refactor

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.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

@@ -9,9 +9,9 @@
 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.database import get_session
+from genotype_api.database.session_handler import get_session
 from genotype_api.file_parsing.files import check_file
-from genotype_api.database.models.models import (
+from genotype_api.database.models import (
     Analysis,
     AnalysisRead,
     User,

genotype_api/api/endpoints/plates.py

@@ -17,10 +17,10 @@
 )
 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.database import get_session
+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.database.models.models import (
+from genotype_api.database.models import (
     Analysis,
     User,
     Plate,

genotype_api/api/endpoints/samples.py

@@ -6,14 +6,14 @@
 
 import genotype_api.database.crud.create
 from genotype_api.constants import SEXES
-from genotype_api.database.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 (
     SampleDetail,
     MatchResult,
     MatchCounts,
 )
-from genotype_api.database.models.models import (
+from genotype_api.database.models import (
     Analysis,
     Sample,
     SampleRead,

genotype_api/api/endpoints/snps.py

@@ -1,10 +1,10 @@
 """Routes for the snps"""
 
-from genotype_api.database.models.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.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

@@ -8,8 +8,8 @@
 from starlette.responses import JSONResponse
 
 from genotype_api.database.crud.read import get_user
-from genotype_api.database.database import get_session
-from genotype_api.database.models.models import User, UserRead, UserCreate, UserReadWithPlates
+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

genotype_api/database/crud/create.py

@@ -4,7 +4,7 @@
 from fastapi import HTTPException
 from sqlmodel import Session
 
-from genotype_api.database.models.models import (
+from genotype_api.database.models import (
     Analysis,
     Sample,
     User,

genotype_api/database/crud/delete.py

@@ -3,7 +3,7 @@
 
 from sqlmodel import Session
 
-from genotype_api.database.models.models import Analysis, Plate
+from genotype_api.database.models import Analysis, Plate
 from sqlmodel.sql.expression import Select, SelectOfScalar
 
 SelectOfScalar.inherit_cache = True

genotype_api/database/crud/read.py

@@ -5,7 +5,7 @@
 from sqlmodel import Session, select
 
 from genotype_api.constants import TYPES
-from genotype_api.database.models.models import Analysis, Sample, User, Plate
+from genotype_api.database.models import Analysis, Sample, User, Plate
 from sqlmodel.sql.expression import Select, SelectOfScalar
 
 SelectOfScalar.inherit_cache = True

genotype_api/database/crud/update.py

@@ -1,7 +1,7 @@
 from sqlmodel import Session
 
 from genotype_api.match import check_sample
-from genotype_api.database.models.models import Sample
+from genotype_api.database.models import Sample
 from sqlmodel.sql.expression import Select, SelectOfScalar
 
 SelectOfScalar.inherit_cache = True

genotype_api/file_parsing/excel.py

@@ -6,7 +6,7 @@
 
 import openpyxl
 from genotype_api.exceptions import SexConflictError
-from genotype_api.database.models.models import Genotype, Analysis
+from genotype_api.database.models import Genotype, Analysis
 
 from openpyxl.workbook import Workbook
 from openpyxl.worksheet.worksheet import Worksheet

genotype_api/file_parsing/vcf.py

@@ -2,7 +2,7 @@
 
 from typing import Dict, Iterable, List, TextIO
 
-from genotype_api.database.models.models import Genotype as DBGenotype, Analysis
+from genotype_api.database.models import Genotype as DBGenotype, Analysis
 from pydantic import BaseModel
 
 

genotype_api/match.py

@@ -4,7 +4,7 @@
 from genotype_api.models import (
     SampleDetail,
 )
-from genotype_api.database.models.models import Sample, check_snps, check_sex
+from genotype_api.database.models import Sample, check_snps, check_sex
 
 log = logging.getLogger(__name__)
 

genotype_api/security.py

@@ -7,8 +7,8 @@
 
 from starlette.requests import Request
 
-from genotype_api.database.database import get_session
-from genotype_api.database.models.models import User
+from genotype_api.database.session_handler import get_session
+from genotype_api.database.models import User
 from genotype_api.config import security_settings
 from genotype_api.database.crud.read import get_user_by_email
 from jose import jwt