Hi John,

I did some investigation.
I added logging statement to line 843 of lib/galaxy/workflow/modules.py
file:

for step in workflow.steps:
        step_args = param_map.get( step.id, {} )
       * log.info <http://log.info>('step.id <http://step.id>=' +
str(step.id <http://step.id>) + ', step_args=' + str(step_args))*
        step_errors = module_injector.inject( step, step_args=step_args )

It gives:
galaxy.workflow.modules INFO 2014-12-18 13:39:31,464 step.id=21,
step_args={'contrast': u'Female-Male'}

See http post below. It looks like somehow runtime parameter appears among
steps.

4 * Client out-bound request
4 > POST
http://galaxy.thehyve.net/api/workflows?key=5c4f870bc0108a60dc7435a000fb7874
4 > Content-Type: application/json
4 > Accept: application/json
{"parameters":{"21":{"contrast":"Female-Male"}},"workflow_id":"d4bec7f9d7e8cf4d","history":"hist_id=59bd7ef52a8ce0e8","ds_map":{"21":{"id":"fb94345e0a2a5a2c","src":"hda"},"22":{"id":"9384bb69863b3f9e","src":"hda"}},"no_add_to_history":"true"}

Here is link to ga file for completeness:
https://github.com/thehyve/trait_workflow_runner/blob/master/src/main/resources/nl/vumc/biomedbridges/galaxy/rna-seq-dge.ga

On Fri, Dec 19, 2014 at 7:47 PM, John Chilton <jmchil...@gmail.com> wrote:

> That is odd. Does that workflow run through the UI? It looks like it
> was missing a tool during import. Certainly the API should indicate
> that overtly instead of failing in this fashion.
>
> If it does run, can you export it to JSON and send it to me?
>
> -John
>
> On Thu, Dec 18, 2014 at 10:55 AM, Ruslan Forostianov <rus...@thehyve.nl>
> wrote:
> > galaxy.web.framework.decorators ERROR 2014-12-18 12:22:04,760 Uncaught
> > exception in exposed API method:
> > Traceback (most recent call last):
> >   File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py",
> > line 244, in decorator
> >     rval = func( self, trans, *args, **kwargs)
> >   File
> > "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/workflows.py",
> line
> > 231, in create
> >     populate_state=True,
> >   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/run.py", line 18, in
> > invoke
> >     modules.populate_module_and_state( trans, workflow,
> > workflow_run_config.param_map )
> >   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line
> 843,
> > in populate_module_and_state
> >     step_errors = module_injector.inject( step, step_args=step_args )
> >   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line
> 830,
> > in inject
> >     state, step_errors = module.compute_runtime_state( trans, step_args )
> >   File "/home/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py", line
> 264,
> > in compute_runtime_state
> >     state = self.decode_runtime_state( trans, step_updates.pop(
> "tool_state"
> > ) )
> > KeyError: 'tool_state'
> >
> > Cheers,
> > Ruslan Forostianov
> >
>



-- 
Ruslan Forostianov,
*Software Developer*
www.thehyve.nl
*E* rus...@thehyve.nl
*M* +31(0)6 83 51 30 81
*Skype* foro.ru
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