cr-connect-workflow/crc/api.yml

openapi: "3.0.2"
info:
  version: 1.0.0
  title: Workflow Microservice
  license:
    name: MIT
servers:
  - url: http://localhost:5000/v1.0
paths:
  # /v1.0/study
  /study:
    get:
      operationId: crc.api.study.all_studies
      summary: Provides a list of studies related to the current user.
      tags:
        - Studies
      responses:
        '200':
          description: An array of studies, ordered by the last modified date.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Study"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"
    post:
      operationId: crc.api.study.add_study
      summary: Creates a new study with the given parameters.
      tags:
        - Studies
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/Study'
      responses:
        '200':
          description: Study created successfully.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Study"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"
  /study/{study_id}:
    get:
      operationId: crc.api.study.get_study
      summary: Provides a single study
      tags:
        - Studies
      parameters:
        - name: study_id
          in: path
          required: true
          description: The id of the study for which workflows should be returned.
          schema:
            type: integer
            format: int32
      responses:
        '200':
          description: An Study Object
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Study"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"
    post:
      operationId: crc.api.study.update_study
      summary: Updates an existing study with the given parameters.
      tags:
        - Studies
      parameters:
        - name: study_id
          in: path
          required: true
          description: The id of the study for which workflows should be returned.
          schema:
            type: integer
            format: int32
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/Study'
      responses:
        '200':
          description: Study updated successfully.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Study"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"
  /study-update/{study_id}:
    post:
      operationId: crc.api.study.post_update_study_from_protocol_builder
      summary: If the study is up-to-date with Protocol Builder, returns a 304 Not Modified. If out of date, return a 202 Accepted and study state changes to updating.
      tags:
        - Study Status
      parameters:
        - name: study_id
          in: path
          required: true
          description: The id of the study that should be checked for updates.
          schema:
            type: integer
            format: int32
      responses:
        '304':
          description: Study is currently up to date and does not need to be reloaded from Protocol Builder
        '202':
          description: Request accepted, will preform an update. Study state set to "updating"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"

  /study/{study_id}/workflows:
    get:
      operationId: crc.api.study.get_study_workflows
      summary: Provides a list of workflows to be completed for the given study.
      tags:
        - Studies
      parameters:
        - name: study_id
          in: path
          required: true
          description: The id of the study for which workflows should be returned.
          schema:
            type: integer
            format: int32
      responses:
        '200':
          description: An array of workflows
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/Workflow"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"
    post:
      operationId: crc.api.study.add_workflow_to_study
      summary: Starts a new workflow for the given study using the provided spec.  This is atypical, and should be left to the protocol builder.
      tags:
        - Studies
      parameters:
        - name: study_id
          in: path
          required: true
          description: The id of the study for which a workflow should start
          schema:
            type: integer
            format: int32
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/WorkflowSpec'
      responses:
        '200':
          description: An array of workflows
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/Workflow"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"
  /workflow-specification:
    get:
      operationId: crc.api.workflow.all_specifications
      summary: Provides a list of workflows specifications that can be added to a study manually. Please note that Protocol Builder will handle this most of the time.
      tags:
        - Workflows and Tasks
      responses:
        '200':
          description: An array of workflow specifications
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/WorkflowSpec"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"
    post:
      operationId: crc.api.workflow.add_workflow_specification
      summary: Creates a new workflow specification with the given parameters.
      tags:
        - Workflows and Tasks
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/WorkflowSpec'
      responses:
        '200':
          description: Workflow specification created successfully.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/WorkflowSpec"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"
  /file:
    parameters:
      - name: spec_id
        in: query
        required: false
        description: The unique name of a specification
        schema:
          type: string
    get:
      operationId: crc.api.file.get_files
      summary: Provides a list of files that match the given parameters (such as a spec id) IMPORTANT, only includes metadata, not the file content.
      tags:
        - Files
      responses:
        '200':
          description: An array of file descriptions (not the file content)
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/File"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"
    post:
      operationId: crc.api.file.add_file
      summary: Add a new file
      tags:
        - Files
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                workflow_spec_id:
                  type: string
                file:
                  type: string
                  format: binary
      responses:
        '200':
          description: Metadata about the uploaded file, but not the file content.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/File"

  /file/{file_id}:
    parameters:
      - name: file_id
        in: path
        required: true
        description: The id of the File requested
        schema:
          type: integer
    get:
      operationId: crc.api.file.get_file_info
      summary: Returns metadata about a file.
      tags:
        - Files
      responses:
        '200':
          description: Returns the file information requested.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/File"
    put:
      operationId: crc.api.file.update_file
      summary: Update a file
      tags:
        - Files
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                workflow_spec_id:
                  type: string
                file:
                  type: string
                  format: binary
      responses:
        '200':
          description: Metadata about the uploaded file, but not the file content.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/File"
    delete:
      operationId: crc.api.file.delete_file
      summary: Removes an existing file
      tags:
        - Files
      responses:
        '204':
          description: The file has been removed.
  /file/{file_id}/data:
    parameters:
      - name: file_id
        in: path
        required: true
        description: The id of the File requested
        schema:
          type: integer
    get:
      operationId: crc.api.file.get_file
      summary: Returns only the file contents
      tags:
        - Files
      responses:
        '200':
          description: Returns the actual file
          content:
            application/octet-stream:
              schema:
                type: string
                format: binary
                example: '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
  # /v1.0/workflow/0
  /workflow/{workflow_id}:
    parameters:
        - name: workflow_id
          in: path
          required: true
          description: The id of the workflow
          schema:
            type: integer
            format: int32
    get:
      operationId: crc.api.workflow.get_workflow
      summary: Detailed information for a specific workflow instance
      tags:
        - Workflows and Tasks
      responses:
        '200':
          description: Returns details about the workflows state and current task
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Workflow"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"
    delete:
      operationId: crc.api.workflow.delete
      summary: Removes an existing workflow
      tags:
        - Workflows and Tasks
      responses:
        '204':
          description: The workflow was removed
  /workflow/{workflow_id}/tasks:
    get:
      operationId: crc.api.workflow.get_tasks
      summary: Return a list of all tasks for this workflow
      tags:
        - Workflows and Tasks
      parameters:
        - name: workflow_id
          in: path
          required: true
          description: The id of the workflow
          schema:
            type: integer
            format: int32
      responses:
        '200':
          description: Expected response to a valid request
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/Task"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"
  # /v1.0/workflow/0/task/0
  /workflow/{workflow_id}/task/{task_name}:
    parameters:
      - name: workflow_id
        in: path
        required: true
        description: The id of the workflow
        schema:
          type: integer
          format: int32
      - name: task_name
        in: path
        required: true
        description: The id of the task
        schema:
          type: string
    get:
      operationId: crc.api.workflow.get_task
      summary: Get details of specific task in specific workflow instance
      tags:
        - Workflows and Tasks
      responses:
        '200':
          description: Expected response to a valid request
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Task"
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"

    put:
      operationId: crc.api.workflow.update_task
      summary: Update, attempt to complete a workflow task
      tags:
        - Workflows and Tasks
      parameters:
        - in: body
          name: task
          schema:
            $ref: '#/components/schemas/Task'
      responses:
        '201':
          description: Null response
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"


components:
  schemas:
    DataModel:
      properties:
        id:
          type: string

    Study:
      properties:
        id:
          type: integer
          example: 1234
        title:
          type: string
          example: The impact of fried pickles on beer consumption in bipedal software developers.
        last_updated:
          type: string
          format: date_time
          example: "2019-12-25T09:12:33.001Z"
        protocol_builder_status:
          type: string
          enum: [out_of_date, in_process, complete, updating]
          example: done
        primary_investigator_id:
          type: string
          example: dhf8r
        sponsor:
          type: string
          example: "Sartography Pharmaceuticals"
        ind_number:
          type: string
          example: "27b-6-42"
    WorkflowSpec:
      properties:
        id:
          type: string
        display_name:
          type: string
        description:
          type: string
        bpmn_url:
          type: string
        svg_url:
          type: string
    File:
      properties:
        id:
          type: number
          readOnly: true
        name:
          type: string
          example: "random_fact.bpmn"
        version:
          type: string
          readOnly: true
        last_updated:
          type: string
          format: date_time
          example: "2019-12-25T09:12:33.001Z"
          readOnly: true
        type:
          type: enum
          enum: ['bpmn','svg', 'dmn']
          readOnly: true
        primary:
          type: boolean
          readOnly: true
        content_type:
          type: string
          example: "application/xml"
        workflow_spec_id:
          type: string
          example: "random_fact"
        file:
          type: file
          format: binary
    Workflow:
      properties:
        id:
          readOnly: true
          type: integer
          format: int64
        status:
          type: enum
          enum: ['user_input_required','waiting','complete']
        study_id:
          readOnly: true
          type: integer
        workflow_spec_id:
          readOnly: true
          type: String
        current_task_ids:
          type: array
          items:
            type: String
        messages:
          type: array
          items:
            type: String
      example:
        id: 291234
        status: 'user_input_required'
        current_task_ids: ['study_identification','Detailed Reports']
        workflow_spec:
          id: 'prot_def'
          display_name: 'Protocol Definition'
          description: 'Collect some additional information about your protocol to complete forms and processes.'
          bpmn_url: 'https://crconnect.viriginia.edu/prot_def.bpmn'
          svg_url: 'https://crconnect.viriginia.edu/prot_def.svg'
        messages: [
          "Protocol Builder reports that the protocol process is complete for this study.",
          "IDS Submission Template was generated successfully."
        ]
    Task:
      properties:
        id:
          readOnly: true
          type: string
        name:
          type: string
        title:
          type: string
        type:
          type: string
        state:
          type: string
        form:
          $ref: "#/components/schemas/Form"
        documentation:
          type: string
      example:
        id: study_identification
        name: Study Identification
        title: IRB Review
        documentation: "# Heading 1\n\nMarkdown documentation text goes here"
        type: form
        state: ready
        form:
          "key": "irb_review_form"
          "fields":
            - "id": "irb_review_type"
              "type": "enum"
              "label": "Select IRB Review Type"
              "options":
                - id: "emergency_use"
                  name: "Emergency Use"
                - id: "humanitarian_device"
                  name: "Humanitarian Device"
                - id: "non_human"
                  name: "Non-Human"
                - id: "non_uva_agent"
                  name: "Non-UVA Agent"
                - id: "exempt"
                  name: "Exempt"
                - id: "non_engaged"
                  name: "Non-Engaged"
                - id: "expedited"
                  name: "Expedited"
                - id: "full_board"
                  name: "Full Board"
              "defaultValue": "Full Board"
              "validation":
                - name: "required"
                  config: "true"
              "properties":
                - id: "description"
                  value: "Description text goes here"
                - id: "help"
                  value: "# Heading 1\n\nMarkdown help text goes here"
                - id: "required_expression"
                  value: "model.my_boolean_field_id && model.my_enum_field_value !== 'something'"
                - id: "hide_expression"
                  value: "model.my_enum_field_value === 'something'"
    Form:
      properties:
        key:
          type: string
        fields:
          type: array
          items:
            $ref: "#/components/schemas/Field"
      example:
        "key": "irb_review_form"
        "fields":
          - "id": "irb_review_type"
            "type": "enum"
            "label": "Select IRB Review Type"
            "options":
              - id: "emergency_use"
                name: "Emergency Use"
              - id: "humanitarian_device"
                name: "Humanitarian Device"
              - id: "non_human"
                name: "Non-Human"
              - id: "non_uva_agent"
                name: "Non-UVA Agent"
              - id: "exempt"
                name: "Exempt"
              - id: "non_engaged"
                name: "Non-Engaged"
              - id: "expedited"
                name: "Expedited"
              - id: "full_board"
                name: "Full Board"
            "defaultValue": "Full Board"
            "validation":
              - name: "required"
                config: "true"
            "properties":
              - id: "description"
                value: "Description text goes here"
              - id: "help"
                value: "# Heading 1\n\nMarkdown help text goes here"
              - id: "required_expression"
                value: "model.my_boolean_field_id && model.my_enum_field_value !== 'something'"
              - id: "hide_expression"
                value: "model.my_enum_field_value === 'something'"
    Field:
      properties:
        id:
          type: string
          readOnly: true
        type:
          type: enum
          enum: ['string', 'long', 'boolean', 'date', 'enum']
          readOnly: true
        label:
          type: string
          readOnly: true
        options:
          type: array
          items:
            $ref: "#/components/schemas/EnumFieldOption"
          readOnly: true
        defaultValue:
          type: string
        validation:
          type: array
          items:
            $ref: "#/components/schemas/FieldValidation"
          readOnly: true
        "properties":
          type: array
          items:
            $ref: "#/components/schemas/FieldProperty"
          readOnly: true
    EnumFieldOption:
      properties:
        id:
          type: string
        name:
          type: string
    FieldValidation:
      properties:
        name:
          type: string
        config:
          type: string
    FieldProperty:
      properties:
        id:
          type: string
        value:
          type: string
      example:
        id: "required_expression"
        value: "model.should_require"
    Error:
      required:
        - code
        - message
      properties:
        code:
          type: string
          format: string
          example: "access_denied"
        message:
          type: string
          example: "You do not have permission to view the requested study."