feat!: add base and aac-2017 models from 1.0.0-ballot.2024-11.2 release (#14)

close #11

Author: korikuzma

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "submodules/va_spec"]
 	path = submodules/va_spec
 	url = https://github.com/ga4gh/va-spec
-	branch = 1.x
+	branch = 1.0.0-ballot.2024-11

pyproject.toml

@@ -31,8 +31,8 @@ keywords = [
 requires-python = ">=3.10"
 dynamic = ["version"]
 dependencies = [
-    "ga4gh.vrs~=2.0.0a12",
-    "ga4gh.cat_vrs~=0.1.0",
+    "ga4gh.vrs==2.0.0a13",
+    "ga4gh.cat_vrs~=0.2.1",
     "pydantic==2.*"
 ]
 
@@ -138,7 +138,7 @@ ignore = [
 # B011 - assert-false
 # N815 - mixed-case-variable-in-class-scope
 "tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011"]
-"src/ga4gh/va_spec/profiles/*" = ["ANN102", "N815"]
+"src/ga4gh/va_spec/*" = ["ANN102", "N815"]
 
 [tool.setuptools.packages.find]
 where = ["src"]

src/ga4gh/va_spec/aac_2017/__init__.py

@@ -0,0 +1,13 @@
+"""Module to load and init namespace at package level."""
+
+from .models import (
+    VariantDiagnosticStudyStatement,
+    VariantPrognosticStudyStatement,
+    VariantTherapeuticResponseStudyStatement,
+)
+
+__all__ = [
+    "VariantDiagnosticStudyStatement",
+    "VariantPrognosticStudyStatement",
+    "VariantTherapeuticResponseStudyStatement",
+]

src/ga4gh/va_spec/aac_2017/models.py

@@ -0,0 +1,48 @@
+"""AMP/ASCO/CAP 2017"""
+
+from ga4gh.va_spec.base.core import (
+    Statement,
+    VariantDiagnosticProposition,
+    VariantPrognosticProposition,
+    VariantTherapeuticResponseProposition,
+)
+from pydantic import (
+    Field,
+)
+
+
+class VariantDiagnosticStudyStatement(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: VariantDiagnosticProposition = 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.",
+    )
+
+
+class VariantPrognosticStudyStatement(Statement):
+    """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: VariantPrognosticProposition = 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.",
+    )
+
+
+class VariantTherapeuticResponseStudyStatement(Statement):
+    """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: VariantTherapeuticResponseProposition = 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.",
+    )

src/ga4gh/va_spec/base/__init__.py

@@ -0,0 +1,66 @@
+"""Module to load and init namespace at package level."""
+
+from .caf_study_result import CohortAlleleFrequencyStudyResult
+from .core import (
+    Agent,
+    ClinicalVariantProposition,
+    Contribution,
+    CoreType,
+    DataSet,
+    DiagnosticPredicate,
+    Direction,
+    Document,
+    EvidenceLine,
+    ExperimentalVariantFunctionalImpactProposition,
+    InformationEntity,
+    Method,
+    PrognosticPredicate,
+    Proposition,
+    Statement,
+    StudyGroup,
+    StudyResult,
+    SubjectVariantProposition,
+    TherapeuticResponsePredicate,
+    VariantDiagnosticProposition,
+    VariantOncogenicityProposition,
+    VariantPathogenicityProposition,
+    VariantPrognosticProposition,
+    VariantTherapeuticResponseProposition,
+)
+from .domain_entities import Condition, Therapeutic, TherapyGroup, TraitSet
+from .experimental_variant_functional_impact import (
+    ExperimentalVariantFunctionalImpactStudyResult,
+)
+
+__all__ = [
+    "CohortAlleleFrequencyStudyResult",
+    "InformationEntity",
+    "StudyResult",
+    "Proposition",
+    "SubjectVariantProposition",
+    "ClinicalVariantProposition",
+    "ExperimentalVariantFunctionalImpactProposition",
+    "DiagnosticPredicate",
+    "VariantDiagnosticProposition",
+    "VariantOncogenicityProposition",
+    "VariantPathogenicityProposition",
+    "PrognosticPredicate",
+    "VariantPrognosticProposition",
+    "TherapeuticResponsePredicate",
+    "VariantTherapeuticResponseProposition",
+    "CoreType",
+    "Method",
+    "Contribution",
+    "Document",
+    "Agent",
+    "Direction",
+    "DataSet",
+    "EvidenceLine",
+    "Statement",
+    "StudyGroup",
+    "TraitSet",
+    "Condition",
+    "TherapyGroup",
+    "Therapeutic",
+    "ExperimentalVariantFunctionalImpactStudyResult",
+]

src/ga4gh/va_spec/base/caf_study_result.py

@@ -0,0 +1,71 @@
+"""Cohort Allele Frequency Study Result Standard Profile"""
+
+from __future__ import annotations
+
+from typing import Any, Literal
+
+from ga4gh.core.models import iriReference
+from ga4gh.va_spec.base.core import DataSet, StudyGroup, StudyResult
+from ga4gh.vrs.models import Allele
+from pydantic import Field, field_validator
+
+
+class CohortAlleleFrequencyStudyResult(StudyResult):
+    """A StudyResult that reports measures related to the frequency of an Allele in a cohort"""
+
+    type: Literal["CohortAlleleFrequencyStudyResult"] = Field(
+        "CohortAlleleFrequencyStudyResult",
+        description="MUST be 'CohortAlleleFrequencyStudyResult'.",
+    )
+    sourceDataSet: DataSet | None = Field(
+        None,
+        description="The dataset from which the CohortAlleleFrequencyStudyResult was reported.",
+    )
+    focus: None = Field(
+        None, exclude=True, repr=False
+    )  # extends property in JSON Schema. Should not be used
+    focusAllele: Allele | iriReference = Field(
+        ..., description="The Allele for which frequency results are reported."
+    )
+    focusAlleleCount: int = Field(
+        ..., description="The number of occurrences of the focusAllele in the cohort."
+    )
+    locusAlleleCount: int = Field(
+        ...,
+        description="The number of occurrences of all alleles at the locus in the cohort.",
+    )
+    focusAlleleFrequency: float = Field(
+        ..., description="The frequency of the focusAllele in the cohort."
+    )
+    cohort: StudyGroup = Field(
+        ..., description="The cohort from which the frequency was derived."
+    )
+    subCohortFrequency: list[CohortAlleleFrequencyStudyResult] | None = Field(
+        None,
+        description="A list of CohortAlleleFrequency objects describing subcohorts of the cohort currently being described. Subcohorts can be further subdivided into more subcohorts. This enables, for example, the description  of different ancestry groups and sexes among those ancestry groups.",
+    )
+    ancillaryResults: dict | None = None
+    qualityMeasures: dict | None = None
+
+    def __getattribute__(self, name: str) -> Any:  # noqa: ANN401
+        """Retrieve the value of the specified attribute
+
+        :param name: Name of attribute being accessed
+        :return: The value of the specified attribute
+        :raises ValueError: If the attribute being accessed is not already defined in
+            CohortAlleleFrequencyStudyResult or the attribute is `focus`
+        """
+        if name == "focus":
+            err_msg = f"'{type(self).__name__!r}' object has no attribute '{name!r}'"
+            raise AttributeError(err_msg)
+        return super().__getattribute__(name)
+
+    @field_validator("focus", mode="before")
+    def set_focus_to_none(cls, v: Any) -> None:  # noqa: ANN401, N805
+        """Set focus to None"""
+        return
+
+
+del CohortAlleleFrequencyStudyResult.model_fields[
+    "focus"
+]  # Need to remove inherited property