MCP Tool System

MCP Tool System

Overview

ADEPT uses the Model Context Protocol (MCP) as its standard for tool communication between the orchestration layer and execution servers. The platform provides 28+ built-in tools distributed across three specialized servers, with support for dynamic registration of external tools at runtime.

Built-in Tools

Tools are organized by domain across three stateless MCP servers:

Server	Domain	Tools
mcp_server	Scientific research	BLAST, UniProt, PubChem, AlphaFold, web search, file management, CSV/PDF RAG
sandbox_mcp_server	Code execution	Secure Python/R execution, calculations, plot generation
hpc_mcp_server	Training/demos	Nextflow workflow execution, video transcription, repository analysis (GitXray)
slurm_mcp_server	Production HPC	Slurm job submission via SSH/REST, workspace file ops, cluster monitoring

The first three servers are built-in to the core stack. The hpc_mcp_server was the original HPC integration designed for workshops and training demonstrations.

The Slurm HPC MCP server (examples/slurm_hpc/slurm_mcp_server/) is an external tool stack that registers with the ADEPT gateway at runtime. It provides 27 tools for submitting and managing batch jobs on production HPC clusters (Deception, Tahoma) via SSH, with session-scoped workspaces for input/output isolation. See Slurm HPC Integration for full documentation.

Each server exposes tools via the @mcp.tool() decorator pattern, making them automatically discoverable through the MCP JSON-RPC protocol.

Tool Discovery

ADEPT uses MCPToolDiscovery for runtime introspection of available tools:

# Runtime discovery via JSON-RPC tools/list
discovered_tools = await mcp_discovery.discover_all_tools()

The discovery system:

• Queries each MCP server's tools/list JSON-RPC endpoint
• Caches results with configurable TTL for performance
• Falls back gracefully when servers are unreachable
• Eliminates dual maintenance of tool configuration

Single Source of Truth: Tool definitions live exclusively in @mcp.tool() decorators on the MCP servers. No separate configuration files need to be maintained.

Dynamic Registration

External tools can be registered at runtime via the /admin/tools/* API endpoints:

# Register an external MCP tool
POST /v1/admin/tools/register
{
  "name": "custom_analysis",
  "type": "mcp",
  "endpoint": "https://tools.example.com/mcp",
  "description": "Custom domain analysis tool"
}

Tool configurations are persisted in Redis, surviving service restarts without requiring redeployment.

ACL-Based Access Control

Tool access is governed by user group membership from Keycloak JWT claims:

1. User authenticates and receives JWT with groups claim
2. Orchestration service extracts groups from the authenticated context
3. Tool manager filters available tools based on ACL rules
4. Only authorized tools are exposed to the agent for that session

# Example ACL configuration
tool: blast_search
allowed_groups: ["scientists", "admin"]

External Tools

ADEPT supports three protocols for external tool integration:

Protocol	Use Case	Communication
MCP	Structured tool servers	JSON-RPC over HTTP/SSE
HTTP	REST APIs and webhooks	Standard HTTP requests
stdio	Local CLI tools	stdin/stdout piping

External tools are combined with built-in tools and passed to worker agents during multi-agent session creation.

Session Isolation

Each MCP server enforces strict session-scoped resource isolation:

• File uploads: Stored in data/uploaded_files/{mcp_session_id}/
• Code execution: Session-scoped containers and filesystems
• RAG indexes: Session-isolated vector stores
• Temporary files: Cleaned up on session termination

Security Boundary: Session isolation prevents cross-user data leakage. Each tool invocation receives the session context and must scope all resources accordingly.

Multi-tier session identifiers (session_id, mcp_session_id, multi_agent_session_id) propagate through all tool calls to maintain proper isolation boundaries.