fix warnings

genotype_api/api/app.py

@@ -7,15 +7,14 @@
 from fastapi.responses import JSONResponse
 from fastapi.middleware.cors import CORSMiddleware
 
-from genotype_api.config import security_settings, DBSettings, settings
+from genotype_api.config import security_settings, settings
 from genotype_api.database.database import create_all_tables, initialise_database, close_session
 from genotype_api.api.endpoints import samples, snps, users, plates, analyses
 from sqlalchemy.exc import NoResultFound
 
 app = FastAPI(
     root_path=security_settings.api_root_path,
     root_path_in_servers=True,
-    openapi_prefix=security_settings.api_root_path,
 )
 app.add_middleware(
     CORSMiddleware,

genotype_api/dto/plate.py

@@ -18,7 +18,7 @@ class PlateStatusCounts(BaseModel):
     commented: int = Field(0, nullable=True)
 
     class Config:
-        allow_population_by_field_name = True
+        populate_by_name = True
 
 
 class UserOnPlate(BaseModel):
@@ -66,4 +66,4 @@ def check_detail(cls, value, values):
         return PlateStatusCounts(**status_counts, total=len(analyses), commented=commented)
 
     class Config:
-        validate_all = True
+        validate_default = True

genotype_api/models.py

@@ -40,7 +40,7 @@ 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):