npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.18 → 2.10.20 - Mend

@cyanheads/pubmed-mcp-server 2.10.18 → 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 (121) hide show

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 }),
     };
 }
 /**
@@ -276,6 +285,33 @@ export function extractPublicationTypes(publicationTypeListXml) {
     const pubTypes = ensureArray(publicationTypeListXml.PublicationType);
     return pubTypes.map((pt) => getText(pt)).filter(Boolean);
 }
+/**
+ * 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 function extractCommentsCorrections(commentsCorrectionsListXml) {
+    return ensureArray(commentsCorrectionsListXml?.CommentsCorrections)
+        .filter((entry) => getAttribute(entry, 'RefType') !== 'Cites')
+        .map((entry) => {
+        const pmid = getOptionalText(entry.PMID);
+        const note = getOptionalText(entry.Note);
+        return {
+            refType: getAttribute(entry, 'RefType'),
+            refSource: getText(entry.RefSource),
+            ...(pmid && { pmid }),
+            ...(note && { note }),
+        };
+    });
+}
 /**
  * Extracts keywords from XML. Handles single or multiple KeywordList elements.
  * @param keywordListsXml - The XML KeywordList element or an array of them.
@@ -372,6 +408,7 @@ export function parseFullArticle(xmlArticle, options = {}) {
     const pmcId = extractPmcId(article, pubmedDataArticleIdList);
     const { authors, affiliations } = extractAuthors(article?.AuthorList);
     const publicationTypes = extractPublicationTypes(article?.PublicationTypeList);
+    const commentsCorrections = extractCommentsCorrections(medlineCitation?.CommentsCorrectionsList);
     const keywords = extractKeywords(medlineCitation?.KeywordList ?? article?.KeywordList);
     const articleDates = extractArticleDates(article);
     const meshTerms = includeMesh ? extractMeshTerms(medlineCitation?.MeshHeadingList) : undefined;
@@ -385,6 +422,7 @@ export function parseFullArticle(xmlArticle, options = {}) {
         authors,
         ...(journalInfo !== undefined && { journalInfo }),
         ...(publicationTypes.length > 0 && { publicationTypes }),
+        ...(commentsCorrections.length > 0 && { commentsCorrections }),
         ...(keywords.length > 0 && { keywords }),
         ...(meshTerms !== undefined && meshTerms.length > 0 && { meshTerms }),
         ...(grantList !== undefined && grantList.length > 0 && { grantList }),
@@ -504,16 +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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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 }),

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

	@@ -1 +1 @@
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