alliance: align ingest patterns with codebase standards #218
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- Use entity_id() from bmt.pydantic instead of uuid.uuid1() for association IDs - Use build_association_knowledge_sources() with sources field instead of deprecated primary_knowledge_source/aggregator_knowledge_source fields - Return KnowledgeGraph objects instead of raw entity/association lists - Remove redundant explicit category assignments on nodes and associations - Update function signatures with proper type hints - Update tests to work with new KnowledgeGraph return type 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
- Switch from qualifiers (list) to qualifier (single value) for expression assay since mouse/rat data always has exactly one assay per record - Change conditionRelations handling to raise ValueError if conditions are found, since mouse/rat phenotype data should not have experimental conditions - This simplifies the code and makes unexpected data visible 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <[email protected]>
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Summary
entity_id()from bmt.pydantic instead ofuuid.uuid1()for association IDsbuild_association_knowledge_sources()withsourcesfield instead of deprecatedprimary_knowledge_source/aggregator_knowledge_sourcefieldsKnowledgeGraphobjects instead of raw entity/association listsKnowledgeGraph | None)Test plan
Notes
The
qualifiersfield usage is kept as-is for now (experimental conditions for phenotypes, assay for expression). This may need a follow-up PR to address potential deprecation concerns, but the current usage appears to be semantically correct for ontology-term qualifiers.🤖 Generated with Claude Code