Add a structured issues model and emit findings from the filename validator

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#85 1 commento 0 reazioni 1 assegnatario Vedi su GitHub

@karellopez ci sta già lavorando.

Dal 10/8/2026.

  • #86 di @karellopez — aperta

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Descrizione

enhancement
Summary

Validation currently answers a yes/no question. BIDSValidator.is_bids() returns a
boolean, and the CLI prints one line per non-compliant file:

/sub-01/anat/oops.nii.gz is not a valid bids filename

That output carries no severity, no stable code, and no structure a program can consume.
It cannot be counted, filtered, serialised, or shown in a UI, and it cannot say why a
name is wrong.

context.py already anticipates this: ValidationError is a stub whose entire body is
"""TODO: Add issue structure.""".

Proposal

Two small pieces.

1. An issue model (bids_validator/issues.py). Pure data, no I/O, attrs to match
the convention already used by context.py, bidsignore.py and types/files.py:

  • Severity (error, warning)
  • Issue with code, severity, location, message, sub_code, rule
  • DatasetIssues, an ordered collection with add, extend, by_severity,
    has_errors, __len__, __iter__

Field names mirror the reference validator so output stays interchangeable.

2. Emit findings from filename validation. Rather than one blanket answer, report the
specific reason using the reference validator's codes: NOT_INCLUDED,
MISSING_REQUIRED_ENTITY, ENTITY_NOT_IN_RULE, ENTITY_WITH_NO_LABEL,
INVALID_ENTITY_LABEL, EXTENSION_MISMATCH, DATATYPE_MISMATCH, INVALID_LOCATION,
FILENAME_MISMATCH, ALL_FILENAME_RULES_HAVE_ISSUES.

Scope is names and paths only. No file contents are read.

BIDSValidator.is_bids() stays untouched, since pybids and mne-bids depend on it.

Why this first

Every later check needs somewhere to report to. Content validation (sidecar fields, NIfTI
headers, tabular columns) produces the same Issue type into the same DatasetIssues,
so the output contract is defined once and does not change as coverage grows.

Questions for maintainers
  1. Is the minimal field set above right, or do you want the reference validator's richer
    fields (rule provenance, machine-actionable fixes, an ignore severity, line spans)
    from the start? I kept them out to keep the first PR small.
  2. The CLI currently prints <path> is not a valid bids filename for each bad file.
    When these findings are wired into it, should that output change to show the
    specific code and reason, or should the current text stay the default with the
    structured output behind a flag? Changing it would be more useful but would break
    anyone parsing the current output.
  3. Any preference on module naming (issues.py / filename_checks.py)?

I have a working implementation with tests and am happy to open a PR, or to adjust the
shape first if you would prefer a different design.

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