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

This reverts commit 4fbdea7.

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 AnalysisGenotypeResponse, AnalysisResponse
+from genotype_api.dto.analysis import AnalysisWithGenotypeResponse, 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=AnalysisGenotypeResponse)
+@router.get("/{analysis_id}", response_model=AnalysisWithGenotypeResponse)
 def read_analysis(
     analysis_id: int,
     session: Session = Depends(get_session),

genotype_api/api/endpoints/plates.py

@@ -1,65 +1,117 @@
 """Routes for plates"""
 
-from typing import Literal
-from fastapi import APIRouter, Depends, File, Query, UploadFile, status
+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 fastapi.responses import JSONResponse
+from sqlalchemy import asc, desc
 from sqlmodel import Session
-from genotype_api.database.filter_models.plate_models import PlateOrderParams
-from genotype_api.database.models import User
+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.session_handler import get_session
-from genotype_api.dto.plate import PlateResponse
+from genotype_api.file_parsing.excel import GenotypeAnalysis
+from genotype_api.file_parsing.files import check_file
 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_service(session: Session = Depends(get_session)) -> PlateService:
-    return PlateService(session)
+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]
 
 
-@router.post(
-    "/plate",
-    response_model=PlateResponse,
-    response_model_exclude={"detail"},
-)
+@router.post("/plate", response_model=PlateReadWithAnalyses)
 def upload_plate(
     file: UploadFile = File(...),
-    plate_service: PlateService = Depends(get_plate_service),
+    session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ):
-    return plate_service.upload_plate(file)
-
-
-@router.patch(
-    "/{plate_id}/sign-off",
-    response_model=PlateResponse,
-    response_model_exclude={"analyses", "user", "detail"},
-)
+    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)
 def sign_off_plate(
     plate_id: int,
     method_document: str = Query(...),
     method_version: str = Query(...),
-    plate_service: PlateService = Depends(get_plate_service),
+    session: Session = Depends(get_session),
     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
     """
-
-    return plate_service.update_plate_sign_off(
-        plate_id=plate_id,
-        user_email=current_user.email,
-        method_version=method_version,
+    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,
+        method_version=method_version,
     )
+    return update_plate_sign_off(session=session, plate=plate, plate_sign_off=plate_sign_off)
 
 
 @router.get(
     "/{plate_id}",
-    response_model=PlateResponse,
+    response_model=PlateReadWithAnalysisDetailSingle,
     response_model_by_alias=False,
     response_model_exclude={
         "analyses": {
@@ -81,17 +133,16 @@ def sign_off_plate(
 )
 def read_plate(
     plate_id: int,
-    plate_service: PlateService = Depends(get_plate_service),
+    session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ):
     """Display information about a plate."""
-
-    return plate_service.read_plate(plate_id=plate_id)
+    return get_plate_read_analysis_single(session=session, plate_id=plate_id)
 
 
 @router.get(
     "/",
-    response_model=list[PlateResponse],
+    response_model=list[PlateReadWithAnalysisDetail],
     response_model_exclude={"analyses"},
     response_model_by_alias=False,
 )
@@ -100,25 +151,33 @@ async def read_plates(
     sort_order: Literal["ascend", "descend"] | None = "descend",
     skip: int | None = 0,
     limit: int | None = 10,
-    plate_service: PlateService = Depends(get_plate_service),
+    session: Session = Depends(get_session),
     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
     )
-    return plate_service.read_plates(order_params=order_params)
+    plates: Sequence[Plate] = get_ordered_plates(session=session, order_params=order_params)
+    return plates
 
 
-@router.delete("/{plate_id}")
+@router.delete("/{plate_id}", response_model=Plate)
 def delete_plate(
     plate_id: int,
-    plate_service: PlateService = Depends(get_plate_service),
+    session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ):
     """Delete plate."""
-    analysis_ids = plate_service.delete_plate(plate_id)
+    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)
+
     return JSONResponse(
-        f"Deleted plate: {plate_id} and analyses: {analysis_ids}",
+        f"Deleted plate: {plate_id} and analyses: {analyse_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_by_id,
+    get_user,
     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_by_id(session=session, user_id=user_id)
+    return get_user(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_by_id(session=session, user_id=user_id)
+    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")
     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_by_id(session=session, user_id=user_id)
+    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: 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

@@ -76,23 +76,33 @@ def get_analysis_by_type_and_sample_id(
     ).one()
 
 
-def get_plate_by_id(session: Session, plate_id: int) -> Plate:
+def get_plate(session: Session, plate_id: int) -> Plate:
+    """Get 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
-    return session.exec(
+    plates: list[Plate] = 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)
@@ -152,7 +162,7 @@ def get_samples(statement: SelectOfScalar, sample_id: str) -> SelectOfScalar:
     return statement.where(Sample.id.contains(sample_id))
 
 
-def get_user_by_id(session: Session, user_id: int):
+def get_user(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

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

genotype_api/dto/dto.py

@@ -4,8 +4,7 @@
 
 import genotype_api.database.models
 from genotype_api.database import models
-from genotype_api.models import SampleDetail
-from genotype_api.dto.plate import PlateStatusCounts
+from genotype_api.models import SampleDetail, 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 GenotypeResponse(BaseModel):
+class GenotypeBase(BaseModel):
     rsnumber: str = Field(max_length=10)
     analysis_id: int
     allele_1: str = Field(max_length=1)