feat: upgrades aind-data-schema (#217)

* feat: upgrades aind-data-schema * feat: adds pydantic settings * feat: updates aind-metadata-mapper
AllenNeuralDynamics · Apr 8, 2024 · d84c2f3 · d84c2f3
1 parent f8232c6
commit d84c2f3
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Showing 13 changed files with 19 additions and 55 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -17,7 +17,8 @@ readme = "README.md"
 dynamic = ["version"]
 
 dependencies = [
-    'aind-metadata-mapper==0.5.0'
+    'aind-metadata-mapper==0.6.1',
+    'pydantic-settings>=2.0'
 ]
 
 [project.optional-dependencies]

diff --git a/src/aind_metadata_service/sharepoint/client.py b/src/aind_metadata_service/sharepoint/client.py
@@ -240,9 +240,9 @@ def _merge_two_responses(
             )
         else:
             left_procedures: List[Procedures] = left_model_response.aind_models
-            right_procedures: List[
-                Procedures
-            ] = right_model_response.aind_models
+            right_procedures: List[Procedures] = (
+                right_model_response.aind_models
+            )
             procedures = self._merge_procedures(
                 left_procedures=left_procedures,
                 right_procedures=right_procedures,

diff --git a/src/aind_metadata_service/sharepoint/nsb2019/mapping.py b/src/aind_metadata_service/sharepoint/nsb2019/mapping.py
@@ -1423,13 +1423,7 @@ def get_craniotomy_procedure(self) -> Craniotomy:
         return Craniotomy.model_construct(
             craniotomy_type=self.aind_craniotomy_type,
             craniotomy_hemisphere=self.aind_hp_loc,
-            craniotomy_coordinates_ml=self.aind_hp_m_l,
-            craniotomy_coordinates_ap=self.aind_hp_a_p,
-            craniotomy_coordinates_reference=(
-                self.aind_craniotomy_coordinates_reference
-            ),
             bregma_to_lambda_distance=self.aind_breg2_lamb,
-            craniotomy_size=self.aind_craniotomy_size,
             dura_removed=self.aind_hp_durotomy,
         )
 

diff --git a/src/aind_metadata_service/smartsheet/protocols/mapping.py b/src/aind_metadata_service/smartsheet/protocols/mapping.py
@@ -81,10 +81,10 @@ def _get_protocol_list(
         """
         rows_associated_with_protocol_name: List[ProtocolInformation] = []
         for row in self.model.rows:
-            opt_protocol: Optional[
-                ProtocolInformation
-            ] = self._map_row_to_protocol(
-                row=row, input_protocol_name=protocol_name
+            opt_protocol: Optional[ProtocolInformation] = (
+                self._map_row_to_protocol(
+                    row=row, input_protocol_name=protocol_name
+                )
             )
             if opt_protocol is not None:
                 rows_associated_with_protocol_name.append(opt_protocol)

diff --git a/src/aind_metadata_service/tars/mapping.py b/src/aind_metadata_service/tars/mapping.py
@@ -265,9 +265,9 @@ def integrate_injection_materials(
                                     new_material.titer = (
                                         injection_material.titer
                                     )
-                                    procedure.injection_materials[
-                                        idx
-                                    ] = new_material
+                                    procedure.injection_materials[idx] = (
+                                        new_material
+                                    )
                                 elif (
                                     tars_response.status_code
                                     == StatusCodes.NO_DATA_FOUND.value

diff --git a/tests/resources/sharepoint/nsb2019/mapped/mapped_list_item2.json b/tests/resources/sharepoint/nsb2019/mapped/mapped_list_item2.json
@@ -23,16 +23,10 @@
       {
         "craniotomy_type": "Whole hemisphere craniotomy",
         "craniotomy_hemisphere": null,
-        "craniotomy_coordinates_ml": "2.8",
-        "craniotomy_coordinates_ap": "1.3",
-        "craniotomy_coordinates_reference": null,
         "bregma_to_lambda_distance": null,
-        "craniotomy_size": null,
         "dura_removed": false,
         "procedure_type": "Craniotomy",
-        "craniotomy_coordinates_unit": "millimeter",
         "bregma_to_lambda_unit": "millimeter",
-        "craniotomy_size_unit": "millimeter",
         "implant_part_number": null,
         "protective_material": null,
         "recovery_time": null,

diff --git a/tests/resources/sharepoint/nsb2019/mapped/mapped_list_item4.json b/tests/resources/sharepoint/nsb2019/mapped/mapped_list_item4.json
@@ -23,16 +23,10 @@
       {
         "craniotomy_type": "Other",
         "craniotomy_hemisphere": null,
-        "craniotomy_coordinates_ml": "2.8",
-        "craniotomy_coordinates_ap": "1.3",
-        "craniotomy_coordinates_reference": null,
         "bregma_to_lambda_distance": null,
-        "craniotomy_size": null,
         "dura_removed": null,
         "procedure_type": "Craniotomy",
-        "craniotomy_coordinates_unit": "millimeter",
         "bregma_to_lambda_unit": "millimeter",
-        "craniotomy_size_unit": "millimeter",
         "implant_part_number": null,
         "protective_material": null,
         "recovery_time": null,

diff --git a/tests/resources/sharepoint/nsb2019/mapped/mapped_list_item7.json b/tests/resources/sharepoint/nsb2019/mapped/mapped_list_item7.json
@@ -23,16 +23,10 @@
       {
         "craniotomy_type": "Other",
         "craniotomy_hemisphere": null,
-        "craniotomy_coordinates_ml": "2.8",
-        "craniotomy_coordinates_ap": "1.3",
-        "craniotomy_coordinates_reference": null,
         "bregma_to_lambda_distance": null,
-        "craniotomy_size": null,
         "dura_removed": false,
         "procedure_type": "Craniotomy",
-        "craniotomy_coordinates_unit": "millimeter",
         "bregma_to_lambda_unit": "millimeter",
-        "craniotomy_size_unit": "millimeter",
         "implant_part_number": null,
         "protective_material": null,
         "recovery_time": null,

diff --git a/tests/resources/sharepoint/nsb2023/mapped/mapped_list_item10.json b/tests/resources/sharepoint/nsb2023/mapped/mapped_list_item10.json
@@ -15,17 +15,11 @@
     "procedures": [
       {
         "craniotomy_type": "3 mm",
-        "craniotomy_coordinates_reference": null,
         "bregma_to_lambda_distance": null,
-        "craniotomy_size": "3",
         "recovery_time": "25.0",
         "procedure_type": "Craniotomy",
         "craniotomy_hemisphere": null,
-        "craniotomy_coordinates_ml": null,
-        "craniotomy_coordinates_ap": null,
-        "craniotomy_coordinates_unit": "millimeter",
         "bregma_to_lambda_unit": "millimeter",
-        "craniotomy_size_unit": "millimeter",
         "implant_part_number": "3mm stacked coverslip",
         "dura_removed": null,
         "protective_material": null,

diff --git a/tests/resources/sharepoint/nsb2023/mapped/mapped_list_item22.json b/tests/resources/sharepoint/nsb2023/mapped/mapped_list_item22.json
@@ -10,17 +10,11 @@
     "procedures": [
       {
         "craniotomy_type": "5 mm",
-        "craniotomy_coordinates_reference": "Lambda",
         "bregma_to_lambda_distance": null,
-        "craniotomy_size": "5",
         "recovery_time": null,
         "procedure_type": "Craniotomy",
         "craniotomy_hemisphere": null,
-        "craniotomy_coordinates_ml": null,
-        "craniotomy_coordinates_ap": null,
-        "craniotomy_coordinates_unit": "millimeter",
         "bregma_to_lambda_unit": "millimeter",
-        "craniotomy_size_unit": "millimeter",
         "implant_part_number": "2006",
         "dura_removed": null,
         "protective_material": null,

diff --git a/tests/resources/sharepoint/nsb2023/mapped/mapped_list_item9.json b/tests/resources/sharepoint/nsb2023/mapped/mapped_list_item9.json
@@ -15,17 +15,11 @@
     "procedures": [
       {
         "craniotomy_type": "5 mm",
-        "craniotomy_coordinates_reference": "Lambda",
         "bregma_to_lambda_distance": null,
-        "craniotomy_size": "5",
         "recovery_time": "30.0",
         "procedure_type": "Craniotomy",
         "craniotomy_hemisphere": null,
-        "craniotomy_coordinates_ml": null,
-        "craniotomy_coordinates_ap": null,
-        "craniotomy_coordinates_unit": "millimeter",
         "bregma_to_lambda_unit": "millimeter",
-        "craniotomy_size_unit": "millimeter",
         "implant_part_number": "5mm stacked coverslip",
         "dura_removed": null,
         "protective_material": null,

diff --git a/tests/slims/test_client.py b/tests/slims/test_client.py
@@ -345,7 +345,10 @@ def test_get_model_response_internal_server_error(
     @patch(
         "aind_metadata_service.slims.client.SlimsClient.get_record_response"
     )
-    def test_get_model_response_exception(self, mock_get_record_response):
+    @patch("logging.error")
+    def test_get_model_response_exception(
+        self, mock_log_error: MagicMock, mock_get_record_response: MagicMock
+    ):
         """Test case: Exception during execution"""
         mock_get_record_response.side_effect = Exception("Some error")
         self.assertEqual(
@@ -356,6 +359,7 @@ def test_get_model_response_exception(self, mock_get_record_response):
             self.client.get_rig_model_response("12345").status_code,
             StatusCodes.INTERNAL_SERVER_ERROR,
         )
+        mock_log_error.assert_called()
 
     @patch("aind_metadata_service.slims.client.requests.get")
     def test_get_response_with_oauth(self, mock_requests_get):

diff --git a/tests/smartsheet/test_perfusions.py b/tests/smartsheet/test_perfusions.py
@@ -38,8 +38,9 @@ def setUpClass(cls):
             contents = json.load(f)
         cls.example_sheet_contents = contents
         cls.example_sheet = json.dumps(contents)
+        # TODO: Add protocol id
         cls.expected_model = [
-            Surgery(
+            Surgery.model_construct(
                 start_date=date(2023, 10, 2),
                 experimenter_full_name="Jane Smith",
                 iacuc_protocol="2109",