# Database upgrade error - 22.05 to 24.01 **URL:** \ **Category:** Uncategorized\ **Tags:** devops-administration, galaxy-local\ **Created:** [February 26, 2025, 11:11pm UTC](https://help.galaxyproject.org/t/database-upgrade-error-22-05-to-24-01/14866 "2025-02-26T23:11:19Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![caldodge](https://avatars.discourse-cdn.com/v4/letter/c/9dc877/32.png) [@caldodge](https://help.galaxyproject.org/u/caldodge)\ **Post date:** [February 26, 2025, 11:11pm UTC](https://help.galaxyproject.org/t/database-upgrade-error-22-05-to-24-01/14866/1 "2025-02-26T23:11:19Z")
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](https://sqlalche.me/e/20/e3q8)) What’s my next step? The URL at the end of the message was no help. ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [February 27, 2025, 6:30pm UTC](https://help.galaxyproject.org/t/database-upgrade-error-22-05-to-24-01/14866/2 "2025-02-27T18:30:59Z")
Welcome @caldodge Your upgrade is making a huge jump between releases and the “FROM” statement seems to be having trouble connecting between the tables changes between them. To migrate between releases, and to incorporate the changes introduced in each, we recommend upgrading one release at a time. This way the changes for each are applied before the next change is applied. Apologies if this is confusing language! In short: upgrade to each release sequentially until you are at the current stable release. Painful, but it is the supported way to do this. Let us know if you need help as you work through this. We’ve had other upgrade out of the 22.NN releases and there were a few hiccups but these were able to be resolved. 🙂 XREf → - [Private Galaxy Servers](https://help.galaxyproject.org/t/private-galaxy-servers/10861) - Recent Q&A [Database upgrade error](https://help.galaxyproject.org/t/database-upgrade-error/13687) ---
**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\ **Post date:** [March 17, 2026, 4:43am UTC](https://help.galaxyproject.org/t/database-upgrade-error-22-05-to-24-01/14866/3 "2026-03-17T04:43:44Z")
Closed on March 17, 2026, 4:43am UTC