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40 fix schema translate map rel class - #41

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40-fix-schema-translate-map-rel-class
Open

40 fix schema translate map rel class#41
nicoloesch wants to merge 5 commits into
mainfrom
40-fix-schema-translate-map-rel-class

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Depends on AustralianCancerDataNetwork/omop-alchemy#57. Requires pyproject.toml version update for oa-configurator, orm-loader, and omop-alchemy

Summary

Root cause

  • relationship-classification was writing outside the configured CDM schema
    • a stale DROP TYPE no-op plus unqualified staging-table SQL.
  • The OAK-lib adapter (OMOPAlchemyImplementation) resolved a database URL but discarded its
    schema_translate_map, silently ignoring the configured schema for all ontology/concept
    traversal, not just this one command.
  • omop_resource()/ OMOPAlchemyImplementation never wired a configured split vocabulary connection through to a real second engine at all
    • KnowledgeGraph silently collapsed to one connection whenever a caller, including every production path, omitted vocab_engine explicitly.

Fix

  • relationship-classification now respects the configured CDM schema end to end
  • The OAK-lib adapter carries its schema_translate_map through to the engine it builds, and skips engine construction entirely when a caller injects kg= directly.
  • omop_resource() now builds both the primary and vocabulary engines via oa-configurator's create_engines(), and OMOPAlchemyImplementation accepts and forwards a real vocab_engine
    • a genuinely separate vocabulary connection is now supported end to end in production

Checklist

  • Applied exactly one label (breaking, feature, fix, dependencies, or chore)
  • Tests pass locally (uv run pytest -q): 46 passed
  • Lint passes (uv run ruff check .)

@nicoloesch nicoloesch added the fix Bug fix, backwards-compatible. PATCH: x.y.z+1 label Sep 7, 2026
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fix Bug fix, backwards-compatible. PATCH: x.y.z+1

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omop-graph relationship-classification load command does not honour non-default schema

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