@cyanheads/pubmed-mcp-server 1.1.2 → 1.2.1

package/README.md

@@ -2,7 +2,7 @@
 
 [![TypeScript](https://img.shields.io/badge/TypeScript-^5.8.3-blue.svg)](https://www.typescriptlang.org/)
 [![Model Context Protocol](https://img.shields.io/badge/MCP%20SDK-^1.12.1-green.svg)](https://modelcontextprotocol.io/)
-[![Version](https://img.shields.io/badge/Version-1.0.16-blue.svg)](./CHANGELOG.md)
+[![Version](https://img.shields.io/badge/Version-1.2.1-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-Stable-green.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)
@@ -17,13 +17,13 @@ Built on the [`cyanheads/mcp-ts-template`](https://github.com/cyanheads/mcp-ts-t
 
 This server equips your AI with specialized tools to interact with PubMed:
 
-| Tool Name                                                                               | Description                                                                                                                                                                                                                                    | Key Features                                                                                                                                                                                                                                                                                                                                                                                         |
-| :-------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| [`search_pubmed_articles`](./src/mcp-server/tools/searchPubMedArticles/)                | Searches PubMed for articles based on your query. (See [Example](./examples/search_pubmed_articles_example.md))                                                                                                                                | - 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.                                                                                                                                                                                                        |
-| [`fetch_pubmed_content`](./src/mcp-server/tools/fetchPubMedContent/)                    | Retrieves detailed information for PubMed articles. Can use a list of PMIDs or ESearch history (queryKey/webEnv) with pagination. (See [Example](./examples/fetch_pubmed_content_example.md))                                                  | - 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. |
-| [`get_pubmed_article_connections`](./src/mcp-server/tools/getPubMedArticleConnections/) | Finds related articles (cited by, similar, references) or formats citations for a PMID. (See [Ex.1](./examples/get_pubmed_article_connections_1.md), [Ex.2](./examples/get_pubmed_article_connections_2.md))                                   | - Uses NCBI ELink for relationships.<br/>- Uses NCBI EFetch for citation data (RIS, BibTeX, APA, MLA).<br/>- Filter by max related results.                                                                                                                                                                                                                                                          |
-| [`pubmed_research_agent`](./src/mcp-server/tools/pubmedResearchAgent/)                  | Generates a standardized JSON research plan outline from component details. (See [Example](./examples/pubmed_research_agent_example.md))                                                                                                       | - 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.                                                                                                                                                                                        |
-| [`generate_pubmed_chart`](./src/mcp-server/tools/generatePubMedChart/)                  | Generates a chart image (PNG) from given input data. (See [Bar](./examples/generate_pubmed_chart_example_bar.svg), [Line](./examples/generate_pubmed_chart_example_line.svg), [Scatter](./examples/generate_pubmed_chart_example_scatter.svg)) | - Supports 'bar', 'line', and 'scatter' chart types.<br/>- Takes data values and field specifications for axes and encoding.<br/>- Constructs a Vega-Lite specification internally and renders it as a PNG.                                                                                                                                                                                          |
+| Tool Name                                                                               | Description                                                                                                                                                                                                  | Key Features                                                                                                                                                                                                                                                                                                                                                                                         |
+| :-------------------------------------------------------------------------------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| [`search_pubmed_articles`](./src/mcp-server/tools/searchPubMedArticles/)                | Searches PubMed for articles based on your query. (See [Example](./examples/search_pubmed_articles_example.md))                                                                                              | - 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.                                                                                                                                                                                                        |
+| [`fetch_pubmed_content`](./src/mcp-server/tools/fetchPubMedContent/)                    | Retrieves detailed information for PubMed articles. Can use a list of PMIDs or ESearch history (queryKey/webEnv) with pagination. (See [Example](./examples/fetch_pubmed_content_example.md))                | - 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. |
+| [`get_pubmed_article_connections`](./src/mcp-server/tools/getPubMedArticleConnections/) | Finds related articles (cited by, similar, references) or formats citations for a PMID. (See [Ex.1](./examples/get_pubmed_article_connections_1.md), [Ex.2](./examples/get_pubmed_article_connections_2.md)) | - Uses NCBI ELink for relationships.<br/>- Uses NCBI EFetch for citation data (RIS, BibTeX, APA, MLA).<br/>- Filter by max related results.                                                                                                                                                                                                                                                          |
+| [`pubmed_research_agent`](./src/mcp-server/tools/pubmedResearchAgent/)                  | Generates a standardized JSON research plan outline from component details. (See [Example](./examples/pubmed_research_agent_example.md))                                                                     | - 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.                                                                                                                                                                                        |
+| [`generate_pubmed_chart`](./src/mcp-server/tools/generatePubMedChart/)                  | Generates a chart image (PNG) from given input data. (See [Examples](./examples/generate_pubmed_chart))                                                                                                      | - Supports a wide range of chart types: `bar`, `line`, `scatter`, `pie`, `doughnut`, `bubble`, `radar`, and `polarArea`.<br/>- Takes data values and field specifications for axes and series.<br/>- Uses `Chart.js` and `chartjs-node-canvas` for direct server-side rendering.                                                                                                                     |
 
 ---
 
@@ -56,14 +56,15 @@ Built on the robust `mcp-ts-template`, this server provides a standardized, secu
 
 Leverages the robust utilities provided by the `mcp-ts-template`:
 
-- **Logging**: Structured, configurable logging (file rotation, console, MCP notifications) with sensitive data redaction.
+- **Logging**: Structured, configurable logging (file rotation, stdout JSON, MCP notifications) with sensitive data redaction.
 - **Error Handling**: Centralized error processing, standardized error types (`McpError`), and automatic logging.
 - **Configuration**: Environment variable loading (`dotenv`) with comprehensive validation.
 - **Input Validation/Sanitization**: Uses `zod` for schema validation and custom sanitization logic.
-- **Request Context**: Tracking and correlation of operations via unique request IDs.
+- **Request Context**: Tracking and correlation of operations via unique request IDs using `AsyncLocalStorage`.
 - **Type Safety**: Strong typing enforced by TypeScript and Zod schemas.
-- **HTTP Transport Option**: Built-in Express server with SSE, session management, CORS support, and JWT authentication.
-- **Rate Limiting**: Built-in request queuing and delay management for NCBI API compliance.
+- **HTTP Transport**: High-performance HTTP server using **Hono**, featuring session management with garbage collection, CORS, and IP-based rate limiting.
+- **Authentication**: Robust authentication layer supporting JWT and OAuth 2.1, with fine-grained scope enforcement.
+- **Deployment**: Multi-stage `Dockerfile` for creating small, secure production images with native dependency support.
 
 ### PubMed Integration
 
@@ -72,7 +73,7 @@ Leverages the robust utilities provided by the `mcp-ts-template`:
 - **Full Article Metadata**: Retrieve complete publication data including abstracts, authors, affiliations, journal information, DOIs, and citation data.
 - **Citation Network Analysis**: Find related articles, citing articles, and reference lists through ELink integration.
 - **Research Planning**: Generate structured research plans with automated literature search strategies.
-- **Data Visualization**: Create PNG charts from publication metadata (bar charts, line graphs, scatter plots).
+- **Data Visualization**: Create PNG charts from publication metadata (bar, line, scatter, pie, bubble, radar, polarArea).
 - **Multiple Output Formats**: Support for JSON, MEDLINE text, full XML, and formatted citations (RIS, BibTeX, APA, MLA).
 - **Batch Processing**: Efficient handling of multiple PMIDs with pagination support.
 
@@ -82,6 +83,7 @@ Leverages the robust utilities provided by the `mcp-ts-template`:
 
 - [Node.js (>=18.0.0)](https://nodejs.org/)
 - [npm](https://www.npmjs.com/) (comes with Node.js)
+- [Docker](https://www.docker.com/) (optional, for containerized deployment)
 - **NCBI API Key** (recommended for higher rate limits) - [Get one here](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/)
 
 ### Install via npm (recommended)
@@ -124,21 +126,23 @@ Configure the server using environment variables. These environmental variables
 | `MCP_HTTP_HOST`        | Host address for the HTTP server (if `MCP_TRANSPORT_TYPE=http`).                         | `127.0.0.1`                    |
 | `MCP_ALLOWED_ORIGINS`  | Comma-separated list of allowed origins for CORS (if `MCP_TRANSPORT_TYPE=http`).         | (none)                         |
 | `MCP_LOG_LEVEL`        | Logging level (`debug`, `info`, `notice`, `warning`, `error`, `crit`, `alert`, `emerg`). | `debug`                        |
-| `MCP_AUTH_SECRET_KEY`  | **Required for HTTP transport.** Minimum 32-character secret key for JWT authentication. | (none)                         |
+| `LOG_OUTPUT_MODE`      | Logging output mode: `file` or `stdout`.                                                 | `file`                         |
+| `MCP_AUTH_MODE`        | Authentication mode for HTTP: `jwt` or `oauth`.                                          | `jwt`                          |
+| `MCP_AUTH_SECRET_KEY`  | **Required for `jwt` auth.** Minimum 32-character secret key for JWT authentication.     | (none)                         |
 | `NCBI_API_KEY`         | **Recommended.** Your NCBI API Key for higher rate limits and reliable access.           | (none)                         |
 | `NCBI_TOOL_IDENTIFIER` | Tool identifier for NCBI E-utility requests.                                             | `@cyanheads/pubmed-mcp-server` |
-| `LOGS_DIR`             | Directory for log file storage.                                                          | `logs/`                        |
+| `LOGS_DIR`             | Directory for log file storage (if `LOG_OUTPUT_MODE=file`).                              | `logs/`                        |
 
 ### MCP Client Settings
 
-Add to your MCP client settings (e.g., `cline_mcp_settings.json`):
+Add the following to your MCP client's configuration file (e.g., `cline_mcp_settings.json`). This configuration uses `npx` to run the server, which will automatically install the package if not already present:
 
 ```json
 {
   "mcpServers": {
     "pubmed-mcp-server": {
-      "command": "node",
-      "args": ["/path/to/your/pubmed-mcp-server/dist/index.js"],
+      "command": "npx",
+      "args": ["@cyanheads/pubmed-mcp-server"],
       "env": {
         "NCBI_API_KEY": "your_ncbi_api_key_here"
       },
@@ -149,8 +153,6 @@ Add to your MCP client settings (e.g., `cline_mcp_settings.json`):
 }
 ```
 
-**Note**: You can see [mcp.json](mcp.json) for an example MCP client configuration file that includes the PubMed MCP Server.
-
 ## Project Structure
 
 The codebase follows a modular structure within the `src/` directory:
@@ -166,8 +168,7 @@ src/
 │   ├── resources/        # MCP Resource implementations
 │   └── tools/            # MCP Tool implementations (subdirs per tool)
 ├── services/             # External service integrations
-│   ├── NCBI/            # NCBI E-utilities API client and parsing
-│   └── llm-providers/   # LLM provider integrations (optional)
+│   └── NCBI/             # NCBI E-utilities API client and parsing
 ├── types-global/         # Shared TypeScript type definitions
 └── utils/                # Common utility functions (logger, error handler, etc.)
 ```
@@ -184,7 +185,7 @@ The PubMed MCP Server provides a comprehensive suite of tools for biomedical lit
 | `fetch_pubmed_content`           | Fetches detailed article information using PMIDs or search history.    | `pmids?`, `queryKey?`, `webEnv?`, `detailLevel?`, `includeMeshTerms?`, `includeGrantInfo?`                |
 | `get_pubmed_article_connections` | Finds related articles, citations, and references for a given PMID.    | `sourcePmid`, `relationshipType?`, `maxRelatedResults?`, `citationStyles?`                                |
 | `pubmed_research_agent`          | Generates structured research plans with literature search strategies. | `project_title_suggestion`, `primary_research_goal`, `research_keywords`, `organism_focus?`, `p1_*`, etc. |
-| `generate_pubmed_chart`          | Creates customizable PNG charts from structured publication data.      | `chartType`, `dataValues`, `xField`, `yField`, `title?`, `colorField?`, `seriesField?`, `sizeField?`      |
+| `generate_pubmed_chart`          | Creates customizable PNG charts from structured publication data.      | `chartType`, `dataValues`, `xField`, `yField`, `title?`, `seriesField?`, `sizeField?`                     |
 
 _Note: All tools support comprehensive error handling and return structured JSON responses._
 
@@ -196,7 +197,7 @@ Comprehensive usage examples are available in the [`examples/`](examples/) direc
 - [Fetch Article Content](examples/fetch_pubmed_content_example.md)
 - [Article Connections](examples/get_pubmed_article_connections_1.md)
 - [Research Planning](examples/pubmed_research_agent_example.md)
-- [Chart Generation](examples/) - Generated chart examples (bar, line, scatter) are available in the `examples/` directory.
+- [Chart Generation](./examples/generate_pubmed_chart/) - Generated chart examples (bar, line, scatter, pie, bubble, radar, polarArea) are available in the `examples/generate_pubmed_chart/` directory.
 
 ## Development
 

package/dist/config/index.js

@@ -71,7 +71,8 @@ catch (error) {
  * Provides type safety, validation, defaults, and clear error messages.
  * @private
  */
-const EnvSchema = z.object({
+const EnvSchema = z
+    .object({
     /** Optional. The desired name for the MCP server. Defaults to `package.json` name. */
     MCP_SERVER_NAME: z.string().optional(),
     /** Optional. The version of the MCP server. Defaults to `package.json` version. */
@@ -146,6 +147,43 @@ const EnvSchema = z.object({
     NCBI_REQUEST_DELAY_MS: z.coerce.number().int().positive().optional(), // Default will be set conditionally
     /** Maximum number of retries for failed NCBI requests. Default: 3. */
     NCBI_MAX_RETRIES: z.coerce.number().int().nonnegative().default(3),
+})
+    .superRefine((data, ctx) => {
+    // Rule 1: MCP_AUTH_SECRET_KEY is required for http transport in production with jwt auth
+    if (data.NODE_ENV === "production" &&
+        data.MCP_TRANSPORT_TYPE === "http" &&
+        data.MCP_AUTH_MODE === "jwt" &&
+        !data.MCP_AUTH_SECRET_KEY) {
+        ctx.addIssue({
+            code: z.ZodIssueCode.custom,
+            path: ["MCP_AUTH_SECRET_KEY"],
+            message: "MCP_AUTH_SECRET_KEY is required for 'jwt' auth with 'http' transport in a 'production' environment.",
+        });
+    }
+    // Rule 2: Core OAuth variables are required when MCP_AUTH_MODE is 'oauth'
+    if (data.MCP_AUTH_MODE === "oauth") {
+        if (!data.OAUTH_ISSUER_URL) {
+            ctx.addIssue({
+                code: z.ZodIssueCode.custom,
+                path: ["OAUTH_ISSUER_URL"],
+                message: "OAUTH_ISSUER_URL is required when MCP_AUTH_MODE is 'oauth'.",
+            });
+        }
+        if (!data.OAUTH_AUDIENCE) {
+            ctx.addIssue({
+                code: z.ZodIssueCode.custom,
+                path: ["OAUTH_AUDIENCE"],
+                message: "OAUTH_AUDIENCE is required when MCP_AUTH_MODE is 'oauth'.",
+            });
+        }
+        if (!data.OAUTH_JWKS_URI) {
+            ctx.addIssue({
+                code: z.ZodIssueCode.custom,
+                path: ["OAUTH_JWKS_URI"],
+                message: "OAUTH_JWKS_URI is required when MCP_AUTH_MODE is 'oauth'.",
+            });
+        }
+    }
 });
 const parsedEnv = EnvSchema.safeParse(process.env);
 if (!parsedEnv.success) {

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

@@ -18,12 +18,5 @@ import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 /**
  * Main application entry point. Initializes and starts the MCP server.
  * Orchestrates server startup, transport selection, and top-level error handling.
- *
- * MCP Spec Relevance:
- * - 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', resolves with `http.Server`.
- *   Rejects on critical failure, leading to process exit.
  */
 export declare function initializeAndStartServer(): Promise<void | McpServer | ServerType>;

package/dist/mcp-server/server.js

@@ -16,6 +16,7 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { config, environment } from "../config/index.js";
 import { ErrorHandler, logger, requestContextService } from "../utils/index.js";
+import { BaseErrorCode } from "../types-global/errors.js";
 import { registerFetchPubMedContentTool } from "./tools/fetchPubMedContent/index.js";
 import { registerGeneratePubMedChartTool } from "./tools/generatePubMedChart/index.js";
 import { registerGetPubMedArticleConnectionsTool } from "./tools/getPubMedArticleConnections/index.js";
@@ -34,10 +35,8 @@ import { connectStdioTransport } from "./transports/stdioTransport.js";
  * - Capabilities Declaration: Declares supported features (logging, dynamic resources/tools).
  * - Resource/Tool Registration: Makes capabilities discoverable and invocable.
  *
- * Design Note: This factory is called once for 'stdio' transport and per session for 'http' transport.
- *
  * @returns A promise resolving with the configured `McpServer` instance.
- * @throws {Error} If any resource or tool registration fails.
+ * @throws {McpError} If any resource or tool registration fails.
  * @private
  */
 async function createMcpServerInstance() {
@@ -50,18 +49,6 @@ async function createMcpServerInstance() {
         appVersion: config.mcpServerVersion,
         environment,
     });
-    logger.debug("Instantiating McpServer with capabilities", {
-        ...context,
-        serverInfo: {
-            name: config.mcpServerName,
-            version: config.mcpServerVersion,
-        },
-        capabilities: {
-            logging: {},
-            resources: { listChanged: true },
-            tools: { listChanged: true },
-        },
-    });
     const server = new McpServer({ name: config.mcpServerName, version: config.mcpServerVersion }, {
         capabilities: {
             logging: {}, // Server can receive logging/setLevel and send notifications/message
@@ -69,7 +56,7 @@ async function createMcpServerInstance() {
             tools: { listChanged: true }, // Server supports dynamic tool lists
         },
     });
-    try {
+    await ErrorHandler.tryCatch(async () => {
         logger.debug("Registering resources and tools...", context);
         // IMPORTANT: Keep tool registrations in alphabetical order. Do not remove this comment.
         await registerFetchPubMedContentTool(server);
@@ -77,17 +64,13 @@ async function createMcpServerInstance() {
         await registerGetPubMedArticleConnectionsTool(server);
         await registerPubMedResearchAgentTool(server);
         await registerSearchPubMedArticlesTool(server);
-        // Add other tool/resource registrations here
         logger.info("Resources and tools registered successfully", context);
-    }
-    catch (err) {
-        logger.error("Failed to register resources/tools", {
-            ...context,
-            error: err instanceof Error ? err.message : String(err),
-            stack: err instanceof Error ? err.stack : undefined,
-        });
-        throw err;
-    }
+    }, {
+        operation: "registerAllTools",
+        context,
+        errorCode: BaseErrorCode.INITIALIZATION_FAILED,
+        critical: true,
+    });
     return server;
 }
 /**
@@ -98,7 +81,7 @@ 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', `http.Server` for 'http', or `void` if http transport manages its own lifecycle without returning a server.
+ * @returns Resolves with `McpServer` for 'stdio', `http.Server` for 'http', or `void`.
  * @throws {Error} If transport type is unsupported or setup fails.
  * @private
  */
@@ -110,32 +93,18 @@ async function startTransport() {
     });
     logger.info(`Starting transport: ${transportType}`, context);
     if (transportType === "http") {
-        logger.debug("Delegating to startHttpTransport...", context);
-        // For HTTP, startHttpTransport now returns the http.Server instance.
-        const httpServerInstance = await startHttpTransport(createMcpServerInstance, context);
-        return httpServerInstance;
+        return startHttpTransport(createMcpServerInstance, context);
     }
     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 McpServer instance for stdio.
+        return server;
     }
-    // Should not be reached if config validation is effective.
-    logger.fatal(`Unsupported transport type configured: ${transportType}`, context);
     throw new Error(`Unsupported transport type: ${transportType}. Must be 'stdio' or 'http'.`);
 }
 /**
  * Main application entry point. Initializes and starts the MCP server.
  * Orchestrates server startup, transport selection, and top-level error handling.
- *
- * MCP Spec Relevance:
- * - 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', resolves with `http.Server`.
- *   Rejects on critical failure, leading to process exit.
  */
 export async function initializeAndStartServer() {
     const context = requestContextService.createRequestContext({
@@ -148,18 +117,13 @@ export async function initializeAndStartServer() {
         return result;
     }
     catch (err) {
-        logger.fatal("Critical error during MCP server initialization.", {
-            ...context,
-            error: err instanceof Error ? err.message : String(err),
-            stack: err instanceof Error ? err.stack : undefined,
-        });
-        // Ensure the error is handled by our centralized handler, which might log more details or perform cleanup.
         ErrorHandler.handleError(err, {
-            operation: "initializeAndStartServer", // More specific operation
-            context: context, // Pass the existing context
-            critical: true, // This is a critical failure
+            operation: "initializeAndStartServer",
+            context: context,
+            critical: true,
+            rethrow: false, // Ensure we don't rethrow, so we can exit gracefully.
         });
         logger.info("Exiting process due to critical initialization error.", context);
-        process.exit(1); // Exit with a non-zero code to indicate failure.
+        process.exit(1);
     }
 }

package/dist/mcp-server/tools/fetchPubMedContent/logic.d.ts

@@ -5,7 +5,6 @@
  * MEDLINE text, and citation data.
  * @module src/mcp-server/tools/fetchPubMedContent/logic
  */
-import { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
 import { z } from "zod";
 import { RequestContext } from "../../../utils/index.js";
 export declare const FetchPubMedContentInputSchema: z.ZodEffects<z.ZodObject<{
@@ -60,4 +59,9 @@ export declare const FetchPubMedContentInputSchema: z.ZodEffects<z.ZodObject<{
     outputFormat?: "json" | "raw_text" | undefined;
 }>;
 export type FetchPubMedContentInput = z.infer<typeof FetchPubMedContentInputSchema>;
-export declare function fetchPubMedContentLogic(input: FetchPubMedContentInput, parentRequestContext: RequestContext): Promise<CallToolResult>;
+export type FetchPubMedContentOutput = {
+    content: string;
+    articlesReturned: number;
+    eFetchUrl: string;
+};
+export declare function fetchPubMedContentLogic(input: FetchPubMedContentInput, parentRequestContext: RequestContext): Promise<FetchPubMedContentOutput>;