@cyanheads/pubmed-mcp-server 2.10.7 → 2.10.9

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

@@ -7,7 +7,42 @@
  * inline children and drops body sections for markup-heavy articles.
  * @module src/services/ncbi/parsing/pmc-article-parser
  */
-import { attrOf, childrenOf, findAll, findOne, tagNameOf, textContent, } from './pmc-xml-helpers.js';
+import { attrOf, childrenOf, findAll, findAllDescendants, findOne, isTextNode, rawTextContent, tagNameOf, textContent, textContentExcluding, textOf, } from './pmc-xml-helpers.js';
+/**
+ * Block content extracted into its own field and therefore excluded from the
+ * prose a paragraph contributes. A `<table-wrap>` nested inside a `<p>` would
+ * otherwise be flattened into the surrounding sentence, concatenating adjacent
+ * cell values into numbers that never existed. (#111)
+ */
+const LIFTED_BLOCK_TAGS = new Set(['table-wrap']);
+/** Prose of one `<p>`, with lifted block content left out. */
+function paragraphText(paragraph) {
+    return textContentExcluding(paragraph, LIFTED_BLOCK_TAGS);
+}
+/** True when a lifted block sits anywhere in this subtree. */
+function containsLiftedBlock(node) {
+    return childrenOf(node).some((child) => LIFTED_BLOCK_TAGS.has(tagNameOf(child) ?? '') || containsLiftedBlock(child));
+}
+/**
+ * True when a `<sec>` carried block content that was extracted into its own
+ * field — a `<table-wrap>` sitting beside its paragraphs, or nested inside one.
+ *
+ * This is what separates a section emptied by the lift from one that never had
+ * readable prose. The first is a real heading a reader needs in order to place
+ * the table that names it; the second is a structural wrapper — a `<sec>` around
+ * a `<ref-list>`, say — which would arrive as a stray empty "References" entry
+ * if every empty section survived. Only this section's own children are
+ * considered: a `<table-wrap>` deeper down belongs to the nested `<sec>` that
+ * holds it, and that section survives on its own account. (#111, #116)
+ */
+function hasLiftedBlockContent(sec) {
+    return childrenOf(sec).some((child) => {
+        const tag = tagNameOf(child) ?? '';
+        if (LIFTED_BLOCK_TAGS.has(tag))
+            return true;
+        return tag === 'p' && containsLiftedBlock(child);
+    });
+}
 // ─── Article IDs ────────────────────────────────────────────────────────────
 function extractArticleId(articleMeta, pubIdType) {
     if (!articleMeta)
@@ -173,7 +208,7 @@ export function extractBodySections(body) {
     for (const child of childrenOf(body)) {
         const tag = tagNameOf(child);
         if (tag === 'p') {
-            const text = textContent(child);
+            const text = paragraphText(child);
             if (text)
                 pendingParagraphs.push(text);
         }
@@ -190,13 +225,16 @@ export function extractBodySections(body) {
 function extractSection(sec) {
     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 textParts = findAll(sec, 'p').map(paragraphText).filter(Boolean);
     const subsections = findAll(sec, 'sec')
         .map(extractSection)
         .filter((s) => s !== null);
     const text = textParts.join('\n\n');
-    if (!text && subsections.length === 0)
+    // A section left empty *because* its block content was lifted into `tables[]`
+    // survives as a heading-only entry: the heading is what places the table for a
+    // reader, and dropping it also erased the section from a `sections` filter's
+    // reach. A section that never carried prose still drops. (#111)
+    if (!text && subsections.length === 0 && !hasLiftedBlockContent(sec))
         return null;
     return {
         ...(title && { title }),
@@ -205,6 +243,179 @@ function extractSection(sec) {
         ...(subsections.length > 0 && { subsections }),
     };
 }
+// ─── Tables ─────────────────────────────────────────────────────────────────
+/**
+ * Extract every `<table-wrap>` under `root` in document order — pass the
+ * `<article>` node.
+ *
+ * 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.
+ *
+ * Only XHTML `<tr>`/`<td>`/`<th>` bodies are read. **Decision, not an
+ * oversight:** across a 283-table survey of open-access records, 276 were XHTML,
+ * 7 were graphic-only deposits and 0 used the CALS `<tgroup>` model. Graphic-only
+ * and CALS bodies therefore take the unextractable path — returned with their
+ * label and caption and a reason — rather than adding a second table model no
+ * observed record needs. Revisit only if CALS shows up in the wild. (#111)
+ */
+export function extractPmcTables(root) {
+    if (!root)
+        return [];
+    const tables = [];
+    collectTables(root, undefined, tables);
+    return tables;
+}
+function collectTables(node, sectionTitle, out) {
+    for (const child of childrenOf(node)) {
+        const tag = tagNameOf(child);
+        if (!tag)
+            continue;
+        if (tag === 'table-wrap') {
+            out.push(parseTableWrap(child, sectionTitle));
+            continue;
+        }
+        // An untitled <sec> keeps its parent's title rather than dropping the
+        // reader's only positional cue.
+        const nested = tag === 'sec' ? textContent(findOne(child, 'title')) || sectionTitle : sectionTitle;
+        collectTables(child, nested, out);
+    }
+}
+function parseTableWrap(tableWrap, sectionTitle) {
+    const id = attrOf(tableWrap, 'id');
+    const label = textContent(findOne(tableWrap, 'label')) || undefined;
+    const caption = textContent(findOne(tableWrap, 'caption')) || undefined;
+    const footnotes = textContent(findOne(tableWrap, 'table-wrap-foot')) || undefined;
+    // Some deposits offer both renderings inside <alternatives>; prefer the markup.
+    const table = findOne(tableWrap, 'table') ?? findOne(findOne(tableWrap, 'alternatives'), 'table');
+    const { rows, headerRowCount } = table
+        ? extractTableRows(table)
+        : { rows: [], headerRowCount: 0 };
+    return {
+        ...(id && { id }),
+        ...(label && { label }),
+        ...(caption && { caption }),
+        ...(sectionTitle && { sectionTitle }),
+        headerRowCount,
+        rows,
+        ...(footnotes && { footnotes }),
+        ...(rows.length === 0 && {
+            unextractableReason: classifyUnextractable(tableWrap, table),
+        }),
+    };
+}
+function classifyUnextractable(tableWrap, table) {
+    if (findOne(tableWrap, 'tgroup') || findOne(table, 'tgroup'))
+        return 'cals-tgroup';
+    if (findOne(tableWrap, 'graphic') || findOne(findOne(tableWrap, 'alternatives'), 'graphic')) {
+        return 'graphic-only';
+    }
+    return 'no-rows';
+}
+/**
+ * Widest grid a single table row may occupy, and the ceiling every declared
+ * span is clamped to. Real deposits are far narrower — the widest row observed
+ * across a live sample was 15 columns — so this bounds a malformed or hostile
+ * span rather than limiting any genuine table: `colspan="99999999"` costs a
+ * bounded row instead of an unbounded allocation, and a `rowspan` that large
+ * carries a bounded number of rows down. How many rows a table has is set by its
+ * source `<tr>` elements and needs no cap of its own. (#111)
+ */
+export const MAX_TABLE_COLUMNS = 512;
+/** A `colspan`/`rowspan` value, clamped to a sane grid. Anything unparseable is 1. */
+function spanOf(cell, name) {
+    const declared = Number.parseInt(attrOf(cell, name) ?? '', 10);
+    if (!Number.isFinite(declared) || declared < 1)
+        return 1;
+    return Math.min(declared, MAX_TABLE_COLUMNS);
+}
+/**
+ * Read an XHTML `<table>` into rows of cell text, expanding `colspan` and
+ * `rowspan` so every entry in a row is one grid column.
+ *
+ * A cell covering N columns occupies N entries and one covering M rows occupies
+ * its column in the M rows below it, repeating its text across the cells it
+ * genuinely covers. Repeating is the honest flattening: the value belongs to
+ * each of those positions, and a reader scanning a column finds it there. The
+ * alternative — keeping the source cell count — leaves the column a value
+ * belongs to unrecoverable downstream, so a renderer padding rows from the left
+ * puts values under the wrong headers. (#111)
+ *
+ * Header rows are those in `<thead>` plus any leading row made entirely of
+ * `<th>` in a table that declares no `<thead>`.
+ */
+function extractTableRows(table) {
+    const parsed = [];
+    /** Live `rowspan` obligations, indexed by grid column. */
+    const carried = [];
+    /** Consume the carried cells sitting at and after `col`, contiguously. */
+    const drainCarried = (row, col) => {
+        let at = col;
+        while (at < MAX_TABLE_COLUMNS) {
+            const carry = carried[at];
+            if (!carry)
+                return at;
+            row[at] = carry.value;
+            carry.remaining -= 1;
+            if (carry.remaining <= 0)
+                carried[at] = undefined;
+            at += 1;
+        }
+        return at;
+    };
+    const pushRow = (tr, inHead) => {
+        const row = [];
+        let col = 0;
+        let sourceCells = 0;
+        let allHeaderCells = true;
+        for (const cell of childrenOf(tr)) {
+            const tag = tagNameOf(cell);
+            if (tag !== 'td' && tag !== 'th')
+                continue;
+            if (tag === 'td')
+                allHeaderCells = false;
+            sourceCells += 1;
+            col = drainCarried(row, col);
+            const value = textContent(cell);
+            const rowspan = spanOf(cell, 'rowspan');
+            const width = Math.min(spanOf(cell, 'colspan'), MAX_TABLE_COLUMNS - col);
+            for (let i = 0; i < width; i++) {
+                row[col] = value;
+                if (rowspan > 1)
+                    carried[col] = { remaining: rowspan - 1, value };
+                col += 1;
+            }
+        }
+        // Carried cells past the last source cell still hold their columns. Walk out
+        // to the rightmost live obligation so they land where they belong; the gaps
+        // in between are columns this row genuinely left empty.
+        const rightmost = carried.reduce((last, carry, i) => (carry ? i : last), -1);
+        while (col <= rightmost)
+            col = carried[col] ? drainCarried(row, col) : col + 1;
+        if (sourceCells === 0)
+            return;
+        for (let i = 0; i < row.length; i++)
+            row[i] ??= '';
+        parsed.push({ cells: row, header: inHead || allHeaderCells });
+    };
+    for (const child of childrenOf(table)) {
+        const tag = tagNameOf(child);
+        if (tag === 'tr')
+            pushRow(child, false);
+        else if (tag === 'thead' || tag === 'tbody' || tag === 'tfoot') {
+            for (const tr of findAll(child, 'tr'))
+                pushRow(tr, tag === 'thead');
+        }
+    }
+    let headerRowCount = 0;
+    while (parsed[headerRowCount]?.header)
+        headerRowCount++;
+    return { headerRowCount, rows: parsed.map((row) => row.cells) };
+}
 // ─── References ─────────────────────────────────────────────────────────────
 /**
  * `pub-id-type` → human label, so the trailing identifiers in a rendered
@@ -264,46 +475,173 @@ function renderElementCitation(node) {
     return parts.join(' ');
 }
 /**
- * Extract references from a `<back>` node. Prefers `<mixed-citation>` over
- * `<element-citation>`, descending into `<citation-alternatives>` when a ref
- * carries both forms there rather than as direct children of `<ref>`. Mixed
- * citations are read verbatim; structured element citations are rendered
- * field-by-field with separators (see `renderElementCitation`).
+ * Author-name wrappers a `<mixed-citation>` can carry as a direct child. Their
+ * parts routinely sit adjacent with zero characters between them, so the
+ * sibling-element spacing rule has to reach inside them rather than stopping at
+ * the wrapper. Scoped to these three deliberately: recursing into arbitrary
+ * elements would change how inline markup inside `<article-title>` and friends
+ * renders. (#124)
  */
-export function extractReferences(back) {
-    if (!back)
-        return [];
-    const refList = findOne(back, 'ref-list');
-    if (!refList)
+const NAME_WRAPPER_TAGS = new Set(['name', 'string-name', 'person-group']);
+/**
+ * Serialize a `<name>` / `<string-name>` / `<person-group>` subtree, applying
+ * the same rule `renderMixedCitation` applies to its own children: a single
+ * space between two adjacent elements that carry nothing between them, and
+ * source text emitted verbatim. `<person-group>` separates its names with real
+ * `, ` text nodes and `<string-name>` usually separates surname from given
+ * names with a newline, so a fixed separator would double punctuation the
+ * source already has — spacing only the zero-gap transitions leaves those
+ * records byte-identical. Returns raw text; the caller collapses whitespace
+ * once over the finished citation.
+ */
+function renderNameWrapper(node) {
+    let rendered = '';
+    let prevWasElement = false;
+    for (const child of childrenOf(node)) {
+        if (isTextNode(child)) {
+            const raw = textOf(child);
+            if (raw) {
+                rendered += raw;
+                prevWasElement = false;
+            }
+            continue;
+        }
+        const tag = tagNameOf(child) ?? '';
+        const part = NAME_WRAPPER_TAGS.has(tag) ? renderNameWrapper(child) : rawTextContent(child);
+        if (!part)
+            continue;
+        if (prevWasElement)
+            rendered += ' ';
+        rendered += part;
+        prevWasElement = true;
+    }
+    return rendered;
+}
+/**
+ * True when the citation text emitted so far already ends with a literal prefix
+ * naming this `pub-id-type` (`doi:`, `PMID `, `pmcid.`), so prepending the label
+ * would read `doi:DOI 10.1111/…`. (#115)
+ */
+function hasLiteralIdPrefix(rendered, pubIdType) {
+    const tail = rendered.trimEnd().replace(/[:.]$/, '').trimEnd();
+    return tail.toLowerCase().endsWith(pubIdType.toLowerCase());
+}
+/**
+ * Render a `<mixed-citation>` as a readable string.
+ *
+ * Mixed citations carry their punctuation in the text nodes between elements,
+ * so a flat `textContent()` reads correctly almost everywhere. Three adjacencies
+ * defeat it, all with zero characters between the elements: consecutive typed
+ * `<pub-id>`s fuse into one unreadable token (#115), an inline title runs
+ * straight into the volume that follows it (#123), and a `<surname>` glues onto
+ * the `<given-names>` beside it inside an author-name wrapper (#124). Walk the
+ * direct children so those cases can be repaired without touching `textContent`,
+ * which abstracts, titles, and body paragraphs share and where zero-gap
+ * adjacency is often intentional.
+ *
+ * Typed `<pub-id>`s are labeled (unless literal prefix text already names the
+ * type), and a single space separates two adjacent elements that carry nothing
+ * between them. A label is text this renderer inserts rather than source
+ * content, so it is separated from whatever precedes it as well — publisher
+ * styles routinely close the prose on punctuation (`… (2020).`, `…021]`) and a
+ * label butted against that reads as one token. Source transitions that already
+ * carry punctuation or whitespace are emitted unchanged; the trailing whitespace
+ * collapse keeps a whitespace-only gap at one space.
+ */
+function renderMixedCitation(node) {
+    let rendered = '';
+    let prevWasElement = false;
+    for (const child of childrenOf(node)) {
+        if (isTextNode(child)) {
+            const raw = textOf(child);
+            if (raw) {
+                rendered += raw;
+                prevWasElement = false;
+            }
+            continue;
+        }
+        const tag = tagNameOf(child) ?? '';
+        let part;
+        let labeled = false;
+        if (tag === 'pub-id') {
+            const value = textContent(child);
+            if (!value)
+                continue;
+            const type = attrOf(child, 'pub-id-type') ?? '';
+            const label = PUB_ID_LABELS[type];
+            if (label && !hasLiteralIdPrefix(rendered, type)) {
+                labeled = true;
+                part = `${label} ${value}`;
+            }
+            else {
+                part = value;
+            }
+        }
+        else if (NAME_WRAPPER_TAGS.has(tag)) {
+            part = renderNameWrapper(child);
+        }
+        else {
+            part = rawTextContent(child);
+        }
+        if (prevWasElement || labeled)
+            rendered += ' ';
+        rendered += part;
+        prevWasElement = true;
+    }
+    return rendered.replace(/\s+/g, ' ').trim();
+}
+/**
+ * Extract references from anywhere under `root` — pass the `<article>` node to
+ * cover a whole document, or a `<back>` node to scope the search to it.
+ *
+ * `<ref-list>` placement is not uniform: roughly 60% of Europe PMC deposits nest
+ * it under `body/sec/sec` and the rest put it directly under `<back>`, so a
+ * search scoped to a direct `<back>` child misses the majority. Every
+ * `<ref-list>` descendant is collected in document order instead, and a `<ref>`
+ * id already seen is skipped so a document exposing the same list under both
+ * containers still yields each reference once. (#116)
+ *
+ * Prefers `<mixed-citation>` over `<element-citation>`, descending into
+ * `<citation-alternatives>` when a ref carries both forms there rather than as
+ * direct children of `<ref>`. Both forms are rendered child-by-child so adjacent
+ * elements stay separable (see `renderMixedCitation` and
+ * `renderElementCitation`).
+ */
+export function extractReferences(root) {
+    if (!root)
         return [];
     const results = [];
-    for (const ref of findAll(refList, 'ref')) {
-        // JATS wraps the two citation forms in <citation-alternatives> (the NLM
-        // construct carrying both a structured <element-citation> and a readable
-        // <mixed-citation>). findOne matches direct children only, so resolve that
-        // container first; refs with a direct citation node fall through to `ref`.
-        const container = findOne(ref, 'citation-alternatives') ?? ref;
-        const mixedCitation = findOne(container, 'mixed-citation');
-        const elementCitation = findOne(container, 'element-citation');
-        // <mixed-citation> carries punctuation in the text nodes between its
-        // elements, so textContent() reads correctly. <element-citation> children
-        // have no separators — render the structured fields explicitly. (#69)
-        let citation = '';
-        if (mixedCitation) {
-            citation = textContent(mixedCitation);
-        }
-        else if (elementCitation) {
-            citation = renderElementCitation(elementCitation);
+    const seenIds = new Set();
+    for (const refList of findAllDescendants(root, 'ref-list')) {
+        for (const ref of findAll(refList, 'ref')) {
+            const id = attrOf(ref, 'id');
+            if (id && seenIds.has(id))
+                continue;
+            // JATS wraps the two citation forms in <citation-alternatives> (the NLM
+            // construct carrying both a structured <element-citation> and a readable
+            // <mixed-citation>). findOne matches direct children only, so resolve that
+            // container first; refs with a direct citation node fall through to `ref`.
+            const container = findOne(ref, 'citation-alternatives') ?? ref;
+            const mixedCitation = findOne(container, 'mixed-citation');
+            const elementCitation = findOne(container, 'element-citation');
+            let citation = '';
+            if (mixedCitation) {
+                citation = renderMixedCitation(mixedCitation);
+            }
+            else if (elementCitation) {
+                citation = renderElementCitation(elementCitation);
+            }
+            if (!citation)
+                continue;
+            if (id)
+                seenIds.add(id);
+            const label = textContent(findOne(ref, 'label')) || undefined;
+            results.push({
+                ...(id && { id }),
+                ...(label && { label }),
+                citation,
+            });
         }
-        if (!citation)
-            continue;
-        const id = attrOf(ref, 'id');
-        const label = textContent(findOne(ref, 'label')) || undefined;
-        results.push({
-            ...(id && { id }),
-            ...(label && { label }),
-            citation,
-        });
     }
     return results;
 }
@@ -319,7 +657,6 @@ export function parsePmcArticle(articleNode) {
     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');
@@ -332,7 +669,8 @@ export function parsePmcArticle(articleNode) {
     const abstract = extractAbstract(articleMeta);
     const keywords = extractKeywords(articleMeta);
     const sections = extractBodySections(body);
-    const references = extractReferences(back);
+    const references = extractReferences(articleNode);
+    const tables = extractPmcTables(articleNode);
     const normalizedPmcId = !pmcId ? '' : pmcId.startsWith('PMC') ? pmcId : `PMC${pmcId}`;
     const articleType = attrOf(articleNode, 'article-type');
     return {
@@ -348,6 +686,7 @@ export function parsePmcArticle(articleNode) {
         ...(keywords.length > 0 && { keywords }),
         sections,
         ...(references.length > 0 && { references }),
+        ...(tables.length > 0 && { tables }),
         ...(articleType && { articleType }),
         pmcUrl: `https://www.ncbi.nlm.nih.gov/pmc/articles/${normalizedPmcId}/`,
         ...(pmid && { pubmedUrl: `https://pubmed.ncbi.nlm.nih.gov/${pmid}/` }),

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

@@ -30,6 +30,14 @@ export declare function attrOf(node: JatsNode, name: string): string | undefined
 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 with the
+ * source spacing intact — no whitespace collapsing, no trimming. Use it when
+ * the caller assembles several fragments itself and needs to collapse once over
+ * the joined result; {@link textContent} is the normalizing form for everything
+ * else.
+ */
+export declare function rawTextContent(input: JatsNode | JatsNodeList | undefined): 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
@@ -37,8 +45,26 @@ export declare function textOf(node: JatsNode): string;
  * children must read back in the order they appear in the source.
  */
 export declare function textContent(input: JatsNode | JatsNodeList | undefined): string;
+/**
+ * {@link textContent}, with the subtree of any element named in `excludedTags`
+ * left out. Block content a publisher nests inside a `<p>` — a `<table-wrap>` in
+ * particular — would otherwise be flattened into the paragraph, running every
+ * cell together into values that never existed. Such content is extracted
+ * separately and must not appear in the prose twice.
+ */
+export declare function textContentExcluding(input: JatsNode | JatsNodeList | undefined, excludedTags: ReadonlySet<string>): 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[];
+/**
+ * Every descendant element with the given tag name, in document order.
+ * {@link findAll} matches direct children only, which is right for reading a
+ * known JATS shape; this is for containers publishers place at varying depths
+ * (a `<ref-list>` under `<back>` in one deposit and under `body/sec/sec` in the
+ * next). The walk keeps descending through a match, so a container nested
+ * inside another of the same tag is reported too. Each node is visited once, so
+ * the result never repeats a node.
+ */
+export declare function findAllDescendants(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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