schema.task_execution_service.d55bf88.openapi.modified.yaml

swagger: '2.0'
info:
  title: Task Execution Service
  version: '0.4.0'
schemes:
  - http
consumes:
  - application/json
produces:
  - application/json
basePath: '/ga4gh/tes/v1'
paths:
  /tasks:
    get:
      summary: |-
        List tasks.
        TaskView is requested as such: "v1/tasks?view=BASIC"
      operationId: ListTasks
      responses:
        '200':
          description: ''
          schema:
            $ref: '#/definitions/tesListTasksResponse'
      parameters:
        - name: name_prefix
          description: |-
            OPTIONAL. Filter the list to include tasks where the name matches this prefix.
            If unspecified, no task name filtering is done.
          in: query
          required: false
          type: string
        - name: page_size
          description: |-
            OPTIONAL. Number of tasks to return in one page.
            Must be less than 2048. Defaults to 256.
          in: query
          required: false
          type: integer
          format: int64
        - name: page_token
          description: |-
            OPTIONAL. Page token is used to retrieve the next page of results.
            If unspecified, returns the first page of results.
            See ListTasksResponse.next_page_token
          in: query
          required: false
          type: string
        - name: view
          description: |-
            OPTIONAL. Affects the fields included in the returned Task messages.
            See TaskView below.

             - MINIMAL: Task message will include ONLY the fields:
              Task.Id
              Task.State
             - BASIC: Task message will include all fields EXCEPT:
              Task.ExecutorLog.stdout
              Task.ExecutorLog.stderr
              Input.content
              TaskLog.system_logs
             - FULL: Task message includes all fields.
          in: query
          required: false
          type: string
          enum:
            - MINIMAL
            - BASIC
            - FULL
          default: MINIMAL
      tags:
        - TaskService
      x-swagger-router-controller: ga4gh.tes.server
    post:
      summary: Create a new task.
      operationId: CreateTask
      responses:
        '200':
          description: ''
          schema:
            $ref: '#/definitions/tesCreateTaskResponse'
      parameters:
        - name: body
          in: body
          required: true
          schema:
            $ref: '#/definitions/tesTask'
      tags:
        - TaskService
      x-swagger-router-controller: ga4gh.tes.server
  /tasks/service-info:
    get:
      summary: |-
        GetServiceInfo provides information about the service,
        such as storage details, resource availability, and 
        other documentation.
      operationId: GetServiceInfo
      responses:
        '200':
          description: ''
          schema:
            $ref: '#/definitions/tesServiceInfo'
      tags:
        - TaskService
      x-swagger-router-controller: ga4gh.tes.server
  /tasks/task-info:
    post:
      summary: |-
        Provides estimates for the queue time and incurred costs for a task
        with the given resource requirements.
      operationId: GetTaskInfo
      responses:
        '200':
          description: ''
          schema:
            $ref: '#/definitions/tesTaskInfo'
      parameters:
        - name: body
          in: body
          required: true
          schema:
            $ref: '#/definitions/tesResources'
      tags:
        - TaskService
      x-swagger-router-controller: ga4gh.tes.server
  '/tasks/{id}':
    get:
      summary: |-
        Get a task.
        TaskView is requested as such: "v1/tasks/{id}?view=FULL"
      operationId: GetTask
      responses:
        '200':
          description: ''
          schema:
            $ref: '#/definitions/tesTask'
      parameters:
        - name: id
          in: path
          required: true
          type: string
        - name: view
          description: |-
            OPTIONAL. Affects the fields included in the returned Task messages.
            See TaskView below.

             - MINIMAL: Task message will include ONLY the fields:
              Task.Id
              Task.State
             - BASIC: Task message will include all fields EXCEPT:
              Task.ExecutorLog.stdout
              Task.ExecutorLog.stderr
              Input.content
              TaskLog.system_logs
             - FULL: Task message includes all fields.
          in: query
          required: false
          type: string
          enum:
            - MINIMAL
            - BASIC
            - FULL
          default: MINIMAL
      tags:
        - TaskService
      x-swagger-router-controller: ga4gh.tes.server
  '/tasks/{id}:cancel':
    post:
      summary: Cancel a task.
      operationId: CancelTask
      responses:
        '200':
          description: ''
          schema:
            $ref: '#/definitions/tesCancelTaskResponse'
      parameters:
        - name: id
          in: path
          required: true
          type: string
      tags:
        - TaskService
      x-swagger-router-controller: ga4gh.tes.server
definitions:
  tesCancelTaskResponse:
    type: object
    description: CancelTaskResponse describes a response from the CancelTask endpoint.
    readOnly: true
  tesCosts:
    type: object
    properties:
      amount:
        type: number
        format: double
        description: Numeric value specifying an amount of money.
      currency:
        type: string
        enum:
          - AUD
          - BRL
          - BTC
          - CAD
          - CHF
          - CNH
          - EUR
          - GBP
          - HKD
          - INR
          - KRW
          - JPY
          - MXN
          - NOK
          - NZD
          - RUB
          - SEK
          - SGD
          - TRY
          - USD
          - ZAR
        description: Currency/unit of the costs.
    description: Generic object specifying an amount of money.
  tesCreateTaskResponse:
    type: object
    properties:
      id:
        type: string
        description: Task identifier assigned by the server.
    description: CreateTaskResponse describes a response from the CreateTask endpoint.
    readOnly: true
    required:
    - id
  tesExecutor:
    type: object
    properties:
      image:
        type: string
        description: |-
          Name of the container image, for example:
          ubuntu
          quay.io/aptible/ubuntu
          gcr.io/my-org/my-image
          etc...
      command:
        type: array
        items:
          type: string
        description: |-
          A sequence of program arguments to execute, where the first argument
          is the program to execute (i.e. argv).
      workdir:
        type: string
        description: |-
          The working directory that the command will be executed in.
          Defaults to the directory set by the container image.
      stdin:
        type: string
        description: |-
          Path inside the container to a file which will be piped
          to the executor's stdin. Must be an absolute path.
      stdout:
        type: string
        description: |-
          Path inside the container to a file where the executor's
          stdout will be written to. Must be an absolute path.
      stderr:
        type: string
        description: |-
          Path inside the container to a file where the executor's
          stderr will be written to. Must be an absolute path.
      env:
        type: object
        additionalProperties:
          type: string
        description: Enviromental variables to set within the container.
    description: 'Executor describes a command to be executed, and its environment.'
    required:
    - image
    - command
  tesExecutorLog:
    type: object
    properties:
      start_time:
        type: string
        description: 'Time the executor started, in RFC 3339 format.'
      end_time:
        type: string
        description: 'Time the executor ended, in RFC 3339 format.'
      stdout:
        type: string
        description: |-
          Stdout content.

          This is meant for convenience. No guarantees are made about the content.
          Implementations may chose different approaches: only the head, only the tail,
          a URL reference only, etc.

          In order to capture the full stdout users should set Executor.stdout
          to a container file path, and use Task.outputs to upload that file
          to permanent storage.
      stderr:
        type: string
        description: |-
          Stderr content.

          This is meant for convenience. No guarantees are made about the content.
          Implementations may chose different approaches: only the head, only the tail,
          a URL reference only, etc.

          In order to capture the full stderr users should set Executor.stderr
          to a container file path, and use Task.outputs to upload that file
          to permanent storage.
      exit_code:
        type: integer
        format: int32
        description: Exit code.
    description: ExecutorLog describes logging information related to an Executor.
    required:
    - exit_code
    readOnly: true
  tesFileType:
    type: string
    enum:
      - FILE
      - DIRECTORY
    default: FILE
  tesInput:
    type: object
    properties:
      name:
        type: string
      description:
        type: string
      url:
        type: string
        description: |-
          REQUIRED, unless "content" is set.

          URL in long term storage, for example:
          s3://my-object-store/file1
          gs://my-bucket/file2
          file:///path/to/my/file
          /path/to/my/file
          etc...
      path:
        type: string
        description: |-
          Path of the file inside the container.
          Must be an absolute path.
      type:
        $ref: '#/definitions/tesFileType'
        description: 'Type of the file, FILE or DIRECTORY'
      content:
        type: string
        description: |-
          File content literal.
          Implementations should support a minimum of 128 KiB in this field and may define its own maximum.
          UTF-8 encoded

          If content is not empty, "url" must be ignored.
    description: Input describes Task input files.
    required:
    - type
    - path
  tesListTasksResponse:
    type: object
    properties:
      tasks:
        type: array
        items:
          $ref: '#/definitions/tesTask'
        description: List of tasks.
      next_page_token:
        type: string
        description: |-
          Token used to return the next page of results.
          See TaskListRequest.next_page_token
    description: ListTasksResponse describes a response from the ListTasks endpoint.
    required:
    - tasks
    readOnly: true
  tesOutput:
    type: object
    properties:
      name:
        type: string
      description:
        type: string
      url:
        type: string
        description: |-
          URL in long term storage, for example:
          s3://my-object-store/file1
          gs://my-bucket/file2
          file:///path/to/my/file
          /path/to/my/file
          etc...
      path:
        type: string
        description: |-
          Path of the file inside the container.
          Must be an absolute path.
      type:
        $ref: '#/definitions/tesFileType'
        description: 'Type of the file, FILE or DIRECTORY'
    description: Output describes Task output files.
    required:
    - url
    - path
    - type
  tesOutputFileLog:
    type: object
    properties:
      url:
        type: string
        description: 'URL of the file in storage, e.g. s3://bucket/file.txt'
      path:
        type: string
        description: Path of the file inside the container. Must be an absolute path.
      size_bytes:
        type: string
        format: int64
        description: Size of the file in bytes.
    description: |-
      OutputFileLog describes a single output file. This describes
      file details after the task has completed successfully,
      for logging purposes.
    readOnly: true
    required:
    - url
    - path
    - size_bytes
  tesResources:
    type: object
    properties:
      execution_time_sec:
        type: integer
        format: int64
        description: Requested execution in seconds (s)
      cpu_cores:
        type: integer
        format: int64
        description: Requested number of CPUs
      preemptible:
        type: boolean
        format: boolean
        description: Is the task allowed to run on preemptible compute instances (e.g. AWS Spot)?
      ram_gb:
        type: number
        format: double
        description: Requested RAM required in gigabytes (GB)
      disk_gb:
        type: number
        format: double
        description: Requested disk size in gigabytes (GB)
      zones:
        type: array
        items:
          type: string
        description: Request that the task be run in these compute zones.
    description: Resources describes the resources requested by a task.
  tesServiceInfo:
    type: object
    properties:
      name:
        type: string
        description: 'Returns the name of the service, e.g. "ohsu-compbio-funnel".'
      doc:
        type: string
        description: 'Returns a documentation string, e.g. "Hey, we''re OHSU Comp. Bio!".'
      storage:
        type: array
        items:
          type: string
        description: |-
          Lists some, but not necessarily all, storage locations supported by the service.

          Must be in a valid URL format.
          e.g.
          file:///path/to/local/funnel-storage
          s3://ohsu-compbio-funnel/storage
          etc.
    description: |-
      ServiceInfo describes information about the service,
      such as storage details, resource availability,
      and other documentation.
    readOnly: true
  tesState:
    type: string
    enum:
      - UNKNOWN
      - QUEUED
      - INITIALIZING
      - RUNNING
      - PAUSED
      - COMPLETE
      - EXECUTOR_ERROR
      - SYSTEM_ERROR
      - CANCELED
    default: UNKNOWN
    description: |-
      Task states.

       - UNKNOWN: The state of the task is unknown.

      This provides a safe default for messages where this field is missing,
      for example, so that a missing field does not accidentally imply that
      the state is QUEUED.
       - QUEUED: The task is queued.
       - INITIALIZING: The task has been assigned to a worker and is currently preparing to run.
      For example, the worker may be turning on, downloading input files, etc.
       - RUNNING: The task is running. Input files are downloaded and the first Executor
      has been started.
       - PAUSED: The task is paused.

      An implementation may have the ability to pause a task, but this is not required.
       - COMPLETE: The task has completed running. Executors have exited without error
      and output files have been successfully uploaded.
       - EXECUTOR_ERROR: The task encountered an error in one of the Executor processes. Generally,
      this means that an Executor exited with a non-zero exit code.
       - SYSTEM_ERROR: The task was stopped due to a system error, but not from an Executor,
      for example an upload failed due to network issues, the worker's ran out
      of disk space, etc.
       - CANCELED: The task was canceled by the user.
    readOnly: true
  tesTask:
    type: object
    properties:
      id:
        type: string
        description: Task identifier assigned by the server.
        readOnly: true
      state:
        $ref: '#/definitions/tesState'
        # AK 01-JUL-2019: `swagger_spec_validator` gave a validation error:
        # SwaggerValidationWarning: Found "$ref: #/definitions/tesState" with
        # siblings that will be overwritten.
        # See https://stackoverflow.com/a/48114924 for more information.
        # Sibling of $ref was commented out.
        #readOnly: true
      name:
        type: string
      description:
        type: string
      inputs:
        type: array
        items:
          $ref: '#/definitions/tesInput'
        description: |-
          Input files.
          Inputs will be downloaded and mounted into the executor container.
      outputs:
        type: array
        items:
          $ref: '#/definitions/tesOutput'
        description: |-
          Output files.
          Outputs will be uploaded from the executor container to long-term storage.
      resources:
        $ref: '#/definitions/tesResources'
        description: Request that the task be run with these resources.
      executors:
        type: array
        items:
          $ref: '#/definitions/tesExecutor'
        description: |-
          A list of executors to be run, sequentially. Execution stops
          on the first error.
      volumes:
        type: array
        items:
          type: string
        description: |-
          Volumes are directories which may be used to share data between
          Executors. Volumes are initialized as empty directories by the
          system when the task starts and are mounted at the same path
          in each Executor.

          For example, given a volume defined at "/vol/A",
          executor 1 may write a file to "/vol/A/exec1.out.txt", then
          executor 2 may read from that file.

          (Essentially, this translates to a `docker run -v` flag where
          the container path is the same for each executor).
      tags:
        type: object
        additionalProperties:
          type: string
        description: A key-value map of arbitrary tags.
      logs:
        type: array
        items:
          $ref: '#/definitions/tesTaskLog'
        description: |-
          Task logging information.
          Normally, this will contain only one entry, but in the case where
          a task fails and is retried, an entry will be appended to this list.
        readOnly: true
      creation_time:
        type: string
        description: |-
          Date + time the task was created, in RFC 3339 format.
          This is set by the system, not the client.
        readOnly: true
    description: Task describes an instance of a task.
    required:
    - executors
  tesTaskInfo:
    type: object
    properties:
      estimated_compute_costs:
        $ref: '#/definitions/tesCosts'
        description: |-
          Estimated total incurred compute costs for running a task with the
          indicated resource requirements on this TES instance. Excludes data
          storage and transfer costs.
      estimated_storage_costs:
        $ref: '#/definitions/tesCosts'
        description: |-
          Estimated total incurred data storage costs for running a task with
          the indicated resource requirements on this TES instance. Excludes
          compute and data transfer costs. Currently this is reported as a flat
          fee for conceptually indefinite storage.
      estimated_queue_time_sec:
        type: number
        format: double
        description: |-
          Given the current load on this TES instance, returns an estimate of
          the time, in seconds (s), that a task with the indicated resource
          requirements will spend in the task queue.
      unit_costs_data_transfer:
        $ref: '#/definitions/tesCosts'
        description: |-
          Unit costs for transferring 1 gigabyte (GB) of data (inputs, outputs)
          across 1000 kilometers (km).
    description: |-
      Given a set of resource requirements, returns the estimated queue time
      and total incurred costs. Allows informed decisions with regard to which
      TES instance a given task should be sent to.
  tesTaskLog:
    type: object
    properties:
      logs:
        type: array
        items:
          $ref: '#/definitions/tesExecutorLog'
        description: Logs for each executor
      metadata:
        type: object
        additionalProperties:
          type: string
        description: Arbitrary logging metadata included by the implementation.
      start_time:
        type: string
        description: 'When the task started, in RFC 3339 format.'
      end_time:
        type: string
        description: 'When the task ended, in RFC 3339 format.'
      outputs:
        type: array
        items:
          $ref: '#/definitions/tesOutputFileLog'
        description: |-
          Information about all output files. Directory outputs are
          flattened into separate items.
      system_logs:
        type: array
        items:
          type: string
        description: |-
          System logs are any logs the system decides are relevant,
          which are not tied directly to an Executor process.
          Content is implementation specific: format, size, etc.

          System logs may be collected here to provide convenient access.

          For example, the system may include the name of the host
          where the task is executing, an error message that caused
          a SYSTEM_ERROR state (e.g. disk is full), etc.

          System logs are only included in the FULL task view.
    description: TaskLog describes logging information related to a Task.
    required:
    - logs
    - outputs
    readOnly: true