@pharmatools/pubcrawl 2.0.0

package/dist/tools/related.js

@@ -0,0 +1,63 @@
+import { z } from "zod";
+import { elink, esummary } from "../lib/ncbi.js";
+import { parseSummaryAuthors } from "../lib/xml-parser.js";
+const schema = {
+    pmid: z.string().describe("PubMed ID to find related articles for"),
+    maxResults: z.number().min(1).max(100).default(10).describe("Maximum number of results"),
+};
+export function registerRelatedTool(server) {
+    server.tool("find_related", "Find related articles for a given PubMed article. Returns similar papers ranked by relevance score using PubMed's neighbor algorithm.", schema, async (params) => {
+        try {
+            const linkResult = await elink({
+                id: params.pmid,
+                cmd: "neighbor_score",
+                linkname: "pubmed_pubmed",
+            });
+            if (linkResult.links.length === 0) {
+                return {
+                    content: [{ type: "text", text: JSON.stringify({ results: [], message: "No related articles found" }, null, 2) }],
+                };
+            }
+            // Take top N results
+            const topLinks = linkResult.links.slice(0, params.maxResults);
+            const ids = topLinks.map((l) => l.id);
+            const scoreMap = new Map(topLinks.map((l) => [l.id, l.score ?? 0]));
+            const summaryData = await esummary({ id: ids });
+            const articles = ids
+                .filter((uid) => summaryData[uid])
+                .map((uid) => {
+                const doc = summaryData[uid];
+                const authors = parseSummaryAuthors(doc.authors);
+                const pubDate = String(doc.pubdate ?? "");
+                const year = pubDate.match(/\d{4}/)?.[0] ?? "";
+                const doi = (doc.elocationid ?? "")
+                    .toString()
+                    .replace(/^doi:\s*/i, "");
+                return {
+                    pmid: uid,
+                    title: String(doc.title ?? ""),
+                    authors,
+                    journal: String(doc.fulljournalname ?? doc.source ?? ""),
+                    year,
+                    doi,
+                    abstract_snippet: String(doc.sorttitle ?? "").slice(0, 200),
+                    relevance_score: scoreMap.get(uid) ?? 0,
+                };
+            });
+            return {
+                content: [{
+                        type: "text",
+                        text: JSON.stringify({ results: articles }, null, 2),
+                    }],
+            };
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            return {
+                content: [{ type: "text", text: `Error finding related articles: ${message}` }],
+                isError: true,
+            };
+        }
+    });
+}
+//# sourceMappingURL=related.js.map

package/dist/tools/related.js.map

@@ -0,0 +1 @@
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package/dist/tools/search-indication.d.ts

@@ -0,0 +1,3 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerSearchIndicationTool(server: McpServer): void;
+//# sourceMappingURL=search-indication.d.ts.map

package/dist/tools/search-indication.d.ts.map

@@ -0,0 +1 @@
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package/dist/tools/search-indication.js

@@ -0,0 +1,73 @@
+import { z } from "zod";
+import { searchByIndication } from "../lib/openfda.js";
+import { searchEmc } from "../lib/emc.js";
+const MAX_CONCURRENT_EMC = 5;
+async function batchEmcLookups(drugNames) {
+    const results = new Map();
+    // Process in batches to cap concurrency
+    for (let i = 0; i < drugNames.length; i += MAX_CONCURRENT_EMC) {
+        const batch = drugNames.slice(i, i + MAX_CONCURRENT_EMC);
+        const settled = await Promise.allSettled(batch.map((name) => searchEmc(name)));
+        for (let j = 0; j < batch.length; j++) {
+            const outcome = settled[j];
+            if (outcome.status === "fulfilled" && outcome.value.length > 0) {
+                results.set(batch[j], outcome.value);
+            }
+        }
+    }
+    return results;
+}
+const schema = {
+    condition: z.string().describe("Medical condition or indication to search for (e.g., 'type 2 diabetes', 'hypertension')"),
+    maxResults: z.number().min(1).max(50).default(10).describe("Maximum number of drug results to return"),
+};
+export function registerSearchIndicationTool(server) {
+    server.tool("search_by_indication", "Find drugs approved for a medical condition. Searches US FDA labelling for the condition, then checks UK (eMC) availability for each drug found.", schema, async (params) => {
+        try {
+            // Step 1: Search OpenFDA for drugs with this indication
+            const fdaDrugs = await searchByIndication(params.condition, params.maxResults);
+            if (fdaDrugs.length === 0) {
+                return {
+                    content: [{
+                            type: "text",
+                            text: JSON.stringify({
+                                error: `No drugs found for "${params.condition}" in FDA labelling`,
+                            }, null, 2),
+                        }],
+                    isError: true,
+                };
+            }
+            // Step 2: For each unique generic name, check eMC for UK availability
+            const genericNames = fdaDrugs.map((d) => d.generic_name);
+            const emcResults = await batchEmcLookups(genericNames);
+            // Step 3: Merge into final results
+            const drugs = fdaDrugs.map((fda) => {
+                const emcMatches = emcResults.get(fda.generic_name);
+                return {
+                    name: fda.generic_name.toLowerCase(),
+                    brand_name: fda.brand_name,
+                    manufacturer: fda.manufacturer,
+                    us_approved: true,
+                    uk_approved: emcMatches !== undefined,
+                    us_setid: fda.set_id || undefined,
+                    uk_product_id: emcMatches?.[0]?.product_id,
+                };
+            });
+            const result = {
+                condition: params.condition,
+                drugs: drugs.slice(0, params.maxResults),
+            };
+            return {
+                content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+            };
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            return {
+                content: [{ type: "text", text: `Error searching by indication: ${message}` }],
+                isError: true,
+            };
+        }
+    });
+}
+//# sourceMappingURL=search-indication.js.map

package/dist/tools/search-indication.js.map

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package/dist/tools/search.d.ts

@@ -0,0 +1,3 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerSearchTool(server: McpServer): void;
+//# sourceMappingURL=search.d.ts.map

package/dist/tools/search.d.ts.map

@@ -0,0 +1 @@
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package/dist/tools/search.js

@@ -0,0 +1,69 @@
+import { z } from "zod";
+import { esearch, esummary } from "../lib/ncbi.js";
+import { parseSummaryAuthors } from "../lib/xml-parser.js";
+const schema = {
+    query: z.string().describe("PubMed search query"),
+    maxResults: z.number().min(1).max(100).default(10).describe("Maximum number of results"),
+    sort: z.enum(["relevance", "date"]).default("relevance").describe("Sort order"),
+    dateFrom: z.string().optional().describe("Start date (YYYY/MM/DD)"),
+    dateTo: z.string().optional().describe("End date (YYYY/MM/DD)"),
+    articleType: z.string().optional().describe("Article type filter (e.g., review, clinical trial)"),
+};
+function formatArticle(uid, doc) {
+    const authors = parseSummaryAuthors(doc.authors);
+    const pubDate = String(doc.pubdate ?? "");
+    const year = pubDate.match(/\d{4}/)?.[0] ?? "";
+    const doi = (doc.elocationid ?? "")
+        .toString()
+        .replace(/^doi:\s*/i, "");
+    return {
+        pmid: uid,
+        title: String(doc.title ?? ""),
+        authors,
+        journal: String(doc.fulljournalname ?? doc.source ?? ""),
+        year,
+        doi,
+        abstract_snippet: String(doc.sorttitle ?? "").slice(0, 200),
+    };
+}
+export function registerSearchTool(server) {
+    server.tool("search_pubmed", "Search PubMed for biomedical literature. Returns article summaries with PMIDs, titles, authors, journals, and DOIs.", schema, async (params) => {
+        try {
+            let term = params.query;
+            if (params.articleType) {
+                term += ` AND ${params.articleType}[pt]`;
+            }
+            const searchResult = await esearch({
+                term,
+                retmax: params.maxResults,
+                sort: params.sort === "date" ? "pub_date" : "relevance",
+                datetype: params.dateFrom || params.dateTo ? "pdat" : undefined,
+                mindate: params.dateFrom,
+                maxdate: params.dateTo,
+            });
+            if (searchResult.idlist.length === 0) {
+                return {
+                    content: [{ type: "text", text: JSON.stringify({ results: [], total_count: 0 }, null, 2) }],
+                };
+            }
+            const summaryData = await esummary({ id: searchResult.idlist });
+            const articles = searchResult.idlist
+                .filter((uid) => summaryData[uid])
+                .map((uid) => formatArticle(uid, summaryData[uid]));
+            return {
+                content: [{
+                        type: "text",
+                        text: JSON.stringify({ results: articles, total_count: searchResult.count }, null, 2),
+                    }],
+            };
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            return {
+                content: [{ type: "text", text: `Error searching PubMed: ${message}` }],
+                isError: true,
+            };
+        }
+    });
+}
+//# sourceMappingURL=search.js.map

package/dist/tools/search.js.map

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package/dist/tools/smpc.d.ts

@@ -0,0 +1,3 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerSmpcTool(server: McpServer): void;
+//# sourceMappingURL=smpc.d.ts.map

package/dist/tools/smpc.d.ts.map

@@ -0,0 +1 @@
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package/dist/tools/smpc.js

@@ -0,0 +1,52 @@
+import { z } from "zod";
+import { searchEmc, fetchSmpcHtml, parseSmpcSections } from "../lib/emc.js";
+const schema = {
+    drug: z.string().describe("Drug name to look up (e.g., 'metformin', 'atorvastatin')"),
+    sections: z
+        .array(z.string())
+        .optional()
+        .describe("Specific sections to retrieve — accepts numbers like '4.1' or names like 'indications'. Returns all sections if omitted."),
+};
+export function registerSmpcTool(server) {
+    server.tool("get_smpc", "Get UK/EU Summary of Product Characteristics (SmPC) for a drug from eMC (medicines.org.uk). Returns structured labelling sections.", schema, async (params) => {
+        try {
+            const searchResults = await searchEmc(params.drug);
+            if (searchResults.length === 0) {
+                return {
+                    content: [{
+                            type: "text",
+                            text: JSON.stringify({ error: `No SmPC found for "${params.drug}" on eMC` }, null, 2),
+                        }],
+                    isError: true,
+                };
+            }
+            // Select best match: prefer name containing the drug
+            const drugLower = params.drug.toLowerCase();
+            const sorted = [...searchResults].sort((a, b) => {
+                const aMatch = a.name.toLowerCase().includes(drugLower) ? 1 : 0;
+                const bMatch = b.name.toLowerCase().includes(drugLower) ? 1 : 0;
+                return bMatch - aMatch;
+            });
+            const best = sorted[0];
+            const html = await fetchSmpcHtml(best.product_id);
+            const sections = parseSmpcSections(html, params.sections);
+            const result = {
+                drug_name: best.name,
+                product_id: best.product_id,
+                sections: sections.map((s) => ({ code: s.code, title: s.title, content: s.content })),
+                url: `https://www.medicines.org.uk/emc/product/${best.product_id}/smpc`,
+            };
+            return {
+                content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+            };
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            return {
+                content: [{ type: "text", text: `Error fetching SmPC: ${message}` }],
+                isError: true,
+            };
+        }
+    });
+}
+//# sourceMappingURL=smpc.js.map

package/dist/tools/smpc.js.map

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package/dist/tools/trending.d.ts

@@ -0,0 +1,3 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerTrendingTool(server: McpServer): void;
+//# sourceMappingURL=trending.d.ts.map

package/dist/tools/trending.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"trending.d.ts","sourceRoot":"","sources":["../../src/tools/trending.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAqCpE,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAmF5D"}

package/dist/tools/trending.js

@@ -0,0 +1,106 @@
+import { z } from "zod";
+import { esearch, esummary } from "../lib/ncbi.js";
+import { parseSummaryAuthors } from "../lib/xml-parser.js";
+const HIGH_IMPACT_JOURNALS = [
+    "nature",
+    "science",
+    "cell",
+    "the new england journal of medicine",
+    "the lancet",
+    "jama",
+    "bmj",
+    "nature medicine",
+    "nature biotechnology",
+    "nature genetics",
+    "nature reviews",
+    "annals of internal medicine",
+    "plos medicine",
+    "circulation",
+    "journal of clinical oncology",
+];
+const schema = {
+    topic: z.string().describe("Topic or search term"),
+    days: z.number().min(1).max(365).default(30).describe("Number of days to look back"),
+    maxResults: z.number().min(1).max(100).default(20).describe("Maximum number of results"),
+    highImpactOnly: z.boolean().default(false).describe("Filter to high-impact journals only"),
+};
+function formatDate(date) {
+    const y = date.getFullYear();
+    const m = String(date.getMonth() + 1).padStart(2, "0");
+    const d = String(date.getDate()).padStart(2, "0");
+    return `${y}/${m}/${d}`;
+}
+export function registerTrendingTool(server) {
+    server.tool("trending_papers", "Find recent/trending papers on a topic. Sorted by date, with optional filtering to high-impact journals.", schema, async (params) => {
+        try {
+            const now = new Date();
+            const from = new Date(now.getTime() - params.days * 24 * 60 * 60 * 1000);
+            let term = params.topic;
+            if (params.highImpactOnly) {
+                const journalFilter = HIGH_IMPACT_JOURNALS
+                    .map((j) => `"${j}"[journal]`)
+                    .join(" OR ");
+                term += ` AND (${journalFilter})`;
+            }
+            const searchResult = await esearch({
+                term,
+                retmax: params.maxResults,
+                sort: "pub_date",
+                datetype: "pdat",
+                mindate: formatDate(from),
+                maxdate: formatDate(now),
+            });
+            if (searchResult.idlist.length === 0) {
+                return {
+                    content: [{
+                            type: "text",
+                            text: JSON.stringify({
+                                results: [],
+                                total_count: 0,
+                                topic: params.topic,
+                                period_days: params.days,
+                            }, null, 2),
+                        }],
+                };
+            }
+            const summaryData = await esummary({ id: searchResult.idlist });
+            const articles = searchResult.idlist
+                .filter((uid) => summaryData[uid])
+                .map((uid) => {
+                const doc = summaryData[uid];
+                const authors = parseSummaryAuthors(doc.authors);
+                const pubDate = String(doc.pubdate ?? "");
+                const year = pubDate.match(/\d{4}/)?.[0] ?? "";
+                const doi = (doc.elocationid ?? "").toString().replace(/^doi:\s*/i, "");
+                return {
+                    pmid: uid,
+                    title: String(doc.title ?? ""),
+                    authors,
+                    journal: String(doc.fulljournalname ?? doc.source ?? ""),
+                    year,
+                    doi,
+                    abstract_snippet: String(doc.sorttitle ?? "").slice(0, 200),
+                };
+            });
+            return {
+                content: [{
+                        type: "text",
+                        text: JSON.stringify({
+                            results: articles,
+                            total_count: searchResult.count,
+                            topic: params.topic,
+                            period_days: params.days,
+                        }, null, 2),
+                    }],
+            };
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            return {
+                content: [{ type: "text", text: `Error finding trending papers: ${message}` }],
+                isError: true,
+            };
+        }
+    });
+}
+//# sourceMappingURL=trending.js.map

package/dist/tools/trending.js.map

@@ -0,0 +1 @@
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package/dist/tools/uspi.d.ts

@@ -0,0 +1,3 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerUspiTool(server: McpServer): void;
+//# sourceMappingURL=uspi.d.ts.map

package/dist/tools/uspi.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"uspi.d.ts","sourceRoot":"","sources":["../../src/tools/uspi.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAmEpE,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAwExD"}

package/dist/tools/uspi.js

@@ -0,0 +1,117 @@
+import { z } from "zod";
+import { searchDrugLabels, fetchSplXml } from "../lib/dailymed.js";
+import { parseXml, parseSplSections } from "../lib/xml-parser.js";
+// LOINC codes for FDA prescribing information sections
+const LOINC_MAP = {
+    "boxed warning": "34071-1",
+    "indications": "34067-9",
+    "indications and usage": "34067-9",
+    "dosage": "34068-7",
+    "dosage and administration": "34068-7",
+    "dosage forms": "43678-2",
+    "contraindications": "34070-3",
+    "warnings": "43685-7",
+    "warnings and precautions": "43685-7",
+    "adverse reactions": "34084-4",
+    "drug interactions": "34073-7",
+    "use in specific populations": "42228-7",
+    "pregnancy": "42228-7",
+    "overdosage": "34088-5",
+    "clinical pharmacology": "34090-1",
+    "description": "34089-3",
+    "how supplied": "34069-5",
+    "storage": "44425-7",
+    "patient counseling": "34076-0",
+    "medication guide": "42231-1",
+};
+// All known PI LOINC codes
+const ALL_PI_CODES = [...new Set(Object.values(LOINC_MAP))];
+function resolveLoincCodes(sections) {
+    if (!sections || sections.length === 0)
+        return undefined;
+    const codes = [];
+    for (const input of sections) {
+        const lower = input.toLowerCase().trim();
+        // Direct LOINC code (e.g., "34067-9")
+        if (/^\d{5}-\d$/.test(lower)) {
+            codes.push(lower);
+            continue;
+        }
+        // Fuzzy match against section names
+        const match = Object.entries(LOINC_MAP).find(([name]) => name.includes(lower) || lower.includes(name));
+        if (match) {
+            codes.push(match[1]);
+        }
+    }
+    return codes.length > 0 ? codes : undefined;
+}
+const schema = {
+    drug: z.string().describe("Drug name to look up (e.g., 'metformin', 'atorvastatin')"),
+    sections: z
+        .array(z.string())
+        .optional()
+        .describe("Specific sections to retrieve (e.g., ['indications', 'adverse reactions', 'contraindications']). Returns all sections if omitted."),
+};
+export function registerUspiTool(server) {
+    server.tool("get_uspi", "Get FDA US Prescribing Information (USPI) for a drug from DailyMed. Returns structured labelling sections with LOINC codes.", schema, async (params) => {
+        try {
+            const searchResults = await searchDrugLabels(params.drug);
+            if (searchResults.length === 0) {
+                return {
+                    content: [{
+                            type: "text",
+                            text: JSON.stringify({ error: `No FDA labelling found for "${params.drug}"` }, null, 2),
+                        }],
+                    isError: true,
+                };
+            }
+            // Select best match: filter by drug name, sort by date descending
+            const drugLower = params.drug.toLowerCase();
+            const sorted = [...searchResults].sort((a, b) => {
+                const aMatch = a.title.toLowerCase().includes(drugLower) ? 1 : 0;
+                const bMatch = b.title.toLowerCase().includes(drugLower) ? 1 : 0;
+                if (aMatch !== bMatch)
+                    return bMatch - aMatch;
+                return b.published_date.localeCompare(a.published_date);
+            });
+            const best = sorted[0];
+            const xml = await fetchSplXml(best.setid);
+            const parsed = parseXml(xml);
+            // Navigate SPL XML structure: document > component > structuredBody
+            // component may be an array due to XML parser isArray config
+            const document = parsed?.document;
+            const docComponent = document?.component;
+            const firstComponent = Array.isArray(docComponent) ? docComponent[0] : docComponent;
+            const structuredBody = firstComponent?.structuredBody;
+            const requestedCodes = resolveLoincCodes(params.sections);
+            const rawSections = parseSplSections(structuredBody, requestedCodes);
+            // If no specific sections requested and we got nothing from filtering, try all PI codes
+            const sections = rawSections.length > 0
+                ? rawSections.map((s) => ({ code: s.code, title: s.title, content: s.content }))
+                : parseSplSections(structuredBody, ALL_PI_CODES).map((s) => ({
+                    code: s.code,
+                    title: s.title,
+                    content: s.content,
+                }));
+            const result = {
+                drug_name: best.title,
+                setid: best.setid,
+                spl_version: best.spl_version,
+                published_date: best.published_date,
+                sections,
+                dailymed_url: `https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=${best.setid}`,
+            };
+            return {
+                content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+            };
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            return {
+                content: [{ type: "text", text: `Error fetching USPI: ${message}` }],
+                isError: true,
+            };
+        }
+    });
+}
+//# sourceMappingURL=uspi.js.map

package/dist/tools/uspi.js.map

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