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

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/res... On Fri, Dec 19, 2014 at 7:47 PM, John Chilton <jmchilton(a)gmail.com&gt; 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 <ruslan(a)thehyve.nl&gt; > 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 ruslan(a)thehyve.nl M +31(0)6 83 51 30 81 Skype foro.ru