cr-connect-workflow/crc/api.yml

1256 lines
36 KiB
YAML

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:
/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.
parameters:
- name: uid
in: query
required: true
schema:
type: string
- name: email_address
in: query
required: false
schema:
type: string
- name: display_name
in: query
required: false
schema:
type: string
- name: affiliation
in: query
required: false
schema:
type: string
- name: eppn
in: query
required: false
schema:
type: string
- name: first_name
in: query
required: false
schema:
type: string
- name: last_name
in: query
required: false
schema:
type: string
- name: title
in: query
required: false
schema:
type: string
- name: redirect_url
in: query
required: false
schema:
type: string
tags:
- Users
responses:
'304':
description: Redirection to the hosted frontend with an auth_token header.
/user:
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.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"
post:
operationId: crc.api.study.add_study
summary: Creates a new study with the given parameters.
tags:
- Studies
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/Study'
responses:
'200':
description: Study created successfully.
content:
application/json:
schema:
$ref: "#/components/schemas/Study"
/study-files:
get:
operationId: crc.api.study.all_studies_and_files
summary: Provides a list of studies with submitted files
tags:
- Studies
responses:
'200':
description: An array of studies, with submitted files, ordered by the last modified date.
content:
application/json:
schema:
$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:
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:
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"
/workflow-specification:
get:
operationId: crc.api.workflow.all_specifications
summary: Provides a list of workflows specifications that can be added to a study manually. Please note that Protocol Builder will handle this most of the time.
tags:
- Workflow Specifications
responses:
'200':
description: An array of workflow specifications
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/WorkflowSpec"
post:
operationId: crc.api.workflow.add_workflow_specification
summary: Creates a new workflow specification with the given parameters.
tags:
- Workflow Specifications
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/WorkflowSpec'
responses:
'200':
description: Workflow specification created successfully.
content:
application/json:
schema:
$ref: "#/components/schemas/WorkflowSpec"
/workflow-specification/{spec_id}:
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:
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"
delete:
operationId: crc.api.workflow.delete_workflow_specification
summary: Removes an existing workflow specification
tags:
- Workflow Specifications
responses:
'204':
description: The workflow specification has been removed.
/workflow-specification/{spec_id}/validate:
parameters:
- name: spec_id
in: path
required: 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
- name: study_id
in: query
required: false
description: The unique id of a study
schema:
type: integer
- name: workflow_id
in: query
required: false
description: The unique id of a workflow instance
schema:
type: integer
- name: task_id
in: query
required: false
description: The unique id of a workflow task
schema:
type: string
- name: form_field_key
in: query
required: false
description: The unique key of a workflow task form field. Make sure this matches a document in the irb_documents.xslx reference sheet.
schema:
type: string
get:
operationId: crc.api.file.get_files
summary: Provides a list of files that match the given parameters (such as a spec id) IMPORTANT, only includes metadata, not the file content.
tags:
- Files
responses:
'200':
description: An array of file descriptions (not the file content)
content:
application/json:
schema:
type: array
items:
$ref: "#/components/schemas/File"
post:
operationId: crc.api.file.add_file
summary: Add a new file
tags:
- Files
requestBody:
content:
multipart/form-data:
schema:
type: object
properties:
file:
type: string
format: binary
responses:
'200':
description: Metadata about the uploaded file, but not the file content.
content:
application/json:
schema:
$ref: "#/components/schemas/File"
/file/{file_id}:
parameters:
- name: file_id
in: path
required: true
description: The id of the File requested
schema:
type: integer
get:
operationId: crc.api.file.get_file_info
summary: Returns metadata about a file.
tags:
- Files
responses:
'200':
description: Returns the file information requested.
content:
application/json:
schema:
$ref: "#/components/schemas/File"
put:
operationId: crc.api.file.update_file_info
summary: Updates existing file info with the given parameters.
tags:
- Files
requestBody:
content:
application/json:
schema:
$ref: '#/components/schemas/File'
responses:
'200':
description: File info updated successfully.
content:
application/json:
schema:
$ref: "#/components/schemas/File"
delete:
operationId: crc.api.file.delete_file
summary: Removes an existing file
tags:
- Files
responses:
'204':
description: The file has been removed.
/file/{file_id}/data:
parameters:
- name: file_id
in: path
required: true
description: The id of the File requested
schema:
type: integer
get:
operationId: crc.api.file.get_file_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}:
parameters:
- name: workflow_id
in: path
required: true
description: The id of the workflow
schema:
type: integer
format: int32
get:
operationId: crc.api.workflow.get_workflow
summary: Returns a workflow, 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
tags:
- Workflows and Tasks
responses:
'200':
description: Returns details about the workflows state and current task
content:
application/json:
schema:
$ref: "#/components/schemas/Workflow"
delete:
operationId: crc.api.workflow.delete_workflow
summary: Removes an existing workflow
tags:
- Workflows and Tasks
responses:
'204':
description: The workflow was removed
/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:
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}/task/{task_id}/lookup/{field_id}:
parameters:
- name: workflow_id
in: path
required: true
description: The id of the workflow
schema:
type: integer
format: int32
- name: task_id
in: path
required: true
description: The id of the task
schema:
type: string
format: uuid
- name: 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:
- name: approver_uid
in: query
required: false
description: Restrict results to a given approver uid, maybe we restrict the use of this at somepoint.
schema:
type: string
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"
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
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
name:
type: string
display_name:
type: string
description:
type: string
primary_process_id:
type: string
nullable: true
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
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"
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
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:
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'"
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