Add a structured issues model and emit findings from the filename validator
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描述
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)Issuewithcode,severity,location,message,sub_code,ruleDatasetIssues, an ordered collection withadd,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
- Is the minimal field set above right, or do you want the reference validator's richer
fields (rule provenance, machine-actionable fixes, anignoreseverity, line spans)
from the start? I kept them out to keep the first PR small. - The CLI currently prints
<path> is not a valid bids filenamefor 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. - 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.
- 主要語言
- Python
- 星號
- 10
- 分支
- 7
- PR 合併指標
- 30 天內沒有已合併 PR
環境準備
- 沒有 Dockerfile 或 Docker Compose 檔案
- 沒有 Pull Request 範本
- 閱讀貢獻指南
從這裡開始
- 先讀完整個 Issue，再讀專案的貢獻指南。
- 在 Issue 下留言說明你要接手 —— 這能避免兩個人做同樣的事。
- Fork 儲存庫，在一個分支上完成修改。
- 送出 Pull Request，並在描述裡引用這個 Issue 編號。
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