BEP042 patches

[drammock]

This is needed for BEP042, specifically for bids-standard/bids-specification@5ea4b08 (#1998)

Code is copied (with minor typo fixes) from this forum answer so I've listed @rwblair in co-authored-by

marking as draft because I'm not 100% sure that just keys will allow us to check everything we want to check.

EDIT: approach changed after real-time convo with @effigies; now this collates multiple coordsystem files

xref

• [ENH] BEP042 - extension for electromyography (EMG) bids-specification#1998
• [ENH] BEP042 - EMG examples bids-examples#480

[drammock]

@effigies I'm doing local-run validation using the current state of this branch (e6de738). If I use the console.log(context) trick that Ross mentioned on the forum, I see this:

  subject: {},
  entities: { sub: "01", recording: "highDensity" },
  datatype: "emg",
  suffix: "electrodes",
  extension: ".tsv",
  modality: "emg",
  sidecar: {},
  associations: {},
  columns: Map(5) {
    "name" => [
   ... rest of context omitted

Notice that associations is empty. I think that means we're not capturing coordsystem.json files that have a space entity when electrodes.tsv does not have the space entity.

EDIT: this is on emg_concurrentIndependentUnits dataset. I think the empty associations is what is causing EMG_COORD_SYS_MISMATCH and EMG_COORD_SYS_PARENTS to fail for me locally

[drammock]

Notice that associations is empty.

looks like you resolved it on the spec end. I guess this is ready for changelog and review/merge then?

[effigies]

Leaving some notes. This PR can be merged once @rwblair is happy with it, or remain open during the BEP42 review period. It would need to be merged (and the dev branch updated) before the examples PR can be merged.

[effigies]

The EMG examples do not have this case, but with multiple coordsystem.jsons, you could imagine having some at the root and some at the leaf.

We currently strongly assume (and implement with .next().value) that the first level found is the level of the association, which has worked for single-file associations. This probably needs to be relaxed, but the logic will be more intricate. I think you would need to take the first coordsystem.json with a given space entity, not the full collection.

For now this could be noted as a limitation in the validator implementation.

[codecov]

Codecov Report

❌ Patch coverage is 30.23256% with 30 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.98%. Comparing base (fe09d89) to head (5cb3dc4).

Files with missing lines	Patch %	Lines
src/schema/associations.ts	30.23%	29 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #268      +/-   ##
==========================================
- Coverage   87.40%   86.98%   -0.43%     
==========================================
  Files          50       50              
  Lines        3677     3702      +25     
  Branches      603      604       +1     
==========================================
+ Hits         3214     3220       +6     
- Misses        453      472      +19     
  Partials       10       10              

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