feat(pep_0604): (#103)

### Changed

- Refactor to pep0605

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 Literal, Optional
+from typing import Literal
 
 from fastapi import APIRouter, Depends, File, HTTPException, Query, UploadFile, status
 from fastapi.responses import JSONResponse
@@ -139,10 +139,10 @@ def read_plate(
     response_model_by_alias=False,
 )
 async def read_plates(
-    order_by: Optional[Literal["created_at", "plate_id", "signed_at", "id"]] = "id",
-    sort_order: Optional[Literal["ascend", "descend"]] = "descend",
-    skip: Optional[int] = 0,
-    limit: Optional[int] = 10,
+    order_by: Literal["created_at", "plate_id", "signed_at", "id"] | None = "id",
+    sort_order: Literal["ascend", "descend"] | None = "descend",
+    skip: int | None = 0,
+    limit: int | None = 10,
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ):

genotype_api/api/endpoints/samples.py

@@ -1,6 +1,6 @@
 from collections import Counter
 from datetime import date, timedelta
-from typing import Literal, Optional
+from typing import Literal
 
 from fastapi import APIRouter, Depends, Query
 from fastapi.responses import JSONResponse
@@ -85,11 +85,11 @@ def read_sample(
 def read_samples(
     skip: int = 0,
     limit: int = Query(default=10, lte=10),
-    sample_id: Optional[str] = None,
-    plate_id: Optional[str] = None,
-    incomplete: Optional[bool] = False,
-    commented: Optional[bool] = False,
-    status_missing: Optional[bool] = False,
+    sample_id: str | None = None,
+    plate_id: str | None = None,
+    incomplete: bool | None = False,
+    commented: bool | None = False,
+    status_missing: bool | None = False,
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ) -> list[Sample]:
@@ -123,8 +123,8 @@ def create_sample(
 def update_sex(
     sample_id: str,
     sex: SEXES = Query(...),
-    genotype_sex: Optional[SEXES] = None,
-    sequence_sex: Optional[SEXES] = None,
+    genotype_sex: SEXES | None = None,
+    sequence_sex: SEXES | None = None,
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ):
@@ -166,7 +166,7 @@ def update_comment(
 def set_sample_status(
     sample_id: str,
     session: Session = Depends(get_session),
-    status: Optional[Literal["pass", "fail", "cancel"]] = None,
+    status: Literal["pass", "fail", "cancel"] | None = None,
     current_user: User = Depends(get_active_user),
 ):
     """Check sample analyses and update sample status accordingly."""
@@ -184,8 +184,8 @@ def match(
     sample_id: str,
     analysis_type: Literal["genotype", "sequence"],
     comparison_set: Literal["genotype", "sequence"],
-    date_min: Optional[date] = date.min,
-    date_max: Optional[date] = date.max,
+    date_min: date | None = date.min,
+    date_max: date | None = date.max,
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ) -> list[MatchResult]:

genotype_api/database/crud/delete.py

@@ -1,10 +1,9 @@
 import logging
-from typing import Optional
 
 from sqlmodel import Session
+from sqlmodel.sql.expression import Select, SelectOfScalar
 
 from genotype_api.database.models import Analysis, Plate
-from sqlmodel.sql.expression import Select, SelectOfScalar
 
 SelectOfScalar.inherit_cache = True
 Select.inherit_cache = True
@@ -19,7 +18,7 @@ def delete_analysis(session: Session, analysis_id: int) -> Analysis:
     return db_analysis
 
 
-def delete_plate(session: Session, plate_id: int) -> Optional[Plate]:
+def delete_plate(session: Session, plate_id: int) -> Plate | None:
     db_plate: Plate = session.get(Plate, plate_id)
     if not db_plate:
         LOG.info(f"Could not find plate {plate_id}")

genotype_api/database/crud/read.py

@@ -1,5 +1,4 @@
 import logging
-from typing import Optional
 
 from sqlalchemy import func
 from sqlmodel import Session, select
@@ -21,7 +20,7 @@ def get_analyses_from_plate(plate_id: int, session: Session) -> list[Analysis]:
 
 def get_analysis_type_sample(
     sample_id: str, analysis_type: str, session: Session
-) -> Optional[Analysis]:
+) -> Analysis | None:
     statement = select(Analysis).where(
         Analysis.sample_id == sample_id, Analysis.type == analysis_type
     )
@@ -86,7 +85,7 @@ def get_user(session: Session, user_id: int):
     return session.exec(statement).one()
 
 
-def get_user_by_email(session: Session, email: str) -> Optional[User]:
+def get_user_by_email(session: Session, email: str) -> User | None:
     statement = select(User).where(User.email == email)
     return session.exec(statement).first()
 

genotype_api/database/models.py

@@ -1,6 +1,5 @@
 from collections import Counter
 from datetime import datetime
-from typing import Optional
 
 from pydantic import EmailStr, constr, validator
 from sqlalchemy import Index
@@ -11,18 +10,18 @@
 
 
 class GenotypeBase(SQLModel):
-    rsnumber: Optional[constr(max_length=10)]
-    analysis_id: Optional[int] = Field(default=None, foreign_key="analysis.id")
-    allele_1: Optional[constr(max_length=1)]
-    allele_2: Optional[constr(max_length=1)]
+    rsnumber: constr(max_length=10) | None
+    analysis_id: int | None = Field(default=None, foreign_key="analysis.id")
+    allele_1: constr(max_length=1) | None
+    allele_2: constr(max_length=1) | None
 
 
 class Genotype(GenotypeBase, table=True):
     __tablename__ = "genotype"
     __table_args__ = (Index("_analysis_rsnumber", "analysis_id", "rsnumber", unique=True),)
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
 
-    analysis: Optional["Analysis"] = Relationship(back_populates="genotypes")
+    analysis: "Analysis" = Relationship(back_populates="genotypes")
 
     @property
     def alleles(self) -> list[str]:
@@ -46,21 +45,21 @@ class GenotypeCreate(GenotypeBase):
 
 class AnalysisBase(SQLModel):
     type: TYPES
-    source: Optional[str]
-    sex: Optional[SEXES]
-    created_at: Optional[datetime] = datetime.now()
-    sample_id: Optional[constr(max_length=32)] = Field(default=None, foreign_key="sample.id")
-    plate_id: Optional[str] = Field(default=None, foreign_key="plate.id")
+    source: str | None
+    sex: SEXES | None
+    created_at: datetime | None = datetime.now()
+    sample_id: constr(max_length=32) | None = Field(default=None, foreign_key="sample.id")
+    plate_id: str | None = Field(default=None, foreign_key="plate.id")
 
 
 class Analysis(AnalysisBase, table=True):
     __tablename__ = "analysis"
     __table_args__ = (Index("_sample_type", "sample_id", "type", unique=True),)
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = 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")
+    sample: "Sample" = Relationship(back_populates="analyses")
+    plate: list["Plate"] = Relationship(back_populates="analyses")
+    genotypes: list["Genotype"] = Relationship(back_populates="analysis")
 
     def check_no_calls(self) -> dict[str, int]:
         """Check that genotypes look ok."""
@@ -77,23 +76,23 @@ class AnalysisCreate(AnalysisBase):
 
 
 class SampleSlim(SQLModel):
-    status: Optional[STATUS]
-    comment: Optional[str]
+    status: STATUS | None
+    comment: str | None
 
 
 class SampleBase(SampleSlim):
-    sex: Optional[SEXES]
-    created_at: Optional[datetime] = datetime.now()
+    sex: SEXES | None
+    created_at: datetime | None = datetime.now()
 
 
 class Sample(SampleBase, table=True):
     __tablename__ = "sample"
-    id: Optional[constr(max_length=32)] = Field(default=None, primary_key=True)
+    id: constr(max_length=32) | None = Field(default=None, primary_key=True)
 
-    analyses: Optional[list["Analysis"]] = Relationship(back_populates="sample")
+    analyses: list["Analysis"] = Relationship(back_populates="sample")
 
     @property
-    def genotype_analysis(self) -> Optional[Analysis]:
+    def genotype_analysis(self) -> Analysis | None:
         """Return genotype analysis."""
 
         for analysis in self.analyses:
@@ -103,7 +102,7 @@ def genotype_analysis(self) -> Optional[Analysis]:
         return None
 
     @property
-    def sequence_analysis(self) -> Optional[Analysis]:
+    def sequence_analysis(self) -> Analysis | None:
         """Return sequence analysis."""
 
         for analysis in self.analyses:
@@ -122,16 +121,16 @@ class SampleCreate(SampleBase):
 
 
 class SNPBase(SQLModel):
-    ref: Optional[constr(max_length=1)]
-    chrom: Optional[constr(max_length=5)]
-    pos: Optional[int]
+    ref: constr(max_length=1) | None
+    chrom: constr(max_length=5) | None
+    pos: int | None
 
 
 class SNP(SNPBase, table=True):
     __tablename__ = "snp"
     """Represent a SNP position under investigation."""
 
-    id: Optional[constr(max_length=32)] = Field(default=None, primary_key=True)
+    id: constr(max_length=32) | None = Field(default=None, primary_key=True)
 
 
 class SNPRead(SNPBase):
@@ -140,13 +139,13 @@ class SNPRead(SNPBase):
 
 class UserBase(SQLModel):
     email: EmailStr = Field(index=True, unique=True)
-    name: Optional[str] = ""
+    name: str | None = ""
 
 
 class User(UserBase, table=True):
     __tablename__ = "user"
-    id: Optional[int] = Field(default=None, primary_key=True)
-    plates: Optional[list["Plate"]] = Relationship(back_populates="user")
+    id: int | None = Field(default=None, primary_key=True)
+    plates: list["Plate"] = Relationship(back_populates="user")
 
 
 class UserRead(UserBase):
@@ -158,45 +157,45 @@ class UserCreate(UserBase):
 
 
 class PlateBase(SQLModel):
-    created_at: Optional[datetime] = datetime.now()
+    created_at: datetime | None = datetime.now()
     plate_id: constr(max_length=16) = Field(index=True, unique=True)
-    signed_by: Optional[int] = Field(default=None, foreign_key="user.id")
-    signed_at: Optional[datetime]
-    method_document: Optional[str]
-    method_version: Optional[str]
+    signed_by: int | None = Field(default=None, foreign_key="user.id")
+    signed_at: datetime | None
+    method_document: str | None
+    method_version: str | None
 
 
 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")
+    id: int | None = Field(default=None, primary_key=True)
+    user: "User" = Relationship(back_populates="plates")
+    analyses: list["Analysis"] = Relationship(back_populates="plate")
 
 
 class PlateRead(PlateBase):
     id: str
-    user: Optional[UserRead]
+    user: UserRead | None
 
 
 class PlateCreate(PlateBase):
-    analyses: Optional[list[Analysis]] = []
+    analyses: list[Analysis] | None = []
 
 
 class UserReadWithPlates(UserRead):
-    plates: Optional[list[Plate]] = []
+    plates: list[Plate] | None = []
 
 
 class SampleReadWithAnalysis(SampleRead):
-    analyses: Optional[list[AnalysisRead]] = []
+    analyses: list[AnalysisRead] | None = []
 
 
 class AnalysisReadWithGenotype(AnalysisRead):
-    genotypes: Optional[list[Genotype]] = []
+    genotypes: list[Genotype] | None = []
 
 
 class SampleReadWithAnalysisDeep(SampleRead):
-    analyses: Optional[list[AnalysisReadWithGenotype]] = []
-    detail: Optional[SampleDetail]
+    analyses: list[AnalysisReadWithGenotype] | None = []
+    detail: SampleDetail | None
 
     @validator("detail")
     def get_detail(cls, value, values) -> SampleDetail:
@@ -221,7 +220,7 @@ class Config:
 
 
 class AnalysisReadWithSample(AnalysisRead):
-    sample: Optional[SampleSlim]
+    sample: SampleSlim | None
 
 
 def compare_genotypes(genotype_1: Genotype, genotype_2: Genotype) -> tuple[str, str]:
@@ -236,16 +235,16 @@ def compare_genotypes(genotype_1: Genotype, genotype_2: Genotype) -> tuple[str,
 
 
 class AnalysisReadWithSampleDeep(AnalysisRead):
-    sample: Optional[SampleReadWithAnalysisDeep]
+    sample: SampleReadWithAnalysisDeep | None
 
 
 class PlateReadWithAnalyses(PlateRead):
-    analyses: Optional[list[AnalysisReadWithSample]] = []
+    analyses: list[AnalysisReadWithSample] | None = []
 
 
 class PlateReadWithAnalysisDetail(PlateRead):
-    analyses: Optional[list[AnalysisReadWithSample]] = []
-    detail: Optional[PlateStatusCounts]
+    analyses: list[AnalysisReadWithSample] | None = []
+    detail: PlateStatusCounts | None
 
     @validator("detail")
     def check_detail(cls, value, values):
@@ -260,8 +259,8 @@ class Config:
 
 
 class PlateReadWithAnalysisDetailSingle(PlateRead):
-    analyses: Optional[list[AnalysisReadWithSample]] = []
-    detail: Optional[PlateStatusCounts]
+    analyses: list[AnalysisReadWithSample] | None = []
+    detail: PlateStatusCounts | None
 
     @validator("detail")
     def check_detail(cls, value, values):

genotype_api/file_parsing/excel.py

@@ -2,7 +2,7 @@
 
 import logging
 from pathlib import Path
-from typing import ByteString, Iterable, Optional
+from typing import ByteString, Iterable
 
 import openpyxl
 from openpyxl.workbook import Workbook
@@ -25,11 +25,11 @@ class GenotypeAnalysis:
 
     """
 
-    def __init__(self, excel_file: ByteString, file_name: str, include_key: Optional[str] = None):
+    def __init__(self, excel_file: ByteString, file_name: str, include_key: str | None = None):
         LOG.info("Loading genotype information from %s", excel_file)
         self.source: str = file_name
         self.wb: Workbook = openpyxl.load_workbook(filename=excel_file)
-        self.include_key: Optional[str] = include_key
+        self.include_key: str | None = include_key
         self.work_sheet: Worksheet = self.find_sheet(excel_db=self.wb)
         self.header_row: list[str] = self.get_header_cols(self.work_sheet)
         self.snp_start: int = GenotypeAnalysis.find_column(self.header_row, pattern="rs")
@@ -60,7 +60,7 @@ def find_column(header_row: list[str], pattern="rs") -> int:
                 return index
 
     @staticmethod
-    def parse_sample_id(sample_id: str, include_key: str = None) -> Optional[str]:
+    def parse_sample_id(sample_id: str, include_key: str = None) -> str | None:
         """Build samples from Excel sheet."""
         LOG.info("Parse sample id from %s using include_key: %s", sample_id, include_key)
         if include_key: