Cache fix(#50)(patch)

### Fixed
* Workaround for SAWarcning in SQLModel (discussed here: tiangolo/sqlmodel#189)
* Handle missing status detail when analysis is not paired

genotype_api/api/endpoints/analyses.py

@@ -14,6 +14,10 @@
 
 from genotype_api.security import get_active_user
 from genotype_api.file_parsing.vcf import SequenceAnalysis
+from sqlmodel.sql.expression import Select, SelectOfScalar
+
+SelectOfScalar.inherit_cache = True
+Select.inherit_cache = True
 
 router = APIRouter()
 

genotype_api/api/endpoints/plates.py

@@ -27,6 +27,10 @@
     PlateRead,
 )
 from genotype_api.security import get_active_user
+from sqlmodel.sql.expression import Select, SelectOfScalar
+
+SelectOfScalar.inherit_cache = True
+Select.inherit_cache = True
 
 router = APIRouter()
 

genotype_api/api/endpoints/samples.py

@@ -28,10 +28,12 @@
     refresh_sample_status,
 )
 from sqlmodel import Session, select
-from sqlmodel.sql.expression import SelectOfScalar
-
+from sqlmodel.sql.expression import Select, SelectOfScalar
 from genotype_api.security import get_active_user
 
+SelectOfScalar.inherit_cache = True
+Select.inherit_cache = True
+
 
 router = APIRouter()
 
@@ -182,6 +184,8 @@ def get_status_detail(
     current_user: User = Depends(get_active_user),
 ):
     sample: Sample = get_sample(session=session, sample_id=sample_id)
+    if len(sample.analyses) != 2:
+        return StatusDetail()
     return check_sample(sample=sample)
 
 

genotype_api/api/endpoints/snps.py

@@ -7,6 +7,10 @@
 from sqlmodel import Session, delete, select
 
 from genotype_api.security import get_active_user
+from sqlmodel.sql.expression import Select, SelectOfScalar
+
+SelectOfScalar.inherit_cache = True
+Select.inherit_cache = True
 
 router = APIRouter()
 

genotype_api/api/endpoints/users.py

@@ -13,6 +13,11 @@
 from sqlmodel import Session, select
 
 from genotype_api.security import get_active_user
+from sqlmodel.sql.expression import Select, SelectOfScalar
+
+SelectOfScalar.inherit_cache = True
+Select.inherit_cache = True
+
 
 router = APIRouter()
 

genotype_api/crud/analyses.py

@@ -5,6 +5,10 @@
 from genotype_api.constants import TYPES
 from genotype_api.models import Analysis
 from sqlmodel import Session, select
+from sqlmodel.sql.expression import Select, SelectOfScalar
+
+SelectOfScalar.inherit_cache = True
+Select.inherit_cache = True
 
 
 def get_analyses_from_plate(plate_id: int, session: Session) -> List[Analysis]:

genotype_api/crud/plates.py

@@ -2,6 +2,10 @@
 from typing import Optional
 from genotype_api.models import Plate, PlateCreate
 from sqlmodel import Session, select
+from sqlmodel.sql.expression import Select, SelectOfScalar
+
+SelectOfScalar.inherit_cache = True
+Select.inherit_cache = True
 
 LOG = logging.getLogger(__name__)
 
@@ -13,11 +17,6 @@ def get_plate(session: Session, plate_id: int) -> Plate:
     return session.exec(statement).one()
 
 
-def get_plate_by_plate_id(session: Session, plate_id: str) -> Optional[Plate]:
-    statement = select(Plate).where(Plate.plate_id == plate_id)
-    return session.exec(statement).first()
-
-
 def create_plate(session: Session, plate: PlateCreate) -> Plate:
     db_plate = Plate.from_orm(plate)
     db_plate.analyses = plate.analyses  # not sure why from_orm wont pick up the analyses

genotype_api/crud/samples.py

@@ -3,8 +3,11 @@
 from genotype_api.match import check_sample
 from genotype_api.models import Sample, Analysis
 from sqlmodel import Session, func, select
-from sqlmodel.sql.expression import SelectOfScalar
 from fastapi import HTTPException
+from sqlmodel.sql.expression import Select, SelectOfScalar
+
+SelectOfScalar.inherit_cache = True
+Select.inherit_cache = True
 
 
 def get_sample(session: Session, sample_id: str) -> Sample:

genotype_api/crud/users.py

@@ -2,6 +2,10 @@
 
 from genotype_api.models import User, UserCreate
 from sqlmodel import select, Session
+from sqlmodel.sql.expression import Select, SelectOfScalar
+
+SelectOfScalar.inherit_cache = True
+Select.inherit_cache = True
 
 
 def get_user(session: Session, user_id: int):