npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.16 → 2.10.18 - Mend

@cyanheads/pubmed-mcp-server 2.10.16 → 2.10.18

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 (47) hide show

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/openalex/openalex-service.d.ts CHANGED Viewed

@@ -12,6 +12,10 @@
  * never minted — and counted, so callers can disclose the shortfall instead of
  * serving an unexplained empty window.
  *
+ * Transient failures retry with capped exponential backoff. Once retries run
+ * out, only a `ServiceUnavailable` is reported as `openalex_unreachable`; a
+ * `Timeout` or `RateLimited` keeps its own code and any upstream `retryAfter`.
+ *
  * Uses the NCBI_ADMIN_EMAIL config (adminEmail) as the OpenAlex polite-pool
  * `mailto=` parameter when set; omits it when unset.
  *
@@ -64,7 +68,13 @@ export declare class OpenAlexService {
      * the walk never reached is flagged rather than served as a silent empty.
      */
     private finish;
-    /** Retry wrapper for transient errors, mirroring the EPMC service pattern. */
+    /**
+     * Retry wrapper for transient errors. On exhaustion the last error keeps its
+     * code and an upstream `retryAfter`, so a 429 still tells the caller how long to
+     * wait. Only a `ServiceUnavailable` gains `openalex_unreachable` and its hint — the
+     * one code that reason is declared for; a `Timeout` or `RateLimited` keeps its
+     * code with no reason, as the NCBI and Europe PMC services report them.
+     */
     private withRetry;
 }
 /** Initialize the OpenAlex service. Call from `setup()` in createApp. */

package/dist/services/openalex/openalex-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;GAsBG;AAOH,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAIL,KAAK,qBAAqB,EAE3B,MAAM,YAAY,CAAC;AA4EpB,gFAAgF;AAChF,qBAAa,eAAe;IAExB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAF7B,YACmB,MAAM,EAAE,iBAAiB,EACzB,UAAU,EAAE,MAAM,EACjC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW3F;IAED;;;;;;;;OAQG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA4B3F;IAED;;;OAGG;IACG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW9F;IAED,8EAA8E;IAC9E,OAAO,CAAC,SAAS;IAQjB;;;;;;;;;OASG;YACW,iBAAiB;IAiC/B;;;;OAIG;IACH,OAAO,CAAC,MAAM;IAcd;;;;;;OAMG;YACW,SAAS;CAkDxB;AAMD,yEAAyE;AACzE,wBAAgB,mBAAmB,IAAI,IAAI,CAmB1C;AAED,uEAAuE;AACvE,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED,kFAAkF;AAClF,wBAAgB,0BAA0B,IAAI,eAAe,GAAG,SAAS,CAExE"}

package/dist/services/openalex/openalex-service.js CHANGED Viewed

@@ -12,12 +12,16 @@
  * never minted — and counted, so callers can disclose the shortfall instead of
  * serving an unexplained empty window.
  *
+ * Transient failures retry with capped exponential backoff. Once retries run
+ * out, only a `ServiceUnavailable` is reported as `openalex_unreachable`; a
+ * `Timeout` or `RateLimited` keeps its own code and any upstream `retryAfter`.
+ *
  * Uses the NCBI_ADMIN_EMAIL config (adminEmail) as the OpenAlex polite-pool
  * `mailto=` parameter when set; omits it when unset.
  *
  * @module src/services/openalex/openalex-service
  */
-import { internalError, McpError } from '@cyanheads/mcp-ts-core/errors';
+import { internalError, JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
 import { defaultIsTransient, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../config/server-config.js';
 import { recoveryFor } from '../error-contracts.js';
@@ -198,7 +202,13 @@ export class OpenAlexService {
             reachCapped: !exhausted && collector.pmids.length < n,
         };
     }
-    /** Retry wrapper for transient errors, mirroring the EPMC service pattern. */
+    /**
+     * Retry wrapper for transient errors. On exhaustion the last error keeps its
+     * code and an upstream `retryAfter`, so a 429 still tells the caller how long to
+     * wait. Only a `ServiceUnavailable` gains `openalex_unreachable` and its hint — the
+     * one code that reason is declared for; a `Timeout` or `RateLimited` keeps its
+     * code with no reason, as the NCBI and Europe PMC services report them.
+     */
     async withRetry(execute, label, signal) {
         for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
             if (signal?.aborted)
@@ -225,19 +235,18 @@ export class OpenAlexService {
                     continue;
                 }
                 const attempts = this.maxRetries + 1;
-                const msg = error instanceof Error ? error.message : String(error);
-                throw new McpError(error.code, `${msg} (failed after ${attempts} attempts)`, {
-                    reason: 'openalex_unreachable',
+                throw new McpError(error.code, `${error.message} (failed after ${attempts} attempts)`, {
+                    ...(error.code === JsonRpcErrorCode.ServiceUnavailable && {
+                        reason: 'openalex_unreachable',
+                        ...recoveryFor('openalex_unreachable'),
+                    }),
                     label,
                     attempts,
-                    ...recoveryFor('openalex_unreachable'),
+                    ...(error.data?.retryAfter !== undefined && { retryAfter: error.data.retryAfter }),
                 }, { cause: error });
             }
         }
-        throw internalError('OpenAlex request failed after all retries.', {
-            reason: 'openalex_unreachable',
-            ...recoveryFor('openalex_unreachable'),
-        });
+        throw internalError('OpenAlex request failed after all retries.', { label });
     }
 }
 // ─── Init / Accessor ────────────────────────────────────────────────────────

package/dist/services/openalex/openalex-service.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/services/unpaywall/types.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

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package/dist/services/unpaywall/unpaywall-service.d.ts CHANGED Viewed

@@ -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.

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