@cyanheads/pubmed-mcp-server 2.6.11 → 2.7.0

package/dist/services/europe-pmc/request-queue.d.ts

@@ -0,0 +1,33 @@
+/**
+ * @fileoverview Rate-limited request scheduler for Europe PMC calls. Caps
+ * concurrent in-flight requests and enforces a minimum start-gap between
+ * dispatches to stay polite with EBI's infrastructure. Independent rate
+ * domain from NCBI's queue — Europe PMC runs on a different host with its
+ * own limits.
+ * @module src/services/europe-pmc/request-queue
+ */
+/**
+ * Schedules Europe PMC requests against two independent ceilings:
+ *
+ *   - **Throughput** (`minStartGapMs`): minimum delay between two consecutive
+ *     dispatch times. Defaults to 200ms to be polite with EBI.
+ *   - **Concurrency** (`maxConcurrent`): maximum simultaneous in-flight
+ *     requests. 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.
+ */
+export declare class EuropePmcRequestQueue {
+    private readonly waiters;
+    private readonly minStartGapMs;
+    private readonly maxConcurrent;
+    private inFlight;
+    private lastStartTime;
+    private nextDispatchTimer;
+    constructor(minStartGapMs: number, maxConcurrent?: number);
+    enqueue<T>(task: () => Promise<T>, label: string, signal?: AbortSignal): Promise<T>;
+    private tryDispatch;
+}
+//# sourceMappingURL=request-queue.d.ts.map

package/dist/services/europe-pmc/request-queue.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/europe-pmc/request-queue.js

@@ -0,0 +1,107 @@
+/**
+ * @fileoverview Rate-limited request scheduler for Europe PMC calls. Caps
+ * concurrent in-flight requests and enforces a minimum start-gap between
+ * dispatches to stay polite with EBI's infrastructure. Independent rate
+ * domain from NCBI's queue — Europe PMC runs on a different host with its
+ * own limits.
+ * @module src/services/europe-pmc/request-queue
+ */
+import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+const DEFAULT_MAX_CONCURRENT = 4;
+/**
+ * Schedules Europe PMC requests against two independent ceilings:
+ *
+ *   - **Throughput** (`minStartGapMs`): minimum delay between two consecutive
+ *     dispatch times. Defaults to 200ms to be polite with EBI.
+ *   - **Concurrency** (`maxConcurrent`): maximum simultaneous in-flight
+ *     requests. 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.
+ */
+export class EuropePmcRequestQueue {
+    waiters = [];
+    minStartGapMs;
+    maxConcurrent;
+    inFlight = 0;
+    lastStartTime = 0;
+    nextDispatchTimer;
+    constructor(minStartGapMs, maxConcurrent = DEFAULT_MAX_CONCURRENT) {
+        this.minStartGapMs = minStartGapMs;
+        this.maxConcurrent = maxConcurrent;
+    }
+    enqueue(task, label, signal) {
+        return new Promise((resolve, reject) => {
+            if (signal?.aborted) {
+                reject(signal.reason);
+                return;
+            }
+            const waiter = {
+                resolve,
+                reject,
+                task,
+                label,
+                ...(signal && { signal }),
+            };
+            if (signal) {
+                const onAbort = () => {
+                    const idx = this.waiters.indexOf(waiter);
+                    if (idx === -1)
+                        return;
+                    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) {
+                this.nextDispatchTimer = setTimeout(() => {
+                    this.nextDispatchTimer = undefined;
+                    this.tryDispatch();
+                }, gap);
+                return;
+            }
+            const waiter = this.waiters.shift();
+            if (!waiter)
+                return;
+            if (waiter.signal && waiter.onAbort) {
+                waiter.signal.removeEventListener('abort', waiter.onAbort);
+            }
+            this.lastStartTime = Date.now();
+            this.inFlight += 1;
+            logger.debug(`Executing Europe PMC request via queue: ${waiter.label}`, requestContextService.createRequestContext({
+                operation: 'EuropePmcQueueDispatch',
+                label: waiter.label,
+                inFlight: this.inFlight,
+                queueDepth: this.waiters.length,
+            }));
+            Promise.resolve()
+                .then(() => waiter.task())
+                .then(waiter.resolve, (err) => {
+                logger.error('Error processing Europe PMC request from queue.', requestContextService.createRequestContext({
+                    operation: 'EuropePmcQueueProcess',
+                    label: waiter.label,
+                    errorMessage: err instanceof Error ? err.message : String(err),
+                }));
+                waiter.reject(err);
+            })
+                .finally(() => {
+                this.inFlight -= 1;
+                this.tryDispatch();
+            });
+        }
+    }
+}
+//# sourceMappingURL=request-queue.js.map

package/dist/services/europe-pmc/request-queue.js.map

@@ -0,0 +1 @@
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package/dist/services/europe-pmc/types.d.ts

@@ -0,0 +1,123 @@
+/**
+ * @fileoverview Types for the Europe PMC REST API. Covers the search response
+ * shape and the fullTextXML endpoint contract.
+ *
+ * See https://europepmc.org/RestfulWebService for the full API. We use only
+ * the search endpoint (`/webservices/rest/search`) and the fullText endpoint
+ * (`/webservices/rest/{id}/fullTextXML`).
+ *
+ * @module src/services/europe-pmc/types
+ */
+/** Base URL for Europe PMC's RESTful web service. */
+export declare const EUROPEPMC_API_BASE = "https://www.ebi.ac.uk/europepmc/webservices/rest";
+/**
+ * Europe PMC source taxonomy. Determines which corpus a record belongs to and
+ * what identifier scheme applies. PubMed-derived records carry a `pmid`; PMC
+ * preprints carry an EPMC id (`source: PPR`) but no PMID; patents and Agricola
+ * records may carry neither.
+ */
+export type EuropePmcSource = 'MED' | 'PMC' | 'PPR' | 'PAT' | 'AGR' | 'CTX' | 'CBA' | 'ETH' | 'HIR';
+/** Allowed sources for `pubmed_europepmc_search` input. */
+export declare const EUROPEPMC_DEFAULT_SOURCES: readonly ["MED", "PMC", "PPR"];
+export declare const EUROPEPMC_ALL_SOURCES: readonly ["MED", "PMC", "PPR", "PAT", "AGR"];
+/**
+ * Single record from a Europe PMC search response. Only fields the server
+ * actually consumes are typed; the upstream payload carries many more under
+ * `resultType=core`. Field optionality reflects EPMC's real-world sparsity —
+ * preprints often lack `journalTitle`; patents lack `authorString`.
+ */
+export interface EuropePmcSearchHit {
+    abstractText?: string;
+    authorString?: string;
+    bookOrReportDetails?: unknown;
+    citedByCount?: number;
+    doi?: string;
+    /** ISO date (YYYY-MM-DD) of first index in EPMC. */
+    firstIndexDate?: string;
+    /** ISO date (YYYY-MM-DD) of publication where known. */
+    firstPublicationDate?: string;
+    hasBook?: 'Y' | 'N';
+    hasPDF?: 'Y' | 'N';
+    /** "Y"/"N" — whether EPMC believes a full-text XML is available for this record. */
+    hasTextMinedTerms?: 'Y' | 'N';
+    /** EPMC's own record identifier — unique within `source`. Always present. */
+    id: string;
+    inEPMC?: 'Y' | 'N';
+    inPMC?: 'Y' | 'N';
+    isOpenAccess?: 'Y' | 'N';
+    issue?: string;
+    journalTitle?: string;
+    journalVolume?: string;
+    /** Some hits carry their own license. Free-form per EPMC. */
+    license?: string;
+    pageInfo?: string;
+    pmcid?: string;
+    pmid?: string;
+    pubYear?: string;
+    source: EuropePmcSource;
+    title?: string;
+    [extra: string]: unknown;
+}
+/** Wrapper for the `resultList` block in a search response. */
+export interface EuropePmcResultList {
+    result?: EuropePmcSearchHit[] | EuropePmcSearchHit;
+}
+/**
+ * Top-level shape of a Europe PMC JSON search response. EPMC returns scalar
+ * `result` when there's exactly one hit; `request.queryString` echoes the
+ * effective query so callers can preview what EPMC actually searched.
+ */
+export interface EuropePmcSearchResponse {
+    /** Total matching records across all pages. */
+    hitCount?: number;
+    /** Cursor token for the next page; absent on the final page. */
+    nextCursorMark?: string;
+    /** Cursor used for this response, echoed back from the request. */
+    request?: {
+        queryString?: string;
+        resultType?: string;
+        cursorMark?: string;
+        pageSize?: number;
+        sort?: string;
+        [extra: string]: unknown;
+    };
+    resultList?: EuropePmcResultList;
+    version?: string;
+    [extra: string]: unknown;
+}
+/** Normalized search result returned by the service layer. */
+export interface EuropePmcSearchResult {
+    /** Cursor used for this response. Returned as-is so callers can echo it. */
+    cursorMark?: string;
+    hitCount: number;
+    hits: EuropePmcSearchHit[];
+    /** Cursor for the next page. `undefined` when no more pages remain. */
+    nextCursorMark?: string;
+    query: string;
+}
+/** Parameters accepted by the EPMC search endpoint. */
+export interface EuropePmcSearchParams {
+    /** EPMC's cursor pagination token; start with `*` for the first page. */
+    cursorMark?: string;
+    /** Max 100 (per EPMC docs). */
+    pageSize?: number;
+    query: string;
+    /** Default `core` — richest payload with abstract, IDs, dates, license. */
+    resultType?: 'core' | 'lite' | 'idlist';
+    signal?: AbortSignal;
+    /** Optional sort spec, e.g. `FIRST_PIDATE desc`. */
+    sort?: string;
+    /** Allowed sources, comma-joined into the query as `(SRC:"MED" OR ...)`. */
+    sources?: readonly EuropePmcSource[];
+}
+/** Outcome of a fullTextXML lookup. */
+export type EuropePmcFullTextResult = {
+    kind: 'found';
+    xml: string;
+    epmcId: string;
+    source: EuropePmcSource;
+} | {
+    kind: 'not-available';
+    reason: string;
+};
+//# sourceMappingURL=types.d.ts.map

package/dist/services/europe-pmc/types.d.ts.map

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package/dist/services/europe-pmc/types.js

@@ -0,0 +1,16 @@
+/**
+ * @fileoverview Types for the Europe PMC REST API. Covers the search response
+ * shape and the fullTextXML endpoint contract.
+ *
+ * See https://europepmc.org/RestfulWebService for the full API. We use only
+ * the search endpoint (`/webservices/rest/search`) and the fullText endpoint
+ * (`/webservices/rest/{id}/fullTextXML`).
+ *
+ * @module src/services/europe-pmc/types
+ */
+/** Base URL for Europe PMC's RESTful web service. */
+export const EUROPEPMC_API_BASE = 'https://www.ebi.ac.uk/europepmc/webservices/rest';
+/** Allowed sources for `pubmed_europepmc_search` input. */
+export const EUROPEPMC_DEFAULT_SOURCES = ['MED', 'PMC', 'PPR'];
+export const EUROPEPMC_ALL_SOURCES = ['MED', 'PMC', 'PPR', 'PAT', 'AGR'];
+//# sourceMappingURL=types.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/services/europe-pmc/types.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,qDAAqD;AACrD,MAAM,CAAC,MAAM,kBAAkB,GAAG,kDAAkD,CAAC;AAUrF,2DAA2D;AAC3D,MAAM,CAAC,MAAM,yBAAyB,GAAG,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,CAAU,CAAC;AACxE,MAAM,CAAC,MAAM,qBAAqB,GAAG,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,CAAU,CAAC"}

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

@@ -56,14 +56,13 @@ export declare class NcbiService {
      */
     private withRetry;
     /**
-     * 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).
+     * 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 both the HTTP fetch
-     * (cancels wedged requests) and the backoff sleep (cancels pending retries),
-     * bounding the total time to `totalDeadlineMs` regardless of retry count.
+     * 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).
      */
     private performRequest;
 }

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

@@ -1 +1 @@
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+{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAEpB,KAAK,aAAa,EAElB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AA0CpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;gBAJf,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM;IAGpC,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC;IAoBrF,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC;IAS7F,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC;IAMb,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC;IAOP,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC;IA2BzF,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC;IAO7E;;;OAGG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;IAsD7B;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;IAwD7B,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;;OAKG;YACW,eAAe;IAkC7B;;;;;OAKG;YACW,SAAS;IAkEvB;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;CA2BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA4BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}

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

@@ -187,7 +187,7 @@ export class NcbiService {
         };
         let text;
         try {
-            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);
+            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);
         }
         catch (error) {
             // PMC ID Converter returns 400 (InvalidParams) for malformed inputs and
@@ -308,23 +308,22 @@ export class NcbiService {
         });
     }
     /**
-     * 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).
+     * 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 both the HTTP fetch
-     * (cancels wedged requests) and the backoff sleep (cancels pending retries),
-     * bounding the total time to `totalDeadlineMs` regardless of retry count.
+     * 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).
      */
     performRequest(endpoint, params, options) {
-        return this.queue.enqueue(() => this.runWithDeadline((signal) => this.withRetry(async () => {
+        return this.runWithDeadline((signal) => this.queue.enqueue(() => this.withRetry(async () => {
             const text = await this.apiClient.makeRequest(endpoint, params, {
                 ...options,
                 signal,
             });
             return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
-        }, endpoint, signal), options?.signal), endpoint, params);
+        }, endpoint, signal), endpoint, params, signal), options?.signal);
     }
 }
 // ─── Init / Accessor ────────────────────────────────────────────────────────
@@ -338,7 +337,7 @@ export function initNcbiService() {
         ...(config.apiKey && { apiKey: config.apiKey }),
         ...(config.adminEmail && { adminEmail: config.adminEmail }),
     });
-    const queue = new NcbiRequestQueue(config.requestDelayMs);
+    const queue = new NcbiRequestQueue(config.requestDelayMs, config.maxConcurrent);
     const responseHandler = new NcbiResponseHandler();
     _service = new NcbiService(apiClient, queue, responseHandler, config.maxRetries, config.totalDeadlineMs);
     logger.info('NCBI service initialized.', requestContextService.createRequestContext({
@@ -346,6 +345,7 @@ export function initNcbiService() {
         toolIdentifier: config.toolIdentifier,
         hasApiKey: !!config.apiKey,
         requestDelayMs: config.requestDelayMs,
+        maxConcurrent: config.maxConcurrent,
         totalDeadlineMs: config.totalDeadlineMs,
     }));
 }

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

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

@@ -1,21 +1,36 @@
 /**
- * @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 type { NcbiRequestParams } from './types.js';
 /**
- * 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 declare class NcbiRequestQueue {
-    private readonly queue;
-    private readonly delayMs;
+    private readonly waiters;
+    private readonly minStartGapMs;
+    private readonly maxConcurrent;
     private readonly maxQueueSize;
-    private processing;
-    private lastRequestTime;
-    constructor(delayMs: number, maxQueueSize?: number);
-    enqueue<T>(task: () => Promise<T>, endpoint: string, params: NcbiRequestParams): Promise<T>;
-    private processQueue;
+    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;
 }
 //# sourceMappingURL=request-queue.d.ts.map

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

@@ -1 +1 @@
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