promote_resolved_unmapped helper + merge duplicate alpha-ketoglutamate → CHEBI:30915#70
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…utamate into CHEBI:30915 Backlog #3 (unmapped curation): - New scripts/promote_resolved_unmapped.py automates the unmapped→mapped migration recipe end to end (move+transform between collections, canonical CHEBI label from the local OAK chebi.db, SSSOM row inserted in subject-label sort order, regenerate per-record + docs, verify reconcile/invariants). Default dry-run; --apply writes. Key safety feature: a PK-collision guard that refuses to create a duplicate CHEBI primary key. Handles exact/close (narrow/broad need registry rows — hand-curate). - That guard immediately earned its keep: the ready-to-map alpha-ketoglutamate (UNMAPPED_0323) targets CHEBI:30915, which is ALREADY a mapped record ("alpha-ketoglutaric acid") — and the anion CHEBI:16810 is too. So it's a DUPLICATE, not a new mapping. Merged it into the existing CHEBI:30915 record (added "alpha-ketoglutamate" as a synonym + a MERGED_FROM_UNMAPPED_DUPLICATE history entry, mirroring the prior a-Ketoglutaric_Acid merge) and removed UNMAPPED_0323. (unmapped 397 → 396) Verified: reconcile_sssom in sync (GAP/ORPHAN/STALE 0); SSSOM invariants A/B1/B2/B3; validate-strict 0 errors; full suite 359 passed. No id/label changes. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Backlog #3 (unmapped curation): builds the promotion helper and resolves the second batch-1 "ready" record.
New helper:
scripts/promote_resolved_unmapped.pyAutomates the multi-surface unmapped→mapped migration recipe end to end:
chebi.db,PROMOTED_TO_MAPPEDhistory, header counts);skos:<predicate>row in subject-label sort order;reconcile_sssom+validate_sssom_invariants.Default dry-run;
--applywrites. Key safety feature: a PK-collision guard that refuses to create a duplicate CHEBI primary key (handles exact/close; narrow/broad need registry SSSOM rows → hand-curate).The guard immediately earned its keep
The ready-to-map
alpha-ketoglutamate(UNMAPPED_0323) targetsCHEBI:30915— which is already a mapped record ("alpha-ketoglutaric acid"), and the anionCHEBI:16810is too. So it's a duplicate, not a new mapping.→ Merged it into the existing
CHEBI:30915record (addedalpha-ketoglutamateas a synonym + aMERGED_FROM_UNMAPPED_DUPLICATEhistory entry, mirroring the priora-Ketoglutaric_Acidmerge) and removedUNMAPPED_0323. Unmapped: 397 → 396.Verification
reconcile_sssom: in sync (GAP/ORPHAN/STALE 0). The merge needed no SSSOM change (survivor already has its row; the removed record had 0 occurrences).validate-strict: 0 errors over 2274 files; full suite 359 passed. No id/label changes.🤖 Generated with Claude Code