UCSC Genome Browser REST API — Genomes

naftiko: 1.0.0-alpha2
info:
  label: UCSC Genome Browser REST API — Genomes
  description: 'UCSC Genome Browser REST API — Genomes. 5 operations. Lead operation: Find Genome. Self-contained Naftiko
    capability covering one Ucsc Genomic Data business surface.'
  tags:
  - Ucsc Genomic Data
  - Genomes
  created: '2026-05-19'
  modified: '2026-05-19'
binds:
- namespace: env
  keys:
    UCSC_GENOMIC_DATA_API_KEY: UCSC_GENOMIC_DATA_API_KEY
capability:
  consumes:
  - type: http
    namespace: ucsc-genomic-data-genomes
    baseUri: https://api.genome.ucsc.edu
    description: UCSC Genome Browser REST API — Genomes business capability. Self-contained, no shared references.
    resources:
    - name: findGenome
      path: /findGenome
      operations:
      - name: findgenome
        method: GET
        description: Find Genome
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: q
          in: query
          type: string
          description: Search query string (genome name, accession, or keyword).
          required: true
        - name: browser
          in: query
          type: string
          description: Filter by browser name.
        - name: year
          in: query
          type: integer
          description: Filter assemblies by year.
        - name: category
          in: query
          type: string
          description: Filter by category.
        - name: status
          in: query
          type: string
          description: Filter by assembly status.
        - name: level
          in: query
          type: string
          description: Filter by assembly level.
        - name: statsOnly
          in: query
          type: integer
          description: Return only statistics if set to 1.
        - name: maxItemsOutput
          in: query
          type: integer
          description: Maximum number of items to return.
    - name: list-chromosomes
      path: /list/chromosomes
      operations:
      - name: listchromosomes
        method: GET
        description: List Chromosomes
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: genome
          in: query
          type: string
          description: Genome assembly identifier (e.g., hg38, mm39).
          required: true
        - name: hubUrl
          in: query
          type: string
          description: URL of the hub.txt file for a track hub.
        - name: track
          in: query
          type: string
          description: Filter chromosomes by a specific track.
    - name: list-files
      path: /list/files
      operations:
      - name: listfiles
        method: GET
        description: List Genome Files
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: genome
          in: query
          type: string
          description: Genome assembly identifier (e.g., hg38, mm39).
          required: true
        - name: format
          in: query
          type: string
          description: File format filter (e.g., bigBed, bigWig).
        - name: maxItemsOutput
          in: query
          type: integer
          description: Maximum number of files to return.
    - name: list-genarkGenomes
      path: /list/genarkGenomes
      operations:
      - name: listgenarkgenomes
        method: GET
        description: List GenArk Genomes
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: genome
          in: query
          type: string
          description: Filter by genome assembly name.
        - name: maxItemsOutput
          in: query
          type: integer
          description: Maximum number of items to return.
    - name: list-ucscGenomes
      path: /list/ucscGenomes
      operations:
      - name: listucscgenomes
        method: GET
        description: List UCSC Genomes
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
  exposes:
  - type: rest
    namespace: ucsc-genomic-data-genomes-rest
    port: 8080
    description: REST adapter for UCSC Genome Browser REST API — Genomes. One Spectral-compliant resource per consumed operation,
      prefixed with /v1.
    resources:
    - path: /v1/findgenome
      name: findgenome
      description: REST surface for findGenome.
      operations:
      - method: GET
        name: findgenome
        description: Find Genome
        call: ucsc-genomic-data-genomes.findgenome
        with:
          q: rest.q
          browser: rest.browser
          year: rest.year
          category: rest.category
          status: rest.status
          level: rest.level
          statsOnly: rest.statsOnly
          maxItemsOutput: rest.maxItemsOutput
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/list/chromosomes
      name: list-chromosomes
      description: REST surface for list-chromosomes.
      operations:
      - method: GET
        name: listchromosomes
        description: List Chromosomes
        call: ucsc-genomic-data-genomes.listchromosomes
        with:
          genome: rest.genome
          hubUrl: rest.hubUrl
          track: rest.track
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/list/files
      name: list-files
      description: REST surface for list-files.
      operations:
      - method: GET
        name: listfiles
        description: List Genome Files
        call: ucsc-genomic-data-genomes.listfiles
        with:
          genome: rest.genome
          format: rest.format
          maxItemsOutput: rest.maxItemsOutput
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/list/genarkgenomes
      name: list-genarkgenomes
      description: REST surface for list-genarkGenomes.
      operations:
      - method: GET
        name: listgenarkgenomes
        description: List GenArk Genomes
        call: ucsc-genomic-data-genomes.listgenarkgenomes
        with:
          genome: rest.genome
          maxItemsOutput: rest.maxItemsOutput
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/list/ucscgenomes
      name: list-ucscgenomes
      description: REST surface for list-ucscGenomes.
      operations:
      - method: GET
        name: listucscgenomes
        description: List UCSC Genomes
        call: ucsc-genomic-data-genomes.listucscgenomes
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    namespace: ucsc-genomic-data-genomes-mcp
    port: 9090
    transport: http
    description: MCP adapter for UCSC Genome Browser REST API — Genomes. One tool per consumed operation, routed inline through
      this capability's consumes block.
    tools:
    - name: find-genome
      description: Find Genome
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: ucsc-genomic-data-genomes.findgenome
      with:
        q: tools.q
        browser: tools.browser
        year: tools.year
        category: tools.category
        status: tools.status
        level: tools.level
        statsOnly: tools.statsOnly
        maxItemsOutput: tools.maxItemsOutput
      outputParameters:
      - type: object
        mapping: $.
    - name: list-chromosomes
      description: List Chromosomes
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: ucsc-genomic-data-genomes.listchromosomes
      with:
        genome: tools.genome
        hubUrl: tools.hubUrl
        track: tools.track
      outputParameters:
      - type: object
        mapping: $.
    - name: list-genome-files
      description: List Genome Files
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: ucsc-genomic-data-genomes.listfiles
      with:
        genome: tools.genome
        format: tools.format
        maxItemsOutput: tools.maxItemsOutput
      outputParameters:
      - type: object
        mapping: $.
    - name: list-genark-genomes
      description: List GenArk Genomes
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: ucsc-genomic-data-genomes.listgenarkgenomes
      with:
        genome: tools.genome
        maxItemsOutput: tools.maxItemsOutput
      outputParameters:
      - type: object
        mapping: $.
    - name: list-ucsc-genomes
      description: List UCSC Genomes
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: ucsc-genomic-data-genomes.listucscgenomes
      outputParameters:
      - type: object
        mapping: $.