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<mailto: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<mailto: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<mailto:langho...@neb.com>






--
Brad Langhorst
langho...@neb.com<mailto:langho...@neb.com>





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--
Brad Langhorst
langho...@neb.com<mailto:langho...@neb.com>





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