn) + - [Apache reverse proxy (container) + Gunicorn](#apache-reverse-proxy-container--gunicorn) - [Cron jobs inside the container](#cron-jobs-inside-the-container) - [Upgrade docker deployment](#upgrade-docker-deployment) - [Upgrade docker deployment v3.0.0 to 3.1.0](#upgrade-docker-deployment-v300-to-310) @@ -145,7 +145,7 @@ Deploy the iSkyLIMS container against external MySQL/Samba services: UID/GID for the container runtime user (default `1212:1212`): -- Export `APP_UID` and `APP_GID` before running `container_install.sh` if you need a different host UID/GID (for example, to write to `/opt/iskylims/static-host`). +- Export `APP_UID` and `APP_GID` before running `container_install.sh` if you need a different host UID/GID. ```bash export APP_UID=1212 @@ -156,32 +156,42 @@ Host directory and ownership preparation is described in [Persist logs/documents #### Persist logs/documents on the host -The production compose file mounts logs on the host and keeps documents in a named volume: +The production compose file uses `INSTALL_PATH` from the selected install config, or `APP_INSTALL_PATH` if exported, as the runtime root for the app and for the Apache config/static mounts. -- `/var/log/apps/iskylims` → `/opt/iskylims/logs` -- `iskylims_documents` → `/opt/iskylims/documents` +Persistence layout: + +- `/var/log/local/apps/iskylims` -> `${INSTALL_PATH}/logs` inside the `app` container +- `/var/local/logs/apache` -> `/var/log/httpd` inside the `apache` container +- `${INSTALL_PATH}/conf/iskylims_apache_reverse_proxy.conf` -> `/etc/httpd/conf.d/iskylims.conf` inside the `apache` container +- `iskylims_documents` named volume -> `${INSTALL_PATH}/documents` +- `iskylims_static` named volume -> `${INSTALL_PATH}/static` If you override the compose file, ensure these mounts exist to keep logs and documents persistent. -Create host directories and set ownership to match the container UID/GID: +Create host directories before the first deployment: ```bash -sudo mkdir -p /var/log/apps/iskylims -sudo mkdir -p /opt/iskylims/static-host -sudo chown -R ${APP_UID:-1212}:${APP_GID:-1212} /var/log/apps/iskylims /opt/iskylims/static-host +sudo mkdir -p /var/log/local/apps/iskylims +sudo mkdir -p /var/local/logs/apache +sudo mkdir -p ${APP_INSTALL_PATH:-/opt/iskylims}/conf +sudo chown -R ${APP_UID:-1212}:${APP_GID:-1212} /var/log/local/apps/iskylims ${APP_INSTALL_PATH:-/opt/iskylims} ``` -#### Apache reverse proxy (host) + Gunicorn +#### Apache reverse proxy (container) + Gunicorn -For production, the container runs `gunicorn` (not `manage.py runserver`). Use Apache on the host as a reverse proxy to `localhost:8001`. +For production, the `app` container runs `gunicorn` (not `manage.py runserver`) and the `apache` service in `docker-compose.prod.yml` acts as the reverse proxy. Static files: -- The container writes collected static files to `/opt/iskylims/static`. -- `docker-compose.prod.yml` bind-mounts that path to `/opt/iskylims/static-host` on the host. -- Configure Apache with `Alias /static/ /opt/iskylims/static-host/`. +- The app collects static files into `${INSTALL_PATH}/static`. +- `docker-compose.prod.yml` shares that directory with the `apache` service through the named volume `iskylims_static`. +- The reverse proxy config serves `/static` directly from `${INSTALL_PATH}/static`. + +During `container_install.sh`, the file `conf/iskylims_apache_reverse_proxy.conf` is copied to `${INSTALL_PATH}/conf/iskylims_apache_reverse_proxy.conf` on the host. Edit that copied file for runtime Apache changes after deployment. + +If you need a different runtime root, set `INSTALL_PATH` in the install config file or export `APP_INSTALL_PATH` before running `container_install.sh`. -See the example config in `conf/iskylims_apache_reverse_proxy.conf` and the [Configure Apache server](#configure-apache-server) section below. +`container_install.sh` creates `${APP_INSTALL_PATH}/conf` before `compose up`, copies `conf/iskylims_apache_reverse_proxy.conf` there, passes `APP_INSTALL_PATH` into Compose, and then runs `install.sh` inside the `app` container. `install.sh` creates `${INSTALL_PATH}/logs`, `${INSTALL_PATH}/documents`, and runs `collectstatic`, while the Apache container keeps using the host log path `/var/local/logs/apache`. #### Cron jobs inside the container @@ -386,7 +396,9 @@ mysqldump -h -P -u iskylims -p iskylims > iskylims_$(date +% Logs archive: ```bash -tar -czf iskylims_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/apps/iskylims . +tar -czf iskylims_app_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/apps/iskylims . + +tar -czf iskylims_apache_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/local/logs/apache . ``` Documents volume archive: @@ -424,8 +436,11 @@ With Podman, use the same command replacing `docker` with `podman`. Restore logs: ```bash -mkdir -p /var/log/apps/iskylims -tar -xzf iskylims_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/apps/iskylims +mkdir -p /var/log/local/apps/iskylims +tar -xzf iskylims_app_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/apps/iskylims + +mkdir -p /var/local/logs/apache +tar -xzf iskylims_apache_logs_YYYYMMDD_HHMMSS.tgz -C /var/local/logs/apache ``` Bare-metal full rollback example: @@ -499,7 +514,9 @@ See [Persist logs/documents on the host](#persist-logsdocuments-on-the-host) in ### Configure Apache server -Copy the apache configuration file according to your distribution inside the apache configuration directory and rename it to iskylims.conf +These steps apply to bare-metal Apache installations. Docker production deployments use the `apache` container described above and do not require copying configs into `/etc/apache2` or `/etc/httpd`. + +Copy the apache configuration file according to your distribution inside the apache configuration directory and rename it to `iskylims.conf`. Typical config locations: @@ -520,12 +537,12 @@ Suggested steps (host Apache as reverse proxy): - Set `ServerName` - Ensure `ProxyPass` points to `http://localhost:8001/` - - Ensure `Alias /static/ /opt/iskylims/static-host/` + - Ensure `Alias /static/ /opt/iskylims/static/` 3. Create the static folder on the host: ```bash - sudo mkdir -p /opt/iskylims/static-host + sudo mkdir -p /opt/iskylims/static ``` 4. Enable required modules (Ubuntu/Debian): From 04210ea61697b6cc17e170a15130037cb016cd19 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 1 Apr 2026 12:47:42 +0200 Subject: [PATCH 404/446] properly implement port and app path configuration. Add gunicorn conf --- Dockerfile | 12 +++++++----- container_install.sh | 3 ++- docker-compose.prod.yml | 9 +++++++++ install.sh | 1 + scripts/container_start.sh | 39 +++++++++++++++++++++++++++++++------- 5 files changed, 51 insertions(+), 13 deletions(-) diff --git a/Dockerfile b/Dockerfile index 18b8d38f1..58226dbac 100644 --- a/Dockerfile +++ b/Dockerfile @@ -6,6 +6,8 @@ RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone ARG APP_UID=1212 ARG APP_GID=1212 ARG APP_SHELL=/sbin/nologin +ARG APP_INSTALL_PATH=/opt/iskylims +ENV APP_INSTALL_PATH=${APP_INSTALL_PATH} # Updates @@ -72,16 +74,16 @@ ARG INSTALL_CONF=conf/docker_test_settings.txt ENV SKIP_SYSTEM_PACKAGES=1 RUN /bin/bash install.sh --install dep --git_revision $GIT_REVISION --conf $INSTALL_CONF --skip_apache_restart # Use the virtualenv created by install.sh -ENV PATH="/opt/iskylims/virtualenv/bin:${PATH}" +ENV PATH="${APP_INSTALL_PATH}/virtualenv/bin:${PATH}" -WORKDIR /opt/iskylims +WORKDIR ${APP_INSTALL_PATH} # Create non-root user and set ownership RUN groupadd -g ${APP_GID} iskylims && \ useradd -m -u ${APP_UID} -g ${APP_GID} -s ${APP_SHELL} iskylims && \ - mkdir -p /opt/iskylims/cron /opt/iskylims/tmp && \ - chown -R ${APP_UID}:${APP_GID} /opt/iskylims /srv/iskylims && \ - chmod 700 /opt/iskylims/cron /opt/iskylims/tmp && \ + mkdir -p ${APP_INSTALL_PATH}/cron ${APP_INSTALL_PATH}/tmp && \ + chown -R ${APP_UID}:${APP_GID} ${APP_INSTALL_PATH} /srv/iskylims && \ + chmod 700 ${APP_INSTALL_PATH}/cron ${APP_INSTALL_PATH}/tmp && \ git config --system --add safe.directory /srv/iskylims # Expose diff --git a/container_install.sh b/container_install.sh index 39c8b9937..2a3efd9ce 100644 --- a/container_install.sh +++ b/container_install.sh @@ -517,7 +517,8 @@ INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_cont compose_exec -f "$compose_file" build --no-cache \ --build-arg INSTALL_TYPE="dep" \ --build-arg GIT_REVISION="$git_revision" \ - --build-arg INSTALL_CONF="$install_conf_container" + --build-arg INSTALL_CONF="$install_conf_container" \ + --build-arg APP_INSTALL_PATH="$app_install_path" print_image_after_build APP_INSTALL_PATH="$app_install_path" compose_exec -f "$compose_file" up -d diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 592a3cf21..728dd102d 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -28,11 +28,20 @@ services: APP_UID: ${APP_UID:-1212} APP_GID: ${APP_GID:-1212} APP_SHELL: ${APP_SHELL:-/sbin/nologin} + APP_INSTALL_PATH: ${APP_INSTALL_PATH:-/opt/iskylims} expose: - "8001" environment: DJANGO_SETTINGS_MODULE: iskylims.settings + DJANGO_DEBUG: "false" APP_MODE: prod + APP_PORT: 8001 + DB_CONN_MAX_AGE: ${DB_CONN_MAX_AGE:-60} + WEB_CONCURRENCY: ${WEB_CONCURRENCY:-2} + GUNICORN_THREADS: ${GUNICORN_THREADS:-2} + GUNICORN_TIMEOUT: ${GUNICORN_TIMEOUT:-120} + GUNICORN_KEEPALIVE: ${GUNICORN_KEEPALIVE:-5} + APP_INSTALL_PATH: ${APP_INSTALL_PATH:-/opt/iskylims} user: "${APP_UID:-1212}:${APP_GID:-1212}" volumes: - /etc/localtime:/etc/localtime:ro diff --git a/install.sh b/install.sh index 123224702..cca681a06 100644 --- a/install.sh +++ b/install.sh @@ -284,6 +284,7 @@ load_install_config() { ensure_file_exists "$conf" "$conf" # shellcheck disable=SC1090 . "$conf" + INSTALL_PATH="${APP_INSTALL_PATH:-$INSTALL_PATH}" } # checkout_git_revision: ensure desired git revision exists and check it out safely. diff --git a/scripts/container_start.sh b/scripts/container_start.sh index 3afdaeac0..c4e18df6f 100644 --- a/scripts/container_start.sh +++ b/scripts/container_start.sh @@ -1,14 +1,26 @@ #!/usr/bin/env bash set -euo pipefail -APP_DIR="/opt/iskylims" +APP_DIR="${APP_INSTALL_PATH:-/opt/iskylims}" CRON_DIR="${APP_DIR}/cron" TMP_DIR="${APP_DIR}/tmp" CRON_FILE="${CRON_DIR}/iskylims" CRON_LOG="${TMP_DIR}/supercronic.log" APP_MODE="${APP_MODE:-prod}" +APP_PORT="${APP_PORT:-8001}" +PROJECT_MODULE="${PROJECT_MODULE:-iskylims}" +GUNICORN_TIMEOUT="${GUNICORN_TIMEOUT:-120}" +GUNICORN_KEEPALIVE="${GUNICORN_KEEPALIVE:-5}" +GUNICORN_THREADS="${GUNICORN_THREADS:-2}" + +WAIT_TIMEOUT_SECONDS=100 +wait_start="${SECONDS}" while [ ! -f "${APP_DIR}/manage.py" ]; do + if (( SECONDS - wait_start >= WAIT_TIMEOUT_SECONDS )); then + echo "Timed out after ${WAIT_TIMEOUT_SECONDS}s waiting for ${APP_DIR}/manage.py" >&2 + exit 1 + fi sleep 2 done @@ -35,7 +47,7 @@ safe_chmod() { safe_chmod 700 "${CRON_DIR}" "${TMP_DIR}" if [ "$APP_MODE" = "dev" ]; then - exec python "${APP_DIR}/manage.py" runserver 0.0.0.0:8001 + exec python "${APP_DIR}/manage.py" runserver "0.0.0.0:${APP_PORT}" fi if command -v supercronic >/dev/null 2>&1; then @@ -58,8 +70,21 @@ else echo "supercronic not found. Skipping cron." fi -exec gunicorn iskylims.wsgi:application \ - --bind 0.0.0.0:8001 \ - --workers 1 \ - --threads 1 \ - --timeout 120 +if [ -n "${WEB_CONCURRENCY:-}" ]; then + GUNICORN_WORKERS="${WEB_CONCURRENCY}" +else + cpu_count="$(getconf _NPROCESSORS_ONLN 2>/dev/null || nproc 2>/dev/null || echo 1)" + if [ "${cpu_count}" -le 2 ]; then + GUNICORN_WORKERS=2 + else + GUNICORN_WORKERS=4 + fi +fi + +exec gunicorn "${PROJECT_MODULE}.wsgi:application" \ + --bind "0.0.0.0:${APP_PORT}" \ + --workers "${GUNICORN_WORKERS}" \ + --threads "${GUNICORN_THREADS}" \ + --keep-alive "${GUNICORN_KEEPALIVE}" \ + --timeout "${GUNICORN_TIMEOUT}" \ + --worker-tmp-dir /dev/shm From 4d789ad4dfea7cc772839c2d6076676dd766e195 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 1 Apr 2026 12:50:26 +0200 Subject: [PATCH 405/446] updated docs with new tunning vars, update supercronic use instead of crond --- LEAME.md | 27 ++++++++++++++++++++++++++- README.md | 27 ++++++++++++++++++++++++++- 2 files changed, 52 insertions(+), 2 deletions(-) diff --git a/LEAME.md b/LEAME.md index 863cf1c7a..693517d4b 100644 --- a/LEAME.md +++ b/LEAME.md @@ -135,6 +135,31 @@ export APP_UID=1212 export APP_GID=1212 ``` +Variables opcionales de build/runtime para produccion: + +- `APP_INSTALL_PATH`: cambia la raiz de instalacion en runtime usada por el contenedor `app`, el montaje de configuracion de Apache, los estaticos/documentos y los scripts de instalacion. Valor por defecto: `/opt/iskylims`. +- `APP_UID` / `APP_GID`: UID/GID de ejecucion del usuario `iskylims` dentro del contenedor. Valor por defecto: `1212:1212`. +- `APP_SHELL`: shell asignada al usuario de runtime durante la build. Valor por defecto: `/sbin/nologin`. +- `APP_PORT`: puerto interno donde Gunicorn escucha dentro del servicio `app`. Valor por defecto: `8001`. +- `DB_CONN_MAX_AGE`: tiempo de vida, en segundos, de las conexiones persistentes de Django a la BD. Valor por defecto: `60`. +- `WEB_CONCURRENCY`: numero de workers de Gunicorn. Valor por defecto en compose: `2`. Si no se define en el entrypoint, se calcula segun CPU disponible. +- `GUNICORN_THREADS`: numero de hilos por worker de Gunicorn. Valor por defecto: `2`. +- `GUNICORN_TIMEOUT`: timeout de peticiones Gunicorn en segundos. Valor por defecto: `120`. +- `GUNICORN_KEEPALIVE`: keep-alive de Gunicorn en segundos. Valor por defecto: `5`. +- `DJANGO_DEBUG`: se pasa al contenedor de produccion. Valor por defecto: `"false"`. Debe mantenerse desactivado en produccion. + +Ejemplo: + +```bash +export APP_INSTALL_PATH=/srv/iskylims +export APP_UID=1500 +export APP_GID=1500 +export WEB_CONCURRENCY=4 +export GUNICORN_THREADS=2 +export GUNICORN_TIMEOUT=180 +bash container_install.sh --install_conf conf/my_prod_settings.txt +``` + Asegura que la carpeta de estaticos en el host sea escribible por ese UID/GID: ```bash @@ -182,7 +207,7 @@ Si necesitas otra raiz de instalacion, define `INSTALL_PATH` en el fichero de co #### Tareas cron dentro del contenedor -Cron se ejecuta mediante un `crond` ligero lanzado por el script de arranque del contenedor. El script escribe las entradas de django-crontab en `/opt/iskylims/cron/iskylims` y arranca `crond` con un PID en una ruta escribible por el usuario. +Cron se ejecuta mediante `supercronic`, lanzado por el script de arranque del contenedor. El script escribe las entradas de django-crontab en `${APP_INSTALL_PATH}/cron/iskylims` y arranca `supercronic` como usuario no root. Si modificas `CRONJOBS`, reconstruye o reinicia el contenedor para regenerar el archivo de cron. diff --git a/README.md b/README.md index 320287208..e3445703f 100644 --- a/README.md +++ b/README.md @@ -152,6 +152,31 @@ export APP_UID=1212 export APP_GID=1212 ``` +Optional production runtime/build variables: + +- `APP_INSTALL_PATH`: overrides the runtime install root used by the app container, Apache config mount, static/documents mounts, and install scripts. Default: `/opt/iskylims`. +- `APP_UID` / `APP_GID`: runtime UID/GID for the `iskylims` user inside the container. Default: `1212:1212`. +- `APP_SHELL`: shell assigned to the runtime user during image build. Default: `/sbin/nologin`. +- `APP_PORT`: internal Gunicorn bind port for the `app` service. Default: `8001`. +- `DB_CONN_MAX_AGE`: Django persistent DB connection lifetime in seconds. Default: `60`. +- `WEB_CONCURRENCY`: Gunicorn worker count. Default: `2`. If unset in the container entrypoint, workers fall back to CPU-based auto-selection. +- `GUNICORN_THREADS`: threads per Gunicorn worker. Default: `2`. +- `GUNICORN_TIMEOUT`: Gunicorn request timeout in seconds. Default: `120`. +- `GUNICORN_KEEPALIVE`: Gunicorn keep-alive in seconds. Default: `5`. +- `DJANGO_DEBUG`: passed to the production app container. Default: `"false"`. Keep it disabled in production. + +Example: + +```bash +export APP_INSTALL_PATH=/srv/iskylims +export APP_UID=1500 +export APP_GID=1500 +export WEB_CONCURRENCY=4 +export GUNICORN_THREADS=2 +export GUNICORN_TIMEOUT=180 +bash container_install.sh --install_conf conf/my_prod_settings.txt +``` + Host directory and ownership preparation is described in [Persist logs/documents on the host](#persist-logsdocuments-on-the-host). #### Persist logs/documents on the host @@ -195,7 +220,7 @@ If you need a different runtime root, set `INSTALL_PATH` in the install config f #### Cron jobs inside the container -Cron runs via a lightweight `crond` started by the container entrypoint script. The script writes the django-crontab entries to `/opt/iskylims/cron/iskylims` and starts `crond` with a user-writable PID file. +Cron runs via `supercronic`, started by the container entrypoint script. The script writes the django-crontab entries to `${APP_INSTALL_PATH}/cron/iskylims` and starts `supercronic` as the non-root app user. If you change `CRONJOBS`, rebuild or restart the container to regenerate the cron file. From a36d10f3ffc7b7b6d5e767732354a3301e5679b1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 1 Apr 2026 13:14:34 +0200 Subject: [PATCH 406/446] fix apache log path --- LEAME.md | 12 ++++++------ README.md | 12 ++++++------ container_install.sh | 2 +- docker-compose.prod.yml | 2 +- 4 files changed, 14 insertions(+), 14 deletions(-) diff --git a/LEAME.md b/LEAME.md index 693517d4b..55899f499 100644 --- a/LEAME.md +++ b/LEAME.md @@ -175,7 +175,7 @@ El compose de produccion usa `INSTALL_PATH` del fichero de configuracion selecci Persistencia actual: - `/var/log/local/apps/iskylims` -> `${INSTALL_PATH}/logs` dentro del contenedor `app` -- `/var/local/logs/apache` -> `/var/log/httpd` dentro del contenedor `apache` +- `/var/log/local/apache` -> `/var/log/httpd` dentro del contenedor `apache` - `${INSTALL_PATH}/conf/iskylims_apache_reverse_proxy.conf` -> `/etc/httpd/conf.d/iskylims.conf` dentro del contenedor `apache` - volumen nombrado `iskylims_documents` -> `${INSTALL_PATH}/documents` - volumen nombrado `iskylims_static` -> `${INSTALL_PATH}/static` @@ -184,7 +184,7 @@ Crea los directorios necesarios en el host: ```bash sudo mkdir -p /var/log/local/apps/iskylims -sudo mkdir -p /var/local/logs/apache +sudo mkdir -p /var/log/local/apache sudo mkdir -p ${APP_INSTALL_PATH:-/opt/iskylims}/conf sudo chown -R 1212:1212 /var/log/local/apps/iskylims ${APP_INSTALL_PATH:-/opt/iskylims} ``` @@ -203,7 +203,7 @@ Durante `container_install.sh`, el fichero `conf/iskylims_apache_reverse_proxy.c Si necesitas otra raiz de instalacion, define `INSTALL_PATH` en el fichero de configuracion o exporta `APP_INSTALL_PATH` antes de ejecutar `container_install.sh`. -`container_install.sh` crea `${APP_INSTALL_PATH}/conf` antes de `compose up`, copia ahi `conf/iskylims_apache_reverse_proxy.conf`, exporta `APP_INSTALL_PATH` a Compose y despues ejecuta `install.sh` dentro del contenedor `app`. `install.sh` crea `${INSTALL_PATH}/logs`, `${INSTALL_PATH}/documents` y ejecuta `collectstatic`, mientras que el contenedor `apache` sigue escribiendo sus logs en el path del host `/var/local/logs/apache`. +`container_install.sh` crea `${APP_INSTALL_PATH}/conf` y `/var/log/local/apache` antes de `compose up`, copia ahi `conf/iskylims_apache_reverse_proxy.conf`, exporta `APP_INSTALL_PATH` a Compose y despues ejecuta `install.sh` dentro del contenedor `app`. `install.sh` crea `${INSTALL_PATH}/logs`, `${INSTALL_PATH}/documents` y ejecuta `collectstatic`, mientras que el contenedor `apache` sigue escribiendo sus logs en el path del host `/var/log/local/apache`. #### Tareas cron dentro del contenedor @@ -238,7 +238,7 @@ La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh` dentr ```bash tar -czf iskylims_app_logs.tgz -C /var/log/local/apps/iskylims . -tar -czf iskylims_apache_logs.tgz -C /var/local/logs/apache . +tar -czf iskylims_apache_logs.tgz -C /var/log/local/apache . docker run --rm \ -v iskylims_documents:/from \ @@ -437,8 +437,8 @@ mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_pro mkdir -p /var/log/local/apps/iskylims tar -xzf iskylims_app_logs.tgz -C /var/log/local/apps/iskylims -mkdir -p /var/local/logs/apache -tar -xzf iskylims_apache_logs.tgz -C /var/local/logs/apache +mkdir -p /var/log/local/apache +tar -xzf iskylims_apache_logs.tgz -C /var/log/local/apache docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ tar -xzf /from/iskylims_documents.tgz -C /to diff --git a/README.md b/README.md index e3445703f..83ea18018 100644 --- a/README.md +++ b/README.md @@ -186,7 +186,7 @@ The production compose file uses `INSTALL_PATH` from the selected install config Persistence layout: - `/var/log/local/apps/iskylims` -> `${INSTALL_PATH}/logs` inside the `app` container -- `/var/local/logs/apache` -> `/var/log/httpd` inside the `apache` container +- `/var/log/local/apache` -> `/var/log/httpd` inside the `apache` container - `${INSTALL_PATH}/conf/iskylims_apache_reverse_proxy.conf` -> `/etc/httpd/conf.d/iskylims.conf` inside the `apache` container - `iskylims_documents` named volume -> `${INSTALL_PATH}/documents` - `iskylims_static` named volume -> `${INSTALL_PATH}/static` @@ -197,7 +197,7 @@ Create host directories before the first deployment: ```bash sudo mkdir -p /var/log/local/apps/iskylims -sudo mkdir -p /var/local/logs/apache +sudo mkdir -p /var/log/local/apache sudo mkdir -p ${APP_INSTALL_PATH:-/opt/iskylims}/conf sudo chown -R ${APP_UID:-1212}:${APP_GID:-1212} /var/log/local/apps/iskylims ${APP_INSTALL_PATH:-/opt/iskylims} ``` @@ -216,7 +216,7 @@ During `container_install.sh`, the file `conf/iskylims_apache_reverse_proxy.conf If you need a different runtime root, set `INSTALL_PATH` in the install config file or export `APP_INSTALL_PATH` before running `container_install.sh`. -`container_install.sh` creates `${APP_INSTALL_PATH}/conf` before `compose up`, copies `conf/iskylims_apache_reverse_proxy.conf` there, passes `APP_INSTALL_PATH` into Compose, and then runs `install.sh` inside the `app` container. `install.sh` creates `${INSTALL_PATH}/logs`, `${INSTALL_PATH}/documents`, and runs `collectstatic`, while the Apache container keeps using the host log path `/var/local/logs/apache`. +`container_install.sh` creates `${APP_INSTALL_PATH}/conf` and `/var/log/local/apache` before `compose up`, copies `conf/iskylims_apache_reverse_proxy.conf` there, passes `APP_INSTALL_PATH` into Compose, and then runs `install.sh` inside the `app` container. `install.sh` creates `${INSTALL_PATH}/logs`, `${INSTALL_PATH}/documents`, and runs `collectstatic`, while the Apache container keeps using the host log path `/var/log/local/apache`. #### Cron jobs inside the container @@ -423,7 +423,7 @@ Logs archive: ```bash tar -czf iskylims_app_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/apps/iskylims . -tar -czf iskylims_apache_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/local/logs/apache . +tar -czf iskylims_apache_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/apache . ``` Documents volume archive: @@ -464,8 +464,8 @@ Restore logs: mkdir -p /var/log/local/apps/iskylims tar -xzf iskylims_app_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/apps/iskylims -mkdir -p /var/local/logs/apache -tar -xzf iskylims_apache_logs_YYYYMMDD_HHMMSS.tgz -C /var/local/logs/apache +mkdir -p /var/log/local/apache +tar -xzf iskylims_apache_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/apache ``` Bare-metal full rollback example: diff --git a/container_install.sh b/container_install.sh index 2a3efd9ce..0eb378e8d 100644 --- a/container_install.sh +++ b/container_install.sh @@ -509,7 +509,7 @@ cleanup_stale_test_containers print_local_source_diagnostics print_existing_artifact_diagnostics echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=dep and GIT_REVISION=$git_revision..." -mkdir -p "$app_install_path/conf" "$app_install_path/logs/apache" +mkdir -p "$app_install_path/conf" "/var/log/local/apache" if [ -f "$repo_root/conf/iskylims_apache_reverse_proxy.conf" ]; then cp "$repo_root/conf/iskylims_apache_reverse_proxy.conf" "$app_install_path/conf/iskylims_apache_reverse_proxy.conf" fi diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 728dd102d..31052ec1a 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -13,7 +13,7 @@ services: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo - ${APP_INSTALL_PATH:-/opt/iskylims}/conf/iskylims_apache_reverse_proxy.conf:/etc/httpd/conf.d/iskylims.conf:Z,ro - - /var/local/logs/apache:/var/log/httpd:Z + - /var/log/local/apache:/var/log/httpd:Z - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static:Z,ro app: From 69261b17089fa084fec0f82c00dd889b598f5c4b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 1 Apr 2026 15:39:21 +0200 Subject: [PATCH 407/446] remove :z to apache log path so it does not try to override selinux permissions --- docker-compose.prod.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 31052ec1a..6e51996c8 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -13,7 +13,7 @@ services: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo - ${APP_INSTALL_PATH:-/opt/iskylims}/conf/iskylims_apache_reverse_proxy.conf:/etc/httpd/conf.d/iskylims.conf:Z,ro - - /var/log/local/apache:/var/log/httpd:Z + - /var/log/local/apache:/var/log/httpd - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static:Z,ro app: From c5e7682e14e94bac5dff751e2e0607bd6a1b9b6a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 1 Apr 2026 15:46:27 +0200 Subject: [PATCH 408/446] add note about selinux configuration for logs folder --- LEAME.md | 18 ++++++++++++++++++ README.md | 18 ++++++++++++++++++ 2 files changed, 36 insertions(+) diff --git a/LEAME.md b/LEAME.md index 55899f499..58d00bb26 100644 --- a/LEAME.md +++ b/LEAME.md @@ -205,6 +205,24 @@ Si necesitas otra raiz de instalacion, define `INSTALL_PATH` en el fichero de co `container_install.sh` crea `${APP_INSTALL_PATH}/conf` y `/var/log/local/apache` antes de `compose up`, copia ahi `conf/iskylims_apache_reverse_proxy.conf`, exporta `APP_INSTALL_PATH` a Compose y despues ejecuta `install.sh` dentro del contenedor `app`. `install.sh` crea `${INSTALL_PATH}/logs`, `${INSTALL_PATH}/documents` y ejecuta `collectstatic`, mientras que el contenedor `apache` sigue escribiendo sus logs en el path del host `/var/log/local/apache`. +Nota SELinux para pre-produccion y produccion: + +- Asegura que `/var/log/local/apache` sea escribible por el runtime de contenedores y tenga una etiqueta valida para contenedores, por ejemplo `container_file_t`. +- Si el path del host ya esta etiquetado como `container_file_t`, no anadas `:Z` al bind mount de logs de Apache. `:Z` fuerza un relabel y puede fallar con `lsetxattr(... container_file_t ...): operation not permitted`. +- Comprobacion rapida: + +```bash +ls -ldZ /var/log/local/apache +``` + +- Ejemplo esperado: + +```text +system_u:object_r:container_file_t:s0 +``` + +- Si Apache falla al arrancar con `ModSecurity: Failed to open debug log file: /var/log/httpd/modsec_debug.log`, elimina cualquier fichero host obsoleto y recrea/reinicia el contenedor. En la practica, borrar `/var/log/local/apache/modsec_debug.log` ha sido suficiente cuando el inode existente tenia permisos o contexto incorrectos. + #### Tareas cron dentro del contenedor Cron se ejecuta mediante `supercronic`, lanzado por el script de arranque del contenedor. El script escribe las entradas de django-crontab en `${APP_INSTALL_PATH}/cron/iskylims` y arranca `supercronic` como usuario no root. diff --git a/README.md b/README.md index 83ea18018..18752ccbd 100644 --- a/README.md +++ b/README.md @@ -218,6 +218,24 @@ If you need a different runtime root, set `INSTALL_PATH` in the install config f `container_install.sh` creates `${APP_INSTALL_PATH}/conf` and `/var/log/local/apache` before `compose up`, copies `conf/iskylims_apache_reverse_proxy.conf` there, passes `APP_INSTALL_PATH` into Compose, and then runs `install.sh` inside the `app` container. `install.sh` creates `${INSTALL_PATH}/logs`, `${INSTALL_PATH}/documents`, and runs `collectstatic`, while the Apache container keeps using the host log path `/var/log/local/apache`. +SELinux note for pre-production and production: + +- Ensure `/var/log/local/apache` is writable by the container runtime and labeled for containers, for example `container_file_t`. +- If the host path is already labeled `container_file_t`, do not add `:Z` to the Apache log bind mount. `:Z` forces a relabel and may fail with `lsetxattr(... container_file_t ...): operation not permitted`. +- A quick check is: + +```bash +ls -ldZ /var/log/local/apache +``` + +- Expected example: + +```text +system_u:object_r:container_file_t:s0 +``` + +- If Apache fails on startup with `ModSecurity: Failed to open debug log file: /var/log/httpd/modsec_debug.log`, remove any stale host file and recreate/restart the container. In practice, deleting `/var/log/local/apache/modsec_debug.log` has been enough when the existing inode had bad permissions/label state. + #### Cron jobs inside the container Cron runs via `supercronic`, started by the container entrypoint script. The script writes the django-crontab entries to `${APP_INSTALL_PATH}/cron/iskylims` and starts `supercronic` as the non-root app user. From e868c59e602ca8dc93d2a8a94c2ee46874df8250 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 6 Apr 2026 13:23:22 +0200 Subject: [PATCH 409/446] fix bug in initial settings, new lab_code where not included in html --- wetlab/templates/wetlab/initial_settings.html | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/wetlab/templates/wetlab/initial_settings.html b/wetlab/templates/wetlab/initial_settings.html index 3a7d881c5..b69e293a2 100644 --- a/wetlab/templates/wetlab/initial_settings.html +++ b/wetlab/templates/wetlab/initial_settings.html @@ -320,10 +320,12 @@
    Define First the cities where the Laboratories are loca Contact phone Email Address + Lab code 1 + Lab code 2 - {% for name, code, dept, contact, phone, email, addr, id in initial_data.lab_request_data %} + {% for name, code, dept, contact, phone, email, addr, lab_code_1, lab_code_2, id in initial_data.lab_request_data %} {{name}} {{code}} @@ -332,6 +334,8 @@
    Define First the cities where the Laboratories are loca {{phone}} {{email}} {{addr}} + {{lab_code_1}} + {{lab_code_2}} {% endfor %} From 40a19cc3c44fa2903bde4aabbaab13637fb7bfc5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 7 Apr 2026 10:25:39 +0200 Subject: [PATCH 410/446] add readme note --- README.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/README.md b/README.md index 18752ccbd..a09aa48c2 100644 --- a/README.md +++ b/README.md @@ -202,6 +202,22 @@ sudo mkdir -p ${APP_INSTALL_PATH:-/opt/iskylims}/conf sudo chown -R ${APP_UID:-1212}:${APP_GID:-1212} /var/log/local/apps/iskylims ${APP_INSTALL_PATH:-/opt/iskylims} ``` +For hardened/rootless Podman hosts, run the host preparation script as the same +user that starts the containers. The script pre-creates Apache log files, fixes +rootless Podman ownership for the UBI httpd user, and applies SELinux container +labels when SELinux is enabled: + +```bash +bash hardening.sh +``` + +If an administrator runs it as root, set `PODMAN_USER` to the user that starts +the rootless containers: + +```bash +PODMAN_USER=bioinfo bash hardening.sh +``` + #### Apache reverse proxy (container) + Gunicorn For production, the `app` container runs `gunicorn` (not `manage.py runserver`) and the `apache` service in `docker-compose.prod.yml` acts as the reverse proxy. From 003e408487b6700d47ae82d575a2b7e187560135 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 7 Apr 2026 10:27:19 +0200 Subject: [PATCH 411/446] removed postgress dependency --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 58226dbac..3998d1ead 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,7 +24,7 @@ RUN dnf -y install \ python3.11 python3.11-pip python3.11-devel python3.11-wheel \ gcc gcc-c++ make \ openssl-devel libffi-devel \ - mariadb mariadb-connector-c-devel postgresql-devel \ + mariadb mariadb-connector-c-devel \ httpd-devel cronie \ rsync tzdata \ pkgconf-pkg-config \ From 60cfa50b5035628a42bf3fa2b7a1c1b6d41e1365 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 7 Apr 2026 10:29:18 +0200 Subject: [PATCH 412/446] minor fix in dep versions --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index a09aa48c2..09e1b9433 100644 --- a/README.md +++ b/README.md @@ -72,10 +72,10 @@ cd iskylims ## Minimum requirements - **sudo privileges** for dependency installation -- MySQL > 8.0 or MariaDB > 10.4 +- MySQL >= 8.0 or MariaDB > 10.4 - Apache 2.4 -- git > 2.34 -- Python > 3.11 +- git >= 2.34 +- Python >= 3.11 - Local email sender configured - Access to the Samba share where run folders live - `lsb_release` package: From d33b26533392bc633b06ac7867219bf1a5a73b5e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 7 Apr 2026 10:40:32 +0200 Subject: [PATCH 413/446] add clarification about minimum requirements --- LEAME.md | 246 +++++++++++++++++++++++++++++++++++++++++++++--------- README.md | 14 +++- 2 files changed, 218 insertions(+), 42 deletions(-) diff --git a/LEAME.md b/LEAME.md index 58d00bb26..b70f284ff 100644 --- a/LEAME.md +++ b/LEAME.md @@ -14,14 +14,17 @@ De acuerdo con la infraestructura existente, la secuenciacion se realiza en un i - [iSkyLIMS](#iskylims) - [Obtener el codigo (obligatorio)](#obtener-el-codigo-obligatorio) - [Elige tu ruta](#elige-tu-ruta) + - [Requisitos minimos](#requisitos-minimos) - [Despliegue con Docker](#despliegue-con-docker) - [Contenedor local de pruebas](#contenedor-local-de-pruebas) - [Contenedor de produccion](#contenedor-de-produccion) + - [Persistir logs/documentos en el host](#persistir-logsdocumentos-en-el-host) - [Proxy inverso con Apache (contenedor) + Gunicorn](#proxy-inverso-con-apache-contenedor--gunicorn) - [Tareas cron dentro del contenedor](#tareas-cron-dentro-del-contenedor) - [Actualizacion del despliegue Docker](#actualizacion-del-despliegue-docker) - [Actualizacion del despliegue Docker v3.0.0 a 3.1.0](#actualizacion-del-despliegue-docker-v300-a-310) - [Haz copia de seguridad](#haz-copia-de-seguridad) + - [Actualizar codigo y ajustes](#actualizar-codigo-y-ajustes) - [Despliegue bare-metal (Ubuntu/CentOS)](#despliegue-bare-metal-ubuntucentos) - [Instalacion](#instalacion) - [Requisitos previos](#requisitos-previos) @@ -31,15 +34,22 @@ De acuerdo con la infraestructura existente, la secuenciacion se realiza en un i - [Ejecutar install.sh](#ejecutar-installsh) - [Actualizacion (3.0.x a 3.1.x)](#actualizacion-30x-a-31x) - [Haz copia de seguridad](#haz-copia-de-seguridad-1) - - [Actualizar codigo y ajustes](#actualizar-codigo-y-ajustes) + - [Actualizar codigo y ajustes](#actualizar-codigo-y-ajustes-1) - [Ejecutar pasos de actualizacion con root](#ejecutar-pasos-de-actualizacion-con-root) - [Ejecutar pasos de actualizacion sin root](#ejecutar-pasos-de-actualizacion-sin-root) + - [Operaciones comunes (Docker + bare-metal)](#operaciones-comunes-docker--bare-metal) + - [Creacion de base de datos, usuarios y permisos](#creacion-de-base-de-datos-usuarios-y-permisos) + - [Copias de seguridad](#copias-de-seguridad) + - [Restauracion / rollback](#restauracion--rollback) - [Que hacer si algo falla](#que-hacer-si-algo-falla) - [Bare-metal](#bare-metal) - [Docker](#docker) - [Pasos finales de configuracion](#pasos-finales-de-configuracion) - [Configuracion de SAMBA](#configuracion-de-samba) - [Verificacion de correo electronico](#verificacion-de-correo-electronico) + - [Notas para desarrolladores](#notas-para-desarrolladores) + - [Flujo de migraciones Django](#flujo-de-migraciones-django) + - [Rutas persistentes en el host](#rutas-persistentes-en-el-host) - [Configurar el servidor Apache](#configurar-el-servidor-apache) - [Verificacion de la instalacion](#verificacion-de-la-instalacion) - [Documentacion de iSkyLIMS](#documentacion-de-iskylims) @@ -61,12 +71,31 @@ cd iskylims - **Docker (contenedor de produccion)**: despliega solo la aplicacion, apuntando a tu DB/Samba existente. - **Bare-metal**: instala o actualiza directamente en hosts Ubuntu/CentOS con `install.sh`. -## Despliegue con Docker +## Requisitos minimos + +Requisitos para despliegue en contenedor: -Requisitos previos para instalaciones con Docker: +- Docker Engine + Docker Compose v2, o Podman + `podman-compose` +- git >= 2.34 para clonar/actualizar el repositorio +- MySQL/MariaDB, Apache, Python y `lsb_release` en el host no son necesarios para el despliegue en contenedor +- Para contenedores locales de prueba: MySQL y Samba se arrancan como contenedores con `container_install.sh --test` +- Para contenedores de produccion: acceso a un servidor MySQL/MariaDB externo y a la carpeta Samba configurados en el fichero de instalacion seleccionado +- Directorios y permisos en el host para logs, documentos y estaticos, como se describe en [Persistir logs/documentos en el host](#persistir-logsdocumentos-en-el-host) -- Docker Engine + Docker Compose v2 -- git (para clonar el repositorio) +Requisitos para despliegue bare-metal: + +- **Privilegios sudo** para instalar dependencias +- MySQL >= 8.0 o MariaDB > 10.4 +- Apache >= 2.4 +- git >= 2.34 +- Python >= 3.11 +- Servidor local configurado para enviar correos +- Acceso a la carpeta Samba donde estan los run folders +- Paquete `lsb_release`: + - RedHat/CentOS: `yum install redhat-lsb-core` + - Ubuntu: `apt install lsb-core lsb-release` + +## Despliegue con Docker ### Contenedor local de pruebas @@ -186,7 +215,19 @@ Crea los directorios necesarios en el host: sudo mkdir -p /var/log/local/apps/iskylims sudo mkdir -p /var/log/local/apache sudo mkdir -p ${APP_INSTALL_PATH:-/opt/iskylims}/conf -sudo chown -R 1212:1212 /var/log/local/apps/iskylims ${APP_INSTALL_PATH:-/opt/iskylims} +sudo chown -R ${APP_UID:-1212}:${APP_GID:-1212} /var/log/local/apps/iskylims ${APP_INSTALL_PATH:-/opt/iskylims} +``` + +En hosts Podman rootless o endurecidos, ejecuta el script de preparacion del host con el mismo usuario que arranca los contenedores. El script pre-crea los ficheros de log de Apache, ajusta la propiedad para el usuario UBI httpd en Podman rootless y aplica etiquetas SELinux de contenedor cuando SELinux esta activo: + +```bash +bash hardening.sh +``` + +Si un administrador lo ejecuta como root, define `PODMAN_USER` con el usuario que arranca los contenedores rootless: + +```bash +PODMAN_USER=bioinfo bash hardening.sh ``` #### Proxy inverso con Apache (contenedor) + Gunicorn @@ -250,30 +291,38 @@ La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh` dentr #### Haz copia de seguridad -- Copia completa de la base de datos `iskylims`. -- Copia completa de las carpetas de logs y documents. +Ejecuta primero los pasos de [Copias de seguridad](#copias-de-seguridad). + +Para 3.0.0 -> 3.1.0, exporta primero el mapeo de LibraryPool y luego ejecuta la actualizacion con scripts pre/post: ```bash -tar -czf iskylims_app_logs.tgz -C /var/log/local/apps/iskylims . +mysql --user= --password= --host= --port= iskylims \ + -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ + > /tmp/library_pool_run_process.tsv +``` -tar -czf iskylims_apache_logs.tgz -C /var/log/local/apache . +#### Actualizar codigo y ajustes -docker run --rm \ - -v iskylims_documents:/from \ - -v "$PWD":/to \ - alpine tar -czf /to/iskylims_documents.tgz -C /from . +```bash +cd /iskylims +git pull +cp conf/docker_production_settings.txt myprod_settings.txt +sudo nano myprod_settings.txt ``` -Antes de actualizar, asegurate de tener una copia completa de la base de datos y de los datos en volumenes que uses. Confirma que `conf/my_prod_settings.txt` tenga el host/usuario/password de la base de datos de produccion, la URL/IP del servidor, correo y ajustes de logging usados por el contenedor. +Si editas el archivo en Windows, asegurate de guardarlo con codificacion UTF-8/ASCII. -Para 3.0.0 -> 3.1.0, exporta primero el mapeo de LibraryPool y luego ejecuta la actualizacion con scripts pre/post: +Si usas `APP_UID`/`APP_GID`, exportalos de nuevo antes de la actualizacion para que el contenedor se ejecute con el mismo UID/GID: ```bash -mysql --user= --password= --host= --port= iskylims \ - -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ - > /tmp/library_pool_run_process.tsv +export APP_UID=1212 +export APP_GID=1212 +``` + +Ejecuta la actualizacion: -bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade \ +```bash +bash container_install.sh --engine podman --install_conf myprod_settings.txt --action upgrade \ --script_before convert_rawtop_counter_to_int \ --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv ``` @@ -303,9 +352,7 @@ cd iskylims #### Preparar la base de datos -1. Crea una base de datos llamada `iskylims`. -2. Crea un usuario con permisos de lectura/escritura sobre esa base. -3. Guarda host, puerto, usuario y password para el archivo de ajustes. +Crea la base de datos y el usuario de aplicacion siguiendo [Creacion de base de datos, usuarios y permisos](#creacion-de-base-de-datos-usuarios-y-permisos). Guarda host, puerto, usuario y password para `install_settings.txt`. #### Configurar install_settings.txt @@ -352,13 +399,14 @@ Sigue estos pasos para pasar de la version 3.0.0 a la serie 3.1.x. #### Haz copia de seguridad -- Copia completa de la base de datos `iskylims`. -- Copia completa de la carpeta de instalacion (por ejemplo `/opt/iskylims`). +- Ejecuta primero los pasos de [Copias de seguridad](#copias-de-seguridad). +- Ademas, guarda una copia completa de la carpeta de instalacion (por ejemplo `/opt/iskylims`) para rollback bare-metal. - Si usas library pools, exportalos antes de actualizar: ```bash mysql --user= --password= --host= --port= iskylims \ - -e "SELECT * FROM wetlab_library_pool" > /backup_lib_pool.sql + -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ + > /tmp/library_pool_run_process.tsv ``` #### Actualizar codigo y ajustes @@ -388,19 +436,6 @@ Actualiza el codigo y la base de datos: ```bash # con restauracion de library pool -bash install.sh --upgrade app --script /backup_lib_pool.sql --git_revision main --tables - -# sin restauracion de library pool -bash install.sh --upgrade app --git_revision main --tables - -# ejemplo ejecutando un script de migracion en la actualizacion -bash install.sh --upgrade app --script migrate_optional_values --git_revision main --tables - -# 3.0.0 -> 3.1.0 (scripts de datos pre/post) -mysql --user= --password= --host= --port= iskylims \ - -e "SELECT id, run_process_id_id FROM wetlab_library_pool" \ - > /tmp/library_pool_run_process.tsv - bash install.sh --upgrade app --git_revision main \ --script_before convert_rawtop_counter_to_int \ --script_after library_pool_to_many_relation,/tmp/library_pool_run_process.tsv @@ -414,9 +449,123 @@ sudo bash install.sh --upgrade full --git_revision main --tables Las actualizaciones regeneran las migraciones y las aplican con `--fake-initial` para conservar las tablas existentes, igual que en Docker. +## Operaciones comunes (Docker + bare-metal) + +### Creacion de base de datos, usuarios y permisos + +Ejecuta como root de MySQL: + +```sql +CREATE DATABASE IF NOT EXISTS iskylims CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci; + +CREATE USER IF NOT EXISTS 'iskylims'@'%' IDENTIFIED BY 'djangopass'; +CREATE USER IF NOT EXISTS 'iskylims'@'localhost' IDENTIFIED BY 'djangopass'; + +GRANT ALL PRIVILEGES ON iskylims.* TO 'iskylims'@'%'; +GRANT ALL PRIVILEGES ON iskylims.* TO 'iskylims'@'localhost'; + +FLUSH PRIVILEGES; +``` + +Verificacion: + +```sql +SHOW GRANTS FOR 'iskylims'@'%'; +``` + +### Copias de seguridad + +Dump de base de datos: + +```bash +mysqldump -h -P -u iskylims -p iskylims > iskylims_$(date +%Y%m%d_%H%M%S).sql +``` + +Archivo de logs: + +```bash +tar -czf iskylims_app_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/apps/iskylims . + +tar -czf iskylims_apache_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/apache . +``` + +Archivo del volumen de documents: + +```bash +docker run --rm -v iskylims_documents:/from -v "$PWD":/to alpine \ + tar -czf /to/iskylims_documents_$(date +%Y%m%d_%H%M%S).tgz -C /from . +``` + +Con Podman, usa el mismo comando sustituyendo `docker` por `podman`. + +Orden recomendado antes de actualizar: + +1. Dump de BD +2. Archivo del volumen de documents +3. Archivo de logs + +### Restauracion / rollback + +Restaurar BD: + +```bash +mysql -h -P -u iskylims -p iskylims < iskylims_YYYYMMDD_HHMMSS.sql +``` + +Restaurar volumen de documents: + +```bash +docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ + sh -lc "cd /to && tar -xzf /from/iskylims_documents_YYYYMMDD_HHMMSS.tgz" +``` + +Con Podman, usa el mismo comando sustituyendo `docker` por `podman`. + +Restaurar logs: + +```bash +mkdir -p /var/log/local/apps/iskylims +tar -xzf iskylims_app_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/apps/iskylims + +mkdir -p /var/log/local/apache +tar -xzf iskylims_apache_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/apache +``` + +Ejemplo de rollback completo bare-metal: + +```bash +sudo rm -rf /opt/iskylims +sudo cp -r /home/dadmin/backup_prod/iSkyLIMS/ /opt/ +sudo /scripts/hardening.sh +mysql -u iskylims -p -h iskylims < /home/dadmin/backup_prod/bk_iSkyLIMS_YYYYMMDDHHMM.sql +``` + ## Que hacer si algo falla -Cuando actualizamos usando el script de instalacion estamos realizando varios cambios en la base de datos. Si algo falla necesitamos restaurar el estado anterior y empezar de nuevo. +Cuando una instalacion o actualizacion falla, restaura el estado anterior y reintenta con logs activados. + +Diagnosticos rapidos: + +```bash +# bare-metal +cd /opt/iskylims +python manage.py check + +# docker +docker compose -f docker-compose.prod.yml ps +docker compose -f docker-compose.prod.yml logs --tail 200 app + +# podman +podman-compose -f docker-compose.prod.yml ps +podman-compose -f docker-compose.prod.yml logs --tail 200 app +``` + +Si sospechas que una imagen o cache de build de Docker esta corrupta: + +```bash +docker compose -f docker-compose.prod.yml build --no-cache app +docker compose -f docker-compose.prod.yml up -d --force-recreate app +``` ### Bare-metal @@ -485,6 +634,23 @@ docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ - Ve a Configuration -> Email configuration - Rellena el formulario con los parametros necesarios y prueba a enviar un correo. +## Notas para desarrolladores + +### Flujo de migraciones Django + +Las migraciones se versionan en el repositorio. No ejecutes `makemigrations` durante la instalacion o actualizacion. + +Flujo base + actualizacion para nuevas releases: + +1. Genera las migraciones base desde el ultimo tag estable (por ejemplo 3.0.0). +2. Versiona las migraciones base. +3. Genera en `develop` las nuevas migraciones para cambios de esquema y versionalas. +4. Las actualizaciones ejecutan una vez `migrate --fake-initial` para alinear tablas existentes, y despues `migrate` para aplicar los nuevos ficheros de migracion. + +### Rutas persistentes en el host + +Consulta [Persistir logs/documentos en el host](#persistir-logsdocumentos-en-el-host) en la seccion de despliegue de produccion. + ### Configurar el servidor Apache Copia el archivo de configuracion de Apache segun tu distribucion dentro del directorio de configuracion de Apache y renombralo a iskylims.conf diff --git a/README.md b/README.md index 09e1b9433..3e789477d 100644 --- a/README.md +++ b/README.md @@ -71,9 +71,20 @@ cd iskylims ## Minimum requirements +Container deployment requirements: + +- Docker Engine + Docker Compose v2, or Podman + `podman-compose` +- git >= 2.34 to clone/update the repository +- Host MySQL/MariaDB, Apache, Python, and `lsb_release` are not required for container deployment +- For local test containers: MySQL and Samba are started as containers by `container_install.sh --test` +- For production containers: access to an external MySQL/MariaDB server and Samba share configured in the selected install config +- Host directories and permissions for logs, documents, and static files, as described in [Persist logs/documents on the host](#persist-logsdocuments-on-the-host) + +Bare-metal deployment requirements: + - **sudo privileges** for dependency installation - MySQL >= 8.0 or MariaDB > 10.4 -- Apache 2.4 +- Apache >= 2.4 - git >= 2.34 - Python >= 3.11 - Local email sender configured @@ -81,7 +92,6 @@ cd iskylims - `lsb_release` package: - RedHat/CentOS: `yum install redhat-lsb-core` - Ubuntu: `apt install lsb-core lsb-release` -- For containers: Docker Engine + Docker Compose v2, or Podman + `podman-compose` ## Docker deployment From 162c4c1145cabb931e33ac1ef2c012a0b12eff6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 7 Apr 2026 11:11:02 +0200 Subject: [PATCH 414/446] change github url for gitlab url in leame --- LEAME.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/LEAME.md b/LEAME.md index b70f284ff..e3fd04535 100644 --- a/LEAME.md +++ b/LEAME.md @@ -61,7 +61,7 @@ Si tienes algun problema o deseas informar de algun error, por favor, publicalo Todas las rutas de instalacion asumen que ya clonaste el repositorio: ```bash -git clone https://github.com/BU-ISCIII/iskylims.git iskylims +git clone https://gitlab.isciii.es/bu-isciii/iSkyLIMS.git iskylims cd iskylims ``` @@ -346,7 +346,7 @@ bash container_install.sh --engine podman --install_conf myprod_settings.txt --a ```bash cd -git clone https://github.com/BU-ISCIII/iskylims.git iskylims +git clone https://gitlab.isciii.es/bu-isciii/iSkyLIMS.git iskylims cd iskylims ``` From 7d034772207325bac9963bbcf71502d16389b570 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 8 Apr 2026 12:40:00 +0200 Subject: [PATCH 415/446] fallback for cp when podman rootless --- container_install.sh | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/container_install.sh b/container_install.sh index 0eb378e8d..8940bbd34 100644 --- a/container_install.sh +++ b/container_install.sh @@ -130,6 +130,24 @@ compose_exec() { "${COMPOSE_CMD[@]}" "$@" } +copy_with_podman_fallback() { + local src="$1" + local dst="$2" + + if cp "$src" "$dst" 2>/dev/null; then + return 0 + fi + + if [ "$engine" = "podman" ]; then + if podman unshare cp "$src" "$dst"; then + return 0 + fi + fi + + echo "Failed to copy '$src' to '$dst'" >&2 + return 1 +} + # PARSE VARIABLE ARGUMENTS WITH getopts options=":d:g:c:s:j:a:m:b:f:e:vhntp" while getopts $options opt; do @@ -511,7 +529,9 @@ print_existing_artifact_diagnostics echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=dep and GIT_REVISION=$git_revision..." mkdir -p "$app_install_path/conf" "/var/log/local/apache" if [ -f "$repo_root/conf/iskylims_apache_reverse_proxy.conf" ]; then - cp "$repo_root/conf/iskylims_apache_reverse_proxy.conf" "$app_install_path/conf/iskylims_apache_reverse_proxy.conf" + copy_with_podman_fallback \ + "$repo_root/conf/iskylims_apache_reverse_proxy.conf" \ + "$app_install_path/conf/iskylims_apache_reverse_proxy.conf" fi INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" APP_INSTALL_PATH="$app_install_path" \ compose_exec -f "$compose_file" build --no-cache \ From 863fa96e4954b80eb9cc5a3c4efd3a49b45ca309 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 13 Apr 2026 13:07:14 +0200 Subject: [PATCH 416/446] apache conf for data size bodies,.. --- conf/iskylims_apache_reverse_proxy.conf | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/conf/iskylims_apache_reverse_proxy.conf b/conf/iskylims_apache_reverse_proxy.conf index 2ab7cde4f..c0a2a727a 100644 --- a/conf/iskylims_apache_reverse_proxy.conf +++ b/conf/iskylims_apache_reverse_proxy.conf @@ -7,6 +7,15 @@ RequestHeader set X-Forwarded-Proto "http" RequestHeader set X-Forwarded-Port "8080" + # Allow larger POST bodies to reach Django instead of being rejected by + # Apache first. Adjust this value if your deployment needs larger uploads. + LimitRequestBody 52428800 + + + SecRequestBodyLimit 52428800 + SecRequestBodyNoFilesLimit 52428800 + + ProxyPass /static ! Alias /static /opt/iskylims/static From 6d7fc5150f31c06b680bd262a94395f5dfcc9f7b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 14 Apr 2026 11:28:39 +0200 Subject: [PATCH 417/446] change container install way separating app install from db aplication --- Dockerfile | 4 +- container_install.sh | 14 ++-- install.sh | 145 +++++++++++++++++++++++++++++++------ scripts/container_start.sh | 19 ++--- 4 files changed, 144 insertions(+), 38 deletions(-) diff --git a/Dockerfile b/Dockerfile index 3998d1ead..ea5a6182d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -70,9 +70,11 @@ ARG INSTALL_TYPE=dep ARG GIT_REVISION=main ARG INSTALL_CONF=conf/docker_test_settings.txt -# Execute the dependency stage only; app migrations run when the container is up. +# Prepare dependencies and stage the application tree in the image so the +# container can restart without rerunning install-time file generation. ENV SKIP_SYSTEM_PACKAGES=1 RUN /bin/bash install.sh --install dep --git_revision $GIT_REVISION --conf $INSTALL_CONF --skip_apache_restart +RUN /bin/bash install.sh --stage install --git_revision $GIT_REVISION --conf $INSTALL_CONF --skip_apache_restart # Use the virtualenv created by install.sh ENV PATH="${APP_INSTALL_PATH}/virtualenv/bin:${PATH}" diff --git a/container_install.sh b/container_install.sh index 8940bbd34..89408aec6 100644 --- a/container_install.sh +++ b/container_install.sh @@ -526,7 +526,7 @@ cleanup_stale_test_containers print_local_source_diagnostics print_existing_artifact_diagnostics -echo "Deploying containers (compose file: $compose_file) with INSTALL_TYPE=dep and GIT_REVISION=$git_revision..." +echo "Deploying containers (compose file: $compose_file) with a pre-staged app image and GIT_REVISION=$git_revision..." mkdir -p "$app_install_path/conf" "/var/log/local/apache" if [ -f "$repo_root/conf/iskylims_apache_reverse_proxy.conf" ]; then copy_with_podman_fallback \ @@ -577,17 +577,17 @@ if [ "$run_script" = true ]; then fi if [ "$action" = "upgrade" ]; then - echo "Running install.sh upgrade inside the container" - engine_exec exec -it "$app_container" bash -c "cd $app_repo_path && bash install.sh --upgrade app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" + echo "Running install.sh bootstrap inside the container (upgrade mode)" + engine_exec exec -it "$app_container" bash -c "cd $app_repo_path && bash install.sh --bootstrap upgrade --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" else - echo "Running install.sh install inside the container" - engine_exec exec -it "$app_container" bash -c "cd $app_repo_path && bash install.sh --install app --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" + echo "Running install.sh bootstrap inside the container (install mode)" + engine_exec exec -it "$app_container" bash -c "cd $app_repo_path && bash install.sh --bootstrap install --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" fi -print_container_source_diagnostics "Container diagnostics after install.sh:" +print_container_source_diagnostics "Container diagnostics after bootstrap:" if ! engine_exec exec -it "$app_container" test -f "$app_install_path/manage.py"; then - echo "Error: $app_install_path/manage.py not found after install.sh. Showing logs:" + echo "Error: $app_install_path/manage.py not found after bootstrap. Showing logs:" engine_exec logs --tail 200 "$app_container" exit 1 fi diff --git a/install.sh b/install.sh index cca681a06..d371636da 100644 --- a/install.sh +++ b/install.sh @@ -11,6 +11,8 @@ usage : $0 --upgrade --git_revision --conf Optional input data: --install | Install iskylims full/dep/app --upgrade | Upgrade iskylims full/dep/app + --stage | Stage app files only (install/upgrade) without DB work. Internal/container use. + --bootstrap | Run DB/bootstrap steps only (install/upgrade) against an existing staged app. Internal/container use. --git_revision | Git revision name to run (branch, tag, commit SHA, or 'current' to use copied local sources as-is) --conf | Select custom configuration file. Default: ./install_settings.txt --tables | Load the first inital tables (from conf folder) @@ -35,6 +37,12 @@ Examples: Upgrade running migration script and update initial tables $0 --upgrade full --script --tables + Stage application files during a container image build + $0 --stage install --git_revision main --conf conf/docker_production_settings.txt + + Bootstrap database/static using an already staged container image + $0 --bootstrap upgrade --git_revision main --conf conf/docker_production_settings.txt + Make adjustments for apps renaming in upgrade 2.3.0 to 2.3.1 $0 --upgrade full --ren_app --script --tables @@ -331,6 +339,20 @@ check_requirements() { fi } +check_stage_requirements() { + log_section "Checking requirements for staged app preparation" + python_check + log_info "Valid version of Python" +} + +check_bootstrap_requirements() { + log_section "Checking requirements for application bootstrap" + python_check + log_info "Valid version of Python" + db_check + log_info "Successful check for database" +} + # rename_apps_if_needed: handles legacy app renaming and DB/migration adjustments when --ren_app is provided. rename_apps_if_needed() { if [ $ren_app != true ]; then @@ -558,6 +580,20 @@ run_django_deploy() { fi } +refresh_static_files() { + echo "Deleting static files..." + if [ -d "$INSTALL_PATH/static" ]; then + if command -v mountpoint >/dev/null 2>&1 && mountpoint -q "$INSTALL_PATH/static"; then + echo "Static directory is a mount point. Skipping delete." + else + rm -rf "$INSTALL_PATH/static" || echo "Skipping static removal (busy)." + fi + fi + echo "Running collect statics..." + python manage.py collectstatic --noinput + echo "Done collect statics" +} + # sync_requirements_file: copy repository requirements into the target installation path. sync_requirements_file() { mkdir -p $INSTALL_PATH/conf @@ -717,6 +753,18 @@ upgrade_application_files() { rename_apps_if_needed + stage_upgrade_application_files + bootstrap_application_runtime "upgrade" + + log_section "Successfuly upgrade of iSKyLIMS version: ${APP_VERSION}" +} + +# stage_upgrade_application_files: sync code/config into INSTALL_PATH without DB work. +stage_upgrade_application_files() { + if [ ! -d $INSTALL_PATH ]; then + abort_install "Unable to start the upgrade. Folder $INSTALL_PATH does not exist." + fi + echo "Copying files to installation folder" rsync -rlv conf/ $INSTALL_PATH/conf/ rsync -rlv --fuzzy --delay-updates --delete-delay \ @@ -737,25 +785,19 @@ upgrade_application_files() { update_settings_and_urls prepare_documents_structure - run_django_deploy "upgrade" - echo "Deleting static files..." - if [ -d "$INSTALL_PATH/static" ]; then - if command -v mountpoint >/dev/null 2>&1 && mountpoint -q "$INSTALL_PATH/static"; then - echo "Static directory is a mount point. Skipping delete." - else - rm -rf "$INSTALL_PATH/static" || echo "Skipping static removal (busy)." - fi - fi - echo "Running collect statics..." - python manage.py collectstatic - echo "Done collect statics" - cd - - log_section "Successfuly upgrade of iSKyLIMS version: ${APP_VERSION}" } # install_application_files: deploy Django project files, update settings, and run initial migrations. install_application_files() { + stage_install_application_files + bootstrap_application_runtime "install" + log_section "Successfuly iSkyLIMS Installation version: ${APP_VERSION}" + echo "Installation completed" +} + +# stage_install_application_files: copy app files into INSTALL_PATH without DB work. +stage_install_application_files() { log_section "Starting iSkyLIMS install version: ${APP_VERSION}" user=${SUDO_USER:-$USER} @@ -813,16 +855,31 @@ install_application_files() { update_settings_and_urls - run_django_deploy "install" + cd - + fi +} - echo "Run collectstatic" - python manage.py collectstatic +# bootstrap_application_runtime: run DB/bootstrap tasks against an already staged INSTALL_PATH. +bootstrap_application_runtime() { + local mode="$1" - cd - + if [ ! -d "$INSTALL_PATH" ]; then + abort_install "Unable to bootstrap application. Folder $INSTALL_PATH does not exist." + fi - log_section "Successfuly iSkyLIMS Installation version: ${APP_VERSION}" - echo "Installation completed" + cd $INSTALL_PATH + ensure_virtualenv_ready + echo "activate the virtualenv" + source virtualenv/bin/activate + + if [ ! -f "$INSTALL_PATH/manage.py" ]; then + abort_install "manage.py not found at $INSTALL_PATH/manage.py. Stage application files first." fi + + run_django_deploy "$mode" + refresh_static_files + + cd - } # translate long options to short @@ -837,6 +894,8 @@ do # OPTIONAL --install) set -- "$@" -i ;; --upgrade) set -- "$@" -u ;; + --stage) set -- "$@" -j ;; + --bootstrap) set -- "$@" -l ;; --script) set -- "$@" -s ;; --script_before) set -- "$@" -p ;; --script_after) set -- "$@" -o ;; @@ -866,6 +925,8 @@ install=true install_type="full" upgrade=false upgrade_type="full" +workflow="standard" +workflow_mode="" docker=false prefilled_tables="conf/first_install_tables.json" restart_apache=true @@ -876,10 +937,11 @@ migration_script_before=() skip_tables=false # PARSE VARIABLE ARGUMENTS WITH getops -options=":c:s:i:u:r:g:tdbkvhao:p:" +options=":c:s:i:u:j:l:r:g:tdbkvhao:p:" while getopts $options opt; do case $opt in i ) + workflow="standard" install=true upgrade=false if [[ "$OPTARG" == "full" || "$OPTARG" == "dep" || "$OPTARG" == "app" ]]; then @@ -891,6 +953,7 @@ while getopts $options opt; do fi ;; u ) + workflow="standard" install=false upgrade=true if [[ "$OPTARG" == "full" || "$OPTARG" == "dep" || "$OPTARG" == "app" ]]; then @@ -901,6 +964,22 @@ while getopts $options opt; do exit 1 fi ;; + j ) + workflow="stage" + workflow_mode=$OPTARG + if [[ "$workflow_mode" != "install" && "$workflow_mode" != "upgrade" ]]; then + echo "Stage is not set to one valid option. Use: --stage install/upgrade" + exit 1 + fi + ;; + l ) + workflow="bootstrap" + workflow_mode=$OPTARG + if [[ "$workflow_mode" != "install" && "$workflow_mode" != "upgrade" ]]; then + echo "Bootstrap is not set to one valid option. Use: --bootstrap install/upgrade" + exit 1 + fi + ;; s ) run_script=true migration_script+=("$OPTARG") @@ -967,6 +1046,10 @@ if [ $upgrade == true ]; then operation="upgrade" operation_scope="$upgrade_type" fi +if [ "$workflow" != "standard" ]; then + operation="$workflow_mode" + operation_scope="app" +fi # Default to loading initial tables on installs unless explicitly skipped. if [ "$operation" = "install" ] && [ "$skip_tables" = false ] && [ "$tables" = false ]; then @@ -977,6 +1060,26 @@ load_install_config PROJECT_NAME="${PROJECT_NAME:-iskylims}" checkout_git_revision user=${SUDO_USER:-$USER} + +if [ "$workflow" = "stage" ]; then + check_stage_requirements + if [ "$workflow_mode" = "install" ]; then + stage_install_application_files + else + stage_upgrade_application_files + fi + exit 0 +fi + +if [ "$workflow" = "bootstrap" ]; then + check_bootstrap_requirements + if [ "$workflow_mode" = "upgrade" ]; then + rename_apps_if_needed + fi + bootstrap_application_runtime "$workflow_mode" + exit 0 +fi + check_requirements if [[ "$operation_scope" == "full" || "$operation_scope" == "dep" ]]; then diff --git a/scripts/container_start.sh b/scripts/container_start.sh index c4e18df6f..c55adb46b 100644 --- a/scripts/container_start.sh +++ b/scripts/container_start.sh @@ -13,16 +13,17 @@ GUNICORN_TIMEOUT="${GUNICORN_TIMEOUT:-120}" GUNICORN_KEEPALIVE="${GUNICORN_KEEPALIVE:-5}" GUNICORN_THREADS="${GUNICORN_THREADS:-2}" -WAIT_TIMEOUT_SECONDS=100 -wait_start="${SECONDS}" +if [ ! -f "${APP_DIR}/manage.py" ]; then + echo "Application entrypoint not found at ${APP_DIR}/manage.py" >&2 + ls -la "${APP_DIR}" >&2 || true + exit 1 +fi -while [ ! -f "${APP_DIR}/manage.py" ]; do - if (( SECONDS - wait_start >= WAIT_TIMEOUT_SECONDS )); then - echo "Timed out after ${WAIT_TIMEOUT_SECONDS}s waiting for ${APP_DIR}/manage.py" >&2 - exit 1 - fi - sleep 2 -done +if [ ! -f "${APP_DIR}/virtualenv/bin/activate" ]; then + echo "Virtualenv activation script not found at ${APP_DIR}/virtualenv/bin/activate" >&2 + ls -la "${APP_DIR}/virtualenv" >&2 || true + exit 1 +fi source "${APP_DIR}/virtualenv/bin/activate" From c9cc472fd1d2a29a432270dc129306d3bd304087 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 14 Apr 2026 11:29:26 +0200 Subject: [PATCH 418/446] modify leame and readme accordingly --- LEAME.md | 10 ++++++++-- README.md | 10 ++++++++-- 2 files changed, 16 insertions(+), 4 deletions(-) diff --git a/LEAME.md b/LEAME.md index e3fd04535..47c7217a1 100644 --- a/LEAME.md +++ b/LEAME.md @@ -128,6 +128,8 @@ bash container_install.sh --test --script migrate_optional_values Cuando el script termine, abre `http://localhost:8001` y crea el superusuario de Django cuando te lo pida. +La imagen ahora incluye el arbol de la aplicacion ya preparado dentro de `${APP_INSTALL_PATH}`. Por tanto, los contenedores de prueba pueden recrearse o reiniciarse sin volver a ejecutar la instalacion de ficheros; `container_install.sh` solo lanza las tareas de bootstrap de BD, scripts opcionales y estaticos. + ### Contenedor de produccion Despliega el contenedor de iSkyLIMS contra servicios MySQL/Samba externos: @@ -155,6 +157,8 @@ Despliega el contenedor de iSkyLIMS contra servicios MySQL/Samba externos: 3. Si es una instalacion nueva, crea el superusuario cuando se solicite y completa la configuracion de Samba en la UI. +Las imagenes de produccion ahora incorporan la aplicacion iSkyLIMS ya preparada. Un reinicio del host o la recreacion del contenedor ya no requiere reinstalar la aplicacion; `container_install.sh` solo ejecuta tareas de bootstrap en runtime, como migraciones, scripts/fixtures opcionales, creacion del superusuario en la primera instalacion y `collectstatic`. + UID/GID del usuario de ejecucion del contenedor (por defecto `1212:1212`): - Exporta `APP_UID` y `APP_GID` antes de ejecutar `container_install.sh` si necesitas un UID/GID distinto. @@ -244,7 +248,7 @@ Durante `container_install.sh`, el fichero `conf/iskylims_apache_reverse_proxy.c Si necesitas otra raiz de instalacion, define `INSTALL_PATH` en el fichero de configuracion o exporta `APP_INSTALL_PATH` antes de ejecutar `container_install.sh`. -`container_install.sh` crea `${APP_INSTALL_PATH}/conf` y `/var/log/local/apache` antes de `compose up`, copia ahi `conf/iskylims_apache_reverse_proxy.conf`, exporta `APP_INSTALL_PATH` a Compose y despues ejecuta `install.sh` dentro del contenedor `app`. `install.sh` crea `${INSTALL_PATH}/logs`, `${INSTALL_PATH}/documents` y ejecuta `collectstatic`, mientras que el contenedor `apache` sigue escribiendo sus logs en el path del host `/var/log/local/apache`. +`container_install.sh` crea `${APP_INSTALL_PATH}/conf` y `/var/log/local/apache` antes de `compose up`, copia ahi `conf/iskylims_apache_reverse_proxy.conf`, exporta `APP_INSTALL_PATH` a Compose y despues ejecuta `install.sh --bootstrap ...` dentro del contenedor `app`. La imagen del contenedor ya contiene el proyecto Django y el virtualenv preparados dentro de `${APP_INSTALL_PATH}`; el bootstrap aplica migraciones, scripts/fixtures opcionales y refresca `${INSTALL_PATH}/static`, mientras que el contenedor `apache` sigue escribiendo sus logs en el path del host `/var/log/local/apache`. Nota SELinux para pre-produccion y produccion: @@ -285,7 +289,7 @@ Re-despliega el contenedor de aplicacion contra una base de datos existente sin bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade ``` -La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh` dentro del contenedor, que regenera migraciones, las aplica con `--fake-initial` y evita cargar superusuario/datos demo/prueba. +La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh --bootstrap upgrade` dentro del contenedor. Los ficheros de la aplicacion ya van incorporados en la nueva imagen; la fase de bootstrap aplica migraciones con `--fake-initial`, refresca los estaticos y evita cargar superusuario/datos demo/prueba. ### Actualizacion del despliegue Docker v3.0.0 a 3.1.0 @@ -371,6 +375,8 @@ iSkyLIMS se instala en `/opt/iskylims` por defecto. El script `install.sh` gesti - `app`: despliega el codigo, actualiza ajustes, ejecuta migraciones y collectstatic (sin sudo). - `full`: ejecuta ambos pasos. +La separacion interna entre preparacion de ficheros y bootstrap se usa solo para las imagenes de contenedor. En bare-metal no cambian los comandos operativos: `--install` y `--upgrade` siguen ejecutando el flujo completo de dependencias, aplicacion y base de datos descrito aqui. + Ejemplos: ```bash diff --git a/README.md b/README.md index 3e789477d..cd4f73b06 100644 --- a/README.md +++ b/README.md @@ -126,6 +126,8 @@ bash container_install.sh --test --script migrate_optional_values 2>&1 | tee tes When the script finishes, open `http://localhost:8001` and follow the prompt to create the Django superuser. +The image now includes the staged application tree under `${APP_INSTALL_PATH}`. Test containers can therefore be recreated or restarted without rerunning the file installation step; only DB/bootstrap tasks are executed by `container_install.sh`. + ### Production container Deploy the iSkyLIMS container against external MySQL/Samba services: @@ -153,6 +155,8 @@ Deploy the iSkyLIMS container against external MySQL/Samba services: 3. If this is a fresh install, create the Django superuser when prompted and complete the Samba configuration in the UI. +Production images now bake the staged iSkyLIMS application into the image itself. Host reboots or container recreation no longer require rerunning the app installation step; `container_install.sh` only performs runtime bootstrap tasks such as migrations, optional fixtures/scripts, superuser creation on first install, and `collectstatic`. + UID/GID for the container runtime user (default `1212:1212`): - Export `APP_UID` and `APP_GID` before running `container_install.sh` if you need a different host UID/GID. @@ -242,7 +246,7 @@ During `container_install.sh`, the file `conf/iskylims_apache_reverse_proxy.conf If you need a different runtime root, set `INSTALL_PATH` in the install config file or export `APP_INSTALL_PATH` before running `container_install.sh`. -`container_install.sh` creates `${APP_INSTALL_PATH}/conf` and `/var/log/local/apache` before `compose up`, copies `conf/iskylims_apache_reverse_proxy.conf` there, passes `APP_INSTALL_PATH` into Compose, and then runs `install.sh` inside the `app` container. `install.sh` creates `${INSTALL_PATH}/logs`, `${INSTALL_PATH}/documents`, and runs `collectstatic`, while the Apache container keeps using the host log path `/var/log/local/apache`. +`container_install.sh` creates `${APP_INSTALL_PATH}/conf` and `/var/log/local/apache` before `compose up`, copies `conf/iskylims_apache_reverse_proxy.conf` there, passes `APP_INSTALL_PATH` into Compose, and then runs `install.sh --bootstrap ...` inside the `app` container. The container image already contains the staged Django project and virtualenv under `${APP_INSTALL_PATH}`; the bootstrap step applies migrations, optional scripts/fixtures, and refreshes `${INSTALL_PATH}/static`, while the Apache container keeps using the host log path `/var/log/local/apache`. SELinux note for pre-production and production: @@ -283,7 +287,7 @@ Re-deploy the application container against an existing production database with bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log ``` -The upgrade path rebuilds/restarts the container and runs `install.sh` inside the app container, which regenerates migrations, applies them with `--fake-initial`, and skips superuser/demo/test data loading. +The upgrade path rebuilds/restarts the container and runs `install.sh --bootstrap upgrade` inside the app container. The app files are already baked into the rebuilt image; the bootstrap phase applies migrations with `--fake-initial`, refreshes static files, and skips superuser/demo/test data loading. ### Upgrade docker deployment v3.0.0 to 3.1.0 @@ -358,6 +362,8 @@ iSkyLIMS is installed to `/opt/iskylims` by default. The single `install.sh` scr - `app`: deploy iSkyLIMS code, update settings, run migrations, and collect static files (no sudo needed). - `full`: run both stages in sequence. +The staged/bootstrap split added for container images is internal. Bare-metal commands do not change: `--install` and `--upgrade` still run the complete dependency, application, and database workflow documented here. + Examples: ```bash From bfef5454f7dec2e8abdf668d4ed1d6305baf435b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 14 Apr 2026 17:20:27 +0200 Subject: [PATCH 419/446] change Z to z in bind mounts with selinux --- docker-compose.prod.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 6e51996c8..4731038bc 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -46,9 +46,9 @@ services: volumes: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo - - /var/log/local/apps/iskylims:${APP_INSTALL_PATH:-/opt/iskylims}/logs:Z + - /var/log/local/apps/iskylims:${APP_INSTALL_PATH:-/opt/iskylims}/logs:z - iskylims_documents:${APP_INSTALL_PATH:-/opt/iskylims}/documents - - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static:Z + - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static:z extra_hosts: - "host.docker.internal:host-gateway" From b4bc46000d6fef5a3a4928d5ce9e87b69e45f4ab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Wed, 15 Apr 2026 13:25:17 +0200 Subject: [PATCH 420/446] updated changelog --- CHANGELOG.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 33fa1d19d..68abd529f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -30,6 +30,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Enabled Docker internal networking for local test installation [#389](https://github.com/BU-ISCIII/iskylims/pull/389) - Opened Docker network to allow localhost MySQL connection when required [#389](https://github.com/BU-ISCIII/iskylims/pull/389) - Added test fixtures and installation updates for the new sequencer and SampleSheet v2 support, including admin test-group assignment and new sequencer bootstrap data. Closes [#388](https://github.com/BU-ISCIII/iskylims/issues/388) [#392](https://github.com/BU-ISCIII/iskylims/pull/392) +- Refactored container installation flow to separate staged application install from runtime bootstrap tasks [#393](https://github.com/BU-ISCIII/iskylims/pull/393) +- Updated Docker image build to stage application files at build time and run bootstrap tasks on container start/upgrade [#393](https://github.com/BU-ISCIII/iskylims/pull/393) +- Replaced container cron runtime with supercronic and improved multi-container install configuration [#391](https://github.com/BU-ISCIII/iskylims/pull/391) #### Fixes @@ -73,6 +76,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Fixed samplesheet parsing error [#389](https://github.com/BU-ISCIII/iskylims/pull/389) - Fixed logger inconsistency that prevented exceptions and error messages from being written to the update crontab log. Closes [#390](https://github.com/BU-ISCIII/iskylims/issues/390) [#392](https://github.com/BU-ISCIII/iskylims/pull/392) - Fixed wetlab crontab processing for the new sequencer, including run discovery, completion checks, RunInfo/RunParameters parsing updates, and SampleSheet v2 handling. Closes [#387](https://github.com/BU-ISCIII/iskylims/issues/387) [#392](https://github.com/BU-ISCIII/iskylims/pull/392) +- Improved Podman compatibility and adjusted SELinux bind mount handling in production compose setup [#393](https://github.com/BU-ISCIII/iskylims/pull/393) #### Changed @@ -87,7 +91,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - API create-sample-data Lab data mapping moved to core_config.LAB_REQUEST_ONTOLOGY_MAP [#377](https://github.com/BU-ISCIII/iskylims/pull/377) - Renamed `docker-compose.yml` to `docker-compose.test.yml` and `docker-compose.prod.yml` for test clarity [#389](https://github.com/BU-ISCIII/iskylims/pull/389) - Refactored Docker runtime handling when path is outside repository [#389](https://github.com/BU-ISCIII/iskylims/pull/389) -- Updated `docker_install.sh` with multiple reliability improvements [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Updated `docker_install.sh` to `container_install.sh` with multiple reliability improvements [#389](https://github.com/BU-ISCIII/iskylims/pull/389) - Updated upgrade scripts documentation to include execution order information and docker upgrade clarifications [#389](https://github.com/BU-ISCIII/iskylims/pull/389) #### Removed From a86cf228234bbeab19cb98f6845941e20ec253fd Mon Sep 17 00:00:00 2001 From: Alejandro Date: Wed, 7 Jan 2026 11:53:23 +0100 Subject: [PATCH 421/446] Update dockerile --- conf/docker_test_settings.txt | 9 ++++----- conf/template_settings.txt | 2 +- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/conf/docker_test_settings.txt b/conf/docker_test_settings.txt index d6546a1ec..646eb75a5 100644 --- a/conf/docker_test_settings.txt +++ b/conf/docker_test_settings.txt @@ -9,10 +9,10 @@ PYTHON_BIN_PATH='python3' # example: /opt/python/3.9.6/bin/python3 ### Settings required to access database -DB_USER='django' -DB_PASS='djangopass' -DB_NAME='iskylims_docker' -DB_SERVER_IP='db' +DB_USER='' +DB_PASS='' +DB_NAME='' +DB_SERVER_IP='host.docker.internal' DB_PORT=3306 ### Settings required for sending emails @@ -32,4 +32,3 @@ DNS_URL='*' ### Logs settings LOG_TYPE="regular_folder" # can be symbolic link, or regular_folder LOG_PATH="" # mandatory if LOG_TYPE="symbolic_link", where is the log folder so we can create a symbolic link in the repository folder. - diff --git a/conf/template_settings.txt b/conf/template_settings.txt index 6367cb736..3c098beb0 100644 --- a/conf/template_settings.txt +++ b/conf/template_settings.txt @@ -25,7 +25,7 @@ SECRET_KEY = SECRET # SECURITY WARNING: don't run with debug turned on in production! DEBUG = True -ALLOWED_HOSTS = ["localhost", "127.0.0.1", "localserverip"] +ALLOWED_HOSTS = ["*", "iskylims_app", "iskylimsapp", "localhost", "127.0.0.1"] # Application definition From f6a6ba128f0f62bc55450be08ebbea7b82051570 Mon Sep 17 00:00:00 2001 From: Alejandro Date: Thu, 16 Apr 2026 08:43:06 +0200 Subject: [PATCH 422/446] Improve supercronic download resilience in Docker build --- Dockerfile | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index ea5a6182d..ef6f5f87a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -40,9 +40,13 @@ RUN set -eux; \ aarch64) supercronic_arch="arm64" ;; \ *) echo "Unsupported architecture for supercronic: $arch" >&2; exit 1 ;; \ esac; \ - wget -q -O /usr/local/bin/supercronic \ - "https://github.com/aptible/supercronic/releases/download/${SUPERCRONIC_VERSION}/supercronic-linux-${supercronic_arch}"; \ - chmod +x /usr/local/bin/supercronic + supercronic_url="https://github.com/aptible/supercronic/releases/download/${SUPERCRONIC_VERSION}/supercronic-linux-${supercronic_arch}"; \ + if wget --tries=3 --waitretry=2 --retry-connrefused -q -O /usr/local/bin/supercronic "${supercronic_url}"; then \ + chmod +x /usr/local/bin/supercronic; \ + else \ + rm -f /usr/local/bin/supercronic; \ + echo "supercronic download failed from ${supercronic_url}; continuing without cron support"; \ + fi # Ensure python3 points to the desired version RUN ln -sf /usr/bin/python3.11 /usr/bin/python3 From 619370facc8ea7dba88d4ba64ebf5fe2e076321d Mon Sep 17 00:00:00 2001 From: Alejandro Date: Thu, 16 Apr 2026 08:47:45 +0200 Subject: [PATCH 423/446] Restore default docker test settings placeholders --- conf/docker_test_settings.txt | 9 +++++---- conf/template_settings.txt | 2 +- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/conf/docker_test_settings.txt b/conf/docker_test_settings.txt index 646eb75a5..d6546a1ec 100644 --- a/conf/docker_test_settings.txt +++ b/conf/docker_test_settings.txt @@ -9,10 +9,10 @@ PYTHON_BIN_PATH='python3' # example: /opt/python/3.9.6/bin/python3 ### Settings required to access database -DB_USER='' -DB_PASS='' -DB_NAME='' -DB_SERVER_IP='host.docker.internal' +DB_USER='django' +DB_PASS='djangopass' +DB_NAME='iskylims_docker' +DB_SERVER_IP='db' DB_PORT=3306 ### Settings required for sending emails @@ -32,3 +32,4 @@ DNS_URL='*' ### Logs settings LOG_TYPE="regular_folder" # can be symbolic link, or regular_folder LOG_PATH="" # mandatory if LOG_TYPE="symbolic_link", where is the log folder so we can create a symbolic link in the repository folder. + diff --git a/conf/template_settings.txt b/conf/template_settings.txt index 3c098beb0..6367cb736 100644 --- a/conf/template_settings.txt +++ b/conf/template_settings.txt @@ -25,7 +25,7 @@ SECRET_KEY = SECRET # SECURITY WARNING: don't run with debug turned on in production! DEBUG = True -ALLOWED_HOSTS = ["*", "iskylims_app", "iskylimsapp", "localhost", "127.0.0.1"] +ALLOWED_HOSTS = ["localhost", "127.0.0.1", "localserverip"] # Application definition From 9b06e1d3eb24e7cd0f7b7a85613ee4d083b1a21f Mon Sep 17 00:00:00 2001 From: Alejandro Date: Thu, 16 Apr 2026 10:32:41 +0200 Subject: [PATCH 424/446] Optimize stats-info aggregation queries --- wetlab/api/utils/sample.py | 116 +++++++++++++++++-------------------- 1 file changed, 53 insertions(+), 63 deletions(-) diff --git a/wetlab/api/utils/sample.py b/wetlab/api/utils/sample.py index 420f2c972..10d274a3e 100644 --- a/wetlab/api/utils/sample.py +++ b/wetlab/api/utils/sample.py @@ -1,5 +1,7 @@ from datetime import datetime +from collections import defaultdict +from django.db.models import Count import core.models import core.utils.samples import core.core_config @@ -520,62 +522,41 @@ def collect_statistics_information(data): if len(query_params) > 2: return {"ERROR": ""} - stats_data = {} - par1_values = ( - core.models.SampleProjectsFieldsValue.objects.filter( - sample_project_field_id__sample_projects_id=s_project_obj, - sample_project_field_id__sample_project_field_name__iexact=query_params[ - 0 - ], - ) - .values_list("sample_project_field_value", flat=True) - .distinct() + base_values = core.models.SampleProjectsFieldsValue.objects.filter( + sample_project_field_id__sample_projects_id=s_project_obj ) - if len(query_params) == 2: - for par1_val in par1_values: - stats_data[par1_val] = {} - - samples = core.models.SampleProjectsFieldsValue.objects.filter( - sample_project_field_id__sample_projects_id=s_project_obj, - sample_project_field_id__sample_project_field_name__iexact=query_params[ - 0 - ], - sample_project_field_value__exact=par1_val, - ).values_list("sample_id", flat=True) - par2_values = ( - core.models.SampleProjectsFieldsValue.objects.filter( - sample_id__in=samples, - sample_project_field_id__sample_project_field_name__iexact=query_params[ - 1 - ], + par1_rows = base_values.filter( + sample_project_field_id__sample_project_field_name__iexact=query_params[ + 0 + ] + ).values_list("sample_id", "sample_project_field_value") + par2_rows = base_values.filter( + sample_project_field_id__sample_project_field_name__iexact=query_params[ + 1 + ] + ).values_list("sample_id", "sample_project_field_value") + + par1_by_sample = defaultdict(list) + for sample_id, par1_val in par1_rows: + par1_by_sample[sample_id].append(par1_val) + + stats_data = defaultdict(dict) + for sample_id, par2_val in par2_rows: + for par1_val in par1_by_sample.get(sample_id, []): + stats_data[par1_val][par2_val] = ( + stats_data[par1_val].get(par2_val, 0) + 1 ) - .values_list("sample_project_field_value", flat=True) - .distinct() - ) - for par2_val in par2_values: - value = core.models.SampleProjectsFieldsValue.objects.filter( - sample_id__in=samples, - sample_project_field_id__sample_project_field_name=query_params[ - 1 - ], - sample_project_field_value__exact=par2_val, - ).count() - if value > 0: - stats_data[par1_val][par2_val] = value - else: - for par1_val in par1_values: - stats_data[par1_val] = ( - core.models.SampleProjectsFieldsValue.objects.filter( - sample_project_field_id__sample_projects_id=s_project_obj, - sample_project_field_id__sample_project_field_name__iexact=query_params[ - 0 - ], - sample_project_field_value=par1_val, - ).count() - ) - - return stats_data + return dict(stats_data) + + counts = base_values.filter( + sample_project_field_id__sample_project_field_name__iexact=query_params[ + 0 + ] + ).values("sample_project_field_value").annotate(count=Count("id")) + return { + item["sample_project_field_value"]: item["count"] for item in counts + } else: # Collect info stats for all fields # Collect the fields utilization for sample projects stats_data = { @@ -591,21 +572,30 @@ def collect_statistics_information(data): s_project_field_objs = core.models.SampleProjectsFields.objects.filter( sample_projects_id=s_project_obj ) + field_ids = list(s_project_field_objs.values_list("id", flat=True)) + total_counts = dict( + core.models.SampleProjectsFieldsValue.objects.filter( + sample_project_field_id__in=field_ids + ) + .values_list("sample_project_field_id") + .annotate(total=Count("id")) + ) + not_none_counts = dict( + core.models.SampleProjectsFieldsValue.objects.filter( + sample_project_field_id__in=field_ids + ) + .exclude(sample_project_field_value__in=["None", ""]) + .values_list("sample_project_field_id") + .annotate(total=Count("id")) + ) for s_project_field_obj in s_project_field_objs: f_name = s_project_field_obj.get_field_name() - if not core.models.SampleProjectsFieldsValue.objects.filter( - sample_project_field_id=s_project_field_obj - ).exists(): + total_count = total_counts.get(s_project_field_obj.pk, 0) + if total_count == 0: stats_data["never_used"].append(f_name) stats_data["fields_value"][f_name] = 0 continue - count_not_none = ( - core.models.SampleProjectsFieldsValue.objects.filter( - sample_project_field_id=s_project_field_obj - ) - .exclude(sample_project_field_value__in=["None", ""]) - .count() - ) + count_not_none = not_none_counts.get(s_project_field_obj.pk, 0) stats_data["fields_value"][f_name] = count_not_none if count_not_none == 0: stats_data["always_none"].append(f_name) From 00f9d9d7a7bae3487331e05336ff9f060b43f231 Mon Sep 17 00:00:00 2001 From: Alejandro Date: Thu, 16 Apr 2026 10:36:52 +0200 Subject: [PATCH 425/446] Fix linting --- wetlab/api/utils/sample.py | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/wetlab/api/utils/sample.py b/wetlab/api/utils/sample.py index 10d274a3e..30613d333 100644 --- a/wetlab/api/utils/sample.py +++ b/wetlab/api/utils/sample.py @@ -549,11 +549,15 @@ def collect_statistics_information(data): ) return dict(stats_data) - counts = base_values.filter( - sample_project_field_id__sample_project_field_name__iexact=query_params[ - 0 - ] - ).values("sample_project_field_value").annotate(count=Count("id")) + counts = ( + base_values.filter( + sample_project_field_id__sample_project_field_name__iexact=query_params[ + 0 + ] + ) + .values("sample_project_field_value") + .annotate(count=Count("id")) + ) return { item["sample_project_field_value"]: item["count"] for item in counts } From 64a797a4a33fed136496c6c32fe2e2c1699a73fa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 14 May 2026 11:49:56 +0200 Subject: [PATCH 426/446] Fix wetlab run configuration tests --- wetlab/models.py | 2 +- .../templates/wetlab/configuration_test.html | 2 +- wetlab/utils/crontab_update_run.py | 16 +++++--- wetlab/utils/fetch_info.py | 12 +++--- wetlab/utils/test_conf.py | 40 +++++++++++-------- wetlab/views.py | 6 +-- 6 files changed, 45 insertions(+), 33 deletions(-) diff --git a/wetlab/models.py b/wetlab/models.py index 184ded6d6..4948ca7c1 100644 --- a/wetlab/models.py +++ b/wetlab/models.py @@ -401,7 +401,7 @@ def set_run_error_code(self, error_code): else: self.run_error = RunErrors.objects.get(error_text__exact="Undefined") self.state_before_error = self.state - self.state = RunStates.objects.get(run_state_name__exact="Error") + self.state = RunStates.objects.get(run_state_name__exact="error") self.save() return True diff --git a/wetlab/templates/wetlab/configuration_test.html b/wetlab/templates/wetlab/configuration_test.html index 41e793c6a..ba20cf0dc 100644 --- a/wetlab/templates/wetlab/configuration_test.html +++ b/wetlab/templates/wetlab/configuration_test.html @@ -263,7 +263,7 @@
    You can not go further in the testing while the Basic test are not passed OK

    Results execution for {{run_test_result.run_test_name}} test Run

    - {% if run_test_result.Completed == "OK" %} + {% if run_test_result.completed == "OK" %}

    Run test was successfully completed

    {% else %} diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index 6fcc4880b..d1bc4ed15 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -87,7 +87,7 @@ def get_list_processed_runs(): return processed_runs -def search_update_new_runs(request_reason): +def search_update_new_runs(request_reason, run_test_folder=None): """ Description: The function will check if there are new run folders in the remote @@ -232,8 +232,14 @@ def search_update_new_runs(request_reason): logger.info(" %s : Deleted temporary run parameter file", new_run) continue else: - if experiment_name != request_reason: - logger.info("ignoring test folder %s", experiment_name) + requested_test_run = run_test_folder or request_reason + current_test_run = new_run if run_test_folder else experiment_name + if current_test_run != requested_test_run: + logger.info( + "ignoring test folder %s in remote folder %s", + experiment_name, + new_run, + ) os.remove(l_run_parameter) logger.info(" %s : Deleted temporary run parameter file", new_run) continue @@ -618,7 +624,7 @@ def manage_run_in_recorded_state(conn, run_process_objs): continue - run_process_obj.set_run_state("Sample Sent") + run_process_obj.set_run_state("sample_sent") logger.info("%s : is now on Sample Sent state", experiment_name) logger.debug(" End function manage_run_in_recorded_state") return @@ -1189,6 +1195,6 @@ def manage_run_in_processed_bcl2fastq_state(conn, run_process_objs): finish_date = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S") run_process_obj.set_run_finish_date(finish_date) # Update the run state to completed - run_process_obj.set_run_state("Completed") + run_process_obj.set_run_state("completed") logger.info("%s : is Completed", experiment_name) logger.debug(" End function manage_run_in_processed_bcl2fastq_state") diff --git a/wetlab/utils/fetch_info.py b/wetlab/utils/fetch_info.py index c4ca33fb3..774f49f77 100644 --- a/wetlab/utils/fetch_info.py +++ b/wetlab/utils/fetch_info.py @@ -545,10 +545,10 @@ def get_information_for_incompleted_run(): data.append(str((today - recorded_date).days)) run_information["recorded"].append(data) - if wetlab.models.RunProcess.objects.filter(state__run_state_name="Error").exists(): + if wetlab.models.RunProcess.objects.filter(state__run_state_name="error").exists(): run_information["error"] = [] run_objs = wetlab.models.RunProcess.objects.filter( - state__run_state_name="Error" + state__run_state_name="error" ).order_by("run_name") for run_obj in run_objs: data = [] @@ -1215,12 +1215,12 @@ def get_sequencers_run_from_time_interval(sequencer, start_date, end_date): used_sequencer=sequencer_obj, run_date__range=(start_date, end_date) ) query_completed = run_objs_found.filter( - state__run_state_name__exact="Completed" + state__run_state_name__exact="completed" ) for item in query_completed: runs_using_sequencer["completed_run_objs"].append(item) query_not_completed = run_objs_found.exclude( - state__run_state_name__exact="Completed" + state__run_state_name__exact="completed" ) for item in query_not_completed: runs_using_sequencer["not_completed_run_objs"].append(item) @@ -1384,13 +1384,13 @@ def get_stats_sequencer_data_from_selected_runs( # get the data for run executed in other sequencers per months if ( wetlab.models.RunProcess.objects.filter( - state__run_state_name__exact="Completed" + state__run_state_name__exact="completed" ) .exclude(used_sequencer__sequencer_name__exact=sequencer) .exists() ): runs_in_other_sequencers = wetlab.models.RunProcess.objects.filter( - state__run_state_name__exact="Completed" + state__run_state_name__exact="completed" ).exclude(used_sequencer__sequencer_name__exact=sequencer) run_time_dict = {} for run_in_other_seq in runs_in_other_sequencers: diff --git a/wetlab/utils/test_conf.py b/wetlab/utils/test_conf.py index 2e1fae7e8..3b5b996c0 100644 --- a/wetlab/utils/test_conf.py +++ b/wetlab/utils/test_conf.py @@ -131,7 +131,7 @@ def delete_test_run(run_obj): return -def execute_test_for_testing_run(run_test_name): +def execute_test_for_testing_run(run_test_name, run_test_folder=None): """ Description: The funtion call the functions used in the crontab to collect run information @@ -163,15 +163,18 @@ def execute_test_for_testing_run(run_test_name): logger.info("----------------------------------") logger.info("###########---Start RUN Testing -----############") logger.info("----------------------------------") - wetlab.utils.crontab_update_run.search_update_new_runs(run_test_name) - conn = wetlab.utils.common.open_samba_connection() + wetlab.utils.crontab_update_run.search_update_new_runs( + run_test_name, run_test_folder + ) # Execute 6 times to be sure it has completed all steps state_run_test = [ - "Sample sent", - "Processed run", - "Processed Bcl2fastq", - "Completed", + "sample_sent", + "processing_run", + "processed_run", + "processing_bcl2fastq", + "processed_bcl2fastq", + "completed", ] for state_run in state_run_test: run_result[state_run] = "NOK" @@ -183,11 +186,13 @@ def execute_test_for_testing_run(run_test_name): run_obj = wetlab.models.RunProcess.objects.filter( run_name__exact=run_test_name ).last() + conn = wetlab.utils.common.open_samba_connection() for _ in range(6): + run_obj.refresh_from_db() state = run_obj.get_state() if state == "error": run_result["ERROR"] = "error" - return run_result + break elif state == "sample_sent": wetlab.utils.crontab_update_run.manage_run_in_sample_sent_processing_state( conn, [run_obj] @@ -196,7 +201,7 @@ def execute_test_for_testing_run(run_test_name): run_result["ERROR"] = "Error when processing run in Sample Sent state" break else: - run_result["Sample sent"] = "OK" + run_result["sample_sent"] = "OK" elif state == "processing_run": wetlab.utils.crontab_update_run.manage_run_in_sample_sent_processing_state( conn, [run_obj] @@ -207,7 +212,7 @@ def execute_test_for_testing_run(run_test_name): ) break else: - run_result["Processing run"] = "OK" + run_result["processing_run"] = "OK" elif state == "processed_run": wetlab.utils.crontab_update_run.manage_run_in_processed_run_state( conn, [run_obj] @@ -216,7 +221,7 @@ def execute_test_for_testing_run(run_test_name): run_result["ERROR"] = "Error when processing run in Processed Run state" break else: - run_result["Processed run"] = "OK" + run_result["processed_run"] = "OK" elif state == "processing_bcl2fastq": wetlab.utils.crontab_update_run.manage_run_in_processing_bcl2fastq_state( conn, [run_obj] @@ -227,7 +232,7 @@ def execute_test_for_testing_run(run_test_name): ) break else: - run_result["Processing Bcl2fastq"] = "OK" + run_result["processing_bcl2fastq"] = "OK" elif state == "processed_bcl2fastq": wetlab.utils.crontab_update_run.manage_run_in_processed_bcl2fastq_state( conn, [run_obj] @@ -238,11 +243,12 @@ def execute_test_for_testing_run(run_test_name): ) break else: - run_result["Processed Bcl2fastq"] = "OK" + run_result["processed_bcl2fastq"] = "OK" elif state == "completed": - run_result["Completed"] = "OK" + run_result["completed"] = "OK" break - logger.info("----------------------------------") - logger.info("###########---End RUN Testing -----############") - logger.info("----------------------------------") + conn.close() + logger.info("----------------------------------") + logger.info("###########---End RUN Testing -----############") + logger.info("----------------------------------") return run_result diff --git a/wetlab/views.py b/wetlab/views.py index 31ceca7e0..1b8ad4346 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -196,7 +196,7 @@ def configuration_test(request): {"error": wetlab.config.ERROR_NOT_FOLDER_RUN_TEST_WAS_FOUND}, ) run_test_result = wetlab.utils.test_conf.execute_test_for_testing_run( - run_test_name + run_test_name, run_test_folder ) run_test_result["run_test_name"] = run_test_name if "ERROR" in run_test_result: @@ -1169,7 +1169,7 @@ def skip_cancel_situation(request): run_id = request.POST["run_id"] if wetlab.models.RunProcess.objects.filter(pk__exact=run_id).exists(): run_name_found = wetlab.models.RunProcess.objects.get(pk__exact=run_id) - run_name_found.set_run_state("Sample Sent") + run_name_found.set_run_state("sample_sent") run_name_found.set_forced_continue_on_error() detail_description = {} detail_description["information"] = ( @@ -1262,7 +1262,7 @@ def incompleted_runs(request): ) if ( wetlab.models.wetlab.models.RunProcess.objects.all() - .exclude(state__run_state_name="Completed") + .exclude(state__run_state_name="completed") .exists() ): display_incompleted_run = ( From 5bc3fa28f0e539a5acfda9a822d766f1fb417a3c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 14 May 2026 11:50:22 +0200 Subject: [PATCH 427/446] Refresh install fixtures on Docker upgrades --- LEAME.md | 6 +++--- README.md | 6 +++--- container_install.sh | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/LEAME.md b/LEAME.md index 47c7217a1..13dc09e6f 100644 --- a/LEAME.md +++ b/LEAME.md @@ -157,7 +157,7 @@ Despliega el contenedor de iSkyLIMS contra servicios MySQL/Samba externos: 3. Si es una instalacion nueva, crea el superusuario cuando se solicite y completa la configuracion de Samba en la UI. -Las imagenes de produccion ahora incorporan la aplicacion iSkyLIMS ya preparada. Un reinicio del host o la recreacion del contenedor ya no requiere reinstalar la aplicacion; `container_install.sh` solo ejecuta tareas de bootstrap en runtime, como migraciones, scripts/fixtures opcionales, creacion del superusuario en la primera instalacion y `collectstatic`. +Las imagenes de produccion ahora incorporan la aplicacion iSkyLIMS ya preparada. Un reinicio del host o la recreacion del contenedor ya no requiere reinstalar la aplicacion; `container_install.sh` solo ejecuta tareas de bootstrap en runtime, como migraciones, refresco de fixtures, scripts opcionales, creacion del superusuario en la primera instalacion y `collectstatic`. UID/GID del usuario de ejecucion del contenedor (por defecto `1212:1212`): @@ -283,13 +283,13 @@ export APP_UID=1212 export APP_GID=1212 ``` -Re-despliega el contenedor de aplicacion contra una base de datos existente sin tocar los datos: +Re-despliega el contenedor de aplicacion contra una base de datos existente: ```bash bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade ``` -La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh --bootstrap upgrade` dentro del contenedor. Los ficheros de la aplicacion ya van incorporados en la nueva imagen; la fase de bootstrap aplica migraciones con `--fake-initial`, refresca los estaticos y evita cargar superusuario/datos demo/prueba. +La actualizacion reconstruye/reinicia el contenedor y ejecuta `install.sh --bootstrap upgrade --tables` dentro del contenedor. Los ficheros de la aplicacion ya van incorporados en la nueva imagen; la fase de bootstrap aplica migraciones con `--fake-initial`, refresca `conf/first_install_tables.json`, refresca los estaticos y evita cargar superusuario/datos demo/prueba. ### Actualizacion del despliegue Docker v3.0.0 a 3.1.0 diff --git a/README.md b/README.md index cd4f73b06..87cf5701a 100644 --- a/README.md +++ b/README.md @@ -155,7 +155,7 @@ Deploy the iSkyLIMS container against external MySQL/Samba services: 3. If this is a fresh install, create the Django superuser when prompted and complete the Samba configuration in the UI. -Production images now bake the staged iSkyLIMS application into the image itself. Host reboots or container recreation no longer require rerunning the app installation step; `container_install.sh` only performs runtime bootstrap tasks such as migrations, optional fixtures/scripts, superuser creation on first install, and `collectstatic`. +Production images now bake the staged iSkyLIMS application into the image itself. Host reboots or container recreation no longer require rerunning the app installation step; `container_install.sh` only performs runtime bootstrap tasks such as migrations, fixture refreshes, optional scripts, superuser creation on first install, and `collectstatic`. UID/GID for the container runtime user (default `1212:1212`): @@ -281,13 +281,13 @@ export APP_UID=1212 export APP_GID=1212 ``` -Re-deploy the application container against an existing production database without touching data: +Re-deploy the application container against an existing production database: ```bash bash container_install.sh --install_conf conf/my_prod_settings.txt --action upgrade 2>&1 | tee ./iskylims_docker_install_$(date +%Y%m%d_%H%M%S).log ``` -The upgrade path rebuilds/restarts the container and runs `install.sh --bootstrap upgrade` inside the app container. The app files are already baked into the rebuilt image; the bootstrap phase applies migrations with `--fake-initial`, refreshes static files, and skips superuser/demo/test data loading. +The upgrade path rebuilds/restarts the container and runs `install.sh --bootstrap upgrade --tables` inside the app container. The app files are already baked into the rebuilt image; the bootstrap phase applies migrations with `--fake-initial`, refreshes `conf/first_install_tables.json`, refreshes static files, and skips superuser/demo/test data loading. ### Upgrade docker deployment v3.0.0 to 3.1.0 diff --git a/container_install.sh b/container_install.sh index 89408aec6..b4b7689ca 100644 --- a/container_install.sh +++ b/container_install.sh @@ -578,7 +578,7 @@ fi if [ "$action" = "upgrade" ]; then echo "Running install.sh bootstrap inside the container (upgrade mode)" - engine_exec exec -it "$app_container" bash -c "cd $app_repo_path && bash install.sh --bootstrap upgrade --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" + engine_exec exec -it "$app_container" bash -c "cd $app_repo_path && bash install.sh --bootstrap upgrade --git_revision \"$git_revision\" --conf \"$install_conf_container\" --tables --skip_apache_restart$script_args_before$script_args_after" else echo "Running install.sh bootstrap inside the container (install mode)" engine_exec exec -it "$app_container" bash -c "cd $app_repo_path && bash install.sh --bootstrap install --git_revision \"$git_revision\" --conf \"$install_conf_container\" --skip_apache_restart$script_args_before$script_args_after" From 1590bd8e240fa14e72660a1a23eb32fc6ad321bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 14 May 2026 11:52:24 +0200 Subject: [PATCH 428/446] update proxy server conf --- conf/iskylims_apache_reverse_proxy.conf | 3 +++ 1 file changed, 3 insertions(+) diff --git a/conf/iskylims_apache_reverse_proxy.conf b/conf/iskylims_apache_reverse_proxy.conf index c0a2a727a..a7c78231d 100644 --- a/conf/iskylims_apache_reverse_proxy.conf +++ b/conf/iskylims_apache_reverse_proxy.conf @@ -6,6 +6,7 @@ ProxyPreserveHost On RequestHeader set X-Forwarded-Proto "http" RequestHeader set X-Forwarded-Port "8080" + RequestHeader set X-Forwarded-Host "iskyimsdocker.isciiides.es" # Allow larger POST bodies to reach Django instead of being rejected by # Apache first. Adjust this value if your deployment needs larger uploads. @@ -24,6 +25,8 @@ ProxyPass / http://app:8001/ ProxyPassReverse / http://app:8001/ + ProxyTimeout 300 + TimeOut 300 ErrorLog /var/log/httpd/iskylims-apache.error.log CustomLog /var/log/httpd/iskylims-apache.access.log combined From 49acfb53cf71fe6f08c070144d1b858f6bd27fca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 14 May 2026 16:26:54 +0200 Subject: [PATCH 429/446] Fix duplicate wetlab run test logging --- wetlab/utils/common.py | 12 ++++++++++++ wetlab/utils/test_conf.py | 2 -- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/wetlab/utils/common.py b/wetlab/utils/common.py index eab207aed..ad107b26f 100644 --- a/wetlab/utils/common.py +++ b/wetlab/utils/common.py @@ -500,4 +500,16 @@ def open_log(config_file): # Keep existing named loggers active; otherwise fileConfig may disable them. fileConfig(config_file, disable_existing_loggers=False) logger = logging.getLogger() + seen_handlers = set() + for handler in logger.handlers[:]: + base_filename = getattr(handler, "baseFilename", None) + if base_filename: + handler_id = (handler.__class__, base_filename) + else: + handler_id = (handler.__class__, getattr(handler, "stream", None)) + if handler_id in seen_handlers: + logger.removeHandler(handler) + handler.close() + else: + seen_handlers.add(handler_id) return logger diff --git a/wetlab/utils/test_conf.py b/wetlab/utils/test_conf.py index 3b5b996c0..4fbeef35c 100644 --- a/wetlab/utils/test_conf.py +++ b/wetlab/utils/test_conf.py @@ -1,6 +1,5 @@ # Generic imports import grp -import logging import os import pwd @@ -159,7 +158,6 @@ def execute_test_for_testing_run(run_test_name, run_test_folder=None): settings.BASE_DIR, "wetlab", wetlab.config.LOGGING_CONFIG_FILE ) logger = wetlab.utils.common.open_log(config_file) - logger = logging.getLogger(__name__) logger.info("----------------------------------") logger.info("###########---Start RUN Testing -----############") logger.info("----------------------------------") From d4bbb4fe3f6bc7a475aa5b2563bf5f5621e06255 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 14 May 2026 16:27:03 +0200 Subject: [PATCH 430/446] Stage Apache configs for production containers --- conf/docker_production_settings.txt | 3 +++ conf/iskylims_apache_logs.conf | 17 +++++++++++++++++ conf/iskylims_apache_reverse_proxy.conf | 19 +++++++++++++------ conf/template_install_settings.txt | 4 +++- container_install.sh | 18 ++++++++++++++---- docker-compose.prod.yml | 19 ++++++++++--------- 6 files changed, 60 insertions(+), 20 deletions(-) create mode 100644 conf/iskylims_apache_logs.conf diff --git a/conf/docker_production_settings.txt b/conf/docker_production_settings.txt index 3f07fbd65..ff77ebd8c 100644 --- a/conf/docker_production_settings.txt +++ b/conf/docker_production_settings.txt @@ -4,6 +4,9 @@ ### Installation path and modules settings INSTALL_PATH='/opt/iskylims' +# Optional host directory for Apache bind-mounted conf files. +# Leave empty to use ${INSTALL_PATH}/conf. +APACHE_CONF_PATH='' REQUIRED_MODULES='core drylab wetlab clinic django_utils' MIGRATION_MODULES='core drylab wetlab django_utils' FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' diff --git a/conf/iskylims_apache_logs.conf b/conf/iskylims_apache_logs.conf new file mode 100644 index 000000000..0ecafdbdd --- /dev/null +++ b/conf/iskylims_apache_logs.conf @@ -0,0 +1,17 @@ +ErrorLog "logs/apache_error.log" + + + LogFormat "%v %a %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\" %D %I %O" combined + LogFormat "%v %{X-Forwarded-For}i %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\" %D %I %O" proxy + LogFormat "%v %{X-Forwarded-For}i %l %u %t \"%r\" %>s %b" common + LogFormat "%{Referer}i -> %U" referer + LogFormat "%{User-agent}i" agent + + + LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" \"%{User-Agent}i\" %I %O" combinedio + + + SetEnvIf X-Forwarded-For "^.*\..*\..*\..*" forwarded + CustomLog "logs/apache.access.log" combined env=!forwarded + CustomLog "logs/apache.access.log" proxy env=forwarded + diff --git a/conf/iskylims_apache_reverse_proxy.conf b/conf/iskylims_apache_reverse_proxy.conf index a7c78231d..3c7f576a7 100644 --- a/conf/iskylims_apache_reverse_proxy.conf +++ b/conf/iskylims_apache_reverse_proxy.conf @@ -1,12 +1,13 @@ # Apache reverse proxy config for iSkyLIMS production container - ServerName iskyimsdocker.isciiides.es + ServerName dockeriskyims.isciiides.es ProxyPreserveHost On - RequestHeader set X-Forwarded-Proto "http" - RequestHeader set X-Forwarded-Port "8080" - RequestHeader set X-Forwarded-Host "iskyimsdocker.isciiides.es" + RequestHeader set X-Forwarded-Proto "https" + RequestHeader set X-Forwarded-Port "443" + RequestHeader set X-Forwarded-Host "dockeriskyims.isciiides.es" + # Allow larger POST bodies to reach Django instead of being rejected by # Apache first. Adjust this value if your deployment needs larger uploads. @@ -28,6 +29,12 @@ ProxyTimeout 300 TimeOut 300 - ErrorLog /var/log/httpd/iskylims-apache.error.log - CustomLog /var/log/httpd/iskylims-apache.access.log combined + #ErrorLog logs/iskylims.pre.isciii.es-apache.error.log + #CustomLog logs/iskylims.pre.isciii.es-apache.access.log combined + + CustomLog logs/dockeriskyims.isciiides.es-apache.access.log combined env=!forwarded + CustomLog logs/dockeriskyims.isciiides.es-apache.access.log proxy env=forwarded + + ErrorLog logs/iskylims.pre.isciii.es-apache.error.log + diff --git a/conf/template_install_settings.txt b/conf/template_install_settings.txt index 43db77dae..2e963bc64 100644 --- a/conf/template_install_settings.txt +++ b/conf/template_install_settings.txt @@ -1,5 +1,8 @@ ### Installation path and modules settings INSTALL_PATH='/opt/iskylims' +# Optional host directory for Apache bind-mounted conf files. +# Leave empty to use ${INSTALL_PATH}/conf. +APACHE_CONF_PATH='' REQUIRED_MODULES='core drylab wetlab clinic django_utils' MIGRATION_MODULES='core drylab wetlab django_utils' FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' @@ -32,4 +35,3 @@ DNS_URL='' ### Logs settings LOG_TYPE="symbolic_link" # can be symbolic link, or regular_folder LOG_PATH="" # mandatory if LOG_TYPE="symbolic_link", where is the log folder so we can create a symbolic link in the repository folder. - diff --git a/container_install.sh b/container_install.sh index b4b7689ca..e83d76b5a 100644 --- a/container_install.sh +++ b/container_install.sh @@ -337,6 +337,11 @@ set_engine app_repo_path="${APP_REPO_PATH:-/srv/iskylims}" config_install_path="$(read_install_conf_value "INSTALL_PATH" "$host_install_conf_path")" app_install_path="${APP_INSTALL_PATH:-${config_install_path:-/opt/iskylims}}" +config_apache_conf_path="$(read_install_conf_value "APACHE_CONF_PATH" "$host_install_conf_path")" +apache_conf_path="${APACHE_CONF_PATH:-${config_apache_conf_path:-}}" +if [ -z "$apache_conf_path" ]; then + apache_conf_path="$app_install_path/conf" +fi app_port="${APP_PORT:-8001}" app_container="" local_head_hash="" @@ -527,20 +532,25 @@ cleanup_stale_test_containers print_local_source_diagnostics print_existing_artifact_diagnostics echo "Deploying containers (compose file: $compose_file) with a pre-staged app image and GIT_REVISION=$git_revision..." -mkdir -p "$app_install_path/conf" "/var/log/local/apache" +mkdir -p "$app_install_path/conf" "$apache_conf_path" "/var/log/local/iskylims/apache" "/var/log/local/iskylims/apps" if [ -f "$repo_root/conf/iskylims_apache_reverse_proxy.conf" ]; then copy_with_podman_fallback \ "$repo_root/conf/iskylims_apache_reverse_proxy.conf" \ - "$app_install_path/conf/iskylims_apache_reverse_proxy.conf" + "$apache_conf_path/iskylims_apache_reverse_proxy.conf" +fi +if [ -f "$repo_root/conf/iskylims_apache_logs.conf" ]; then + copy_with_podman_fallback \ + "$repo_root/conf/iskylims_apache_logs.conf" \ + "$apache_conf_path/iskylims_apache_logs.conf" fi -INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" APP_INSTALL_PATH="$app_install_path" \ +INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" APP_INSTALL_PATH="$app_install_path" APACHE_CONF_PATH="$apache_conf_path" \ compose_exec -f "$compose_file" build --no-cache \ --build-arg INSTALL_TYPE="dep" \ --build-arg GIT_REVISION="$git_revision" \ --build-arg INSTALL_CONF="$install_conf_container" \ --build-arg APP_INSTALL_PATH="$app_install_path" print_image_after_build -APP_INSTALL_PATH="$app_install_path" compose_exec -f "$compose_file" up -d +APP_INSTALL_PATH="$app_install_path" APACHE_CONF_PATH="$apache_conf_path" compose_exec -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." sleep 20 diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 4731038bc..2b821242f 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -11,10 +11,11 @@ services: - "8080:8080" volumes: - /etc/localtime:/etc/localtime:ro - - /usr/share/zoneinfo:/usr/share/zoneinfo - - ${APP_INSTALL_PATH:-/opt/iskylims}/conf/iskylims_apache_reverse_proxy.conf:/etc/httpd/conf.d/iskylims.conf:Z,ro - - /var/log/local/apache:/var/log/httpd - - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static:Z,ro + - /usr/share/zoneinfo:/usr/share/zoneinfo:ro + - ${APACHE_CONF_PATH:-/opt/iskylims/conf}/iskylims_apache_reverse_proxy.conf:/etc/httpd/conf.d/iskylims.conf:ro + - ${APACHE_CONF_PATH:-/opt/iskylims/conf}/iskylims_apache_logs.conf:/etc/httpd/conf.d/logformat.conf:ro + - /var/log/local/iskylims/apache:/var/log/httpd:U + - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static:ro app: container_name: iskylims_app @@ -39,16 +40,16 @@ services: DB_CONN_MAX_AGE: ${DB_CONN_MAX_AGE:-60} WEB_CONCURRENCY: ${WEB_CONCURRENCY:-2} GUNICORN_THREADS: ${GUNICORN_THREADS:-2} - GUNICORN_TIMEOUT: ${GUNICORN_TIMEOUT:-120} + GUNICORN_TIMEOUT: ${GUNICORN_TIMEOUT:-300} GUNICORN_KEEPALIVE: ${GUNICORN_KEEPALIVE:-5} APP_INSTALL_PATH: ${APP_INSTALL_PATH:-/opt/iskylims} - user: "${APP_UID:-1212}:${APP_GID:-1212}" + user: "${APP_UID:-1005}:${APP_GID:-1005}" volumes: - /etc/localtime:/etc/localtime:ro - - /usr/share/zoneinfo:/usr/share/zoneinfo - - /var/log/local/apps/iskylims:${APP_INSTALL_PATH:-/opt/iskylims}/logs:z + - /usr/share/zoneinfo:/usr/share/zoneinfo:ro + - /var/log/local/iskylims/apps/:${APP_INSTALL_PATH:-/opt/iskylims}/logs:U - iskylims_documents:${APP_INSTALL_PATH:-/opt/iskylims}/documents - - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static:z + - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static extra_hosts: - "host.docker.internal:host-gateway" From e605673bd1a29d11d8a28f83875085d53014c0fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 14 May 2026 16:27:12 +0200 Subject: [PATCH 431/446] Document production container bind mounts --- LEAME.md | 50 ++++++++++++++++++++++++++------------------------ README.md | 42 ++++++++++++++++++++++-------------------- 2 files changed, 48 insertions(+), 44 deletions(-) diff --git a/LEAME.md b/LEAME.md index 13dc09e6f..2f43f9774 100644 --- a/LEAME.md +++ b/LEAME.md @@ -170,14 +170,15 @@ export APP_GID=1212 Variables opcionales de build/runtime para produccion: -- `APP_INSTALL_PATH`: cambia la raiz de instalacion en runtime usada por el contenedor `app`, el montaje de configuracion de Apache, los estaticos/documentos y los scripts de instalacion. Valor por defecto: `/opt/iskylims`. +- `APP_INSTALL_PATH`: cambia la raiz de instalacion en runtime usada por el contenedor `app`, los estaticos/documentos y los scripts de instalacion. Valor por defecto: `/opt/iskylims`. +- `APACHE_CONF_PATH`: cambia el directorio host usado para los ficheros de configuracion de Apache montados por bind mount. Si esta vacio, `container_install.sh` usa `${APP_INSTALL_PATH}/conf`. - `APP_UID` / `APP_GID`: UID/GID de ejecucion del usuario `iskylims` dentro del contenedor. Valor por defecto: `1212:1212`. - `APP_SHELL`: shell asignada al usuario de runtime durante la build. Valor por defecto: `/sbin/nologin`. - `APP_PORT`: puerto interno donde Gunicorn escucha dentro del servicio `app`. Valor por defecto: `8001`. - `DB_CONN_MAX_AGE`: tiempo de vida, en segundos, de las conexiones persistentes de Django a la BD. Valor por defecto: `60`. - `WEB_CONCURRENCY`: numero de workers de Gunicorn. Valor por defecto en compose: `2`. Si no se define en el entrypoint, se calcula segun CPU disponible. - `GUNICORN_THREADS`: numero de hilos por worker de Gunicorn. Valor por defecto: `2`. -- `GUNICORN_TIMEOUT`: timeout de peticiones Gunicorn en segundos. Valor por defecto: `120`. +- `GUNICORN_TIMEOUT`: timeout de peticiones Gunicorn en segundos. Valor por defecto: `300`. - `GUNICORN_KEEPALIVE`: keep-alive de Gunicorn en segundos. Valor por defecto: `5`. - `DJANGO_DEBUG`: se pasa al contenedor de produccion. Valor por defecto: `"false"`. Debe mantenerse desactivado en produccion. @@ -207,19 +208,20 @@ El compose de produccion usa `INSTALL_PATH` del fichero de configuracion selecci Persistencia actual: -- `/var/log/local/apps/iskylims` -> `${INSTALL_PATH}/logs` dentro del contenedor `app` -- `/var/log/local/apache` -> `/var/log/httpd` dentro del contenedor `apache` -- `${INSTALL_PATH}/conf/iskylims_apache_reverse_proxy.conf` -> `/etc/httpd/conf.d/iskylims.conf` dentro del contenedor `apache` +- `/var/log/local/iskylims/apps` -> `${INSTALL_PATH}/logs` dentro del contenedor `app` +- `/var/log/local/iskylims/apache` -> `/var/log/httpd` dentro del contenedor `apache` +- `${APACHE_CONF_PATH:-${INSTALL_PATH}/conf}/iskylims_apache_reverse_proxy.conf` -> `/etc/httpd/conf.d/iskylims.conf` dentro del contenedor `apache` +- `${APACHE_CONF_PATH:-${INSTALL_PATH}/conf}/iskylims_apache_logs.conf` -> `/etc/httpd/conf.d/logformat.conf` dentro del contenedor `apache` - volumen nombrado `iskylims_documents` -> `${INSTALL_PATH}/documents` - volumen nombrado `iskylims_static` -> `${INSTALL_PATH}/static` Crea los directorios necesarios en el host: ```bash -sudo mkdir -p /var/log/local/apps/iskylims -sudo mkdir -p /var/log/local/apache +sudo mkdir -p /var/log/local/iskylims/apps +sudo mkdir -p /var/log/local/iskylims/apache sudo mkdir -p ${APP_INSTALL_PATH:-/opt/iskylims}/conf -sudo chown -R ${APP_UID:-1212}:${APP_GID:-1212} /var/log/local/apps/iskylims ${APP_INSTALL_PATH:-/opt/iskylims} +sudo chown -R ${APP_UID:-1212}:${APP_GID:-1212} /var/log/local/iskylims/apps ${APP_INSTALL_PATH:-/opt/iskylims} ``` En hosts Podman rootless o endurecidos, ejecuta el script de preparacion del host con el mismo usuario que arranca los contenedores. El script pre-crea los ficheros de log de Apache, ajusta la propiedad para el usuario UBI httpd en Podman rootless y aplica etiquetas SELinux de contenedor cuando SELinux esta activo: @@ -244,20 +246,20 @@ Archivos estaticos: - `docker-compose.prod.yml` comparte ese directorio con `apache` mediante el volumen nombrado `iskylims_static`. - La configuracion del proxy sirve `/static` directamente desde `${INSTALL_PATH}/static`. -Durante `container_install.sh`, el fichero `conf/iskylims_apache_reverse_proxy.conf` se copia al host en `${INSTALL_PATH}/conf/iskylims_apache_reverse_proxy.conf`. A partir de ese momento, los cambios de runtime deben hacerse sobre esa copia. +Durante `container_install.sh`, los ficheros `conf/iskylims_apache_reverse_proxy.conf` y `conf/iskylims_apache_logs.conf` se copian al host en `${APACHE_CONF_PATH}`. Si `APACHE_CONF_PATH` esta vacio, se copian a `${INSTALL_PATH}/conf`. A partir de ese momento, los cambios de runtime deben hacerse sobre esas copias. -Si necesitas otra raiz de instalacion, define `INSTALL_PATH` en el fichero de configuracion o exporta `APP_INSTALL_PATH` antes de ejecutar `container_install.sh`. +Si necesitas otra raiz de instalacion, define `INSTALL_PATH` en el fichero de configuracion o exporta `APP_INSTALL_PATH` antes de ejecutar `container_install.sh`. Si necesitas que los ficheros de Apache queden fuera de la raiz de runtime de la app, define `APACHE_CONF_PATH` en el fichero de configuracion o exportalo antes de ejecutar `container_install.sh`. -`container_install.sh` crea `${APP_INSTALL_PATH}/conf` y `/var/log/local/apache` antes de `compose up`, copia ahi `conf/iskylims_apache_reverse_proxy.conf`, exporta `APP_INSTALL_PATH` a Compose y despues ejecuta `install.sh --bootstrap ...` dentro del contenedor `app`. La imagen del contenedor ya contiene el proyecto Django y el virtualenv preparados dentro de `${APP_INSTALL_PATH}`; el bootstrap aplica migraciones, scripts/fixtures opcionales y refresca `${INSTALL_PATH}/static`, mientras que el contenedor `apache` sigue escribiendo sus logs en el path del host `/var/log/local/apache`. +`container_install.sh` crea `${APP_INSTALL_PATH}/conf`, `${APACHE_CONF_PATH:-${APP_INSTALL_PATH}/conf}`, `/var/log/local/iskylims/apps` y `/var/log/local/iskylims/apache` antes de `compose up`, copia ahi los dos ficheros de configuracion de Apache, exporta `APP_INSTALL_PATH` y `APACHE_CONF_PATH` a Compose y despues ejecuta `install.sh --bootstrap ...` dentro del contenedor `app`. La imagen del contenedor ya contiene el proyecto Django y el virtualenv preparados dentro de `${APP_INSTALL_PATH}`; el bootstrap aplica migraciones, scripts/fixtures opcionales y refresca `${INSTALL_PATH}/static`, mientras que el contenedor `apache` sigue escribiendo sus logs en el path del host `/var/log/local/iskylims/apache`. Nota SELinux para pre-produccion y produccion: -- Asegura que `/var/log/local/apache` sea escribible por el runtime de contenedores y tenga una etiqueta valida para contenedores, por ejemplo `container_file_t`. +- Asegura que `/var/log/local/iskylims/apache` sea escribible por el runtime de contenedores y tenga una etiqueta valida para contenedores, por ejemplo `container_file_t`. - Si el path del host ya esta etiquetado como `container_file_t`, no anadas `:Z` al bind mount de logs de Apache. `:Z` fuerza un relabel y puede fallar con `lsetxattr(... container_file_t ...): operation not permitted`. - Comprobacion rapida: ```bash -ls -ldZ /var/log/local/apache +ls -ldZ /var/log/local/iskylims/apache ``` - Ejemplo esperado: @@ -266,7 +268,7 @@ ls -ldZ /var/log/local/apache system_u:object_r:container_file_t:s0 ``` -- Si Apache falla al arrancar con `ModSecurity: Failed to open debug log file: /var/log/httpd/modsec_debug.log`, elimina cualquier fichero host obsoleto y recrea/reinicia el contenedor. En la practica, borrar `/var/log/local/apache/modsec_debug.log` ha sido suficiente cuando el inode existente tenia permisos o contexto incorrectos. +- Si Apache falla al arrancar con `ModSecurity: Failed to open debug log file: /var/log/httpd/modsec_debug.log`, elimina cualquier fichero host obsoleto y recrea/reinicia el contenedor. En la practica, borrar `/var/log/local/iskylims/apache/modsec_debug.log` ha sido suficiente cuando el inode existente tenia permisos o contexto incorrectos. #### Tareas cron dentro del contenedor @@ -490,9 +492,9 @@ mysqldump -h -P -u iskylims -p iskylims > iskylims_$(date +% Archivo de logs: ```bash -tar -czf iskylims_app_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/apps/iskylims . +tar -czf iskylims_app_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/iskylims/apps . -tar -czf iskylims_apache_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/apache . +tar -czf iskylims_apache_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/iskylims/apache . ``` Archivo del volumen de documents: @@ -530,11 +532,11 @@ Con Podman, usa el mismo comando sustituyendo `docker` por `podman`. Restaurar logs: ```bash -mkdir -p /var/log/local/apps/iskylims -tar -xzf iskylims_app_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/apps/iskylims +mkdir -p /var/log/local/iskylims/apps +tar -xzf iskylims_app_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/iskylims/apps -mkdir -p /var/log/local/apache -tar -xzf iskylims_apache_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/apache +mkdir -p /var/log/local/iskylims/apache +tar -xzf iskylims_apache_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/iskylims/apache ``` Ejemplo de rollback completo bare-metal: @@ -607,11 +609,11 @@ mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_pro 4. Si los volumenes estan comprometidos, restauralos desde los tar: ```bash -mkdir -p /var/log/local/apps/iskylims -tar -xzf iskylims_app_logs.tgz -C /var/log/local/apps/iskylims +mkdir -p /var/log/local/iskylims/apps +tar -xzf iskylims_app_logs.tgz -C /var/log/local/iskylims/apps -mkdir -p /var/log/local/apache -tar -xzf iskylims_apache_logs.tgz -C /var/log/local/apache +mkdir -p /var/log/local/iskylims/apache +tar -xzf iskylims_apache_logs.tgz -C /var/log/local/iskylims/apache docker run --rm -v iskylims_documents:/to -v "$PWD":/from alpine \ tar -xzf /from/iskylims_documents.tgz -C /to diff --git a/README.md b/README.md index 87cf5701a..343c1f37e 100644 --- a/README.md +++ b/README.md @@ -168,14 +168,15 @@ export APP_GID=1212 Optional production runtime/build variables: -- `APP_INSTALL_PATH`: overrides the runtime install root used by the app container, Apache config mount, static/documents mounts, and install scripts. Default: `/opt/iskylims`. +- `APP_INSTALL_PATH`: overrides the runtime install root used by the app container, static/documents mounts, and install scripts. Default: `/opt/iskylims`. +- `APACHE_CONF_PATH`: overrides the host directory used for Apache bind-mounted config files. If empty, `container_install.sh` uses `${APP_INSTALL_PATH}/conf`. - `APP_UID` / `APP_GID`: runtime UID/GID for the `iskylims` user inside the container. Default: `1212:1212`. - `APP_SHELL`: shell assigned to the runtime user during image build. Default: `/sbin/nologin`. - `APP_PORT`: internal Gunicorn bind port for the `app` service. Default: `8001`. - `DB_CONN_MAX_AGE`: Django persistent DB connection lifetime in seconds. Default: `60`. - `WEB_CONCURRENCY`: Gunicorn worker count. Default: `2`. If unset in the container entrypoint, workers fall back to CPU-based auto-selection. - `GUNICORN_THREADS`: threads per Gunicorn worker. Default: `2`. -- `GUNICORN_TIMEOUT`: Gunicorn request timeout in seconds. Default: `120`. +- `GUNICORN_TIMEOUT`: Gunicorn request timeout in seconds. Default: `300`. - `GUNICORN_KEEPALIVE`: Gunicorn keep-alive in seconds. Default: `5`. - `DJANGO_DEBUG`: passed to the production app container. Default: `"false"`. Keep it disabled in production. @@ -199,9 +200,10 @@ The production compose file uses `INSTALL_PATH` from the selected install config Persistence layout: -- `/var/log/local/apps/iskylims` -> `${INSTALL_PATH}/logs` inside the `app` container -- `/var/log/local/apache` -> `/var/log/httpd` inside the `apache` container -- `${INSTALL_PATH}/conf/iskylims_apache_reverse_proxy.conf` -> `/etc/httpd/conf.d/iskylims.conf` inside the `apache` container +- `/var/log/local/iskylims/apps` -> `${INSTALL_PATH}/logs` inside the `app` container +- `/var/log/local/iskylims/apache` -> `/var/log/httpd` inside the `apache` container +- `${APACHE_CONF_PATH:-${INSTALL_PATH}/conf}/iskylims_apache_reverse_proxy.conf` -> `/etc/httpd/conf.d/iskylims.conf` inside the `apache` container +- `${APACHE_CONF_PATH:-${INSTALL_PATH}/conf}/iskylims_apache_logs.conf` -> `/etc/httpd/conf.d/logformat.conf` inside the `apache` container - `iskylims_documents` named volume -> `${INSTALL_PATH}/documents` - `iskylims_static` named volume -> `${INSTALL_PATH}/static` @@ -210,10 +212,10 @@ If you override the compose file, ensure these mounts exist to keep logs and doc Create host directories before the first deployment: ```bash -sudo mkdir -p /var/log/local/apps/iskylims -sudo mkdir -p /var/log/local/apache +sudo mkdir -p /var/log/local/iskylims/apps +sudo mkdir -p /var/log/local/iskylims/apache sudo mkdir -p ${APP_INSTALL_PATH:-/opt/iskylims}/conf -sudo chown -R ${APP_UID:-1212}:${APP_GID:-1212} /var/log/local/apps/iskylims ${APP_INSTALL_PATH:-/opt/iskylims} +sudo chown -R ${APP_UID:-1212}:${APP_GID:-1212} /var/log/local/iskylims/apps ${APP_INSTALL_PATH:-/opt/iskylims} ``` For hardened/rootless Podman hosts, run the host preparation script as the same @@ -242,20 +244,20 @@ Static files: - `docker-compose.prod.yml` shares that directory with the `apache` service through the named volume `iskylims_static`. - The reverse proxy config serves `/static` directly from `${INSTALL_PATH}/static`. -During `container_install.sh`, the file `conf/iskylims_apache_reverse_proxy.conf` is copied to `${INSTALL_PATH}/conf/iskylims_apache_reverse_proxy.conf` on the host. Edit that copied file for runtime Apache changes after deployment. +During `container_install.sh`, `conf/iskylims_apache_reverse_proxy.conf` and `conf/iskylims_apache_logs.conf` are copied to `${APACHE_CONF_PATH}` on the host. If `APACHE_CONF_PATH` is empty, they are copied to `${INSTALL_PATH}/conf`. Edit those copied files for runtime Apache changes after deployment. -If you need a different runtime root, set `INSTALL_PATH` in the install config file or export `APP_INSTALL_PATH` before running `container_install.sh`. +If you need a different runtime root, set `INSTALL_PATH` in the install config file or export `APP_INSTALL_PATH` before running `container_install.sh`. If you need Apache configs outside the app runtime root, set `APACHE_CONF_PATH` in the install config file or export it before running `container_install.sh`. -`container_install.sh` creates `${APP_INSTALL_PATH}/conf` and `/var/log/local/apache` before `compose up`, copies `conf/iskylims_apache_reverse_proxy.conf` there, passes `APP_INSTALL_PATH` into Compose, and then runs `install.sh --bootstrap ...` inside the `app` container. The container image already contains the staged Django project and virtualenv under `${APP_INSTALL_PATH}`; the bootstrap step applies migrations, optional scripts/fixtures, and refreshes `${INSTALL_PATH}/static`, while the Apache container keeps using the host log path `/var/log/local/apache`. +`container_install.sh` creates `${APP_INSTALL_PATH}/conf`, `${APACHE_CONF_PATH:-${APP_INSTALL_PATH}/conf}`, `/var/log/local/iskylims/apps`, and `/var/log/local/iskylims/apache` before `compose up`, copies both Apache config files there, passes `APP_INSTALL_PATH` and `APACHE_CONF_PATH` into Compose, and then runs `install.sh --bootstrap ...` inside the `app` container. The container image already contains the staged Django project and virtualenv under `${APP_INSTALL_PATH}`; the bootstrap step applies migrations, optional scripts/fixtures, and refreshes `${INSTALL_PATH}/static`, while the Apache container keeps using the host log path `/var/log/local/iskylims/apache`. SELinux note for pre-production and production: -- Ensure `/var/log/local/apache` is writable by the container runtime and labeled for containers, for example `container_file_t`. +- Ensure `/var/log/local/iskylims/apache` is writable by the container runtime and labeled for containers, for example `container_file_t`. - If the host path is already labeled `container_file_t`, do not add `:Z` to the Apache log bind mount. `:Z` forces a relabel and may fail with `lsetxattr(... container_file_t ...): operation not permitted`. - A quick check is: ```bash -ls -ldZ /var/log/local/apache +ls -ldZ /var/log/local/iskylims/apache ``` - Expected example: @@ -264,7 +266,7 @@ ls -ldZ /var/log/local/apache system_u:object_r:container_file_t:s0 ``` -- If Apache fails on startup with `ModSecurity: Failed to open debug log file: /var/log/httpd/modsec_debug.log`, remove any stale host file and recreate/restart the container. In practice, deleting `/var/log/local/apache/modsec_debug.log` has been enough when the existing inode had bad permissions/label state. +- If Apache fails on startup with `ModSecurity: Failed to open debug log file: /var/log/httpd/modsec_debug.log`, remove any stale host file and recreate/restart the container. In practice, deleting `/var/log/local/iskylims/apache/modsec_debug.log` has been enough when the existing inode had bad permissions/label state. #### Cron jobs inside the container @@ -471,9 +473,9 @@ mysqldump -h -P -u iskylims -p iskylims > iskylims_$(date +% Logs archive: ```bash -tar -czf iskylims_app_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/apps/iskylims . +tar -czf iskylims_app_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/iskylims/apps . -tar -czf iskylims_apache_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/apache . +tar -czf iskylims_apache_logs_$(date +%Y%m%d_%H%M%S).tgz -C /var/log/local/iskylims/apache . ``` Documents volume archive: @@ -511,11 +513,11 @@ With Podman, use the same command replacing `docker` with `podman`. Restore logs: ```bash -mkdir -p /var/log/local/apps/iskylims -tar -xzf iskylims_app_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/apps/iskylims +mkdir -p /var/log/local/iskylims/apps +tar -xzf iskylims_app_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/iskylims/apps -mkdir -p /var/log/local/apache -tar -xzf iskylims_apache_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/apache +mkdir -p /var/log/local/iskylims/apache +tar -xzf iskylims_apache_logs_YYYYMMDD_HHMMSS.tgz -C /var/log/local/iskylims/apache ``` Bare-metal full rollback example: From c53142ec81a7c8228e297b6e03b7dd76f6413c3d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 14 May 2026 18:45:42 +0200 Subject: [PATCH 432/446] Bind mount production Django settings --- LEAME.md | 8 ++++++-- README.md | 8 ++++++-- conf/docker_production_settings.txt | 3 +++ conf/template_install_settings.txt | 3 +++ container_install.sh | 23 +++++++++++++++++++++-- docker-compose.prod.yml | 1 + install.sh | 16 ++++++++++++++-- 7 files changed, 54 insertions(+), 8 deletions(-) diff --git a/LEAME.md b/LEAME.md index 2f43f9774..c234c007f 100644 --- a/LEAME.md +++ b/LEAME.md @@ -172,6 +172,7 @@ Variables opcionales de build/runtime para produccion: - `APP_INSTALL_PATH`: cambia la raiz de instalacion en runtime usada por el contenedor `app`, los estaticos/documentos y los scripts de instalacion. Valor por defecto: `/opt/iskylims`. - `APACHE_CONF_PATH`: cambia el directorio host usado para los ficheros de configuracion de Apache montados por bind mount. Si esta vacio, `container_install.sh` usa `${APP_INSTALL_PATH}/conf`. +- `DJANGO_SETTINGS_PATH`: cambia el path host usado para el `settings.py` de Django montado por bind mount. Si esta vacio, `container_install.sh` usa `${APP_INSTALL_PATH}/iskylims/settings.py`. - `APP_UID` / `APP_GID`: UID/GID de ejecucion del usuario `iskylims` dentro del contenedor. Valor por defecto: `1212:1212`. - `APP_SHELL`: shell asignada al usuario de runtime durante la build. Valor por defecto: `/sbin/nologin`. - `APP_PORT`: puerto interno donde Gunicorn escucha dentro del servicio `app`. Valor por defecto: `8001`. @@ -212,6 +213,7 @@ Persistencia actual: - `/var/log/local/iskylims/apache` -> `/var/log/httpd` dentro del contenedor `apache` - `${APACHE_CONF_PATH:-${INSTALL_PATH}/conf}/iskylims_apache_reverse_proxy.conf` -> `/etc/httpd/conf.d/iskylims.conf` dentro del contenedor `apache` - `${APACHE_CONF_PATH:-${INSTALL_PATH}/conf}/iskylims_apache_logs.conf` -> `/etc/httpd/conf.d/logformat.conf` dentro del contenedor `apache` +- `${DJANGO_SETTINGS_PATH:-${INSTALL_PATH}/iskylims/settings.py}` -> `${INSTALL_PATH}/iskylims/settings.py` dentro del contenedor `app` - volumen nombrado `iskylims_documents` -> `${INSTALL_PATH}/documents` - volumen nombrado `iskylims_static` -> `${INSTALL_PATH}/static` @@ -248,9 +250,11 @@ Archivos estaticos: Durante `container_install.sh`, los ficheros `conf/iskylims_apache_reverse_proxy.conf` y `conf/iskylims_apache_logs.conf` se copian al host en `${APACHE_CONF_PATH}`. Si `APACHE_CONF_PATH` esta vacio, se copian a `${INSTALL_PATH}/conf`. A partir de ese momento, los cambios de runtime deben hacerse sobre esas copias. -Si necesitas otra raiz de instalacion, define `INSTALL_PATH` en el fichero de configuracion o exporta `APP_INSTALL_PATH` antes de ejecutar `container_install.sh`. Si necesitas que los ficheros de Apache queden fuera de la raiz de runtime de la app, define `APACHE_CONF_PATH` en el fichero de configuracion o exportalo antes de ejecutar `container_install.sh`. +`container_install.sh` prepara un fichero host `settings.py` de Django para el bind mount en `${DJANGO_SETTINGS_PATH}`, o en `${INSTALL_PATH}/iskylims/settings.py` si `DJANGO_SETTINGS_PATH` esta vacio. Durante el bootstrap, `install.sh` actualiza ese fichero montado a partir de `conf/template_settings.txt` y el fichero de configuracion seleccionado, conservando el `SECRET_KEY` si ya existe. Despues se pueden editar settings de runtime y reiniciar el contenedor sin reconstruir la imagen. -`container_install.sh` crea `${APP_INSTALL_PATH}/conf`, `${APACHE_CONF_PATH:-${APP_INSTALL_PATH}/conf}`, `/var/log/local/iskylims/apps` y `/var/log/local/iskylims/apache` antes de `compose up`, copia ahi los dos ficheros de configuracion de Apache, exporta `APP_INSTALL_PATH` y `APACHE_CONF_PATH` a Compose y despues ejecuta `install.sh --bootstrap ...` dentro del contenedor `app`. La imagen del contenedor ya contiene el proyecto Django y el virtualenv preparados dentro de `${APP_INSTALL_PATH}`; el bootstrap aplica migraciones, scripts/fixtures opcionales y refresca `${INSTALL_PATH}/static`, mientras que el contenedor `apache` sigue escribiendo sus logs en el path del host `/var/log/local/iskylims/apache`. +Si necesitas otra raiz de instalacion, define `INSTALL_PATH` en el fichero de configuracion o exporta `APP_INSTALL_PATH` antes de ejecutar `container_install.sh`. Si necesitas que los ficheros de Apache o los settings de Django queden fuera de la raiz de runtime de la app, define `APACHE_CONF_PATH` o `DJANGO_SETTINGS_PATH` en el fichero de configuracion, o exportalos antes de ejecutar `container_install.sh`. + +`container_install.sh` crea `${APP_INSTALL_PATH}/conf`, `${APACHE_CONF_PATH:-${APP_INSTALL_PATH}/conf}`, `/var/log/local/iskylims/apps` y `/var/log/local/iskylims/apache` antes de `compose up`, copia ahi los dos ficheros de configuracion de Apache, prepara el fichero de settings montado por bind mount si no existe, exporta `APP_INSTALL_PATH`, `APACHE_CONF_PATH` y `DJANGO_SETTINGS_PATH` a Compose y despues ejecuta `install.sh --bootstrap ...` dentro del contenedor `app`. La imagen del contenedor ya contiene el proyecto Django y el virtualenv preparados dentro de `${APP_INSTALL_PATH}`; el bootstrap actualiza settings, aplica migraciones, scripts/fixtures opcionales y refresca `${INSTALL_PATH}/static`, mientras que el contenedor `apache` sigue escribiendo sus logs en el path del host `/var/log/local/iskylims/apache`. Nota SELinux para pre-produccion y produccion: diff --git a/README.md b/README.md index 343c1f37e..2cec01f5e 100644 --- a/README.md +++ b/README.md @@ -170,6 +170,7 @@ Optional production runtime/build variables: - `APP_INSTALL_PATH`: overrides the runtime install root used by the app container, static/documents mounts, and install scripts. Default: `/opt/iskylims`. - `APACHE_CONF_PATH`: overrides the host directory used for Apache bind-mounted config files. If empty, `container_install.sh` uses `${APP_INSTALL_PATH}/conf`. +- `DJANGO_SETTINGS_PATH`: overrides the host path used for the bind-mounted Django `settings.py`. If empty, `container_install.sh` uses `${APP_INSTALL_PATH}/iskylims/settings.py`. - `APP_UID` / `APP_GID`: runtime UID/GID for the `iskylims` user inside the container. Default: `1212:1212`. - `APP_SHELL`: shell assigned to the runtime user during image build. Default: `/sbin/nologin`. - `APP_PORT`: internal Gunicorn bind port for the `app` service. Default: `8001`. @@ -204,6 +205,7 @@ Persistence layout: - `/var/log/local/iskylims/apache` -> `/var/log/httpd` inside the `apache` container - `${APACHE_CONF_PATH:-${INSTALL_PATH}/conf}/iskylims_apache_reverse_proxy.conf` -> `/etc/httpd/conf.d/iskylims.conf` inside the `apache` container - `${APACHE_CONF_PATH:-${INSTALL_PATH}/conf}/iskylims_apache_logs.conf` -> `/etc/httpd/conf.d/logformat.conf` inside the `apache` container +- `${DJANGO_SETTINGS_PATH:-${INSTALL_PATH}/iskylims/settings.py}` -> `${INSTALL_PATH}/iskylims/settings.py` inside the `app` container - `iskylims_documents` named volume -> `${INSTALL_PATH}/documents` - `iskylims_static` named volume -> `${INSTALL_PATH}/static` @@ -246,9 +248,11 @@ Static files: During `container_install.sh`, `conf/iskylims_apache_reverse_proxy.conf` and `conf/iskylims_apache_logs.conf` are copied to `${APACHE_CONF_PATH}` on the host. If `APACHE_CONF_PATH` is empty, they are copied to `${INSTALL_PATH}/conf`. Edit those copied files for runtime Apache changes after deployment. -If you need a different runtime root, set `INSTALL_PATH` in the install config file or export `APP_INSTALL_PATH` before running `container_install.sh`. If you need Apache configs outside the app runtime root, set `APACHE_CONF_PATH` in the install config file or export it before running `container_install.sh`. +`container_install.sh` prepares a host-side Django `settings.py` bind source at `${DJANGO_SETTINGS_PATH}`, or at `${INSTALL_PATH}/iskylims/settings.py` when `DJANGO_SETTINGS_PATH` is empty. During the bootstrap step, `install.sh` updates that bind-mounted file from `conf/template_settings.txt` and the selected install config, preserving an existing `SECRET_KEY`. Runtime settings can then be edited and the container restarted without rebuilding the image. -`container_install.sh` creates `${APP_INSTALL_PATH}/conf`, `${APACHE_CONF_PATH:-${APP_INSTALL_PATH}/conf}`, `/var/log/local/iskylims/apps`, and `/var/log/local/iskylims/apache` before `compose up`, copies both Apache config files there, passes `APP_INSTALL_PATH` and `APACHE_CONF_PATH` into Compose, and then runs `install.sh --bootstrap ...` inside the `app` container. The container image already contains the staged Django project and virtualenv under `${APP_INSTALL_PATH}`; the bootstrap step applies migrations, optional scripts/fixtures, and refreshes `${INSTALL_PATH}/static`, while the Apache container keeps using the host log path `/var/log/local/iskylims/apache`. +If you need a different runtime root, set `INSTALL_PATH` in the install config file or export `APP_INSTALL_PATH` before running `container_install.sh`. If you need Apache configs or Django settings outside the app runtime root, set `APACHE_CONF_PATH` or `DJANGO_SETTINGS_PATH` in the install config file, or export them before running `container_install.sh`. + +`container_install.sh` creates `${APP_INSTALL_PATH}/conf`, `${APACHE_CONF_PATH:-${APP_INSTALL_PATH}/conf}`, `/var/log/local/iskylims/apps`, and `/var/log/local/iskylims/apache` before `compose up`, copies both Apache config files there, prepares the bind-mounted Django settings file if it does not exist, passes `APP_INSTALL_PATH`, `APACHE_CONF_PATH`, and `DJANGO_SETTINGS_PATH` into Compose, and then runs `install.sh --bootstrap ...` inside the `app` container. The container image already contains the staged Django project and virtualenv under `${APP_INSTALL_PATH}`; the bootstrap step updates settings, applies migrations, optional scripts/fixtures, and refreshes `${INSTALL_PATH}/static`, while the Apache container keeps using the host log path `/var/log/local/iskylims/apache`. SELinux note for pre-production and production: diff --git a/conf/docker_production_settings.txt b/conf/docker_production_settings.txt index ff77ebd8c..f2ba9d292 100644 --- a/conf/docker_production_settings.txt +++ b/conf/docker_production_settings.txt @@ -7,6 +7,9 @@ INSTALL_PATH='/opt/iskylims' # Optional host directory for Apache bind-mounted conf files. # Leave empty to use ${INSTALL_PATH}/conf. APACHE_CONF_PATH='' +# Optional host path for bind-mounted Django settings.py. +# Leave empty to use ${INSTALL_PATH}/iskylims/settings.py. +DJANGO_SETTINGS_PATH='' REQUIRED_MODULES='core drylab wetlab clinic django_utils' MIGRATION_MODULES='core drylab wetlab django_utils' FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' diff --git a/conf/template_install_settings.txt b/conf/template_install_settings.txt index 2e963bc64..a088b771f 100644 --- a/conf/template_install_settings.txt +++ b/conf/template_install_settings.txt @@ -3,6 +3,9 @@ INSTALL_PATH='/opt/iskylims' # Optional host directory for Apache bind-mounted conf files. # Leave empty to use ${INSTALL_PATH}/conf. APACHE_CONF_PATH='' +# Optional host path for bind-mounted Django settings.py. +# Leave empty to use ${INSTALL_PATH}/iskylims/settings.py. +DJANGO_SETTINGS_PATH='' REQUIRED_MODULES='core drylab wetlab clinic django_utils' MIGRATION_MODULES='core drylab wetlab django_utils' FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' diff --git a/container_install.sh b/container_install.sh index e83d76b5a..289355358 100644 --- a/container_install.sh +++ b/container_install.sh @@ -148,6 +148,19 @@ copy_with_podman_fallback() { return 1 } +prepare_django_settings_bind_mount() { + local settings_path="$1" + + if [ "$mode" != "production" ]; then + return 0 + fi + + mkdir -p "$(dirname "$settings_path")" + if [ ! -f "$settings_path" ]; then + copy_with_podman_fallback "$repo_root/conf/template_settings.txt" "$settings_path" + fi +} + # PARSE VARIABLE ARGUMENTS WITH getopts options=":d:g:c:s:j:a:m:b:f:e:vhntp" while getopts $options opt; do @@ -342,6 +355,11 @@ apache_conf_path="${APACHE_CONF_PATH:-${config_apache_conf_path:-}}" if [ -z "$apache_conf_path" ]; then apache_conf_path="$app_install_path/conf" fi +config_django_settings_path="$(read_install_conf_value "DJANGO_SETTINGS_PATH" "$host_install_conf_path")" +django_settings_path="${DJANGO_SETTINGS_PATH:-${config_django_settings_path:-}}" +if [ -z "$django_settings_path" ]; then + django_settings_path="$app_install_path/iskylims/settings.py" +fi app_port="${APP_PORT:-8001}" app_container="" local_head_hash="" @@ -533,6 +551,7 @@ print_local_source_diagnostics print_existing_artifact_diagnostics echo "Deploying containers (compose file: $compose_file) with a pre-staged app image and GIT_REVISION=$git_revision..." mkdir -p "$app_install_path/conf" "$apache_conf_path" "/var/log/local/iskylims/apache" "/var/log/local/iskylims/apps" +prepare_django_settings_bind_mount "$django_settings_path" if [ -f "$repo_root/conf/iskylims_apache_reverse_proxy.conf" ]; then copy_with_podman_fallback \ "$repo_root/conf/iskylims_apache_reverse_proxy.conf" \ @@ -543,14 +562,14 @@ if [ -f "$repo_root/conf/iskylims_apache_logs.conf" ]; then "$repo_root/conf/iskylims_apache_logs.conf" \ "$apache_conf_path/iskylims_apache_logs.conf" fi -INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" APP_INSTALL_PATH="$app_install_path" APACHE_CONF_PATH="$apache_conf_path" \ +INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" APP_INSTALL_PATH="$app_install_path" APACHE_CONF_PATH="$apache_conf_path" DJANGO_SETTINGS_PATH="$django_settings_path" \ compose_exec -f "$compose_file" build --no-cache \ --build-arg INSTALL_TYPE="dep" \ --build-arg GIT_REVISION="$git_revision" \ --build-arg INSTALL_CONF="$install_conf_container" \ --build-arg APP_INSTALL_PATH="$app_install_path" print_image_after_build -APP_INSTALL_PATH="$app_install_path" APACHE_CONF_PATH="$apache_conf_path" compose_exec -f "$compose_file" up -d +APP_INSTALL_PATH="$app_install_path" APACHE_CONF_PATH="$apache_conf_path" DJANGO_SETTINGS_PATH="$django_settings_path" compose_exec -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." sleep 20 diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 2b821242f..a9ccbe710 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -48,6 +48,7 @@ services: - /etc/localtime:/etc/localtime:ro - /usr/share/zoneinfo:/usr/share/zoneinfo:ro - /var/log/local/iskylims/apps/:${APP_INSTALL_PATH:-/opt/iskylims}/logs:U + - ${DJANGO_SETTINGS_PATH:-/opt/iskylims/iskylims/settings.py}:${APP_INSTALL_PATH:-/opt/iskylims}/iskylims/settings.py:U - iskylims_documents:${APP_INSTALL_PATH:-/opt/iskylims}/documents - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static extra_hosts: diff --git a/install.sh b/install.sh index d371636da..423b870da 100644 --- a/install.sh +++ b/install.sh @@ -151,16 +151,27 @@ root_check(){ fi } +generate_django_secret_key(){ + "$PYTHON_BIN_PATH" -c "import secrets; print(''.join(secrets.choice('abcdefghijklmnopqrstuvwxyz0123456789!@#$%^&*(-_=+)') for _ in range(50)))" +} + # update_settings_and_urls: rewrite Django settings and urls with deployment values. update_settings_and_urls(){ log "INFO" "Updating settings.py and urls.py with deployment values" local project_dir="$INSTALL_PATH/$PROJECT_NAME" - grep ^SECRET "$project_dir/settings.py" > ~/.secret + local secret_line="" + + if [ -f "$project_dir/settings.py" ]; then + secret_line="$(grep -E "^SECRET_KEY[[:space:]]*=" "$project_dir/settings.py" | tail -n 1)" + fi + if [ -z "$secret_line" ] || [[ "$secret_line" =~ SECRET_KEY[[:space:]]*=[[:space:]]*SECRET ]]; then + secret_line="SECRET_KEY = '$(generate_django_secret_key)'" + fi cp conf/template_settings.txt "$project_dir/settings.py" cp conf/urls.py "$project_dir" - sed -i "/^SECRET/c\\$(cat ~/.secret)" "$project_dir/settings.py" + sed -i "/^SECRET_KEY/c\\$secret_line" "$project_dir/settings.py" sed -i "s/djangouser/${DB_USER}/g" "$project_dir/settings.py" sed -i "s/djangopass/${DB_PASS}/g" "$project_dir/settings.py" sed -i "s/djangohost/${DB_SERVER_IP}/g" "$project_dir/settings.py" @@ -876,6 +887,7 @@ bootstrap_application_runtime() { abort_install "manage.py not found at $INSTALL_PATH/manage.py. Stage application files first." fi + update_settings_and_urls run_django_deploy "$mode" refresh_static_files From c45324cdb54af5d1f2cb477e7ac7eb88c50d463f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 14 May 2026 18:45:51 +0200 Subject: [PATCH 433/446] Show skipped wetlab run test states --- wetlab/templates/wetlab/configuration_test.html | 2 ++ wetlab/utils/test_conf.py | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/wetlab/templates/wetlab/configuration_test.html b/wetlab/templates/wetlab/configuration_test.html index ba20cf0dc..236ab6d87 100644 --- a/wetlab/templates/wetlab/configuration_test.html +++ b/wetlab/templates/wetlab/configuration_test.html @@ -302,6 +302,8 @@
    You can not go further in the testing while the Basic test are not passed OK

    Result of run test for the state {{key}} {% if value == 'OK' %} + {% elif value == 'SKIP' %} + {% else %} {% endif %} diff --git a/wetlab/utils/test_conf.py b/wetlab/utils/test_conf.py index 4fbeef35c..5c2a400cd 100644 --- a/wetlab/utils/test_conf.py +++ b/wetlab/utils/test_conf.py @@ -175,7 +175,7 @@ def execute_test_for_testing_run(run_test_name, run_test_folder=None): "completed", ] for state_run in state_run_test: - run_result[state_run] = "NOK" + run_result[state_run] = "SKIP" if not wetlab.models.RunProcess.objects.filter( run_name__exact=run_test_name ).exists(): From 62bd4e7e476d5f0d09e9e794909425a59fb3c6ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 18 May 2026 14:54:10 +0200 Subject: [PATCH 434/446] Generate production compose env file --- .gitignore | 1 + LEAME.md | 88 ++++++++++++++--------------- README.md | 84 +++++++++++++-------------- conf/docker_production_settings.txt | 33 +++++++++-- conf/docker_test_settings.txt | 27 +++++++++ conf/template_install_settings.txt | 33 +++++++++-- container_install.sh | 87 +++++++++++++++++++++++++--- docker-compose.prod.yml | 6 +- 8 files changed, 245 insertions(+), 114 deletions(-) diff --git a/.gitignore b/.gitignore index 1c0f66014..3ba26fc9a 100644 --- a/.gitignore +++ b/.gitignore @@ -102,6 +102,7 @@ celerybeat-schedule # dotenv .env +.env.prod.file # virtualenv .venv diff --git a/LEAME.md b/LEAME.md index c234c007f..9c478599b 100644 --- a/LEAME.md +++ b/LEAME.md @@ -21,6 +21,7 @@ De acuerdo con la infraestructura existente, la secuenciacion se realiza en un i - [Persistir logs/documentos en el host](#persistir-logsdocumentos-en-el-host) - [Proxy inverso con Apache (contenedor) + Gunicorn](#proxy-inverso-con-apache-contenedor--gunicorn) - [Tareas cron dentro del contenedor](#tareas-cron-dentro-del-contenedor) + - [Gestionar contenedores despues de la instalacion](#gestionar-contenedores-despues-de-la-instalacion) - [Actualizacion del despliegue Docker](#actualizacion-del-despliegue-docker) - [Actualizacion del despliegue Docker v3.0.0 a 3.1.0](#actualizacion-del-despliegue-docker-v300-a-310) - [Haz copia de seguridad](#haz-copia-de-seguridad) @@ -159,46 +160,27 @@ Despliega el contenedor de iSkyLIMS contra servicios MySQL/Samba externos: Las imagenes de produccion ahora incorporan la aplicacion iSkyLIMS ya preparada. Un reinicio del host o la recreacion del contenedor ya no requiere reinstalar la aplicacion; `container_install.sh` solo ejecuta tareas de bootstrap en runtime, como migraciones, refresco de fixtures, scripts opcionales, creacion del superusuario en la primera instalacion y `collectstatic`. -UID/GID del usuario de ejecucion del contenedor (por defecto `1212:1212`): +Los valores de build/runtime del contenedor se configuran en el fichero de instalacion seleccionado, no exportando variables en la shell. Edita estos campos en `conf/my_prod_settings.txt` antes de ejecutar `container_install.sh`: -- Exporta `APP_UID` y `APP_GID` antes de ejecutar `container_install.sh` si necesitas un UID/GID distinto. - -```bash -export APP_UID=1212 -export APP_GID=1212 -``` - -Variables opcionales de build/runtime para produccion: - -- `APP_INSTALL_PATH`: cambia la raiz de instalacion en runtime usada por el contenedor `app`, los estaticos/documentos y los scripts de instalacion. Valor por defecto: `/opt/iskylims`. -- `APACHE_CONF_PATH`: cambia el directorio host usado para los ficheros de configuracion de Apache montados por bind mount. Si esta vacio, `container_install.sh` usa `${APP_INSTALL_PATH}/conf`. -- `DJANGO_SETTINGS_PATH`: cambia el path host usado para el `settings.py` de Django montado por bind mount. Si esta vacio, `container_install.sh` usa `${APP_INSTALL_PATH}/iskylims/settings.py`. +- `APP_INSTALL_PATH`: raiz de instalacion en runtime usada por el contenedor `app`, los estaticos/documentos y los scripts de instalacion. Dejalo vacio para reutilizar `INSTALL_PATH`. +- `APACHE_CONF_PATH`: directorio host usado para los ficheros de configuracion de Apache montados por bind mount. Dejalo vacio para usar `${APP_INSTALL_PATH}/conf`. +- `DJANGO_SETTINGS_PATH`: path host usado para el `settings.py` de Django montado por bind mount. Dejalo vacio para usar `${APP_INSTALL_PATH}/iskylims/settings.py`. - `APP_UID` / `APP_GID`: UID/GID de ejecucion del usuario `iskylims` dentro del contenedor. Valor por defecto: `1212:1212`. - `APP_SHELL`: shell asignada al usuario de runtime durante la build. Valor por defecto: `/sbin/nologin`. - `APP_PORT`: puerto interno donde Gunicorn escucha dentro del servicio `app`. Valor por defecto: `8001`. +- `DJANGO_DEBUG`: flag de debug de Django que se pasa al contenedor de produccion. Valor por defecto: `false`; mantenlo desactivado en produccion. - `DB_CONN_MAX_AGE`: tiempo de vida, en segundos, de las conexiones persistentes de Django a la BD. Valor por defecto: `60`. -- `WEB_CONCURRENCY`: numero de workers de Gunicorn. Valor por defecto en compose: `2`. Si no se define en el entrypoint, se calcula segun CPU disponible. +- `WEB_CONCURRENCY`: numero de workers de Gunicorn. Valor por defecto: `2`. - `GUNICORN_THREADS`: numero de hilos por worker de Gunicorn. Valor por defecto: `2`. - `GUNICORN_TIMEOUT`: timeout de peticiones Gunicorn en segundos. Valor por defecto: `300`. - `GUNICORN_KEEPALIVE`: keep-alive de Gunicorn en segundos. Valor por defecto: `5`. -- `DJANGO_DEBUG`: se pasa al contenedor de produccion. Valor por defecto: `"false"`. Debe mantenerse desactivado en produccion. -Ejemplo: - -```bash -export APP_INSTALL_PATH=/srv/iskylims -export APP_UID=1500 -export APP_GID=1500 -export WEB_CONCURRENCY=4 -export GUNICORN_THREADS=2 -export GUNICORN_TIMEOUT=180 -bash container_install.sh --install_conf conf/my_prod_settings.txt -``` +Durante una instalacion/actualizacion de produccion, `container_install.sh` escribe `.env.prod.file` en la raiz del repositorio. Este fichero esta ignorado por git y Compose lo usa para interpolar variables en `docker-compose.prod.yml`. Intencionadamente contiene metadatos de Compose/runtime, no passwords de base de datos ni de correo. Asegura que la carpeta de estaticos en el host sea escribible por ese UID/GID: ```bash -sudo chown -R 1212:1212 ${APP_INSTALL_PATH:-/opt/iskylims} +sudo chown -R : ``` #### Persistir logs/documentos en el host @@ -222,8 +204,8 @@ Crea los directorios necesarios en el host: ```bash sudo mkdir -p /var/log/local/iskylims/apps sudo mkdir -p /var/log/local/iskylims/apache -sudo mkdir -p ${APP_INSTALL_PATH:-/opt/iskylims}/conf -sudo chown -R ${APP_UID:-1212}:${APP_GID:-1212} /var/log/local/iskylims/apps ${APP_INSTALL_PATH:-/opt/iskylims} +sudo mkdir -p /conf +sudo chown -R : /var/log/local/iskylims/apps ``` En hosts Podman rootless o endurecidos, ejecuta el script de preparacion del host con el mismo usuario que arranca los contenedores. El script pre-crea los ficheros de log de Apache, ajusta la propiedad para el usuario UBI httpd en Podman rootless y aplica etiquetas SELinux de contenedor cuando SELinux esta activo: @@ -280,15 +262,34 @@ Cron se ejecuta mediante `supercronic`, lanzado por el script de arranque del co Si modificas `CRONJOBS`, reconstruye o reinicia el contenedor para regenerar el archivo de cron. -### Actualizacion del despliegue Docker +### Gestionar contenedores despues de la instalacion -Si usas `APP_UID`/`APP_GID`, exportalos de nuevo antes de la actualizacion para mantener el mismo UID/GID: +Despues de una instalacion de produccion, usa el fichero generado `.env.prod.file` siempre que ejecutes Compose directamente. Asi las rutas, UID/GID, puertos y ajustes de Gunicorn siguen alineados con el fichero de instalacion. + +Ejemplos con Docker Compose: ```bash -export APP_UID=1212 -export APP_GID=1212 +docker compose --env-file .env.prod.file -f docker-compose.prod.yml ps +docker compose --env-file .env.prod.file -f docker-compose.prod.yml logs --tail 200 app +docker compose --env-file .env.prod.file -f docker-compose.prod.yml restart app +docker compose --env-file .env.prod.file -f docker-compose.prod.yml up -d ``` +Ejemplos con Podman Compose: + +```bash +podman compose --env-file .env.prod.file -f docker-compose.prod.yml ps +podman compose --env-file .env.prod.file -f docker-compose.prod.yml logs --tail 200 app +podman compose --env-file .env.prod.file -f docker-compose.prod.yml restart app +podman compose --env-file .env.prod.file -f docker-compose.prod.yml up -d +``` + +Si editas valores de runtime del contenedor en el fichero de instalacion, vuelve a ejecutar `container_install.sh --install_conf ` para regenerar `.env.prod.file` y los contenedores de forma consistente. + +### Actualizacion del despliegue Docker + +Mantén los mismos valores de `APP_UID`/`APP_GID` en el fichero de instalacion seleccionado antes de actualizar. + Re-despliega el contenedor de aplicacion contra una base de datos existente: ```bash @@ -322,12 +323,7 @@ sudo nano myprod_settings.txt Si editas el archivo en Windows, asegurate de guardarlo con codificacion UTF-8/ASCII. -Si usas `APP_UID`/`APP_GID`, exportalos de nuevo antes de la actualizacion para que el contenedor se ejecute con el mismo UID/GID: - -```bash -export APP_UID=1212 -export APP_GID=1212 -``` +Mantén los mismos valores de `APP_UID`/`APP_GID` en el fichero de instalacion seleccionado antes de ejecutar la actualizacion 3.0.0 -> 3.1.0. Ejecuta la actualizacion: @@ -564,19 +560,19 @@ cd /opt/iskylims python manage.py check # docker -docker compose -f docker-compose.prod.yml ps -docker compose -f docker-compose.prod.yml logs --tail 200 app +docker compose --env-file .env.prod.file -f docker-compose.prod.yml ps +docker compose --env-file .env.prod.file -f docker-compose.prod.yml logs --tail 200 app # podman -podman-compose -f docker-compose.prod.yml ps -podman-compose -f docker-compose.prod.yml logs --tail 200 app +podman compose --env-file .env.prod.file -f docker-compose.prod.yml ps +podman compose --env-file .env.prod.file -f docker-compose.prod.yml logs --tail 200 app ``` Si sospechas que una imagen o cache de build de Docker esta corrupta: ```bash -docker compose -f docker-compose.prod.yml build --no-cache app -docker compose -f docker-compose.prod.yml up -d --force-recreate app +docker compose --env-file .env.prod.file -f docker-compose.prod.yml build --no-cache app +docker compose --env-file .env.prod.file -f docker-compose.prod.yml up -d --force-recreate app ``` ### Bare-metal @@ -598,7 +594,7 @@ mysql -u iskylims -p -h dmysqlps.isciiides.es iskylims < /home/dadmin/backup_pro 1. Para el contenedor: ```bash - docker compose -f docker-compose.prod.yml down + docker compose --env-file .env.prod.file -f docker-compose.prod.yml down ``` 2. Restaura la base de datos desde tu backup. diff --git a/README.md b/README.md index 2cec01f5e..86e4e40bd 100644 --- a/README.md +++ b/README.md @@ -22,6 +22,7 @@ Application servers run web applications for bioinformatics analysis (GALAXY), t - [Persist logs/documents on the host](#persist-logsdocuments-on-the-host) - [Apache reverse proxy (container) + Gunicorn](#apache-reverse-proxy-container--gunicorn) - [Cron jobs inside the container](#cron-jobs-inside-the-container) + - [Manage containers after installation](#manage-containers-after-installation) - [Upgrade docker deployment](#upgrade-docker-deployment) - [Upgrade docker deployment v3.0.0 to 3.1.0](#upgrade-docker-deployment-v300-to-310) - [Back up first](#back-up-first) @@ -157,41 +158,22 @@ Deploy the iSkyLIMS container against external MySQL/Samba services: Production images now bake the staged iSkyLIMS application into the image itself. Host reboots or container recreation no longer require rerunning the app installation step; `container_install.sh` only performs runtime bootstrap tasks such as migrations, fixture refreshes, optional scripts, superuser creation on first install, and `collectstatic`. -UID/GID for the container runtime user (default `1212:1212`): +Container build/runtime values are configured in the selected install config, not by exporting shell variables. Edit these fields in `conf/my_prod_settings.txt` before running `container_install.sh`: -- Export `APP_UID` and `APP_GID` before running `container_install.sh` if you need a different host UID/GID. - -```bash -export APP_UID=1212 -export APP_GID=1212 -``` - -Optional production runtime/build variables: - -- `APP_INSTALL_PATH`: overrides the runtime install root used by the app container, static/documents mounts, and install scripts. Default: `/opt/iskylims`. -- `APACHE_CONF_PATH`: overrides the host directory used for Apache bind-mounted config files. If empty, `container_install.sh` uses `${APP_INSTALL_PATH}/conf`. -- `DJANGO_SETTINGS_PATH`: overrides the host path used for the bind-mounted Django `settings.py`. If empty, `container_install.sh` uses `${APP_INSTALL_PATH}/iskylims/settings.py`. +- `APP_INSTALL_PATH`: runtime install root used by the app container, static/documents mounts, and install scripts. Leave empty to reuse `INSTALL_PATH`. +- `APACHE_CONF_PATH`: host directory used for Apache bind-mounted config files. Leave empty to use `${APP_INSTALL_PATH}/conf`. +- `DJANGO_SETTINGS_PATH`: host path used for the bind-mounted Django `settings.py`. Leave empty to use `${APP_INSTALL_PATH}/iskylims/settings.py`. - `APP_UID` / `APP_GID`: runtime UID/GID for the `iskylims` user inside the container. Default: `1212:1212`. - `APP_SHELL`: shell assigned to the runtime user during image build. Default: `/sbin/nologin`. - `APP_PORT`: internal Gunicorn bind port for the `app` service. Default: `8001`. +- `DJANGO_DEBUG`: Django debug flag passed to the production app container. Default: `false`; keep it disabled in production. - `DB_CONN_MAX_AGE`: Django persistent DB connection lifetime in seconds. Default: `60`. -- `WEB_CONCURRENCY`: Gunicorn worker count. Default: `2`. If unset in the container entrypoint, workers fall back to CPU-based auto-selection. +- `WEB_CONCURRENCY`: Gunicorn worker count. Default: `2`. - `GUNICORN_THREADS`: threads per Gunicorn worker. Default: `2`. - `GUNICORN_TIMEOUT`: Gunicorn request timeout in seconds. Default: `300`. - `GUNICORN_KEEPALIVE`: Gunicorn keep-alive in seconds. Default: `5`. -- `DJANGO_DEBUG`: passed to the production app container. Default: `"false"`. Keep it disabled in production. -Example: - -```bash -export APP_INSTALL_PATH=/srv/iskylims -export APP_UID=1500 -export APP_GID=1500 -export WEB_CONCURRENCY=4 -export GUNICORN_THREADS=2 -export GUNICORN_TIMEOUT=180 -bash container_install.sh --install_conf conf/my_prod_settings.txt -``` +During production install/upgrade, `container_install.sh` writes `.env.prod.file` in the repository root. This file is ignored by git and is used by Compose for variable interpolation in `docker-compose.prod.yml`. It intentionally contains Compose/runtime metadata, not database or email passwords. Host directory and ownership preparation is described in [Persist logs/documents on the host](#persist-logsdocuments-on-the-host). @@ -216,8 +198,8 @@ Create host directories before the first deployment: ```bash sudo mkdir -p /var/log/local/iskylims/apps sudo mkdir -p /var/log/local/iskylims/apache -sudo mkdir -p ${APP_INSTALL_PATH:-/opt/iskylims}/conf -sudo chown -R ${APP_UID:-1212}:${APP_GID:-1212} /var/log/local/iskylims/apps ${APP_INSTALL_PATH:-/opt/iskylims} +sudo mkdir -p /conf +sudo chown -R : /var/log/local/iskylims/apps ``` For hardened/rootless Podman hosts, run the host preparation script as the same @@ -278,15 +260,34 @@ Cron runs via `supercronic`, started by the container entrypoint script. The scr If you change `CRONJOBS`, rebuild or restart the container to regenerate the cron file. -### Upgrade docker deployment +### Manage containers after installation -If you set `APP_UID`/`APP_GID`, export them again before upgrade so the container runs with the same UID/GID: +After a production install, use the generated `.env.prod.file` whenever you run Compose directly. This keeps paths, UID/GID, ports, and Gunicorn settings aligned with the install config. + +Docker Compose examples: ```bash -export APP_UID=1212 -export APP_GID=1212 +docker compose --env-file .env.prod.file -f docker-compose.prod.yml ps +docker compose --env-file .env.prod.file -f docker-compose.prod.yml logs --tail 200 app +docker compose --env-file .env.prod.file -f docker-compose.prod.yml restart app +docker compose --env-file .env.prod.file -f docker-compose.prod.yml up -d ``` +Podman Compose examples: + +```bash +podman compose --env-file .env.prod.file -f docker-compose.prod.yml ps +podman compose --env-file .env.prod.file -f docker-compose.prod.yml logs --tail 200 app +podman compose --env-file .env.prod.file -f docker-compose.prod.yml restart app +podman compose --env-file .env.prod.file -f docker-compose.prod.yml up -d +``` + +If you edit container runtime values in the install config, rerun `container_install.sh --install_conf ` so `.env.prod.file` and the running containers are regenerated consistently. + +### Upgrade docker deployment + +Keep the same `APP_UID`/`APP_GID` values in the selected install config before running an upgrade. + Re-deploy the application container against an existing production database: ```bash @@ -320,12 +321,7 @@ sudo nano myprod_settings.txt Ensure the file uses Linux-friendly encoding (UTF-8/ASCII) if you edit it on Windows. -If you set `APP_UID`/`APP_GID`, export them again before upgrade so the container runs with the same UID/GID: - -```bash -export APP_UID=1212 -export APP_GID=1212 -``` +Keep the same `APP_UID`/`APP_GID` values in the selected install config before running the 3.0.0 -> 3.1.0 upgrade. Run upgrade command: @@ -545,18 +541,18 @@ cd /opt/iskylims python manage.py check # docker -docker compose -f docker-compose.prod.yml ps -docker compose -f docker-compose.prod.yml logs --tail 200 app +docker compose --env-file .env.prod.file -f docker-compose.prod.yml ps +docker compose --env-file .env.prod.file -f docker-compose.prod.yml logs --tail 200 app # podman -podman-compose -f docker-compose.prod.yml ps -podman-compose -f docker-compose.prod.yml logs --tail 200 app +podman compose --env-file .env.prod.file -f docker-compose.prod.yml ps +podman compose --env-file .env.prod.file -f docker-compose.prod.yml logs --tail 200 app ``` If you suspect a corrupted image/build cache in Docker: ```bash -docker compose -f docker-compose.prod.yml build --no-cache app -docker compose -f docker-compose.prod.yml up -d --force-recreate app +docker compose --env-file .env.prod.file -f docker-compose.prod.yml build --no-cache app +docker compose --env-file .env.prod.file -f docker-compose.prod.yml up -d --force-recreate app ``` ## Final configuration steps diff --git a/conf/docker_production_settings.txt b/conf/docker_production_settings.txt index f2ba9d292..a7427d65b 100644 --- a/conf/docker_production_settings.txt +++ b/conf/docker_production_settings.txt @@ -4,16 +4,37 @@ ### Installation path and modules settings INSTALL_PATH='/opt/iskylims' -# Optional host directory for Apache bind-mounted conf files. -# Leave empty to use ${INSTALL_PATH}/conf. -APACHE_CONF_PATH='' -# Optional host path for bind-mounted Django settings.py. -# Leave empty to use ${INSTALL_PATH}/iskylims/settings.py. -DJANGO_SETTINGS_PATH='' REQUIRED_MODULES='core drylab wetlab clinic django_utils' MIGRATION_MODULES='core drylab wetlab django_utils' FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' +### Container build/runtime settings +# Runtime installation root used by the app container. +# Leave empty to reuse INSTALL_PATH. +APP_INSTALL_PATH='' +# Host directory for Apache bind-mounted configuration files. +# Leave empty to use ${APP_INSTALL_PATH}/conf. +APACHE_CONF_PATH='' +# Host path for the bind-mounted Django settings.py. +# Leave empty to use ${APP_INSTALL_PATH}/iskylims/settings.py. +DJANGO_SETTINGS_PATH='' +# UID/GID for the non-root iskylims user inside the app container. +APP_UID='1212' +APP_GID='1212' +# Shell assigned to the container runtime user during image build. +APP_SHELL='/sbin/nologin' +# Internal app port used by Gunicorn. +APP_PORT='8001' +# Django production debug flag. Keep disabled in production. +DJANGO_DEBUG='false' +# Django persistent database connection lifetime in seconds. +DB_CONN_MAX_AGE='60' +# Gunicorn runtime tuning. +WEB_CONCURRENCY='2' +GUNICORN_THREADS='2' +GUNICORN_TIMEOUT='300' +GUNICORN_KEEPALIVE='5' + ### (optional) Python installation path where pip and python executables are located PYTHON_BIN_PATH='python3.11' diff --git a/conf/docker_test_settings.txt b/conf/docker_test_settings.txt index d6546a1ec..30f16bf70 100644 --- a/conf/docker_test_settings.txt +++ b/conf/docker_test_settings.txt @@ -4,6 +4,33 @@ REQUIRED_MODULES='core drylab wetlab clinic django_utils' MIGRATION_MODULES='core drylab wetlab django_utils' FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' +### Container build/runtime settings +# Runtime installation root used by the app container. +# Leave empty to reuse INSTALL_PATH. +APP_INSTALL_PATH='' +# Host directory for Apache bind-mounted configuration files. +# Leave empty to use ${APP_INSTALL_PATH}/conf. +APACHE_CONF_PATH='' +# Host path for the bind-mounted Django settings.py. +# Leave empty to use ${APP_INSTALL_PATH}/iskylims/settings.py. +DJANGO_SETTINGS_PATH='' +# UID/GID for the non-root iskylims user inside the app container. +APP_UID='1212' +APP_GID='1212' +# Shell assigned to the container runtime user during image build. +APP_SHELL='/bin/bash' +# Internal app port used by Django runserver/Gunicorn. +APP_PORT='8001' +# Django production debug flag. Keep disabled in production. +DJANGO_DEBUG='false' +# Django persistent database connection lifetime in seconds. +DB_CONN_MAX_AGE='60' +# Gunicorn runtime tuning. +WEB_CONCURRENCY='2' +GUNICORN_THREADS='2' +GUNICORN_TIMEOUT='300' +GUNICORN_KEEPALIVE='5' + ### (optional) Python installation path where pip and python executables are located PYTHON_BIN_PATH='python3' # example: /opt/python/3.9.6/bin/python3 diff --git a/conf/template_install_settings.txt b/conf/template_install_settings.txt index a088b771f..70b969736 100644 --- a/conf/template_install_settings.txt +++ b/conf/template_install_settings.txt @@ -1,15 +1,36 @@ ### Installation path and modules settings INSTALL_PATH='/opt/iskylims' -# Optional host directory for Apache bind-mounted conf files. -# Leave empty to use ${INSTALL_PATH}/conf. -APACHE_CONF_PATH='' -# Optional host path for bind-mounted Django settings.py. -# Leave empty to use ${INSTALL_PATH}/iskylims/settings.py. -DJANGO_SETTINGS_PATH='' REQUIRED_MODULES='core drylab wetlab clinic django_utils' MIGRATION_MODULES='core drylab wetlab django_utils' FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' +### Container build/runtime settings +# Runtime installation root used by the app container. +# Leave empty to reuse INSTALL_PATH. +APP_INSTALL_PATH='' +# Host directory for Apache bind-mounted configuration files. +# Leave empty to use ${APP_INSTALL_PATH}/conf. +APACHE_CONF_PATH='' +# Host path for the bind-mounted Django settings.py. +# Leave empty to use ${APP_INSTALL_PATH}/iskylims/settings.py. +DJANGO_SETTINGS_PATH='' +# UID/GID for the non-root iskylims user inside the app container. +APP_UID='1212' +APP_GID='1212' +# Shell assigned to the container runtime user during image build. +APP_SHELL='/sbin/nologin' +# Internal app port used by Gunicorn. +APP_PORT='8001' +# Django production debug flag. Keep disabled in production. +DJANGO_DEBUG='false' +# Django persistent database connection lifetime in seconds. +DB_CONN_MAX_AGE='60' +# Gunicorn runtime tuning. +WEB_CONCURRENCY='2' +GUNICORN_THREADS='2' +GUNICORN_TIMEOUT='300' +GUNICORN_KEEPALIVE='5' + ### (optional) Python installation path where pip and python executables are located PYTHON_BIN_PATH='python3' # example: /opt/python/3.9.6/bin/python3 diff --git a/container_install.sh b/container_install.sh index 289355358..ba157d529 100644 --- a/container_install.sh +++ b/container_install.sh @@ -345,11 +345,68 @@ read_install_conf_value() { grep -E "^${key}=" "$file" | tail -n 1 | cut -d= -f2- | sed "s/^['\"]//;s/['\"]$//" } +config_value_or_default() { + local key="$1" + local default_value="$2" + local config_value="" + local env_value="${!key:-}" + + if [ -n "$env_value" ]; then + echo "$env_value" + return 0 + fi + + config_value="$(read_install_conf_value "$key" "$host_install_conf_path")" + if [ -n "$config_value" ]; then + echo "$config_value" + else + echo "$default_value" + fi +} + +write_compose_env_file() { + if [ "$mode" != "production" ]; then + return 0 + fi + + cat > "$compose_env_file" << EOF +# Generated by container_install.sh from $install_conf_container. +# Used by Docker Compose/Podman Compose for docker-compose.prod.yml interpolation. +INSTALL_TYPE=dep +GIT_REVISION=$git_revision +INSTALL_CONF=$install_conf_container +APP_INSTALL_PATH=$app_install_path +APACHE_CONF_PATH=$apache_conf_path +DJANGO_SETTINGS_PATH=$django_settings_path +APP_UID=$app_uid +APP_GID=$app_gid +APP_SHELL=$app_shell +APP_PORT=$app_port +DJANGO_DEBUG=$django_debug +DB_CONN_MAX_AGE=$db_conn_max_age +WEB_CONCURRENCY=$web_concurrency +GUNICORN_THREADS=$gunicorn_threads +GUNICORN_TIMEOUT=$gunicorn_timeout +GUNICORN_KEEPALIVE=$gunicorn_keepalive +EOF + + echo "Wrote Compose environment file: $compose_env_file" +} + +compose_with_env_exec() { + if [ "$mode" = "production" ] && [ -f "$compose_env_file" ]; then + compose_exec --env-file "$compose_env_file" "$@" + else + compose_exec "$@" + fi +} + set_engine app_repo_path="${APP_REPO_PATH:-/srv/iskylims}" config_install_path="$(read_install_conf_value "INSTALL_PATH" "$host_install_conf_path")" -app_install_path="${APP_INSTALL_PATH:-${config_install_path:-/opt/iskylims}}" +config_app_install_path="$(read_install_conf_value "APP_INSTALL_PATH" "$host_install_conf_path")" +app_install_path="${APP_INSTALL_PATH:-${config_app_install_path:-${config_install_path:-/opt/iskylims}}}" config_apache_conf_path="$(read_install_conf_value "APACHE_CONF_PATH" "$host_install_conf_path")" apache_conf_path="${APACHE_CONF_PATH:-${config_apache_conf_path:-}}" if [ -z "$apache_conf_path" ]; then @@ -360,7 +417,17 @@ django_settings_path="${DJANGO_SETTINGS_PATH:-${config_django_settings_path:-}}" if [ -z "$django_settings_path" ]; then django_settings_path="$app_install_path/iskylims/settings.py" fi -app_port="${APP_PORT:-8001}" +app_uid="$(config_value_or_default APP_UID 1212)" +app_gid="$(config_value_or_default APP_GID 1212)" +app_shell="$(config_value_or_default APP_SHELL /sbin/nologin)" +app_port="$(config_value_or_default APP_PORT 8001)" +django_debug="$(config_value_or_default DJANGO_DEBUG false)" +db_conn_max_age="$(config_value_or_default DB_CONN_MAX_AGE 60)" +web_concurrency="$(config_value_or_default WEB_CONCURRENCY 2)" +gunicorn_threads="$(config_value_or_default GUNICORN_THREADS 2)" +gunicorn_timeout="$(config_value_or_default GUNICORN_TIMEOUT 300)" +gunicorn_keepalive="$(config_value_or_default GUNICORN_KEEPALIVE 5)" +compose_env_file="$repo_root/.env.prod.file" app_container="" local_head_hash="" local_head_short="" @@ -376,7 +443,7 @@ image_id_after_build="" # Returns: # 0 if the service exists, 1 otherwise service_exists() { - compose_exec -f "$compose_file" ps --services 2>/dev/null | grep -Fxq "$1" + compose_with_env_exec -f "$compose_file" ps --services 2>/dev/null | grep -Fxq "$1" } # Return the name of the container for a given service name. @@ -562,22 +629,24 @@ if [ -f "$repo_root/conf/iskylims_apache_logs.conf" ]; then "$repo_root/conf/iskylims_apache_logs.conf" \ "$apache_conf_path/iskylims_apache_logs.conf" fi -INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" APP_INSTALL_PATH="$app_install_path" APACHE_CONF_PATH="$apache_conf_path" DJANGO_SETTINGS_PATH="$django_settings_path" \ - compose_exec -f "$compose_file" build --no-cache \ +write_compose_env_file +INSTALL_TYPE="dep" GIT_REVISION="$git_revision" INSTALL_CONF="$install_conf_container" APP_INSTALL_PATH="$app_install_path" APACHE_CONF_PATH="$apache_conf_path" DJANGO_SETTINGS_PATH="$django_settings_path" APP_UID="$app_uid" APP_GID="$app_gid" APP_SHELL="$app_shell" APP_PORT="$app_port" DJANGO_DEBUG="$django_debug" DB_CONN_MAX_AGE="$db_conn_max_age" WEB_CONCURRENCY="$web_concurrency" GUNICORN_THREADS="$gunicorn_threads" GUNICORN_TIMEOUT="$gunicorn_timeout" GUNICORN_KEEPALIVE="$gunicorn_keepalive" \ + compose_with_env_exec -f "$compose_file" build --no-cache \ --build-arg INSTALL_TYPE="dep" \ --build-arg GIT_REVISION="$git_revision" \ --build-arg INSTALL_CONF="$install_conf_container" \ - --build-arg APP_INSTALL_PATH="$app_install_path" + --build-arg APP_INSTALL_PATH="$app_install_path" \ + --build-arg APP_UID="$app_uid" \ + --build-arg APP_GID="$app_gid" \ + --build-arg APP_SHELL="$app_shell" print_image_after_build -APP_INSTALL_PATH="$app_install_path" APACHE_CONF_PATH="$apache_conf_path" DJANGO_SETTINGS_PATH="$django_settings_path" compose_exec -f "$compose_file" up -d +APP_INSTALL_PATH="$app_install_path" APACHE_CONF_PATH="$apache_conf_path" DJANGO_SETTINGS_PATH="$django_settings_path" APP_UID="$app_uid" APP_GID="$app_gid" APP_SHELL="$app_shell" APP_PORT="$app_port" DJANGO_DEBUG="$django_debug" DB_CONN_MAX_AGE="$db_conn_max_age" WEB_CONCURRENCY="$web_concurrency" GUNICORN_THREADS="$gunicorn_threads" GUNICORN_TIMEOUT="$gunicorn_timeout" GUNICORN_KEEPALIVE="$gunicorn_keepalive" compose_with_env_exec -f "$compose_file" up -d echo "Waiting 20 seconds for starting database and web services..." sleep 20 ensure_app_running print_container_source_diagnostics "Container diagnostics after startup:" -app_uid="${APP_UID:-1212}" -app_gid="${APP_GID:-1212}" echo "Ensuring runtime directories are writable by ${app_uid}:${app_gid}" engine_exec exec -u 0 -it "$app_container" sh -lc "mkdir -p ${app_install_path}/documents ${app_install_path}/logs ${app_install_path}/static ${app_install_path}/cron ${app_install_path}/tmp && chown -R ${app_uid}:${app_gid} ${app_install_path}/documents ${app_install_path}/logs ${app_install_path}/static ${app_install_path}/cron ${app_install_path}/tmp" diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index a9ccbe710..28deaa30c 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -31,12 +31,12 @@ services: APP_SHELL: ${APP_SHELL:-/sbin/nologin} APP_INSTALL_PATH: ${APP_INSTALL_PATH:-/opt/iskylims} expose: - - "8001" + - "${APP_PORT:-8001}" environment: DJANGO_SETTINGS_MODULE: iskylims.settings - DJANGO_DEBUG: "false" + DJANGO_DEBUG: ${DJANGO_DEBUG:-false} APP_MODE: prod - APP_PORT: 8001 + APP_PORT: ${APP_PORT:-8001} DB_CONN_MAX_AGE: ${DB_CONN_MAX_AGE:-60} WEB_CONCURRENCY: ${WEB_CONCURRENCY:-2} GUNICORN_THREADS: ${GUNICORN_THREADS:-2} From f49a6926844d0f9489d96bdfbf3beaab7c0e8651 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 18 May 2026 14:56:09 +0200 Subject: [PATCH 435/446] Remove runtime ownership fix from container install --- container_install.sh | 3 --- 1 file changed, 3 deletions(-) diff --git a/container_install.sh b/container_install.sh index ba157d529..ee91e00e9 100644 --- a/container_install.sh +++ b/container_install.sh @@ -647,9 +647,6 @@ sleep 20 ensure_app_running print_container_source_diagnostics "Container diagnostics after startup:" -echo "Ensuring runtime directories are writable by ${app_uid}:${app_gid}" -engine_exec exec -u 0 -it "$app_container" sh -lc "mkdir -p ${app_install_path}/documents ${app_install_path}/logs ${app_install_path}/static ${app_install_path}/cron ${app_install_path}/tmp && chown -R ${app_uid}:${app_gid} ${app_install_path}/documents ${app_install_path}/logs ${app_install_path}/static ${app_install_path}/cron ${app_install_path}/tmp" - container_install_conf_path="$install_conf_container" if [[ "$container_install_conf_path" != /* ]]; then container_install_conf_path="$app_repo_path/$container_install_conf_path" From daf94fa0d4b8a2d6cb2ca6a07f695594ff43e46b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 18 May 2026 16:31:09 +0200 Subject: [PATCH 436/446] add servername and custom log naming automatically with the config file --- LEAME.md | 2 +- README.md | 2 +- conf/iskylims_apache_reverse_proxy.conf | 26 ++++++-------- container_install.sh | 45 +++++++++++++++++++++++-- 4 files changed, 56 insertions(+), 19 deletions(-) diff --git a/LEAME.md b/LEAME.md index 9c478599b..0218860d6 100644 --- a/LEAME.md +++ b/LEAME.md @@ -230,7 +230,7 @@ Archivos estaticos: - `docker-compose.prod.yml` comparte ese directorio con `apache` mediante el volumen nombrado `iskylims_static`. - La configuracion del proxy sirve `/static` directamente desde `${INSTALL_PATH}/static`. -Durante `container_install.sh`, los ficheros `conf/iskylims_apache_reverse_proxy.conf` y `conf/iskylims_apache_logs.conf` se copian al host en `${APACHE_CONF_PATH}`. Si `APACHE_CONF_PATH` esta vacio, se copian a `${INSTALL_PATH}/conf`. A partir de ese momento, los cambios de runtime deben hacerse sobre esas copias. +Durante `container_install.sh`, los ficheros `conf/iskylims_apache_reverse_proxy.conf` y `conf/iskylims_apache_logs.conf` se renderizan y se copian al host en `${APACHE_CONF_PATH}`. Si `APACHE_CONF_PATH` esta vacio, se copian a `${INSTALL_PATH}/conf`. El `ServerName`, el forwarded host y los nombres de logs access/error del proxy inverso se generan desde `DNS_URL` en el fichero de instalacion seleccionado. A partir de ese momento, los cambios de runtime deben hacerse sobre esas copias. `container_install.sh` prepara un fichero host `settings.py` de Django para el bind mount en `${DJANGO_SETTINGS_PATH}`, o en `${INSTALL_PATH}/iskylims/settings.py` si `DJANGO_SETTINGS_PATH` esta vacio. Durante el bootstrap, `install.sh` actualiza ese fichero montado a partir de `conf/template_settings.txt` y el fichero de configuracion seleccionado, conservando el `SECRET_KEY` si ya existe. Despues se pueden editar settings de runtime y reiniciar el contenedor sin reconstruir la imagen. diff --git a/README.md b/README.md index 86e4e40bd..99834cc64 100644 --- a/README.md +++ b/README.md @@ -228,7 +228,7 @@ Static files: - `docker-compose.prod.yml` shares that directory with the `apache` service through the named volume `iskylims_static`. - The reverse proxy config serves `/static` directly from `${INSTALL_PATH}/static`. -During `container_install.sh`, `conf/iskylims_apache_reverse_proxy.conf` and `conf/iskylims_apache_logs.conf` are copied to `${APACHE_CONF_PATH}` on the host. If `APACHE_CONF_PATH` is empty, they are copied to `${INSTALL_PATH}/conf`. Edit those copied files for runtime Apache changes after deployment. +During `container_install.sh`, `conf/iskylims_apache_reverse_proxy.conf` and `conf/iskylims_apache_logs.conf` are rendered and copied to `${APACHE_CONF_PATH}` on the host. If `APACHE_CONF_PATH` is empty, they are copied to `${INSTALL_PATH}/conf`. The reverse proxy `ServerName`, forwarded host, and access/error log file names are generated from `DNS_URL` in the selected install config. Edit those copied files for runtime Apache changes after deployment. `container_install.sh` prepares a host-side Django `settings.py` bind source at `${DJANGO_SETTINGS_PATH}`, or at `${INSTALL_PATH}/iskylims/settings.py` when `DJANGO_SETTINGS_PATH` is empty. During the bootstrap step, `install.sh` updates that bind-mounted file from `conf/template_settings.txt` and the selected install config, preserving an existing `SECRET_KEY`. Runtime settings can then be edited and the container restarted without rebuilding the image. diff --git a/conf/iskylims_apache_reverse_proxy.conf b/conf/iskylims_apache_reverse_proxy.conf index 3c7f576a7..07d526b39 100644 --- a/conf/iskylims_apache_reverse_proxy.conf +++ b/conf/iskylims_apache_reverse_proxy.conf @@ -1,12 +1,12 @@ # Apache reverse proxy config for iSkyLIMS production container - ServerName dockeriskyims.isciiides.es + ServerName __ISKYLIMS_SERVER_NAME__ ProxyPreserveHost On RequestHeader set X-Forwarded-Proto "https" RequestHeader set X-Forwarded-Port "443" - RequestHeader set X-Forwarded-Host "dockeriskyims.isciiides.es" + RequestHeader set X-Forwarded-Host "__ISKYLIMS_SERVER_NAME__" # Allow larger POST bodies to reach Django instead of being rejected by @@ -19,22 +19,18 @@ ProxyPass /static ! - Alias /static /opt/iskylims/static - + Alias /static __APP_INSTALL_PATH__/static + Require all granted - ProxyPass / http://app:8001/ - ProxyPassReverse / http://app:8001/ - ProxyTimeout 300 - TimeOut 300 + ProxyPass / http://app:__APP_PORT__/ + ProxyPassReverse / http://app:__APP_PORT__/ + ProxyTimeout __GUNICORN_TIMEOUT__ + TimeOut __GUNICORN_TIMEOUT__ - #ErrorLog logs/iskylims.pre.isciii.es-apache.error.log - #CustomLog logs/iskylims.pre.isciii.es-apache.access.log combined - - CustomLog logs/dockeriskyims.isciiides.es-apache.access.log combined env=!forwarded - CustomLog logs/dockeriskyims.isciiides.es-apache.access.log proxy env=forwarded - - ErrorLog logs/iskylims.pre.isciii.es-apache.error.log + CustomLog logs/__ISKYLIMS_LOG_NAME__-apache.access.log combined env=!forwarded + CustomLog logs/__ISKYLIMS_LOG_NAME__-apache.access.log proxy env=forwarded + ErrorLog logs/__ISKYLIMS_LOG_NAME__-apache.error.log diff --git a/container_install.sh b/container_install.sh index ee91e00e9..18fd2d402 100644 --- a/container_install.sh +++ b/container_install.sh @@ -148,6 +148,44 @@ copy_with_podman_fallback() { return 1 } +normalize_apache_server_name() { + local value="$1" + + value="${value#http://}" + value="${value#https://}" + value="${value%%/*}" + value="${value%%:*}" + + if [ -z "$value" ] || [ "$value" = "*" ]; then + value="localhost" + fi + + echo "$value" +} + +render_apache_config() { + local src="$1" + local dst="$2" + local tmp_file="" + + tmp_file="$(mktemp)" + sed \ + -e "s|__ISKYLIMS_SERVER_NAME__|$apache_server_name|g" \ + -e "s|__ISKYLIMS_LOG_NAME__|$apache_log_name|g" \ + -e "s|__APP_INSTALL_PATH__|$app_install_path|g" \ + -e "s|__APP_PORT__|$app_port|g" \ + -e "s|__GUNICORN_TIMEOUT__|$gunicorn_timeout|g" \ + "$src" > "$tmp_file" + + if copy_with_podman_fallback "$tmp_file" "$dst"; then + rm -f "$tmp_file" + return 0 + fi + + rm -f "$tmp_file" + return 1 +} + prepare_django_settings_bind_mount() { local settings_path="$1" @@ -427,6 +465,9 @@ web_concurrency="$(config_value_or_default WEB_CONCURRENCY 2)" gunicorn_threads="$(config_value_or_default GUNICORN_THREADS 2)" gunicorn_timeout="$(config_value_or_default GUNICORN_TIMEOUT 300)" gunicorn_keepalive="$(config_value_or_default GUNICORN_KEEPALIVE 5)" +config_dns_url="$(read_install_conf_value "DNS_URL" "$host_install_conf_path")" +apache_server_name="$(normalize_apache_server_name "${APACHE_SERVER_NAME:-${config_dns_url:-localhost}}")" +apache_log_name="$(printf '%s' "$apache_server_name" | tr -c 'A-Za-z0-9._-' '_' | sed 's/_$//')" compose_env_file="$repo_root/.env.prod.file" app_container="" local_head_hash="" @@ -620,12 +661,12 @@ echo "Deploying containers (compose file: $compose_file) with a pre-staged app i mkdir -p "$app_install_path/conf" "$apache_conf_path" "/var/log/local/iskylims/apache" "/var/log/local/iskylims/apps" prepare_django_settings_bind_mount "$django_settings_path" if [ -f "$repo_root/conf/iskylims_apache_reverse_proxy.conf" ]; then - copy_with_podman_fallback \ + render_apache_config \ "$repo_root/conf/iskylims_apache_reverse_proxy.conf" \ "$apache_conf_path/iskylims_apache_reverse_proxy.conf" fi if [ -f "$repo_root/conf/iskylims_apache_logs.conf" ]; then - copy_with_podman_fallback \ + render_apache_config \ "$repo_root/conf/iskylims_apache_logs.conf" \ "$apache_conf_path/iskylims_apache_logs.conf" fi From 901a90421f8290ef90718b907b27ba82b08280cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 18 May 2026 16:32:26 +0200 Subject: [PATCH 437/446] add network to docker compose --- docker-compose.prod.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/docker-compose.prod.yml b/docker-compose.prod.yml index 28deaa30c..7e9776d08 100644 --- a/docker-compose.prod.yml +++ b/docker-compose.prod.yml @@ -16,6 +16,8 @@ services: - ${APACHE_CONF_PATH:-/opt/iskylims/conf}/iskylims_apache_logs.conf:/etc/httpd/conf.d/logformat.conf:ro - /var/log/local/iskylims/apache:/var/log/httpd:U - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static:ro + networks: + - iskylims_net app: container_name: iskylims_app @@ -53,6 +55,11 @@ services: - iskylims_static:${APP_INSTALL_PATH:-/opt/iskylims}/static extra_hosts: - "host.docker.internal:host-gateway" + networks: + - iskylims_net + +networks: + iskylims_net: volumes: iskylims_documents: From 29489a19ba1a67ad2a6ea6345270fe6b2331ea69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 18 May 2026 16:50:30 +0200 Subject: [PATCH 438/446] Normalize Django settings bind path --- LEAME.md | 2 +- README.md | 2 +- conf/docker_production_settings.txt | 1 + conf/docker_test_settings.txt | 1 + conf/template_install_settings.txt | 1 + container_install.sh | 27 +++++++++++++++++++++++---- 6 files changed, 28 insertions(+), 6 deletions(-) diff --git a/LEAME.md b/LEAME.md index 0218860d6..fc8d24d9a 100644 --- a/LEAME.md +++ b/LEAME.md @@ -164,7 +164,7 @@ Los valores de build/runtime del contenedor se configuran en el fichero de insta - `APP_INSTALL_PATH`: raiz de instalacion en runtime usada por el contenedor `app`, los estaticos/documentos y los scripts de instalacion. Dejalo vacio para reutilizar `INSTALL_PATH`. - `APACHE_CONF_PATH`: directorio host usado para los ficheros de configuracion de Apache montados por bind mount. Dejalo vacio para usar `${APP_INSTALL_PATH}/conf`. -- `DJANGO_SETTINGS_PATH`: path host usado para el `settings.py` de Django montado por bind mount. Dejalo vacio para usar `${APP_INSTALL_PATH}/iskylims/settings.py`. +- `DJANGO_SETTINGS_PATH`: path host usado para el `settings.py` de Django montado por bind mount. Dejalo vacio para usar `${APP_INSTALL_PATH}/iskylims/settings.py`. Si el valor es un directorio o termina en `/`, `container_install.sh` anade `settings.py`. - `APP_UID` / `APP_GID`: UID/GID de ejecucion del usuario `iskylims` dentro del contenedor. Valor por defecto: `1212:1212`. - `APP_SHELL`: shell asignada al usuario de runtime durante la build. Valor por defecto: `/sbin/nologin`. - `APP_PORT`: puerto interno donde Gunicorn escucha dentro del servicio `app`. Valor por defecto: `8001`. diff --git a/README.md b/README.md index 99834cc64..3a6a3c646 100644 --- a/README.md +++ b/README.md @@ -162,7 +162,7 @@ Container build/runtime values are configured in the selected install config, no - `APP_INSTALL_PATH`: runtime install root used by the app container, static/documents mounts, and install scripts. Leave empty to reuse `INSTALL_PATH`. - `APACHE_CONF_PATH`: host directory used for Apache bind-mounted config files. Leave empty to use `${APP_INSTALL_PATH}/conf`. -- `DJANGO_SETTINGS_PATH`: host path used for the bind-mounted Django `settings.py`. Leave empty to use `${APP_INSTALL_PATH}/iskylims/settings.py`. +- `DJANGO_SETTINGS_PATH`: host path used for the bind-mounted Django `settings.py`. Leave empty to use `${APP_INSTALL_PATH}/iskylims/settings.py`. If the value is a directory or ends with `/`, `container_install.sh` appends `settings.py`. - `APP_UID` / `APP_GID`: runtime UID/GID for the `iskylims` user inside the container. Default: `1212:1212`. - `APP_SHELL`: shell assigned to the runtime user during image build. Default: `/sbin/nologin`. - `APP_PORT`: internal Gunicorn bind port for the `app` service. Default: `8001`. diff --git a/conf/docker_production_settings.txt b/conf/docker_production_settings.txt index a7427d65b..88f2089e4 100644 --- a/conf/docker_production_settings.txt +++ b/conf/docker_production_settings.txt @@ -17,6 +17,7 @@ APP_INSTALL_PATH='' APACHE_CONF_PATH='' # Host path for the bind-mounted Django settings.py. # Leave empty to use ${APP_INSTALL_PATH}/iskylims/settings.py. +# If this is a directory or ends with /, container_install.sh appends settings.py. DJANGO_SETTINGS_PATH='' # UID/GID for the non-root iskylims user inside the app container. APP_UID='1212' diff --git a/conf/docker_test_settings.txt b/conf/docker_test_settings.txt index 30f16bf70..1c310116b 100644 --- a/conf/docker_test_settings.txt +++ b/conf/docker_test_settings.txt @@ -13,6 +13,7 @@ APP_INSTALL_PATH='' APACHE_CONF_PATH='' # Host path for the bind-mounted Django settings.py. # Leave empty to use ${APP_INSTALL_PATH}/iskylims/settings.py. +# If this is a directory or ends with /, container_install.sh appends settings.py. DJANGO_SETTINGS_PATH='' # UID/GID for the non-root iskylims user inside the app container. APP_UID='1212' diff --git a/conf/template_install_settings.txt b/conf/template_install_settings.txt index 70b969736..b55a1ad2a 100644 --- a/conf/template_install_settings.txt +++ b/conf/template_install_settings.txt @@ -13,6 +13,7 @@ APP_INSTALL_PATH='' APACHE_CONF_PATH='' # Host path for the bind-mounted Django settings.py. # Leave empty to use ${APP_INSTALL_PATH}/iskylims/settings.py. +# If this is a directory or ends with /, container_install.sh appends settings.py. DJANGO_SETTINGS_PATH='' # UID/GID for the non-root iskylims user inside the app container. APP_UID='1212' diff --git a/container_install.sh b/container_install.sh index 18fd2d402..33fec7bc7 100644 --- a/container_install.sh +++ b/container_install.sh @@ -163,6 +163,22 @@ normalize_apache_server_name() { echo "$value" } +normalize_settings_bind_path() { + local value="$1" + + if [ -z "$value" ]; then + echo "$app_install_path/iskylims/settings.py" + return 0 + fi + + if [ -d "$value" ] || [[ "$value" = */ ]]; then + echo "${value%/}/settings.py" + return 0 + fi + + echo "$value" +} + render_apache_config() { local src="$1" local dst="$2" @@ -193,6 +209,12 @@ prepare_django_settings_bind_mount() { return 0 fi + if [ -d "$settings_path" ]; then + echo "DJANGO_SETTINGS_PATH must resolve to a file path, but '$settings_path' is a directory." >&2 + echo "Use a full path like '$settings_path/settings.py' or remove the directory and rerun." >&2 + return 1 + fi + mkdir -p "$(dirname "$settings_path")" if [ ! -f "$settings_path" ]; then copy_with_podman_fallback "$repo_root/conf/template_settings.txt" "$settings_path" @@ -451,10 +473,7 @@ if [ -z "$apache_conf_path" ]; then apache_conf_path="$app_install_path/conf" fi config_django_settings_path="$(read_install_conf_value "DJANGO_SETTINGS_PATH" "$host_install_conf_path")" -django_settings_path="${DJANGO_SETTINGS_PATH:-${config_django_settings_path:-}}" -if [ -z "$django_settings_path" ]; then - django_settings_path="$app_install_path/iskylims/settings.py" -fi +django_settings_path="$(normalize_settings_bind_path "${DJANGO_SETTINGS_PATH:-${config_django_settings_path:-}}")" app_uid="$(config_value_or_default APP_UID 1212)" app_gid="$(config_value_or_default APP_GID 1212)" app_shell="$(config_value_or_default APP_SHELL /sbin/nologin)" From f02f68c59baaa1a0a4ce1afe5e6c009fabf0ff4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 18 May 2026 17:49:00 +0200 Subject: [PATCH 439/446] Render mounted settings before container start --- .dockerignore | 53 +++++++++++++++++++++++++++++ Dockerfile | 28 ++++++++++------ container_install.sh | 80 ++++++++++++++++++++++++++++++++++++++++++-- 3 files changed, 148 insertions(+), 13 deletions(-) create mode 100644 .dockerignore diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 000000000..25b5269f2 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,53 @@ +# Keep .git: install/build diagnostics use git metadata inside the image. + +# Local Python environments and caches +.venv/ +venv/ +env/ +ENV/ +virtualenv/ +__pycache__/ +*.py[cod] +.pytest_cache/ +.mypy_cache/ +.hypothesis/ +.coverage +.coverage.* +htmlcov/ +.tox/ + +# Local editor and OS files +.vscode/ +.idea/ +.DS_Store +*.swp +*.swo + +# Local runtime/generated deployment files +.env +.env.* +!.env.example +.env.prod.file +install_settings.txt +wetlab/logging_config.ini +logs/ +tmp/ +documents/ +outputs/ +catboost_info/ + +# Build, package, and generated archives +build/ +dist/ +*.egg-info/ +.eggs/ +*.egg +*.log +*.gz +*.zip +*.tar +*.tgz + +# Generated Django/runtime files at repo root +/manage.py +/static/ diff --git a/Dockerfile b/Dockerfile index ef6f5f87a..113e635e9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -8,18 +8,21 @@ ARG APP_GID=1212 ARG APP_SHELL=/sbin/nologin ARG APP_INSTALL_PATH=/opt/iskylims ENV APP_INSTALL_PATH=${APP_INSTALL_PATH} - +ENV PIP_NO_CACHE_DIR=1 # Updates -RUN dnf -y update +RUN dnf -y update \ + && dnf clean all \ + && rm -rf /var/cache/dnf /tmp/* /var/tmp/* # Add EPEL for packages not available in default UBI repositories -RUN dnf -y install \ +RUN dnf -y install --setopt=install_weak_deps=False --nodocs \ https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm \ - && dnf clean all + && dnf clean all \ + && rm -rf /var/cache/dnf /tmp/* /var/tmp/* # Essential software -RUN dnf -y install \ +RUN dnf -y install --setopt=install_weak_deps=False --nodocs \ git wget \ python3.11 python3.11-pip python3.11-devel python3.11-wheel \ gcc gcc-c++ make \ @@ -29,7 +32,8 @@ RUN dnf -y install \ rsync tzdata \ pkgconf-pkg-config \ gnuplot-minimal \ - && dnf clean all + && dnf clean all \ + && rm -rf /var/cache/dnf /tmp/* /var/tmp/* # Install supercronic (rootless-friendly cron runner) RUN set -eux; \ @@ -46,7 +50,8 @@ RUN set -eux; \ else \ rm -f /usr/local/bin/supercronic; \ echo "supercronic download failed from ${supercronic_url}; continuing without cron support"; \ - fi + fi; \ + rm -rf /tmp/* /var/tmp/* # Ensure python3 points to the desired version RUN ln -sf /usr/bin/python3.11 /usr/bin/python3 @@ -57,7 +62,8 @@ RUN set -eux; \ wget -q https://github.com/Illumina/interop/releases/download/v1.1.15/InterOp-1.1.15-Linux-GNU.tar.gz; \ tar -xf InterOp-1.1.15-Linux-GNU.tar.gz; \ ln -s InterOp-1.1.15-Linux-GNU interop; \ - rm InterOp-1.1.15-Linux-GNU.tar.gz + rm InterOp-1.1.15-Linux-GNU.tar.gz; \ + rm -rf /tmp/* /var/tmp/* # Set git repository RUN mkdir /srv/iskylims @@ -77,8 +83,10 @@ ARG INSTALL_CONF=conf/docker_test_settings.txt # Prepare dependencies and stage the application tree in the image so the # container can restart without rerunning install-time file generation. ENV SKIP_SYSTEM_PACKAGES=1 -RUN /bin/bash install.sh --install dep --git_revision $GIT_REVISION --conf $INSTALL_CONF --skip_apache_restart -RUN /bin/bash install.sh --stage install --git_revision $GIT_REVISION --conf $INSTALL_CONF --skip_apache_restart +RUN /bin/bash install.sh --install dep --git_revision $GIT_REVISION --conf $INSTALL_CONF --skip_apache_restart \ + && rm -rf /root/.cache/pip /tmp/* /var/tmp/* +RUN /bin/bash install.sh --stage install --git_revision $GIT_REVISION --conf $INSTALL_CONF --skip_apache_restart \ + && rm -rf /root/.cache/pip /tmp/* /var/tmp/* # Use the virtualenv created by install.sh ENV PATH="${APP_INSTALL_PATH}/virtualenv/bin:${PATH}" diff --git a/container_install.sh b/container_install.sh index 33fec7bc7..cf9214239 100644 --- a/container_install.sh +++ b/container_install.sh @@ -163,6 +163,74 @@ normalize_apache_server_name() { echo "$value" } +generate_django_secret_key() { + if command -v python3 >/dev/null 2>&1; then + python3 -c "import secrets; print(''.join(secrets.choice('abcdefghijklmnopqrstuvwxyz0123456789!@#$%^&*(-_=+)') for _ in range(50)))" + else + LC_ALL=C tr -dc 'A-Za-z0-9!@#$%^&*(-_=+)' < /dev/urandom | head -c 50 + printf "\n" + fi +} + +sed_replacement_escape() { + printf '%s' "$1" | sed -e 's/[\\&|]/\\&/g' +} + +render_django_settings_file() { + local settings_path="$1" + local secret_line="" + local tmp_file="" + local db_user db_pass db_name db_host db_port + local email_host email_port email_user email_pass email_tls + local local_server_ip dns_url + + if [ -f "$settings_path" ]; then + secret_line="$(grep -E "^SECRET_KEY[[:space:]]*=" "$settings_path" | tail -n 1)" + fi + if [ -z "$secret_line" ] || [[ "$secret_line" =~ SECRET_KEY[[:space:]]*=[[:space:]]*SECRET ]]; then + secret_line="SECRET_KEY = '$(generate_django_secret_key)'" + fi + + db_user="$(read_install_conf_value DB_USER "$host_install_conf_path")" + db_pass="$(read_install_conf_value DB_PASS "$host_install_conf_path")" + db_name="$(read_install_conf_value DB_NAME "$host_install_conf_path")" + db_host="$(read_install_conf_value DB_SERVER_IP "$host_install_conf_path")" + db_port="$(read_install_conf_value DB_PORT "$host_install_conf_path")" + email_host="$(read_install_conf_value EMAIL_HOST_SERVER "$host_install_conf_path")" + email_port="$(read_install_conf_value EMAIL_PORT "$host_install_conf_path")" + email_user="$(read_install_conf_value EMAIL_HOST_USER "$host_install_conf_path")" + email_pass="$(read_install_conf_value EMAIL_HOST_PASSWORD "$host_install_conf_path")" + email_tls="$(read_install_conf_value EMAIL_USE_TLS "$host_install_conf_path")" + local_server_ip="$(read_install_conf_value LOCAL_SERVER_IP "$host_install_conf_path")" + dns_url="$(read_install_conf_value DNS_URL "$host_install_conf_path")" + + tmp_file="$(mktemp)" + cp "$repo_root/conf/template_settings.txt" "$tmp_file" + sed -i \ + -e "s|^SECRET_KEY.*|$(sed_replacement_escape "$secret_line")|" \ + -e "s|djangouser|$(sed_replacement_escape "$db_user")|g" \ + -e "s|djangopass|$(sed_replacement_escape "$db_pass")|g" \ + -e "s|djangohost|$(sed_replacement_escape "$db_host")|g" \ + -e "s|djangoport|$(sed_replacement_escape "$db_port")|g" \ + -e "s|djangodbname|$(sed_replacement_escape "$db_name")|g" \ + -e "s|emailhostserver|$(sed_replacement_escape "$email_host")|g" \ + -e "s|emailport|$(sed_replacement_escape "$email_port")|g" \ + -e "s|emailhostuser|$(sed_replacement_escape "$email_user")|g" \ + -e "s|emailhostpassword|$(sed_replacement_escape "$email_pass")|g" \ + -e "s|emailhosttls|$(sed_replacement_escape "$email_tls")|g" \ + -e "s|localserverip|$(sed_replacement_escape "$local_server_ip")|g" \ + -e "s|localhost|$(sed_replacement_escape "$dns_url")|g" \ + "$tmp_file" + + if copy_with_podman_fallback "$tmp_file" "$settings_path"; then + rm -f "$tmp_file" + return 0 + fi + + rm -f "$tmp_file" + return 1 +} + normalize_settings_bind_path() { local value="$1" @@ -216,8 +284,8 @@ prepare_django_settings_bind_mount() { fi mkdir -p "$(dirname "$settings_path")" - if [ ! -f "$settings_path" ]; then - copy_with_podman_fallback "$repo_root/conf/template_settings.txt" "$settings_path" + if [ ! -f "$settings_path" ] || grep -Eq "SECRET_KEY[[:space:]]*=[[:space:]]*SECRET|emailhosttls|djangouser|djangopass|djangohost|djangodbname" "$settings_path"; then + render_django_settings_file "$settings_path" fi } @@ -402,7 +470,13 @@ fi read_install_conf_value() { local key="$1" local file="$2" - grep -E "^${key}=" "$file" | tail -n 1 | cut -d= -f2- | sed "s/^['\"]//;s/['\"]$//" + + bash -c ' + set -a + . "$1" + key="$2" + printf "%s" "${!key-}" + ' _ "$file" "$key" } config_value_or_default() { From d85cc124d72e6bd1a1549a8d9d83a910a88a507e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Mon, 18 May 2026 18:24:55 +0200 Subject: [PATCH 440/446] sed to a tmp setting file and then copy in install.sh --- install.sh | 42 ++++++++++++++++++++++++++---------------- 1 file changed, 26 insertions(+), 16 deletions(-) diff --git a/install.sh b/install.sh index 423b870da..c1d601cc4 100644 --- a/install.sh +++ b/install.sh @@ -155,11 +155,16 @@ generate_django_secret_key(){ "$PYTHON_BIN_PATH" -c "import secrets; print(''.join(secrets.choice('abcdefghijklmnopqrstuvwxyz0123456789!@#$%^&*(-_=+)') for _ in range(50)))" } +sed_replacement_escape(){ + printf '%s' "$1" | sed -e 's/[\&|]/\\&/g' +} + # update_settings_and_urls: rewrite Django settings and urls with deployment values. update_settings_and_urls(){ log "INFO" "Updating settings.py and urls.py with deployment values" local project_dir="$INSTALL_PATH/$PROJECT_NAME" local secret_line="" + local tmp_settings="" if [ -f "$project_dir/settings.py" ]; then secret_line="$(grep -E "^SECRET_KEY[[:space:]]*=" "$project_dir/settings.py" | tail -n 1)" @@ -168,23 +173,28 @@ update_settings_and_urls(){ secret_line="SECRET_KEY = '$(generate_django_secret_key)'" fi - cp conf/template_settings.txt "$project_dir/settings.py" + tmp_settings="$(mktemp)" + cp conf/template_settings.txt "$tmp_settings" cp conf/urls.py "$project_dir" - - sed -i "/^SECRET_KEY/c\\$secret_line" "$project_dir/settings.py" - sed -i "s/djangouser/${DB_USER}/g" "$project_dir/settings.py" - sed -i "s/djangopass/${DB_PASS}/g" "$project_dir/settings.py" - sed -i "s/djangohost/${DB_SERVER_IP}/g" "$project_dir/settings.py" - sed -i "s/djangoport/${DB_PORT}/g" "$project_dir/settings.py" - sed -i "s/djangodbname/${DB_NAME}/g" "$project_dir/settings.py" - - sed -i "s/emailhostserver/${EMAIL_HOST_SERVER}/g" "$project_dir/settings.py" - sed -i "s/emailport/${EMAIL_PORT}/g" "$project_dir/settings.py" - sed -i "s/emailhostuser/${EMAIL_HOST_USER}/g" "$project_dir/settings.py" - sed -i "s/emailhostpassword/${EMAIL_HOST_PASSWORD}/g" "$project_dir/settings.py" - sed -i "s/emailhosttls/${EMAIL_USE_TLS}/g" "$project_dir/settings.py" - sed -i "s/localserverip/${LOCAL_SERVER_IP}/g" "$project_dir/settings.py" - sed -i "s/localhost/${DNS_URL}/g" "$project_dir/settings.py" + + sed -i \ + -e "s|^SECRET_KEY.*|$(sed_replacement_escape "$secret_line")|" \ + -e "s|djangouser|$(sed_replacement_escape "$DB_USER")|g" \ + -e "s|djangopass|$(sed_replacement_escape "$DB_PASS")|g" \ + -e "s|djangohost|$(sed_replacement_escape "$DB_SERVER_IP")|g" \ + -e "s|djangoport|$(sed_replacement_escape "$DB_PORT")|g" \ + -e "s|djangodbname|$(sed_replacement_escape "$DB_NAME")|g" \ + -e "s|emailhostserver|$(sed_replacement_escape "$EMAIL_HOST_SERVER")|g" \ + -e "s|emailport|$(sed_replacement_escape "$EMAIL_PORT")|g" \ + -e "s|emailhostuser|$(sed_replacement_escape "$EMAIL_HOST_USER")|g" \ + -e "s|emailhostpassword|$(sed_replacement_escape "$EMAIL_HOST_PASSWORD")|g" \ + -e "s|emailhosttls|$(sed_replacement_escape "$EMAIL_USE_TLS")|g" \ + -e "s|localserverip|$(sed_replacement_escape "$LOCAL_SERVER_IP")|g" \ + -e "s|localhost|$(sed_replacement_escape "$DNS_URL")|g" \ + "$tmp_settings" + + cp "$tmp_settings" "$project_dir/settings.py" + rm -f "$tmp_settings" } # restore_git_ref: reset repository to branch/tag/commit active before script ran. From a8be20a7d29f2a396c490c77dafba2ea7255e2ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 19 May 2026 15:25:45 +0200 Subject: [PATCH 441/446] Fix Samba cron path validation --- .../templates/wetlab/configuration_samba.html | 2 +- wetlab/utils/crontab_update_run.py | 27 ++++++++++++++++--- wetlab/views.py | 7 ++++- 3 files changed, 31 insertions(+), 5 deletions(-) diff --git a/wetlab/templates/wetlab/configuration_samba.html b/wetlab/templates/wetlab/configuration_samba.html index dcfcf1b81..0a2e4ee8d 100644 --- a/wetlab/templates/wetlab/configuration_samba.html +++ b/wetlab/templates/wetlab/configuration_samba.html @@ -97,7 +97,7 @@

    Your Samba settings are OK
    - +
    diff --git a/wetlab/utils/crontab_update_run.py b/wetlab/utils/crontab_update_run.py index d1bc4ed15..9ca684f3b 100644 --- a/wetlab/utils/crontab_update_run.py +++ b/wetlab/utils/crontab_update_run.py @@ -807,14 +807,35 @@ def manage_run_in_processed_run_state(conn, run_process_objs): run_process_obj, experiment_name ) # Check run_folder time creation - created_time = _as_utc_datetime( - wetlab.utils.common.get_samba_atribute_data( + try: + created_time = wetlab.utils.common.get_samba_atribute_data( conn, wetlab.utils.crontab_process.get_samba_shared_folder(), root_run_folder, "create_time", ) - ) + except Exception: + logger.exception( + "%s : Unable to access remote run folder %s", + experiment_name, + root_run_folder, + ) + wetlab.utils.common.logging_errors( + ( + experiment_name + + " : Unable to access remote run folder " + + root_run_folder + ), + True, + False, + ) + wetlab.utils.crontab_process.manage_errors_in_run(experiment_name, 9) + logger.debug( + "%s : End manage_run_in_processed_run_state function", + experiment_name, + ) + continue + created_time = _as_utc_datetime(created_time) if created_time is None: logger.warning( "%s : Unable to determine creation time for run folder %s", diff --git a/wetlab/views.py b/wetlab/views.py index 1b8ad4346..2039bce8e 100644 --- a/wetlab/views.py +++ b/wetlab/views.py @@ -114,7 +114,12 @@ def configuration_samba(request): {"samba_conf_data": samba_user_field, "error_message": error_message}, ) try: - conn.listPath(samba_user_field["shared_folder_name"], "/") + samba_application_folder = os.path.join( + "/", samba_user_field.get("samba_folder_name", "") + ) + conn.listPath( + samba_user_field["shared_folder_name"], samba_application_folder + ) return render( request, "wetlab/configuration_samba.html", From 59655a1827dadf6e897fd4266cf6d4515b6a7191 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 19 May 2026 17:21:27 +0200 Subject: [PATCH 442/446] Document bind mount config examples --- conf/docker_production_settings.txt | 2 ++ conf/docker_test_settings.txt | 2 ++ conf/template_install_settings.txt | 2 ++ 3 files changed, 6 insertions(+) diff --git a/conf/docker_production_settings.txt b/conf/docker_production_settings.txt index 88f2089e4..f77ecd4b2 100644 --- a/conf/docker_production_settings.txt +++ b/conf/docker_production_settings.txt @@ -14,10 +14,12 @@ FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' APP_INSTALL_PATH='' # Host directory for Apache bind-mounted configuration files. # Leave empty to use ${APP_INSTALL_PATH}/conf. +# Example: APACHE_CONF_PATH='/srv/containers/bind/iskylims_apache_conf' APACHE_CONF_PATH='' # Host path for the bind-mounted Django settings.py. # Leave empty to use ${APP_INSTALL_PATH}/iskylims/settings.py. # If this is a directory or ends with /, container_install.sh appends settings.py. +# Example: DJANGO_SETTINGS_PATH='/srv/containers/bind/iskylims_app_setting' DJANGO_SETTINGS_PATH='' # UID/GID for the non-root iskylims user inside the app container. APP_UID='1212' diff --git a/conf/docker_test_settings.txt b/conf/docker_test_settings.txt index 1c310116b..7ffabfbac 100644 --- a/conf/docker_test_settings.txt +++ b/conf/docker_test_settings.txt @@ -10,10 +10,12 @@ FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' APP_INSTALL_PATH='' # Host directory for Apache bind-mounted configuration files. # Leave empty to use ${APP_INSTALL_PATH}/conf. +# Example: APACHE_CONF_PATH='/srv/containers/bind/iskylims_apache_conf' APACHE_CONF_PATH='' # Host path for the bind-mounted Django settings.py. # Leave empty to use ${APP_INSTALL_PATH}/iskylims/settings.py. # If this is a directory or ends with /, container_install.sh appends settings.py. +# Example: DJANGO_SETTINGS_PATH='/srv/containers/bind/iskylims_app_setting' DJANGO_SETTINGS_PATH='' # UID/GID for the non-root iskylims user inside the app container. APP_UID='1212' diff --git a/conf/template_install_settings.txt b/conf/template_install_settings.txt index b55a1ad2a..7d1c2cea0 100644 --- a/conf/template_install_settings.txt +++ b/conf/template_install_settings.txt @@ -10,10 +10,12 @@ FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' APP_INSTALL_PATH='' # Host directory for Apache bind-mounted configuration files. # Leave empty to use ${APP_INSTALL_PATH}/conf. +# Example: APACHE_CONF_PATH='/srv/containers/bind/iskylims_apache_conf' APACHE_CONF_PATH='' # Host path for the bind-mounted Django settings.py. # Leave empty to use ${APP_INSTALL_PATH}/iskylims/settings.py. # If this is a directory or ends with /, container_install.sh appends settings.py. +# Example: DJANGO_SETTINGS_PATH='/srv/containers/bind/iskylims_app_setting' DJANGO_SETTINGS_PATH='' # UID/GID for the non-root iskylims user inside the app container. APP_UID='1212' From 9bbdb12ff6724e0dce836313bfa3918d5b5ef46d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 19 May 2026 18:15:28 +0200 Subject: [PATCH 443/446] keep dnf clean only in last dnf step --- Dockerfile | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/Dockerfile b/Dockerfile index 113e635e9..149e68ba0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,15 +11,11 @@ ENV APP_INSTALL_PATH=${APP_INSTALL_PATH} ENV PIP_NO_CACHE_DIR=1 # Updates -RUN dnf -y update \ - && dnf clean all \ - && rm -rf /var/cache/dnf /tmp/* /var/tmp/* +RUN dnf -y update # Add EPEL for packages not available in default UBI repositories RUN dnf -y install --setopt=install_weak_deps=False --nodocs \ - https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm \ - && dnf clean all \ - && rm -rf /var/cache/dnf /tmp/* /var/tmp/* + https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm # Essential software RUN dnf -y install --setopt=install_weak_deps=False --nodocs \ From 78c479b28e7cb9ad106f0fb97fc5d8c2b1a2bc00 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Tue, 19 May 2026 18:43:36 +0200 Subject: [PATCH 444/446] better info in config files --- conf/docker_production_settings.txt | 6 +++--- conf/docker_test_settings.txt | 4 ++-- conf/template_install_settings.txt | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/conf/docker_production_settings.txt b/conf/docker_production_settings.txt index f77ecd4b2..ff4582770 100644 --- a/conf/docker_production_settings.txt +++ b/conf/docker_production_settings.txt @@ -10,7 +10,7 @@ FAKEINITIAL_MODULES='django_utils iSkyLIMS_core iSkyLIMS_wetlab iSkyLIMS_drylab' ### Container build/runtime settings # Runtime installation root used by the app container. -# Leave empty to reuse INSTALL_PATH. +# Leave empty to reuse INSTALL_PATH. If you are not sure leave it empty. APP_INSTALL_PATH='' # Host directory for Apache bind-mounted configuration files. # Leave empty to use ${APP_INSTALL_PATH}/conf. @@ -49,9 +49,9 @@ DB_SERVER_IP='host.docker.internal' # hostname or IP of the production DB (use DB_PORT=3306 ### Settings required for sending emails -EMAIL_HOST_SERVER='smtp.yourdomain' +EMAIL_HOST_SERVER='host.docker.internal' EMAIL_PORT='25' -EMAIL_HOST_USER='bioinfo' +EMAIL_HOST_USER='bioinformatica@isciii.es' EMAIL_HOST_PASSWORD='' EMAIL_USE_TLS='False' diff --git a/conf/docker_test_settings.txt b/conf/docker_test_settings.txt index 7ffabfbac..c288c3d21 100644 --- a/conf/docker_test_settings.txt +++ b/conf/docker_test_settings.txt @@ -47,9 +47,9 @@ DB_PORT=3306 ### Settings required for sending emails -EMAIL_HOST_SERVER='localhost' +EMAIL_HOST_SERVER='host.docker.internal' EMAIL_PORT='25' -EMAIL_HOST_USER='bioinfo' +EMAIL_HOST_USER='bioinformatica@isciii.es' EMAIL_HOST_PASSWORD='' EMAIL_USE_TLS='False' diff --git a/conf/template_install_settings.txt b/conf/template_install_settings.txt index 7d1c2cea0..3b3cc004a 100644 --- a/conf/template_install_settings.txt +++ b/conf/template_install_settings.txt @@ -47,9 +47,9 @@ DB_PORT=3306 ### Settings required for sending emails -EMAIL_HOST_SERVER='localhost' +EMAIL_HOST_SERVER='host.docker.internal' EMAIL_PORT='25' -EMAIL_HOST_USER='bioinfo' +EMAIL_HOST_USER='bioinformatica@isciii.es' EMAIL_HOST_PASSWORD='' EMAIL_USE_TLS='False' From b63f322768f96d34c78b2139aa4e5844af35c269 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 21 May 2026 09:48:42 +0200 Subject: [PATCH 445/446] changelog update --- CHANGELOG.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 68abd529f..957400a19 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -33,6 +33,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Refactored container installation flow to separate staged application install from runtime bootstrap tasks [#393](https://github.com/BU-ISCIII/iskylims/pull/393) - Updated Docker image build to stage application files at build time and run bootstrap tasks on container start/upgrade [#393](https://github.com/BU-ISCIII/iskylims/pull/393) - Replaced container cron runtime with supercronic and improved multi-container install configuration [#391](https://github.com/BU-ISCIII/iskylims/pull/391) +- Added production container support for bind-mounted Django settings and generated Apache configuration files. +- Added production compose environment file generation during container installation. +- Added configurable ServerName and Apache log naming from installation settings. +- Added dedicated Docker network configuration to the production compose file. +- Added configuration examples for container bind mounts in installation settings templates. #### Fixes @@ -77,6 +82,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Fixed logger inconsistency that prevented exceptions and error messages from being written to the update crontab log. Closes [#390](https://github.com/BU-ISCIII/iskylims/issues/390) [#392](https://github.com/BU-ISCIII/iskylims/pull/392) - Fixed wetlab crontab processing for the new sequencer, including run discovery, completion checks, RunInfo/RunParameters parsing updates, and SampleSheet v2 handling. Closes [#387](https://github.com/BU-ISCIII/iskylims/issues/387) [#392](https://github.com/BU-ISCIII/iskylims/pull/392) - Improved Podman compatibility and adjusted SELinux bind mount handling in production compose setup [#393](https://github.com/BU-ISCIII/iskylims/pull/393) +- Fixed production container Django settings rendering when settings are provided through bind mounts. +- Fixed duplicate wetlab run configuration test logging. +- Fixed wetlab run configuration tests, including run discovery and completion checks. +- Fixed skipped wetlab run test states so they are displayed in the configuration test view. +- Fixed Samba cron path validation in wetlab configuration checks. +- Fixed Docker build cleanup so DNF cache cleanup only runs in the final DNF step. #### Changed @@ -93,11 +104,18 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), - Refactored Docker runtime handling when path is outside repository [#389](https://github.com/BU-ISCIII/iskylims/pull/389) - Updated `docker_install.sh` to `container_install.sh` with multiple reliability improvements [#389](https://github.com/BU-ISCIII/iskylims/pull/389) - Updated upgrade scripts documentation to include execution order information and docker upgrade clarifications [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Improved wetlab API stats-info aggregation queries. +- Improved supercronic download resilience in the Docker build. +- Refreshed install fixtures during Docker upgrades. +- Updated production container documentation for bind mounts and generated configuration files. +- Normalized the Django settings bind path used by container installation. +- Updated installation configuration templates with clearer container configuration guidance. #### Removed - Dummy fix in usage line [#271](https://github.com/BU-ISCIII/iskylims/pull/271) - Removed migrations from `.gitignore` and app-level `.gitignore` to ensure version control of schema changes [#389](https://github.com/BU-ISCIII/iskylims/pull/389) +- Removed runtime ownership fixes from container installation. #### Requirements From c37ba0c5cd1e8aeec339fa0cb74c080f1a4e2a26 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sara=20Monz=C3=B3n?= Date: Thu, 21 May 2026 09:50:38 +0200 Subject: [PATCH 446/446] Release version 3.1.0 --- CHANGELOG.md | 2 +- install.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 957400a19..185f49603 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [3.1.0dev] - 2025-XX-XX : +## [3.1.0] - 2026-05-21 : ### Credits diff --git a/install.sh b/install.sh index c1d601cc4..14835a067 100644 --- a/install.sh +++ b/install.sh @@ -1,6 +1,6 @@ #!/bin/bash -APP_VERSION="3.1.0dev" +APP_VERSION="3.1.0" # usage: prints the command line help and usage examples. usage() {