feat: expose json schema metadata to va models

pyproject.toml

@@ -1,55 +1,37 @@
 [project]
 name = "ga4gh.va_spec"
-authors = [
-    {name = "Matt Brush"},
-    {name = "Javier Lopez"},
-]
+authors = [{ name = "Matt Brush" }, { name = "Javier Lopez" }]
 readme = "README.md"
 description = "GA4GH Variant Annotation (VA) reference implementation"
-license = {file = "LICENSE"}
+license = { file = "LICENSE" }
 classifiers = [
-    "Development Status :: 3 - Alpha",
-    "Intended Audience :: Developers",
-    "Intended Audience :: Healthcare Industry",
-    "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: Apache Software License",
-    "Operating System :: OS Independent",
-    "Programming Language :: Python",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-    "Topic :: Scientific/Engineering :: Medical Science Apps.",
-]
-keywords = [
-    "bioinformatics",
-    "ga4gh",
-    "genomics",
-    "variation"
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Healthcare Industry",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: Apache Software License",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Topic :: Scientific/Engineering :: Medical Science Apps.",
 ]
+keywords = ["bioinformatics", "ga4gh", "genomics", "variation"]
 requires-python = ">=3.10"
 dynamic = ["version"]
 dependencies = [
-    "ga4gh.vrs~=2.4.0-a1",
-    "ga4gh.cat_vrs~=0.8.0-a1",
-    "pydantic>=2.0,<3.0",
-    "typing_extensions",
+  "ga4gh.cat_vrs @ git+https://github.com/ga4gh/cat-vrs-python.git@30d6c5035fb7cd000bf637d8f03069633dd10ff1",
+  "pydantic>=2.0,<3.0",
+  "typing_extensions",
 ]
 
 [project.optional-dependencies]
-dev = [
-    "pre-commit",
-    "ruff==0.4.9",
-]
-tests = [
-    "pytest",
-    "pytest-cov",
-    "pyyaml"
-]
-notebooks = [
-    "jupyter",
-]
+dev = ["pre-commit", "ruff==0.4.9"]
+tests = ["pytest", "pytest-cov", "pyyaml"]
+notebooks = ["jupyter"]
 
 [project.urls]
 Homepage = "https://github.com/ga4gh/va-spec-python"
@@ -64,53 +46,52 @@ build-backend = "setuptools.build_meta"
 
 [tool.ruff]
 src = ["src"]
-exclude = [
-    "submodules"
-]
+exclude = ["submodules"]
 
 [tool.ruff.lint]
 select = [
-    "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
-    "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
-    "I",  # https://docs.astral.sh/ruff/rules/#isort-i
-    "N",  # https://docs.astral.sh/ruff/rules/#pep8-naming-n
-    "D",  # https://docs.astral.sh/ruff/rules/#pydocstyle-d
-    "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
-    "ANN",  # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
-    "ASYNC",  # https://docs.astral.sh/ruff/rules/#flake8-async-async
-    "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
-    "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
-    "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
-    "C4",  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
-    "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
-    "T10",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
-    "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
-    "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
-    "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
-    "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
-    "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
-    "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
-    "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
-    "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
-    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
-    "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
-    "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
-    "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+  "F",     # https://docs.astral.sh/ruff/rules/#pyflakes-f
+  "E",
+  "W",     # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
+  "I",     # https://docs.astral.sh/ruff/rules/#isort-i
+  "N",     # https://docs.astral.sh/ruff/rules/#pep8-naming-n
+  "D",     # https://docs.astral.sh/ruff/rules/#pydocstyle-d
+  "UP",    # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+  "ANN",   # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+  "ASYNC", # https://docs.astral.sh/ruff/rules/#flake8-async-async
+  "S",     # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+  "B",     # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+  "A",     # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+  "C4",    # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+  "DTZ",   # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+  "T10",   # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+  "EM",    # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+  "G",     # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+  "PIE",   # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+  "T20",   # https://docs.astral.sh/ruff/rules/#flake8-print-t20
+  "PT",    # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
+  "Q",     # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
+  "RSE",   # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
+  "RET",   # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+  "SIM",   # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+  "PTH",   # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+  "PGH",   # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+  "RUF",   # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
 ]
 fixable = [
-    "I",
-    "F401",
-    "D",
-    "UP",
-    "ANN",
-    "B",
-    "C4",
-    "G",
-    "PIE",
-    "PT",
-    "RSE",
-    "SIM",
-    "RUF"
+  "I",
+  "F401",
+  "D",
+  "UP",
+  "ANN",
+  "B",
+  "C4",
+  "G",
+  "PIE",
+  "PT",
+  "RSE",
+  "SIM",
+  "RUF",
 ]
 # ANN101 - missing-type-self
 # ANN003 - missing-type-kwargs
@@ -129,11 +110,21 @@ fixable = [
 # S321 - suspicious-ftp-lib-usage
 # *ignored for compatibility with formatter
 ignore = [
-    "ANN101", "ANN003",
-    "D203", "D205", "D206", "D213", "D300", "D400", "D415",
-    "E111", "E114", "E117", "E501",
-    "W191",
-    "S321",
+  "ANN101",
+  "ANN003",
+  "D203",
+  "D205",
+  "D206",
+  "D213",
+  "D300",
+  "D400",
+  "D415",
+  "E111",
+  "E114",
+  "E117",
+  "E501",
+  "W191",
+  "S321",
 ]
 
 [tool.ruff.lint.per-file-ignores]

src/ga4gh/va_spec/__init__.py

@@ -1,13 +1,15 @@
 """Package for VA-Spec Python implementation"""
 
-from importlib.metadata import PackageNotFoundError, version
+from importlib.metadata import PackageNotFoundError
+from importlib.metadata import version as package_version
+
+from ga4gh.va_spec.version import VASPEC_VERSION
 
 try:
-    __version__ = version(__name__)
+    __version__ = package_version(__name__)
 except PackageNotFoundError:  # pragma: nocover
     __version__ = "unknown"
 finally:
-    del version, PackageNotFoundError
-
+    del package_version, PackageNotFoundError
 
-VASPEC_VERSION = "1.1.0-snapshot.2026-06.1"
+__all__ = ["VASPEC_VERSION", "__version__"]

src/ga4gh/va_spec/aac_2017/metadata.py

@@ -0,0 +1,9 @@
+"""Provide metadata for AAC 2017 VA-Spec models."""
+
+from ga4gh.va_spec.metadata import VASpecMetadataMixin
+
+
+class AAC2017MetadataMixin(VASpecMetadataMixin):
+    """Provide metadata shared by models in the AAC 2017 namespace."""
+
+    _schema_namespace = "aac-2017"

src/ga4gh/va_spec/aac_2017/models.py

@@ -6,12 +6,15 @@
 
 from enum import Enum
 from types import MappingProxyType
+from typing import ClassVar
 
 from pydantic import Field, RootModel, field_validator, model_validator
 from pydantic.dataclasses import dataclass
 from typing_extensions import Self
 
+from ga4gh.core.metadata import Maturity
 from ga4gh.core.models import BaseModelForbidExtra, MappableConcept, iriReference
+from ga4gh.va_spec.aac_2017.metadata import AAC2017MetadataMixin
 from ga4gh.va_spec.base.core import (
     Direction,
     Document,
@@ -58,9 +61,11 @@ class AmpAscoCapEvidenceLineStrength(str, Enum):
 ]
 
 
-class AmpAscoCapEvidenceLine(EvidenceLine):
+class AmpAscoCapEvidenceLine(AAC2017MetadataMixin, EvidenceLine):
     """Evidence line for AMP/ASCO/CAP"""
 
+    _maturity: ClassVar[Maturity] = Maturity.DRAFT
+
     targetProposition: (
         VariantPrognosticProposition
         | VariantDiagnosticProposition
@@ -88,29 +93,41 @@ class _PrognosticEvidenceLineObject(AmpAscoCapEvidenceLine):
     targetProposition: VariantPrognosticProposition
 
 
-class PrognosticEvidenceLine(RootModel[_PrognosticEvidenceLineObject | iriReference]):
+class PrognosticEvidenceLine(
+    AAC2017MetadataMixin, RootModel[_PrognosticEvidenceLineObject | iriReference]
+):
     """Prognostic evidence line for AMP/ASCO/CAP"""
 
+    _maturity: ClassVar[Maturity] = Maturity.DRAFT
+
 
 class _DiagnosticEvidenceLineObject(AmpAscoCapEvidenceLine):
     """Internal diagnostic evidence line for AMP/ASCO/CAP"""
 
     targetProposition: VariantDiagnosticProposition
 
 
-class DiagnosticEvidenceLine(RootModel[_DiagnosticEvidenceLineObject | iriReference]):
+class DiagnosticEvidenceLine(
+    AAC2017MetadataMixin, RootModel[_DiagnosticEvidenceLineObject | iriReference]
+):
     """Diagnostic evidence line for AMP/ASCO/CAP"""
 
+    _maturity: ClassVar[Maturity] = Maturity.DRAFT
+
 
 class _TherapeuticEvidenceLineObject(AmpAscoCapEvidenceLine):
     """Internal therapeutic evidence line for AMP/ASCO/CAP"""
 
     targetProposition: VariantTherapeuticResponseProposition
 
 
-class TherapeuticEvidenceLine(RootModel[_TherapeuticEvidenceLineObject | iriReference]):
+class TherapeuticEvidenceLine(
+    AAC2017MetadataMixin, RootModel[_TherapeuticEvidenceLineObject | iriReference]
+):
     """Therapeutic evidence line for AMP/ASCO/CAP"""
 
+    _maturity: ClassVar[Maturity] = Maturity.DRAFT
+
 
 class AmpAscoCapStrengthCode(str, Enum):
     """Define constraints for AMP/ASCO/CAP strength coding"""
@@ -177,12 +194,16 @@ class AmpAscoCapConfig:
 )
 
 
-class VariantClinicalSignificanceStatement(Statement, BaseModelForbidExtra):
+class VariantClinicalSignificanceStatement(
+    AAC2017MetadataMixin, Statement, BaseModelForbidExtra
+):
     """A statement reporting a conclusion from a single study about the clinical
     significance of a variant with respect to a condition, based on interpretation of
     the study's results.
     """
 
+    _maturity: ClassVar[Maturity] = Maturity.DRAFT
+
     proposition: VariantClinicalSignificanceProposition
     strength: MappableConcept | None = Field(
         default=None,

src/ga4gh/va_spec/acmg_2015/metadata.py

@@ -0,0 +1,9 @@
+"""Provide metadata for ACMG 2015 VA-Spec models."""
+
+from ga4gh.va_spec.metadata import VASpecMetadataMixin
+
+
+class ACMG2015MetadataMixin(VASpecMetadataMixin):
+    """Provide metadata shared by models in the ACMG 2015 namespace."""
+
+    _schema_namespace = "acmg-2015"

src/ga4gh/va_spec/acmg_2015/models.py

@@ -10,7 +10,9 @@
 from pydantic import Field, field_validator, model_validator
 from typing_extensions import Self
 
+from ga4gh.core.metadata import Maturity
 from ga4gh.core.models import MappableConcept, iriReference
+from ga4gh.va_spec.acmg_2015.metadata import ACMG2015MetadataMixin
 from ga4gh.va_spec.base.core import (
     Direction,
     Document,
@@ -62,7 +64,7 @@ class AcmgClassification(str, Enum):
 
 
 class VariantPathogenicityEvidenceLine(
-    EvidenceLine, MethodTypeCriterionValidationMixin
+    ACMG2015MetadataMixin, EvidenceLine, MethodTypeCriterionValidationMixin
 ):
     """An Evidence Line that describes how a specific type of information was
     interpreted as evidence for or against a variant's pathogenicity. In the ACMG
@@ -71,6 +73,8 @@ class VariantPathogenicityEvidenceLine(
     adjusting the default strength based on the quality and abundance of evidence.
     """
 
+    _maturity: ClassVar[Maturity] = Maturity.DRAFT
+
     targetProposition: VariantPathogenicityProposition | None = Field(
         default=None,
         description="A Variant Pathogenicity Proposition against which a specific type of evidence was assessed, to determine the strength and direction of support this evidence provides for or against the proposition's validity.",
@@ -320,9 +324,11 @@ def validate_model(self) -> Self:
         return self
 
 
-class VariantPathogenicityStatement(Statement):
+class VariantPathogenicityStatement(ACMG2015MetadataMixin, Statement):
     """A Statement describing the role of a variant in causing an inherited condition."""
 
+    _maturity: ClassVar[Maturity] = Maturity.DRAFT
+
     proposition: VariantPathogenicityProposition = Field(
         ...,
         description="A proposition about the pathogenicity of a variant, the validity of which is assessed and reported by the Statement. A Statement can put forth the proposition as being true, false, or uncertain, and may provide an assessment of the level of confidence/evidence supporting this claim.",