[24.1] Fix importing shared workflows with deeply nested subworkflows

[mvdbeek]

We need to pass the user also to the workflow copy method when copying subworkflow steps. Adds a few bonus type annotations that made it easier to debug.

Fixes
https://sentry.galaxyproject.org/share/issue/454be6bbb98b43a1aa504309e1c6bc7b/::

NotNullViolation: null value in column "user_id" of relation "stored_workflow" violates not-null constraint
DETAIL:  Failing row contains (296863, 2024-12-16 17:04:34.329066, 2024-12-16 17:04:34.329067, null, null, TreeValGal bed to bigwig, f, f, null, f, null, t).

  File "sqlalchemy/engine/base.py", line 2116, in _exec_insertmany_context
    dialect.do_execute(
  File "sqlalchemy/engine/default.py", line 924, in do_execute
    cursor.execute(statement, parameters)
IntegrityError: (psycopg2.errors.NotNullViolation) null value in column "user_id" of relation "stored_workflow" violates not-null constraint
DETAIL:  Failing row contains (296863, 2024-12-16 17:04:34.329066, 2024-12-16 17:04:34.329067, null, null, TreeValGal bed to bigwig, f, f, null, f, null, t).

[SQL: INSERT INTO stored_workflow (create_time, update_time, user_id, latest_workflow_id, name, deleted, hidden, importable, slug, from_path, published) SELECT p0::TIMESTAMP WITHOUT TIME ZONE, p1::TIMESTAMP WITHOUT TIME ZONE, p2::INTEGER, p3::INTEGER, p4:: ... 1138 characters truncated ... p9, p10, sen_counter) ORDER BY sen_counter RETURNING stored_workflow.id, stored_workflow.id AS id__1]
[parameters: {'from_path__0': None, 'user_id__0': 91803, 'name__0': 'TreeValGalBaseOneHaplotype', 'create_time__0': datetime.datetime(2024, 12, 16, 17, 4, 34, 329062), 'update_time__0': datetime.datetime(2024, 12, 16, 17, 4, 34, 329065), 'deleted__0': False, 'published__0': False, 'importable__0': False, 'latest_workflow_id__0': None, 'hidden...
  File "galaxy/web/framework/middleware/error.py", line 167, in __call__
    app_iter = self.application(environ, sr_checker)
  File "/cvmfs/main.galaxyproject.org/venv/lib/python3.11/site-packages/paste/httpexceptions.py", line 635, in __call__
    return self.application(environ, start_response)
  File "galaxy/web/framework/base.py", line 176, in __call__
    return self.handle_request(request_id, path_info, environ, start_response)
  File "galaxy/web/framework/base.py", line 271, in handle_request
    body = method(trans, **kwargs)
  File "galaxy/web/framework/decorators.py", line 94, in decorator
    return func(self, trans, *args, **kwargs)
  File "galaxy/webapps/galaxy/controllers/workflow.py", line 125, in imp
    self._import_shared_workflow(trans, stored)
  File "galaxy/webapps/base/controller.py", line 1161, in _import_shared_workflow
    session.commit()
  File "sqlalchemy/orm/scoping.py", line 597, in commit
    return self._proxied.commit()
  File "sqlalchemy/orm/session.py", line 2017, in commit
    trans.commit(_to_root=True)
  File "<string>", line 2, in commit
    # Copyright (C) 2005-2024 the SQLAlchemy authors and contributors
  File "sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
  File "sqlalchemy/orm/session.py", line 1302, in commit
    self._prepare_impl()
  File "<string>", line 2, in _prepare_impl
    # Copyright (C) 2005-2024 the SQLAlchemy authors and contributors
  File "sqlalchemy/orm/state_changes.py", line 139, in _go
    ret_value = fn(self, *arg, **kw)
  File "sqlalchemy/orm/session.py", line 1277, in _prepare_impl
    self.session.flush()
  File "sqlalchemy/orm/session.py", line 4341, in flush
    self._flush(objects)
  File "sqlalchemy/orm/session.py", line 4476, in _flush
    with util.safe_reraise():
  File "sqlalchemy/util/langhelpers.py", line 146, in __exit__
    raise exc_value.with_traceback(exc_tb)
  File "sqlalchemy/orm/session.py", line 4437, in _flush
    flush_context.execute()
  File "sqlalchemy/orm/unitofwork.py", line 466, in execute
    rec.execute(self)
  File "sqlalchemy/orm/unitofwork.py", line 642, in execute
    util.preloaded.orm_persistence.save_obj(
  File "sqlalchemy/orm/persistence.py", line 93, in save_obj
    _emit_insert_statements(
  File "sqlalchemy/orm/persistence.py", line 1143, in _emit_insert_statements
    result = connection.execute(
  File "sqlalchemy/engine/base.py", line 1418, in execute
    return meth(
  File "sqlalchemy/sql/elements.py", line 515, in _execute_on_connection
    return connection._execute_clauseelement(
  File "sqlalchemy/engine/base.py", line 1640, in _execute_clauseelement
    ret = self._execute_context(
  File "sqlalchemy/engine/base.py", line 1844, in _execute_context
    return self._exec_insertmany_context(dialect, context)
  File "sqlalchemy/engine/base.py", line 2124, in _exec_insertmany_context
    self._handle_dbapi_exception(
  File "sqlalchemy/engine/base.py", line 2353, in _handle_dbapi_exception
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "sqlalchemy/engine/base.py", line 2116, in _exec_insertmany_context
    dialect.do_execute(
  File "sqlalchemy/engine/default.py", line 924, in do_execute
    cursor.execute(statement, parameters)

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• I've included appropriate automated tests.
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  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

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[nsoranzo]

Thanks!