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
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 <langhorst@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






--
Brad Langhorst





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