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&_=13576... 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 <dan@bx.psu.edumailto:dan@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&_=13575... 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.commailto: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 langhorst@neb.commailto:langhorst@neb.com

-- Brad Langhorst langhorst@neb.commailto:langhorst@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 langhorst@neb.commailto:langhorst@neb.com

Dan: Nice job! That did it.

[cid:BA83181D-A7AD-4E81-A01B-EB30EED822FE@neb.com]

Brad On Jan 8, 2013, at 10:52 AM, Daniel Blankenberg <dan@bx.psu.edumailto:dan@bx.psu.edu> wrote:

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&_=13576... 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 <dan@bx.psu.edumailto:dan@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&_=13575... 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.commailto: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 langhorst@neb.commailto:langhorst@neb.com

-- Brad Langhorst langhorst@neb.commailto:langhorst@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 langhorst@neb.commailto:langhorst@neb.com

-- Brad Langhorst langhorst@neb.commailto:langhorst@neb.com