@cyanheads/pubmed-mcp-server 1.0.16 → 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". */
@@ -39,26 +41,14 @@ export declare const config: {
     mcpAllowedOrigins: string[] | undefined;
     /** Auth secret key (JWTs, http transport). From `MCP_AUTH_SECRET_KEY`. CRITICAL. */
     mcpAuthSecretKey: string | undefined;
-    /** OpenRouter App URL. From `OPENROUTER_APP_URL`. Default: "http://localhost:3000". */
-    openrouterAppUrl: string;
-    /** OpenRouter App Name. From `OPENROUTER_APP_NAME`. Defaults to `mcpServerName`. */
-    openrouterAppName: string;
-    /** OpenRouter API Key. From `OPENROUTER_API_KEY`. */
-    openrouterApiKey: string | undefined;
-    /** Default LLM model. From `LLM_DEFAULT_MODEL`. */
-    llmDefaultModel: string;
-    /** Default LLM temperature. From `LLM_DEFAULT_TEMPERATURE`. */
-    llmDefaultTemperature: number | undefined;
-    /** Default LLM top_p. From `LLM_DEFAULT_TOP_P`. */
-    llmDefaultTopP: number | undefined;
-    /** Default LLM max tokens. From `LLM_DEFAULT_MAX_TOKENS`. */
-    llmDefaultMaxTokens: number | undefined;
-    /** Default LLM top_k. From `LLM_DEFAULT_TOP_K`. */
-    llmDefaultTopK: number | undefined;
-    /** Default LLM min_p. From `LLM_DEFAULT_MIN_P`. */
-    llmDefaultMinP: number | undefined;
-    /** Gemini API Key. From `GEMINI_API_KEY`. */
-    geminiApiKey: string | undefined;
+    /** Auth mode ('jwt' or 'oauth'). From `MCP_AUTH_MODE`. */
+    mcpAuthMode: "jwt" | "oauth";
+    /** OAuth Issuer URL. From `OAUTH_ISSUER_URL`. */
+    oauthIssuerUrl: string | undefined;
+    /** OAuth Audience. From `OAUTH_AUDIENCE`. */
+    oauthAudience: string | undefined;
+    /** OAuth JWKS URI. From `OAUTH_JWKS_URI`. */
+    oauthJwksUri: string | undefined;
     /** NCBI API Key. From `NCBI_API_KEY`. */
     ncbiApiKey: string | undefined;
     /** NCBI Tool Identifier. From `NCBI_TOOL_IDENTIFIER`. Defaults to server name/version. */

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". */
@@ -95,31 +97,14 @@ const EnvSchema = z.object({
         .string()
         .min(32, "MCP_AUTH_SECRET_KEY must be at least 32 characters long for security reasons.")
         .optional(),
-    /** Optional. Application URL for OpenRouter integration. */
-    OPENROUTER_APP_URL: z
-        .string()
-        .url("OPENROUTER_APP_URL must be a valid URL (e.g., http://localhost:3000)")
-        .optional(),
-    /** Optional. Application name for OpenRouter. Defaults to MCP_SERVER_NAME or package name. */
-    OPENROUTER_APP_NAME: z.string().optional(),
-    /** Optional. API key for OpenRouter services. */
-    OPENROUTER_API_KEY: z.string().optional(),
-    /** Default LLM model. Default: "google/gemini-2.5-flash-preview:thinking". */
-    LLM_DEFAULT_MODEL: z
-        .string()
-        .default("google/gemini-2.5-flash-preview-05-20"),
-    /** Optional. Default LLM temperature (0.0-2.0). */
-    LLM_DEFAULT_TEMPERATURE: z.coerce.number().min(0).max(2).optional(),
-    /** Optional. Default LLM top_p (0.0-1.0). */
-    LLM_DEFAULT_TOP_P: z.coerce.number().min(0).max(1).optional(),
-    /** Optional. Default LLM max tokens (positive integer). */
-    LLM_DEFAULT_MAX_TOKENS: z.coerce.number().int().positive().optional(),
-    /** Optional. Default LLM top_k (non-negative integer). */
-    LLM_DEFAULT_TOP_K: z.coerce.number().int().nonnegative().optional(),
-    /** Optional. Default LLM min_p (0.0-1.0). */
-    LLM_DEFAULT_MIN_P: z.coerce.number().min(0).max(1).optional(),
-    /** Optional. API key for Google Gemini services. */
-    GEMINI_API_KEY: z.string().optional(),
+    /** Authentication mode ('jwt' or 'oauth'). Default: 'jwt'. */
+    MCP_AUTH_MODE: z.enum(["jwt", "oauth"]).default("jwt"),
+    /** OAuth: The expected issuer of the JWT. */
+    OAUTH_ISSUER_URL: z.string().url().optional(),
+    /** OAuth: The expected audience of the JWT. */
+    OAUTH_AUDIENCE: z.string().optional(),
+    /** OAuth: The URI of the JWKS endpoint. */
+    OAUTH_JWKS_URI: z.string().url().optional(),
     /** Optional. OAuth provider authorization endpoint URL. */
     OAUTH_PROXY_AUTHORIZATION_URL: z
         .string()
@@ -226,12 +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 ---
 /**
@@ -245,7 +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,
@@ -261,26 +251,14 @@ export const config = {
         .filter(Boolean),
     /** Auth secret key (JWTs, http transport). From `MCP_AUTH_SECRET_KEY`. CRITICAL. */
     mcpAuthSecretKey: env.MCP_AUTH_SECRET_KEY,
-    /** OpenRouter App URL. From `OPENROUTER_APP_URL`. Default: "http://localhost:3000". */
-    openrouterAppUrl: env.OPENROUTER_APP_URL || "http://localhost:3000",
-    /** OpenRouter App Name. From `OPENROUTER_APP_NAME`. Defaults to `mcpServerName`. */
-    openrouterAppName: env.OPENROUTER_APP_NAME || pkg.name || "MCP TS App",
-    /** OpenRouter API Key. From `OPENROUTER_API_KEY`. */
-    openrouterApiKey: env.OPENROUTER_API_KEY,
-    /** Default LLM model. From `LLM_DEFAULT_MODEL`. */
-    llmDefaultModel: env.LLM_DEFAULT_MODEL,
-    /** Default LLM temperature. From `LLM_DEFAULT_TEMPERATURE`. */
-    llmDefaultTemperature: env.LLM_DEFAULT_TEMPERATURE,
-    /** Default LLM top_p. From `LLM_DEFAULT_TOP_P`. */
-    llmDefaultTopP: env.LLM_DEFAULT_TOP_P,
-    /** Default LLM max tokens. From `LLM_DEFAULT_MAX_TOKENS`. */
-    llmDefaultMaxTokens: env.LLM_DEFAULT_MAX_TOKENS,
-    /** Default LLM top_k. From `LLM_DEFAULT_TOP_K`. */
-    llmDefaultTopK: env.LLM_DEFAULT_TOP_K,
-    /** Default LLM min_p. From `LLM_DEFAULT_MIN_P`. */
-    llmDefaultMinP: env.LLM_DEFAULT_MIN_P,
-    /** Gemini API Key. From `GEMINI_API_KEY`. */
-    geminiApiKey: env.GEMINI_API_KEY,
+    /** Auth mode ('jwt' or 'oauth'). From `MCP_AUTH_MODE`. */
+    mcpAuthMode: env.MCP_AUTH_MODE,
+    /** OAuth Issuer URL. From `OAUTH_ISSUER_URL`. */
+    oauthIssuerUrl: env.OAUTH_ISSUER_URL,
+    /** OAuth Audience. From `OAUTH_AUDIENCE`. */
+    oauthAudience: env.OAUTH_AUDIENCE,
+    /** OAuth JWKS URI. From `OAUTH_JWKS_URI`. */
+    oauthJwksUri: env.OAUTH_JWKS_URI,
     // NCBI Configuration
     /** NCBI API Key. From `NCBI_API_KEY`. */
     ncbiApiKey: env.NCBI_API_KEY,

package/dist/index.js

@@ -22,16 +22,21 @@
  * @module src/index
  */
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import http from "http"; // Import http module
 import { config, environment } from "./config/index.js";
 import { initializeAndStartServer } from "./mcp-server/server.js";
 import { requestContextService } from "./utils/index.js";
 import { logger } from "./utils/internal/logger.js";
 /**
  * Holds the main MCP server instance, primarily for STDIO transport.
- * For HTTP transport, server instances are typically managed per session.
  * @private
  */
-let server;
+let mcpStdioServer;
+/**
+ * Holds the Node.js HTTP server instance if HTTP transport is used.
+ * @private
+ */
+let actualHttpServer;
 /**
  * Gracefully shuts down the main MCP server and associated resources.
  * Called on process termination signals or critical unhandled errors.
@@ -46,25 +51,70 @@ const shutdown = async (signal) => {
         triggerEvent: signal,
     });
     logger.info(`Received ${signal}. Initiating graceful shutdown...`, shutdownContext);
-    try {
-        if (server) {
-            logger.info("Attempting to close main MCP server...", shutdownContext);
-            await server.close();
-            logger.info("Main MCP server closed successfully.", shutdownContext);
+    let mcpClosed = false;
+    let httpClosed = false;
+    let closeError = null;
+    const checkAndExit = () => {
+        if (closeError) {
+            logger.error("Critical error encountered during shutdown process.", {
+                ...shutdownContext,
+                errorMessage: closeError.message,
+                errorStack: closeError.stack,
+            });
+            process.exit(1);
         }
-        else {
-            logger.notice("No global server instance found to close during shutdown (this may be normal for HTTP transport).", shutdownContext);
+        else if (mcpClosed && httpClosed) {
+            logger.info("Graceful shutdown completed successfully. Exiting.", shutdownContext);
+            process.exit(0);
         }
-        logger.info("Graceful shutdown completed successfully. Exiting.", shutdownContext);
-        process.exit(0);
+    };
+    if (mcpStdioServer) {
+        logger.info("Attempting to close main MCP server (STDIO)...", shutdownContext);
+        mcpStdioServer
+            .close()
+            .then(() => {
+            logger.info("Main MCP server (STDIO) closed successfully.", shutdownContext);
+            mcpClosed = true;
+            checkAndExit();
+        })
+            .catch((err) => {
+            logger.error("Error closing MCP server (STDIO).", {
+                ...shutdownContext,
+                error: err,
+            });
+            mcpClosed = true; // Consider it closed even on error to allow exit
+            if (!closeError)
+                closeError = err;
+            checkAndExit();
+        });
     }
-    catch (error) {
-        logger.error("Critical error encountered during shutdown process.", {
-            ...shutdownContext,
-            errorMessage: error instanceof Error ? error.message : String(error),
-            errorStack: error instanceof Error ? error.stack : undefined,
+    else {
+        mcpClosed = true; // No STDIO McpServer to close
+    }
+    if (actualHttpServer) {
+        logger.info("Attempting to close HTTP server...", shutdownContext);
+        actualHttpServer.close((err) => {
+            if (err) {
+                logger.error("Error closing HTTP server.", {
+                    ...shutdownContext,
+                    error: err,
+                });
+                if (!closeError)
+                    closeError = err;
+            }
+            else {
+                logger.info("HTTP server closed successfully.", shutdownContext);
+            }
+            httpClosed = true;
+            checkAndExit();
         });
-        process.exit(1);
+    }
+    else {
+        httpClosed = true; // No HTTP server to close
+    }
+    // Initial check in case no servers needed closing
+    if (mcpClosed && httpClosed) {
+        checkAndExit();
     }
 };
 /**
@@ -100,13 +150,6 @@ const start = async () => {
     }
     await logger.initialize(validatedMcpLogLevel);
     logger.info(`Logger has been initialized by start(). Effective MCP logging level set to: ${validatedMcpLogLevel}.`);
-    // Configure RequestContextService once globally
-    requestContextService.configure({
-        appName: config.mcpServerName,
-        appVersion: config.mcpServerVersion,
-        environment,
-    });
-    logger.debug("RequestContextService configured with app name, version, and environment.");
     const transportType = config.mcpTransportType;
     const startupContext = requestContextService.createRequestContext({
         operation: `ServerStartupSequence_${transportType}`,
@@ -129,14 +172,19 @@ const start = async () => {
     logger.info(`Starting ${config.mcpServerName} (Version: ${config.mcpServerVersion}, Transport: ${transportType}, Env: ${environment})...`, startupContext);
     try {
         logger.debug("Calling initializeAndStartServer to set up MCP transport...", startupContext);
-        const potentialServerInstance = await initializeAndStartServer();
-        if (transportType === "stdio" &&
-            potentialServerInstance instanceof McpServer) {
-            server = potentialServerInstance;
+        const serverInstance = await initializeAndStartServer();
+        if (transportType === "stdio" && serverInstance instanceof McpServer) {
+            mcpStdioServer = serverInstance;
             logger.info("STDIO McpServer instance stored globally for shutdown.", startupContext);
         }
+        else if (transportType === "http" &&
+            serverInstance instanceof http.Server) {
+            actualHttpServer = serverInstance;
+            logger.info("HTTP transport initialized, http.Server instance stored globally for shutdown.", startupContext);
+        }
         else if (transportType === "http") {
-            logger.info("HTTP transport initialized. Server lifecycle managed by HTTP listener and session handlers.", startupContext);
+            // This case should ideally not be reached if initializeAndStartServer correctly returns http.Server
+            logger.warning("HTTP transport initialized, but no http.Server instance was returned to index.ts. Shutdown might be incomplete.", startupContext);
         }
         logger.info(`${config.mcpServerName} is now running and ready to accept connections via ${transportType} transport.`, {
             ...startupContext,

package/dist/mcp-server/server.d.ts

@@ -13,6 +13,7 @@
  * - Transports: https://github.com/modelcontextprotocol/modelcontextprotocol/blob/main/docs/specification/2025-03-26/basic/transports.mdx
  * @module src/mcp-server/server
  */
+import { ServerType } from "@hono/node-server";
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 /**
  * Main application entry point. Initializes and starts the MCP server.
@@ -22,7 +23,7 @@ import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
  * - Manages server startup, leading to a server ready for MCP messages.
  * - Handles critical startup failures, ensuring appropriate process exit.
  *
- * @returns For 'stdio', resolves with `McpServer`. For 'http', runs indefinitely.
+ * @returns For 'stdio', resolves with `McpServer`. For 'http', resolves with `http.Server`.
  *   Rejects on critical failure, leading to process exit.
  */
-export declare function initializeAndStartServer(): Promise<void | McpServer>;
+export declare function initializeAndStartServer(): Promise<void | McpServer | ServerType>;

package/dist/mcp-server/server.js

@@ -14,14 +14,12 @@
  * @module src/mcp-server/server
  */
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { config } from "../config/index.js";
+import { config, environment } from "../config/index.js";
 import { ErrorHandler, logger, requestContextService } from "../utils/index.js";
-// import { registerEchoResource } from "./resources/echoResource/index.js"; // To be removed after resource implementations.
 import { registerFetchPubMedContentTool } from "./tools/fetchPubMedContent/index.js";
-// Removed: import { registerFetchImageTestTool } from "./tools/imageTest/index.js";
-import { registerGeneratePubMedChartTool } from "./tools/generatePubMedChart/index.js"; // Added import
+import { registerGeneratePubMedChartTool } from "./tools/generatePubMedChart/index.js";
 import { registerGetPubMedArticleConnectionsTool } from "./tools/getPubMedArticleConnections/index.js";
-import { registerPubMedResearchAgentTool } from "./tools/pubmedResearchAgent/index.js"; // Added import
+import { registerPubMedResearchAgentTool } from "./tools/pubmedResearchAgent/index.js";
 import { registerSearchPubMedArticlesTool } from "./tools/searchPubMedArticles/index.js";
 import { startHttpTransport } from "./transports/httpTransport.js";
 import { connectStdioTransport } from "./transports/stdioTransport.js";
@@ -47,6 +45,11 @@ async function createMcpServerInstance() {
         operation: "createMcpServerInstance",
     });
     logger.info("Initializing MCP server instance", context);
+    requestContextService.configure({
+        appName: config.mcpServerName,
+        appVersion: config.mcpServerVersion,
+        environment,
+    });
     logger.debug("Instantiating McpServer with capabilities", {
         ...context,
         serverInfo: {
@@ -70,10 +73,9 @@ async function createMcpServerInstance() {
         logger.debug("Registering resources and tools...", context);
         // IMPORTANT: Keep tool registrations in alphabetical order. Do not remove this comment.
         await registerFetchPubMedContentTool(server);
-        // Removed: await registerFetchImageTestTool(server);
-        await registerGeneratePubMedChartTool(server); // Added new tool registration
+        await registerGeneratePubMedChartTool(server);
         await registerGetPubMedArticleConnectionsTool(server);
-        await registerPubMedResearchAgentTool(server); // Added new tool registration
+        await registerPubMedResearchAgentTool(server);
         await registerSearchPubMedArticlesTool(server);
         // Add other tool/resource registrations here
         logger.info("Resources and tools registered successfully", context);
@@ -96,7 +98,7 @@ async function createMcpServerInstance() {
  * - Transport Connection: Calls dedicated functions for chosen transport.
  * - Server Instance Lifecycle: Single instance for 'stdio', per-session for 'http'.
  *
- * @returns Resolves with `McpServer` for 'stdio', or `void` for 'http'.
+ * @returns Resolves with `McpServer` for 'stdio', `http.Server` for 'http', or `void` if http transport manages its own lifecycle without returning a server.
  * @throws {Error} If transport type is unsupported or setup fails.
  * @private
  */
@@ -109,16 +111,16 @@ async function startTransport() {
     logger.info(`Starting transport: ${transportType}`, context);
     if (transportType === "http") {
         logger.debug("Delegating to startHttpTransport...", context);
-        // For HTTP, startHttpTransport manages its own lifecycle and server instances per session.
-        await startHttpTransport(createMcpServerInstance, context);
-        return; // HTTP server runs indefinitely, no single server instance returned here.
+        // For HTTP, startHttpTransport now returns the http.Server instance.
+        const httpServerInstance = await startHttpTransport(createMcpServerInstance, context);
+        return httpServerInstance;
     }
     if (transportType === "stdio") {
         logger.debug("Creating single McpServer instance for stdio transport...", context);
         const server = await createMcpServerInstance();
         logger.debug("Delegating to connectStdioTransport...", context);
         await connectStdioTransport(server, context);
-        return server; // Return the single server instance for stdio.
+        return server; // Return the single McpServer instance for stdio.
     }
     // Should not be reached if config validation is effective.
     logger.fatal(`Unsupported transport type configured: ${transportType}`, context);
@@ -132,7 +134,7 @@ async function startTransport() {
  * - Manages server startup, leading to a server ready for MCP messages.
  * - Handles critical startup failures, ensuring appropriate process exit.
  *
- * @returns For 'stdio', resolves with `McpServer`. For 'http', runs indefinitely.
+ * @returns For 'stdio', resolves with `McpServer`. For 'http', resolves with `http.Server`.
  *   Rejects on critical failure, leading to process exit.
  */
 export async function initializeAndStartServer() {

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

@@ -6,7 +6,7 @@
  * @module src/mcp-server/tools/fetchPubMedContent/logic
  */
 import { z } from "zod";
-import { ncbiService } from "../../../services/NCBI/ncbiService.js";
+import { getNcbiService } from "../../../services/NCBI/ncbiService.js";
 import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
 import { logger, requestContextService, sanitizeInputForLogging, } from "../../../utils/index.js";
 import { ensureArray, extractAbstractText, extractArticleDates, extractAuthors, extractDoi, extractGrants, extractJournalInfo, extractKeywords, extractMeshTerms, extractPmid, extractPublicationTypes, getText, } from "../../../utils/parsing/ncbi-parsing/index.js";
@@ -292,6 +292,7 @@ export async function fetchPubMedContentLogic(input, parentRequestContext) {
             isError: true,
         };
     }
+    const ncbiService = getNcbiService();
     const toolLogicContext = requestContextService.createRequestContext({
         parentRequestId: parentRequestContext.requestId,
         operation: "fetchPubMedContentLogic",

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/generatePubMedChart/registration.js

@@ -5,11 +5,11 @@ export function registerGeneratePubMedChartTool(server) {
     const operation = "registerGeneratePubMedChartTool";
     const regContext = requestContextService.createRequestContext({ operation });
     try {
-        server.tool("generate_pubmed_chart", "Generates a customizable chart (SVG) from structured data. " +
+        server.tool("generate_pubmed_chart", "Generates a customizable chart (PNG) from structured data. " +
             "Supports 'bar', 'line', and 'scatter' plots. " +
             "Requires data values and field mappings for axes. " +
             "Optional parameters allow for titles, dimensions, and color/size/series encoding. " +
-            "Internally uses Vega-Lite to produce an SVG image.", GeneratePubMedChartInputSchema.shape, async (validatedInput, mcpProvidedContext) => {
+            "Internally uses Vega-Lite and a canvas renderer to produce a Base64-encoded PNG image.", GeneratePubMedChartInputSchema.shape, async (validatedInput, mcpProvidedContext) => {
             const handlerRequestContext = requestContextService.createRequestContext({
                 parentRequestId: regContext.requestId,
                 operation: "generatePubMedChartToolHandler",

package/dist/mcp-server/tools/getPubMedArticleConnections/logic/citationFormatter.js

@@ -3,7 +3,7 @@
  * Fetches article details using EFetch and formats them into various citation styles.
  * @module src/mcp-server/tools/getPubMedArticleConnections/logic/citationFormatter
  */
-import { ncbiService } from "../../../../services/NCBI/ncbiService.js";
+import { getNcbiService } from "../../../../services/NCBI/ncbiService.js";
 import { logger, requestContextService, } from "../../../../utils/index.js";
 import { extractAuthors, extractDoi, extractJournalInfo, extractPmid, getText, } from "../../../../utils/parsing/ncbi-parsing/index.js";
 // Main handler for citation formats
@@ -17,6 +17,7 @@ export async function handleCitationFormats(input, outputData, context) {
     const eFetchBaseUrl = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi";
     const searchParamsString = new URLSearchParams(eFetchParams).toString();
     outputData.eUtilityUrl = `${eFetchBaseUrl}?${searchParamsString}`;
+    const ncbiService = getNcbiService();
     const eFetchResult = await ncbiService.eFetch(eFetchParams, context);
     if (!eFetchResult?.PubmedArticleSet?.PubmedArticle?.[0]) {
         outputData.message =

package/dist/mcp-server/tools/getPubMedArticleConnections/logic/elinkHandler.js

@@ -3,7 +3,7 @@
  * for the getPubMedArticleConnections tool.
  * @module src/mcp-server/tools/getPubMedArticleConnections/logic/elinkHandler
  */
-import { ncbiService } from "../../../../services/NCBI/ncbiService.js";
+import { getNcbiService } from "../../../../services/NCBI/ncbiService.js";
 import { logger } from "../../../../utils/index.js";
 import { extractBriefSummaries } from "../../../../utils/parsing/ncbi-parsing/index.js";
 import { ensureArray } from "../../../../utils/parsing/ncbi-parsing/xmlGenericHelpers.js"; // Added import
@@ -33,6 +33,7 @@ export async function handleELinkRelationships(input, outputData, context) {
     const tempUrl = new URL("https://dummy.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi");
     Object.keys(eLinkParams).forEach((key) => tempUrl.searchParams.append(key, String(eLinkParams[key])));
     outputData.eUtilityUrl = `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?${tempUrl.search.substring(1)}`;
+    const ncbiService = getNcbiService();
     const eLinkResult = await ncbiService.eLink(eLinkParams, context);
     // Log the full eLinkResult for debugging
     logger.debug("Raw eLinkResult from ncbiService:", {

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

@@ -141,7 +141,7 @@ export const PubMedResearchAgentInputSchema = z.object({
         .optional()
         .describe("Ethical considerations, IRB/IACUC approval plans, data privacy, RCR training."),
     // Meta-parameter from previous iterations, still useful
-    include_detailed_prompts_for_agent: z // Renamed from include_edge_cases_and_challenges_in_plan
+    include_detailed_prompts_for_agent: z
         .boolean()
         .optional()
         .default(false) // Default to false, meaning the tool primarily structures the detailed input.

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

@@ -27,39 +27,48 @@ function G(notes, includePrompts) {
 function allPropertiesUndefined(obj) {
     return Object.values(obj).every((value) => value === undefined);
 }
-// Helper function to recursively remove keys with empty object values
+// Helper function to recursively remove keys with empty object or empty array values
 function removeEmptyObjectsRecursively(obj) {
     // Base cases for recursion
     if (typeof obj !== "object" || obj === null) {
         return obj; // Not an object or array, return as is
     }
     if (Array.isArray(obj)) {
-        // If it's an array, recurse on each element
-        // And filter out any elements that become empty objects after recursion
-        return obj.map(removeEmptyObjectsRecursively).filter((item) => {
+        // If it's an array, recurse on each element and filter out empty objects/arrays
+        const newArr = obj.map(removeEmptyObjectsRecursively).filter((item) => {
+            if (item === null || item === undefined)
+                return false;
+            if (Array.isArray(item) && item.length === 0)
+                return false; // Filter out empty arrays
             if (typeof item === "object" &&
-                item !== null &&
                 !Array.isArray(item) &&
                 Object.keys(item).length === 0) {
-                return false; // Filter out empty objects from arrays
+                return false; // Filter out empty objects
             }
             return true;
         });
+        return newArr;
     }
     // If it's an object, create a new object with non-empty properties
     const newObj = {};
     for (const key in obj) {
         if (Object.prototype.hasOwnProperty.call(obj, key)) {
             const value = removeEmptyObjectsRecursively(obj[key]);
-            // Check if the recursed value is an empty object
+            // Skip null or undefined values
+            if (value === null || value === undefined) {
+                continue;
+            }
+            // Skip empty arrays
+            if (Array.isArray(value) && value.length === 0) {
+                continue;
+            }
+            // Skip empty objects
             if (typeof value === "object" &&
-                value !== null &&
                 !Array.isArray(value) &&
                 Object.keys(value).length === 0) {
-                // It's an empty object, so we don't add this key-value pair to newObj
                 continue;
             }
-            // If value is not an empty object (or not an object at all), add it
+            // If value is not empty, add it
             newObj[key] = value;
         }
     }

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

@@ -5,7 +5,7 @@
  * @module src/mcp-server/tools/searchPubMedArticles/logic
  */
 import { z } from "zod";
-import { ncbiService } from "../../../services/NCBI/ncbiService.js";
+import { getNcbiService } from "../../../services/NCBI/ncbiService.js";
 import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
 import { logger, requestContextService, sanitizeInputForLogging, } from "../../../utils/index.js";
 import { extractBriefSummaries } from "../../../utils/parsing/ncbi-parsing/index.js";
@@ -70,6 +70,7 @@ export const SearchPubMedArticlesInputSchema = z.object({
  * @returns A promise resolving to a CallToolResult.
  */
 export async function searchPubMedArticlesLogic(input, parentRequestContext) {
+    const ncbiService = getNcbiService();
     const toolLogicContext = requestContextService.createRequestContext({
         parentRequestId: parentRequestContext.requestId,
         operation: "searchPubMedArticlesLogic",

package/dist/mcp-server/transports/authentication/authContext.d.ts

@@ -0,0 +1,33 @@
+/**
+ * @fileoverview Defines the AsyncLocalStorage context for authentication information.
+ * This module provides a mechanism to store and retrieve authentication details
+ * (like scopes and client ID) across asynchronous operations, making it available
+ * from the middleware layer down to the tool and resource handlers without
+ * drilling props.
+ *
+ * @module src/mcp-server/transports/authentication/authContext
+ */
+import { AsyncLocalStorage } from "async_hooks";
+import type { AuthInfo } from "./types.js";
+/**
+ * Defines the structure of the store used within the AsyncLocalStorage.
+ * It holds the authentication information for the current request context.
+ */
+interface AuthStore {
+    authInfo: AuthInfo;
+}
+/**
+ * An instance of AsyncLocalStorage to hold the authentication context (`AuthStore`).
+ * This allows `authInfo` to be accessible throughout the async call chain of a request
+ * after being set in the authentication middleware.
+ *
+ * @example
+ * // In middleware:
+ * await authContext.run({ authInfo }, next);
+ *
+ * // In a deeper handler:
+ * const store = authContext.getStore();
+ * const scopes = store?.authInfo.scopes;
+ */
+export declare const authContext: AsyncLocalStorage<AuthStore>;
+export {};