arazzo: 1.0.1
info:
  title: Amazon HealthOmics Export a Read Set to S3
  summary: Start a read set export job to Amazon S3 and poll it to completion.
  description: >-
    Read sets stored in a HealthOmics sequence store can be exported back to
    Amazon S3 for downstream tooling. This workflow starts a read set export job
    that writes the supplied read sets to an S3 destination and polls
    GetReadSetExportJob until the job reaches a terminal state. 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: healthOmicsApi
  url: ../openapi/amazon-healthomics-openapi.yaml
  type: openapi
workflows:
- workflowId: export-read-set
  summary: Start a read set export job to S3 and wait for it to complete.
  description: >-
    Starts a read set export job that writes the supplied read sets to an S3
    destination and polls GetReadSetExportJob until the job is COMPLETED,
    COMPLETED_WITH_FAILURES, CANCELLED, or FAILED.
  inputs:
    type: object
    required:
    - sequenceStoreId
    - destination
    - roleArn
    - sources
    properties:
      sequenceStoreId:
        type: string
        description: The sequence store ID that holds the read sets to export.
      destination:
        type: string
        description: The S3 location (s3://...) for the exported files.
      roleArn:
        type: string
        description: The service role ARN that HealthOmics assumes to write to S3.
      sources:
        type: array
        description: The export job sources, each with a readSetId.
        items:
          type: object
  steps:
  - stepId: startExportJob
    description: Start a read set export job that writes the supplied read sets to S3.
    operationId: StartReadSetExportJob
    parameters:
    - name: sequenceStoreId
      in: path
      value: $inputs.sequenceStoreId
    requestBody:
      contentType: application/json
      payload:
        destination: $inputs.destination
        roleArn: $inputs.roleArn
        sources: $inputs.sources
    successCriteria:
    - condition: $statusCode == 200
    outputs:
      exportJobId: $response.body#/id
      exportStatus: $response.body#/status
  - stepId: pollExportJob
    description: >-
      Poll the export job until it reaches a terminal status. The status enum is
      SUBMITTED, IN_PROGRESS, CANCELLING, CANCELLED, FAILED, COMPLETED, or
      COMPLETED_WITH_FAILURES.
    operationId: GetReadSetExportJob
    parameters:
    - name: sequenceStoreId
      in: path
      value: $inputs.sequenceStoreId
    - name: id
      in: path
      value: $steps.startExportJob.outputs.exportJobId
    successCriteria:
    - condition: $statusCode == 200
    outputs:
      jobStatus: $response.body#/status
      statusMessage: $response.body#/statusMessage
      completionTime: $response.body#/completionTime
    onSuccess:
    - name: exportComplete
      type: end
      criteria:
      - context: $response.body
        condition: $.status == "COMPLETED"
        type: jsonpath
    - name: exportFailed
      type: end
      criteria:
      - context: $response.body
        condition: $.status == "FAILED" || $.status == "CANCELLED"
        type: jsonpath
    - name: exportStillRunning
      type: goto
      stepId: pollExportJob
      criteria:
      - context: $response.body
        condition: $.status == "IN_PROGRESS" || $.status == "SUBMITTED"
        type: jsonpath
  outputs:
    exportJobId: $steps.startExportJob.outputs.exportJobId
    finalStatus: $steps.pollExportJob.outputs.jobStatus