Hi all,
Here’s a mail for heads up and googleable error message in case someone finds a similar error and scratches her/his head.
So (some time) after the very nice API class we had at GCC2015 I am now trying my hand at running workflows using Bioblend. I had some frustration trying to invoke a simple WF, but now found out that the inputs parameter to invoke_workflow is not as I thought it would be. I’m on the latest galaxy-dist and using Bioblend 0.7 in Python3.4.
So I thought I’d call e.g.:
gi.workflows.invoke_workflow(workflow_id, inputs={‘9678’: {’src’: ‘hda’, ‘id’: ‘abcdef12345’}} , history_id=‘abc1234’)
Where the keys in inputs dict represent the ids from: gi.workflows.get_workflow(workflow_id)[‘inputs’]
But apparently the new standard is to use the step_order (so 0 for the first step) instead of the step_id, as shown in the code at lib/galaxy/workflow/run_request.py So this gave me the HTTP 400 error "Workflow cannot be run because an expected input step '84' has no input dataset."
I have reverted to using legacy code with run_workflow and dataset_map, which circumvents the problem: gi.workflows.run_workflow(workflow_id, dataset_map={‘9678’: {’src’: ‘hda’, ‘id’: ‘abcdef12345’}} , history_id=‘abc1234’)
Is there any way to specify inputs_by in the payload or am I on the wrong bioblend version? Otherwise I can file a request on the Bioblend github.
cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden