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❯ ./manage_db.sh downgrade release_25.0
Activating virtualenv at .venv
/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/edam_ontology/streams.py:8: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
from pkg_resources import resource_stream
INFO:alembic.runtime.migration:Context impl PostgresqlImpl.
INFO:alembic.runtime.migration:Will assume transactional DDL.
INFO:alembic.runtime.migration:Running downgrade 3af58c192752 -> 338d0e5deb03, Implement sample sheets
DEBUG:alembic.runtime.migration:update 3af58c192752 to 338d0e5deb03
INFO:alembic.runtime.migration:Running downgrade 338d0e5deb03 -> c44ae5f3dcf1, Add cleanup_event_user_assoc table
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/sqlalchemy/engine/base.py", line 1964, in _exec_single_context
self.dialect.do_execute(
~~~~~~~~~~~~~~~~~~~~~~~^
cursor, str_statement, effective_parameters, context
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/sqlalchemy/engine/default.py", line 945, in do_execute
cursor.execute(statement, parameters)
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
psycopg2.errors.UndefinedTable: table "cleanup_event_user_association" does not exist
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/./scripts/db.py", line 37, in <module>
main()
~~~~^^
File "/Users/mvandenb/src/galaxy/./scripts/db.py", line 33, in main
args.func(args)
~~~~~~~~~^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/model/migrations/base.py", line 266, in downgrade
self._exec_command("downgrade", args)
~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/model/migrations/base.py", line 287, in _exec_command
getattr(dbscript, command)(args)
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/model/migrations/base.py", line 205, in downgrade
command.downgrade(self.alembic_config, revision, args.sql)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/alembic/command.py", line 455, in downgrade
script.run_env()
~~~~~~~~~~~~~~^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/alembic/script/base.py", line 586, in run_env
util.load_python_file(self.dir, "env.py")
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/alembic/util/pyfiles.py", line 95, in load_python_file
module = load_module_py(module_id, path)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/alembic/util/pyfiles.py", line 113, in load_module_py
spec.loader.exec_module(module) # type: ignore
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^
File "<frozen importlib._bootstrap_external>", line 1026, in exec_module
File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
File "/Users/mvandenb/src/galaxy/lib/galaxy/model/migrations/alembic/env.py", line 157, in <module>
run_migrations_online()
~~~~~~~~~~~~~~~~~~~~~^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/model/migrations/alembic/env.py", line 40, in run_migrations_online
_configure_and_run_migrations_online(url)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/model/migrations/alembic/env.py", line 121, in _configure_and_run_migrations_online
_run_migrations()
~~~~~~~~~~~~~~~^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/model/migrations/alembic/env.py", line 128, in _run_migrations
context.run_migrations()
~~~~~~~~~~~~~~~~~~~~~~^^
File "<string>", line 8, in run_migrations
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/alembic/runtime/environment.py", line 946, in run_migrations
self.get_context().run_migrations(**kw)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/alembic/runtime/migration.py", line 623, in run_migrations
step.migration_fn(**kw)
~~~~~~~~~~~~~~~~~^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/model/migrations/alembic/versions_gxy/338d0e5deb03_add_cleanup_event_user_assoc_table.py", line 44, in downgrade
drop_table(TABLE_NAME)
~~~~~~~~~~^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/model/migrations/util.py", line 305, in drop_table
DropTable(table_name).run()
~~~~~~~~~~~~~~~~~~~~~~~~~^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/model/migrations/util.py", line 28, in run
return self.execute()
~~~~~~~~~~~~^^
File "/Users/mvandenb/src/galaxy/lib/galaxy/model/migrations/util.py", line 111, in execute
op.drop_table(self.table_name)
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^
File "<string>", line 8, in drop_table
File "<string>", line 3, in drop_table
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/alembic/operations/ops.py", line 1421, in drop_table
operations.invoke(op)
~~~~~~~~~~~~~~~~~^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/alembic/operations/base.py", line 441, in invoke
return fn(self, operation)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/alembic/operations/toimpl.py", line 84, in drop_table
operations.impl.drop_table(
~~~~~~~~~~~~~~~~~~~~~~~~~~^
operation.to_table(operations.migration_context), **kw
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/alembic/ddl/impl.py", line 428, in drop_table
self._exec(schema.DropTable(table, **kw))
~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/alembic/ddl/impl.py", line 246, in _exec
return conn.execute(construct, params)
~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/sqlalchemy/engine/base.py", line 1416, in execute
return meth(
self,
distilled_parameters,
execution_options or NO_OPTIONS,
)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/sqlalchemy/sql/ddl.py", line 187, in _execute_on_connection
return connection._execute_ddl(
~~~~~~~~~~~~~~~~~~~~~~~^
self, distilled_params, execution_options
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/sqlalchemy/engine/base.py", line 1527, in _execute_ddl
ret = self._execute_context(
dialect,
...<4 lines>...
compiled,
)
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/sqlalchemy/engine/base.py", line 1843, in _execute_context
return self._exec_single_context(
~~~~~~~~~~~~~~~~~~~~~~~~~^
dialect, context, statement, parameters
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/sqlalchemy/engine/base.py", line 1983, in _exec_single_context
self._handle_dbapi_exception(
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
e, str_statement, effective_parameters, cursor, context
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/sqlalchemy/engine/base.py", line 2352, in _handle_dbapi_exception
raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/sqlalchemy/engine/base.py", line 1964, in _exec_single_context
self.dialect.do_execute(
~~~~~~~~~~~~~~~~~~~~~~~^
cursor, str_statement, effective_parameters, context
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/Users/mvandenb/src/galaxy/.venv/lib/python3.13/site-packages/sqlalchemy/engine/default.py", line 945, in do_execute
cursor.execute(statement, parameters)
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
sqlalchemy.exc.ProgrammingError: (psycopg2.errors.UndefinedTable) table "cleanup_event_user_association" does not exist
[SQL:
DROP TABLE cleanup_event_user_association]
(Background on this error at: https://sqlalche.me/e/20/f405)
I think that used to be a table created by external scripts ?
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