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
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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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/ee11198392fe25328b96fc036367f29e5d01... 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 marten@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 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
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/
galaxy-dev@lists.galaxyproject.org
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Dannon Baker -
Langhorst, Brad -
Martin Čech