Allow ontology term ids instead of general metadata#5
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Pull Request Overview
This PR allows the validator to accept ontology term IDs as alternatives to general metadata fields. The validation now passes if either the standard metadata column (e.g., "tissue") or its corresponding ontology term ID column (e.g., "tissue_ontology_term_id") is present and contains valid values.
Key changes:
- Modified obs column validation to accept either standard metadata or ontology term ID columns
- Added new exception type for handling None/empty values in metadata fields
- Updated error messages to reflect the new ontology term ID support
Reviewed Changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.
| File | Description |
|---|---|
| src/cap_upload_validator/upload_validator.py | Updated validation logic to check for either metadata columns or ontology term ID columns, refactored validation helper methods |
| src/cap_upload_validator/errors.py | Added new exception class and updated existing exception messages to include ontology term ID alternatives |
| test/test_upload_validator.py | Added comprehensive test coverage for ontology term ID validation scenarios and corrected typos in exception names |
| CHANGELOG.md | Documented the new feature and breaking changes |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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