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 <Langhorst@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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