refactor( analysis dependency injection)

genotype_api/api/endpoints/analyses.py

@@ -4,61 +4,60 @@
 from fastapi.responses import JSONResponse
 from sqlmodel import Session
 
-from genotype_api.database.crud.delete import delete_analysis
-from genotype_api.database.crud.read import (
-    get_analysis_by_id,
-)
-from genotype_api.database.models import Analysis, User
-from genotype_api.dto.analysis import AnalysisWithGenotypeResponse, AnalysisResponse
+from genotype_api.database.models import User
+from genotype_api.dto.analysis import 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)
+def get_analysis_service(session: Session = Depends(get_session)):
+    return AnalysisService(session)
+
+
+@router.get("/{analysis_id}", response_model=AnalysisResponse)
 def read_analysis(
     analysis_id: int,
-    session: Session = Depends(get_session),
+    analysis_service: AnalysisService = Depends(get_analysis_service),
     current_user: User = Depends(get_active_user),
 ):
     """Return analysis."""
-    analysis_service = AnalysisService(session)
     return analysis_service.get_analysis_with_genotype(analysis_id)
 
 
-@router.get("/", response_model=list[AnalysisResponse])
+@router.get("/", response_model=list[AnalysisResponse], response_model_exclude={"genotypes"})
 def read_analyses(
     skip: int = 0,
     limit: int = Query(default=100, lte=100),
-    session: Session = Depends(get_session),
+    analysis_service: AnalysisService = Depends(get_analysis_service),
     current_user: User = Depends(get_active_user),
 ):
     """Return all analyses."""
-    analysis_service = AnalysisService(session)
     return analysis_service.get_analyses_to_display(skip=skip, limit=limit)
 
 
 @router.delete("/{analysis_id}")
 def delete_analysis(
     analysis_id: int,
-    session: Session = Depends(get_session),
+    analysis_service: AnalysisService = Depends(get_analysis_service),
     current_user: User = Depends(get_active_user),
 ):
     """Delete analysis based on analysis_id"""
-    analysis: Analysis = get_analysis_by_id(session=session, analysis_id=analysis_id)
-    delete_analysis(session=session, analysis=analysis)
+    analysis_service.delete_analysis(analysis_id)
     return JSONResponse(f"Deleted analysis: {analysis_id}", status_code=status.HTTP_200_OK)
 
 
-@router.post("/sequence", response_model=list[AnalysisResponse])
+@router.post(
+    "/sequence", response_model=list[AnalysisResponse], response_model_exclude={"genotypes"}
+)
 def upload_sequence_analysis(
     file: UploadFile = File(...),
-    session: Session = Depends(get_session),
+    analysis_service: AnalysisService = Depends(get_analysis_service),
     current_user: User = Depends(get_active_user),
 ):
     """Reading VCF file, creating and uploading sequence analyses and sample objects to the database."""
-    analysis_service = AnalysisService(session)
+
     analyses: list[AnalysisResponse] = analysis_service.get_upload_sequence_analyses(file)
     return analyses

genotype_api/dto/analysis.py

@@ -16,14 +16,4 @@ class AnalysisResponse(BaseModel):
     sample_id: str | None
     plate_id: str | None
     id: int | None
-
-
-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[GenotypeBase] | None

genotype_api/services/analysis_service/analysis_service.py

@@ -7,14 +7,15 @@
 
 from genotype_api.constants import Types, FileExtension
 from genotype_api.database.crud.create import create_analyses_samples, create_analysis
+from genotype_api.database.crud.delete import delete_analysis
 from genotype_api.database.crud.read import (
     get_analysis_by_id,
     get_analyses_with_skip_and_limit,
     check_analyses_objects,
 )
 from genotype_api.database.crud.update import refresh_sample_status
 from genotype_api.database.models import Analysis
-from genotype_api.dto.analysis import AnalysisWithGenotypeResponse, AnalysisResponse
+from genotype_api.dto.analysis import AnalysisResponse
 from genotype_api.file_parsing.files import check_file
 from genotype_api.file_parsing.vcf import SequenceAnalysis
 
@@ -25,24 +26,15 @@ class AnalysisService:
     def __init__(self, session: Session):
         self.session: Session = session
 
-    def get_analysis_with_genotype(self, analysis_id: int) -> AnalysisWithGenotypeResponse:
+    def get_analysis_with_genotype(self, analysis_id: int) -> AnalysisResponse:
         analysis: Analysis = get_analysis_by_id(session=self.session, analysis_id=analysis_id)
-        return AnalysisWithGenotypeResponse(
-            type=analysis.type,
-            source=analysis.source,
-            sex=analysis.sex,
-            created_at=analysis.created_at,
-            sample_id=analysis.sample_id,
-            plate_id=analysis.plate_id,
-            id=analysis.id,
-            genotypes=analysis.genotypes,
-        )
+        return self._get_analyses_response(analysis)
 
     def get_analyses_to_display(self, skip: int, limit: int) -> list[AnalysisResponse]:
         analyses: list[Analysis] = get_analyses_with_skip_and_limit(
             session=self.session, skip=skip, limit=limit
         )
-        return self.create_analyses_response(analyses)
+        return [self._get_analyses_response(analysis) for analysis in analyses]
 
     def get_upload_sequence_analyses(self, file: UploadFile) -> list[AnalysisResponse]:
         """
@@ -60,19 +52,21 @@ def get_upload_sequence_analyses(self, file: UploadFile) -> list[AnalysisRespons
             analysis: Analysis = create_analysis(session=self.session, analysis=analysis)
             refresh_sample_status(session=self.session, sample=analysis.sample)
 
-        return self.create_analyses_response(analyses)
+        return [self._get_analyses_response(analysis) for analysis in analyses]
 
     @staticmethod
-    def create_analyses_response(analyses: list[Analysis]) -> list[AnalysisResponse]:
-        return [
-            AnalysisResponse(
-                type=analysis.type,
-                source=analysis.source,
-                sex=analysis.sex,
-                created_at=analysis.created_at,
-                sample_id=analysis.sample_id,
-                plate_id=analysis.plate_id,
-                id=analysis.id,
-            )
-            for analysis in analyses
-        ]
+    def _get_analyses_response(analysis: Analysis) -> AnalysisResponse:
+        return AnalysisResponse(
+            type=analysis.type,
+            source=analysis.source,
+            sex=analysis.sex,
+            created_at=analysis.created_at,
+            sample_id=analysis.sample_id,
+            plate_id=analysis.plate_id,
+            id=analysis.id,
+            genotypes=analysis.genotypes,
+        )
+
+    def delete_analysis(self, analysis_id: int) -> None:
+        analysis: Analysis = get_analysis_by_id(session=self.session, analysis_id=analysis_id)
+        delete_analysis(session=self.session, analysis=analysis)