packages/cdk/lib/wes_adapter/rest_api/openapi/openapi.yaml [334:697]:
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components:
  schemas:
    DefaultWorkflowEngineParameter:
      description: A message that allows one to describe default parameters for a
        workflow engine.
      example:
        name: name
        default_value: default_value
        type: type
      properties:
        name:
          description: The name of the parameter
          type: string
        type:
          description: Describes the type of the parameter, e.g. float.
          type: string
        default_value:
          description: The stringified version of the default parameter. e.g. "2.45".
          type: string
      type: object
    Log:
      description: Log and other info
      example:
        start_time: start_time
        stdout: stdout
        name: name
        end_time: end_time
        exit_code: 0
        cmd:
        - cmd
        - cmd
        stderr: stderr
      properties:
        name:
          description: The task or workflow name
          type: string
        cmd:
          description: The command line that was executed
          items:
            type: string
          type: array
        start_time:
          description: When the command started executing, in ISO 8601 format "%Y-%m-%dT%H:%M:%SZ"
          type: string
        end_time:
          description: When the command stopped executing (completed, failed, or cancelled),
            in ISO 8601 format "%Y-%m-%dT%H:%M:%SZ"
          type: string
        stdout:
          description: A URL to retrieve standard output logs of the workflow run
            or task.  This URL may change between status requests, or may not be available
            until the task or workflow has finished execution.  Should be available
            using the same credentials used to access the WES endpoint.
          type: string
        stderr:
          description: A URL to retrieve standard error logs of the workflow run or
            task.  This URL may change between status requests, or may not be available
            until the task or workflow has finished execution.  Should be available
            using the same credentials used to access the WES endpoint.
          type: string
        exit_code:
          description: Exit code of the program
          format: int32
          type: integer
      type: object
    ServiceInfo:
      description: A message containing useful information about the running service,
        including supported versions and default settings.
      example:
        system_state_counts:
          key: 0
        supported_wes_versions:
        - supported_wes_versions
        - supported_wes_versions
        supported_filesystem_protocols:
        - supported_filesystem_protocols
        - supported_filesystem_protocols
        auth_instructions_url: auth_instructions_url
        workflow_engine_versions:
          key: workflow_engine_versions
        contact_info_url: contact_info_url
        workflow_type_versions:
          key:
            workflow_type_version:
            - workflow_type_version
            - workflow_type_version
        default_workflow_engine_parameters:
        - name: name
          default_value: default_value
          type: type
        - name: name
          default_value: default_value
          type: type
        tags:
          key: tags
      properties:
        workflow_type_versions:
          additionalProperties:
            $ref: '#/components/schemas/WorkflowTypeVersion'
          description: A map with keys as the workflow format type name (currently
            only CWL and WDL are used although a service may support others) and value
            is a workflow_type_version object which simply contains an array of one
            or more version strings
          type: object
        supported_wes_versions:
          description: The version(s) of the WES schema supported by this service
          items:
            type: string
          type: array
        supported_filesystem_protocols:
          description: The filesystem protocols supported by this service, currently
            these may include common protocols using the terms 'http', 'https', 'sftp',
            's3', 'gs', 'file', or 'synapse', but others  are possible and the terms
            beyond these core protocols are currently not fixed.   This section reports
            those protocols (either common or not) supported by this WES service.
          items:
            type: string
          type: array
        workflow_engine_versions:
          additionalProperties:
            type: string
          description: The engine(s) used by this WES service, key is engine name
            (e.g. Cromwell) and value is version
          type: object
        default_workflow_engine_parameters:
          description: Each workflow engine can present additional parameters that
            can be sent to the workflow engine. This message will list the default
            values, and their types for each workflow engine.
          items:
            $ref: '#/components/schemas/DefaultWorkflowEngineParameter'
          type: array
        system_state_counts:
          additionalProperties:
            format: int64
            type: integer
          description: The system statistics, key is the statistic, value is the count
            of runs in that state. See the State enum for the possible keys.
          type: object
        auth_instructions_url:
          description: 'A web page URL with human-readable instructions on how to
            get an authorization token for use with a specific WES endpoint.          '
          type: string
        contact_info_url:
          description: An email address URL (mailto:) or web page URL with contact
            information for the operator of a specific WES endpoint.  Users of the
            endpoint should use this to report problems or security vulnerabilities.
          type: string
        tags:
          additionalProperties:
            type: string
          description: A key-value map of arbitrary, extended metadata outside the
            scope of the above but useful to report back
          type: object
      type: object
    State:
      default: UNKNOWN
      description: "- 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.\n\n\n\
        \ - QUEUED: The task is queued.\n\n\n- 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.\n\n- RUNNING: The task is running.\
        \ Input files are downloaded and the first Executor has been started.\n\n\
        - PAUSED: The task is paused. An implementation may have the ability to pause\
        \ a task, but this is not required.\n\n\n - COMPLETE: The task has completed\
        \ running. Executors have exited without error\nand output files have been\
        \ successfully uploaded.\n\n\n - EXECUTOR_ERROR: The task encountered an error\
        \ in one of the Executor processes. Generally,\nthis means that an Executor\
        \ exited with a non-zero exit code.\n\n\n - SYSTEM_ERROR: The task was stopped\
        \ due to a system error, but not from an Executor,\nfor example an upload\
        \ failed due to network issues, the worker's ran out of disk space, etc.\n\
        \n\n - CANCELED: The task was canceled by the user.\n\n\n  - CANCELING: The\
        \ task was canceled by the user, and is in the process of stopping.       "
      enum:
      - UNKNOWN
      - QUEUED
      - INITIALIZING
      - RUNNING
      - PAUSED
      - COMPLETE
      - EXECUTOR_ERROR
      - SYSTEM_ERROR
      - CANCELED
      - CANCELING
      type: string
    RunListResponse:
      description: The service will return a RunListResponse when receiving a successful
        RunListRequest.
      example:
        next_page_token: next_page_token
        runs:
        - run_id: run_id
        - run_id: run_id
      properties:
        runs:
          description: A list of workflow runs that the service has executed or is
            executing. The list is filtered to only include runs that the caller has
            permission to see.
          items:
            $ref: '#/components/schemas/RunStatus'
          type: array
        next_page_token:
          description: A token which may be supplied as `page_token` in workflow run
            list request to get the next page of results.  An empty string indicates
            there are no more items to return.
          type: string
      type: object
    RunLog:
      example:
        outputs: '{}'
        request:
          workflow_engine_parameters:
            key: workflow_engine_parameters
          workflow_url: workflow_url
          workflow_params: '{}'
          workflow_type: workflow_type
          workflow_type_version: workflow_type_version
          tags:
            key: tags
        run_id: run_id
        run_log:
          start_time: start_time
          stdout: stdout
          name: name
          end_time: end_time
          exit_code: 0
          cmd:
          - cmd
          - cmd
          stderr: stderr
        task_logs:
        - start_time: start_time
          stdout: stdout
          name: name
          end_time: end_time
          exit_code: 0
          cmd:
          - cmd
          - cmd
          stderr: stderr
        - start_time: start_time
          stdout: stdout
          name: name
          end_time: end_time
          exit_code: 0
          cmd:
          - cmd
          - cmd
          stderr: stderr
      properties:
        run_id:
          description: workflow run ID
          type: string
        request:
          $ref: '#/components/schemas/RunRequest'
        state:
          $ref: '#/components/schemas/State'
        run_log:
          $ref: '#/components/schemas/Log'
        task_logs:
          description: The logs, and other key info like timing and exit code, for
            each step in the workflow run.
          items:
            $ref: '#/components/schemas/Log'
          type: array
        outputs:
          description: The outputs from the workflow run.
          properties: {}
          type: object
      type: object
    RunRequest:
      description: |-
        To execute a workflow, send a run request including all the details needed to begin downloading
        and executing a given workflow.
      example:
        workflow_engine_parameters:
          key: workflow_engine_parameters
        workflow_url: workflow_url
        workflow_params: '{}'
        workflow_type: workflow_type
        workflow_type_version: workflow_type_version
        tags:
          key: tags
      properties:
        workflow_params:
          description: |-
            REQUIRED
            The workflow run parameterizations (JSON encoded), including input and output file locations
          properties: {}
          type: object
        workflow_type:
          description: |-
            REQUIRED
            The workflow descriptor type, must be "CWL" or "WDL" currently (or another alternative supported by this WES instance)
          type: string
        workflow_type_version:
          description: |-
            REQUIRED
            The workflow descriptor type version, must be one supported by this WES instance
          type: string
        tags:
          additionalProperties:
            type: string
          description: |-
            OPTIONAL
            A key-value map of arbitrary metadata outside the scope of `workflow_params` but useful to track with this run request
          type: object
        workflow_engine_parameters:
          additionalProperties:
            type: string
          description: |-
            OPTIONAL
            Additional parameters can be sent to the workflow engine using this field. Default values for these parameters can be obtained using the ServiceInfo endpoint.
          type: object
        workflow_url:
          description: |-
            REQUIRED
            The workflow CWL or WDL document. When `workflow_attachments` is used to attach files, the `workflow_url` may be a relative path to one of the attachments.
          type: string
      type: object
    RunId:
      example:
        run_id: run_id
      properties:
        run_id:
          description: workflow run ID
          type: string
      type: object
    RunStatus:
      description: Small description of a workflow run, returned by server during
        listing
      example:
        run_id: run_id
      properties:
        run_id:
          type: string
        state:
          $ref: '#/components/schemas/State'
      required:
      - run_id
      type: object
    WorkflowTypeVersion:
      description: Available workflow types supported by a given instance of the service.
      example:
        workflow_type_version:
        - workflow_type_version
        - workflow_type_version
      properties:
        workflow_type_version:
          description: an array of one or more acceptable types for the `workflow_type`
          items:
            type: string
          type: array
      type: object
    ErrorResponse:
      description: An object that can optionally include information about the error.
      properties:
        msg:
          description: A detailed error message.
          type: string
        status_code:
          description: The integer representing the HTTP status code (e.g. 200, 404).
          type: integer
      type: object
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packages/wes_api/client/api/openapi.yaml [327:690]:
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components:
  schemas:
    DefaultWorkflowEngineParameter:
      description: A message that allows one to describe default parameters for a
        workflow engine.
      example:
        name: name
        default_value: default_value
        type: type
      properties:
        name:
          description: The name of the parameter
          type: string
        type:
          description: Describes the type of the parameter, e.g. float.
          type: string
        default_value:
          description: The stringified version of the default parameter. e.g. "2.45".
          type: string
      type: object
    Log:
      description: Log and other info
      example:
        start_time: start_time
        stdout: stdout
        name: name
        end_time: end_time
        exit_code: 0
        cmd:
        - cmd
        - cmd
        stderr: stderr
      properties:
        name:
          description: The task or workflow name
          type: string
        cmd:
          description: The command line that was executed
          items:
            type: string
          type: array
        start_time:
          description: When the command started executing, in ISO 8601 format "%Y-%m-%dT%H:%M:%SZ"
          type: string
        end_time:
          description: When the command stopped executing (completed, failed, or cancelled),
            in ISO 8601 format "%Y-%m-%dT%H:%M:%SZ"
          type: string
        stdout:
          description: A URL to retrieve standard output logs of the workflow run
            or task.  This URL may change between status requests, or may not be available
            until the task or workflow has finished execution.  Should be available
            using the same credentials used to access the WES endpoint.
          type: string
        stderr:
          description: A URL to retrieve standard error logs of the workflow run or
            task.  This URL may change between status requests, or may not be available
            until the task or workflow has finished execution.  Should be available
            using the same credentials used to access the WES endpoint.
          type: string
        exit_code:
          description: Exit code of the program
          format: int32
          type: integer
      type: object
    ServiceInfo:
      description: A message containing useful information about the running service,
        including supported versions and default settings.
      example:
        system_state_counts:
          key: 0
        supported_wes_versions:
        - supported_wes_versions
        - supported_wes_versions
        supported_filesystem_protocols:
        - supported_filesystem_protocols
        - supported_filesystem_protocols
        auth_instructions_url: auth_instructions_url
        workflow_engine_versions:
          key: workflow_engine_versions
        contact_info_url: contact_info_url
        workflow_type_versions:
          key:
            workflow_type_version:
            - workflow_type_version
            - workflow_type_version
        default_workflow_engine_parameters:
        - name: name
          default_value: default_value
          type: type
        - name: name
          default_value: default_value
          type: type
        tags:
          key: tags
      properties:
        workflow_type_versions:
          additionalProperties:
            $ref: '#/components/schemas/WorkflowTypeVersion'
          description: A map with keys as the workflow format type name (currently
            only CWL and WDL are used although a service may support others) and value
            is a workflow_type_version object which simply contains an array of one
            or more version strings
          type: object
        supported_wes_versions:
          description: The version(s) of the WES schema supported by this service
          items:
            type: string
          type: array
        supported_filesystem_protocols:
          description: The filesystem protocols supported by this service, currently
            these may include common protocols using the terms 'http', 'https', 'sftp',
            's3', 'gs', 'file', or 'synapse', but others  are possible and the terms
            beyond these core protocols are currently not fixed.   This section reports
            those protocols (either common or not) supported by this WES service.
          items:
            type: string
          type: array
        workflow_engine_versions:
          additionalProperties:
            type: string
          description: The engine(s) used by this WES service, key is engine name
            (e.g. Cromwell) and value is version
          type: object
        default_workflow_engine_parameters:
          description: Each workflow engine can present additional parameters that
            can be sent to the workflow engine. This message will list the default
            values, and their types for each workflow engine.
          items:
            $ref: '#/components/schemas/DefaultWorkflowEngineParameter'
          type: array
        system_state_counts:
          additionalProperties:
            format: int64
            type: integer
          description: The system statistics, key is the statistic, value is the count
            of runs in that state. See the State enum for the possible keys.
          type: object
        auth_instructions_url:
          description: 'A web page URL with human-readable instructions on how to
            get an authorization token for use with a specific WES endpoint.          '
          type: string
        contact_info_url:
          description: An email address URL (mailto:) or web page URL with contact
            information for the operator of a specific WES endpoint.  Users of the
            endpoint should use this to report problems or security vulnerabilities.
          type: string
        tags:
          additionalProperties:
            type: string
          description: A key-value map of arbitrary, extended metadata outside the
            scope of the above but useful to report back
          type: object
      type: object
    State:
      default: UNKNOWN
      description: "- 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.\n\n\n\
        \ - QUEUED: The task is queued.\n\n\n- 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.\n\n- RUNNING: The task is running.\
        \ Input files are downloaded and the first Executor has been started.\n\n\
        - PAUSED: The task is paused. An implementation may have the ability to pause\
        \ a task, but this is not required.\n\n\n - COMPLETE: The task has completed\
        \ running. Executors have exited without error\nand output files have been\
        \ successfully uploaded.\n\n\n - EXECUTOR_ERROR: The task encountered an error\
        \ in one of the Executor processes. Generally,\nthis means that an Executor\
        \ exited with a non-zero exit code.\n\n\n - SYSTEM_ERROR: The task was stopped\
        \ due to a system error, but not from an Executor,\nfor example an upload\
        \ failed due to network issues, the worker's ran out of disk space, etc.\n\
        \n\n - CANCELED: The task was canceled by the user.\n\n\n  - CANCELING: The\
        \ task was canceled by the user, and is in the process of stopping.       "
      enum:
      - UNKNOWN
      - QUEUED
      - INITIALIZING
      - RUNNING
      - PAUSED
      - COMPLETE
      - EXECUTOR_ERROR
      - SYSTEM_ERROR
      - CANCELED
      - CANCELING
      type: string
    RunListResponse:
      description: The service will return a RunListResponse when receiving a successful
        RunListRequest.
      example:
        next_page_token: next_page_token
        runs:
        - run_id: run_id
        - run_id: run_id
      properties:
        runs:
          description: A list of workflow runs that the service has executed or is
            executing. The list is filtered to only include runs that the caller has
            permission to see.
          items:
            $ref: '#/components/schemas/RunStatus'
          type: array
        next_page_token:
          description: A token which may be supplied as `page_token` in workflow run
            list request to get the next page of results.  An empty string indicates
            there are no more items to return.
          type: string
      type: object
    RunLog:
      example:
        outputs: '{}'
        request:
          workflow_engine_parameters:
            key: workflow_engine_parameters
          workflow_url: workflow_url
          workflow_params: '{}'
          workflow_type: workflow_type
          workflow_type_version: workflow_type_version
          tags:
            key: tags
        run_id: run_id
        run_log:
          start_time: start_time
          stdout: stdout
          name: name
          end_time: end_time
          exit_code: 0
          cmd:
          - cmd
          - cmd
          stderr: stderr
        task_logs:
        - start_time: start_time
          stdout: stdout
          name: name
          end_time: end_time
          exit_code: 0
          cmd:
          - cmd
          - cmd
          stderr: stderr
        - start_time: start_time
          stdout: stdout
          name: name
          end_time: end_time
          exit_code: 0
          cmd:
          - cmd
          - cmd
          stderr: stderr
      properties:
        run_id:
          description: workflow run ID
          type: string
        request:
          $ref: '#/components/schemas/RunRequest'
        state:
          $ref: '#/components/schemas/State'
        run_log:
          $ref: '#/components/schemas/Log'
        task_logs:
          description: The logs, and other key info like timing and exit code, for
            each step in the workflow run.
          items:
            $ref: '#/components/schemas/Log'
          type: array
        outputs:
          description: The outputs from the workflow run.
          properties: {}
          type: object
      type: object
    RunRequest:
      description: |-
        To execute a workflow, send a run request including all the details needed to begin downloading
        and executing a given workflow.
      example:
        workflow_engine_parameters:
          key: workflow_engine_parameters
        workflow_url: workflow_url
        workflow_params: '{}'
        workflow_type: workflow_type
        workflow_type_version: workflow_type_version
        tags:
          key: tags
      properties:
        workflow_params:
          description: |-
            REQUIRED
            The workflow run parameterizations (JSON encoded), including input and output file locations
          properties: {}
          type: object
        workflow_type:
          description: |-
            REQUIRED
            The workflow descriptor type, must be "CWL" or "WDL" currently (or another alternative supported by this WES instance)
          type: string
        workflow_type_version:
          description: |-
            REQUIRED
            The workflow descriptor type version, must be one supported by this WES instance
          type: string
        tags:
          additionalProperties:
            type: string
          description: |-
            OPTIONAL
            A key-value map of arbitrary metadata outside the scope of `workflow_params` but useful to track with this run request
          type: object
        workflow_engine_parameters:
          additionalProperties:
            type: string
          description: |-
            OPTIONAL
            Additional parameters can be sent to the workflow engine using this field. Default values for these parameters can be obtained using the ServiceInfo endpoint.
          type: object
        workflow_url:
          description: |-
            REQUIRED
            The workflow CWL or WDL document. When `workflow_attachments` is used to attach files, the `workflow_url` may be a relative path to one of the attachments.
          type: string
      type: object
    RunId:
      example:
        run_id: run_id
      properties:
        run_id:
          description: workflow run ID
          type: string
      type: object
    RunStatus:
      description: Small description of a workflow run, returned by server during
        listing
      example:
        run_id: run_id
      properties:
        run_id:
          type: string
        state:
          $ref: '#/components/schemas/State'
      required:
      - run_id
      type: object
    WorkflowTypeVersion:
      description: Available workflow types supported by a given instance of the service.
      example:
        workflow_type_version:
        - workflow_type_version
        - workflow_type_version
      properties:
        workflow_type_version:
          description: an array of one or more acceptable types for the `workflow_type`
          items:
            type: string
          type: array
      type: object
    ErrorResponse:
      description: An object that can optionally include information about the error.
      properties:
        msg:
          description: A detailed error message.
          type: string
        status_code:
          description: The integer representing the HTTP status code (e.g. 200, 404).
          type: integer
      type: object
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