Maxime's branch - #1397
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* move the sourcing of the python environment up as this erase the PATH configuration when done at the end of the file * Update comment for the python environment sourcingg
…#1455) * remove update of session scan done field from the delete script now that the Scan_done field has been removed from the DB * update MD file --------- Co-authored-by: lorisadmin <lorisadmin@cbrain.mcgill.ca>
* Validate config-provided CenterID against the psc table in getPSC * Validate config CenterID and finish removing MRI_alias from Perl * shorten comment section * address Nics comments: generate associated .md file for documentation changes in MRI.pm file. better validation strategy with PSCOB class rather than database check. Improved order of code for readability in tarchiveLoader.pl
* add a few test plans * fix typo
* add dicom and bids importer documentation * fix whoopsie
Co-authored-by: cmadjar <lorisadmin@cbrain.mcgill.ca>
incremental bids importer bids session dataclass bids participants dataclass factorize combination iteration fix layout ignore skip files already inserted wip fix mri path join rebase commit migrate to new database abstraction rewrite optional dataset_description.json return an error on unknown scan types fix wrong counter and memory use fix eeg path concatenation fix cli options make profile cli argument optional add missing candidate and session fields fix print statement use lists instead of tuples for eeg paths rename bids classes migrate bids importer from str to path add specialized data types add modalities-specific bids modules change nifti class to bids mri acquisiton wip vibe coding vibe coding wip 2 meegqc rename tracking factorize meegqc endpoints update meegqc wip improve permissions
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Do not merge.
Branch with lots of stuff to be merge in other PRs.