@cyanheads/pubmed-mcp-server 2.10.21 → 2.10.22

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

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

@@ -98,6 +98,53 @@ export function isMathTag(tag) {
 }
 /** MathML token elements, which contribute their text as deposited. */
 const MATH_TOKEN_TAGS = new Set(['mi', 'mn', 'mo', 'mtext', 'ms']);
+/** The alternate renderings a `<semantics>` carries after its expression. (#230) */
+const MATH_ANNOTATION_TAGS = new Set(['annotation', 'annotation-xml']);
+/**
+ * Content MathML elements that can stand as a whole expression: the strict
+ * set plus the containers pragmatic markup writes directly. Read as
+ * presentation they contribute only their leaves (`x2` for x²). (#230)
+ */
+const CONTENT_MATH_TAGS = new Set([
+    'apply',
+    'bind',
+    'cbytes',
+    'cerror',
+    'ci',
+    'cn',
+    'cs',
+    'csymbol',
+    'interval',
+    'lambda',
+    'list',
+    'matrix',
+    'piecewise',
+    'set',
+    'share',
+    'vector',
+]);
+/** `<annotation-xml>` encodings that mark a Presentation MathML rendering. (#230) */
+const PRESENTATION_ENCODINGS = new Set([
+    'mathml-presentation',
+    'application/mathml-presentation+xml',
+]);
+/**
+ * The child a MathML `<semantics>` renders through: its expression — the first
+ * child that is not an annotation — or, when that expression is Content
+ * MathML, a Presentation MathML `<annotation-xml>` beside it (MathML 3
+ * §5.1.3, §5.2.1). Every other annotation is an alternate spelling of the same
+ * expression (TeX source, MathType data, Content markup) and never reads.
+ */
+function semanticsRendering(args) {
+    const isAnnotation = (node) => MATH_ANNOTATION_TAGS.has(localName(tagNameOf(node) ?? ''));
+    const expression = args.find((arg) => !isAnnotation(arg));
+    if (!expression || !CONTENT_MATH_TAGS.has(localName(tagNameOf(expression) ?? ''))) {
+        return expression;
+    }
+    const presentation = args.find((arg) => localName(tagNameOf(arg) ?? '') === 'annotation-xml' &&
+        PRESENTATION_ENCODINGS.has(attrOf(arg, 'encoding')?.toLowerCase() ?? ''));
+    return presentation ?? expression;
+}
 /**
  * A MathML `<math>` element in a TeX-style linear form — the notation a
  * formula deposited as `<tex-math>` already reads in — so a formula keeps the
@@ -113,6 +160,7 @@ const MATH_TOKEN_TAGS = new Set(['mi', 'mn', 'mo', 'mtext', 'ms']);
  * | `mfenced` | `open`, the children split by `separators`, `close` (defaults `(`, `,`, `)`) |
  * | `mtable` | cells split by ` & `, rows by ` \\ ` |
  * | `mspace` / `mphantom` | one space / nothing |
+ * | `semantics` | one rendering of its expression, never an annotation (see `semanticsRendering`) |
  * | anything else | its children in order |
  *
  * An empty script slot is left out (`x^{2}`, not `x_{}^{2}`). Whitespace-only
@@ -239,6 +287,9 @@ export function linearMath(math) {
                 return;
             case 'mphantom':
                 return;
+            case 'semantics':
+                write(semanticsRendering(args));
+                return;
             default:
                 for (const child of childrenOf(node))
                     write(child);
@@ -311,6 +362,12 @@ const LINE_SEPARATOR = 2;
 const WHITESPACE_CHAR = /\s/;
 /** Any character other than whitespace. */
 const VISIBLE_CHAR = /\S/;
+/**
+ * Punctuation that closes the text before it — `L<0.`, `Henry L,`, `(2020)` —
+ * so whitespace a pretty-printed deposit leaves in front of it is formatting,
+ * not spacing. (#219, #225)
+ */
+export const CLOSING_PUNCTUATION = new Set(['.', ',', ';', ':', ')', ']']);
 /**
  * Accumulates JATS text in document order and decides every separator the
  * markup implies in the same pass, from state it carries rather than by
@@ -327,6 +384,12 @@ const VISIBLE_CHAR = /\S/;
  *   between them is preceded by a comma: `[1,2,3,4]`, not `[1234]`, which reads
  *   as one reference. Any source text between them, whitespace included, means
  *   the source already separated them. (#197)
+ * - Whitespace between an element and the {@link CLOSING_PUNCTUATION} after it
+ *   is dropped when it holds a line break, whether the punctuation follows in
+ *   plain text or opens the next element: `</inline-formula>\n<italic>.</italic>`
+ *   reads `L<0.`, not `L<0 .`. A gap with no line break, one before `(` or a
+ *   word, and a line boundary owed there are kept, and so is a line break
+ *   between a word and punctuation with no element closing between them. (#225)
  *
  * An owed separator is only written between two pieces of content, so a reader
  * adds nothing at the edges of what it reads. By default the source text is
@@ -353,6 +416,12 @@ export class TextAssembler {
     #commaOwed = false;
     /** {@link #written} at each open `<label>` and `<xref>`, innermost last. */
     #marks = [];
+    /** An element closed since the last visible character was written. */
+    #elementClosed = false;
+    /** The whitespace written since the last visible character holds a line break. */
+    #gapHasLineBreak = false;
+    /** Where that whitespace starts in {@link #out}: every piece from here on is whitespace. */
+    #gapStart = 0;
     constructor(options = {}) {
         this.#lines = options.lines ?? false;
     }
@@ -361,25 +430,44 @@ export class TextAssembler {
         if (value === '')
             return;
         this.#afterXref = false;
-        if (!VISIBLE_CHAR.test(value)) {
+        const lead = value.search(VISIBLE_CHAR);
+        if (lead === -1) {
             this.#out.push(this.#lines ? ' ' : value);
             this.#endsWithSpace = true;
+            if (value.includes('\n'))
+                this.#gapHasLineBreak = true;
             return;
         }
+        let start = 0;
         if (this.#written > 0 && this.#owed !== NO_SEPARATOR) {
             const separator = this.#owed === LINE_SEPARATOR ? '\n' : ' ';
-            const sourceSpaced = this.#endsWithSpace || WHITESPACE_CHAR.test(value.charAt(0));
+            const sourceSpaced = this.#endsWithSpace || lead > 0;
             if (this.#lines || !sourceSpaced)
                 this.#out.push(separator);
         }
         else if (this.#commaOwed) {
             this.#out.push(',');
         }
+        else if (this.#lineBreakBeforePunctuation(value, lead)) {
+            this.#out.length = this.#gapStart;
+            start = lead;
+        }
         this.#owed = NO_SEPARATOR;
         this.#afterLabel = false;
         this.#commaOwed = false;
-        this.#out.push(this.#lines ? value.replace(/\s+/g, ' ') : value);
-        this.#endsWithSpace = WHITESPACE_CHAR.test(value.charAt(value.length - 1));
+        // The trailing whitespace goes in a piece of its own, so the gap it opens can be dropped whole.
+        let end = value.length;
+        while (WHITESPACE_CHAR.test(value.charAt(end - 1)))
+            end -= 1;
+        const body = value.slice(start, end);
+        const trail = value.slice(end);
+        this.#out.push(this.#lines ? body.replace(/\s+/g, ' ') : body);
+        this.#gapStart = this.#out.length;
+        if (trail)
+            this.#out.push(this.#lines ? ' ' : trail);
+        this.#endsWithSpace = trail !== '';
+        this.#gapHasLineBreak = trail.includes('\n');
+        this.#elementClosed = false;
         this.#written += 1;
     }
     /** Enter an element, before its children are read. */
@@ -401,6 +489,7 @@ export class TextAssembler {
      * block nested in inline markup — owes nothing.
      */
     close(tag) {
+        this.#elementClosed = true;
         if (LINE_BOUNDARY_TAGS.has(tag)) {
             this.#oweLine();
             return;
@@ -436,6 +525,17 @@ export class TextAssembler {
         if (!this.#afterLabel)
             this.#owed = LINE_SEPARATOR;
     }
+    /**
+     * True when `value`, visible from `lead`, opens with closing punctuation, an
+     * element closed since the last visible character, and the whitespace between
+     * them holds a line break.
+     */
+    #lineBreakBeforePunctuation(value, lead) {
+        return (this.#written > 0 &&
+            this.#elementClosed &&
+            CLOSING_PUNCTUATION.has(value.charAt(lead)) &&
+            (this.#gapHasLineBreak || value.lastIndexOf('\n', lead) !== -1));
+    }
 }
 /**
  * Drive `sink` through a node or sibling list in document order. `excluded`
@@ -458,12 +558,10 @@ function readInto(input, sink, excluded) {
         const tag = tagNameOf(node) ?? '';
         if (IDENTIFIER_TAGS.has(tag) || excluded?.has(tag))
             continue;
-        if (tag === TEX_MATH_TAG) {
-            sink.text(texMathExpression(readText(childrenOf(node))));
-            continue;
-        }
-        if (isMathTag(tag)) {
-            sink.text(linearMath(node));
+        if (tag === TEX_MATH_TAG || isMathTag(tag)) {
+            sink.open(tag);
+            sink.text(tag === TEX_MATH_TAG ? texMathExpression(readText(childrenOf(node))) : linearMath(node));
+            sink.close(tag);
             continue;
         }
         if (tag === ALTERNATIVES_TAG) {

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

@@ -1 +1 @@
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package/dist/services/ncbi/parsing/text-helpers.d.ts

@@ -28,4 +28,14 @@ export declare function decodeHtmlEntities(text: string): string;
  * character budget is spent on text rather than markup.
  */
 export declare function toDisplayText(text: string): string;
+/**
+ * Drop {@link INVISIBLE_FORMAT_CHARS_RE} from a raw XML body before it is
+ * parsed, once for every reader of the tree. JavaScript's `\s` matches U+FEFF,
+ * so each whitespace collapse downstream turned one inside a word into a space
+ * that split it (`hepatopulmonary s yndrome`); U+00AD and U+200B survive every
+ * collapse and break a search for the word (`employ` + U+00AD + `ment`). The
+ * characters never stand for spacing, so a real space beside one stays one
+ * space. (#224)
+ */
+export declare function stripInvisibleFormatChars(xml: 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;AAsHH;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAcvD;AAED;;;;;;;;;;GAUG;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;AAUD;;;;;;;;GAQG;AACH,wBAAgB,yBAAyB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAE7D"}

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

@@ -152,4 +152,23 @@ export function toDisplayText(text) {
         .replace(WHITESPACE_RE, ' ')
         .trim();
 }
+/**
+ * U+FEFF (zero width no-break space), U+00AD (soft hyphen) and U+200B (zero
+ * width space): invisible characters PMC deposits carry inside words. U+200C
+ * and U+200D, joiners that carry meaning in some scripts, are left alone, and so
+ * is U+2060, which no deposit sampled carries.
+ */
+const INVISIBLE_FORMAT_CHARS_RE = /[\uFEFF\u00AD\u200B]/g;
+/**
+ * Drop {@link INVISIBLE_FORMAT_CHARS_RE} from a raw XML body before it is
+ * parsed, once for every reader of the tree. JavaScript's `\s` matches U+FEFF,
+ * so each whitespace collapse downstream turned one inside a word into a space
+ * that split it (`hepatopulmonary s yndrome`); U+00AD and U+200B survive every
+ * collapse and break a search for the word (`employ` + U+00AD + `ment`). The
+ * characters never stand for spacing, so a real space beside one stays one
+ * space. (#224)
+ */
+export function stripInvisibleFormatChars(xml) {
+    return xml.replace(INVISIBLE_FORMAT_CHARS_RE, '');
+}
 //# sourceMappingURL=text-helpers.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"text-helpers.js","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/text-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,mFAAmF;AACnF,MAAM,cAAc,GAAqC;IACvD,GAAG,EAAE,GAAG;IACR,EAAE,EAAE,GAAG;IACP,EAAE,EAAE,GAAG;IACP,IAAI,EAAE,GAAG;IACT,IAAI,EAAE,GAAG;IACT,IAAI,EAAE,GAAG;IACT,GAAG,EAAE,GAAG;CACT,CAAC;AAEF,yFAAyF;AACzF,MAAM,SAAS,GAAG,uCAAuC,CAAC;AAC1D;;;;GAIG;AACH,MAAM,oBAAoB,GAAG;IAC3B,GAAG;IACH,MAAM;IACN,IAAI;IACJ,GAAG;IACH,KAAK;IACL,QAAQ;IACR,IAAI;IACJ,QAAQ;IACR,KAAK;IACL,KAAK;IACL,GAAG;IACH,WAAW;CACH,CAAC;AACX,MAAM,uBAAuB,GAAwB,IAAI,GAAG,CAAC,oBAAoB,CAAC,CAAC;AACnF,MAAM,0BAA0B,GAAG,oBAAoB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;AAClE;;;;;;;;;;;;;;;;;;;;;GAqBG;AACH,MAAM,aAAa,GAAG,IAAI,MAAM,CAC9B,yDAAyD,0BAA0B,OAAO,EAC1F,IAAI,CACL,CAAC;AACF,0EAA0E;AAC1E,MAAM,YAAY,GAAG,IAAI,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC;AACnD,uEAAuE;AACvE,MAAM,oBAAoB,GAAG,IAAI,MAAM,CACrC,WAAW,0BAA0B,iBAAiB,0BAA0B,OAAO,EACvF,IAAI,CACL,CAAC;AACF,gDAAgD;AAChD,MAAM,oBAAoB,GAAG,gBAAgB,CAAC;AAC9C,MAAM,cAAc,GAAG,OAAO,CAAC;AAC/B,MAAM,cAAc,GAAG,IAAI,CAAC;AAC5B,MAAM,aAAa,GAAG,MAAM,CAAC;AAE7B;;;;;;;;GAQG;AACH,SAAS,gBAAgB,CACvB,GAAW,EACX,OAA2B,EAC3B,OAA2B,EAC3B,MAAc,EACd,IAAY;IAEZ,MAAM,UAAU,GACd,OAAO,KAAK,SAAS;QACrB,CAAC,OAAO,KAAK,SAAS,IAAI,uBAAuB,CAAC,GAAG,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC;IAChF,OAAO,UAAU,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;AACrF,CAAC;AAED;;;;;;;;GAQG;AACH,SAAS,cAAc,CAAC,IAAY,EAAE,KAAa,EAAE,GAAW;IAC9D,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;IAC/B,IAAI,MAAM,KAAK,SAAS,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,MAAM,CAAC;QAAE,OAAO,KAAK,CAAC;IACpE,IAAI,MAAM,KAAK,GAAG,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,GAAG;QAAE,OAAO,KAAK,CAAC;IAC5D,IAAI,IAAI,GAAG,GAAG,CAAC;IACf,oBAAoB,CAAC,SAAS,GAAG,IAAI,CAAC;IACtC,OAAO,oBAAoB,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,IAAI,GAAG,oBAAoB,CAAC,SAAS,CAAC;IAC9E,oBAAoB,CAAC,SAAS,GAAG,IAAI,CAAC;IACtC,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,KAAK,CAAC;IACnD,OAAO,CAAC,CAAC,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;AAChG,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,kBAAkB,CAAC,IAAY;IAC7C,OAAO,IAAI,CAAC,OAAO,CAAC,SAAS,EAAE,CAAC,KAAK,EAAE,IAAY,EAAE,EAAE;QACrD,IAAI,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,SAAS,EAAE,CAAC;YACxC,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,eAAe;YACtF,MAAM,SAAS,GAAG,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACpF,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,IAAI,SAAS,GAAG,CAAC,IAAI,SAAS,GAAG,QAAQ;gBAAE,OAAO,KAAK,CAAC;YACvF,IAAI,CAAC;gBACH,OAAO,MAAM,CAAC,aAAa,CAAC,SAAS,CAAC,CAAC;YACzC,CAAC;YAAC,MAAM,CAAC;gBACP,OAAO,KAAK,CAAC;YACf,CAAC;QACH,CAAC;QACD,OAAO,cAAc,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC,IAAI,KAAK,CAAC;IACrD,CAAC,CAAC,CAAC;AACL,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,aAAa,CAAC,IAAY;IACxC,OAAO,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,EAAE,gBAAgB,CAAC,CAAC;SACrE,OAAO,CAAC,cAAc,EAAE,EAAE,CAAC;SAC3B,OAAO,CAAC,aAAa,EAAE,GAAG,CAAC;SAC3B,IAAI,EAAE,CAAC;AACZ,CAAC"}
+{"version":3,"file":"text-helpers.js","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/text-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,mFAAmF;AACnF,MAAM,cAAc,GAAqC;IACvD,GAAG,EAAE,GAAG;IACR,EAAE,EAAE,GAAG;IACP,EAAE,EAAE,GAAG;IACP,IAAI,EAAE,GAAG;IACT,IAAI,EAAE,GAAG;IACT,IAAI,EAAE,GAAG;IACT,GAAG,EAAE,GAAG;CACT,CAAC;AAEF,yFAAyF;AACzF,MAAM,SAAS,GAAG,uCAAuC,CAAC;AAC1D;;;;GAIG;AACH,MAAM,oBAAoB,GAAG;IAC3B,GAAG;IACH,MAAM;IACN,IAAI;IACJ,GAAG;IACH,KAAK;IACL,QAAQ;IACR,IAAI;IACJ,QAAQ;IACR,KAAK;IACL,KAAK;IACL,GAAG;IACH,WAAW;CACH,CAAC;AACX,MAAM,uBAAuB,GAAwB,IAAI,GAAG,CAAC,oBAAoB,CAAC,CAAC;AACnF,MAAM,0BAA0B,GAAG,oBAAoB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;AAClE;;;;;;;;;;;;;;;;;;;;;GAqBG;AACH,MAAM,aAAa,GAAG,IAAI,MAAM,CAC9B,yDAAyD,0BAA0B,OAAO,EAC1F,IAAI,CACL,CAAC;AACF,0EAA0E;AAC1E,MAAM,YAAY,GAAG,IAAI,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,CAAC,CAAC;AACnD,uEAAuE;AACvE,MAAM,oBAAoB,GAAG,IAAI,MAAM,CACrC,WAAW,0BAA0B,iBAAiB,0BAA0B,OAAO,EACvF,IAAI,CACL,CAAC;AACF,gDAAgD;AAChD,MAAM,oBAAoB,GAAG,gBAAgB,CAAC;AAC9C,MAAM,cAAc,GAAG,OAAO,CAAC;AAC/B,MAAM,cAAc,GAAG,IAAI,CAAC;AAC5B,MAAM,aAAa,GAAG,MAAM,CAAC;AAE7B;;;;;;;;GAQG;AACH,SAAS,gBAAgB,CACvB,GAAW,EACX,OAA2B,EAC3B,OAA2B,EAC3B,MAAc,EACd,IAAY;IAEZ,MAAM,UAAU,GACd,OAAO,KAAK,SAAS;QACrB,CAAC,OAAO,KAAK,SAAS,IAAI,uBAAuB,CAAC,GAAG,CAAC,OAAO,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC;IAChF,OAAO,UAAU,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;AACrF,CAAC;AAED;;;;;;;;GAQG;AACH,SAAS,cAAc,CAAC,IAAY,EAAE,KAAa,EAAE,GAAW;IAC9D,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC;IAC/B,IAAI,MAAM,KAAK,SAAS,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,MAAM,CAAC;QAAE,OAAO,KAAK,CAAC;IACpE,IAAI,MAAM,KAAK,GAAG,IAAI,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,GAAG;QAAE,OAAO,KAAK,CAAC;IAC5D,IAAI,IAAI,GAAG,GAAG,CAAC;IACf,oBAAoB,CAAC,SAAS,GAAG,IAAI,CAAC;IACtC,OAAO,oBAAoB,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,IAAI,GAAG,oBAAoB,CAAC,SAAS,CAAC;IAC9E,oBAAoB,CAAC,SAAS,GAAG,IAAI,CAAC;IACtC,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,IAAI,CAAC;QAAE,OAAO,KAAK,CAAC;IACnD,OAAO,CAAC,CAAC,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,IAAI,cAAc,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;AAChG,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,kBAAkB,CAAC,IAAY;IAC7C,OAAO,IAAI,CAAC,OAAO,CAAC,SAAS,EAAE,CAAC,KAAK,EAAE,IAAY,EAAE,EAAE;QACrD,IAAI,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,SAAS,EAAE,CAAC;YACxC,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,eAAe;YACtF,MAAM,SAAS,GAAG,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACpF,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,IAAI,SAAS,GAAG,CAAC,IAAI,SAAS,GAAG,QAAQ;gBAAE,OAAO,KAAK,CAAC;YACvF,IAAI,CAAC;gBACH,OAAO,MAAM,CAAC,aAAa,CAAC,SAAS,CAAC,CAAC;YACzC,CAAC;YAAC,MAAM,CAAC;gBACP,OAAO,KAAK,CAAC;YACf,CAAC;QACH,CAAC;QACD,OAAO,cAAc,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC,IAAI,KAAK,CAAC;IACrD,CAAC,CAAC,CAAC;AACL,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,aAAa,CAAC,IAAY;IACxC,OAAO,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,EAAE,gBAAgB,CAAC,CAAC;SACrE,OAAO,CAAC,cAAc,EAAE,EAAE,CAAC;SAC3B,OAAO,CAAC,aAAa,EAAE,GAAG,CAAC;SAC3B,IAAI,EAAE,CAAC;AACZ,CAAC;AAED;;;;;GAKG;AACH,MAAM,yBAAyB,GAAG,uBAAuB,CAAC;AAE1D;;;;;;;;GAQG;AACH,MAAM,UAAU,yBAAyB,CAAC,GAAW;IACnD,OAAO,GAAG,CAAC,OAAO,CAAC,yBAAyB,EAAE,EAAE,CAAC,CAAC;AACpD,CAAC"}

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

@@ -65,17 +65,6 @@ export declare class NcbiResponseHandler {
      * uses, so the two JATS paths cannot drift apart. (#69, #127)
      */
     private readonly orderedXmlParser;
-    /**
-     * Flat, named-key parser with `parseTagValue: false`. Same shape as
-     * `xmlParser` — `response.eSpellResult.Query` still resolves — but tag text
-     * arrives verbatim. Used where a response echoes an arbitrary caller-supplied
-     * token: ESpell's `<Query>` is the only such field today, and coercion there
-     * destroys the text before application code runs (`007` → `7`, `1e5` →
-     * `100000`), which no read-site `String()` can undo. `orderedXmlParser` is
-     * not a substitute — it also sets `preserveOrder`, returning a node array
-     * rather than the property access the ESpell read depends on. (#108)
-     */
-    private readonly verbatimXmlParser;
     constructor();
     /**
      * Extract a structured error from a parsed NCBI XML body and throw it as

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

@@ -1 +1 @@
-{"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;AAgJrD;;;;;;;;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"}
+{"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;AAqJrD;;;;;;;;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;IAEjD,cAeC;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,CA6NH;CACF"}

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

@@ -21,7 +21,7 @@ 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 { ORDERED_XML_PARSER_OPTIONS, XML_PROCESS_ENTITIES_OPTIONS, } from './parsing/ordered-xml-parser-options.js';
-import { decodeHtmlEntities } from './parsing/text-helpers.js';
+import { decodeHtmlEntities, stripInvisibleFormatChars } 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.
@@ -90,10 +90,11 @@ const NCBI_ARRAY_JPATHS = new Set([
  * 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.
+ * children — the version-1 fallback in `esummary-parser` reads an `AuthorList`
+ * and `ArticleIds` this way. 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)+$/;
@@ -106,6 +107,10 @@ const ERROR_PATHS = [
     'eSearchResult.ERROR',
     'eSummaryResult.ERROR',
     'eFetchResult.ERROR',
+    // ESpell is parsed on the ordered path, which reaches this list only for a
+    // non-empty `<ERROR>`. The empty `<ERROR/>` it sends with every answer would
+    // read as an error on the flat path. (#241)
+    'eSpellResult.ERROR',
     'PubmedArticleSet.ErrorList.CannotRetrievePMID',
     'ERROR',
 ];
@@ -466,7 +471,7 @@ const VERBATIM_TEXT_JPATHS = new Set([
  * `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.
+ * The flat parser keeps the default `jPath: true`, so the path arrives as a string.
  */
 const preserveVerbatimText = (tagName, tagValue, jPath) => tagName === 'Isbn' || VERBATIM_TEXT_JPATHS.has(jPath) ? undefined : tagValue;
 /**
@@ -481,33 +486,20 @@ export class NcbiResponseHandler {
      * uses, so the two JATS paths cannot drift apart. (#69, #127)
      */
     orderedXmlParser;
-    /**
-     * Flat, named-key parser with `parseTagValue: false`. Same shape as
-     * `xmlParser` — `response.eSpellResult.Query` still resolves — but tag text
-     * arrives verbatim. Used where a response echoes an arbitrary caller-supplied
-     * token: ESpell's `<Query>` is the only such field today, and coercion there
-     * destroys the text before application code runs (`007` → `7`, `1e5` →
-     * `100000`), which no read-site `String()` can undo. `orderedXmlParser` is
-     * not a substitute — it also sets `preserveOrder`, returning a node array
-     * rather than the property access the ESpell read depends on. (#108)
-     */
-    verbatimXmlParser;
     constructor() {
-        // The two flat, named-key parsers differ only in `parseTagValue`.
-        const flatOptions = {
+        this.xmlParser = new FastXmlParser({
             ignoreAttributes: false,
             attributeNamePrefix: '@_',
             processEntities: XML_PROCESS_ENTITIES_OPTIONS,
             htmlEntities: true,
+            parseTagValue: true,
             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: preserveVerbatimText,
-        };
-        this.xmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: true });
-        this.verbatimXmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: false });
+        });
         this.orderedXmlParser = new FastXmlParser(ORDERED_XML_PARSER_OPTIONS);
     }
     /**
@@ -619,17 +611,13 @@ export class NcbiResponseHandler {
                 const errorParsed = this.xmlParser.parse(responseText);
                 this.throwNcbiError(errorParsed, endpoint);
             }
-            // Ordered wins when both are set: it is the JATS mixed-content path, and
-            // it already parses tag values verbatim.
-            const parser = useOrdered
-                ? this.orderedXmlParser
-                : options?.useVerbatimParser
-                    ? this.verbatimXmlParser
-                    : this.xmlParser;
-            // 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);
+            const parser = useOrdered ? this.orderedXmlParser : this.xmlParser;
+            // Invisible characters a deposit carries inside words go before either
+            // parser sees them (#224). Then 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 visibleXml = stripInvisibleFormatChars(responseText);
+            const xmlForParse = useOrdered ? visibleXml : flattenInlineMarkup(visibleXml);
             let parsedXml;
             try {
                 parsedXml = parser.parse(xmlForParse);

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

@@ -1 +1 @@
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