feat: update models vrs 2.1.1-ballot.2026-09.1

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "submodules/vrs"]
 	path = submodules/vrs
 	url = https://github.com/ga4gh/vrs.git
-	branch = 2.1
+	branch = 2.1.1-ballot.2026-09

README.md

@@ -18,7 +18,7 @@
 
 ## Features
 
-- Pydantic implementation of GKS core models and VRS models
+- Pydantic implementation of GKM-Core models and VRS models
 - Algorithm for generating consistent, globally unique identifiers for variation without a central authority
 - Algorithm for performing fully justified allele normalization
 - Translating from and to other variant formats

src/ga4gh/core/__init__.py

@@ -21,12 +21,15 @@
     use_ga4gh_compute_identifier_when,
 )
 from ga4gh.core.metadata import (
+    GKMMaturityMixin,
+    GKMMetadataMixin,
+    GKMSchemaMixin,
     GKSMaturityMixin,
     GKSMetadataMixin,
     GKSSchemaMixin,
     Maturity,
 )
-from ga4gh.core.models import GKSCoreMetadataMixin
+from ga4gh.core.models import GKMCoreMetadataMixin, GKSCoreMetadataMixin
 from ga4gh.core.pydantic import is_curie_type, is_pydantic_instance, pydantic_copy
 from ga4gh.core.version import CORE_VERSION
 
@@ -45,6 +48,10 @@
     "GA4GH_DIGEST_REGEXP",
     "GA4GH_IR_REGEXP",
     "GA4GH_PREFIX_SEP",
+    "GKMCoreMetadataMixin",
+    "GKMMaturityMixin",
+    "GKMMetadataMixin",
+    "GKMSchemaMixin",
     "GKSCoreMetadataMixin",
     "GKSMaturityMixin",
     "GKSMetadataMixin",

src/ga4gh/core/metadata.py

@@ -1,9 +1,10 @@
-"""Provide shared metadata types for GA4GH GKS models."""
+"""Provide shared metadata types for GA4GH GKM models."""
 
 from enum import Enum
 from typing import Any, ClassVar
 
 from pydantic.json_schema import GenerateJsonSchema, JsonSchemaMode
+from typing_extensions import deprecated
 
 
 class Maturity(str, Enum):
@@ -15,19 +16,19 @@ class Maturity(str, Enum):
     DEPRECATED = "deprecated"
 
 
-class GKSMaturityMixin:
-    """Provide maturity metadata for a GA4GH GKS model."""
+class GKMMaturityMixin:
+    """Provide maturity metadata for a GA4GH GKM model."""
 
     _maturity: ClassVar[Maturity]
 
     @classmethod
     def maturity(cls) -> Maturity:
-        """Return the GKS maturity level for the model."""
+        """Return the GKM maturity level for the model."""
         return cls._maturity
 
 
-class GKSSchemaMixin:
-    """Provide a canonical JSON Schema identifier for a GA4GH GKS model."""
+class GKMSchemaMixin:
+    """Provide a canonical JSON Schema identifier for a GA4GH GKM model."""
 
     _schema_base_uri: ClassVar[str] = "https://w3id.org/ga4gh/schema"
     _product_name: ClassVar[str]
@@ -39,8 +40,44 @@ def schema_id(cls) -> str:
         return f"{cls._schema_base_uri}/{cls._product_name}/{cls._product_version}/json/{cls.__name__}"
 
 
-class GKSMetadataMixin(GKSMaturityMixin, GKSSchemaMixin):
-    """Provide maturity and schema metadata for a concrete GKS model."""
+class GKMMetadataMixin(GKMMaturityMixin, GKMSchemaMixin):
+    """Provide maturity and schema metadata for a GKM model."""
+
+    _abstract: ClassVar[bool] = False
+
+    @staticmethod
+    def apply_schema_metadata(
+        model_class: type, schema: dict[str, Any]
+    ) -> dict[str, Any]:
+        """Add GKM metadata to a generated JSON Schema.
+
+        :param model_class: Pydantic model class that produced the schema.
+        :param schema: Generated JSON Schema to annotate.
+        :returns: The annotated JSON Schema.
+        """
+        schema["$id"] = model_class.schema_id()
+        schema["maturity"] = model_class.maturity().value
+
+        if model_class.__dict__.get("_abstract", False):
+            schema["abstract"] = True
+
+        # GA4GH identifier metadata is optional and applies only when declared.
+        ga4gh_class = getattr(model_class, "ga4gh", None)
+        if not ga4gh_class:
+            return schema
+
+        ga4gh_metadata = {}
+
+        if prefix := getattr(ga4gh_class, "prefix", None):
+            ga4gh_metadata["prefix"] = prefix
+
+        if inherent := getattr(ga4gh_class, "inherent", None):
+            ga4gh_metadata["inherent"] = list(inherent)
+
+        if ga4gh_metadata:
+            schema["ga4gh"] = ga4gh_metadata
+
+        return schema
 
     @classmethod
     def model_json_schema(
@@ -50,30 +87,34 @@ def model_json_schema(
         schema_generator: type[GenerateJsonSchema] = GenerateJsonSchema,
         mode: JsonSchemaMode = "validation",
     ) -> dict[str, Any]:
-        """Generate JSON Schema with GKS metadata."""
+        """Generate JSON Schema with GKM metadata.
+
+        :param by_alias: Whether to use field aliases.
+        :param ref_template: Template for schema references.
+        :param schema_generator: Pydantic schema generator class.
+        :param mode: Pydantic schema generation mode.
+        :returns: JSON Schema annotated with GKM metadata.
+        """
         schema = super().model_json_schema(
             by_alias=by_alias,
             ref_template=ref_template,
             schema_generator=schema_generator,
             mode=mode,
         )
 
-        schema["$id"] = cls.schema_id()
-        schema["maturity"] = cls.maturity().value
+        return cls.apply_schema_metadata(cls, schema)
 
-        ga4gh_class = getattr(cls, "ga4gh", None)
-        if not ga4gh_class:
-            return schema
 
-        ga4gh_metadata = {}
+@deprecated("GKSMaturityMixin is deprecated; use GKMMaturityMixin instead.")
+class GKSMaturityMixin(GKMMaturityMixin):
+    """Deprecated alias for :class:`GKMMaturityMixin`."""
 
-        if prefix := getattr(ga4gh_class, "prefix", None):
-            ga4gh_metadata["prefix"] = prefix
 
-        if inherent := getattr(ga4gh_class, "inherent", None):
-            ga4gh_metadata["inherent"] = list(inherent)
+@deprecated("GKSSchemaMixin is deprecated; use GKMSchemaMixin instead.")
+class GKSSchemaMixin(GKMSchemaMixin):
+    """Deprecated alias for :class:`GKMSchemaMixin`."""
 
-        if ga4gh_metadata:
-            schema["ga4gh"] = ga4gh_metadata
 
-        return schema
+@deprecated("GKSMetadataMixin is deprecated; use GKMMetadataMixin instead.")
+class GKSMetadataMixin(GKMMetadataMixin):
+    """Deprecated alias for :class:`GKMMetadataMixin`."""

src/ga4gh/core/models.py

@@ -1,4 +1,4 @@
-"""GKS Core Class Definitions"""
+"""GKM Core Class Definitions"""
 
 from __future__ import annotations
 
@@ -14,20 +14,25 @@
     StringConstraints,
     model_validator,
 )
-from typing_extensions import Self
+from typing_extensions import Self, deprecated
 
 from ga4gh.core.identifiers import GA4GH_IR_REGEXP
-from ga4gh.core.metadata import GKSMaturityMixin, GKSMetadataMixin, Maturity
+from ga4gh.core.metadata import GKMMetadataMixin, Maturity
 from ga4gh.core.version import CORE_VERSION
 
 
-class GKSCoreMetadataMixin(GKSMetadataMixin):
+class GKMCoreMetadataMixin(GKMMetadataMixin):
     """Provide gkm-core model metadata."""
 
     _product_name = "gkm-core"
     _product_version = CORE_VERSION
 
 
+@deprecated("GKSCoreMetadataMixin is deprecated; use GKMCoreMetadataMixin instead.")
+class GKSCoreMetadataMixin(GKMCoreMetadataMixin):
+    """Deprecated alias for :class:`GKMCoreMetadataMixin`."""
+
+
 class BaseModelForbidExtra(BaseModel):
     """Base Pydantic model class with extra attributes forbidden."""
 
@@ -65,7 +70,7 @@ class MembershipOperator(str, Enum):
 #########################################
 
 
-class code(GKSCoreMetadataMixin, RootModel):  # noqa: N801
+class code(GKMCoreMetadataMixin, RootModel):  # noqa: N801
     """Indicates that the value is taken from a set of controlled strings defined
     elsewhere. Technically, a code is restricted to a string which has at least one
     character and no leading or trailing whitespace, and where there is no whitespace
@@ -83,7 +88,7 @@ class code(GKSCoreMetadataMixin, RootModel):  # noqa: N801
     )
 
 
-class iriReference(GKSCoreMetadataMixin, RootModel):  # noqa: N801
+class iriReference(GKMCoreMetadataMixin, RootModel):  # noqa: N801
     """An IRI Reference (either an IRI or a relative-reference), according to `RFC3986
     section 4.1 <https://datatracker.ietf.org/doc/html/rfc3986#section-4.1>`_ and
     `RFC3987 section 2.1 <https://datatracker.ietf.org/doc/html/rfc3987#section-2.1>`_.
@@ -115,13 +120,14 @@ def ga4gh_serialize(self) -> str:  # noqa: D102
 #########################################
 
 
-class Entity(GKSMaturityMixin, BaseModel, ABC):
+class Entity(GKMCoreMetadataMixin, BaseModel, ABC):
     """Anything that exists, has existed, or will exist.
 
     Abstract base class to be extended by other classes. Do NOT instantiate directly.
     """
 
     _maturity: ClassVar[Maturity] = Maturity.TRIAL_USE
+    _abstract: ClassVar[bool] = True
 
     id: str | None = Field(
         default=None,
@@ -144,13 +150,14 @@ class Entity(GKSMaturityMixin, BaseModel, ABC):
     )
 
 
-class Element(GKSMaturityMixin, BaseModel, ABC):
+class Element(GKMCoreMetadataMixin, BaseModel, ABC):
     """The base definition for all identifiable data objects.
 
     Abstract base class to be extended by other classes. Do NOT instantiate directly.
     """
 
     _maturity: ClassVar[Maturity] = Maturity.TRIAL_USE
+    _abstract: ClassVar[bool] = True
 
     id: str | None = Field(
         default=None,
@@ -177,7 +184,7 @@ def get_extensions_by_name(self, name: str) -> list[Extension]:
 #########################################
 
 
-class Coding(GKSCoreMetadataMixin, Element, BaseModelForbidExtra):
+class Coding(Element, BaseModelForbidExtra):
     """A structured representation of a code for a defined concept in a terminology or
     code system.
     """
@@ -203,7 +210,7 @@ class Coding(GKSCoreMetadataMixin, Element, BaseModelForbidExtra):
     )
 
 
-class ConceptMapping(GKSCoreMetadataMixin, Element, BaseModelForbidExtra):
+class ConceptMapping(Element, BaseModelForbidExtra):
     """A mapping to a concept in a terminology or code system."""
 
     model_config = ConfigDict(use_enum_values=True)
@@ -220,7 +227,7 @@ class ConceptMapping(GKSCoreMetadataMixin, Element, BaseModelForbidExtra):
     )
 
 
-class ConceptSet(GKSCoreMetadataMixin, Entity, BaseModelForbidExtra):
+class ConceptSet(Entity, BaseModelForbidExtra):
     """A set of concepts that may be considered as dependent (occurring together), or
     independent (existing separately) in the context of some knowledge reported about
     them, as indicated by a set membership operator. e.g. a set of independent molecular
@@ -236,6 +243,10 @@ class ConceptSet(GKSCoreMetadataMixin, Entity, BaseModelForbidExtra):
         default="ConceptSet",
         description='MUST be "ConceptSet".',
     )
+    conceptSetType: str | None = Field(  # noqa: N815
+        default=None,
+        description="A term indicating the type of concept being represented by the ConceptSet.",
+    )
     concepts: list[MappableConcept] | list[ConceptSet] = Field(
         ...,
         description="A list of concepts that are dependent (occurring together), or independent (existing separately), depending on the membership operator.",
@@ -247,7 +258,7 @@ class ConceptSet(GKSCoreMetadataMixin, Entity, BaseModelForbidExtra):
     )
 
 
-class Extension(GKSCoreMetadataMixin, Element, BaseModelForbidExtra):
+class Extension(Element, BaseModelForbidExtra):
     """The Extension class provides entities with a means to include additional
     attributes that are outside of the specified standard but needed by a given content
     provider or system implementer. These extensions are not expected to be natively
@@ -271,7 +282,7 @@ class Extension(GKSCoreMetadataMixin, Element, BaseModelForbidExtra):
     )
 
 
-class MappableConcept(GKSCoreMetadataMixin, Entity, BaseModelForbidExtra):
+class MappableConcept(Entity, BaseModelForbidExtra):
     """A concept based on a primaryCoding and/or name that may be mapped to one or more other `Codings`."""
 
     _maturity: ClassVar[Maturity] = Maturity.TRIAL_USE

src/ga4gh/core/version.py

@@ -1,3 +1,3 @@
 """Define GKM-Core version"""
 
-CORE_VERSION = "1.2.0"
+CORE_VERSION = "1.3.0-ballot.2026-09.1"