@cyanheads/pubmed-mcp-server 1.0.14 → 1.1.1

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.d.ts

@@ -12,7 +12,7 @@ export declare const GeneratePubMedChartInputSchema: z.ZodObject<{
     width: z.ZodDefault<z.ZodOptional<z.ZodNumber>>;
     height: z.ZodDefault<z.ZodOptional<z.ZodNumber>>;
     dataValues: z.ZodArray<z.ZodRecord<z.ZodString, z.ZodAny>, "many">;
-    outputFormat: z.ZodDefault<z.ZodEnum<["svg"]>>;
+    outputFormat: z.ZodDefault<z.ZodEnum<["png"]>>;
     xField: z.ZodString;
     yField: z.ZodString;
     xFieldType: z.ZodOptional<z.ZodEnum<["nominal", "ordinal", "quantitative", "temporal"]>>;
@@ -26,7 +26,7 @@ export declare const GeneratePubMedChartInputSchema: z.ZodObject<{
 }, "strip", z.ZodTypeAny, {
     width: number;
     height: number;
-    outputFormat: "svg";
+    outputFormat: "png";
     chartType: "bar" | "line" | "scatter";
     dataValues: Record<string, any>[];
     xField: string;
@@ -48,7 +48,7 @@ export declare const GeneratePubMedChartInputSchema: z.ZodObject<{
     title?: string | undefined;
     width?: number | undefined;
     height?: number | undefined;
-    outputFormat?: "svg" | undefined;
+    outputFormat?: "png" | undefined;
     xFieldType?: "nominal" | "ordinal" | "quantitative" | "temporal" | undefined;
     yFieldType?: "nominal" | "ordinal" | "quantitative" | "temporal" | undefined;
     colorField?: string | undefined;

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

@@ -30,9 +30,9 @@ export const GeneratePubMedChartInputSchema = z.object({
         .min(1)
         .describe("Required. An array of data objects used to plot the chart. Each object represents a data point or bar, structured as key-value pairs (e.g., [{ 'year': '2020', 'articles': 150 }, { 'year': '2021', 'articles': 180 }]). Must contain at least one data object."),
     outputFormat: z
-        .enum(["svg"])
-        .default("svg")
-        .describe("Specifies the output format for the chart. Currently, only 'svg' (Scalable Vector Graphics) is supported and is the default."),
+        .enum(["png"]) // Changed from svg to png
+        .default("png") // Changed default to png
+        .describe("Specifies the output format for the chart. Currently, only 'png' (Portable Network Graphics) is supported and is the default."),
     xField: z
         .string()
         .describe("Required. The name of the field in `dataValues` to be used for the X-axis (horizontal). This field determines the categories or values along the bottom of the chart (e.g., 'year', 'geneName', 'publicationCount')."),
@@ -83,8 +83,9 @@ 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 !== "svg") {
-        const unsupportedFormatError = new McpError(BaseErrorCode.VALIDATION_ERROR, `Unsupported output format: ${input.outputFormat}. Currently, only 'svg' is supported.`, { requestedFormat: input.outputFormat });
+    if (input.outputFormat !== "png") { // Changed from svg to png
+        const unsupportedFormatError = new McpError(BaseErrorCode.VALIDATION_ERROR, `Unsupported output format: ${input.outputFormat}. Currently, only 'png' is supported.`, // Changed message
+        { requestedFormat: input.outputFormat });
         logger.warning(unsupportedFormatError.message, operationContext);
         return {
             content: [
@@ -203,14 +204,24 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
         }
         const compiledVegaSpec = vegaLite.compile(vegaLiteSpec).spec;
         const view = new vega.View(vega.parse(compiledVegaSpec), {
-            renderer: "none",
+            renderer: "canvas", // Explicitly set renderer to 'canvas'
         });
-        const svgString = await view.toSVG();
-        const imageBuffer = Buffer.from(svgString, "utf-8");
+        // const svgString = await view.toSVG(); // Old SVG method
+        // New PNG method
+        // Initialize the view to ensure canvas is ready
+        await view.runAsync(); // Initialize and run the view
+        const canvas = await view.toCanvas(); // Render to canvas
+        // Cast to 'any' to access toBuffer, assuming it's a Node Canvas instance at runtime
+        const imageBuffer = await canvas.toBuffer("image/png"); // Get PNG buffer from canvas
         const base64Data = imageBuffer.toString("base64");
-        const dataUriSvg = `data:image/svg+xml;base64,${base64Data}`;
         return {
-            content: [{ type: "text", text: dataUriSvg }],
+            content: [
+                {
+                    type: "image",
+                    data: base64Data,
+                    mimeType: "image/png", // Changed MIME type to image/png
+                },
+            ],
             isError: false,
         };
     }

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 +27,50 @@ 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 {};

package/dist/mcp-server/transports/authentication/authContext.js

@@ -0,0 +1,24 @@
+/**
+ * @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";
+/**
+ * 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 const authContext = new AsyncLocalStorage();

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

@@ -1,5 +1,5 @@
 /**
- * @fileoverview MCP Authentication Middleware for Bearer Token Validation (JWT).
+ * @fileoverview MCP Authentication Middleware for Bearer Token Validation (JWT) for Hono.
  *
  * This middleware validates JSON Web Tokens (JWT) passed via the 'Authorization' header
  * using the 'Bearer' scheme (e.g., "Authorization: Bearer <your_token>").
@@ -7,23 +7,29 @@
  * in the configuration (`config.mcpAuthSecretKey`).
  *
  * If the token is valid, an object conforming to the MCP SDK's `AuthInfo` type
- * (expected to contain `token`, `clientId`, and `scopes`) is attached to `req.auth`.
- * If the token is missing, invalid, or expired, it sends an HTTP 401 Unauthorized response.
+ * is attached to `c.env.incoming.auth`. This direct attachment to the raw Node.js
+ * request object is for compatibility with the underlying SDK transport, which is
+ * not Hono-context-aware.
+ * If the token is missing, invalid, or expired, it returns an HTTP 401 Unauthorized response.
  *
  * @see {@link https://github.com/modelcontextprotocol/modelcontextprotocol/blob/main/docs/specification/2025-03-26/basic/authorization.mdx | MCP Authorization Specification}
  * @module src/mcp-server/transports/authentication/authMiddleware
  */
-import { NextFunction, Request, Response } from "express";
-import { AuthInfo } from "@modelcontextprotocol/sdk/server/auth/types.js";
-declare global {
-    namespace Express {
-        interface Request {
-            /** Authentication information derived from the JWT, conforming to MCP SDK's AuthInfo. */
-            auth?: AuthInfo;
-        }
-    }
-}
+import { HttpBindings } from "@hono/node-server";
+import { Context, Next } from "hono";
 /**
- * Express middleware for verifying JWT Bearer token authentication.
+ * Validates the presence of the MCP_AUTH_SECRET_KEY at startup.
+ * This should be called once when the application is initializing.
  */
-export declare function mcpAuthMiddleware(req: Request, res: Response, next: NextFunction): void;
+export declare function initializeAuthMiddleware(): void;
+/**
+ * Hono middleware for verifying JWT Bearer token authentication.
+ * It attaches authentication info to `c.env.incoming.auth` for SDK compatibility with the node server.
+ */
+export declare function mcpAuthMiddleware(c: Context<{
+    Bindings: HttpBindings;
+}>, next: Next): Promise<void | (Response & import("hono").TypedResponse<{
+    error: string;
+}, 500, "json">) | (Response & import("hono").TypedResponse<{
+    error: string;
+}, 401, "json">)>;