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 <asmariya...@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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