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
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@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
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/resour...
On Fri, Dec 19, 2014 at 7:47 PM, John Chilton jmchilton@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 ruslan@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
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 ruslan@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/resour...
On Fri, Dec 19, 2014 at 7:47 PM, John Chilton jmchilton@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 ruslan@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 ruslan@thehyve.nl M +31(0)6 83 51 30 81 Skype foro.ru
galaxy-dev@lists.galaxyproject.org
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John Chilton -
Ruslan Forostianov