anybody seen this class of error before?

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anybody seen this class of error before?

Langhorst, Brad
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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Re: anybody seen this class of error before?

Martin Čech
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 <[hidden email]> 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/

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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: anybody seen this class of error before?

Dannon Baker-2
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 <[hidden email]> 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 <[hidden email]> 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/

___________________________________________________________
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/