@cyanheads/pubmed-mcp-server 1.3.5 → 1.4.3

package/README.md

@@ -5,15 +5,15 @@
 **Empower your AI agents and research tools with seamless PubMed integration!**
 
 [![TypeScript](https://img.shields.io/badge/TypeScript-^5.8.3-blue.svg?style=flat-square)](https://www.typescriptlang.org/)
-[![Model Context Protocol](https://img.shields.io/badge/MCP%20SDK-^1.17.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
-[![Version](https://img.shields.io/badge/Version-1.3.5-blue.svg?style=flat-square)](./CHANGELOG.md)
+[![Model Context Protocol](https://img.shields.io/badge/MCP%20SDK-^1.17.2-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
+[![Version](https://img.shields.io/badge/Version-1.4.2-blue.svg?style=flat-square)](./CHANGELOG.md)
 [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg?style=flat-square)](https://opensource.org/licenses/Apache-2.0)
 [![Status](https://img.shields.io/badge/Status-Stable-green.svg?style=flat-square)](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)
 
 </div>
 
-Model Context Protocol (MCP) Server providing comprehensive access to PubMed's biomedical literature database. Enables LLMs and AI agents to search, retrieve, analyze, and visualize scientific publications through NCBI's E-utilities API with advanced research workflow capabilities.
+A production-grade Model Context Protocol (MCP) server that empowers AI agents and research tools with comprehensive access to PubMed. Enables advanced, automated workflows for searching, retrieving, analyzing, and visualizing biomedical and scientific literature via NCBI E-utilities.
 
 Built on the [`cyanheads/mcp-ts-template`](https://github.com/cyanheads/mcp-ts-template), this server follows a modular architecture with robust error handling, logging, and security features.
 
@@ -21,13 +21,13 @@ 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                                                                             | Example                                                                                                          |
-| :-------------------------------------------------------------------------------------- | :-------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------- |
-| [`search_pubmed_articles`](./src/mcp-server/tools/searchPubMedArticles/)                | Searches PubMed for articles based on your query.                                       | [View Example](./examples/search_pubmed_articles_example.md)                                                     |
-| [`fetch_pubmed_content`](./src/mcp-server/tools/fetchPubMedContent/)                    | Retrieves detailed information for PubMed articles.                                     | [View Example](./examples/fetch_pubmed_content_example.md)                                                       |
-| [`get_pubmed_article_connections`](./src/mcp-server/tools/getPubMedArticleConnections/) | Finds related articles (cited by, similar, references) or formats citations for a PMID. | [Ex. 1](./examples/get_pubmed_article_connections_1.md), [Ex. 2](./examples/get_pubmed_article_connections_2.md) |
-| [`pubmed_research_agent`](./src/mcp-server/tools/pubmedResearchAgent/)                  | Generates a standardized JSON research plan outline from component details.             | [View Example](./examples/pubmed_research_agent_example.md)                                                      |
-| [`generate_pubmed_chart`](./src/mcp-server/tools/generatePubMedChart/)                  | Generates a chart image (PNG) from given input data.                                    | [View Examples](./examples/generate_pubmed_chart/)                                                               |
+| Tool Name                                                                        | Description                                                                             | Example                                                                                                  |
+| :------------------------------------------------------------------------------- | :-------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------------- |
+| [`pubmed_search_articles`](./src/mcp-server/tools/pubmedSearchArticles/)         | Searches PubMed for articles based on your query.                                       | [View Example](./examples/pubmed_search_articles_example.md)                                             |
+| [`pubmed_fetch_contents`](./src/mcp-server/tools/pubmedFetchContents/)           | Retrieves detailed information for PubMed articles.                                     | [View Example](./examples/pubmed_fetch_contents_example.md)                                              |
+| [`pubmed_article_connections`](./src/mcp-server/tools/pubmedArticleConnections/) | Finds related articles (cited by, similar, references) or formats citations for a PMID. | [Ex. 1](./examples/pubmed_article_connections_1.md), [Ex. 2](./examples/pubmed_article_connections_2.md) |
+| [`pubmed_research_agent`](./src/mcp-server/tools/pubmedResearchAgent/)           | Generates a standardized JSON research plan outline from component details.             | [View Example](./examples/pubmed_research_agent_example.md)                                              |
+| [`pubmed_generate_chart`](./src/mcp-server/tools/pubmedGenerateChart/)           | Generates a chart image (PNG) from given input data.                                    | [View Examples](./examples/generate_pubmed_chart/)                                                       |
 
 ---
 
@@ -179,13 +179,13 @@ For a detailed file tree, run `npm run tree` or see [docs/tree.md](docs/tree.md)
 
 The PubMed MCP Server provides a comprehensive suite of tools for biomedical literature research, callable via the Model Context Protocol.
 
-| Tool Name                        | Description                                                            | Key Arguments                                                                                             |
-| :------------------------------- | :--------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------- |
-| `search_pubmed_articles`         | Searches PubMed for articles using queries, filters, and date ranges.  | `queryTerm`, `maxResults?`, `sortBy?`, `dateRange?`, `filterByPublicationTypes?`, `fetchBriefSummaries?`  |
-| `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?`, `seriesField?`, `sizeField?`                     |
+| Tool Name                    | Description                                                            | Key Arguments                                                                                             |
+| :--------------------------- | :--------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------- |
+| `pubmed_search_articles`     | Searches PubMed for articles using queries, filters, and date ranges.  | `queryTerm`, `maxResults?`, `sortBy?`, `dateRange?`, `filterByPublicationTypes?`, `fetchBriefSummaries?`  |
+| `pubmed_fetch_contents`      | Fetches detailed article information using PMIDs or search history.    | `pmids?`, `queryKey?`, `webEnv?`, `detailLevel?`, `includeMeshTerms?`, `includeGrantInfo?`                |
+| `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. |
+| `pubmed_generate_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._
 
@@ -193,11 +193,11 @@ _Note: All tools support comprehensive error handling and return structured JSON
 
 Comprehensive usage examples for each tool are available in the [`examples/`](examples/) directory.
 
-- **`search_pubmed_articles`**: [View Example](./examples/search_pubmed_articles_example.md)
-- **`fetch_pubmed_content`**: [View Example](./examples/fetch_pubmed_content_example.md)
-- **`get_pubmed_article_connections`**: [Ex. 1](./examples/get_pubmed_article_connections_1.md), [Ex. 2](./examples/get_pubmed_article_connections_2.md)
+- **`pubmed_search_articles`**: [View Example](./examples/pubmed_search_articles_example.md)
+- **`pubmed_fetch_contents`**: [View Example](./examples/pubmed_fetch_contents_example.md)
+- **`pubmed_article_connections`**: [Ex. 1](./examples/pubmed_article_connections_1.md), [Ex. 2](./examples/pubmed_article_connections_2.md)
 - **`pubmed_research_agent`**: [View Example](./examples/pubmed_research_agent_example.md)
-- **`generate_pubmed_chart`**: [View Examples](./examples/generate_pubmed_chart/)
+- **`pubmed_generate_chart`**: [View Examples](./examples/generate_pubmed_chart/)
 
 ## Development & Testing
 
@@ -213,6 +213,9 @@ npm run clean
 # Clean build artifacts and then rebuild the project
 npm run rebuild
 
+# Lint the codebase
+npm run lint
+
 # Format code with Prettier
 npm run format
 

package/dist/config/index.d.ts

@@ -10,9 +10,11 @@ export declare const config: {
     pkg: {
         name: string;
         version: string;
+        description: string;
     };
     mcpServerName: string;
     mcpServerVersion: string;
+    mcpServerDescription: string;
     logLevel: string;
     logsPath: string | null;
     environment: string;
@@ -37,6 +39,15 @@ export declare const config: {
     ncbiAdminEmail: string | undefined;
     ncbiRequestDelayMs: number;
     ncbiMaxRetries: number;
+    openTelemetry: {
+        enabled: boolean;
+        serviceName: string;
+        serviceVersion: string;
+        tracesEndpoint: string | undefined;
+        metricsEndpoint: string | undefined;
+        samplingRatio: number;
+        logLevel: "NONE" | "ERROR" | "WARN" | "INFO" | "DEBUG" | "VERBOSE" | "ALL";
+    };
 };
 export declare const logLevel: string;
 export declare const environment: string;

package/dist/config/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/config/index.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAkPH,eAAO,MAAM,MAAM;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAiClB,CAAC;AAEF,eAAO,MAAM,QAAQ,EAAE,MAAwB,CAAC;AAChD,eAAO,MAAM,WAAW,EAAE,MAA2B,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/config/index.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAkTH,eAAO,MAAM,MAAM;;cA7PX,MAAM;iBACH,MAAM;qBACF,MAAM;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;CAuSpB,CAAC;AAEF,eAAO,MAAM,QAAQ,EAAE,MAAwB,CAAC;AAChD,eAAO,MAAM,WAAW,EAAE,MAA2B,CAAC"}

package/dist/config/index.js

@@ -15,6 +15,10 @@ dotenv.config();
 // --- Determine Project Root ---
 const findProjectRoot = (startDir) => {
     let currentDir = startDir;
+    // If the start directory is in `dist`, start searching from the parent directory.
+    if (path.basename(currentDir) === "dist") {
+        currentDir = path.dirname(currentDir);
+    }
     while (true) {
         const packageJsonPath = join(currentDir, "package.json");
         if (existsSync(packageJsonPath)) {
@@ -33,21 +37,51 @@ try {
     projectRoot = findProjectRoot(currentModuleDir);
 }
 catch (error) {
-    console.error(`FATAL: Error determining project root: ${error.message}`);
+    const errorMessage = error instanceof Error ? error.message : String(error);
+    console.error(`FATAL: Error determining project root: ${errorMessage}`);
     projectRoot = process.cwd();
-    console.warn(`Warning: Using process.cwd() (${projectRoot}) as fallback project root.`);
-}
-// --- End Determine Project Root ---
-const pkgPath = join(projectRoot, "package.json");
-let pkg = { name: "pubmed-mcp-server", version: "0.0.0" };
-try {
-    pkg = JSON.parse(readFileSync(pkgPath, "utf-8"));
-}
-catch (error) {
     if (process.stdout.isTTY) {
-        console.error("Warning: Could not read package.json for default config values. Using hardcoded defaults.", error);
+        console.warn(`Warning: Using process.cwd() (${projectRoot}) as fallback project root.`);
     }
 }
+// --- End Determine Project Root ---
+/**
+ * Loads and parses the package.json file from the project root.
+ * @returns The parsed package.json object or a fallback default.
+ * @private
+ */
+const loadPackageJson = () => {
+    const pkgPath = join(projectRoot, "package.json");
+    const fallback = {
+        name: "pubmed-mcp-server",
+        version: "0.0.0",
+        description: "No description provided.",
+    };
+    if (!existsSync(pkgPath)) {
+        if (process.stdout.isTTY) {
+            console.warn(`Warning: package.json not found at ${pkgPath}. Using fallback values. This is expected in some environments (e.g., Docker) but may indicate an issue with project root detection.`);
+        }
+        return fallback;
+    }
+    try {
+        const fileContents = readFileSync(pkgPath, "utf-8");
+        const parsed = JSON.parse(fileContents);
+        return {
+            name: typeof parsed.name === "string" ? parsed.name : fallback.name,
+            version: typeof parsed.version === "string" ? parsed.version : fallback.version,
+            description: typeof parsed.description === "string"
+                ? parsed.description
+                : fallback.description,
+        };
+    }
+    catch (error) {
+        if (process.stdout.isTTY) {
+            console.error("Warning: Could not read or parse package.json. Using hardcoded defaults.", error);
+        }
+        return fallback;
+    }
+};
+const pkg = loadPackageJson();
 const EnvSchema = z
     .object({
     // Core Server Config
@@ -97,6 +131,26 @@ const EnvSchema = z
     NCBI_ADMIN_EMAIL: z.string().email().optional(),
     NCBI_REQUEST_DELAY_MS: z.coerce.number().int().positive().optional(),
     NCBI_MAX_RETRIES: z.coerce.number().int().nonnegative().default(3),
+    // --- START: OpenTelemetry Configuration ---
+    /** If 'true', OpenTelemetry will be initialized and enabled. Default: 'false'. */
+    OTEL_ENABLED: z
+        .string()
+        .transform((v) => v.toLowerCase() === "true")
+        .default("false"),
+    /** The logical name of the service. Defaults to MCP_SERVER_NAME or package name. */
+    OTEL_SERVICE_NAME: z.string().optional(),
+    /** The version of the service. Defaults to MCP_SERVER_VERSION or package version. */
+    OTEL_SERVICE_VERSION: z.string().optional(),
+    /** The OTLP endpoint for traces. If not set, traces are logged to a file in development. */
+    OTEL_EXPORTER_OTLP_TRACES_ENDPOINT: z.string().url().optional(),
+    /** The OTLP endpoint for metrics. If not set, metrics are not exported. */
+    OTEL_EXPORTER_OTLP_METRICS_ENDPOINT: z.string().url().optional(),
+    /** Sampling ratio for traces (0.0 to 1.0). 1.0 means sample all. Default: 1.0 */
+    OTEL_TRACES_SAMPLER_ARG: z.coerce.number().min(0).max(1).default(1.0),
+    /** Log level for OpenTelemetry's internal diagnostic logger. Default: "INFO". */
+    OTEL_LOG_LEVEL: z
+        .enum(["NONE", "ERROR", "WARN", "INFO", "DEBUG", "VERBOSE", "ALL"])
+        .default("INFO"),
 })
     .superRefine((data, ctx) => {
     if (data.NODE_ENV === "production" &&
@@ -198,6 +252,7 @@ export const config = {
     pkg,
     mcpServerName: env.MCP_SERVER_NAME || pkg.name,
     mcpServerVersion: env.MCP_SERVER_VERSION || pkg.version,
+    mcpServerDescription: pkg.description,
     logLevel: env.MCP_LOG_LEVEL,
     logsPath: validatedLogsPath,
     environment: env.NODE_ENV,
@@ -225,6 +280,15 @@ export const config = {
     ncbiAdminEmail: env.NCBI_ADMIN_EMAIL,
     ncbiRequestDelayMs: env.NCBI_REQUEST_DELAY_MS ?? (env.NCBI_API_KEY ? 100 : 334),
     ncbiMaxRetries: env.NCBI_MAX_RETRIES,
+    openTelemetry: {
+        enabled: env.OTEL_ENABLED,
+        serviceName: env.OTEL_SERVICE_NAME || env.MCP_SERVER_NAME || pkg.name,
+        serviceVersion: env.OTEL_SERVICE_VERSION || env.MCP_SERVER_VERSION || pkg.version,
+        tracesEndpoint: env.OTEL_EXPORTER_OTLP_TRACES_ENDPOINT,
+        metricsEndpoint: env.OTEL_EXPORTER_OTLP_METRICS_ENDPOINT,
+        samplingRatio: env.OTEL_TRACES_SAMPLER_ARG,
+        logLevel: env.OTEL_LOG_LEVEL,
+    },
 };
 export const logLevel = config.logLevel;
 export const environment = config.environment;

package/dist/config/index.js.map

@@ -1 +1 @@
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package/dist/index.js.map

@@ -1 +1 @@
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package/dist/mcp-server/server.d.ts

@@ -11,8 +11,21 @@
  */
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import http from "http";
+type SdkToolSpec = Parameters<McpServer["registerTool"]>[1];
+type ServerIdentity = ConstructorParameters<typeof McpServer>[0];
+type McpServerOptions = NonNullable<ConstructorParameters<typeof McpServer>[1]>;
+export interface DescribedTool extends SdkToolSpec {
+    title: string;
+}
+export interface ServerInstanceInfo {
+    server: McpServer;
+    tools: DescribedTool[];
+    identity: ServerIdentity;
+    options: McpServerOptions;
+}
 /**
  * Main application entry point. Initializes and starts the MCP server.
  */
 export declare function initializeAndStartServer(): Promise<McpServer | http.Server>;
+export {};
 //# sourceMappingURL=server.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../../src/mcp-server/server.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACpE,OAAO,IAAI,MAAM,MAAM,CAAC;AAWxB,KAAK,WAAW,GAAG,UAAU,CAAC,SAAS,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AAC5D,KAAK,cAAc,GAAG,qBAAqB,CAAC,OAAO,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC;AACjE,KAAK,gBAAgB,GAAG,WAAW,CACjC,qBAAqB,CAAC,OAAO,SAAS,CAAC,CAAC,CAAC,CAAC,CAC3C,CAAC;AAEF,MAAM,WAAW,aAAc,SAAQ,WAAW;IAChD,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,kBAAkB;IACjC,MAAM,EAAE,SAAS,CAAC;IAClB,KAAK,EAAE,aAAa,EAAE,CAAC;IACvB,QAAQ,EAAE,cAAc,CAAC;IACzB,OAAO,EAAE,gBAAgB,CAAC;CAC3B;AA6GD;;GAEG;AACH,wBAAsB,wBAAwB,IAAI,OAAO,CACvD,SAAS,GAAG,IAAI,CAAC,MAAM,CACxB,CA6BA"}

package/dist/mcp-server/server.js

@@ -12,17 +12,17 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { config, environment } from "../config/index.js";
 import { ErrorHandler, logger, requestContextService } from "../utils/index.js";
-import { registerFetchPubMedContentTool } from "./tools/fetchPubMedContent/index.js";
-import { registerGeneratePubMedChartTool } from "./tools/generatePubMedChart/index.js";
-import { registerGetPubMedArticleConnectionsTool } from "./tools/getPubMedArticleConnections/index.js";
+import { registerPubMedArticleConnectionsTool } from "./tools/pubmedArticleConnections/index.js";
+import { registerPubMedFetchContentsTool } from "./tools/pubmedFetchContents/index.js";
+import { registerPubMedGenerateChartTool } from "./tools/pubmedGenerateChart/index.js";
 import { registerPubMedResearchAgentTool } from "./tools/pubmedResearchAgent/index.js";
-import { registerSearchPubMedArticlesTool } from "./tools/searchPubMedArticles/index.js";
+import { registerPubMedSearchArticlesTool } from "./tools/pubmedSearchArticles/index.js";
 import { startHttpTransport } from "./transports/http/index.js";
 import { startStdioTransport } from "./transports/stdio/index.js";
 /**
  * Creates and configures a new instance of the `McpServer`.
  *
- * @returns A promise resolving with the configured `McpServer` instance.
+ * @returns A promise resolving with the configured `McpServer` instance and its tool metadata.
  * @throws {McpError} If any resource or tool registration fails.
  * @private
  */
@@ -36,21 +36,39 @@ async function createMcpServerInstance() {
         appVersion: config.mcpServerVersion,
         environment,
     });
-    const server = new McpServer({ name: config.mcpServerName, version: config.mcpServerVersion }, {
+    const identity = {
+        name: config.mcpServerName,
+        version: config.mcpServerVersion,
+        description: config.mcpServerDescription,
+    };
+    const options = {
         capabilities: {
             logging: {},
             resources: { listChanged: true },
             tools: { listChanged: true },
         },
-    });
+    };
+    const server = new McpServer(identity, options);
+    const registeredTools = [];
+    const originalRegisterTool = server.registerTool.bind(server);
+    server.registerTool = (name, spec, implementation) => {
+        registeredTools.push({
+            title: name,
+            description: spec.description,
+            inputSchema: spec.inputSchema,
+            outputSchema: spec.outputSchema,
+            annotations: spec.annotations,
+        });
+        return originalRegisterTool(name, spec, implementation);
+    };
     try {
         logger.debug("Registering resources and tools...", context);
         // IMPORTANT: Keep tool registrations in alphabetical order.
-        await registerFetchPubMedContentTool(server);
-        await registerGeneratePubMedChartTool(server);
-        await registerGetPubMedArticleConnectionsTool(server);
+        await registerPubMedArticleConnectionsTool(server);
+        await registerPubMedFetchContentsTool(server);
+        await registerPubMedGenerateChartTool(server);
         await registerPubMedResearchAgentTool(server);
-        await registerSearchPubMedArticlesTool(server);
+        await registerPubMedSearchArticlesTool(server);
         logger.info("Resources and tools registered successfully", context);
     }
     catch (err) {
@@ -61,7 +79,7 @@ async function createMcpServerInstance() {
         });
         throw err;
     }
-    return server;
+    return { server, tools: registeredTools, identity, options };
 }
 /**
  * Selects, sets up, and starts the appropriate MCP transport layer based on configuration.
@@ -82,7 +100,7 @@ async function startTransport() {
         return server;
     }
     if (transportType === "stdio") {
-        const server = await createMcpServerInstance();
+        const { server } = await createMcpServerInstance();
         await startStdioTransport(server, context);
         return server;
     }

package/dist/mcp-server/server.js.map

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package/dist/mcp-server/tools/pubmedArticleConnections/index.d.ts

@@ -0,0 +1,7 @@
+/**
+ * @fileoverview Barrel file for the pubmedArticleConnections tool.
+ * Exports the registration function for this tool.
+ * @module src/mcp-server/tools/pubmedArticleConnections/index
+ */
+export { registerPubMedArticleConnectionsTool } from "./registration.js";
+//# sourceMappingURL=index.d.ts.map

package/dist/mcp-server/tools/pubmedArticleConnections/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedArticleConnections/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,oCAAoC,EAAE,MAAM,mBAAmB,CAAC"}

package/dist/mcp-server/tools/pubmedArticleConnections/index.js

@@ -0,0 +1,7 @@
+/**
+ * @fileoverview Barrel file for the pubmedArticleConnections tool.
+ * Exports the registration function for this tool.
+ * @module src/mcp-server/tools/pubmedArticleConnections/index
+ */
+export { registerPubMedArticleConnectionsTool } from "./registration.js";
+//# sourceMappingURL=index.js.map

package/dist/mcp-server/tools/pubmedArticleConnections/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/pubmedArticleConnections/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,oCAAoC,EAAE,MAAM,mBAAmB,CAAC"}

package/dist/mcp-server/tools/pubmedArticleConnections/logic/citationFormatter.d.ts

@@ -0,0 +1,10 @@
+/**
+ * @fileoverview Handles citation formatting for the pubmedArticleConnections tool.
+ * Fetches article details using EFetch and formats them into various citation styles.
+ * @module src/mcp-server/tools/pubmedArticleConnections/logic/citationFormatter
+ */
+import { RequestContext } from "../../../../utils/index.js";
+import type { PubMedArticleConnectionsInput } from "./index.js";
+import type { ToolOutputData } from "./types.js";
+export declare function handleCitationFormats(input: PubMedArticleConnectionsInput, outputData: ToolOutputData, context: RequestContext): Promise<void>;
+//# sourceMappingURL=citationFormatter.d.ts.map

package/dist/mcp-server/tools/pubmedArticleConnections/logic/citationFormatter.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"citationFormatter.d.ts","sourceRoot":"","sources":["../../../../../src/mcp-server/tools/pubmedArticleConnections/logic/citationFormatter.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAQH,OAAO,EAEL,cAAc,EAEf,MAAM,4BAA4B,CAAC;AASpC,OAAO,KAAK,EAAE,6BAA6B,EAAE,MAAM,YAAY,CAAC;AAChE,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAGjD,wBAAsB,qBAAqB,CACzC,KAAK,EAAE,6BAA6B,EACpC,UAAU,EAAE,cAAc,EAC1B,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,IAAI,CAAC,CAyDf"}

package/dist/mcp-server/tools/{getPubMedArticleConnections → pubmedArticleConnections}/logic/citationFormatter.js

@@ -1,12 +1,13 @@
 /**
- * @fileoverview Handles citation formatting for the getPubMedArticleConnections tool.
+ * @fileoverview Handles citation formatting for the pubmedArticleConnections tool.
  * Fetches article details using EFetch and formats them into various citation styles.
- * @module src/mcp-server/tools/getPubMedArticleConnections/logic/citationFormatter
+ * @module src/mcp-server/tools/pubmedArticleConnections/logic/citationFormatter
  */
 import Cite from "citation-js";
 import { getNcbiService } from "../../../../services/NCBI/core/ncbiService.js";
 import { logger, requestContextService, } from "../../../../utils/index.js";
 import { extractAuthors, extractDoi, extractJournalInfo, extractPmid, getText, } from "../../../../services/NCBI/parsing/index.js";
+import { ensureArray } from "../../../../services/NCBI/parsing/index.js";
 // Main handler for citation formats
 export async function handleCitationFormats(input, outputData, context) {
     const eFetchParams = {
@@ -18,14 +19,15 @@ export async function handleCitationFormats(input, outputData, context) {
     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]) {
+    const eFetchResult = (await ncbiService.eFetch(eFetchParams, context));
+    const pubmedArticles = ensureArray(eFetchResult?.PubmedArticleSet?.PubmedArticle);
+    if (pubmedArticles.length === 0) {
         outputData.message =
             "Could not retrieve article details for citation formatting.";
         logger.warning(outputData.message, context);
         return;
     }
-    const article = eFetchResult.PubmedArticleSet.PubmedArticle[0];
+    const article = pubmedArticles[0];
     const csl = pubmedArticleToCsl(article, context);
     const cite = new Cite(csl);
     if (input.citationStyles?.includes("ris")) {
@@ -105,8 +107,8 @@ function pubmedArticleToCsl(article, context) {
         URL: pmid ? `https://pubmed.ncbi.nlm.nih.gov/${pmid}` : undefined,
     };
     // Clean up any undefined/null properties
-    for (const key in cslData) {
-        if (cslData[key] === undefined || cslData[key] === null) {
+    for (const [key, value] of Object.entries(cslData)) {
+        if (value === undefined || value === null) {
             delete cslData[key];
         }
     }

package/dist/mcp-server/tools/pubmedArticleConnections/logic/citationFormatter.js.map

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package/dist/mcp-server/tools/pubmedArticleConnections/logic/elinkHandler.d.ts

@@ -0,0 +1,10 @@
+/**
+ * @fileoverview Handles ELink requests and enriches results with ESummary data
+ * for the pubmedArticleConnections tool.
+ * @module src/mcp-server/tools/pubmedArticleConnections/logic/elinkHandler
+ */
+import { RequestContext } from "../../../../utils/index.js";
+import type { PubMedArticleConnectionsInput } from "./index.js";
+import type { ToolOutputData } from "./types.js";
+export declare function handleELinkRelationships(input: PubMedArticleConnectionsInput, outputData: ToolOutputData, context: RequestContext): Promise<void>;
+//# sourceMappingURL=elinkHandler.d.ts.map

package/dist/mcp-server/tools/pubmedArticleConnections/logic/elinkHandler.d.ts.map

@@ -0,0 +1 @@
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