naftiko: 1.0.0-alpha2
info:
  label: CyVerse Data Science Workflow
  description: Unified workflow capability for bioinformatics and data science on the CyVerse Discovery Environment. Enables
    researchers, bioinformaticians, and data scientists to manage data in iRODS, discover and launch analysis applications,
    monitor jobs, annotate datasets with metadata, share data with collaborators, and request persistent identifiers for publication-ready
    datasets.
  tags:
  - CyVerse
  - Bioinformatics
  - Data Science
  - iRODS
  - Life Sciences
  - Research Computing
  - Open Science
  created: '2026-05-03'
  modified: '2026-05-06'
binds:
- namespace: env
  keys:
    TERRAIN_JWT_TOKEN: TERRAIN_JWT_TOKEN
capability:
  consumes:
  - type: http
    namespace: terrain
    baseUri: https://de.cyverse.org/terrain
    description: Terrain Discovery Environment primary REST API
    authentication:
      type: bearer
      token: '{{TERRAIN_JWT_TOKEN}}'
    resources:
    - name: filesystem-directory
      path: /secured/filesystem/directory
      description: Browse and create iRODS directories
      operations:
      - name: list-directory
        method: GET
        description: List contents of a directory in iRODS
        inputParameters:
        - name: path
          in: query
          type: string
          required: true
          description: iRODS path of the directory
        - name: limit
          in: query
          type: integer
          required: false
          description: Max entries to return
        - name: offset
          in: query
          type: integer
          required: false
          description: Pagination offset
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: filesystem-root
      path: /secured/filesystem/root
      description: Get root directory for the user
      operations:
      - name: get-root-directory
        method: GET
        description: Get the root directory listing
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: filesystem-stat
      path: /secured/filesystem/stat
      description: Get file or directory statistics
      operations:
      - name: get-file-stats
        method: GET
        description: Get metadata and stats for a file or directory
        inputParameters:
        - name: path
          in: query
          type: string
          required: true
          description: iRODS path
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: filesystem-search
      path: /secured/filesystem/search
      description: Search the iRODS filesystem
      operations:
      - name: search-filesystem
        method: GET
        description: Full-text search across iRODS data store
        inputParameters:
        - name: search
          in: query
          type: string
          required: true
          description: Search query
        - name: limit
          in: query
          type: integer
          required: false
          description: Max results
        - name: type
          in: query
          type: string
          required: false
          description: 'Filter: file, folder, any'
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: filesystem-move
      path: /secured/filesystem/move
      description: Move files and directories
      operations:
      - name: move-files
        method: POST
        description: Move files or directories to a new location
        body:
          type: json
          data:
            sources: '{{tools.sources}}'
            dest: '{{tools.dest}}'
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: filesystem-delete
      path: /secured/filesystem/delete
      description: Delete files and directories
      operations:
      - name: delete-files
        method: POST
        description: Move files or directories to the trash
        body:
          type: json
          data:
            paths: '{{tools.paths}}'
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: filesystem-metadata
      path: /secured/filesystem/metadata
      description: Manage iRODS metadata AVUs
      operations:
      - name: get-file-metadata
        method: GET
        description: Get metadata AVUs for a file or directory
        inputParameters:
        - name: path
          in: query
          type: string
          required: true
          description: iRODS path
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: filesystem-share
      path: /secured/filesystem/share
      description: Share data with other users
      operations:
      - name: share-data
        method: POST
        description: Share files or directories with specified users
        body:
          type: json
          data:
            sharing: '{{tools.sharing}}'
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: apps
      path: /secured/apps
      description: Browse available applications
      operations:
      - name: list-apps
        method: GET
        description: List available applications in the Discovery Environment
        inputParameters:
        - name: search
          in: query
          type: string
          required: false
          description: Filter apps by name
        - name: limit
          in: query
          type: integer
          required: false
          description: Max apps to return
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: analyses
      path: /secured/analyses
      description: Submit and list analysis jobs
      operations:
      - name: list-analyses
        method: GET
        description: List analyses for the current user
        inputParameters:
        - name: limit
          in: query
          type: integer
          required: false
          description: Max analyses to return
        - name: offset
          in: query
          type: integer
          required: false
          description: Pagination offset
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
      - name: submit-analysis
        method: POST
        description: Submit a new analysis job
        body:
          type: json
          data:
            name: '{{tools.name}}'
            app_id: '{{tools.app_id}}'
            system_id: '{{tools.system_id}}'
            config: '{{tools.config}}'
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
    - name: notifications
      path: /secured/notifications
      description: Manage user notifications
      operations:
      - name: list-notifications
        method: GET
        description: List notifications for the current user
        inputParameters:
        - name: limit
          in: query
          type: integer
          required: false
          description: Max notifications
        - name: seen
          in: query
          type: boolean
          required: false
          description: Filter by read/unread
        outputRawFormat: json
        outputParameters:
        - name: result
          type: object
          value: $.
  exposes:
  - type: rest
    port: 8080
    namespace: cyverse-data-science-api
    description: Unified REST API for CyVerse Discovery Environment data science workflows.
    resources:
    - path: /v1/filesystem
      name: filesystem
      description: iRODS data store browsing
      operations:
      - method: GET
        name: list-directory
        description: List directory contents in iRODS
        call: terrain.list-directory
        with:
          path: rest.path
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/filesystem/root
      name: filesystem-root
      description: User root directory
      operations:
      - method: GET
        name: get-root-directory
        description: Get user's root iRODS directory
        call: terrain.get-root-directory
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/filesystem/search
      name: filesystem-search
      description: Search data store
      operations:
      - method: GET
        name: search-filesystem
        description: Search iRODS for files and directories
        call: terrain.search-filesystem
        with:
          search: rest.search
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/filesystem/metadata
      name: metadata
      description: File metadata (AVUs)
      operations:
      - method: GET
        name: get-file-metadata
        description: Get AVU metadata for a path
        call: terrain.get-file-metadata
        with:
          path: rest.path
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/apps
      name: apps
      description: Application discovery
      operations:
      - method: GET
        name: list-apps
        description: Browse available bioinformatics apps
        call: terrain.list-apps
        with:
          search: rest.search
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/analyses
      name: analyses
      description: Analysis job management
      operations:
      - method: GET
        name: list-analyses
        description: List user's analysis jobs
        call: terrain.list-analyses
        outputParameters:
        - type: object
          mapping: $.
      - method: POST
        name: submit-analysis
        description: Submit a new analysis job
        call: terrain.submit-analysis
        with:
          name: rest.name
          app_id: rest.app_id
          system_id: rest.system_id
          config: rest.config
        outputParameters:
        - type: object
          mapping: $.
    - path: /v1/notifications
      name: notifications
      description: User notifications
      operations:
      - method: GET
        name: list-notifications
        description: List user notifications
        call: terrain.list-notifications
        outputParameters:
        - type: object
          mapping: $.
  - type: mcp
    port: 9090
    namespace: cyverse-data-science-mcp
    transport: http
    description: MCP server for AI-assisted CyVerse Discovery Environment data science workflows.
    tools:
    - name: list-directory
      description: Browse an iRODS directory in the CyVerse data store
      hints:
        readOnly: true
        openWorld: true
      call: terrain.list-directory
      with:
        path: tools.path
      outputParameters:
      - type: object
        mapping: $.
    - name: get-root-directory
      description: Get the root directory structure for the CyVerse user account
      hints:
        readOnly: true
        openWorld: false
      call: terrain.get-root-directory
      outputParameters:
      - type: object
        mapping: $.
    - name: get-file-stats
      description: Get size, permissions, and modification dates for an iRODS file or directory
      hints:
        readOnly: true
        openWorld: false
      call: terrain.get-file-stats
      with:
        path: tools.path
      outputParameters:
      - type: object
        mapping: $.
    - name: search-filesystem
      description: Search the CyVerse iRODS data store for files and folders by name
      hints:
        readOnly: true
        openWorld: true
      call: terrain.search-filesystem
      with:
        search: tools.search
        type: tools.type
      outputParameters:
      - type: object
        mapping: $.
    - name: move-files
      description: Move files or directories to a new location in iRODS
      hints:
        readOnly: false
        destructive: false
        idempotent: false
      call: terrain.move-files
      with:
        sources: tools.sources
        dest: tools.dest
      outputParameters:
      - type: object
        mapping: $.
    - name: delete-files
      description: Move files or directories to the user's iRODS trash
      hints:
        readOnly: false
        destructive: true
        idempotent: false
      call: terrain.delete-files
      with:
        paths: tools.paths
      outputParameters:
      - type: object
        mapping: $.
    - name: get-file-metadata
      description: Get iRODS AVU metadata triples for a file or directory
      hints:
        readOnly: true
        openWorld: false
      call: terrain.get-file-metadata
      with:
        path: tools.path
      outputParameters:
      - type: object
        mapping: $.
    - name: share-data
      description: Share iRODS data (files/folders) with other CyVerse users
      hints:
        readOnly: false
        destructive: false
      call: terrain.share-data
      with:
        sharing: tools.sharing
      outputParameters:
      - type: object
        mapping: $.
    - name: list-apps
      description: Browse bioinformatics and data science apps in the Discovery Environment
      hints:
        readOnly: true
        openWorld: true
      call: terrain.list-apps
      with:
        search: tools.search
      outputParameters:
      - type: object
        mapping: $.
    - name: list-analyses
      description: List the user's analysis job history in the Discovery Environment
      hints:
        readOnly: true
        openWorld: true
      call: terrain.list-analyses
      outputParameters:
      - type: object
        mapping: $.
    - name: submit-analysis
      description: Submit a new bioinformatics analysis job using a Discovery Environment application
      hints:
        readOnly: false
        destructive: false
      call: terrain.submit-analysis
      with:
        name: tools.name
        app_id: tools.app_id
        system_id: tools.system_id
        config: tools.config
      outputParameters:
      - type: object
        mapping: $.
    - name: list-notifications
      description: Get recent notifications about completed analyses and system events
      hints:
        readOnly: true
        openWorld: true
      call: terrain.list-notifications
      outputParameters:
      - type: object
        mapping: $.