MyOme Resources API

openapi: 3.2.0
info:
  title: MyOme Resources API
  version: 2.51.0
  contact:
    email: support@myome.com
  description: "The MyOme API enables clients to:\n- List sequencing and analysis products available to the client.\n- Submit requisitions for sequencing for new samples.\n- Check status of requisitions and orders.\n- Retrieve order results, including sequencing data, structured interpretation\n  data, and PDF reports.\n\n# API Overview\n\n## Terminology\n\n- A *Product* is a specific assay or intepretation service. Product\n  identifiers begin with `PR`.\n- A *Requisition* is a request for one or more Products for a single sample.\n  Requisition identifiers begin with `RQ`.\n- An *Order* is\n  a request for a specific service for a specific sample.  An Order is created for each\n  Product requested in a Requisition Order identifiers\n  begin with `OR`.   \n- A *Report* is the end result of a successful Order. An Order typically has one\n  associated Report, but may have zero in the case of failure or multiple in\n  the case of amended or corrected reports.\n\n## Typical flow\n\n- Client obtains JWT from auth.myome.com. All of the following interactions with the MyOme API include\n  this JWT for authorization (details below).\n- Client sends a requisition to MyOme with product ID(s). Each product will generate a distinct order attached to that requisition. \n  The MyOme API returns a MyOme requisition id.\n- Client fetches information about the Requisition. The response includes an order id for each Order placed.\n- Client fetches information about each Order. The response includes the status and, if\n  available, links to results.\n\n## Order Statuses\n\nOrder status:\n- SUBMITTED - Order has been received\n- DENIED - Denied by physician of record (only relevant for patient-initiated testing requests)\n- CANCELED - Order was canceled\n- AWAITING_SAMPLE - Sample has not arrived yet\n- ANALYZING - Order is being processed\n- CLINICIAN_REVIEW - Order results sent to clinician and waiting for review\n- COMPLETED - Order has been completed\n\n# API Conventions\n\n## Authorization\n\nAll endpoints require authorization using JSON Web Tokens (JWT) using the header: `Authorization: Bearer <token>`. `<token>` is a JWT generated using Keycloak with partner-specific credientials. \nNote that the token refreshes every hour. MyOme will provide credentials to partners via secure email during account creation. Those credentials should be kept confidential.\n\n## HTTP Status Codes\n\nThe MyOme API uses the following standard HTTP status codes to indicate the success or failure\nof an API request.\n\n    200 Success\n    201 Created\n    204 No Content\n    400 Bad Request\n    401 Unauthorized\n    403 Forbidden\n    404 Resource Not Found\n    415 Unsupported Media Type\n    500 Internal Server Error\n\nA successful create request returns 201 Created along with the created object identifier. A successful\nupdate request returns 200 OK along with the updated object. An unsuccessful API request returns\na relevant HTTP status code along with an error response."
servers:
- url: /0/
  description: local development server
- url: https://api.sbx.myome.com/0/
  description: External sandbox instance for partner testing/development
- url: https://api.myome.com/0/
  description: Production API
tags:
- name: Resources
  description: Reference data—orderable products and consent types (general and product-specific).
paths:
  /consent:
    get:
      operationId: myome.api.endpoints.consent.consent_get
      security: []
      summary: List consent types
      description: Returns available consent types (general and, when requested via query, product-specific). Used to know which consent URIs to send when granting consent.
      tags:
      - Resources
      responses:
        '200':
          $ref: '#/components/responses/ConsentListResponse'
        '401':
          $ref: '#/components/responses/StructuredError'
      parameters:
      - name: consents
        in: query
        required: true
        example:
        - DNAVISIT
        - PR-2019
        schema:
          type: array
          items:
            type: string
            pattern: '[A-Z_0-9]+(-\d+\.\d+\.\d+)?$'
  /product:
    get:
      operationId: myome.api.endpoints.product.product_get
      security:
      - jwt: []
      tags:
      - Resources
      summary: List orderable products
      description: 'Returns the list of products that can be ordered (for use when creating requisitions).

        '
      responses:
        '200':
          $ref: '#/components/responses/ProductListResponse'
        '401':
          $ref: '#/components/responses/StructuredError'
components:
  responses:
    ProductListResponse:
      description: List of products
      content:
        application/json:
          schema:
            type: array
            items:
              $ref: '#/components/schemas/Product'
          example:
          - - description: MyOme product for analysis of ACMG Secondary Findings Version 3.
              name: MyOme Personal Genome, Proactive Health, 81 Genes
              product_id: PR-2019
    StructuredError:
      description: Generic structured error message
      content:
        application/json:
          schema:
            type: object
            additionalProperties: false
            required:
            - title
            - detail
            properties:
              title:
                type: string
              detail:
                type: string
              code:
                type:
                - string
                - 'null'
                description: The type of error that occurred
              errors:
                type:
                - object
                - 'null'
                additionalProperties: true
                description: Dictionary of field names and error messages
              extra:
                oneOf:
                - type: object
                  additionalProperties: true
                - type: string
          examples:
            simple_error:
              value:
                detail: There was an error validating the request
                title: Validation error
            flat_field_errors:
              value:
                code: validation_error
                detail: Validation error
                title: Validation error
                errors:
                  field1: field is required
            nested_field_errors:
              value:
                code: validation_error
                detail: Validation error
                title: Validation error
                errors:
                  field1: field is required
                  field2:
                    field3: field is invalid
            no_field_errors:
              value:
                code: validation_error
                detail: Validation error
                title: Validation error
    ConsentListResponse:
      description: List of general and product specific consents
      content:
        application/json:
          schema:
            type: array
            items:
              type: object
              additionalProperties: false
              properties:
                consent_uri:
                  allOf:
                  - $ref: '#/components/schemas/ConsentUri'
                name:
                  type:
                  - string
                  - 'null'
                  description: Consent name
                consent_text:
                  type:
                  - string
                  - 'null'
          example:
          - - consent_uri: myome:consent:GENERAL-0.0.1
              name: MyOme General Consent
              consent_text: Example consent text
  schemas:
    ProductId:
      type: string
      description: A reference to an ordered product.
      pattern: ^PR-?\d+$
      examples:
      - PR-0123456
      - PR0123456
    Product:
      type: object
      required:
      - product_id
      properties:
        description:
          type:
          - string
          - 'null'
          description: Description of analysis product
        name:
          type:
          - string
          - 'null'
          description: Short analysis product name
        product_id:
          $ref: '#/components/schemas/ProductId'
    ConsentUri:
      type: string
      pattern: ^myome:consent:[A-Z_0-9]+(-\d+\.\d+\.\d+)?(-dev\.\d+)?$
      examples:
      - myome:consent:GENERAL-0.1.4
      - myome:consent:PR2008-0.0.1
      - myome:consent:DNAVISIT
      - myome:consent:PRODUCT_NOTIFICATIONS-0.0.1
      - myome:consent:PR5004-0.0.1-dev.0
      - myome:consent:HIE_ACCESS__TREATMENT
      - myome:consent:CONTACT__RESEARCH_OPPORTUNITIES
      - myome:consent:CONTACT__TRANSACTIONAL_SMS
      - myome:consent:CONTACT__MARKETING
  securitySchemes:
    jwt:
      type: http
      scheme: bearer
      bearerFormat: JWT
      description: 'JSON Web Token (JWT) obtained from Keycloak.

        '
      x-bearerInfoFunc: myome.api.support.auth.validate_kc_token