Add HINT validation result suggesting .bidsignore for dandiset.yaml #1741
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Copilot AI changed the title [WIP] Add hint for user to create .bidsignore for dandiset.yaml Add HINT validation result suggesting .bidsignore for dandiset.yaml Nov 12, 2025
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When BIDS validator encounters dandiset.yaml (not part of BIDS spec), now: - Keeps the existing ERROR about the file not matching BIDS patterns - Adds a new HINT level validation result suggesting to create/update .bidsignore Includes test to verify both ERROR and HINT are generated Co-authored-by: yarikoptic <39889+yarikoptic@users.noreply.github.com>
yarikoptic force-pushed the copilot/add-hint-for-dandiset-yaml branch from 5d5dd81 to 957da04 Compare 
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| @yarikoptic I don't get the point of this or #1740. If we don't want the problem with |
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| We don't want to "cheat" bids validator, so if people run it directly they get the same result. AI we want to instruct for to mitigate that error consistently |
Member
| Tested against dandiset 001442 (chosen because it is a smallish BIDS dataset, though lots of validation noise). The PR works as described - the IMO this is fine, the HINT probably will be easier to understand for unfamiliar users, even though the duplication and extra noise are somewhat undesirable. trimmed raw output: master branchtrimmed output: PR branchDiff between master and branch5a6,7 > [DANDI.BIDSIGNORE_DANDISET_YAML] /home/austin/devel/dandi-cli/001442 — Consider creating or updating a `.bidsignore` file in the root of your BIDS dataset to ignore `dandiset.yaml`. Add the following line to `.bidsignore`: > dandiset.yaml |
asmacdo approved these changes Dec 12, 2025
candleindark requested changes Dec 12, 2025
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candleindark left a comment
candleindark left a comment There was a problem hiding this comment.
Proposed some changes.
Additionally, if we want this custom validation hint to show up in the dandi upload command as well, we need to move this logic to an earlier point the in the calling process. The current setup only affect dandi validate not dandi upload where the issue was originally reported at #1734 (comment).
Comment on lines 198 to 206
| if is_dandiset_yaml_error: | ||
| r.message = ( | ||
| f"The dandiset metadata file, `{dandiset_metadata_file}`, " | ||
| f"is not a part of BIDS specification. Please include a " | ||
| f"`.bidsignore` file with specification to ignore the " | ||
| f"metadata file in your dataset. For more details, see " | ||
| f"https://github.com/bids-standard/bids-specification/" | ||
| f"issues/131#issuecomment-461060166." | ||
| ) |
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Since we now have a separate hind for to suggest for modifying .bidsignore, and we want to preserve the original error from BIDS deno validator as much as possible, we can remove this modification of the original error message.
Comment on lines +213 to +228
| hint = ValidationResult( | ||
| id="DANDI.BIDSIGNORE_DANDISET_YAML", | ||
| origin=ORIGIN_VALIDATION_DANDI_LAYOUT, | ||
| severity=Severity.HINT, | ||
| scope=Scope.DATASET, | ||
| path=r.dataset_path, | ||
| dataset_path=r.dataset_path, | ||
| dandiset_path=dandiset_path, | ||
| message=( | ||
| f"Consider creating or updating a `.bidsignore` file " | ||
| f"in the root of your BIDS dataset to ignore " | ||
| f"`{dandiset_metadata_file}`. " | ||
| f"Add the following line to `.bidsignore`:\n" | ||
| f"{dandiset_metadata_file}" | ||
| ), | ||
| ) |
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Suggested change
| hint = ValidationResult( | |
| id="DANDI.BIDSIGNORE_DANDISET_YAML", | |
| origin=ORIGIN_VALIDATION_DANDI_LAYOUT, | |
| severity=Severity.HINT, | |
| scope=Scope.DATASET, | |
| path=r.dataset_path, | |
| dataset_path=r.dataset_path, | |
| dandiset_path=dandiset_path, | |
| message=( | |
| f"Consider creating or updating a `.bidsignore` file " | |
| f"in the root of your BIDS dataset to ignore " | |
| f"`{dandiset_metadata_file}`. " | |
| f"Add the following line to `.bidsignore`:\n" | |
| f"{dandiset_metadata_file}" | |
| ), | |
| ) | |
| hint = ValidationResult( | |
| id="DANDI.BIDSIGNORE_DANDISET_YAML", | |
| origin=ORIGIN_VALIDATION_DANDI_LAYOUT, | |
| scope=Scope.DATASET, | |
| origin_result=r, | |
| severity=Severity.HINT, | |
| dandiset_path=r.dandiset_path, | |
| dataset_path=r.dataset_path, | |
| path=r.path, | |
| message=( | |
| f"Consider creating or updating a `.bidsignore` file " | |
| f"in the root of your BIDS dataset to ignore " | |
| f"`{dandiset_metadata_file}`. " | |
| f"Add the following line to `.bidsignore`:\n" | |
| f"{dandiset_metadata_file}" | |
| ), | |
| ) |
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When BIDS validator encounters
dandiset.yaml(not part of BIDS spec), users now receive both the ERROR and a HINT suggesting to add the file to.bidsignore.Changes
dandi/validate.py
DANDI.BIDSIGNORE_DANDISET_YAML, severity:Severity.HINT, scope:DATASET.bidsignoredandi/tests/test_validate.py
test_validate_bids()to verify both ERROR and HINT are generatedExample Output
Original prompt
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