fix: oncogenicity evidence lines should accept null evidence outcomes

src/ga4gh/va_spec/base/validators.py

@@ -114,19 +114,21 @@ def _get_base_criterion_from_code(cls, evidence_outcome_code: str) -> CriterionT
     def _validate_method_type_evidence_outcome(
         cls,
         method_type: str,
-        evidence_outcome_code: str,
+        evidence_outcome_code: str | None,
     ) -> None:
         """Validate that ``evidenceOutcome`` is compatible with a method type.
 
         :param method_type: Method type value from ``specifiedBy.methodType``.
         :param evidence_outcome_code: Evidence outcome to validate.
         :raises ValueError: If the evidence outcome criterion is invalid or is
-            not valid for the specified method type.
-        :return: None.
+            not valid for the specified method type, or if method type is invalid
         """
         parsed_method_type = cls.MethodType(method_type)
         allowed_criteria = cls.ALLOWED_CRITERIA_BY_METHOD_TYPE[parsed_method_type]
 
+        if not evidence_outcome_code:
+            return
+
         criterion = cls._get_base_criterion_from_code(evidence_outcome_code)
 
         if criterion not in allowed_criteria:

src/ga4gh/va_spec/ccv_2022/models.py

@@ -234,10 +234,16 @@ def validate_model(self) -> Self:
             ``directionOfEvidenceProvided`` is neutral
         """
         self._validate_direction_of_evidence_provided()
-        self._validate_evidence_outcome(SYSTEM, CCV_CODE_PATTERN, is_required=True)
+        self._validate_evidence_outcome(SYSTEM, CCV_CODE_PATTERN, is_required=False)
         self._validate_criterion_specified_by()
+
+        evidence_outcome = (
+            self.evidenceOutcome.primaryCoding.code.root
+            if self.evidenceOutcome
+            else None
+        )
         self._validate_method_type_evidence_outcome(
-            self.specifiedBy.methodType, self.evidenceOutcome.primaryCoding.code.root
+            self.specifiedBy.methodType, evidence_outcome
         )
         return self
 

tests/validation/test_va_spec_models.py

@@ -21,6 +21,7 @@
     ExperimentalVariantFunctionalImpactStudyResult,
 )
 from ga4gh.va_spec.base.core import (
+    Direction,
     EvidenceLine,
     Method,
     Statement,
@@ -611,6 +612,38 @@ def test_variant_onco_el():
         VariantOncogenicityEvidenceLine(**invalid_params)
 
 
+def test_variant_onco_el_no_evidence_outcome():
+    """Test that VariantOncogenicityEvidenceLine validates without evidence
+    outcome
+    """
+    valid = VariantOncogenicityEvidenceLine(
+        type="EvidenceLine",
+        specifiedBy={
+            "type": "Method",
+            "reportedIn": {
+                "type": "Document",
+                "pmid": "35101336",
+                "name": "ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022",
+            },
+            "methodType": "functional_assay",
+        },
+        directionOfEvidenceProvided=Direction.NEUTRAL,
+        scoreOfEvidenceProvided=0,
+        evidenceOutcome=None,
+    )
+
+    assert valid
+
+    invalid = valid.model_dump()
+    invalid["specifiedBy"]["methodType"] = "dummy"
+
+    with pytest.raises(
+        ValueError,
+        match="'dummy' is not a valid VariantOncogenicityEvidenceLine.MethodType",
+    ):
+        VariantOncogenicityEvidenceLine.model_validate(invalid)
+
+
 def test_aac_statement():
     """Test that AMP/ASCO/CAP statement model validators work correctly"""
     prop = {