build!: update ga4gh.vrs version (#193)

pyproject.toml

@@ -29,7 +29,7 @@ dependencies = [
     "uvicorn",
     "click",
     "boto3",
-    "ga4gh.vrs~=2.0.0a1",
+    "ga4gh.vrs~=2.0.0a8",
 ]
 dynamic = ["version"]
 

src/disease/query.py

@@ -5,7 +5,7 @@
 import re
 
 from botocore.exceptions import ClientError
-from ga4gh.core import core_models
+from ga4gh.core import domain_models, entity_models
 
 from disease import NAMESPACE_LOOKUP, PREFIX_LOOKUP, SOURCES_LOWER_LOOKUP
 from disease.database.database import AbstractDatabase
@@ -320,7 +320,7 @@ def _add_disease(
         :param match_type: type of match achieved
         :return: completed normalized response object ready to return to user
         """
-        disease_obj = core_models.Disease(
+        disease_obj = domain_models.Disease(
             id=f"normalize.disease.{record['concept_id']}", label=record["label"]
         )
 
@@ -329,22 +329,22 @@ def _add_disease(
         for source_id in source_ids:
             system, code = source_id.split(":")
             mappings.append(
-                core_models.Mapping(
-                    coding=core_models.Coding(
-                        code=core_models.Code(code), system=system.lower()
+                entity_models.ConceptMapping(
+                    coding=entity_models.Coding(
+                        code=entity_models.Code(code), system=system.lower()
                     ),
-                    relation=core_models.Relation.RELATED_MATCH,
+                    relation=entity_models.Relation.RELATED_MATCH,
                 )
             )
         if mappings:
             disease_obj.mappings = mappings
 
         if "aliases" in record:
-            disease_obj.aliases = record["aliases"]
+            disease_obj.alternativeLabels = record["aliases"]
 
         if "pediatric_disease" in record and record["pediatric_disease"] is not None:
             disease_obj.extensions = [
-                core_models.Extension(
+                entity_models.Extension(
                     name="pediatric_disease",
                     value=record["pediatric_disease"],
                 )

src/disease/schemas.py

@@ -4,7 +4,7 @@
 from enum import Enum, IntEnum
 from typing import Literal
 
-from ga4gh.core import core_models
+from ga4gh.core import domain_models
 from pydantic import BaseModel, ConfigDict, StrictBool, StrictStr
 
 from disease.version import __version__
@@ -261,7 +261,7 @@ class NormalizationService(BaseModel):
     warnings: dict | None = None
     match_type: MatchType
     normalized_id: str | None = None
-    disease: core_models.Disease | None = None
+    disease: domain_models.Disease | None = None
     source_meta_: dict[SourceName, SourceMeta] | None = None
     service_meta_: ServiceMeta
 
@@ -299,7 +299,6 @@ class NormalizationService(BaseModel):
                     ],
                     "extensions": [
                         {
-                            "type": "Extension",
                             "name": "pediatric_disease",
                             "value": True,
                         },

tests/unit/test_query.py

@@ -3,7 +3,7 @@
 from datetime import datetime
 
 import pytest
-from ga4gh.core import core_models
+from ga4gh.core import domain_models
 
 from disease.query import InvalidParameterException, QueryHandler
 from disease.schemas import MatchType, SourceName
@@ -18,7 +18,7 @@ def query_handler(database):
 @pytest.fixture(scope="module")
 def neuroblastoma():
     """Create neuroblastoma fixture."""
-    return core_models.Disease(
+    return domain_models.Disease(
         type="Disease",
         id="normalize.disease.ncit:C3270",
         label="Neuroblastoma",
@@ -68,7 +68,7 @@ def neuroblastoma():
                 "relation": "relatedMatch",
             },
         ],
-        aliases=[
+        alternativeLabels=[
             "NB",
             "neuroblastoma",
             "Neural Crest Tumor, Malignant",
@@ -87,11 +87,11 @@ def neuroblastoma():
 @pytest.fixture(scope="module")
 def skin_myo():
     """Create a test fixture for skin myopithelioma"""
-    return core_models.Disease(
+    return domain_models.Disease(
         type="Disease",
         id="normalize.disease.ncit:C167370",
         label="Skin Myoepithelioma",
-        aliases=["Cutaneous Myoepithelioma"],
+        alternativeLabels=["Cutaneous Myoepithelioma"],
     )
 
 
@@ -100,11 +100,11 @@ def mafd2():
     """Create a test fixture for major affective disorder 2. Query should not
     include a "pediatric_disease" Extension object.
     """
-    return core_models.Disease(
+    return domain_models.Disease(
         type="Disease",
         id="normalize.disease.mondo:0010648",
         label="major affective disorder 2",
-        aliases=[
+        alternativeLabels=[
             "MAFD2",
             "MDI",
             "MDX",
@@ -158,9 +158,9 @@ def compare_disease(actual, fixture):
         assert no_matches == [], no_matches
         assert len(actual.mappings) == len(fixture.mappings)
 
-    assert bool(actual.aliases) == bool(fixture.aliases)
-    if actual.aliases:
-        assert set(actual.aliases) == set(fixture.aliases)
+    assert bool(actual.alternativeLabels) == bool(fixture.alternativeLabels)
+    if actual.alternativeLabels:
+        assert set(actual.alternativeLabels) == set(fixture.alternativeLabels)
 
     def get_extension(extensions, name):
         matches = [e for e in extensions if e.name == name]