@cyanheads/pubmed-mcp-server 2.10.10 → 2.10.12

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

@@ -41,10 +41,77 @@ export function textOf(node) {
     const v = node[TEXT_KEY];
     return v == null ? '' : String(v);
 }
+/** JATS element carrying a LaTeX rendering of a formula. */
+const TEX_MATH_TAG = 'tex-math';
+/** JATS container holding equivalent renderings of one object. */
+const ALTERNATIVES_TAG = 'alternatives';
+/**
+ * JATS pointers to an external rendering: a file reference, not a rendering of
+ * the object itself.
+ */
+const POINTER_TAGS = new Set([
+    'graphic',
+    'inline-graphic',
+    'media',
+    'inline-media',
+]);
+/**
+ * The `\begin{document}` … `\end{document}` body of a LaTeX document. The
+ * closing marker is optional so a deposit that opens the document and never
+ * closes it still yields its expression rather than falling back to the whole
+ * document, preamble included.
+ */
+const TEX_DOCUMENT_BODY = /\\begin\{document\}([\s\S]*?)(?:\\end\{document\}|$)/;
+/**
+ * The expression a `<tex-math>` contributes: the body between
+ * `\begin{document}` and `\end{document}`.
+ *
+ * Publishers deposit `<tex-math>` as a complete LaTeX document —
+ * `\documentclass[12pt]{minimal}\usepackage{amsmath}…\begin{document}$$…$$\end{document}`
+ * — and every character of that preamble reached prose before this rule
+ * existed, once per formula (312 times in one Scientific Reports record). The
+ * math delimiters inside the body are kept, so the expression still reads as
+ * math rather than as bare tokens. A body deposited without the wrapper is
+ * already the expression and is returned unchanged. (#135)
+ */
+function texMathExpression(raw) {
+    return TEX_DOCUMENT_BODY.exec(raw)?.[1] ?? raw;
+}
+/**
+ * The single child of an `<alternatives>` whose text stands for the whole
+ * element.
+ *
+ * `<alternatives>` offers equivalent renderings of one object — a TeX and a
+ * MathML spelling of the same formula, a graphic and a marked-up table — so
+ * reading every child states the object twice in the same sentence. The
+ * `<tex-math>` is preferred because it survives as readable math, then any other
+ * rendering that carries text, and a pointer's own `<alt-text>` only when the
+ * deposit offers nothing else. Every candidate must carry text under the
+ * caller's `excluded` set, which is what keeps the selection from landing on a
+ * rendering that would then contribute nothing: an empty `<tex-math>`, a
+ * `<graphic>` naming its file, or a child the caller excludes by tag. Returns
+ * undefined when no child qualifies. (#135)
+ *
+ * Structural selections are unaffected: `<table-wrap>` and `<disp-formula>`
+ * resolve their own `<alternatives>` children by tag.
+ */
+export function selectAlternative(node, excluded) {
+    const children = childrenOf(node);
+    const carriesText = (child) => concatText(child, excluded).trim() !== '';
+    return (children.find((child) => tagNameOf(child) === TEX_MATH_TAG && carriesText(child)) ??
+        children.find((child) => !POINTER_TAGS.has(tagNameOf(child) ?? '') && carriesText(child)) ??
+        children.find(carriesText));
+}
 /**
  * Concatenate text content in document order without normalizing whitespace.
  * Internal helper so recursion preserves the original spacing between siblings.
  * `excluded` skips a whole subtree by tag name; omitting it reads everything.
+ *
+ * Two JATS elements do not contribute the plain concatenation of their subtree:
+ * a `<tex-math>` contributes only its LaTeX document body, and an
+ * `<alternatives>` contributes exactly one child. Both rules live here so every
+ * prose consumer inherits them — paragraphs, table cells, captions, abstracts.
+ * (#135)
  */
 function concatText(input, excluded) {
     const nodes = Array.isArray(input) ? input : [input];
@@ -52,10 +119,22 @@ function concatText(input, excluded) {
     for (const node of nodes) {
         if (isTextNode(node)) {
             parts.push(textOf(node));
+            continue;
+        }
+        const tag = tagNameOf(node) ?? '';
+        if (excluded?.has(tag))
+            continue;
+        if (tag === TEX_MATH_TAG) {
+            parts.push(texMathExpression(concatText(childrenOf(node))));
+            continue;
         }
-        else if (!excluded?.has(tagNameOf(node) ?? '')) {
-            parts.push(concatText(childrenOf(node), excluded));
+        if (tag === ALTERNATIVES_TAG) {
+            const chosen = selectAlternative(node, excluded);
+            if (chosen)
+                parts.push(concatText(chosen, excluded));
+            continue;
         }
+        parts.push(concatText(childrenOf(node), excluded));
     }
     return parts.join('');
 }

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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+{"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

@@ -19,43 +19,78 @@ import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { XMLParser as FastXmlParser, XMLValidator } from 'fast-xml-parser';
 import { recoveryFor } from '../error-contracts.js';
 import { ORDERED_XML_PARSER_OPTIONS, XML_PROCESS_ENTITIES_OPTIONS, } from './parsing/ordered-xml-parser-options.js';
+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.
+ *
+ * **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)+$/;
 /**
  * Ordered paths to check for NCBI error messages in parsed XML.
  * More specific paths come first so they take precedence.
@@ -134,6 +169,11 @@ const ERROR_TAG_REGEX = /<ERROR(?:\s[^>]*)?>/;
  * Unicode superscript map. Covers digits, common operators, and the few
  * letters that have superscript codepoints (n, i). `−` (U+2212, the proper
  * minus) is normalized to U+207B alongside ASCII `-`.
+ *
+ * `®` and `™` map to themselves. They have no superscript codepoint because
+ * they need none — the glyphs are already raised, and the `<sup>` around them
+ * (`GeneReviews<sup>&#xae;</sup>`) is presentation, not content. Without an
+ * entry the `^` fallback fires and a book title renders `GeneReviews^®`. (#114)
  */
 const SUPERSCRIPT_MAP = {
     '0': '⁰',
@@ -154,6 +194,8 @@ const SUPERSCRIPT_MAP = {
     ')': '⁾',
     n: 'ⁿ',
     i: 'ⁱ',
+    '®': '®',
+    '™': '™',
 };
 /**
  * Unicode subscript map. Covers digits and operators; alphabetic subscripts
@@ -178,9 +220,19 @@ const SUBSCRIPT_MAP = {
     '(': '₍',
     ')': '₎',
 };
+/**
+ * Map one `<sup>`/`<sub>` payload, or fall back to the ASCII prefix form.
+ *
+ * Lookup runs on the decoded text because this pass happens before the XML
+ * parser: a registered mark reaches it as `&#xae;`, not `®`, and a per-character
+ * lookup over the entity's own characters can only ever miss. The fallback
+ * returns the *original* content, so an unmappable payload keeps whatever
+ * encoding it arrived in and the string stays valid XML for the parser that
+ * follows — nothing in either table decodes to `&`, `<` or `>`.
+ */
 function mapInlineContent(content, table, asciiPrefix) {
     let out = '';
-    for (const ch of content) {
+    for (const ch of decodeHtmlEntities(content)) {
         const mapped = table[ch];
         if (mapped === undefined)
             return `${asciiPrefix}${content}`;
@@ -212,6 +264,17 @@ export function flattenInlineMarkup(xml) {
         .replace(/<inf>([^<]*)<\/inf>/g, (_, c) => mapInlineContent(c, SUBSCRIPT_MAP, '_'))
         .replace(/<\/?(?:i|b|u|sc)>/g, '');
 }
+/**
+ * Keeps `Book/Isbn` out of fast-xml-parser's numeric coercion.
+ *
+ * An ISBN-10 can start with a zero (`0309605393`); coerced, it becomes the
+ * number 309605393 and the leading digit is gone before any read site sees it,
+ * so the record ships a wrong ISBN with no error anywhere. The processor's
+ * contract does the work: returning `undefined` leaves the raw text alone,
+ * while returning the value unchanged for every other tag keeps the existing
+ * coercion exactly as it was. (#114)
+ */
+const preserveIsbnText = (tagName, tagValue) => tagName === 'Isbn' ? undefined : tagValue;
 /**
  * Parses NCBI E-utility responses (XML, JSON, text) and checks for NCBI-specific
  * error structures embedded in response bodies.
@@ -242,7 +305,12 @@ 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 });
         this.verbatimXmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: false });

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

@@ -1 +1 @@
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