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[ENH] Add derivatives command and
pipeline-catalog
submodule (#349)
* add examples of nipoppy proc status files * add skeleton derivatives command * add basic smoke test of derivatives cmd * load TSV and check for missing IDs in derivatives cmd * generalize util to load a tabular file * Test added for load_tabular * Added nipoppy pipeline catalogue as submodule * Add loading of pipeline names and versions * validate pipeline names & versions and store expected col names in a dict * update help text & docstrings * refactor unique subject check to generic util * refactor pipeline name / version validation * add example proc status file w/ subjects not in the synthetic dataset - participant_id col of existing examples also updated to match Nipoppy * check that proc status subs are in pheno-containing JSONLD * refactor out jsonld validation & move IO utils into new module - prevents circular import errors since some utils require models.py, which in turn requires IO utils * switch to typer echo statement for model validation error * factor out context extraction * add logic to add completed pipelines to existing or new imaging sessions * create utility for extracting imaging sessions from a JSONLD * create util for creating completed pipelines * handle missing BIDS sessions * refine smoke test and add test using pheno-bids JSONLD * refactor out custom session ID * refactor out jsonld subject extraction * create list of namespaces & update tests to catch outdated @context * regenerate context in each cmd to ensure they are up-to-date * add short option for overwrite to error msg * update test data README * handle jsonld loading tgt with dataset parsing * create global vars for known pipelines + vers * handle error for mismatched subs in separate func * update bagel bids to add metadata to existing sessions * update derivatives cmd to add to existing custom ses * make get_imaging_session_instances a shared util * update tests of bids command
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