npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.19 → 2.10.20 - Mend

@cyanheads/pubmed-mcp-server 2.10.19 → 2.10.20

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 (84) hide show

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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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"}

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

@@ -20,22 +20,96 @@ const NAMED_ENTITIES = {
 /** A well-formed numeric (`&#173;`, `&#xAD;`) or named (`&amp;`) 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 CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ncbi/response-handler.d.ts CHANGED Viewed

@@ -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
  */

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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;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 CHANGED Viewed

@@ -327,29 +327,122 @@ 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('');
 }
 /**
  * Free-text elements of a linked notice, matched by path: an element named `Note`
@@ -530,8 +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;

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	@@ -1 +1 @@
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package/dist/services/ncbi/types.d.ts CHANGED Viewed

@@ -820,8 +820,8 @@ export interface ECitMatchCitation {
     journal?: string | undefined;
     /**
      * Arbitrary label echoed onto this citation's result. Not a correlation key:
-     * it may repeat across citations, so `eCitMatch` submits a separate
-     * per-request token and matches upstream rows on that instead.
+     * it may repeat across citations, so `eCitMatch` submits the citation's
+     * position in the call as its token and matches upstream rows on that instead.
      */
     key: string;
     /** Volume number */

package/dist/services/openalex/openalex-service.d.ts CHANGED Viewed

@@ -13,8 +13,10 @@
  * serving an unexplained empty window.
  *
  * Transient failures retry with capped exponential backoff. Once retries run
- * out, only a `ServiceUnavailable` is reported as `openalex_unreachable`; a
- * `Timeout` or `RateLimited` keeps its own code and any upstream `retryAfter`.
+ * out, the last attempt's `data.reason` is kept (`openalex_invalid_response` for
+ * a body that is not JSON), and only a `ServiceUnavailable` with no reason is
+ * reported as `openalex_unreachable`; a `Timeout` or `RateLimited` keeps its own
+ * code and any upstream `retryAfter`.
  *
  * Uses the NCBI_ADMIN_EMAIL config (adminEmail) as the OpenAlex polite-pool
  * `mailto=` parameter when set; omits it when unset.
@@ -70,10 +72,12 @@ export declare class OpenAlexService {
     private finish;
     /**
      * Retry wrapper for transient errors. On exhaustion the last error keeps its
-     * code and an upstream `retryAfter`, so a 429 still tells the caller how long to
-     * wait. Only a `ServiceUnavailable` gains `openalex_unreachable` — the one code
-     * that reason is declared for; a `Timeout` or `RateLimited` keeps its
-     * code with no reason, as the Europe PMC service reports them.
+     * code, its `data.reason`, and an upstream `retryAfter`, so a 429 still tells the
+     * caller how long to wait and an unparseable body stays
+     * `openalex_invalid_response`. Only a `ServiceUnavailable` carrying no reason
+     * gains `openalex_unreachable` — the one code that reason is declared for; a
+     * `Timeout` or `RateLimited` keeps its code with no reason, as the Europe PMC
+     * service reports them.
      */
     private withRetry;
 }

package/dist/services/openalex/openalex-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA~~;;;;;;;;;;;;;;;;;;;;;;GAsBG~~;AAMH,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAIL,KAAK,qBAAqB,EAE3B,MAAM,YAAY,CAAC;AA4EpB,gFAAgF;AAChF,qBAAa,eAAe;IAExB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAF7B,YACmB,MAAM,EAAE,iBAAiB,EACzB,UAAU,EAAE,MAAM,EACjC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW3F;IAED;;;;;;;;OAQG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA4B3F;IAED;;;OAGG;IACG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW9F;IAED,8EAA8E;IAC9E,OAAO,CAAC,SAAS;IAQjB;;;;;;;;;OASG;YACW,iBAAiB;IAiC/B;;;;OAIG;IACH,OAAO,CAAC,MAAM;IAcd~~;;;;;;OAMG~~;YACW,SAAS;~~CAiDxB~~;AAMD,yEAAyE;AACzE,wBAAgB,mBAAmB,IAAI,IAAI,CAmB1C;AAED,uEAAuE;AACvE,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED,kFAAkF;AAClF,wBAAgB,0BAA0B,IAAI,eAAe,GAAG,SAAS,CAExE"}
1	+ {"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;GAwBG;AAMH,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAIL,KAAK,qBAAqB,EAE3B,MAAM,YAAY,CAAC;AA4EpB,gFAAgF;AAChF,qBAAa,eAAe;IAExB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAF7B,YACmB,MAAM,EAAE,iBAAiB,EACzB,UAAU,EAAE,MAAM,EACjC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW3F;IAED;;;;;;;;OAQG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA4B3F;IAED;;;OAGG;IACG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW9F;IAED,8EAA8E;IAC9E,OAAO,CAAC,SAAS;IAQjB;;;;;;;;;OASG;YACW,iBAAiB;IAiC/B;;;;OAIG;IACH,OAAO,CAAC,MAAM;IAcd;;;;;;;;OAQG;YACW,SAAS;CAkDxB;AAMD,yEAAyE;AACzE,wBAAgB,mBAAmB,IAAI,IAAI,CAmB1C;AAED,uEAAuE;AACvE,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED,kFAAkF;AAClF,wBAAgB,0BAA0B,IAAI,eAAe,GAAG,SAAS,CAExE"}

package/dist/services/openalex/openalex-service.js CHANGED Viewed

@@ -13,8 +13,10 @@
  * serving an unexplained empty window.
  *
  * Transient failures retry with capped exponential backoff. Once retries run
- * out, only a `ServiceUnavailable` is reported as `openalex_unreachable`; a
- * `Timeout` or `RateLimited` keeps its own code and any upstream `retryAfter`.
+ * out, the last attempt's `data.reason` is kept (`openalex_invalid_response` for
+ * a body that is not JSON), and only a `ServiceUnavailable` with no reason is
+ * reported as `openalex_unreachable`; a `Timeout` or `RateLimited` keeps its own
+ * code and any upstream `retryAfter`.
  *
  * Uses the NCBI_ADMIN_EMAIL config (adminEmail) as the OpenAlex polite-pool
  * `mailto=` parameter when set; omits it when unset.
@@ -203,10 +205,12 @@ export class OpenAlexService {
     }
     /**
      * Retry wrapper for transient errors. On exhaustion the last error keeps its
-     * code and an upstream `retryAfter`, so a 429 still tells the caller how long to
-     * wait. Only a `ServiceUnavailable` gains `openalex_unreachable` — the one code
-     * that reason is declared for; a `Timeout` or `RateLimited` keeps its
-     * code with no reason, as the Europe PMC service reports them.
+     * code, its `data.reason`, and an upstream `retryAfter`, so a 429 still tells the
+     * caller how long to wait and an unparseable body stays
+     * `openalex_invalid_response`. Only a `ServiceUnavailable` carrying no reason
+     * gains `openalex_unreachable` — the one code that reason is declared for; a
+     * `Timeout` or `RateLimited` keeps its code with no reason, as the Europe PMC
+     * service reports them.
      */
     async withRetry(execute, label, signal) {
         for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
@@ -234,10 +238,10 @@ export class OpenAlexService {
                     continue;
                 }
                 const attempts = this.maxRetries + 1;
+                const reason = error.data?.reason ??
+                    (error.code === JsonRpcErrorCode.ServiceUnavailable ? 'openalex_unreachable' : undefined);
                 throw new McpError(error.code, `${error.message} (failed after ${attempts} attempt${attempts === 1 ? '' : 's'})`, {
-                    ...(error.code === JsonRpcErrorCode.ServiceUnavailable && {
-                        reason: 'openalex_unreachable',
-                    }),
+                    ...(reason !== undefined && { reason }),
                     label,
                     attempts,
                     ...(error.data?.retryAfter !== undefined && { retryAfter: error.data.retryAfter }),

package/dist/services/openalex/openalex-service.js.map CHANGED Viewed

	@@ -1 +1 @@
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