@cyanheads/pubmed-mcp-server 1.0.12

package/LICENSE

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package/README.md

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+# PubMed MCP Server Pubmed
+
+[![TypeScript](https://img.shields.io/badge/TypeScript-^5.8.3-blue.svg)](https://www.typescriptlang.org/)
+[![Model Context Protocol SDK](https://img.shields.io/badge/MCP%20SDK-1.12.0-green.svg)](https://github.com/modelcontextprotocol/typescript-sdk)
+[![MCP Spec Version](https://img.shields.io/badge/MCP%20Spec-2025--03--26-lightgrey.svg)](https://github.com/modelcontextprotocol/modelcontextprotocol/blob/main/docs/specification/2025-03-26/changelog.mdx)
+[![Version](https://img.shields.io/badge/Version-1.0.12-blue.svg)](./CHANGELOG.md)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Status](https://img.shields.io/badge/Status-Beta-orange.svg)](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)
+
+**Unlock the power of biomedical literature for your AI agents with the PubMed MCP Server!**
+
+This server acts as a bridge, connecting your AI to NCBI's PubMed and E-utilities through the [Model Context Protocol (MCP)](https://modelcontextprotocol.io/). It empowers language models to seamlessly search, retrieve, and analyze biomedical articles and data. Built with TypeScript and adhering to the **MCP 2025-03-26 specification**, it's designed for robustness and includes production-grade utilities.
+
+## 🚀 Core Capabilities: PubMed Tools 🛠️
+
+This server equips your AI with specialized tools to interact with PubMed:
+
+| Tool Name                        | Description                                                                                                                       | Key Features                                                                                                                                                                                                                                                                                                                                                                                         | Output Structure (JSON Example)                                                                                                                                                                                                                                                                                                 |
+| :------------------------------- | :-------------------------------------------------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| `search_pubmed_articles`         | Searches PubMed for articles based on your query.                                                                                 | - Filter by max results, sort order, date range, publication types.<br/>- Uses NCBI ESearch for PMIDs.<br/>- Optionally fetches brief summaries (title, authors, source, dates) via ESummary.                                                                                                                                                                                                        | `{"searchParameters": {"queryTerm": "oncology", "maxResults": 5},"effectiveESearchTerm": "oncology","totalFound": 250,"retrievedPmidCount": 5,"pmids": ["12345", "67890"],"briefSummaries": [{"pmid": "12345", "title": "Example Title"}],"eSearchUrl": "https://ncbi...","eSummaryUrl": "https://ncbi..."}`                    |
+| `fetch_pubmed_content`           | Retrieves detailed information for PubMed articles. Can use a list of PMIDs or ESearch history (queryKey/webEnv) with pagination. | - Flexible `detailLevel`: `abstract_plus` (parsed details, optional MeSH/grant), `full_xml` (JSON representation of the PubMedArticle XML structure), `medline_text` (MEDLINE format), `citation_data` (minimal for citations).<br/>- Supports direct PMID list or `queryKey`/`webEnv` from ESearch history.<br/>- Supports `retstart`/`retmax` for pagination with history.<br/>- Uses NCBI EFetch. | `{"requestedPmids": ["12345"],"articles": [{"pmid": "12345", "title": "Example Title", "abstractText": "..."}],"notFoundPmids": [],"eFetchDetails": {"urls": ["https://ncbi..."], "requestMethod": "GET"}}` (Or raw string for`detailLevel: 'full_xml'/'medline_text'`with`outputFormat: 'raw_text'`)                           |
+| `get_pubmed_article_connections` | Finds related articles (cited by, similar, references) or formats citations for a PMID.                                           | - Uses NCBI ELink for relationships.<br/>- Uses NCBI EFetch for citation data (RIS, BibTeX, APA, MLA).<br/>- Filter by max related results.                                                                                                                                                                                                                                                          | `{"sourcePmid": "12345","relationshipType": "pubmed_similar_articles","relatedArticles": [{"pmid": "67890", "title": "Related Title"}],"citations": {"ris": "RIS formatted citation..." },"retrievedCount": 1,"eUtilityUrl": "https://ncbi...","message": "Success"}`                                                           |
+| `pubmed_research_agent`          | Generates a standardized JSON research plan outline from component details.                                                       | - Accepts granular inputs for all research phases.<br/>- Optionally embeds instructive prompts for agent execution.<br/>- Structures rough ideas into a formal, machine-readable plan for further processing.                                                                                                                                                                                        | `{"plan_title": "Comprehensive Research Plan on Topic X","input_summary": {"keywords_received": ["Topic X", "Gene Y"]},"phase_1_conception_and_planning": {"step_1_1_research_question_and_hypothesis": {"primary_research_question": "What is the role of Gene Y in Topic X?"}},"phase_2_data_collection_and_processing": {}}` |
+
+---
+
+## ✨ Key Features Beyond Tools
+
+| Feature Category               | Description                                                                                                                                                                  |
+| :----------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| **🔌 MCP Compliant**           | Fully functional server supporting `stdio` and `http` (SSE) transports.                                                                                                      |
+| **🚀 Production-Ready Utils**  | Includes robust logging, error handling, ID generation, rate limiting, request context tracking, and input sanitization.                                                     |
+| **🔒 Secure & Type-Safe**      | Built with TypeScript & Zod for strong type checking and input validation. Manages NCBI API keys, implements rate limiting, and features JWT-based auth middleware for HTTP. |
+| **⚙️ Advanced Error Handling** | Consistent error categorization, detailed logging, and centralized handling, including specific error types for NCBI interactions.                                           |
+| **📚 Well-Documented**         | Comprehensive JSDoc comments, API references, and project specifications.                                                                                                    |
+| **🤖 Agent-Friendly**          | Includes a `.clinerules` developer cheatsheet tailored for LLM coding agents using this server.                                                                              |
+| **🛠️ Developer Utilities**     | Scripts for cleaning builds, setting executable permissions, generating directory trees, and fetching OpenAPI specifications.                                                |
+
+## 🚀 Quick Start
+
+Get the PubMed MCP server running in minutes:
+
+1.  **Clone the repository:**
+
+    ```bash
+    git clone https://github.com/cyanheads/pubmed-mcp-server.git
+    cd pubmed-mcp-server
+    ```
+
+2.  **Install dependencies:**
+
+    ```bash
+    npm install
+    ```
+
+3.  **Configure Environment Variables (`.env` file):**
+    Create a `.env` file in the project root. Key variables:
+
+    ```env
+    # REQUIRED FOR HTTP TRANSPORT
+    MCP_AUTH_SECRET_KEY=generate_a_strong_random_32_plus_char_secret_key
+
+    # RECOMMENDED FOR NCBI E-UTILITIES (for higher rate limits)
+    # NCBI_API_KEY=your_ncbi_api_key_here
+    # NCBI_ADMIN_EMAIL=your_email@example.com # Recommended if using an API key
+    # NCBI_TOOL_IDENTIFIER=@cyanheads/pubmed-mcp-server/1.0.11 # Optional: Tool identifier for NCBI (defaults to current version)
+    ```
+
+    For all options, see the [Configuration](#⚙️-configuration) section below or the [Developer Cheatsheet (.clinerules)](./.clinerules).
+
+4.  **Build the project:**
+
+    ```bash
+    npm run build
+    # Or use 'npm run rebuild' for a clean install (deletes node_modules, logs, dist)
+    ```
+
+5.  **Format the code (Optional but Recommended):**
+
+    ```bash
+    npm run format
+    ```
+
+6.  **Run the Server:**
+
+    - **Via Stdio (Default):** Many MCP host applications will run this automatically using `stdio`. To run manually for testing:
+      ```bash
+      npm start
+      # or 'npm run start:stdio'
+      ```
+    - **Via HTTP (SSE):** (Ensure `MCP_TRANSPORT_TYPE=http` and `MCP_AUTH_SECRET_KEY` are set in your `.env`)
+      ```bash
+      npm run start:http
+      ```
+      This starts an HTTP server (default: `http://127.0.0.1:3010`) using Server-Sent Events.
+
+## ⚙️ Configuration
+
+### Server Configuration (Environment Variables)
+
+Configure the PubMed MCP server's behavior using environment variables (typically in a `.env` file).
+
+| Variable                | Description                                                                                            | Default                                  |
+| :---------------------- | :----------------------------------------------------------------------------------------------------- | :--------------------------------------- |
+| `MCP_TRANSPORT_TYPE`    | Server transport: `stdio` or `http`.                                                                   | `stdio`                                  |
+| `MCP_HTTP_PORT`         | Port for the HTTP server (if `MCP_TRANSPORT_TYPE=http`).                                               | `3010`                                   |
+| `MCP_HTTP_HOST`         | Host address for the HTTP server (if `MCP_TRANSPORT_TYPE=http`).                                       | `127.0.0.1`                              |
+| `MCP_ALLOWED_ORIGINS`   | Comma-separated allowed origins for CORS (if `MCP_TRANSPORT_TYPE=http`).                               | (none)                                   |
+| `MCP_LOG_LEVEL`         | Server logging level (`debug`, `info`, `warning`, `error`, etc.).                                      | `debug`                                  |
+| `LOGS_DIR`              | Directory for log files.                                                                               | `logs/` (in project root)                |
+| `NODE_ENV`              | Runtime environment (`development`, `production`).                                                     | `development`                            |
+| `MCP_AUTH_SECRET_KEY`   | **Required for HTTP transport.** Secret key (min 32 chars) for signing/verifying auth tokens (JWT).    | (none - **MUST be set in production**)   |
+| `NCBI_API_KEY`          | **Optional, but highly recommended.** Your NCBI API Key for higher rate limits (10/sec vs 3/sec).      | (none)                                   |
+| `NCBI_ADMIN_EMAIL`      | **Optional, but recommended if using an API key.** Your email for NCBI contact.                        | (none)                                   |
+| `NCBI_TOOL_IDENTIFIER`  | Optional. Tool identifier sent to NCBI.                                                                | `@cyanheads/pubmed-mcp-server/<version>` |
+| `NCBI_REQUEST_DELAY_MS` | Milliseconds to wait between NCBI requests. Dynamically set (e.g., 100ms with API key, 334ms without). | (see `src/config/index.ts`)              |
+| `NCBI_MAX_RETRIES`      | Maximum number of retries for failed NCBI requests.                                                    | `3`                                      |
+
+**Note on HTTP Port Retries:** If the `MCP_HTTP_PORT` is busy, the server automatically tries the next port (up to 15 times).
+
+**Security Note for HTTP Transport:** When using `MCP_TRANSPORT_TYPE=http`, authentication is **mandatory** as per the MCP specification. This server includes JWT-based authentication middleware. You **MUST** set a strong, unique `MCP_AUTH_SECRET_KEY` in your production environment.
+
+For a **comprehensive list of all available environment variables**, their descriptions, and default values, please review the configuration loader at `src/config/index.ts`.
+
+## 🏗️ Project Structure Overview
+
+The `src/` directory contains the core logic:
+
+- `config/`: Environment variable loading and package information.
+- `mcp-server/`: The heart of the PubMed MCP server.
+  - `server.ts`: Initializes the server instance and registers all tools and resources.
+  - `resources/`: Implementations for MCP resources (e.g., server status, PubMed statistics).
+  - `tools/`: Implementations for MCP tools (like `searchPubMedArticles`, `fetchPubMedContent`, `getPubMedArticleConnections`).
+  - `transports/`: Handles `stdio` and `http` (SSE) communication, including authentication for HTTP.
+- `services/`: Integrations with external services.
+  - `NCBI/ncbiService.ts`: Manages all interactions with NCBI E-utilities, including API calls, rate limiting, and response parsing.
+  - `llm-providers/`: (Optional) For integrating LLM capabilities directly within the server.
+- `types-global/`: Shared TypeScript definitions, especially for errors and MCP types.
+- `utils/`: A comprehensive suite of reusable utilities for logging, error handling, security, parsing, metrics, and more.
+
+For a detailed file tree, run: `npm run tree` or see [Directory Tree](./docs/tree.md).
+
+## 🧩 Extending with More PubMed Capabilities
+
+Adding new tools or resources is straightforward:
+
+1.  **Directory Setup**: Create a new directory under `src/mcp-server/tools/yourNewTool/` or `src/mcp-server/resources/yourNewResource/`.
+2.  **Implement Core Logic (`logic.ts`)**:
+    - Define Zod schemas for input validation.
+    - Write the function that interacts with `src/services/NCBI/ncbiService.ts` (e.g., `ncbiService.eLink(...)`).
+    - Parse the NCBI response and format it according to MCP specifications (`CallToolResult` or `ReadResourceResult`).
+3.  **Register the Capability (`registration.ts`)**:
+    - For tools: `server.tool(name, description, zodSchemaShape, handlerFunction)`
+    - For resources: `server.resource(registrationName, template, metadata, handlerFunction)`
+    - Always wrap your logic in `ErrorHandler.tryCatch` for robust error management.
+4.  **Export and Integrate**: Export the registration function from your new directory's `index.ts` and call it within `src/mcp-server/server.ts`.
+
+## 🌍 Learn More
+
+- **[Model Context Protocol Official Site](https://modelcontextprotocol.io/)**
+- **[MCP Specification (2025-03-26)](https://github.com/modelcontextprotocol/modelcontextprotocol/blob/main/docs/specification/2025-03-26/changelog.mdx)**
+- **[TypeScript SDK for MCP](https://github.com/modelcontextprotocol/typescript-sdk)**
+- **[NCBI E-utilities Documentation](https://www.ncbi.nlm.nih.gov/books/NBK25501/)**
+
+## 📜 License
+
+This project is licensed under the Apache License 2.0. See the [LICENSE](LICENSE) file for details.
+
+---
+
+<div align="center">
+  Empowering AI with PubMed | Built on the <a href="https://modelcontextprotocol.io/">Model Context Protocol</a>
+</div>

package/dist/config/index.d.ts

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+/**
+ * @fileoverview Loads, validates, and exports application configuration.
+ * This module centralizes configuration management, sourcing values from
+ * environment variables and `package.json`. It uses Zod for schema validation
+ * to ensure type safety and correctness of configuration parameters.
+ *
+ * Key responsibilities:
+ * - Load environment variables from a `.env` file.
+ * - Read `package.json` for default server name and version.
+ * - Define a Zod schema for all expected environment variables.
+ * - Validate environment variables against the schema.
+ * - Construct and export a comprehensive `config` object.
+ * - Export individual configuration values like `logLevel` and `environment` for convenience.
+ *
+ * @module src/config/index
+ */
+/**
+ * Main application configuration object.
+ * Aggregates settings from validated environment variables and `package.json`.
+ */
+export declare const config: {
+    /** MCP server name. Env `MCP_SERVER_NAME` > `package.json` name > "mcp-ts-template". */
+    mcpServerName: string;
+    /** MCP server version. Env `MCP_SERVER_VERSION` > `package.json` version > "0.0.0". */
+    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;
+    /** 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". */
+    mcpTransportType: "stdio" | "http";
+    /** HTTP server port (if http transport). From `MCP_HTTP_PORT` env var. Default: 3010. */
+    mcpHttpPort: number;
+    /** HTTP server host (if http transport). From `MCP_HTTP_HOST` env var. Default: "127.0.0.1". */
+    mcpHttpHost: string;
+    /** Array of allowed CORS origins (http transport). From `MCP_ALLOWED_ORIGINS` (comma-separated). */
+    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;
+    /** NCBI API Key. From `NCBI_API_KEY`. */
+    ncbiApiKey: string | undefined;
+    /** NCBI Tool Identifier. From `NCBI_TOOL_IDENTIFIER`. Defaults to server name/version. */
+    ncbiToolIdentifier: string;
+    /** NCBI Admin Email. From `NCBI_ADMIN_EMAIL`. */
+    ncbiAdminEmail: string | undefined;
+    /** NCBI Request Delay in MS. From `NCBI_REQUEST_DELAY_MS`. Dynamically set based on API key presence. */
+    ncbiRequestDelayMs: number;
+    /** NCBI Max Retries. From `NCBI_MAX_RETRIES`. */
+    ncbiMaxRetries: number;
+    /** OAuth Proxy configurations. Undefined if no related env vars are set. */
+    oauthProxy: {
+        authorizationUrl: string | undefined;
+        tokenUrl: string | undefined;
+        revocationUrl: string | undefined;
+        issuerUrl: string | undefined;
+        serviceDocumentationUrl: string | undefined;
+        defaultClientRedirectUris: string[] | undefined;
+    } | undefined;
+};
+/**
+ * Configured logging level for the application.
+ * Exported for convenience.
+ */
+export declare const logLevel: string;
+/**
+ * Configured runtime environment ("development", "production", etc.).
+ * Exported for convenience.
+ */
+export declare const environment: string;