@cyanheads/pubmed-mcp-server 2.3.9 → 2.3.10

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

@@ -1,126 +1,78 @@
 /**
  * @fileoverview Parser for PMC full-text articles in JATS XML format.
- * Extracts metadata, body sections, and references from PMC EFetch responses.
+ * Consumes the ordered tree shape from fast-xml-parser's `preserveOrder: true`
+ * mode (see `pmc-xml-helpers.ts`) so that mixed-content elements — `<p>`,
+ * `<abstract>`, `<title>` with inline `<italic>`, `<xref>`, `<sup>`, etc. —
+ * read back in document order. Parsing in the default object shape scrambles
+ * inline children and drops body sections for markup-heavy articles.
  * @module src/services/ncbi/parsing/pmc-article-parser
  */
-import { ensureArray, getAttribute, getText } from './xml-helpers.js';
-// ─── Text Extraction ────────────────────────────────────────────────────────
-/**
- * Recursively extracts plain text content from a JATS XML node.
- * Handles mixed content where text and child elements are interleaved.
- * fast-xml-parser with `preserveOrder: false` stores text in `#text` and
- * child elements as named properties — document order is lost, but all
- * text content is preserved.
- */
-export function extractTextContent(node) {
-    if (node == null)
-        return '';
-    if (typeof node === 'string')
-        return node;
-    if (typeof node === 'number' || typeof node === 'boolean')
-        return String(node);
-    if (Array.isArray(node)) {
-        return node.map(extractTextContent).filter(Boolean).join(' ');
-    }
-    if (typeof node === 'object') {
-        const obj = node;
-        const parts = [];
-        // Collect #text from this node
-        if (obj['#text'] !== undefined) {
-            const text = typeof obj['#text'] === 'string' ? obj['#text'] : String(obj['#text']);
-            if (text)
-                parts.push(text);
-        }
-        // Recurse into child elements (skip attributes prefixed with @_)
-        for (const key of Object.keys(obj)) {
-            if (key === '#text' || key.startsWith('@_'))
-                continue;
-            const childText = extractTextContent(obj[key]);
-            if (childText)
-                parts.push(childText);
-        }
-        return parts.join(' ').replace(/\s+/g, ' ').trim();
-    }
-    return '';
-}
-// ─── Article ID Extraction ──────────────────────────────────────────────────
-/**
- * Extracts a specific article ID by pub-id-type from article-meta.
- */
-function extractArticleId(articleIds, pubIdType) {
-    for (const id of ensureArray(articleIds)) {
-        if (getAttribute(id, 'pub-id-type') === pubIdType) {
-            const val = id['#text'];
-            if (val !== undefined)
-                return String(val);
+import { attrOf, childrenOf, findAll, findOne, tagNameOf, textContent, } from './pmc-xml-helpers.js';
+// ─── Article IDs ────────────────────────────────────────────────────────────
+function extractArticleId(articleMeta, pubIdType) {
+    if (!articleMeta)
+        return;
+    for (const idNode of findAll(articleMeta, 'article-id')) {
+        if (attrOf(idNode, 'pub-id-type') === pubIdType) {
+            return textContent(idNode) || undefined;
         }
     }
     return;
 }
-// ─── Author Extraction ──────────────────────────────────────────────────────
-/**
- * Extracts authors from JATS contrib-group elements.
- * Only includes contributors with contrib-type="author".
- */
-export function extractJatsAuthors(contribGroups) {
-    if (!contribGroups)
+// ─── Authors & Affiliations ─────────────────────────────────────────────────
+/** Extract authors from a single `<contrib-group>` node. Non-author contributors are skipped. */
+export function extractJatsAuthors(contribGroup) {
+    if (!contribGroup)
         return [];
     const authors = [];
-    for (const group of ensureArray(contribGroups)) {
-        for (const contrib of ensureArray(group.contrib)) {
-            // Only include authors (skip editors, etc.)
-            if (contrib['@_contrib-type'] && contrib['@_contrib-type'] !== 'author')
-                continue;
-            const collectiveName = extractTextContent(contrib.collab);
-            if (collectiveName) {
+    for (const contrib of findAll(contribGroup, 'contrib')) {
+        const contribType = attrOf(contrib, 'contrib-type');
+        if (contribType && contribType !== 'author')
+            continue;
+        const collab = findOne(contrib, 'collab');
+        if (collab) {
+            const collectiveName = textContent(collab);
+            if (collectiveName)
                 authors.push({ collectiveName });
-                continue;
-            }
-            if (contrib.name) {
-                const lastName = extractTextContent(contrib.name.surname) || undefined;
-                const givenNames = extractTextContent(contrib.name['given-names']) || undefined;
-                authors.push({
-                    ...(lastName && { lastName }),
-                    ...(givenNames && { givenNames }),
-                });
-            }
+            continue;
+        }
+        const nameNode = findOne(contrib, 'name');
+        if (nameNode) {
+            const lastName = textContent(findOne(nameNode, 'surname')) || undefined;
+            const givenNames = textContent(findOne(nameNode, 'given-names')) || undefined;
+            authors.push({
+                ...(lastName && { lastName }),
+                ...(givenNames && { givenNames }),
+            });
         }
     }
     return authors;
 }
-// ─── Affiliation Extraction ─────────────────────────────────────────────────
-/**
- * Extracts affiliation strings from JATS aff elements.
- */
-function extractAffiliations(affs) {
-    if (!affs)
+function extractAffiliations(articleMeta) {
+    if (!articleMeta)
         return [];
     const result = [];
-    for (const aff of ensureArray(affs)) {
-        const text = extractTextContent(aff);
+    for (const aff of findAll(articleMeta, 'aff')) {
+        const text = textContent(aff);
         if (text)
             result.push(text);
     }
     return result;
 }
-// ─── Journal Extraction ─────────────────────────────────────────────────────
-/**
- * Extracts journal metadata from JATS journal-meta.
- */
+// ─── Journal & Publication Date ─────────────────────────────────────────────
 function extractJournal(journalMeta, articleMeta) {
     if (!journalMeta)
         return;
-    const title = extractTextContent(journalMeta['journal-title-group']?.['journal-title']) ||
-        extractTextContent(journalMeta['journal-title']) ||
+    const titleGroup = findOne(journalMeta, 'journal-title-group');
+    const title = textContent(findOne(titleGroup, 'journal-title')) ||
+        textContent(findOne(journalMeta, 'journal-title')) ||
         undefined;
-    const issns = ensureArray(journalMeta.issn);
-    const issn = issns.length > 0 ? getText(issns[0]) || undefined : undefined;
-    const volume = articleMeta?.volume
-        ? extractTextContent(articleMeta.volume) || undefined
-        : undefined;
-    const issue = articleMeta?.issue ? extractTextContent(articleMeta.issue) || undefined : undefined;
-    const fpage = articleMeta?.fpage ? extractTextContent(articleMeta.fpage) : undefined;
-    const lpage = articleMeta?.lpage ? extractTextContent(articleMeta.lpage) : undefined;
+    const firstIssn = findAll(journalMeta, 'issn')[0];
+    const issn = firstIssn ? textContent(firstIssn) || undefined : undefined;
+    const volume = articleMeta ? textContent(findOne(articleMeta, 'volume')) || undefined : undefined;
+    const issue = articleMeta ? textContent(findOne(articleMeta, 'issue')) || undefined : undefined;
+    const fpage = articleMeta ? textContent(findOne(articleMeta, 'fpage')) : '';
+    const lpage = articleMeta ? textContent(findOne(articleMeta, 'lpage')) : '';
     const pages = fpage && lpage ? `${fpage}-${lpage}` : fpage || undefined;
     if (!title && !issn && !volume && !issue && !pages)
         return;
@@ -132,157 +84,147 @@ function extractJournal(journalMeta, articleMeta) {
         ...(pages && { pages }),
     };
 }
-// ─── Publication Date Extraction ────────────────────────────────────────────
-/**
- * Extracts publication date from JATS pub-date elements.
- * Prefers epub date, falls back to ppub, then any available.
- */
-function extractPubDate(pubDates) {
-    if (!pubDates)
+function extractPubDate(articleMeta) {
+    if (!articleMeta)
+        return;
+    const dates = findAll(articleMeta, 'pub-date');
+    if (dates.length === 0)
         return;
-    const dates = ensureArray(pubDates);
-    // Prefer epub, then ppub, then first available
-    const preferred = dates.find((d) => getAttribute(d, 'pub-type') === 'epub') ??
-        dates.find((d) => getAttribute(d, 'pub-type') === 'ppub') ??
-        dates.find((d) => getAttribute(d, 'date-type') === 'pub') ??
+    const preferred = dates.find((d) => attrOf(d, 'pub-type') === 'epub') ??
+        dates.find((d) => attrOf(d, 'pub-type') === 'ppub') ??
+        dates.find((d) => attrOf(d, 'date-type') === 'pub') ??
         dates[0];
     if (!preferred)
         return;
-    const year = extractTextContent(preferred.year) || undefined;
-    const month = extractTextContent(preferred.month) || undefined;
-    const day = extractTextContent(preferred.day) || undefined;
+    const year = textContent(findOne(preferred, 'year')) || undefined;
     if (!year)
         return;
+    const month = textContent(findOne(preferred, 'month')) || undefined;
+    const day = textContent(findOne(preferred, 'day')) || undefined;
     return {
         year,
         ...(month && { month }),
         ...(day && { day }),
     };
 }
-// ─── Abstract Extraction ────────────────────────────────────────────────────
-/**
- * Extracts abstract text from JATS abstract element.
- * Handles both simple and structured abstracts (with titled sections).
- */
-function extractAbstract(abstractNode) {
+// ─── Abstract & Keywords ────────────────────────────────────────────────────
+function extractAbstract(articleMeta) {
+    if (!articleMeta)
+        return;
+    const abstractNode = findOne(articleMeta, 'abstract');
     if (!abstractNode)
         return;
-    // Structured abstract with sections
-    if (typeof abstractNode === 'object' && !Array.isArray(abstractNode)) {
-        const obj = abstractNode;
-        // Check for sectioned abstract (<abstract><sec><title>...<p>...</sec></abstract>)
-        if (obj.sec) {
-            const sections = ensureArray(obj.sec);
-            const parts = [];
-            for (const sec of sections) {
-                const secObj = sec;
-                const title = extractTextContent(secObj.title);
-                const text = extractTextContent(secObj.p);
-                if (title && text) {
-                    parts.push(`${title}: ${text}`);
-                }
-                else if (text) {
-                    parts.push(text);
-                }
-            }
-            const result = parts.join('\n\n').trim();
-            return result || undefined;
-        }
-        // Simple abstract with just <p> elements
-        if (obj.p) {
-            const text = extractTextContent(obj.p);
-            return text || undefined;
+    const sections = findAll(abstractNode, 'sec');
+    if (sections.length > 0) {
+        const parts = [];
+        for (const sec of sections) {
+            const title = textContent(findOne(sec, 'title'));
+            const text = findAll(sec, 'p')
+                .map((p) => textContent(p))
+                .filter(Boolean)
+                .join(' ');
+            if (title && text)
+                parts.push(`${title}: ${text}`);
+            else if (text)
+                parts.push(text);
         }
+        return parts.join('\n\n').trim() || undefined;
+    }
+    const paragraphs = findAll(abstractNode, 'p');
+    if (paragraphs.length > 0) {
+        return (paragraphs
+            .map((p) => textContent(p))
+            .filter(Boolean)
+            .join(' ') || undefined);
     }
-    // Fallback: extract all text
-    const text = extractTextContent(abstractNode);
-    return text || undefined;
+    return textContent(abstractNode) || undefined;
 }
-// ─── Keywords Extraction ────────────────────────────────────────────────────
-/**
- * Extracts keywords from JATS kwd-group elements.
- */
-function extractKeywords(kwdGroups) {
-    if (!kwdGroups)
+function extractKeywords(articleMeta) {
+    if (!articleMeta)
         return [];
     const keywords = [];
-    for (const group of ensureArray(kwdGroups)) {
-        for (const kwd of ensureArray(group.kwd)) {
-            const text = extractTextContent(kwd);
+    for (const group of findAll(articleMeta, 'kwd-group')) {
+        for (const kwd of findAll(group, 'kwd')) {
+            const text = textContent(kwd);
             if (text)
                 keywords.push(text);
         }
     }
     return keywords;
 }
-// ─── Body Section Extraction ────────────────────────────────────────────────
+// ─── Body Sections ──────────────────────────────────────────────────────────
 /**
- * Recursively extracts body sections from JATS sec elements.
+ * Extract body sections from a `<body>` node, walking children in document order.
+ * Consecutive bare `<p>` siblings are collected into an untitled section so
+ * articles with mixed structure (direct paragraphs + trailing `<sec>`, common
+ * in manuscript-submitted PMC deposits) preserve their main text.
  */
 export function extractBodySections(body) {
     if (!body)
         return [];
-    // Some articles have paragraphs directly in body without section wrappers
-    if (!body.sec) {
-        if (body.p) {
-            const text = extractTextContent(body.p);
-            return text ? [{ text }] : [];
+    const sections = [];
+    let pendingParagraphs = [];
+    const flushPending = () => {
+        if (pendingParagraphs.length > 0) {
+            sections.push({ text: pendingParagraphs.join('\n\n') });
+            pendingParagraphs = [];
+        }
+    };
+    for (const child of childrenOf(body)) {
+        const tag = tagNameOf(child);
+        if (tag === 'p') {
+            const text = textContent(child);
+            if (text)
+                pendingParagraphs.push(text);
+        }
+        else if (tag === 'sec') {
+            flushPending();
+            const section = extractSection(child);
+            if (section)
+                sections.push(section);
         }
-        return [];
     }
-    return ensureArray(body.sec)
-        .map(extractSection)
-        .filter((s) => s !== null);
+    flushPending();
+    return sections;
 }
-/**
- * Extracts a single JATS section, recursing into subsections.
- */
 function extractSection(sec) {
-    const title = extractTextContent(sec.title) || undefined;
-    const label = extractTextContent(sec.label) || undefined;
-    // Collect text from paragraphs
-    const paragraphs = ensureArray(sec.p);
-    const textParts = [];
-    for (const p of paragraphs) {
-        const text = extractTextContent(p);
-        if (text)
-            textParts.push(text);
-    }
-    // Recurse into subsections
-    const subsections = sec.sec
-        ? ensureArray(sec.sec)
-            .map(extractSection)
-            .filter((s) => s !== null)
-        : undefined;
+    const title = textContent(findOne(sec, 'title')) || undefined;
+    const label = textContent(findOne(sec, 'label')) || undefined;
+    const paragraphs = findAll(sec, 'p');
+    const textParts = paragraphs.map((p) => textContent(p)).filter(Boolean);
+    const subsections = findAll(sec, 'sec')
+        .map(extractSection)
+        .filter((s) => s !== null);
     const text = textParts.join('\n\n');
-    // Skip empty sections with no subsections
-    if (!text && (!subsections || subsections.length === 0))
+    if (!text && subsections.length === 0)
         return null;
     return {
         ...(title && { title }),
         ...(label && { label }),
         text,
-        ...(subsections && subsections.length > 0 && { subsections }),
+        ...(subsections.length > 0 && { subsections }),
     };
 }
-// ─── Reference Extraction ───────────────────────────────────────────────────
-/**
- * Extracts references from JATS back matter ref-list.
- */
+// ─── References ─────────────────────────────────────────────────────────────
+/** Extract references from a `<back>` node. Prefers mixed-citation over element-citation. */
 export function extractReferences(back) {
-    if (!back?.['ref-list']?.ref)
+    if (!back)
+        return [];
+    const refList = findOne(back, 'ref-list');
+    if (!refList)
         return [];
-    const refs = ensureArray(back['ref-list'].ref);
     const results = [];
-    for (const ref of refs) {
-        // Try mixed-citation first, then element-citation
-        const citationNode = ref['mixed-citation'] ?? ref['element-citation'];
-        const citation = extractTextContent(citationNode);
+    for (const ref of findAll(refList, 'ref')) {
+        const citationNode = findOne(ref, 'mixed-citation') ?? findOne(ref, 'element-citation');
+        if (!citationNode)
+            continue;
+        const citation = textContent(citationNode);
         if (!citation)
             continue;
-        const label = ref.label ? extractTextContent(ref.label) || undefined : undefined;
+        const id = attrOf(ref, 'id');
+        const label = textContent(findOne(ref, 'label')) || undefined;
         results.push({
-            ...(ref['@_id'] && { id: ref['@_id'] }),
+            ...(id && { id }),
             ...(label && { label }),
             citation,
         });
@@ -291,31 +233,32 @@ export function extractReferences(back) {
 }
 // ─── Main Parser ────────────────────────────────────────────────────────────
 /**
- * Parses a JATS XML article (from PMC EFetch) into a structured ParsedPmcArticle.
- * @param xmlArticle - The parsed JATS article object from fast-xml-parser.
- * @returns A fully parsed PMC article with metadata, body sections, and optional references.
+ * Parse a single JATS `<article>` node (from PMC EFetch via the ordered parser)
+ * into a structured `ParsedPmcArticle`. The input node is the element wrapper
+ * itself — `{ article: [...], ':@': { '@_article-type': ... } }` — not the
+ * outer `<pmc-articleset>`.
  */
-export function parsePmcArticle(xmlArticle) {
-    const front = xmlArticle.front;
-    const articleMeta = front?.['article-meta'];
-    const journalMeta = front?.['journal-meta'];
-    const articleIds = articleMeta?.['article-id'];
-    const pmcId = extractArticleId(articleIds, 'pmcid') ?? extractArticleId(articleIds, 'pmc-uid') ?? '';
-    const pmid = extractArticleId(articleIds, 'pmid');
-    const doi = extractArticleId(articleIds, 'doi');
-    const title = articleMeta?.['title-group']
-        ? extractTextContent(articleMeta['title-group']['article-title']) || undefined
-        : undefined;
-    const authors = extractJatsAuthors(articleMeta?.['contrib-group']);
-    const affiliations = extractAffiliations(articleMeta?.aff);
+export function parsePmcArticle(articleNode) {
+    const front = findOne(articleNode, 'front');
+    const articleMeta = findOne(front, 'article-meta');
+    const journalMeta = findOne(front, 'journal-meta');
+    const body = findOne(articleNode, 'body');
+    const back = findOne(articleNode, 'back');
+    const pmcId = extractArticleId(articleMeta, 'pmcid') ?? extractArticleId(articleMeta, 'pmc-uid') ?? '';
+    const pmid = extractArticleId(articleMeta, 'pmid');
+    const doi = extractArticleId(articleMeta, 'doi');
+    const titleGroup = findOne(articleMeta, 'title-group');
+    const title = textContent(findOne(titleGroup, 'article-title')) || undefined;
+    const authors = collectAuthors(articleMeta);
+    const affiliations = extractAffiliations(articleMeta);
     const journal = extractJournal(journalMeta, articleMeta);
-    const publicationDate = extractPubDate(articleMeta?.['pub-date']);
-    const abstract = extractAbstract(articleMeta?.abstract);
-    const keywords = extractKeywords(articleMeta?.['kwd-group']);
-    const sections = extractBodySections(xmlArticle.body);
-    const references = extractReferences(xmlArticle.back);
-    // Normalize PMCID — ensure it has the PMC prefix (skip if empty)
+    const publicationDate = extractPubDate(articleMeta);
+    const abstract = extractAbstract(articleMeta);
+    const keywords = extractKeywords(articleMeta);
+    const sections = extractBodySections(body);
+    const references = extractReferences(back);
     const normalizedPmcId = !pmcId ? '' : pmcId.startsWith('PMC') ? pmcId : `PMC${pmcId}`;
+    const articleType = attrOf(articleNode, 'article-type');
     return {
         pmcId: normalizedPmcId,
         ...(pmid && { pmid }),
@@ -329,9 +272,19 @@ export function parsePmcArticle(xmlArticle) {
         ...(keywords.length > 0 && { keywords }),
         sections,
         ...(references.length > 0 && { references }),
-        ...(xmlArticle['@_article-type'] && { articleType: xmlArticle['@_article-type'] }),
+        ...(articleType && { articleType }),
         pmcUrl: `https://www.ncbi.nlm.nih.gov/pmc/articles/${normalizedPmcId}/`,
         ...(pmid && { pubmedUrl: `https://pubmed.ncbi.nlm.nih.gov/${pmid}/` }),
     };
 }
+/** Collect authors across every `<contrib-group>` under `<article-meta>`. */
+function collectAuthors(articleMeta) {
+    if (!articleMeta)
+        return [];
+    const result = [];
+    for (const group of findAll(articleMeta, 'contrib-group')) {
+        result.push(...extractJatsAuthors(group));
+    }
+    return result;
+}
 //# sourceMappingURL=pmc-article-parser.js.map

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

@@ -1 +1 @@
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package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts

@@ -0,0 +1,44 @@
+/**
+ * @fileoverview Helpers for fast-xml-parser output in `preserveOrder: true` mode.
+ * Each element node is `{ tagName: JatsNode[] }` with an optional `:@` carrying
+ * attributes; text nodes are `{ "#text": value }`. Preserving order is critical
+ * for JATS mixed content (e.g. `<p>text <italic>inline</italic> more text</p>`)
+ * — the default object shape collapses all text into a single string keyed by
+ * `#text`, dropping inline children's position. PMC full-text articles rely on
+ * this order for readable abstracts and body sections.
+ * @module src/services/ncbi/parsing/pmc-xml-helpers
+ */
+/**
+ * A node in the ordered XML tree.
+ * - Element: `{ tagName: JatsNode[] }`, optionally with `:@` carrying attributes
+ * - Text:    `{ "#text": string | number | boolean }`
+ */
+export type JatsNode = Record<string, unknown>;
+/**
+ * Ordered sibling list — every children array and the document root.
+ * Plain `JatsNode[]` (not readonly) so `Array.isArray` narrows inputs cleanly
+ * in `findOne` / `findAll`; callers should not mutate the list.
+ */
+export type JatsNodeList = JatsNode[];
+/** Tag name of an element (the single non-attribute key); undefined for text nodes. */
+export declare function tagNameOf(node: JatsNode): string | undefined;
+/** Ordered children of an element node. Empty for text nodes or missing tags. */
+export declare function childrenOf(node: JatsNode): JatsNodeList;
+/** Attribute value (caller omits the `@_` prefix). */
+export declare function attrOf(node: JatsNode, name: string): string | undefined;
+/** True for `{ "#text": ... }` nodes. */
+export declare function isTextNode(node: JatsNode): boolean;
+/** Stringified text value of a text node. */
+export declare function textOf(node: JatsNode): string;
+/**
+ * Extract all text from a node or sibling list in document order, collapsing
+ * runs of whitespace to a single space and trimming the result. Use this for
+ * mixed-content elements (`<p>`, `<title>`, `<abstract>`, …) where inline
+ * children must read back in the order they appear in the source.
+ */
+export declare function textContent(input: JatsNode | JatsNodeList | undefined): string;
+/** First direct child with the given tag name. */
+export declare function findOne(input: JatsNode | JatsNodeList | undefined, tagName: string): JatsNode | undefined;
+/** All direct children with the given tag name. */
+export declare function findAll(input: JatsNode | JatsNodeList | undefined, tagName: string): JatsNode[];
+//# sourceMappingURL=pmc-xml-helpers.d.ts.map

package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map

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