@cyanheads/pubmed-mcp-server 2.10.20 → 2.10.22

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

@@ -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.
@@ -15,41 +55,14 @@ 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) => {
-        // 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) {
-            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;
-                }
-            }
-        }
+        const indices = affiliations.of(auth.AffiliationInfo);
+        const orcid = extractOrcid(auth.Identifier);
         const collectiveName = getText(auth.CollectiveName);
+        const suffix = getOptionalText(auth.Suffix);
         return {
             ...(collectiveName
                 ? { collectiveName }
@@ -57,12 +70,45 @@ export function extractAuthors(authorListXml) {
                     lastName: getText(auth.LastName),
                     firstName: getText(auth.ForeName), // XML uses ForeName
                     initials: getText(auth.Initials),
+                    ...(suffix && { suffix }),
                 }),
             ...(indices.length > 0 && { affiliationIndices: indices }),
             ...(orcid && { orcid }),
         };
     });
-    return { authors, affiliations: affiliationList };
+    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` included.
+ * (#216, #226)
+ * @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 suffix = getOptionalText(inv.Suffix);
+        const indices = affiliations.of(inv.AffiliationInfo);
+        const orcid = extractOrcid(inv.Identifier);
+        return {
+            ...(lastName && { lastName }),
+            ...(firstName && { firstName }),
+            ...(initials && { initials }),
+            ...(suffix && { suffix }),
+            ...(indices.length > 0 && { affiliationIndices: indices }),
+            ...(orcid && { orcid }),
+        };
+    });
+    return { investigators, affiliations: affiliations.list };
 }
 /**
  * Picks the electronic article locator from an Article's `ELocationID` list —
@@ -112,7 +158,9 @@ export function extractJournalInfo(journalXml, articleXml) {
     const isoAbbreviation = getOptionalText(journalXml.ISOAbbreviation);
     const volume = getOptionalText(journalXml.JournalIssue?.Volume);
     const issue = getOptionalText(journalXml.JournalIssue?.Issue);
-    const pages = getOptionalText(articleXml?.Pagination?.MedlinePgn);
+    const medlinePgn = getOptionalText(articleXml?.Pagination?.MedlinePgn);
+    // NCBI writes the literal `None` where a record has no pagination. (#248)
+    const pages = medlinePgn === 'None' ? undefined : medlinePgn;
     const publicationDate = {
         ...(year && { year }),
         ...(month && { month }),
@@ -400,13 +448,16 @@ 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);
@@ -420,6 +471,7 @@ 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 }),
@@ -471,10 +523,11 @@ function mergeAuthorLists(lists) {
 export function extractBookInfo(bookDocumentXml) {
     const book = bookDocumentXml.Book;
     const editorLists = ensureArray(book?.AuthorList).filter((list) => getAttribute(list, 'Type') === 'editors');
-    const editors = extractAuthors(mergeAuthorLists(editorLists)).authors.map(({ lastName, firstName, initials, collectiveName }) => ({
+    const editors = extractAuthors(mergeAuthorLists(editorLists)).authors.map(({ lastName, firstName, initials, suffix, collectiveName }) => ({
         ...(lastName && { lastName }),
         ...(firstName && { firstName }),
         ...(initials && { initials }),
+        ...(suffix && { suffix }),
         ...(collectiveName && { collectiveName }),
     }));
     const isbns = ensureArray(book?.Isbn)

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

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

@@ -9,7 +9,11 @@
  */
 import type { ParsedPmcArticle, ParsedPmcAsset, ParsedPmcAuthor, ParsedPmcReference, ParsedPmcSection, ParsedPmcTable } from '../types.js';
 import { type JatsNode } from './pmc-xml-helpers.js';
-/** Extract authors from a single `<contrib-group>` node. Non-author contributors are skipped. */
+/**
+ * Extract authors from a single `<contrib-group>` node. Non-author contributors
+ * are skipped. A name part the deposit lacks is omitted; a `<suffix>` is kept
+ * verbatim (`IV`, never rewritten to `4th`). (#226)
+ */
 export declare function extractJatsAuthors(contribGroup: JatsNode | undefined): ParsedPmcAuthor[];
 /**
  * Extract body sections from a `<body>` node, walking children in document order.
@@ -40,10 +44,10 @@ 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 +75,10 @@ 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

@@ -1 +1 @@
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+{"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,cAAc,EAEd,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EAChB,cAAc,EAEf,MAAM,aAAa,CAAC;AACrB,OAAO,EAUL,KAAK,QAAQ,EAWd,MAAM,sBAAsB,CAAC;AAkI9B;;;;GAIG;AACH,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA4BxF;AA4wBD;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CAElF;AA6SD;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,cAAc,EAAE,CAO7E;AAgGD;;;;;;;;GAQG;AACH,eAAO,MAAM,iBAAiB,MAAM,CAAC;AAoGrC;;;;;;;;;;;;GAYG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,cAAc,EAAE,CAQ7E;AA8TD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,CAsClF;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CAkDvE"}