Merging and Metadata improvements#390
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EvanDietzMorris merged 14 commits intomasterfrom Apr 15, 2026
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option to overwrite existing edge ids, record mappings of pre and post merge edge ids when they change
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- improved normalization and merging metadata - allow edge_id passthrough and write edge_id mapping metadata - implemented merging handling of all dictionary properties see these ORION prs for more detail: RobokopU24/ORION#390 RobokopU24/ORION#377
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Metadata and Merging Improvements
Normalization metadata by prefix
KGXFileNormalizer now computes and records per-curie-prefix normalization stats (succeeded, failed, total, success_rate, normalized_to), sorted by prevalence, under normalization_metadata. Logs warnings on prefixes below 50% success and logs errors on prefixes that fail outright.
Edge-id preservation and pre-merge mapping
New overwrite_edge_ids flag on GraphSpec (default True, preserves existing behavior). When add_edge_id=True and overwrite_edge_ids=False, unmerged edges keep their original ids, and merged edges get the generated merge key as their new id while the mapping from new id → original pre-merge ids is recorded. DiskGraphMerger streams this mapping to a file as merges finalize instead of buffering it in memory.
Dict-shaped biolink slot merging
entity_merging_function now merges dict-valued slots (e.g. has_supporting_study_result) instead of silently keeping entity_1's dict.
Truthy-prefer scalar collision policy
Scalar/scalar merges now prefer the truthy value: falsy values (None, 0, "", False) lose to any populated value on the other side. Only two genuinely different truthy values count as a collision. Also fixed a latent bug where a None in entity_2 could clobber an existing value in entity_1.
Merge warnings in merge_metadata
Collisions surface as metadata and logs: merge_metadata['merge_warnings'] contains mismatched_properties (a dict slot on one side, non-dict on the other) and dropped_properties (genuine collisions). Collected per merger, flushed at generator completion, unioned across node and edge mergers.