apply VariantClinicalSignificanceStatement + evidence line changes

Author: korikuzma

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "submodules/va_spec"]
 	path = submodules/va_spec
 	url = https://github.com/ga4gh/va-spec
-	branch = issue-293
+	branch = fix-aac

src/ga4gh/va_spec/aac_2017/__init__.py

@@ -6,11 +6,13 @@
     AMP_ASCO_CAP_EVIDENCE_LINE_STRENGTHS,
     AmpAscoCapClassificationCode,
     AmpAscoCapClassificationName,
+    AmpAscoCapEvidenceLine,
     AmpAscoCapEvidenceLineStrength,
     AsmpAscoCapStrengthCode,
-    VariantDiagnosticStatement,
-    VariantPrognosticStatement,
-    VariantTherapeuticResponseStatement,
+    DiagnosticEvidenceLine,
+    PrognosticEvidenceLine,
+    TherapeuticEvidenceLine,
+    VariantClinicalSignificanceStatement,
 )
 
 __all__ = [
@@ -19,9 +21,11 @@
     "AMP_ASCO_CAP_EVIDENCE_LINE_STRENGTHS",
     "AmpAscoCapClassificationCode",
     "AmpAscoCapClassificationName",
+    "AmpAscoCapEvidenceLine",
     "AmpAscoCapEvidenceLineStrength",
     "AsmpAscoCapStrengthCode",
-    "VariantDiagnosticStatement",
-    "VariantPrognosticStatement",
-    "VariantTherapeuticResponseStatement",
+    "DiagnosticEvidenceLine",
+    "PrognosticEvidenceLine",
+    "TherapeuticEvidenceLine",
+    "VariantClinicalSignificanceStatement",
 ]

src/ga4gh/va_spec/aac_2017/models.py

@@ -4,11 +4,10 @@
 sequence variants in cancer.
 """
 
-from abc import ABC
 from enum import Enum
 from types import MappingProxyType
 
-from pydantic import Field, model_validator
+from pydantic import Field, field_validator, model_validator
 from pydantic.dataclasses import dataclass
 from typing_extensions import Self
 
@@ -27,6 +26,57 @@
 from ga4gh.va_spec.base.validators import validate_mappable_concept
 
 
+class AmpAscoCapEvidenceLineStrength(str, Enum):
+    """Define constraints for AMP/ASCO/CAP `EvidenceLine.strengthOfEvidenceProvided`"""
+
+    A = "A"
+    B = "B"
+    C = "C"
+    D = "D"
+
+
+class AmpAscoCapEvidenceLine(EvidenceLine):
+    """Evidence line for AMP/ASCO/CAP"""
+
+    targetProposition: (
+        VariantDiagnosticProposition
+        | VariantPrognosticProposition
+        | VariantTherapeuticResponseProposition
+    )
+
+    @field_validator("strengthOfEvidenceProvided", mode="after")
+    @classmethod
+    def validate_strength_of_evidence_provided(
+        cls, v: MappableConcept | None
+    ) -> MappableConcept | None:
+        """Validate strengthOfEvidenceProvided"""
+        validate_mappable_concept(
+            v,
+            System.AMP_ASCO_CAP,
+            valid_codes=AMP_ASCO_CAP_EVIDENCE_LINE_STRENGTHS,
+            mc_is_required=False,
+        )
+        return v
+
+
+class DiagnosticEvidenceLine(AmpAscoCapEvidenceLine):
+    """Diagnostic evidence line for AMP/ASCO/CAP"""
+
+    targetProposition: VariantDiagnosticProposition
+
+
+class PrognosticEvidenceLine(AmpAscoCapEvidenceLine):
+    """Prognostic evidence line for AMP/ASCO/CAP"""
+
+    targetProposition: VariantPrognosticProposition
+
+
+class TherapeuticEvidenceLine(AmpAscoCapEvidenceLine):
+    """Therapeutic evidence line for AMP/ASCO/CAP"""
+
+    targetProposition: VariantTherapeuticResponseProposition
+
+
 class AsmpAscoCapStrengthCode(str, Enum):
     """Define constraints for AMP/ASCO/CAP strength coding"""
 
@@ -37,10 +87,10 @@ class AsmpAscoCapStrengthCode(str, Enum):
 class AmpAscoCapClassificationCode(str, Enum):
     """Define constraints for AMP/ASCO/CAP classification coding"""
 
-    TIER_1 = "tier 1"
-    TIER_2 = "tier 2"
-    TIER_3 = "tier 3"
-    TIER_4 = "tier 4"
+    TIER_1 = "tier i"
+    TIER_2 = "tier ii"
+    TIER_3 = "tier iii"
+    TIER_4 = "tier iv"
 
 
 AMP_ASCO_CAP_CLASSIFICATION_CODES = [
@@ -57,15 +107,6 @@ 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()
 ]
@@ -106,20 +147,39 @@ class AmpAscoCapConfig:
 )
 
 
-class _AmpAscoCapStatement(Statement, ABC):
-    """Abstract base class for AAC 2017 statements"""
+class VariantClinicalSignificanceStatement(Statement):
+    """A statement reporting a conclusion from a single study about whether a variant is
+    associated with a disease (a diagnostic inclusion criterion), or absence of a
+    disease (diagnostic exclusion criterion) - based on interpretation of the study's
+    results.
+    """
+
+    proposition: VariantClinicalSignificanceProposition = Field(
+        ...,
+        description="A proposition about a diagnostic association between a variant and condition, for which the study provides evidence. The validity of this proposition, and the level of confidence/evidence supporting it, may be assessed and reported by the Statement.",
+    )
+    strength: MappableConcept | None = Field(
+        default=None,
+        description="The strength of support that the Statement is determined to provide for or against the Diagnostic Proposition for the assessed variant, based on the curation and reporting conventions of the AMP/ASCO/CAP 2017 Guidelines.",
+    )
+    classification: MappableConcept = Field(
+        ...,
+        description="A single term or phrase classifying the subject variant based on the outcome of direction and strength assessments of the Statement's Proposition, using terms from the AMP/ASCO/CAP 2017 Guidelines.",
+    )
+    specifiedBy: Method | iriReference
 
     @model_validator(mode="after")
     def validate_aac_statement(self) -> Self:
-        """Validate AMP/ASCO/CAP statements"""
+        """Validate VariantClinicalSignificanceStatement"""
 
         def _validate_classification_config(
             classification_code: AmpAscoCapClassificationCode,
             classification_name: str,
             direction: str,
             strength_code: MappableConcept | None,
+            has_evidence_lines: list,
         ) -> None:
-            """Validate that classificati"""
+            """Validate that classification config is correct"""
             expected_config = AMP_ASCO_CAP_CLASSIFICATION_MAP[classification_code]
             actual_strength = (
                 strength_code.primaryCoding.code.root
@@ -143,6 +203,30 @@ def _validate_classification_config(
                 msg = f"`direction` must be: {expected_config.direction.value}"
                 raise ValueError(msg)
 
+            if classification_code in {
+                AmpAscoCapClassificationCode.TIER_1,
+                AmpAscoCapClassificationCode.TIER_2,
+            }:
+                for evidence_line in has_evidence_lines:
+                    found_approved_el_clas = False
+                    for approved_el_cls in [
+                        DiagnosticEvidenceLine,
+                        PrognosticEvidenceLine,
+                        TherapeuticEvidenceLine,
+                        iriReference,
+                    ]:
+                        try:
+                            approved_el_cls(**evidence_line.model_dump())
+                        except Exception:  # noqa: S110
+                            pass
+                        else:
+                            found_approved_el_clas = True
+                            break
+
+                    if not found_approved_el_clas:
+                        msg = "`hasEvidenceLines` must be one of: `DiagnosticEvidenceLine`, `PrognosticEvidenceLine`, `TherapeuticEvidenceLine`, or `iriReference`"
+                        raise ValueError(msg)
+
         # Validate strength
         validate_mappable_concept(
             self.strength,
@@ -162,99 +246,7 @@ def _validate_classification_config(
             self.classification.name,
             self.direction,
             self.strength,
+            self.hasEvidenceLines or [],
         )
 
-        # Validate hasEvidenceLines
-        for evidence_line in self.hasEvidenceLines or []:
-            if isinstance(evidence_line, EvidenceLine):
-                target_proposition = evidence_line.targetProposition
-                if target_proposition and not isinstance(
-                    target_proposition,
-                    VariantDiagnosticProposition
-                    | VariantPrognosticProposition
-                    | VariantTherapeuticResponseProposition,
-                ):
-                    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
-
-
-class VariantDiagnosticStatement(_AmpAscoCapStatement):
-    """A statement reporting a conclusion from a single study about whether a variant is
-    associated with a disease (a diagnostic inclusion criterion), or absence of a
-    disease (diagnostic exclusion criterion) - based on interpretation of the study's
-    results.
-    """
-
-    proposition: VariantClinicalSignificanceProposition = Field(
-        ...,
-        description="A proposition about a diagnostic association between a variant and condition, for which the study provides evidence. The validity of this proposition, and the level of confidence/evidence supporting it, may be assessed and reported by the Statement.",
-    )
-    strength: MappableConcept | None = Field(
-        default=None,
-        description="The strength of support that the Statement is determined to provide for or against the Diagnostic Proposition for the assessed variant, based on the curation and reporting conventions of the AMP/ASCO/CAP (AAC) 2017 Guidelines.",
-    )
-    classification: MappableConcept = Field(
-        ...,
-        description="A single term or phrase classifying the subject variant based on the outcome of direction and strength assessments of the Statement's Proposition - reported here using terms from the AMP/ASCO/CAP (AAC) 2017 Guidelines.",
-    )
-    specifiedBy: Method | iriReference = Field(
-        ...,
-        description="A method that specifies how the diagnostic classification was ultimately assigned to the variant, based on assessment of evidence.",
-    )
-
-
-class VariantPrognosticStatement(_AmpAscoCapStatement):
-    """A statement reporting a conclusion from a single study about whether a variant is
-    associated with a disease prognosis - based on interpretation of the study's
-    results.
-    """
-
-    proposition: VariantClinicalSignificanceProposition = Field(
-        ...,
-        description="A proposition about a prognostic association between a variant and condition, for which the study provides evidence. The validity of this proposition, and the level of confidence/evidence supporting it, may be assessed and reported by the Statement.",
-    )
-    strength: MappableConcept | None = Field(
-        default=None,
-        description="The strength of support that the Statement is determined to provide for or against the Prognostic Proposition for the assessed variant, based on the curation and reporting conventions of the AMP/ASCO/CAP (AAC) 2017 Guidelines.",
-    )
-    classification: MappableConcept = Field(
-        ...,
-        description="A single term or phrase classifying the subject variant based on the outcome of direction and strength assessments of the Statement's Proposition - reported here using terms from the AMP/ASCO/CAP (AAC) 2017 Guidelines. Note that the enumerated value set here is bound to the `code` field of the Coding object that is nested inside a MappableConcept's primary coding.",
-    )
-    specifiedBy: Method | iriReference = Field(
-        ...,
-        description="A method that specifies how the prognostic classification was ultimately assigned to the variant, based on assessment of evidence.",
-    )
-
-
-class VariantTherapeuticResponseStatement(_AmpAscoCapStatement):
-    """A statement reporting a conclusion from a single study about whether a variant is
-    associated with a therapeutic response (positive or negative) - based on
-    interpretation of the study's results.
-    """
-
-    proposition: VariantClinicalSignificanceProposition = Field(
-        ...,
-        description="A proposition about the therapeutic response associated with a variant, for which the study provides evidence. The validity of this proposition, and the level of confidence/evidence supporting it, may be assessed and reported by the Statement.",
-    )
-    strength: MappableConcept | None = Field(
-        default=None,
-        description="The strength of support that the Statement is determined to provide for or against the Therapeutic Response Proposition for the assessed variant, based on the curation and reporting conventions of the AMP/ASCO/CAP (AAC) 2017 Guidelines.",
-    )
-    classification: MappableConcept = Field(
-        ...,
-        description="A single term or phrase classifying the subject variant based on the outcome of direction and strength assessments of the Statement's Proposition - reported here using terms from the AMP/ASCO/CAP (AAC) 2017 Guidelines.",
-    )
-    specifiedBy: Method | iriReference = Field(
-        ...,
-        description="A method that specifies how the therapeutic response classification was ultimately assigned to the variant, based on assessment of evidence.",
-    )

src/ga4gh/va_spec/base/core.py

@@ -392,7 +392,7 @@ class ClinicalVariantProposition(_SubjectVariantPropositionBase):
     )
     alleleOriginQualifier: MappableConcept | iriReference | None = Field(
         default=None,
-        description="Reports whether the Proposition should be interpreted in the context of a heritable 'germline' variant, an acquired 'somatic' variant in a tumor,  post-zygotic 'mosaic' variant. While these are the most commonly reported allele origins, other more nuanced concepts can be captured  (e.g. 'maternal' vs 'paternal' allele origin'). In practice, populating this field may be complicated by the fact that some sources report allele origin based on the type of tissue that was sequenced to identify the variant, and others use it more generally to specify a category of variant for which the proposition holds. The stated intent of this attribute is the latter. However, if an implementer is not sure about which is reported in their data, it may be safer to create an Extension to hold this information, where they can explicitly acknowledge this ambiguity.",
+        description='Reports whether the Proposition should be interpreted in the context of a heritable "germline" variant, an acquired "somatic" variant in a tumor, or a post-zygotic "mosaic" variant. While these are the most commonly reported allele origins, other more nuanced concepts can be captured  (e.g. "maternal" vs "paternal" allele origin). In practice, populating this field may be complicated by the fact that some sources report allele origin based on the type of tissue that was sequenced to identify the variant, and others use it more generally to specify a category of variant for which the proposition holds. The stated intent of this attribute is the latter. However, if an implementer is not sure about which is reported in their data, it may be safer to create an Extension to hold this information, where they can explicitly acknowledge this ambiguity.',
     )
 
 
@@ -438,7 +438,7 @@ class VariantClinicalSignificanceProposition(
         description="The predicate associating the subject variant to clinical significance for the object Condition. MUST be 'hasClinicalSignificanceFor'.",
     )
     objectCondition: Condition | iriReference = Field(
-        ..., description="The disease that is evaluated."
+        ..., description="The condition that is evaluated."
     )