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 <[email protected]> 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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