openapi: "3.0.2"
info:
  version: 1.0.0
  title: Workflow Microservice
  license:
    name: MIT
servers:
  - url: http://localhost:5000/v1.0
security:
  - jwt: ['secret']
paths:
  /login:
    get:
      operationId: crc.api.user.login
      summary: In production, logs the user in via SSO. If not in production, logs in as a specific user for testing.
      security: []  # Disable security for this endpoint only.
      parameters:
        - name: uid
          in: query
          required: false
          schema:
            type: string
        - name: redirect_url
          in: query
          required: false
          schema:
            type: string
      tags:
        - Users
      responses:
        '304':
          description: Redirection to the hosted frontend with an auth_token header.
  /user:
    parameters:
      - name: admin_impersonate_uid
        in: query
        required: false
        description: For admins, the unique uid of an existing user to impersonate.
        schema:
          type: string
    get:
      operationId: crc.api.user.get_current_user
      summary: Returns the current user.
      tags:
        - Users
      responses:
        '200':
          description: The currently-authenticated user, or, if the current user is an admin and admin_impersonate_uid is provided, this will be the user with the given uid.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/User"
  /list_users:
    get:
      operationId: crc.api.user.get_all_users
      security:
        - auth_admin: ['secret']
      summary: Returns a list of all users in the database.
      tags:
        - Users
      responses:
        '200':
          description: All users in the database.
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/User"
  # /v1.0/document_directory/{study_id}
  /document_directory/{study_id}:
    parameters :
      - name : study_id
        required : true
        in : path
        description : The unique id of a study.
        schema :
          type : integer
      - name : workflow_id
        in : query
        required : false
        schema :
          type : integer
    get:
      operationId: crc.api.document.get_document_directory
      summary: Returns a directory of all files for study in a nested structure
      tags:
        - Document Categories
      responses:
        '200':
          description: All IRB Categories defined in the file document.
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/DocumentDirectory"

  # /v1.0/study
  /study:
    get:
      operationId: crc.api.study.user_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:
                type: array
                items:
                  $ref: "#/components/schemas/Study"
    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:
                type: array
                items:
                  $ref: "#/components/schemas/Study"
  /workflow_sync/pullall:
    get:
      operationId: crc.api.workflow_sync.sync_all_changed_workflows
      summary: Sync all workflows that have changed on the remote side and provide a list of the results
      security:
        - ApiKeyAuth : []
      # in the endpoint
      parameters:
        - name: remote
          in: query
          required: true
          description: The remote endpoint
          schema:
            type: string
      tags:
        - Workflow Sync API
      responses:
        '200':
          description: An array of workflow specs that were synced from remote.
          content:
            application/json:
              schema:
                type: array
                items:
                  type: string
                example : ['top_level_workflow','3b495037-f7d4-4509-bf58-cee41c0c6b0e']




  /workflow_sync/diff:
    get:
      operationId: crc.api.workflow_sync.get_changed_workflows
      summary: Provides a list of workflow that differ from remote and if it is new or not
      security :
        - ApiKeyAuth : []
      # in the endpoint
      parameters:
        - name: remote
          in: query
          required: true
          description: The remote endpoint
          schema:
            type: string
      tags:
        - Workflow Sync API
      responses:
        '200':
          description: An array of workflow specs, with last touched date and which one is most recent.
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/WorkflowSpecDiffList"

  /workflow_sync/{workflow_spec_id}/spec:
    parameters:
      - name: workflow_spec_id
        in: path
        required: true
        description: The unique id of an existing workflow specification to modify.
        schema:
          type: string
    get:
      operationId: crc.api.workflow_sync.get_sync_workflow_specification
      summary: Returns a single workflow specification
      security:
        - ApiKeyAuth: []
      tags:
        - Workflow Sync API
      responses:
        '200':
          description: Workflow specification.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/WorkflowSpec"


  /workflow_sync/{workflow_spec_id}/files:
    get:
      operationId: crc.api.workflow_sync.get_workflow_spec_files
      summary: Provides a list of files for a workflow spec on this machine.
      security :
        - ApiKeyAuth : []
      parameters:
        - name: workflow_spec_id
          in: path
          required: true
          description: The workflow_spec id
          schema:
            type: string

      tags:
        - Workflow Sync API
      responses:
        '200':
          description: An array of files for a workflow spec on the local system, with details.
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/WorkflowSpecFilesList"

  /workflow_sync/{workflow_spec_id}/files/sync:
    get:
      operationId: crc.api.workflow_sync.sync_changed_files
      summary: Syncs files from a workflow on a remote system and provides a list of files that were updated
      security :
        - ApiKeyAuth : []
      parameters:
        - name: workflow_spec_id
          in: path
          required: true
          description: The workflow_spec id
          schema:
            type: string
        - name: remote
          in: query
          required: true
          description: The remote endpoint
          schema:
            type: string

      tags:
        - Workflow Sync API
      responses:
        '200':
          description: A list of files that were synced for the workflow.
          content:
            application/json:
              schema:
                type: array
                items:
                  type : string
                example : ["data_security_plan.dmn",'some_other_file.xml']


  /workflow_sync/{workflow_spec_id}/files/diff:
    get:
      operationId: crc.api.workflow_sync.get_changed_files
      summary: Provides a list of files for a workflow specs that differ from remote and their signature.
      security :
        - ApiKeyAuth : []

      parameters:
        - name: workflow_spec_id
          in: path
          required: true
          description: The workflow_spec id
          schema:
            type: string
        - name: remote
          in: query
          required: true
          description: The remote endpoint
          schema:
            type: string

      tags:
        - Workflow Sync API
      responses:
        '200':
          description: An array of files that are different from remote, with last touched date and file signature.
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/WorkflowSpecFilesDiff"


  /workflow_sync/all:
    get:
      operationId: crc.api.workflow_sync.get_all_spec_state
      summary: Provides a list of workflow specs, last update date and thumbprint
      security:
        - ApiKeyAuth : []

      tags:
        - Workflow Sync API
      responses:
        '200':
          description: An array of workflow specs, with last touched date and file signature.
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/WorkflowSpecAll"


  /study/all:
    get:
      operationId: crc.api.study.all_studies
      summary: Provides a list of studies
      tags:
        - Studies
      responses:
        '200':
          description: An array of studies, with submitted files, ordered by the last modified date.
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/Study"
  /study/{study_id}:
    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
      - name: update_status
        in: query
        required: false
        description: If set to true, will synch the study with protocol builder and assure the status of all workflows is up to date (expensive).
        schema:
          type: boolean
    get:
      operationId: crc.api.study.get_study
      summary: Provides a single study
      tags:
        - Studies
      responses:
        '200':
          description: An Study Object
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Study"
    delete:
      operationId: crc.api.study.delete_study
      security:
        - auth_admin: ['secret']
      summary: Removes the given study completely.
      tags:
        - Studies
      responses:
        '204':
          description: The study has been removed.
    put:
      operationId: crc.api.study.update_study
      summary: Updates an existing study with the given parameters.
      tags:
        - Studies
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/Study'
      responses:
        '200':
          description: Study updated successfully.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Study"
  /study/{study_id}/associates:
    parameters:
      - name: study_id
        in: path
        required: true
        description: The id of the study for which associates should be returned.
        schema:
          type: integer
          format: int32
    get:
      operationId: crc.api.study.get_study_associates
      summary: Provides a list of associates for a particular study
      tags:
        - Studies
      responses:
        '200':
          description: list of Study Associate Objects
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/StudyAssociate"

  /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:
        - Workflow Specifications
      parameters :
        - name : libraries
          in : query
          required : false
          description : True if we should return just library schemas
          schema :
            type : boolean
        - name : standalone
          in : query
          required : false
          description : True if we should return just standalone schemas
          schema :
            type : boolean
      responses:
        '200':
          description: An array of workflow specifications
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/WorkflowSpec"
    post:
      operationId: crc.api.workflow.add_workflow_specification
      summary: Creates a new workflow specification with the given parameters.
      tags:
        - Workflow Specifications
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/WorkflowSpec'
      responses:
        '200':
          description: Workflow specification created successfully.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/WorkflowSpec"


  /workflow-specification/{spec_id}/library/{library_id}:
    parameters:
      - name: spec_id
        in: path
        required: true
        description: The unique id of an existing workflow specification.
        schema:
          type: string
      - name: library_id
        in: path
        required: true
        description: The unique id of an existing library specification.
        schema:
          type: string


    post:
      operationId: crc.api.workflow.add_workflow_spec_library
      summary: Adds a library to a workflow spec
      tags:
        - Workflow Specifications
      responses:
        '200':
          description: Workflow specification.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/WorkflowSpec"
    delete:
      operationId: crc.api.workflow.drop_workflow_spec_library
      summary: Delete a library from a workflow
      tags:
        - Workflow Specifications
      responses:
        '200':
          description: Workflow specification.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/WorkflowSpec"


  /workflow-specification/{spec_id}:
    parameters:
      - name: spec_id
        in: path
        required: true
        description: The unique id of an existing workflow specification.
        schema:
          type: string
    get:
      operationId: crc.api.workflow.get_workflow_specification
      summary: Returns a single workflow specification
      tags:
        - Workflow Specifications
      responses:
        '200':
          description: Workflow specification.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/WorkflowSpec"
    post:
      operationId: crc.api.workflow.get_workflow_from_spec
      summary: Creates a workflow from a workflow spec and returns the workflow
      tags:
        - Workflow Specifications
      responses:
        '200':
          description: Workflow generated successfully
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Workflow"
    put:
      operationId: crc.api.workflow.update_workflow_specification
      security:
        - auth_admin: ['secret']
      summary: Modifies an existing workflow specification with the given parameters.
      tags:
        - Workflow Specifications
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/WorkflowSpec'
      responses:
        '200':
          description: Workflow specification created successfully.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/WorkflowSpec"
    delete:
      operationId: crc.api.workflow.delete_workflow_specification
      security:
        - auth_admin: ['secret']
      summary: Removes an existing workflow specification
      tags:
        - Workflow Specifications
      responses:
        '204':
          description: The workflow specification has been removed.
  /workflow-specification/{spec_id}/validate:
    parameters:
      - name: spec_id
        in: path
        required: true
        description: The unique id of an existing workflow specification to validate.
        schema:
          type: string
      - name: study_id
        in: query
        required: false
        description: Optional id of study to test under different scenarios
        schema:
          type: string
      - name: test_until
        in: query
        required: false
        description: Optional name of task to stop validating at
        schema:
          type: string
    get:
      operationId: crc.api.workflow.validate_workflow_specification
      summary: Loads and attempts to execute a Workflow Specification, returning a list of errors encountered
      tags:
        - Workflow Specifications
      responses:
        '200':
          description: Workflow specification.
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/Error"
  /workflow-specification-category:
    get:
      operationId: crc.api.workflow.list_workflow_spec_categories
      summary: Provides a list of categories that can be added to a workflow spec.
      tags:
        - Workflow Specification Category
      responses:
        '200':
          description: An array of workflow specification categories
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/WorkflowSpecCategory"
    post:
      operationId: crc.api.workflow.add_workflow_spec_category
      security:
        - auth_admin: ['secret']
      summary: Creates a new workflow spec category with the given parameters.
      tags:
        - Workflow Specification Category
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/WorkflowSpecCategory'
      responses:
        '200':
          description: Workflow spec category created successfully.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/WorkflowSpecCategory"
  /workflow-specification-category/{cat_id}:
    parameters:
      - name: cat_id
        in: path
        required: true
        description: The unique id of an existing workflow spec category to modify.
        schema:
          type: string
    get:
      operationId: crc.api.workflow.get_workflow_spec_category
      summary: Returns a single workflow spec category
      tags:
        - Workflow Specification Category
      responses:
        '200':
          description: Workflow spec category.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/WorkflowSpecCategory"
    put:
      operationId: crc.api.workflow.update_workflow_spec_category
      security:
        - auth_admin: ['secret']
      summary: Modifies an existing workflow spec category with the given parameters.
      tags:
        - Workflow Specification Category
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/WorkflowSpecCategory'
      responses:
        '200':
          description: Workflow spec category created successfully.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/WorkflowSpecCategory"
    delete:
      operationId: crc.api.workflow.delete_workflow_spec_category
      security:
        - auth_admin: ['secret']
      summary: Removes an existing workflow spec category
      tags:
        - Workflow Specification Category
      responses:
        '204':
          description: The workflow spec category has been removed.
  /file:
    parameters:
      - name: workflow_spec_id
        in: query
        required: false
        description: The unique id of a workflow specification
        schema:
          type: string
      - name: workflow_id
        in: query
        required: false
        description: The unique id of a workflow instance
        schema:
          type: integer
      - name: form_field_key
        in: query
        required: false
        description: The unique key of a workflow task form field.  Make sure this matches a document in the irb_documents.xslx reference sheet.
        schema:
          type: string
      - name: study_id
        in: query
        required: false
        description: The study that the files are related to
        schema:
          type: integer
    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"

    post:
      operationId: crc.api.file.add_file
      summary: Add a new file
      tags:
        - Files
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                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_info
      summary: Updates existing file info with the given parameters.
      tags:
        - Files
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/File'
      responses:
        '200':
          description: File info updated successfully.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/File"
    delete:
      operationId: crc.api.file.delete_file
      summary: Removes an existing file.  In the event the file can not be deleted, it is marked as "archived" in the database and is no longer returned unless specifically requested by id.
      tags:
        - Files
      responses:
        '204':
          description: The file has been removed.
  /file/{md5_hash}/hash_data:
    parameters:
      - name: md5_hash
        in: path
        required: true
        description: The md5 hash of the file requested
        schema:
          type: string
    get:
      operationId: crc.api.file.get_file_data_by_hash
      summary: Returns only the file contents
      security:
        - ApiKeyAuth: []
      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>'
  /file/{file_id}/download :
    parameters :
      - name : file_id
        in : path
        required : true
        description : The id of the File requested
        schema :
          type : integer
      - name : auth_token
        in : query
        required : true
        description : User Auth Toeken
        schema :
          type : string
      - name : version
        in : query
        required : false
        description : The version of the file, or none for latest version
        schema :
          type : integer
    get :
      operationId : crc.api.file.get_file_data_link
      summary : Returns only the file contents
      security: []
      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>'
  /file/{file_id}/data:
    parameters:
      - name: file_id
        in: path
        required: true
        description: The id of the File requested
        schema:
          type: integer
      - name: version
        in: query
        required: false
        description: The version of the file, or none for latest version
        schema:
          type: integer
    get:
      operationId: crc.api.file.get_file_data
      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>'
    put:
      operationId: crc.api.file.update_file_data
      summary: Update only the file contents for a given file
      tags:
        - Files
      requestBody:
        content:
          multipart/form-data:
            schema:
              x-body-name: file
              type: object
              properties:
                file:
                  type: string
                  format: binary
              required:
                - file
      responses:
        '200':
          description: Returns the updated file model with the new version information.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/File"
  /reference_file:
    get:
      operationId: crc.api.file.get_reference_files
      summary: Provides a list of existing reference files that are available in the system.
      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"
  /reference_file/{name}:
    parameters:
      - name: name
        in: path
        required: true
        description: The special name of the reference file.
        schema:
          type: string
    get:
      operationId: crc.api.file.get_reference_file
      summary: Reference files are called by name rather than by id.
      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>'
    put:
      operationId: crc.api.file.set_reference_file
      security:
        - auth_admin: ['secret']
      summary: Update the contents of a named reference file.
      tags:
        - Files
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                file:
                  type: string
                  format: binary
      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>'
  /task_events:
    parameters:
      - name: action
        in: query
        required: false
        description: The type of action the event documents, options include "ASSIGNMENT" for tasks that are waiting on you, "COMPLETE" for things have completed.
        schema:
          type: string
      - name: workflow
        in: query
        required: false
        description: Restrict results to the given workflow.
        schema:
          type: number
      - name: study
        in: query
        required: false
        description: Restrict results to the given study.
        schema:
          type: number
    get:
      operationId: crc.api.workflow.get_task_events
      summary: Returns a list of task events related to the current user.  Can be filtered by type.
      tags:
        - Workflows and Tasks
      responses:
        '200':
          description: Returns details about tasks that are waiting on the current user.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/TaskEvent"
  # /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: Returns a workflow.
      parameters:
        - name: do_engine_steps
          in: query
          required: false
          description: Defaults to true, can be set to false if you are just looking at the workflow not completeing it.
          schema:
            type: boolean
      tags:
        - Workflows and Tasks
      responses:
        '200':
          description: Returns details about the workflows state and current task
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Workflow"
    delete:
      operationId: crc.api.workflow.delete_workflow
      security:
        - auth_admin: ['secret']
      summary: Removes an existing workflow
      tags:
        - Workflows and Tasks
      responses:
        '204':
          description: The workflow was removed
  /workflow/{workflow_id}/restart:
    parameters:
      - name: workflow_id
        in: path
        required: true
        description: The id of the workflow
        schema:
          type: integer
          format: int32
    get:
      operationId: crc.api.workflow.restart_workflow
      summary: Restarts a workflow with the latest spec. Can also clear data.
      parameters:
        - name: clear_data
          in: query
          required: false
          description: Set this to true to clear data when starting workflow.
          schema:
            type: boolean
        - name: delete_files
          in: query
          required: false
          description: Set this to true to delete associated files when starting workflow.
          schema:
            type: boolean
      tags:
        - Workflows and Tasks
      responses:
        '200':
          description: Returns updated workflow, possibly without data.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Workflow"

  /workflow/{workflow_id}/task/{task_id}/data:
    parameters:
      - name: workflow_id
        in: path
        required: true
        description: The id of the workflow
        schema:
          type: integer
          format: int32
      - name: task_id
        in: path
        required: true
        description: The id of the task
        schema:
          type: string
          format: uuid
      - name: terminate_loop
        in: query
        required: false
        description: Terminate the loop on a looping task
        schema:
          type: boolean
      - name: update_all
        in: query
        required: false
        description: In the case of a multi-instance user task, update all tasks with the submitted values.
        schema:
          type: boolean
    put:
      operationId: crc.api.workflow.update_task
      summary: Exclusively for User Tasks, submits form data as a flat set of key/values.
      tags:
        - Workflows and Tasks
      requestBody:
        description: Key / Value pairs in JSON format.
        required: true
        content:
          application/json:
            schema:
              type: object
              example:
                favorite_color: blue
                capital_assyria: Assur
      responses:
        '201':
          description: Returns the updated workflow with this task as the current task.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Workflow"
  /workflow/{workflow_id}/task/{task_id}/set_token:
    parameters:
      - name: workflow_id
        in: path
        required: true
        description: The id of the workflow
        schema:
          type: integer
          format: int32
      - name: task_id
        in: path
        required: true
        description: The id of the task
        schema:
          type: string
          format: uuid
    put:
      operationId: crc.api.workflow.set_current_task
      summary: Attempts to make the given task the Current Active Task
      tags:
        - Workflows and Tasks
      responses:
        '201':
          description: Returns the updated workflow with this task as the current task.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Workflow"
  /workflow/{workflow_id}/lookup/{task_spec_name}/{field_id}:
    parameters:
      - name: workflow_id
        in: path
        required: true
        description: The id of the workflow
        schema:
          type: integer
          format: int32
      - name: task_spec_name
        in: path
        required: true
        description: The name of the current task
        schema:
          type: string
      - name: field_id
        in: path
        required: true
        description: The id of the field (as set in the bpmn editor) on which to do a lookup.
        schema:
          type: string
      - name: query
        in: query
        required: false
        description: The string to search for in the Value column of the lookup table.
        schema:
          type: string
      - name: value
        in: query
        required: false
        description: An alternative to query, this accepts the specific value or id selected in a dropdown list or auto-complete, and will return the one matching record. Useful for getting additional details about an item selected in a dropdown.
        schema:
          type: string
      - name: limit
        in: query
        required: false
        description: The total number of records to return, defaults to 10.
        schema:
          type: integer

    get:
      operationId: crc.api.workflow.lookup
      summary: Provides type-ahead search against a lookup table associted with a form field.
      tags:
        - Workflows and Tasks
      responses:
        '201':
          description: Returns the a list of values and labels for a lookup form.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/LookupItem"
  /render_markdown:
    parameters:
      - name: data
        in: query
        required: true
        description: The json data to use in populating the template
        schema:
          type: string
      - name: template
        in: query
        required: true
        description: The markdown template to process.
        schema:
          type: string
    get:
      operationId: crc.api.tools.render_markdown
      security: []  # Disable security for this endpoint only.
      summary: Processes the markdown template using the data provided.
      tags:
        - Configurator Tools
      responses:
        '201':
          description: Returns the updated workflow with the task completed.
          content:
            text/plain:
              schema:
                type: string
  /send_email:
    parameters:
      - in: query
        name: subject
        required: true
        description: The subject of the email.
        schema:
          type: string
      - in: query
        name: address
        required: true
        description: The address to send a test email to.
        schema:
          type: string
      - in: query
        name: data
        required: false
        description:
          The data to use in populating the message.
        schema:
          type: string
        example: {"id_1": "value_1", "id_2": "value_2"}
    put:
      operationId: crc.api.tools.send_email
      summary: Sends an email so we can see what the message will look like.
      tags:
        - Configurator Tools
      requestBody:
        required: true
        content:
          text/plain:
            schema:
              type: string
      responses:
        '201':
          description: Returns any error messages that might come back from sending the email.
          content:
            text/plain:
              schema:
                type: string
  /render_docx:
    put:
      operationId: crc.api.tools.render_docx
      security: []  # Disable security for this endpoint only.
      summary: Renders a docx template with embedded jinja2 markup.
      tags:
        - Configurator Tools
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                file:
                  type: string
                  format: binary
                data:
                  type: string
                  format: json
      responses:
        '200':
          description: Returns the generated document.
          content:
            application/octet-stream:
              schema:
                type: string
                format: binary
                example: '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
  /list_scripts:
    get:
      operationId: crc.api.tools.list_scripts
      security: []  # Disable security for this endpoint only.
      summary: Returns an list of scripts, along with their descriptions
      tags:
        - Configurator Tools
      responses:
        '201':
          description: The list of scripts
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: "#/components/schemas/Script"
  /eval:
    put:
      operationId: crc.api.tools.evaluate_python_expression
      summary: Execute the given python expression, with the given json data structure used as local variables, returns the result of the evaluation.
      tags:
        - Configurator Tools
      requestBody:
        description: The expression and the json data to use as local variables when evaluating the expresson.
        required: true
        content:
          application/json:
            schema:
              type: object
      responses:
        '200':
          description: Returns the result of executing the given python script.
          content:
            text/plain:
              schema:
                type: string
  /datastore:
    post:
      operationId: crc.api.data_store.add_datastore
      summary: Add datastore item with the given parameters.
      tags:
        - DataStore
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DataStore'
      responses:
        '200':
          description: Datastore updated successfully.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/DataStore"

  /datastore/{id}:
    parameters:
      - name: id
        in: path
        required: true
        description: The key to lookup.
        schema:
          type: string
          format: string

    get:
      operationId: crc.api.data_store.datastore_get
      summary: Get a datastore item by id
      tags:
        - DataStore
      responses:
        '200':
          description: A value from the data store, or a default if provided, or None if not found.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/DataStore"
    put:
      operationId: crc.api.data_store.update_datastore
      summary: Updates an existing datastore item with the given parameters.
      tags:
        - DataStore
      requestBody:
        content:
          application/json:
            schema:
              $ref: '#/components/schemas/DataStore'
      responses:
        '200':
          description: Datastore updated successfully.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/DataStore"


    delete:
      operationId: crc.api.data_store.datastore_del
      summary: Deletes a value from the data store by id
      tags:
        - DataStore
      responses:
        '200':
          description: Deletes a value from a data store.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/DataStore"


  /datastore/study/{study_id}:
    parameters:
      - name: study_id
        in: path
        required: true
        description: The study id we are concerned with .
        schema:
          type: integer
          format: int32
    get:
      operationId: crc.api.data_store.study_multi_get
      summary: Gets all datastore items for a study_id
      tags:
        - DataStore
      responses:
        '200':
          description: Get all values from the data store for a study_id
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/DataStore"
  /datastore/user/{user_id}:
    parameters:
      - name: user_id
        in: path
        required: true
        description: The user id we are concerned with .
        schema:
          type: string
          format: string
    get:
      operationId: crc.api.data_store.user_multi_get
      summary: Gets all datastore items by user_id
      tags:
        - DataStore
      responses:
        '200':
          description: Get all values from the data store for a user_id.
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/DataStore"
  /datastore/file/{file_id}:
    parameters:
      - name: file_id
        in: path
        required: true
        description: The file id we are concerned with
        schema:
          type: string
          format: string
    get:
      operationId: crc.api.data_store.file_multi_get
      summary: Gets all datastore items by file_id
      tags:
        - DataStore
      responses:
        '200':
          description: Get all values from the data store for a file_id
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/DataStore"
components:
  securitySchemes:
    jwt:
      type: http
      scheme: bearer
      bearerFormat: JWT
      x-bearerInfoFunc: crc.api.user.verify_token
    auth_admin:
      type: http
      scheme: bearer
      bearerFormat: JWT
      x-bearerInfoFunc: crc.api.user.verify_token_admin
    ApiKeyAuth :
        type : apiKey
        in : header
        name : X-CR-API-KEY
        x-apikeyInfoFunc: crc.api.workflow_sync.verify_token

  schemas:
    User:
      properties:
        uid:
          type: string
        email_address:
          type: string
        display_name:
          type: string
        affiliation:
          type: string
        eppn:
          type: string
        first_name:
          type: string
        last_name:
          type: string
        title:
          type: string
    DataModel:
      properties:
        id:
          type: string
    WorkflowSpecDiffList:
      properties:
        workflow_spec_id:
          type: string
          example : top_level_workflow
        date_created :
          type: string
          example : 2020-12-09 16:55:12.951500+00:00
        location :
          type : string
          example : remote
        new :
          type : boolean
          example : false
    WorkflowSpecFilesList:
      properties:
        file_model_id:
          type : integer
          example : 171
        workflow_spec_id :
          type: string
          example : top_level_workflow
        filename :
          type: string
          example : data_security_plan.dmn
        date_created :
          type: string
          example : 2020-12-01 13:58:12.420333+00:00
        type:
          type : string
          example : dmn
        primary :
          type : boolean
          example : false
        content_type:
          type: string
          example : text/xml
        primary_process_id:
          type : string
          example : null
        md5_hash:
          type: string
          example: f12e2bbd-a20c-673b-ccb8-a8a1ea9c5b7b


    WorkflowSpecFilesDiff:
      properties:
        filename :
          type: string
          example : data_security_plan.dmn
        date_created :
          type: string
          example : 2020-12-01 13:58:12.420333+00:00
        type:
          type : string
          example : dmn
        primary :
          type : boolean
          example : false
        content_type:
          type: string
          example : text/xml
        primary_process_id:
          type : string
          example : null
        md5_hash:
          type: string
          example: f12e2bbd-a20c-673b-ccb8-a8a1ea9c5b7b
        location:
          type : string
          example : remote
        new:
          type: boolean
          example : false

    WorkflowSpecAll:
      properties:
        workflow_spec_id :
          type: string
          example : acaf1258-43b4-437e-8846-f612afa66811
        date_created :
          type: string
          example : 2020-12-01 13:58:12.420333+00:00
        md5_hash:
          type: string
          example: c30fd597f21715018eab12f97f9d4956
    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"
        primary_investigator_id:
          type: string
          x-nullable: true
          example: dhf8r
        user_uid:
          type: string
          example: dhf8r
        status:
          type: string
          enum: ['in_progress', 'hold', 'open_for_enrollment', 'abandoned']
          example: done
        sponsor:
          type: string
          x-nullable: true
          example: "Sartography Pharmaceuticals"
        ind_number:
          type: string
          x-nullable: true
          example: "27b-6-42"
        hsr_number:
          type: string
          x-nullable: true
          example: "27b-6-1212"
    StudyAssociate:
      properties:
        uid:
          type: string
          example: "dhf8r"
        access:
          type: boolean
          example: False
        role:
          type: string
          example: "TODO"
    DocumentDirectory:
      properties:
        level:
          type: string
          x-nullable: true
          example: "Ancillary Document"
        description:
          type: string
          x-nullable: true
          example: "Documents that are ancillary to the study"
        file:
          $ref: "#/components/schemas/File"
          x-nullable: true
        expanded:
          type: boolean
          example: False
        filecount:
          type: integer
          example: 1
        children:
          type: array
          items:
            $ref: "#/components/schemas/File"
    DataStore:
      properties:
        id:
          type: integer
          example: 1234
        key:
          type: string
          example: MyKey
        workflow_id:
          type: integer
          x-nullable: true
          example: 12
        study_id:
          type: integer
          x-nullable: true
          example: 42
        user_id:
          type: string
          x-nullable: true
          example: dhf8r
        task_id:
          type: string
          x-nullable: true
          example: MyTask
        spec_id:
          type: string
          x-nullable: true
          example: My Spec Name
        value:
          type: string
          x-nullable: true
          example: Some Value

    WorkflowSpec:
      properties:
        id:
          type: string
        name:
          type: string
        display_name:
          type: string
        description:
          type: string
        primary_process_id:
          type: string
          nullable: true
        category_id:
          type: integer
          nullable: true
        standalone:
          type: boolean
          example: false
          default: false
        workflow_spec_category:
          $ref: "#/components/schemas/WorkflowSpecCategory"
        is_status:
          type: boolean
          nullable: true
    WorkflowSpecCategory:
      properties:
        id:
          type: integer
        name:
          type: string
        display_name:
          type: string
        display_order:
          type: integer
        workflows:
          type: array
          items:
            $ref: "#/components/schemas/Workflow"
    File:
      properties:
        id:
          type: number
        name:
          type: string
          example: "random_fact.bpmn"
        version:
          type: integer
        last_updated:
          type: string
          format: date_time
          example: "2019-12-25T09:12:33.001Z"
        type:
          type: string
        primary:
          type: boolean
        content_type:
          type: string
          example: "application/xml"
        workflow_spec_id:
          type: string
          example: "random_fact"
          x-nullable: true
        file:
          type: string
    Workflow:
      properties:
        id:
          readOnly: true
          type: integer
          format: int64
        status:
          type: string
          enum: ['new','user_input_required','waiting','complete']
        navigation:
          type: array
          items:
            $ref: "#/components/schemas/NavigationItem"
        next_task:
          $ref: "#/components/schemas/Task"
        workflow_spec_id:
          type: string
        spec_version:
          type: string
        is_latest_spec:
          type: boolean
        num_tasks_total:
          type: integer
        num_tasks_complete:
          type: integer
        num_tasks_incomplete:
          type: integer
        study_id:
          type: integer

      example:
        id: 291234
        status: 'user_input_required'
        workflow_spec_id: 'random_fact'
        spec_version: 'v1.1 [22,23]'
        is_latest_spec: True
        next_task:
          id: study_identification
          name: Study Identification
          title: IRB Review
          documentation: "# Heading 1\n\nMarkdown documentation text goes here"
          type: form
          state: ready
    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
        data:
          type: object
        multi_instance_type:
          type: string
          enum: ['none', 'looping', 'parallel', 'sequential']
        multi_instance_count:
          type: number
        multi_instance_index:
          type: number
        process_name:
          type: string
        properties:
          type: object
      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"
              "default_value": "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'"
    TaskEvent:
      properties:
          workflow:
            $ref: "#/components/schemas/Workflow"
          study:
            $ref: "#/components/schemas/Study"
          workflow_sec:
            $ref: "#/components/schemas/WorkflowSpec"
          spec_version:
            type: string
          action:
            type: string
          task_id:
            type: string
          task_type:
            type: string
          task_lane:
            type: string
          form_data:
            type: object
          mi_type:
            type: string
          mi_count:
            type: integer
          mi_index:
            type: integer
          process_name:
            type: string
          date:
            type: string
    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"
            "default_value": "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: string
          enum: ['string', 'long', 'boolean', 'date', 'enum']
          readOnly: true
        label:
          type: string
          readOnly: true
        options:
          type: array
          items:
            $ref: "#/components/schemas/EnumFieldOption"
          readOnly: true
        default_value:
          type: string
          readOnly: true
        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."
    Script:
      properties:
        name:
          type: string
          format: string
          example: "random_fact"
        description:
          type: string
          example: "Returns a random fact about a topic.  Provide an argument of either 'cat', 'norris', or 'buzzword'"
    LookupItem:
      properties:
        value:
          type: string
          format: string
          example: "1000"
        label:
          type: string
          example: "Chuck Norris"
        data:
          type: string
    NavigationItem:
      properties:
        id:
          type: number
          format: integer
          example: 5
        task_id:
          type: string
          format: uuid
          example: "1234123uuid1234"
        name:
          type: string
          example: "Task_Has_bananas"
        description:
          type: string
          example: "Has Bananas?"
        backtracks:
          type: boolean
          example: false
        level:
          type: integer
          example: 1
        indent:
          type: integer
          example: 2
        child_count:
          type: integer
          example: 4
        state:
          type: string
          enum: ['FUTURE', 'WAITING', 'READY', 'CANCELLED', 'COMPLETED','LIKELY','MAYBE']
          readOnly: true
        is_decision:
          type: boolean
          example: False
          readOnly: true
        task:
          $ref: "#/components/schemas/Task"
    Approval:
      properties:
        id:
          type: number
          format: integer
          example: 5
    ApprovalCounts:
      properties:
        PENDING:
          type: number
          format: integer
          example: 5
        APPROVED:
          type: number
          format: integer
          example: 5
        DECLINED:
          type: number
          format: integer
          example: 5
        CANCELED:
          type: number
          format: integer
          example: 5
        AWAITING:
          type: number
          format: integer
          example: 5