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Validate stored clique types before normalization - #46
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Return null for affected inputs when base or conflation source types are malformed, and emit structured diagnostics. Preserve ancestry order while removing duplicate types and every biolink:Entity. Add regression coverage for invalid sources, batch isolation, valid conflation, individual types, and GET/POST all-null responses. Validation: 53 focused tests passed.
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🟢 Approval recommended
No blocking issues were identified, and focused regression coverage addresses the changed behavior.
Review effort: Balanced
Findings: None
What changed in this PR
Adds API-side safeguards for malformed stored clique types associated with #41 while preserving valid normalization and conflation behavior.
Changes:
- Returns null for inputs with invalid base or conflation types and logs structured diagnostics.
- Deduplicates ancestry and removes every
biolink:Entity. - Adds regression coverage for batch isolation, conflation, fallbacks, and HTTP responses.
| File | Description |
|---|---|
| tests/test_normalized_nodes_lookup.py | Tests invalid types, ancestry cleanup, and preserved valid behavior. |
| src/nodenorm/handlers/normalized_nodes.py | Validates stored types and filters ancestry output. |
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Add safeguard for #41 on the API side