npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.19 → 2.10.20 - Mend

@cyanheads/pubmed-mcp-server 2.10.19 → 2.10.20

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (84) hide show

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

@@ -6,7 +6,7 @@
  * 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 { NcbiApiClient } from './api-client.js';
@@ -40,19 +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;
@@ -240,60 +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' };
@@ -335,14 +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;
         }
@@ -366,11 +401,17 @@ 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. 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;
@@ -384,8 +425,8 @@ export class NcbiService {
                     if (error instanceof McpError && error.data?.ncbiErrors !== undefined) {
                         ncbiErrors = error.data.ncbiErrors;
                     }
-                    if (attempt <= this.maxRetries && isTransient(error)) {
-                        logger.warning(`NCBI request to ${endpoint} failed on attempt ${attempt} of ${this.maxRetries + 1}.`, requestContextService.createRequestContext({
+                    if (attempt <= maxRetries && isTransient(error)) {
+                        logger.warning(`NCBI request to ${endpoint} failed on attempt ${attempt} of ${maxRetries + 1}.`, requestContextService.createRequestContext({
                             operation: 'NcbiRetry',
                             additionalContext: {
                                 endpoint,
@@ -397,9 +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 }),
@@ -414,13 +455,17 @@ export class NcbiService {
                 ncbiErrors,
             });
         }
+        finally {
+            if (budget)
+                budget.retriesLeft -= attempt - 1;
+        }
     }
     /**
      * 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) {
+    performRequest(endpoint, params, options, budget) {
         return this.runPaced(endpoint, options?.signal, async (signal) => {
             const text = await this.apiClient
                 .makeRequest(endpoint, params, { ...options, signal })
@@ -431,7 +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 CHANGED Viewed

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

	@@ -1 +1 @@
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package/dist/services/ncbi/parsing/article-parser.js CHANGED Viewed

@@ -28,11 +28,8 @@ export function extractAuthors(authorListXml) {
     }
     const xmlAuthors = ensureArray(authorListXml.Author);
     const authors = xmlAuthors.map((auth) => {
-        const collectiveName = getText(auth.CollectiveName);
-        if (collectiveName) {
-            return { collectiveName };
-        }
-        // Collect all affiliations for this author, deduplicated at article level
+        // Collect all affiliations for this author, deduplicated at article level.
+        // A collective author carries its own `AffiliationInfo` too. (#212)
         const authorAffiliationInfos = ensureArray(auth.AffiliationInfo);
         const indices = [];
         for (const info of authorAffiliationInfos) {
@@ -52,10 +49,15 @@ export function extractAuthors(authorListXml) {
                 }
             }
         }
+        const collectiveName = getText(auth.CollectiveName);
         return {
-            lastName: getText(auth.LastName),
-            firstName: getText(auth.ForeName), // XML uses ForeName
-            initials: getText(auth.Initials),
+            ...(collectiveName
+                ? { collectiveName }
+                : {
+                    lastName: getText(auth.LastName),
+                    firstName: getText(auth.ForeName), // XML uses ForeName
+                    initials: getText(auth.Initials),
+                }),
             ...(indices.length > 0 && { affiliationIndices: indices }),
             ...(orcid && { orcid }),
         };
@@ -105,22 +107,29 @@ export function extractJournalInfo(journalXml, articleXml) {
     const day = getText(pubDate?.Day);
     const medlineDate = getText(pubDate?.MedlineDate);
     const locator = extractELocationId(articleXml);
+    // A field the record does not carry is omitted, never written as "". (#137, #213)
+    const title = getOptionalText(journalXml.Title);
+    const isoAbbreviation = getOptionalText(journalXml.ISOAbbreviation);
+    const volume = getOptionalText(journalXml.JournalIssue?.Volume);
+    const issue = getOptionalText(journalXml.JournalIssue?.Issue);
+    const pages = getOptionalText(articleXml?.Pagination?.MedlinePgn);
+    const publicationDate = {
+        ...(year && { year }),
+        ...(month && { month }),
+        ...(day && { day }),
+        ...(medlineDate && { medlineDate }),
+    };
     return {
-        title: getText(journalXml.Title),
-        isoAbbreviation: getText(journalXml.ISOAbbreviation),
+        ...(title && { title }),
+        ...(isoAbbreviation && { isoAbbreviation }),
         ...(issn && { issn }),
         ...(eIssn && { eIssn }),
-        volume: getText(journalXml.JournalIssue?.Volume),
-        issue: getText(journalXml.JournalIssue?.Issue),
-        pages: getText(articleXml?.Pagination?.MedlinePgn),
+        ...(volume && { volume }),
+        ...(issue && { issue }),
+        ...(pages && { pages }),
         ...(locator && { elocationId: locator.value }),
         ...(locator?.type && { elocationIdType: locator.type }),
-        publicationDate: {
-            ...(year && { year }),
-            ...(month && { month }),
-            ...(day && { day }),
-            ...(medlineDate && { medlineDate }),
-        },
+        ...(Object.keys(publicationDate).length > 0 && { publicationDate }),
     };
 }
 /**
@@ -533,16 +542,16 @@ export function parseFullBookArticle(xmlBookArticle) {
     const articleDates = [
         ['ContributionDate', bookDocument?.ContributionDate],
         ['DateRevised', bookDocument?.DateRevised],
-    ].flatMap(([dateType, dateXml]) => dateXml
-        ? [
-            {
-                dateType,
-                year: getText(dateXml.Year),
-                month: getText(dateXml.Month),
-                day: getText(dateXml.Day),
-            },
-        ]
-        : []);
+    ].flatMap(([dateType, dateXml]) => {
+        if (!dateXml)
+            return [];
+        // A `ContributionDate` may carry no `Month` or `Day` (or a `Season` instead),
+        // unlike a journal `ArticleDate`; an absent part is omitted, never "". (#213)
+        const year = getOptionalText(dateXml.Year);
+        const month = getOptionalText(dateXml.Month);
+        const day = getOptionalText(dateXml.Day);
+        return [{ dateType, ...(year && { year }), ...(month && { month }), ...(day && { day }) }];
+    });
     const doi = findArticleId(bookDocument?.ArticleIdList, 'doi') ??
         findArticleId(xmlBookArticle.PubmedBookData?.ArticleIdList, 'doi');
     const title = chapterTitle ?? book.title;

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	@@ -1 +1 @@
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package/dist/services/ncbi/parsing/esummary-parser.d.ts CHANGED Viewed

@@ -20,6 +20,15 @@ export declare function formatESummaryAuthors(authors?: XmlESummaryAuthor[]): st
  * option causes "2023 Dec" to resolve to a future December, ignoring the year.
  */
 export declare function parseNcbiDate(dateStr: string): string | undefined;
+/**
+ * A Bookshelf chapter's own date from its ESummary `DocDate` — `1998 Oct 23
+ * [updated 2018 Dec 20]`, `2025 Jul 3`, `2021 Sep`, or `2026`: the revision when
+ * there is one, otherwise the contribution date, as `pubmed_format_citations`
+ * dates the chapter (#189). An unreadable revision falls back to the
+ * contribution date; undefined when neither is one of ESummary's date forms, so
+ * the caller keeps the book's date rather than guessing. (#199)
+ */
+export declare function chapterDateFromDocDate(docDate: string): string | undefined;
 /**
  * Standardizes date strings from ESummary to 'YYYY-MM-DD' format.
  * Uses a dedicated NCBI date parser for known formats, falling back to

package/dist/services/ncbi/parsing/esummary-parser.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,EAGV,uBAAuB,EAEvB,cAAc,EACd,kBAAkB,EAClB,cAAc,IAAI,iBAAiB,EAEpC,MAAM,aAAa,CAAC;AAGrB;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,CAAC,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAQ3E;AA8BD;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAajE;AAKD;;;;;;;GAOG;AACH,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAW1E;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,MAAM,EAChB,aAAa,CAAC,EAAE,cAAc,GAC7B,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CA+B7B;AAmBD;;;;;;;;GAQG;AACH,wBAAgB,uCAAuC,CACrD,UAAU,EAAE,uBAAuB,GAClC,iBAAiB,EAAE,CAuGrB;AA6KD;;;GAGG;AACH,wBAAsB,qBAAqB,CACzC,cAAc,CAAC,EAAE,cAAc,EAC/B,OAAO,CAAC,EAAE,cAAc,GACvB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAwD/B"}

package/dist/services/ncbi/parsing/esummary-parser.js CHANGED Viewed

@@ -68,6 +68,27 @@ export function parseNcbiDate(dateStr) {
         return `${year}-${month}-01`;
     return `${year}-01-01`;
 }
+/** Opens the revision date inside a Bookshelf chapter's `DocDate`. */
+const DOC_DATE_UPDATED = '[updated ';
+/**
+ * A Bookshelf chapter's own date from its ESummary `DocDate` — `1998 Oct 23
+ * [updated 2018 Dec 20]`, `2025 Jul 3`, `2021 Sep`, or `2026`: the revision when
+ * there is one, otherwise the contribution date, as `pubmed_format_citations`
+ * dates the chapter (#189). An unreadable revision falls back to the
+ * contribution date; undefined when neither is one of ESummary's date forms, so
+ * the caller keeps the book's date rather than guessing. (#199)
+ */
+export function chapterDateFromDocDate(docDate) {
+    const readable = (part) => {
+        const trimmed = part.trim();
+        return parseNcbiDate(trimmed) ? trimmed : undefined;
+    };
+    const updated = docDate.indexOf(DOC_DATE_UPDATED);
+    const close = updated === -1 ? -1 : docDate.indexOf(']', updated);
+    const revised = close === -1 ? undefined : readable(docDate.slice(updated + DOC_DATE_UPDATED.length, close));
+    const bracket = docDate.indexOf('[');
+    return revised ?? readable(docDate.slice(0, bracket === -1 ? undefined : bracket));
+}
 /**
  * Standardizes date strings from ESummary to 'YYYY-MM-DD' format.
  * Uses a dedicated NCBI date parser for known formats, falling back to
@@ -253,13 +274,16 @@ function parseSingleDocumentSummary(docSummary) {
     const pmcIdValue = pmcEntry ? getOptionalText(getArticleIdValue(pmcEntry)) : undefined;
     const title = getText(docSummary.Title);
     const source = getText(docSummary.Source) || getText(docSummary.FullJournalName) || getText(docSummary.SO);
-    const rawPubDate = getText(docSummary.PubDate);
-    const rawEPubDate = getText(docSummary.EPubDate);
     // A Bookshelf record leaves Source and FullJournalName empty and carries its
     // venue here instead, so without these a book summary renders with none. (#114)
     const bookTitle = getText(docSummary.BookTitle);
     const publisherName = getText(docSummary.PublisherName);
     const docType = getText(docSummary.DocType);
+    // A chapter's PubDate is its book's (GeneReviews: 1993); its own dates are in
+    // DocDate, which ESummary sets on chapters only. (#199)
+    const chapterDate = docType === 'chapter' ? chapterDateFromDocDate(getText(docSummary.DocDate)) : undefined;
+    const rawPubDate = chapterDate ?? getText(docSummary.PubDate);
+    const rawEPubDate = getText(docSummary.EPubDate);
     return {
         pmid: String(pmid),
         ...(title && { title }),