openapi: 3.0.1
info:
  title: Pathway Analysis Service database report API
  description: Provides an API for pathway over-representation and expression analysis as well as species comparison tool.
  termsOfService: /license
  contact:
    name: Reactome
    url: https://reactome.org
    email: help@reactome.org
  license:
    name: Creative Commons Attribution 3.0 Unsupported License
    url: https://creativecommons.org/licenses/by/3.0/legalcode
  version: '2.0'
servers:
- url: /AnalysisService
tags:
- name: report
  description: Retrieves report files in PDF format
paths:
  /report/{token}/{species}/{filename}.pdf:
    get:
      tags:
      - report
      summary: Downloads a report for a given pathway analysis result
      description: This method provides a report for a given pathway analysis result in a PDF document. This document contains data about the analysis itself followed by the pathways overview and the most significant pathways overlaid with the analysis result. Users can download and store this information in a convenient format to be checked in the future when the 'token' is not longer available.
      operationId: generatePdfReport
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: species
        in: path
        description: The species for which results will be reported
        required: true
        schema:
          type: string
        example: Homo sapiens
      - name: filename
        in: path
        description: The name of the file to be downloaded
        required: true
        schema:
          type: string
        example: report
      - name: number
        in: query
        description: Number of pathways reported (max 50)
        required: false
        schema:
          type: integer
          format: int32
          default: 25
        example: 25
      - name: resource
        in: query
        required: false
        schema:
          type: string
          description: the resource to sort
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      - name: importableOnly
        in: query
        description: Filters resources to only includes importable ones
        required: false
        schema:
          type: boolean
          default: false
      - name: diagramProfile
        in: query
        required: false
        schema:
          type: string
          description: Diagram Color Profile
          example: Modern
          enum:
          - Modern
          - Standard
      - name: analysisProfile
        in: query
        required: false
        schema:
          type: string
          description: Analysis  Color Profile
          example: Standard
          enum:
          - Standard
          - Strosobar
          - Copper Plus
      - name: fireworksProfile
        in: query
        required: false
        schema:
          type: string
          description: Diagram Color Profile
          example: Barium Lithium
          enum:
          - Cooper
          - Cooper Plus
          - Barium Lithium
          - Calcium Salts
      responses:
        '404':
          description: No result corresponding to the token was found
        '410':
          description: Result deleted due to a new data release