@cyanheads/pubmed-mcp-server 2.10.18 → 2.10.20

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

@@ -6,10 +6,9 @@
  * deadline that covers queue wait, attempts, and backoff. Uses init/accessor pattern.
  * @module src/services/ncbi/ncbi-service
  */
-import { JsonRpcErrorCode, McpError, rateLimited, serializationError, timeout, validationError, } from '@cyanheads/mcp-ts-core/errors';
+import { invalidParams, 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 { createNcbiRequestQueue } from './request-queue.js';
 import { emptyEFetchResultFor, NcbiResponseHandler, reclassifyNcbiHttpError, } from './response-handler.js';
@@ -41,19 +40,63 @@ function normalizeDiagnosticList(list) {
     return normalized;
 }
 /**
- * The tracking token each citation is submitted to ECitMatch under — echoed
- * back verbatim on that citation's response row, and unique within the request.
+ * The tracking token a citation is submitted to ECitMatch under — echoed back
+ * verbatim on that citation's response row, and unique within the call.
  *
- * Always the citation's 1-based position, never `ECitMatchCitation.key`. That
- * label is caller-supplied, so reconciling response rows on it collapses two
- * citations carrying the same label onto one row and hands the second
- * citation's PMID to the first (#113); and a `|` inside it shifts the
- * pipe-delimited field layout of the submitted line, so NCBI's echoed row no
- * longer reconciles and a citation it matched comes back as not_found (#125).
- * Keeping the label off the wire entirely removes both.
+ * Always the citation's 1-based position in the call, never
+ * `ECitMatchCitation.key`, and the same in every request that carries it, so a
+ * re-requested line reconciles without renumbering (#193). The label is
+ * caller-supplied, so reconciling response rows on it collapses two citations
+ * carrying the same label onto one row and hands the second citation's PMID to
+ * the first (#113); and a `|` inside it shifts the pipe-delimited field layout
+ * of the submitted line, so NCBI's echoed row no longer reconciles and a
+ * citation it matched comes back as not_found (#125). Keeping the label off the
+ * wire entirely removes both.
  */
-function wireKeysFor(citations) {
-    return citations.map((_, i) => String(i + 1));
+function wireKeyFor(index) {
+    return String(index + 1);
+}
+/** One submitted citation as an ECitMatch `bdata` line. */
+function bdataLine(c, index) {
+    return `${c.journal ?? ''}|${c.year ?? ''}|${c.volume ?? ''}|${c.firstPage ?? ''}|${c.authorName ?? ''}|${wireKeyFor(index)}|`;
+}
+/** ECitMatch's response rows, each carrying the wire key its line was submitted under. */
+function parseECitMatchRows(text) {
+    return text
+        .split(/[\r\n]+/)
+        .filter((line) => line.trim().length > 0)
+        .map((line) => {
+        const parts = line.split('|');
+        const key = parts[5]?.trim() ?? '';
+        const rawOutcome = parts[6]?.trim() ?? '';
+        if (/^\d+$/.test(rawOutcome)) {
+            return { key, matched: true, pmid: rawOutcome, status: 'matched' };
+        }
+        if (rawOutcome.startsWith('AMBIGUOUS')) {
+            const csv = /^AMBIGUOUS\s+([\d,\s]+)/.exec(rawOutcome)?.[1];
+            const candidatePmids = csv
+                ? csv
+                    .split(',')
+                    .map((p) => p.trim())
+                    .filter((p) => /^\d+$/.test(p))
+                : undefined;
+            return {
+                key,
+                matched: false,
+                pmid: null,
+                status: 'ambiguous',
+                detail: rawOutcome,
+                ...(candidatePmids?.length && { candidatePmids }),
+            };
+        }
+        return {
+            key,
+            matched: false,
+            pmid: null,
+            status: 'not_found',
+            ...(rawOutcome && { detail: rawOutcome }),
+        };
+    });
 }
 /** Ceiling on one backoff sleep, so a high retry count cannot grow it without bound. */
 const MAX_BACKOFF_MS = 30_000;
@@ -72,18 +115,50 @@ const QUEUE_WAIT_MARGIN_MS = 1;
  * loop is a defect or a response that cannot parse — retrying it only repeats it.
  */
 const isTransient = (error) => error instanceof McpError && defaultIsTransient(error);
+/** The reason each code a retry loop can end on is stamped with; a Timeout gets none. */
+const REASON_BY_CODE = new Map([
+    [JsonRpcErrorCode.ServiceUnavailable, 'ncbi_unreachable'],
+    [JsonRpcErrorCode.RateLimited, 'ncbi_rate_limited'],
+]);
+/**
+ * A retry loop that ran out, reported as its last attempt's failure: that attempt's
+ * code with `endpoint`, `attempts`, and NCBI's `ncbiErrors` when the attempt carried
+ * them. A ServiceUnavailable is stamped `ncbi_unreachable`; a RateLimited is stamped
+ * `ncbi_rate_limited` and keeps the `retryAfter` its 429 named; a Timeout keeps its
+ * code with no reason.
+ */
+function retriesSpent(last, message, attempts, endpoint, cause) {
+    const reason = REASON_BY_CODE.get(last.code);
+    const retryAfter = last.code === JsonRpcErrorCode.RateLimited ? last.data?.retryAfter : undefined;
+    return new McpError(last.code, message, {
+        ...(reason && { reason }),
+        endpoint,
+        attempts,
+        ...(last.data?.ncbiErrors !== undefined && { ncbiErrors: last.data.ncbiErrors }),
+        ...(retryAfter !== undefined && { retryAfter }),
+    }, { cause });
+}
 /**
  * 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`.
+ * - `retry_deadline_exceeded` with the deadline fired — mid-request, in the queue, or
+ *   mid-backoff → `ncbi_deadline_exceeded` (Timeout), with NCBI's `ncbiErrors` from the
+ *   latest attempt that carried any, wherever the timer landed.
+ * - `retry_deadline_exceeded` with the deadline not fired — the loop stopped because
+ *   the next backoff would not fit the time left → retries spent, as below. The error's
+ *   own cause or timing cannot tell the two apart (a request aborted mid-flight fails as
+ *   the client's ServiceUnavailable, and timers can fire early), so `deadlineFired` — the
+ *   loop's own signal — does. (#174)
+ * - Retries exhausted → retries spent: the last attempt's code and message (the
+ *   framework appends the attempt count) with `endpoint`, `attempts`, and `ncbiErrors`.
+ * - A 429 never retried because its `Retry-After` outlasts the time left or the backoff
+ *   cap → the attempt's own error, stamped `ncbi_rate_limited`.
  * - Anything else — a failure that was never retried — passes through unchanged.
  */
-function toServiceError(error, endpoint, deadlineMs) {
+function toServiceError(error, endpoint, loop) {
     if (!(error instanceof McpError))
         return error;
     const data = error.data ?? {};
@@ -93,22 +168,28 @@ function toServiceError(error, endpoint, deadlineMs) {
             endpoint,
             queueSize: data.queueDepth,
             retryAfter: data.retryAfter,
-            ...recoveryFor('queue_full'),
         }, { cause: error });
     }
     if (data.reason === 'retry_deadline_exceeded') {
-        return timeout(`NCBI request deadline (${deadlineMs}ms) exceeded`, { reason: 'ncbi_deadline_exceeded', deadlineMs, ...recoveryFor('ncbi_deadline_exceeded') }, { cause: error });
+        const last = error.cause;
+        const attempts = data.retryAttempts;
+        if (!loop.deadlineFired && last instanceof McpError && typeof attempts === 'number') {
+            const count = `${attempts} attempt${attempts > 1 ? 's' : ''}`;
+            return retriesSpent(last, `${last.message} (failed after ${count})`, attempts, endpoint, error);
+        }
+        return timeout(`NCBI request deadline (${loop.deadlineMs}ms) exceeded`, {
+            reason: 'ncbi_deadline_exceeded',
+            deadlineMs: loop.deadlineMs,
+            ...(loop.ncbiErrors !== undefined && { ncbiErrors: loop.ncbiErrors }),
+        }, { 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 });
+    if (typeof data.retryAttempts === 'number') {
+        return retriesSpent(error, error.message, data.retryAttempts, endpoint, error.cause ?? error);
+    }
+    if (error.code === JsonRpcErrorCode.RateLimited) {
+        return new McpError(error.code, error.message, { ...data, reason: 'ncbi_rate_limited' }, { cause: error });
+    }
+    return error;
 }
 /**
  * Facade over NCBI's E-utility suite. Each public method corresponds to a
@@ -203,60 +284,50 @@ export class NcbiService {
      *
      * Results come back one per submitted citation, in submission order, carrying
      * the caller's `key`. Correlation runs on the wire key (see
-     * {@link wireKeysFor}), never on `key` itself — that label is caller-supplied,
+     * {@link wireKeyFor}), never on `key` itself — that label is caller-supplied,
      * so it may repeat and may carry characters that break the wire format.
      * (#113, #125)
+     *
+     * A journal-less citation ECitMatch finds no candidate for ends the response:
+     * that line and every line after it come back with no row. So the response
+     * stops at the line after the last one answered; that line is reported
+     * `not_found`, and the lines after it are requested again without it, until
+     * every line has a result. A complete response costs one request, each
+     * dropped line at most one more — 25 requests for 25 such citations. Every
+     * request draws on one deadline and one retry allowance for the whole call.
+     * A line with no row ahead of one that has a row is not a stop and is never
+     * re-requested; it stays `not_found`, as every missing row did before. (#54, #193)
      */
     async eCitMatch(citations, options) {
-        const wireKeys = wireKeysFor(citations);
-        const bdata = citations
-            .map((c, i) => `${c.journal ?? ''}|${c.year ?? ''}|${c.volume ?? ''}|${c.firstPage ?? ''}|${c.authorName ?? ''}|${wireKeys[i]}|`)
-            .join('\r');
-        const text = await this.performRequest('ecitmatch.cgi', { db: 'pubmed', retmode: 'xml', bdata }, { retmode: 'text', ...(options?.signal && { signal: options.signal }) });
-        const parsed = text
-            .split(/[\r\n]+/)
-            .filter((line) => line.trim().length > 0)
-            .map((line) => {
-            const parts = line.split('|');
-            const key = parts[5]?.trim() ?? '';
-            const rawOutcome = parts[6]?.trim() ?? '';
-            if (/^\d+$/.test(rawOutcome)) {
-                return { key, matched: true, pmid: rawOutcome, status: 'matched' };
-            }
-            if (rawOutcome.startsWith('AMBIGUOUS')) {
-                const csv = /^AMBIGUOUS\s+([\d,\s]+)/.exec(rawOutcome)?.[1];
-                const candidatePmids = csv
-                    ? csv
-                        .split(',')
-                        .map((p) => p.trim())
-                        .filter((p) => /^\d+$/.test(p))
-                    : undefined;
-                return {
-                    key,
-                    matched: false,
-                    pmid: null,
-                    status: 'ambiguous',
-                    detail: rawOutcome,
-                    ...(candidatePmids?.length && { candidatePmids }),
-                };
+        const budget = {
+            expiresAt: Date.now() + this.totalDeadlineMs,
+            retriesLeft: this.maxRetries,
+        };
+        const rowByIndex = new Map();
+        let pending = citations.map((citation, index) => ({ citation, index }));
+        while (pending.length > 0) {
+            const bdata = pending.map(({ citation, index }) => bdataLine(citation, index)).join('\r');
+            const text = await this.performRequest('ecitmatch.cgi', { db: 'pubmed', retmode: 'xml', bdata }, { retmode: 'text', ...(options?.signal && { signal: options.signal }) }, budget);
+            // Reconcile on the wire key each line was submitted under — unique within
+            // the call, so one row can never stand in for a second citation. The line
+            // after the last one answered is where the response stopped: it keeps no
+            // row, and only the lines after it go out again.
+            const rowByWireKey = new Map(parseECitMatchRows(text).map((r) => [r.key, r]));
+            let lastAnswered = -1;
+            for (const [position, { index }] of pending.entries()) {
+                const row = rowByWireKey.get(wireKeyFor(index));
+                if (!row)
+                    continue;
+                rowByIndex.set(index, row);
+                lastAnswered = position;
             }
-            return {
-                key,
-                matched: false,
-                pmid: null,
-                status: 'not_found',
-                ...(rawOutcome && { detail: rawOutcome }),
-            };
-        });
-        // ECitMatch omits lines for citations it cannot classify. Reconcile on the
-        // wire key each citation was submitted under — unique within the request, so
-        // one row can never stand in for a second citation — then restore the
-        // caller's label on the way out. Every input gets a result row, so callers
-        // can rely on results.length === citations.length and on results[i]
-        // describing citations[i]. (#54, #113, #125)
-        const parsedByWireKey = new Map(parsed.map((r) => [r.key, r]));
+            pending = pending.slice(lastAnswered + 2);
+        }
+        // Every input gets a result row, so callers can rely on results.length ===
+        // citations.length and on results[i] describing citations[i]; the caller's
+        // label is restored on the way out. (#54, #113, #125)
         return citations.map((c, i) => {
-            const row = parsedByWireKey.get(wireKeys[i] ?? '');
+            const row = rowByIndex.get(i);
             return row
                 ? { ...row, key: c.key }
                 : { key: c.key, matched: false, pmid: null, status: 'not_found' };
@@ -298,14 +369,15 @@ export class NcbiService {
         }
         catch (error) {
             // PMC ID Converter returns 400 (InvalidParams) for malformed inputs and
-            // leaks the upstream HTML/text body into `data.body`. Rewrite to a typed
-            // validation error with idType-specific guidance and drop the leaky body.
+            // leaks the upstream HTML/text body into `data.body`. Rewrite the message
+            // with idType-specific guidance and drop the leaky body, keeping the
+            // InvalidParams code every other NCBI 400 carries.
             if (error instanceof McpError && error.code === JsonRpcErrorCode.InvalidParams) {
                 const hint = ID_CONVERT_FORMAT_HINTS[idtype ?? ''];
                 const message = hint
                     ? `PMC ID Converter rejected one or more inputs as malformed (idType="${idtype}"). Expected: ${hint}.`
                     : `PMC ID Converter rejected the input as malformed (idType="${idtype ?? 'unspecified'}").`;
-                throw validationError(message, { idType: idtype, idCount: ids.length }, { cause: error });
+                throw invalidParams(message, { idType: idtype, idCount: ids.length }, { cause: error });
             }
             throw error;
         }
@@ -317,7 +389,6 @@ export class NcbiService {
             throw serializationError('Failed to parse ID Converter JSON response.', {
                 reason: 'ncbi_invalid_response',
                 responseSnippet: text.substring(0, 200),
-                ...recoveryFor('ncbi_invalid_response'),
             }, { cause: error });
         }
         return parsed.records ?? [];
@@ -330,19 +401,32 @@ export class NcbiService {
      * 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.
      *
+     * With a `budget`, the request is one of several in a call: its deadline is the
+     * time the call has left and its retries are the ones the call has not spent,
+     * which it then spends from. A failure is still reported against the call's
+     * full deadline.
+     *
      * 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.
+     * onto this service's reasons by {@link toServiceError}, after the loop. Once the
+     * caller is ruled out, the loop's signal has aborted only if the deadline fired.
      */
-    async runPaced(endpoint, callerSignal, execute) {
+    async runPaced(endpoint, callerSignal, execute, budget) {
+        const maxRetries = budget?.retriesLeft ?? this.maxRetries;
         let attempt = 0;
+        let loopSignal;
+        let ncbiErrors;
         try {
             return await withRetry(({ signal, remainingMs }) => {
+                loopSignal = signal;
                 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({
+                    if (error instanceof McpError && error.data?.ncbiErrors !== undefined) {
+                        ncbiErrors = error.data.ncbiErrors;
+                    }
+                    if (attempt <= maxRetries && isTransient(error)) {
+                        logger.warning(`NCBI request to ${endpoint} failed on attempt ${attempt} of ${maxRetries + 1}.`, requestContextService.createRequestContext({
                             operation: 'NcbiRetry',
                             additionalContext: {
                                 endpoint,
@@ -354,9 +438,9 @@ export class NcbiService {
                     throw error;
                 });
             }, {
-                maxRetries: this.maxRetries,
+                maxRetries,
                 maxDelayMs: MAX_BACKOFF_MS,
-                deadlineMs: this.totalDeadlineMs,
+                deadlineMs: budget ? Math.max(0, budget.expiresAt - Date.now()) : this.totalDeadlineMs,
                 isTransient,
                 operation: `NCBI ${endpoint}`,
                 ...(callerSignal && { signal: callerSignal }),
@@ -365,7 +449,15 @@ export class NcbiService {
         catch (error) {
             if (callerSignal?.aborted)
                 throw callerSignal.reason;
-            throw toServiceError(error, endpoint, this.totalDeadlineMs);
+            throw toServiceError(error, endpoint, {
+                deadlineMs: this.totalDeadlineMs,
+                deadlineFired: loopSignal?.aborted === true,
+                ncbiErrors,
+            });
+        }
+        finally {
+            if (budget)
+                budget.retriesLeft -= attempt - 1;
         }
     }
     /**
@@ -373,7 +465,7 @@ export class NcbiService {
      * 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) {
+    performRequest(endpoint, params, options, budget) {
         return this.runPaced(endpoint, options?.signal, async (signal) => {
             const text = await this.apiClient
                 .makeRequest(endpoint, params, { ...options, signal })
@@ -384,7 +476,7 @@ export class NcbiService {
                 throw reclassifyNcbiHttpError(error, endpoint);
             });
             return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
-        });
+        }, budget);
     }
 }
 // ─── Init / Accessor ────────────────────────────────────────────────────────

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

@@ -1 +1 @@
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package/dist/services/ncbi/parsing/article-parser.d.ts

@@ -3,7 +3,7 @@
  * typically from EFetch results.
  * @module src/services/ncbi/parsing/article-parser
  */
-import type { ParsedArticle, ParsedArticleAuthor, ParsedArticleDate, ParsedBookInfo, ParsedGrant, ParsedJournalInfo, ParsedMeshTerm, ParseFullArticleOptions, XmlArticle, XmlArticleIdList, XmlAuthorList, XmlBookDocument, XmlGrantList, XmlJournal, XmlKeywordList, XmlMedlineCitation, XmlMeshHeadingList, XmlPublicationTypeList, XmlPubmedArticle, XmlPubmedArticleSet, XmlPubmedBookArticle } from '../types.js';
+import type { ParsedArticle, ParsedArticleAuthor, ParsedArticleDate, ParsedBookInfo, ParsedCommentsCorrection, ParsedGrant, ParsedJournalInfo, ParsedMeshTerm, ParseFullArticleOptions, XmlArticle, XmlArticleIdList, XmlAuthorList, XmlBookDocument, XmlCommentsCorrectionsList, XmlGrantList, XmlJournal, XmlKeywordList, XmlMedlineCitation, XmlMeshHeadingList, XmlPublicationTypeList, XmlPubmedArticle, XmlPubmedArticleSet, XmlPubmedBookArticle } from '../types.js';
 /**
  * Result of extracting authors with deduplicated affiliations.
  */
@@ -61,6 +61,20 @@ export declare function extractPmcId(articleXml?: XmlArticle, pubmedDataArticleI
  * @returns An array of publication type strings.
  */
 export declare function extractPublicationTypes(publicationTypeListXml?: XmlPublicationTypeList): string[];
+/**
+ * Extracts the linked notices from `MedlineCitation/CommentsCorrectionsList` —
+ * retractions, errata, expressions of concern, comments, updates — in upstream
+ * order. `Cites` entries are dropped: they list a bibliography rather than a
+ * linked record, which NLM now carries in `PubmedData/ReferenceList`. (#178)
+ *
+ * `RefSource` and `Note` reach this function as the text NCBI wrote: the response
+ * handler exempts both from numeric coercion, which would otherwise reduce `007` to
+ * `7`. A `PMID` is still coerced, and `getText` turns it back into a string — PMIDs
+ * carry no leading zeros, so none is lost.
+ * @param commentsCorrectionsListXml - The XML CommentsCorrectionsList element.
+ * @returns The linked notices; empty when the record carries none.
+ */
+export declare function extractCommentsCorrections(commentsCorrectionsListXml?: XmlCommentsCorrectionsList): ParsedCommentsCorrection[];
 /**
  * Extracts keywords from XML. Handles single or multiple KeywordList elements.
  * @param keywordListsXml - The XML KeywordList element or an array of them.

package/dist/services/ncbi/parsing/article-parser.d.ts.map

@@ -1 +1 @@
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