@cyanheads/pubmed-mcp-server 1.0.16 → 1.1.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "1.0.16",
+  "version": "1.1.1",
   "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": [
@@ -33,10 +33,11 @@
     "start:client-cli": "node dist/mcp-client/cli/mcp-client-cli.js"
   },
   "dependencies": {
-    "@google/genai": "^1.3.0",
+    "@hono/node-server": "^1.14.4",
     "@modelcontextprotocol/sdk": "^1.12.1",
+    "@node-oauth/oauth2-server": "^5.2.0",
     "@types/jsonwebtoken": "^9.0.9",
-    "@types/node": "^22.15.29",
+    "@types/node": "^24.0.1",
     "@types/sanitize-html": "^2.16.0",
     "@types/validator": "13.15.1",
     "axios": "^1.9.0",
@@ -46,10 +47,12 @@
     "cli-table3": "^0.6.5",
     "dotenv": "^16.5.0",
     "express": "^5.1.0",
-    "fast-xml-parser": "^5.2.3",
+    "fast-xml-parser": "^5.2.5",
+    "hono": "^4.7.11",
     "ignore": "^7.0.5",
+    "jose": "^6.0.11",
     "jsonwebtoken": "^9.0.2",
-    "openai": "^5.1.0",
+    "openai": "^5.3.0",
     "partial-json": "^0.1.7",
     "sanitize-html": "^2.17.0",
     "tiktoken": "^1.0.21",
@@ -61,7 +64,7 @@
     "winston": "^3.17.0",
     "winston-daily-rotate-file": "^5.0.0",
     "yargs": "^18.0.0",
-    "zod": "^3.25.50"
+    "zod": "^3.25.64"
   },
   "keywords": [
     "mcp",
@@ -84,6 +87,16 @@
   ],
   "author": "cyanheads <casey@caseyjhand.com> (https://github.com/cyanheads/pubmed-mcp-server#readme)",
   "license": "Apache-2.0",
+  "funding": [
+    {
+      "type": "github",
+      "url": "https://github.com/sponsors/cyanheads"
+    },
+    {
+      "type": "buy_me_a_coffee",
+      "url": "https://www.buymeacoffee.com/cyanheads"
+    }
+  ],
   "publishConfig": {
     "access": "public"
   },
@@ -91,7 +104,7 @@
     "node": ">=16.0.0"
   },
   "devDependencies": {
-    "@types/express": "^5.0.2",
+    "@types/express": "^5.0.3",
     "@types/js-yaml": "^4.0.9",
     "js-yaml": "^4.1.0",
     "prettier": "^3.5.3",

package/dist/services/index.d.ts

@@ -1,7 +0,0 @@
-/**
- * @fileoverview Main barrel file for all services.
- * This file re-exports all service modules, providing a single entry point
- * for accessing various services within the application.
- * @module src/services/index
- */
-export * from "./llm-providers/index.js";

package/dist/services/index.js

@@ -1,7 +0,0 @@
-/**
- * @fileoverview Main barrel file for all services.
- * This file re-exports all service modules, providing a single entry point
- * for accessing various services within the application.
- * @module src/services/index
- */
-export * from "./llm-providers/index.js";

package/dist/services/llm-providers/index.d.ts

@@ -1,7 +0,0 @@
-/**
- * @fileoverview Barrel file for LLM provider services.
- * This file re-exports all services related to different Large Language Model providers,
- * making them easily accessible from a single import path.
- * @module src/services/llm-providers/index
- */
-export * from "./openRouter/index.js";

package/dist/services/llm-providers/index.js

@@ -1,7 +0,0 @@
-/**
- * @fileoverview Barrel file for LLM provider services.
- * This file re-exports all services related to different Large Language Model providers,
- * making them easily accessible from a single import path.
- * @module src/services/llm-providers/index
- */
-export * from "./openRouter/index.js"; // Changed to export from the new barrel file

package/dist/services/llm-providers/llmFactory.d.ts

@@ -1,69 +0,0 @@
-/**
- * @fileoverview Factory for creating LLM client instances.
- * Provides a centralized way to instantiate clients for different LLM providers
- * like OpenRouter and Google Gemini, handling API key configuration and
- * basic client setup.
- * @module src/services/llm-providers/llmFactory
- */
-import { GoogleGenAI } from "@google/genai";
-import OpenAI from "openai";
-import { RequestContext } from "../../utils/index.js";
-/**
- * Defines the supported LLM providers.
- */
-export type LlmProviderType = "openrouter" | "gemini";
-/**
- * Options for configuring the OpenRouter client.
- */
-export interface OpenRouterClientOptions {
-    apiKey?: string;
-    baseURL?: string;
-    siteUrl?: string;
-    siteName?: string;
-}
-/**
- * Options for configuring the Gemini client using @google/genai.
- * The factory will return a GoogleGenAI instance.
- * Vertex AI specific options are included here.
- */
-export interface GeminiClientOptions {
-    apiKey?: string;
-    useVertexAi?: boolean;
-    project?: string;
-    location?: string;
-}
-/**
- * Union type for all LLM client options.
- */
-export type LlmClientOptions = OpenRouterClientOptions | GeminiClientOptions;
-/**
- * LLM Factory class to create and configure LLM clients.
- */
-declare class LlmFactory {
-    /**
-     * Creates and returns an LLM client instance for the specified provider.
-     *
-     * @param provider - The LLM provider to create a client for.
-     * @param context - The request context for logging.
-     * @param options - Optional provider-specific configuration options.
-     * @returns A Promise resolving to an instance of OpenAI (for OpenRouter)
-     *          or GoogleGenAI (for Gemini).
-     * @throws {McpError} If the provider is unsupported or API key/config is missing.
-     */
-    getLlmClient(provider: LlmProviderType, context: RequestContext, options?: LlmClientOptions): Promise<OpenAI | GoogleGenAI>;
-    /**
-     * Creates an OpenAI client configured for OpenRouter.
-     * @private
-     */
-    private createOpenRouterClient;
-    /**
-     * Creates a GoogleGenAI client for Gemini, supporting standard API key or Vertex AI.
-     * @private
-     */
-    private createGeminiClient;
-}
-/**
- * Singleton instance of the LlmFactory.
- */
-export declare const llmFactory: LlmFactory;
-export {};

package/dist/services/llm-providers/llmFactory.js

@@ -1,132 +0,0 @@
-/**
- * @fileoverview Factory for creating LLM client instances.
- * Provides a centralized way to instantiate clients for different LLM providers
- * like OpenRouter and Google Gemini, handling API key configuration and
- * basic client setup.
- * @module src/services/llm-providers/llmFactory
- */
-import { GoogleGenAI } from "@google/genai"; // Updated import path
-import OpenAI from "openai";
-import { config } from "../../config/index.js";
-import { BaseErrorCode, McpError } from "../../types-global/errors.js";
-import { logger } from "../../utils/index.js";
-/**
- * LLM Factory class to create and configure LLM clients.
- */
-class LlmFactory {
-    /**
-     * Creates and returns an LLM client instance for the specified provider.
-     *
-     * @param provider - The LLM provider to create a client for.
-     * @param context - The request context for logging.
-     * @param options - Optional provider-specific configuration options.
-     * @returns A Promise resolving to an instance of OpenAI (for OpenRouter)
-     *          or GoogleGenAI (for Gemini).
-     * @throws {McpError} If the provider is unsupported or API key/config is missing.
-     */
-    async getLlmClient(provider, context, options) {
-        // Return type changed for Gemini
-        const operation = `LlmFactory.getLlmClient.${provider}`;
-        logger.info(`[${operation}] Requesting LLM client`, {
-            ...context,
-            provider,
-        });
-        switch (provider) {
-            case "openrouter":
-                return this.createOpenRouterClient(context, options);
-            case "gemini":
-                return this.createGeminiClient(context, options);
-            default:
-                logger.error(`[${operation}] Unsupported LLM provider requested: ${provider}`, context);
-                throw new McpError(BaseErrorCode.CONFIGURATION_ERROR, `Unsupported LLM provider: ${provider}`, { operation, provider });
-        }
-    }
-    /**
-     * Creates an OpenAI client configured for OpenRouter.
-     * @private
-     */
-    createOpenRouterClient(context, options) {
-        const operation = "LlmFactory.createOpenRouterClient";
-        const apiKey = options?.apiKey || config.openrouterApiKey;
-        const baseURL = options?.baseURL || "https://openrouter.ai/api/v1";
-        const siteUrl = options?.siteUrl || config.openrouterAppUrl;
-        const siteName = options?.siteName || config.openrouterAppName;
-        if (!apiKey) {
-            logger.error(`[${operation}] OPENROUTER_API_KEY is not set.`, context);
-            throw new McpError(BaseErrorCode.CONFIGURATION_ERROR, "OpenRouter API key is not configured.", { operation });
-        }
-        try {
-            const client = new OpenAI({
-                baseURL,
-                apiKey,
-                defaultHeaders: {
-                    "HTTP-Referer": siteUrl,
-                    "X-Title": siteName,
-                },
-            });
-            logger.info(`[${operation}] OpenRouter client created successfully.`, context);
-            return client;
-        }
-        catch (error) {
-            logger.error(`[${operation}] Failed to create OpenRouter client`, {
-                ...context,
-                error: error.message,
-            });
-            throw new McpError(BaseErrorCode.INITIALIZATION_FAILED, `Failed to initialize OpenRouter client: ${error.message}`, { operation, cause: error });
-        }
-    }
-    /**
-     * Creates a GoogleGenAI client for Gemini, supporting standard API key or Vertex AI.
-     * @private
-     */
-    createGeminiClient(context, options) {
-        const operation = "LlmFactory.createGeminiClient";
-        if (options?.useVertexAi) {
-            if (!options.project || !options.location) {
-                logger.error(`[${operation}] Vertex AI project and location are required when useVertexAi is true.`, context);
-                throw new McpError(BaseErrorCode.CONFIGURATION_ERROR, "Vertex AI project and location must be configured if useVertexAi is true.", { operation });
-            }
-            try {
-                // For Vertex AI, apiKey in GoogleGenAI constructor is optional if ADC are set up.
-                // The SDK handles ADC automatically if apiKey is not provided.
-                const clientConfig = {
-                    project: options.project,
-                    location: options.location,
-                    vertexai: true,
-                };
-                if (options.apiKey) {
-                    // Allow API key to be passed for Vertex if specific auth needed
-                    clientConfig.apiKey = options.apiKey;
-                }
-                const genAI = new GoogleGenAI(clientConfig);
-                logger.info(`[${operation}] GoogleGenAI client for Vertex AI created successfully.`, context);
-                return genAI;
-            }
-            catch (error) {
-                logger.error(`[${operation}] Failed to create Gemini client for Vertex AI`, { ...context, error: error.message });
-                throw new McpError(BaseErrorCode.INITIALIZATION_FAILED, `Failed to initialize Gemini client for Vertex AI: ${error.message}`, { operation, cause: error });
-            }
-        }
-        else {
-            // Standard Gemini API key authentication
-            const apiKey = options?.apiKey || config.geminiApiKey;
-            if (!apiKey) {
-                logger.error(`[${operation}] GEMINI_API_KEY is not set for standard API usage.`, context);
-                throw new McpError(BaseErrorCode.CONFIGURATION_ERROR, "Gemini API key is not configured for standard API usage.", { operation });
-            }
-            try {
-                const genAI = new GoogleGenAI({ apiKey });
-                logger.info(`[${operation}] GoogleGenAI client (standard API key) created successfully.`, context);
-                return genAI;
-            }
-            catch (error) {
-                logger.error(`[${operation}] Failed to create Gemini client (standard API key)`, { ...context, error: error.message });
-                throw new McpError(BaseErrorCode.INITIALIZATION_FAILED, `Failed to initialize Gemini client (standard API key): ${error.message}`, { operation, cause: error });
-            }
-        }
-    }
-}
-/**
- * Singleton instance of the LlmFactory.
- */
-export const llmFactory = new LlmFactory();

package/dist/services/llm-providers/openRouter/index.d.ts

@@ -1,6 +0,0 @@
-/**
- * @fileoverview Barrel file for the OpenRouter provider service.
- * Exports the OpenRouterProvider class and any related types.
- * @module services/llm-providers/openRouter/index
- */
-export * from "./openRouterProvider.js";

package/dist/services/llm-providers/openRouter/index.js

@@ -1,7 +0,0 @@
-/**
- * @fileoverview Barrel file for the OpenRouter provider service.
- * Exports the OpenRouterProvider class and any related types.
- * @module services/llm-providers/openRouter/index
- */
-export * from "./openRouterProvider.js";
-// Add other exports from this module if any in the future

package/dist/services/llm-providers/openRouter/openRouterProvider.d.ts

@@ -1,99 +0,0 @@
-import { OpenRouterClientOptions } from "../llmFactory.js";
-import { ChatCompletion, ChatCompletionChunk, ChatCompletionCreateParamsNonStreaming, ChatCompletionCreateParamsStreaming } from "openai/resources/chat/completions";
-import { Stream } from "openai/streaming";
-import { OperationContext, RequestContext } from "../../../utils/internal/requestContext.js";
-/**
- * Defines the parameters for an OpenRouter chat completion request.
- * This type extends standard OpenAI chat completion parameters and includes
- * OpenRouter-specific fields.
- *
- * @property top_k - OpenRouter specific: Sample from the k most likely next tokens.
- * @property min_p - OpenRouter specific: Minimum probability for a token to be considered.
- * @property transforms - OpenRouter specific: Apply transformations to the request or response.
- * @property models - OpenRouter specific: A list of models to use, often for fallback or routing.
- * @property route - OpenRouter specific: Specifies routing strategy, e.g., 'fallback'.
- * @property provider - OpenRouter specific: Provider-specific parameters or routing preferences.
- * @property stream - If true, the response will be a stream of `ChatCompletionChunk` objects.
- *   If false or undefined, a single `ChatCompletion` object is returned.
- */
-export type OpenRouterChatParams = (ChatCompletionCreateParamsNonStreaming | ChatCompletionCreateParamsStreaming) & {
-    top_k?: number;
-    min_p?: number;
-    transforms?: string[];
-    models?: string[];
-    route?: "fallback";
-    provider?: Record<string, any>;
-};
-/**
- * Service class for interacting with the OpenRouter API.
- * Uses the OpenAI SDK for chat completions, configured for OpenRouter.
- * Handles API key management, default headers, model-specific parameter adjustments,
- * and provides methods for chat completions and listing models.
- */
-declare class OpenRouterProvider {
-    /**
-     * The OpenAI SDK client instance configured for OpenRouter.
-     * @private
-     */
-    private client?;
-    /**
-     * Current status of the OpenRouter service.
-     * - `unconfigured`: API key is missing.
-     * - `initializing`: Constructor is running.
-     * - `ready`: Client initialized successfully and service is usable.
-     * - `error`: An error occurred during initialization.
-     */
-    status: "unconfigured" | "initializing" | "ready" | "error";
-    /**
-     * Stores any error that occurred during client initialization.
-     * @private
-     */
-    private initializationError;
-    /**
-     * Constructs an `OpenRouterProvider` instance.
-     * Initializes the OpenAI client for OpenRouter if an API key is provided.
-     * Sets default headers required by OpenRouter.
-     * @param apiKey - The OpenRouter API key. If undefined, the service remains 'unconfigured'.
-     * @param parentOpContext - Optional parent operation context for linked logging.
-     */
-    constructor(options?: OpenRouterClientOptions, parentOpContext?: OperationContext);
-    /**
-     * Checks if the service is ready to make API calls.
-     * @param operation - The name of the operation attempting to use the service.
-     * @param context - The request context for logging.
-     * @throws {McpError} If the service is not ready.
-     * @private
-     */
-    private checkReady;
-    /**
-     * Creates a chat completion using the OpenRouter API.
-     * Can return either a single response or a stream of chunks.
-     * Applies rate limiting and handles model-specific parameter adjustments.
-     *
-     * @param params - Parameters for the chat completion request.
-     * @param context - Request context for logging, error handling, and rate limiting.
-     * @returns A promise resolving with either a `ChatCompletion` or a `Stream<ChatCompletionChunk>`.
-     * @throws {McpError} If service not ready, rate limit exceeded, or API call fails.
-     */
-    chatCompletion(params: OpenRouterChatParams, context: RequestContext): Promise<ChatCompletion | Stream<ChatCompletionChunk>>;
-    /**
-     * Lists available models from the OpenRouter API.
-     * Makes a direct `fetch` call to the `/models` endpoint.
-     *
-     * @param context - Request context for logging and error handling.
-     * @returns A promise resolving with the JSON response from the OpenRouter API.
-     * @throws {McpError} If the service is not ready, or if the API call fails.
-     */
-    listModels(context: RequestContext): Promise<any>;
-}
-/**
- * Singleton instance of the `OpenRouterProvider`.
- * Initialized with the OpenRouter API key from application configuration.
- */
-declare const openRouterProviderInstance: OpenRouterProvider;
-export { openRouterProviderInstance as openRouterProvider };
-/**
- * Exporting the type of the OpenRouterProvider class for use in dependency injection
- * or for type hinting elsewhere in the application.
- */
-export type { OpenRouterProvider };