@cyanheads/pubmed-mcp-server 1.1.1 → 1.1.2

package/dist/config/index.d.ts

@@ -25,8 +25,10 @@ export declare const config: {
     mcpServerVersion: string;
     /** Logging level. From `MCP_LOG_LEVEL` env var. Default: "debug". */
     logLevel: string;
-    /** Absolute path to the logs directory. From `LOGS_DIR` env var. */
-    logsPath: string;
+    /** Defines the logging output mode ('file' or 'stdout'). From `LOG_OUTPUT_MODE`. */
+    logOutputMode: "file" | "stdout";
+    /** Absolute path to the logs directory (if logOutputMode is 'file'). From `LOGS_DIR`. */
+    logsPath: string | null;
     /** Runtime environment. From `NODE_ENV` env var. Default: "development". */
     environment: string;
     /** MCP transport type ('stdio' or 'http'). From `MCP_TRANSPORT_TYPE` env var. Default: "stdio". */

package/dist/config/index.js

@@ -80,6 +80,8 @@ const EnvSchema = z.object({
     MCP_LOG_LEVEL: z.string().default("debug"),
     /** Directory for log files. Defaults to "logs" in project root. */
     LOGS_DIR: z.string().default(path.join(projectRoot, "logs")),
+    /** Defines the logging output mode. "file" for logs in LOGS_DIR, "stdout" for console logging. */
+    LOG_OUTPUT_MODE: z.enum(["file", "stdout"]).default("file"),
     /** Runtime environment (e.g., "development", "production"). Default: "development". */
     NODE_ENV: z.string().default("development"),
     /** MCP communication transport ("stdio" or "http"). Default: "stdio". */
@@ -209,12 +211,15 @@ const ensureDirectory = (dirPath, rootDir, dirName) => {
 };
 // --- End Directory Ensurance Function ---
 // --- Logs Directory Handling ---
-const validatedLogsPath = ensureDirectory(env.LOGS_DIR, projectRoot, "logs");
-if (!validatedLogsPath) {
-    if (process.stdout.isTTY) {
-        console.error("FATAL: Logs directory configuration is invalid or could not be created. Please check permissions and path. Exiting.");
+let validatedLogsPath = null;
+if (env.LOG_OUTPUT_MODE === "file") {
+    validatedLogsPath = ensureDirectory(env.LOGS_DIR, projectRoot, "logs");
+    if (!validatedLogsPath) {
+        if (process.stdout.isTTY) {
+            console.error("FATAL: Log mode is 'file' but logs directory is invalid or could not be created. Please check LOGS_DIR, permissions, and path. Exiting.");
+        }
+        process.exit(1); // Exit if file logging is configured but directory is not usable
     }
-    process.exit(1); // Exit if logs directory is not usable
 }
 // --- End Logs Directory Handling ---
 /**
@@ -228,7 +233,9 @@ export const config = {
     mcpServerVersion: env.MCP_SERVER_VERSION || pkg.version,
     /** Logging level. From `MCP_LOG_LEVEL` env var. Default: "debug". */
     logLevel: env.MCP_LOG_LEVEL,
-    /** Absolute path to the logs directory. From `LOGS_DIR` env var. */
+    /** Defines the logging output mode ('file' or 'stdout'). From `LOG_OUTPUT_MODE`. */
+    logOutputMode: env.LOG_OUTPUT_MODE,
+    /** Absolute path to the logs directory (if logOutputMode is 'file'). From `LOGS_DIR`. */
     logsPath: validatedLogsPath,
     /** Runtime environment. From `NODE_ENV` env var. Default: "development". */
     environment: env.NODE_ENV,

package/dist/mcp-server/tools/generatePubMedChart/logic.js

@@ -83,7 +83,8 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
         input: sanitizeInputForLogging(input),
     });
     logger.info(`Executing 'generate_pubmed_chart'. Chart type: ${input.chartType}, Output format: ${input.outputFormat}`, operationContext);
-    if (input.outputFormat !== "png") { // Changed from svg to png
+    if (input.outputFormat !== "png") {
+        // Changed from svg to png
         const unsupportedFormatError = new McpError(BaseErrorCode.VALIDATION_ERROR, `Unsupported output format: ${input.outputFormat}. Currently, only 'png' is supported.`, // Changed message
         { requestedFormat: input.outputFormat });
         logger.warning(unsupportedFormatError.message, operationContext);

package/dist/mcp-server/tools/pubmedResearchAgent/logic/planOrchestrator.js

@@ -35,9 +35,7 @@ function removeEmptyObjectsRecursively(obj) {
     }
     if (Array.isArray(obj)) {
         // If it's an array, recurse on each element and filter out empty objects/arrays
-        const newArr = obj
-            .map(removeEmptyObjectsRecursively)
-            .filter((item) => {
+        const newArr = obj.map(removeEmptyObjectsRecursively).filter((item) => {
             if (item === null || item === undefined)
                 return false;
             if (Array.isArray(item) && item.length === 0)

package/dist/utils/internal/logger.js

@@ -35,11 +35,8 @@ const mcpToWinstonLevel = {
     alert: "error",
     emerg: "error",
 };
-// The logsPath from config is already resolved and validated by src/config/index.ts
-const resolvedLogsDir = config.logsPath;
-const isLogsDirSafe = !!resolvedLogsDir; // If logsPath is set, it's considered safe by config logic.
 /**
- * Creates the Winston console log format.
+ * Creates the Winston console log format for interactive TTY sessions.
  * @returns The Winston log format for console output.
  * @private
  */
@@ -103,47 +100,45 @@ export class Logger {
             });
             return;
         }
-        // Set initialized to true at the beginning of the initialization process.
         this.initialized = true;
         this.currentMcpLevel = level;
         this.currentWinstonLevel = mcpToWinstonLevel[level];
-        // The logs directory (config.logsPath / resolvedLogsDir) is expected to be created and validated
-        // by the configuration module (src/config/index.ts) before logger initialization.
-        // If isLogsDirSafe is true, we assume resolvedLogsDir exists and is usable.
-        // No redundant directory creation logic here.
-        const fileFormat = winston.format.combine(winston.format.timestamp(), winston.format.errors({ stack: true }), winston.format.json());
         const transports = [];
-        const fileTransportOptions = {
-            format: fileFormat,
-            maxsize: this.LOG_FILE_MAX_SIZE,
-            maxFiles: this.LOG_MAX_FILES,
-            tailable: true,
-        };
-        if (isLogsDirSafe) {
-            transports.push(new winston.transports.File({
-                filename: path.join(resolvedLogsDir, "error.log"),
-                level: "error",
-                ...fileTransportOptions,
-            }), new winston.transports.File({
-                filename: path.join(resolvedLogsDir, "warn.log"),
-                level: "warn",
-                ...fileTransportOptions,
-            }), new winston.transports.File({
-                filename: path.join(resolvedLogsDir, "info.log"),
-                level: "info",
-                ...fileTransportOptions,
-            }), new winston.transports.File({
-                filename: path.join(resolvedLogsDir, "debug.log"),
-                level: "debug",
-                ...fileTransportOptions,
-            }), new winston.transports.File({
-                filename: path.join(resolvedLogsDir, "combined.log"),
-                ...fileTransportOptions,
+        if (config.logOutputMode === "stdout") {
+            transports.push(new winston.transports.Console({
+                format: winston.format.combine(winston.format.timestamp(), winston.format.errors({ stack: true }), winston.format.json()),
             }));
         }
         else {
-            if (process.stdout.isTTY) {
-                console.warn("File logging disabled as logsPath is not configured or invalid.");
+            const resolvedLogsDir = config.logsPath;
+            if (resolvedLogsDir) {
+                const fileFormat = winston.format.combine(winston.format.timestamp(), winston.format.errors({ stack: true }), winston.format.json());
+                const fileTransportOptions = {
+                    format: fileFormat,
+                    maxsize: this.LOG_FILE_MAX_SIZE,
+                    maxFiles: this.LOG_MAX_FILES,
+                    tailable: true,
+                };
+                transports.push(new winston.transports.File({
+                    filename: path.join(resolvedLogsDir, "error.log"),
+                    level: "error",
+                    ...fileTransportOptions,
+                }), new winston.transports.File({
+                    filename: path.join(resolvedLogsDir, "warn.log"),
+                    level: "warn",
+                    ...fileTransportOptions,
+                }), new winston.transports.File({
+                    filename: path.join(resolvedLogsDir, "info.log"),
+                    level: "info",
+                    ...fileTransportOptions,
+                }), new winston.transports.File({
+                    filename: path.join(resolvedLogsDir, "debug.log"),
+                    level: "debug",
+                    ...fileTransportOptions,
+                }), new winston.transports.File({
+                    filename: path.join(resolvedLogsDir, "combined.log"),
+                    ...fileTransportOptions,
+                }));
             }
         }
         this.winstonLogger = winston.createLogger({
@@ -151,23 +146,20 @@ export class Logger {
             transports,
             exitOnError: false,
         });
-        // Configure console transport after Winston logger is created
         const consoleStatus = this._configureConsoleTransport();
         const initialContext = {
             loggerSetup: true,
             requestId: "logger-init-deferred",
             timestamp: new Date().toISOString(),
         };
-        // Removed logging of logsDirCreatedMessage as it's no longer set
         if (consoleStatus.message) {
             this.info(consoleStatus.message, initialContext);
         }
-        this.initialized = true; // Ensure this is set after successful setup
-        this.info(`Logger initialized. File logging level: ${this.currentWinstonLevel}. MCP logging level: ${this.currentMcpLevel}. Console logging: ${consoleStatus.enabled ? "enabled" : "disabled"}`, {
+        this.info(`Logger initialized. Mode: ${config.logOutputMode}. File logging level: ${this.currentWinstonLevel}. MCP logging level: ${this.currentMcpLevel}.`, {
             loggerSetup: true,
             requestId: "logger-post-init",
             timestamp: new Date().toISOString(),
-            logsPathUsed: resolvedLogsDir,
+            logsPathUsed: config.logsPath,
         });
     }
     /**
@@ -207,7 +199,6 @@ export class Logger {
         this.currentMcpLevel = newLevel;
         this.currentWinstonLevel = mcpToWinstonLevel[newLevel];
         if (this.winstonLogger) {
-            // Ensure winstonLogger is defined
             this.winstonLogger.level = this.currentWinstonLevel;
         }
         const consoleStatus = this._configureConsoleTransport();
@@ -226,6 +217,12 @@ export class Logger {
      * @private
      */
     _configureConsoleTransport() {
+        if (config.logOutputMode === "stdout") {
+            return {
+                enabled: true,
+                message: "Stdout logging is enabled by configuration.",
+            };
+        }
         if (!this.winstonLogger) {
             return {
                 enabled: false,
@@ -238,17 +235,19 @@ export class Logger {
         if (shouldHaveConsole && !consoleTransport) {
             const consoleFormat = createWinstonConsoleFormat();
             this.winstonLogger.add(new winston.transports.Console({
-                level: "debug", // Console always logs debug if enabled
+                level: "debug",
                 format: consoleFormat,
             }));
-            message = "Console logging enabled (level: debug, stdout is TTY).";
+            message =
+                "Interactive console logging enabled (level: debug, stdout is TTY).";
         }
         else if (!shouldHaveConsole && consoleTransport) {
             this.winstonLogger.remove(consoleTransport);
-            message = "Console logging disabled (level not debug or stdout not TTY).";
+            message =
+                "Interactive console logging disabled (level not debug or stdout not TTY).";
         }
         else {
-            message = "Console logging status unchanged.";
+            message = "Interactive console logging status unchanged.";
         }
         return { enabled: shouldHaveConsole, message };
     }
@@ -288,7 +287,7 @@ export class Logger {
         if (!this.ensureInitialized())
             return;
         if (mcpLevelSeverity[level] > mcpLevelSeverity[this.currentMcpLevel]) {
-            return; // Do not log if message level is less severe than currentMcpLevel
+            return;
         }
         const logData = { ...context };
         const winstonLevel = mcpToWinstonLevel[level];
@@ -304,7 +303,6 @@ export class Logger {
                 mcpDataPayload.context = context;
             if (error) {
                 mcpDataPayload.error = { message: error.message };
-                // Include stack trace in debug mode for MCP notifications, truncated for brevity
                 if (this.currentMcpLevel === "debug" && error.stack) {
                     mcpDataPayload.error.stack = error.stack.substring(0, this.MCP_NOTIFICATION_STACK_TRACE_MAX_LENGTH);
                 }
@@ -321,7 +319,7 @@ export class Logger {
                     originalLevel: level,
                     originalMessage: msg,
                     sendError: errorMessage,
-                    mcpPayload: JSON.stringify(mcpDataPayload).substring(0, 500), // Log a preview
+                    mcpPayload: JSON.stringify(mcpDataPayload).substring(0, 500),
                 };
                 this.winstonLogger.error("Failed to send MCP log notification", internalErrorContext);
             }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "1.1.1",
+  "version": "1.1.2",
   "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": [
@@ -29,8 +29,7 @@
     "tree": "ts-node --esm scripts/tree.ts",
     "fetch-spec": "ts-node --esm scripts/fetch-openapi-spec.ts",
     "format": "prettier --write \"**/*.{ts,js,json,md,html,css}\"",
-    "inspector": "mcp-inspector --config mcp.json --server pubmed-mcp-server",
-    "start:client-cli": "node dist/mcp-client/cli/mcp-client-cli.js"
+    "inspector": "mcp-inspector --config mcp.json --server pubmed-mcp-server"
   },
   "dependencies": {
     "@hono/node-server": "^1.14.4",