test: add tests for validating va-spec test fixtures against pydantic models (#36)

close #33

Author: korikuzma

tests/conftest.py

@@ -1,5 +1,34 @@
 """Provide utilities for test cases."""
 
+from enum import Enum
 from pathlib import Path
 
 SUBMODULES_DIR = Path(__file__).parents[1] / "submodules" / "va_spec"
+
+
+class VaSpecSchema(str, Enum):
+    """Enum for VA-Spec schema"""
+
+    AAC_2017 = "aac-2017"
+    ACMG_2015 = "acmg-2015"
+    BASE = "base"
+    CCV_2022 = "ccv-2022"
+
+
+def get_va_spec_schema(label: str) -> str | None:
+    """Get VA-Spec schema given label
+
+    :param label: Label
+    :return: VA-Spec label
+    """
+    if label.endswith(VaSpecSchema.AAC_2017):
+        schema = VaSpecSchema.AAC_2017
+    elif label.endswith(VaSpecSchema.ACMG_2015):
+        schema = VaSpecSchema.ACMG_2015
+    elif label.endswith(VaSpecSchema.BASE):
+        schema = VaSpecSchema.BASE
+    elif label.endswith(VaSpecSchema.CCV_2022):
+        schema = VaSpecSchema.CCV_2022
+    else:
+        schema = None
+    return schema

tests/validation/test_va_spec_fixtures_validation.py

@@ -0,0 +1,42 @@
+"""Ensure that VA-Spec test fixtures validate against Pydantic models"""
+
+import yaml
+from ga4gh.va_spec import aac_2017, acmg_2015, base, ccv_2022
+
+from tests.conftest import SUBMODULES_DIR, VaSpecSchema, get_va_spec_schema
+
+VA_SPEC_TESTS_DIR = SUBMODULES_DIR / "tests"
+
+
+with (VA_SPEC_TESTS_DIR / "test_definitions.yaml").open() as f:
+    data = yaml.load(f, Loader=yaml.SafeLoader)
+    test_definitions = data["tests"]
+
+SCHEMA_TO_PYDANTIC_MODULE = {
+    VaSpecSchema.AAC_2017: aac_2017,
+    VaSpecSchema.ACMG_2015: acmg_2015,
+    VaSpecSchema.CCV_2022: ccv_2022,
+    VaSpecSchema.BASE: base,
+}
+VA_SPEC_TEST_DEFINITIONS = {schema: [] for schema in VaSpecSchema}
+
+
+for test_def in test_definitions:
+    if test_def["namespace"].startswith("va-spec."):
+        schema = get_va_spec_schema(test_def["namespace"].split("va-spec.")[-1])
+        VA_SPEC_TEST_DEFINITIONS[schema].append(test_def)
+
+
+def test_va_spec_fixtures():
+    """Test that VA-Spec test fixtures validate against Pydantic models"""
+    for va_spec_schema, schema_test_defs in VA_SPEC_TEST_DEFINITIONS.items():
+        pydantic_module = SCHEMA_TO_PYDANTIC_MODULE[va_spec_schema]
+
+        for schema_test_def in schema_test_defs:
+            with (
+                VA_SPEC_TESTS_DIR / "fixtures" / schema_test_def["test_file"]
+            ).open() as f:
+                test_fixture_dict = yaml.load(f, Loader=yaml.SafeLoader)
+                va_spec_class = schema_test_def["definition"]
+                pydantic_model = getattr(pydantic_module, va_spec_class)
+                assert pydantic_model(**test_fixture_dict)

tests/validation/test_va_spec_schema.py

@@ -1,27 +1,21 @@
 """Test that VA-Spec Python Pydantic models match corresponding JSON schemas"""
 
 import json
-from enum import Enum
 from pathlib import Path
 
 import pytest
 from ga4gh.va_spec import aac_2017, acmg_2015, base, ccv_2022
 from pydantic import BaseModel
 
-from tests.conftest import SUBMODULES_DIR
+from tests.conftest import (
+    SUBMODULES_DIR,
+    VaSpecSchema,
+    get_va_spec_schema,
+)
 
 VA_SCHEMA_DIR = SUBMODULES_DIR / "schema" / "va-spec"
 
 
-class VaSpecSchema(str, Enum):
-    """Enum for VA-Spec schema"""
-
-    AAC_2017 = "aac-2017"
-    ACMG_2015 = "acmg-2015"
-    BASE = "base"
-    CCV_2022 = "ccv-2022"
-
-
 class VaSpecSchemaMapping(BaseModel):
     """Model for representing VA-Spec Schema concrete classes, primitives, and schema"""
 
@@ -59,15 +53,8 @@ def _update_va_spec_schema_mapping(
 # Get core + profiles classes
 for child in VA_SCHEMA_DIR.iterdir():
     child_str = str(child)
-    if child_str.endswith(VaSpecSchema.AAC_2017):
-        mapping_key = VaSpecSchema.AAC_2017
-    elif child_str.endswith(VaSpecSchema.ACMG_2015):
-        mapping_key = VaSpecSchema.ACMG_2015
-    elif child_str.endswith(VaSpecSchema.BASE):
-        mapping_key = VaSpecSchema.BASE
-    elif child_str.endswith(VaSpecSchema.CCV_2022):
-        mapping_key = VaSpecSchema.CCV_2022
-    else:
+    mapping_key = get_va_spec_schema(child_str)
+    if not mapping_key:
         continue
 
     mapping = VA_SPEC_SCHEMA_MAPPING[mapping_key]