apply system + evidence line strength updates

Author: korikuzma

src/ga4gh/va_spec/aac_2017/__init__.py

@@ -3,8 +3,10 @@
 from .models import (
     AMP_ASCO_CAP_CLASSIFICATION_CODES,
     AMP_ASCO_CAP_CLASSIFICATION_MAP,
+    AMP_ASCO_CAP_EVIDENCE_LINE_STRENGTHS,
     AmpAscoCapClassificationCode,
     AmpAscoCapClassificationName,
+    AmpAscoCapEvidenceLineStrength,
     AsmpAscoCapStrengthCode,
     VariantDiagnosticStatement,
     VariantPrognosticStatement,
@@ -14,8 +16,10 @@
 __all__ = [
     "AMP_ASCO_CAP_CLASSIFICATION_CODES",
     "AMP_ASCO_CAP_CLASSIFICATION_MAP",
+    "AMP_ASCO_CAP_EVIDENCE_LINE_STRENGTHS",
     "AmpAscoCapClassificationCode",
     "AmpAscoCapClassificationName",
+    "AmpAscoCapEvidenceLineStrength",
     "AsmpAscoCapStrengthCode",
     "VariantDiagnosticStatement",
     "VariantPrognosticStatement",

src/ga4gh/va_spec/aac_2017/models.py

@@ -57,6 +57,20 @@ class AmpAscoCapClassificationName(str, Enum):
     TIER_4 = "Tier IV"
 
 
+class AmpAscoCapEvidenceLineStrength(str, Enum):
+    """Define constraints for AMP/ASCO/CAP `EvidenceLine.strengthOfEvidenceProvided`"""
+
+    A = "A"
+    B = "B"
+    C = "C"
+    D = "D"
+
+
+AMP_ASCO_CAP_EVIDENCE_LINE_STRENGTHS = [
+    v.value for v in AmpAscoCapEvidenceLineStrength.__members__.values()
+]
+
+
 @dataclass
 class AmpAscoCapConfig:
     """AMP/ASCO/CAP config for expected values"""
@@ -163,6 +177,13 @@ def _validate_classification_config(
                     msg = "`targetProposition` must be one of: `VariantDiagnosticProposition`, `VariantPrognosticProposition`, `VariantTherapeuticResponseProposition`"
                     raise ValueError(msg)
 
+                validate_mappable_concept(
+                    evidence_line.strengthOfEvidenceProvided,
+                    System.AMP_ASCO_CAP,
+                    valid_codes=AMP_ASCO_CAP_EVIDENCE_LINE_STRENGTHS,
+                    mc_is_required=False,
+                )
+
         return self
 
 

src/ga4gh/va_spec/base/enums.py

@@ -95,6 +95,6 @@ class System(str, Enum):
     """Define constraints for systems"""
 
     ACMG = "ACMG Guidelines, 2015"
-    AMP_ASCO_CAP = "AMP/ASCO/CAP (AAC) Guidelines, 2017"
+    AMP_ASCO_CAP = "AMP/ASCO/CAP Guidelines, 2017"
     CLIN_GEN = "ClinGen Low Penetrance and Risk Allele Recommendations, 2024"
     CCV = "ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022"

submodules/va_spec

@@ -239,13 +239,13 @@ def test_evidence_line(caf):
                 },
                 "strength": {
                     "primaryCoding": {
-                        "system": "AMP/ASCO/CAP (AAC) Guidelines, 2017",
+                        "system": "AMP/ASCO/CAP Guidelines, 2017",
                         "code": "strong",
                     }
                 },
                 "classification": {
                     "primaryCoding": {
-                        "system": "AMP/ASCO/CAP (AAC) Guidelines, 2017",
+                        "system": "AMP/ASCO/CAP Guidelines, 2017",
                         "code": "tier 1",
                     }
                 },
@@ -352,7 +352,7 @@ def test_variant_pathogenicity_stmt():
 
     invalid_params = deepcopy(params)
     invalid_params["classification"]["primaryCoding"]["system"] = (
-        "AMP/ASCO/CAP (AAC) Guidelines, 2017"
+        "AMP/ASCO/CAP Guidelines, 2017"
     )
     with pytest.raises(ValueError, match="`primaryCoding.system` must be one of"):
         VariantPathogenicityStatement(**invalid_params)
@@ -459,7 +459,7 @@ def test_variant_pathogenicity_el():
     invalid_params = deepcopy(params)
     invalid_params["strengthOfEvidenceProvided"] = {
         "primaryCoding": {
-            "system": "AMP/ASCO/CAP (AAC) Guidelines, 2017",
+            "system": "AMP/ASCO/CAP Guidelines, 2017",
             "code": "strong",
         }
     }
@@ -624,24 +624,24 @@ def test_aac_statement():
         "strength": {
             "primaryCoding": {
                 "code": "strong",
-                "system": "AMP/ASCO/CAP (AAC) Guidelines, 2017",
+                "system": "AMP/ASCO/CAP Guidelines, 2017",
             }
         },
         "specifiedBy": "documents.json#/1",
         "classification": {
             "name": "Tier I",
             "primaryCoding": {
                 "code": "tier 1",
-                "system": "AMP/ASCO/CAP (AAC) Guidelines, 2017",
+                "system": "AMP/ASCO/CAP Guidelines, 2017",
             },
         },
         "hasEvidenceLines": [
             {
                 "directionOfEvidenceProvided": "supports",
                 "strengthOfEvidenceProvided": {
                     "primaryCoding": {
-                        "code": "Level A",
-                        "system": "AMP/ASCO/CAP (AAC) Guidelines, 2017",
+                        "code": "A",
+                        "system": "AMP/ASCO/CAP Guidelines, 2017",
                     }
                 },
                 "hasEvidenceItems": [
@@ -669,6 +669,13 @@ def test_aac_statement():
     }
     assert VariantTherapeuticResponseStatement(**params)
 
+    # No strengthOfEvidenceProvided
+    no_evidence_line_strength_params = deepcopy(params)
+    no_evidence_line_strength_params["hasEvidenceLines"][0].pop(
+        "strengthOfEvidenceProvided"
+    )
+    assert VariantTherapeuticResponseStatement(**no_evidence_line_strength_params)
+
     # Invalid strength
     invalid_params = deepcopy(params)
     invalid_params["strength"]["primaryCoding"]["code"] = "Strong"