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 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: 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: get: operationId: crc.api.study.all_studies summary: Provides a list of studies tags: - Studies responses: '200': description: An array of studies, with submitted files, ordered by the last modified date. content: application/json: schema: type: array items: $ref: "#/components/schemas/Study" /study/{study_id}: parameters: - name: study_id in: path required: true description: The id of the study for which workflows should be returned. schema: type: integer format: int32 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" /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: 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: workflow_id in: query required: false description: The unique id of a workflow instance schema: type: integer - name: form_field_key in: query required: false description: The unique key of a workflow task form field. Make sure this matches a document in the irb_documents.xslx reference sheet. schema: type: string 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 - name: version in: query required: false description: The version of the file, or none for latest version schema: type: integer get: operationId: crc.api.file.get_file_data summary: Returns only the file contents tags: - Files responses: '200': description: Returns the actual file content: application/octet-stream: schema: type: string format: binary example: '' 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: '' 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: '' # /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}/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: '' /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: everything in: query required: false description: If set to true, returns all the approvals known to the system. schema: 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 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