Hi Brad,
Like Martin mentioned, this is something I've been trying to fix for a
while now in various ways, but none 100% successful so far. If you have an
environment where you can reliably reproduce this (and are able to test
things), you could try
https://github.com/dannon/galaxy/commit/ee11198392fe25328b96fc036367f29e5d0141b1
if the kombu and sqlalchemy upgrades I pushed Friday don't resolve it.
-Dannon
On Sun, Apr 19, 2015 at 4:14 PM Martin Čech mar...@bx.psu.edu wrote:
Hi Brad,
this is known somewhat rare startup error. Please restart your Galaxy and
it should go away.
Dannon is tracking it down and this recent change might solve it:
https://github.com/galaxyproject/galaxy/pull/128
Martin
On Sun, Apr 19, 2015 at 2:53 PM Langhorst, Brad langho...@neb.com wrote:
InvalidRequestError: One or more mappers failed to initialize - can't
proceed with initialization of other mappers. Original exception was:
Class 'kombu.transport.sqlalchemy.Message' is not mapped
galaxy.jobs.handler ERROR 2015-04-19 14:46:00,794 Exception in
monitor_step
Traceback (most recent call last):
File /mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py,
line 177, in __monitor
self.__monitor_step()
File /mnt/galaxy/data/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py,
line 229, in __monitor_step
jobs_to_check =
self.sa_session.query(model.Job).enable_eagerloads(False) \
File
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/scoping.py,
line 150, in do
return getattr(self.registry(), name)(*args, **kwargs)
File
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/session.py,
line 1165, in query
return self._query_cls(entities, self, **kwargs)
File
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py,
line 108, in __init__
self._set_entities(entities)
File
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py,
line 118, in _set_entities
self._set_entity_selectables(self._entities)
File
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py,
line 151, in _set_entity_selectables
ent.setup_entity(*d[entity])
File
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/query.py,
line 3036, in setup_entity
self._with_polymorphic = ext_info.with_polymorphic_mappers
File
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/util/langhelpers.py,
line 725, in __get__
obj.__dict__[self.__name__] = result = self.fget(obj)
File
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/mapper.py,
line 1877, in _with_polymorphic_mappers
configure_mappers()
File
/mnt/galaxy/data/galaxy/galaxy-dist/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/mapper.py,
line 2586, in configure_mappers
raise e
Once this error occurs, no more jobs execute on the cluster.
Restarting the handler seems to get things moving again, but I’d like
to find the source of the failure.
Any ideas?
Brad
--
Brad Langhorst, Ph.D.
Applications and Product Development Scientist
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