Upgrade sqlalchemy

Adapt code to prevent new warnings and errors (as of SQLAlchemy 1.4):
- Overlapping foreign key columns could be set in a conflicting way
  => This is prevented by the application logic
  => Ignore the warning by setting a `overlaps` flag
- Transaction already rolled back
  => This only happens when tests cause an `IntegrityError` on purpose
  => Filter away the corresponding warning in the fixture
- Query returns `Row` objects and not scalars
  => Add genexpr to pull out `primary_id`