Ref #12541

The only fix that was required was a fix to a unit test setup. Here're the details:

Commit instead of flushing in unit test

Rationale:
We use an in-memory sqlite database for quota tests. With SA 2.0 (or with the future flag enabled on the engine), the following conflict happens: (this is a simplified model)

foo = Foo()
session.add(foo)
session.flush()

engine = session.get_bind()
with engine.connect() as conn:
    conn.execute(some-sql)

foo.bar = "new value"
session.commit() # BOOM!!!!  sqlalchemy.orm.exc.StaleDataError: UPDATE statement on table 'galaxy_user' expected to update 1 row(s); 0 were matched.

Reason for BOOM:
With an in-memory database, the underlying dbapi_connection object is the same for the session and the engine.connect(). Here's what happens:

line 10: foo is flushed to the db tmp buffer
line 14: conn is closed on exit from context manager, which issues a rollback, which rolls back whatever is in the tmp buffer - so foo is never inserted.
line 16: foo is updated
line 17: error happens: the session thinks it's updating foo's record in the db, but that record does not exist therefore, "0 rows matched".

Solution: commit instead of flushing - then foo is inserted.

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.