MCP Server Security

# /etc/nginx/sites-enabled/mcp-server.conf
server {
    listen 443 ssl http2;
    server_name mcp.internal.example.com;

    ssl_certificate     /etc/ssl/certs/mcp-server.crt;
    ssl_certificate_key /etc/ssl/private/mcp-server.key;
    ssl_protocols       TLSv1.3;
    ssl_ciphers         TLS_AES_256_GCM_SHA384:TLS_CHACHA20_POLY1305_SHA256;
    ssl_prefer_server_ciphers on;
    ssl_session_timeout 1d;
    ssl_session_tickets off;

    # HSTS header
    add_header Strict-Transport-Security "max-age=63072000; includeSubDomains" always;

    location / {
        proxy_pass http://127.0.0.1:3001;
        proxy_http_version 1.1;
        proxy_set_header Upgrade $http_upgrade;
        proxy_set_header Connection "upgrade";
        proxy_set_header Host $host;
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-Proto $scheme;

        # SSE-specific: disable buffering so events stream immediately
        proxy_buffering off;
        proxy_cache off;
        proxy_read_timeout 86400s;
    }
}

# Add to the server block above
ssl_client_certificate /etc/ssl/certs/agent-ca.crt;
ssl_verify_client on;
ssl_verify_depth 2;

# Create CA (one-time)
openssl req -x509 -newkey ec -pkeyopt ec_paramgen_curve:P-256 \
  -days 365 -noenc -keyout ca-key.pem -out ca-cert.pem \
  -subj "/CN=MCP Agent CA"

# Create agent client cert signed by the CA
openssl req -newkey ec -pkeyopt ec_paramgen_curve:P-256 \
  -noenc -keyout agent-key.pem -out agent-csr.pem \
  -subj "/CN=agent-orchestrator-01"

openssl x509 -req -in agent-csr.pem -CA ca-cert.pem -CAkey ca-key.pem \
  -CAcreateserial -out agent-cert.pem -days 90

// claude_desktop_config.json - restrict stdio server permissions
{
  "mcpServers": {
    "filesystem": {
      "command": "npx",
      "args": ["-y", "@modelcontextprotocol/server-filesystem", "/home/user/safe-dir"],
      "env": {
        "NODE_OPTIONS": "--experimental-permission --allow-fs-read=/home/user/safe-dir --allow-fs-write=/home/user/safe-dir"
      }
    }
  }
}

// src/auth.ts - OAuth 2.1 token validation middleware for an MCP server
import { createServer } from "@modelcontextprotocol/sdk/server/index.js";
import { StreamableHTTPServerTransport } from "@modelcontextprotocol/sdk/server/streamableHttp.js";
import express from "express";
import jwt from "jsonwebtoken";

const app = express();

// OAuth 2.1 token validation middleware
function validateBearerToken(req: express.Request, res: express.Response, next: express.NextFunction) {
  const authHeader = req.headers.authorization;
  if (!authHeader?.startsWith("Bearer ")) {
    return res.status(401).json({ error: "missing_token" });
  }

  const token = authHeader.slice(7);
  try {
    const payload = jwt.verify(token, process.env.OAUTH_PUBLIC_KEY!, {
      algorithms: ["RS256"],
      issuer: "https://auth.example.com",
      audience: "mcp-server",
    });
    // Attach scopes for downstream authorization
    (req as any).tokenScopes = (payload as any).scope?.split(" ") || [];
    (req as any).userId = (payload as any).sub;
    next();
  } catch {
    return res.status(403).json({ error: "invalid_token" });
  }
}

app.use("/mcp", validateBearerToken);

// src/apikeys.ts
import { createHash, timingSafeEqual } from "crypto";

interface ApiKeyRecord {
  hashedKey: string;
  userId: string;
  allowedTools: string[];
  rateLimit: number;        // requests per minute
  expiresAt: Date;
}

// Store hashed keys, never plaintext
const apiKeyStore: Map<string, ApiKeyRecord> = new Map();

export function registerApiKey(plainKey: string, record: Omit<ApiKeyRecord, "hashedKey">) {
  const hashed = createHash("sha256").update(plainKey).digest("hex");
  apiKeyStore.set(hashed, { ...record, hashedKey: hashed });
}

export function validateApiKey(plainKey: string): ApiKeyRecord | null {
  const hashed = createHash("sha256").update(plainKey).digest("hex");
  const record = apiKeyStore.get(hashed);
  if (!record) return null;
  if (new Date() > record.expiresAt) {
    apiKeyStore.delete(hashed);
    return null;
  }
  return record;
}