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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