Merge pull request #333 from AllenNeuralDynamics/release-v0.19.1

release-v0.19.1

src/aind_metadata_service/__init__.py

@@ -1,3 +1,3 @@
 """REST service to retrieve metadata from databases."""
 
-__version__ = "0.19.0"
+__version__ = "0.19.1"

src/aind_metadata_service/tars/mapping.py

@@ -232,8 +232,9 @@ def get_virus_strains(response: ModelResponse) -> List:
                         viruses.extend(virus_strains)
         return viruses
 
+    # TODO: Refactor this method
     @staticmethod
-    def integrate_injection_materials(
+    def integrate_injection_materials(  # noqa: C901
         response: ModelResponse, tars_mapping: Dict[str, JSONResponse]
     ) -> ModelResponse:
         """
@@ -262,7 +263,8 @@ def integrate_injection_materials(
                                 virus_strain = injection_material.name.strip()
                                 tars_response = tars_mapping.get(virus_strain)
                                 if (
-                                    tars_response.status_code
+                                    tars_response
+                                    and tars_response.status_code
                                     == StatusCodes.DB_RESPONDED.value
                                     or tars_response.status_code
                                     == StatusCodes.VALID_DATA.value
@@ -272,10 +274,21 @@ def integrate_injection_materials(
                                     data = json.loads(tars_response.body)[
                                         "data"
                                     ]
-                                    new_material = ViralMaterial(**data)
-                                    new_material.titer = (
-                                        injection_material.titer
-                                    )
+                                    try:
+                                        new_material = ViralMaterial(**data)
+                                        new_material.titer = (
+                                            injection_material.titer
+                                        )
+                                    except ValidationError as e:
+                                        logging.error(f"{e}")
+                                        new_material = (
+                                            ViralMaterial.model_construct(
+                                                **data
+                                            )
+                                        )
+                                        new_material.titer = (
+                                            injection_material.titer
+                                        )
                                     procedure.injection_materials[idx] = (
                                         new_material
                                     )

tests/tars/test_mapping.py

@@ -1,6 +1,7 @@
 """Module to test TARS mapping."""
 
 import unittest
+from copy import deepcopy
 from datetime import date
 from unittest.mock import MagicMock, patch
 
@@ -365,7 +366,7 @@ def test_integrate_injection_materials(self):
             "12345": tars_response1.map_to_json_response(),
             "67890": tars_response2.map_to_json_response(),
         }
-        procedures_response = self.procedures_response
+        procedures_response = deepcopy(self.procedures_response)
         merged_response = self.handler.integrate_injection_materials(
             response=procedures_response, tars_mapping=tars_mapping
         )
@@ -487,6 +488,76 @@ def test_integrate_injection_materials_no_data(self):
         )
         self.assertEqual(merged_response.status_code, StatusCodes.DB_RESPONDED)
 
+    @patch("logging.error")
+    def test_integrate_injection_materials_no_name(
+        self, mock_error: MagicMock
+    ):
+        """Tests that injection materials are integrated into
+        procedures response as expected and invalid viral material"""
+        expected_injection_material = ViralMaterial.model_construct(
+            name="rAAV-MGT_789",
+            tars_identifiers=TarsVirusIdentifiers.model_construct(
+                virus_tars_id="AiV456",
+                plasmid_tars_alias="AiP123",
+                prep_lot_number="12345",
+                prep_date=date(2023, 12, 15),
+                prep_type=VirusPrepType.CRUDE.value,
+                prep_protocol="SOP#VC002",
+            ),
+        )
+        expected_injection_material2 = ViralMaterial.model_construct(
+            tars_identifiers=TarsVirusIdentifiers.model_construct(
+                virus_tars_id="AiV456",
+                plasmid_tars_alias="AiP123",
+                prep_lot_number="12345",
+                prep_date=date(2023, 12, 15),
+                prep_type=VirusPrepType.CRUDE.value,
+                prep_protocol="SOP#VC002",
+            ),
+        )
+        tars_response1 = ModelResponse(
+            aind_models=[expected_injection_material],
+            status_code=StatusCodes.DB_RESPONDED,
+        )
+        tars_response2 = ModelResponse(
+            aind_models=[expected_injection_material2],
+            status_code=StatusCodes.DB_RESPONDED,
+        )
+        tars_mapping = {
+            "12345": tars_response1.map_to_json_response(),
+            "67890": tars_response2.map_to_json_response(),
+        }
+        procedures_response = self.procedures_response
+        merged_response = self.handler.integrate_injection_materials(
+            response=procedures_response, tars_mapping=tars_mapping
+        )
+        expected_surgery = Surgery.model_construct(
+            procedures=[
+                NanojectInjection.model_construct(
+                    injection_materials=[expected_injection_material]
+                ),
+                NanojectInjection.model_construct(
+                    injection_materials=[expected_injection_material2]
+                ),
+            ]
+        )
+        expected_merged_response = ModelResponse(
+            aind_models=[
+                Procedures(
+                    subject_id="12345",
+                    subject_procedures=[expected_surgery],
+                )
+            ],
+            status_code=StatusCodes.DB_RESPONDED,
+        )
+        self.assertEqual(
+            expected_merged_response.aind_models[0].model_dump_json(
+                warnings=False
+            ),
+            merged_response.aind_models[0].model_dump_json(warnings=False),
+        )
+        mock_error.assert_called_once()
+
 
 if __name__ == "__main__":
     unittest.main()