@cyanheads/pubmed-mcp-server 2.10.11 → 2.10.12

package/dist/services/ncbi/parsing/xml-helpers.js

@@ -16,6 +16,17 @@ export function ensureArray(item) {
     }
     return Array.isArray(item) ? item : [item];
 }
+/**
+ * Safely extracts text content from an XML element, which might be a string or an object with a '#text' property.
+ * Handles cases where #text might be a number or boolean by converting to string.
+ *
+ * Always returns a string. Use {@link getOptionalText} where an absent element
+ * must stay distinguishable from an empty one — a default parameter fires on an
+ * explicit `undefined`, so this function cannot report absence. (#137)
+ * @param element - The XML element (string, object with #text, or undefined).
+ * @param defaultValue - The value to return if text cannot be extracted. Defaults to an empty string.
+ * @returns The text content or the default value.
+ */
 export function getText(element, defaultValue = '') {
     if (element == null) {
         return defaultValue;
@@ -38,6 +49,31 @@ export function getText(element, defaultValue = '') {
     }
     return defaultValue;
 }
+/**
+ * Text of an XML element, with an absent or empty element reported as absent.
+ *
+ * NCBI ships a field it carries with no value as an empty element — `<AuthType/>`,
+ * `<ClusterID/>`, `<ELocationID></ELocationID>` — and a caller cannot act on the
+ * difference between that and no element at all. Both are `undefined` here, so
+ * a conditional spread (`...(v !== undefined && { v })`) omits the key instead
+ * of writing an empty string into the parsed record. (#137)
+ * @param element - The XML element (string, object with #text, or undefined).
+ * @returns The text content, or undefined when the element is absent or empty.
+ */
+export function getOptionalText(element) {
+    return getText(element) || undefined;
+}
+/**
+ * Safely extracts an attribute value from an XML element.
+ * Assumes attributes are prefixed with '@_' by fast-xml-parser.
+ *
+ * Always returns a string; {@link getOptionalAttribute} is the form that reports
+ * absence. (#137)
+ * @param element - The XML element object.
+ * @param attributeName - The name of the attribute (e.g., 'UI', 'MajorTopicYN', without the '@_' prefix).
+ * @param defaultValue - The value to return if the attribute is not found. Defaults to an empty string.
+ * @returns The attribute value or the default value.
+ */
 export function getAttribute(element, attributeName, // e.g., 'UI', 'MajorTopicYN'
 defaultValue = '') {
     const fullAttributeName = `@_${attributeName}`; // As per fast-xml-parser config
@@ -53,4 +89,14 @@ defaultValue = '') {
     }
     return defaultValue;
 }
+/**
+ * Attribute value of an XML element, with a missing or empty attribute reported
+ * as absent — the {@link getOptionalText} rule applied to attributes. (#137)
+ * @param element - The XML element object.
+ * @param attributeName - The attribute name, without the '@_' prefix.
+ * @returns The attribute value, or undefined when it is missing or empty.
+ */
+export function getOptionalAttribute(element, attributeName) {
+    return getAttribute(element, attributeName) || undefined;
+}
 //# sourceMappingURL=xml-helpers.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"xml-helpers.js","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/xml-helpers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH;;;;;;GAMG;AACH,MAAM,UAAU,WAAW,CAAI,IAAgC;IAC7D,IAAI,IAAI,IAAI,IAAI,EAAE,CAAC;QACjB,OAAO,EAAE,CAAC;IACZ,CAAC;IACD,OAAO,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;AAC7C,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,OAAO,CAAC,OAAgB,EAAE,YAAY,GAAG,EAAE;IACzD,IAAI,OAAO,IAAI,IAAI,EAAE,CAAC;QACpB,OAAO,YAAY,CAAC;IACtB,CAAC;IACD,IAAI,OAAO,OAAO,KAAK,QAAQ,EAAE,CAAC;QAChC,OAAO,OAAO,CAAC;IACjB,CAAC;IACD,IAAI,OAAO,OAAO,KAAK,QAAQ,IAAI,OAAO,OAAO,KAAK,SAAS,EAAE,CAAC;QAChE,OAAO,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,wCAAwC;IAClE,CAAC;IACD,IAAI,OAAO,OAAO,KAAK,QAAQ,EAAE,CAAC;QAChC,MAAM,GAAG,GAAG,OAAkC,CAAC;QAC/C,IAAI,GAAG,CAAC,OAAO,CAAC,KAAK,SAAS,EAAE,CAAC;YAC/B,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAC,CAAC;YACzB,IAAI,OAAO,GAAG,KAAK,QAAQ;gBAAE,OAAO,GAAG,CAAC;YACxC,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,OAAO,GAAG,KAAK,SAAS;gBAAE,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC;QAC9E,CAAC;IACH,CAAC;IACD,OAAO,YAAY,CAAC;AACtB,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,eAAe,CAAC,OAAgB;IAC9C,OAAO,OAAO,CAAC,OAAO,CAAC,IAAI,SAAS,CAAC;AACvC,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,YAAY,CAC1B,OAAgB,EAChB,aAAqB,EAAE,6BAA6B;AACpD,YAAY,GAAG,EAAE;IAEjB,MAAM,iBAAiB,GAAG,KAAK,aAAa,EAAE,CAAC,CAAC,gCAAgC;IAChF,IAAI,OAAO,IAAI,OAAO,OAAO,KAAK,QAAQ,EAAE,CAAC;QAC3C,MAAM,GAAG,GAAG,OAAkC,CAAC;QAC/C,MAAM,GAAG,GAAG,GAAG,CAAC,iBAAiB,CAAC,CAAC;QACnC,IAAI,OAAO,GAAG,KAAK,QAAQ;YAAE,OAAO,GAAG,CAAC;QACxC,IAAI,OAAO,GAAG,KAAK,SAAS;YAAE,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,uCAAuC;QACzF,IAAI,OAAO,GAAG,KAAK,QAAQ;YAAE,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,sCAAsC;IACzF,CAAC;IACD,OAAO,YAAY,CAAC;AACtB,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,oBAAoB,CAAC,OAAgB,EAAE,aAAqB;IAC1E,OAAO,YAAY,CAAC,OAAO,EAAE,aAAa,CAAC,IAAI,SAAS,CAAC;AAC3D,CAAC"}

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

@@ -1 +1 @@
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+{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAsBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AA2OrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAeD;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;OAIG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IACjD;;;;;;;;;OASG;IACH,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAgB;IAElD,cAkBC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA2BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,CAsOH;CACF"}

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

@@ -24,50 +24,73 @@ import { decodeHtmlEntities } from './parsing/text-helpers.js';
  * jpaths that NCBI may return as either a single value or an array.
  * The `isArray` callback forces these to always parse as arrays for consistency.
  *
- * A jpath is the **full** dotted path from the document root, so only an entry
- * that spells out every ancestor matches. Read sites still pass values through
- * `ensureArray`, which is what makes the shorter, ancestor-less entries below
- * harmless.
+ * **Convention: one entry per shape, spelling the full path from the document
+ * root.** fast-xml-parser supplies that full dotted path and the lookup is an
+ * exact match, so an entry naming only its last segments never fires. Where a
+ * child is shared between record kinds, both ancestries are listed —
+ * `PubmedArticle` and `PubmedBookArticle.BookDocument` each get their own line.
+ * (#138)
+ *
+ * Two absences are deliberate. `<Link>` carries exactly one `<Id>`, which
+ * `find-related` reads without `ensureArray`, so listing it would strand every
+ * related PMID; and the JATS paths a PMC full-text response uses are governed by
+ * {@link ORDERED_XML_PARSER_OPTIONS}, which declares no `isArray` at all, so an
+ * entry for one here could never fire.
+ *
+ * Read sites still pass values through `ensureArray`, which is why correcting
+ * the previously ancestor-less entries changes nothing downstream. It stays.
  */
 const NCBI_ARRAY_JPATHS = new Set([
-    'IdList.Id',
+    // ESearch
     'eSearchResult.IdList.Id',
+    // EFetch — journal articles
     'PubmedArticleSet.PubmedArticle',
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.Article.AuthorList.Author',
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.Article.AuthorList.Author.AffiliationInfo',
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.Article.GrantList.Grant',
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.Article.PublicationTypeList.PublicationType',
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.KeywordList.Keyword',
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.MeshHeadingList.MeshHeading',
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.MeshHeadingList.MeshHeading.QualifierName',
+    'PubmedArticleSet.PubmedArticle.PubmedData.History.PubMedPubDate',
+    // EFetch — Bookshelf records
     'PubmedArticleSet.PubmedBookArticle',
     'PubmedArticleSet.PubmedBookArticle.BookDocument.AuthorList',
+    'PubmedArticleSet.PubmedBookArticle.BookDocument.AuthorList.Author',
+    'PubmedArticleSet.PubmedBookArticle.BookDocument.AuthorList.Author.AffiliationInfo',
+    'PubmedArticleSet.PubmedBookArticle.BookDocument.KeywordList.Keyword',
     'PubmedArticleSet.PubmedBookArticle.BookDocument.PublicationType',
     'PubmedArticleSet.PubmedBookArticle.BookDocument.Book.AuthorList',
+    'PubmedArticleSet.PubmedBookArticle.BookDocument.Book.AuthorList.Author',
     'PubmedArticleSet.PubmedBookArticle.BookDocument.Book.ELocationID',
     'PubmedArticleSet.PubmedBookArticle.BookDocument.Book.Isbn',
+    'PubmedArticleSet.PubmedBookArticle.PubmedBookData.History.PubMedPubDate',
     'PubmedArticleSet.DeleteCitation.PMID',
-    'AuthorList.Author',
-    'AffiliationInfo',
-    'MeshHeadingList.MeshHeading',
-    'MeshHeading.QualifierName',
-    'GrantList.Grant',
-    'KeywordList.Keyword',
-    'PublicationTypeList.PublicationType',
-    'History.PubMedPubDate',
-    'LinkSet.LinkSetDb.Link',
-    'Link.Id',
-    'DbInfo.FieldList.Field',
-    'DbInfo.LinkList.Link',
+    // ELink
+    'eLinkResult.LinkSet.LinkSetDb',
+    'eLinkResult.LinkSet.LinkSetDb.Link',
+    // EInfo
+    'eInfoResult.DbInfo.FieldList.Field',
+    'eInfoResult.DbInfo.LinkList.Link',
+    // ESummary
     'eSummaryResult.DocSum',
-    'DocSum.Item',
+    // EFetch — MeSH descriptor records
     'DescriptorRecordSet.DescriptorRecord',
-    'ConceptList.Concept',
-    'TermList.Term',
-    'TreeNumberList.TreeNumber',
-    'pmc-articleset.article',
-    'article-meta.article-id',
-    'article-meta.pub-date',
-    'contrib-group.contrib',
-    'kwd-group.kwd',
-    'body.sec',
-    'sec.sec',
-    'sec.p',
-    'ref-list.ref',
+    'DescriptorRecordSet.DescriptorRecord.ConceptList.Concept',
+    'DescriptorRecordSet.DescriptorRecord.ConceptList.Concept.TermList.Term',
+    'DescriptorRecordSet.DescriptorRecord.TreeNumberList.TreeNumber',
 ]);
+/**
+ * ESummary version-1 `<Item>` elements, at any nesting depth.
+ *
+ * A `DocSum` item of `Type="List"` or `Type="Structure"` holds further `<Item>`
+ * children, and `lookup-mesh` walks three levels of them to reach a tree number.
+ * The nesting is open-ended, so one anchored pattern covers it where a fixed
+ * list of paths would silently cap the depth. Anchored at the root for the same
+ * reason the set is: a suffix match would catch an unrelated `Item` elsewhere.
+ * (#138)
+ */
+const ESUMMARY_ITEM_JPATH = /^eSummaryResult\.DocSum(?:\.Item)+$/;
 /**
  * Ordered paths to check for NCBI error messages in parsed XML.
  * More specific paths come first so they take precedence.
@@ -282,7 +305,11 @@ export class NcbiResponseHandler {
             attributeNamePrefix: '@_',
             processEntities: XML_PROCESS_ENTITIES_OPTIONS,
             htmlEntities: true,
-            isArray: (_name, jpath) => NCBI_ARRAY_JPATHS.has(jpath),
+            isArray: (_name, jpath) => {
+                // `jPathOrMatcher` is a string unless `jPath: false` is set, which it is not.
+                const path = jpath;
+                return NCBI_ARRAY_JPATHS.has(path) || ESUMMARY_ITEM_JPATH.test(path);
+            },
             tagValueProcessor: preserveIsbnText,
         };
         this.xmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: true });

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

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

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.10.11",
+  "version": "2.10.12",
   "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": "2.10.11",
+  "version": "2.10.12",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.11",
+      "version": "2.10.12",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.11",
+      "version": "2.10.12",
       "packageArguments": [
         {
           "type": "positional",