1:52 a.m.
Hi Dannon,
Here is the full trace from the log:
===
138.253.25.15 - - [29/Aug/2014:19:16:01 +0100]
"POST /galaxy/workflow/run?id=f597429621d6eb2b HTTP/1.1" 500 -
"http://138.253.25.15/galaxy/workflow/run?id=f597429621d6eb2b"
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:31.0) Gecko/20100101
Firefox/31.0"
Error - <type 'exceptions.AttributeError'>: 'WorkflowStep' object
has no
attribute 'module'
URL: http://138.253.25.15/galaxy/workflow/run?id=f597429621d6eb2b
File
'/usr/lib/galaxy-server/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/usr/lib/galaxy-server/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84
in __call__
return self.application(environ, start_response)
File
'/usr/lib/galaxy-server/lib/galaxy/web/framework/middleware/remoteuser.py', line
94 in __call__
return self.app( environ, start_response )
File
'/usr/lib/galaxy-server/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/usr/lib/galaxy-server/lib/galaxy/web/framework/base.py', line 132
in __call__
return self.handle_request( environ, start_response )
File '/usr/lib/galaxy-server/lib/galaxy/web/framework/base.py', line 190
in handle_request
body = method( trans, **kwargs )
File
'/usr/lib/galaxy-server/lib/galaxy/webapps/galaxy/controllers/workflow.py', line
1410 in run
enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults)
File '/usr/lib/galaxy-server/lib/galaxy/web/framework/__init__.py', line
1194 in fill_template
return self.fill_template_mako( filename, **kwargs )
File '/usr/lib/galaxy-server/lib/galaxy/web/framework/__init__.py', line
1209 in fill_template_mako
return template.render( **data )
File
'/usr/lib/galaxy-server/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
line 296 in render
return runtime._render(self, self.callable_, args, data)
File '/usr/lib/galaxy-server/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 660 in _render
**_kwargs_for_callable(callable_, data))
File '/usr/lib/galaxy-server/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 692 in _render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File '/usr/lib/galaxy-server/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 718 in _exec_template
callable_(context, *args, **kwargs)
File '/usr/lib/galaxy-server/database/compiled_templates/base.mako.py',
line 66 in render_body
__M_writer(unicode(next.body()))
File
'/usr/lib/galaxy-server/database/compiled_templates/workflow/run.mako.py', line
257 in render_body
for ic in oc.input_step.module.get_data_inputs():
AttributeError: 'WorkflowStep' object has no attribute 'module'
===
Cheers,
TIM
On Thu, 2014-09-18 at 22:12 +0100, Dannon Baker wrote:
Hi Tim,
Thanks for this. If you still have it handy, what was the exact
attribute error?
-Dannon
On Thu, Sep 18, 2014 at 10:28 AM, Tim Booth <tbooth(a)ceh.ac.uk> wrote:
Dear Devs,
I recently ran into a problem where attempting to run a
workflow
resulted in an uninformative error and a traceback in the
logs, that I
put into Google. This led me to the message below from 2012.
As far as
I can see it got no reply at the time and I have hit the same
issue.
I modified database/compiled_templates/workflow/run.mako.py
and this
resulted in a much more useful error report appearing in the
browser.
Obviously this is a generated file, so attached is a patch for
templates/webapps/galaxy/workflow/run.mako that I propose you
add to
Galaxy. As you'll see it just adds a single "try" block and
then
ignores the exception, which I would say in this case is not
actually a
bad thing to do even if it is not the ideal fix. Should be
fairly
explanatory from the patch.
Cheers,
TIM
Way way back in Jun 2012, Paul-Michael.Agapow at hpa.org.uk
wrote:
> Looking for pointers on what might be causing this problem:
>
> A user had a moderately complicated workflow that when run
under certain parameter values results in a traceback that
ends:
>
> Module workflow_run_mako:232 in render_body
> >> for ic in oc.input_step.module.get_data_inputs():
> AttributeError: 'WorkflowStep' object has no attribute
'module'
>
> After some puzzling, I realized one of the parameters was
outside the allowed range (a max on an integer param) and that
Galaxy was trying to render "run.mako" flagging up the error
but erroring out. Why Galaxy tries to call this non-existent
member is unclear to me. Any insight or places I should start
exploring?
>
> Galaxy version: various (started with an 6-month old one,
upgraded to latest production to see if it would fix error, it
didn't)
> Hosting OS: CentOS 6
>
> ------
> Paul Agapow (paul-michael.agapow at hpa.org.uk)
> Bioinformatics, Health Protection Agency (UK)
>
--
Tim Booth <tbooth(a)ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
___________________________________________________________
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Tim Booth <tbooth(a)ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705