@pharmatools/pubcrawl 2.0.0

package/dist/lib/ncbi.d.ts

@@ -0,0 +1,37 @@
+export declare function setApiKey(key: string): void;
+export declare function esearch(params: {
+    db?: string;
+    term: string;
+    retmax?: number;
+    sort?: string;
+    datetype?: string;
+    mindate?: string;
+    maxdate?: string;
+}): Promise<{
+    idlist: string[];
+    count: number;
+}>;
+export declare function esummary(params: {
+    db?: string;
+    id: string[];
+}): Promise<Record<string, unknown>>;
+export declare function efetch(params: {
+    db?: string;
+    id: string;
+    rettype?: string;
+    retmode?: string;
+}): Promise<string>;
+export declare function elink(params: {
+    dbfrom?: string;
+    db?: string;
+    id: string;
+    cmd?: string;
+    linkname?: string;
+}): Promise<{
+    links: Array<{
+        id: string;
+        score?: number;
+    }>;
+}>;
+export declare function pmidToPmcid(pmid: string): Promise<string | null>;
+//# sourceMappingURL=ncbi.d.ts.map

package/dist/lib/ncbi.d.ts.map

@@ -0,0 +1 @@
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package/dist/lib/ncbi.js

@@ -0,0 +1,175 @@
+import { cache, TTL } from "./cache.js";
+const BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils";
+const TOOL = "pubcrawl";
+const EMAIL = "nick@pharmatools.ai";
+const REQUEST_DELAY_MS = 300;
+const TIMEOUT_MS = 15000;
+let apiKey;
+let lastRequestTime = 0;
+export function setApiKey(key) {
+    apiKey = key;
+}
+function buildParams(extra) {
+    const params = new URLSearchParams();
+    params.set("tool", TOOL);
+    params.set("email", EMAIL);
+    if (apiKey)
+        params.set("api_key", apiKey);
+    for (const [key, value] of Object.entries(extra)) {
+        if (value !== undefined)
+            params.set(key, value);
+    }
+    return params;
+}
+async function rateLimitedFetch(url) {
+    const minDelay = apiKey ? 100 : REQUEST_DELAY_MS;
+    const now = Date.now();
+    const elapsed = now - lastRequestTime;
+    if (elapsed < minDelay) {
+        await new Promise((resolve) => setTimeout(resolve, minDelay - elapsed));
+    }
+    lastRequestTime = Date.now();
+    const controller = new AbortController();
+    const timeout = setTimeout(() => controller.abort(), TIMEOUT_MS);
+    try {
+        const response = await fetch(url, { signal: controller.signal });
+        if (!response.ok) {
+            throw new Error(`NCBI API error: ${response.status} ${response.statusText}`);
+        }
+        return response;
+    }
+    finally {
+        clearTimeout(timeout);
+    }
+}
+export async function esearch(params) {
+    const cacheKey = `esearch:${JSON.stringify(params)}`;
+    const cached = cache.get(cacheKey);
+    if (cached)
+        return cached;
+    const urlParams = buildParams({
+        db: params.db ?? "pubmed",
+        term: params.term,
+        retmax: String(params.retmax ?? 10),
+        sort: params.sort,
+        datetype: params.datetype,
+        mindate: params.mindate,
+        maxdate: params.maxdate,
+        retmode: "json",
+    });
+    const url = `${BASE_URL}/esearch.fcgi?${urlParams}`;
+    const response = await rateLimitedFetch(url);
+    const data = await response.json();
+    const result = {
+        idlist: data.esearchresult?.idlist ?? [],
+        count: parseInt(data.esearchresult?.count ?? "0", 10),
+    };
+    cache.set(cacheKey, result, TTL.SEARCH);
+    return result;
+}
+export async function esummary(params) {
+    if (params.id.length === 0)
+        return {};
+    const cacheKey = `esummary:${params.db ?? "pubmed"}:${params.id.join(",")}`;
+    const cached = cache.get(cacheKey);
+    if (cached)
+        return cached;
+    const urlParams = buildParams({
+        db: params.db ?? "pubmed",
+        id: params.id.join(","),
+        retmode: "json",
+    });
+    const url = `${BASE_URL}/esummary.fcgi?${urlParams}`;
+    const response = await rateLimitedFetch(url);
+    const data = await response.json();
+    const result = data.result ?? {};
+    cache.set(cacheKey, result, TTL.SUMMARY);
+    return result;
+}
+export async function efetch(params) {
+    const cacheKey = `efetch:${params.db ?? "pubmed"}:${params.id}:${params.rettype ?? "xml"}`;
+    const cached = cache.get(cacheKey);
+    if (cached)
+        return cached;
+    const urlParams = buildParams({
+        db: params.db ?? "pubmed",
+        id: params.id,
+        rettype: params.rettype ?? "xml",
+        retmode: params.retmode ?? "xml",
+    });
+    const url = `${BASE_URL}/efetch.fcgi?${urlParams}`;
+    const response = await rateLimitedFetch(url);
+    const text = await response.text();
+    const ttl = params.db === "pmc" ? TTL.FULLTEXT : TTL.ABSTRACT;
+    cache.set(cacheKey, text, ttl);
+    return text;
+}
+export async function elink(params) {
+    const cacheKey = `elink:${JSON.stringify(params)}`;
+    const cached = cache.get(cacheKey);
+    if (cached)
+        return cached;
+    const urlParams = buildParams({
+        dbfrom: params.dbfrom ?? "pubmed",
+        db: params.db ?? "pubmed",
+        id: params.id,
+        cmd: params.cmd,
+        linkname: params.linkname,
+        retmode: "json",
+    });
+    const url = `${BASE_URL}/elink.fcgi?${urlParams}`;
+    const response = await rateLimitedFetch(url);
+    const data = await response.json();
+    const linkSets = data.linksets ?? [];
+    const links = [];
+    for (const linkSet of linkSets) {
+        const linkSetDbs = linkSet.linksetdbs ?? [];
+        for (const lsdb of linkSetDbs) {
+            const dbLinks = lsdb.links ?? [];
+            for (const link of dbLinks) {
+                if (typeof link === "object" && link !== null) {
+                    links.push({ id: String(link.id), score: link.score ? Number(link.score) : undefined });
+                }
+                else {
+                    links.push({ id: String(link) });
+                }
+            }
+        }
+    }
+    const result = { links };
+    cache.set(cacheKey, result, TTL.RELATED);
+    return result;
+}
+export async function pmidToPmcid(pmid) {
+    const cacheKey = `pmid2pmc:${pmid}`;
+    const cached = cache.get(cacheKey);
+    if (cached !== undefined)
+        return cached;
+    const urlParams = buildParams({
+        dbfrom: "pubmed",
+        db: "pmc",
+        id: pmid,
+        linkname: "pubmed_pmc",
+        retmode: "json",
+    });
+    const url = `${BASE_URL}/elink.fcgi?${urlParams}`;
+    const response = await rateLimitedFetch(url);
+    const data = await response.json();
+    const linkSets = data.linksets ?? [];
+    let pmcid = null;
+    for (const linkSet of linkSets) {
+        const linkSetDbs = linkSet.linksetdbs ?? [];
+        for (const lsdb of linkSetDbs) {
+            if (lsdb.linkname === "pubmed_pmc" && lsdb.links?.length > 0) {
+                const rawId = lsdb.links[0];
+                pmcid = `PMC${typeof rawId === "object" ? rawId.id : rawId}`;
+                break;
+            }
+        }
+        if (pmcid)
+            break;
+    }
+    cache.set(cacheKey, pmcid, TTL.ABSTRACT);
+    return pmcid;
+}
+//# sourceMappingURL=ncbi.js.map

package/dist/lib/ncbi.js.map

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package/dist/lib/openfda.d.ts

@@ -0,0 +1,8 @@
+export interface OpenFdaDrug {
+    generic_name: string;
+    brand_name: string;
+    manufacturer: string;
+    set_id: string;
+}
+export declare function searchByIndication(condition: string, limit?: number): Promise<OpenFdaDrug[]>;
+//# sourceMappingURL=openfda.d.ts.map

package/dist/lib/openfda.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"openfda.d.ts","sourceRoot":"","sources":["../../src/lib/openfda.ts"],"names":[],"mappings":"AAgCA,MAAM,WAAW,WAAW;IAC1B,YAAY,EAAE,MAAM,CAAC;IACrB,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;IACrB,MAAM,EAAE,MAAM,CAAC;CAChB;AAmBD,wBAAsB,kBAAkB,CACtC,SAAS,EAAE,MAAM,EACjB,KAAK,SAAK,GACT,OAAO,CAAC,WAAW,EAAE,CAAC,CAyDxB"}

package/dist/lib/openfda.js

@@ -0,0 +1,83 @@
+import { cache, TTL } from "./cache.js";
+const BASE_URL = "https://api.fda.gov/drug/label.json";
+const REQUEST_DELAY_MS = 300;
+const TIMEOUT_MS = 15000;
+let lastRequestTime = 0;
+async function rateLimitedFetch(url) {
+    const now = Date.now();
+    const elapsed = now - lastRequestTime;
+    if (elapsed < REQUEST_DELAY_MS) {
+        await new Promise((resolve) => setTimeout(resolve, REQUEST_DELAY_MS - elapsed));
+    }
+    lastRequestTime = Date.now();
+    const controller = new AbortController();
+    const timeout = setTimeout(() => controller.abort(), TIMEOUT_MS);
+    try {
+        const response = await fetch(url, { signal: controller.signal });
+        if (!response.ok) {
+            throw new Error(`OpenFDA API error: ${response.status} ${response.statusText}`);
+        }
+        return response;
+    }
+    finally {
+        clearTimeout(timeout);
+    }
+}
+// OpenFDA max per request (unauthenticated)
+const MAX_PER_PAGE = 99;
+const MAX_PAGES = 3;
+export async function searchByIndication(condition, limit = 20) {
+    const cacheKey = `openfda:indication:${condition.toLowerCase()}:${limit}`;
+    const cached = cache.get(cacheKey);
+    if (cached)
+        return cached;
+    // Use AND of individual terms so "rheumatoid arthritis" matches labels
+    // that say "moderately to severely active rheumatoid arthritis" etc.
+    const terms = condition.trim().split(/\s+/);
+    const query = terms
+        .map((t) => `indications_and_usage:${encodeURIComponent(t)}`)
+        .join("+AND+");
+    const seen = new Map();
+    // Always fetch all pages to maximise drug diversity, then trim.
+    // Page 1 is mostly NSAIDs; biologics appear on later pages.
+    for (let page = 0; page < MAX_PAGES; page++) {
+        const skip = page * MAX_PER_PAGE;
+        const url = `${BASE_URL}?search=${query}&limit=${MAX_PER_PAGE}&skip=${skip}`;
+        let data;
+        try {
+            const response = await rateLimitedFetch(url);
+            data = await response.json();
+        }
+        catch {
+            break;
+        }
+        if (!data.results || data.results.length === 0)
+            break;
+        for (const result of data.results) {
+            const openfda = result.openfda;
+            if (!openfda)
+                continue;
+            const genericName = openfda.generic_name?.[0] ?? "";
+            if (!genericName)
+                continue;
+            // Skip multi-ingredient kits/combos (e.g. "methylprednisolone acetate,
+            // lidocaine hydrochloride, bupivacaine hydrochloride") — these fill
+            // slots that should go to distinct therapeutic agents
+            if (genericName.includes(","))
+                continue;
+            const key = genericName.toLowerCase();
+            if (seen.has(key))
+                continue;
+            seen.set(key, {
+                generic_name: genericName,
+                brand_name: openfda.brand_name?.[0] ?? "",
+                manufacturer: openfda.manufacturer_name?.[0] ?? "",
+                set_id: openfda.spl_set_id?.[0] ?? "",
+            });
+        }
+    }
+    const drugs = [...seen.values()].slice(0, limit);
+    cache.set(cacheKey, drugs, TTL.SEARCH);
+    return drugs;
+}
+//# sourceMappingURL=openfda.js.map

package/dist/lib/openfda.js.map

@@ -0,0 +1 @@
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package/dist/lib/xml-parser.d.ts

@@ -0,0 +1,23 @@
+export declare function parseXml(xml: string): any;
+export declare function extractText(node: unknown): string;
+export declare function parseAuthors(authorList: unknown): string[];
+export declare function parseSummaryAuthors(authors: unknown): string[];
+export declare function parseAbstractSections(abstractNode: unknown): Array<{
+    label: string;
+    text: string;
+}>;
+export declare function parseMeshTerms(meshList: unknown): string[];
+export declare function parseKeywords(keywordList: unknown): string[];
+export declare function parseJatsSections(body: unknown): Array<{
+    title: string;
+    content: string;
+}>;
+export declare function parseFigureCaptions(body: unknown): string[];
+export declare function parseTableCaptions(body: unknown): string[];
+export declare function countReferences(back: unknown): number;
+export declare function parseSplSections(structuredBody: unknown, requestedCodes?: string[]): Array<{
+    code: string;
+    title: string;
+    content: string;
+}>;
+//# sourceMappingURL=xml-parser.d.ts.map

package/dist/lib/xml-parser.d.ts.map

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package/dist/lib/xml-parser.js

@@ -0,0 +1,273 @@
+import { XMLParser } from "fast-xml-parser";
+const parser = new XMLParser({
+    ignoreAttributes: false,
+    attributeNamePrefix: "@_",
+    textNodeName: "#text",
+    isArray: (name) => {
+        const arrayTags = [
+            "PubmedArticle",
+            "Author",
+            "AbstractText",
+            "MeshHeading",
+            "Keyword",
+            "sec",
+            "fig",
+            "table-wrap",
+            "ref",
+            "IdList",
+            "Link",
+            "LinkSet",
+            // SPL (DailyMed) tags
+            "component",
+            "section",
+            "paragraph",
+            "table",
+            "list",
+            "item",
+            "tbody",
+            "tr",
+            "td",
+            "thead",
+            "content",
+            "linkHtml",
+        ];
+        return arrayTags.includes(name);
+    },
+    trimValues: true,
+});
+// eslint-disable-next-line @typescript-eslint/no-explicit-any
+export function parseXml(xml) {
+    return parser.parse(xml);
+}
+export function extractText(node) {
+    if (typeof node === "string")
+        return node;
+    if (typeof node === "number")
+        return String(node);
+    if (node === null || node === undefined)
+        return "";
+    if (typeof node === "object") {
+        const obj = node;
+        if ("#text" in obj)
+            return String(obj["#text"]);
+        // Concatenate text from child elements
+        const parts = [];
+        for (const [key, value] of Object.entries(obj)) {
+            if (!key.startsWith("@_")) {
+                if (Array.isArray(value)) {
+                    parts.push(value.map(extractText).join(" "));
+                }
+                else {
+                    parts.push(extractText(value));
+                }
+            }
+        }
+        return parts.join(" ").trim();
+    }
+    return String(node);
+}
+function ensureArray(val) {
+    if (val === undefined || val === null)
+        return [];
+    return Array.isArray(val) ? val : [val];
+}
+export function parseAuthors(authorList) {
+    if (!authorList)
+        return [];
+    const list = authorList?.Author;
+    const authors = ensureArray(list);
+    return authors.map((a) => {
+        const author = a;
+        const last = author.LastName ? String(author.LastName) : "";
+        const first = author.ForeName ? String(author.ForeName) : "";
+        const initials = author.Initials ? String(author.Initials) : "";
+        if (last && first)
+            return `${last} ${first}`;
+        if (last && initials)
+            return `${last} ${initials}`;
+        // CollectiveName for group authors
+        if (author.CollectiveName)
+            return String(author.CollectiveName);
+        return last || first || "";
+    }).filter(Boolean);
+}
+export function parseSummaryAuthors(authors) {
+    if (!authors)
+        return [];
+    const list = ensureArray(authors);
+    return list.map((a) => {
+        if (typeof a === "string")
+            return a;
+        const author = a;
+        return author.name ? String(author.name) : extractText(a);
+    }).filter(Boolean);
+}
+export function parseAbstractSections(abstractNode) {
+    if (!abstractNode)
+        return [];
+    const obj = abstractNode;
+    const textNodes = obj.AbstractText;
+    if (!textNodes)
+        return [];
+    const sections = ensureArray(textNodes);
+    return sections.map((section) => {
+        if (typeof section === "string") {
+            return { label: "", text: section };
+        }
+        const s = section;
+        const label = s["@_Label"] ? String(s["@_Label"]) : "";
+        const text = extractText(section);
+        return { label, text };
+    });
+}
+export function parseMeshTerms(meshList) {
+    if (!meshList)
+        return [];
+    const headings = ensureArray(meshList?.MeshHeading);
+    return headings.map((h) => {
+        const heading = h;
+        const descriptor = heading.DescriptorName;
+        return extractText(descriptor);
+    }).filter(Boolean);
+}
+export function parseKeywords(keywordList) {
+    if (!keywordList)
+        return [];
+    const keywords = ensureArray(keywordList?.Keyword);
+    return keywords.map(extractText).filter(Boolean);
+}
+export function parseJatsSections(body) {
+    if (!body)
+        return [];
+    const obj = body;
+    const sections = ensureArray(obj.sec);
+    return sections.map((sec) => {
+        const s = sec;
+        const title = s.title ? extractText(s.title) : "";
+        const content = extractJatsContent(s);
+        return { title, content };
+    });
+}
+function extractJatsContent(node) {
+    if (!node || typeof node !== "object")
+        return extractText(node);
+    const obj = node;
+    const parts = [];
+    for (const [key, value] of Object.entries(obj)) {
+        if (key === "title" || key.startsWith("@_"))
+            continue;
+        if (key === "p") {
+            const paragraphs = ensureArray(value);
+            parts.push(...paragraphs.map(extractText));
+        }
+        else if (key === "sec") {
+            // Nested sections
+            const subsections = ensureArray(value);
+            for (const sub of subsections) {
+                const subObj = sub;
+                if (subObj.title)
+                    parts.push(`\n### ${extractText(subObj.title)}`);
+                parts.push(extractJatsContent(sub));
+            }
+        }
+    }
+    return parts.join("\n\n");
+}
+export function parseFigureCaptions(body) {
+    if (!body)
+        return [];
+    const figures = findAllElements(body, "fig");
+    return figures.map((fig) => {
+        const f = fig;
+        const label = f.label ? extractText(f.label) : "";
+        const caption = f.caption ? extractText(f.caption) : "";
+        return label ? `${label}: ${caption}` : caption;
+    }).filter(Boolean);
+}
+export function parseTableCaptions(body) {
+    if (!body)
+        return [];
+    const tables = findAllElements(body, "table-wrap");
+    return tables.map((tw) => {
+        const t = tw;
+        const label = t.label ? extractText(t.label) : "";
+        const caption = t.caption ? extractText(t.caption) : "";
+        return label ? `${label}: ${caption}` : caption;
+    }).filter(Boolean);
+}
+export function countReferences(back) {
+    if (!back)
+        return 0;
+    const refs = findAllElements(back, "ref");
+    return refs.length;
+}
+export function parseSplSections(structuredBody, requestedCodes) {
+    if (!structuredBody)
+        return [];
+    const obj = structuredBody;
+    const components = ensureArray(obj.component);
+    const results = [];
+    for (const comp of components) {
+        const c = comp;
+        const sections = ensureArray(c.section);
+        for (const sec of sections) {
+            extractSplSection(sec, results, requestedCodes);
+        }
+    }
+    return results;
+}
+function extractSplSection(section, results, requestedCodes) {
+    if (!section || typeof section !== "object")
+        return;
+    const s = section;
+    // Extract LOINC code from <code @_code>
+    const codeNode = s.code;
+    const code = codeNode?.["@_code"] ? String(codeNode["@_code"]) : "";
+    const title = s.title ? extractText(s.title) : "";
+    // Extract text content from <text> > <paragraph> elements
+    const textNode = s.text;
+    let content = "";
+    if (textNode) {
+        const paragraphs = ensureArray(textNode.paragraph);
+        content = paragraphs.map(extractText).filter(Boolean).join("\n\n");
+        if (!content) {
+            content = extractText(textNode);
+        }
+    }
+    if (code && (!requestedCodes || requestedCodes.includes(code))) {
+        results.push({ code, title, content });
+    }
+    // Recurse into nested components > sections
+    const nestedComponents = ensureArray(s.component);
+    for (const nc of nestedComponents) {
+        const ncObj = nc;
+        const nestedSections = ensureArray(ncObj.section);
+        for (const ns of nestedSections) {
+            extractSplSection(ns, results, requestedCodes);
+        }
+    }
+}
+function findAllElements(node, tagName) {
+    const results = [];
+    if (!node || typeof node !== "object")
+        return results;
+    const obj = node;
+    for (const [key, value] of Object.entries(obj)) {
+        if (key === tagName) {
+            const items = ensureArray(value);
+            results.push(...items);
+        }
+        else if (typeof value === "object" && value !== null) {
+            if (Array.isArray(value)) {
+                for (const item of value) {
+                    results.push(...findAllElements(item, tagName));
+                }
+            }
+            else {
+                results.push(...findAllElements(value, tagName));
+            }
+        }
+    }
+    return results;
+}
+//# sourceMappingURL=xml-parser.js.map

package/dist/lib/xml-parser.js.map

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

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

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

@@ -0,0 +1 @@
+{"version":3,"file":"abstract.d.ts","sourceRoot":"","sources":["../../src/tools/abstract.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAiBpE,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAkH5D"}