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Drop SNOMED, EFO and NCIT from the shared-case known_gaps - #18
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ndi-ontology-matlab 36d7814 added cases for all three to ontology_lookup_tests.json, so every ported provider now has a case and known_gaps is empty. The NCIT rows also exercise this branch's obo_id lookup live. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CgkxUSKbSBq9Js9q871BNE
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Oct 21, 2026
…ed helpers main brought #14 (EMPTY), #15 (NCIT codes by obo_id), #17 (lookup trimming, the same fix as this branch's) and #18 (known_gaps). #15's NCITProvider.lookup_term called OLSProvider._search_ols, which this branch replaces; git merged it cleanly, and every NCIT lookup would have raised AttributeError. It now does what NCIT.m does on the ported helpers: preprocessLookupInput, then searchOLSAndPerformIRILookup on obo_id for ['NCIT:', search_query]. Its tests move to FakeOLS, plus one for the prefixed and numeric forms. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_017iFBFMQmEZaz21d9ZFJbiH
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Follow-up to #15 and item 4 of #11.
Waltham-Data-Science/ndi-ontology-matlab#13 (merged as 36d7814) added SNOMED, EFO and NCIT cases to
ontology_lookup_tests.json. Every ported provider now has at least one shared case, soknown_gapsintest_case_table_covers_every_ported_provideris now an empty set. The NCIT bridge entry's note now says NCIT is covered instead of pointing at the pending upstream PR.This commit was pushed to #15's branch a few seconds after #15 merged, so it was not part of that merge.
Tests
black --check,ruff checkandpytest -m "not live"pass locally (169 passed, 2 skipped).test_case_table_covers_every_ported_providerpasses against ndi-ontology-matlab 36d7814.Generated by Claude Code