cr-connect-workflow/crc/api.yml

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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:
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/sso_backdoor:
get:
operationId: crc.api.user.backdoor
summary: A backdoor that allows someone to log in as a specific user, if they
are in a staging environment.
security: [] # Disable security for this endpoint only.
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parameters:
- name: uid
in: query
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required: true
schema:
type: string
- name: email_address
in: query
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required: false
schema:
type: string
- name: display_name
in: query
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required: false
schema:
type: string
- name: affiliation
in: query
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required: false
schema:
type: string
- name: eppn
in: query
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required: false
schema:
type: string
- name: first_name
in: query
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required: false
schema:
type: string
- name: last_name
in: query
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required: false
schema:
type: string
- name: title
in: query
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required: false
schema:
type: string
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- name: redirect
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in: query
required: false
schema:
type: string
tags:
- Users
responses:
'304':
description: Redirection to the hosted frontend with an auth_token header.
/user:
get:
operationId: crc.api.user.get_current_user
summary: Returns the current user.
tags:
- Users
responses:
'200':
description: The currently authenticated user.
content:
application/json:
schema:
$ref: "#/components/schemas/User"
# /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:
$ref: "#/components/schemas/Study"
post:
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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"
/study/all:
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get:
operationId: crc.api.study.all_studies
summary: Provides a list of studies
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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
get:
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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
summary: Removes the given study completely.
tags:
- Studies
responses:
'204':
description: The study has been removed.
put:
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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}/approvals:
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
get:
operationId: crc.api.approval.get_approvals_for_study
summary: Returns approvals for a single study
tags:
- Studies
- Approvals
responses:
'200':
description: An array of approvals
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/Approval"
/workflow-specification:
get:
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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
responses:
'200':
description: An array of workflow specifications
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/WorkflowSpec"
post:
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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}:
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parameters:
- name: spec_id
in: path
required: false
description: The unique id of an existing workflow specification to modify.
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"
put:
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operationId: crc.api.workflow.update_workflow_specification
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"
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delete:
operationId: crc.api.workflow.delete_workflow_specification
summary: Removes an existing workflow specification
tags:
- Workflow Specifications
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responses:
'204':
description: The workflow specification has been removed.
/workflow-specification/{spec_id}/validate:
parameters:
- name: spec_id
in: path
required: false
description: The unique id of an existing workflow specification to validate.
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
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: false
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
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
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
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- name: workflow_id
in: query
required: false
description: The unique id of a workflow instance
schema:
type: integer
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- 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.
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schema:
type: string
get:
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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:
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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:
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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:
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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/{file_id}/data:
parameters:
- name: file_id
in: path
required: true
description: The id of the File requested
schema:
type: integer
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- name: version
in: query
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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"
# /v1.0/workflow/0
/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
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>'
# /v1.0/workflow/0
/workflow/{workflow_id}:
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parameters:
- name: workflow_id
in: path
required: true
description: The id of the workflow
schema:
type: integer
format: int32
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get:
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operationId: crc.api.workflow.get_workflow
summary: Returns a workflow, can also be used to do a soft or hard reset on the workflow.
parameters:
- name: soft_reset
in: query
required: false
description: Set this to true to use the latest workflow specification to load minor modifications to the spec.
schema:
type: boolean
- name: hard_reset
in: query
required: false
description: Set this to true to reset the workflow
schema:
type: boolean
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tags:
- Workflows and Tasks
responses:
'200':
description: Returns details about the workflows state and current task
content:
application/json:
schema:
$ref: "#/components/schemas/Workflow"
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delete:
operationId: crc.api.workflow.delete_workflow
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summary: Removes an existing workflow
tags:
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- Workflows and Tasks
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responses:
'204':
description: The workflow was removed
/workflow/{workflow_id}/task/{task_id}/data:
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parameters:
- name: workflow_id
in: path
required: true
description: The id of the workflow
schema:
type: integer
format: int32
- name: task_id
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in: path
required: true
description: The id of the task
schema:
type: string
format: uuid
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/{field_id}:
parameters:
- name: workflow_id
in: path
required: true
description: The id of the workflow
schema:
type: integer
format: int32
- 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: 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
/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"
/approval:
parameters:
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- name: everything
in: query
required: false
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description: If set to true, returns all the approvals known to the system.
schema:
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type: boolean
get:
operationId: crc.api.approval.get_approvals
summary: Provides a list of workflows approvals
tags:
- Approvals
responses:
'200':
description: An array of approvals
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/Approval"
/approval/{approval_id}:
parameters:
- name: approval_id
in: path
required: true
description: The id of the approval in question.
schema:
type: integer
format: int32
put:
operationId: crc.api.approval.update_approval
summary: Updates an approval with the given parameters
tags:
- Approvals
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/Approval'
responses:
'200':
description: Study updated successfully.
content:
application/json:
schema:
$ref: "#/components/schemas/Approval"
/approval/csv:
get:
operationId: crc.api.approval.get_csv
summary: Provides a list of all users for all approved studies
tags:
- Approvals
responses:
'200':
description: An array of approvals
content:
application/json:
schema:
type: object
components:
securitySchemes:
jwt:
type: http
scheme: bearer
bearerFormat: JWT
x-bearerInfoFunc: crc.api.user.verify_token
schemas:
User:
properties:
uid:
type: string
email_address:
type: string
display_name:
type: string
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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"
primary_investigator_id:
type: string
example: dhf8r
user_uid:
type: string
example: dhf8r
protocol_builder_status:
type: string
enum: [INCOMPLETE, ACTIVE, HOLD, OPEN, ABANDONED]
example: done
sponsor:
type: string
example: "Sartography Pharmaceuticals"
ind_number:
type: string
example: "27b-6-42"
hsr_number:
type: string
x-nullable: true
example: "27b-6-1212"
categories:
type: array
items:
$ref: "#/components/schemas/WorkflowSpecCategory"
WorkflowSpec:
properties:
id:
type: string
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name:
type: string
display_name:
type: string
description:
type: string
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primary_process_id:
type: string
nullable: true
category_id:
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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
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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: file
format: binary
Workflow:
properties:
id:
readOnly: true
type: integer
format: int64
status:
type: enum
enum: ['new','user_input_required','waiting','complete']
navigation:
type: array
items:
$ref: "#/components/schemas/NavigationItem"
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next_task:
$ref: "#/components/schemas/Task"
workflow_spec_id:
type: string
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spec_version:
type: string
is_latest_spec:
type: boolean
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num_tasks_total:
type: integer
num_tasks_complete:
type: integer
num_tasks_incomplete:
type: integer
example:
id: 291234
status: 'user_input_required'
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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
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type: string
name:
type: string
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title:
type: string
type:
type: string
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state:
type: string
form:
$ref: "#/components/schemas/Form"
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documentation:
type: string
data:
type: object
multi_instance_type:
type: enum
enum: ['none', 'looping', 'parallel', 'sequential']
multi_instance_count:
type: number
multi_instance_index:
type: number
process_name:
type: string
properties:
type: object
example:
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id: study_identification
name: Study Identification
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title: IRB Review
documentation: "# Heading 1\n\nMarkdown documentation text goes here"
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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"
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"default_value": "Full Board"
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"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:
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key:
type: string
fields:
type: array
items:
$ref: "#/components/schemas/Field"
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example:
"key": "irb_review_form"
"fields":
- "id": "irb_review_type"
"type": "enum"
"label": "Select IRB Review Type"
"options":
- id: "emergency_use"
name: "Emergency Use"
- id: "humanitarian_device"
name: "Humanitarian Device"
- id: "non_human"
name: "Non-Human"
- id: "non_uva_agent"
name: "Non-UVA Agent"
- id: "exempt"
name: "Exempt"
- id: "non_engaged"
name: "Non-Engaged"
- id: "expedited"
name: "Expedited"
- id: "full_board"
name: "Full Board"
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"default_value": "Full Board"
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"validation":
- name: "required"
config: "true"
"properties":
- id: "description"
value: "Description text goes here"
- id: "help"
value: "# Heading 1\n\nMarkdown help text goes here"
- id: "required_expression"
value: "model.my_boolean_field_id && model.my_enum_field_value !== 'something'"
- id: "hide_expression"
value: "model.my_enum_field_value === 'something'"
Field:
properties:
id:
type: string
readOnly: true
type:
type: enum
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enum: ['string', 'long', 'boolean', 'date', 'enum']
readOnly: true
label:
type: string
readOnly: true
options:
type: array
items:
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$ref: "#/components/schemas/EnumFieldOption"
readOnly: true
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default_value:
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type: string
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readOnly: true
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validation:
type: array
items:
$ref: "#/components/schemas/FieldValidation"
readOnly: true
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"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
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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: any
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: enum
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