Merge pull request #331 from AllenNeuralDynamics/release-v0.19.0

Release v0.19.0

.github/workflows/add_issue_to_project_board.yml

@@ -0,0 +1,15 @@
+name: Auto add issues to project board
+on:
+  issues:
+    types:
+      - opened
+
+jobs:
+  add-to-project:
+    name: Add issue to project
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+        with:
+          project-url: https://github.com/orgs/AllenNeuralDynamics/projects/9
+          github-token: ${{ secrets.SERVICE_TOKEN }}

.github/workflows/publish_dev.yml

@@ -8,7 +8,7 @@ jobs:
   publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Compute new docker image tag
         run: |
           echo "sha_short=$(git rev-parse --short "$GITHUB_SHA")" >> "$GITHUB_ENV"

.github/workflows/publish_main.yml

@@ -11,7 +11,7 @@ jobs:
     outputs:
       pkg_version: ${{ steps.output_version.outputs.pkg_version }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Get version from file
       run: |
         pkg_name=$(grep -P 'version = \{attr = .*\}' pyproject.toml | grep -oP '\w+.__version__')
@@ -42,7 +42,7 @@ jobs:
           ghcr.io/allenneuraldynamics/aind-metadata-service:${{ env.docker_tag }}
           ghcr.io/allenneuraldynamics/aind-metadata-service:latest
     - name: Set up Python 3.10
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.10'
     - name: Install dependencies

.github/workflows/run_dev_tests.yml

@@ -12,9 +12,9 @@ jobs:
       matrix:
         python-version: [ '3.10', '3.11' ]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

.github/workflows/run_main_tests.yml

@@ -13,9 +13,9 @@ jobs:
       matrix:
         python-version: [ '3.10', '3.11' ]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -28,7 +28,7 @@ jobs:
   verify_version:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Check version incremented
         run: |
           pkg_name=$(grep -P 'version = \{attr = .*\}' pyproject.toml | grep -oP '\w+.__version__')

pyproject.toml

@@ -43,7 +43,7 @@ server = [
     'fastapi==0.115.0',
     'uvicorn[standard]==0.31.0',
     'python-dateutil',
-    'aind-slims-api==0.1.17',
+    'aind-slims-api==0.1.19',
     'azure-identity==1.15.0'
 ]
 

src/aind_metadata_service/__init__.py

@@ -1,3 +1,3 @@
 """REST service to retrieve metadata from databases."""
 
-__version__ = "0.18.1"
+__version__ = "0.19.0"

src/aind_metadata_service/server.py

@@ -281,8 +281,14 @@ async def retrieve_procedures(subject_id):
         subject_id=subject_id,
         list_title=sharepoint_settings.las_2020_list,
     )
+    # merge subject procedures
     merged_response = sharepoint_client.merge_responses(
-        [lb_response, sp2019_response, sp2023_response, las2020_response]
+        [
+            lb_response,
+            sp2019_response,
+            sp2023_response,
+            las2020_response,
+        ]
     )
     # integrate TARS response
     mapper = TarsResponseHandler()
@@ -316,7 +322,15 @@ async def retrieve_procedures(subject_id):
     integrated_response = protocols_integrator.integrate_protocols(
         response=integrated_response, protocols_mapping=protocols_mapping
     )
-    return integrated_response.map_to_json_response()
+    # merge specimen procedures
+    slims_response = await run_in_threadpool(
+        slims_client.get_specimen_procedures_model_response,
+        specimen_id=subject_id,
+    )
+    merged_response = sharepoint_client.merge_responses(
+        [integrated_response, slims_response]
+    )
+    return merged_response.map_to_json_response()
 
 
 @app.get(

src/aind_metadata_service/sharepoint/client.py

@@ -212,10 +212,15 @@ def _merge_procedures(
                 left_procedures[0].subject_procedures
                 + right_procedures[0].subject_procedures
             )
+            new_specimen_procedures = (
+                left_procedures[0].specimen_procedures
+                + right_procedures[0].specimen_procedures
+            )
             return [
                 Procedures.model_construct(
                     subject_id=subject_id,
                     subject_procedures=new_subject_procedures,
+                    specimen_procedures=new_specimen_procedures,
                 )
             ]
 

src/aind_metadata_service/slims/client.py

@@ -3,19 +3,24 @@
 import logging
 
 from aind_data_schema.core.instrument import Instrument
+from aind_data_schema.core.procedures import Procedures
 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 aind_slims_api.operations import (
+    fetch_ecephys_sessions,
+    fetch_histology_procedures,
+)
 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_metadata_service.slims.mapping import SlimsSessionMapper
+from aind_metadata_service.slims.procedures.mapping import SlimsHistologyMapper
+from aind_metadata_service.slims.sessions.mapping import SlimsSessionMapper
 
 
 class SlimsSettings(BaseSettings):
@@ -139,3 +144,32 @@ def get_sessions_model_response(self, subject_id: str) -> ModelResponse:
         except Exception as e:
             logging.error(repr(e))
             return ModelResponse.internal_server_error_response()
+
+    def get_specimen_procedures_model_response(
+        self, specimen_id: str
+    ) -> ModelResponse:
+        """
+        Fetches specimen procedures for a given specimen ID from SLIMS.
+        """
+        try:
+            procs = fetch_histology_procedures(
+                specimen_id=specimen_id, client=self.client
+            )
+            if procs:
+                mapper = SlimsHistologyMapper()
+                mapped_procedures = mapper.map_specimen_procedures(
+                    procs, specimen_id
+                )
+                procedures = Procedures.model_construct(subject_id=specimen_id)
+                procedures.specimen_procedures = mapped_procedures
+                return ModelResponse(
+                    aind_models=[procedures],
+                    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()

src/aind_metadata_service/slims/procedures/__init__.py

@@ -0,0 +1 @@
+"""Package to handle retrieving procedures information from SLIMS"""