@cyanheads/pubmed-mcp-server 1.1.4 → 1.2.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +8 -10
- package/dist/mcp-server/server.d.ts +0 -7
- package/dist/mcp-server/server.js +17 -53
- package/dist/mcp-server/tools/fetchPubMedContent/logic.d.ts +6 -2
- package/dist/mcp-server/tools/fetchPubMedContent/logic.js +94 -202
- package/dist/mcp-server/tools/fetchPubMedContent/registration.js +43 -7
- package/dist/mcp-server/tools/generatePubMedChart/logic.d.ts +9 -28
- package/dist/mcp-server/tools/generatePubMedChart/logic.js +133 -192
- package/dist/mcp-server/tools/generatePubMedChart/registration.js +57 -13
- package/dist/mcp-server/tools/getPubMedArticleConnections/logic/citationFormatter.d.ts +1 -1
- package/dist/mcp-server/tools/getPubMedArticleConnections/logic/elinkHandler.d.ts +1 -1
- package/dist/mcp-server/tools/getPubMedArticleConnections/logic/index.d.ts +27 -4
- package/dist/mcp-server/tools/getPubMedArticleConnections/logic/index.js +50 -45
- package/dist/mcp-server/tools/getPubMedArticleConnections/logic/types.d.ts +1 -1
- package/dist/mcp-server/tools/getPubMedArticleConnections/registration.d.ts +0 -24
- package/dist/mcp-server/tools/getPubMedArticleConnections/registration.js +51 -45
- package/dist/mcp-server/tools/pubmedResearchAgent/logic.d.ts +2 -4
- package/dist/mcp-server/tools/pubmedResearchAgent/logic.js +7 -41
- package/dist/mcp-server/tools/pubmedResearchAgent/registration.js +49 -8
- package/dist/mcp-server/tools/searchPubMedArticles/logic.d.ts +12 -10
- package/dist/mcp-server/tools/searchPubMedArticles/logic.js +68 -126
- package/dist/mcp-server/tools/searchPubMedArticles/registration.js +46 -6
- package/dist/mcp-server/transports/httpTransport.d.ts +0 -8
- package/dist/mcp-server/transports/httpTransport.js +57 -354
- package/package.json +7 -15
- package/dist/mcp-server/resources/echoResource/echoResourceLogic.d.ts +0 -79
- package/dist/mcp-server/resources/echoResource/echoResourceLogic.js +0 -82
- package/dist/mcp-server/resources/echoResource/index.d.ts +0 -13
- package/dist/mcp-server/resources/echoResource/index.js +0 -13
- package/dist/mcp-server/resources/echoResource/registration.d.ts +0 -30
- package/dist/mcp-server/resources/echoResource/registration.js +0 -168
- package/dist/mcp-server/tools/getPubMedArticleConnections/logic.d.ts +0 -6
- package/dist/mcp-server/tools/getPubMedArticleConnections/logic.js +0 -6
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@@ -19,84 +19,17 @@ import http from "http";
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import { randomUUID } from "node:crypto";
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import { config } from "../../config/index.js";
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import { BaseErrorCode, McpError } from "../../types-global/errors.js";
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import { logger, rateLimiter, requestContextService, } from "../../utils/index.js";
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import { ErrorHandler, logger, rateLimiter, requestContextService, } from "../../utils/index.js";
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import { initializeAuthMiddleware, mcpAuthMiddleware, } from "./authentication/authMiddleware.js";
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import { oauthMiddleware } from "./authentication/oauthMiddleware.js";
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/**
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* The port number for the HTTP transport, configured via `MCP_HTTP_PORT` environment variable.
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* Defaults to 3010 if not specified (default is managed by the config module).
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* @constant {number} HTTP_PORT
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* @private
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*/
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const HTTP_PORT = config.mcpHttpPort;
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/**
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* The host address for the HTTP transport, configured via `MCP_HTTP_HOST` environment variable.
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* Defaults to '127.0.0.1' if not specified (default is managed by the config module).
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* MCP Spec Security Note: Recommends binding to localhost for local servers to minimize exposure.
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* @private
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*/
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const HTTP_HOST = config.mcpHttpHost;
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/**
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* The single HTTP endpoint path for all MCP communication, as required by the MCP specification.
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* This endpoint supports POST, GET, DELETE, and OPTIONS methods.
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* @constant {string} MCP_ENDPOINT_PATH
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* @private
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*/
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const MCP_ENDPOINT_PATH = "/mcp";
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/**
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* Maximum number of attempts to find an available port if the initial `HTTP_PORT` is in use.
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* The server will try ports sequentially: `HTTP_PORT`, `HTTP_PORT + 1`, ..., up to `MAX_PORT_RETRIES`.
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* @constant {number} MAX_PORT_RETRIES
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* @private
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*/
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const MAX_PORT_RETRIES = 15;
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* This is essential for routing subsequent HTTP requests (GET, DELETE, non-initialize POST)
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* to the correct stateful session transport instance.
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*
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* @scalability Note: This is an in-memory store. For horizontal scaling across
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* multiple processes or machines, this state would need to be moved to a shared,
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* distributed store like Redis or a database.
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*
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* @type {Record<string, StreamableHTTPServerTransport>}
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* @private
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*/
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const SESSION_TIMEOUT_MS = 30 * 60 * 1000;
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const SESSION_GC_INTERVAL_MS = 60 * 1000;
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const httpTransports = {};
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/**
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* Stores the last activity timestamp for each session, keyed by session ID.
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* Used for garbage collecting stale/abandoned sessions.
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*
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* @scalability Note: This is an in-memory store. Like `httpTransports`, this
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* would need to be moved to a distributed store for multi-instance deployments.
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*
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* @type {Record<string, number>}
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* @private
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*/
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const sessionActivity = {};
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/**
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* The timeout period in milliseconds for inactive sessions. If a session has no
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* activity for this duration, it will be considered stale and garbage collected.
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* Defaults to 30 minutes.
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* @constant {number} SESSION_TIMEOUT_MS
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* @private
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*/
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const SESSION_TIMEOUT_MS = 30 * 60 * 1000; // 30 minutes
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/**
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* The interval in milliseconds at which the session garbage collector runs to
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* clean up stale sessions. Defaults to 1 minute.
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* @constant {number} SESSION_GC_INTERVAL_MS
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* @private
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*/
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const SESSION_GC_INTERVAL_MS = 60 * 1000; // 1 minute
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/**
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* Proactively checks if a specific network port is already in use.
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* @param port - The port number to check.
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* @param host - The host address to check the port on.
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* @param parentContext - Logging context from the caller.
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* @returns A promise that resolves to `true` if the port is in use, or `false` otherwise.
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* @private
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*/
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async function isPortInUse(port, host, parentContext) {
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const checkContext = requestContextService.createRequestContext({
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...parentContext,
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@@ -104,133 +37,66 @@ async function isPortInUse(port, host, parentContext) {
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port,
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host,
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});
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logger.debug(`Proactively checking port usability...`, checkContext);
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return new Promise((resolve) => {
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const tempServer = http.createServer();
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tempServer
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.once("error", (err) => {
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logger.debug(`Proactive check: Port confirmed in use (EADDRINUSE).`, checkContext);
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resolve(true);
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}
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else {
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logger.debug(`Proactive check: Non-EADDRINUSE error encountered: ${err.message}`, { ...checkContext, errorCode: err.code });
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resolve(false);
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}
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resolve(err.code === "EADDRINUSE");
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})
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.once("listening", () => {
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logger.debug(`Proactive check: Port is available.`, checkContext);
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tempServer.close(() => resolve(false));
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})
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.listen(port, host);
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});
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}
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/**
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* Attempts to start the HTTP server, retrying on incrementing ports if `EADDRINUSE` occurs.
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*
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* @param app - The Hono application instance.
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* @param initialPort - The initial port number to try.
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* @param host - The host address to bind to.
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* @param maxRetries - Maximum number of additional ports to attempt.
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* @param parentContext - Logging context from the caller.
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* @returns A promise that resolves with the Node.js `http.Server` instance the server successfully bound to.
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* @throws {Error} If binding fails after all retries or for a non-EADDRINUSE error.
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* @private
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*/
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function startHttpServerWithRetry(app, initialPort, host, maxRetries, parentContext) {
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const startContext = requestContextService.createRequestContext({
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...parentContext,
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operation: "startHttpServerWithRetry",
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initialPort,
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host,
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maxRetries,
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});
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logger.debug(`Attempting to start HTTP server...`, startContext);
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return new Promise(async (resolve, reject) => {
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let lastError = null;
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for (let i = 0; i <= maxRetries; i++) {
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const currentPort = initialPort + i;
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const attemptContext =
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...startContext,
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port: currentPort,
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attempt: i + 1,
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maxAttempts: maxRetries + 1,
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});
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logger.debug(`Attempting port ${currentPort} (${attemptContext.attempt}/${attemptContext.maxAttempts})`, attemptContext);
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const attemptContext = { ...startContext, port: currentPort, attempt: i + 1 };
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if (await isPortInUse(currentPort, host, attemptContext)) {
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logger.warning(`
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lastError = new Error(`EADDRINUSE: Port ${currentPort} detected as in use by proactive check.`);
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await new Promise((res) => setTimeout(res, 100));
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logger.warning(`Port ${currentPort} is in use, retrying...`, attemptContext);
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continue;
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}
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try {
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const serverInstance = serve({ fetch: app.fetch, port: currentPort, hostname: host }, (info) => {
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const serverAddress = `http://${info.address}:${info.port}${MCP_ENDPOINT_PATH}`;
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logger.info(`HTTP transport
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// Display user-friendly startup message only after server is confirmed listening
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let serverAddressLog = serverAddress;
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let productionNote = "";
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if (config.environment === "production") {
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serverAddressLog = `https://${info.address}:${info.port}${MCP_ENDPOINT_PATH}`;
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productionNote = ` (via HTTPS, ensure reverse proxy is configured)`;
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}
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logger.info(`HTTP transport listening at ${serverAddress}`, { ...attemptContext, address: serverAddress });
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if (process.stdout.isTTY) {
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console.log(`\n🚀 MCP Server running
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console.log(`\n🚀 MCP Server running at: ${serverAddress}\n`);
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}
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});
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resolve(serverInstance);
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return;
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}
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catch (err) {
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logger.debug(`Listen error on port ${currentPort}: Code=${err.code}, Message=${err.message}`, { ...attemptContext, errorCode: err.code, errorMessage: err.message });
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if (err.code === "EADDRINUSE") {
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logger.warning(`Port ${currentPort} already in use (EADDRINUSE), retrying...`, attemptContext);
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await new Promise((res) => setTimeout(res, 100));
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}
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else {
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logger.error(`Failed to bind to port ${currentPort} due to non-EADDRINUSE error: ${err.message}`, { ...attemptContext, error: err.message });
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if (err.code !== "EADDRINUSE") {
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reject(err);
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return;
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}
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}
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}
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reject(lastError ||
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new Error("Failed to bind to any port after multiple retries."));
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reject(new Error("Failed to bind to any port after multiple retries."));
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});
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}
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/**
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* Sets up and starts the Streamable HTTP transport layer for the MCP server.
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*
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* @param createServerInstanceFn - An asynchronous factory function that returns a new `McpServer` instance.
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* @param parentContext - Logging context from the main server startup process.
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* @returns A promise that resolves with the Node.js `http.Server` instance when the HTTP server is successfully listening.
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* @throws {Error} If the server fails to start after all port retries.
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*/
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export async function startHttpTransport(createServerInstanceFn, parentContext) {
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initializeAuthMiddleware();
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initializeAuthMiddleware();
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const app = new Hono();
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const transportContext = requestContextService.createRequestContext({
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...parentContext,
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transportType: "HTTP",
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component: "HttpTransportSetup",
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});
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logger.debug("Setting up Hono app for HTTP transport...", transportContext);
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// Start the session garbage collector
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setInterval(() => {
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const now = Date.now();
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const gcContext = requestContextService.createRequestContext({
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operation: "SessionGarbageCollector",
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});
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logger.debug("Running session garbage collector...", gcContext);
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const gcContext = requestContextService.createRequestContext({ operation: "SessionGarbageCollector" });
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for (const sessionId in sessionActivity) {
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if (now - sessionActivity[sessionId] > SESSION_TIMEOUT_MS) {
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logger.info(`Session ${sessionId} timed out
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if (transport) {
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transport.close(); // This will trigger the onclose handler to delete it from httpTransports
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}
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logger.info(`Session ${sessionId} timed out. Cleaning up.`, { ...gcContext, sessionId });
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}
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}
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app.use("*", cors({
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origin: config.mcpAllowedOrigins || [],
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allowMethods: ["GET", "POST", "DELETE", "OPTIONS"],
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allowHeaders: [
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"Authorization",
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allowHeaders: ["Content-Type", "Mcp-Session-Id", "Last-Event-ID", "Authorization"],
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credentials: true,
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}));
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app.use("*", async (c, next) => {
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const securityContext = requestContextService.createRequestContext({
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...transportContext,
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operation: "securityMiddleware",
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path: c.req.path,
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method: c.req.method,
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origin: c.req.header("origin"),
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});
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logger.debug(`Applying security middleware...`, securityContext);
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c.res.headers.set("X-Content-Type-Options", "nosniff");
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c.res.headers.set("Referrer-Policy", "strict-origin-when-cross-origin");
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c.res.headers.set("Content-Security-Policy", "default-src 'self'; script-src 'self'; object-src 'none'; style-src 'self'; img-src 'self'; media-src 'self'; frame-src 'none'; font-src 'self'; connect-src 'self'");
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logger.debug("Security middleware passed.", securityContext);
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await next();
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});
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app.use(MCP_ENDPOINT_PATH, async (c, next) => {
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const
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const
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const rateLimitKey = clientIp || c.req.header("host") || "unknown_ip_for_rate_limit";
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const context = requestContextService.createRequestContext({
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operation: "httpRateLimitCheck",
|
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ipAddress: rateLimitKey,
|
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method: c.req.method,
|
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|
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});
|
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const clientIp = c.req.header("x-forwarded-for")?.split(",")[0].trim() || "unknown_ip";
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|
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|
try {
|
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rateLimiter.check(
|
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logger.debug("Rate limit check passed.", context);
|
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rateLimiter.check(clientIp, context);
|
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|
await next();
|
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|
}
|
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catch (error) {
|
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});
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error: { code: -32000, message: "Too Many Requests" },
|
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id: (await c.req.json().catch(() => ({})))?.id || null,
|
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|
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}, 429);
|
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}
|
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|
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|
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|
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|
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error: error instanceof Error ? error.message : String(error),
|
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|
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|
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|
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}
|
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const handledError = ErrorHandler.handleError(error, { operation: "rateLimitMiddleware", context });
|
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return c.json({
|
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|
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error: { code: -32000, message: handledError.message },
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id: (await c.req.json().catch(() => ({})))?.id || null,
|
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}, 429);
|
|
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}
|
|
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|
});
|
|
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|
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// Use the appropriate authentication middleware based on config
|
|
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130
|
if (config.mcpAuthMode === "oauth") {
|
|
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|
app.use(MCP_ENDPOINT_PATH, oauthMiddleware);
|
|
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132
|
}
|
|
@@ -307,200 +134,76 @@ export async function startHttpTransport(createServerInstanceFn, parentContext)
|
|
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134
|
app.use(MCP_ENDPOINT_PATH, mcpAuthMiddleware);
|
|
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|
}
|
|
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|
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|
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const
|
|
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|
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|
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|
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operation: "handlePost",
|
|
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method: "POST",
|
|
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path: c.req.path,
|
|
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|
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origin: c.req.header("origin"),
|
|
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|
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});
|
|
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|
-
const body = await c.req.json();
|
|
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|
-
logger.debug(`Received POST request on ${MCP_ENDPOINT_PATH}`, {
|
|
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|
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...basePostContext,
|
|
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|
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headers: c.req.header(),
|
|
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|
-
bodyPreview: JSON.stringify(body).substring(0, 100),
|
|
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|
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});
|
|
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|
-
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|
|
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|
-
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|
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|
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...basePostContext,
|
|
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|
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sessionId,
|
|
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|
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});
|
|
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|
-
let transport = sessionId ? httpTransports[sessionId] : undefined;
|
|
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|
-
if (transport && sessionId) {
|
|
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|
-
sessionActivity[sessionId] = Date.now(); // Update activity timestamp
|
|
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|
-
}
|
|
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|
-
logger.debug(`Found existing transport for session ID: ${!!transport}`, {
|
|
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|
-
...basePostContext,
|
|
334
|
-
sessionId,
|
|
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|
-
});
|
|
336
|
-
const isInitReq = isInitializeRequest(body);
|
|
337
|
-
logger.debug(`Is InitializeRequest: ${isInitReq}`, {
|
|
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|
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|
|
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|
-
sessionId,
|
|
340
|
-
});
|
|
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|
-
const requestId = body?.id || null;
|
|
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|
+
const postContext = requestContextService.createRequestContext({ ...transportContext, operation: "handlePost" });
|
|
138
|
+
let transport;
|
|
342
139
|
try {
|
|
343
|
-
|
|
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|
+
const body = await c.req.json();
|
|
141
|
+
const sessionId = c.req.header("mcp-session-id");
|
|
142
|
+
transport = sessionId ? httpTransports[sessionId] : undefined;
|
|
143
|
+
if (transport && sessionId)
|
|
144
|
+
sessionActivity[sessionId] = Date.now();
|
|
145
|
+
if (isInitializeRequest(body)) {
|
|
344
146
|
if (transport) {
|
|
345
|
-
logger.warning("
|
|
147
|
+
logger.warning("Re-initializing existing session.", { ...postContext, sessionId });
|
|
346
148
|
await transport.close();
|
|
347
|
-
// onclose handler will delete from httpTransports and sessionActivity
|
|
348
149
|
}
|
|
349
|
-
logger.info("Handling Initialize Request: Creating new session...", {
|
|
350
|
-
...basePostContext,
|
|
351
|
-
sessionId,
|
|
352
|
-
});
|
|
353
150
|
transport = new StreamableHTTPServerTransport({
|
|
354
|
-
sessionIdGenerator: () =>
|
|
355
|
-
const newId = randomUUID();
|
|
356
|
-
logger.debug(`Generated new session ID: ${newId}`, basePostContext);
|
|
357
|
-
return newId;
|
|
358
|
-
},
|
|
151
|
+
sessionIdGenerator: () => randomUUID(),
|
|
359
152
|
onsessioninitialized: (newId) => {
|
|
360
|
-
logger.debug(`Session initialized callback triggered for ID: ${newId}`, { ...basePostContext, newSessionId: newId });
|
|
361
153
|
httpTransports[newId] = transport;
|
|
362
|
-
sessionActivity[newId] = Date.now();
|
|
363
|
-
logger.info(`HTTP Session created: ${newId}`, {
|
|
364
|
-
...basePostContext,
|
|
365
|
-
newSessionId: newId,
|
|
366
|
-
});
|
|
154
|
+
sessionActivity[newId] = Date.now();
|
|
155
|
+
logger.info(`HTTP Session created: ${newId}`, { ...postContext, newSessionId: newId });
|
|
367
156
|
},
|
|
368
157
|
});
|
|
369
158
|
transport.onclose = () => {
|
|
370
159
|
const closedSessionId = transport.sessionId;
|
|
371
160
|
if (closedSessionId) {
|
|
372
|
-
logger.debug(`onclose handler triggered for session ID: ${closedSessionId}`, { ...basePostContext, closedSessionId });
|
|
373
161
|
delete httpTransports[closedSessionId];
|
|
374
|
-
delete sessionActivity[closedSessionId];
|
|
375
|
-
logger.info(`HTTP Session closed: ${closedSessionId}`, {
|
|
376
|
-
...basePostContext,
|
|
377
|
-
closedSessionId,
|
|
378
|
-
});
|
|
379
|
-
}
|
|
380
|
-
else {
|
|
381
|
-
logger.debug("onclose handler triggered for transport without session ID (likely init failure).", basePostContext);
|
|
162
|
+
delete sessionActivity[closedSessionId];
|
|
163
|
+
logger.info(`HTTP Session closed: ${closedSessionId}`, { ...postContext, closedSessionId });
|
|
382
164
|
}
|
|
383
165
|
};
|
|
384
|
-
logger.debug("Creating McpServer instance for new session...", basePostContext);
|
|
385
166
|
const server = await createServerInstanceFn();
|
|
386
|
-
logger.debug("Connecting McpServer to new transport...", basePostContext);
|
|
387
167
|
await server.connect(transport);
|
|
388
|
-
logger.debug("McpServer connected to transport.", basePostContext);
|
|
389
168
|
}
|
|
390
169
|
else if (!transport) {
|
|
391
|
-
|
|
392
|
-
return c.json({
|
|
393
|
-
jsonrpc: "2.0",
|
|
394
|
-
error: { code: -32004, message: "Invalid or expired session ID" },
|
|
395
|
-
id: requestId,
|
|
396
|
-
}, 404);
|
|
170
|
+
throw new McpError(BaseErrorCode.NOT_FOUND, "Invalid or expired session ID.");
|
|
397
171
|
}
|
|
398
|
-
|
|
399
|
-
logger.debug(`Processing POST request content for session ${currentSessionId}...`, { ...basePostContext, sessionId: currentSessionId, isInitReq });
|
|
400
|
-
const response = await transport.handleRequest(c.env.incoming, c.env.outgoing, body);
|
|
401
|
-
logger.debug(`Finished processing POST request content for session ${currentSessionId}.`, { ...basePostContext, sessionId: currentSessionId });
|
|
402
|
-
return response;
|
|
172
|
+
return await transport.handleRequest(c.env.incoming, c.env.outgoing, body);
|
|
403
173
|
}
|
|
404
174
|
catch (err) {
|
|
405
|
-
const
|
|
406
|
-
|
|
407
|
-
...basePostContext,
|
|
408
|
-
sessionId: errorSessionId,
|
|
409
|
-
isInitReq,
|
|
410
|
-
error: err instanceof Error ? err.message : String(err),
|
|
411
|
-
stack: err instanceof Error ? err.stack : undefined,
|
|
412
|
-
});
|
|
413
|
-
if (isInitReq && transport && !transport.sessionId) {
|
|
414
|
-
logger.debug("Cleaning up transport after initialization failure.", {
|
|
415
|
-
...basePostContext,
|
|
416
|
-
sessionId: errorSessionId,
|
|
417
|
-
});
|
|
418
|
-
await transport.close().catch((closeErr) => logger.error("Error closing transport after init failure", {
|
|
419
|
-
...basePostContext,
|
|
420
|
-
sessionId: errorSessionId,
|
|
421
|
-
closeError: closeErr,
|
|
422
|
-
}));
|
|
423
|
-
}
|
|
175
|
+
const handledError = ErrorHandler.handleError(err, { operation: "handlePost", context: postContext });
|
|
176
|
+
const requestId = (await c.req.json().catch(() => ({})))?.id || null;
|
|
424
177
|
return c.json({
|
|
425
178
|
jsonrpc: "2.0",
|
|
426
|
-
error: {
|
|
427
|
-
code: -32603,
|
|
428
|
-
message: "Internal server error during POST handling",
|
|
429
|
-
},
|
|
179
|
+
error: { code: -32603, message: handledError.message },
|
|
430
180
|
id: requestId,
|
|
431
|
-
}, 500);
|
|
181
|
+
}, handledError instanceof McpError && handledError.code === BaseErrorCode.NOT_FOUND ? 404 : 500);
|
|
432
182
|
}
|
|
433
183
|
});
|
|
434
184
|
const handleSessionReq = async (c) => {
|
|
435
185
|
const method = c.req.method;
|
|
436
|
-
const
|
|
437
|
-
...transportContext,
|
|
438
|
-
operation: `handle${method}`,
|
|
439
|
-
method,
|
|
440
|
-
path: c.req.path,
|
|
441
|
-
origin: c.req.header("origin"),
|
|
442
|
-
});
|
|
443
|
-
logger.debug(`Received ${method} request on ${MCP_ENDPOINT_PATH}`, {
|
|
444
|
-
...baseSessionReqContext,
|
|
445
|
-
headers: c.req.header(),
|
|
446
|
-
});
|
|
447
|
-
const sessionId = c.req.header("mcp-session-id");
|
|
448
|
-
logger.debug(`Extracted session ID: ${sessionId}`, {
|
|
449
|
-
...baseSessionReqContext,
|
|
450
|
-
sessionId,
|
|
451
|
-
});
|
|
452
|
-
const transport = sessionId ? httpTransports[sessionId] : undefined;
|
|
453
|
-
if (transport && sessionId) {
|
|
454
|
-
sessionActivity[sessionId] = Date.now(); // Update activity timestamp
|
|
455
|
-
}
|
|
456
|
-
logger.debug(`Found existing transport for session ID: ${!!transport}`, {
|
|
457
|
-
...baseSessionReqContext,
|
|
458
|
-
sessionId,
|
|
459
|
-
});
|
|
460
|
-
if (!transport) {
|
|
461
|
-
logger.warning(`Session not found for ${method} request`, {
|
|
462
|
-
...baseSessionReqContext,
|
|
463
|
-
sessionId,
|
|
464
|
-
});
|
|
465
|
-
return c.json({
|
|
466
|
-
jsonrpc: "2.0",
|
|
467
|
-
error: { code: -32004, message: "Session not found or expired" },
|
|
468
|
-
id: null,
|
|
469
|
-
}, 404);
|
|
470
|
-
}
|
|
186
|
+
const sessionReqContext = requestContextService.createRequestContext({ ...transportContext, operation: `handle${method}` });
|
|
471
187
|
try {
|
|
472
|
-
|
|
473
|
-
const
|
|
474
|
-
|
|
475
|
-
|
|
188
|
+
const sessionId = c.req.header("mcp-session-id");
|
|
189
|
+
const transport = sessionId ? httpTransports[sessionId] : undefined;
|
|
190
|
+
if (!transport) {
|
|
191
|
+
throw new McpError(BaseErrorCode.NOT_FOUND, "Session not found or expired.");
|
|
192
|
+
}
|
|
193
|
+
if (sessionId)
|
|
194
|
+
sessionActivity[sessionId] = Date.now();
|
|
195
|
+
return await transport.handleRequest(c.env.incoming, c.env.outgoing);
|
|
476
196
|
}
|
|
477
197
|
catch (err) {
|
|
478
|
-
|
|
479
|
-
...baseSessionReqContext,
|
|
480
|
-
sessionId,
|
|
481
|
-
error: err instanceof Error ? err.message : String(err),
|
|
482
|
-
stack: err instanceof Error ? err.stack : undefined,
|
|
483
|
-
});
|
|
198
|
+
const handledError = ErrorHandler.handleError(err, { operation: `handle${method}`, context: sessionReqContext });
|
|
484
199
|
return c.json({
|
|
485
200
|
jsonrpc: "2.0",
|
|
486
|
-
error: { code: -32603, message:
|
|
201
|
+
error: { code: -32603, message: handledError.message },
|
|
487
202
|
id: null,
|
|
488
|
-
}, 500);
|
|
203
|
+
}, handledError instanceof McpError && handledError.code === BaseErrorCode.NOT_FOUND ? 404 : 500);
|
|
489
204
|
}
|
|
490
205
|
};
|
|
491
206
|
app.get(MCP_ENDPOINT_PATH, handleSessionReq);
|
|
492
207
|
app.delete(MCP_ENDPOINT_PATH, handleSessionReq);
|
|
493
|
-
|
|
494
|
-
try {
|
|
495
|
-
logger.debug("Attempting to start HTTP server with retry logic...", transportContext);
|
|
496
|
-
const serverInstance = await startHttpServerWithRetry(app, config.mcpHttpPort, config.mcpHttpHost, MAX_PORT_RETRIES, transportContext);
|
|
497
|
-
return serverInstance;
|
|
498
|
-
}
|
|
499
|
-
catch (err) {
|
|
500
|
-
logger.fatal("HTTP server failed to start after multiple port retries.", {
|
|
501
|
-
...transportContext,
|
|
502
|
-
error: err instanceof Error ? err.message : String(err),
|
|
503
|
-
});
|
|
504
|
-
throw err;
|
|
505
|
-
}
|
|
208
|
+
return startHttpServerWithRetry(app, HTTP_PORT, HTTP_HOST, MAX_PORT_RETRIES, transportContext);
|
|
506
209
|
}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "1.1
|
|
3
|
+
"version": "1.2.1",
|
|
4
4
|
"description": "A Model Context Protocol (MCP) server enabling AI agents to intelligently search, retrieve, and analyze biomedical literature from PubMed via NCBI E-utilities. Built on the mcp-ts-template for robust, production-ready performance.",
|
|
5
5
|
"main": "dist/index.js",
|
|
6
6
|
"files": [
|
|
@@ -33,22 +33,16 @@
|
|
|
33
33
|
},
|
|
34
34
|
"dependencies": {
|
|
35
35
|
"@hono/node-server": "^1.14.4",
|
|
36
|
-
"@modelcontextprotocol/sdk": "^1.12.
|
|
37
|
-
"@node-oauth/oauth2-server": "^5.2.0",
|
|
36
|
+
"@modelcontextprotocol/sdk": "^1.12.3",
|
|
38
37
|
"@types/jsonwebtoken": "^9.0.9",
|
|
39
38
|
"@types/node": "^24.0.1",
|
|
40
39
|
"@types/sanitize-html": "^2.16.0",
|
|
41
40
|
"@types/validator": "13.15.1",
|
|
42
|
-
"axios": "^1.
|
|
43
|
-
"
|
|
44
|
-
"chalk": "^5.4.1",
|
|
45
|
-
"chrono-node": "^2.8.2",
|
|
46
|
-
"cli-table3": "^0.6.5",
|
|
41
|
+
"axios": "^1.10.0",
|
|
42
|
+
"chrono-node": "^2.8.3",
|
|
47
43
|
"dotenv": "^16.5.0",
|
|
48
|
-
"express": "^5.1.0",
|
|
49
44
|
"fast-xml-parser": "^5.2.5",
|
|
50
45
|
"hono": "^4.7.11",
|
|
51
|
-
"ignore": "^7.0.5",
|
|
52
46
|
"jose": "^6.0.11",
|
|
53
47
|
"jsonwebtoken": "^9.0.2",
|
|
54
48
|
"openai": "^5.3.0",
|
|
@@ -58,11 +52,10 @@
|
|
|
58
52
|
"ts-node": "^10.9.2",
|
|
59
53
|
"typescript": "^5.8.3",
|
|
60
54
|
"validator": "13.15.15",
|
|
61
|
-
"
|
|
62
|
-
"
|
|
55
|
+
"chart.js": "^4.5.0",
|
|
56
|
+
"chartjs-node-canvas": "^5.0.0",
|
|
63
57
|
"winston": "^3.17.0",
|
|
64
|
-
"winston-
|
|
65
|
-
"yargs": "^18.0.0",
|
|
58
|
+
"winston-transport": "^4.9.0",
|
|
66
59
|
"zod": "^3.25.64"
|
|
67
60
|
},
|
|
68
61
|
"keywords": [
|
|
@@ -103,7 +96,6 @@
|
|
|
103
96
|
"node": ">=16.0.0"
|
|
104
97
|
},
|
|
105
98
|
"devDependencies": {
|
|
106
|
-
"@types/express": "^5.0.3",
|
|
107
99
|
"@types/js-yaml": "^4.0.9",
|
|
108
100
|
"js-yaml": "^4.1.0",
|
|
109
101
|
"prettier": "^3.5.3",
|