update(pydantic)

genotype_api/api/endpoints/samples.py

@@ -9,7 +9,6 @@
 from starlette import status
 
 import genotype_api.database.crud.create
-from genotype_api.constants import SEXES
 from genotype_api.database.crud.read import (
     get_commented_samples,
     get_incomplete_samples,
@@ -26,6 +25,7 @@
     SampleReadWithAnalysisDeep,
     User,
     compare_genotypes,
+    Sexes,
 )
 from genotype_api.database.session_handler import get_session
 from genotype_api.match import check_sample
@@ -122,9 +122,9 @@ def create_sample(
 @router.put("/{sample_id}/sex", response_model=SampleRead)
 def update_sex(
     sample_id: str,
-    sex: SEXES = Query(...),
-    genotype_sex: SEXES | None = None,
-    sequence_sex: SEXES | None = None,
+    sex: Sexes = Query(...),
+    genotype_sex: Sexes | None = None,
+    sequence_sex: Sexes | None = None,
     session: Session = Depends(get_session),
     current_user: User = Depends(get_active_user),
 ):

genotype_api/config.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from pydantic import BaseSettings
+from pydantic_settings import BaseSettings
 
 GENOTYPE_PACKAGE = Path(__file__).parent
 PACKAGE_ROOT: Path = GENOTYPE_PACKAGE.parent
@@ -22,10 +22,10 @@ class Config:
 class SecuritySettings(BaseSettings):
     """Settings for serving the genotype-api app"""
 
-    client_id = ""
-    algorithm = ""
-    jwks_uri = "https://www.googleapis.com/oauth2/v3/certs"
-    api_root_path = "/"
+    client_id: str = ""
+    algorithm: str = ""
+    jwks_uri: str = "https://www.googleapis.com/oauth2/v3/certs"
+    api_root_path: str = "/"
 
     class Config:
         env_file = str(ENV_FILE)

genotype_api/constants.py

@@ -1,24 +1 @@
 """Constants used over the package"""
-
-from enum import Enum
-from pydantic import BaseModel
-
-
-class TYPES(str, Enum):
-    GENOTYPE = "genotype"
-    SEQUENCE = "sequence"
-
-
-class SEXES(str, Enum):
-    MALE = "male"
-    FEMALE = "female"
-    UNKNOWN = "unknown"
-
-
-class STATUS(str, Enum):
-    PASS = "pass"
-    FAIL = "fail"
-    CANCEL = "cancel"
-
-
-CUTOFS = dict(max_nocalls=15, max_mismatch=3, min_matches=35)

genotype_api/database/crud/read.py

@@ -4,8 +4,7 @@
 from sqlmodel import Session, select
 from sqlmodel.sql.expression import Select, SelectOfScalar
 
-from genotype_api.constants import TYPES
-from genotype_api.database.models import Analysis, Plate, Sample, User
+from genotype_api.database.models import Analysis, Plate, Sample, User, AnalysisTypes
 
 SelectOfScalar.inherit_cache = True
 Select.inherit_cache = True
@@ -96,7 +95,7 @@ def get_users(session: Session, skip: int = 0, limit: int = 100) -> list[User]:
 
 
 def check_analyses_objects(
-    session: Session, analyses: list[Analysis], analysis_type: TYPES
+    session: Session, analyses: list[Analysis], analysis_type: AnalysisTypes
 ) -> None:
     """Raising 400 if any analysis in the list already exist in the database"""
     for analysis_obj in analyses:

genotype_api/database/models.py

@@ -1,19 +1,39 @@
+import enum
 from collections import Counter
 from datetime import datetime
 
-from pydantic import EmailStr, constr, validator
+
+from pydantic import validator
 from sqlalchemy import Index
 from sqlmodel import Field, Relationship, SQLModel
-
-from genotype_api.constants import CUTOFS, SEXES, STATUS, TYPES
 from genotype_api.models import PlateStatusCounts, SampleDetail
 
 
+class AnalysisTypes(enum.Enum):
+    GENOTYPE: str = "genotype"
+    SEQUENCE: str = "sequence"
+
+
+class Sexes(enum.Enum):
+    MALE: str = "male"
+    FEMALE: str = "female"
+    UNKNOWN: str = "unknown"
+
+
+class Status(enum.Enum):
+    PASS: str = "pass"
+    FAIL: str = "fail"
+    CANCEL: str = "cancel"
+
+
+CUTOFS = dict(max_nocalls=15, max_mismatch=3, min_matches=35)
+
+
 class GenotypeBase(SQLModel):
-    rsnumber: constr(max_length=10) | None
+    rsnumber: str | None = Field(max_length=10)
     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
+    allele_1: str | None = Field(max_length=1)
+    allele_2: str | None = Field(max_length=1)
 
 
 class Genotype(GenotypeBase, table=True):
@@ -44,11 +64,11 @@ class GenotypeCreate(GenotypeBase):
 
 
 class AnalysisBase(SQLModel):
-    type: TYPES
+    type: AnalysisTypes
     source: str | None
-    sex: SEXES | None
+    sex: Sexes | None
     created_at: datetime | None = datetime.now()
-    sample_id: constr(max_length=32) | None = Field(default=None, foreign_key="sample.id")
+    sample_id: str | None = Field(default=None, foreign_key="sample.id", max_length=32)
     plate_id: str | None = Field(default=None, foreign_key="plate.id")
 
 
@@ -76,18 +96,18 @@ class AnalysisCreate(AnalysisBase):
 
 
 class SampleSlim(SQLModel):
-    status: STATUS | None
+    status: Status | None
     comment: str | None
 
 
 class SampleBase(SampleSlim):
-    sex: SEXES | None
+    sex: Sexes | None
     created_at: datetime | None = datetime.now()
 
 
 class Sample(SampleBase, table=True):
     __tablename__ = "sample"
-    id: constr(max_length=32) | None = Field(default=None, primary_key=True)
+    id: str | None = Field(default=None, primary_key=True, max_length=32)
 
     analyses: list["Analysis"] = Relationship(back_populates="sample")
 
@@ -113,32 +133,32 @@ def sequence_analysis(self) -> Analysis | None:
 
 
 class SampleRead(SampleBase):
-    id: constr(max_length=32)
+    id: str = Field(max_length=32)
 
 
 class SampleCreate(SampleBase):
     pass
 
 
 class SNPBase(SQLModel):
-    ref: constr(max_length=1) | None
-    chrom: constr(max_length=5) | None
+    ref: str | None = Field(max_length=1)
+    chrom: str | None = Field(max_length=5)
     pos: int | None
 
 
 class SNP(SNPBase, table=True):
     __tablename__ = "snp"
     """Represent a SNP position under investigation."""
 
-    id: constr(max_length=32) | None = Field(default=None, primary_key=True)
+    id: str | None = Field(default=None, primary_key=True, max_length=32)
 
 
 class SNPRead(SNPBase):
-    id: constr(max_length=32)
+    id: str = Field(max_length=32)
 
 
 class UserBase(SQLModel):
-    email: EmailStr = Field(index=True, unique=True)
+    email: str = Field(index=True, unique=True)
     name: str | None = ""
 
 
@@ -158,7 +178,7 @@ class UserCreate(UserBase):
 
 class PlateBase(SQLModel):
     created_at: datetime | None = datetime.now()
-    plate_id: constr(max_length=16) = Field(index=True, unique=True)
+    plate_id: str = Field(index=True, unique=True, max_length=16)
     signed_by: int | None = Field(default=None, foreign_key="user.id")
     signed_at: datetime | None
     method_document: str | None
@@ -216,7 +236,7 @@ def get_detail(cls, value, values) -> SampleDetail:
         return SampleDetail(**status, sex=sex)
 
     class Config:
-        validate_all = True
+        validate_default = True
 
 
 class AnalysisReadWithSample(AnalysisRead):
@@ -255,7 +275,7 @@ def check_detail(cls, value, values):
         return PlateStatusCounts(**status_counts, total=len(analyses), commented=commented)
 
     class Config:
-        validate_all = True
+        validate_default = True
 
 
 class PlateReadWithAnalysisDetailSingle(PlateRead):
@@ -271,7 +291,7 @@ def check_detail(cls, value, values):
         return PlateStatusCounts(**status_counts, total=len(analyses), commented=commented)
 
     class Config:
-        validate_all = True
+        validate_default = True
 
 
 def check_snps(genotype_analysis, sequence_analysis):
@@ -303,9 +323,9 @@ def check_snps(genotype_analysis, sequence_analysis):
 
 def check_sex(sample_sex, genotype_analysis, sequence_analysis):
     """Check if any source disagrees on the sex"""
-    if not sample_sex or genotype_analysis.sex == SEXES.UNKNOWN:
+    if not sample_sex or genotype_analysis.sex == Sexes.UNKNOWN:
         return "fail"
     sexes = {genotype_analysis.sex, sequence_analysis.sex, sample_sex}
-    if {SEXES.MALE, SEXES.FEMALE}.issubset(sexes):
+    if {Sexes.MALE, Sexes.FEMALE}.issubset(sexes):
         return "fail"
     return "pass"

genotype_api/models.py

@@ -11,7 +11,7 @@ class PlateStatusCounts(BaseModel):
     commented: int = Field(0, nullable=True)
 
     class Config:
-        allow_population_by_field_name = True
+        populate_by_name = True
 
 
 class SampleDetailStats(BaseModel):
@@ -53,7 +53,7 @@ def validate_status(cls, value, values) -> SampleDetailStatus:
         return SampleDetailStatus(sex=sex, snps=snps, nocalls=nocalls)
 
     class Config:
-        validate_all = True
+        validate_default = True
 
 
 class MatchCounts(BaseModel):

requirements.txt

@@ -1,18 +1,19 @@
-SQLAlchemy==1.4.30
+SQLAlchemy
 aiofiles
 bcrypt
 bump2version
 click
 coloredlogs
 email-validator
-fastapi==0.75.0
+fastapi
 google-auth
 gunicorn
 httptools
 numpy
 openpyxl
 passlib
-pydantic==1.10.14
+pydantic
+pydantic-settings
 pymysql
 python-dotenv
 python-jose[cryptography]