bids-validator

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I am preparing example for the - https://github.com/bids-standard/bids-specification/pull/1861 and upon initial validation receiving NO error although it should be there since I entered (for extra check) a completely unknown value....

yarikoptic

Got ``` [WARNING] The onset column in events.tsv files should be sorted. (EVENT_ONSET_ORDER) ./sub-0001/ses-02/func/sub-0001_ses-02_task-narratives_acq-mb8_run-01_events.tsv Evidence: schema.rules.rules.checks.events.SortedOnsets ... ./sub-0131/ses-04/func/sub-0131_ses-04_task-social_acq-mb8_run-02_events.tsv Evidence: schema.rules.rules.checks.events.SortedOnsets ... ./sub-0147/ses-04/func/sub-0147_ses-04_task-fractional_acq-mb8_run-01_desc-posner_events.tsv Evidence: schema.rules.rules.checks.events.SortedOnsets Please visit https://neurostars.org/search?q=EVENT_ONSET_ORDER for existing conversations...

yarikoptic

chore(deps-dev): bump ws from 8.13.0 to 8.17.1

1

Bumps [ws](https://github.com/websockets/ws) from 8.13.0 to 8.17.1. Release notes Sourced from ws's releases. 8.17.1 Bug fixes Fixed a DoS vulnerability (#2231). A request with a number of headers exceeding the[server.maxHeadersCount][] threshold...

dependabot[bot]

Make bids-validator conform to BIDS-App (or execution-spec right away) specification

2

ATM it is ``` Usage: bids-validator [options] ``` whenever BIDS-app interface, as described in new exec spec (bep027) https://bids-standard.github.io/execution-spec/inputs.html#backwards-compatibility ``` bids-app InputDataset OutputLocation AnalysisLevel [options] ... CLI flag: --subject-label ```...

yarikoptic

Introspect values in failing checks

3

ATM ``` [ERROR] Participant labels found in this dataset did not match the values in participant_id column found in the participants.tsv file. (PARTICIPANT_ID_MISMATCH) ./participants.tsv Evidence: schema.rules.rules.checks.dataset.ParticipantIDMismatch 1 more files with...

yarikoptic

in relation to - https://github.com/bids-standard/bids-validator/issues/1999 to avoid waiting the validation of hundreds of subjects just to see the effect on `README_FILE_MISSING` . Probably would relate to discussion - https://github.com/bids-standard/bids-validator/issues/1937#issuecomment-2156630201 since...

yarikoptic

do not add ANSI coloring if stdout is not a tty -- add `--color=auto,yes,no`

1

It has bugged me for a while, even with original bids-validator and now with deno version: if output is redirected to a file we still get ANSI characters in there...

yarikoptic

Making a distinction between OPTIONAL and RECOMMENDED fields in the json files

2

Is there a way yet in which the validator gives a warning for missing recommended fields in json files?

dorahermes

allow multiple configs

1

E.g. if we have "center-wide" one, and then per-dataset specific (btw -- what would be the logical location to keep it around under?), it would be cool if I could...

yarikoptic

Warn for empty directories

2

I have a bids dataset with empty anat directories. It passed bids validator test without reporting for these empty anat directories or other empty directories.

suyashdb