@cyanheads/pubmed-mcp-server 2.10.16 → 2.10.17

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

@@ -398,9 +398,35 @@ function renderBlock(node) {
 /**
  * The `<graphic>`/`<media>` pointer an asset hangs its file on, and the element
  * a deposit may hang the label and caption on instead of on the asset itself.
+ *
+ * A direct child wins, a `<graphic>` before a `<media>`. Without one, the
+ * pointer is read from the asset's `<alternatives>`, where publishers offer the
+ * same figure in several file formats — the fallback `<table-wrap>` and
+ * `<disp-formula>` already apply to their own `<alternatives>` children. (#142)
  */
 function assetPointer(node) {
-    return findOne(node, 'graphic') ?? findOne(node, 'media');
+    return (findOne(node, 'graphic') ??
+        findOne(node, 'media') ??
+        alternativePointer(findOne(node, 'alternatives')));
+}
+/** Pointer elements an asset's `<alternatives>` can offer its file through. */
+const ASSET_POINTER_TAGS = new Set(['graphic', 'media']);
+/**
+ * The `<graphic>`/`<media>` an `<alternatives>` offers for display: one whose
+ * `@specific-use` names the web (`web`, `web-version`, `web-only`), else the
+ * first in document order. JATS4R marks the renderings of one figure `web` and
+ * `print` exactly this way, and keying on that attribute needs no list of file
+ * formats to rank, which would have to track every publisher's spelling of
+ * them. Not {@link selectAlternative}: that picks the rendering whose *text*
+ * stands for the element, and a pointer carries a file reference, not text.
+ * (#142)
+ */
+function alternativePointer(alternatives) {
+    if (!alternatives)
+        return;
+    const pointers = childrenOf(alternatives).filter((child) => ASSET_POINTER_TAGS.has(tagNameOf(child) ?? ''));
+    return (pointers.find((pointer) => attrOf(pointer, 'specific-use')?.toLowerCase().includes('web')) ??
+        pointers[0]);
 }
 /**
  * An asset's display label: its own `<label>`, else one the deposit hung on the
@@ -431,12 +457,15 @@ function assetMarker(node, kind) {
  * `<title>` takes a line of its own above the items, and a `<list>` or
  * `<def-list>` nested inside a `<list-item>` — both in the JATS content model —
  * indents one level per depth. (#130)
+ *
+ * `withTitle: false` leaves the title out, for a list whose title has become
+ * the heading of the section it forms (see {@link extractBodySections}).
  */
-function renderList(list, depth) {
+function renderList(list, depth, withTitle = true) {
     const pad = NESTED_LIST_INDENT.repeat(depth);
     const listType = attrOf(list, 'list-type');
     const lines = [];
-    const title = textContent(findOne(list, 'title'));
+    const title = withTitle ? textContent(findOne(list, 'title')) : '';
     if (title)
         lines.push(`${pad}${title}`);
     let ordinal = 0;
@@ -465,11 +494,15 @@ function renderList(list, depth) {
     }
     return lines.join('\n');
 }
-/** Render a `<def-list>`: its title on a line of its own, then `- term — definition` per item. */
-function renderDefList(defList, depth) {
+/**
+ * Render a `<def-list>`: its title on a line of its own, then
+ * `- term — definition` per item. `withTitle: false` leaves the title out, as
+ * {@link renderList} does.
+ */
+function renderDefList(defList, depth, withTitle = true) {
     const pad = NESTED_LIST_INDENT.repeat(depth);
     const lines = [];
-    const title = textContent(findOne(defList, 'title'));
+    const title = withTitle ? textContent(findOne(defList, 'title')) : '';
     if (title)
         lines.push(`${pad}${title}`);
     for (const item of findAll(defList, 'def-item')) {
@@ -502,12 +535,24 @@ function renderDispQuote(quote) {
  * container rather than a captioned box — 13 of the 14 in a 68-record draw carry
  * `<sec>` children and nothing else — so rendering it as a caption plus
  * paragraphs would drop the nested headings entirely. (#130)
+ *
+ * The `<caption>`'s `<title>` and `<p>`s are statements of their own and render
+ * as separate blocks, never run together. (#169)
+ *
+ * `withTitle: false` leaves out the `<caption>`'s `<title>` — the box's title in
+ * the JATS content model — for a box whose title has become the heading of the
+ * section it forms (see {@link extractBodySections}).
  */
-function renderBoxedText(boxedText) {
+function renderBoxedText(boxedText, withTitle = true) {
     const blocks = [];
     for (const child of childrenOf(boxedText)) {
-        if (tagNameOf(child) === 'sec')
+        const tag = tagNameOf(child);
+        if (tag === 'sec')
             blocks.push(...flattenSec(child));
+        else if (tag === 'caption') {
+            const parts = childrenOf(child).filter((c) => withTitle || tagNameOf(c) !== 'title');
+            blocks.push(...flowBlocks(parts, STATEMENT_BLOCK_TAGS));
+        }
         else
             blocks.push(...flowBlocks([child]));
     }
@@ -583,6 +628,14 @@ function renderDispFormula(formula) {
  * reads as an article with no body at all. Legacy
  * `<preformat preformat-type="pmc-ocr-text">` deposits, which put the entire
  * article in one such element, are the case that matters. (#130)
+ *
+ * A body-level block that carries a title of its own — a `<def-list>` or
+ * `<list>` `<title>`, a `<boxed-text>` `<caption>` title — forms a section of
+ * its own under that title, and the title leaves the block's text. PMC13546078
+ * opens its `<body>` with its abbreviations `<def-list>` this way; reporting it
+ * as an untitled section left `content[]` with no heading to separate the list
+ * from the abstract above it. Untitled blocks on either side of it are not its
+ * content and stay in untitled sections of their own. (#148)
  */
 export function extractBodySections(body) {
     if (!body)
@@ -603,19 +656,93 @@ export function extractBodySections(body) {
                 sections.push(section);
             continue;
         }
+        const title = ownBlockTitle(child);
+        if (title) {
+            flushPending();
+            sections.push({ title, text: renderBlockWithoutTitle(child) });
+            continue;
+        }
         pendingBlocks.push(...flowBlocks([child]));
     }
     flushPending();
     return sections;
 }
+/**
+ * The title a block carries of its own, where the JATS content model puts one:
+ * a direct `<title>` on a `<def-list>` or `<list>`, the `<caption>` title on a
+ * `<boxed-text>`. Undefined for every other element. (#148)
+ */
+function ownBlockTitle(node) {
+    switch (tagNameOf(node)) {
+        case 'def-list':
+        case 'list':
+            return textContent(findOne(node, 'title')) || undefined;
+        case 'boxed-text':
+            return textContent(findOne(findOne(node, 'caption'), 'title')) || undefined;
+        default:
+            return;
+    }
+}
+/** A `<sec>`'s own metadata children, which carry no body content. */
+const SECTION_META_TAGS = new Set(['title', 'label']);
+/**
+ * The titled `<def-list>`, `<list>` or `<boxed-text>` an untitled `<sec>`
+ * carries as its only content — its `<label>` and an empty `<title>` aside —
+ * and that block's title. A `<sec>` holding nothing but its abbreviations list
+ * (PMC12696417) is that list; the list's title is the section's title the way
+ * a body-level block's is. Undefined for a `<sec>` with a title of its own or
+ * any other content. (#148, #169)
+ */
+function loneTitledBlock(sec) {
+    if (textContent(findOne(sec, 'title')))
+        return;
+    const content = childrenOf(sec).filter((child) => isTextNode(child)
+        ? textOf(child).trim() !== ''
+        : !SECTION_META_TAGS.has(tagNameOf(child) ?? ''));
+    const [node] = content;
+    if (content.length !== 1 || !node || isTextNode(node))
+        return;
+    const title = ownBlockTitle(node);
+    return title ? { node, title } : undefined;
+}
+/**
+ * The title a `<sec>` goes by in the output: its own `<title>`, else the one
+ * {@link loneTitledBlock} lifts. {@link extractSection} titles the section and
+ * {@link collectSectioned} names the tables and assets inside it from this one
+ * rule, so a `sections` filter keeps them together. (#169)
+ */
+function secTitle(sec) {
+    return textContent(findOne(sec, 'title')) || loneTitledBlock(sec)?.title;
+}
+/** A block whose {@link ownBlockTitle} became its section's title, rendered without it. */
+function renderBlockWithoutTitle(node) {
+    switch (tagNameOf(node)) {
+        case 'def-list':
+            return renderDefList(node, 0, false);
+        case 'list':
+            return renderList(node, 0, false);
+        case 'boxed-text':
+            return renderBoxedText(node, false);
+        default:
+            return renderBlock(node);
+    }
+}
 /**
  * Read one `<sec>`, walking every child in document order. The first `<title>`
  * and `<label>` are the section's own metadata, a `<sec>` is a subsection, and
  * everything else — `<p>` and block elements alike — contributes text at the
  * position it occupies. Reading `<p>` and `<sec>` alone is what dropped a
  * section's lists, figures, formulae and boxed text outright. (#130)
+ *
+ * An untitled `<sec>` whose only content is a titled block takes that block's
+ * title, and the block renders without it (see {@link loneTitledBlock}). (#169)
  */
 function extractSection(sec) {
+    const lone = loneTitledBlock(sec);
+    if (lone) {
+        const label = textContent(findOne(sec, 'label')) || undefined;
+        return { title: lone.title, ...(label && { label }), text: renderBlockWithoutTitle(lone.node) };
+    }
     let title;
     let label;
     const textParts = [];
@@ -681,15 +808,24 @@ export function extractPmcTables(root) {
 }
 /**
  * Walk a subtree in document order, collecting whatever `take` recognizes and
- * carrying the innermost enclosing `<sec>` title down to it. An untitled `<sec>`
- * keeps its parent's title rather than dropping the reader's only positional
- * cue, and an element inside no `<sec>` at all gets none. A recognized element
- * is not descended into — it parses its own subtree.
+ * carrying the title of the innermost enclosing section down to it. An untitled
+ * `<sec>` keeps its parent's title rather than dropping the reader's only
+ * positional cue, and an element inside no section at all gets none. A
+ * recognized element is not descended into — it parses its own subtree.
+ *
+ * A section here is whatever {@link extractBodySections} reports as one, under
+ * the title it reports: a `<sec>` by {@link secTitle}, and a titled block
+ * sitting directly in `<body>` by its own title — so a figure in a titled
+ * body-level box names the box, and a `sections` filter on the box keeps it.
+ * A `<sec>` inside a `<boxed-text>` is no section: the box flattens it into its
+ * text (see {@link renderBoxedText}), so what sits in it names the section the
+ * box belongs to. (#169)
  *
  * Shared by the table and asset walks so the section-title rule has one
  * definition and cannot drift between them.
  */
-function collectSectioned(node, sectionTitle, out, take) {
+function collectSectioned(node, sectionTitle, out, take, inBox = false) {
+    const inBody = tagNameOf(node) === 'body';
     for (const child of childrenOf(node)) {
         const tag = tagNameOf(child);
         if (!tag)
@@ -699,8 +835,14 @@ function collectSectioned(node, sectionTitle, out, take) {
             out.push(collected);
             continue;
         }
-        const nested = tag === 'sec' ? textContent(findOne(child, 'title')) || sectionTitle : sectionTitle;
-        collectSectioned(child, nested, out, take);
+        const own = inBox
+            ? undefined
+            : tag === 'sec'
+                ? secTitle(child)
+                : inBody
+                    ? ownBlockTitle(child)
+                    : undefined;
+        collectSectioned(child, own || sectionTitle, out, take, inBox || tag === 'boxed-text');
     }
 }
 function parseTableWrap(tableWrap, sectionTitle) {
@@ -865,7 +1007,8 @@ const ASSET_TAG_TYPES = {
 function parseAsset(node, assetType, sectionTitle) {
     const id = attrOf(node, 'id');
     // Both `fig` and `supplementary-material` carry the pointer on a child
-    // element: a `<graphic>` for images, a `<media>` for everything else.
+    // element — a `<graphic>` for images, a `<media>` for everything else — or on
+    // one of the renderings their `<alternatives>` offers.
     const pointer = assetPointer(node);
     const href = pointer ? attrOf(pointer, 'xlink:href') : undefined;
     // `label?, caption?` are in the JATS content model of `<media>` and

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

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package/dist/services/unpaywall/types.d.ts

@@ -22,20 +22,34 @@ export interface UnpaywallLocation {
     version?: 'submittedVersion' | 'acceptedVersion' | 'publishedVersion' | string | null;
 }
 /**
- * Subset of the Unpaywall `/v2/{doi}` response this server consumes.
+ * Subset of the Unpaywall `/v2/{doi}` DOI object this server consumes.
  * Upstream response has many more fields — we narrow to what's actually used.
+ * The bibliographic fields are nullable per the data format.
  */
 export interface UnpaywallResponse {
     best_oa_location?: UnpaywallLocation | null;
     doi?: string;
     is_oa?: boolean;
+    /** Journal or repository name the DOI is registered under (`medRxiv` for a medRxiv preprint). */
+    journal_name?: string | null;
     oa_locations?: UnpaywallLocation[];
     oa_status?: 'gold' | 'green' | 'hybrid' | 'bronze' | 'closed' | string;
+    /** Title of the work the DOI names. */
+    title?: string | null;
+    /** Publication year, an integer. */
+    year?: number | null;
 }
-/** Outcome of resolving a DOI to an OA copy. */
+/**
+ * Outcome of resolving a DOI to an OA copy. A `found` resolution also carries
+ * the DOI object's own title, journal name, and year — each present only when
+ * Unpaywall supplies a usable value.
+ */
 export type UnpaywallResolution = {
     kind: 'found';
     location: UnpaywallLocation;
+    journalName?: string;
+    title?: string;
+    year?: number;
 } | {
     kind: 'no-oa';
     reason: string;

package/dist/services/unpaywall/types.d.ts.map

@@ -1 +1 @@
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package/dist/services/unpaywall/unpaywall-service.d.ts

@@ -1,7 +1,8 @@
 /**
- * @fileoverview Unpaywall service. Resolves a DOI to an open-access location
- * and fetches the raw content (HTML or PDF) for downstream extraction. Enabled
- * only when `UNPAYWALL_EMAIL` is set — absence leaves the fallback disabled.
+ * @fileoverview Unpaywall service. Resolves a DOI to an open-access location —
+ * together with the title, journal name, and year the DOI object carries — and
+ * fetches the raw content (HTML or PDF) for downstream extraction. Enabled only
+ * when `UNPAYWALL_EMAIL` is set — absence leaves the fallback disabled.
  *
  * Philosophy: best-effort. Upstream 404s and non-OA DOIs return a `no-oa`
  * resolution; only genuine service failures (5xx, network, timeout) throw.

package/dist/services/unpaywall/unpaywall-service.d.ts.map

@@ -1 +1 @@
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package/dist/services/unpaywall/unpaywall-service.js

@@ -1,7 +1,8 @@
 /**
- * @fileoverview Unpaywall service. Resolves a DOI to an open-access location
- * and fetches the raw content (HTML or PDF) for downstream extraction. Enabled
- * only when `UNPAYWALL_EMAIL` is set — absence leaves the fallback disabled.
+ * @fileoverview Unpaywall service. Resolves a DOI to an open-access location —
+ * together with the title, journal name, and year the DOI object carries — and
+ * fetches the raw content (HTML or PDF) for downstream extraction. Enabled only
+ * when `UNPAYWALL_EMAIL` is set — absence leaves the fallback disabled.
  *
  * Philosophy: best-effort. Upstream 404s and non-OA DOIs return a `no-oa`
  * resolution; only genuine service failures (5xx, network, timeout) throw.
@@ -82,7 +83,13 @@ export class UnpaywallService {
                 version: location.version ?? null,
             },
         }));
-        return { kind: 'found', location };
+        return {
+            kind: 'found',
+            location,
+            ...(nonBlank(data.title) && { title: data.title }),
+            ...(nonBlank(data.journal_name) && { journalName: data.journal_name }),
+            ...(typeof data.year === 'number' && Number.isInteger(data.year) && { year: data.year }),
+        };
     }
     /**
      * Fetch the content at an Unpaywall location. Prefers `url_for_pdf` when
@@ -182,6 +189,10 @@ export class UnpaywallService {
         return { kind: 'html', fetchedUrl, body: new TextDecoder().decode(bytes) };
     }
 }
+/** True for a string carrying more than whitespace — Unpaywall sends `null` for a field it has no value for. */
+function nonBlank(value) {
+    return typeof value === 'string' && value.trim().length > 0;
+}
 /** `%PDF-`, the five bytes every PDF file opens with. */
 const PDF_MAGIC = Uint8Array.of(0x25, 0x50, 0x44, 0x46, 0x2d);
 /** Whether the received bytes are a PDF, independent of any declared type. */

package/dist/services/unpaywall/unpaywall-service.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.10.16",
+  "version": "2.10.17",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
   "type": "module",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.10.16",
+  "version": "2.10.17",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.16",
+      "version": "2.10.17",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.16",
+      "version": "2.10.17",
       "packageArguments": [
         {
           "type": "positional",