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

___________________________________________________________ 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/