Hi Brad,

Thanks for reporting this issue. I've committed what I hope is a fix for your 
issue in changeset 8527:eb4dac39eed5 in galaxy-central.  Once you are able to 
apply these changes, would you mind letting us know if this resolves your 
broken workflows? 


Thanks for using Galaxy,

Dan


On Jan 7, 2013, at 9:11 AM, Langhorst, Brad wrote:

> I've recently updated to the december 20th revision of galaxy and still have 
> a problem with a few workflows.
> You can find the backtraces below.
> 
> based on these I'm starting to look in 
> /mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py - but any 
> hints would be appreciated.
> 
> 
> thanks
> 
> Brad
> 
> here's a backtrace from an attempt to edit the problem workflow 
> 
> Error - <type 'exceptions.TypeError'>: 'NoneType' object is unsubscriptable
> URL: 
> http://galaxy.neb.com/workflow/load_workflow?id=4280bfc7d7999071&_=1357567007122
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
>  line 143 in __call__
>   app_iter = self.application(environ, start_response)
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
>  line 80 in __call__
>   return self.application(environ, start_response)
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
>  line 91 in __call__
>   return self.app( environ, start_response )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
>  line 632 in __call__
>   return self.application(environ, start_response)
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 
> 160 in __call__
>   body = method( trans, **kwargs )
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', 
> line 73 in decorator
>   return simplejson.dumps( func( self, trans, *args, **kwargs ) )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py',
>  line 676 in load_workflow
>   module = module_factory.from_workflow_step( trans, step )
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 
> 402 in from_workflow_step
>   return self.module_types[type].from_workflow_step( trans, step )
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 
> 217 in from_workflow_step
>   module.state.inputs = module.tool.params_from_strings( step.tool_inputs, 
> trans.app, ignore_errors=True )
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 
> 2130 in params_from_strings
>   return params_from_strings( self.inputs, params, app, ignore_errors )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/__init__.py', 
> line 94 in params_from_strings
>   value = params[key].value_from_basic( value, app, ignore_errors )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py', 
> line 444 in value_from_basic
>   current_case = rval['__current_case__'] = value['__current_case__']
> TypeError: 'NoneType' object is unsubscriptable
> 
> 
> here's one attempting to run it
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
>  line 143 in __call__
>   app_iter = self.application(environ, start_response)
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
>  line 80 in __call__
>   return self.application(environ, start_response)
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
>  line 91 in __call__
>   return self.app( environ, start_response )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
>  line 632 in __call__
>   return self.application(environ, start_response)
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 
> 160 in __call__
>   body = method( trans, **kwargs )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py',
>  line 1473 in run
>   step.module = module_factory.from_workflow_step( trans, step )
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 
> 402 in from_workflow_step
>   return self.module_types[type].from_workflow_step( trans, step )
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 
> 217 in from_workflow_step
>   module.state.inputs = module.tool.params_from_strings( step.tool_inputs, 
> trans.app, ignore_errors=True )
> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 
> 2130 in params_from_strings
>   return params_from_strings( self.inputs, params, app, ignore_errors )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/__init__.py', 
> line 94 in params_from_strings
>   value = params[key].value_from_basic( value, app, ignore_errors )
> File 
> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py', 
> line 444 in value_from_basic
>   current_case = rval['__current_case__'] = value['__current_case__']
> TypeError: 'NoneType' object is unsubscriptable
> 
> 
> and here's the original report from an attempt to view a shared a workflow
> 
> On Jan 2, 2013, at 9:59 PM, Brad Langhorst <langho...@neb.com> wrote:
> 
>> File 
>> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py',
>>  line 202 in display_by_username_and_slug
>>   return self.display(trans, stored_workflow)
>> File 
>> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py',
>>  line 218 in display
>>   self.get_stored_workflow_steps( trans, stored_workflow )
>> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/web/base/controller.py', 
>> line 668 in get_stored_workflow_steps
>>   module = module_factory.from_workflow_step( trans, step )
>> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 
>> 402 in from_workflow_step
>>   return self.module_types[type].from_workflow_step( trans, step )
>> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py', line 
>> 217 in from_workflow_step
>>   module.state.inputs = module.tool.params_from_strings( step.tool_inputs, 
>> trans.app, ignore_errors=True )
>> File '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py', line 
>> 2120 in params_from_strings
>>   return params_from_strings( self.inputs, params, app, ignore_errors )
>> File 
>> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/__init__.py', 
>> line 94 in params_from_strings
>>   value = params[key].value_from_basic( value, app, ignore_errors )
>> File 
>> '/mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/tools/parameters/grouping.py', 
>> line 444 in value_from_basic
>>   current_case = rval['__current_case__'] = value['__current_case__']
>> TypeError: 'NoneType' object is unsubscriptable
>> 
>> --
>> Brad Langhorst
>> langho...@neb.com
>> 
>> 
>> 
>> 
>> 
> 
> --
> Brad Langhorst
> langho...@neb.com
> 
> 
> 
> 
> 
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