Useful when creating virtual environments for several Python versions
(e.g. `.venv38`, `.venv312`), which otherwise are linted by tools like
black, isort and flake8.
Sorry, I guess the idea was to not have to build a full MockApp ?
Realisitically all tasks access the database at this point.
I suppose we could make the decorators more specific if necessary ?
Running the test without removing the session yields:
```
celery.app.trace ERROR 2024-01-17 11:49:42,502 [pN:main,p:81158,tN:Thread-2 (start)] Task integration.test_celery_tasks.use_session[0f89df2c-4960-4aac-8e1a-ce431dae6749] raised unexpected: PendingRollbackError("Can't reconnect until invalid transaction is rolled back.")
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/celery/app/trace.py", line 477, in trace_task
R = retval = fun(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/celery/__init__.py", line 181, in wrapper
rval = app.magic_partial(func)(*args, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/lagom/wrapping.py", line 28, in _bound_func
return inner_func(*bound_args, **bound_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/lagom/wrapping.py", line 45, in _error_handling_func
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/test/integration/test_celery_tasks.py", line 42, in use_session
sa_session().query(HistoryDatasetAssociation).get(1)
File "<string>", line 2, in get
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/util/deprecations.py", line 468, in warned
return fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 947, in get
return self._get_impl(ident, loading.load_on_pk_identity)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/query.py", line 951, in _get_impl
return self.session._get_impl(
^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 2975, in _get_impl
return db_load_fn(
^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/loading.py", line 530, in load_on_pk_identity
session.execute(
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/orm/session.py", line 1717, in execute
result = conn._execute_20(statement, params or {}, execution_options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1710, in _execute_20
return meth(self, args_10style, kwargs_10style, execution_options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/sql/elements.py", line 334, in _execute_on_connection
return connection._execute_clauseelement(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1577, in _execute_clauseelement
ret = self._execute_context(
^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 1808, in _execute_context
conn = self._revalidate_connection()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 650, in _revalidate_connection
self._invalid_transaction()
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/base.py", line 622, in _invalid_transaction
raise exc.PendingRollbackError(
sqlalchemy.exc.PendingRollbackError: Can't reconnect until invalid transaction is rolled back. (Background on this error at: https://sqlalche.me/e/14/8s2b)
FAILEDINFO: 127.0.0.1:59776 - "GET /api/jobs?state=running HTTP/1.1" 200 OK
```
The fix here is to set a unique scope for the session registry.
This means that the task is guranteed to get a new, unshared session,
and this session gets removed after completing the task.
The docstring of session.remove says:
```
This will first call :meth:`.Session.close` method
on the current :class:`.Session`, which releases any existing
transactional/connection resources still being held; transactions
specifically are rolled back. The :class:`.Session` is then
discarded. Upon next usage within the same scope,
the :class:`.scoped_session` will produce a new
:class:`.Session` object.
```
which I think is what we want after every celery task (for now, at least).
It might make sense to discard the session for any long-running task
that doesn't require database access in the future.
Fix scope
fixes#16947
also adds a setter to `MockApp` in order to fix the following
which was shown during tests
```
/home/berntm/projects/galaxy/.venv/lib/python3.10/site-packages/_pytest/threadexception.py:73: PytestUnhandledThreadExceptionWarning: Exception in thread Thread-7 (check)
Traceback (most recent call last):
File "/usr/lib/python3.10/threading.py", line 1016, in _bootstrap_inner
self.run()
File "/usr/lib/python3.10/threading.py", line 953, in run
self._target(*self._args, **self._kwargs)
File "/home/berntm/projects/galaxy/lib/galaxy/tool_util/toolbox/watcher.py", line 153, in check
self.reload_callback()
File "/home/berntm/projects/galaxy/lib/galaxy/app_unittest_utils/toolbox_support.py", line 44, in <lambda>
app.watchers.tool_config_watcher.reload_callback = lambda: reload_callback(test_case)
File "/home/berntm/projects/galaxy/lib/galaxy/app_unittest_utils/toolbox_support.py", line 193, in reload_callback
test_case._toolbox = test_case.app.toolbox = SimplifiedToolBox(test_case)
AttributeError: can't set attribute 'toolbox'
warnings.warn(pytest.PytestUnhandledThreadExceptionWarning(msg))
```
Lucille Delisle