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
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