binding_scanner_api.yaml

openapi: 3.0.0
info:
  title: Binding Scanner API Specification
  license:
    name: Apache 2.0
  description: >-
    BindingScanner is a tool for predicting binding sites of distinct regulators
    in an RNA sequence by calculating posterior probabilities with MotEvo, given
    the sequence specificity of regulators, represented as position-specific
    weight matrices. It is intended to help in the analysis of individual
    reporter sequences, by predicting regulatory that may act on the sequence as
    well as how the binding may be affected by specific mutations introduced in
    the reporter sequences. The tools scans the input sequence with a set of
    position-specific weight matrices (PWMs) representing the binding
    specificity of individual RNA-binding proteins.
  version: 1.0.0
paths:
  /runs/{id}/status:
    get:
      summary: 'Returns status of the run'
      operationId: statusGet
      description: This endpoint returns status corresponding to the id in path.
      parameters:
        - name: id
          in: path
          required: true
          description: A unique identifier of the pipeline information.
          example: 1234
          schema:
            type: string
      responses:
        '200':
          description: 'Status of the run'
          content:
            application/json:
              schema:
                type: string
        '404':
          description: 'Status unavailable for the run.'
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Error'
            text/plain:
              schema:
                $ref: '#/components/schemas/Error'
  /runs/{id}/table:
    get:
      summary: 'Returns merged tsv file'
      operationId: TsvGet
      description: This endpoint returns merged tsv file corresponding to the id in path.
      parameters:
        - name: id
          in: path
          required: true
          description: A unique identifier of the pipeline information.
          example: 1234
          schema:
            type: string
      responses:
        '200':
          description: 'Merged tsv file.'
          content:
            text/tsv:
              schema:
                type: string
        '404':
          description: File cannot be found.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Error'
            text/plain:
              schema:
                $ref: '#/components/schemas/Error'
  /runs/{id}/heatmap:
    get:
      summary: 'Returns a pdf file with heatmap of binding sites'
      operationId: HeatmapGet
      description: This endpoint returns a heatmap pdf file corresponding to the id in path.
      parameters:
        - name: id
          in: path
          required: true
          description: A unique identifier of the pipeline information.
          example: 1234
          schema:
            type: string
      responses:
        '200':
          description: 'Heatmap pdf file.'
          content:
            application/pdf:
              schema:
                type: string
                format: binary
        '404':
          description: File cannot be found.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Error'
            text/plain:
              schema:
                $ref: '#/components/schemas/Error'
  /runs:
    post:
      summary: Register pipeline info.
      description: Inputs for the binding scanner to process.
      operationId: infoPost
      requestBody:
        description: Pipeline info to add.
        required: true
        content:
          applcation/json:
            schema:
              type: object
              properties:
                sequence:
                  type: string
                  example: ATGTGAGTGAAGTGTGGGAAAGATGACTCGATATATCTGGATGCTAGGGATCGGATGGCGATACG
                pwm_directory:
                  type: string
                  example: ATtRACT_hsa
                background_binding_prior:
                  type: number
                  example: 0.99
                  default: 0.99
                min_binding_posterior:
                  type: number
                  example: 0.01
                  default: 0.01
                markov_chain_order:
                  type: number
                  example: 1
                  default: 1
      responses:
        '201':
          description: Pipeline information was successfully uploaded.
          content:
            application/json:
              schema:
                description: Pipeline information identifier.
                type: string
                example: 1234
        '400':
          description: The request is malformed.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Error'
        '500':
          description: An unexpected error occurred.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Error'
components:
  schemas:
    Error:
      type: object
      required:
        - code
      properties:
        code:
          type: integer
          format: int32
          default: 500
        message:
          type: string
          default: Internal Server Error
servers:
  # Added by API Auto Mocking Plugin
  - description: SwaggerHub API Auto Mocking
    url: https://virtserver.swaggerhub.com/krish8484/Binding-Scanner/1.0.0