fix(build): update ga4gh.vrs/submodules + forbid extra attrs (#11)

* Update ga4gh.vrs + submodules 
* forbid extra attributes when additionalProperties is set to False

Author: korikuzma

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "submodules/cat_vrs"]
 	path = submodules/cat_vrs
 	url = https://github.com/ga4gh/cat-vrs
-	branch = 1.0.0-ballot.2024-11
+	branch = 1.0.0-snapshot.2025-02

pyproject.toml

@@ -32,7 +32,7 @@ keywords = [
 requires-python = ">=3.10"
 dynamic = ["version"]
 dependencies = [
-    "ga4gh.vrs==2.0.0a13",
+    "ga4gh.vrs==2.0.0a14",
     "pydantic==2.*",
 ]
 

src/ga4gh/cat_vrs/models.py

@@ -8,13 +8,14 @@
 from typing import Literal
 
 from ga4gh.core.models import (
+    BaseModelForbidExtra,
     ConceptMapping,
     Entity,
     MappableConcept,
     iriReference,
 )
 from ga4gh.vrs.models import Allele, CopyChange, Range, SequenceLocation, Variation
-from pydantic import BaseModel, Field, RootModel, field_validator
+from pydantic import Field, RootModel, field_validator
 
 
 class Relation(str, Enum):
@@ -27,7 +28,7 @@ class Relation(str, Enum):
     TRANSCRIBES_TO = "transcribes_to"
 
 
-class DefiningAlleleConstraint(BaseModel):
+class DefiningAlleleConstraint(BaseModelForbidExtra):
     """The defining allele and its associated relationships that are congruent with
     member variants.
     """
@@ -42,7 +43,7 @@ class DefiningAlleleConstraint(BaseModel):
     )
 
 
-class DefiningLocationConstraint(BaseModel):
+class DefiningLocationConstraint(BaseModelForbidExtra):
     """The defining location and its associated relationships that are congruent with
     member locations.
     """
@@ -61,7 +62,7 @@ class DefiningLocationConstraint(BaseModel):
     )
 
 
-class CopyCountConstraint(BaseModel):
+class CopyCountConstraint(BaseModelForbidExtra):
     """The exact or range of copies that members of this categorical variant must
     satisfy.
     """
@@ -75,7 +76,7 @@ class CopyCountConstraint(BaseModel):
     )
 
 
-class CopyChangeConstraint(BaseModel):
+class CopyChangeConstraint(BaseModelForbidExtra):
     """A representation of copy number change"""
 
     type: Literal["CopyChangeConstraint"] = Field(
@@ -114,7 +115,7 @@ class Constraint(RootModel):
     ) = Field(..., discriminator="type")
 
 
-class CategoricalVariant(Entity):
+class CategoricalVariant(Entity, BaseModelForbidExtra):
     """A representation of a categorically-defined domain for variation, in which
     individual Constraintual variation instances may be members of the domain.
     """

submodules/cat_vrs

@@ -46,7 +46,7 @@ def defining_loc_constr():
             MappableConcept(primaryCode=code(models.Relation.LIFTOVER_TO.value))
         ],
         location="location.json#/1",
-        matchCharacteristic=MappableConcept(label="test"),
+        matchCharacteristic=MappableConcept(name="test"),
     )
 
 
@@ -119,7 +119,7 @@ def test_protein_sequence_consequence(defining_loc_constr, members):
     invalid_params["constraints"] = [
         models.Constraint(
             root=models.DefiningAlleleConstraint(
-                relations=[MappableConcept(label=models.Relation.LIFTOVER_TO.value)],
+                relations=[MappableConcept(name=models.Relation.LIFTOVER_TO.value)],
                 allele=DUMMY_ALLELE_IRI,
             )
         )