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.cock@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/
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