-----Original Message----- From: jmchilton@gmail.com [mailto:jmchilton@gmail.com] On Behalf Of John Chilton Sent: Thursday, February 28, 2013 11:27 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] blend4j
This is not a blend4j issue, it is more of a Galaxy API issue. I think it is essentially a known problem that you cannot specify runtime parameters for workflow, only data inputs. Here the relevant piece of Galaxy code:
inputs = {} for step in latest_workflow.steps: if step.type == 'data_input': inputs[step.id] = {'label':step.tool_inputs['name'], 'value':""} else: pass # Eventually, allow regular tool parameters to be inserted and modified at runtime. # p = step.get_required_parameters()
I think the meantime, the work around is not define these are workflow parameters but instead hard code some values, and then pull down, rewrite, and reupload a new workflow for each execution:
WorkflowsClient client = galaxyInstance.getWorkflowsClient(); String workflowJson = client.exportWorkflow(originalWorkflowId); // modify workflow json Workflow importedWorkflow = client.importWorkflow(workflowJson); String importedWorkflowId = importedWorkflow.getId();
It is not pretty obviously. They are pretty good about responding to API pull requests so if you have the time to fix the Galaxy code itself I think everyone would appreciate that fix.
-John
Hi John Thanks for the quick answer; I'll give it a try. Regarding the fix: you need to give me some time, started with a python tutorial only 2 days ago ;-)
Regards, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________