Internal server error when importing workflows!

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Internal server error when importing workflows!

Hakeem Almabrazi

Hi,

 

I have upgraded my local galaxy to the latest stable version and it works fine but I get an error when I try to import workflows that were created older version of Galaxy.  Here is the error I keep getting.

 

Internal Server Error

Galaxy was unable to successfully complete your request

URL: http://10.7.10.21/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:1072 in import_workflow
>>  workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source=src, add_to_menu=add_to_menu )
Module galaxy.web.base.controller:1639 in _workflow_from_dict
>>  module.save_to_step( step )
Module galaxy.workflow.modules:274 in save_to_step
>>  step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app )
Module galaxy.tools:2418 in params_to_strings
>>  return params_to_strings( self.inputs, params, app )
Module galaxy.tools.parameters:85 in params_to_strings
>>  value = params[ key ].value_to_basic( value, app )
Module galaxy.tools.parameters.grouping:468 in value_to_basic
>>  rval[ input.name ] = input.value_to_basic( value[ input.name ], app )
KeyError: 'index'

 

Can someone let me know how to fix this issue?

 

Thank you

Hakeem

 

 


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Re: Internal server error when importing workflows!

Hakeem Almabrazi

Does anyone have any idea if there is any compatibility issues when it comes to import workflow files across different releases?   My issue is described below.  Please let me know if you have any clues.

 

I appreciate it.

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Hakeem Almabrazi
Sent: Tuesday, March 11, 2014 11:44 AM
To: [hidden email]
Subject: [galaxy-dev] Internal server error when importing workflows!

 

Hi,

 

I have upgraded my local galaxy to the latest stable version and it works fine but I get an error when I try to import workflows that were created older version of Galaxy.  Here is the error I keep getting.

 

Internal Server Error

Galaxy was unable to successfully complete your request

URL: http://10.7.10.21/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:1072 in import_workflow
>>  workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source=src, add_to_menu=add_to_menu )
Module galaxy.web.base.controller:1639 in _workflow_from_dict
>>  module.save_to_step( step )
Module galaxy.workflow.modules:274 in save_to_step
>>  step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app )
Module galaxy.tools:2418 in params_to_strings
>>  return params_to_strings( self.inputs, params, app )
Module galaxy.tools.parameters:85 in params_to_strings
>>  value = params[ key ].value_to_basic( value, app )
Module galaxy.tools.parameters.grouping:468 in value_to_basic
>>  rval[ input.name ] = input.value_to_basic( value[ input.name ], app )
KeyError: 'index'

 

Can someone let me know how to fix this issue?

 

Thank you

Hakeem

 

 


___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: Internal server error when importing workflows!

John Chilton-4
In reply to this post by Hakeem Almabrazi
Hmm... I can import older workflows on usegalaxy.org so I don't think
it is a general problem with all workflows as a part of the latest
release. That said I don't know what the problem is - if it is a bug
with a new release or a problem with one of your tools etc....

If I had to guess I would say you updated a tool has been updated
changing its "interface" without changing its version? Can you send
the list (or me) the workflow and any custom tool XML files it uses?
Do you still have access to the original Galaxy instance with the
workflow in it - if you could try to trim the number of steps down and
retry until it works or try a completely new workflow that might help
track down the particular circumstances surrounding the problem.

-John


On Tue, Mar 11, 2014 at 11:43 AM, Hakeem Almabrazi
<[hidden email]> wrote:

> Hi,
>
>
>
> I have upgraded my local galaxy to the latest stable version and it works
> fine but I get an error when I try to import workflows that were created
> older version of Galaxy.  Here is the error I keep getting.
>
>
>
> Internal Server Error
>
> Galaxy was unable to successfully complete your request
>
> URL: http://10.7.10.21/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:1072 in import_workflow
>>>  workflow, missing_tool_tups = self._workflow_from_dict( trans, data,
>>> source=src, add_to_menu=add_to_menu )
> Module galaxy.web.base.controller:1639 in _workflow_from_dict
>>>  module.save_to_step( step )
> Module galaxy.workflow.modules:274 in save_to_step
>>>  step.tool_inputs = self.tool.params_to_strings( self.state.inputs,
>>> self.trans.app )
> Module galaxy.tools:2418 in params_to_strings
>>>  return params_to_strings( self.inputs, params, app )
> Module galaxy.tools.parameters:85 in params_to_strings
>>>  value = params[ key ].value_to_basic( value, app )
> Module galaxy.tools.parameters.grouping:468 in value_to_basic
>>>  rval[ input.name ] = input.value_to_basic( value[ input.name ], app )
> KeyError: 'index'
>
>
>
> Can someone let me know how to fix this issue?
>
>
>
> Thank you
>
> Hakeem
>
>
>
>
>
>
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/