@cyanheads/pubmed-mcp-server 2.10.18 → 2.10.20

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

@@ -18,12 +18,14 @@
 export declare function decodeHtmlEntities(text: string): string;
 /**
  * Turn an upstream string that may carry JATS/HTML markup into display-ready
- * plain text: strip structural tags, decode character references, drop soft
- * hyphens (U+00AD — invisible, and it corrupts token matching mid-word), and
- * collapse the resulting whitespace. Tags are stripped before decoding so a
- * structural `<bold>` is removed while an entity-escaped `&lt;gene&gt;` survives
- * as literal text. Used for Europe PMC abstract snippets before truncation, so
- * the character budget is spent on text rather than markup.
+ * plain text: strip tags, decode character references, drop soft hyphens
+ * (U+00AD — invisible, and it corrupts token matching mid-word), and collapse
+ * the resulting whitespace. Tags are stripped in one pass before decoding, so a
+ * raw `<bold>` and an encoded `&lt;i&gt;` are removed while an escaped
+ * `&lt;gene&gt;` survives as literal text — and nothing a removal joins or a
+ * decode produces is scanned again (`&lt;&lt;i&gt;i&gt;` reads `<i>`). Used for
+ * Europe PMC titles, authors, journals, and abstracts before truncation, so the
+ * character budget is spent on text rather than markup.
  */
 export declare function toDisplayText(text: string): string;
 //# sourceMappingURL=text-helpers.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"text-helpers.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/text-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAiCH;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAcvD;AAED;;;;;;;;GAQG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAKlD"}
+{"version":3,"file":"text-helpers.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/text-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAsHH;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAcvD;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAKlD"}

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

@@ -20,22 +20,96 @@ const NAMED_ENTITIES = {
 /** A well-formed numeric (`­`, `­`) or named (`&`) character reference. */
 const ENTITY_RE = /&(#x[0-9a-f]+|#\d+|[a-z][a-z0-9]*);/gi;
 /**
- * A structural tag: `<` immediately followed by an optional `/` and a tag-name
- * letter, then a tag body carrying no further angle bracket.
+ * Inline formatting elements (PubMed, JATS, HTML). Removing one reproduces what
+ * a renderer shows, so `D<sub>2</sub>O` reads `D2O`, never `D 2 O` — except
+ * after sentence-closing punctuation, where it keeps the break. (#181)
+ */
+const FORMATTING_TAG_NAMES = [
+    'b',
+    'bold',
+    'em',
+    'i',
+    'inf',
+    'italic',
+    'sc',
+    'strong',
+    'sub',
+    'sup',
+    'u',
+    'underline',
+];
+const FORMATTING_TAG_NAME_SET = new Set(FORMATTING_TAG_NAMES);
+const FORMATTING_TAG_ALTERNATION = FORMATTING_TAG_NAMES.join('|');
+/**
+ * A markup tag, in one of two forms, recognized in a single left-to-right pass.
+ *
+ * Raw: `<`, an optional `/`, a tag name that starts with a letter, then either
+ * `>` or a body that opens with whitespace or `/` and carries no further angle
+ * bracket. Each restriction keeps notation intact. A leading letter leaves
+ * `P<0.001` alone; a name ends only at whitespace, `/`, or `>`, never at `=`, so
+ * PubMed's legacy `<or= 20 or > 20` (≤) is not read as a tag that deletes the
+ * text up to the next `>` (#195); and a body free of `<` stops a match opened on
+ * a stray `<` from spanning the next real tag (`n<N ... <bold>` keeps its text,
+ * #94). The remaining gap is a stray `<letter …>` pair — `a<b and c>d` still
+ * strips to `a d`, and `HuMab<CD20>` loses `<CD20>`. Closing it would take a
+ * tag-name allowlist that silently drops unknown JATS elements, so the looser
+ * shape is deliberate. The name class excludes the delimiter the body must
+ * start with, so a failed match costs only the characters up to the next angle
+ * bracket and the scan stays linear.
  *
- * Both restrictions exist to keep statistical notation intact. Requiring a
- * leading letter leaves `P<0.001` alone; forbidding `<` inside the body stops a
- * match that opened on a stray `<` from spanning across the next real tag and
- * swallowing the prose between them (`n<N ... <bold>` keeps its text). The
- * remaining gap is a stray `<` and `>` pair with a letter after the `<` and no
- * tag between them — `a<b and c>d` still strips to `a d`. Closing it would take
- * a tag-name allowlist, which would silently drop unknown JATS elements, so the
- * looser pattern is deliberate: it errs toward leaving markup visible rather
- * than deleting text. (#94)
+ * Entity-encoded: a bare formatting tag as Europe PMC escapes it in PubMed
+ * titles (`&lt;i&gt;`, `&lt;/sup&gt;`). Only these names, with nothing else
+ * inside the brackets, are recognized — every other escaped `&lt;…&gt;` stays
+ * literal text. (#181)
  */
-const MARKUP_TAG_RE = /<\/?[A-Za-z][^<>]*>/g;
+const MARKUP_TAG_RE = new RegExp(`<\\/?([A-Za-z][^\\s/<>=]*)([\\s/][^<>]*)?>|&lt;\\/?(?:${FORMATTING_TAG_ALTERNATION})&gt;`, 'gi');
+/** Punctuation that closes a sentence or a heading label (`Results:`). */
+const SENTENCE_END = new Set(['.', ':', '!', '?']);
+/** Sticky: one bare formatting tag, raw or encoded, at `lastIndex`. */
+const FORMATTING_TAG_AT_RE = new RegExp(`<\\/?(?:${FORMATTING_TAG_ALTERNATION})>|&lt;\\/?(?:${FORMATTING_TAG_ALTERNATION})&gt;`, 'iy');
+/** Sticky: a letter or digit at `lastIndex`. */
+const WORD_CHARACTER_AT_RE = /[\p{L}\p{N}]/uy;
+const ASCII_DIGIT_RE = /[0-9]/;
 const SOFT_HYPHEN_RE = /­/g;
 const WHITESPACE_RE = /\s+/g;
+/**
+ * Replacement for one {@link MARKUP_TAG_RE} match: a bare formatting tag, raw or
+ * encoded, is removed outright; any other raw tag becomes a space so the words
+ * on either side of a structural boundary stay apart. A formatting tag that
+ * sits between a sentence's closing punctuation and the next word also becomes
+ * a space: abstracts set headings in bold or italic with no whitespace around
+ * them (`children.<b>Aim.</b> The`, `<i>Objective.</i>Quantitative`), and
+ * joining there fuses the sentences.
+ */
+function replaceMarkupTag(tag, rawName, rawBody, offset, text) {
+    const formatting = rawName === undefined ||
+        (rawBody === undefined && FORMATTING_TAG_NAME_SET.has(rawName.toLowerCase()));
+    return formatting && !breaksSentence(text, offset, offset + tag.length) ? '' : ' ';
+}
+/**
+ * Whether the tag spanning `start`–`end` follows sentence-closing punctuation
+ * and leads, past any further formatting tags, into a letter or digit. A `::`
+ * separator (`T2::<i>Nluc</i>`) closes no sentence, and neither does
+ * punctuation between two digits (`0.<b>05</b>`, `10:<b>30</b>`). Only a tag
+ * preceded by that punctuation reads ahead, and the run it reads ends at the
+ * first character that is not a formatting tag, so the read-ahead stays linear
+ * overall.
+ */
+function breaksSentence(text, start, end) {
+    const before = text[start - 1];
+    if (before === undefined || !SENTENCE_END.has(before))
+        return false;
+    if (before === ':' && text[start - 2] === ':')
+        return false;
+    let next = end;
+    FORMATTING_TAG_AT_RE.lastIndex = next;
+    while (FORMATTING_TAG_AT_RE.test(text))
+        next = FORMATTING_TAG_AT_RE.lastIndex;
+    WORD_CHARACTER_AT_RE.lastIndex = next;
+    if (!WORD_CHARACTER_AT_RE.test(text))
+        return false;
+    return !(ASCII_DIGIT_RE.test(text[start - 2] ?? '') && ASCII_DIGIT_RE.test(text[next] ?? ''));
+}
 /**
  * Decode well-formed named and numeric HTML/XML character references in a plain
  * string. A bare `&` (e.g. `AT&T`) is left untouched — only `&name;` / `&#NN;` /
@@ -63,15 +137,17 @@ export function decodeHtmlEntities(text) {
 }
 /**
  * Turn an upstream string that may carry JATS/HTML markup into display-ready
- * plain text: strip structural tags, decode character references, drop soft
- * hyphens (U+00AD — invisible, and it corrupts token matching mid-word), and
- * collapse the resulting whitespace. Tags are stripped before decoding so a
- * structural `<bold>` is removed while an entity-escaped `&lt;gene&gt;` survives
- * as literal text. Used for Europe PMC abstract snippets before truncation, so
- * the character budget is spent on text rather than markup.
+ * plain text: strip tags, decode character references, drop soft hyphens
+ * (U+00AD — invisible, and it corrupts token matching mid-word), and collapse
+ * the resulting whitespace. Tags are stripped in one pass before decoding, so a
+ * raw `<bold>` and an encoded `&lt;i&gt;` are removed while an escaped
+ * `&lt;gene&gt;` survives as literal text — and nothing a removal joins or a
+ * decode produces is scanned again (`&lt;&lt;i&gt;i&gt;` reads `<i>`). Used for
+ * Europe PMC titles, authors, journals, and abstracts before truncation, so the
+ * character budget is spent on text rather than markup.
  */
 export function toDisplayText(text) {
-    return decodeHtmlEntities(text.replace(MARKUP_TAG_RE, ' '))
+    return decodeHtmlEntities(text.replace(MARKUP_TAG_RE, replaceMarkupTag))
         .replace(SOFT_HYPHEN_RE, '')
         .replace(WHITESPACE_RE, ' ')
         .trim();

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

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

@@ -28,19 +28,27 @@ export declare function emptyEFetchResultFor(error: unknown, endpoint: string, d
  */
 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
- * runs. The non-ordered parser used for EFetch responses doesn't preserve
- * mixed content — `1.73 m<sup>2</sup>` parses to `{ '#text': '1.73 m', sup:
- * 2 }`, and `extractAbstractText` only reads `#text`, so the superscript
- * digit is silently dropped from abstracts and titles.
+ * Flattens inline mixed-content markup inside PubMed/MEDLINE XML before
+ * fast-xml-parser runs. The non-ordered parser used for EFetch responses
+ * doesn't preserve mixed content — `1.73 m<sup>2</sup>` parses to `{ '#text':
+ * '1.73 m', sup: 2 }`, and every read site takes only `#text`, so a child
+ * element is dropped and the trimmed text around it is joined with no space.
  *
- * Numeric and operator characters map to Unicode (²/³/⁻²/₂…); anything else
- * falls back to a `^X` / `_X` ASCII prefix so the content survives in a
- * recognizable form. Italic / bold / underline / small-caps tags are
- * stripped (content kept) since they don't carry meaning in our text
- * rendering. Only invoked on the regular parser path; the PMC JATS path
- * already preserves inline markup via `preserveOrder: true`.
+ * PubMed's `%text;` content model (`b | i | sup | sub | u`) nests without limit,
+ * and titles, abstracts and keywords also take `mml:math` (an abstract's
+ * `DispFormula` wraps one). One pass handles all of it:
+ * - `<i>`, `<b>`, `<u>`, `<sc>` are removed, content kept, wherever they sit.
+ * - A `<sup>`/`<sub>`/`<inf>` maps numeric and operator characters to Unicode
+ *   (²/³/⁻²/₂…) and otherwise falls back to a `^X` / `_X` prefix, so the
+ *   content survives in a recognizable form. Emphasis inside it no longer
+ *   blocks the mapping (`<sup>-/<i>y</i></sup>` → `^-/y`); a script holding
+ *   another script takes the prefix, with the inner one rendered in place.
+ * - `mml:math` becomes its text, inter-element whitespace dropped: the scripts
+ *   of `msub`/`msup`/`msubsup` render like `<sub>`/`<sup>`, and `mfrac` is
+ *   written `a/b`. `DispFormula` tags are removed. (#211)
+ *
+ * Only invoked on the regular parser path; the PMC JATS path already preserves
+ * inline markup via `preserveOrder: true`.
  *
  * @internal exported for direct unit tests
  */

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;;;;;;;;GAQG;AA0BH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AA6IrD;;;;;;;;GAQG;AACH,wBAAgB,oBAAoB,CAClC,KAAK,EAAE,OAAO,EACd,QAAQ,EAAE,MAAM,EAChB,EAAE,EAAE,OAAO,GACV,MAAM,GAAG,SAAS,CAKpB;AAED;;;;;;;GAOG;AACH,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAmBjF;AA+MD;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAmDvD;AA+BD;;;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;IAyBtB,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,CAiOH;CACF"}

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

@@ -20,7 +20,6 @@ import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
  */
 // biome-ignore lint/suspicious/noDeprecatedImports: staying on in-tree XMLValidator — see block comment above
 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';
 /**
@@ -52,6 +51,7 @@ const NCBI_ARRAY_JPATHS = new Set([
     'PubmedArticleSet.PubmedArticle.MedlineCitation.Article.AuthorList.Author.AffiliationInfo',
     'PubmedArticleSet.PubmedArticle.MedlineCitation.Article.GrantList.Grant',
     'PubmedArticleSet.PubmedArticle.MedlineCitation.Article.PublicationTypeList.PublicationType',
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.CommentsCorrectionsList.CommentsCorrections',
     'PubmedArticleSet.PubmedArticle.MedlineCitation.KeywordList.Keyword',
     'PubmedArticleSet.PubmedArticle.MedlineCitation.MeshHeadingList.MeshHeading',
     'PubmedArticleSet.PubmedArticle.MedlineCitation.MeshHeadingList.MeshHeading.QualifierName',
@@ -187,7 +187,6 @@ export function reclassifyNcbiHttpError(error, endpoint) {
         endpoint,
         status: error.data?.status,
         ncbiErrors,
-        ...recoveryFor('ncbi_unreachable'),
     }, { cause: error });
 }
 /**
@@ -328,41 +327,145 @@ function mapInlineContent(content, table, asciiPrefix) {
     }
     return out;
 }
+/** A superscript or subscript, with the table and fallback prefix that render it. */
+const SUPERSCRIPT = { table: SUPERSCRIPT_MAP, prefix: '^' };
+const SUBSCRIPT = { table: SUBSCRIPT_MAP, prefix: '_' };
 /**
- * Flattens inline mixed-content markup (`<sup>`, `<sub>`, `<inf>`, `<i>`,
- * `<b>`, `<u>`, `<sc>`) inside PubMed/MEDLINE XML before fast-xml-parser
- * runs. The non-ordered parser used for EFetch responses doesn't preserve
- * mixed content — `1.73 m<sup>2</sup>` parses to `{ '#text': '1.73 m', sup:
- * 2 }`, and `extractAbstractText` only reads `#text`, so the superscript
- * digit is silently dropped from abstracts and titles.
+ * One inline token, in a single left-to-right pass: a `b|i|u|sc|sup|sub|inf` tag
+ * (PubMed's `%text;` elements, plus two legacy names), or a MathML or
+ * `DispFormula` tag with optional attributes and self-closing slash. Attribute
+ * text excludes `<`, as XML requires, so a match opened on a tag that never
+ * closes fails at the next `<` and the scan stays linear.
+ */
+const INLINE_TOKEN_RE = /<(\/?)(sup|sub|inf|i|b|u|sc)>|<(\/?)(mml:[A-Za-z][\w.-]*|DispFormula)(?:\s(?:[^<>"'/]|"[^"<]*"|'[^'<]*')*)?(\/?)>/g;
+/**
+ * Count one more child of `parent` and name the slot it fills: the script of
+ * `msub`/`msup`, either script of `msubsup`, or the denominator of `mfrac`.
+ */
+function claimMathChildSlot(parent) {
+    if (!parent)
+        return;
+    const index = parent.children++;
+    switch (parent.name) {
+        case 'mml:msub':
+            return index === 1 ? SUBSCRIPT : undefined;
+        case 'mml:msup':
+            return index === 1 ? SUPERSCRIPT : undefined;
+        case 'mml:msubsup':
+            return index === 1 ? SUBSCRIPT : index === 2 ? SUPERSCRIPT : undefined;
+        case 'mml:mfrac':
+            return index === 1 ? 'denominator' : undefined;
+        default:
+            return;
+    }
+}
+/**
+ * Flattens inline mixed-content markup inside PubMed/MEDLINE XML before
+ * fast-xml-parser runs. The non-ordered parser used for EFetch responses
+ * doesn't preserve mixed content — `1.73 m<sup>2</sup>` parses to `{ '#text':
+ * '1.73 m', sup: 2 }`, and every read site takes only `#text`, so a child
+ * element is dropped and the trimmed text around it is joined with no space.
  *
- * Numeric and operator characters map to Unicode (²/³/⁻²/₂…); anything else
- * falls back to a `^X` / `_X` ASCII prefix so the content survives in a
- * recognizable form. Italic / bold / underline / small-caps tags are
- * stripped (content kept) since they don't carry meaning in our text
- * rendering. Only invoked on the regular parser path; the PMC JATS path
- * already preserves inline markup via `preserveOrder: true`.
+ * PubMed's `%text;` content model (`b | i | sup | sub | u`) nests without limit,
+ * and titles, abstracts and keywords also take `mml:math` (an abstract's
+ * `DispFormula` wraps one). One pass handles all of it:
+ * - `<i>`, `<b>`, `<u>`, `<sc>` are removed, content kept, wherever they sit.
+ * - A `<sup>`/`<sub>`/`<inf>` maps numeric and operator characters to Unicode
+ *   (²/³/⁻²/₂…) and otherwise falls back to a `^X` / `_X` prefix, so the
+ *   content survives in a recognizable form. Emphasis inside it no longer
+ *   blocks the mapping (`<sup>-/<i>y</i></sup>` → `^-/y`); a script holding
+ *   another script takes the prefix, with the inner one rendered in place.
+ * - `mml:math` becomes its text, inter-element whitespace dropped: the scripts
+ *   of `msub`/`msup`/`msubsup` render like `<sub>`/`<sup>`, and `mfrac` is
+ *   written `a/b`. `DispFormula` tags are removed. (#211)
+ *
+ * Only invoked on the regular parser path; the PMC JATS path already preserves
+ * inline markup via `preserveOrder: true`.
  *
  * @internal exported for direct unit tests
  */
 export function flattenInlineMarkup(xml) {
-    return xml
-        .replace(/<sup>([^<]*)<\/sup>/g, (_, c) => mapInlineContent(c, SUPERSCRIPT_MAP, '^'))
-        .replace(/<sub>([^<]*)<\/sub>/g, (_, c) => mapInlineContent(c, SUBSCRIPT_MAP, '_'))
-        .replace(/<inf>([^<]*)<\/inf>/g, (_, c) => mapInlineContent(c, SUBSCRIPT_MAP, '_'))
-        .replace(/<\/?(?:i|b|u|sc)>/g, '');
+    const out = [];
+    const scripts = [];
+    const math = [];
+    const write = (text) => {
+        if (text === '' || (math.length > 0 && text.trim() === ''))
+            return;
+        const top = scripts.at(-1);
+        if (top?.plain)
+            top.text += text;
+        else
+            out.push(text);
+    };
+    const openScript = (style) => {
+        const top = scripts.at(-1);
+        if (top?.plain) {
+            top.plain = false;
+            out.push(top.style.prefix + top.text);
+        }
+        scripts.push({ plain: true, style, text: '' });
+    };
+    const closeScript = () => {
+        const frame = scripts.pop();
+        if (frame?.plain) {
+            out.push(mapInlineContent(frame.text, frame.style.table, frame.style.prefix));
+        }
+    };
+    let last = 0;
+    for (const match of xml.matchAll(INLINE_TOKEN_RE)) {
+        write(xml.slice(last, match.index));
+        last = match.index + match[0].length;
+        const [, inlineClose, inlineName, otherClose, otherName, selfClosing] = match;
+        if (inlineName === 'sup' || inlineName === 'sub' || inlineName === 'inf') {
+            if (inlineClose)
+                closeScript();
+            else
+                openScript(inlineName === 'sup' ? SUPERSCRIPT : SUBSCRIPT);
+        }
+        else if (otherName?.startsWith('mml:')) {
+            if (otherClose) {
+                if (math.pop()?.opensScript)
+                    closeScript();
+                continue;
+            }
+            const slot = claimMathChildSlot(math.at(-1));
+            if (slot === 'denominator')
+                write('/');
+            const opensScript = slot !== undefined && slot !== 'denominator';
+            if (opensScript)
+                openScript(slot);
+            if (!selfClosing)
+                math.push({ children: 0, name: otherName, opensScript });
+            else if (opensScript)
+                closeScript();
+        }
+        // Emphasis and `DispFormula` tags are dropped; their content stays.
+    }
+    write(xml.slice(last));
+    return out.join('');
 }
 /**
- * Keeps `Book/Isbn` out of fast-xml-parser's numeric coercion.
+ * Free-text elements of a linked notice, matched by path: an element named `Note`
+ * elsewhere keeps the default coercion. (#178)
+ */
+const VERBATIM_TEXT_JPATHS = new Set([
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.CommentsCorrectionsList.CommentsCorrections.RefSource',
+    'PubmedArticleSet.PubmedArticle.MedlineCitation.CommentsCorrectionsList.CommentsCorrections.Note',
+]);
+/**
+ * Keeps text that must survive exactly as NCBI wrote it out of fast-xml-parser's
+ * numeric coercion: `Book/Isbn`, and a linked notice's `RefSource` and `Note`.
  *
  * 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)
+ * so the record ships a wrong ISBN with no error anywhere (#114). A purely
+ * numeric `RefSource` or `Note` loses its spelling the same way — `1.50` → `1.5`,
+ * `007` → `7`, `0x1A` → `26` (#178). 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.
+ * The flat parsers keep the default `jPath: true`, so the path arrives as a string.
  */
-const preserveIsbnText = (tagName, tagValue) => tagName === 'Isbn' ? undefined : tagValue;
+const preserveVerbatimText = (tagName, tagValue, jPath) => tagName === 'Isbn' || VERBATIM_TEXT_JPATHS.has(jPath) ? undefined : tagValue;
 /**
  * Parses NCBI E-utility responses (XML, JSON, text) and checks for NCBI-specific
  * error structures embedded in response bodies.
@@ -398,7 +501,7 @@ export class NcbiResponseHandler {
                 const path = jpath;
                 return NCBI_ARRAY_JPATHS.has(path) || ESUMMARY_ITEM_JPATH.test(path);
             },
-            tagValueProcessor: preserveIsbnText,
+            tagValueProcessor: preserveVerbatimText,
         };
         this.xmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: true });
         this.verbatimXmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: false });
@@ -424,14 +527,12 @@ export class NcbiResponseHandler {
                 reason: 'ncbi_resource_not_found',
                 endpoint,
                 ncbiErrors: errorMessages,
-                ...recoveryFor('ncbi_resource_not_found'),
             });
         }
         throw serviceUnavailable(`NCBI API Error: ${errorMessages.join('; ')}`, {
             reason: 'ncbi_unreachable',
             endpoint,
             ncbiErrors: errorMessages,
-            ...recoveryFor('ncbi_unreachable'),
         });
     }
     extractNcbiErrorMessages(parsedXml) {
@@ -472,7 +573,7 @@ export class NcbiResponseHandler {
                     operation: 'NcbiHtmlResponse',
                     additionalContext: { endpoint },
                 }));
-                throw serviceUnavailable('NCBI API returned an HTML response instead of XML — likely rate-limited.', { reason: 'ncbi_unreachable', endpoint, ...recoveryFor('ncbi_unreachable') });
+                throw serviceUnavailable('NCBI API returned an HTML response instead of XML — likely rate-limited.', { reason: 'ncbi_unreachable', endpoint });
             }
             // NCBI's eLink (and occasionally other endpoints) drops the root element
             // when the upstream backend connection fails mid-response, yielding just
@@ -489,7 +590,7 @@ export class NcbiResponseHandler {
                     operation: 'NcbiEmptyResponse',
                     additionalContext: { endpoint, responseLength: responseText.length },
                 }));
-                throw serviceUnavailable('NCBI returned an empty response body — the upstream backend likely failed mid-request.', { reason: 'ncbi_unreachable', endpoint, ...recoveryFor('ncbi_unreachable') });
+                throw serviceUnavailable('NCBI returned an empty response body — the upstream backend likely failed mid-request.', { reason: 'ncbi_unreachable', endpoint });
             }
             const xmlForValidation = responseText.replace(/<!DOCTYPE[^>]*>/gi, '');
             const validationResult = XMLValidator.validate(xmlForValidation);
@@ -505,7 +606,6 @@ export class NcbiResponseHandler {
                     reason: 'ncbi_invalid_response',
                     endpoint,
                     responseSnippet: responseText.substring(0, 200),
-                    ...recoveryFor('ncbi_invalid_response'),
                 });
             }
             const useOrdered = options?.useOrderedParser ?? false;
@@ -523,8 +623,8 @@ export class NcbiResponseHandler {
                 : options?.useVerbatimParser
                     ? this.verbatimXmlParser
                     : this.xmlParser;
-            // Pre-flatten <sup>/<sub>/<inf>/<i>/<b>/<u>/<sc> on the regular parser
-            // path. The ordered parser walks mixed content correctly via
+            // Pre-flatten inline markup (scripts, emphasis, MathML) on the regular
+            // parser path. The ordered parser walks mixed content correctly via
             // preserveOrder; the regular parser does not.
             const xmlForParse = useOrdered ? responseText : flattenInlineMarkup(responseText);
             let parsedXml;
@@ -546,7 +646,6 @@ export class NcbiResponseHandler {
                     endpoint,
                     parserError,
                     responseSnippet: responseText.substring(0, 200),
-                    ...recoveryFor('ncbi_invalid_response'),
                 }, { cause: error });
             }
             if (!useOrdered) {
@@ -583,7 +682,6 @@ export class NcbiResponseHandler {
                     reason: 'ncbi_invalid_response',
                     endpoint,
                     responseSnippet: responseText.substring(0, 200),
-                    ...recoveryFor('ncbi_invalid_response'),
                 }, { cause: error });
             }
             if (parsed && typeof parsed === 'object' && 'error' in parsed) {
@@ -597,14 +695,12 @@ export class NcbiResponseHandler {
                         reason: 'ncbi_resource_not_found',
                         endpoint,
                         ncbiErrors: [errorMessage],
-                        ...recoveryFor('ncbi_resource_not_found'),
                     });
                 }
                 throw serviceUnavailable(`NCBI API Error: ${errorMessage}`, {
                     reason: 'ncbi_unreachable',
                     endpoint,
-                    ncbiError: errorMessage,
-                    ...recoveryFor('ncbi_unreachable'),
+                    ncbiErrors: [errorMessage],
                 });
             }
             logger.debug('Successfully parsed JSON response.', requestContextService.createRequestContext({

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

@@ -1 +1 @@
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