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Track ndi-ontology-matlab PR #9: WormBase via WormMine, NCBITaxon synonyms - #8
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…onyms Ports ndi-ontology-matlab at 9d8fc03 (0c18bf8, ff3c3fd): - WBStrainProvider becomes WormBaseProvider, mirroring the MATLAB rename. Strains are read from WormMine's InterMine query service, because wormbase.org and rest.wormbase.org answer scripts with a Cloudflare 403. The `wormbase:WBStrain00000001` CURIE is accepted and returned in that form. A non-strain WormBase id, "*", an ambiguous or mismatched name and a WormMine error now raise, as in MATLAB, rather than being swallowed into an empty result. parseStrain is public, as in MATLAB. - NCBITaxonProvider.parseOtherNames ports MATLAB's new synonym parser: common names, synonyms, equivalent names and acronyms; no authority citations, misspellings or <Includes>. - ontology_list.json copied from MATLAB (WBStrain and wormbase -> WormBase). - Ports TestNCBITaxonOtherNames, TestWormBaseParsing, TestLookupStringInput and TestLookupSynonyms (live). WormBase is now covered by the shared case table, so it leaves the known gaps. - Bridge, README updated. MATLAB's string-scalar fix in lookup has no Python counterpart (one string type); recorded in the bridge. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01AkGucMfJVpwrBRyjNLpdcw
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Brings the port in line with ndi-ontology-matlab at 9d8fc03 (Waltham-Data-Science/ndi-ontology-matlab#9: commits 0c18bf8 and ff3c3fd).
Changes
WBStrainProvideris renamedWormBaseProvider, matching the MATLAB class rename.wormbase:WBStrain00000001is accepted and returned in that form.WBStrain:lookups behave as before.*, a name matching more than one strain, a returned name that doesn't match, and a WormMine error.parseStrainis public, as it is in MATLAB.NCBITaxonProvider.parseOtherNamesports MATLAB's new parser. It keeps common names, synonyms, equivalent names and acronyms, and drops authority citations, misspellings and<Includes>. The old code returned every<DispName>and missed<Synonym>and<GenbankCommonName>.ontology_list.jsonis now an exact copy of MATLAB's:WBStrainandwormbaseboth map toWormBase.TestNCBITaxonOtherNames,TestWormBaseParsing,TestLookupStringInputandTestLookupSynonyms(live) intotests/matlab_tests/test_ontology_parsing.py, and rewrites the WormBase unit tests. The shared case table now has WormBase cases, so WormBase is removed fromknown_gaps.lookuphas no Python counterpart, since Python has only one string type; the bridge records this.Testing
black --check,ruff checkandpytest -m "not live"pass: 112 passed, 3 skipped.TestLookupSynonymsLivewill run for the first time in the live CI job.🤖 Generated with Claude Code
https://claude.ai/code/session_01AkGucMfJVpwrBRyjNLpdcw
Generated by Claude Code