@cyanheads/pubmed-mcp-server 1.2.3 → 1.3.0

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

@@ -22,17 +22,17 @@ export declare const FetchPubMedContentInputSchema: z.ZodEffects<z.ZodObject<{
     includeMeshTerms: boolean;
     includeGrantInfo: boolean;
     outputFormat: "json" | "raw_text";
-    pmids?: string[] | undefined;
     queryKey?: string | undefined;
     webEnv?: string | undefined;
-    retstart?: number | undefined;
     retmax?: number | undefined;
-}, {
+    retstart?: number | undefined;
     pmids?: string[] | undefined;
+}, {
     queryKey?: string | undefined;
     webEnv?: string | undefined;
-    retstart?: number | undefined;
     retmax?: number | undefined;
+    retstart?: number | undefined;
+    pmids?: string[] | undefined;
     detailLevel?: "abstract_plus" | "full_xml" | "medline_text" | "citation_data" | undefined;
     includeMeshTerms?: boolean | undefined;
     includeGrantInfo?: boolean | undefined;
@@ -42,17 +42,17 @@ export declare const FetchPubMedContentInputSchema: z.ZodEffects<z.ZodObject<{
     includeMeshTerms: boolean;
     includeGrantInfo: boolean;
     outputFormat: "json" | "raw_text";
-    pmids?: string[] | undefined;
     queryKey?: string | undefined;
     webEnv?: string | undefined;
-    retstart?: number | undefined;
     retmax?: number | undefined;
-}, {
+    retstart?: number | undefined;
     pmids?: string[] | undefined;
+}, {
     queryKey?: string | undefined;
     webEnv?: string | undefined;
-    retstart?: number | undefined;
     retmax?: number | undefined;
+    retstart?: number | undefined;
+    pmids?: string[] | undefined;
     detailLevel?: "abstract_plus" | "full_xml" | "medline_text" | "citation_data" | undefined;
     includeMeshTerms?: boolean | undefined;
     includeGrantInfo?: boolean | undefined;

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

@@ -6,10 +6,10 @@
  * @module src/mcp-server/tools/fetchPubMedContent/logic
  */
 import { z } from "zod";
-import { getNcbiService } from "../../../services/NCBI/ncbiService.js";
+import { getNcbiService } from "../../../services/NCBI/core/ncbiService.js";
 import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
 import { logger, requestContextService, sanitizeInputForLogging, } from "../../../utils/index.js";
-import { ensureArray, extractAbstractText, extractArticleDates, extractAuthors, extractDoi, extractGrants, extractJournalInfo, extractKeywords, extractMeshTerms, extractPmid, extractPublicationTypes, getText, } from "../../../utils/parsing/ncbi-parsing/index.js";
+import { ensureArray, extractAbstractText, extractArticleDates, extractAuthors, extractDoi, extractGrants, extractJournalInfo, extractKeywords, extractMeshTerms, extractPmid, extractPublicationTypes, getText, } from "../../../services/NCBI/parsing/index.js";
 export const FetchPubMedContentInputSchema = z
     .object({
     pmids: z
@@ -242,13 +242,14 @@ export async function fetchPubMedContentLogic(input, parentRequestContext) {
         }
     }
     else if (input.detailLevel === "full_xml") {
+        const articlesXml = ensureArray(eFetchResponseData?.PubmedArticleSet?.PubmedArticle || []);
+        articlesCount = articlesXml.length;
         if (input.outputFormat === "raw_text") {
+            // Note: Raw XML output is requested, but we still parse to get an accurate count.
+            // This is a trade-off for robustness over performance in this specific case.
             finalOutputText = String(eFetchResponseData);
-            articlesCount = (finalOutputText.match(/<PubmedArticle>/g) || []).length;
         }
         else {
-            const articlesXml = ensureArray(eFetchResponseData?.PubmedArticleSet?.PubmedArticle || []);
-            articlesCount = articlesXml.length;
             const foundPmidsInXml = new Set();
             const articlesPayload = articlesXml.map((articleXml) => {
                 const pmid = extractPmid(articleXml.MedlineCitation) || "unknown_pmid";

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

@@ -1,9 +1,3 @@
-/**
- * @fileoverview Core logic for the generate_pubmed_chart tool.
- * Generates charts from parameterized input by creating Chart.js configurations
- * and rendering them on the server using chartjs-node-canvas.
- * @module src/mcp-server/tools/generatePubMedChart/logic
- */
 import { ChartJSNodeCanvas } from "chartjs-node-canvas";
 import { z } from "zod";
 import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
@@ -96,8 +90,8 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
         const groupedData = groupDataBySeries(dataValues, xField, yField, seriesField);
         datasets = Array.from(groupedData.entries()).map(([seriesName, data]) => ({
             label: seriesName,
-            data: labels.map(label => {
-                const point = data.find(p => p.x === label);
+            data: labels.map((label) => {
+                const point = data.find((p) => p.x === label);
                 return point ? point.y : null;
             }),
             // You can add backgroundColor, borderColor etc. here for styling
@@ -107,41 +101,45 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
         datasets = [
             {
                 label: yField,
-                data: labels.map(label => {
-                    const item = dataValues.find(d => d[xField] === label);
+                data: labels.map((label) => {
+                    const item = dataValues.find((d) => d[xField] === label);
                     return item ? item[yField] : null;
                 }),
             },
         ];
     }
     // For scatter and bubble charts, the data format is different
-    if (chartType === 'scatter' || chartType === 'bubble') {
+    if (chartType === "scatter" || chartType === "bubble") {
         if (seriesField) {
             const groupedData = groupDataBySeries(dataValues, xField, yField, seriesField);
             datasets = Array.from(groupedData.entries()).map(([seriesName, data]) => ({
                 label: seriesName,
-                data: data.map(point => ({
+                data: data.map((point) => ({
                     x: point.x,
                     y: point.y,
-                    r: chartType === 'bubble' && sizeField ? dataValues.find(d => d[xField] === point.x)[sizeField] : undefined
+                    r: chartType === "bubble" && sizeField
+                        ? dataValues.find((d) => d[xField] === point.x)[sizeField]
+                        : undefined,
                 })),
             }));
         }
         else {
-            datasets = [{
+            datasets = [
+                {
                     label: yField,
-                    data: dataValues.map(item => ({
+                    data: dataValues.map((item) => ({
                         x: item[xField],
                         y: item[yField],
-                        r: chartType === 'bubble' && sizeField ? item[sizeField] : undefined
+                        r: chartType === "bubble" && sizeField ? item[sizeField] : undefined,
                     })),
-                }];
+                },
+            ];
         }
     }
     const configuration = {
         type: chartType,
         data: {
-            labels: (chartType !== 'scatter' && chartType !== 'bubble') ? labels : undefined,
+            labels: chartType !== "scatter" && chartType !== "bubble" ? labels : undefined,
             datasets: datasets,
         },
         options: {
@@ -151,7 +149,9 @@ export async function generatePubMedChartLogic(input, parentRequestContext) {
                     text: title,
                 },
             },
-            scales: chartType === "pie" || chartType === "doughnut" || chartType === "polarArea"
+            scales: chartType === "pie" ||
+                chartType === "doughnut" ||
+                chartType === "polarArea"
                 ? undefined
                 : {
                     x: {

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

@@ -3,16 +3,16 @@
  * Fetches article details using EFetch and formats them into various citation styles.
  * @module src/mcp-server/tools/getPubMedArticleConnections/logic/citationFormatter
  */
-import { getNcbiService } from "../../../../services/NCBI/ncbiService.js";
+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 "../../../../utils/parsing/ncbi-parsing/index.js";
+import { extractAuthors, extractDoi, extractJournalInfo, extractPmid, getText, } from "../../../../services/NCBI/parsing/index.js";
 // Main handler for citation formats
 export async function handleCitationFormats(input, outputData, context) {
     const eFetchParams = {
         db: "pubmed",
         id: input.sourcePmid,
         retmode: "xml",
-        // Omitting rettype to hopefully get the fullest XML record by default
     };
     const eFetchBaseUrl = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi";
     const searchParamsString = new URLSearchParams(eFetchParams).toString();
@@ -26,264 +26,89 @@ export async function handleCitationFormats(input, outputData, context) {
         return;
     }
     const article = eFetchResult.PubmedArticleSet.PubmedArticle[0];
+    const csl = pubmedArticleToCsl(article, context);
+    const cite = new Cite(csl);
     if (input.citationStyles?.includes("ris")) {
-        outputData.citations.ris = formatAsRIS(article, context);
+        outputData.citations.ris = cite.format("ris");
     }
     if (input.citationStyles?.includes("bibtex")) {
-        outputData.citations.bibtex = formatAsBibTeX(article, context);
+        outputData.citations.bibtex = cite.format("bibtex");
     }
     if (input.citationStyles?.includes("apa_string")) {
-        outputData.citations.apa_string = formatAsAPA(article, context);
+        outputData.citations.apa_string = cite.format("bibliography", {
+            format: "text",
+            template: "apa",
+        });
     }
     if (input.citationStyles?.includes("mla_string")) {
-        outputData.citations.mla_string = formatAsMLA(article, context);
+        outputData.citations.mla_string = cite.format("bibliography", {
+            format: "text",
+            template: "mla",
+        });
     }
     outputData.retrievedCount = 1;
 }
-// --- Citation Formatting Helper Functions ---
-function formatAsRIS(article, context) {
+/**
+ * Converts an XML PubMed Article object to a CSL-JSON object.
+ * @param article The PubMed article in XML format.
+ * @param context The request context for logging.
+ * @returns A CSL-JSON object compatible with citation-js.
+ */
+function pubmedArticleToCsl(article, context) {
     const medlineCitation = article.MedlineCitation;
     const articleDetails = medlineCitation?.Article;
     const pmid = extractPmid(medlineCitation);
-    logger.debug("Formatting RIS for article", requestContextService.createRequestContext({ ...context, pmid }));
-    if (!articleDetails)
-        return "TY  - ERROR\nTI  - Article details not found\nER  - \n";
-    const authors = extractAuthors(articleDetails.AuthorList);
-    const journalInfo = extractJournalInfo(articleDetails.Journal, medlineCitation);
-    const title = getText(articleDetails.ArticleTitle);
-    const doi = extractDoi(articleDetails);
-    let risString = "TY  - JOUR\n";
-    authors.forEach((author) => {
-        if (author.lastName && author.firstName) {
-            risString += `AU  - ${author.lastName}, ${author.firstName}\n`;
-        }
-        else if (author.lastName) {
-            // Handle collective name or incomplete author
-            risString += `AU  - ${author.lastName}\n`;
-        }
+    const cslContext = requestContextService.createRequestContext({
+        ...context,
+        pmid,
     });
-    risString += `TI  - ${title || "N/A"}\n`;
-    risString += `JO  - ${journalInfo?.title || "N/A"}\n`;
-    risString += `VL  - ${journalInfo?.volume || ""}\n`;
-    risString += `IS  - ${journalInfo?.issue || ""}\n`;
-    if (journalInfo?.pages) {
-        const pages = journalInfo.pages.split("-");
-        risString += `SP  - ${pages[0] || ""}\n`;
-        if (pages.length > 1)
-            risString += `EP  - ${pages[1] || ""}\n`;
+    logger.debug("Converting PubMed XML to CSL-JSON", cslContext);
+    if (!articleDetails) {
+        logger.warning("Article details not found for CSL conversion", cslContext);
+        return { id: pmid || "unknown", title: "Article details not found" };
     }
-    risString += `PY  - ${journalInfo?.publicationDate?.year || ""}\n`;
-    if (doi)
-        risString += `DO  - ${doi}\n`;
-    if (pmid)
-        risString += `UR  - https://pubmed.ncbi.nlm.nih.gov/${pmid}\n`;
-    risString += "ER  - \n";
-    return risString;
-}
-function formatAsBibTeX(article, context) {
-    const medlineCitation = article.MedlineCitation;
-    const articleDetails = medlineCitation?.Article;
-    const pmid = extractPmid(medlineCitation);
-    logger.debug("Formatting BibTeX for article", requestContextService.createRequestContext({ ...context, pmid }));
-    if (!articleDetails)
-        return `@article{ERROR_ArticleNotFound${pmid || ""},\n  title = {Article details not found}\n}\n`;
-    const parsedAuthors = extractAuthors(articleDetails.AuthorList);
-    const journalInfo = extractJournalInfo(articleDetails.Journal, medlineCitation);
-    const title = getText(articleDetails.ArticleTitle) || "N/A";
-    const doi = extractDoi(articleDetails);
-    const authorsBibtex = parsedAuthors
-        .map((author) => {
-        if (author.lastName && author.firstName)
-            return `${author.lastName}, ${author.firstName}`;
-        if (author.lastName)
-            return `{${author.lastName}}`; // For collective names or single names
-        return "";
-    })
-        .filter(Boolean)
-        .join(" and ");
-    const year = journalInfo?.publicationDate?.year || "ND";
-    const firstAuthorLastName = parsedAuthors[0]?.lastName?.replace(/\s+/g, "") || "Unknown";
-    const bibKey = `${firstAuthorLastName}${year}`;
-    let bibtexString = `@article{${bibKey},\n`;
-    if (authorsBibtex)
-        bibtexString += `  author    = {${authorsBibtex}},\n`;
-    bibtexString += `  title     = {${title}},\n`;
-    bibtexString += `  journal   = {${journalInfo?.title || "N/A"}},\n`;
-    if (journalInfo?.publicationDate?.year)
-        bibtexString += `  year      = {${journalInfo.publicationDate.year}},\n`;
-    if (journalInfo?.volume)
-        bibtexString += `  volume    = {${journalInfo.volume}},\n`;
-    if (journalInfo?.issue)
-        bibtexString += `  number    = {${journalInfo.issue}},\n`;
-    if (journalInfo?.pages)
-        bibtexString += `  pages     = {${journalInfo.pages.replace("-", "--")}},\n`;
-    if (journalInfo?.publicationDate?.month)
-        bibtexString += `  month     = {${journalInfo.publicationDate.month.toLowerCase()}},\n`;
-    if (doi)
-        bibtexString += `  doi       = {${doi}},\n`;
-    if (pmid)
-        bibtexString += `  pmid      = {${pmid}}\n`;
-    bibtexString += `}\n`;
-    return bibtexString;
-}
-function formatAsAPA(article, context) {
-    const medlineCitation = article.MedlineCitation;
-    const articleDetails = medlineCitation?.Article;
-    const pmid = extractPmid(medlineCitation);
-    logger.debug("Formatting APA for article", requestContextService.createRequestContext({ ...context, pmid }));
-    if (!articleDetails)
-        return "Article details not found.";
-    const parsedAuthors = extractAuthors(articleDetails.AuthorList);
-    const journalInfo = extractJournalInfo(articleDetails.Journal, medlineCitation);
-    const titleText = getText(articleDetails.ArticleTitle) || "N/A";
-    const doi = extractDoi(articleDetails);
-    let authorsString = "N/A";
-    if (parsedAuthors.length > 0) {
-        if (parsedAuthors.length <= 20) {
-            authorsString = parsedAuthors
-                .map((author) => {
-                if (author.lastName && author.firstName) {
-                    const initials = author.firstName
-                        .split(/\s+|-/)
-                        .map((namePart) => namePart.charAt(0).toUpperCase() + ".")
-                        .join("");
-                    return `${author.lastName}, ${initials}`;
-                }
-                if (author.lastName)
-                    return author.lastName; // Collective name
-                return "";
-            })
-                .filter(Boolean)
-                .join(", ");
-            if (parsedAuthors.length > 1) {
-                const lastCommaIndex = authorsString.lastIndexOf(", ");
-                if (lastCommaIndex !== -1) {
-                    authorsString =
-                        authorsString.substring(0, lastCommaIndex) +
-                            " & " +
-                            authorsString.substring(lastCommaIndex + 2);
-                }
-            }
-        }
-        else {
-            const first19 = parsedAuthors
-                .slice(0, 19)
-                .map((author) => {
-                if (author.lastName && author.firstName) {
-                    const initials = author.firstName
-                        .split(/\s+|-/)
-                        .map((namePart) => namePart.charAt(0).toUpperCase() + ".")
-                        .join("");
-                    return `${author.lastName}, ${initials}`;
-                }
-                if (author.lastName)
-                    return author.lastName;
-                return "";
-            })
-                .filter(Boolean)
-                .join(", ");
-            const lastAuthor = parsedAuthors[parsedAuthors.length - 1];
-            let lastAuthorString = "";
-            if (lastAuthor.lastName && lastAuthor.firstName) {
-                const initials = lastAuthor.firstName
-                    .split(/\s+|-/)
-                    .map((namePart) => namePart.charAt(0).toUpperCase() + ".")
-                    .join("");
-                lastAuthorString = `${lastAuthor.lastName}, ${initials}`;
-            }
-            else if (lastAuthor.lastName) {
-                lastAuthorString = lastAuthor.lastName;
-            }
-            authorsString = `${first19}, ..., ${lastAuthorString}`;
-        }
-    }
-    const year = journalInfo?.publicationDate?.year || "n.d.";
-    const apaTitle = titleText.charAt(0).toUpperCase() + titleText.slice(1); // APA typically sentence case for article titles.
-    const journal = journalInfo?.title || "N/A";
-    const volume = journalInfo?.volume || "";
-    const issue = journalInfo?.issue ? `(${journalInfo.issue})` : "";
-    const pages = journalInfo?.pages || "";
-    const doiLink = doi ? ` https://doi.org/${doi}` : "";
-    let apaString = `${authorsString}. (${year}). ${apaTitle}. ${journal}`;
-    if (volume)
-        apaString += `, ${volume}`;
-    if (issue)
-        apaString += issue;
-    if (pages)
-        apaString += `, ${pages}`;
-    apaString += `.${doiLink}`;
-    return apaString;
-}
-function formatAsMLA(article, context) {
-    const medlineCitation = article.MedlineCitation;
-    const articleDetails = medlineCitation?.Article;
-    const pmid = extractPmid(medlineCitation);
-    logger.debug("Formatting MLA for article", requestContextService.createRequestContext({ ...context, pmid }));
-    if (!articleDetails)
-        return "Article details not found.";
-    const parsedAuthors = extractAuthors(articleDetails.AuthorList);
+    const authors = extractAuthors(articleDetails.AuthorList);
     const journalInfo = extractJournalInfo(articleDetails.Journal, medlineCitation);
-    const titleText = getText(articleDetails.ArticleTitle);
+    const title = getText(articleDetails.ArticleTitle);
     const doi = extractDoi(articleDetails);
-    let authorsString = "N/A";
-    if (parsedAuthors.length > 0) {
-        if (parsedAuthors.length <= 2) {
-            authorsString = parsedAuthors
-                .map((author, index) => {
-                if (author.lastName && author.firstName) {
-                    return index === 0
-                        ? `${author.lastName}, ${author.firstName}`
-                        : `${author.firstName} ${author.lastName}`;
+    const cslAuthors = authors.map((author) => author.collectiveName
+        ? { literal: author.collectiveName }
+        : { family: author.lastName, given: author.firstName });
+    const dateParts = [];
+    if (journalInfo?.publicationDate?.year) {
+        dateParts.push(parseInt(journalInfo.publicationDate.year, 10));
+        if (journalInfo.publicationDate.month) {
+            // Convert month name/number to number
+            const monthNumber = new Date(`${journalInfo.publicationDate.month} 1, 2000`).getMonth();
+            if (!isNaN(monthNumber)) {
+                dateParts.push(monthNumber + 1);
+                if (journalInfo.publicationDate.day) {
+                    dateParts.push(parseInt(journalInfo.publicationDate.day, 10));
                 }
-                if (author.lastName)
-                    return author.lastName;
-                return "";
-            })
-                .filter(Boolean)
-                .join(" and ");
-        }
-        else {
-            const firstAuthor = parsedAuthors[0];
-            if (firstAuthor.lastName && firstAuthor.firstName) {
-                authorsString = `${firstAuthor.lastName}, ${firstAuthor.firstName}, et al`;
-            }
-            else if (firstAuthor.lastName) {
-                authorsString = `${firstAuthor.lastName}, et al`;
             }
         }
     }
-    const title = titleText ? `"${titleText}."` : "N/A.";
-    const journal = journalInfo?.title || "N/A";
-    let publicationDateString = journalInfo?.publicationDate?.year || "";
-    if (journalInfo?.publicationDate?.month && journalInfo.publicationDate.year) {
-        const month = journalInfo.publicationDate.month.substring(0, 3) + "."; // Abbreviate month
-        publicationDateString = `${month} ${journalInfo.publicationDate.year}`;
-        if (journalInfo.publicationDate.day) {
-            publicationDateString = `${journalInfo.publicationDate.day} ${month} ${journalInfo.publicationDate.year}`;
+    const cslData = {
+        id: pmid,
+        type: "article-journal",
+        title: title,
+        author: cslAuthors,
+        issued: {
+            "date-parts": [dateParts],
+        },
+        "container-title": journalInfo?.title,
+        volume: journalInfo?.volume,
+        issue: journalInfo?.issue,
+        page: journalInfo?.pages,
+        DOI: doi,
+        PMID: pmid,
+        URL: pmid ? `https://pubmed.ncbi.nlm.nih.gov/${pmid}` : undefined,
+    };
+    // Clean up any undefined/null properties
+    for (const key in cslData) {
+        if (cslData[key] === undefined || cslData[key] === null) {
+            delete cslData[key];
         }
     }
-    else if (journalInfo?.publicationDate?.medlineDate) {
-        publicationDateString = journalInfo.publicationDate.medlineDate;
-    }
-    const volume = journalInfo?.volume ? `vol. ${journalInfo.volume}` : "";
-    const issue = journalInfo?.issue ? `no. ${journalInfo.issue}` : "";
-    const pages = journalInfo?.pages
-        ? `pp. ${journalInfo.pages.replace("-", "–")}`
-        : ""; // en-dash for MLA
-    const accessUrl = doi
-        ? `doi:${doi}`
-        : pmid
-            ? `https://pubmed.ncbi.nlm.nih.gov/${pmid}`
-            : "";
-    let mlaString = `${authorsString}. ${title} ${journal}`;
-    if (volume)
-        mlaString += `, ${volume}`;
-    if (issue)
-        mlaString += `, ${issue}`;
-    if (publicationDateString)
-        mlaString += `, ${publicationDateString}`;
-    if (pages)
-        mlaString += `, ${pages}`;
-    mlaString += `. PubMed Central, ${accessUrl}.`; // Assuming PubMed Central or just PubMed
-    return mlaString;
+    return cslData;
 }

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

@@ -3,10 +3,10 @@
  * for the getPubMedArticleConnections tool.
  * @module src/mcp-server/tools/getPubMedArticleConnections/logic/elinkHandler
  */
-import { getNcbiService } from "../../../../services/NCBI/ncbiService.js";
+import { getNcbiService } from "../../../../services/NCBI/core/ncbiService.js";
 import { logger } from "../../../../utils/index.js";
-import { extractBriefSummaries } from "../../../../utils/parsing/ncbi-parsing/index.js";
-import { ensureArray } from "../../../../utils/parsing/ncbi-parsing/xmlGenericHelpers.js"; // Added import
+import { extractBriefSummaries } from "../../../../services/NCBI/parsing/index.js";
+import { ensureArray } from "../../../../services/NCBI/parsing/xmlGenericHelpers.js"; // Added import
 export async function handleELinkRelationships(input, outputData, context) {
     const eLinkParams = {
         dbfrom: "pubmed",

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

@@ -5,10 +5,10 @@
  * @module src/mcp-server/tools/searchPubMedArticles/logic
  */
 import { z } from "zod";
-import { getNcbiService } from "../../../services/NCBI/ncbiService.js";
+import { getNcbiService } from "../../../services/NCBI/core/ncbiService.js";
 import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
 import { logger, requestContextService, sanitizeInputForLogging, } from "../../../utils/index.js";
-import { extractBriefSummaries } from "../../../utils/parsing/ncbi-parsing/index.js";
+import { extractBriefSummaries } from "../../../services/NCBI/parsing/index.js";
 import { sanitization } from "../../../utils/security/sanitization.js";
 export const SearchPubMedArticlesInputSchema = z.object({
     queryTerm: z
@@ -99,7 +99,7 @@ export async function searchPubMedArticlesLogic(input, parentRequestContext) {
         sort: input.sortBy,
         usehistory: currentFetchBriefSummaries > 0 ? "y" : "n",
     };
-    const eSearchResponse = await ncbiService.eSearch(eSearchParams, toolLogicContext);
+    const esResult = await ncbiService.eSearch(eSearchParams, toolLogicContext);
     const eSearchBase = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi";
     const eSearchQueryStringParams = {};
     for (const key in eSearchParams) {
@@ -109,15 +109,14 @@ export async function searchPubMedArticlesLogic(input, parentRequestContext) {
     }
     const eSearchQueryString = new URLSearchParams(eSearchQueryStringParams).toString();
     const eSearchUrl = `${eSearchBase}?${eSearchQueryString}`;
-    if (!eSearchResponse || !eSearchResponse.eSearchResult) {
+    if (!esResult) {
         throw new McpError(BaseErrorCode.NCBI_PARSING_ERROR, "Invalid or empty ESearch response from NCBI.", {
             ...toolLogicContext,
-            responsePreview: sanitizeInputForLogging(JSON.stringify(eSearchResponse).substring(0, 200)),
+            responsePreview: sanitizeInputForLogging(JSON.stringify(esResult).substring(0, 200)),
         });
     }
-    const esResult = eSearchResponse.eSearchResult;
-    const pmids = esResult.IdList?.Id || [];
-    const totalFound = parseInt(esResult.Count || "0", 10);
+    const pmids = esResult.idList || [];
+    const totalFound = esResult.count || 0;
     const retrievedPmidCount = pmids.length;
     let briefSummaries = [];
     let eSummaryUrl;
@@ -127,9 +126,9 @@ export async function searchPubMedArticlesLogic(input, parentRequestContext) {
             version: "2.0",
             retmode: "xml",
         };
-        if (esResult.WebEnv && esResult.QueryKey) {
-            eSummaryParams.WebEnv = esResult.WebEnv;
-            eSummaryParams.query_key = esResult.QueryKey;
+        if (esResult.webEnv && esResult.queryKey) {
+            eSummaryParams.WebEnv = esResult.webEnv;
+            eSummaryParams.query_key = esResult.queryKey;
             eSummaryParams.retmax = currentFetchBriefSummaries;
         }
         else {

package/dist/mcp-server/transports/auth/authFactory.d.ts

@@ -0,0 +1,10 @@
+import { AuthStrategy } from "./strategies/authStrategy.js";
+/**
+ * Creates and returns an authentication strategy instance based on the
+ * application's configuration (`config.mcpAuthMode`).
+ *
+ * @returns An instance of a class that implements the `AuthStrategy` interface,
+ *          or `null` if authentication is disabled (`none`).
+ * @throws {Error} If the auth mode is unknown or misconfigured.
+ */
+export declare function createAuthStrategy(): AuthStrategy | null;

package/dist/mcp-server/transports/auth/authFactory.js

@@ -0,0 +1,41 @@
+/**
+ * @fileoverview Factory for creating an authentication strategy based on configuration.
+ * This module centralizes the logic for selecting and instantiating the correct
+ * authentication strategy, promoting loose coupling and easy extensibility.
+ * @module src/mcp-server/transports/auth/authFactory
+ */
+import { config } from "../../../config/index.js";
+import { logger, requestContextService } from "../../../utils/index.js";
+import { JwtStrategy } from "./strategies/jwtStrategy.js";
+import { OauthStrategy } from "./strategies/oauthStrategy.js";
+/**
+ * Creates and returns an authentication strategy instance based on the
+ * application's configuration (`config.mcpAuthMode`).
+ *
+ * @returns An instance of a class that implements the `AuthStrategy` interface,
+ *          or `null` if authentication is disabled (`none`).
+ * @throws {Error} If the auth mode is unknown or misconfigured.
+ */
+export function createAuthStrategy() {
+    const context = requestContextService.createRequestContext({
+        operation: "createAuthStrategy",
+        authMode: config.mcpAuthMode,
+    });
+    logger.info("Creating authentication strategy...", context);
+    switch (config.mcpAuthMode) {
+        case "jwt":
+            logger.debug("Instantiating JWT authentication strategy.", context);
+            return new JwtStrategy();
+        case "oauth":
+            logger.debug("Instantiating OAuth authentication strategy.", context);
+            return new OauthStrategy();
+        case "none":
+            logger.info("Authentication is disabled ('none' mode).", context);
+            return null; // No authentication
+        default:
+            // This ensures that if a new auth mode is added to the config type
+            // but not to this factory, we get a compile-time or runtime error.
+            logger.error(`Unknown authentication mode: ${config.mcpAuthMode}`, context);
+            throw new Error(`Unknown authentication mode: ${config.mcpAuthMode}`);
+    }
+}

package/dist/mcp-server/transports/auth/authMiddleware.d.ts

@@ -0,0 +1,19 @@
+/**
+ * @fileoverview Defines a unified Hono middleware for authentication.
+ * This middleware is strategy-agnostic. It extracts a Bearer token,
+ * delegates verification to the provided authentication strategy, and
+ * populates the async-local storage context with the resulting auth info.
+ * @module src/mcp-server/transports/auth/authMiddleware
+ */
+import type { HttpBindings } from "@hono/node-server";
+import type { Context, Next } from "hono";
+import type { AuthStrategy } from "./strategies/authStrategy.js";
+/**
+ * Creates a Hono middleware function that enforces authentication using a given strategy.
+ *
+ * @param strategy - An instance of a class that implements the `AuthStrategy` interface.
+ * @returns A Hono middleware function.
+ */
+export declare function createAuthMiddleware(strategy: AuthStrategy): (c: Context<{
+    Bindings: HttpBindings;
+}>, next: Next) => Promise<void>;