Hi Peter, Yes, this is a known recent issue that I'm actually at work fixing right now.
-Dannon On Tue Feb 24 2015 at 9:53:24 AM Peter Cock <p.j.a.c...@googlemail.com> wrote: > Hi all, > > I'm trying the (BETA 2) GitHub repository with a view to switching > from hg for my Galaxy development. There are a couple of big > scary tracebacks in the stdout which look like SQLalchemy > incompatibilities - are these a recent issue? > > $ git clone > $ cd galaxy > $ cp config/galaxy.ini.sample config/galaxy.ini > $ emacs config/galaxy.ini > (set port and a few misc settings like admin users) > $ ./run.sh > ... > galaxy.jobs.handler DEBUG 2015-02-24 14:49:20,223 Loaded job runners > plugins: lwr:local > galaxy.jobs.handler INFO 2015-02-24 14:49:20,224 job handler stop queue > started > galaxy.jobs.handler INFO 2015-02-24 14:49:20,238 job handler queue started > galaxy.sample_tracking.external_service_types ERROR 2015-02-24 > 14:49:20,240 error reading external_service_type from path: > simple_unknown_sequencer.xml > Traceback (most recent call last): > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ > tracking/external_service_types.py", > line 32, in load_all > external_service_type = self.load_external_service_type( > os.path.join( self.root_dir, file_path ), visible ) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ > tracking/external_service_types.py", > line 43, in load_external_service_type > return ExternalServiceType( config_file, root, visible ) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ > tracking/external_service_types.py", > line 60, in __init__ > self.parse( root ) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ > tracking/external_service_types.py", > line 78, in parse > self.form_definition = form_factory.from_elem( root.find( 'form' ) ) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/forms/forms.py", > line 59, in from_elem > return self.new( form_type, name, description=description, > fields=fields, layout=layout, > form_definition_current=form_definition_current ) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/forms/forms.py", > line 32, in new > rval = FormDefinition( name=name, desc=description, > form_type=self.form_types[form_type], > form_definition_current=form_definition_current, layout=layout, > fields=fields ) > File "<string>", line 4, in __init__ > File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- > py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/state.py", > line 260, in _initialize_instance > return manager.original_init(*mixed[1:], **kwargs) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/model/__init__.py", > line 3417, in __init__ > self.fields = fields > File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- > py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", > line 226, in __set__ > instance_dict(instance), value, None) > File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- > py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", > line 693, in set > value, old, initiator) > File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- > py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", > line 712, in fire_replace_event > state, value, previous, initiator or self._replace_token) > File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- > py2.6-linux-x86_64-ucs4.egg/sqlalchemy/ext/mutable.py", > line 445, in set > value = cls.coerce(key, value) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/model/custom_types.py", > line 48, in coerce > return Mutable.coerce(key, value) > File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- > py2.6-linux-x86_64-ucs4.egg/sqlalchemy/ext/mutable.py", > line 403, in coerce > raise ValueError(msg % (key, type(value))) > ValueError: Attribute 'fields' does not accept objects of type <type > 'list'> > galaxy.sample_tracking.external_service_types ERROR 2015-02-24 > 14:49:20,244 error reading external_service_type from path: > applied_biosystems_solid.xml > Traceback (most recent call last): > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ > tracking/external_service_types.py", > line 32, in load_all > external_service_type = self.load_external_service_type( > os.path.join( self.root_dir, file_path ), visible ) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ > tracking/external_service_types.py", > line 43, in load_external_service_type > return ExternalServiceType( config_file, root, visible ) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ > tracking/external_service_types.py", > line 60, in __init__ > self.parse( root ) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/sample_ > tracking/external_service_types.py", > line 78, in parse > self.form_definition = form_factory.from_elem( root.find( 'form' ) ) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/forms/forms.py", > line 59, in from_elem > return self.new( form_type, name, description=description, > fields=fields, layout=layout, > form_definition_current=form_definition_current ) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/forms/forms.py", > line 32, in new > rval = FormDefinition( name=name, desc=description, > form_type=self.form_types[form_type], > form_definition_current=form_definition_current, layout=layout, > fields=fields ) > File "<string>", line 4, in __init__ > File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- > py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/state.py", > line 260, in _initialize_instance > return manager.original_init(*mixed[1:], **kwargs) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/model/__init__.py", > line 3417, in __init__ > self.fields = fields > File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- > py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", > line 226, in __set__ > instance_dict(instance), value, None) > File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- > py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", > line 693, in set > value, old, initiator) > File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- > py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/attributes.py", > line 712, in fire_replace_event > state, value, previous, initiator or self._replace_token) > File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- > py2.6-linux-x86_64-ucs4.egg/sqlalchemy/ext/mutable.py", > line 445, in set > value = cls.coerce(key, value) > File "/mnt/galaxy/repositories/galaxy/lib/galaxy/model/custom_types.py", > line 48, in coerce > return Mutable.coerce(key, value) > File "/mnt/galaxy/repositories/galaxy/eggs/SQLAlchemy-0.9.8- > py2.6-linux-x86_64-ucs4.egg/sqlalchemy/ext/mutable.py", > line 403, in coerce > raise ValueError(msg % (key, type(value))) > ValueError: Attribute 'fields' does not accept objects of type <type > 'list'> > galaxy.workflow.scheduling_manager DEBUG 2015-02-24 14:49:20,247 > Starting workflow schedulers > ... > Starting server in PID 360. > serving on http://127.0.0.1:8081 > > Peter > ___________________________________________________________ > 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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