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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