@cyanheads/pubmed-mcp-server 2.10.11 → 2.10.13

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

@@ -1 +1 @@
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+{"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,4DAA4D;AAC5D,MAAM,YAAY,GAAG,UAAU,CAAC;AAEhC,kEAAkE;AAClE,MAAM,gBAAgB,GAAG,cAAc,CAAC;AAExC;;;GAGG;AACH,MAAM,YAAY,GAAwB,IAAI,GAAG,CAAC;IAChD,SAAS;IACT,gBAAgB;IAChB,OAAO;IACP,cAAc;CACf,CAAC,CAAC;AAEH;;;;;GAKG;AACH,MAAM,iBAAiB,GAAG,sDAAsD,CAAC;AAEjF;;;;;;;;;;;GAWG;AACH,SAAS,iBAAiB,CAAC,GAAW;IACpC,OAAO,iBAAiB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC;AACjD,CAAC;AAED;;;;;;;;;;;;;;;;;GAiBG;AACH,MAAM,UAAU,iBAAiB,CAC/B,IAAc,EACd,QAA8B;IAE9B,MAAM,QAAQ,GAAG,UAAU,CAAC,IAAI,CAAC,CAAC;IAClC,MAAM,WAAW,GAAG,CAAC,KAAe,EAAW,EAAE,CAAC,UAAU,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,IAAI,EAAE,KAAK,EAAE,CAAC;IAC5F,OAAO,CACL,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,KAAK,YAAY,IAAI,WAAW,CAAC,KAAK,CAAC,CAAC;QACjF,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,YAAY,CAAC,GAAG,CAAC,SAAS,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,IAAI,WAAW,CAAC,KAAK,CAAC,CAAC;QACzF,QAAQ,CAAC,IAAI,CAAC,WAAW,CAAC,CAC3B,CAAC;AACJ,CAAC;AAED;;;;;;;;;;GAUG;AACH,SAAS,UAAU,CAAC,KAA8B,EAAE,QAA8B;IAChF,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;YACzB,SAAS;QACX,CAAC;QACD,MAAM,GAAG,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC;QAClC,IAAI,QAAQ,EAAE,GAAG,CAAC,GAAG,CAAC;YAAE,SAAS;QACjC,IAAI,GAAG,KAAK,YAAY,EAAE,CAAC;YACzB,KAAK,CAAC,IAAI,CAAC,iBAAiB,CAAC,UAAU,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;YAC5D,SAAS;QACX,CAAC;QACD,IAAI,GAAG,KAAK,gBAAgB,EAAE,CAAC;YAC7B,MAAM,MAAM,GAAG,iBAAiB,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC;YACjD,IAAI,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC;YACrD,SAAS;QACX,CAAC;QACD,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,QAAQ,CAAC,CAAC,CAAC;IACrD,CAAC;IACD,OAAO,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;AACxB,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,cAAc,CAAC,KAA0C;IACvE,OAAO,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AACxC,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;;;;;;GAMG;AACH,MAAM,UAAU,oBAAoB,CAClC,KAA0C,EAC1C,YAAiC;IAEjC,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,OAAO,UAAU,CAAC,KAAK,EAAE,YAAY,CAAC,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;AACrE,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;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,kBAAkB,CAChC,KAA0C,EAC1C,OAAe;IAEf,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IACtB,MAAM,KAAK,GAAe,EAAE,CAAC;IAC7B,MAAM,KAAK,GAAG,CAAC,KAAmB,EAAQ,EAAE;QAC1C,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;YACzB,IAAI,SAAS,CAAC,IAAI,CAAC,KAAK,OAAO;gBAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YAClD,KAAK,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC;QAC1B,CAAC;IACH,CAAC,CAAC;IACF,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,CAAC;IACxD,OAAO,KAAK,CAAC;AACf,CAAC"}

package/dist/services/ncbi/parsing/xml-helpers.d.ts

@@ -14,20 +14,46 @@ export declare function ensureArray<T>(item: T | T[] | undefined | null): T[];
 /**
  * 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 declare function getText(element: unknown, defaultValue: undefined): string | undefined;
 export declare function getText(element: unknown, defaultValue?: string): string;
+/**
+ * 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 declare function getOptionalText(element: unknown): string | 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 declare function getAttribute(element: unknown, attributeName: string, defaultValue: undefined): string | undefined;
-export declare function getAttribute(element: unknown, attributeName: string, defaultValue?: string): string;
+export declare function getAttribute(element: unknown, attributeName: string, // e.g., 'UI', 'MajorTopicYN'
+defaultValue?: string): string;
+/**
+ * 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 declare function getOptionalAttribute(element: unknown, attributeName: string): string | undefined;
 //# sourceMappingURL=xml-helpers.d.ts.map

package/dist/services/ncbi/parsing/xml-helpers.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"xml-helpers.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/xml-helpers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH;;;;;;GAMG;AACH,wBAAgB,WAAW,CAAC,CAAC,EAAE,IAAI,EAAE,CAAC,GAAG,CAAC,EAAE,GAAG,SAAS,GAAG,IAAI,GAAG,CAAC,EAAE,CAKpE;AAED;;;;;;GAMG;AACH,wBAAgB,OAAO,CAAC,OAAO,EAAE,OAAO,EAAE,YAAY,EAAE,SAAS,GAAG,MAAM,GAAG,SAAS,CAAC;AACvF,wBAAgB,OAAO,CAAC,OAAO,EAAE,OAAO,EAAE,YAAY,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;AAyBzE;;;;;;;GAOG;AACH,wBAAgB,YAAY,CAC1B,OAAO,EAAE,OAAO,EAChB,aAAa,EAAE,MAAM,EACrB,YAAY,EAAE,SAAS,GACtB,MAAM,GAAG,SAAS,CAAC;AACtB,wBAAgB,YAAY,CAC1B,OAAO,EAAE,OAAO,EAChB,aAAa,EAAE,MAAM,EACrB,YAAY,CAAC,EAAE,MAAM,GACpB,MAAM,CAAC"}
+{"version":3,"file":"xml-helpers.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/xml-helpers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH;;;;;;GAMG;AACH,wBAAgB,WAAW,CAAC,CAAC,EAAE,IAAI,EAAE,CAAC,GAAG,CAAC,EAAE,GAAG,SAAS,GAAG,IAAI,GAAG,CAAC,EAAE,CAKpE;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,OAAO,CAAC,OAAO,EAAE,OAAO,EAAE,YAAY,SAAK,GAAG,MAAM,CAmBnE;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CAEpE;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,YAAY,CAC1B,OAAO,EAAE,OAAO,EAChB,aAAa,EAAE,MAAM,EAAE,6BAA6B;AACpD,YAAY,SAAK,GAChB,MAAM,CAUR;AAED;;;;;;GAMG;AACH,wBAAgB,oBAAoB,CAAC,OAAO,EAAE,OAAO,EAAE,aAAa,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAEhG"}

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

@@ -5,6 +5,15 @@
  * @module src/services/ncbi/response-handler
  */
 import type { NcbiRequestOptions } from './types.js';
+/**
+ * Reclassifies an HTTP error from a eutils request whose captured body is an NCBI
+ * `<ERROR>` envelope reporting a backend failure. The status-derived code reads such a
+ * response as caller error (400 → InvalidParams), which the retry gate never retries.
+ * Any other error — including a genuine invalid-parameter 400 — is returned unchanged.
+ * Matches the body text rather than parsing it, since the framework captures only a
+ * bounded prefix. (#153)
+ */
+export declare function reclassifyNcbiHttpError(error: unknown, endpoint: string): unknown;
 /**
  * Flattens inline mixed-content markup (`<sup>`, `<sub>`, `<inf>`, `<i>`,
  * `<b>`, `<u>`, `<sc>`) inside PubMed/MEDLINE XML before fast-xml-parser

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

@@ -1 +1 @@
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package/dist/services/ncbi/response-handler.js

@@ -4,7 +4,7 @@
  * NCBI's inconsistent XML structures where single-element lists are collapsed to scalars.
  * @module src/services/ncbi/response-handler
  */
-import { notFound, serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
+import { McpError, notFound, serializationError, serviceUnavailable, } from '@cyanheads/mcp-ts-core/errors';
 import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 /**
  * fast-xml-parser 5.8.0 marks the in-tree `XMLValidator` as `@deprecated` in
@@ -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.
@@ -76,9 +99,41 @@ const ERROR_PATHS = [
     'eLinkResult.ERROR',
     'eSearchResult.ERROR',
     'eSummaryResult.ERROR',
+    'eFetchResult.ERROR',
     'PubmedArticleSet.ErrorList.CannotRetrievePMID',
     'ERROR',
 ];
+/**
+ * NCBI `<ERROR>` messages describing a backend failure rather than the request.
+ * EFetch sends the viewer-timeout envelope under HTTP 200 and HTTP 400 alike, so
+ * the status cannot tell it from a malformed request; the message can. (#153)
+ */
+const NCBI_TRANSIENT_ERROR_PATTERNS = [/External viewer error/i, /Status:\s*Timeout/i];
+/** Captures the text of each uppercase `<ERROR>` element in a raw response body. */
+const ERROR_TEXT_REGEX = /<ERROR(?:\s[^>]*)?>([^<]*)<\/ERROR>/g;
+/**
+ * Reclassifies an HTTP error from a eutils request whose captured body is an NCBI
+ * `<ERROR>` envelope reporting a backend failure. The status-derived code reads such a
+ * response as caller error (400 → InvalidParams), which the retry gate never retries.
+ * Any other error — including a genuine invalid-parameter 400 — is returned unchanged.
+ * Matches the body text rather than parsing it, since the framework captures only a
+ * bounded prefix. (#153)
+ */
+export function reclassifyNcbiHttpError(error, endpoint) {
+    if (!(error instanceof McpError) || typeof error.data?.body !== 'string')
+        return error;
+    const ncbiErrors = [...error.data.body.matchAll(ERROR_TEXT_REGEX)].map((match) => decodeHtmlEntities(match[1] ?? '').trim());
+    if (!ncbiErrors.some((msg) => NCBI_TRANSIENT_ERROR_PATTERNS.some((p) => p.test(msg)))) {
+        return error;
+    }
+    return serviceUnavailable(`NCBI API Error: ${ncbiErrors.join('; ')}`, {
+        reason: 'ncbi_unreachable',
+        endpoint,
+        status: error.data.status,
+        ncbiErrors,
+        ...recoveryFor('ncbi_unreachable'),
+    }, { cause: error });
+}
 /**
  * NCBI error messages indicating the requested record doesn't exist (permanent
  * failure). Throwing NotFound for these prevents the retry loop from hammering
@@ -282,7 +337,11 @@ 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": "2.10.13",
   "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",
@@ -19,6 +19,8 @@
     "format": "biome check --write .",
     "format:unsafe": "biome check --write --unsafe .",
     "test": "bunx vitest run",
+    "test:coverage": "bunx vitest run --coverage",
+    "audit:fix": "bun audit fix",
     "audit:refresh": "rm -f bun.lock && bun install && bun audit",
     "list-skills": "bun run scripts/list-skills.ts",
     "lint:mcp": "bun run scripts/lint-mcp.ts",
@@ -74,31 +76,31 @@
   "license": "Apache-2.0",
   "packageManager": "bun@1.4.0",
   "engines": {
-    "bun": ">=1.3.0",
+    "bun": ">=1.4.0",
     "node": ">=24.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.12.8",
+    "@cyanheads/mcp-ts-core": "^0.13.0",
     "defuddle": "^0.19.3",
     "fast-xml-parser": "^5.11.1",
     "linkedom": "^0.18.13",
     "pino-pretty": "^13.1.3",
     "sanitize-html": "^2.17.7",
     "unpdf": "^1.8.1",
-    "zod": "^4.5.4"
+    "zod": "^4.6.1"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.5.12",
+    "@biomejs/biome": "^2.5.13",
     "@socketsecurity/bun-security-scanner": "^1.1.2",
-    "@types/node": "^26.4.1",
+    "@types/node": "^26.5.1",
     "@types/sanitize-html": "^2.16.1",
     "@vitest/coverage-istanbul": "^5.0.0",
     "depcheck": "^1.4.7",
     "fast-check": "^4.9.0",
-    "ignore": "^7.0.8",
+    "ignore": "^7.0.9",
     "tsc-alias": "^1.9.4",
     "typescript": "^7.0.2",
     "vitest": "^5.0.0"

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.10.11",
+  "version": "2.10.13",
   "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": "2.10.13",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.11",
+      "version": "2.10.13",
       "packageArguments": [
         {
           "type": "positional",