Amazon HealthOmics Run a Private Workflow

arazzo: 1.0.1
info:
  title: Amazon HealthOmics Run a Private Workflow
  summary: Register a private workflow, start a run, poll it to completion, and list its tasks.
  description: >-
    The end-to-end bioinformatics execution flow for Amazon HealthOmics. The
    workflow registers a private WDL/Nextflow/CWL workflow definition, starts a
    run against it with a service role and run parameters, polls GetRun until
    the run reaches a terminal state, and then lists the run's tasks for
    inspection. Each step spells out its AWS REST-JSON request inline so the
    flow can be read and executed without opening the underlying OpenAPI
    description.
  version: 1.0.0
sourceDescriptions:
- name: runApi
  url: ../openapi/amazon-healthomics-run-api-openapi.yml
  type: openapi
- name: workflowApi
  url: ../openapi/amazon-healthomics-workflow-api-openapi.yml
  type: openapi
workflows:
- workflowId: run-private-workflow
  summary: Create a private workflow, start a run, wait for it to finish, then list tasks.
  description: >-
    Registers a private workflow definition, starts a run, polls GetRun until
    the run status is COMPLETED, CANCELLED, DELETED, or FAILED, and on
    completion enumerates the run's tasks via ListRunTasks.
  inputs:
    type: object
    required:
    - workflowName
    - engine
    - definitionUri
    - requestId
    - roleArn
    - runRequestId
    properties:
      workflowName:
        type: string
        description: A name for the workflow.
      engine:
        type: string
        description: The workflow engine (WDL, NEXTFLOW, or CWL).
      definitionUri:
        type: string
        description: The URI of the workflow definition.
      main:
        type: string
        description: The path of the main definition file.
      requestId:
        type: string
        description: Idempotency token for the CreateWorkflow request.
      roleArn:
        type: string
        description: The service role ARN the run assumes.
      runName:
        type: string
        description: A name for the run.
      parameters:
        type: object
        description: Parameters passed to the run.
      runRequestId:
        type: string
        description: Idempotency token for the StartRun request.
  steps:
  - stepId: createWorkflow
    description: Register the private workflow definition with HealthOmics.
    operationId: CreateWorkflow
    requestBody:
      contentType: application/json
      payload:
        name: $inputs.workflowName
        engine: $inputs.engine
        definitionUri: $inputs.definitionUri
        main: $inputs.main
        requestId: $inputs.requestId
    successCriteria:
    - condition: $statusCode == 201
    outputs:
      workflowId: $response.body#/id
      workflowArn: $response.body#/arn
      workflowStatus: $response.body#/status
  - stepId: startRun
    description: Start a run against the newly created private workflow.
    operationId: StartRun
    requestBody:
      contentType: application/json
      payload:
        workflowId: $steps.createWorkflow.outputs.workflowId
        workflowType: PRIVATE
        roleArn: $inputs.roleArn
        name: $inputs.runName
        parameters: $inputs.parameters
        requestId: $inputs.runRequestId
    successCriteria:
    - condition: $statusCode == 201
    outputs:
      runId: $response.body#/id
      runStatus: $response.body#/status
  - stepId: pollRun
    description: >-
      Poll the run until it reaches a terminal status. The status enum is
      PENDING, STARTING, RUNNING, STOPPING, COMPLETED, DELETED, CANCELLED, or
      FAILED.
    operationId: GetRun
    parameters:
    - name: id
      in: path
      value: $steps.startRun.outputs.runId
    successCriteria:
    - condition: $statusCode == 200
    outputs:
      runStatus: $response.body#/status
    onSuccess:
    - name: runComplete
      type: goto
      stepId: listRunTasks
      criteria:
      - context: $response.body
        condition: $.status == "COMPLETED"
        type: jsonpath
    - name: runFailed
      type: end
      criteria:
      - context: $response.body
        condition: $.status == "FAILED" || $.status == "CANCELLED"
        type: jsonpath
    - name: runStillRunning
      type: goto
      stepId: pollRun
      criteria:
      - context: $response.body
        condition: $.status == "PENDING" || $.status == "STARTING" || $.status == "RUNNING"
        type: jsonpath
  - stepId: listRunTasks
    description: List the tasks for the completed run so individual task results can be inspected.
    operationId: ListRunTasks
    parameters:
    - name: id
      in: path
      value: $steps.startRun.outputs.runId
    successCriteria:
    - condition: $statusCode == 200
    outputs:
      tasks: $response.body#/items
  outputs:
    workflowId: $steps.createWorkflow.outputs.workflowId
    runId: $steps.startRun.outputs.runId
    finalRunStatus: $steps.pollRun.outputs.runStatus
    tasks: $steps.listRunTasks.outputs.tasks