refactor(backend): replace db.query() with select()

[eatyourgreens]

Replace the legacy SQLAlchemy Query API with select() in the backend API.

• closes The query API is legacy in SQLAlchemy 2 #209.

[eatyourgreens]

@tomalrussell @mz8i I think these changes can also be applied to https://github.com/nismod/infra-risk-vis.

[tomalrussell]

A couple of queries here (and with deleting app/dependencies.py)

First, if we drop the use sessionmaker, do we also want to go back to default autoflush=True? I think dropping the other arguments wouldn't make a difference: autocommit=False is already the default, and bind can be replaced by passing engine as the first parameter.

https://docs.sqlalchemy.org/en/20/orm/session_basics.html#using-a-sessionmaker

Second, as I read the docs, it's not thread-safe to create a single module-level session variable, and for FastAPI these should be constructed once per request. FastAPI have a slightly lighter recommendation now, where we can pass in session: SessionDep as a parameter instead of db: Session = Depends(get_db):

# in backend.db.database:
def get_session():
    with Session(engine) as session:
        yield session


SessionDep = Annotated[Session, Depends(get_session)]

# in e.g. backend.app.routers.features:
@router.get("/{feature_id}", response_model=schemas.FeatureOut)
def read_feature(feature_id: int, session: SessionDep):

https://fastapi.tiangolo.com/tutorial/sql-databases/#create-a-session-dependency

[eatyourgreens]

Thanks for taking a look. I've updated this to follow the changes in nismod/infra-risk-vis#190, and added sessionmaker back in with autoFlush=False for all sessions.

[eatyourgreens]

Hmmmm, might have spoken too soon. I'm now seeing this in the backend logs on this branch.

TypeError: Session.__init__() got an unexpected keyword argument 'autoFlush'

[eatyourgreens]

My mistake, there's a typo in autoFlush.

[eatyourgreens]

Should all be working now.