@cyanheads/pubmed-mcp-server 1.3.5 → 1.4.3

package/dist/mcp-server/transports/core/statelessTransportManager.js

@@ -1,9 +1,16 @@
 /**
- * @fileoverview Stateless Transport Manager implementation for MCP SDK.
- * This manager handles single-request operations without maintaining sessions.
- * Each request creates a temporary server instance that is cleaned up immediately.
- * This version is adapted for Hono by bridging the SDK's Node.js-style
- * request handling with Hono's stream-based response model.
+ * @fileoverview Implements a stateless transport manager for the MCP SDK.
+ *
+ * This manager handles single, ephemeral MCP operations. For each incoming request,
+ * it dynamically creates a temporary McpServer and transport instance, processes the
+ * request, and then immediately schedules the resources for cleanup. This approach
+ * is ideal for simple, one-off tool calls that do not require persistent session state.
+ *
+ * The key challenge addressed here is bridging the Node.js-centric MCP SDK with
+ * modern, Web Standards-based frameworks like Hono. This is achieved by deferring
+ * resource cleanup until the response stream has been fully consumed by the web
+ * framework, preventing premature closure and truncated responses.
+ *
  * @module src/mcp-server/transports/core/statelessTransportManager
  */
 import { StreamableHTTPServerTransport } from "@modelcontextprotocol/sdk/server/streamableHttp.js";
@@ -11,10 +18,23 @@ import { Readable } from "stream";
 import { ErrorHandler, logger, requestContextService, } from "../../../utils/index.js";
 import { BaseTransportManager } from "./baseTransportManager.js";
 import { HonoStreamResponse } from "./honoNodeBridge.js";
+import { convertNodeHeadersToWebHeaders } from "./headerUtils.js";
 /**
- * Stateless Transport Manager that handles ephemeral MCP operations.
+ * Manages ephemeral, single-request MCP operations.
  */
 export class StatelessTransportManager extends BaseTransportManager {
+    /**
+     * Handles a single, stateless MCP request.
+     *
+     * This method orchestrates the creation of temporary server and transport instances,
+     * handles the request, and ensures resources are cleaned up only after the
+     * response stream is closed.
+     *
+     * @param headers - The incoming request headers.
+     * @param body - The parsed body of the request.
+     * @param context - The request context for logging and tracing.
+     * @returns A promise resolving to a streaming TransportResponse.
+     */
     async handleRequest(headers, body, context) {
         const opContext = {
             ...context,
@@ -24,6 +44,7 @@ export class StatelessTransportManager extends BaseTransportManager {
         let server;
         let transport;
         try {
+            // 1. Create ephemeral instances for this request.
             server = await this.createServerInstanceFn();
             transport = new StreamableHTTPServerTransport({
                 sessionIdGenerator: undefined,
@@ -31,45 +52,73 @@ export class StatelessTransportManager extends BaseTransportManager {
             });
             await server.connect(transport);
             logger.debug("Ephemeral server connected to transport.", opContext);
+            // 2. Set up the Node.js-to-Web stream bridge.
             const mockReq = {
                 headers,
                 method: "POST",
             };
-            const mockRes = new HonoStreamResponse();
+            const mockResBridge = new HonoStreamResponse();
+            // 3. Defer cleanup until the stream is fully processed.
+            // This is the critical fix to prevent premature resource release.
+            this.setupDeferredCleanup(mockResBridge, server, transport, opContext);
+            // 4. Process the request using the MCP transport.
+            const mockRes = mockResBridge;
             await transport.handleRequest(mockReq, mockRes, body);
             logger.info("Stateless request handled successfully.", opContext);
-            const responseHeaders = new Headers();
-            for (const [key, value] of Object.entries(mockRes.getHeaders())) {
-                responseHeaders.set(key, Array.isArray(value) ? value.join(", ") : String(value));
-            }
-            // Bridge the Node.js stream (PassThrough) to a Web Stream (ReadableStream)
-            const webStream = Readable.toWeb(mockRes);
+            // 5. Convert headers and create the final streaming response.
+            const responseHeaders = convertNodeHeadersToWebHeaders(mockRes.getHeaders());
+            const webStream = Readable.toWeb(mockResBridge);
             return {
+                type: "stream",
                 headers: responseHeaders,
                 statusCode: mockRes.statusCode,
                 stream: webStream,
             };
         }
         catch (error) {
+            // If an error occurs before the stream is returned, we must clean up immediately.
+            if (server || transport) {
+                this.cleanup(server, transport, opContext);
+            }
             throw ErrorHandler.handleError(error, {
                 operation: "StatelessTransportManager.handleRequest",
                 context: opContext,
                 rethrow: true,
             });
         }
-        finally {
-            if (server || transport) {
-                this.cleanup(server, transport, opContext);
-            }
-        }
     }
-    async shutdown() {
-        const context = requestContextService.createRequestContext({
-            operation: "StatelessTransportManager.shutdown",
-        });
-        logger.info("Stateless transport manager shutdown - no persistent resources to clean up.", context);
-        return Promise.resolve();
+    /**
+     * Attaches listeners to the response stream to trigger resource cleanup
+     * only after the stream has been fully consumed or has errored.
+     *
+     * @param stream - The response stream bridge.
+     * @param server - The ephemeral McpServer instance.
+     * @param transport - The ephemeral transport instance.
+     * @param context - The request context for logging.
+     */
+    setupDeferredCleanup(stream, server, transport, context) {
+        let cleanedUp = false;
+        const cleanupFn = (error) => {
+            if (cleanedUp)
+                return;
+            cleanedUp = true;
+            if (error) {
+                logger.warning("Stream ended with an error, proceeding to cleanup.", {
+                    ...context,
+                    error: error.message,
+                });
+            }
+            // Cleanup is fire-and-forget.
+            this.cleanup(server, transport, context);
+        };
+        // 'close' is the most reliable event, firing on both normal completion and abrupt termination.
+        stream.on("close", () => cleanupFn());
+        stream.on("error", (err) => cleanupFn(err));
     }
+    /**
+     * Performs the actual cleanup of ephemeral resources.
+     * This method is designed to be "fire-and-forget".
+     */
     cleanup(server, transport, context) {
         const opContext = {
             ...context,
@@ -89,5 +138,16 @@ export class StatelessTransportManager extends BaseTransportManager {
             });
         });
     }
+    /**
+     * Shuts down the manager. For the stateless manager, this is a no-op
+     * as there are no persistent resources to manage.
+     */
+    async shutdown() {
+        const context = requestContextService.createRequestContext({
+            operation: "StatelessTransportManager.shutdown",
+        });
+        logger.info("Stateless transport manager shutdown - no persistent resources to clean up.", context);
+        return Promise.resolve();
+    }
 }
 //# sourceMappingURL=statelessTransportManager.js.map

package/dist/mcp-server/transports/core/statelessTransportManager.js.map

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package/dist/mcp-server/transports/core/transportTypes.d.ts

@@ -1,69 +1,106 @@
 /**
- * @fileoverview Core types and interfaces for the transport layer abstraction.
+ * @fileoverview Defines the core types and interfaces for the transport layer abstraction.
+ * This module establishes the data contracts and abstract interfaces that decouple
+ * the MCP server's core logic from specific transport implementations like HTTP or stdio.
  * @module src/mcp-server/transports/core/transportTypes
  */
 import type { IncomingHttpHeaders } from "http";
 import { RequestContext } from "../../../utils/index.js";
 /**
- * Valid HTTP status codes for transport responses.
+ * Defines the set of valid HTTP status codes that the transport layer can return.
+ * This ensures type safety and consistency in response handling.
  */
 export type HttpStatusCode = 200 | 201 | 400 | 401 | 403 | 404 | 409 | 429 | 500 | 502 | 503;
 /**
- * Represents the result of a transport operation.
+ * A base interface for all transport responses, containing common properties.
  */
-export interface TransportResponse {
+interface BaseTransportResponse {
     sessionId?: string;
     headers: Headers;
     statusCode: HttpStatusCode;
-    body?: unknown;
-    stream?: ReadableStream<Uint8Array>;
 }
 /**
- * Represents an active transport session.
+ * Represents a transport response where the entire body is buffered in memory.
+ * Suitable for small, non-streamed responses.
+ */
+export interface BufferedTransportResponse extends BaseTransportResponse {
+    type: "buffered";
+    body: unknown;
+}
+/**
+ * Represents a transport response that streams its body.
+ * Essential for handling large or chunked responses efficiently without high memory usage.
+ */
+export interface StreamingTransportResponse extends BaseTransportResponse {
+    type: "stream";
+    stream: ReadableStream<Uint8Array>;
+}
+/**
+ * A discriminated union representing the possible types of a transport response.
+ * Using a discriminated union on the `type` property allows for type-safe handling
+ * of different response formats (buffered vs. streamed).
+ */
+export type TransportResponse = BufferedTransportResponse | StreamingTransportResponse;
+/**
+ * Represents the state of an active, persistent transport session.
  */
 export interface TransportSession {
     id: string;
     createdAt: Date;
     lastAccessedAt: Date;
+    /**
+     * A counter for requests currently being processed for this session.
+     * This is a critical mechanism to prevent race conditions where a session
+     * might be garbage-collected while a long-running request is still in flight.
+     * It is incremented when a request begins and decremented when it finishes.
+     */
+    activeRequests: number;
 }
 /**
- * Abstract interface for managing MCP transport operations.
- * This interface separates transport logic from HTTP routing concerns.
+ * Defines the abstract interface for a transport manager.
+ * This contract ensures that any transport manager, regardless of its statefulness,
+ * provides a consistent way to handle requests and manage its lifecycle.
  */
 export interface TransportManager {
     /**
      * Handles an incoming request.
-     * @param headers The request headers.
+     * @param headers The incoming request headers.
      * @param body The parsed body of the request.
-     * @param context Request context for logging and tracing.
-     * @param sessionId Optional session identifier for stateful operations.
-     * @returns A promise resolving to a TransportResponse.
+     * @param context The request context for logging, tracing, and metadata.
+     * @param sessionId An optional session identifier for stateful operations.
+     * @returns A promise that resolves to a TransportResponse object.
      */
     handleRequest(headers: IncomingHttpHeaders, body: unknown, context: RequestContext, sessionId?: string): Promise<TransportResponse>;
     /**
-     * Clean up resources.
+     * Gracefully shuts down the transport manager, cleaning up any resources.
      */
     shutdown(): Promise<void>;
 }
 /**
- * Extends the base TransportManager with session-specific operations.
+ * Extends the base TransportManager with operations specific to stateful sessions.
  */
 export interface StatefulTransportManager extends TransportManager {
     /**
-     * Initializes a new session and handles the request.
-     * @param headers The request headers.
+     * Initializes a new stateful session and handles the first request.
+     * @param headers The incoming request headers.
      * @param body The parsed body of the request.
-     * @param context Request context for logging and tracing.
-     * @returns A promise resolving to a TransportResponse.
+     * @param context The request context.
+     * @returns A promise resolving to a TransportResponse, which will include a session ID.
      */
     initializeAndHandle(headers: IncomingHttpHeaders, body: unknown, context: RequestContext): Promise<TransportResponse>;
     /**
-     * Handles a DELETE request to close a session.
+     * Handles a request to explicitly delete a session.
+     * @param sessionId The ID of the session to delete.
+     * @param context The request context.
+     * @returns A promise resolving to a TransportResponse confirming closure.
      */
     handleDeleteRequest(sessionId: string, context: RequestContext): Promise<TransportResponse>;
     /**
-     * Retrieves session information.
+     * Retrieves information about a specific session.
+     * @param sessionId The ID of the session to retrieve.
+     * @returns A TransportSession object if the session exists, otherwise undefined.
      */
     getSession(sessionId: string): TransportSession | undefined;
 }
+export {};
 //# sourceMappingURL=transportTypes.d.ts.map

package/dist/mcp-server/transports/core/transportTypes.d.ts.map

@@ -1 +1 @@
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package/dist/mcp-server/transports/core/transportTypes.js

@@ -1,5 +1,7 @@
 /**
- * @fileoverview Core types and interfaces for the transport layer abstraction.
+ * @fileoverview Defines the core types and interfaces for the transport layer abstraction.
+ * This module establishes the data contracts and abstract interfaces that decouple
+ * the MCP server's core logic from specific transport implementations like HTTP or stdio.
  * @module src/mcp-server/transports/core/transportTypes
  */
 export {};

package/dist/mcp-server/transports/core/transportTypes.js.map

@@ -1 +1 @@
-{"version":3,"file":"transportTypes.js","sourceRoot":"","sources":["../../../../src/mcp-server/transports/core/transportTypes.ts"],"names":[],"mappings":"AAAA;;;GAGG"}
+{"version":3,"file":"transportTypes.js","sourceRoot":"","sources":["../../../../src/mcp-server/transports/core/transportTypes.ts"],"names":[],"mappings":"AAAA;;;;;GAKG"}

package/dist/mcp-server/transports/http/httpTransport.d.ts

@@ -5,15 +5,15 @@
  * @module src/mcp-server/transports/http/httpTransport
  */
 import { ServerType } from "@hono/node-server";
-import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { Hono } from "hono";
 import { RequestContext } from "../../../utils/index.js";
+import { ServerInstanceInfo } from "../../server.js";
 import { TransportManager } from "../core/transportTypes.js";
 import { HonoNodeBindings } from "./httpTypes.js";
-export declare function createHttpApp(transportManager: TransportManager, createServerInstanceFn: () => Promise<McpServer>, parentContext: RequestContext): Hono<{
+export declare function createHttpApp(transportManager: TransportManager, createServerInstanceFn: () => Promise<ServerInstanceInfo>, parentContext: RequestContext): Hono<{
     Bindings: HonoNodeBindings;
 }>;
-export declare function startHttpTransport(createServerInstanceFn: () => Promise<McpServer>, parentContext: RequestContext): Promise<{
+export declare function startHttpTransport(createServerInstanceFn: () => Promise<ServerInstanceInfo>, parentContext: RequestContext): Promise<{
     app: Hono<{
         Bindings: HonoNodeBindings;
     }>;

package/dist/mcp-server/transports/http/httpTransport.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"httpTransport.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/transports/http/httpTransport.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAS,UAAU,EAAE,MAAM,mBAAmB,CAAC;AACtD,OAAO,EAAW,IAAI,EAAQ,MAAM,MAAM,CAAC;AAK3C,OAAO,EAGL,cAAc,EAEf,MAAM,yBAAyB,CAAC;AACjC,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AAGrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,2BAA2B,CAAC;AAG7D,OAAO,EAAE,gBAAgB,EAAE,MAAM,gBAAgB,CAAC;AAkMlD,wBAAgB,aAAa,CAC3B,gBAAgB,EAAE,gBAAgB,EAClC,sBAAsB,EAAE,MAAM,OAAO,CAAC,kBAAkB,CAAC,EACzD,aAAa,EAAE,cAAc,GAC5B,IAAI,CAAC;IAAE,QAAQ,EAAE,gBAAgB,CAAA;CAAE,CAAC,CAiMtC;AAED,wBAAsB,kBAAkB,CACtC,sBAAsB,EAAE,MAAM,OAAO,CAAC,kBAAkB,CAAC,EACzD,aAAa,EAAE,cAAc,GAC5B,OAAO,CAAC;IACT,GAAG,EAAE,IAAI,CAAC;QAAE,QAAQ,EAAE,gBAAgB,CAAA;KAAE,CAAC,CAAC;IAC1C,MAAM,EAAE,UAAU,CAAC;IACnB,gBAAgB,EAAE,gBAAgB,CAAC;CACpC,CAAC,CA4BD"}

package/dist/mcp-server/transports/http/httpTransport.js

@@ -12,13 +12,24 @@ import http from "http";
 import { config } from "../../../config/index.js";
 import { logger, rateLimiter, requestContextService, } from "../../../utils/index.js";
 import { createAuthMiddleware, createAuthStrategy } from "../auth/index.js";
-import { StatefulTransportManager } from "../core/statefulTransportManager.js";
 import { StatelessTransportManager } from "../core/statelessTransportManager.js";
+import { StatefulTransportManager } from "./../core/statefulTransportManager.js";
 import { httpErrorHandler } from "./httpErrorHandler.js";
 import { mcpTransportMiddleware } from "./mcpTransportMiddleware.js";
 const HTTP_PORT = config.mcpHttpPort;
 const HTTP_HOST = config.mcpHttpHost;
 const MCP_ENDPOINT_PATH = config.mcpHttpEndpointPath;
+/**
+ * Extracts the client IP address from the request, prioritizing common proxy headers.
+ * @param c - The Hono context object.
+ * @returns The client's IP address or a default string if not found.
+ */
+function getClientIp(c) {
+    const forwardedFor = c.req.header("x-forwarded-for");
+    return ((forwardedFor?.split(",")[0] ?? "").trim() ||
+        c.req.header("x-real-ip") ||
+        "unknown_ip");
+}
 /**
  * Converts a Fetch API Headers object to Node.js IncomingHttpHeaders.
  * Hono uses Fetch API Headers, but the underlying transport managers expect
@@ -94,7 +105,8 @@ function startHttpServerWithRetry(app, initialPort, host, maxRetries, parentCont
                 }
             })
                 .catch((err) => {
-                logger.fatal("Failed to check if port is in use.", err, attemptContext);
+                const error = err instanceof Error ? err : new Error(String(err));
+                logger.fatal("Failed to check if port is in use.", error, attemptContext);
                 reject(err);
             });
         };
@@ -108,15 +120,20 @@ function createTransportManager(createServerInstanceFn, sessionMode, context) {
         sessionMode,
     };
     logger.info(`Creating transport manager for session mode: ${sessionMode}`, opContext);
+    const statefulOptions = {
+        staleSessionTimeoutMs: config.mcpStatefulSessionStaleTimeoutMs,
+        mcpHttpEndpointPath: config.mcpHttpEndpointPath,
+    };
+    const getMcpServer = async () => (await createServerInstanceFn()).server;
     switch (sessionMode) {
         case "stateless":
-            return new StatelessTransportManager(createServerInstanceFn);
+            return new StatelessTransportManager(getMcpServer);
         case "stateful":
-            return new StatefulTransportManager(createServerInstanceFn);
+            return new StatefulTransportManager(getMcpServer, statefulOptions);
         case "auto":
         default:
             logger.info("Defaulting to 'auto' mode (stateful with stateless fallback).", opContext);
-            return new StatefulTransportManager(createServerInstanceFn);
+            return new StatefulTransportManager(getMcpServer, statefulOptions);
     }
 }
 export function createHttpApp(transportManager, createServerInstanceFn, parentContext) {
@@ -142,10 +159,7 @@ export function createHttpApp(transportManager, createServerInstanceFn, parentCo
         await next();
     });
     app.use(MCP_ENDPOINT_PATH, async (c, next) => {
-        const forwardedFor = c.req.header("x-forwarded-for");
-        const clientIp = (forwardedFor?.split(",")[0] ?? "").trim() ||
-            c.req.header("x-real-ip") ||
-            "unknown_ip";
+        const clientIp = getClientIp(c);
         const context = requestContextService.createRequestContext({
             operation: "httpRateLimitCheck",
             ipAddress: clientIp,
@@ -178,15 +192,33 @@ export function createHttpApp(transportManager, createServerInstanceFn, parentCo
             timestamp: new Date().toISOString(),
         });
     });
-    app.get(MCP_ENDPOINT_PATH, (c) => {
+    app.get(MCP_ENDPOINT_PATH, async (c) => {
         const sessionId = c.req.header("mcp-session-id");
         if (sessionId) {
             return c.text("GET requests to existing sessions are not supported.", 405);
         }
+        // Since this is a stateless endpoint, we create a temporary instance
+        // to report on the server's configuration.
+        const { tools, identity, options } = await createServerInstanceFn();
+        const effectiveSessionMode = transportManager instanceof StatefulTransportManager
+            ? "stateful"
+            : "stateless";
         return c.json({
             status: "ok",
-            mode: "stateless",
-            message: "Server is running. Provide a Mcp-Session-Id header to stream from a session.",
+            server: {
+                name: identity.name,
+                version: identity.version,
+                description: identity.description || "No description provided.",
+                nodeVersion: process.version,
+                environment: config.environment,
+                capabilities: options.capabilities,
+            },
+            sessionMode: {
+                configured: config.mcpSessionMode,
+                effective: effectiveSessionMode,
+            },
+            tools: tools,
+            message: "Server is running. POST to this endpoint to execute a tool call.",
         });
     });
     app.post(MCP_ENDPOINT_PATH, mcpTransportMiddleware(transportManager, createServerInstanceFn), (c) => {
@@ -198,16 +230,16 @@ export function createHttpApp(transportManager, createServerInstanceFn, parentCo
             c.header(key, value);
         });
         c.status(response.statusCode);
-        if (response.stream) {
+        if (response.type === "stream") {
             return stream(c, async (s) => {
-                if (response.stream) {
-                    await s.pipe(response.stream);
-                }
+                await s.pipe(response.stream);
             });
         }
         else {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            return c.json(response.body);
+            const body = typeof response.body === "object" && response.body !== null
+                ? response.body
+                : { body: response.body };
+            return c.json(body);
         }
     });
     app.delete(MCP_ENDPOINT_PATH, async (c) => {
@@ -220,8 +252,14 @@ export function createHttpApp(transportManager, createServerInstanceFn, parentCo
         if (sessionId) {
             if (transportManager instanceof StatefulTransportManager) {
                 const response = await transportManager.handleDeleteRequest(sessionId, context);
-                // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                return c.json(response.body, response.statusCode);
+                if (response.type === "buffered") {
+                    const body = typeof response.body === "object" && response.body !== null
+                        ? response.body
+                        : { body: response.body };
+                    return c.json(body, response.statusCode);
+                }
+                // Fallback for unexpected stream response on DELETE
+                return c.body(null, response.statusCode);
             }
             else {
                 return c.json({

package/dist/mcp-server/transports/http/httpTransport.js.map

@@ -1 +1 @@
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package/dist/mcp-server/transports/http/mcpTransportMiddleware.d.ts

@@ -5,7 +5,8 @@
  * response for Hono to send.
  * @module src/mcp-server/transports/http/mcpTransportMiddleware
  */
-import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { MiddlewareHandler } from "hono";
+import { ServerInstanceInfo } from "../../server.js";
 import { TransportManager, TransportResponse } from "../core/transportTypes.js";
 import { HonoNodeBindings } from "./httpTypes.js";
 /**
@@ -19,8 +20,8 @@ type McpMiddlewareEnv = {
         mcpResponse: TransportResponse;
     };
 };
-export declare const mcpTransportMiddleware: (transportManager: TransportManager, createServerInstanceFn: () => Promise<McpServer>) => import("hono").MiddlewareHandler<McpMiddlewareEnv & {
+export declare const mcpTransportMiddleware: (transportManager: TransportManager, createServerInstanceFn: () => Promise<ServerInstanceInfo>) => MiddlewareHandler<McpMiddlewareEnv & {
     Bindings: HonoNodeBindings;
-}, string, {}>;
+}>;
 export {};
 //# sourceMappingURL=mcpTransportMiddleware.d.ts.map

package/dist/mcp-server/transports/http/mcpTransportMiddleware.d.ts.map

@@ -1 +1 @@
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