diff --git a/database.db b/database.db new file mode 100644 index 0000000..e064415 Binary files /dev/null and b/database.db differ diff --git a/genotype_api/api/app.py b/genotype_api/api/app.py index 96b4b91..e83b4f8 100644 --- a/genotype_api/api/app.py +++ b/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 diff --git a/genotype_api/api/endpoints/analyses.py b/genotype_api/api/endpoints/analyses.py index aeb3197..c5a754f 100644 --- a/genotype_api/api/endpoints/analyses.py +++ b/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, diff --git a/genotype_api/api/endpoints/plates.py b/genotype_api/api/endpoints/plates.py index 039b1d3..016c63c 100644 --- a/genotype_api/api/endpoints/plates.py +++ b/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, diff --git a/genotype_api/api/endpoints/samples.py b/genotype_api/api/endpoints/samples.py index a42ba6d..89c71e7 100644 --- a/genotype_api/api/endpoints/samples.py +++ b/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, diff --git a/genotype_api/api/endpoints/snps.py b/genotype_api/api/endpoints/snps.py index c9086b5..157399d 100644 --- a/genotype_api/api/endpoints/snps.py +++ b/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 diff --git a/genotype_api/api/endpoints/users.py b/genotype_api/api/endpoints/users.py index e85a371..75180e6 100644 --- a/genotype_api/api/endpoints/users.py +++ b/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 diff --git a/genotype_api/database/crud/create.py b/genotype_api/database/crud/create.py index a1c9031..e66527d 100644 --- a/genotype_api/database/crud/create.py +++ b/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, diff --git a/genotype_api/database/crud/delete.py b/genotype_api/database/crud/delete.py index 3bfb3bf..924722d 100644 --- a/genotype_api/database/crud/delete.py +++ b/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 diff --git a/genotype_api/database/crud/read.py b/genotype_api/database/crud/read.py index 74e3e76..5615957 100644 --- a/genotype_api/database/crud/read.py +++ b/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 diff --git a/genotype_api/database/crud/update.py b/genotype_api/database/crud/update.py index e6b1250..845ca7c 100644 --- a/genotype_api/database/crud/update.py +++ b/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 diff --git a/genotype_api/database/models/models.py b/genotype_api/database/models.py similarity index 100% rename from genotype_api/database/models/models.py rename to genotype_api/database/models.py diff --git a/genotype_api/database/models/__init__.py b/genotype_api/database/models/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/genotype_api/database/database.py b/genotype_api/database/session_handler.py similarity index 100% rename from genotype_api/database/database.py rename to genotype_api/database/session_handler.py diff --git a/genotype_api/file_parsing/excel.py b/genotype_api/file_parsing/excel.py index ef3243b..a88b682 100644 --- a/genotype_api/file_parsing/excel.py +++ b/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 diff --git a/genotype_api/file_parsing/vcf.py b/genotype_api/file_parsing/vcf.py index 4e4d394..9d08d90 100644 --- a/genotype_api/file_parsing/vcf.py +++ b/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 diff --git a/genotype_api/match.py b/genotype_api/match.py index ab6439a..203e94d 100644 --- a/genotype_api/match.py +++ b/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__) diff --git a/genotype_api/security.py b/genotype_api/security.py index fa6f53e..5bb59c7 100644 --- a/genotype_api/security.py +++ b/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