@djmima/pubmed-mcp 0.0.0-stage → 1.0.0

package/dist/pubmed/client.js

@@ -0,0 +1,315 @@
+/**
+ * NCBI E-utilities HTTP client.
+ * Handles rate limiting, API key injection, and request construction.
+ *
+ * Base URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/
+ * Rate limits:
+ *   - Without API key: 3 requests/sec
+ *   - With API key:   10 requests/sec
+ * NCBI counts requests by arrival time, so we send at 8 req/s with a key to
+ * absorb network jitter, and retry briefly on HTTP 429.
+ */
+import https from 'node:https';
+import axios from 'axios';
+const NCBI_BASE_URL = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/';
+const PMC_ID_CONVERTER_URL = 'https://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/';
+/**
+ * Shared agent for every NCBI request.
+ * - ALPN: pmc.ncbi.nlm.nih.gov answers 403 to Node's default TLS handshake,
+ *   which advertises no ALPN protocol; offering http/1.1 is accepted.
+ * - keepAlive: reuse TLS connections across calls instead of re-handshaking.
+ */
+const HTTPS_AGENT = new https.Agent({
+    ALPNProtocols: ['http/1.1'],
+    keepAlive: true,
+});
+const TOOL_NAME = 'pubmed-mcp';
+const TOOL_EMAIL = 'pubmed-mcp@example.com';
+// ─── Rate limiter ────────────────────────────────────────────────────────────
+class RateLimiter {
+    nextSlot = 0;
+    minInterval; // ms
+    constructor(requestsPerSecond) {
+        this.minInterval = 1000 / requestsPerSecond;
+    }
+    /**
+     * Reserve the next send slot synchronously, then wait for it.
+     * Reserving before awaiting keeps concurrent callers spaced out instead of
+     * letting them all read the same timestamp and fire together.
+     */
+    async throttle() {
+        const now = Date.now();
+        const slot = Math.max(now, this.nextSlot);
+        this.nextSlot = slot + this.minInterval;
+        if (slot > now) {
+            await sleep(slot - now);
+        }
+    }
+}
+function sleep(ms) {
+    return new Promise((resolve) => setTimeout(resolve, ms));
+}
+/** Retries after an HTTP 429 before giving up. */
+const MAX_RATE_LIMIT_RETRIES = 2;
+/** Backoff per retry when NCBI sends no usable Retry-After header. */
+const RATE_LIMIT_BACKOFF_MS = 1000;
+// ─── Error types ─────────────────────────────────────────────────────────────
+export class NcbiNetworkError extends Error {
+    cause;
+    constructor(message, cause) {
+        super(message);
+        this.cause = cause;
+        this.name = 'NcbiNetworkError';
+    }
+}
+export class NcbiApiError extends Error {
+    statusCode;
+    constructor(message, statusCode) {
+        super(message);
+        this.statusCode = statusCode;
+        this.name = 'NcbiApiError';
+    }
+}
+export class NcbiParseError extends Error {
+    cause;
+    constructor(message, cause) {
+        super(message);
+        this.cause = cause;
+        this.name = 'NcbiParseError';
+    }
+}
+// ─── Client ──────────────────────────────────────────────────────────────────
+export class NcbiClient {
+    apiKey;
+    rateLimiter;
+    constructor(apiKey) {
+        // Trim whitespace/newlines that can sneak in from Secret Manager or .env files.
+        const raw = apiKey ?? process.env.NCBI_API_KEY;
+        this.apiKey = raw?.trim() || undefined;
+        const rps = this.apiKey ? 8 : 3; // 8 req/s (margin below NCBI's 10 req/s limit for arrival jitter)
+        this.rateLimiter = new RateLimiter(rps);
+    }
+    commonParams() {
+        const params = {
+            tool: TOOL_NAME,
+            email: TOOL_EMAIL,
+        };
+        if (this.apiKey) {
+            params['api_key'] = this.apiKey;
+        }
+        return params;
+    }
+    /**
+     * Throttle, send, and retry on HTTP 429. Every NCBI call goes through here
+     * so each attempt (including retries) takes its own rate-limiter slot.
+     */
+    async request(operation, send) {
+        for (let attempt = 0;; attempt++) {
+            await this.rateLimiter.throttle();
+            try {
+                return await send();
+            }
+            catch (err) {
+                if (attempt < MAX_RATE_LIMIT_RETRIES && isRateLimited(err)) {
+                    await sleep(retryDelayMs(err, attempt));
+                    continue;
+                }
+                throw wrapAxiosError(err, operation);
+            }
+        }
+    }
+    /**
+     * ESearch — search PubMed for article IDs.
+     * Returns the raw JSON response from NCBI.
+     */
+    async esearch(params) {
+        const response = await this.request('esearch', () => axios.get(`${NCBI_BASE_URL}esearch.fcgi`, {
+            httpsAgent: HTTPS_AGENT,
+            params: {
+                ...this.commonParams(),
+                db: 'pubmed',
+                retmode: 'json',
+                retmax: params.retmax ?? 20,
+                retstart: params.retstart ?? 0,
+                term: params.term,
+                ...(params.sort ? { sort: params.sort } : {}),
+                ...(params.field ? { field: params.field } : {}),
+                ...(params.datetype ? { datetype: params.datetype } : {}),
+                ...(params.mindate ? { mindate: params.mindate } : {}),
+                ...(params.maxdate ? { maxdate: params.maxdate } : {}),
+            },
+        }));
+        return response.data.esearchresult;
+    }
+    /**
+     * EFetch — retrieve full records from PubMed or PMC.
+     * Returns raw XML text.
+     */
+    async efetch(params) {
+        const idStr = Array.isArray(params.id) ? params.id.join(',') : params.id;
+        const response = await this.request('efetch', () => axios.get(`${NCBI_BASE_URL}efetch.fcgi`, {
+            httpsAgent: HTTPS_AGENT,
+            params: {
+                ...this.commonParams(),
+                db: params.db,
+                id: idStr,
+                retmode: params.retmode ?? 'xml',
+                ...(params.rettype ? { rettype: params.rettype } : {}),
+            },
+            responseType: 'text',
+        }));
+        return response.data;
+    }
+    /**
+     * ELink — find related articles or cross-database links.
+     * Accepts multiple IDs and returns the raw JSON response.
+     */
+    async elink(params) {
+        // Build URL manually to allow repeated id= params
+        const searchParams = new URLSearchParams({
+            ...this.commonParams(),
+            dbfrom: params.dbfrom,
+            linkname: params.linkname,
+            cmd: params.cmd ?? 'neighbor',
+            retmode: 'json',
+        });
+        for (const id of params.id) {
+            searchParams.append('id', id);
+        }
+        const response = await this.request('elink', () => axios.get(`${NCBI_BASE_URL}elink.fcgi?${searchParams.toString()}`, {
+            httpsAgent: HTTPS_AGENT,
+        }));
+        return response.data;
+    }
+    /**
+     * ECitmatch — look up PubMed IDs from structured citation data.
+     * Returns raw text with pipe-delimited fields.
+     */
+    async ecitmatch(citations) {
+        const bdata = citations
+            .map((c) => `${c.journal}|${c.year}|${c.volume}|${c.first_page}|${c.author}|${c.key}|`)
+            .join('\r');
+        const response = await this.request('ecitmatch', () => axios.get(`${NCBI_BASE_URL}ecitmatch.cgi`, {
+            httpsAgent: HTTPS_AGENT,
+            params: {
+                ...this.commonParams(),
+                db: 'pubmed',
+                retmode: 'xml',
+                rettype: 'xml',
+                bdata,
+            },
+            responseType: 'text',
+        }));
+        const contentType = String(response.headers?.['content-type'] ?? '').toLowerCase();
+        const text = String(response.data ?? '');
+        if (contentType.includes('html') || looksLikeHtml(text)) {
+            throw new NcbiApiError('NCBI ecitmatch returned HTML instead of citation match text. ' +
+                'Check the ECitMatch endpoint and bdata parameter format.', response.status);
+        }
+        return text;
+    }
+    /**
+     * PMC ID Converter — convert between PMID, PMCID, and DOI.
+     */
+    async idConvert(params) {
+        const response = await this.request('idConvert', () => axios.get(PMC_ID_CONVERTER_URL, {
+            httpsAgent: HTTPS_AGENT,
+            params: {
+                tool: TOOL_NAME,
+                email: TOOL_EMAIL,
+                ...(this.apiKey ? { api_key: this.apiKey } : {}),
+                format: 'json',
+                ids: params.ids.join(','),
+                idtype: params.idtype ?? 'pmid',
+                versions: 'no',
+            },
+        }));
+        return sanitizeIdConvResponse(response.data);
+    }
+}
+// ─── Helpers ─────────────────────────────────────────────────────────────────
+function wrapAxiosError(err, operation) {
+    if (err instanceof NcbiApiError || err instanceof NcbiNetworkError) {
+        return err;
+    }
+    if (axios.isAxiosError(err)) {
+        const status = err.response?.status;
+        if (status !== undefined) {
+            const body = describeResponseBody(err.response?.data);
+            const message = redactApiKey(body || err.message);
+            return new NcbiApiError(`NCBI ${operation} returned HTTP ${status}: ${message}`, status);
+        }
+        return new NcbiNetworkError(`Network error during NCBI ${operation}: ${err.message}`, err);
+    }
+    if (err instanceof Error)
+        return err;
+    return new Error(`Unknown error during NCBI ${operation}`);
+}
+const MAX_ERROR_BODY_LENGTH = 300;
+/** Render an error response body (JSON object, string, or buffer) as readable text. */
+function describeResponseBody(data) {
+    if (data === undefined || data === null)
+        return '';
+    let text;
+    if (typeof data === 'string') {
+        text = data;
+    }
+    else if (data instanceof ArrayBuffer || ArrayBuffer.isView(data)) {
+        text = Buffer.from(data).toString('utf8');
+    }
+    else {
+        try {
+            text = JSON.stringify(data);
+        }
+        catch {
+            text = String(data);
+        }
+    }
+    text = text.trim();
+    return text.length > MAX_ERROR_BODY_LENGTH
+        ? `${text.slice(0, MAX_ERROR_BODY_LENGTH)}…`
+        : text;
+}
+function isRateLimited(err) {
+    return axios.isAxiosError(err) && err.response?.status === 429;
+}
+/** Honor a numeric Retry-After header (seconds, capped); otherwise back off linearly. */
+function retryDelayMs(err, attempt) {
+    const fallback = RATE_LIMIT_BACKOFF_MS * (attempt + 1);
+    if (!axios.isAxiosError(err))
+        return fallback;
+    const headers = err.response?.headers;
+    const seconds = Number(headers?.['retry-after']);
+    if (Number.isFinite(seconds) && seconds > 0) {
+        return Math.min(seconds * 1000, 10_000);
+    }
+    return fallback;
+}
+function looksLikeHtml(text) {
+    return /^\s*(?:<!doctype\s+html|<html\b)/i.test(text);
+}
+function sanitizeIdConvResponse(response) {
+    return {
+        ...response,
+        request: {
+            ...response.request,
+            echo: redactApiKey(response.request.echo),
+        },
+        records: response.records.map((record) => ({
+            ...record,
+            ...(record.pmid !== undefined ? { pmid: String(record.pmid) } : {}),
+            ...(record.pmcid !== undefined ? { pmcid: String(record.pmcid) } : {}),
+            ...(record.doi !== undefined ? { doi: String(record.doi) } : {}),
+            ...(record['requested-id'] !== undefined
+                ? { 'requested-id': String(record['requested-id']) }
+                : {}),
+        })),
+    };
+}
+function redactApiKey(value) {
+    // NCBI echoes the key both as a query param and as "api-key" in JSON error bodies.
+    return value
+        .replace(/(^|[?&])(api_key=)[^&\s]+/gi, '$1$2<redacted>')
+        .replace(/("api[-_]key"\s*:\s*")[^"]*/gi, '$1<redacted>');
+}
+//# sourceMappingURL=client.js.map

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@@ -0,0 +1 @@
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package/dist/pubmed/types.d.ts

@@ -0,0 +1,159 @@
+/**
+ * TypeScript types for PubMed MCP tool responses.
+ * These match the exact API surface of the official Anthropic PubMed connector.
+ */
+export interface SearchArticlesWarnings {
+    phrases_ignored: string[];
+    quoted_phrases_not_found: string[];
+    output_messages: string[];
+}
+/** NCBI ESearch query diagnostics, not transport or MCP execution errors. */
+export interface SearchArticlesErrors {
+    phrases_not_found: string[];
+    fields_not_found: string[];
+}
+export interface SearchArticlesResponse {
+    pmids: string[];
+    total_count: number;
+    returned_count: number;
+    query: string;
+    query_translation: string;
+    has_more: boolean;
+    warnings: SearchArticlesWarnings;
+    errors: SearchArticlesErrors;
+}
+export interface ArticleIdentifiers {
+    pmid: string;
+    doi?: string;
+    pii?: string;
+    pmcid?: string;
+}
+export interface ArticleJournal {
+    title: string;
+    iso_abbreviation: string;
+}
+export interface ArticleAuthor {
+    last_name: string;
+    fore_name: string;
+    initials: string;
+    /** Group author (e.g. a study group); the name fields above are empty for it. */
+    collective_name?: string;
+    affiliations?: string[];
+}
+export interface ArticlePublicationDate {
+    year: string;
+    month?: string;
+    day?: string;
+}
+export interface ArticleCitation {
+    volume?: string;
+    issue?: string;
+    pages?: string;
+}
+export interface ArticleMetadata {
+    identifiers: ArticleIdentifiers;
+    title: string;
+    abstract: string;
+    doi?: string;
+    journal: ArticleJournal;
+    authors: ArticleAuthor[];
+    /** Number of authors PubMed lists, even when `authors` was cut down. */
+    author_count: number;
+    publication_date: ArticlePublicationDate;
+    keywords: string[];
+    mesh_terms: string[];
+    article_types: string[];
+    language: string;
+    citation: ArticleCitation;
+}
+export interface GetArticleMetadataResponse {
+    articles: ArticleMetadata[];
+    count: number;
+    important_legal_notice: string;
+}
+export interface LinksetDb {
+    dbto: string;
+    linkname: string;
+    links: string[];
+}
+export interface Linkset {
+    dbfrom: string;
+    ids: string[];
+    linksetdbs: LinksetDb[];
+}
+export interface FindRelatedArticlesResponse {
+    linksets: Linkset[];
+}
+export interface CitationResult {
+    journal: string;
+    year: string;
+    volume: string;
+    first_page: string;
+    author: string;
+    pmid: string;
+    key: string;
+}
+export interface LookupArticleByCitationResponse {
+    citations: CitationResult[];
+}
+export interface IdConversionRecord {
+    pmid?: string;
+    pmcid?: string;
+    doi?: string;
+    'requested-id': string;
+    errmsg?: string;
+    [key: string]: string | undefined;
+}
+export interface IdConversionRequest {
+    warnings: string[];
+    format: string;
+    idtype: string;
+    ids: string[];
+    email: string;
+    tool: string;
+    echo: string;
+    versions: string;
+    showaiid: string;
+}
+export interface ConvertArticleIdsResponse {
+    status: string;
+    'response-date': string;
+    request: IdConversionRequest;
+    records: IdConversionRecord[];
+}
+export interface FullTextIdentifiers {
+    pmcid: string;
+    pmid?: string;
+    doi?: string;
+}
+export interface FullTextArticle {
+    identifiers: FullTextIdentifiers;
+    title: string;
+    abstract: string;
+    doi?: string;
+    full_text: string;
+}
+export interface FullTextArticleError {
+    pmcid: string;
+    error: string;
+}
+export interface GetFullTextArticleResponse {
+    important_legal_notice: string;
+    articles: FullTextArticle[];
+    errors: FullTextArticleError[];
+    count: number;
+}
+export interface CopyrightStatus {
+    pmid: string;
+    pmcid?: string;
+    has_full_text: boolean;
+    license?: string;
+    copyright_statement?: string;
+    is_open_access?: boolean;
+}
+export interface GetCopyrightStatusResponse {
+    statuses: CopyrightStatus[];
+    count: number;
+}
+export declare const IMPORTANT_LEGAL_NOTICE: string;
+//# sourceMappingURL=types.d.ts.map

package/dist/pubmed/types.d.ts.map

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package/dist/pubmed/types.js

@@ -0,0 +1,11 @@
+/**
+ * TypeScript types for PubMed MCP tool responses.
+ * These match the exact API surface of the official Anthropic PubMed connector.
+ */
+// ─── Shared constants ────────────────────────────────────────────────────────
+export const IMPORTANT_LEGAL_NOTICE = 'PubMed data is provided by the National Library of Medicine (NLM). ' +
+    'When citing articles, include the complete DOI as required by the journal and publisher. ' +
+    'Use of this data is subject to NLM copyright and terms of use. ' +
+    'For PubMed Central full-text articles, proper attribution including the PMCID is required. ' +
+    'See: https://www.ncbi.nlm.nih.gov/home/about/policies/';
+//# sourceMappingURL=types.js.map

package/dist/pubmed/types.js.map

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package/dist/server.d.ts

@@ -0,0 +1,18 @@
+/**
+ * MCP server setup and tool registration.
+ *
+ * All seven PubMed tools are registered here. Each tool handler calls
+ * the appropriate function from src/tools/, catches errors, and returns
+ * a text content block (never throws — MCP protocol requires graceful errors).
+ */
+import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
+import { NcbiClient } from './pubmed/client.js';
+/**
+ * Create and return a configured MCP server instance.
+ *
+ * @param client NCBI client used by every tool. Rate limiting is per client,
+ *   so pass one shared client when creating several servers (HTTP mode
+ *   creates one per request). Defaults to a new client.
+ */
+export declare function createServer(client?: NcbiClient): McpServer;
+//# sourceMappingURL=server.d.ts.map

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