naftiko: 1.0.0-alpha2
info:
  label: NCI Genomic Data Commons (GDC) API
  description: The GDC API provides programmatic access to cancer genomic and clinical data hosted by the National Cancer
    Institute Genomic Data Commons. The API supports search and retrieval of projects, cases, files, and annotations, along
    with file download, BAM slicing, and data submission workflows.
  tags:
  - National
  - Cancer
  - Institute
  - API
  created: '2026-05-06'
  modified: '2026-05-06'
capability:
  consumes:
  - type: http
    namespace: national-cancer-institute
    baseUri: https://api.gdc.cancer.gov
    description: NCI Genomic Data Commons (GDC) API HTTP API.
    authentication:
      type: apikey
      in: header
      name: X-Auth-Token
      value: '{{NATIONAL_CANCER_INSTITUTE_TOKEN}}'
    resources:
    - name: status
      path: /status
      operations:
      - name: getstatus
        method: GET
        description: Get API status
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: projects
      path: /projects
      operations:
      - name: searchprojects
        method: GET
        description: Search projects
        inputParameters:
        - name: filters
          in: query
          type: string
        - name: fields
          in: query
          type: string
        - name: size
          in: query
          type: integer
        - name: from
          in: query
          type: integer
        - name: sort
          in: query
          type: string
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: projects-project-id
      path: /projects/{project_id}
      operations:
      - name: getproject
        method: GET
        description: Get project by ID
        inputParameters:
        - name: project_id
          in: path
          type: string
          required: true
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: cases
      path: /cases
      operations:
      - name: searchcases
        method: GET
        description: Search cases
        inputParameters:
        - name: filters
          in: query
          type: string
        - name: fields
          in: query
          type: string
        - name: size
          in: query
          type: integer
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: cases-case-id
      path: /cases/{case_id}
      operations:
      - name: getcase
        method: GET
        description: Get case by ID
        inputParameters:
        - name: case_id
          in: path
          type: string
          required: true
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: files
      path: /files
      operations:
      - name: searchfiles
        method: GET
        description: Search files
        inputParameters:
        - name: filters
          in: query
          type: string
        - name: fields
          in: query
          type: string
        - name: size
          in: query
          type: integer
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: files-file-id
      path: /files/{file_id}
      operations:
      - name: getfile
        method: GET
        description: Get file metadata by ID
        inputParameters:
        - name: file_id
          in: path
          type: string
          required: true
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: annotations
      path: /annotations
      operations:
      - name: searchannotations
        method: GET
        description: Search annotations
        inputParameters:
        - name: filters
          in: query
          type: string
        - name: fields
          in: query
          type: string
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: data-file-id
      path: /data/{file_id}
      operations:
      - name: downloadfile
        method: GET
        description: Download a file
        inputParameters:
        - name: file_id
          in: path
          type: string
          required: true
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: manifest
      path: /manifest
      operations:
      - name: getmanifest
        method: GET
        description: Generate manifest
        inputParameters:
        - name: filters
          in: query
          type: string
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: slicing-view-file-id
      path: /slicing/view/{file_id}
      operations:
      - name: slicebam
        method: GET
        description: BAM slicing
        inputParameters:
        - name: file_id
          in: path
          type: string
          required: true
        - name: region
          in: query
          type: string
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: submission-program-project
      path: /submission/{program}/{project}
      operations:
      - name: getsubmissionproject
        method: GET
        description: Get submission program/project resources
        inputParameters:
        - name: program
          in: path
          type: string
          required: true
        - name: project
          in: path
          type: string
          required: true
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
  exposes:
  - type: rest
    port: 8080
    namespace: national-cancer-institute-rest
    description: REST adapter for NCI Genomic Data Commons (GDC) API.
    resources:
    - path: /status
      name: getstatus
      operations:
      - method: GET
        name: getstatus
        description: Get API status
        call: national-cancer-institute.getstatus
        outputParameters:
        - type: object
          mapping: $.
    - path: /projects
      name: searchprojects
      operations:
      - method: GET
        name: searchprojects
        description: Search projects
        call: national-cancer-institute.searchprojects
        outputParameters:
        - type: object
          mapping: $.
    - path: /projects/{project_id}
      name: getproject
      operations:
      - method: GET
        name: getproject
        description: Get project by ID
        call: national-cancer-institute.getproject
        with:
          project_id: rest.project_id
        outputParameters:
        - type: object
          mapping: $.
    - path: /cases
      name: searchcases
      operations:
      - method: GET
        name: searchcases
        description: Search cases
        call: national-cancer-institute.searchcases
        outputParameters:
        - type: object
          mapping: $.
    - path: /cases/{case_id}
      name: getcase
      operations:
      - method: GET
        name: getcase
        description: Get case by ID
        call: national-cancer-institute.getcase
        with:
          case_id: rest.case_id
        outputParameters:
        - type: object
          mapping: $.
    - path: /files
      name: searchfiles
      operations:
      - method: GET
        name: searchfiles
        description: Search files
        call: national-cancer-institute.searchfiles
        outputParameters:
        - type: object
          mapping: $.
    - path: /files/{file_id}
      name: getfile
      operations:
      - method: GET
        name: getfile
        description: Get file metadata by ID
        call: national-cancer-institute.getfile
        with:
          file_id: rest.file_id
        outputParameters:
        - type: object
          mapping: $.
    - path: /annotations
      name: searchannotations
      operations:
      - method: GET
        name: searchannotations
        description: Search annotations
        call: national-cancer-institute.searchannotations
        outputParameters:
        - type: object
          mapping: $.
    - path: /data/{file_id}
      name: downloadfile
      operations:
      - method: GET
        name: downloadfile
        description: Download a file
        call: national-cancer-institute.downloadfile
        with:
          file_id: rest.file_id
        outputParameters:
        - type: object
          mapping: $.
    - path: /manifest
      name: getmanifest
      operations:
      - method: GET
        name: getmanifest
        description: Generate manifest
        call: national-cancer-institute.getmanifest
        outputParameters:
        - type: object
          mapping: $.
    - path: /slicing/view/{file_id}
      name: slicebam
      operations:
      - method: GET
        name: slicebam
        description: BAM slicing
        call: national-cancer-institute.slicebam
        with:
          file_id: rest.file_id
        outputParameters:
        - type: object
          mapping: $.
    - path: /submission/{program}/{project}
      name: getsubmissionproject
      operations:
      - method: GET
        name: getsubmissionproject
        description: Get submission program/project resources
        call: national-cancer-institute.getsubmissionproject
        with:
          program: rest.program
          project: rest.project
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    port: 9090
    namespace: national-cancer-institute-mcp
    transport: http
    description: MCP adapter for NCI Genomic Data Commons (GDC) API for AI agent use.
    tools:
    - name: getstatus
      description: Get API status
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute.getstatus
      outputParameters:
      - type: object
        mapping: $.
    - name: searchprojects
      description: Search projects
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute.searchprojects
      with:
        filters: tools.filters
        fields: tools.fields
        size: tools.size
        from: tools.from
        sort: tools.sort
      inputParameters:
      - name: filters
        type: string
        description: filters
      - name: fields
        type: string
        description: fields
      - name: size
        type: integer
        description: size
      - name: from
        type: integer
        description: from
      - name: sort
        type: string
        description: sort
      outputParameters:
      - type: object
        mapping: $.
    - name: getproject
      description: Get project by ID
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute.getproject
      with:
        project_id: tools.project_id
      inputParameters:
      - name: project_id
        type: string
        description: project_id
        required: true
      outputParameters:
      - type: object
        mapping: $.
    - name: searchcases
      description: Search cases
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute.searchcases
      with:
        filters: tools.filters
        fields: tools.fields
        size: tools.size
      inputParameters:
      - name: filters
        type: string
        description: filters
      - name: fields
        type: string
        description: fields
      - name: size
        type: integer
        description: size
      outputParameters:
      - type: object
        mapping: $.
    - name: getcase
      description: Get case by ID
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute.getcase
      with:
        case_id: tools.case_id
      inputParameters:
      - name: case_id
        type: string
        description: case_id
        required: true
      outputParameters:
      - type: object
        mapping: $.
    - name: searchfiles
      description: Search files
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute.searchfiles
      with:
        filters: tools.filters
        fields: tools.fields
        size: tools.size
      inputParameters:
      - name: filters
        type: string
        description: filters
      - name: fields
        type: string
        description: fields
      - name: size
        type: integer
        description: size
      outputParameters:
      - type: object
        mapping: $.
    - name: getfile
      description: Get file metadata by ID
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute.getfile
      with:
        file_id: tools.file_id
      inputParameters:
      - name: file_id
        type: string
        description: file_id
        required: true
      outputParameters:
      - type: object
        mapping: $.
    - name: searchannotations
      description: Search annotations
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute.searchannotations
      with:
        filters: tools.filters
        fields: tools.fields
      inputParameters:
      - name: filters
        type: string
        description: filters
      - name: fields
        type: string
        description: fields
      outputParameters:
      - type: object
        mapping: $.
    - name: downloadfile
      description: Download a file
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute.downloadfile
      with:
        file_id: tools.file_id
      inputParameters:
      - name: file_id
        type: string
        description: file_id
        required: true
      outputParameters:
      - type: object
        mapping: $.
    - name: getmanifest
      description: Generate manifest
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute.getmanifest
      with:
        filters: tools.filters
      inputParameters:
      - name: filters
        type: string
        description: filters
      outputParameters:
      - type: object
        mapping: $.
    - name: slicebam
      description: BAM slicing
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute.slicebam
      with:
        file_id: tools.file_id
        region: tools.region
      inputParameters:
      - name: file_id
        type: string
        description: file_id
        required: true
      - name: region
        type: string
        description: region
      outputParameters:
      - type: object
        mapping: $.
    - name: getsubmissionproject
      description: Get submission program/project resources
      hints:
        readOnly: true
        destructive: false
        idempotent: true
      call: national-cancer-institute.getsubmissionproject
      with:
        program: tools.program
        project: tools.project
      inputParameters:
      - name: program
        type: string
        description: program
        required: true
      - name: project
        type: string
        description: project
        required: true
      outputParameters:
      - type: object
        mapping: $.
binds:
- namespace: env
  keys:
    NATIONAL_CANCER_INSTITUTE_TOKEN: NATIONAL_CANCER_INSTITUTE_TOKEN