api_doc.yml

openapi: "3.0.0"
info:
  version: 1.0.0
  title: Swagger Petstore
  license:
    name: MIT
servers:
  - url: http://petstore.swagger.io/v1
paths:
  # analysis_results.py
  /analysis_results/{result_uuid}:
    get:
      summary: Get a specific AnalysisResult
      operationId: showAnalysisResultById
      parameters:
        - name: result_uuid
          in: path
          description: uuid of the analysis result_uuid
          required: true
          schema:
            type: string
      responses:
        '200':
          content:
            '#/components/schemas/AnalysisResult'
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"
  /analysis_results:
    get:
      summary: Get all AnalysisResults
      operationId: showAnalysisResults
      responses:
        '200':
          content:
            '#/components/schemas/AnalysisResults'
        default:
          description: unexpected error
          content:
            application/json:
              schema:
                $ref: "#/components/schemas/Error"

  # auth.py
  /auth/register:
    post:
      summary: Register a new user and log them in
  /auth/login:
    post:
      summary: Log current user in
  /auth/logout:
    get:
      summary: Log current user out
  /auth/status:
    get:
      summary: get status of current user
  /organizations:
    post:
      summary: Create a new organization
    get:
      summary: List all organizations the current user is allowed to see
  /organizations/{organization_uuid}:
    get:
      summary: Get a specified organization
  /organizations/{organization_uuid}/users:
    post:
      summary: Add a user to an organization
    get:
      summary: List all users in an organization

  # ping.py
  /ping:
    get:
      summary: Return a pong

  # sample_groups.py
  /sample_groups:
    post:
      summary: Add a sample group
    get:
      summary: Get all sample groups the user is allowed to see
  /sample_groups/{group_uuid}:
    get:
      summary: Get a specified sample group
    delete:
      summary: Delete a specified sample group
  /sample_groups/{group_uuid}/samples:
    get:
      summary: Get all samples in a specified group
    post:
      summary: Add samples to a specified group
  /sample_groups/{group_uuid}/middleware:
    post:
      summary: Run requested middleware/analysis modules for the specified group
  /libraries/{library_uuid}/metadata:
    post:
      summary: Upload metadata to a library 
  /organizations/{organization_uuid}/sample_groups:
    post:
      summary: Add a sample group to an organization
    get:
      summary: Get all sample groups owned by an organization

  # samples.py
  /samples:
    post:
      summary: Create a sample and add it to a library
    get:
      summary: Get all samples the current user is allowed to see
  /samples/{sample_uuid}:
    get:
      summary: Get a specified sample
  /samples/{sample_uuid}/metadata:
    get:
      summary: Get metadata for a specified sample
    post:
      summary: Upload metadata for specified sample
  /samples/getid/{sample_name}:
    get:
      summary: Get the uuid for a specific sample name
  /samples/{sample_uuid}/middleware:
    post:
      summary: Run requested middleware/analysis modules for the specified sample


components:
  schemas:
    AnalysisResult:
      type: object
      required:
        - uuid
        - module_name
      properties:
        uuid:
          type: string
        module_name:
          type: string
    AnalysisResults:
      type: array
      items:
        $ref: "#/components/schemas/AnalysisResult"
    Error:
      type: object
      required:
        - code
        - message
      properties:
        code:
          type: integer
          format: int32
        message:
          type: string