Merge branch 'main' into update-python

# Conflicts:
#	poetry.lock
#	pyproject.toml

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.18
+current_version = 3.0.19
 commit = True
 tag = True
 tag_name = v{new_version}

genotype_api/__init__.py

@@ -1 +1 @@
-__version__ = "3.0.18"
+__version__ = "3.0.19"

genotype_api/api/app.py

@@ -3,29 +3,46 @@
 
 """
 
-from fastapi import FastAPI, status, Request
-from fastapi.responses import JSONResponse
+import logging
+from contextlib import asynccontextmanager
+
+from fastapi import FastAPI, Request, status
 from fastapi.middleware.cors import CORSMiddleware
+from fastapi.responses import JSONResponse
+from sqlalchemy.exc import NoResultFound, OperationalError
 
-from genotype_api.api.middleware import DBSessionMiddleware
-from genotype_api.config import security_settings, settings
-from genotype_api.database.database import create_all_tables, initialise_database
-from genotype_api.api.endpoints import samples, snps, users, plates, analyses
-from sqlalchemy.exc import NoResultFound
+from genotype_api.api.endpoints import analyses, plates, samples, snps, users
+from genotype_api.config import security_settings
 
-app = FastAPI(
-    root_path=security_settings.api_root_path,
-    root_path_in_servers=True,
-    openapi_prefix=security_settings.api_root_path,
-)
+LOG = logging.getLogger(__name__)
+
+
+@asynccontextmanager
+async def lifespan(app: FastAPI):
+    # Startup actions, like connecting to the database
+    LOG.debug("Starting up...")
+    yield  # This is important, it must yield control
+    # Shutdown actions, like closing the database connection
+    LOG.debug("Shutting down...")
+
+
+app = FastAPI(lifespan=lifespan, root_path=security_settings.api_root_path)
 app.add_middleware(
     CORSMiddleware,
     allow_origins=["*"],
     allow_credentials=True,
     allow_methods=["*"],
     allow_headers=["*"],
 )
-app.add_middleware(DBSessionMiddleware)
+
+
+@app.exception_handler(OperationalError)
+async def db_connection_exception_handler(request: Request, exc: OperationalError):
+    LOG.error(f"Database connection error: {exc}")
+    return JSONResponse(
+        content={"detail": "Database connection error. Please try again later."},
+        status_code=status.HTTP_503_SERVICE_UNAVAILABLE,
+    )
 
 
 @app.exception_handler(NoResultFound)
@@ -72,9 +89,3 @@ def welcome():
     tags=["analyses"],
     responses={status.HTTP_404_NOT_FOUND: {"description": "Not found"}},
 )
-
-
-@app.on_event("startup")
-def on_startup():
-    initialise_database(settings.db_uri)
-    create_all_tables()

genotype_api/api/endpoints/analyses.py

@@ -2,19 +2,15 @@
 
 from http import HTTPStatus
 
-from fastapi import APIRouter, Depends, File, Query, UploadFile, status, HTTPException
+from fastapi import APIRouter, Depends, File, HTTPException, Query, UploadFile, status
 from fastapi.responses import JSONResponse
 
 from genotype_api.database.store import Store, get_store
 from genotype_api.dto.analysis import AnalysisResponse
 from genotype_api.dto.user import CurrentUser
-
 from genotype_api.exceptions import AnalysisNotFoundError
 from genotype_api.security import get_active_user
-from genotype_api.services.endpoint_services.analysis_service import (
-    AnalysisService,
-)
-
+from genotype_api.services.endpoint_services.analysis_service import AnalysisService
 
 router = APIRouter()
 
@@ -24,14 +20,14 @@ def get_analysis_service(store: Store = Depends(get_store)) -> AnalysisService:
 
 
 @router.get("/{analysis_id}", response_model=AnalysisResponse)
-def read_analysis(
+async def read_analysis(
     analysis_id: int,
     analysis_service: AnalysisService = Depends(get_analysis_service),
     current_user: CurrentUser = Depends(get_active_user),
 ):
     """Return analysis."""
     try:
-        return analysis_service.get_analysis(analysis_id)
+        return await analysis_service.get_analysis(analysis_id)
     except AnalysisNotFoundError:
         raise HTTPException(
             detail=f"Could not find analysis with id: {analysis_id}",
@@ -40,15 +36,15 @@ def read_analysis(
 
 
 @router.get("/", response_model=list[AnalysisResponse], response_model_exclude={"genotypes"})
-def read_analyses(
+async def read_analyses(
     skip: int = 0,
     limit: int = Query(default=100, lte=100),
     analysis_service: AnalysisService = Depends(get_analysis_service),
     current_user: CurrentUser = Depends(get_active_user),
 ):
     """Return all analyses."""
     try:
-        return analysis_service.get_analyses(skip=skip, limit=limit)
+        return await analysis_service.get_analyses(skip=skip, limit=limit)
     except AnalysisNotFoundError:
         raise HTTPException(
             detail="Could not fetch analyses from backend.",
@@ -57,14 +53,14 @@ def read_analyses(
 
 
 @router.delete("/{analysis_id}")
-def delete_analysis(
+async def delete_analysis(
     analysis_id: int,
     analysis_service: AnalysisService = Depends(get_analysis_service),
     current_user: CurrentUser = Depends(get_active_user),
 ):
     """Delete analysis based on analysis id."""
     try:
-        analysis_service.delete_analysis(analysis_id)
+        await analysis_service.delete_analysis(analysis_id)
     except AnalysisNotFoundError:
         raise HTTPException(
             detail=f"Could not find analysis with id: {analysis_id}",
@@ -76,12 +72,12 @@ def delete_analysis(
 @router.post(
     "/sequence", response_model=list[AnalysisResponse], response_model_exclude={"genotypes"}
 )
-def upload_sequence_analysis(
+async def upload_sequence_analysis(
     file: UploadFile = File(...),
     analysis_service: AnalysisService = Depends(get_analysis_service),
     current_user: CurrentUser = Depends(get_active_user),
 ):
     """Reading VCF file, creating and uploading sequence analyses and sample objects to the database."""
 
-    analyses: list[AnalysisResponse] = analysis_service.get_upload_sequence_analyses(file)
+    analyses: list[AnalysisResponse] = await analysis_service.get_upload_sequence_analyses(file)
     return analyses

genotype_api/api/endpoints/plates.py

@@ -2,19 +2,18 @@
 
 from http import HTTPStatus
 from typing import Literal
-from fastapi import APIRouter, Depends, File, Query, UploadFile, status, HTTPException
-from fastapi.responses import JSONResponse
-from genotype_api.database.filter_models.plate_models import PlateOrderParams
 
+from fastapi import APIRouter, Depends, File, HTTPException, Query, UploadFile, status
+from fastapi.responses import JSONResponse
 
+from genotype_api.database.filter_models.plate_models import PlateOrderParams
 from genotype_api.database.store import Store, get_store
 from genotype_api.dto.plate import PlateResponse
 from genotype_api.dto.user import CurrentUser
-from genotype_api.exceptions import PlateNotFoundError, PlateExistsError
+from genotype_api.exceptions import PlateExistsError, PlateNotFoundError
 from genotype_api.security import get_active_user
 from genotype_api.services.endpoint_services.plate_service import PlateService
 
-
 router = APIRouter()
 
 
@@ -25,14 +24,14 @@ def get_plate_service(store: Store = Depends(get_store)) -> PlateService:
 @router.post(
     "/plate",
 )
-def upload_plate(
+async def upload_plate(
     file: UploadFile = File(...),
     plate_service: PlateService = Depends(get_plate_service),
     current_user: CurrentUser = Depends(get_active_user),
 ):
 
     try:
-        plate_service.upload_plate(file)
+        await plate_service.upload_plate(file)
     except PlateExistsError:
         raise HTTPException(
             detail="Plate already exists in the database.", status_code=HTTPStatus.BAD_REQUEST
@@ -45,7 +44,7 @@ def upload_plate(
     response_model=PlateResponse,
     response_model_exclude={"analyses", "user", "plate_status_counts"},
 )
-def sign_off_plate(
+async def sign_off_plate(
     plate_id: int,
     method_document: str = Query(...),
     method_version: str = Query(...),
@@ -57,7 +56,7 @@ def sign_off_plate(
     Add Depends with current user
     """
 
-    return plate_service.update_plate_sign_off(
+    return await plate_service.update_plate_sign_off(
         plate_id=plate_id,
         user_email=current_user.email,
         method_version=method_version,
@@ -87,14 +86,14 @@ def sign_off_plate(
         }
     },
 )
-def read_plate(
+async def read_plate(
     plate_id: int,
     plate_service: PlateService = Depends(get_plate_service),
     current_user: CurrentUser = Depends(get_active_user),
 ):
     """Display information about a plate."""
     try:
-        return plate_service.get_plate(plate_id=plate_id)
+        return await plate_service.get_plate(plate_id=plate_id)
     except PlateNotFoundError:
         raise HTTPException(
             detail=f"Could not find plate with id: {plate_id}", status_code=HTTPStatus.BAD_REQUEST
@@ -120,22 +119,22 @@ async def read_plates(
         order_by=order_by, skip=skip, limit=limit, sort_order=sort_order
     )
     try:
-        return plate_service.get_plates(order_params=order_params)
+        return await plate_service.get_plates(order_params=order_params)
     except PlateNotFoundError:
         raise HTTPException(
             detail="Could not fetch plates from backend.", status_code=HTTPStatus.BAD_REQUEST
         )
 
 
 @router.delete("/{plate_id}")
-def delete_plate(
+async def delete_plate(
     plate_id: int,
     plate_service: PlateService = Depends(get_plate_service),
     current_user: CurrentUser = Depends(get_active_user),
 ):
     """Delete plate."""
     try:
-        analysis_ids = plate_service.delete_plate(plate_id)
+        analysis_ids = await plate_service.delete_plate(plate_id)
         return JSONResponse(
             f"Deleted plate: {plate_id} and analyses: {analysis_ids}",
             status_code=status.HTTP_200_OK,