config/server_config.yaml

# OpenProblems Spatial Transcriptomics MCP Server Configuration

server:
  name: "OpenProblems-SpatialAI-MCP"
  version: "0.1.0"
  description: "Model Context Protocol server for spatial transcriptomics workflows"

  # Communication settings
  transport:
    primary: "stdio"     # Primary transport method
    secondary: "http"    # Optional HTTP transport
    http_port: 8000

  # Resource limits
  execution:
    nextflow_timeout: 3600     # 1 hour timeout for Nextflow workflows
    viash_timeout: 1800        # 30 minutes timeout for Viash components
    docker_timeout: 1800       # 30 minutes timeout for Docker builds
    max_concurrent_jobs: 3     # Maximum concurrent tool executions

  # Logging configuration
  logging:
    level: "INFO"
    format: "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
    file: "/app/logs/mcp_server.log"
    max_size: "10MB"
    backup_count: 5

# Directory paths
paths:
  data_dir: "/app/data"
  work_dir: "/app/work"
  logs_dir: "/app/logs"
  cache_dir: "/app/cache"

# Tool configurations
tools:
  nextflow:
    default_profile: "docker"
    config_file: null
    enable_resume: true
    enable_tower: false

  viash:
    default_engine: "docker"
    cache_docker_images: true

  docker:
    registry: "docker.io"
    enable_buildkit: true
    default_platform: "linux/amd64"

# Resource configurations
resources:
  documentation:
    auto_update: false
    cache_duration: 3600  # Cache docs for 1 hour

  templates:
    source_repos:
      - "https://github.com/openproblems-bio/task_ist_preprocessing"
      - "https://github.com/openproblems-bio/task_spatial_simulators"
      - "https://github.com/openpipelines-bio/openpipeline"
      - "https://github.com/aertslab/SpatialNF"

  spatial_data:
    supported_formats: ["h5ad", "zarr", "csv", "tsv"]
    max_file_size: "10GB"

# Security settings
security:
  enable_authentication: false
  allowed_hosts: ["localhost", "127.0.0.1"]
  sandbox_mode: true  # Run tools in sandboxed environment

# Feature flags
features:
  enable_experimental_tools: false
  enable_remote_execution: false
  enable_gpu_support: false
  enable_notifications: true

# Environment-specific configurations
environments:
  development:
    logging:
      level: "DEBUG"
    security:
      sandbox_mode: false
    features:
      enable_experimental_tools: true

  production:
    logging:
      level: "INFO"
    security:
      sandbox_mode: true
      enable_authentication: true
    execution:
      max_concurrent_jobs: 5