@cyanheads/pubmed-mcp-server 2.10.14 → 2.10.16

package/dist/services/europe-pmc/europe-pmc-service.js.map

@@ -1 +1 @@
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package/dist/services/ncbi/ncbi-service.d.ts

@@ -1,11 +1,13 @@
 /**
  * @fileoverview High-level service for interacting with NCBI E-utilities.
  * Orchestrates the API client, request queue, and response handler to provide
- * typed methods for each E-utility endpoint. Uses init/accessor pattern.
+ * typed methods for each E-utility endpoint. Every call runs as a retry loop around
+ * the shared request queue — each attempt re-queued and re-paced — under one total
+ * deadline that covers queue wait, attempts, and backoff. Uses init/accessor pattern.
  * @module src/services/ncbi/ncbi-service
  */
+import { type Pacer } from '@cyanheads/mcp-ts-core/utils';
 import { NcbiApiClient } from './api-client.js';
-import { NcbiRequestQueue } from './request-queue.js';
 import { NcbiResponseHandler } from './response-handler.js';
 import { type ECitMatchCitation, type ECitMatchResult, type ESearchResult, type ESpellResult, type ESummaryResult, type IdConvertRecord, type NcbiCallOptions, type NcbiRequestOptions, type NcbiRequestParams, type XmlPubmedArticleSet } from './types.js';
 /**
@@ -18,7 +20,7 @@ export declare class NcbiService {
     private readonly responseHandler;
     private readonly maxRetries;
     private readonly totalDeadlineMs;
-    constructor(apiClient: NcbiApiClient, queue: NcbiRequestQueue, responseHandler: NcbiResponseHandler, maxRetries: number, totalDeadlineMs: number);
+    constructor(apiClient: NcbiApiClient, queue: Pacer, responseHandler: NcbiResponseHandler, maxRetries: number, totalDeadlineMs: number);
     eSearch(params: NcbiRequestParams, options?: NcbiCallOptions): Promise<ESearchResult>;
     eSummary(params: NcbiRequestParams, options?: NcbiCallOptions): Promise<ESummaryResult>;
     eFetch<T = {
@@ -43,30 +45,22 @@ export declare class NcbiService {
      * Accepts up to 200 IDs in a single request. Only works for articles in PMC.
      */
     idConvert(ids: string[], idtype?: string, options?: NcbiCallOptions): Promise<IdConvertRecord[]>;
-    /** Maximum backoff delay per retry (prevents exponential explosion at high retry counts). */
-    private static readonly MAX_BACKOFF_MS;
     /**
-     * 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.
-     */
-    private runWithDeadline;
-    /**
-     * Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout, RateLimited).
-     * Non-transient McpErrors and unexpected plain Errors fail immediately.
-     * Uses capped exponential backoff with jitter. Backoff sleep is abortable via
-     * `signal`, so deadline expiration or caller cancel short-circuits the chain.
+     * Runs one NCBI call: a retry loop around the shared request queue, so every
+     * attempt re-queues and is re-paced (and a 429 closes the gate for all callers,
+     * not just this one). One deadline covers queue wait, attempts, and backoff. Its
+     * signal — joined with the caller's — reaches the queue wait, the backoff sleep,
+     * and the HTTP request, and each attempt offers the queue only the time left, so
+     * a call that cannot start in time is shed at once instead of waiting it out.
+     *
+     * A caller abort rethrows the caller's own reason; every other failure is mapped
+     * onto this service's reasons by {@link toServiceError}, after the loop.
      */
-    private withRetry;
+    private runPaced;
     /**
-     * Runs a request under a service-level deadline that bounds queue wait time
-     * + retry chain + HTTP execution. The deadline is constructed *outside* the
-     * queue so a backlog can't burn a request's budget before it even dispatches.
-     *
-     * The combined deadline+caller signal is threaded into the queue (cancels a
-     * still-waiting task), the retry chain (cancels pending backoff sleeps),
-     * and the HTTP fetch (cancels wedged requests).
+     * One eutils request through {@link runPaced}: fetch, classify, parse. EFetch's
+     * all-invalid-ID rejection resolves as the empty set NCBI returns for an unknown
+     * ID, and a backend-failure envelope is reclassified as transient so it retries.
      */
     private performRequest;
 }

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

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

@@ -1,16 +1,18 @@
 /**
  * @fileoverview High-level service for interacting with NCBI E-utilities.
  * Orchestrates the API client, request queue, and response handler to provide
- * typed methods for each E-utility endpoint. Uses init/accessor pattern.
+ * typed methods for each E-utility endpoint. Every call runs as a retry loop around
+ * the shared request queue — each attempt re-queued and re-paced — under one total
+ * deadline that covers queue wait, attempts, and backoff. Uses init/accessor pattern.
  * @module src/services/ncbi/ncbi-service
  */
-import { internalError, JsonRpcErrorCode, McpError, serializationError, timeout, validationError, } from '@cyanheads/mcp-ts-core/errors';
-import { defaultIsTransient, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { JsonRpcErrorCode, McpError, rateLimited, serializationError, timeout, validationError, } from '@cyanheads/mcp-ts-core/errors';
+import { defaultIsTransient, logger, requestContextService, withRetry, } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../config/server-config.js';
 import { recoveryFor } from '../error-contracts.js';
 import { NcbiApiClient } from './api-client.js';
-import { NcbiRequestQueue } from './request-queue.js';
-import { NcbiResponseHandler, reclassifyNcbiHttpError } from './response-handler.js';
+import { createNcbiRequestQueue } from './request-queue.js';
+import { emptyEFetchResultFor, NcbiResponseHandler, reclassifyNcbiHttpError, } from './response-handler.js';
 import { NCBI_PMC_IDCONV_URL, } from './types.js';
 /**
  * Per-idType expected-format hints surfaced when PMC ID Converter rejects a
@@ -53,33 +55,60 @@ function normalizeDiagnosticList(list) {
 function wireKeysFor(citations) {
     return citations.map((_, i) => String(i + 1));
 }
-/** 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';
-    }
-}
+/** Ceiling on one backoff sleep, so a high retry count cannot grow it without bound. */
+const MAX_BACKOFF_MS = 30_000;
 /**
- * Sleep that resolves after `ms`, or rejects immediately if `signal` aborts.
- * Cleans up both timer and listener when either side wins.
+ * Margin added to the time left on the deadline when it is offered to the queue as a
+ * wait budget. The queue sheds an arrival whose projected wait exceeds the budget, and
+ * separately times out a caller still waiting when the budget runs out; that second
+ * timer would otherwise land on the same instant as the deadline itself. Setting it just
+ * past the deadline leaves expiry to the deadline, so a call still queued when its time
+ * is up always reports `ncbi_deadline_exceeded`, never `queue_full`.
  */
-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 });
-    });
+const QUEUE_WAIT_MARGIN_MS = 1;
+/**
+ * Retry gate: the framework's transient set, narrowed to `McpError`s. The client and
+ * response handler classify every upstream failure, so a plain `Error` reaching the
+ * loop is a defect or a response that cannot parse — retrying it only repeats it.
+ */
+const isTransient = (error) => error instanceof McpError && defaultIsTransient(error);
+/**
+ * Maps what the retry loop throws onto this service's declared failure reasons. Runs
+ * outside the loop, so the loop itself still sees the framework's `pacer_shed` — which
+ * it never retries — and `retry_deadline_exceeded`.
+ *
+ * - `pacer_shed` → `queue_full` (RateLimited), keeping the shed's `retryAfter`.
+ * - `retry_deadline_exceeded` → `ncbi_deadline_exceeded` (Timeout).
+ * - Retries exhausted → the last attempt's code and message with `endpoint` and
+ *   `attempts`; a ServiceUnavailable is stamped `ncbi_unreachable`.
+ * - Anything else — a failure that was never retried — passes through unchanged.
+ */
+function toServiceError(error, endpoint, deadlineMs) {
+    if (!(error instanceof McpError))
+        return error;
+    const data = error.data ?? {};
+    if (data.reason === 'pacer_shed') {
+        return rateLimited(`NCBI request queue is full or cannot start this call before its deadline (${String(data.queueDepth)} requests waiting).`, {
+            reason: 'queue_full',
+            endpoint,
+            queueSize: data.queueDepth,
+            retryAfter: data.retryAfter,
+            ...recoveryFor('queue_full'),
+        }, { cause: error });
+    }
+    if (data.reason === 'retry_deadline_exceeded') {
+        return timeout(`NCBI request deadline (${deadlineMs}ms) exceeded`, { reason: 'ncbi_deadline_exceeded', deadlineMs, ...recoveryFor('ncbi_deadline_exceeded') }, { cause: error });
+    }
+    if (typeof data.retryAttempts !== 'number')
+        return error;
+    // Other retryable codes (Timeout, RateLimited) keep their code with no reason.
+    const reason = error.code === JsonRpcErrorCode.ServiceUnavailable ? 'ncbi_unreachable' : undefined;
+    return new McpError(error.code, error.message, {
+        ...(reason && { reason, ...recoveryFor(reason) }),
+        endpoint,
+        attempts: data.retryAttempts,
+        ...(data.ncbiErrors !== undefined && { ncbiErrors: data.ncbiErrors }),
+    }, { cause: error.cause ?? error });
 }
 /**
  * Facade over NCBI's E-utility suite. Each public method corresponds to a
@@ -265,7 +294,7 @@ export class NcbiService {
         };
         let text;
         try {
-            text = await this.runWithDeadline((signal) => this.queue.enqueue(() => this.withRetry(() => this.apiClient.makeExternalRequest(NCBI_PMC_IDCONV_URL, params, signal), 'idconv', signal), 'idconv', params, signal), options?.signal);
+            text = await this.runPaced('idconv', options?.signal, (signal) => this.apiClient.makeExternalRequest(NCBI_PMC_IDCONV_URL, params, signal));
         }
         catch (error) {
             // PMC ID Converter returns 400 (InvalidParams) for malformed inputs and
@@ -293,110 +322,69 @@ export class NcbiService {
         }
         return parsed.records ?? [];
     }
-    /** 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.
+     * Runs one NCBI call: a retry loop around the shared request queue, so every
+     * attempt re-queues and is re-paced (and a 429 closes the gate for all callers,
+     * not just this one). One deadline covers queue wait, attempts, and backoff. Its
+     * signal — joined with the caller's — reaches the queue wait, the backoff sleep,
+     * and the HTTP request, and each attempt offers the queue only the time left, so
+     * a call that cannot start in time is shed at once instead of waiting it out.
+     *
+     * A caller abort rethrows the caller's own reason; every other failure is mapped
+     * onto this service's reasons by {@link toServiceError}, after the loop.
      */
-    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;
+    async runPaced(endpoint, callerSignal, execute) {
+        let attempt = 0;
         try {
-            return await task(signal);
+            return await withRetry(({ signal, remainingMs }) => {
+                attempt += 1;
+                return this.queue
+                    .run(execute, { signal, maxWaitMs: remainingMs + QUEUE_WAIT_MARGIN_MS })
+                    .catch((error) => {
+                    if (attempt <= this.maxRetries && isTransient(error)) {
+                        logger.warning(`NCBI request to ${endpoint} failed on attempt ${attempt} of ${this.maxRetries + 1}.`, requestContextService.createRequestContext({
+                            operation: 'NcbiRetry',
+                            additionalContext: {
+                                endpoint,
+                                attempt,
+                                error: error instanceof Error ? error.message : String(error),
+                            },
+                        }));
+                    }
+                    throw error;
+                });
+            }, {
+                maxRetries: this.maxRetries,
+                maxDelayMs: MAX_BACKOFF_MS,
+                deadlineMs: this.totalDeadlineMs,
+                isTransient,
+                operation: `NCBI ${endpoint}`,
+                ...(callerSignal && { signal: callerSignal }),
+            });
         }
         catch (error) {
-            if (error instanceof NcbiDeadlineExceeded) {
-                throw timeout(error.message, {
-                    reason: 'ncbi_deadline_exceeded',
-                    deadlineMs: this.totalDeadlineMs,
-                    ...recoveryFor('ncbi_deadline_exceeded'),
-                }, { cause: error });
-            }
-            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. Backoff sleep is abortable via
-     * `signal`, so deadline expiration or caller cancel short-circuits the chain.
-     */
-    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;
-                }
-                if (!defaultIsTransient(error)) {
-                    throw error;
-                }
-                if (attempt < this.maxRetries) {
-                    const baseDelay = Math.min(1000 * 2 ** attempt, NcbiService.MAX_BACKOFF_MS);
-                    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 ${retryDelay}ms.`, requestContextService.createRequestContext({
-                        operation: 'NcbiRetry',
-                        additionalContext: { endpoint: label, attempt: attempt + 1, retryDelay },
-                    }));
-                    await abortableSleep(retryDelay, signal);
-                    continue;
-                }
-                const attempts = this.maxRetries + 1;
-                const msg = error instanceof Error ? error.message : String(error);
-                // Tag transient ServiceUnavailable retries-exhausted with `ncbi_unreachable` so
-                // tool callers can switch on a stable reason. Other retryable codes (Timeout,
-                // RateLimited) keep their original code with no reason — `ncbi_deadline_exceeded`
-                // and `queue_full` are stamped at their own throw sites.
-                const reason = error.code === JsonRpcErrorCode.ServiceUnavailable ? 'ncbi_unreachable' : undefined;
-                const ncbiErrors = error.data?.ncbiErrors;
-                throw new McpError(error.code, `${msg} (failed after ${attempts} attempts)`, {
-                    ...(reason && { reason, ...recoveryFor(reason) }),
-                    endpoint: label,
-                    attempts,
-                    ...(ncbiErrors !== undefined && { ncbiErrors }),
-                }, { cause: error });
-            }
+            if (callerSignal?.aborted)
+                throw callerSignal.reason;
+            throw toServiceError(error, endpoint, this.totalDeadlineMs);
         }
-        throw internalError('Request failed after all retries.', {
-            reason: 'ncbi_unreachable',
-            endpoint: label,
-            ...recoveryFor('ncbi_unreachable'),
-        });
     }
     /**
-     * Runs a request under a service-level deadline that bounds queue wait time
-     * + retry chain + HTTP execution. The deadline is constructed *outside* the
-     * queue so a backlog can't burn a request's budget before it even dispatches.
-     *
-     * The combined deadline+caller signal is threaded into the queue (cancels a
-     * still-waiting task), the retry chain (cancels pending backoff sleeps),
-     * and the HTTP fetch (cancels wedged requests).
+     * One eutils request through {@link runPaced}: fetch, classify, parse. EFetch's
+     * all-invalid-ID rejection resolves as the empty set NCBI returns for an unknown
+     * ID, and a backend-failure envelope is reclassified as transient so it retries.
      */
     performRequest(endpoint, params, options) {
-        return this.runWithDeadline((signal) => this.queue.enqueue(() => this.withRetry(async () => {
+        return this.runPaced(endpoint, options?.signal, async (signal) => {
             const text = await this.apiClient
                 .makeRequest(endpoint, params, { ...options, signal })
                 .catch((error) => {
+                const empty = emptyEFetchResultFor(error, endpoint, params.db);
+                if (empty !== undefined)
+                    return empty;
                 throw reclassifyNcbiHttpError(error, endpoint);
             });
             return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
-        }, endpoint, signal), endpoint, params, signal), options?.signal);
+        });
     }
 }
 // ─── Init / Accessor ────────────────────────────────────────────────────────
@@ -410,7 +398,10 @@ export function initNcbiService() {
         ...(config.apiKey && { apiKey: config.apiKey }),
         ...(config.adminEmail && { adminEmail: config.adminEmail }),
     });
-    const queue = new NcbiRequestQueue(config.requestDelayMs, config.maxConcurrent);
+    const queue = createNcbiRequestQueue({
+        minStartGapMs: config.requestDelayMs,
+        maxConcurrent: config.maxConcurrent,
+    });
     const responseHandler = new NcbiResponseHandler();
     _service = new NcbiService(apiClient, queue, responseHandler, config.maxRetries, config.totalDeadlineMs);
     logger.info('NCBI service initialized.', requestContextService.createRequestContext({

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

@@ -1 +1 @@
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package/dist/services/ncbi/request-queue.d.ts

@@ -1,36 +1,28 @@
 /**
- * @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 type { NcbiRequestParams } from './types.js';
+import { type Pacer } from '@cyanheads/mcp-ts-core/utils';
+/** Settings for {@link createNcbiRequestQueue}. */
+export interface NcbiRequestQueueOptions {
+    /** Maximum requests in flight at once. */
+    maxConcurrent: number;
+    /** Waiting callers past which a new arrival is shed. Defaults to 100. */
+    maxQueueDepth?: number;
+    /** Minimum gap between two request starts — NCBI's per-second ceiling. */
+    minStartGapMs: number;
+}
 /**
- * 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.
+ * 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 declare class NcbiRequestQueue {
-    private readonly waiters;
-    private readonly minStartGapMs;
-    private readonly maxConcurrent;
-    private readonly maxQueueSize;
-    private inFlight;
-    private lastStartTime;
-    private nextDispatchTimer;
-    constructor(minStartGapMs: number, maxConcurrent?: number, maxQueueSize?: number);
-    enqueue<T>(task: () => Promise<T>, endpoint: string, params: NcbiRequestParams, signal?: AbortSignal): Promise<T>;
-    private tryDispatch;
-}
+export declare function createNcbiRequestQueue({ maxConcurrent, maxQueueDepth, minStartGapMs, }: NcbiRequestQueueOptions): Pacer;
 //# sourceMappingURL=request-queue.d.ts.map

package/dist/services/ncbi/request-queue.d.ts.map

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