fix(annotation): handle all VRS allele state types in deserialization#737
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bencap wants to merge 2 commits into
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fix(annotation): handle all VRS allele state types in deserialization#737bencap wants to merge 2 commits into
bencap wants to merge 2 commits into
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allele_from_mapped_variant_dictionary_result unconditionally constructed a LiteralSequenceExpression from the stored state dict, causing a Pydantic ValidationError (500) for score sets containing reference-identical variants whose state is a ReferenceLengthExpression. - Dispatch on state type to construct RLE, LengthExpression, or LSE - Raise ValueError with an actionable message for unknown state types, replacing the cryptic multi-field Pydantic error as the failure mode - Add test constants for RLE and LengthExpression allele dicts - Parametrize state-type and CisPhasedBlock member tests to cover all three state types and enforce coverage of future additions
…elds Serializing evidence to dicts via `serialize_evidence_items` before assigning to `hasEvidenceItems`/`hasEvidenceLines` caused `VariantPathogenicityEvidenceLine` validation to fail for Statement objects containing nested VRS Alleles with production genomic data (regex constraints on `digest`, `refgetAccession`, etc. failed during dict reconstruction). - Remove `serialize_evidence_items` from `util.py` entirely - `acmg_evidence_line`: pass `list(evidence)` directly; Statement is in `has_evidence_items_models` and passes the isinstance check - `functional_evidence_line`: wrap items as `StudyResult(root=item)`; `ExperimentalVariantFunctionalImpactStudyResult` does not inherit `StudyResult` so direct instances fail the isinstance check - `mapped_variant_to_pathogenicity_statement`: pass `list(evidence)` - Add regression tests in `test_evidence_line.py` and `test_annotate.py` that assert evidence items are model instances, not raw dicts - Remove `TestSerializeEvidenceItems` from `test_util.py`
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allele_from_mapped_variant_dictionary_resultunconditionally constructed aLiteralSequenceExpressionfrom the stored state dict, causing a PydanticValidationError(500) for score sets containing reference-identical variants whose state is aReferenceLengthExpression.Additionally, fixes a bug where certain evidence lines were unable to be regenerated via a serialized dict. Evidence generation now proceeds directly via models.