@cyanheads/pubmed-mcp-server 2.10.14 → 2.10.16

package/dist/services/ncbi/request-queue.js

@@ -1,135 +1,36 @@
 /**
- * @fileoverview Rate-limited request scheduler for NCBI E-utility calls. Caps
- * concurrent in-flight requests and enforces a minimum start-gap between
- * dispatches to stay within NCBI's documented per-second ceiling. Supports
- * abort-during-wait so callers' deadlines can bound queue time end-to-end.
+ * @fileoverview Request queue for NCBI E-utility calls, built on the framework pacer.
+ * Spaces request starts to NCBI's per-second ceiling, caps concurrent in-flight
+ * requests and queue depth, releases a waiting caller the moment its signal aborts,
+ * and closes one shared cooldown gate for every queued caller when NCBI answers 429.
+ * Each retry attempt re-enters the queue, so a throttled upstream paces the whole
+ * server rather than each caller retrying into it on its own backoff.
  * @module src/services/ncbi/request-queue
  */
-import { rateLimited } from '@cyanheads/mcp-ts-core/errors';
-import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
-import { recoveryFor } from '../error-contracts.js';
-const DEFAULT_MAX_CONCURRENT = 8;
-const DEFAULT_MAX_QUEUE_SIZE = 100;
+import { createPacer } from '@cyanheads/mcp-ts-core/utils';
+/** Waiting callers past which a new arrival is shed at once. */
+const DEFAULT_MAX_QUEUE_DEPTH = 100;
 /**
- * Schedules NCBI API requests against two independent ceilings:
- *
- *   - **Throughput** (`minStartGapMs`): minimum delay between two consecutive
- *     dispatch times. Matches NCBI's per-second start-rate cap (≈3/s without
- *     an API key, ≈10/s with one).
- *   - **Concurrency** (`maxConcurrent`): maximum number of requests in flight
- *     simultaneously. Decouples concurrency from rate, so slow upstream
- *     responses don't block new dispatches.
- *
- * Enqueue accepts an optional `AbortSignal` so callers can bound their total
- * time inside the scheduler — when the signal fires, a still-waiting task
- * rejects immediately instead of sitting behind a saturated worker for
- * minutes.
+ * Gate closed on an NCBI 429: one second — the width of NCBI's rate window — doubled
+ * per consecutive 429 and reset by the first success. An honored `Retry-After` is capped
+ * by the same ceiling, a quarter of the default total deadline, so a caller queued
+ * behind the longest gate still has budget left for its request.
  */
-export class NcbiRequestQueue {
-    waiters = [];
-    minStartGapMs;
-    maxConcurrent;
-    maxQueueSize;
-    inFlight = 0;
-    lastStartTime = 0;
-    nextDispatchTimer;
-    constructor(minStartGapMs, maxConcurrent = DEFAULT_MAX_CONCURRENT, maxQueueSize = DEFAULT_MAX_QUEUE_SIZE) {
-        this.minStartGapMs = minStartGapMs;
-        this.maxConcurrent = maxConcurrent;
-        this.maxQueueSize = maxQueueSize;
-    }
-    enqueue(task, endpoint, params, signal) {
-        if (this.waiters.length >= this.maxQueueSize) {
-            return Promise.reject(rateLimited(`NCBI request queue is full (max ${this.maxQueueSize}).`, {
-                reason: 'queue_full',
-                endpoint,
-                queueSize: this.waiters.length,
-                ...recoveryFor('queue_full'),
-            }));
-        }
-        return new Promise((resolve, reject) => {
-            if (signal?.aborted) {
-                reject(signal.reason);
-                return;
-            }
-            const waiter = {
-                resolve,
-                reject,
-                task,
-                endpoint,
-                params,
-                ...(signal && { signal }),
-            };
-            if (signal) {
-                const onAbort = () => {
-                    const idx = this.waiters.indexOf(waiter);
-                    if (idx === -1)
-                        return; // already dispatched — the task forwards its own signal
-                    this.waiters.splice(idx, 1);
-                    reject(signal.reason);
-                };
-                waiter.onAbort = onAbort;
-                signal.addEventListener('abort', onAbort, { once: true });
-            }
-            this.waiters.push(waiter);
-            this.tryDispatch();
-        });
-    }
-    tryDispatch() {
-        if (this.nextDispatchTimer !== undefined)
-            return;
-        while (this.inFlight < this.maxConcurrent && this.waiters.length > 0) {
-            const now = Date.now();
-            const gap = this.minStartGapMs - (now - this.lastStartTime);
-            if (gap > 0) {
-                logger.debug(`Delaying next NCBI dispatch by ${gap}ms to respect rate limit.`, requestContextService.createRequestContext({
-                    operation: 'NcbiQueueWait',
-                    additionalContext: { delayMs: gap },
-                }));
-                this.nextDispatchTimer = setTimeout(() => {
-                    this.nextDispatchTimer = undefined;
-                    this.tryDispatch();
-                }, gap);
-                return;
-            }
-            const waiter = this.waiters.shift();
-            if (!waiter)
-                return;
-            // Detach the cancel listener now that we're about to start; the task is
-            // responsible for forwarding its own signal to downstream I/O.
-            if (waiter.signal && waiter.onAbort) {
-                waiter.signal.removeEventListener('abort', waiter.onAbort);
-            }
-            this.lastStartTime = Date.now();
-            this.inFlight += 1;
-            logger.info(`Executing NCBI request via queue: ${waiter.endpoint}`, requestContextService.createRequestContext({
-                operation: 'NcbiQueueDispatch',
-                additionalContext: {
-                    endpoint: waiter.endpoint,
-                    inFlight: this.inFlight,
-                    queueDepth: this.waiters.length,
-                },
-            }));
-            // `Promise.resolve().then(() => task())` converts any sync throw from
-            // `task()` into a rejected promise so the finally() bookkeeping always
-            // runs.
-            Promise.resolve()
-                .then(() => waiter.task())
-                .then(waiter.resolve, (err) => {
-                logger.error('Error processing NCBI request from queue.', requestContextService.createRequestContext({
-                    operation: 'NcbiQueueProcess',
-                    additionalContext: {
-                        endpoint: waiter.endpoint,
-                        errorMessage: err instanceof Error ? err.message : String(err),
-                    },
-                }));
-                waiter.reject(err);
-            })
-                .finally(() => {
-                this.inFlight -= 1;
-                this.tryDispatch();
-            });
-        }
-    }
+const RATE_LIMIT_COOLDOWN = { baseMs: 1_000, maxMs: 15_000 };
+/**
+ * Creates the pacer every NCBI E-utility call runs through. A caller passes its
+ * remaining deadline as `maxWaitMs`: a call whose projected wait already exceeds it
+ * — behind a deep queue or a closed cooldown gate — is shed at enqueue with a
+ * `pacer_shed` rejection carrying `retryAfter`, rather than waiting out a deadline
+ * it cannot meet.
+ */
+export function createNcbiRequestQueue({ maxConcurrent, maxQueueDepth = DEFAULT_MAX_QUEUE_DEPTH, minStartGapMs, }) {
+    return createPacer({
+        name: 'ncbi',
+        minStartGapMs,
+        maxConcurrent,
+        maxQueueDepth,
+        cooldown: RATE_LIMIT_COOLDOWN,
+    });
 }
 //# sourceMappingURL=request-queue.js.map

package/dist/services/ncbi/request-queue.js.map

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package/dist/services/ncbi/response-handler.d.ts

@@ -2,16 +2,29 @@
  * @fileoverview Handles parsing of NCBI E-utility responses and NCBI-specific error extraction.
  * Creates an NCBI-specific XMLParser instance with `isArray` callback support for handling
  * NCBI's inconsistent XML structures where single-element lists are collapsed to scalars.
+ * Also reads the `<ERROR>` envelope of a failed eutils response: a backend failure is
+ * reclassified as transient, and EFetch's all-invalid-ID rejection becomes the empty set
+ * NCBI returns for an unknown ID.
  * @module src/services/ncbi/response-handler
  */
 import type { NcbiRequestOptions } from './types.js';
+/**
+ * The response NCBI would have sent had it answered an all-invalid EFetch ID list the
+ * way it answers an unknown well-formed one. EFetch rejects a list in which no ID is a
+ * real UID (`id=00000000`) with an HTTP 400 `ID list is empty!` envelope, but answers an
+ * unassigned UID (`id=99999999`) with HTTP 200 and an empty set, so the same question —
+ * "which of these exist?" — would otherwise split into an error and an answer depending
+ * on the ID's spelling. Returns the empty-set document to parse in place of the error,
+ * or `undefined` when the error is anything else. (#155)
+ */
+export declare function emptyEFetchResultFor(error: unknown, endpoint: string, db: unknown): string | undefined;
 /**
  * Reclassifies an HTTP error from a eutils request whose captured body is an NCBI
  * `<ERROR>` envelope reporting a backend failure. The status-derived code reads such a
  * response as caller error (400 → InvalidParams), which the retry gate never retries.
  * Any other error — including a genuine invalid-parameter 400 — is returned unchanged.
  * Matches the body text rather than parsing it, since the framework captures only a
- * bounded prefix. (#153)
+ * bounded prefix. (#153, #155)
  */
 export declare function reclassifyNcbiHttpError(error: unknown, endpoint: string): unknown;
 /**

package/dist/services/ncbi/response-handler.d.ts.map

@@ -1 +1 @@
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package/dist/services/ncbi/response-handler.js

@@ -2,6 +2,9 @@
  * @fileoverview Handles parsing of NCBI E-utility responses and NCBI-specific error extraction.
  * Creates an NCBI-specific XMLParser instance with `isArray` callback support for handling
  * NCBI's inconsistent XML structures where single-element lists are collapsed to scalars.
+ * Also reads the `<ERROR>` envelope of a failed eutils response: a backend failure is
+ * reclassified as transient, and EFetch's all-invalid-ID rejection becomes the empty set
+ * NCBI returns for an unknown ID.
  * @module src/services/ncbi/response-handler
  */
 import { McpError, notFound, serializationError, serviceUnavailable, } from '@cyanheads/mcp-ts-core/errors';
@@ -107,29 +110,82 @@ const ERROR_PATHS = [
  * NCBI `<ERROR>` messages describing a backend failure rather than the request.
  * EFetch sends the viewer-timeout envelope under HTTP 200 and HTTP 400 alike, so
  * the status cannot tell it from a malformed request; the message can. (#153)
+ *
+ * `proxy_stream()` is the EFetch front end's own backend-proxy method: it prefixes
+ * every failure relayed from the service behind it (a 502 page, "Failed to connect
+ * to PubOne service"), so a client-side 400 cannot carry it. (#155)
+ */
+const NCBI_TRANSIENT_ERROR_PATTERNS = [
+    /External viewer error/i,
+    /Status:\s*Timeout/i,
+    /proxy_stream\(\)/,
+];
+/**
+ * Captures the text of each uppercase `<ERROR>` element in a raw response body. The
+ * framework keeps only the first 500 bytes of an error body, so an envelope relaying a
+ * backend page is cut before its `</ERROR>`: an unterminated element runs to the end of
+ * the capture. Content may hold markup, raw or entity-escaped.
+ */
+const ERROR_TEXT_REGEX = /<ERROR(?:\s[^>]*)?>([\s\S]*?)(?:<\/ERROR>|$)/g;
+/** NCBI's whole-list rejection when not one supplied ID is a real UID. (#155) */
+const EMPTY_ID_LIST_PATTERN = /^ID list is empty\b/i;
+/**
+ * What EFetch answers, HTTP 200, when every requested ID is well-formed but unknown —
+ * an empty set in the database's own wrapper. Keyed by `db`; a database missing here
+ * keeps the rejection as an error.
+ */
+const EMPTY_EFETCH_RESULTS = {
+    pubmed: '<?xml version="1.0" ?>\n<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2025//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_250101.dtd">\n<PubmedArticleSet></PubmedArticleSet>\n',
+    pmc: '<?xml version="1.0" ?>\n<!DOCTYPE pmc-articleset PUBLIC "-//NLM//DTD ARTICLE SET 2.0//EN" "https://dtd.nlm.nih.gov/ncbi/pmc/articleset/nlm-articleset-2.0.dtd">\n<pmc-articleset></pmc-articleset>\n',
+};
+/**
+ * The `<ERROR>` messages in the captured body of a non-2xx eutils response, as plain
+ * text: entities decoded, markup dropped (including a tag the capture cut in half),
+ * whitespace collapsed. `undefined` when the error carries no captured body.
+ */
+function ncbiErrorTexts(error) {
+    if (!(error instanceof McpError) || typeof error.data?.body !== 'string')
+        return;
+    return [...error.data.body.matchAll(ERROR_TEXT_REGEX)].map((match) => decodeHtmlEntities(match[1] ?? '')
+        .replace(/<\/?[a-z!][^>]*(?:>|$)/gi, ' ')
+        .replace(/\s+/g, ' ')
+        .trim());
+}
+/**
+ * The response NCBI would have sent had it answered an all-invalid EFetch ID list the
+ * way it answers an unknown well-formed one. EFetch rejects a list in which no ID is a
+ * real UID (`id=00000000`) with an HTTP 400 `ID list is empty!` envelope, but answers an
+ * unassigned UID (`id=99999999`) with HTTP 200 and an empty set, so the same question —
+ * "which of these exist?" — would otherwise split into an error and an answer depending
+ * on the ID's spelling. Returns the empty-set document to parse in place of the error,
+ * or `undefined` when the error is anything else. (#155)
  */
-const NCBI_TRANSIENT_ERROR_PATTERNS = [/External viewer error/i, /Status:\s*Timeout/i];
-/** Captures the text of each uppercase `<ERROR>` element in a raw response body. */
-const ERROR_TEXT_REGEX = /<ERROR(?:\s[^>]*)?>([^<]*)<\/ERROR>/g;
+export function emptyEFetchResultFor(error, endpoint, db) {
+    if (endpoint !== 'efetch' || typeof db !== 'string')
+        return;
+    const empty = EMPTY_EFETCH_RESULTS[db];
+    if (empty === undefined)
+        return;
+    return ncbiErrorTexts(error)?.some((msg) => EMPTY_ID_LIST_PATTERN.test(msg)) ? empty : undefined;
+}
 /**
  * Reclassifies an HTTP error from a eutils request whose captured body is an NCBI
  * `<ERROR>` envelope reporting a backend failure. The status-derived code reads such a
  * response as caller error (400 → InvalidParams), which the retry gate never retries.
  * Any other error — including a genuine invalid-parameter 400 — is returned unchanged.
  * Matches the body text rather than parsing it, since the framework captures only a
- * bounded prefix. (#153)
+ * bounded prefix. (#153, #155)
  */
 export function reclassifyNcbiHttpError(error, endpoint) {
-    if (!(error instanceof McpError) || typeof error.data?.body !== 'string')
-        return error;
-    const ncbiErrors = [...error.data.body.matchAll(ERROR_TEXT_REGEX)].map((match) => decodeHtmlEntities(match[1] ?? '').trim());
-    if (!ncbiErrors.some((msg) => NCBI_TRANSIENT_ERROR_PATTERNS.some((p) => p.test(msg)))) {
+    const ncbiErrors = ncbiErrorTexts(error);
+    if (!(error instanceof McpError) ||
+        !ncbiErrors?.some((msg) => NCBI_TRANSIENT_ERROR_PATTERNS.some((p) => p.test(msg)))) {
         return error;
     }
     return serviceUnavailable(`NCBI API Error: ${ncbiErrors.join('; ')}`, {
         reason: 'ncbi_unreachable',
         endpoint,
-        status: error.data.status,
+        status: error.data?.status,
         ncbiErrors,
         ...recoveryFor('ncbi_unreachable'),
     }, { cause: error });

package/dist/services/ncbi/response-handler.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.10.14",
+  "version": "2.10.16",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
   "type": "module",
@@ -92,8 +92,8 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.13.4",
-    "defuddle": "^0.19.3",
+    "@cyanheads/mcp-ts-core": "^0.13.6",
+    "defuddle": "^0.19.4",
     "fast-xml-parser": "^5.11.1",
     "linkedom": "^0.18.13",
     "pino-pretty": "^13.1.3",
@@ -102,13 +102,13 @@
     "zod": "^4.6.5"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.5.13",
+    "@biomejs/biome": "^2.5.14",
     "@socketsecurity/bun-security-scanner": "^1.1.2",
-    "@types/node": "^26.5.1",
+    "@types/node": "^26.6.2",
     "@types/sanitize-html": "^2.16.1",
     "@vitest/coverage-istanbul": "^5.0.1",
     "depcheck": "^1.4.7",
-    "fast-check": "^4.10.0",
+    "fast-check": "^4.10.2",
     "ignore": "^7.0.9",
     "tsc-alias": "^1.9.5",
     "typescript": "^7.0.2",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.10.14",
+  "version": "2.10.16",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.14",
+      "version": "2.10.16",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.14",
+      "version": "2.10.16",
       "packageArguments": [
         {
           "type": "positional",