@cyanheads/pubmed-mcp-server 2.4.1 → 2.5.1

package/dist/services/ncbi/ncbi-service.js

@@ -11,6 +11,34 @@ import { NcbiApiClient } from './api-client.js';
 import { NcbiRequestQueue } from './request-queue.js';
 import { NcbiResponseHandler } from './response-handler.js';
 import { NCBI_PMC_IDCONV_URL, } from './types.js';
+/** Sentinel reason used when the service-level deadline expires. */
+class NcbiDeadlineExceeded extends Error {
+    constructor(deadlineMs) {
+        super(`NCBI request deadline (${deadlineMs}ms) exceeded`);
+        this.name = 'NcbiDeadlineExceeded';
+    }
+}
+/**
+ * Sleep that resolves after `ms`, or rejects immediately if `signal` aborts.
+ * Cleans up both timer and listener when either side wins.
+ */
+function abortableSleep(ms, signal) {
+    if (!signal)
+        return new Promise((r) => setTimeout(r, ms));
+    if (signal.aborted)
+        return Promise.reject(signal.reason);
+    return new Promise((resolve, reject) => {
+        const onAbort = () => {
+            clearTimeout(timer);
+            reject(signal.reason);
+        };
+        const timer = setTimeout(() => {
+            signal.removeEventListener('abort', onAbort);
+            resolve();
+        }, ms);
+        signal.addEventListener('abort', onAbort, { once: true });
+    });
+}
 /**
  * Facade over NCBI's E-utility suite. Each public method corresponds to a
  * single E-utility endpoint.
@@ -20,15 +48,18 @@ export class NcbiService {
     queue;
     responseHandler;
     maxRetries;
-    constructor(apiClient, queue, responseHandler, maxRetries) {
+    totalDeadlineMs;
+    constructor(apiClient, queue, responseHandler, maxRetries, totalDeadlineMs) {
         this.apiClient = apiClient;
         this.queue = queue;
         this.responseHandler = responseHandler;
         this.maxRetries = maxRetries;
+        this.totalDeadlineMs = totalDeadlineMs;
     }
-    async eSearch(params) {
+    async eSearch(params, options) {
         const response = await this.performRequest('esearch', params, {
             retmode: 'xml',
+            ...(options?.signal && { signal: options.signal }),
         });
         const esResult = response.eSearchResult;
         return {
@@ -43,10 +74,11 @@ export class NcbiService {
             ...(esResult.WarningList !== undefined && { warningList: esResult.WarningList }),
         };
     }
-    async eSummary(params) {
+    async eSummary(params, options) {
         const retmode = params.version === '2.0' && params.retmode === 'json' ? 'json' : 'xml';
         const response = await this.performRequest('esummary', params, {
             retmode,
+            ...(options?.signal && { signal: options.signal }),
         });
         return response.eSummaryResult;
     }
@@ -54,12 +86,16 @@ export class NcbiService {
         const usePost = options.usePost || (typeof params.id === 'string' && params.id.split(',').length > 200);
         return this.performRequest('efetch', params, { ...options, usePost });
     }
-    eLink(params) {
-        return this.performRequest('elink', params, { retmode: 'xml' });
+    eLink(params, options) {
+        return this.performRequest('elink', params, {
+            retmode: 'xml',
+            ...(options?.signal && { signal: options.signal }),
+        });
     }
-    async eSpell(params) {
+    async eSpell(params, options) {
         const response = await this.performRequest('espell', params, {
             retmode: 'xml',
+            ...(options?.signal && { signal: options.signal }),
         });
         const spellResult = response.eSpellResult;
         const original = spellResult.Query ?? params.term ?? '';
@@ -75,18 +111,21 @@ export class NcbiService {
             hasSuggestion: corrected.length > 0 && corrected !== original,
         };
     }
-    eInfo(params) {
-        return this.performRequest('einfo', params, { retmode: 'xml' });
+    eInfo(params, options) {
+        return this.performRequest('einfo', params, {
+            retmode: 'xml',
+            ...(options?.signal && { signal: options.signal }),
+        });
     }
     /**
      * Look up PMIDs from partial citation strings via NCBI ECitMatch.
      * Each citation can include journal, year, volume, first page, and author name.
      */
-    async eCitMatch(citations) {
+    async eCitMatch(citations, options) {
         const bdata = citations
             .map((c) => `${c.journal ?? ''}|${c.year ?? ''}|${c.volume ?? ''}|${c.firstPage ?? ''}|${c.authorName ?? ''}|${c.key}|`)
             .join('\r');
-        const text = await this.performRequest('ecitmatch.cgi', { db: 'pubmed', retmode: 'xml', bdata }, { retmode: 'text' });
+        const text = await this.performRequest('ecitmatch.cgi', { db: 'pubmed', retmode: 'xml', bdata }, { retmode: 'text', ...(options?.signal && { signal: options.signal }) });
         return text
             .split(/[\r\n]+/)
             .filter((line) => line.trim().length > 0)
@@ -119,13 +158,13 @@ export class NcbiService {
      * Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converter API.
      * Accepts up to 200 IDs in a single request. Only works for articles in PMC.
      */
-    async idConvert(ids, idtype) {
+    async idConvert(ids, idtype, options) {
         const params = {
             ids: ids.join(','),
             format: 'json',
             ...(idtype && { idtype }),
         };
-        const text = await this.queue.enqueue(() => this.withRetry(() => this.apiClient.makeExternalRequest(NCBI_PMC_IDCONV_URL, params), 'idconv'), 'idconv', params);
+        const text = await this.queue.enqueue(() => this.runWithDeadline((signal) => this.withRetry(() => this.apiClient.makeExternalRequest(NCBI_PMC_IDCONV_URL, params, signal), 'idconv', signal), options?.signal), 'idconv', params);
         let parsed;
         try {
             parsed = JSON.parse(text);
@@ -143,17 +182,49 @@ export class NcbiService {
     ]);
     /** Maximum backoff delay per retry (prevents exponential explosion at high retry counts). */
     static MAX_BACKOFF_MS = 30_000;
+    /**
+     * Wraps a task with a service-level deadline. Returns a combined AbortSignal
+     * (internal deadline OR'd with the caller's `ctx.signal`, if any) that the
+     * task must forward to both the HTTP call and any backoff sleep so cancellation
+     * interrupts the full retry chain — not just the next attempt.
+     */
+    async runWithDeadline(task, callerSignal) {
+        const deadlineController = new AbortController();
+        const deadlineTimer = setTimeout(() => deadlineController.abort(new NcbiDeadlineExceeded(this.totalDeadlineMs)), this.totalDeadlineMs);
+        const signal = callerSignal
+            ? AbortSignal.any([deadlineController.signal, callerSignal])
+            : deadlineController.signal;
+        try {
+            return await task(signal);
+        }
+        catch (error) {
+            if (error instanceof NcbiDeadlineExceeded) {
+                throw new McpError(JsonRpcErrorCode.Timeout, error.message, {
+                    deadlineMs: this.totalDeadlineMs,
+                });
+            }
+            throw error;
+        }
+        finally {
+            clearTimeout(deadlineTimer);
+        }
+    }
     /**
      * Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout, RateLimited).
      * Non-transient McpErrors and unexpected plain Errors fail immediately.
-     * Uses capped exponential backoff with jitter.
+     * Uses capped exponential backoff with jitter. Backoff sleep is abortable via
+     * `signal`, so deadline expiration or caller cancel short-circuits the chain.
      */
-    async withRetry(execute, label) {
+    async withRetry(execute, label, signal) {
         for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
+            if (signal?.aborted)
+                throw signal.reason;
             try {
                 return await execute();
             }
             catch (error) {
+                if (signal?.aborted)
+                    throw signal.reason;
                 if (!(error instanceof McpError)) {
                     throw error;
                 }
@@ -165,7 +236,7 @@ export class NcbiService {
                     const jitter = baseDelay * (0.75 + 0.5 * Math.random()); // ±25%
                     const retryDelay = Math.round(jitter);
                     logger.warning(`NCBI request to ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, { endpoint: label, attempt: attempt + 1, retryDelay });
-                    await new Promise((r) => setTimeout(r, retryDelay));
+                    await abortableSleep(retryDelay, signal);
                     continue;
                 }
                 const attempts = this.maxRetries + 1;
@@ -181,16 +252,23 @@ export class NcbiService {
         });
     }
     /**
-     * Enqueues a request with retry logic that covers both HTTP-level failures
-     * (network errors, timeouts) and XML-level errors (NCBI returning 200 OK
-     * with an error structure in the response body, e.g. connection resets
-     * surfaced as C++ exception traces).
+     * Enqueues a request with a service-level deadline and retry logic that covers
+     * both HTTP-level failures (network errors, timeouts) and XML-level errors
+     * (NCBI returning 200 OK with an error structure in the response body, e.g.
+     * connection resets surfaced as C++ exception traces).
+     *
+     * The combined deadline+caller signal is threaded into both the HTTP fetch
+     * (cancels wedged requests) and the backoff sleep (cancels pending retries),
+     * bounding the total time to `totalDeadlineMs` regardless of retry count.
      */
     performRequest(endpoint, params, options) {
-        return this.queue.enqueue(() => this.withRetry(async () => {
-            const text = await this.apiClient.makeRequest(endpoint, params, options);
+        return this.queue.enqueue(() => this.runWithDeadline((signal) => this.withRetry(async () => {
+            const text = await this.apiClient.makeRequest(endpoint, params, {
+                ...options,
+                signal,
+            });
             return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
-        }, endpoint), endpoint, params);
+        }, endpoint, signal), options?.signal), endpoint, params);
     }
 }
 // ─── Init / Accessor ────────────────────────────────────────────────────────
@@ -206,11 +284,12 @@ export function initNcbiService() {
     });
     const queue = new NcbiRequestQueue(config.requestDelayMs);
     const responseHandler = new NcbiResponseHandler();
-    _service = new NcbiService(apiClient, queue, responseHandler, config.maxRetries);
+    _service = new NcbiService(apiClient, queue, responseHandler, config.maxRetries, config.totalDeadlineMs);
     logger.info('NCBI service initialized.', {
         toolIdentifier: config.toolIdentifier,
         hasApiKey: !!config.apiKey,
         requestDelayMs: config.requestDelayMs,
+        totalDeadlineMs: config.totalDeadlineMs,
     });
 }
 /** Get the initialized NCBI service. Throws if not initialized. */

package/dist/services/ncbi/ncbi-service.js.map

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package/dist/services/ncbi/types.d.ts

@@ -26,6 +26,12 @@ export interface NcbiRequestOptions {
     rettype?: string;
     /** When true and retmode is 'xml', return the raw XML string after error checking. */
     returnRawXml?: boolean;
+    /**
+     * Combined abort signal — internal service-level deadline OR'd with the
+     * caller's `ctx.signal`. Cancels the in-flight fetch and short-circuits
+     * backoff sleeps.
+     */
+    signal?: AbortSignal;
     /**
      * Parse XML in `preserveOrder: true` mode (returns `JatsNodeList`). Required
      * for JATS mixed-content responses (PMC full-text) where inline element order
@@ -35,6 +41,14 @@ export interface NcbiRequestOptions {
     /** Force HTTP POST (for large payloads). */
     usePost?: boolean;
 }
+/**
+ * Runtime options accepted by public NCBI service methods.
+ * Lets callers thread `ctx.signal` (from tool handlers) through the retry layer.
+ */
+export interface NcbiCallOptions {
+    /** Caller-provided abort signal; combined with the service's internal deadline. */
+    signal?: AbortSignal;
+}
 /**
  * Options for the parseFullArticle convenience function.
  */

package/dist/services/ncbi/types.d.ts.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.4.1",
+  "version": "2.5.1",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
   "type": "module",
@@ -67,7 +67,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.5.3",
+    "@cyanheads/mcp-ts-core": "^0.6.5",
     "fast-xml-parser": "^5.7.1",
     "pino-pretty": "^13.1.3",
     "sanitize-html": "^2.17.3"
@@ -76,11 +76,11 @@
     "@biomejs/biome": "^2.4.12",
     "@types/node": "^25.6.0",
     "@types/sanitize-html": "^2.16.1",
-    "@vitest/coverage-istanbul": "^4.1.4",
+    "@vitest/coverage-istanbul": "^4.1.5",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.16",
     "typescript": "^6.0.3",
-    "vitest": "^4.1.4"
+    "vitest": "^4.1.5"
   }
 }

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.4.1",
+  "version": "2.5.1",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.4.1",
+      "version": "2.5.1",
       "packageArguments": [
         {
           "type": "positional",
@@ -60,7 +60,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.4.1",
+      "version": "2.5.1",
       "packageArguments": [
         {
           "type": "positional",