@cyanheads/pubmed-mcp-server 1.3.1 → 1.3.3

package/README.md

@@ -6,7 +6,7 @@
 
 [![TypeScript](https://img.shields.io/badge/TypeScript-^5.8.3-blue.svg?style=flat-square)](https://www.typescriptlang.org/)
 [![Model Context Protocol](https://img.shields.io/badge/MCP%20SDK-^1.17.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
-[![Version](https://img.shields.io/badge/Version-1.3.1-blue.svg?style=flat-square)](./CHANGELOG.md)
+[![Version](https://img.shields.io/badge/Version-1.3.2-blue.svg?style=flat-square)](./CHANGELOG.md)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg?style=flat-square)](https://opensource.org/licenses/Apache-2.0)
 [![Status](https://img.shields.io/badge/Status-Stable-green.svg?style=flat-square)](https://github.com/cyanheads/pubmed-mcp-server/issues)
 [![GitHub](https://img.shields.io/github/stars/cyanheads/pubmed-mcp-server?style=social)](https://github.com/cyanheads/pubmed-mcp-server)

package/dist/config/index.js

@@ -137,30 +137,63 @@ const ensureDirectory = (dirPath, rootDir, dirName) => {
     const resolvedDirPath = path.isAbsolute(dirPath)
         ? dirPath
         : path.resolve(rootDir, dirPath);
-    if (!resolvedDirPath.startsWith(rootDir)) {
+    if (!resolvedDirPath.startsWith(rootDir + path.sep) &&
+        resolvedDirPath !== rootDir) {
         if (process.stdout.isTTY) {
-            console.error(`Error: ${dirName} path "${dirPath}" is outside the project boundary "${rootDir}".`);
+            console.error(`Error: ${dirName} path "${dirPath}" resolves to "${resolvedDirPath}", which is outside the project boundary "${rootDir}".`);
         }
         return null;
     }
-    try {
-        if (!existsSync(resolvedDirPath)) {
+    if (!existsSync(resolvedDirPath)) {
+        try {
             mkdirSync(resolvedDirPath, { recursive: true });
+            if (process.stdout.isTTY) {
+                console.log(`Created ${dirName} directory: ${resolvedDirPath}`);
+            }
         }
-        else {
-            if (!statSync(resolvedDirPath).isDirectory()) {
-                console.error(`Error: ${dirName} path ${resolvedDirPath} exists but is not a directory.`);
-                return null;
+        catch (err) {
+            const errorMessage = err instanceof Error ? err.message : String(err);
+            if (process.stdout.isTTY) {
+                console.error(`Error creating ${dirName} directory at ${resolvedDirPath}: ${errorMessage}`);
             }
+            return null;
         }
-        return resolvedDirPath;
     }
-    catch (error) {
-        console.error(`Error ensuring ${dirName} directory at ${resolvedDirPath}: ${error.message}`);
-        return null;
+    else {
+        try {
+            const stats = statSync(resolvedDirPath);
+            if (!stats.isDirectory()) {
+                if (process.stdout.isTTY) {
+                    console.error(`Error: ${dirName} path ${resolvedDirPath} exists but is not a directory.`);
+                }
+                return null;
+            }
+        }
+        catch (statError) {
+            const errorMessage = statError instanceof Error
+                ? statError.message
+                : "An unknown error occurred";
+            if (process.stdout.isTTY) {
+                console.error(`Error accessing ${dirName} path ${resolvedDirPath}: ${errorMessage}`);
+            }
+            return null;
+        }
     }
+    return resolvedDirPath;
 };
-const validatedLogsPath = ensureDirectory(env.LOGS_DIR, projectRoot, "logs");
+let validatedLogsPath = ensureDirectory(env.LOGS_DIR, projectRoot, "logs");
+if (!validatedLogsPath) {
+    if (process.stdout.isTTY) {
+        console.warn(`Warning: Custom logs directory ('${env.LOGS_DIR}') is invalid or outside the project boundary. Falling back to default.`);
+    }
+    const defaultLogsDir = path.join(projectRoot, "logs");
+    validatedLogsPath = ensureDirectory(defaultLogsDir, projectRoot, "logs");
+    if (!validatedLogsPath) {
+        if (process.stdout.isTTY) {
+            console.warn("Warning: Default logs directory could not be created. File logging will be disabled.");
+        }
+    }
+}
 export const config = {
     pkg,
     mcpServerName: env.MCP_SERVER_NAME || pkg.name,

package/dist/mcp-server/server.js

@@ -32,6 +32,11 @@ async function createMcpServerInstance() {
         operation: "createMcpServerInstance",
     });
     logger.info("Initializing MCP server instance", context);
+    requestContextService.configure({
+        appName: config.mcpServerName,
+        appVersion: config.mcpServerVersion,
+        environment,
+    });
     const server = new McpServer({ name: config.mcpServerName, version: config.mcpServerVersion }, {
         capabilities: {
             logging: {},
@@ -90,11 +95,6 @@ export async function initializeAndStartServer() {
         operation: "initializeAndStartServer",
     });
     logger.info("MCP Server initialization sequence started.", context);
-    requestContextService.configure({
-        appName: config.mcpServerName,
-        appVersion: config.mcpServerVersion,
-        environment,
-    });
     try {
         const result = await startTransport();
         logger.info("MCP Server initialization sequence completed successfully.", context);

package/dist/services/NCBI/core/ncbiRequestQueueManager.d.ts

@@ -19,6 +19,7 @@ export declare class NcbiRequestQueueManager {
     private requestQueue;
     private isProcessingQueue;
     private lastRequestTime;
+    private keepAliveInterval;
     constructor();
     /**
      * Processes the request queue, ensuring delays between requests to respect NCBI rate limits.

package/dist/services/NCBI/core/ncbiRequestQueueManager.js

@@ -9,8 +9,11 @@ export class NcbiRequestQueueManager {
         this.requestQueue = [];
         this.isProcessingQueue = false;
         this.lastRequestTime = 0;
-        // Constructor should not have side-effects like logging.
-        // The service that uses this manager can log its creation if needed.
+        // This interval's purpose is to keep the Node.js event loop alive
+        // so the process doesn't exit prematurely when running in stdio mode.
+        this.keepAliveInterval = setInterval(() => {
+            // This empty interval keeps the event loop active.
+        }, 1000000);
     }
     /**
      * Processes the request queue, ensuring delays between requests to respect NCBI rate limits.

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "1.3.1",
+  "version": "1.3.3",
   "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.",
   "main": "dist/index.js",
   "files": [