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 On Thu, Feb 28, 2013 at 3:24 PM, Marc Logghe <Marc.Logghe@ablynx.com> wrote:
Hi all,
Is this the correct forum to post blend4j issues ? Apologies if this is not the case.
I was trying to run a custom workflow via blend4j, according to https://github.com/jmchilton/blend4j
In my hands, the call to workflowDetails.getInputs() returns an empty Map. I believe the corresponding REST request looks like:
/galaxy/api/workflows/<workflow id>?key=<API key>
In the JSON response, the ‘inputs’ attribute is empty indeed ({"url": "/galaxy/api/workflows/f09437b8822035f7", "inputs": {}, …).
I do not understand why this is the case because 2 steps require inputs to be set at runtime. Via the Galaxy web interface those required parameters can be set and the workflow is running smoothly.
Or has the term ‘inputs’ nothing to do with ‘parameters’ ?
Regards,
Marc
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