Upgrade to latest technologies across all components

db/Dockerfile

@@ -1,4 +1,3 @@
-FROM postgres:11.5
+FROM postgres:16-alpine
 
 COPY ./initdb.sql /docker-entrypoint-initdb.d/initdb.sql
-

embedding-calculator/Dockerfile

@@ -1,5 +1,5 @@
 ARG BASE_IMAGE
-FROM ${BASE_IMAGE:-python:3.8-slim-bullseye}
+FROM ${BASE_IMAGE:-python:3.11-slim-bookworm}
 
 RUN apt-get update && apt-get install -y build-essential cmake git wget unzip \
         curl yasm pkg-config libswscale-dev libtbb2 libtbb-dev libjpeg-dev \
@@ -20,14 +20,14 @@ RUN git clone --depth=1 --shallow-submodules --recursive -b v0.1 https://github.
 	rm -rf /tmp/brunsli
 
 # libjxl
-RUN git clone --depth=1 --shallow-submodules --recursive -b v0.7.0 https://github.com/libjxl/libjxl && \
+RUN git clone --depth=1 --shallow-submodules --recursive -b v0.10.2 https://github.com/libjxl/libjxl && \
 	cd libjxl && \
 	cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=OFF . && \
 	make -j$(nproc) install && \
 	rm -rf /tmp/libjxl
 
 # zfp
-RUN git clone --depth=1 -b 0.5.5 https://github.com/LLNL/zfp && \
+RUN git clone --depth=1 -b 1.0.1 https://github.com/LLNL/zfp && \
 	cd zfp && \
 	mkdir build && \
 	cd build && \
@@ -40,8 +40,7 @@ RUN git clone --depth=1 -b 0.5.5 https://github.com/LLNL/zfp && \
 SHELL ["/bin/bash", "-c"]
 WORKDIR /app/ml
 COPY requirements.txt .
-# Ensure numpy is installed first as imagecodecs doesn't declare dependencies correctly until 2022.9.26,
-# which is not compatible with Python 3.7
+# Ensure numpy is installed first as imagecodecs doesn't declare dependencies correctly until 2022.9.26
 RUN pip --no-cache-dir install $(grep ^numpy requirements.txt)
 RUN pip --no-cache-dir install -r requirements.txt
 

embedding-calculator/gpu.Dockerfile

@@ -1,8 +1,8 @@
 ARG BASE_IMAGE
-FROM ${BASE_IMAGE:-nvidia/cuda:11.8.0-cudnn8-runtime-ubuntu20.04}
+FROM ${BASE_IMAGE:-nvidia/cuda:12.3.1-cudnn9-runtime-ubuntu22.04}
 
 ENV DEBIAN_FRONTEND=noninteractive
-ENV CUDA=11.8
+ENV CUDA=12.3
 
 RUN apt-get update && apt-get install -y --no-install-recommends \
         build-essential \

embedding-calculator/requirements.txt

@@ -1,99 +1,123 @@
-absl-py==1.4.0
+# Core ML dependencies
+tensorflow==2.15.0
+keras==2.15.0
+tensorflow-estimator==2.15.0
+tensorboard==2.15.2
+tensorboard-data-server==0.7.2
+tensorboard-plugin-wit==1.8.1
+tf-slim==1.1.0
+
+# Scientific computing
+numpy==1.26.4
+scipy==1.12.0
+scikit-learn==1.4.0
+scikit-image==0.22.0
+joblib==1.3.2
+
+# Image processing
+Pillow==10.2.0
+opencv-python==4.9.0.80
+imageio==2.33.1
+imagecodecs==2024.1.1
+tifffile==2024.1.30
+
+# Web framework
+Flask==3.0.2
+Werkzeug==3.0.1
+uWSGI==2.0.24
+flasgger==0.9.7.1
+itsdangerous==2.1.2
+Jinja2==3.1.3
+MarkupSafe==2.1.5
+click==8.1.7
+
+# API & networking
+requests==2.31.0
+urllib3==2.2.0
+certifi==2024.2.2
+charset-normalizer==3.3.2
+idna==3.6
+
+# Google/TensorFlow utilities
+absl-py==2.1.0
 astunparse==1.6.3
-attrs==20.2.0
-beautifulsoup4==4.12.2
-cached-property==1.5.2
-cachetools==4.2.4
-certifi==2023.7.22
-charset-normalizer==3.2.0
-click==8.1.6
-colour==0.1.5
-contourpy==1.1.0
-cycler==0.11.0
-exceptiongroup==1.1.3
-filelock==3.12.2
-flasgger==0.9.5
-Flask==1.1.2
-fonttools==4.42.0
-gast==0.3.3
-gdown==4.5.4
-google-auth==1.35.0
-google-auth-oauthlib==0.4.6
+cachetools==5.3.2
+google-auth==2.27.0
+google-auth-oauthlib==1.2.0
 google-pasta==0.2.0
-grpcio==1.57.0
-h5py==2.10.0
-idna==3.4
-imageio==2.31.1
-importlib-metadata==6.8.0
-importlib-resources==6.0.1
-iniconfig==2.0.0
-itsdangerous==2.0.1
-Jinja2==3.0.3
-jsonschema==4.17.3
-Keras-Preprocessing==1.1.2
-kiwisolver==1.4.4
-Markdown==3.4.4
-MarkupSafe==2.1.3
-matplotlib==3.6.3
-mccabe==0.7.0
-mistune==3.0.1
-networkx==3.1
-oauthlib==3.2.2
+grpcio==1.60.1
+gast==0.5.4
+h5py==3.10.0
 opt-einsum==3.3.0
-packaging==23.1
-pip==23.0.1
-pkgutil_resolve_name==1.3.10
-pluggy==1.2.0
-protobuf==3.19.6
-pyasn1==0.5.0
-pyasn1-modules==0.3.0
-pycodestyle==2.11.0
-pydocstyle==6.3.0
-pyflakes==3.1.0
+protobuf==4.25.2
+wrapt==1.16.0
+flatbuffers==23.5.26
+libclang==16.0.6
+ml-dtypes==0.2.0
+termcolor==2.4.0
+typing_extensions==4.9.0
+
+# Data processing
+PyYAML==6.0.1
+beautifulsoup4==4.12.3
+soupsieve==2.5
+jsonschema==4.21.1
+jsonschema-specifications==2023.12.1
+referencing==0.33.0
+rpds-py==0.17.1
+attrs==23.2.0
+pyrsistent==0.20.0
+
+# Visualization
+matplotlib==3.8.2
+contourpy==1.2.0
+cycler==0.12.1
+fonttools==4.47.2
+kiwisolver==1.4.5
 pyparsing==3.1.1
-pyrsistent==0.19.3
-PySocks==1.7.1
 python-dateutil==2.8.2
-PyWavelets==1.4.1
-PyYAML==5.4.1
+
+# Authentication
+oauthlib==3.2.2
+pyasn1==0.5.1
+pyasn1-modules==0.3.0
 requests-oauthlib==1.3.1
 rsa==4.9
-setuptools==57.5.0
+
+# Utilities
+packaging==23.2
 six==1.16.0
-snowballstemmer==2.2.0
-soupsieve==2.4.1
-tensorboard==2.2.2
-tensorboard-plugin-wit==1.8.1
-tensorflow==2.2.0
-tensorflow-estimator==2.2.0
-termcolor==2.3.0
-tf-slim==1.1.0
-threadpoolctl==3.2.0
-tifffile==2023.7.10
-tomli==2.0.1
+filelock==3.13.1
 tqdm==4.66.1
-urllib3==2.0.4
-Werkzeug==1.0.1
-wheel==0.41.1
-wrapt==1.15.0
-zipp==3.16.2
+gdown==5.1.0
+PySocks==1.7.1
+networkx==3.2.1
+PyWavelets==1.5.0
+colour==0.1.5
+Markdown==3.5.2
+mistune==3.0.2
+zipp==3.17.0
+importlib-metadata==7.0.1
+importlib-resources==6.1.1
+pkgutil_resolve_name==1.3.10
+cached-property==1.5.2
+
+# Build/setup
+pip>=23.3.2
+setuptools>=69.0.3
+wheel>=0.42.0
 
-# tests
+# Tests
 mock==5.1.0
-pytest==7.4.0
-pytest-mock==3.11.1
-requests==2.31.0
+pytest==8.0.0
+pytest-mock==3.12.0
 pylama==8.4.1
-
-# dependencies for both scanner backends
-Pillow==8.3.2
-imagecodecs==2020.5.30
-numpy==1.19.5
-scipy==1.4.1
-opencv-python==4.4.0.46
-scikit-image==0.17.2
-scikit-learn==0.23.2
-joblib==0.17.0
-
-# web server
-uWSGI==2.0.19
+mccabe==0.7.0
+pycodestyle==2.11.1
+pydocstyle==6.3.0
+pyflakes==3.2.0
+snowballstemmer==2.2.0
+exceptiongroup==1.2.0
+iniconfig==2.0.0
+pluggy==1.4.0
+tomli==2.0.1

java/admin/pom.xml

@@ -35,13 +35,10 @@
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-web</artifactId>
         </dependency>
+        <!-- Springdoc OpenAPI (replacement for Springfox) -->
         <dependency>
-            <groupId>io.springfox</groupId>
-            <artifactId>springfox-swagger2</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>io.springfox</groupId>
-            <artifactId>springfox-swagger-ui</artifactId>
+            <groupId>org.springdoc</groupId>
+            <artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
         </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
@@ -80,6 +77,14 @@
             <groupId>io.jsonwebtoken</groupId>
             <artifactId>jjwt-api</artifactId>
         </dependency>
+        <dependency>
+            <groupId>io.jsonwebtoken</groupId>
+            <artifactId>jjwt-impl</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>io.jsonwebtoken</groupId>
+            <artifactId>jjwt-jackson</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
@@ -90,8 +95,8 @@
             <artifactId>spring-boot-starter-data-jpa</artifactId>
         </dependency>
         <dependency>
-            <groupId>com.vladmihalcea</groupId>
-            <artifactId>hibernate-types-52</artifactId>
+            <groupId>io.hypersistence</groupId>
+            <artifactId>hypersistence-utils-hibernate-63</artifactId>
         </dependency>
         <dependency>
             <groupId>org.liquibase</groupId>
@@ -108,12 +113,8 @@
             <artifactId>spring-boot-starter-security</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.springframework.security</groupId>
-            <artifactId>spring-security-jwt</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.springframework.security.oauth</groupId>
-            <artifactId>spring-security-oauth2</artifactId>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-oauth2-resource-server</artifactId>
         </dependency>
         <!-- TEST -->
         <dependency>