@cyanheads/pubmed-mcp-server 1.1.2 → 1.2.1

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

@@ -61,14 +61,6 @@ export const SearchPubMedArticlesInputSchema = z.object({
         .default(0)
         .describe("Number of top PMIDs for which to fetch brief summaries using ESummary v2.0. Set to 0 to disable. Maximum is 50 for this tool. Default is 0."),
 });
-/**
- * Logic for the searchPubMedArticles tool.
- * Constructs and executes ESearch and optionally ESummary queries via NcbiService,
- * then formats the results into a CallToolResult.
- * @param input - Validated input arguments for the tool.
- * @param parentRequestContext - The parent request context for logging and correlation.
- * @returns A promise resolving to a CallToolResult.
- */
 export async function searchPubMedArticlesLogic(input, parentRequestContext) {
     const ncbiService = getNcbiService();
     const toolLogicContext = requestContextService.createRequestContext({
@@ -107,124 +99,79 @@ export async function searchPubMedArticlesLogic(input, parentRequestContext) {
         sort: input.sortBy,
         usehistory: currentFetchBriefSummaries > 0 ? "y" : "n",
     };
-    let eSearchUrl = "";
-    let eSummaryUrl = "";
-    try {
-        const eSearchResponse = await ncbiService.eSearch(eSearchParams, toolLogicContext);
-        const eSearchBase = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi";
-        const eSearchQueryStringParams = {};
-        for (const key in eSearchParams) {
-            if (eSearchParams[key] !== undefined) {
-                eSearchQueryStringParams[key] = String(eSearchParams[key]);
-            }
+    const eSearchResponse = await ncbiService.eSearch(eSearchParams, toolLogicContext);
+    const eSearchBase = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi";
+    const eSearchQueryStringParams = {};
+    for (const key in eSearchParams) {
+        if (eSearchParams[key] !== undefined) {
+            eSearchQueryStringParams[key] = String(eSearchParams[key]);
         }
-        const eSearchQueryString = new URLSearchParams(eSearchQueryStringParams).toString();
-        eSearchUrl = `${eSearchBase}?${eSearchQueryString}`;
-        if (!eSearchResponse || !eSearchResponse.eSearchResult) {
-            throw new McpError(BaseErrorCode.NCBI_PARSING_ERROR, "Invalid or empty ESearch response from NCBI.", {
-                responsePreview: sanitizeInputForLogging(JSON.stringify(eSearchResponse).substring(0, 200)),
-                requestId: toolLogicContext.requestId,
-            });
+    }
+    const eSearchQueryString = new URLSearchParams(eSearchQueryStringParams).toString();
+    const eSearchUrl = `${eSearchBase}?${eSearchQueryString}`;
+    if (!eSearchResponse || !eSearchResponse.eSearchResult) {
+        throw new McpError(BaseErrorCode.NCBI_PARSING_ERROR, "Invalid or empty ESearch response from NCBI.", {
+            ...toolLogicContext,
+            responsePreview: sanitizeInputForLogging(JSON.stringify(eSearchResponse).substring(0, 200)),
+        });
+    }
+    const esResult = eSearchResponse.eSearchResult;
+    const pmids = esResult.IdList?.Id || [];
+    const totalFound = parseInt(esResult.Count || "0", 10);
+    const retrievedPmidCount = pmids.length;
+    let briefSummaries = [];
+    let eSummaryUrl;
+    if (currentFetchBriefSummaries > 0 && pmids.length > 0) {
+        const eSummaryParams = {
+            db: "pubmed",
+            version: "2.0",
+            retmode: "xml",
+        };
+        if (esResult.WebEnv && esResult.QueryKey) {
+            eSummaryParams.WebEnv = esResult.WebEnv;
+            eSummaryParams.query_key = esResult.QueryKey;
+            eSummaryParams.retmax = currentFetchBriefSummaries;
         }
-        const esResult = eSearchResponse.eSearchResult;
-        const pmids = esResult.IdList?.Id || [];
-        const totalFound = parseInt(esResult.Count || "0", 10);
-        const retrievedPmidCount = pmids.length;
-        let briefSummaries = [];
-        if (currentFetchBriefSummaries > 0 && pmids.length > 0) {
-            const eSummaryParams = {
-                db: "pubmed",
-                version: "2.0",
-                retmode: "xml",
-            };
-            if (esResult.WebEnv && esResult.QueryKey) {
-                eSummaryParams.WebEnv = esResult.WebEnv;
-                eSummaryParams.query_key = esResult.QueryKey;
-                eSummaryParams.retmax = currentFetchBriefSummaries; // Use history with retmax
-            }
-            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(",");
-                eSummaryParams.id = pmidsForSummary;
-            }
-            const eSummaryBase = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi";
-            const eSummaryQueryStringParams = {};
-            for (const key in eSummaryParams) {
-                if (eSummaryParams[key] !== undefined) {
-                    eSummaryQueryStringParams[key] = String(eSummaryParams[key]);
-                }
+        else {
+            const pmidsForSummary = pmids
+                .slice(0, currentFetchBriefSummaries)
+                .join(",");
+            eSummaryParams.id = pmidsForSummary;
+        }
+        const eSummaryBase = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi";
+        const eSummaryQueryStringParams = {};
+        for (const key in eSummaryParams) {
+            if (eSummaryParams[key] !== undefined) {
+                eSummaryQueryStringParams[key] = String(eSummaryParams[key]);
             }
-            const eSummaryQueryString = new URLSearchParams(eSummaryQueryStringParams).toString();
-            eSummaryUrl = `${eSummaryBase}?${eSummaryQueryString}`;
-            const eSummaryResponseXml = await ncbiService.eSummary(eSummaryParams, toolLogicContext);
-            logger.debug("Raw ESummary Response (XML parsed by ncbiService):", {
+        }
+        const eSummaryQueryString = new URLSearchParams(eSummaryQueryStringParams).toString();
+        eSummaryUrl = `${eSummaryBase}?${eSummaryQueryString}`;
+        const eSummaryResponseXml = await ncbiService.eSummary(eSummaryParams, toolLogicContext);
+        if (eSummaryResponseXml && eSummaryResponseXml.eSummaryResult) {
+            briefSummaries = await extractBriefSummaries(eSummaryResponseXml.eSummaryResult, toolLogicContext);
+        }
+        else if (eSummaryResponseXml && eSummaryResponseXml.ERROR) {
+            logger.warning("ESummary returned a top-level error", {
                 ...toolLogicContext,
-                eSummaryResponse: sanitizeInputForLogging(eSummaryResponseXml),
+                errorDetails: eSummaryResponseXml.ERROR,
             });
-            if (eSummaryResponseXml && eSummaryResponseXml.eSummaryResult) {
-                briefSummaries = await extractBriefSummaries(eSummaryResponseXml.eSummaryResult, toolLogicContext);
-            }
-            else if (eSummaryResponseXml && eSummaryResponseXml.ERROR) {
-                logger.warning("ESummary returned a top-level error", {
-                    ...toolLogicContext,
-                    errorDetails: eSummaryResponseXml.ERROR,
-                });
-            }
         }
-        const resultPayload = {
-            searchParameters: {
-                queryTerm: input.queryTerm,
-                maxResults: input.maxResults,
-                sortBy: input.sortBy,
-                dateRange: input.dateRange,
-                filterByPublicationTypes: input.filterByPublicationTypes,
-                fetchBriefSummaries: currentFetchBriefSummaries,
-            },
-            effectiveESearchTerm: effectiveQuery,
-            totalFound,
-            retrievedPmidCount,
-            pmids, // These are the PMIDs from ESearch, limited by input.maxResults
-            briefSummaries, // These should now be limited by currentFetchBriefSummaries
-            eSearchUrl,
-            eSummaryUrl: currentFetchBriefSummaries > 0 && pmids.length > 0
-                ? eSummaryUrl
-                : undefined,
-        };
-        return {
-            content: [{ type: "text", text: JSON.stringify(resultPayload) }],
-            isError: false,
-        };
-    }
-    catch (error) {
-        logger.error("Error in searchPubMedArticlesLogic", error, toolLogicContext);
-        const mcpError = error instanceof McpError
-            ? error
-            : new McpError(BaseErrorCode.INTERNAL_ERROR, "Failed to search PubMed articles due to an unexpected error.", {
-                originalErrorName: error.name,
-                originalErrorMessage: error.message,
-                requestId: toolLogicContext.requestId,
-            });
-        return {
-            content: [
-                {
-                    type: "text",
-                    text: JSON.stringify({
-                        error: {
-                            code: mcpError.code,
-                            message: mcpError.message,
-                            details: mcpError.details,
-                        },
-                        searchParameters: sanitizeInputForLogging(input),
-                        eSearchUrl,
-                        eSummaryUrl: (input.fetchBriefSummaries ?? 0) > 0 && eSummaryUrl
-                            ? eSummaryUrl
-                            : undefined,
-                    }),
-                },
-            ],
-            isError: true,
-        };
     }
+    logger.notice("Successfully executed searchPubMedArticles tool.", {
+        ...toolLogicContext,
+        totalFound,
+        retrievedPmidCount,
+        summariesFetched: briefSummaries.length,
+    });
+    return {
+        searchParameters: input,
+        effectiveESearchTerm: effectiveQuery,
+        totalFound,
+        retrievedPmidCount,
+        pmids,
+        briefSummaries,
+        eSearchUrl,
+        eSummaryUrl,
+    };
 }

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 +2,70 @@
  * @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, McpError } 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 toolName = "search_pubmed_articles";
+    const toolDescription = "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.";
     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(async () => {
+        server.tool(toolName, toolDescription, SearchPubMedArticlesInputSchema.shape, async (input, mcpProvidedContext) => {
             const richContext = requestContextService.createRequestContext({
                 parentRequestId: context.requestId,
                 operation: "searchPubMedArticlesToolHandler",
-                mcpToolContext: toolContext, // Include MCP-provided context if any
+                mcpToolContext: mcpProvidedContext,
+                input,
             });
-            return searchPubMedArticlesLogic(input, richContext);
+            try {
+                const result = await searchPubMedArticlesLogic(input, richContext);
+                return {
+                    content: [
+                        { type: "text", text: JSON.stringify(result, null, 2) },
+                    ],
+                    isError: false,
+                };
+            }
+            catch (error) {
+                const handledError = ErrorHandler.handleError(error, {
+                    operation: "searchPubMedArticlesToolHandler",
+                    context: richContext,
+                    input,
+                    rethrow: false,
+                });
+                const mcpError = handledError instanceof McpError
+                    ? handledError
+                    : new McpError(BaseErrorCode.INTERNAL_ERROR, "An unexpected error occurred while searching PubMed articles.", {
+                        originalErrorName: handledError.name,
+                        originalErrorMessage: handledError.message,
+                    });
+                return {
+                    content: [
+                        {
+                            type: "text",
+                            text: JSON.stringify({
+                                error: {
+                                    code: mcpError.code,
+                                    message: mcpError.message,
+                                    details: mcpError.details,
+                                },
+                            }),
+                        },
+                    ],
+                    isError: true,
+                };
+            }
         });
-    }
-    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 '${toolName}' registered.`, context);
+    }, {
+        operation,
+        context,
+        errorCode: BaseErrorCode.INITIALIZATION_FAILED,
+        critical: true,
+    });
 }

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

@@ -13,12 +13,4 @@
 import { ServerType } from "@hono/node-server";
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { RequestContext } from "../../utils/index.js";
-/**
- * Sets up and starts the Streamable HTTP transport layer for the MCP server.
- *
- * @param createServerInstanceFn - An asynchronous factory function that returns a new `McpServer` instance.
- * @param parentContext - Logging context from the main server startup process.
- * @returns A promise that resolves with the Node.js `http.Server` instance when the HTTP server is successfully listening.
- * @throws {Error} If the server fails to start after all port retries.
- */
 export declare function startHttpTransport(createServerInstanceFn: () => Promise<McpServer>, parentContext: RequestContext): Promise<ServerType>;