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
paths:
# /v1.0/study
/study:
get:
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operationId: crc.api.study.all_studies
summary: Provides a list of studies related to the current user.
tags:
- Studies
responses:
'200':
description: An array of studies, ordered by the last modified date.
content:
application/json:
schema:
$ref: "#/components/schemas/Study"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
post:
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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:
$ref: "#/components/schemas/Study"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
/study/{study_id}:
get:
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operationId: crc.api.study.get_study
summary: Provides a single study
tags:
- Studies
parameters:
- name: study_id
in: path
required: true
description: The id of the study for which workflows should be returned.
schema:
type: integer
format: int32
responses:
'200':
description: An Study Object
content:
application/json:
schema:
$ref: "#/components/schemas/Study"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
post:
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operationId: crc.api.study.update_study
summary: Updates an existing study with the given parameters.
tags:
- Studies
parameters:
- name: study_id
in: path
required: true
description: The id of the study for which workflows should be returned.
schema:
type: integer
format: int32
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/Study'
responses:
'200':
description: Study updated successfully.
content:
application/json:
schema:
$ref: "#/components/schemas/Study"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
/study-update/{study_id}:
post:
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operationId: crc.api.study.post_update_study_from_protocol_builder
summary: If the study is up-to-date with Protocol Builder, returns a 304 Not Modified. If out of date, return a 202 Accepted and study state changes to updating.
tags:
- Study Status
parameters:
- name: study_id
in: path
required: true
description: The id of the study that should be checked for updates.
schema:
type: integer
format: int32
responses:
'304':
description: Study is currently up to date and does not need to be reloaded from Protocol Builder
'202':
description: Request accepted, will preform an update. Study state set to "updating"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
/study/{study_id}/workflows:
get:
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operationId: crc.api.study.get_study_workflows
summary: Provides a list of workflows to be completed for the given study.
tags:
- Studies
parameters:
- name: study_id
in: path
required: true
description: The id of the study for which workflows should be returned.
schema:
type: integer
format: int32
responses:
'200':
description: An array of workflows
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/Workflow"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
post:
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operationId: crc.api.study.add_workflow_to_study
summary: Starts a new workflow for the given study using the provided spec. This is atypical, and should be left to the protocol builder.
tags:
- Studies
parameters:
- name: study_id
in: path
required: true
description: The id of the study for which a workflow should start
schema:
type: integer
format: int32
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requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/WorkflowSpec'
responses:
'200':
description: An array of workflows
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/Workflow"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
/workflow-specification:
get:
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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:
- Workflows and Tasks
responses:
'200':
description: An array of workflow specifications
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/WorkflowSpec"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
post:
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operationId: crc.api.workflow.add_workflow_specification
summary: Creates a new workflow specification with the given parameters.
tags:
- Workflows and Tasks
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/WorkflowSpec'
responses:
'200':
description: Workflow specification created successfully.
content:
application/json:
schema:
$ref: "#/components/schemas/WorkflowSpec"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
/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
put:
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operationId: crc.api.workflow.update_workflow_specification
summary: Modifies an existing workflow specification with the given parameters.
tags:
- Workflows and Tasks
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/WorkflowSpec'
responses:
'200':
description: Workflow specification created successfully.
content:
application/json:
schema:
$ref: "#/components/schemas/WorkflowSpec"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
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delete:
operationId: crc.api.workflow.delete_workflow_specification
summary: Removes an existing workflow specification
tags:
- Workflows and Tasks
responses:
'204':
description: The workflow specification has been removed.
/file:
parameters:
- name: spec_id
in: query
required: false
description: The unique name of a specification
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"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
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:
workflow_spec_id:
type: string
file:
type: string
format: binary
responses:
'200':
description: Metadata about the uploaded file, but not the file content.
content:
application/json:
schema:
$ref: "#/components/schemas/File"
/file/{file_id}:
parameters:
- name: file_id
in: path
required: true
description: The id of the File requested
schema:
type: integer
get:
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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:
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operationId: crc.api.file.update_file
summary: Update a file
tags:
- Files
requestBody:
content:
multipart/form-data:
schema:
type: object
properties:
workflow_spec_id:
type: string
file:
type: string
format: binary
responses:
'200':
description: Metadata about the uploaded file, but not the file content.
content:
application/json:
schema:
$ref: "#/components/schemas/File"
delete:
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operationId: crc.api.file.delete_file
summary: Removes an existing file
tags:
- Files
responses:
'204':
description: The file has been removed.
/file/{file_id}/data:
parameters:
- name: file_id
in: path
required: true
description: The id of the File requested
schema:
type: integer
get:
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operationId: crc.api.file.get_file
summary: Returns only the file contents
tags:
- Files
responses:
'200':
description: Returns the actual file
content:
application/octet-stream:
schema:
type: string
format: binary
example: '<?xml version="1.0" encoding="UTF-8"?><bpmn:definitions></bpmn:definitions>'
# /v1.0/workflow/0
/workflow/{workflow_id}:
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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
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summary: Detailed information for a specific workflow instance
tags:
- Workflows and Tasks
responses:
'200':
description: Returns details about the workflows state and current task
content:
application/json:
schema:
$ref: "#/components/schemas/Workflow"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
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delete:
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operationId: crc.api.workflow.delete
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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}/tasks:
get:
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operationId: crc.api.workflow.get_tasks
summary: Return a list of all tasks for this workflow
tags:
- Workflows and Tasks
parameters:
- name: workflow_id
in: path
required: true
description: The id of the workflow
schema:
type: integer
format: int32
responses:
'200':
description: Expected response to a valid request
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/Task"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
# /v1.0/workflow/0/task/0
/workflow/{workflow_id}/task/{task_id}:
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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
get:
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operationId: crc.api.workflow.get_task
summary: Get details of specific task in specific workflow instance
tags:
- Workflows and Tasks
responses:
'200':
description: Expected response to a valid request
content:
application/json:
schema:
$ref: "#/components/schemas/Task"
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
/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
put:
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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: Null response
default:
description: unexpected error
content:
application/json:
schema:
$ref: "#/components/schemas/Error"
components:
schemas:
DataModel:
properties:
id:
type: string
Study:
properties:
id:
type: integer
example: 1234
title:
type: string
example: The impact of fried pickles on beer consumption in bipedal software developers.
last_updated:
type: string
format: date_time
example: "2019-12-25T09:12:33.001Z"
protocol_builder_status:
type: string
enum: [out_of_date, in_process, complete, updating]
example: done
primary_investigator_id:
type: string
example: dhf8r
sponsor:
type: string
example: "Sartography Pharmaceuticals"
ind_number:
type: string
example: "27b-6-42"
WorkflowSpec:
properties:
id:
type: string
display_name:
type: string
description:
type: string
File:
properties:
id:
type: number
readOnly: true
name:
type: string
example: "random_fact.bpmn"
version:
type: string
readOnly: true
last_updated:
type: string
format: date_time
example: "2019-12-25T09:12:33.001Z"
readOnly: true
type:
type: enum
enum: ['bpmn','svg', 'dmn']
readOnly: true
primary:
type: boolean
readOnly: true
content_type:
type: string
example: "application/xml"
workflow_spec_id:
type: string
example: "random_fact"
file:
type: file
format: binary
Workflow:
properties:
id:
readOnly: true
type: integer
format: int64
status:
type: enum
enum: ['user_input_required','waiting','complete']
study_id:
readOnly: true
type: integer
workflow_spec_id:
readOnly: true
type: String
current_task_ids:
type: array
items:
type: String
messages:
type: array
items:
type: String
example:
id: 291234
status: 'user_input_required'
current_task_ids: ['study_identification','Detailed Reports']
workflow_spec:
id: 'prot_def'
display_name: 'Protocol Definition'
description: 'Collect some additional information about your protocol to complete forms and processes.'
bpmn_url: 'https://crconnect.viriginia.edu/prot_def.bpmn'
svg_url: 'https://crconnect.viriginia.edu/prot_def.svg'
messages: [
"Protocol Builder reports that the protocol process is complete for this study.",
"IDS Submission Template was generated successfully."
]
Task:
properties:
id:
readOnly: true
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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
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"
"defaultValue": "Full Board"
"validation":
- name: "required"
config: "true"
"properties":
- id: "description"
value: "Description text goes here"
- id: "help"
value: "# Heading 1\n\nMarkdown help text goes here"
- id: "required_expression"
value: "model.my_boolean_field_id && model.my_enum_field_value !== 'something'"
- id: "hide_expression"
value: "model.my_enum_field_value === 'something'"
Form:
properties:
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key:
type: string
fields:
type: array
items:
$ref: "#/components/schemas/Field"
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example:
"key": "irb_review_form"
"fields":
- "id": "irb_review_type"
"type": "enum"
"label": "Select IRB Review Type"
"options":
- id: "emergency_use"
name: "Emergency Use"
- id: "humanitarian_device"
name: "Humanitarian Device"
- id: "non_human"
name: "Non-Human"
- id: "non_uva_agent"
name: "Non-UVA Agent"
- id: "exempt"
name: "Exempt"
- id: "non_engaged"
name: "Non-Engaged"
- id: "expedited"
name: "Expedited"
- id: "full_board"
name: "Full Board"
"defaultValue": "Full Board"
"validation":
- name: "required"
config: "true"
"properties":
- id: "description"
value: "Description text goes here"
- id: "help"
value: "# Heading 1\n\nMarkdown help text goes here"
- id: "required_expression"
value: "model.my_boolean_field_id && model.my_enum_field_value !== 'something'"
- id: "hide_expression"
value: "model.my_enum_field_value === 'something'"
Field:
properties:
id:
type: string
readOnly: true
type:
type: enum
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enum: ['string', 'long', 'boolean', 'date', 'enum']
readOnly: true
label:
type: string
readOnly: true
options:
type: array
items:
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$ref: "#/components/schemas/EnumFieldOption"
readOnly: true
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defaultValue:
type: string
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."