Amazon HealthOmics Import API

openapi: 3.1.0
info:
  title: Amazon Omics Import API
  version: '2022-11-28'
  description: Generated from AWS's published Smithy model for Amazon Omics. 8 operation(s).
  contact:
    name: Amazon Web Services
    url: https://aws.amazon.com/contact-us/
  license:
    name: Apache 2.0
    identifier: Apache-2.0
    url: https://github.com/aws/api-models-aws/blob/main/LICENSE
servers:
- url: https://omics.{region}.amazonaws.com
  variables:
    region:
      default: us-east-1
security:
- sigv4: []
paths:
  /import/annotation:
    post:
      operationId: StartAnnotationImportJob
      summary: Start Annotation Import Job
      description: Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers.
        Existing customers can continue to use the service as normal. For more information, see Amazon Web Services HealthOmics
        variant store and annotation store availability change. Starts an annotation import job.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/StartAnnotationImportResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '402':
          description: ServiceQuotaExceededException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ServiceQuotaExceededException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/StartAnnotationImportRequest'
      tags:
      - Import
  /import/annotation/{jobId}:
    get:
      operationId: GetAnnotationImportJob
      summary: Get Annotation Import Job
      description: Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers.
        Existing customers can continue to use the service as normal. For more information, see Amazon Web Services HealthOmics
        variant store and annotation store availability change. Gets information about an annotation import job.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/GetAnnotationImportResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/GetAnnotationImportRequest'
      tags:
      - Import
    delete:
      operationId: CancelAnnotationImportJob
      summary: Cancel Annotation Import Job
      description: Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers.
        Existing customers can continue to use the service as normal. For more information, see Amazon Web Services HealthOmics
        variant store and annotation store availability change. Cancels an annotation import job.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/CancelAnnotationImportResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/CancelAnnotationImportRequest'
      tags:
      - Import
  /import/annotations:
    post:
      operationId: ListAnnotationImportJobs
      summary: List Annotation Import Jobs
      description: Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers.
        Existing customers can continue to use the service as normal. For more information, see Amazon Web Services HealthOmics
        variant store and annotation store availability change. Retrieves a list of annotation import jobs.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ListAnnotationImportJobsResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/ListAnnotationImportJobsRequest'
      tags:
      - Import
  /import/variant:
    post:
      operationId: StartVariantImportJob
      summary: Start Variant Import Job
      description: Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers.
        Existing customers can continue to use the service as normal. For more information, see Amazon Web Services HealthOmics
        variant store and annotation store availability change. Starts a variant import job.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/StartVariantImportResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '402':
          description: ServiceQuotaExceededException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ServiceQuotaExceededException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/StartVariantImportRequest'
      tags:
      - Import
  /import/variant/{jobId}:
    get:
      operationId: GetVariantImportJob
      summary: Get Variant Import Job
      description: Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers.
        Existing customers can continue to use the service as normal. For more information, see Amazon Web Services HealthOmics
        variant store and annotation store availability change. Gets information about a variant import job.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/GetVariantImportResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/GetVariantImportRequest'
      tags:
      - Import
    delete:
      operationId: CancelVariantImportJob
      summary: Cancel Variant Import Job
      description: Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers.
        Existing customers can continue to use the service as normal. For more information, see Amazon Web Services HealthOmics
        variant store and annotation store availability change. Cancels a variant import job.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/CancelVariantImportResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/CancelVariantImportRequest'
      tags:
      - Import
  /import/variants:
    post:
      operationId: ListVariantImportJobs
      summary: List Variant Import Jobs
      description: Amazon Web Services HealthOmics variant stores and annotation stores are no longer open to new customers.
        Existing customers can continue to use the service as normal. For more information, see Amazon Web Services HealthOmics
        variant store and annotation store availability change. Retrieves a list of variant import jobs.
      responses:
        '200':
          description: Success
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ListVariantImportJobsResponse'
        '403':
          description: AccessDeniedException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AccessDeniedException'
        '500':
          description: InternalServerException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/InternalServerException'
        '404':
          description: ResourceNotFoundException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ResourceNotFoundException'
        '429':
          description: ThrottlingException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ThrottlingException'
        '400':
          description: ValidationException
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ValidationException'
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/ListVariantImportJobsRequest'
      tags:
      - Import
components:
  securitySchemes:
    sigv4:
      type: apiKey
      in: header
      name: Authorization
      description: AWS Signature Version 4. The Authorization header carries an AWS4-HMAC-SHA256 signature over the canonical
        request, with X-Amz-Date (and X-Amz-Security-Token for temporary credentials). Not a bearer token.
      x-aws-sigv4:
        signingName: omics
  schemas:
    AccessDeniedException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    AnnotationImportItemDetail:
      type: object
      properties:
        source:
          type: string
          description: The source file's location in Amazon S3.
        jobStatus:
          type: string
          description: The item's job status.
      required:
      - source
      - jobStatus
    AnnotationImportItemSource:
      type: object
      properties:
        source:
          type: string
          description: The source file's location in Amazon S3.
      required:
      - source
    AnnotationImportJobItem:
      type: object
      properties:
        id:
          type: string
          description: The job's ID.
        destinationName:
          type: string
          description: The job's destination annotation store.
        versionName:
          type: string
          description: The name of the annotation store version.
        roleArn:
          type: string
          description: The job's service role ARN.
        status:
          type: string
          description: The job's status.
        creationTime:
          type: string
          format: date-time
          description: When the job was created.
        updateTime:
          type: string
          format: date-time
          description: When the job was updated.
        completionTime:
          type: string
          format: date-time
          description: When the job completed.
        runLeftNormalization:
          type: boolean
          description: The job's left normalization setting.
        annotationFields:
          type: object
          additionalProperties:
            type: string
          description: The annotation schema generated by the parsed annotation data.
      required:
      - id
      - destinationName
      - versionName
      - roleArn
      - status
      - creationTime
      - updateTime
    CancelAnnotationImportRequest:
      type: object
      properties:
        jobId:
          type: string
          description: The job's ID.
      required:
      - jobId
    CancelAnnotationImportResponse:
      type: object
      properties: {}
    CancelVariantImportRequest:
      type: object
      properties:
        jobId:
          type: string
          description: The job's ID.
      required:
      - jobId
    CancelVariantImportResponse:
      type: object
      properties: {}
    FormatOptions:
      type: object
      properties:
        tsvOptions:
          $ref: '#/components/schemas/TsvOptions'
        vcfOptions:
          $ref: '#/components/schemas/VcfOptions'
      description: Exactly one member is set.
    GetAnnotationImportRequest:
      type: object
      properties:
        jobId:
          type: string
          description: The job's ID.
      required:
      - jobId
    GetAnnotationImportResponse:
      type: object
      properties:
        id:
          type: string
          description: The job's ID.
        destinationName:
          type: string
          description: The job's destination annotation store.
        versionName:
          type: string
          description: The name of the annotation store version.
        roleArn:
          type: string
          description: The job's service role ARN.
        status:
          type: string
          description: The job's status.
        statusMessage:
          type: string
          description: The job's status message.
        creationTime:
          type: string
          format: date-time
          description: When the job was created.
        updateTime:
          type: string
          format: date-time
          description: When the job was updated.
        completionTime:
          type: string
          format: date-time
          description: When the job completed.
        items:
          type: array
          items:
            $ref: '#/components/schemas/AnnotationImportItemDetail'
          description: The job's imported items.
        runLeftNormalization:
          type: boolean
          description: The job's left normalization setting.
        formatOptions:
          $ref: '#/components/schemas/FormatOptions'
        annotationFields:
          type: object
          additionalProperties:
            type: string
          description: The annotation schema generated by the parsed annotation data.
      required:
      - id
      - destinationName
      - versionName
      - roleArn
      - status
      - statusMessage
      - creationTime
      - updateTime
      - completionTime
      - items
      - runLeftNormalization
      - formatOptions
    GetVariantImportRequest:
      type: object
      properties:
        jobId:
          type: string
          description: The job's ID.
      required:
      - jobId
    GetVariantImportResponse:
      type: object
      properties:
        id:
          type: string
          description: The job's ID.
        destinationName:
          type: string
          description: The job's destination variant store.
        roleArn:
          type: string
          description: The job's service role ARN.
        status:
          type: string
          description: The job's status.
        statusMessage:
          type: string
          description: The job's status message.
        creationTime:
          type: string
          format: date-time
          description: When the job was created.
        updateTime:
          type: string
          format: date-time
          description: When the job was updated.
        completionTime:
          type: string
          format: date-time
          description: When the job completed.
        items:
          type: array
          items:
            $ref: '#/components/schemas/VariantImportItemDetail'
          description: The job's items.
        runLeftNormalization:
          type: boolean
          description: The job's left normalization setting.
        annotationFields:
          type: object
          additionalProperties:
            type: string
          description: The annotation schema generated by the parsed annotation data.
      required:
      - id
      - destinationName
      - roleArn
      - status
      - statusMessage
      - creationTime
      - updateTime
      - items
      - runLeftNormalization
    InternalServerException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    ListAnnotationImportJobsFilter:
      type: object
      properties:
        status:
          type: string
          description: A status to filter on.
        storeName:
          type: string
          description: A store name to filter on.
    ListAnnotationImportJobsRequest:
      type: object
      properties:
        maxResults:
          type: integer
          description: The maximum number of jobs to return in one page of results.
        ids:
          type: array
          items:
            type: string
          description: IDs of annotation import jobs to retrieve.
        nextToken:
          type: string
          description: Specifies the pagination token from a previous request to retrieve the next page of results.
        filter:
          $ref: '#/components/schemas/ListAnnotationImportJobsFilter'
    ListAnnotationImportJobsResponse:
      type: object
      properties:
        annotationImportJobs:
          type: array
          items:
            $ref: '#/components/schemas/AnnotationImportJobItem'
          description: A list of jobs.
        nextToken:
          type: string
          description: Specifies the pagination token from a previous request to retrieve the next page of results.
    ListVariantImportJobsFilter:
      type: object
      properties:
        status:
          type: string
          description: A status to filter on.
        storeName:
          type: string
          description: A store name to filter on.
    ListVariantImportJobsRequest:
      type: object
      properties:
        maxResults:
          type: integer
          description: The maximum number of import jobs to return in one page of results.
        ids:
          type: array
          items:
            type: string
          description: A list of job IDs.
        nextToken:
          type: string
          description: Specify the pagination token from a previous request to retrieve the next page of results.
        filter:
          $ref: '#/components/schemas/ListVariantImportJobsFilter'
    ListVariantImportJobsResponse:
      type: object
      properties:
        variantImportJobs:
          type: array
          items:
            $ref: '#/components/schemas/VariantImportJobItem'
          description: A list of jobs.
        nextToken:
          type: string
          description: A pagination token that's included if more results are available.
    ReadOptions:
      type: object
      properties:
        sep:
          type: string
          description: The file's field separator.
        encoding:
          type: string
          description: The file's encoding.
        quote:
          type: string
          description: The file's quote character.
        quoteAll:
          type: boolean
          description: Whether all values need to be quoted, or just those that contain quotes.
        escape:
          type: string
          description: A character for escaping quotes in the file.
        escapeQuotes:
          type: boolean
          description: Whether quotes need to be escaped in the file.
        comment:
          type: string
          description: The file's comment character.
        header:
          type: boolean
          description: Whether the file has a header row.
        lineSep:
          type: string
          description: A line separator for the file.
    ResourceNotFoundException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    ServiceQuotaExceededException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    StartAnnotationImportRequest:
      type: object
      properties:
        destinationName:
          type: string
          description: A destination annotation store for the job.
        roleArn:
          type: string
          description: A service role for the job.
        items:
          type: array
          items:
            $ref: '#/components/schemas/AnnotationImportItemSource'
          description: Items to import.
        versionName:
          type: string
          description: The name of the annotation store version.
        formatOptions:
          $ref: '#/components/schemas/FormatOptions'
        runLeftNormalization:
          type: boolean
          description: The job's left normalization setting.
        annotationFields:
          type: object
          additionalProperties:
            type: string
          description: The annotation schema generated by the parsed annotation data.
      required:
      - destinationName
      - roleArn
      - items
    StartAnnotationImportResponse:
      type: object
      properties:
        jobId:
          type: string
          description: The job's ID.
      required:
      - jobId
    StartVariantImportRequest:
      type: object
      properties:
        destinationName:
          type: string
          description: The destination variant store for the job.
        roleArn:
          type: string
          description: A service role for the job.
        items:
          type: array
          items:
            $ref: '#/components/schemas/VariantImportItemSource'
          description: Items to import.
        runLeftNormalization:
          type: boolean
          description: The job's left normalization setting.
        annotationFields:
          type: object
          additionalProperties:
            type: string
          description: The annotation schema generated by the parsed annotation data.
      required:
      - destinationName
      - roleArn
      - items
    StartVariantImportResponse:
      type: object
      properties:
        jobId:
          type: string
          description: The job's ID.
      required:
      - jobId
    ThrottlingException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    TsvOptions:
      type: object
      properties:
        readOptions:
          $ref: '#/components/schemas/ReadOptions'
    ValidationException:
      type: object
      properties:
        message:
          type: string
      required:
      - message
    VariantImportItemDetail:
      type: object
      properties:
        source:
          type: string
          description: The source file's location in Amazon S3.
        jobStatus:
          type: string
          description: The item's job status.
        statusMessage:
          type: string
          description: A message that provides additional context about a job
      required:
      - source
      - jobStatus
    VariantImportItemSource:
      type: object
      properties:
        source:
          type: string
          description: The source file's location in Amazon S3.
      required:
      - source
    VariantImportJobItem:
      type: object
      properties:
        id:
          type: string
          description: The job's ID.
        destinationName:
          type: string
          description: The job's destination variant store.
        roleArn:
          type: string
          description: The job's service role ARN.
        status:
          type: string
          description: The job's status.
        creationTime:
          type: string
          format: date-time
          description: When the job was created.
        updateTime:
          type: string
          format: date-time
          description: When the job was updated.
        completionTime:
          type: string
          format: date-time
          description: When the job completed.
        runLeftNormalization:
          type: boolean
          description: The job's left normalization setting.
        annotationFields:
          type: object
          additionalProperties:
            type: string
          description: The annotation schema generated by the parsed annotation data.
      required:
      - id
      - destinationName
      - roleArn
      - status
      - creationTime
      - updateTime
    VcfOptions:
      type: object
      properties:
        ignoreQualField:
          type: boolean
          description: The file's ignore qual field setting.
        ignoreFilterField:
          type: boolean
          description: The file's ignore filter field setting.
x-provenance:
  method: harvested
  publisher: Amazon Web Services
  source: https://raw.githubusercontent.com/aws/api-models-aws/582e55931c45b944739742a2c1620b6026dd2d13/models/omics/service/2022-11-28/omics-2022-11-28.json
  note: converted by smithy-to-openapi.py from AWS's Smithy model (roadmap#1001)