⚡ Improvement: BIDS Inheritance

[shnizzedy]

Related problem

If a BIDS directory contains sidecar information split between file-level and directory-level, C-PAC produces outputs like the following if the parameters C-PAC is looking for are in a higher-level sidecar.

Parsing /bids_dataset..
{'site': 'none', 'sub': '17', 'ses': 'localizer', 'task': 'objectcategories', 'run': '3', 'scantype': 'bold'}
Did not receive any parameters for sub-17/ses-localizer/func/sub-17_ses-localizer_task-objectcategories_run-3_bold.nii.gz, is this a problem?
{'site': 'none', 'sub': '17', 'ses': 'localizer', 'task': 'retmapclw', 'run': '1', 'scantype': 'bold'}
Did not receive any parameters for sub-17/ses-localizer/func/sub-17_ses-localizer_task-retmapclw_run-1_bold.nii.gz, is this a problem?
{'site': 'none', 'sub': '17', 'ses': 'localizer', 'task': 'objectcategories', 'run': '1', 'scantype': 'bold'}
Did not receive any parameters for sub-17/ses-localizer/func/sub-17_ses-localizer_task-objectcategories_run-1_bold.nii.gz, is this a problem?
{'site': 'none', 'sub': '17', 'ses': 'localizer', 'task': 'retmapcon', 'run': '1', 'scantype': 'bold'}
Did not receive any parameters for sub-17/ses-localizer/func/sub-17_ses-localizer_task-retmapcon_run-1_bold.nii.gz, is this a problem?
{'site': 'none', 'sub': '17', 'ses': 'localizer', 'task': 'movielocalizer', 'run': '1', 'scantype': 'bold'}
Did not receive any parameters for sub-17/ses-localizer/func/sub-17_ses-localizer_task-movielocalizer_run-1_bold.nii.gz, is this a problem?
{'site': 'none', 'sub': '17', 'ses': 'localizer', 'task': 'retmapexp', 'run': '1', 'scantype': 'bold'}
Did not receive any parameters for sub-17/ses-localizer/func/sub-17_ses-localizer_task-retmapexp_run-1_bold.nii.gz, is this a problem?
{'site': 'none', 'sub': '17', 'ses': 'localizer', 'task': 'objectcategories', 'run': '2', 'scantype': 'bold'}
Did not receive any parameters for sub-17/ses-localizer/func/sub-17_ses-localizer_task-objectcategories_run-2_bold.nii.gz, is this a problem?
{'site': 'none', 'sub': '17', 'ses': 'localizer', 'task': 'retmapccw', 'run': '1', 'scantype': 'bold'}
Did not receive any parameters for sub-17/ses-localizer/func/sub-17_ses-localizer_task-retmapccw_run-1_bold.nii.gz, is this a problem?
{'site': 'none', 'sub': '17', 'ses': 'localizer', 'task': 'objectcategories', 'run': '4', 'scantype': 'bold'}
Did not receive any parameters for sub-17/ses-localizer/func/sub-17_ses-localizer_task-objectcategories_run-4_bold.nii.gz, is this a problem?

Parsing /bids_dataset..
{'site': 'site1', 'sub': '18', 'ses': 'movie', 'scantype': 'T1w'}
Did not receive any parameters for site-1/sub-18/ses-movie/anat/sub-18_ses-movie_T1w.nii.gz, is this a problem?
{'site': 'site1', 'sub': '18', 'ses': 'movie', 'task': 'movie', 'run': '1', 'scantype': 'bold'}
Did not receive any parameters for site-1/sub-18/ses-movie/func/sub-18_ses-movie_task-movie_run-1_bold.nii.gz, is this a problem?
{'site': 'site1', 'sub': '18', 'ses': 'movie', 'task': 'movie', 'run': '8', 'scantype': 'bold'}
Did not receive any parameters for site-1/sub-18/ses-movie/func/sub-18_ses-movie_task-movie_run-8_bold.nii.gz, is this a problem?
{'site': 'site1', 'sub': '18', 'ses': 'movie', 'task': 'movie', 'run': '7', 'scantype': 'bold'}
Did not receive any parameters for site-1/sub-18/ses-movie/func/sub-18_ses-movie_task-movie_run-7_bold.nii.gz, is this a problem?
{'site': 'site1', 'sub': '18', 'ses': 'movie', 'task': 'movie', 'run': '5', 'scantype': 'bold'}
Did not receive any parameters for site-1/sub-18/ses-movie/func/sub-18_ses-movie_task-movie_run-5_bold.nii.gz, is this a problem?
{'site': 'site1', 'sub': '18', 'ses': 'movie', 'task': 'movie', 'run': '6', 'scantype': 'bold'}
Did not receive any parameters for site-1/sub-18/ses-movie/func/sub-18_ses-movie_task-movie_run-6_bold.nii.gz, is this a problem?
{'site': 'site1', 'sub': '18', 'ses': 'movie', 'task': 'movie', 'run': '4', 'scantype': 'bold'}
Did not receive any parameters for site-1/sub-18/ses-movie/func/sub-18_ses-movie_task-movie_run-4_bold.nii.gz, is this a problem?
{'site': 'site1', 'sub': '18', 'ses': 'movie', 'task': 'movie', 'run': '2', 'scantype': 'bold'}
Did not receive any parameters for site-1/sub-18/ses-movie/func/sub-18_ses-movie_task-movie_run-2_bold.nii.gz, is this a problem?

If the more specific sidecars are removed, however, C-PAC discovers the parameters in the higher-level sidecar.

Proposed feature

Update C-PAC's sidecar discovery to follow BIDS' Inheritance Principle

There is no notion of "unsetting" a key/value pair. Once a key/value pair is set in a given level in the dataset, lower down in the hierarchy that key/value pair will always have some assigned value.
[…]
If the .json file at the more shallow level contains key-value-pairs that are not present in the .json file at the deeper level, these key-value-pairs are inherited by the .json file at the deeper level (but NOT vice versa!).

[shnizzedy]

Possibly related: #2103

[sgiavasis]

We'll be considering migrating to either bids2table, or possibly but less likely, PyBIDS in the near future (v1.8.8).
@e-kenneally is starting to look into it.