NCI Genomic Data Commons (GDC) API — Download

naftiko: 1.0.0-alpha2
info:
  label: NCI Genomic Data Commons (GDC) API — Download
  description: 'NCI Genomic Data Commons (GDC) API — Download. 3 operations. Lead operation: Download a file. Self-contained
    Naftiko capability covering one National Cancer Institute business surface.'
  tags:
  - National Cancer Institute
  - Download
  created: '2026-05-19'
  modified: '2026-05-19'
binds:
- namespace: env
  keys:
    NATIONAL_CANCER_INSTITUTE_API_KEY: NATIONAL_CANCER_INSTITUTE_API_KEY
capability:
  consumes:
  - type: http
    namespace: national-cancer-institute-download
    baseUri: https://api.gdc.cancer.gov
    description: NCI Genomic Data Commons (GDC) API — Download business capability. Self-contained, no shared references.
    resources:
    - name: data-file_id
      path: /data/{file_id}
      operations:
      - name: downloadfile
        method: GET
        description: Download a file
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: file_id
          in: path
          type: string
          required: true
    - name: manifest
      path: /manifest
      operations:
      - name: getmanifest
        method: GET
        description: Generate manifest
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: filters
          in: query
          type: string
    - name: slicing-view-file_id
      path: /slicing/view/{file_id}
      operations:
      - name: slicebam
        method: GET
        description: BAM slicing
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
        inputParameters:
        - name: file_id
          in: path
          type: string
          required: true
        - name: region
          in: query
          type: string
    authentication:
      type: apikey
      key: X-Auth-Token
      value: '{{env.NATIONAL_CANCER_INSTITUTE_API_KEY}}'
      placement: header
  exposes:
  - type: rest
    namespace: national-cancer-institute-download-rest
    port: 8080
    description: REST adapter for NCI Genomic Data Commons (GDC) API — Download. One Spectral-compliant resource per consumed
      operation, prefixed with /v1.
    resources:
    - path: /v1/data/{file-id}
      name: data-file-id
      description: REST surface for data-file_id.
      operations:
      - method: GET
        name: downloadfile
        description: Download a file
        call: national-cancer-institute-download.downloadfile
        with:
          file_id: rest.file_id
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/manifest
      name: manifest
      description: REST surface for manifest.
      operations:
      - method: GET
        name: getmanifest
        description: Generate manifest
        call: national-cancer-institute-download.getmanifest
        with:
          filters: rest.filters
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/slicing/view/{file-id}
      name: slicing-view-file-id
      description: REST surface for slicing-view-file_id.
      operations:
      - method: GET
        name: slicebam
        description: BAM slicing
        call: national-cancer-institute-download.slicebam
        with:
          file_id: rest.file_id
          region: rest.region
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    namespace: national-cancer-institute-download-mcp
    port: 9090
    transport: http
    description: MCP adapter for NCI Genomic Data Commons (GDC) API — Download. One tool per consumed operation, routed inline
      through this capability's consumes block.
    tools:
    - name: download-file
      description: Download a file
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute-download.downloadfile
      with:
        file_id: tools.file_id
      outputParameters:
      - type: object
        mapping: $.
    - name: generate-manifest
      description: Generate manifest
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute-download.getmanifest
      with:
        filters: tools.filters
      outputParameters:
      - type: object
        mapping: $.
    - name: bam-slicing
      description: BAM slicing
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute-download.slicebam
      with:
        file_id: tools.file_id
        region: tools.region
      outputParameters:
      - type: object
        mapping: $.