Bids curation in mulitple JSON files

Motivation

One giant json config file is hard to inspect. Breaking rules into their own file makes debuging more managable. And we can add comments.

Iterating

1. change e.g. LunaHabit/SEFieldMap.json
2. run ./bundler.py (or make, see Makefile for bundler.py syntax)
3. upload bundle to flywheel (e.g fw upload LunaHabit_curate.json fw://mrrc/playground)
4. rerun BIDS. ./run_curate-gear.py. prints log, writes to /tmp/nii.csv.
5. look at output: grep nii.gz /tmp/nii.csv| cut -d, -f5,6,9|column -ts,
6. repeat

Offline Check

As of 2024-12, fw-template-check is out-of-date with upstream curate-bids. Use the old version like (likely in a dedicate python virtual machine):

pip install git+https://gitlab.com/will.foran/curate-bids.git@check-cli-old

fw-template-check -t LunaHabit_curate.json "33 - dMRI_b0_AP" "37 - dMRI_b0_AP"

33 - dMRI_b0_AP dMRI_b0 sub-{session.info.BIDS.Subject}_acq-b0_epi.nii.gz
37 - dMRI_b0_AP dMRI_b0 sub-{session.info.BIDS.Subject}_acq-b0_epi.nii.gz

TODO

intendedFor regex pairs. can be set in ./run_curate-gear.py

https://docs.flywheel.io/Developer_Guides/dev_bids_curation_6_fmaps_and_intendedfors/#how-to-include-regular-expressions-during-bids-curation

Flywheel documentation

https://docs.flywheel.io/Developer_Guides/dev_bids_template_file/

[Watch out for missing currly's and parrens]

Flywheel examples can be found in https://gitlab.com/flywheel-io/public/bids-client/ within flywheel_bids/templates/flywheel_curated/

Bids Curate Notes

$run_counter

From LunaHabit/dMRI_b0.json

    "run": {
        // bids-client/tests/test_templates_unittest.py
        // + always increments?
        "$value": "+",
        // flywheel_curated/nyu-bair-vfs-project-template.json
        "$run_counter": {
            "key": "field_map.{file.info.BIDS.Dir}.{file.info.BIDS.Acq}.{file.info.BIDS.Suffix}"
          }
    },

bids-client/flywheel_bids/supporting_files/templates.py appears to only update the $run_couter if the current value is "+". The only place I've found this referenced is in bids-client/tests/test_templates_unittest.py.

Format

Format can be used with auto_update defnitiions, espeically for session and subject: definitions.session.{Label,Subject}.auto_update.

"$format":[{
 "$replace": {
  "$pattern": "bad",
  "$replacement": "good"}
 }]
}

from LunaHabit/template.jsonc

    "definitions": {
        "session": {
            "properties": {
                "Label": {
                    "auto_update": {
                        "$process": true,
                        "$value": "<session.label>", // this is yyyymmddhhmmss... '<>' is autoformat lowercase + rm spaces; {} is literal value
                        "$format": [{
                            "$replace": { // keep only the first 8 digits
                                "$pattern": "(?<=[0-9]{8}).*",
                                "$replacement": ""}
                        }]
                    }