promote to main (2/4): structure-guided re-resolution of conflated commits (fork #60) - #95
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…r-window fix(annotators): text/vector search scan the window for the first on-category node (port of fork #59)
…s + lipid independent-structure source (port of fork #60) Port of trentleslie/biomapper2 PR #60 (merged to fork dev 2026-09-01) to Phenome-Health. src/ + tests only — the studies/external_benchmarks benchmark harness (fork #61) stays off-org. Applied as a 3-way port onto org dev; verified green on the org base: pyright 0 errors, ruff clean, 776 passed / 227 skipped. Reviewer note: org dev has diverged resolver work (#75/#77/#82/#83 source-weighting / URL-resolver / InChIKey-blocks) — the port merged cleanly and the full suite passes, but confirm the re-resolution logic composes as intended with those. This promotion is the prerequisite for the D2 RefMet-bridge re-resolution work. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
This was referenced Sep 9, 2026
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Stacked promotion dev→main, 2 of 4. #94 (#59) merged; this is #60 on top.
This PR (#60 port)
Structure-guided re-resolution: when a committed KG node's structure disagrees with the query's INDEPENDENT structure, disambiguate to the correct distinct KG candidate; plus the lipid independent-structure resolver. Benchmark-gated; part of the validated determinism/re-resolution program already on org
dev.Series
Handle accidental double colons in input curies #59 text/vector window✅ merged (promote to main (1/4): text/vector search window scan (fork #59) #94)dev→main; no
studies/; org CIgateruns. No RefMet freeze in prod (consumer code inert unless configured).🤖 Generated with Claude Code