990 lines
28 KiB
YAML
990 lines
28 KiB
YAML
openapi: "3.0.2"
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info:
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version: 1.0.0
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title: Workflow Microservice
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license:
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name: MIT
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servers:
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- url: http://localhost:5000/v1.0
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paths:
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/sso_backdoor:
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get:
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operationId: crc.api.user.backdoor
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summary: A backdoor that allows someone to log in as a specific user, if they
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are in a staging environment.
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parameters:
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- name: uid
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in: query
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required: true
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schema:
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type: string
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- name: email_address
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in: query
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required: false
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schema:
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type: string
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- name: display_name
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in: query
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required: false
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schema:
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type: string
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- name: affiliation
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in: query
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required: false
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schema:
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type: string
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- name: eppn
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in: query
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required: false
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schema:
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type: string
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- name: first_name
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in: query
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required: false
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schema:
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type: string
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- name: last_name
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in: query
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required: false
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schema:
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type: string
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- name: title
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in: query
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required: false
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schema:
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type: string
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- name: redirect_url
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in: query
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required: false
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schema:
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type: string
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tags:
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- Users
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responses:
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'304':
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description: Redirection to the hosted frontend with an auth_token header.
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/user:
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get:
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operationId: crc.api.user.get_current_user
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summary: Returns the current user.
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tags:
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- Users
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responses:
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'200':
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description: The currently authenticated user.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/User"
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# /v1.0/study
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/study:
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get:
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operationId: crc.api.study.all_studies
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summary: Provides a list of studies related to the current user.
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tags:
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- Studies
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responses:
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'200':
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description: An array of studies, ordered by the last modified date.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/Study"
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post:
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operationId: crc.api.study.add_study
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summary: Creates a new study with the given parameters.
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tags:
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- Studies
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requestBody:
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content:
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application/json:
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schema:
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$ref: '#/components/schemas/Study'
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responses:
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'200':
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description: Study created successfully.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/Study"
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/study/{study_id}:
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parameters:
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- name: study_id
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in: path
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required: true
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description: The id of the study for which workflows should be returned.
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schema:
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type: integer
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format: int32
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get:
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operationId: crc.api.study.get_study
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summary: Provides a single study
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tags:
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- Studies
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responses:
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'200':
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description: An Study Object
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/Study"
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delete:
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operationId: crc.api.study.delete_study
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summary: Removes the given study completely.
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tags:
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- Studies
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responses:
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'204':
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description: The study has been removed.
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put:
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operationId: crc.api.study.update_study
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summary: Updates an existing study with the given parameters.
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tags:
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- Studies
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requestBody:
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content:
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application/json:
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schema:
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$ref: '#/components/schemas/Study'
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responses:
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'200':
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description: Study updated successfully.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/Study"
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/study-update/{study_id}:
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post:
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operationId: crc.api.study.post_update_study_from_protocol_builder
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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.
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tags:
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- Study Status
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parameters:
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- name: study_id
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in: path
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required: true
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description: The id of the study that should be checked for updates.
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schema:
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type: integer
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format: int32
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responses:
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'304':
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description: Study is currently up to date and does not need to be reloaded from Protocol Builder
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'202':
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description: Request accepted, will preform an update. Study state set to "updating"
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/study/{study_id}/workflows:
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get:
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operationId: crc.api.study.get_study_workflows
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summary: Provides a list of workflows to be completed for the given study.
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tags:
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- Studies
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parameters:
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- name: study_id
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in: path
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required: true
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description: The id of the study for which workflows should be returned.
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schema:
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type: integer
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format: int32
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responses:
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'200':
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description: An array of workflows
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content:
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application/json:
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schema:
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type: array
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items:
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$ref: "#/components/schemas/Workflow"
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post:
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operationId: crc.api.study.add_workflow_to_study
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summary: Starts a new workflow for the given study using the provided spec. This is atypical, and should be left to the protocol builder.
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tags:
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- Studies
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parameters:
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- name: study_id
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in: path
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required: true
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description: The id of the study for which a workflow should start
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schema:
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type: integer
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format: int32
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requestBody:
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content:
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application/json:
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schema:
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$ref: '#/components/schemas/WorkflowSpec'
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responses:
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'200':
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description: An array of workflows
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content:
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application/json:
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schema:
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type: array
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items:
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$ref: "#/components/schemas/Workflow"
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/workflow-specification:
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get:
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operationId: crc.api.workflow.all_specifications
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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.
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tags:
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- Workflow Specifications
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responses:
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'200':
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description: An array of workflow specifications
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content:
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application/json:
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schema:
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type: array
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items:
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$ref: "#/components/schemas/WorkflowSpec"
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post:
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operationId: crc.api.workflow.add_workflow_specification
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summary: Creates a new workflow specification with the given parameters.
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tags:
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- Workflow Specifications
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requestBody:
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content:
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application/json:
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schema:
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$ref: '#/components/schemas/WorkflowSpec'
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responses:
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'200':
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description: Workflow specification created successfully.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/WorkflowSpec"
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/workflow-specification/{spec_id}:
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parameters:
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- name: spec_id
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in: path
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required: false
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description: The unique id of an existing workflow specification to modify.
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schema:
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type: string
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get:
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operationId: crc.api.workflow.get_workflow_specification
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summary: Returns a single workflow specification
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tags:
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- Workflow Specifications
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responses:
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'200':
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description: Workflow specification.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/WorkflowSpec"
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put:
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operationId: crc.api.workflow.update_workflow_specification
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summary: Modifies an existing workflow specification with the given parameters.
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tags:
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- Workflow Specifications
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requestBody:
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content:
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application/json:
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schema:
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$ref: '#/components/schemas/WorkflowSpec'
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responses:
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'200':
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description: Workflow specification created successfully.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/WorkflowSpec"
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delete:
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operationId: crc.api.workflow.delete_workflow_specification
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summary: Removes an existing workflow specification
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tags:
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- Workflow Specifications
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responses:
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'204':
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description: The workflow specification has been removed.
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/file:
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parameters:
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- name: workflow_spec_id
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in: query
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required: false
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description: The unique id of a workflow specification
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schema:
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type: string
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- name: study_id
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in: query
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required: false
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description: The unique id of a study
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schema:
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type: integer
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- name: workflow_id
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in: query
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required: false
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description: The unique id of a workflow instance
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schema:
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type: integer
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- name: task_id
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in: query
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required: false
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description: The unique id of a workflow task
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schema:
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type: string
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- name: form_field_key
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in: query
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required: false
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description: The unique key of a workflow task form field
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schema:
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type: string
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get:
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operationId: crc.api.file.get_files
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summary: Provides a list of files that match the given parameters (such as a spec id) IMPORTANT, only includes metadata, not the file content.
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tags:
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- Files
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responses:
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'200':
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description: An array of file descriptions (not the file content)
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content:
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application/json:
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schema:
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type: array
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items:
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$ref: "#/components/schemas/File"
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post:
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operationId: crc.api.file.add_file
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summary: Add a new file
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tags:
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- Files
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requestBody:
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content:
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multipart/form-data:
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schema:
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type: object
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properties:
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file:
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type: string
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format: binary
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responses:
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'200':
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description: Metadata about the uploaded file, but not the file content.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/File"
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/file/{file_id}:
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parameters:
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- name: file_id
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in: path
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required: true
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description: The id of the File requested
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schema:
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type: integer
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get:
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operationId: crc.api.file.get_file_info
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summary: Returns metadata about a file.
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tags:
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- Files
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responses:
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'200':
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description: Returns the file information requested.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/File"
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put:
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operationId: crc.api.file.update_file_info
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summary: Updates existing file info with the given parameters.
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tags:
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- Files
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requestBody:
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content:
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application/json:
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schema:
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$ref: '#/components/schemas/File'
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responses:
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'200':
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description: File info updated successfully.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/File"
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delete:
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operationId: crc.api.file.delete_file
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summary: Removes an existing file
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tags:
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- Files
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responses:
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'204':
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description: The file has been removed.
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/file/{file_id}/data:
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parameters:
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- name: file_id
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in: path
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required: true
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description: The id of the File requested
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schema:
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type: integer
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get:
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operationId: crc.api.file.get_file_data
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summary: Returns only the file contents
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tags:
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- Files
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responses:
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'200':
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description: Returns the actual file
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content:
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application/octet-stream:
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schema:
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type: string
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format: binary
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example: '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
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put:
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operationId: crc.api.file.update_file_data
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summary: Update only the file contents for a given file
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tags:
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- Files
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requestBody:
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content:
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multipart/form-data:
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schema:
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type: object
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properties:
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file:
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type: string
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format: binary
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responses:
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'200':
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description: Returns the actual file
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content:
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application/octet-stream:
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schema:
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type: string
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format: binary
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example: '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
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# /v1.0/workflow/0
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/workflow/{workflow_id}:
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parameters:
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- name: workflow_id
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in: path
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required: true
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description: The id of the workflow
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schema:
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type: integer
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format: int32
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get:
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operationId: crc.api.workflow.get_workflow
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summary: Detailed information for a specific workflow instance
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parameters:
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- name: soft_reset
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in: query
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required: false
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description: Set this to true to use the latest workflow specification to load minor modifications to the spec.
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schema:
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type: boolean
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- name: hard_reset
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in: query
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required: false
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description: Set this to true to reset the workflow
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schema:
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type: boolean
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tags:
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- Workflows and Tasks
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responses:
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'200':
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description: Returns details about the workflows state and current task
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/Workflow"
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delete:
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operationId: crc.api.workflow.delete
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summary: Removes an existing workflow
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tags:
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- Workflows and Tasks
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responses:
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'204':
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description: The workflow was removed
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/workflow/{workflow_id}/stats:
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parameters:
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- name: workflow_id
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in: path
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required: true
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description: The id of the workflow
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schema:
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type: integer
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format: int32
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get:
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operationId: crc.api.stats.get_workflow_stats
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summary: Stats about a given workflow
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tags:
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- Workflows and Tasks
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responses:
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'200':
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description: Returns counts of complete, incomplete, and total number of tasks
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/Workflow"
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# /v1.0/workflow/0/task/0
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/workflow/{workflow_id}/task/{task_id}:
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parameters:
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- name: workflow_id
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in: path
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required: true
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description: The id of the workflow
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schema:
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type: integer
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format: int32
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- name: task_id
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in: path
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required: true
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description: The id of the task
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schema:
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type: string
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format: uuid
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get:
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operationId: crc.api.workflow.get_task
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summary: Get details of specific task in specific workflow instance
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tags:
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- Workflows and Tasks
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responses:
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'200':
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description: Expected response to a valid request
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/Task"
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/workflow/{workflow_id}/task/{task_id}/data:
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parameters:
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- name: workflow_id
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in: path
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required: true
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description: The id of the workflow
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schema:
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type: integer
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format: int32
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- name: task_id
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in: path
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required: true
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description: The id of the task
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schema:
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type: string
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format: uuid
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put:
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operationId: crc.api.workflow.update_task
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summary: Exclusively for User Tasks, submits form data as a flat set of key/values.
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tags:
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- Workflows and Tasks
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requestBody:
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description: Key / Value pairs in JSON format.
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required: true
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content:
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application/json:
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schema:
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type: object
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example:
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favorite_color: blue
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capital_assyria: Assur
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responses:
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'201':
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description: Returns the updated workflow with the task completed.
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content:
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application/json:
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schema:
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$ref: "#/components/schemas/Workflow"
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/render_markdown:
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parameters:
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- name: data
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in: query
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required: true
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description: The json data to use in populating the template
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schema:
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type: string
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- name: template
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in: query
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required: true
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description: The markdown template to process.
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schema:
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type: string
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get:
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operationId: crc.api.tools.render_markdown
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summary: Processes the markdown template using the data provided.
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tags:
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- Configurator Tools
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responses:
|
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'201':
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description: Returns the updated workflow with the task completed.
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content:
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text/plain:
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schema:
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|
type: string
|
|
/render_docx:
|
|
parameters:
|
|
- name: data
|
|
in: query
|
|
required: true
|
|
description: The json data to use in populating the template
|
|
schema:
|
|
type: string
|
|
put:
|
|
operationId: crc.api.tools.render_docx
|
|
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
|
|
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
|
|
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"
|
|
components:
|
|
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
|
|
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: [DRAFT, IN_PROCESS, IN_REVIEW, REVIEW_COMPLETE, INACTIVE]
|
|
example: done
|
|
user_uid:
|
|
type: string
|
|
example: dhf8r
|
|
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
|
|
name:
|
|
type: string
|
|
display_name:
|
|
type: string
|
|
description:
|
|
type: string
|
|
primary_process_id:
|
|
type: string
|
|
nullable: true
|
|
workflow_spec_category_id:
|
|
type: integer
|
|
nullable: true
|
|
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
|
|
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
|
|
enum: ['bpmn','svg', 'dmn']
|
|
primary:
|
|
type: boolean
|
|
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: ['new','user_input_required','waiting','complete']
|
|
user_tasks:
|
|
type: array
|
|
items:
|
|
$ref: "#/components/schemas/Task"
|
|
last_task:
|
|
$ref: "#/components/schemas/Task"
|
|
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
|
|
|
|
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
|
|
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'"
|
|
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: enum
|
|
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'"
|