@cyanheads/pubmed-mcp-server 2.6.11 → 2.7.0

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

@@ -1,88 +1,130 @@
 /**
- * @fileoverview FIFO request queue for NCBI E-utility calls that enforces a minimum
- * delay between requests to comply with NCBI rate limits.
+ * @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.
  * @module src/services/ncbi/request-queue
  */
 import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
 import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { recoveryFor } from '../../services/error-contracts.js';
+const DEFAULT_MAX_CONCURRENT = 8;
 const DEFAULT_MAX_QUEUE_SIZE = 100;
 /**
- * Processes NCBI API requests through a FIFO queue, inserting a configurable
- * delay between consecutive calls to stay within NCBI's rate-limit window.
+ * 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.
  */
 export class NcbiRequestQueue {
-    queue = [];
-    delayMs;
+    waiters = [];
+    minStartGapMs;
+    maxConcurrent;
     maxQueueSize;
-    processing = false;
-    lastRequestTime = 0;
-    constructor(delayMs, maxQueueSize = DEFAULT_MAX_QUEUE_SIZE) {
-        this.delayMs = delayMs;
+    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) {
-        if (this.queue.length >= this.maxQueueSize) {
+    enqueue(task, endpoint, params, signal) {
+        if (this.waiters.length >= this.maxQueueSize) {
             return Promise.reject(new McpError(JsonRpcErrorCode.RateLimited, `NCBI request queue is full (max ${this.maxQueueSize}).`, {
                 reason: 'queue_full',
                 endpoint,
-                queueSize: this.queue.length,
+                queueSize: this.waiters.length,
                 ...recoveryFor('queue_full'),
             }));
         }
         return new Promise((resolve, reject) => {
-            this.queue.push({
-                resolve: resolve,
+            if (signal?.aborted) {
+                reject(signal.reason);
+                return;
+            }
+            const waiter = {
+                resolve,
                 reject,
                 task,
                 endpoint,
                 params,
-            });
-            if (!this.processing) {
-                queueMicrotask(() => this.processQueue());
+                ...(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();
         });
     }
-    async processQueue() {
-        if (this.processing || this.queue.length === 0)
-            return;
-        this.processing = true;
-        const item = this.queue.shift();
-        if (!item) {
-            this.processing = false;
+    tryDispatch() {
+        if (this.nextDispatchTimer !== undefined)
             return;
-        }
-        const { resolve, reject, task, endpoint } = item;
-        try {
+        while (this.inFlight < this.maxConcurrent && this.waiters.length > 0) {
             const now = Date.now();
-            const elapsed = now - this.lastRequestTime;
-            const wait = this.delayMs - elapsed;
-            if (wait > 0) {
-                logger.debug(`Delaying NCBI request by ${wait}ms to respect rate limit.`, requestContextService.createRequestContext({
+            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',
-                    endpoint,
-                    delayMs: wait,
+                    delayMs: gap,
                 }));
-                await new Promise((r) => setTimeout(r, wait));
+                this.nextDispatchTimer = setTimeout(() => {
+                    this.nextDispatchTimer = undefined;
+                    this.tryDispatch();
+                }, gap);
+                return;
             }
-            this.lastRequestTime = Date.now();
-            logger.info(`Executing NCBI request via queue: ${endpoint}`, requestContextService.createRequestContext({ operation: 'NcbiQueueDispatch', endpoint }));
-            const result = await task();
-            resolve(result);
-        }
-        catch (error) {
-            logger.error('Error processing NCBI request from queue.', requestContextService.createRequestContext({
-                operation: 'NcbiQueueProcess',
-                endpoint,
-                errorMessage: error instanceof Error ? error.message : String(error),
-            }));
-            reject(error);
-        }
-        finally {
-            this.processing = false;
-            if (this.queue.length > 0) {
-                queueMicrotask(() => this.processQueue());
+            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',
+                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',
+                    endpoint: waiter.endpoint,
+                    errorMessage: err instanceof Error ? err.message : String(err),
+                }));
+                waiter.reject(err);
+            })
+                .finally(() => {
+                this.inFlight -= 1;
+                this.tryDispatch();
+            });
         }
     }
 }

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

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

@@ -133,7 +133,7 @@ function sanitizeNcbiError(message) {
  * E-utilities use `<ERROR>` for response-level failures, while PMC EFetch
  * uses lowercase `<error id="…">` to flag a single unavailable PMCID. The
  * latter is data (a missing ID), not a transport error, so it falls through
- * to the caller which reports it via `unavailablePmcIds`.
+ * to the caller which reports it via the unified `unavailable[]` list.
  */
 const ERROR_TAG_REGEX = /<ERROR(?:\s[^>]*)?>/;
 /**

package/dist/services/unpaywall/unpaywall-service.d.ts.map

@@ -1 +1 @@
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package/dist/services/unpaywall/unpaywall-service.js

@@ -7,7 +7,7 @@
  * resolution; only genuine service failures (5xx, network, timeout) throw.
  * @module src/services/unpaywall/unpaywall-service
  */
-import { serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
+import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../config/server-config.js';
 import { recoveryFor } from '../../services/error-contracts.js';
@@ -35,6 +35,11 @@ export class UnpaywallService {
             return { kind: 'no-oa', reason: 'Invalid DOI' };
         const url = `${UNPAYWALL_API_BASE}/${encodeURIComponent(normalized)}?email=${encodeURIComponent(this.email)}`;
         const ctx = requestContextService.createRequestContext({ operation: 'UnpaywallResolve', doi });
+        // `fetchWithTimeout` throws on any non-2xx response, so the explicit
+        // `response.status === 404` / `=== 422` checks the API actually returns
+        // arrive as `McpError(NotFound)` / `McpError(ValidationError)` here, not as
+        // a response object. Translate those into the documented `no-oa` outcomes
+        // before falling back to the service-unavailable wrap.
         let response;
         try {
             response = await fetchWithTimeout(url, this.timeoutMs, ctx, {
@@ -43,6 +48,14 @@ export class UnpaywallService {
             });
         }
         catch (error) {
+            if (error instanceof McpError) {
+                if (error.code === JsonRpcErrorCode.NotFound) {
+                    return { kind: 'no-oa', reason: 'DOI unknown to Unpaywall' };
+                }
+                if (error.code === JsonRpcErrorCode.ValidationError) {
+                    return { kind: 'no-oa', reason: 'Invalid DOI format' };
+                }
+            }
             const msg = error instanceof Error ? error.message : String(error);
             throw serviceUnavailable(`Unpaywall request failed: ${msg}`, {
                 reason: 'unpaywall_unreachable',
@@ -50,18 +63,6 @@ export class UnpaywallService {
                 ...recoveryFor('unpaywall_unreachable'),
             }, { cause: error });
         }
-        if (response.status === 404)
-            return { kind: 'no-oa', reason: 'DOI unknown to Unpaywall' };
-        if (response.status === 422)
-            return { kind: 'no-oa', reason: 'Invalid DOI format' };
-        if (!response.ok) {
-            const body = await response.text().catch(() => '');
-            throw await httpErrorFromResponse(response, {
-                service: 'Unpaywall',
-                captureBody: false,
-                data: { doi: normalized, body: body.substring(0, 300) },
-            });
-        }
         const data = (await response.json());
         if (!data.is_oa)
             return { kind: 'no-oa', reason: 'No open-access copy indexed' };

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

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package/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.6.11",
+  "version": "2.7.0",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
-  "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata and open-access full text (PMC + Unpaywall), generate citations, explore MeSH terms, and discover related research.",
+  "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -40,7 +40,8 @@
     "e-utilities",
     "open-access",
     "full-text",
-    "unpaywall"
+    "unpaywall",
+    "europe-pmc"
   ],
   "repository": {
     "type": "git",
@@ -71,17 +72,17 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.9.0",
+    "@cyanheads/mcp-ts-core": "^0.9.1",
     "defuddle": "^0.18.1",
     "fast-xml-parser": "~5.7.3",
     "linkedom": "^0.18.12",
     "pino-pretty": "^13.1.3",
-    "sanitize-html": "^2.17.3",
+    "sanitize-html": "^2.17.4",
     "unpdf": "^1.6.2"
   },
   "devDependencies": {
     "@biomejs/biome": "^2.4.15",
-    "@types/node": "^25.7.0",
+    "@types/node": "^25.9.0",
     "@types/sanitize-html": "^2.16.1",
     "@vitest/coverage-istanbul": "^4.1.6",
     "depcheck": "^1.4.7",

package/server.json

@@ -1,12 +1,12 @@
 {
   "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
   "name": "io.github.cyanheads/pubmed-mcp-server",
-  "description": "Search PubMed, fetch articles and full text, generate citations, and explore MeSH terms via NCBI.",
+  "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms.",
   "repository": {
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.6.11",
+  "version": "2.7.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.6.11",
+      "version": "2.7.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.6.11",
+      "version": "2.7.0",
       "packageArguments": [
         {
           "type": "positional",