Amazon HealthOmics Import Annotations

arazzo: 1.0.1
info:
  title: Amazon HealthOmics Import Annotations
  summary: Create an annotation store, start an annotation import job, and poll it to completion.
  description: >-
    Annotation stores hold genomic annotations (GFF, TSV, or VCF) in a queryable
    form. This workflow creates an annotation store in a chosen format, starts an
    annotation import job that loads source items from Amazon S3 into the store,
    and polls GetAnnotationImportJob 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: import-annotations
  summary: Create an annotation store then import annotations and wait for completion.
  description: >-
    Creates an annotation store in the chosen storeFormat, starts an annotation
    import job against it by destination store name, and polls
    GetAnnotationImportJob until the job is COMPLETED, COMPLETED_WITH_FAILURES,
    CANCELLED, or FAILED.
  inputs:
    type: object
    required:
    - storeName
    - storeFormat
    - roleArn
    - items
    properties:
      storeName:
        type: string
        description: A name for the new annotation store (lowercase, starts with a letter).
      storeFormat:
        type: string
        description: The annotation file format of the store (GFF, TSV, or VCF).
      referenceArn:
        type: string
        description: An optional genome reference ARN to bind the store to.
      roleArn:
        type: string
        description: The service role ARN that HealthOmics assumes to read source files.
      items:
        type: array
        description: The annotation import items, each with an S3 source URI.
        items:
          type: object
  steps:
  - stepId: createAnnotationStore
    description: Create an annotation store in the chosen format.
    operationId: CreateAnnotationStore
    requestBody:
      contentType: application/json
      payload:
        name: $inputs.storeName
        storeFormat: $inputs.storeFormat
        reference:
          referenceArn: $inputs.referenceArn
    successCriteria:
    - condition: $statusCode == 200
    outputs:
      annotationStoreId: $response.body#/id
      annotationStoreName: $response.body#/name
      storeStatus: $response.body#/status
  - stepId: startImportJob
    description: Start an annotation import job that loads the source items into the new store.
    operationId: StartAnnotationImportJob
    requestBody:
      contentType: application/json
      payload:
        destinationName: $steps.createAnnotationStore.outputs.annotationStoreName
        roleArn: $inputs.roleArn
        items: $inputs.items
    successCriteria:
    - condition: $statusCode == 200
    outputs:
      importJobId: $response.body#/jobId
  - stepId: pollImportJob
    description: >-
      Poll the annotation import job until it reaches a terminal status. The
      status enum is SUBMITTED, IN_PROGRESS, CANCELLED, COMPLETED, FAILED, or
      COMPLETED_WITH_FAILURES.
    operationId: GetAnnotationImportJob
    parameters:
    - name: jobId
      in: path
      value: $steps.startImportJob.outputs.importJobId
    successCriteria:
    - condition: $statusCode == 200
    outputs:
      jobStatus: $response.body#/status
      statusMessage: $response.body#/statusMessage
    onSuccess:
    - name: importComplete
      type: end
      criteria:
      - context: $response.body
        condition: $.status == "COMPLETED"
        type: jsonpath
    - name: importFailed
      type: end
      criteria:
      - context: $response.body
        condition: $.status == "FAILED" || $.status == "CANCELLED"
        type: jsonpath
    - name: importStillRunning
      type: goto
      stepId: pollImportJob
      criteria:
      - context: $response.body
        condition: $.status == "IN_PROGRESS" || $.status == "SUBMITTED"
        type: jsonpath
  outputs:
    annotationStoreId: $steps.createAnnotationStore.outputs.annotationStoreId
    importJobId: $steps.startImportJob.outputs.importJobId
    finalStatus: $steps.pollImportJob.outputs.jobStatus