We needed to upgrade from 22.05 to 24.01 to support the new Slurm version.
sh manage_db.sh upgrade fails. If I could find the SQL lines being executed, I would try to do so manually. But they appear to be buried inside layers of objects. Here’s the full message:
sh manage_db.sh upgrade
Activating virtualenv at .venv
INFO:alembic.runtime.migration:Context impl SQLiteImpl.
INFO:alembic.runtime.migration:Will assume non-transactional DDL.
INFO:alembic.runtime.migration:Running upgrade c63848676caf → 04288b6a5b25, make dataset uuids unique
Traceback (most recent call last):
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1967, in _exec_single_context
self.dialect.do_execute(
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/sqlalchemy/engine/default.py”, line 924, in do_execute
cursor.execute(statement, parameters)
sqlite3.OperationalError: near “FROM”: syntax error
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/./scripts/db.py”, line 37, in
main()
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/./scripts/db.py”, line 33, in main
args.func(args)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/lib/galaxy/model/migrations/base.py”, line 265, in upgrade
self._exec_command(“upgrade”, args)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/lib/galaxy/model/migrations/base.py”, line 289, in _exec_command
getattr(dbscript, command)(args)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/lib/galaxy/model/migrations/base.py”, line 202, in upgrade
self._upgrade_to_head(args.sql)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/lib/galaxy/model/migrations/dbscript.py”, line 88, in _upgrade_to_head
self._upgrade_to_revision(“gxy@head”, is_sql_mode)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/lib/galaxy/model/migrations/base.py”, line 234, in _upgrade_to_revision
command.upgrade(self.alembic_config, rev, is_sql_mode)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/alembic/command.py”, line 403, in upgrade
script.run_env()
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/alembic/script/base.py”, line 583, in run_env
util.load_python_file(self.dir, “env.py”)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/alembic/util/pyfiles.py”, line 95, in load_python_file
module = load_module_py(module_id, path)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/alembic/util/pyfiles.py”, line 113, in load_module_py
spec.loader.exec_module(module) # type: ignore
File “”, line 883, in exec_module
File “”, line 241, in _call_with_frames_removed
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/lib/galaxy/model/migrations/alembic/env.py”, line 146, in
run_migrations_online()
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/lib/galaxy/model/migrations/alembic/env.py”, line 40, in run_migrations_online
_configure_and_run_migrations_online(url)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/lib/galaxy/model/migrations/alembic/env.py”, line 123, in _configure_and_run_migrations_online
context.run_migrations()
File “”, line 8, in run_migrations
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/alembic/runtime/environment.py”, line 948, in run_migrations
self.get_context().run_migrations(**kw)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/alembic/runtime/migration.py”, line 627, in run_migrations
step.migration_fn(**kw)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/lib/galaxy/model/migrations/alembic/versions_gxy/04288b6a5b25_make_dataset_uuids_unique.py”, line 73, in upgrade
_update_dataset_associations_to_point_to_latest_active_datasets(connection)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/lib/galaxy/model/migrations/alembic/versions_gxy/04288b6a5b25_make_dataset_uuids_unique.py”, line 292, in _update_dataset_associations_to_point_to_latest_active_datasets
connection.execute(update_hda_links)
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1418, in execute
return meth(
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/sqlalchemy/sql/elements.py”, line 515, in _execute_on_connection
return connection._execute_clauseelement(
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1640, in _execute_clauseelement
ret = self._execute_context(
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1846, in _execute_context
return self._exec_single_context(
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1986, in _exec_single_context
self._handle_dbapi_exception(
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 2353, in _handle_dbapi_exception
raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1967, in _exec_single_context
self.dialect.do_execute(
File “/common/compbiomed-galaxy/galaxy/24.01/galaxy/.venv/lib/python3.10/site-packages/sqlalchemy/engine/default.py”, line 924, in do_execute
cursor.execute(statement, parameters)
sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) near “FROM”: syntax error
[SQL:
UPDATE history_dataset_association
SET dataset_id=t.to_dataset_id
FROM temp_active_mapping t
WHERE t.from_dataset_id = dataset_id
]
(Background on this error at: Error Messages — SQLAlchemy 2.0 Documentation)
What’s my next step? The URL at the end of the message was no help.
