Hi Brad,

Sorry that didn't fix your issue and I agree that your traceback hasn't changed.

I've committed another potential fix in galaxy-central changeset 
8542:530fb4f8204f, but it is hard to be certain that I have replicated your 
exact issue. Could you try that changeset to see if that resolves this issue?


Thanks for using Galaxy,

Dan


On Jan 7, 2013, at 9:17 PM, Langhorst, Brad wrote:

> Hi Dan:
> 
> After much wrestling with hg graft and gnashing of teeth I failed to cherry 
> pick that changeset and just added the code manually in 
> lib/galaxy/tools/__init__.py
> 
> However, I'm not observing any change as a result. I cannot clone, view, 
> export or edit this workflow (or the other problem workflow).
> 
> I don't know what these workflows might share in common, since I don't 
> remember and I can't tell what the steps are.
> 
> I'll try to turn around quicker in future debug loops… 
> 
> here is the current backtrace from an attempt to edit (to my eye this is 
> unchanged)
> 
> URL: 
> http://galaxy.neb.com/workflow/load_workflow?id=4280bfc7d7999071&_=1357611376884
> 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
> 
> Brad
> 
> 
> 
> On Jan 7, 2013, at 11:21 AM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> 
>> 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
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ___________________________________________________________
>>> 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/
>> 
> 
> --
> Brad Langhorst
> langho...@neb.com
> 
> 
> 
> 
> 

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