That post looks like it might be wrong. If 21 is the step id of the
tool (edgeR) then ds_map should probably reference steps 19 and 20
right?
Also - I will see what I can do about improving these workflow API
error messages - it is never exactly clear to me what is wrong when
there are problems.
-John
On Fri, Dec 19, 2014 at 4:21 PM, Ruslan Forostianov <rus...@thehyve.nl> wrote:
> 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('step.id=' + str(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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