Hi Asma, This is a known issue I'm still working on a permanent fix for. For right now, you can simply restart the process and it'll hopefully work fine -- we'll have a much better fix out soon. -Dannon On Thu, Apr 23, 2015 at 2:12 PM Asma Riyaz <asmariyaz23@gmail.com> wrote:
Hi,
I am receiving this traceback when I do restart Apache and not sure what to make of it:
Exception in thread WorkflowRequestMonitor.monitor_thread:
Traceback (most recent call last):
File "/broad/software/free/Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/threading.py", line 530, in __bootstrap_inner
self.run()
File "/broad/software/free/Linux/redhat_6_x86_64/pkgs/python_2.7.1-sqlite3-rtrees/lib/python2.7/threading.py", line 483, in run
self.__target(*self.__args, **self.__kwargs)
File "/seq/regev_genome_portal/SOFTWARE/galaxy/lib/galaxy/workflow/scheduling_manager.py", line 158, in __monitor
self.__schedule( workflow_scheduler_id, workflow_scheduler )
File "/seq/regev_genome_portal/SOFTWARE/galaxy/lib/galaxy/workflow/scheduling_manager.py", line 162, in __schedule
invocation_ids = self.__active_invocation_ids( workflow_scheduler_id )
File "/seq/regev_genome_portal/SOFTWARE/galaxy/lib/galaxy/workflow/scheduling_manager.py", line 191, in __active_invocation_ids
handler=handler,
File "/seq/regev_genome_portal/SOFTWARE/galaxy/lib/galaxy/model/__init__.py", line 3254, in poll_active_workflow_ids
WorkflowInvocation
File "/seq/regev_genome_portal/SOFTWARE/galaxy/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 "/seq/regev_genome_portal/SOFTWARE/galaxy/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 "/seq/regev_genome_portal/SOFTWARE/galaxy/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 "/seq/regev_genome_portal/SOFTWARE/galaxy/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 "/seq/regev_genome_portal/SOFTWARE/galaxy/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 "/seq/regev_genome_portal/SOFTWARE/galaxy/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 "/seq/regev_genome_portal/SOFTWARE/galaxy/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 "/seq/regev_genome_portal/SOFTWARE/galaxy/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 "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/mapper.py", line 2589, in configure_mappers
mapper._post_configure_properties()
File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/mapper.py", line 1694, in _post_configure_properties
prop.init()
File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/interfaces.py", line 144, in init
self.do_init()
File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/relationships.py", line 1549, in do_init
self._process_dependent_arguments()
File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/relationships.py", line 1605, in _process_dependent_arguments
self.target = self.mapper.mapped_table
File "/seq/regev_genome_portal/SOFTWARE/galaxy/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 "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/orm/relationships.py", line 1522, in mapper
argument = self.argument()
File "/seq/regev_genome_portal/SOFTWARE/galaxy/eggs/SQLAlchemy-0.9.8-py2.7-linux-x86_64-ucs2.egg/sqlalchemy/ext/declarative/clsregistry.py", line 283, in __call__
(self.prop.parent, self.arg, n.args[0], self.cls)
InvalidRequestError: When initializing mapper Mapper|Queue|kombu_queue, expression 'Message' failed to locate a name ("name 'Message' is not defined"). If this is a class name, consider adding this relationship() to the <class 'kombu.transport.sqlalchemy.Queue'> class after both dependent classes have been defined.
This happens sometimes but when I shut down galaxy and re-start I don't get it anymore.
Can someone guide me to a more permanent solution to this?
Asma
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