npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.19 → 2.10.21 - Mend

@cyanheads/pubmed-mcp-server 2.10.19 → 2.10.21

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 (110) hide show

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

@@ -5,6 +5,46 @@
  */
 import { decodeHtmlEntities } from './text-helpers.js';
 import { ensureArray, getAttribute, getOptionalAttribute, getOptionalText, getText, } from './xml-helpers.js';
+/**
+ * An article's deduplicated affiliation list: one index per distinct text, a new
+ * text appended at the end. Seeded with an existing list, it continues that
+ * list's numbering, so the seed's indices never move.
+ */
+function affiliationIndex(seed = []) {
+    const list = [...seed];
+    const indexOf = new Map(list.map((text, index) => [text, index]));
+    return {
+        list,
+        /** Indices of one contributor's `AffiliationInfo` texts, in order. */
+        of(infos) {
+            const indices = [];
+            for (const info of ensureArray(infos)) {
+                const text = getText(info?.Affiliation);
+                if (!text)
+                    continue;
+                let index = indexOf.get(text);
+                if (index === undefined) {
+                    index = list.length;
+                    list.push(text);
+                    indexOf.set(text, index);
+                }
+                indices.push(index);
+            }
+            return indices;
+        },
+    };
+}
+/** The first ORCID among a contributor's `Identifier` elements (`Source="ORCID"`). */
+function extractOrcid(identifiers) {
+    for (const id of ensureArray(identifiers)) {
+        if (getAttribute(id, 'Source') === 'ORCID') {
+            const value = getText(id);
+            if (value)
+                return value;
+        }
+    }
+    return;
+}
 /**
  * Extracts and formats author information from XML, deduplicating affiliations.
  * Affiliations are collected into a single array; each author references them by index.
@@ -15,52 +55,56 @@ import { ensureArray, getAttribute, getOptionalAttribute, getOptionalText, getTe
 export function extractAuthors(authorListXml) {
     if (!authorListXml)
         return { authors: [], affiliations: [] };
-    const affiliationMap = new Map();
-    const affiliationList = [];
-    function getAffiliationIndex(text) {
-        const existing = affiliationMap.get(text);
-        if (existing !== undefined)
-            return existing;
-        const idx = affiliationList.length;
-        affiliationList.push(text);
-        affiliationMap.set(text, idx);
-        return idx;
-    }
+    const affiliations = affiliationIndex();
     const xmlAuthors = ensureArray(authorListXml.Author);
     const authors = xmlAuthors.map((auth) => {
+        // A collective author carries its own `AffiliationInfo` too. (#212)
+        const indices = affiliations.of(auth.AffiliationInfo);
+        const orcid = extractOrcid(auth.Identifier);
         const collectiveName = getText(auth.CollectiveName);
-        if (collectiveName) {
-            return { collectiveName };
-        }
-        // Collect all affiliations for this author, deduplicated at article level
-        const authorAffiliationInfos = ensureArray(auth.AffiliationInfo);
-        const indices = [];
-        for (const info of authorAffiliationInfos) {
-            const text = getText(info?.Affiliation);
-            if (text)
-                indices.push(getAffiliationIndex(text));
-        }
-        // Extract ORCID from Identifier elements with Source="ORCID"
-        let orcid;
-        const identifiers = ensureArray(auth.Identifier);
-        for (const id of identifiers) {
-            if (getAttribute(id, 'Source') === 'ORCID') {
-                const val = getText(id);
-                if (val) {
-                    orcid = val;
-                    break;
-                }
-            }
-        }
         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 }),
+        };
+    });
+    return { authors, affiliations: affiliations.list };
+}
+/**
+ * Extracts the members of a collective author from every `InvestigatorList`,
+ * flattened in upstream order and uncapped. Investigator affiliations join the
+ * article's deduplicated list after the authors' entries, so an author's indices
+ * never shift. A name part the record lacks is omitted; `Suffix` is not read,
+ * as for authors. (#216)
+ * @param investigatorListsXml - The record's `InvestigatorList` elements.
+ * @param authorAffiliations - The authors' affiliations, from {@link extractAuthors}.
+ * @returns The investigators, and the affiliation list extended with theirs.
+ */
+function extractInvestigators(investigatorListsXml, authorAffiliations) {
+    const affiliations = affiliationIndex(authorAffiliations);
+    const investigators = ensureArray(investigatorListsXml)
+        .flatMap((list) => ensureArray(list.Investigator))
+        .map((inv) => {
+        const lastName = getOptionalText(inv.LastName);
+        const firstName = getOptionalText(inv.ForeName);
+        const initials = getOptionalText(inv.Initials);
+        const indices = affiliations.of(inv.AffiliationInfo);
+        const orcid = extractOrcid(inv.Identifier);
+        return {
+            ...(lastName && { lastName }),
+            ...(firstName && { firstName }),
+            ...(initials && { initials }),
             ...(indices.length > 0 && { affiliationIndices: indices }),
             ...(orcid && { orcid }),
         };
     });
-    return { authors, affiliations: affiliationList };
+    return { investigators, affiliations: affiliations.list };
 }
 /**
  * Picks the electronic article locator from an Article's `ELocationID` list —
@@ -105,22 +149,29 @@ 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 }),
     };
 }
 /**
@@ -391,13 +442,16 @@ export function extractArticleDates(articleXml) {
 export function parseFullArticle(xmlArticle, options = {}) {
     const medlineCitation = xmlArticle.MedlineCitation;
     const article = medlineCitation?.Article;
-    const { includeMesh = true, includeGrants = false } = options;
+    const { includeMesh = true, includeGrants = false, includeInvestigators = false } = options;
     const abstractText = extractAbstractText(article?.Abstract);
     const journalInfo = extractJournalInfo(article?.Journal, article);
     const pubmedDataArticleIdList = xmlArticle.PubmedData?.ArticleIdList;
     const doi = extractDoi(article, pubmedDataArticleIdList);
     const pmcId = extractPmcId(article, pubmedDataArticleIdList);
-    const { authors, affiliations } = extractAuthors(article?.AuthorList);
+    const { authors, affiliations: authorAffiliations } = extractAuthors(article?.AuthorList);
+    const { investigators, affiliations } = includeInvestigators
+        ? extractInvestigators(medlineCitation?.InvestigatorList, authorAffiliations)
+        : { investigators: [], affiliations: authorAffiliations };
     const publicationTypes = extractPublicationTypes(article?.PublicationTypeList);
     const commentsCorrections = extractCommentsCorrections(medlineCitation?.CommentsCorrectionsList);
     const keywords = extractKeywords(medlineCitation?.KeywordList ?? article?.KeywordList);
@@ -411,6 +465,7 @@ export function parseFullArticle(xmlArticle, options = {}) {
         ...(abstractText !== undefined && { abstractText }),
         ...(affiliations.length > 0 && { affiliations }),
         authors,
+        ...(investigators.length > 0 && { investigators }),
         ...(journalInfo !== undefined && { journalInfo }),
         ...(publicationTypes.length > 0 && { publicationTypes }),
         ...(commentsCorrections.length > 0 && { commentsCorrections }),
@@ -533,16 +588,16 @@ 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;

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

	@@ -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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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 }),

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

@@ -40,10 +40,10 @@ export declare function extractBodySections(body: JatsNode | undefined): ParsedP
  * The walk covers the whole article rather than `<body>` alone: about a quarter
  * of real tables sit in `<floats-group>`, `<back>/<sec>`, `<table-wrap-group>`
  * or `<app-group>/<app>`, so a body-scoped extractor drops them. Each table
- * names the innermost enclosing `<sec>` wherever that sits — a back-matter or
- * appendix section counts, and naming it is the reader's only positional cue
- * there. Only a table inside no `<sec>` at all, such as a `<floats-group>`
- * deposit, carries no section name.
+ * names the innermost enclosing section wherever that sits — a back-matter
+ * `<sec>`, `<app>`, `<notes>` or `<fn-group>` counts, and naming it is the
+ * reader's only positional cue there. Only a table inside no section at all,
+ * such as a `<floats-group>` deposit, carries no section name. (#206)
  *
  * Only XHTML `<tr>`/`<td>`/`<th>` bodies are read. **Decision, not an
  * oversight:** across a 283-table survey of open-access records, 276 were XHTML,
@@ -71,9 +71,10 @@ export declare const MAX_TABLE_COLUMNS = 512;
  * supplementary material sit outside `<body>` entirely — `<floats-group>`
  * deposits, `<back>/<sec>` and `<app-group>/<app>` placements, and figures
  * hanging off the abstract in `<front>`. Each asset names the innermost
- * enclosing `<sec>` wherever that sits, an untitled one inheriting its parent's
- * title, so the reader keeps a positional cue; an asset inside no `<sec>` at all
- * carries no section name. (#130)
+ * enclosing section wherever that sits — a back-matter element read as one
+ * included — an untitled `<sec>` inheriting its parent's title, so the reader
+ * keeps a positional cue; an asset inside no section at all carries no section
+ * name. (#130, #206)
  */
 export declare function extractPmcAssets(root: JatsNode | undefined): ParsedPmcAsset[];
 /**

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

	@@ -1 +1 @@
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