EcephysSessions from SLIMS

pyproject.toml

@@ -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/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

@@ -22,6 +22,7 @@
     SharePointClient,
     SharepointSettings,
 )
+from aind_metadata_service.slims.client import SlimsHandler, SlimsSettings
 from aind_metadata_service.smartsheet.client import (
     SmartSheetClient,
     SmartsheetSettings,
@@ -36,7 +37,6 @@
 )
 from aind_metadata_service.tars.client import AzureSettings, TarsClient
 from aind_metadata_service.tars.mapping import TarsResponseHandler
-from aind_metadata_service.slims.client import SlimsSettings, SlimsHandler
 
 SMARTSHEET_FUNDING_ID = os.getenv("SMARTSHEET_FUNDING_ID")
 SMARTSHEET_FUNDING_TOKEN = os.getenv("SMARTSHEET_API_TOKEN")
@@ -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/slims/client.py

@@ -4,16 +4,18 @@
 
 from aind_data_schema.core.instrument import Instrument
 from aind_data_schema.core.rig import Rig
+from aind_slims_api import SlimsClient
+from aind_slims_api.exceptions import SlimsRecordNotFound
+from aind_slims_api.models.instrument import SlimsInstrumentRdrc
+from aind_slims_api.operations.ecephys_session import fetch_ecephys_sessions
 from pydantic import Extra, Field, SecretStr
 from pydantic_settings import BaseSettings
 from requests.models import Response
 from slims.criteria import equals
 
 from aind_metadata_service.client import StatusCodes
 from aind_metadata_service.response_handler import ModelResponse
-from aind_slims_api.exceptions import SlimsRecordNotFound
-from aind_slims_api import SlimsClient
-from aind_slims_api.models.instrument import SlimsInstrumentRdrc
+from aind_metadata_service.slims.mapping import SlimsSessionMapper
 
 
 class SlimsSettings(BaseSettings):
@@ -114,3 +116,26 @@ def get_rig_model_response(self, input_id) -> ModelResponse:
         except Exception as e:
             logging.error(repr(e))
             return ModelResponse.internal_server_error_response()
+
+    def get_sessions_model_response(self, subject_id: str) -> ModelResponse:
+        """
+        Fetches sessions for a given subject ID from SLIMS.
+        """
+        try:
+            sessions = fetch_ecephys_sessions(
+                subject_id=subject_id, client=self.client
+            )
+            if sessions:
+                mapper = SlimsSessionMapper()
+                mapped_sessions = mapper.map_sessions(sessions, subject_id)
+                return ModelResponse(
+                    aind_models=mapped_sessions,
+                    status_code=StatusCodes.DB_RESPONDED,
+                )
+            else:
+                return ModelResponse.no_data_found_error_response()
+        except SlimsRecordNotFound:
+            return ModelResponse.no_data_found_error_response()
+        except Exception as e:
+            logging.error(repr(e))
+            return ModelResponse.internal_server_error_response()