Ref/linkml ingestion#16
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The doc still described registry_version as a field on RegistryClass/ RegistryProperty (excluded from the hash) from before it was moved to ProvenanceEntry. Fixed the build_registry_entities() section and the data model table, and added a note pointing at test_required_does_not_affect_property_identity as the end-to-end proof that usage constraints like required do not leak into identity. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…be set The whole-registry version only gets computed at the very end of a submission, in export_json.py - seed.py/ingest_linkml.py/align.py all run before that, so there is no correct value to stamp on ProvenanceEntry at ingest time yet. Passing the current pre-bump version would record the wrong version (the one being replaced, not the one the entity is part of). The consistent fix would be computing the bump once up front and threading it through every step, but that is a workflow restructuring decision, not a mechanical fix - left unresolved and documented rather than guessed at. schema_submission.yml intentionally still does not pass --registry-version to ingest_linkml.py/align.py. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
export_snapshot()'s class query still asked for n.registry_version, which was removed from RegistryClass when that field moved to ProvenanceEntry - export_json.py and align.py were fixed for the earlier field renames (class_uri, description, etc.) before that move happened, so this one slipped through. LadybugDB raised "Cannot find property registry_version for n" on every real GA run past that point (reported from a live failure on issue #11). Removed the column from the query and the per-class registry_version key from the exported JSON - there's no longer a meaningful class-level value to put there (see docs/ingestion.md's open question on when ProvenanceEntry.registry_version even gets populated). Verified against the exact failing command (seed -> ingest bbqs -> align -> export --bump minor --issue 11 --agent djarecka --schema my_schema1) plus the full pytest suite. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
# Conflicts: # neuro_ghost/export_json.py
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fixing GA ingestion