npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.11 → 2.10.12 - Mend

@cyanheads/pubmed-mcp-server 2.10.11 → 2.10.12

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 (32) hide show

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

@@ -5,7 +5,7 @@
  * @module src/services/ncbi/parsing/esummary-parser
  */
 import { dateParser, logger, requestContextService, withExtra } from '@cyanheads/mcp-ts-core/utils';
-import { ensureArray, getAttribute, getText } from './xml-helpers.js';
+import { ensureArray, getAttribute, getOptionalText, getText } from './xml-helpers.js';
 /**
  * Formats an array of ESummary authors into a string.
  * Limits to the first 3 authors and adds 'et al.' if more exist.
@@ -114,7 +114,16 @@ function getArticleIdType(id) {
 function getArticleIdValue(id) {
     return id.value ?? id.Value;
 }
-function parseESummaryAuthorsFromDocumentSummary(docSummary) {
+/**
+ * Read the contributor list of a `DocumentSummarySet` summary.
+ *
+ * `authtype` and `clusterid` are omitted rather than written as empty strings
+ * when the record carries neither — NCBI ships `<ClusterID/>` on every author of
+ * a Bookshelf summary, and a field present with no value is the same absence to
+ * every consumer. (#137)
+ * @internal exported for direct unit tests
+ */
+export function parseESummaryAuthorsFromDocumentSummary(docSummary) {
     const authorsProp = docSummary.Authors;
     if (!authorsProp)
         return [];
@@ -132,8 +141,8 @@ function parseESummaryAuthorsFromDocumentSummary(docSummary) {
             if (!name) {
                 name = getText(authorObj.Name || authorObj.name, '');
             }
-            authtype = getText(authorObj.AuthType || authorObj.authtype, undefined);
-            clusterid = getText(authorObj.ClusterId || authorObj.clusterid, undefined);
+            authtype = getOptionalText(authorObj.AuthType || authorObj.authtype);
+            clusterid = getOptionalText(authorObj.ClusterId || authorObj.clusterid);
             if (!name) {
                 const authInputString = JSON.stringify(authorObj);
                 logger.warning(`Unhandled author structure in parseESummaryAuthorsFromDocumentSummary. authInput: ${authInputString.substring(0, 100)}`, requestContextService.createRequestContext({
@@ -233,15 +242,15 @@ function parseSingleDocumentSummary(docSummary) {
             ? articleIdsProp
             : ensureArray(articleIdsProp.ArticleId);
     }
-    let doiValue = getText(docSummary.DOI, undefined);
+    let doiValue = getOptionalText(docSummary.DOI);
     if (!doiValue) {
         const doiEntry = idsArray.find((id) => getArticleIdType(id) === 'doi');
         if (doiEntry) {
-            doiValue = getText(getArticleIdValue(doiEntry), undefined);
+            doiValue = getOptionalText(getArticleIdValue(doiEntry));
         }
     }
     const pmcEntry = idsArray.find((id) => getArticleIdType(id) === 'pmc');
-    const pmcIdValue = pmcEntry ? getText(getArticleIdValue(pmcEntry), undefined) : undefined;
+    const pmcIdValue = pmcEntry ? getOptionalText(getArticleIdValue(pmcEntry)) : undefined;
     const title = getText(docSummary.Title);
     const source = getText(docSummary.Source) || getText(docSummary.FullJournalName) || getText(docSummary.SO);
     const rawPubDate = getText(docSummary.PubDate);

package/dist/services/ncbi/parsing/esummary-parser.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,cAAc,EAEd,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EAChB,cAAc,EAEf,MAAM,aAAa,CAAC;AACrB,OAAO,EAOL,KAAK,QAAQ,EAQd,MAAM,sBAAsB,CAAC;AAwH9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;AAycD;;;;;;;;;;;;GAYG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CAyBlF;AAkDD;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,cAAc,EAAE,CAO7E;AAqED;;;;;;;;GAQG;AACH,eAAO,MAAM,iBAAiB,MAAM,CAAC;AAmGrC;;;;;;;;;;;GAWG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,cAAc,EAAE,CAQ7E;AAuND;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,CAsClF;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CA+CvE"}

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

@@ -7,7 +7,7 @@
  * inline children and drops body sections for markup-heavy articles.
  * @module src/services/ncbi/parsing/pmc-article-parser
  */
-import { attrOf, childrenOf, findAll, findAllDescendants, findOne, isTextNode, rawTextContent, tagNameOf, textContent, textContentExcluding, textOf, } from './pmc-xml-helpers.js';
+import { attrOf, childrenOf, findAll, findAllDescendants, findOne, isTextNode, rawTextContent, selectAlternative, tagNameOf, textContent, textContentExcluding, textOf, } from './pmc-xml-helpers.js';
 /**
  * Block content extracted into a field of its own and therefore left out of the
  * prose a section contributes. Each one nested inside a `<p>` would otherwise be
@@ -49,8 +49,10 @@ const LIFTED_BLOCK_TAGS = new Set([
  * right, so its placement is whatever holds it: naming it here broke the
  * standard `<inline-formula><alternatives><tex-math/><mml:math/></alternatives>`
  * deposit out of the sentence it belonged to and split that sentence in two.
- * `<disp-formula>`, `<table-wrap>` and `<fig>` resolve their own
- * `<alternatives>` children, so nothing depends on it flushing the run. (#130)
+ * `<disp-formula>` and `<table-wrap>` resolve their own `<alternatives>`
+ * children, and a `<fig>` is a block in its own right, so nothing depends on it
+ * flushing the run. What it contributes is one of those renderings rather than
+ * all of them — see `selectAlternative`. (#130, #135)
  */
 const BLOCK_TAGS = new Set([
     ...LIFTED_BLOCK_TAGS,
@@ -296,6 +298,13 @@ function flushRun(flow) {
  * `blockTags` names what interrupts the run: {@link BLOCK_TAGS} for article
  * prose, {@link STATEMENT_BLOCK_TAGS} for a container whose `<title>` and `<p>`
  * children are separate statements rather than one continuous sentence.
+ *
+ * `<tex-math>` and `<alternatives>` are the two elements whose text is not the
+ * concatenation of their subtree, so this walk defers to the shared rule rather
+ * than reading their children one at a time: a `<tex-math>` contributes its
+ * LaTeX document body via `rawTextContent`, and an `<alternatives>` re-enters
+ * this walk with its single chosen child, which keeps a `<disp-formula>` found
+ * there at block position. (#135)
  */
 function walkFlow(nodes, flow, blockTags) {
     for (const node of nodes) {
@@ -304,6 +313,16 @@ function walkFlow(nodes, flow, blockTags) {
             continue;
         }
         const tag = tagNameOf(node) ?? '';
+        if (tag === 'alternatives') {
+            const chosen = selectAlternative(node);
+            if (chosen)
+                walkFlow([chosen], flow, blockTags);
+            continue;
+        }
+        if (tag === 'tex-math') {
+            flow.run += rawTextContent(node);
+            continue;
+        }
         if (blockTags.has(tag)) {
             flushRun(flow);
             const rendered = renderBlock(node);
@@ -538,6 +557,10 @@ const DISP_FORMULA_NON_BODY = new Set(['label', 'graphic', 'media']);
  * 68-record draw against 3 for `<tex-math>`. A graphic-only deposit has no
  * fallback text and contributes nothing at all rather than a bare label on an
  * otherwise empty line. (#130)
+ *
+ * A `<tex-math>` contributes only the expression between `\begin{document}` and
+ * `\end{document}`; `textContent` applies that rule, so the LaTeX preamble
+ * publishers wrap around every formula never reaches the rendered line. (#135)
  */
 function renderDispFormula(formula) {
     const texMath = findOne(formula, 'tex-math') ?? findOne(findOne(formula, 'alternatives'), 'tex-math');

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

	@@ -1 +1 @@
1	- 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package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts CHANGED Viewed

@@ -30,6 +30,25 @@ export declare function attrOf(node: JatsNode, name: string): string | undefined
 export declare function isTextNode(node: JatsNode): boolean;
 /** Stringified text value of a text node. */
 export declare function textOf(node: JatsNode): string;
+/**
+ * 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 declare function selectAlternative(node: JatsNode, excluded?: ReadonlySet<string>): JatsNode | undefined;
 /**
  * Extract all text from a node or sibling list in document order with the
  * source spacing intact — no whitespace collapsing, no trimming. Use it when

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

	@@ -1 +1 @@
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package/dist/services/ncbi/parsing/pmc-xml-helpers.js CHANGED Viewed

@@ -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('');
 }

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	@@ -1 +1 @@
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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,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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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