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.log...@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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