Importing workflow from file fails in Galaxy instance on Amazon Cloud

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Importing workflow from file fails in Galaxy instance on Amazon Cloud

Sébastien Vigneau
Hi,

I can't import workflows from file on a freshly installed instance of Galaxy on Amazon Cloud. The error message is copied below. Do you have some idea on how to fix this?

Thanks,

Sébastien


Internal Server Error
Galaxy was unable to sucessfully complete your request
URL: http://ec2-50-19-79-199.compute-1.amazonaws.com/workflow/import_workflow
Module galaxy.web.framework.middleware.error:149 in __call__
>>  app_iter = self.application(environ, sr_checker)
Module paste.recursive:84 in __call__
>>  return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
>>  body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.workflow:1127 in import_workflow
>>  workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source=src,add_to_menu=add_to_menu )
Module galaxy.webapps.galaxy.controllers.workflow:1823 in _workflow_from_dict
>>  module = module_factory.from_dict( trans, step_dict, secure=False )
Module galaxy.workflow.modules:428 in from_dict
>>  return self.module_types[type].from_dict( trans, d, **kwargs )
Module galaxy.workflow.modules:222 in from_dict
>>  module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure )
Module galaxy.tools:849 in decode
>>  self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True )
Module galaxy.tools.parameters:92 in params_from_strings
>>  value = json_fix( from_json_string( value ) )
Module simplejson:384 in loads
Module simplejson.decoder:402 in decode
TypeError: expected string or buffer

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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

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Re: Importing workflow from file fails in Galaxy instance on Amazon Cloud

Dannon Baker-2
Sébastien,

This seems to be a galaxy bug from a little while back.  To fix your cloud instance, go to the cloud admin console and click "Update Galaxy", and the problem should be resolved once galaxy updates and restarts.

-Dannon


On Fri, Jan 3, 2014 at 6:42 PM, Sébastien Vigneau <[hidden email]> wrote:
Hi,

I can't import workflows from file on a freshly installed instance of Galaxy on Amazon Cloud. The error message is copied below. Do you have some idea on how to fix this?

Thanks,

Sébastien


Internal Server Error
Galaxy was unable to sucessfully complete your request
URL: http://ec2-50-19-79-199.compute-1.amazonaws.com/workflow/import_workflow
Module galaxy.web.framework.middleware.error:149 in __call__
>>  app_iter = self.application(environ, sr_checker)
Module paste.recursive:84 in __call__
>>  return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
>>  return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
>>  body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.workflow:1127 in import_workflow
>>  workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source=src,add_to_menu=add_to_menu )
Module galaxy.webapps.galaxy.controllers.workflow:1823 in _workflow_from_dict
>>  module = module_factory.from_dict( trans, step_dict, secure=False )
Module galaxy.workflow.modules:428 in from_dict
>>  return self.module_types[type].from_dict( trans, d, **kwargs )
Module galaxy.workflow.modules:222 in from_dict
>>  module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure )
Module galaxy.tools:849 in decode
>>  self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True )
Module galaxy.tools.parameters:92 in params_from_strings
>>  value = json_fix( from_json_string( value ) )
Module simplejson:384 in loads
Module simplejson.decoder:402 in decode
TypeError: expected string or buffer

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/