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fix(reactome): preserve unmatched selection schema - #57

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FuqingZh merged 1 commit into
mainfrom
codex-reactome-unmatched-schema
Aug 18, 2026
Merged

fix(reactome): preserve unmatched selection schema#57
FuqingZh merged 1 commit into
mainfrom
codex-reactome-unmatched-schema

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Summary

  • Project the publication-backed single-selection unmatched frame to the public input_id schema.
  • Add source/publication regression coverage across four namespaces and three selection modes.

Root cause

Reactome selection normalization retains the internal lookup_id column. The publication-backed single-selection iterator passed that internal column through while declaring the public schema as only input_id, causing selection.unmatched_ids().collect() to raise a Polars SchemaError.

Validation

  • BIOEXTRACT_TEST_THREADS=1 pdm run check
  • 848 tests passed in 305.44s
  • Focused Reactome, cross-resource publication, lint, format, and direct formal-publication readback checks passed.

@FuqingZh
FuqingZh merged commit 64a8802 into main Aug 18, 2026
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