update tests

tests/__init__.py

@@ -0,0 +1 @@
+"""Initialize the tests namespace for shared utilities."""

tests/conftest.py

@@ -6,10 +6,12 @@
 
 import pytest
 from deepdiff import DeepDiff
+from ga4gh.core.models import ConceptMapping
 
 from metakb.harvesters.base import Harvester
 from metakb.normalizers import ViccNormalizers
 from metakb.query import QueryHandler
+from metakb.transformers.base import NORMALIZER_PRIORITY_EXT_NAME
 
 TEST_DATA_DIR = Path(__file__).resolve().parents[0] / "data"
 TEST_HARVESTERS_DIR = TEST_DATA_DIR / "harvesters"
@@ -64,6 +66,24 @@ def get_vicc_normalizer_ext(is_priority: bool):
     return [{"name": "vicc_normalizer_priority", "value": is_priority}]
 
 
+def get_mappings_normalizer_id(mappings: list[dict | ConceptMapping]) -> str | None:
+    """Get normalizer ID from list of concept mappings
+
+    :param mappings: List of concept mappings
+    :return: Normalizer ID
+    """
+    normalizer_id = None
+    for mapping in mappings:
+        if isinstance(mapping, ConceptMapping):
+            mapping = mapping.model_dump()
+        extensions = mapping.get("extensions") or []
+        for ext in extensions:
+            if ext["name"] == NORMALIZER_PRIORITY_EXT_NAME and ext["value"]:
+                normalizer_id = mapping["coding"]["code"]
+                break
+    return normalizer_id
+
+
 @pytest.fixture(scope="session")
 def braf_normalizer_mappings():
     """Create test fixture for braf normalizer mappings"""

tests/unit/database/test_database.py

@@ -5,10 +5,10 @@
 import pytest
 from neo4j import Driver
 from neo4j.graph import Node
+from tests.conftest import get_mappings_normalizer_id
 
 from metakb.database import get_driver
 from metakb.schemas.app import SourceName
-from metakb.transformers.base import NORMALIZER_PRIORITY_EXT_NAME
 
 
 @pytest.fixture(scope="module")
@@ -184,11 +184,8 @@ def _check_function(
             if k == "mappings" or (k == "subtype" and isinstance(fixture[k], dict)):
                 assert json.loads(node[k]) == fixture[k]
             elif k == "normalizer_id":
-                for mapping in fixture["mappings"]:
-                    extensions = mapping.get("extensions") or []
-                    for ext in extensions:
-                        if ext["name"] == NORMALIZER_PRIORITY_EXT_NAME and ext["value"]:
-                            assert node[k] == mapping["coding"]["code"]
+                normalizer_id = get_mappings_normalizer_id(fixture["mappings"])
+                assert node[k] == normalizer_id
             elif isinstance(fixture[k], list):
                 assert set(node[k]) == set(fixture[k])
             else:

tests/unit/search/test_search_statements.py

@@ -1,27 +1,13 @@
 """Test search statement methods"""
 
 import pytest
-from ga4gh.core.models import MappableConcept
+from tests.conftest import get_mappings_normalizer_id
 
 from metakb.query import QueryHandler
 
 from .utils import assert_no_match, find_and_check_stmt
 
 
-def _get_normalizer_id(mappings: list[MappableConcept]) -> str | None:
-    """Get normalized ID from list of extensions
-
-    :param mappings: List of mappable concepts
-    :return: Normalized concept ID if found in extensions
-    """
-    normalizer_id = None
-    for mapping in mappings:
-        if mapping.extensions == "from_vicc_normalizer":
-            normalizer_id = mapping.code.root
-            break
-    return normalizer_id
-
-
 def assert_general_search_stmts(response):
     """Check that general search_statements queries return a valid response"""
     len_stmt_id_matches = len(response.statement_ids)
@@ -216,11 +202,14 @@ async def test_general_search_statements(query_handler):
         tp = statement.proposition.objectTherapeutic.root
 
         if hasattr(tp, "conceptType"):
-            assert _get_normalizer_id(tp.mappings) == expected_therapy_id
+            assert get_mappings_normalizer_id(tp.mappings) == expected_therapy_id
         else:
             found_expected = False
             for therapeutic in tp.therapies:
-                if _get_normalizer_id(therapeutic.mappings) == expected_therapy_id:
+                if (
+                    get_mappings_normalizer_id(therapeutic.mappings)
+                    == expected_therapy_id
+                ):
                     found_expected = True
                     break
             assert found_expected
@@ -245,11 +234,15 @@ async def test_general_search_statements(query_handler):
             == expected_variation_id
         )
         assert (
-            _get_normalizer_id(statement.proposition.objectTherapeutic.root.extensions)
+            get_mappings_normalizer_id(
+                statement.proposition.objectTherapeutic.root.mappings
+            )
             == expected_therapy_id
         )
         assert (
-            _get_normalizer_id(statement.proposition.conditionQualifier.root.extensions)
+            get_mappings_normalizer_id(
+                statement.proposition.conditionQualifier.root.mappings
+            )
             == expected_disease_id
         )