Broad Institute Womtool API

openapi: 3.2.0
info:
  title: Terra Womtool API
  description: Terra API
  termsOfService: https://app.terra.bio/#terms-of-service
  license:
    name: BSD
    url: http://opensource.org/licenses/BSD-3-Clause
  version: '0.1'
servers:
- url: /
security:
- oidc: []
tags:
- name: Womtool
paths:
  /api/womtool/{version}/describe:
    post:
      tags:
      - Womtool
      summary: Machine-readable description of a workflow, including inputs and outputs
      operationId: describe
      parameters:
      - $ref: '#/components/parameters/versionParam'
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                workflowSource:
                  type: string
                  description: The workflow source file to submit for execution. Either workflow source or workflow url is required.
                  format: binary
                workflowUrl:
                  type: string
                  description: URL which points to the workflow. Either workflow source or workflow url is required.
                workflowInputs:
                  type: string
                  description: JSON or YAML file containing the inputs as an object.
                  format: binary
                workflowType:
                  type: string
                  description: The workflow language for the file you submitted. Cromwell currently supports WDL and CWL.
                  enum:
                  - WDL
                  - CWL
                workflowTypeVersion:
                  type: string
                  description: The specification version for the workflow language being used. For WDL, Cromwell currently supports draft-2 and 1.0. For CWL, Cromwell currently supports v1.0.
                  enum:
                  - draft-2
                  - '1.0'
                  - v1.0
      responses:
        200:
          description: Workflow description.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/WorkflowDescription'
      x-passthrough: true
      x-passthrough-target: cromiam
components:
  schemas:
    WorkflowDescription:
      required:
      - errors
      - inputs
      - name
      - outputs
      - submittedDescriptorType
      - valid
      type: object
      properties:
        valid:
          type: boolean
          description: Whether the workflow and inputs as submitted passed validation
        errors:
          type: array
          description: The set of validation failure messages
          example:
          - The 'errors' field will be filled if 'valid' is false
          - We might also provide warnings to a 'valid' workflow here
          - Otherwise, 'errors' will be the empty array
          items:
            type: string
        name:
          type: string
          description: For a source file with one workflow and zero or more tasks, the name of the workflow. For a single task, the name of the task. For a source file with multiple tasks but no workflows, the empty string.
        inputs:
          type: array
          description: A list of inputs for this tool
          example:
          - name: my_wf.string_input
            valueType:
              typeName: String
            optional: false
            typeDisplayName: String
          - name: my_wf.array_input
            valueType:
              typeName: Array
              arrayType:
                typeName: String
            optional: false
            typeDisplayName: Array[String]
          - name: my_wf.optional_input
            valueType:
              typeName: Optional
              optionalType:
                typeName: String
            optional: true
            default: hello
            typeDisplayName: String?
          - name: my_wf.map_input
            valueType:
              typeName: Map
              mapType:
                keyType:
                  typeName: String
                valueType:
                  typeName: Int
            optional: false
            typeDisplayName: Map[String, Int]
          - name: my_wf.object_input
            valueType:
              typeName: Object
              objectFieldTypes:
              - fieldName: int_field
                fieldType:
                  typeName: Int
              - fieldName: int_array_field
                fieldType:
                  typeName: Array
                  arrayType:
                    typeName: Int
            optional: false
            typeDisplayName: Object
          - name: my_wf.int_string_pair_input
            valueType:
              typeName: Pair
              pairTypes:
              - leftType:
                - typeName: Int
              - rightType:
                - typeName: String
            optional: false
            typeDisplayName: Pair[Int, String]
          items:
            $ref: '#/components/schemas/ToolInputParameter'
        outputs:
          type: array
          description: A list of outputs for this tool
          example:
          - name: my_wf.string_output
            valueType:
              typeName: String
            typeDisplayName: String
          - name: my_wf.array_output
            valueType:
              typeName: Array
              arrayType:
                typeName: String
            typeDisplayName: Array[String]
          - name: my_wf.map_output
            valueType:
              typeName: Map
              mapType:
                keyType:
                  typeName: String
                valueType:
                  typeName: Int
            typeDisplayName: Map[String, Int]
          - name: my_wf.object_output
            valueType:
              typeName: Object
              objectFieldTypes:
              - fieldName: int_field
                fieldType:
                  typeName: Int
              - fieldName: int_array_field
                fieldType:
                  typeName: Array
                  arrayType:
                    typeName: Int
            typeDisplayName: Object
          - name: my_wf.int_string_pair_output
            valueType:
              typeName: Pair
              tupleTypes:
              - typeName: Int
              - typeName: String
            typeDisplayName: Pair[Int, String]
          items:
            $ref: '#/components/schemas/ToolOutputParameter'
        submittedDescriptorType:
          $ref: '#/components/schemas/DescriptorTypeAndVersion'
    ToolInputParameter:
      required:
      - default
      - name
      - optional
      - valueType
      type: object
      properties:
        name:
          type: string
          description: The name of this input value (formatted as expected by the tool)
        valueType:
          $ref: '#/components/schemas/ValueType'
        optional:
          type: boolean
          description: Whether the tool allows this value to not be specified
        default:
          type: string
          description: The in-language expression used to evaluate a default value for this parameter, if none is supplied.
      description: An input parameter for a tool or workflow.
    MapValueType:
      required:
      - keyType
      - valueType
      type: object
      properties:
        keyType:
          $ref: '#/components/schemas/ValueType'
        valueType:
          $ref: '#/components/schemas/ValueType'
      description: A type representing a map from one type to another.
    ValueType:
      type: object
      properties:
        typeName:
          type: string
          description: The type of this value
          enum:
          - String
          - File
          - Directory
          - Float
          - Int
          - Boolean
          - Optional
          - Array
          - Tuple
          - Map
          - Object
        optionalType:
          $ref: '#/components/schemas/ValueType'
        arrayType:
          $ref: '#/components/schemas/ValueType'
        mapType:
          $ref: '#/components/schemas/MapValueType'
        tupleTypes:
          type: array
          items:
            $ref: '#/components/schemas/ValueType'
        objectFieldTypes:
          type: array
          items:
            type: object
            properties:
              fieldName:
                type: string
              fieldType:
                $ref: '#/components/schemas/ValueType'
      description: The type expected for a given value.
    ToolOutputParameter:
      required:
      - name
      - valueType
      type: object
      properties:
        name:
          type: string
          description: The name of this input value (formatted as expected by the tool)
        valueType:
          $ref: '#/components/schemas/ValueType'
      description: An output parameter for a tool or workflow.
    DescriptorType:
      type: string
      description: One from a list of descriptor type strings (e.g. CWL, WDL). Note that these files can also include associated Docker/container files and test parameters that further describe a version of a tool
      example: WDL
      enum:
      - CWL
      - WDL
    DescriptorTypeAndVersion:
      required:
      - descriptorType
      - descriptorTypeVersion
      type: object
      properties:
        descriptorType:
          $ref: '#/components/schemas/DescriptorType'
        descriptorTypeVersion:
          type: string
          example: '1.0'
      description: A workflow descriptor file type and version.
  parameters:
    versionParam:
      name: version
      in: path
      description: Cromwell API Version
      required: true
      schema:
        type: string
        default: v1
  securitySchemes:
    oidc:
      type: oauth2
      x-tokenName: id_token
      flows:
        authorizationCode:
          authorizationUrl: OAUTH_AUTHORIZATION_URL
          scopes: {}
          tokenUrl: OAUTH_TOKEN_URL
    oidc_google_billing_scope:
      type: oauth2
      x-tokenName: id_token
      flows:
        authorizationCode:
          authorizationUrl: OAUTH_AUTHORIZATION_URL_WITH_GOOGLE_BILLING_SCOPE
          scopes: {}
          tokenUrl: OAUTH_TOKEN_URL_WITH_GOOGLE_BILLING_SCOPE