refactor(crud and models) (#99) (patch)

# Description

Refactor crud models

genotype_api/api/app.py

@@ -8,7 +8,7 @@
 from fastapi.middleware.cors import CORSMiddleware
 
 from genotype_api.config import security_settings
-from genotype_api.database import create_db_and_tables
+from genotype_api.database.session_handler import create_db_and_tables
 from genotype_api.api.endpoints import samples, snps, users, plates, analyses
 from sqlalchemy.exc import NoResultFound
 

genotype_api/api/endpoints/analyses.py

@@ -6,18 +6,17 @@
 from fastapi import APIRouter, Depends, status, Query, UploadFile, File
 from fastapi.responses import JSONResponse
 
-from genotype_api.crud.analyses import (
-    get_analysis,
-    check_analyses_objects,
-    create_analysis,
-)
-from genotype_api.crud.samples import (
-    create_analyses_sample_objects,
-    refresh_sample_status,
-)
-from genotype_api.database import get_session
+from genotype_api.database.crud.read import get_analysis, check_analyses_objects
+from genotype_api.database.crud.create import create_analysis, create_analyses_sample_objects
+from genotype_api.database.crud.update import refresh_sample_status
+from genotype_api.database.session_handler import get_session
 from genotype_api.file_parsing.files import check_file
-from genotype_api.models import Analysis, AnalysisRead, AnalysisReadWithGenotype, User
+from genotype_api.database.models import (
+    Analysis,
+    AnalysisRead,
+    User,
+    AnalysisReadWithGenotype,
+)
 from sqlmodel import Session, select
 
 from genotype_api.security import get_active_user

genotype_api/api/endpoints/plates.py

@@ -9,26 +9,23 @@
 from sqlalchemy import desc, asc
 from sqlmodel import Session, select
 
-from genotype_api.crud.analyses import (
+from genotype_api.database.crud.read import (
     get_analyses_from_plate,
+    get_plate,
+    get_user_by_email,
     check_analyses_objects,
 )
-from genotype_api.crud.samples import (
-    create_analyses_sample_objects,
-    refresh_sample_status,
-)
-from genotype_api.crud.plates import create_plate, get_plate
-from genotype_api.crud.users import get_user_by_email
-from genotype_api.database import get_session
+from genotype_api.database.crud.update import refresh_sample_status
+from genotype_api.database.crud.create import create_plate, create_analyses_sample_objects
+from genotype_api.database.session_handler import get_session
 from genotype_api.file_parsing.excel import GenotypeAnalysis
 from genotype_api.file_parsing.files import check_file
-from genotype_api.models import (
-    Plate,
-    PlateReadWithAnalyses,
+from genotype_api.database.models import (
     Analysis,
-    PlateCreate,
     User,
-    PlateRead,
+    Plate,
+    PlateCreate,
+    PlateReadWithAnalyses,
     PlateReadWithAnalysisDetail,
     PlateReadWithAnalysisDetailSingle,
 )

genotype_api/api/endpoints/samples.py

@@ -1,33 +1,34 @@
 from typing import List, Optional, Literal
 from fastapi import APIRouter, Depends, Query
 from fastapi.responses import JSONResponse
-from datetime import datetime, timedelta, date
+from datetime import timedelta, date
 from starlette import status
 
+import genotype_api.database.crud.create
 from genotype_api.constants import SEXES
-from genotype_api.database import get_session
+from genotype_api.database.session_handler import get_session
 from genotype_api.match import check_sample
 from genotype_api.models import (
-    Sample,
-    SampleReadWithAnalysis,
-    SampleRead,
-    User,
     SampleDetail,
-    Analysis,
     MatchResult,
     MatchCounts,
+)
+from genotype_api.database.models import (
+    Analysis,
+    Sample,
+    SampleRead,
+    User,
     SampleReadWithAnalysisDeep,
     compare_genotypes,
 )
 from collections import Counter
-from genotype_api import crud
-from genotype_api.crud.samples import (
+from genotype_api.database.crud.update import refresh_sample_status
+from genotype_api.database.crud.read import (
     get_incomplete_samples,
     get_plate_samples,
     get_commented_samples,
-    get_sample,
     get_status_missing_samples,
-    refresh_sample_status,
+    get_sample,
     get_samples,
 )
 from sqlmodel import Session, select
@@ -118,7 +119,7 @@ def create_sample(
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ):
-    return crud.samples.create_sample(session=session, sample=sample)
+    return genotype_api.database.database.crud.create.create_sample(session=session, sample=sample)
 
 
 @router.put("/{sample_id}/sex", response_model=SampleRead)

genotype_api/api/endpoints/snps.py

@@ -1,10 +1,10 @@
 """Routes for the snps"""
 
-from genotype_api.models import SNP, User
+from genotype_api.database.models import SNP, User
 from typing import List
 
-from fastapi import APIRouter, Depends, HTTPException, Query, File, UploadFile
-from genotype_api.database import get_session
+from fastapi import APIRouter, Depends, HTTPException, Query, UploadFile
+from genotype_api.database.session_handler import get_session
 from sqlmodel import Session, delete, select
 
 from genotype_api.security import get_active_user

genotype_api/api/endpoints/users.py

@@ -1,15 +1,15 @@
 """Routes for users"""
 
-from typing import List, Optional
+from typing import List
 
 from fastapi import APIRouter, Depends, HTTPException, Query
 from pydantic import EmailStr
 from starlette import status
 from starlette.responses import JSONResponse
 
-from genotype_api.crud.users import get_user
-from genotype_api.database import get_session
-from genotype_api.models import User, UserRead, UserCreate, UserReadWithPlates
+from genotype_api.database.crud.read import get_user
+from genotype_api.database.session_handler import get_session
+from genotype_api.database.models import User, UserRead, UserCreate, UserReadWithPlates
 from sqlmodel import Session, select
 
 from genotype_api.security import get_active_user