conflicts

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.0.7
+current_version = 3.0.9
 commit = True
 tag = True
 tag_name = v{new_version}

genotype_api/__init__.py

@@ -1 +1 @@
-__version__ = "3.0.7"
+__version__ = "3.0.9"

genotype_api/api/app.py

@@ -7,8 +7,9 @@
 from fastapi.responses import JSONResponse
 from fastapi.middleware.cors import CORSMiddleware
 
+from genotype_api.api.middleware import DBSessionMiddleware
 from genotype_api.config import security_settings, settings
-from genotype_api.database.database import create_all_tables, initialise_database, close_session
+from genotype_api.database.database import create_all_tables, initialise_database
 from genotype_api.api.endpoints import samples, snps, users, plates, analyses
 from sqlalchemy.exc import NoResultFound
 
@@ -24,6 +25,7 @@
     allow_methods=["*"],
     allow_headers=["*"],
 )
+app.add_middleware(DBSessionMiddleware)
 
 
 @app.exception_handler(NoResultFound)

genotype_api/api/endpoints/plates.py

@@ -10,7 +10,7 @@
 from genotype_api.database.store import Store, get_store
 from genotype_api.dto.plate import PlateResponse
 from genotype_api.dto.user import CurrentUser
-from genotype_api.exceptions import PlateNotFoundError
+from genotype_api.exceptions import PlateNotFoundError, PlateExistsError
 from genotype_api.security import get_active_user
 from genotype_api.services.endpoint_services.plate_service import PlateService
 
@@ -24,15 +24,20 @@ def get_plate_service(store: Store = Depends(get_store)) -> PlateService:
 
 @router.post(
     "/plate",
-    response_model=PlateResponse,
-    response_model_exclude={"plate_status_counts"},
 )
 def upload_plate(
     file: UploadFile = File(...),
     plate_service: PlateService = Depends(get_plate_service),
     current_user: CurrentUser = Depends(get_active_user),
 ):
-    return plate_service.upload_plate(file)
+
+    try:
+        plate_service.upload_plate(file)
+    except PlateExistsError:
+        raise HTTPException(
+            detail="Plate already exists in the database.", status_code=HTTPStatus.BAD_REQUEST
+        )
+    return JSONResponse("Plate uploaded successfully", status_code=status.HTTP_201_CREATED)
 
 
 @router.patch(

genotype_api/api/middleware.py

@@ -0,0 +1,13 @@
+from fastapi import Request
+from starlette.middleware.base import BaseHTTPMiddleware
+from genotype_api.database.database import close_session
+
+
+class DBSessionMiddleware(BaseHTTPMiddleware):
+    def __init__(self, app):
+        super().__init__(app)
+
+    async def dispatch(self, request: Request, call_next):
+        response = await call_next(request)
+        close_session()
+        return response

genotype_api/exceptions.py

@@ -51,3 +51,7 @@ class SampleExistsError(Exception):
 
 class SNPExistsError(Exception):
     pass
+
+
+class PlateExistsError(Exception):
+    pass

genotype_api/file_parsing/excel.py

@@ -1,6 +1,7 @@
 """Code to work with excel files"""
 
 import logging
+from datetime import datetime
 from pathlib import Path
 from typing import ByteString, Iterable
 
@@ -70,7 +71,7 @@ def parse_sample_id(sample_id: str, include_key: str = None) -> str | None:
         LOG.info("Use sample id %s", sample_id)
         return sample_id
 
-    def generate_analyses(self) -> Iterable[Analysis]:
+    def generate_analyses(self, plate_id: int) -> Iterable[Analysis]:
         """Loop over the rows and create one analysis for each individual"""
         nr_row: int
         row: list[str]
@@ -95,6 +96,8 @@ def generate_analyses(self) -> Iterable[Analysis]:
                 sample_id=sample_id,
                 sex=sex,
                 genotypes=genotypes,
+                plate_id=plate_id,
+                created_at=datetime.now(),
             )
 
     @staticmethod
@@ -134,18 +137,3 @@ def parse_sex(sex_cells: list[str]) -> str:
             # assays returned conflicting results
             message = "conflicting sex predictions: {}".format(sex_cells)
             raise SexConflictError(message)
-
-
-if __name__ == "__main__":
-    import sys
-
-    import coloredlogs
-
-    coloredlogs.install()
-
-    in_file = Path(sys.argv[1])
-    # include_key = "ID-CG-"
-    include_key = "-CG-"
-    genotype_analysis = GenotypeAnalysis(in_file, include_key)
-    for analysis in genotype_analysis.generate_analyses():
-        print(analysis)

genotype_api/services/endpoint_services/plate_service.py

@@ -1,19 +1,20 @@
 """Module to holds the plate service."""
 
+import logging
 from datetime import datetime
-from http.client import HTTPException
+
 from io import BytesIO
 from pathlib import Path
 
 
 from fastapi import UploadFile
 from pydantic import EmailStr
-from starlette import status
+
 from genotype_api.constants import Types
 from genotype_api.database.filter_models.plate_models import PlateSignOff, PlateOrderParams
-from genotype_api.database.models import Plate, Analysis, User
+from genotype_api.database.models import Plate, Analysis, User, Sample
 from genotype_api.dto.plate import PlateResponse, UserOnPlate, AnalysisOnPlate, SampleStatus
-from genotype_api.exceptions import PlateNotFoundError, UserNotFoundError
+from genotype_api.exceptions import PlateNotFoundError, UserNotFoundError, PlateExistsError
 from genotype_api.file_parsing.excel import GenotypeAnalysis
 from genotype_api.file_parsing.files import check_file
 from genotype_api.services.endpoint_services.base_service import BaseService
@@ -68,33 +69,33 @@ 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 upload_plate(self, file: UploadFile) -> PlateResponse:
+    def upload_plate(self, file: UploadFile) -> None:
         file_name: Path = check_file(file_path=file.filename, extension=".xlsx")
         plate_id: str = self._get_plate_id_from_file(file_name)
         db_plate = self.store.get_plate_by_plate_id(plate_id)
         if db_plate:
-            raise HTTPException(
-                status_code=status.HTTP_409_CONFLICT,
-                detail=f"Plate with id {db_plate.id} already exists",
-            )
+            raise PlateExistsError
 
         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())
+
+        plate_obj = Plate(plate_id=plate_id)
+        plate: Plate = self.store.create_plate(plate=plate_obj)
+        new_plate: Plate = self.store.get_plate_by_plate_id(plate_id=plate_id)
+        analyses: list[Analysis] = list(excel_parser.generate_analyses(plate_id=new_plate.id))
         self.store.check_analyses_objects(analyses=analyses, analysis_type=Types.GENOTYPE)
         self.store.create_analyses_samples(analyses=analyses)
-        plate_obj = Plate(plate_id=plate_id)
+        for analysis in analyses:
+            self.store.create_analysis(analysis=analysis)
         plate_obj.analyses = analyses
-        plate: Plate = self.store.create_plate(plate=plate_obj)
-        for analysis in plate.analyses:
-            self.store.refresh_sample_status(sample=analysis.sample)
+        for analysis in analyses:
+            sample: Sample = self.store.get_sample_by_id(sample_id=analysis.sample_id)
+            self.store.refresh_sample_status(sample=sample)
         self.store.refresh_plate(plate=plate)
 
-        return self._create_plate_response(plate)
-
     def update_plate_sign_off(
         self, plate_id: int, user_email: EmailStr, method_document: str, method_version: str
     ) -> PlateResponse:

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "genotype-api"
-version = "3.0.7"
+version = "3.0.9"
 description = "Genotype-api"
 authors = ["Christian Oertlin <[email protected]>"]
 readme = "README.md"