[23.1] Remove more flushes in database operation tools

[mvdbeek]

We sort of rely on the dataset not being flushed yet in order to bypass the security check for tagging post job actions, so this fixes:

ItemOwnershipException: User does not own item.
  File "galaxy/workflow/run.py", line 233, in invoke
    incomplete_or_none = self._invoke_step(workflow_invocation_step)
  File "galaxy/workflow/run.py", line 309, in _invoke_step
    incomplete_or_none = invocation_step.workflow_step.module.execute(
  File "galaxy/workflow/modules.py", line 2274, in execute
    workflow_invocation_uuid=invocation.uuid.hex,
  File "galaxy/tools/execute.py", line 169, in execute
    execute_single_job(execution_slice, completed_jobs[i], skip=skip)
  File "galaxy/tools/execute.py", line 116, in execute_single_job
    job, result = tool.handle_single_execution(
  File "galaxy/tools/__init__.py", line 1957, in handle_single_execution
    execution_cache=execution_cache,
  File "galaxy/tools/__init__.py", line 1937, in handle_single_execution
    execution_slice,
  File "galaxy/tools/__init__.py", line 2034, in execute
    args[key] = model.User.expand_user_properties(trans.user, param.value)
  File "galaxy/tools/actions/model_operations.py", line 102, in execute
    job_callback(job)
  File "galaxy/workflow/modules.py", line 2284, in <lambda>
    complete = True
  File "galaxy/workflow/modules.py", line 2351, in _handle_post_job_actions
    self.trans.sa_session.add(pjaa)
  File "galaxy/job_execution/actions/post.py", line 575, in execute
    ActionBox.actions[pja.action_type].execute(
  File "galaxy/job_execution/actions/post.py", line 473, in execute
    cls._execute(tag_handler, job.user, dataset_assoc.dataset, tags)
  File "galaxy/job_execution/actions/post.py", line 481, in _execute
    tag_handler.add_tags_from_list(user, output, tags, flush=False)
  File "galaxy/model/tags.py", line 74, in add_tags_from_list
    return self.set_tags_from_list(user, item, new_tags_set, flush=flush)
  File "galaxy/model/tags.py", line 92, in set_tags_from_list
    self.delete_item_tags(user, item)
  File "galaxy/model/tags.py", line 165, in delete_item_tags
    self._ensure_user_owns_item(user, item)
  File "galaxy/model/tags.py", line 193, in _ensure_user_owns_item
    raise ItemOwnershipException("User does not own item.")

(once again).

From https://sentry.galaxyproject.org/share/issue/5b44d1ec20094a2ebe8331b1ef6e58a8/

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[jdavcs]

so, commit depending on the value of flush? (there are 2 unconditional commits at the end of the method)

[mvdbeek]

They can't be eliminated, but the point is to have a uniform interface for the copy method