refactore(add store) (#125)(major)

# Description

Rewrites of the sql backend to phase out sqlmodel and update to pydantic2

genotype_api/api/app.py

@@ -7,8 +7,8 @@
 from fastapi.responses import JSONResponse
 from fastapi.middleware.cors import CORSMiddleware
 
-from genotype_api.config import security_settings
-from genotype_api.database.session_handler import create_db_and_tables
+from genotype_api.config import security_settings, settings
+from genotype_api.database.database import create_all_tables, initialise_database, close_session
 from genotype_api.api.endpoints import samples, snps, users, plates, analyses
 from sqlalchemy.exc import NoResultFound
 
@@ -74,4 +74,10 @@ def welcome():
 
 @app.on_event("startup")
 def on_startup():
-    create_db_and_tables()
+    initialise_database(settings.db_uri)
+    create_all_tables()
+
+
+@app.on_event("shutdown")
+async def on_shutdown():
+    close_session()

genotype_api/api/endpoints/analyses.py

@@ -4,29 +4,30 @@
 
 from fastapi import APIRouter, Depends, File, Query, UploadFile, status, HTTPException
 from fastapi.responses import JSONResponse
-from sqlmodel import Session
 
-
-from genotype_api.database.models import User
+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.database.session_handler import get_session
 from genotype_api.exceptions import AnalysisNotFoundError
 from genotype_api.security import get_active_user
-from genotype_api.services.analysis_service.analysis_service import AnalysisService
+from genotype_api.services.endpoint_services.analysis_service import (
+    AnalysisService,
+)
+
 
 router = APIRouter()
 
 
-def get_analysis_service(session: Session = Depends(get_session)):
-    return AnalysisService(session)
+def get_analysis_service(store: Store = Depends(get_store)) -> AnalysisService:
+    return AnalysisService(store)
 
 
 @router.get("/{analysis_id}", response_model=AnalysisResponse)
 def read_analysis(
     analysis_id: int,
     analysis_service: AnalysisService = Depends(get_analysis_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Return analysis."""
     try:
@@ -43,7 +44,7 @@ def read_analyses(
     skip: int = 0,
     limit: int = Query(default=100, lte=100),
     analysis_service: AnalysisService = Depends(get_analysis_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Return all analyses."""
     try:
@@ -59,7 +60,7 @@ def read_analyses(
 def delete_analysis(
     analysis_id: int,
     analysis_service: AnalysisService = Depends(get_analysis_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Delete analysis based on analysis id."""
     try:
@@ -78,7 +79,7 @@ def delete_analysis(
 def upload_sequence_analysis(
     file: UploadFile = File(...),
     analysis_service: AnalysisService = Depends(get_analysis_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Reading VCF file, creating and uploading sequence analyses and sample objects to the database."""
 

genotype_api/api/endpoints/plates.py

@@ -4,21 +4,22 @@
 from typing import Literal
 from fastapi import APIRouter, Depends, File, Query, UploadFile, status, HTTPException
 from fastapi.responses import JSONResponse
-from sqlmodel import Session
 from genotype_api.database.filter_models.plate_models import PlateOrderParams
-from genotype_api.database.models import User
-from genotype_api.database.session_handler import get_session
+
+
+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
 from genotype_api.security import get_active_user
-from genotype_api.services.plate_service.plate_service import PlateService
+from genotype_api.services.endpoint_services.plate_service import PlateService
 
 
 router = APIRouter()
 
 
-def get_plate_service(session: Session = Depends(get_session)) -> PlateService:
-    return PlateService(session)
+def get_plate_service(store: Store = Depends(get_store)) -> PlateService:
+    return PlateService(store)
 
 
 @router.post(
@@ -29,7 +30,7 @@ def get_plate_service(session: Session = Depends(get_session)) -> PlateService:
 def upload_plate(
     file: UploadFile = File(...),
     plate_service: PlateService = Depends(get_plate_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     return plate_service.upload_plate(file)
 
@@ -44,10 +45,10 @@ def sign_off_plate(
     method_document: str = Query(...),
     method_version: str = Query(...),
     plate_service: PlateService = Depends(get_plate_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Sign off a plate.
-    This means that current User sign off that the plate is checked
+    This means that current CurrentUser sign off that the plate is checked
     Add Depends with current user
     """
 
@@ -84,7 +85,7 @@ def sign_off_plate(
 def read_plate(
     plate_id: int,
     plate_service: PlateService = Depends(get_plate_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Display information about a plate."""
     try:
@@ -107,7 +108,7 @@ async def read_plates(
     skip: int | None = 0,
     limit: int | None = 10,
     plate_service: PlateService = Depends(get_plate_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Display all plates"""
     order_params = PlateOrderParams(
@@ -125,7 +126,7 @@ async def read_plates(
 def delete_plate(
     plate_id: int,
     plate_service: PlateService = Depends(get_plate_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Delete plate."""
     try:

genotype_api/api/endpoints/samples.py

@@ -4,27 +4,24 @@
 
 from fastapi import APIRouter, Depends, Query
 from fastapi.responses import JSONResponse
-from sqlmodel import Session
 from starlette import status
 
 from genotype_api.constants import Sexes, Types
 from genotype_api.database.filter_models.sample_models import SampleFilterParams
-from genotype_api.database.models import (
-    Sample,
-    User,
-)
-from genotype_api.database.session_handler import get_session
-from genotype_api.dto.sample import SampleResponse
+
+from genotype_api.database.store import Store, get_store
+from genotype_api.dto.sample import SampleResponse, SampleCreate
+from genotype_api.dto.user import CurrentUser
 from genotype_api.exceptions import SampleNotFoundError, SampleExistsError
 from genotype_api.models import MatchResult, SampleDetail
 from genotype_api.security import get_active_user
-from genotype_api.services.sample_service.sample_service import SampleService
+from genotype_api.services.endpoint_services.sample_service import SampleService
 
 router = APIRouter()
 
 
-def get_sample_service(session: Session = Depends(get_session)) -> SampleService:
-    return SampleService(session)
+def get_sample_service(store: Store = Depends(get_store)) -> SampleService:
+    return SampleService(store)
 
 
 @router.get(
@@ -34,7 +31,7 @@ def get_sample_service(session: Session = Depends(get_session)) -> SampleService
 def read_sample(
     sample_id: str,
     sample_service: SampleService = Depends(get_sample_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     try:
         return sample_service.get_sample(sample_id)
@@ -48,12 +45,12 @@ def read_sample(
     "/",
 )
 def create_sample(
-    sample: Sample,
+    sample: SampleCreate,
     sample_service: SampleService = Depends(get_sample_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     try:
-        sample_service.create_sample(sample=sample)
+        sample_service.create_sample(sample_create=sample)
         new_sample: SampleResponse = sample_service.get_sample(sample_id=sample.id)
         if not new_sample:
             return JSONResponse(
@@ -90,7 +87,7 @@ def read_samples(
     commented: bool | None = False,
     status_missing: bool | None = False,
     sample_service: SampleService = Depends(get_sample_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Returns a list of samples matching the provided filters."""
     filter_params = SampleFilterParams(
@@ -113,7 +110,7 @@ def update_sex(
     genotype_sex: Sexes | None = None,
     sequence_sex: Sexes | None = None,
     sample_service: SampleService = Depends(get_sample_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Updating sex field on sample and sample analyses."""
     try:
@@ -135,7 +132,7 @@ def update_comment(
     sample_id: str,
     comment: str = Query(...),
     sample_service: SampleService = Depends(get_sample_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Updating comment field on sample."""
     try:
@@ -155,7 +152,7 @@ def set_sample_status(
     sample_id: str,
     sample_service: SampleService = Depends(get_sample_service),
     status: Literal["pass", "fail", "cancel"] | None = None,
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Check sample analyses and update sample status accordingly."""
     try:
@@ -175,7 +172,7 @@ def match(
     date_min: date | None = date.min,
     date_max: date | None = date.max,
     sample_service: SampleService = Depends(get_sample_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ) -> list[MatchResult]:
     """Match sample genotype against all other genotypes."""
     return sample_service.get_match_results(
@@ -196,7 +193,7 @@ def match(
 def get_status_detail(
     sample_id: str,
     sample_service: SampleService = Depends(get_sample_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     try:
         return sample_service.get_status_detail(sample_id)
@@ -210,7 +207,7 @@ def get_status_detail(
 def delete_sample(
     sample_id: str,
     sample_service: SampleService = Depends(get_sample_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Delete sample and its Analyses."""
     sample_service.delete_sample(sample_id)

genotype_api/api/endpoints/snps.py

@@ -1,46 +1,40 @@
 """Routes for the snps"""
 
-from fastapi import APIRouter, Depends, HTTPException, Query, UploadFile
-from sqlmodel import Session
-from sqlmodel.sql.expression import Select, SelectOfScalar
-from starlette.responses import JSONResponse
+from fastapi import APIRouter, Depends, Query, UploadFile
+
 
-from genotype_api.database.crud.create import create_snps
-from genotype_api.database.crud.read import get_snps, get_snps_by_limit_and_skip
-from genotype_api.database.models import SNP, User
-from genotype_api.database.crud import delete
-from genotype_api.database.session_handler import get_session
+from starlette.responses import JSONResponse
+from genotype_api.database.store import Store, get_store
 from genotype_api.dto.snp import SNPResponse
+from genotype_api.dto.user import CurrentUser
 from genotype_api.exceptions import SNPExistsError
 from genotype_api.security import get_active_user
-from genotype_api.services.snp_reader_service.snp_reader import SNPReaderService
-from genotype_api.services.snp_service.snp_service import SNPService
 
-SelectOfScalar.inherit_cache = True
-Select.inherit_cache = True
+from genotype_api.services.endpoint_services.snp_service import SNPService
+
 
 router = APIRouter()
 
 
-def get_snp_service(session: Session = Depends(get_session)) -> SNPService:
-    return SNPService(session)
+def get_snp_service(store: Store = Depends(get_store)) -> SNPService:
+    return SNPService(store)
 
 
 @router.get("/", response_model=list[SNPResponse])
 def read_snps(
     skip: int = 0,
     limit: int = Query(default=100, lte=100),
     snp_service: SNPService = Depends(get_snp_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     return snp_service.get_snps(skip=skip, limit=limit)
 
 
-@router.post("/", response_model=list[SNP])
+@router.post("/", response_model=list[SNPResponse])
 async def upload_snps(
     snps_file: UploadFile,
     snp_service: SNPService = Depends(get_snp_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     try:
         return snp_service.upload_snps(snps_file)
@@ -51,7 +45,7 @@ async def upload_snps(
 @router.delete("/")
 def delete_snps(
     snp_service: SNPService = Depends(get_snp_service),
-    current_user: User = Depends(get_active_user),
+    current_user: CurrentUser = Depends(get_active_user),
 ):
     """Delete all SNPs"""