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jupyterhub / the-littlest-jupyterhub

Simple JupyterHub distribution for 1-100 users on a single server
https://tljh.jupyter.org
BSD 3-Clause "New" or "Revised" License
1.03k stars 339 forks source link

tljh hub breaks with SQLalchemy 2.0.0 #847

Closed pnasrat closed 1 year ago

pnasrat commented 1 year ago

Bug description

Hub fails to start on developer builds post release of SQLAlchemy 2.0.0.

Reported via https://discourse.jupyter.org/t/tljh-failure-setting-up-development-environment-failed-to-start-jupyterhub-service/17748

Expected behaviour

Running local tljh instance

Actual behaviour

Fails to start with traceback in journalctl logs

How to reproduce

  1. Follow TLJH Development Environment as described here: https://tljh.jupyter.org/en/latest/contributing/dev-setup.htm
Logs ``` Jan 30 15:05:51 1a4911f9df26 python3[2771]: [I 2023-01-30 15:05:51.650 JupyterHub app:2480] Running JupyterHub version 1.5.1 Jan 30 15:05:51 1a4911f9df26 python3[2771]: [I 2023-01-30 15:05:51.650 JupyterHub app:2510] Using Authenticator: firstuseauthenticator.firstuseauthenticator.FirstUseAuthenticator Jan 30 15:05:51 1a4911f9df26 python3[2771]: [I 2023-01-30 15:05:51.650 JupyterHub app:2510] Using Spawner: traitlets.traitlets.UserCreatingSpawner-5.9.0 Jan 30 15:05:51 1a4911f9df26 python3[2771]: [I 2023-01-30 15:05:51.650 JupyterHub app:2510] Using Proxy: jupyterhub_traefik_proxy.toml.TraefikTomlProxy-0+unknown Jan 30 15:05:51 1a4911f9df26 python3[2771]: [I 2023-01-30 15:05:51.660 JupyterHub app:1554] Loading cookie_secret from /opt/tljh/state/jupyterhub_cookie_secret Jan 30 15:05:51 1a4911f9df26 python3[2771]: [I 2023-01-30 15:05:51.735 alembic.runtime.migration migration:205] Context impl SQLiteImpl. Jan 30 15:05:51 1a4911f9df26 python3[2771]: [I 2023-01-30 15:05:51.735 alembic.runtime.migration migration:208] Will assume non-transactional DDL. Jan 30 15:05:51 1a4911f9df26 python3[2771]: [E 2023-01-30 15:05:51.744 JupyterHub app:2991] Jan 30 15:05:51 1a4911f9df26 python3[2771]: Traceback (most recent call last): Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/jupyterhub/app.py", line 2988, in launch_instance_async Jan 30 15:05:51 1a4911f9df26 python3[2771]: await self.initialize(argv) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/jupyterhub/app.py", line 2522, in initialize Jan 30 15:05:51 1a4911f9df26 python3[2771]: self.init_db() Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/jupyterhub/app.py", line 1726, in init_db Jan 30 15:05:51 1a4911f9df26 python3[2771]: self.session_factory = orm.new_session_factory( Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/jupyterhub/orm.py", line 880, in new_session_factory Jan 30 15:05:51 1a4911f9df26 python3[2771]: check_db_revision(engine) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/jupyterhub/orm.py", line 771, in check_db_revision Jan 30 15:05:51 1a4911f9df26 python3[2771]: current_table_names = set(inspect(engine).get_table_names()) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/inspection.py", line 111, in inspect Jan 30 15:05:51 1a4911f9df26 python3[2771]: ret = reg(subject) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/engine/reflection.py", line 304, in _engine_insp Jan 30 15:05:51 1a4911f9df26 python3[2771]: return Inspector._construct(Inspector._init_engine, bind) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/engine/reflection.py", line 237, in _construct Jan 30 15:05:51 1a4911f9df26 python3[2771]: init(self, bind) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/engine/reflection.py", line 248, in _init_engine Jan 30 15:05:51 1a4911f9df26 python3[2771]: engine.connect().close() Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 3245, in connect Jan 30 15:05:51 1a4911f9df26 python3[2771]: return self._connection_cls(self) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 174, in __init__ Jan 30 15:05:51 1a4911f9df26 python3[2771]: self.dispatch.engine_connect(self) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/event/attr.py", line 487, in __call__ Jan 30 15:05:51 1a4911f9df26 python3[2771]: fn(*args, **kw) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/event/legacy.py", line 100, in wrap_leg Jan 30 15:05:51 1a4911f9df26 python3[2771]: return fn(*conv(*args)) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/jupyterhub/orm.py", line 737, in ping_connection Jan 30 15:05:51 1a4911f9df26 python3[2771]: connection.scalar(select([1])) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/sql/_selectable_constructors.py", line 493, in select Jan 30 15:05:51 1a4911f9df26 python3[2771]: return Select(*entities) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/sql/selectable.py", line 5219, in __init__ Jan 30 15:05:51 1a4911f9df26 python3[2771]: self._raw_columns = [ Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/sql/selectable.py", line 5220, in Jan 30 15:05:51 1a4911f9df26 python3[2771]: coercions.expect( Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/sql/coercions.py", line 413, in expect Jan 30 15:05:51 1a4911f9df26 python3[2771]: resolved = impl._literal_coercion( Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/sql/coercions.py", line 652, in _literal_coercion Jan 30 15:05:51 1a4911f9df26 python3[2771]: self._raise_for_expected(element, argname) Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/sql/coercions.py", line 1143, in _raise_for_expected Jan 30 15:05:51 1a4911f9df26 python3[2771]: return super()._raise_for_expected( Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/sql/coercions.py", line 711, in _raise_for_expected Jan 30 15:05:51 1a4911f9df26 python3[2771]: super()._raise_for_expected( Jan 30 15:05:51 1a4911f9df26 python3[2771]: File "/opt/tljh/hub/lib/python3.8/site-packages/sqlalchemy/sql/coercions.py", line 536, in _raise_for_expected Jan 30 15:05:51 1a4911f9df26 python3[2771]: raise exc.ArgumentError(msg, code=code) from err Jan 30 15:05:51 1a4911f9df26 python3[2771]: sqlalchemy.exc.ArgumentError: Column expression, FROM clause, or other columns clause element expected, got [1]. Did you mean to say select(1)? Jan 30 15:05:51 1a4911f9df26 python3[2771]: ```
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pnasrat commented 1 year ago

Note upstream jupyterhub has fixed in jupyterhub/jupyterhub#4312 but as tljh uses jupyterhub 1.5.1 the installer probably needs to ensure 1.x SQLAlchemy is installed

jrdnbradford commented 1 year ago

Looks like this issue is the same problem I encountered in #846. See that issue for some extra logs and discussion.

pnasrat commented 1 year ago

Closed as duplicate. Sorry I searched for SQLAlchemy but for some reason didn't see that issue.