@cyanheads/pubmed-mcp-server 1.1.1 → 1.1.4

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

@@ -2,6 +2,11 @@ import * as vega from "vega";
 import * as vegaLite from "vega-lite";
 import { z } from "zod";
 import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
+// IMPORTANT DEPLOYMENT NOTE:
+// This tool uses the 'canvas' package to render PNG images on the server.
+// The 'canvas' package has native system dependencies (e.g., cairo, pango, libjpeg).
+// Ensure these are installed on the deployment environment.
+// See: https://www.npmjs.com/package/canvas#compiling
 import { logger, requestContextService, sanitizeInputForLogging, } from "../../../utils/index.js";
 export const GeneratePubMedChartInputSchema = z.object({
     chartType: z
@@ -73,8 +78,6 @@ export const GeneratePubMedChartInputSchema = z.object({
         .enum(["quantitative", "ordinal"])
         .optional()
         .describe("Optional. Specifies the data type of the `sizeField`. Options: 'quantitative', 'ordinal'. Defaults to 'quantitative' if `sizeField` is provided and this is omitted."),
-    // shapeField: z.string().optional().describe("Optional field for encoding point shape in scatter plots."), // Future enhancement
-    // shapeFieldType: z.enum(["nominal", "ordinal"]).optional().describe("Type of the shape field."), // Future enhancement
 });
 export async function generatePubMedChartLogic(input, parentRequestContext) {
     const operationContext = requestContextService.createRequestContext({
@@ -83,9 +86,8 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
         input: sanitizeInputForLogging(input),
     });
     logger.info(`Executing 'generate_pubmed_chart'. Chart type: ${input.chartType}, Output format: ${input.outputFormat}`, operationContext);
-    if (input.outputFormat !== "png") { // Changed from svg to png
-        const unsupportedFormatError = new McpError(BaseErrorCode.VALIDATION_ERROR, `Unsupported output format: ${input.outputFormat}. Currently, only 'png' is supported.`, // Changed message
-        { requestedFormat: input.outputFormat });
+    if (input.outputFormat !== "png") {
+        const unsupportedFormatError = new McpError(BaseErrorCode.VALIDATION_ERROR, `Unsupported output format: ${input.outputFormat}. Currently, only 'png' is supported.`, { requestedFormat: input.outputFormat });
         logger.warning(unsupportedFormatError.message, operationContext);
         return {
             content: [
@@ -104,15 +106,14 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
         };
     }
     try {
-        let vegaLiteSpec = {
+        const vegaLiteSpec = {
             $schema: "https://vega.github.io/schema/vega-lite/v5.json",
             title: input.title,
             width: input.width,
             height: input.height,
             data: { values: input.dataValues },
-            encoding: {}, // To be populated by chart type specific logic
+            encoding: {},
         };
-        // Default field types if not provided
         const yEncType = input.yFieldType || "quantitative";
         const colorEncType = input.colorFieldType || "nominal";
         const seriesEncType = input.seriesFieldType || "nominal";
@@ -157,14 +158,12 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
                     },
                 };
                 if (input.seriesField) {
-                    // For line charts, seriesField is typically used for color
                     vegaLiteSpec.encoding.color = {
                         field: input.seriesField,
                         type: seriesEncType,
                     };
                 }
                 else if (input.colorField) {
-                    // Allow direct colorField as well
                     vegaLiteSpec.encoding.color = {
                         field: input.colorField,
                         type: colorEncType,
@@ -173,7 +172,7 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
                 break;
             case "scatter":
                 xEncType = input.xFieldType || "quantitative";
-                vegaLiteSpec.mark = "point"; // "circle" is also an option
+                vegaLiteSpec.mark = "point";
                 vegaLiteSpec.encoding = {
                     x: {
                         field: input.xField,
@@ -198,28 +197,28 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
                         type: sizeEncType,
                     };
                 }
-                // Add shape encoding here if shapeField is implemented
                 break;
-            // No default case needed as chartType is an enum and Zod validates it.
         }
         const compiledVegaSpec = vegaLite.compile(vegaLiteSpec).spec;
         const view = new vega.View(vega.parse(compiledVegaSpec), {
-            renderer: "canvas", // Explicitly set renderer to 'canvas'
+            renderer: "canvas",
         });
-        // const svgString = await view.toSVG(); // Old SVG method
-        // New PNG method
-        // Initialize the view to ensure canvas is ready
-        await view.runAsync(); // Initialize and run the view
-        const canvas = await view.toCanvas(); // Render to canvas
-        // Cast to 'any' to access toBuffer, assuming it's a Node Canvas instance at runtime
-        const imageBuffer = await canvas.toBuffer("image/png"); // Get PNG buffer from canvas
+        await view.runAsync();
+        const canvas = await view.toCanvas();
+        const imageBuffer = await canvas.toBuffer("image/png");
         const base64Data = imageBuffer.toString("base64");
+        logger.notice("Successfully generated chart.", {
+            ...operationContext,
+            chartType: input.chartType,
+            outputFormat: input.outputFormat,
+            dataPoints: input.dataValues.length,
+        });
         return {
             content: [
                 {
                     type: "image",
                     data: base64Data,
-                    mimeType: "image/png", // Changed MIME type to image/png
+                    mimeType: "image/png",
                 },
             ],
             isError: false,

package/dist/mcp-server/tools/generatePubMedChart/registration.d.ts

@@ -4,4 +4,4 @@
  * @module src/mcp-server/tools/generatePubMedChart/registration
  */
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-export declare function registerGeneratePubMedChartTool(server: McpServer): void;
+export declare function registerGeneratePubMedChartTool(server: McpServer): Promise<void>;

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

@@ -1,10 +1,10 @@
-import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
+import { BaseErrorCode } from "../../../types-global/errors.js";
 import { ErrorHandler, logger, requestContextService, } from "../../../utils/index.js";
 import { GeneratePubMedChartInputSchema, generatePubMedChartLogic, } from "./logic.js";
-export function registerGeneratePubMedChartTool(server) {
+export async function registerGeneratePubMedChartTool(server) {
     const operation = "registerGeneratePubMedChartTool";
     const regContext = requestContextService.createRequestContext({ operation });
-    try {
+    await ErrorHandler.tryCatch(() => {
         server.tool("generate_pubmed_chart", "Generates a customizable chart (PNG) from structured data. " +
             "Supports 'bar', 'line', and 'scatter' plots. " +
             "Requires data values and field mappings for axes. " +
@@ -17,20 +17,11 @@ export function registerGeneratePubMedChartTool(server) {
             });
             return generatePubMedChartLogic(validatedInput, handlerRequestContext);
         });
-        logger.notice(`Tool 'generate_pubmed_chart' registered with updated schema (added scatter).`, regContext);
-    }
-    catch (error) {
-        const mcpError = error instanceof McpError
-            ? error
-            : new McpError(BaseErrorCode.INITIALIZATION_FAILED, `Failed to register 'generate_pubmed_chart': ${error instanceof Error ? error.message : String(error)}`, {
-                originalErrorName: error instanceof Error ? error.name : "UnknownError",
-                details: "Error during server.tool() call for generate_pubmed_chart.",
-            });
-        ErrorHandler.handleError(mcpError, {
-            operation,
-            context: regContext,
-            errorCode: BaseErrorCode.INITIALIZATION_FAILED,
-            critical: true,
-        });
-    }
+        logger.notice("Tool 'generate_pubmed_chart' registered.", regContext);
+    }, {
+        operation,
+        context: regContext,
+        errorCode: BaseErrorCode.INITIALIZATION_FAILED,
+        critical: true,
+    });
 }

package/dist/mcp-server/tools/getPubMedArticleConnections/logic/citationFormatter.js

@@ -199,8 +199,8 @@ function formatAsAPA(article, context) {
     }
     const year = journalInfo?.publicationDate?.year || "n.d.";
     const apaTitle = titleText.charAt(0).toUpperCase() + titleText.slice(1); // APA typically sentence case for article titles.
-    const journal = journalInfo?.title ? `<em>${journalInfo.title}</em>` : "N/A";
-    const volume = journalInfo?.volume ? `<em>${journalInfo.volume}</em>` : "";
+    const journal = journalInfo?.title || "N/A";
+    const volume = journalInfo?.volume || "";
     const issue = journalInfo?.issue ? `(${journalInfo.issue})` : "";
     const pages = journalInfo?.pages || "";
     const doiLink = doi ? ` https://doi.org/${doi}` : "";
@@ -253,7 +253,7 @@ function formatAsMLA(article, context) {
         }
     }
     const title = titleText ? `"${titleText}."` : "N/A.";
-    const journal = journalInfo?.title ? `<em>${journalInfo.title}</em>` : "N/A";
+    const journal = journalInfo?.title || "N/A";
     let publicationDateString = journalInfo?.publicationDate?.year || "";
     if (journalInfo?.publicationDate?.month && journalInfo.publicationDate.year) {
         const month = journalInfo.publicationDate.month.substring(0, 3) + "."; // Abbreviate month

package/dist/mcp-server/tools/getPubMedArticleConnections/logic/index.js

@@ -15,7 +15,7 @@ import { handleELinkRelationships } from "./elinkHandler.js";
  */
 export async function handleGetPubMedArticleConnections(input, context) {
     const toolLogicContext = requestContextService.createRequestContext({
-        parentRequestId: context.requestId, // Link to parent context
+        parentRequestId: context.requestId,
         operation: "handleGetPubMedArticleConnections",
         toolName: "get_pubmed_article_connections",
         input: sanitizeInputForLogging(input),
@@ -27,8 +27,8 @@ export async function handleGetPubMedArticleConnections(input, context) {
         relatedArticles: [],
         citations: {},
         retrievedCount: 0,
-        eUtilityUrl: undefined, // Initialize
-        message: undefined, // Initialize
+        eUtilityUrl: undefined,
+        message: undefined,
     };
     try {
         switch (input.relationshipType) {
@@ -41,10 +41,8 @@ export async function handleGetPubMedArticleConnections(input, context) {
                 await handleCitationFormats(input, outputData, toolLogicContext);
                 break;
             default:
-                // This case should ideally be caught by Zod schema validation beforehand
                 throw new McpError(BaseErrorCode.VALIDATION_ERROR, `Unsupported relationshipType: ${input.relationshipType}`, { receivedType: input.relationshipType });
         }
-        // Ensure message is set if no specific error but also no results from handlers
         if (outputData.retrievedCount === 0 &&
             !outputData.message &&
             (input.relationshipType !== "citation_formats" ||
@@ -58,7 +56,6 @@ export async function handleGetPubMedArticleConnections(input, context) {
             error instanceof McpError
                 ? error.message
                 : "An unexpected error occurred while processing the request.";
-        // Ensure critical details from McpError are passed through if available
         const errorDetails = error instanceof McpError
             ? error.details
             : { originalError: error.message };
@@ -75,6 +72,12 @@ export async function handleGetPubMedArticleConnections(input, context) {
         ];
         return { content, isError: true };
     }
+    logger.notice("Successfully executed get_pubmed_article_connections tool.", {
+        ...toolLogicContext,
+        relationshipType: input.relationshipType,
+        retrievedCount: outputData.retrievedCount,
+        citationsGenerated: Object.keys(outputData.citations).length,
+    });
     const responseContent = [
         { type: "text", text: JSON.stringify(outputData) },
     ];

package/dist/mcp-server/tools/getPubMedArticleConnections/registration.d.ts

@@ -31,6 +31,5 @@ export type GetPubMedArticleConnectionsInput = z.infer<typeof GetPubMedArticleCo
 /**
  * Registers the 'get_pubmed_article_connections' tool with the given MCP server instance.
  * @param {McpServer} server - The MCP server instance.
- * @param {RequestContext} registrationContext - The context for this registration operation.
  */
-export declare function registerGetPubMedArticleConnectionsTool(server: McpServer): void;
+export declare function registerGetPubMedArticleConnectionsTool(server: McpServer): Promise<void>;

package/dist/mcp-server/tools/getPubMedArticleConnections/registration.js

@@ -4,8 +4,8 @@
  * @module src/mcp-server/tools/getPubMedArticleConnections/registration
  */
 import { z } from "zod";
-import { BaseErrorCode, McpError } from "../../../types-global/errors.js"; // Import McpError
-import { ErrorHandler, requestContextService, } from "../../../utils/index.js"; // Import requestContextService
+import { BaseErrorCode } from "../../../types-global/errors.js";
+import { ErrorHandler, logger, requestContextService, } from "../../../utils/index.js";
 import { handleGetPubMedArticleConnections } from "./logic.js";
 /**
  * Zod schema for the input parameters of the 'get_pubmed_article_connections' tool.
@@ -23,7 +23,7 @@ export const GetPubMedArticleConnectionsInputSchema = z.object({
         "citation_formats",
     ])
         .default("pubmed_similar_articles")
-        .describe("Specifies the type of connection or action: \n- 'pubmed_similar_articles': Finds articles similar to the source PMID (uses ELink `cmd=neighbor`). \n- 'pubmed_citedin': Finds articles in PubMed that cite the source PMID (uses ELink `linkname=pubmed_pubmed_citedin`). \n- 'pubmed_references': Finds articles in PubMed referenced by the source PMID (uses ELink `linkname=pubmed_pubmed_refs`). \n- 'citation_formats': Retrieves data for the source PMID and formats it into specified citation styles (uses EFetch)."),
+        .describe("Specifies the type of connection or action: \n- 'pubmed_similar_articles': Finds articles similar to the source PMID (uses ELink `cmd=neighbor`). \n- 'pubmed_citedin': Finds articles in PubMed that cite the source PMID (uses ELink `linkname=pubmed_pubmed_citedin`). \n- 'pubmed_references': Finds articles in PubMed referenced by the source PMID (uses ELink `linkname=pubmed_pubmed_refs`). \n- 'citation_formats': Retrieves data for the source PMID and formats it into specified citation styles (RIS, BibTeX, APA, MLA via NCBI EFetch and server-side formatting)."),
     maxRelatedResults: z
         .number()
         .int()
@@ -41,36 +41,26 @@ export const GetPubMedArticleConnectionsInputSchema = z.object({
 /**
  * Registers the 'get_pubmed_article_connections' tool with the given MCP server instance.
  * @param {McpServer} server - The MCP server instance.
- * @param {RequestContext} registrationContext - The context for this registration operation.
  */
-export function registerGetPubMedArticleConnectionsTool(server) {
+export async function registerGetPubMedArticleConnectionsTool(server) {
     const operation = "registerGetPubMedArticleConnectionsTool";
     const registrationContext = requestContextService.createRequestContext({
         operation,
     });
-    try {
-        server.tool("get_pubmed_article_connections", "Finds articles related to a source PubMed ID (PMID) or retrieves formatted citations for it. Supports finding similar articles, articles that cite the source, articles referenced by the source (via NCBI ELink), or fetching data to generate citations in various styles (RIS, BibTeX, APA, MLA via NCBI EFetch and server-side formatting). Returns a JSON object detailing the connections or formatted citations.", GetPubMedArticleConnectionsInputSchema.shape, // Pass .shape
-        async (validatedInput, toolContext) => {
-            // Create a new rich context for the logic handler
+    await ErrorHandler.tryCatch(() => {
+        server.tool("get_pubmed_article_connections", "Finds articles related to a source PubMed ID (PMID) or retrieves formatted citations for it. Supports finding similar articles, articles that cite the source, articles referenced by the source (via NCBI ELink), or fetching data to generate citations in various styles (RIS, BibTeX, APA, MLA via NCBI EFetch and server-side formatting). Returns a JSON object detailing the connections or formatted citations.", GetPubMedArticleConnectionsInputSchema.shape, async (validatedInput, toolContext) => {
             const richLogicContext = requestContextService.createRequestContext({
-                parentRequestId: registrationContext.requestId, // Link to registration context
+                parentRequestId: registrationContext.requestId,
                 operation: "getPubMedArticleConnectionsToolHandler",
-                mcpToolContext: toolContext, // Include MCP-provided context
+                mcpToolContext: toolContext,
             });
-            return await handleGetPubMedArticleConnections(validatedInput, richLogicContext);
+            return handleGetPubMedArticleConnections(validatedInput, richLogicContext);
         });
-        // Consistent with other tools, explicit success logging here might be omitted,
-        // relying on ErrorHandler for issues or higher-level logging.
-    }
-    catch (error) {
-        ErrorHandler.handleError(new McpError(// Create an McpError for consistent handling
-        BaseErrorCode.INITIALIZATION_FAILED, "Failed to register 'get_pubmed_article_connections' tool.", {
-            originalError: error instanceof Error ? error.message : String(error),
-        }), {
-            operation,
-            context: registrationContext, // Use the context of the registration operation
-            errorCode: BaseErrorCode.INITIALIZATION_FAILED,
-            critical: true, // Registration failure is critical
-        });
-    }
+        logger.notice("Tool 'get_pubmed_article_connections' registered.", registrationContext);
+    }, {
+        operation,
+        context: registrationContext,
+        errorCode: BaseErrorCode.INITIALIZATION_FAILED,
+        critical: true,
+    });
 }

package/dist/mcp-server/tools/pubmedResearchAgent/logic/planOrchestrator.js

@@ -35,9 +35,7 @@ function removeEmptyObjectsRecursively(obj) {
     }
     if (Array.isArray(obj)) {
         // If it's an array, recurse on each element and filter out empty objects/arrays
-        const newArr = obj
-            .map(removeEmptyObjectsRecursively)
-            .filter((item) => {
+        const newArr = obj.map(removeEmptyObjectsRecursively).filter((item) => {
             if (item === null || item === undefined)
                 return false;
             if (Array.isArray(item) && item.length === 0)

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

@@ -6,7 +6,6 @@
  */
 import { CallToolResult } from "@modelcontextprotocol/sdk/types.js";
 import { RequestContext } from "../../../utils/index.js";
-import { // Re-export for registration
-PubMedResearchAgentInput, PubMedResearchAgentInputSchema } from "./logic/index.js";
+import { PubMedResearchAgentInput, PubMedResearchAgentInputSchema } from "./logic/index.js";
 export { PubMedResearchAgentInput, PubMedResearchAgentInputSchema };
 export declare function pubmedResearchAgentLogic(input: PubMedResearchAgentInput, parentRequestContext: RequestContext): Promise<CallToolResult>;

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

@@ -6,9 +6,7 @@
  */
 import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
 import { logger, requestContextService, sanitizeInputForLogging, } from "../../../utils/index.js";
-import { generateFullResearchPlanOutline, PubMedResearchAgentInputSchema, // Re-export for registration
- } from "./logic/index.js";
-// Re-export schema and input type for easy access by registration.ts
+import { generateFullResearchPlanOutline, PubMedResearchAgentInputSchema, } from "./logic/index.js";
 export { PubMedResearchAgentInputSchema };
 export async function pubmedResearchAgentLogic(input, parentRequestContext) {
     const operationContext = requestContextService.createRequestContext({
@@ -19,6 +17,10 @@ export async function pubmedResearchAgentLogic(input, parentRequestContext) {
     logger.info(`Executing 'pubmed_research_agent' to generate research plan outline. Keywords: ${input.research_keywords.join(", ")}`, operationContext);
     try {
         const researchPlanOutline = generateFullResearchPlanOutline(input, operationContext);
+        logger.notice("Successfully generated research plan outline.", {
+            ...operationContext,
+            projectTitle: input.project_title_suggestion,
+        });
         return {
             content: [
                 { type: "text", text: JSON.stringify(researchPlanOutline, null, 2) },
@@ -30,11 +32,10 @@ export async function pubmedResearchAgentLogic(input, parentRequestContext) {
         logger.error("Execution failed for 'pubmed_research_agent'", error, operationContext);
         const mcpError = error instanceof McpError
             ? error
-            : new McpError(BaseErrorCode.INTERNAL_ERROR, // Using a generic internal error
-            `'pubmed_research_agent' tool failed during plan outline generation: ${error.message || "Internal server error."}`, {
+            : new McpError(BaseErrorCode.INTERNAL_ERROR, `'pubmed_research_agent' tool failed during plan outline generation: ${error.message || "Internal server error."}`, {
                 originalErrorName: error.name,
                 requestId: operationContext.requestId,
-                inputKeywords: input.research_keywords, // Adding some input context to error
+                inputKeywords: input.research_keywords,
             });
         return {
             content: [

package/dist/mcp-server/tools/pubmedResearchAgent/registration.d.ts

@@ -7,4 +7,4 @@ import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
  * Registers the pubmed_research_agent tool with the MCP server.
  * @param server - The McpServer instance.
  */
-export declare function registerPubMedResearchAgentTool(server: McpServer): void;
+export declare function registerPubMedResearchAgentTool(server: McpServer): Promise<void>;

package/dist/mcp-server/tools/pubmedResearchAgent/registration.js

@@ -2,17 +2,17 @@
  * @fileoverview Registration for the pubmed_research_agent tool.
  * @module pubmedResearchAgent/registration
  */
-import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
+import { BaseErrorCode } from "../../../types-global/errors.js";
 import { ErrorHandler, logger, requestContextService, } from "../../../utils/index.js";
 import { PubMedResearchAgentInputSchema, pubmedResearchAgentLogic, } from "./logic.js";
 /**
  * Registers the pubmed_research_agent tool with the MCP server.
  * @param server - The McpServer instance.
  */
-export function registerPubMedResearchAgentTool(server) {
+export async function registerPubMedResearchAgentTool(server) {
     const operation = "registerPubMedResearchAgentTool";
     const context = requestContextService.createRequestContext({ operation });
-    try {
+    await ErrorHandler.tryCatch(() => {
         server.tool("pubmed_research_agent", "Generates a standardized JSON research plan outline from component details you provide. It accepts granular inputs for all research phases (conception, data collection, analysis, dissemination, cross-cutting concerns). If `include_detailed_prompts_for_agent` is true, the output plan will embed instructive prompts and detailed guidance notes to aid the research agent. The tool's primary function is to organize and structure your rough ideas into a formal, machine-readable plan. This plan is intended for further processing; as the research agent, you should then utilize your full suite of tools (e.g., file manipulation, `get_pubmed_article_connections` for literature/data search via PMID) to execute the outlined research, tailored to the user's request.", PubMedResearchAgentInputSchema.shape, async (validatedInput, mcpProvidedContext) => {
             const handlerRequestContext = requestContextService.createRequestContext({
                 parentRequestId: context.requestId,
@@ -22,15 +22,10 @@ export function registerPubMedResearchAgentTool(server) {
             return pubmedResearchAgentLogic(validatedInput, handlerRequestContext);
         });
         logger.notice(`Tool 'pubmed_research_agent' registered.`, context);
-    }
-    catch (error) {
-        ErrorHandler.handleError(new McpError(BaseErrorCode.INITIALIZATION_FAILED, "Failed to register pubmed_research_agent tool", {
-            originalError: error instanceof Error ? error.message : String(error),
-        }), {
-            operation,
-            context,
-            errorCode: BaseErrorCode.INITIALIZATION_FAILED,
-            critical: true,
-        });
-    }
+    }, {
+        operation,
+        context,
+        errorCode: BaseErrorCode.INITIALIZATION_FAILED,
+        critical: true,
+    });
 }

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

@@ -140,10 +140,9 @@ export async function searchPubMedArticlesLogic(input, parentRequestContext) {
             if (esResult.WebEnv && esResult.QueryKey) {
                 eSummaryParams.WebEnv = esResult.WebEnv;
                 eSummaryParams.query_key = esResult.QueryKey;
-                eSummaryParams.retmax = currentFetchBriefSummaries; // Use history with retmax
+                eSummaryParams.retmax = currentFetchBriefSummaries;
             }
             else {
-                // Fallback to using explicit IDs if history is not available (should not happen if usehistory='y' was successful)
                 const pmidsForSummary = pmids
                     .slice(0, currentFetchBriefSummaries)
                     .join(",");
@@ -185,13 +184,19 @@ export async function searchPubMedArticlesLogic(input, parentRequestContext) {
             effectiveESearchTerm: effectiveQuery,
             totalFound,
             retrievedPmidCount,
-            pmids, // These are the PMIDs from ESearch, limited by input.maxResults
-            briefSummaries, // These should now be limited by currentFetchBriefSummaries
+            pmids,
+            briefSummaries,
             eSearchUrl,
             eSummaryUrl: currentFetchBriefSummaries > 0 && pmids.length > 0
                 ? eSummaryUrl
                 : undefined,
         };
+        logger.notice("Successfully executed searchPubMedArticles tool.", {
+            ...toolLogicContext,
+            totalFound,
+            retrievedPmidCount,
+            summariesFetched: briefSummaries.length,
+        });
         return {
             content: [{ type: "text", text: JSON.stringify(resultPayload) }],
             isError: false,

package/dist/mcp-server/tools/searchPubMedArticles/registration.d.ts

@@ -7,4 +7,4 @@ import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
  * Registers the searchPubMedArticles tool with the MCP server.
  * @param server - The McpServer instance.
  */
-export declare function registerSearchPubMedArticlesTool(server: McpServer): void;
+export declare function registerSearchPubMedArticlesTool(server: McpServer): Promise<void>;

package/dist/mcp-server/tools/searchPubMedArticles/registration.js

@@ -2,37 +2,30 @@
  * @fileoverview Registration for the searchPubMedArticles MCP tool.
  * @module src/mcp-server/tools/searchPubMedArticles/registration
  */
-import { BaseErrorCode, McpError } from "../../../types-global/errors.js"; // Import McpError
-import { ErrorHandler, requestContextService } from "../../../utils/index.js";
+import { BaseErrorCode } from "../../../types-global/errors.js";
+import { ErrorHandler, logger, requestContextService, } from "../../../utils/index.js";
 import { SearchPubMedArticlesInputSchema, searchPubMedArticlesLogic, } from "./logic.js";
 /**
  * Registers the searchPubMedArticles tool with the MCP server.
  * @param server - The McpServer instance.
  */
-export function registerSearchPubMedArticlesTool(server) {
+export async function registerSearchPubMedArticlesTool(server) {
     const operation = "registerSearchPubMedArticlesTool";
     const context = requestContextService.createRequestContext({ operation });
-    try {
-        server.tool("search_pubmed_articles", "Searches PubMed for articles using a query term and optional filters (max results, sort, date range, publication types). Uses NCBI ESearch to find PMIDs and ESummary (optional) for brief summaries. Returns a JSON object with search parameters, ESearch term, result counts, PMIDs, optional summaries (PMID, title, authors, source, dates), and E-utility URLs.", SearchPubMedArticlesInputSchema.shape, // Pass the .shape for ZodRawShape
-        async (input, toolContext) => {
-            // Explicitly type input
+    await ErrorHandler.tryCatch(() => {
+        server.tool("search_pubmed_articles", "Searches PubMed for articles using a query term and optional filters (max results, sort, date range, publication types). Uses NCBI ESearch to find PMIDs and ESummary (optional) for brief summaries. Returns a JSON object with search parameters, ESearch term, result counts, PMIDs, optional summaries (PMID, title, authors, source, dates), and E-utility URLs.", SearchPubMedArticlesInputSchema.shape, async (input, toolContext) => {
             const richContext = requestContextService.createRequestContext({
                 parentRequestId: context.requestId,
                 operation: "searchPubMedArticlesToolHandler",
-                mcpToolContext: toolContext, // Include MCP-provided context if any
+                mcpToolContext: toolContext,
             });
             return searchPubMedArticlesLogic(input, richContext);
         });
-    }
-    catch (error) {
-        ErrorHandler.handleError(new McpError(// Create an McpError for consistent handling
-        BaseErrorCode.INITIALIZATION_FAILED, "Failed to register searchPubMedArticles tool", {
-            originalError: error instanceof Error ? error.message : String(error),
-        }), {
-            operation,
-            context,
-            errorCode: BaseErrorCode.INITIALIZATION_FAILED, // errorCode is still useful for categorization
-            critical: true,
-        });
-    }
+        logger.notice("Tool 'search_pubmed_articles' registered.", context);
+    }, {
+        operation,
+        context,
+        errorCode: BaseErrorCode.INITIALIZATION_FAILED,
+        critical: true,
+    });
 }

package/dist/mcp-server/transports/httpTransport.js

@@ -54,6 +54,11 @@ const MAX_PORT_RETRIES = 15;
  * Stores active `StreamableHTTPServerTransport` instances from the SDK, keyed by their session ID.
  * This is essential for routing subsequent HTTP requests (GET, DELETE, non-initialize POST)
  * to the correct stateful session transport instance.
+ *
+ * @scalability Note: This is an in-memory store. For horizontal scaling across
+ * multiple processes or machines, this state would need to be moved to a shared,
+ * distributed store like Redis or a database.
+ *
  * @type {Record<string, StreamableHTTPServerTransport>}
  * @private
  */
@@ -61,6 +66,10 @@ const httpTransports = {};
 /**
  * Stores the last activity timestamp for each session, keyed by session ID.
  * Used for garbage collecting stale/abandoned sessions.
+ *
+ * @scalability Note: This is an in-memory store. Like `httpTransports`, this
+ * would need to be moved to a distributed store for multi-instance deployments.
+ *
  * @type {Record<string, number>}
  * @private
  */