feat(pep_0585):

genotype_api/api/endpoints/analyses.py

@@ -1,7 +1,6 @@
 """Routes for analysis"""
 
 from pathlib import Path
-from typing import List
 
 from fastapi import APIRouter, Depends, status, Query, UploadFile, File
 from fastapi.responses import JSONResponse
@@ -40,15 +39,15 @@ def read_analysis(
     return get_analysis(session=session, analysis_id=analysis_id)
 
 
-@router.get("/", response_model=List[AnalysisRead])
+@router.get("/", response_model=list[AnalysisRead])
 def read_analyses(
     skip: int = 0,
     limit: int = Query(default=100, lte=100),
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
-) -> List[Analysis]:
+) -> list[Analysis]:
     """Return all analyses."""
-    analyses: List[Analysis] = session.exec(select(Analysis).offset(skip).limit(limit)).all()
+    analyses: list[Analysis] = session.exec(select(Analysis).offset(skip).limit(limit)).all()
 
     return analyses
 
@@ -67,7 +66,7 @@ def delete_analysis(
     return JSONResponse(f"Deleted analysis: {analysis_id}", status_code=status.HTTP_200_OK)
 
 
-@router.post("/sequence", response_model=List[Analysis])
+@router.post("/sequence", response_model=list[Analysis])
 def upload_sequence_analysis(
     file: UploadFile = File(...),
     session: Session = Depends(get_session),
@@ -78,7 +77,7 @@ def upload_sequence_analysis(
     file_name: Path = check_file(file_path=file.filename, extension=".vcf")
     content = file.file.read().decode("utf-8")
     sequence_analysis = SequenceAnalysis(vcf_file=content, source=str(file_name))
-    analyses: List[Analysis] = list(sequence_analysis.generate_analyses())
+    analyses: list[Analysis] = list(sequence_analysis.generate_analyses())
     check_analyses_objects(session=session, analyses=analyses, analysis_type="sequence")
     create_analyses_sample_objects(session=session, analyses=analyses)
     for analysis in analyses:

genotype_api/api/endpoints/plates.py

@@ -3,7 +3,7 @@
 from datetime import datetime
 from io import BytesIO
 from pathlib import Path
-from typing import List, Optional, Literal
+from typing import Optional, Literal
 
 from fastapi import APIRouter, Depends, File, HTTPException, UploadFile, Query, status
 from sqlalchemy import desc, asc
@@ -66,7 +66,7 @@ def upload_plate(
         file_name=str(file_name),
         include_key="-CG-",
     )
-    analyses: List[Analysis] = list(excel_parser.generate_analyses())
+    analyses: list[Analysis] = list(excel_parser.generate_analyses())
     check_analyses_objects(session=session, analyses=analyses, analysis_type="genotype")
     create_analyses_sample_objects(session=session, analyses=analyses)
     plate_obj = PlateCreate(plate_id=plate_id)
@@ -136,7 +136,7 @@ def read_plate(
 
 @router.get(
     "/",
-    response_model=List[PlateReadWithAnalysisDetail],
+    response_model=list[PlateReadWithAnalysisDetail],
     response_model_exclude={"analyses"},
     response_model_by_alias=False,
 )
@@ -150,7 +150,7 @@ async def read_plates(
 ):
     """Display all plates"""
     sort_func = desc if sort_order == "descend" else asc
-    plates: List[Plate] = session.exec(
+    plates: list[Plate] = session.exec(
         select(Plate).order_by(sort_func(order_by)).offset(skip).limit(limit)
     ).all()
 
@@ -165,7 +165,7 @@ def delete_plate(
 ):
     """Delete plate."""
     plate = session.get(Plate, plate_id)
-    analyses: List[Analysis] = get_analyses_from_plate(session=session, plate_id=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:
         session.delete(analysis)

genotype_api/api/endpoints/samples.py

@@ -1,4 +1,4 @@
-from typing import List, Optional, Literal
+from typing import Optional, Literal
 from fastapi import APIRouter, Depends, Query
 from fastapi.responses import JSONResponse
 from datetime import timedelta, date
@@ -71,7 +71,7 @@ def read_sample(
 
 @router.get(
     "/",
-    response_model=List[SampleReadWithAnalysisDeep],
+    response_model=list[SampleReadWithAnalysisDeep],
     response_model_by_alias=False,
     response_model_exclude={
         "analyses": {"__all__": {"genotypes": True, "source": True, "created_at": True}},
@@ -95,7 +95,7 @@ def read_samples(
     status_missing: Optional[bool] = False,
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
-) -> List[Sample]:
+) -> list[Sample]:
     """Returns a list of samples matching the provided filters."""
     statement: SelectOfScalar = select(Sample).distinct().join(Analysis)
     if sample_id:
@@ -182,7 +182,7 @@ def set_sample_status(
     return sample
 
 
-@router.get("/{sample_id}/match", response_model=List[MatchResult])
+@router.get("/{sample_id}/match", response_model=list[MatchResult])
 def match(
     sample_id: str,
     analysis_type: Literal["genotype", "sequence"],
@@ -191,7 +191,7 @@ def match(
     date_max: Optional[date] = date.max,
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
-) -> List[MatchResult]:
+) -> list[MatchResult]:
     """Match sample genotype against all other genotypes."""
 
     all_genotypes: Analysis = session.query(Analysis).filter(

genotype_api/api/endpoints/snps.py

@@ -1,7 +1,6 @@
 """Routes for the snps"""
 
 from genotype_api.database.models.models import SNP, User
-from typing import List
 
 from fastapi import APIRouter, Depends, HTTPException, Query, File, UploadFile
 from genotype_api.database import get_session
@@ -16,23 +15,23 @@
 router = APIRouter()
 
 
-@router.get("/", response_model=List[SNP])
+@router.get("/", response_model=list[SNP])
 def read_snps(
     skip: int = 0,
     limit: int = Query(default=100, lte=100),
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
-) -> List[SNP]:
+) -> list[SNP]:
     return session.exec(select(SNP).offset(skip).limit(limit)).all()
 
 
-@router.post("/", response_model=List[SNP])
+@router.post("/", response_model=list[SNP])
 async def upload_snps(
     snps_file: UploadFile,
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ):
-    db_snps: List[SNP] = session.exec(select(SNP)).all()
+    db_snps: list[SNP] = session.exec(select(SNP)).all()
     if db_snps:
         raise HTTPException(status_code=400, detail="SNPs already uploaded")
     snps = []

genotype_api/api/endpoints/users.py

@@ -1,7 +1,5 @@
 """Routes for users"""
 
-from typing import List
-
 from fastapi import APIRouter, Depends, HTTPException, Query
 from pydantic import EmailStr
 from starlette import status
@@ -67,14 +65,14 @@ def change_user_email(
     return user
 
 
-@router.get("/", response_model=List[UserRead])
+@router.get("/", response_model=list[UserRead])
 def read_users(
     skip: int = 0,
     limit: int = Query(default=100, lte=100),
     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()
+) -> list[User]:
+    users: list[User] = session.exec(select(User).offset(skip).limit(limit)).all()
     return users
 
 
@@ -84,7 +82,7 @@ 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()
+    user_in_db: list[User] = session.exec(select(User).where(User.email == user.email)).all()
     if user_in_db:
         raise HTTPException(status_code=409, detail="Email already registered")
     db_user = User.from_orm(user)

genotype_api/database/crud/create.py

@@ -1,5 +1,4 @@
 import logging
-from typing import List
 
 from fastapi import HTTPException
 from sqlmodel import Session
@@ -49,7 +48,7 @@ def create_sample(session: Session, sample: Sample) -> Sample:
     return sample
 
 
-def create_analyses_sample_objects(session: Session, analyses: List[Analysis]) -> List[Sample]:
+def create_analyses_sample_objects(session: Session, analyses: list[Analysis]) -> list[Sample]:
     """creating samples in an analysis if not already in db."""
     return [
         create_sample(session=session, sample=Sample(id=analysis_obj.sample_id))

genotype_api/database/crud/read.py

@@ -1,5 +1,5 @@
 import logging
-from typing import List, Optional
+list[, Optional
 
 from sqlalchemy import func
 from sqlmodel import Session, select
@@ -14,7 +14,7 @@
 LOG = logging.getLogger(__name__)
 
 
-def get_analyses_from_plate(plate_id: int, session: Session) -> List[Analysis]:
+def get_analyses_from_plate(plate_id: int, session: Session) -> list[Analysis]:
     statement = select(Analysis).where(Analysis.plate_id == plate_id)
     return session.exec(statement).all()
 
@@ -91,13 +91,13 @@ def get_user_by_email(session: Session, email: str) -> Optional[User]:
     return session.exec(statement).first()
 
 
-def get_users(session: Session, skip: int = 0, limit: int = 100) -> List[User]:
+def get_users(session: Session, skip: int = 0, limit: int = 100) -> list[User]:
     statement = select(User).offset(skip).limit(limit)
     return session.exec(statement).all()
 
 
 def check_analyses_objects(
-    session: Session, analyses: List[Analysis], analysis_type: TYPES
+    session: Session, analyses: list[Analysis], analysis_type: TYPES
 ) -> None:
     """Raising 400 if any analysis in the list already exist in the database"""
     for analysis_obj in analyses:

genotype_api/database/models/models.py

@@ -1,6 +1,6 @@
 from collections import Counter
 from datetime import datetime
-from typing import Optional, List, Dict, Tuple
+from typing import Optional
 
 from pydantic import constr, EmailStr, validator
 from sqlalchemy import Index
@@ -25,7 +25,7 @@ class Genotype(GenotypeBase, table=True):
     analysis: Optional["Analysis"] = Relationship(back_populates="genotypes")
 
     @property
-    def alleles(self) -> List[str]:
+    def alleles(self) -> list[str]:
         """Return sorted because we are not dealing with phased data."""
 
         return sorted([self.allele_1, self.allele_2])
@@ -59,10 +59,10 @@ class Analysis(AnalysisBase, table=True):
     id: Optional[int] = Field(default=None, primary_key=True)
 
     sample: Optional["Sample"] = Relationship(back_populates="analyses")
-    plate: Optional[List["Plate"]] = Relationship(back_populates="analyses")
-    genotypes: Optional[List["Genotype"]] = Relationship(back_populates="analysis")
+    plate: Optional[list["Plate"]] = Relationship(back_populates="analyses")
+    genotypes: Optional[list["Genotype"]] = Relationship(back_populates="analysis")
 
-    def check_no_calls(self) -> Dict[str, int]:
+    def check_no_calls(self) -> dict[str, int]:
         """Check that genotypes look ok."""
         calls = ["known" if genotype.is_ok else "unknown" for genotype in self.genotypes]
         return Counter(calls)
@@ -90,7 +90,7 @@ class Sample(SampleBase, table=True):
     __tablename__ = "sample"
     id: Optional[constr(max_length=32)] = Field(default=None, primary_key=True)
 
-    analyses: Optional[List["Analysis"]] = Relationship(back_populates="sample")
+    analyses: Optional[list["Analysis"]] = Relationship(back_populates="sample")
 
     @property
     def genotype_analysis(self) -> Optional[Analysis]:
@@ -146,7 +146,7 @@ class UserBase(SQLModel):
 class User(UserBase, table=True):
     __tablename__ = "user"
     id: Optional[int] = Field(default=None, primary_key=True)
-    plates: Optional[List["Plate"]] = Relationship(back_populates="user")
+    plates: Optional[list["Plate"]] = Relationship(back_populates="user")
 
 
 class UserRead(UserBase):
@@ -170,7 +170,7 @@ class Plate(PlateBase, table=True):
     __tablename__ = "plate"
     id: Optional[int] = Field(default=None, primary_key=True)
     user: Optional["User"] = Relationship(back_populates="plates")
-    analyses: Optional[List["Analysis"]] = Relationship(back_populates="plate")
+    analyses: Optional[list["Analysis"]] = Relationship(back_populates="plate")
 
 
 class PlateRead(PlateBase):
@@ -179,23 +179,23 @@ class PlateRead(PlateBase):
 
 
 class PlateCreate(PlateBase):
-    analyses: Optional[List[Analysis]] = []
+    analyses: Optional[list[Analysis]] = []
 
 
 class UserReadWithPlates(UserRead):
-    plates: Optional[List[Plate]] = []
+    plates: Optional[list[Plate]] = []
 
 
 class SampleReadWithAnalysis(SampleRead):
-    analyses: Optional[List[AnalysisRead]] = []
+    analyses: Optional[list[AnalysisRead]] = []
 
 
 class AnalysisReadWithGenotype(AnalysisRead):
-    genotypes: Optional[List[Genotype]] = []
+    genotypes: Optional[list[Genotype]] = []
 
 
 class SampleReadWithAnalysisDeep(SampleRead):
-    analyses: Optional[List[AnalysisReadWithGenotype]] = []
+    analyses: Optional[list[AnalysisReadWithGenotype]] = []
     detail: Optional[SampleDetail]
 
     @validator("detail")
@@ -224,7 +224,7 @@ class AnalysisReadWithSample(AnalysisRead):
     sample: Optional[SampleSlim]
 
 
-def compare_genotypes(genotype_1: Genotype, genotype_2: Genotype) -> Tuple[str, str]:
+def compare_genotypes(genotype_1: Genotype, genotype_2: Genotype) -> tuple[str, str]:
     """Compare two genotypes if they have the same alleles."""
 
     if "0" in genotype_1.alleles or "0" in genotype_2.alleles:
@@ -240,11 +240,11 @@ class AnalysisReadWithSampleDeep(AnalysisRead):
 
 
 class PlateReadWithAnalyses(PlateRead):
-    analyses: Optional[List[AnalysisReadWithSample]] = []
+    analyses: Optional[list[AnalysisReadWithSample]] = []
 
 
 class PlateReadWithAnalysisDetail(PlateRead):
-    analyses: Optional[List[AnalysisReadWithSample]] = []
+    analyses: Optional[list[AnalysisReadWithSample]] = []
     detail: Optional[PlateStatusCounts]
 
     @validator("detail")
@@ -260,7 +260,7 @@ class Config:
 
 
 class PlateReadWithAnalysisDetailSingle(PlateRead):
-    analyses: Optional[List[AnalysisReadWithSample]] = []
+    analyses: Optional[list[AnalysisReadWithSample]] = []
     detail: Optional[PlateStatusCounts]
 
     @validator("detail")