[24.0] Fix InvalidRequestError: Can't operate on closed transaction inside context manager. Please complete the context manager before emitting further commands.

[mvdbeek]

This reverts commit 061d4c3.

Fixes:

Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/handler.py", line 1083, in __monitor
    self.__monitor_step()
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/handler.py", line 1115, in __monitor_step
    self._check_jobs(session, jobs_to_check)
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/handler.py", line 1181, in _check_jobs
    self.__stop(job, session)
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/handler.py", line 1099, in __stop
    job.set_state(job.states.STOPPED)
  File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/__init__.py", line 1703, in set_state
    self.state_history.append(JobStateHistory(self))
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/attributes.py", line 487, in __get__
    return self.impl.get(state, dict_)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/attributes.py", line 959, in get
    value = self._fire_loader_callables(state, key, passive)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/attributes.py", line 995, in _fire_loader_callables
    return self.callable_(state, passive)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/strategies.py", line 912, in _load_for_state
    return self._emit_lazyload(
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/strategies.py", line 1022, in _emit_lazyload
    lazy_clause, params = self._generate_lazy_clause(state, passive)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/strategies.py", line 807, in _generate_lazy_clause
    value = mapper._get_state_attr_by_column(
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/mapper.py", line 3018, in _get_state_attr_by_column
    return state.manager[prop.key].impl.get(state, dict_, passive=passive)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/attributes.py", line 959, in get
    value = self._fire_loader_callables(state, key, passive)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/attributes.py", line 990, in _fire_loader_callables
    return state._load_expired(state, passive)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/state.py", line 712, in _load_expired
    self.manager.expired_attribute_loader(self, toload, passive)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/loading.py", line 1451, in load_scalar_attributes
    result = load_on_ident(
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/loading.py", line 407, in load_on_ident
    return load_on_pk_identity(
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/loading.py", line 530, in load_on_pk_identity
    session.execute(
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1716, in execute
    conn = self._connection_for_bind(bind)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1552, in _connection_for_bind
    TransactionalContext._trans_ctx_check(self)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.8/site-packages/sqlalchemy/engine/util.py", line 199, in _trans_ctx_check
    raise exc.InvalidRequestError(
sqlalchemy.exc.InvalidRequestError: Can't operate on closed transaction inside context manager.  Please complete the context manager before emitting further commands.

at the cost of larger transactions that are more likely to deadlock. Still likely a better tradeoff. Probably fixes
test/integration/test_interactivetools_api.py::TestInteractiveToolsIntegration::test_multi_server_realtime_tool.

(Please replace this header with a description of your pull request. Please include BOTH what you did and why you made the changes. The "why" may simply be citing a relevant Galaxy issue.)
(If fixing a bug, please add any relevant error or traceback)
(For UI components, it is recommended to include screenshots or screencasts)

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.