I am a little paranoid that I am the one that broke something (I guess
that is pattern matching more than paranoia), but I have looked
through that code and it is not immediately obvious to me what the
problem is. If you have some time, can you try cloning the workflow
and ripping various parts out to see what the nature of the problem
is? Is it a particular tool or combination of tools? Being able to
describe the smallest workflow that exhibits this behavior would be
very helpful. I would be happy to fix this problem, but I need help
tracking it down.

Thanks,
-John

On Mon, Jan 7, 2013 at 8:11 AM, Langhorst, Brad <langho...@neb.com> 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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