Operate on git-annexed structure

[bpinsard]

We are using the bids-validator on the git-part of datalad repos in CI, and so we don't pull annexed files for performances.
In the previous versions, using --ignoreNiftiHeaders made it work.
I don't know which recent changes caused the validator to still try to stat the files, and I don't see which option would prevent that.

traceback is

bids-validator --debug DEBUG  --ignoreNiftiHeaders --color true --config /tmp/bids-validator_config.json /bids/
error: Uncaught (in promise) NotFound: No such file or directory (os error 2): stat '/bids/sub-2449/ses-1a/anat/sub-2449_ses-1a_rec-orig_mod-T1w_defacemask.nii.gz'
  for (var i6 = 0, len = code2.length; i6 < len; ++i6) {
                         ^
    at async Object.stat (ext:deno_fs/30_fs.js:410:15)
    at async _readFileTree (https://raw.githubusercontent.com/bids-standard/bids-validator/refs/heads/deno-build/bids-validator.js:52:26)
    at async _readFileTree (https://raw.githubusercontent.com/bids-standard/bids-validator/refs/heads/deno-build/bids-validator.js:65:23)
    at async _readFileTree (https://raw.githubusercontent.com/bids-standard/bids-validator/refs/heads/deno-build/bids-validator.js:65:23)
    at async _readFileTree (https://raw.githubusercontent.com/bids-standard/bids-validator/refs/heads/deno-build/bids-validator.js:65:23)
    at async readFileTree (https://raw.githubusercontent.com/bids-standard/bids-validator/refs/heads/deno-build/bids-validator.js:89:16)
    at async main (https://raw.githubusercontent.com/bids-standard/bids-validator/refs/heads/deno-build/bids-validator.js:29:16)
    at async https://raw.githubusercontent.com/bids-standard/bids-validator/refs/heads/deno-build/bids-validator.js:3:16

config is:

{
        "ignore": [
          {"code": "TSV_COLUMN_MISSING", "location": "**_scans.tsv"},
          {"code": "TSV_ADDITIONAL_COLUMNS_UNDEFINED", "location": "**_scans.tsv"},
          {"code": "TSV_COLUMN_MISSING", "location": "**_events.tsv"},
          {"code": "SCANS_FILENAME_NOT_MATCH_DATASET"},
          {"code": "FILE_READ", "location": "**_scans.tsv"},
          {"code": "FILE_READ", "location": "**_events.tsv"}
        ],
        "warning": [
          {"code": "SIDECAR_KEY_REQUIRED", "subCode": "Units"},
          {"code": "REPETITION_TIME_AND_ACQUISITION_DURATION_MUTUALLY_EXCLUSIVE"}
        ]
      }

Thanks for your help!

[bpinsard]

I guess that is introduced in #281 @effigies
Ideally, this would be optional.

[yarikoptic]

overall there could be a bit more specific option added since it is not per se about nifti headers any longer as annexed could be .tsv and .json files, and also some other binary files which eventually should be subject to validation (e.g. nwb ref #23 ). So there could be --ignore with options for globs or regex on file names, and --annexed=ignore,s3-url-remote,...later-more? to be more specific about what to do about annexed files.

[effigies]

Check out #287. You can test with:

git clone https://github.com/bids-standard/bids-validator
cd bids-validator
git fetch upstream refs/pull/287/head
git checkout FETCH_HEAD -b pr-287
deno run -A src/bids-validator.ts

[bpinsard]

Thanks, it works with that fix!