refactor user and snp endpoints (#108) (patch)

Refactor user and SNP endpoints

genotype_api/api/endpoints/samples.py

@@ -31,7 +31,7 @@
 from genotype_api.database.session_handler import get_session
 from genotype_api.models import MatchResult, SampleDetail
 from genotype_api.security import get_active_user
-from genotype_api.service.match_genotype_service.match_genotype import MatchGenotypeService
+from genotype_api.services.match_genotype_service.match_genotype import MatchGenotypeService
 
 SelectOfScalar.inherit_cache = True
 Select.inherit_cache = True

genotype_api/api/endpoints/snps.py

@@ -1,12 +1,16 @@
 """Routes for the snps"""
 
 from fastapi import APIRouter, Depends, HTTPException, Query, UploadFile
-from sqlmodel import Session, delete, select
+from sqlmodel import Session
 from sqlmodel.sql.expression import Select, SelectOfScalar
 
+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 genotype_api.security import get_active_user
+from genotype_api.services.snp_reader.snp_reader import SNPReaderService
 
 SelectOfScalar.inherit_cache = True
 Select.inherit_cache = True
@@ -21,7 +25,7 @@ def read_snps(
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ) -> list[SNP]:
-    return session.exec(select(SNP).offset(skip).limit(limit)).all()
+    return get_snps_by_limit_and_skip(session=session, skip=skip, limit=limit)
 
 
 @router.post("/", response_model=list[SNP])
@@ -30,21 +34,12 @@ async def upload_snps(
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ):
-    db_snps: list[SNP] = session.exec(select(SNP)).all()
-    if db_snps:
+    existing_snps: list[SNP] = get_snps(session)
+    if existing_snps:
         raise HTTPException(status_code=400, detail="SNPs already uploaded")
-    snps = []
-    content = await snps_file.read()
-
-    header = ["id", "ref", "chrom", "pos"]
-    for line in content.decode().split("\n"):
-        if len(line) <= 10:
-            continue
-        snp = SNP(**dict(zip(header, line.split())))
-        session.add(snp)
-        snps.append(snp)
-    session.commit()
-    return snps
+    snps: list[SNP] = SNPReaderService.read_snps_from_file(snps_file)
+    new_snps: list[snps] = create_snps(session=session, snps=snps)
+    return new_snps
 
 
 @router.delete("/")
@@ -54,6 +49,5 @@ def delete_snps(
 ):
     """Delete all SNPs"""
 
-    result = session.exec(delete(SNP))
-    session.commit()
+    result = delete.delete_snps(session)
     return {"message": f"all snps deleted ({result.rowcount} snps)"}

genotype_api/api/endpoints/users.py

@@ -7,7 +7,13 @@
 from starlette import status
 from starlette.responses import JSONResponse
 
-from genotype_api.database.crud.read import get_user
+from genotype_api.database.crud.read import (
+    get_user,
+    get_user_by_email,
+    get_users_with_skip_and_limit,
+)
+from genotype_api.database.crud.update import update_user_email
+from genotype_api.database.crud import delete, create
 from genotype_api.database.models import User
 from genotype_api.dto.dto import UserRead, UserCreate, UserReadWithPlates
 from genotype_api.database.session_handler import get_session
@@ -43,8 +49,7 @@ def delete_user(
             status_code=status.HTTP_406_NOT_ACCEPTABLE,
             detail="User previously signed plates, please archive instead",
         )
-    session.delete(user)
-    session.commit()
+    delete.delete_user(session=session, user=user)
     return JSONResponse(content="User deleted successfully", status_code=status.HTTP_200_OK)
 
 
@@ -58,10 +63,7 @@ def change_user_email(
     user: User = get_user(session=session, user_id=user_id)
     if not user:
         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="User not found")
-    user.email = email
-    session.add(user)
-    session.commit()
-    session.refresh(user)
+    user: User = update_user_email(session=session, user=user, email=email)
     return user
 
 
@@ -72,8 +74,7 @@ def read_users(
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ) -> list[User]:
-    users: list[User] = session.exec(select(User).offset(skip).limit(limit)).all()
-    return users
+    return get_users_with_skip_and_limit(session=session, skip=skip, limit=limit)
 
 
 @router.post("/", response_model=User)
@@ -82,11 +83,8 @@ def create_user(
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ):
-    user_in_db: list[User] = session.exec(select(User).where(User.email == user.email)).all()
-    if user_in_db:
+    existing_user: User = get_user_by_email(session=session, email=user.email)
+    if existing_user:
         raise HTTPException(status_code=409, detail="Email already registered")
-    db_user = User.from_orm(user)
-    session.add(db_user)
-    session.commit()
-    session.refresh(db_user)
-    return db_user
+    new_user: User = create.create_user(session=session, user=user)
+    return new_user

genotype_api/database/crud/create.py

@@ -4,7 +4,7 @@
 from sqlmodel import Session
 from sqlmodel.sql.expression import Select, SelectOfScalar
 
-from genotype_api.database.models import Analysis, Plate, Sample, User
+from genotype_api.database.models import Analysis, Plate, Sample, User, SNP
 from genotype_api.dto.dto import UserCreate, PlateCreate
 
 SelectOfScalar.inherit_cache = True
@@ -51,10 +51,15 @@ def create_analyses_sample_objects(session: Session, analyses: list[Analysis]) -
     ]
 
 
-def create_user(db: Session, user: UserCreate):
-    fake_hashed_password = user.password + "notreallyhashed"
-    db_user = User(email=user.email, hashed_password=fake_hashed_password)
-    db.add(db_user)
-    db.commit()
-    db.refresh(db_user)
+def create_user(session: Session, user: UserCreate):
+    db_user = User.from_orm(user)
+    session.add(db_user)
+    session.commit()
+    session.refresh(db_user)
     return db_user
+
+
+def create_snps(session: Session, snps: list[SNP]) -> list[SNP]:
+    session.add_all(snps)
+    session.commit()
+    return snps

genotype_api/database/crud/delete.py

@@ -1,9 +1,10 @@
 import logging
 
+from sqlalchemy import delete
 from sqlmodel import Session
 from sqlmodel.sql.expression import Select, SelectOfScalar
 
-from genotype_api.database.models import Analysis, Plate, Sample
+from genotype_api.database.models import Analysis, Plate, Sample, User, SNP
 
 SelectOfScalar.inherit_cache = True
 Select.inherit_cache = True
@@ -24,3 +25,14 @@ def delete_plate(session: Session, plate: Plate) -> None:
 def delete_sample(session: Session, sample: Sample) -> None:
     session.delete(sample)
     session.commit()
+
+
+def delete_user(session: Session, user: User) -> None:
+    session.delete(user)
+    session.commit()
+
+
+def delete_snps(session) -> any:
+    result = session.exec(delete(SNP))
+    session.commit()
+    return result

genotype_api/database/crud/read.py

@@ -15,6 +15,7 @@
     Plate,
     Sample,
     User,
+    SNP,
 )
 from genotype_api.dto.dto import PlateReadWithAnalysisDetailSingle
 
@@ -173,6 +174,10 @@ def get_users(session: Session, skip: int = 0, limit: int = 100) -> list[User]:
     return session.exec(statement).all()
 
 
+def get_users_with_skip_and_limit(session: Session, skip: int, limit: int) -> list[User]:
+    return session.exec(select(User).offset(skip).limit(limit)).all()
+
+
 def check_analyses_objects(
     session: Session, analyses: list[Analysis], analysis_type: TYPES
 ) -> None:
@@ -185,3 +190,11 @@ def check_analyses_objects(
         )
         if db_analysis:
             session.delete(db_analysis)
+
+
+def get_snps(session) -> list[SNP]:
+    return session.exec(select(SNP)).all()
+
+
+def get_snps_by_limit_and_skip(session: Session, skip: int, limit: int) -> list[SNP]:
+    return session.exec(select(SNP).offset(skip).limit(limit)).all()

genotype_api/database/crud/update.py

@@ -1,15 +1,16 @@
 import types
 
+from pydantic import EmailStr
 from sqlmodel import Session
 
 from genotype_api.constants import TYPES
 from genotype_api.database.crud.read import get_sample
 from genotype_api.database.filter_models.plate_models import PlateSignOff
 from genotype_api.database.filter_models.sample_models import SampleSexesUpdate
-from genotype_api.database.models import Sample, Plate
+from genotype_api.database.models import Sample, Plate, User
 from sqlmodel.sql.expression import Select, SelectOfScalar
 
-from genotype_api.service.match_genotype_service.match_genotype import MatchGenotypeService
+from genotype_api.services.match_genotype_service.match_genotype import MatchGenotypeService
 
 SelectOfScalar.inherit_cache = True
 Select.inherit_cache = True
@@ -74,3 +75,11 @@ def update_sample_sex(session: Session, sexes_update: SampleSexesUpdate) -> Samp
     session.refresh(sample)
     sample: Sample = refresh_sample_status(session=session, sample=sample)
     return sample
+
+
+def update_user_email(session: Session, user: User, email: EmailStr) -> User:
+    user.email = email
+    session.add(user)
+    session.commit()
+    session.refresh(user)
+    return user

genotype_api/dto/dto.py

@@ -5,7 +5,7 @@
 import genotype_api.database.models
 from genotype_api.database import models
 from genotype_api.models import SampleDetail, PlateStatusCounts
-from genotype_api.service.match_genotype_service.utils import check_snps, check_sex
+from genotype_api.services.match_genotype_service.utils import check_snps, check_sex
 
 
 class GenotypeRead(models.GenotypeBase):

genotype_api/service/match_genotype_service/match_genotype.py → genotype_api/services/match_genotype_service/match_genotype.py

@@ -1,10 +1,10 @@
-"""Module for the match genotype service."""
+"""Module for the match genotype services."""
 
 from collections import Counter
 
 from genotype_api.database.models import Analysis, Sample
 from genotype_api.models import MatchResult, MatchCounts, SampleDetail
-from genotype_api.service.match_genotype_service.utils import (
+from genotype_api.services.match_genotype_service.utils import (
     compare_genotypes,
     check_snps,
     check_sex,

genotype_api/service/match_genotype_service/utils.py → genotype_api/services/match_genotype_service/utils.py

@@ -1,4 +1,4 @@
-"""Utils functions for the match genotype service."""
+"""Utils functions for the match genotype services."""
 
 from collections import Counter
 

genotype_api/services/snp_reader/snp_reader.py

@@ -0,0 +1,21 @@
+"""This module holds the SNP reader server."""
+
+from fastapi.datastructures import UploadFile
+
+from genotype_api.database.models import SNP
+
+SNP_HEADER = ["id", "ref", "chrom", "pos"]
+
+
+class SNPReaderService:
+    @staticmethod
+    def read_snps_from_file(snps_file: UploadFile) -> list[SNP]:
+        snps: list[SNP] = []
+        content = snps_file.read()
+        header = SNP_HEADER
+        for line in content.decode().split("\n"):
+            if len(line) <= 10:
+                continue
+            snp = SNP(**dict(zip(header, line.split())))
+            snps.append(snp)
+        return snps