npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.3.8 → 2.3.10 - Mend

@cyanheads/pubmed-mcp-server 2.3.8 → 2.3.10

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Files changed (31) hide show

package/dist/services/ncbi/parsing/pmc-xml-helpers.js ADDED Viewed

@@ -0,0 +1,86 @@
+/**
+ * @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
+ */
+const ATTR_KEY = ':@';
+const TEXT_KEY = '#text';
+/** Tag name of an element (the single non-attribute key); undefined for text nodes. */
+export function tagNameOf(node) {
+    for (const key in node) {
+        if (key !== ATTR_KEY && key !== TEXT_KEY)
+            return key;
+    }
+    return;
+}
+/** Ordered children of an element node. Empty for text nodes or missing tags. */
+export function childrenOf(node) {
+    const tag = tagNameOf(node);
+    if (!tag)
+        return [];
+    const value = node[tag];
+    return Array.isArray(value) ? value : [];
+}
+/** Attribute value (caller omits the `@_` prefix). */
+export function attrOf(node, name) {
+    const attrs = node[ATTR_KEY];
+    const val = attrs?.[`@_${name}`];
+    return val == null ? undefined : String(val);
+}
+/** True for `{ "#text": ... }` nodes. */
+export function isTextNode(node) {
+    return TEXT_KEY in node;
+}
+/** Stringified text value of a text node. */
+export function textOf(node) {
+    const v = node[TEXT_KEY];
+    return v == null ? '' : String(v);
+}
+/**
+ * Concatenate text content in document order without normalizing whitespace.
+ * Internal helper so recursion preserves the original spacing between siblings.
+ */
+function concatText(input) {
+    const nodes = Array.isArray(input) ? input : [input];
+    const parts = [];
+    for (const node of nodes) {
+        if (isTextNode(node)) {
+            parts.push(textOf(node));
+        }
+        else {
+            parts.push(concatText(childrenOf(node)));
+        }
+    }
+    return parts.join('');
+}
+/**
+ * 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 function textContent(input) {
+    if (!input)
+        return '';
+    return concatText(input).replace(/\s+/g, ' ').trim();
+}
+/** First direct child with the given tag name. */
+export function findOne(input, tagName) {
+    if (!input)
+        return;
+    const children = Array.isArray(input) ? input : childrenOf(input);
+    return children.find((c) => tagNameOf(c) === tagName);
+}
+/** All direct children with the given tag name. */
+export function findAll(input, tagName) {
+    if (!input)
+        return [];
+    const children = Array.isArray(input) ? input : childrenOf(input);
+    return children.filter((c) => tagNameOf(c) === tagName);
+}
+//# sourceMappingURL=pmc-xml-helpers.js.map

package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"pmc-xml-helpers.js","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-xml-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAgBH,MAAM,QAAQ,GAAG,IAAI,CAAC;AACtB,MAAM,QAAQ,GAAG,OAAO,CAAC;AAEzB,uFAAuF;AACvF,MAAM,UAAU,SAAS,CAAC,IAAc;IACtC,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,IAAI,GAAG,KAAK,QAAQ,IAAI,GAAG,KAAK,QAAQ;YAAE,OAAO,GAAG,CAAC;IACvD,CAAC;IACD,OAAO;AACT,CAAC;AAED,iFAAiF;AACjF,MAAM,UAAU,UAAU,CAAC,IAAc;IACvC,MAAM,GAAG,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC;IAC5B,IAAI,CAAC,GAAG;QAAE,OAAO,EAAE,CAAC;IACpB,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC;IACxB,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAE,KAAsB,CAAC,CAAC,CAAC,EAAE,CAAC;AAC7D,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,MAAM,CAAC,IAAc,EAAE,IAAY;IACjD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAwC,CAAC;IACpE,MAAM,GAAG,GAAG,KAAK,EAAE,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC;IACjC,OAAO,GAAG,IAAI,IAAI,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;AAC/C,CAAC;AAED,yCAAyC;AACzC,MAAM,UAAU,UAAU,CAAC,IAAc;IACvC,OAAO,QAAQ,IAAI,IAAI,CAAC;AAC1B,CAAC;AAED,6CAA6C;AAC7C,MAAM,UAAU,MAAM,CAAC,IAAc;IACnC,MAAM,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC;IACzB,OAAO,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;AACpC,CAAC;AAED;;;GAGG;AACH,SAAS,UAAU,CAAC,KAA8B;IAChD,MAAM,KAAK,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;IACrD,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC;YACrB,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC;QAC3B,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAC3C,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;AACxB,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,WAAW,CAAC,KAA0C;IACpE,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,OAAO,UAAU,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;AACvD,CAAC;AAED,kDAAkD;AAClD,MAAM,UAAU,OAAO,CACrB,KAA0C,EAC1C,OAAe;IAEf,IAAI,CAAC,KAAK;QAAE,OAAO;IACnB,MAAM,QAAQ,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;IAClE,OAAO,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC;AACxD,CAAC;AAED,mDAAmD;AACnD,MAAM,UAAU,OAAO,CAAC,KAA0C,EAAE,OAAe;IACjF,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,MAAM,QAAQ,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;IAClE,OAAO,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC;AAC1D,CAAC"}

package/dist/services/ncbi/response-handler.d.ts CHANGED Viewed

@@ -11,7 +11,19 @@ import type { NcbiRequestOptions } from './types.js';
  */
 export declare class NcbiResponseHandler {
     private readonly xmlParser;
+    /**
+     * Parser configured for JATS mixed content (PMC full-text). `preserveOrder`
+     * keeps document order so inline markup in `<p>`, `<abstract>`, `<title>`
+     * doesn't collapse into reordered text. `trimValues: false` retains spacing
+     * between text nodes and adjacent inline children.
+     */
+    private readonly orderedXmlParser;
     constructor();
+    /**
+     * Extract a structured error from a parsed NCBI XML body and throw it as an
+     * `McpError`. Never returns.
+     */
+    private throwNcbiError;
     extractNcbiErrorMessages(parsedXml: Record<string, unknown>): string[];
     parseAndHandleResponse<T>(responseText: string, endpoint: string, options?: NcbiRequestOptions): T;
 }

package/dist/services/ncbi/response-handler.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;~~AA4GrD~~;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;;~~IAa1C~~,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;~~CAoHL~~"}
1	+ {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAsHrD;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;OAGG;IACH,OAAO,CAAC,cAAc;IAatB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CAyHL"}

package/dist/services/ncbi/response-handler.js CHANGED Viewed

@@ -108,12 +108,28 @@ function sanitizeNcbiError(message) {
     }
     return message;
 }
+/**
+ * Matches `<ERROR>` (uppercase, optionally with attributes) for a cheap
+ * pre-parse check in ordered mode. Intentionally case-sensitive: NCBI's
+ * E-utilities use `<ERROR>` for response-level failures, while PMC EFetch
+ * uses lowercase `<error id="…">` to flag a single unavailable PMCID. The
+ * latter is data (a missing ID), not a transport error, so it falls through
+ * to the caller which reports it via `unavailablePmcIds`.
+ */
+const ERROR_TAG_REGEX = /<ERROR(?:\s[^>]*)?>/;
 /**
  * Parses NCBI E-utility responses (XML, JSON, text) and checks for NCBI-specific
  * error structures embedded in response bodies.
  */
 export class NcbiResponseHandler {
     xmlParser;
+    /**
+     * Parser configured for JATS mixed content (PMC full-text). `preserveOrder`
+     * keeps document order so inline markup in `<p>`, `<abstract>`, `<title>`
+     * doesn't collapse into reordered text. `trimValues: false` retains spacing
+     * between text nodes and adjacent inline children.
+     */
+    orderedXmlParser;
     constructor() {
         this.xmlParser = new FastXmlParser({
             ignoreAttributes: false,
@@ -123,6 +139,27 @@ export class NcbiResponseHandler {
             htmlEntities: true,
             isArray: (_name, jpath) => NCBI_ARRAY_JPATHS.has(jpath),
         });
+        this.orderedXmlParser = new FastXmlParser({
+            preserveOrder: true,
+            ignoreAttributes: false,
+            attributeNamePrefix: '@_',
+            parseTagValue: true,
+            trimValues: false,
+            processEntities: NCBI_PROCESS_ENTITIES_OPTIONS,
+            htmlEntities: true,
+        });
+    }
+    /**
+     * Extract a structured error from a parsed NCBI XML body and throw it as an
+     * `McpError`. Never returns.
+     */
+    throwNcbiError(parsedXml, endpoint) {
+        const errorMessages = this.extractNcbiErrorMessages(parsedXml);
+        logger.error('NCBI API returned an error in XML response.', {
+            endpoint,
+            errors: errorMessages,
+        });
+        throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI API Error: ${errorMessages.join('; ')}`, { endpoint, ncbiErrors: errorMessages });
     }
     extractNcbiErrorMessages(parsedXml) {
         const messages = [];
@@ -169,9 +206,18 @@ export class NcbiResponseHandler {
                     responseSnippet: responseText.substring(0, 200),
                 });
             }
+            const useOrdered = options?.useOrderedParser ?? false;
+            if (useOrdered && ERROR_TAG_REGEX.test(responseText)) {
+                // Ordered parser lacks the named-key shape error extraction relies on.
+                // Errors are rare, so fall back to the regular parser just to surface a
+                // structured message.
+                const errorParsed = this.xmlParser.parse(responseText);
+                this.throwNcbiError(errorParsed, endpoint);
+            }
+            const parser = useOrdered ? this.orderedXmlParser : this.xmlParser;
             let parsedXml;
             try {
-                parsedXml = this.xmlParser.parse(responseText);
+                parsedXml = parser.parse(responseText);
             }
             catch (error) {
                 const parserError = error instanceof Error ? error.message : String(error);
@@ -186,14 +232,12 @@ export class NcbiResponseHandler {
                     responseSnippet: responseText.substring(0, 200),
                 });
             }
-            const hasError = ERROR_PATHS.some((path) => resolvePath(parsedXml, path) !== undefined);
-            if (hasError) {
-                const errorMessages = this.extractNcbiErrorMessages(parsedXml);
-                logger.error('NCBI API returned an error in XML response.', {
-                    endpoint,
-                    errors: errorMessages,
-                });
-                throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI API Error: ${errorMessages.join('; ')}`, { endpoint, ncbiErrors: errorMessages });
+            if (!useOrdered) {
+                const parsedObj = parsedXml;
+                const hasError = ERROR_PATHS.some((path) => resolvePath(parsedObj, path) !== undefined);
+                if (hasError) {
+                    this.throwNcbiError(parsedObj, endpoint);
+                }
             }
             if (options?.returnRawXml) {
                 logger.debug('Returning raw XML string after validation.', { endpoint });

package/dist/services/ncbi/response-handler.js.map CHANGED Viewed

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

@@ -26,6 +26,12 @@ export interface NcbiRequestOptions {
     rettype?: string;
     /** When true and retmode is 'xml', return the raw XML string after error checking. */
     returnRawXml?: boolean;
+    /**
+     * Parse XML in `preserveOrder: true` mode (returns `JatsNodeList`). Required
+     * for JATS mixed-content responses (PMC full-text) where inline element order
+     * must be preserved in the output. Leave false for all other E-utilities.
+     */
+    useOrderedParser?: boolean;
     /** Force HTTP POST (for large payloads). */
     usePost?: boolean;
 }
@@ -282,10 +288,22 @@ export interface ESummaryAuthor {
     clusterid?: string;
     name: string;
 }
+/**
+ * NCBI returns ArticleId entries in two shapes depending on retmode:
+ * - JSON (`retmode=json&version=2.0`): lowercase keys `{ idtype, idtypen, value }`
+ * - XML  (`retmode=xml&version=2.0`):  capitalized child elements parsed as
+ *   `{ IdType, IdTypeN, Value }` by fast-xml-parser.
+ *
+ * Both shapes are supported so callers don't have to care which retmode produced
+ * the summary. Use the helpers in `esummary-parser.ts` to read them safely.
+ */
 export interface ESummaryArticleId {
-    idtype: string;
-    idtypen: number;
-    value: string;
+    IdType?: string;
+    IdTypeN?: number;
+    idtype?: string;
+    idtypen?: number;
+    Value?: string | number;
+    value?: string | number;
     [key: string]: unknown;
 }
 export interface ESummaryHistory {
@@ -422,130 +440,6 @@ export interface ESpellResponseContainer {
 export interface EFetchArticleSet {
     articles: ParsedArticle[];
 }
-/** Top-level PMC EFetch response container. */
-export interface XmlPmcArticleSet {
-    article?: XmlJatsArticle | XmlJatsArticle[];
-}
-/** JATS `<article>` element. */
-export interface XmlJatsArticle {
-    '@_article-type'?: string;
-    '@_xml:lang'?: string;
-    back?: XmlJatsBack;
-    body?: XmlJatsBody;
-    front?: XmlJatsFront;
-}
-/** JATS `<front>` element containing journal and article metadata. */
-export interface XmlJatsFront {
-    'article-meta'?: XmlJatsArticleMeta;
-    'journal-meta'?: XmlJatsJournalMeta;
-}
-/** JATS `<journal-meta>` element. */
-export interface XmlJatsJournalMeta {
-    issn?: XmlTextElement | XmlTextElement[];
-    'journal-id'?: XmlTextElement | XmlTextElement[];
-    'journal-title'?: unknown;
-    'journal-title-group'?: {
-        'journal-title'?: unknown;
-    };
-    publisher?: {
-        'publisher-name'?: unknown;
-    };
-}
-/** JATS `<article-meta>` element. */
-export interface XmlJatsArticleMeta {
-    abstract?: unknown;
-    aff?: XmlJatsAff | XmlJatsAff[];
-    'article-id'?: XmlJatsArticleId | XmlJatsArticleId[];
-    'contrib-group'?: XmlJatsContribGroup | XmlJatsContribGroup[];
-    fpage?: unknown;
-    issue?: unknown;
-    'kwd-group'?: XmlJatsKwdGroup | XmlJatsKwdGroup[];
-    lpage?: unknown;
-    permissions?: {
-        'copyright-statement'?: unknown;
-        license?: unknown;
-    };
-    'pub-date'?: XmlJatsPubDate | XmlJatsPubDate[];
-    'title-group'?: {
-        'article-title'?: unknown;
-    };
-    volume?: unknown;
-}
-/** JATS `<article-id>` element with pub-id-type attribute. */
-export interface XmlJatsArticleId {
-    '@_pub-id-type'?: string;
-    '#text'?: string | number;
-}
-/** JATS `<contrib-group>` element. */
-export interface XmlJatsContribGroup {
-    contrib?: XmlJatsContrib | XmlJatsContrib[];
-}
-/** JATS `<contrib>` element (author or other contributor). */
-export interface XmlJatsContrib {
-    '@_contrib-type'?: string;
-    collab?: unknown;
-    name?: {
-        surname?: unknown;
-        'given-names'?: unknown;
-    };
-    xref?: unknown;
-}
-/** JATS `<aff>` element (affiliation). */
-export interface XmlJatsAff {
-    '@_id'?: string;
-    '#text'?: string;
-    'addr-line'?: unknown;
-    country?: unknown;
-    institution?: unknown;
-    label?: unknown;
-    [key: string]: unknown;
-}
-/** JATS `<pub-date>` element. */
-export interface XmlJatsPubDate {
-    '@_date-type'?: string;
-    '@_pub-type'?: string;
-    day?: unknown;
-    month?: unknown;
-    year?: unknown;
-}
-/** JATS `<kwd-group>` element. */
-export interface XmlJatsKwdGroup {
-    '@_kwd-group-type'?: string;
-    kwd?: unknown;
-}
-/** JATS `<body>` element containing article full text. */
-export interface XmlJatsBody {
-    p?: unknown;
-    sec?: XmlJatsSection | XmlJatsSection[];
-}
-/** JATS `<sec>` element (article section, may nest recursively). */
-export interface XmlJatsSection {
-    '@_id'?: string;
-    '@_sec-type'?: string;
-    fig?: unknown;
-    label?: unknown;
-    p?: unknown;
-    sec?: XmlJatsSection | XmlJatsSection[];
-    'table-wrap'?: unknown;
-    title?: unknown;
-    [key: string]: unknown;
-}
-/** JATS `<back>` element containing references and supplementary material. */
-export interface XmlJatsBack {
-    'ref-list'?: XmlJatsRefList;
-}
-/** JATS `<ref-list>` element. */
-export interface XmlJatsRefList {
-    ref?: XmlJatsRef | XmlJatsRef[];
-    title?: unknown;
-}
-/** JATS `<ref>` element. */
-export interface XmlJatsRef {
-    '@_id'?: string;
-    'element-citation'?: unknown;
-    label?: unknown;
-    'mixed-citation'?: unknown;
-}
 /** Parsed full-text article from PMC. */
 export interface ParsedPmcArticle {
     abstract?: string;

package/dist/services/ncbi/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.3.8",
+  "version": "2.3.10",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
   "type": "module",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.3.8",
+  "version": "2.3.10",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.3.8",
+      "version": "2.3.10",
       "packageArguments": [
         {
           "type": "positional",
@@ -60,7 +60,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.3.8",
+      "version": "2.3.10",
       "packageArguments": [
         {
           "type": "positional",