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 >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/
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