Page tree

Versions Compared


  • This line was added.
  • This line was removed.
  • Formatting was changed.


  • Get a list of all workflow results satisfying the given query: POST /rest/workflow-results
  • Refresh the whole WorkflowResults table iteratively by retrieving and processing workflow invocations per primaryfile, unless the lumpsum mode is specified and true, in which case, retrieve and process all workflow invocations at once:  POST    /rest/workflow-results/refresh
  • Set the WorkflowResults matching the given list of workflow-step-output maps as relevant/irrelevant, and update their corresponding output datasets in Galaxy as visible/invisible accordingly.
    Note: if a wild card is used in a field of a search criteria map, then that criteria match all values of that field:  POST    /rest/workflow-results/relevant?relevant={relevant}
  • Sets the specified WorkflowResult according to the specified final status POST /rest/workflow-results/{id}?isFinal={isFinal}
  • Set and export workflow result csv file as part of response POST /rest/workflow-results/export


  • Create an AMP job (i.e. submit a Galaxy workflow against an AMP primaryfile):POST /jobsAMP jobs by submitting to Galaxy the given workflow against the given primaryfiles, along with the given parameters: POST   /rest/jobs/submitFiles?workflowId={workflowId}&primaryfileIdprimaryfileIds={primaryfileId}&parameters={parameters}
  • Note: 

    • parameters refers to the parameters for each Galaxy workflow step,

    • It's a map in the following format { stepId: { paramName: paramValue } }

    • stepId is the ID returned in workflow details inputs field.
    • paramName and paramValue are defined as part of the configuration of the tool used in that step (refer to the param name and value fields in the tool xml config file). Their values shall also be available in workflow details.
  • Examples
    • Execute workflow #0a248a1f62a0cc04 on primaryfile #4 with empty parameters (i.e. (using the default): POST https://localhost:8200/jobs?workflowId=0a248a1f62a0cc04&primaryfileId=4&parameters={}
    • Execute same workflow on same primaryfile as above but setting Sample Size of the first step (in this case, this step uses the Audio Extraction tool) to 24 Bits per Sample: same request as above but with parameters={ "0": {"samplesize": "pcm_s24le"} }
  • Create a bundle of AMP jobs (i.e. submit a Galaxy workflow against an AMP bundle): this creates multiple primaryfileId1, primaryfileId1, ...}
  • Create a bundle of AMP jobs, one for each primaryfile included in the given bundle, by submitting to Galaxy the given workflow with the given step parameters : POST  /rest/jobs/submitBundle?workflowId={workflowId}&bundleId={bundleId}
  •  Create AMP jobs, one for each row of WorkflowResult outputs specified in the given list of arrays, to invoke the given workflow in Galaxy along with the given parameters, including their associated primaryfile as the first input if the given indicator is true: POST     /rest/jobs/submitResults?workflowId={workflowId}&resultIdss={id1,id2,id3}
  • Create AMP jobs, one for each row of the primary files included in the items of the bundlePOST /jobs/bundleprimaryfile and outputs specified in the given csvFile, by submitting to Galaxy the given workflow along with the given parameters: POST    /rest/jobs/submitCsv?workflowId={workflowId}&bundleId={bundleId}&parameters={parameters}workflowId and parameters refer to the same concepts as submitting a workflow against a primary file, while bundleId refers to the ID of the bundle.}
  • List all AMP jobs with step details, i.e. all workflow invocations submitted via AMPPD UI to Galaxy: GET     /rest/jobs/details
  • List all AMP jobs (corresponding to Galaxy workflow invocations) that have been run with a particular workflow on a particular primaryfile:
    • GET /jobs?workflowId={workflowId}&primaryfileId={primaryfileId}
    • Note: workflowId is the same Galaxy workflow ID used to submit an AMP job
    • Example: /jobs?workflowId=0a248a1f62a0cc04&primaryfileId=35
  • Show brief information of the inquired AMP job, which includes basic information of each step within the job: 
    • GET /jobs/invocationId?workflowId=0a248a1f62a0cc04
    • Note: invocationId is the ID of the invocation, which is returned when request to list jobs
    • Example: /jobs/33c1d4ca9f8bc33c?workflowId=0a248a1f62a0cc04
  • Show detailed information of the inquired step within the inquired AMP job:
    • GET /jobs/{invocationId}/steps/{stepId}
    • Note: stepId is the ID of the step within an invocation; it's returned when request to show an AMP job.
    • Example: /jobs/33c1d4ca9f8bc33c/steps/747a3db1339e88fd?workflowId=0a248a1f62a0cc04
  • Show detailed information of the inquired AMP job step output: