Merge pull request #301 from AllenNeuralDynamics/release-v0.16.0

Release v0.16.0

pyproject.toml

@@ -18,9 +18,9 @@ dynamic = ["version"]
 
 dependencies = [
     'pydantic-settings>=2.0',
-    'pydantic>=2.7,<2.9',
-    'aind-metadata-mapper[bergamo]==0.18.0',
-    'aind-data-schema==1.1.1',
+    'pydantic>=2.10',
+    'aind-metadata-mapper[bergamo]==0.21.0',
+    'aind-data-schema==1.2.0',
     'typing-extensions==4.12.2'
 ]
 
@@ -43,7 +43,7 @@ server = [
     'fastapi==0.115.0',
     'uvicorn[standard]==0.31.0',
     'python-dateutil',
-    'aind-slims-api==0.1.15',
+    'aind-slims-api==0.1.17',
     'azure-identity==1.15.0'
 ]
 

src/aind_metadata_service/__init__.py

@@ -1,3 +1,3 @@
 """REST service to retrieve metadata from databases."""
 
-__version__ = "0.15.1"
+__version__ = "0.16.0"

src/aind_metadata_service/response_handler.py

@@ -13,6 +13,7 @@
     ViralMaterial,
 )
 from aind_data_schema.core.rig import Rig
+from aind_data_schema.core.session import Session
 from aind_data_schema.core.subject import Subject
 from aind_metadata_mapper.core import JobResponse
 from fastapi import Response
@@ -35,6 +36,7 @@
     ProtocolInformation,
     Instrument,
     Rig,
+    Session,
 )
 
 
@@ -89,37 +91,42 @@ def no_data_found_error_response(cls):
             message="No Data Found.",
         )
 
+    @staticmethod
+    def _validate_model(model) -> Optional[str]:
+        """Helper method to validate a model and return validation errors."""
+        validation_error = None
+        try:
+            model.__class__.model_validate(model.model_dump())
+        except ValidationError as e:
+            validation_error = repr(e)
+        except (AttributeError, ValueError, KeyError) as oe:
+            validation_error = repr(oe)
+        return validation_error
+
     def _map_data_response(  # noqa: C901
         self, validate: bool = True
     ) -> Union[Response, JSONResponse]:
         """Map ModelResponse with StatusCodes.DB_RESPONDED to a JSONResponse.
         Perform validations, bypasses validation if flag is set to False."""
+
         if len(self.aind_models) == 0:
             status_code = StatusCodes.NO_DATA_FOUND.value
             content_data = None
             message = "No Data Found."
+
         elif len(self.aind_models) == 1:
             aind_model = self.aind_models[0]
             content_data = jsonable_encoder(
                 json.loads(aind_model.model_dump_json())
             )
             if validate:
-                validation_error = None
-                try:
-                    aind_model.__class__.model_validate(
-                        aind_model.model_dump()
-                    )
-                except ValidationError as e:
-                    validation_error = repr(e)
-                except (AttributeError, ValueError, KeyError) as oe:
-                    validation_error = repr(oe)
+                validation_error = self._validate_model(aind_model)
                 if validation_error:
                     status_code = StatusCodes.INVALID_DATA.value
                     message = f"Validation Errors: {validation_error}"
                 else:
                     status_code = StatusCodes.VALID_DATA.value
                     message = "Valid Model."
-            # if validate flag is False
             else:
                 status_code = StatusCodes.UNPROCESSIBLE_ENTITY.value
                 message = (
@@ -132,13 +139,33 @@ def _map_data_response(  # noqa: C901
                     "There was an error retrieving records from one or more of"
                     " the databases."
                 )
+
         else:
             status_code = StatusCodes.MULTIPLE_RESPONSES.value
             message = "Multiple Items Found."
             content_data = [
                 jsonable_encoder(json.loads(model.model_dump_json()))
                 for model in self.aind_models
             ]
+
+            if validate:
+                # Validate each model and accumulate errors
+                validation_errors = []
+                for model in self.aind_models:
+                    error = self._validate_model(model)
+                    print(error)
+                    if error:
+                        validation_errors.append(error)
+
+                if validation_errors:
+                    message += (
+                        f" Validation Errors: {', '.join(validation_errors)}"
+                    )
+                else:
+                    message += " All Models Valid."
+            else:
+                message += " Models have not been validated."
+
         return JSONResponse(
             status_code=status_code,
             content=({"message": message, "data": content_data}),

src/aind_metadata_service/server.py

@@ -122,6 +122,15 @@ async def retrieve_rig(rig_id):
     return model_response.map_to_json_response(validate=False)
 
 
+@app.get("/ecephys_sessions_by_subject/{subject_id}")
+async def retrieve_sessions(subject_id):
+    """Retrieves sessions from slims"""
+    model_response = await run_in_threadpool(
+        slims_client.get_sessions_model_response, subject_id=subject_id
+    )
+    return model_response.map_to_json_response()
+
+
 @app.get("/protocols/{protocol_name}")
 async def retrieve_protocols(
     protocol_name,

src/aind_metadata_service/sharepoint/las2020/mapping.py

@@ -2094,7 +2094,7 @@ def map_viral_materials(injectable_materials: List[InjectableMaterial]):
             )
         return viral_materials
 
-    def get_procedure(self, subject_id) -> Surgery:
+    def get_procedure(self, subject_id) -> Optional[Surgery]:
         """Return Surgery as best as possible from a record."""
         subject_procedures = []
         if self.has_ip_injection():
@@ -2118,10 +2118,13 @@ def get_procedure(self, subject_id) -> Surgery:
                         injection_materials=injection_materials,
                     )
                     subject_procedures.append(ro_injection)
-        return Surgery.model_construct(
-            experimenter_full_name=self.aind_author_id,
-            iacuc_protocol=self.aind_protocol,
-            start_date=self.aind_n_start_date,
-            end_date=self.aind_n_end_date,
-            procedures=subject_procedures,
-        )
+        if subject_procedures:
+            return Surgery.model_construct(
+                experimenter_full_name=self.aind_author_id,
+                iacuc_protocol=self.aind_protocol,
+                start_date=self.aind_n_start_date,
+                end_date=self.aind_n_end_date,
+                procedures=subject_procedures,
+            )
+        else:
+            return None

src/aind_metadata_service/sharepoint/las2020/procedures.py

@@ -49,5 +49,6 @@ def get_procedures_from_sharepoint(
                 las_model = LASList.model_validate(list_item.to_json())
                 mapped_model = MappedLASList(las=las_model)
                 procedure = mapped_model.get_procedure(subject_id=subject_id)
-                list_of_procedures.append(procedure)
+                if procedure:
+                    list_of_procedures.append(procedure)
         return list_of_procedures