neurobagel / bagel-cli / 11238955293

98%

Build Type

push

github

Committed by web-flow

Commit Message

[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* create list of namespaces & update tests to catch outdated @context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 ... (continued)

Run Details

295 of 297 new or added lines in 10 files covered. (99.33%)

2 existing lines in 2 files now uncovered.

967 of 983 relevant lines covered (98.37%)

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