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__
http://10.7.10.21/workflow/import_workflow app_iter = self.application(environ, sr_checker)
Module paste.recursive:84 in __call__
http://10.7.10.21/workflow/import_workflow return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
http://10.7.10.21/workflow/import_workflow return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
http://10.7.10.21/workflow/import_workflow return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
http://10.7.10.21/workflow/import_workflow body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.workflow:1072 in import_workflow
http://10.7.10.21/workflow/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
http://10.7.10.21/workflow/import_workflow module.save_to_step( step )
Module galaxy.workflow.modules:274 in save_to_step
http://10.7.10.21/workflow/import_workflow step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app )
Module galaxy.tools:2418 in params_to_strings
http://10.7.10.21/workflow/import_workflow return params_to_strings( self.inputs, params, app )
Module galaxy.tools.parameters:85 in params_to_strings
http://10.7.10.21/workflow/import_workflow value = params[ key ].value_to_basic( value, app )
Module galaxy.tools.parameters.grouping:468 in value_to_basic
http://10.7.10.21/workflow/import_workflow 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
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: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Hakeem Almabrazi Sent: Tuesday, March 11, 2014 11:44 AM To: galaxy-dev@lists.bx.psu.edu 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__
http://10.7.10.21/workflow/import_workflow app_iter = self.application(environ, sr_checker)
Module paste.recursive:84 in __call__
http://10.7.10.21/workflow/import_workflow return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
http://10.7.10.21/workflow/import_workflow return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
http://10.7.10.21/workflow/import_workflow return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
http://10.7.10.21/workflow/import_workflow body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.workflow:1072 in import_workflow
http://10.7.10.21/workflow/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
http://10.7.10.21/workflow/import_workflow module.save_to_step( step )
Module galaxy.workflow.modules:274 in save_to_step
http://10.7.10.21/workflow/import_workflow step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app )
Module galaxy.tools:2418 in params_to_strings
http://10.7.10.21/workflow/import_workflow return params_to_strings( self.inputs, params, app )
Module galaxy.tools.parameters:85 in params_to_strings
http://10.7.10.21/workflow/import_workflow value = params[ key ].value_to_basic( value, app )
Module galaxy.tools.parameters.grouping:468 in value_to_basic
http://10.7.10.21/workflow/import_workflow 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
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 halmabrazi@idtdna.com 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
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-
Hakeem Almabrazi -
John Chilton