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 <tbo...@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
# This patch addresses 
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010303.html
--- a/templates/webapps/galaxy/workflow/run.mako
+++ b/templates/webapps/galaxy/workflow/run.mako
@@ -582,9 +582,12 @@
               # Filter possible inputs to data types that are valid for 
subsequent steps
               type_filter = []
               for oc in step.output_connections:
+                try:
                   for ic in oc.input_step.module.get_data_inputs():
                       if 'extensions' in ic and ic['name'] == oc.input_name:
                           type_filter += ic['extensions']
+                except AttributeError:
+                      pass
               if not type_filter:
                   type_filter = ['data']
               %>
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