bids-validator

bids-validator copied to clipboard

inconsistent behavior for files of the form <suffix>.json files when in the root of the dataset

2

For some data types the validator is fine with having `.json` files in the root of the dataset: - pet.json - T1.json But for some others it will throw an...

Remi-Gau

Make bids-validator more git-annex friendly.

2

There is now a number of options which could be used to provide some partial remedy: `--ignoreSymlinks` (its --help output talks about directories but I think it was meant about...

yarikoptic

Remove warning for tsv data files without headers (motion/physio...)

1

Hi everyone, I noticed that .tsv data without headers (for example [this one](https://github.com/bids-standard/bids-examples/tree/bep029_motion/motion_systemvalidation)) lead to warning [Code 82] CUSTOM_COLUMN_WITHOUT_DESCRIPTION (see [this PR](https://github.com/bids-standard/bids-examples/pull/354#issuecomment-1426844837) for context). A few modalities including motion (currently...

sjeung

Validate TSV column contents using schema.objects.columns type and format information

1

Example rule: `ASLCONTEXT_TSV_INCONSISTENT`: `In the 'sub-[_ses-][_acq-][_rec-][_run-]_aslcontext.tsv', the 'volume_type' can only be filled with volumes ['cbf' ,'m0scan', 'label', 'control', 'deltam'].` From [objects.columns](https://github.com/bids-standard/bids-specification/blob/eb658db44deade3ef3eb0ffaa192bb5b77d78de0/src/schema/objects/columns.yaml#L775-L787): ```YAML volume_type: name: volume_type display_name: ASL volume type description:...

effigies

Does not have a check in the current schema.

rwblair

Would be nice to have it spit out tsv/json via cli flag instead of printing the table. Table is not great for copying and pasting.

rwblair

Old validator looked for `n/a` like things and throw an error: ``` (value === 'NA' || value === 'na' || value === 'nan' || value === 'NaN') && ```

rwblair

Node validator can take filenames from standard input separated by newlines and returns if they are valid are not. No file contents or metadata passed.

rwblair

Annexed files without local content crash validation

1

This is for the schema validator. ``` error: Uncaught NotFound: No such file or directory (os error 2), open '/home/nell/Git/crn/datasets/ds000117/sub-01/ses-mri/anat/sub-01_ses-mri_acq-mprage_T1w.nii.gz' return Deno.openSync(this._getPath(), openOptions) ^ at Object.openSync (deno:runtime/js/40_files.js:40:21) at BIDSFileDeno.#openHandle (file:///home/nell/Git/crn/bids-validator/bids-validator/src/files/deno.ts:108:17)...

nellh

Add debug messages to filename validation in schema validator.

3

Seems like another good spot for --debug level warnings. _Originally posted by @nellh in https://github.com/bids-standard/bids-validator/pull/1547#discussion_r1093675127_

rwblair