openapi: 3.0.1
info:
  title: Pathway Analysis Service database download 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: download
  description: Methods to download different views of a result
paths:
  /download/{token}/entities/found/{resource}/{filename}.csv:
    get:
      tags:
      - download
      summary: Downloads found identifiers for a given analysis and resource
      description: The identifiers are filtered by the selected resource. The filename is the one to be suggested in the download window.
      operationId: downloadMappingResult
      parameters:
      - name: token
        in: path
        description: The token associated with the data to download
        required: true
        schema:
          type: string
      - name: resource
        in: path
        required: true
        schema:
          type: string
          description: the preferred resource
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      - name: filename
        in: path
        description: the file name for the downloaded information
        required: true
        schema:
          type: string
        example: result
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            text/csv:
              schema:
                type: string
                format: binary
        '410':
          description: Result deleted due to a new data release
          content:
            text/csv:
              schema:
                type: string
                format: binary
  /download/{token}/entities/notfound/{filename}.csv:
    get:
      tags:
      - download
      summary: Downloads a list of the not found identifiers
      description: Those identifiers from the user sample that are not present up to the current data version. The filename is the one to be suggested in the download window.
      operationId: downloadNotFound
      parameters:
      - name: token
        in: path
        description: The token associated with the data to download
        required: true
        schema:
          type: string
      - name: filename
        in: path
        description: the file name for the downloaded information
        required: true
        schema:
          type: string
        example: result
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            text/csv:
              schema:
                type: string
                format: binary
        '410':
          description: Result deleted due to a new data release
          content:
            text/csv:
              schema:
                type: string
                format: binary
  /download/{token}/pathways/{resource}/{filename}.csv:
    get:
      tags:
      - download
      summary: Downloads all hit pathways for a given analysis
      description: The results are filtered by the selected resource. The filename is the one to be suggested in the download window.
      operationId: downloadResultCSV
      parameters:
      - name: token
        in: path
        description: The token associated with the data to download
        required: true
        schema:
          type: string
      - name: resource
        in: path
        required: true
        schema:
          type: string
          description: the preferred resource
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI
          - PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      - name: filename
        in: path
        description: the file name for the downloaded information
        required: true
        schema:
          type: string
        example: result
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            text/csv:
              schema:
                type: string
                format: binary
        '410':
          description: Result deleted due to a new data release
          content:
            text/csv:
              schema:
                type: string
                format: binary
  /download/{token}/result.json:
    get:
      tags:
      - download
      summary: Returns the complete result in json format
      description: The results are not filtered by any means. The json file contains the whole stored result based on chosen analysis options and submitted data.
      operationId: downloadResultJSON
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: importableOnly
        in: query
        description: Only include resources which can be later imported
        required: false
        schema:
          type: boolean
          default: false
        example: false
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ExternalAnalysisResult'
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ExternalAnalysisResult'
  /download/{token}/result.json.gz:
    get:
      tags:
      - download
      summary: Returns the complete result in json format (gzipped)
      description: The results are not filtered by any means. The json file contains the whole stored result based on chosen analysis options and submitted data.
      operationId: downloadResultGZIP
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/gzip:
              schema:
                type: string
                format: binary
            application/x-gzip:
              schema:
                type: string
                format: binary
        '410':
          description: Result deleted due to a new data release
          content:
            application/gzip:
              schema:
                type: string
                format: binary
            application/x-gzip:
              schema:
                type: string
                format: binary
components:
  schemas:
    ExternalStatistics:
      type: object
      properties:
        entitiesAndInteractorsCount:
          type: integer
          format: int32
        entitiesAndInteractorsFound:
          type: integer
          format: int32
        entitiesCount:
          type: integer
          format: int32
        entitiesFDR:
          type: number
          format: double
        entitiesFound:
          type: integer
          format: int32
        entitiesPValue:
          type: number
          format: double
        entitiesRatio:
          type: number
          format: double
        exp:
          type: array
          items:
            type: number
            format: double
        interactorsCount:
          type: integer
          format: int32
        interactorsFound:
          type: integer
          format: int32
        interactorsRatio:
          type: number
          format: double
        reactionsCount:
          type: integer
          format: int32
        reactionsFound:
          type: integer
          format: int32
        reactionsRatio:
          type: number
          format: double
        resource:
          type: string
    ExternalAnalysisSummary:
      type: object
      properties:
        gsaMethod:
          type: string
        gsaToken:
          type: string
        includeDisease:
          type: boolean
        interactors:
          type: boolean
        projection:
          type: boolean
        sampleName:
          type: string
        server:
          type: string
        token:
          type: string
        type:
          type: string
          enum:
          - SPECIES_COMPARISON
          - OVERREPRESENTATION
          - EXPRESSION
          - GSA_REGULATION
          - GSA_STATISTICS
          - GSVA
        version:
          type: integer
          format: int32
    ExternalPathwayNodeSummary:
      type: object
      properties:
        data:
          $ref: '#/components/schemas/ExternalPathwayNodeData'
        dbId:
          type: integer
          format: int64
        inDisease:
          type: boolean
        llp:
          type: boolean
        name:
          type: string
        species:
          $ref: '#/components/schemas/ExternalSpeciesNode'
        stId:
          type: string
    ExternalMainIdentifier:
      type: object
      properties:
        id:
          type: string
        resource:
          type: string
    ExternalIdentifier:
      type: object
      properties:
        exp:
          type: array
          items:
            type: number
            format: double
        id:
          type: string
        mapsTo:
          type: array
          items:
            $ref: '#/components/schemas/ExternalMainIdentifier'
    ExternalPathwayNodeData:
      type: object
      properties:
        entities:
          type: array
          items:
            $ref: '#/components/schemas/ExternalIdentifier'
        interactors:
          type: array
          items:
            $ref: '#/components/schemas/ExternalInteractor'
        reactions:
          type: array
          items:
            $ref: '#/components/schemas/ExternalAnalysisReaction'
        statistics:
          type: array
          items:
            $ref: '#/components/schemas/ExternalStatistics'
    ExternalInteraction:
      type: object
      properties:
        id:
          type: string
        interactsWith:
          type: array
          items:
            $ref: '#/components/schemas/ExternalMainIdentifier'
    ExternalAnalysisResult:
      type: object
      properties:
        expressionSummary:
          $ref: '#/components/schemas/ExternalExpressionSummary'
        notFound:
          type: array
          items:
            $ref: '#/components/schemas/ExternalIdentifier'
        pathways:
          type: array
          items:
            $ref: '#/components/schemas/ExternalPathwayNodeSummary'
        summary:
          $ref: '#/components/schemas/ExternalAnalysisSummary'
        warnings:
          type: array
          items:
            type: string
    ExternalExpressionSummary:
      type: object
      properties:
        columnNames:
          type: array
          items:
            type: string
        max:
          type: number
          format: double
        min:
          type: number
          format: double
    ExternalAnalysisReaction:
      type: object
      properties:
        dbId:
          type: integer
          format: int64
        resources:
          type: array
          items:
            type: string
        stId:
          type: string
    ExternalInteractor:
      type: object
      properties:
        exp:
          type: array
          items:
            type: number
            format: double
        id:
          type: string
        mapsTo:
          type: array
          items:
            $ref: '#/components/schemas/ExternalInteraction'
    ExternalSpeciesNode:
      type: object
      properties:
        name:
          type: string
        speciesID:
          type: integer
          format: int64
        taxID:
          type: string