[galaxy-dev] Extract Workflow Error

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[galaxy-dev] Extract Workflow Error

Dennis Gascoigne-2
Can anyone shed any light on the following erro I get when trying to extract a workflow from my history?

 TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0xa5ca790> is not JSON serializable
URL: http://localhost:8082/workflow/build_from_current_history
Module weberror.evalexception.middleware:364 in respond          view
>>  app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__          view
>>  environ, self.app)
Module paste.wsgilib:539 in intercept_output          view
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__          view
>>  return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__          view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:126 in __call__          view
>>  body = method( trans, **kwargs )
Module galaxy.web.controllers.workflow:921 in build_from_current_history          view
>>  step.tool_inputs = tool.params_to_strings( param_values, trans.app )
Module galaxy.tools:1110 in params_to_strings          view
>>  return params_to_strings( self.inputs, params, app )
Module galaxy.tools.parameters:80 in params_to_strings          view
>>  rval[ key ] = str( to_json_string( value ) )
Module simplejson:182 in dumps          view
Module simplejson.encoder:312 in encode          view
Module simplejson.encoder:265 in _iterencode          view
Module simplejson.encoder:235 in _iterencode_dict          view
Module simplejson.encoder:265 in _iterencode          view
Module simplejson.encoder:235 in _iterencode_dict          view
Module simplejson.encoder:273 in _iterencode          view
Module simplejson.encoder:279 in _iterencode_default          view
Module simplejson.encoder:300 in default          view
TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0xa5ca790> is not JSON serializable

--
Dennis Gascoigne
0407 639 995
[hidden email]

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Re: [galaxy-dev] Extract Workflow Error

Jeremy Goecks
Hi Dennis,

It seems that a tool in your history is producing parameters that aren't amenable to building a workflow. To help you, we need more information/help:

What tools are you using in this history? Can you try creating histories with a subset of tools in order to identify the problematic tool? Alternatively, you could recreate the history on our main server ( http://main.g2.bx.psu.edu/ ) and then, assuming you run into the same problem, share it with me.

Thanks,
J.



On May 20, 2010, at 1:59 AM, Dennis Gascoigne wrote:

Can anyone shed any light on the following erro I get when trying to extract a workflow from my history?

 TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0xa5ca790> is not JSON serializable
URL: http://localhost:8082/workflow/build_from_current_history
Module weberror.evalexception.middleware:364 in respond          view
>>  app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__          view
>>  environ, self.app)
Module paste.wsgilib:539 in intercept_output          view
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__          view
>>  return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__          view
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:126 in __call__          view
>>  body = method( trans, **kwargs )
Module galaxy.web.controllers.workflow:921 in build_from_current_history          view
>>  step.tool_inputs = tool.params_to_strings( param_values, trans.app )
Module galaxy.tools:1110 in params_to_strings          view
>>  return params_to_strings( self.inputs, params, app )
Module galaxy.tools.parameters:80 in params_to_strings          view
>>  rval[ key ] = str( to_json_string( value ) )
Module simplejson:182 in dumps          view
Module simplejson.encoder:312 in encode          view
Module simplejson.encoder:265 in _iterencode          view
Module simplejson.encoder:235 in _iterencode_dict          view
Module simplejson.encoder:265 in _iterencode          view
Module simplejson.encoder:235 in _iterencode_dict          view
Module simplejson.encoder:273 in _iterencode          view
Module simplejson.encoder:279 in _iterencode_default          view
Module simplejson.encoder:300 in default          view
TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0xa5ca790> is not JSON serializable

--
Dennis Gascoigne
0407 639 995
[hidden email]
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Re: [galaxy-dev] Extract Workflow Error

James Taylor
In reply to this post by Dennis Gascoigne-2
Hi Dennis,

To debug this, we need a better idea of what is in your history. Is  
there one particular step/dataset that causes this problem? What  
revision of Galaxy are you running (I've fixed bugs that manifest this  
way in the past -- shouldn't currently be possible ;)

Thanks,
James

On May 20, 2010, at 1:59 AM, Dennis Gascoigne wrote:

> Can anyone shed any light on the following erro I get when trying to  
> extract a workflow from my history?
>
> ⇝ TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object  
> at 0xa5ca790> is not JSON serializable
> URL: http://localhost:8082/workflow/build_from_current_history
> Module weberror.evalexception.middleware:364 in respond          view
> >>  app_iter = self.application(environ, detect_start_response)
> Module paste.debug.prints:98 in __call__          view
> >>  environ, self.app)
> Module paste.wsgilib:539 in intercept_output          view
> >>  app_iter = application(environ, replacement_start_response)
> Module paste.recursive:80 in __call__          view
> >>  return self.application(environ, start_response)
> Module paste.httpexceptions:632 in __call__          view
> >>  return self.application(environ, start_response)
> Module galaxy.web.framework.base:126 in __call__          view
> >>  body = method( trans, **kwargs )
> Module galaxy.web.controllers.workflow:921 in  
> build_from_current_history          view
> >>  step.tool_inputs = tool.params_to_strings( param_values,  
> trans.app )
> Module galaxy.tools:1110 in params_to_strings          view
> >>  return params_to_strings( self.inputs, params, app )
> Module galaxy.tools.parameters:80 in params_to_strings          view
> >>  rval[ key ] = str( to_json_string( value ) )
> Module simplejson:182 in dumps          view
> Module simplejson.encoder:312 in encode          view
> Module simplejson.encoder:265 in _iterencode          view
> Module simplejson.encoder:235 in _iterencode_dict          view
> Module simplejson.encoder:265 in _iterencode          view
> Module simplejson.encoder:235 in _iterencode_dict          view
> Module simplejson.encoder:273 in _iterencode          view
> Module simplejson.encoder:279 in _iterencode_default          view
> Module simplejson.encoder:300 in default          view
> TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at  
> 0xa5ca790> is not JSON serializable
>
> --
> Dennis Gascoigne
> 0407 639 995
> [hidden email]
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev


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