add(plate service) (#111) (patch)

# Description

add plate service

genotype_api/api/endpoints/analyses.py

@@ -9,15 +9,15 @@
     get_analysis_by_id,
 )
 from genotype_api.database.models import Analysis, User
-from genotype_api.dto.analysis import AnalysisWithGenotypeResponse, AnalysisResponse
+from genotype_api.dto.analysis import AnalysisGenotypeResponse, AnalysisResponse
 from genotype_api.database.session_handler import get_session
 from genotype_api.security import get_active_user
 from genotype_api.services.analysis_service.analysis_service import AnalysisService
 
 router = APIRouter()
 
 
-@router.get("/{analysis_id}", response_model=AnalysisWithGenotypeResponse)
+@router.get("/{analysis_id}", response_model=AnalysisGenotypeResponse)
 def read_analysis(
     analysis_id: int,
     session: Session = Depends(get_session),

genotype_api/api/endpoints/plates.py

@@ -1,117 +1,65 @@
 """Routes for plates"""
 
-from datetime import datetime
-from io import BytesIO
-from pathlib import Path
-from typing import Literal, Sequence
-
-from fastapi import APIRouter, Depends, File, HTTPException, Query, UploadFile, status
+from typing import Literal
+from fastapi import APIRouter, Depends, File, Query, UploadFile, status
 from fastapi.responses import JSONResponse
-from sqlalchemy import asc, desc
 from sqlmodel import Session
-from sqlmodel.sql.expression import Select, SelectOfScalar
-
-from genotype_api.database.crud.create import create_analyses_samples, create_plate
-from genotype_api.database.crud.delete import delete_analysis
-from genotype_api.database.crud.read import (
-    check_analyses_objects,
-    get_analyses_from_plate,
-    get_plate,
-    get_plate_read_analysis_single,
-    get_ordered_plates,
-    get_user_by_email,
-)
-from genotype_api.database.crud.update import (
-    refresh_sample_status,
-    refresh_plate,
-    update_plate_sign_off,
-)
-from genotype_api.database.filter_models.plate_models import PlateSignOff, PlateOrderParams
-from genotype_api.database.models import (
-    Analysis,
-    Plate,
-    User,
-)
-from genotype_api.dto.dto import (
-    PlateCreate,
-    PlateReadWithAnalyses,
-    PlateReadWithAnalysisDetail,
-    PlateReadWithAnalysisDetailSingle,
-)
+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.file_parsing.excel import GenotypeAnalysis
-from genotype_api.file_parsing.files import check_file
+from genotype_api.dto.plate import PlateResponse
 from genotype_api.security import get_active_user
+from genotype_api.services.plate_service.plate_service import PlateService
 
-SelectOfScalar.inherit_cache = True
-Select.inherit_cache = True
 
 router = APIRouter()
 
 
-def get_plate_id_from_file(file_name: Path) -> str:
-    # Get the plate id from the standardized name of the plate
-    return file_name.name.split("_", 1)[0]
+def get_plate_service(session: Session = Depends(get_session)) -> PlateService:
+    return PlateService(session)
 
 
-@router.post("/plate", response_model=PlateReadWithAnalyses)
+@router.post(
+    "/plate",
+    response_model=PlateResponse,
+    response_model_exclude={"detail"},
+)
 def upload_plate(
     file: UploadFile = File(...),
-    session: Session = Depends(get_session),
+    plate_service: PlateService = Depends(get_plate_service),
     current_user: User = Depends(get_active_user),
 ):
-    file_name: Path = check_file(file_path=file.filename, extension=".xlsx")
-    plate_id: str = get_plate_id_from_file(file_name)
-    db_plate = session.get(Plate, plate_id)
-    if db_plate:
-        raise HTTPException(
-            status_code=status.HTTP_409_CONFLICT,
-            detail=f"Plate with id {db_plate.id} already exists",
-        )
-
-    excel_parser = GenotypeAnalysis(
-        excel_file=BytesIO(file.file.read()),
-        file_name=str(file_name),
-        include_key="-CG-",
-    )
-    analyses: list[Analysis] = list(excel_parser.generate_analyses())
-    check_analyses_objects(session=session, analyses=analyses, analysis_type="genotype")
-    create_analyses_samples(session=session, analyses=analyses)
-    plate_obj = PlateCreate(plate_id=plate_id)
-    plate_obj.analyses = analyses
-    plate: Plate = create_plate(session=session, plate=plate_obj)
-    for analysis in plate.analyses:
-        refresh_sample_status(sample=analysis.sample, session=session)
-    refresh_plate(session=session, plate=plate)
-    return plate
-
-
-@router.patch("/{plate_id}/sign-off", response_model=Plate)
+    return plate_service.upload_plate(file)
+
+
+@router.patch(
+    "/{plate_id}/sign-off",
+    response_model=PlateResponse,
+    response_model_exclude={"analyses", "user", "detail"},
+)
 def sign_off_plate(
     plate_id: int,
     method_document: str = Query(...),
     method_version: str = Query(...),
-    session: Session = Depends(get_session),
+    plate_service: PlateService = Depends(get_plate_service),
     current_user: User = Depends(get_active_user),
 ):
     """Sign off a plate.
     This means that current User sign off that the plate is checked
     Add Depends with current user
     """
-    user: User = get_user_by_email(session=session, email=current_user.email)
-    plate: Plate = get_plate(session=session, plate_id=plate_id)
-    plate_sign_off = PlateSignOff(
-        user_id=user.id,
-        signed_at=datetime.now(),
-        method_document=method_document,
+
+    return plate_service.update_plate_sign_off(
+        plate_id=plate_id,
+        user_email=current_user.email,
         method_version=method_version,
+        method_document=method_document,
     )
-    return update_plate_sign_off(session=session, plate=plate, plate_sign_off=plate_sign_off)
 
 
 @router.get(
     "/{plate_id}",
-    response_model=PlateReadWithAnalysisDetailSingle,
+    response_model=PlateResponse,
     response_model_by_alias=False,
     response_model_exclude={
         "analyses": {
@@ -133,16 +81,17 @@ def sign_off_plate(
 )
 def read_plate(
     plate_id: int,
-    session: Session = Depends(get_session),
+    plate_service: PlateService = Depends(get_plate_service),
     current_user: User = Depends(get_active_user),
 ):
     """Display information about a plate."""
-    return get_plate_read_analysis_single(session=session, plate_id=plate_id)
+
+    return plate_service.read_plate(plate_id=plate_id)
 
 
 @router.get(
     "/",
-    response_model=list[PlateReadWithAnalysisDetail],
+    response_model=list[PlateResponse],
     response_model_exclude={"analyses"},
     response_model_by_alias=False,
 )
@@ -151,33 +100,25 @@ async def read_plates(
     sort_order: Literal["ascend", "descend"] | None = "descend",
     skip: int | None = 0,
     limit: int | None = 10,
-    session: Session = Depends(get_session),
+    plate_service: PlateService = Depends(get_plate_service),
     current_user: User = Depends(get_active_user),
-) -> Sequence[Plate]:
+):
     """Display all plates"""
-
     order_params = PlateOrderParams(
         order_by=order_by, skip=skip, limit=limit, sort_order=sort_order
     )
-    plates: Sequence[Plate] = get_ordered_plates(session=session, order_params=order_params)
-    return plates
+    return plate_service.read_plates(order_params=order_params)
 
 
-@router.delete("/{plate_id}", response_model=Plate)
+@router.delete("/{plate_id}")
 def delete_plate(
     plate_id: int,
-    session: Session = Depends(get_session),
+    plate_service: PlateService = Depends(get_plate_service),
     current_user: User = Depends(get_active_user),
 ):
     """Delete plate."""
-    plate = session.get(Plate, plate_id)
-    analyses: list[Analysis] = get_analyses_from_plate(session=session, plate_id=plate_id)
-    analyse_ids = [analyse.id for analyse in analyses]
-    for analysis in analyses:
-        delete_analysis(session=session, analysis=analysis)
-    delete_plate(session=session, plate=plate)
-
+    analysis_ids = plate_service.delete_plate(plate_id)
     return JSONResponse(
-        f"Deleted plate: {plate_id} and analyses: {analyse_ids}",
+        f"Deleted plate: {plate_id} and analyses: {analysis_ids}",
         status_code=status.HTTP_200_OK,
     )

genotype_api/api/endpoints/users.py

@@ -8,7 +8,7 @@
 from starlette.responses import JSONResponse
 
 from genotype_api.database.crud.read import (
-    get_user,
+    get_user_by_id,
     get_user_by_email,
     get_users_with_skip_and_limit,
 )
@@ -32,7 +32,7 @@ def read_user(
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ) -> User:
-    return get_user(session=session, user_id=user_id)
+    return get_user_by_id(session=session, user_id=user_id)
 
 
 @router.delete("/{user_id}")
@@ -41,7 +41,7 @@ def delete_user(
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ) -> JSONResponse:
-    user: User = get_user(session=session, user_id=user_id)
+    user: User = get_user_by_id(session=session, user_id=user_id)
     if not user:
         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="User not found")
     if user.plates:
@@ -60,7 +60,7 @@ def change_user_email(
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ) -> User:
-    user: User = get_user(session=session, user_id=user_id)
+    user: User = get_user_by_id(session=session, user_id=user_id)
     if not user:
         raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="User not found")
     user: User = update_user_email(session=session, user=user, email=email)

genotype_api/constants.py

@@ -19,7 +19,7 @@ class Sexes(str, Enum):
     UNKNOWN = "unknown"
 
 
-class STATUS(str, Enum):
+class Status(str, Enum):
     PASS = "pass"
     FAIL = "fail"
     CANCEL = "cancel"

genotype_api/database/crud/read.py

@@ -76,33 +76,23 @@ def get_analysis_by_type_and_sample_id(
     ).one()
 
 
-def get_plate(session: Session, plate_id: int) -> Plate:
-    """Get plate"""
+def get_plate_by_id(session: Session, plate_id: int) -> Plate:
     statement = select(Plate).where(Plate.id == plate_id)
     return session.exec(statement).one()
 
 
-def get_plate_read_analysis_single(
-    session: Session, plate_id: int
-) -> PlateReadWithAnalysisDetailSingle:
-    plate: Plate = get_plate(session=session, plate_id=plate_id)
-    return PlateReadWithAnalysisDetailSingle.from_orm(plate)
-
-
 def get_ordered_plates(session: Session, order_params: PlateOrderParams) -> list[Plate]:
     sort_func = desc if order_params.sort_order == "descend" else asc
-    plates: list[Plate] = session.exec(
+    return session.exec(
         select(Plate)
         .order_by(sort_func(order_params.order_by))
         .offset(order_params.skip)
         .limit(order_params.limit)
     ).all()
-    return plates
 
 
 def get_incomplete_samples(statement: SelectOfScalar) -> SelectOfScalar:
     """Returning sample query statement for samples with less than two analyses."""
-
     return (
         statement.group_by(Analysis.sample_id)
         .order_by(Analysis.created_at)
@@ -162,7 +152,7 @@ def get_samples(statement: SelectOfScalar, sample_id: str) -> SelectOfScalar:
     return statement.where(Sample.id.contains(sample_id))
 
 
-def get_user(session: Session, user_id: int):
+def get_user_by_id(session: Session, user_id: int):
     statement = select(User).where(User.id == user_id)
     return session.exec(statement).one()
 

genotype_api/database/models.py

@@ -5,7 +5,7 @@
 from sqlalchemy import Index
 from sqlmodel import Field, Relationship, SQLModel
 
-from genotype_api.constants import Sexes, STATUS, Types
+from genotype_api.constants import Sexes, Status, Types
 
 
 class GenotypeBase(SQLModel):
@@ -59,7 +59,7 @@ def check_no_calls(self) -> dict[str, int]:
 
 
 class SampleSlim(SQLModel):
-    status: STATUS | None
+    status: Status | None
     comment: str | None
 
 

genotype_api/dto/analysis.py

@@ -5,7 +5,8 @@
 from pydantic import BaseModel
 
 from genotype_api.constants import Sexes, Types
-from genotype_api.dto.genotype import GenotypeBase
+from genotype_api.dto.genotype import GenotypeResponse
+from genotype_api.dto.sample import SampleStatusResponse
 
 
 class AnalysisResponse(BaseModel):
@@ -18,12 +19,23 @@ class AnalysisResponse(BaseModel):
     id: int | None
 
 
-class AnalysisWithGenotypeResponse(BaseModel):
+class AnalysisGenotypeResponse(BaseModel):
     type: Types | None
     source: str | None
     sex: Sexes | None
     created_at: datetime | None
     sample_id: str | None
     plate_id: str | None
     id: int | None
-    genotypes: list[GenotypeBase] | None
+    genotypes: list[GenotypeResponse] | None = None
+
+
+class AnalysisSampleResponse(BaseModel):
+    type: Types | None
+    source: str | None
+    sex: Sexes | None
+    created_at: datetime | None
+    sample_id: str | None
+    plate_id: str | None
+    id: int | None
+    sample: SampleStatusResponse | None = None

genotype_api/dto/dto.py

@@ -4,7 +4,8 @@
 
 import genotype_api.database.models
 from genotype_api.database import models
-from genotype_api.models import SampleDetail, PlateStatusCounts
+from genotype_api.models import SampleDetail
+from genotype_api.dto.plate import PlateStatusCounts
 from genotype_api.services.match_genotype_service.utils import check_snps, check_sex
 
 

genotype_api/dto/genotype.py

@@ -3,7 +3,7 @@
 from pydantic import BaseModel, Field
 
 
-class GenotypeBase(BaseModel):
+class GenotypeResponse(BaseModel):
     rsnumber: str = Field(max_length=10)
     analysis_id: int
     allele_1: str = Field(max_length=1)