@cyanheads/pubmed-mcp-server 2.10.7 → 2.10.9

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

@@ -44,20 +44,31 @@ export function textOf(node) {
 /**
  * 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.
  */
-function concatText(input) {
+function concatText(input, excluded) {
     const nodes = Array.isArray(input) ? input : [input];
     const parts = [];
     for (const node of nodes) {
         if (isTextNode(node)) {
             parts.push(textOf(node));
         }
-        else {
-            parts.push(concatText(childrenOf(node)));
+        else if (!excluded?.has(tagNameOf(node) ?? '')) {
+            parts.push(concatText(childrenOf(node), excluded));
         }
     }
     return parts.join('');
 }
+/**
+ * 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
+ * the caller assembles several fragments itself and needs to collapse once over
+ * the joined result; {@link textContent} is the normalizing form for everything
+ * else.
+ */
+export function rawTextContent(input) {
+    return input ? concatText(input) : '';
+}
 /**
  * Extract all text from a node or sibling list in document order, collapsing
  * runs of whitespace to a single space and trimming the result. Use this for
@@ -69,6 +80,18 @@ export function textContent(input) {
         return '';
     return concatText(input).replace(/\s+/g, ' ').trim();
 }
+/**
+ * {@link textContent}, with the subtree of any element named in `excludedTags`
+ * left out. Block content a publisher nests inside a `<p>` — a `<table-wrap>` in
+ * particular — would otherwise be flattened into the paragraph, running every
+ * cell together into values that never existed. Such content is extracted
+ * separately and must not appear in the prose twice.
+ */
+export function textContentExcluding(input, excludedTags) {
+    if (!input)
+        return '';
+    return concatText(input, excludedTags).replace(/\s+/g, ' ').trim();
+}
 /** First direct child with the given tag name. */
 export function findOne(input, tagName) {
     if (!input)
@@ -83,4 +106,27 @@ export function findAll(input, tagName) {
     const children = Array.isArray(input) ? input : childrenOf(input);
     return children.filter((c) => tagNameOf(c) === tagName);
 }
+/**
+ * Every descendant element with the given tag name, in document order.
+ * {@link findAll} matches direct children only, which is right for reading a
+ * known JATS shape; this is for containers publishers place at varying depths
+ * (a `<ref-list>` under `<back>` in one deposit and under `body/sec/sec` in the
+ * next). The walk keeps descending through a match, so a container nested
+ * inside another of the same tag is reported too. Each node is visited once, so
+ * the result never repeats a node.
+ */
+export function findAllDescendants(input, tagName) {
+    if (!input)
+        return [];
+    const found = [];
+    const visit = (nodes) => {
+        for (const node of nodes) {
+            if (tagNameOf(node) === tagName)
+                found.push(node);
+            visit(childrenOf(node));
+        }
+    };
+    visit(Array.isArray(input) ? input : childrenOf(input));
+    return found;
+}
 //# sourceMappingURL=pmc-xml-helpers.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"pmc-xml-helpers.js","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-xml-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAgBH,MAAM,QAAQ,GAAG,IAAI,CAAC;AACtB,MAAM,QAAQ,GAAG,OAAO,CAAC;AAEzB,uFAAuF;AACvF,MAAM,UAAU,SAAS,CAAC,IAAc;IACtC,KAAK,MAAM,GAAG,IAAI,IAAI,EAAE,CAAC;QACvB,IAAI,GAAG,KAAK,QAAQ,IAAI,GAAG,KAAK,QAAQ;YAAE,OAAO,GAAG,CAAC;IACvD,CAAC;IACD,OAAO;AACT,CAAC;AAED,iFAAiF;AACjF,MAAM,UAAU,UAAU,CAAC,IAAc;IACvC,MAAM,GAAG,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC;IAC5B,IAAI,CAAC,GAAG;QAAE,OAAO,EAAE,CAAC;IACpB,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC;IACxB,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAE,KAAsB,CAAC,CAAC,CAAC,EAAE,CAAC;AAC7D,CAAC;AAED,sDAAsD;AACtD,MAAM,UAAU,MAAM,CAAC,IAAc,EAAE,IAAY;IACjD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAwC,CAAC;IACpE,MAAM,GAAG,GAAG,KAAK,EAAE,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC;IACjC,OAAO,GAAG,IAAI,IAAI,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;AAC/C,CAAC;AAED,yCAAyC;AACzC,MAAM,UAAU,UAAU,CAAC,IAAc;IACvC,OAAO,QAAQ,IAAI,IAAI,CAAC;AAC1B,CAAC;AAED,6CAA6C;AAC7C,MAAM,UAAU,MAAM,CAAC,IAAc;IACnC,MAAM,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC;IACzB,OAAO,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;AACpC,CAAC;AAED;;;;GAIG;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;QAC3B,CAAC;aAAM,IAAI,CAAC,QAAQ,EAAE,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,EAAE,CAAC;YACjD,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,IAAI,CAAC,EAAE,QAAQ,CAAC,CAAC,CAAC;QACrD,CAAC;IACH,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/response-handler.d.ts

@@ -30,15 +30,9 @@ export declare function flattenInlineMarkup(xml: string): string;
 export declare class NcbiResponseHandler {
     private readonly xmlParser;
     /**
-     * Parser configured for JATS mixed content (PMC full-text). `preserveOrder`
-     * keeps document order so inline markup in `<p>`, `<abstract>`, `<title>`
-     * doesn't collapse into reordered text. `trimValues: false` retains spacing
-     * between text nodes and adjacent inline children. `parseTagValue: false`
-     * keeps bibliographic tokens verbatim — page ranges like `4002.e26` and
-     * zero-padded pages would otherwise coerce to `Number` (→ `4.002e+29`, `123`);
-     * every value on this path is `String()`-ed downstream, so coercion is pure
-     * downside. Entity decoding is unaffected (it's governed by `processEntities`/
-     * `htmlEntities`), so page-range en-dashes still resolve. (#69)
+     * Parser configured for JATS mixed content (PMC full-text), built from
+     * {@link ORDERED_XML_PARSER_OPTIONS} — the same constant `EuropePmcService`
+     * uses, so the two JATS paths cannot drift apart. (#69, #127)
      */
     private readonly orderedXmlParser;
     /**

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;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAkMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;;;;;;OAUG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IACjD;;;;;;;;;OASG;IACH,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAgB;IAElD,cAqBC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA2BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,CAsOH;CACF"}
+{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAqBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAuLrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;OAIG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IACjD;;;;;;;;;OASG;IACH,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAgB;IAElD,cAaC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA2BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,CAsOH;CACF"}

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

@@ -18,6 +18,7 @@ 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 { recoveryFor } from '../error-contracts.js';
+import { ORDERED_XML_PARSER_OPTIONS, XML_PROCESS_ENTITIES_OPTIONS, } from './parsing/ordered-xml-parser-options.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.
@@ -82,16 +83,6 @@ const WARNING_PATHS = [
     'eSearchResult.WarningList.QuotedPhraseNotFound',
     'eSearchResult.WarningList.OutputMessage',
 ];
-/**
- * NCBI responses routinely contain numeric character references for punctuation
- * and diacritics, especially in page ranges and author names. Keep entity
- * processing enabled, but raise the aggregate expansion ceiling high enough for
- * trusted PubMed payloads.
- */
-const NCBI_PROCESS_ENTITIES_OPTIONS = {
-    enabled: true,
-    maxTotalExpansions: 100_000,
-};
 function resolvePath(obj, path) {
     let current = obj;
     for (const part of path.split('.')) {
@@ -228,15 +219,9 @@ export function flattenInlineMarkup(xml) {
 export class NcbiResponseHandler {
     xmlParser;
     /**
-     * Parser configured for JATS mixed content (PMC full-text). `preserveOrder`
-     * keeps document order so inline markup in `<p>`, `<abstract>`, `<title>`
-     * doesn't collapse into reordered text. `trimValues: false` retains spacing
-     * between text nodes and adjacent inline children. `parseTagValue: false`
-     * keeps bibliographic tokens verbatim — page ranges like `4002.e26` and
-     * zero-padded pages would otherwise coerce to `Number` (→ `4.002e+29`, `123`);
-     * every value on this path is `String()`-ed downstream, so coercion is pure
-     * downside. Entity decoding is unaffected (it's governed by `processEntities`/
-     * `htmlEntities`), so page-range en-dashes still resolve. (#69)
+     * Parser configured for JATS mixed content (PMC full-text), built from
+     * {@link ORDERED_XML_PARSER_OPTIONS} — the same constant `EuropePmcService`
+     * uses, so the two JATS paths cannot drift apart. (#69, #127)
      */
     orderedXmlParser;
     /**
@@ -255,21 +240,13 @@ export class NcbiResponseHandler {
         const flatOptions = {
             ignoreAttributes: false,
             attributeNamePrefix: '@_',
-            processEntities: NCBI_PROCESS_ENTITIES_OPTIONS,
+            processEntities: XML_PROCESS_ENTITIES_OPTIONS,
             htmlEntities: true,
             isArray: (_name, jpath) => NCBI_ARRAY_JPATHS.has(jpath),
         };
         this.xmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: true });
         this.verbatimXmlParser = new FastXmlParser({ ...flatOptions, parseTagValue: false });
-        this.orderedXmlParser = new FastXmlParser({
-            preserveOrder: true,
-            ignoreAttributes: false,
-            attributeNamePrefix: '@_',
-            parseTagValue: false,
-            trimValues: false,
-            processEntities: NCBI_PROCESS_ENTITIES_OPTIONS,
-            htmlEntities: true,
-        });
+        this.orderedXmlParser = new FastXmlParser(ORDERED_XML_PARSER_OPTIONS);
     }
     /**
      * Extract a structured error from a parsed NCBI XML body and throw it as

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

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

@@ -496,6 +496,7 @@ export interface ParsedPmcArticle {
     pubmedUrl?: string;
     references?: ParsedPmcReference[];
     sections: ParsedPmcSection[];
+    tables?: ParsedPmcTable[];
     title?: string;
 }
 /** Parsed PMC author. */
@@ -525,6 +526,44 @@ export interface ParsedPmcReference {
     id?: string;
     label?: string;
 }
+/**
+ * Why a `<table-wrap>` yielded no rows. Not an error — the table is still
+ * returned with its label and caption so a reader is never shown a response
+ * that silently omits it.
+ * - `graphic-only` — the deposit is a scanned image, with no markup to read.
+ * - `cals-tgroup` — a CALS `<tgroup>` body, deliberately not extracted.
+ * - `no-rows` — an XHTML `<table>` with no `<tr>` carrying cells.
+ */
+export type ParsedPmcTableUnextractableReason = 'cals-tgroup' | 'graphic-only' | 'no-rows';
+/**
+ * Parsed `<table-wrap>` from a PMC full-text article. Rows are a plain
+ * `string[][]` of cell text, one entry per grid column: `colspan` and `rowspan`
+ * are expanded, so a cell covering several columns or rows repeats its text
+ * across the cells it covers and a well-formed table comes back rectangular.
+ * Nothing deeper than a string hangs off a row — the tool-layer schema that
+ * renders these sits at the framework's parity-walker depth cap.
+ */
+export interface ParsedPmcTable {
+    /** Caption text, without the label. */
+    caption?: string;
+    /** `<table-wrap-foot>` text, flattened. */
+    footnotes?: string;
+    /** Leading rows of {@link rows} that came from `<thead>` or are all `<th>`. */
+    headerRowCount: number;
+    /** The `id` attribute, when the deposit carries one. */
+    id?: string;
+    /** Display label, e.g. `TABLE 1`. */
+    label?: string;
+    /** Cell text by grid column, spans expanded. Empty when unextractable. */
+    rows: string[][];
+    /**
+     * Title of the innermost enclosing `<sec>` wherever it sits — body, back
+     * matter, or appendix. Absent only for a table inside no section at all.
+     */
+    sectionTitle?: string;
+    /** Set only when {@link rows} is empty. */
+    unextractableReason?: ParsedPmcTableUnextractableReason;
+}
 /** Single citation for ECitMatch lookup. */
 export interface ECitMatchCitation {
     /** Author name (e.g., "mann bj") */
@@ -533,7 +572,11 @@ export interface ECitMatchCitation {
     firstPage?: string | undefined;
     /** Journal title or ISO abbreviation */
     journal?: string | undefined;
-    /** Arbitrary key for tracking this citation in results */
+    /**
+     * 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.
+     */
     key: string;
     /** Volume number */
     volume?: string | undefined;
@@ -549,7 +592,7 @@ export interface ECitMatchResult {
     candidatePmids?: string[];
     /** Raw non-match detail returned by ECitMatch when present */
     detail?: string;
-    /** The tracking key from the input citation */
+    /** The label from the input citation this result describes, echoed verbatim */
     key: string;
     /** Whether a PMID was found */
     matched: boolean;

package/dist/services/ncbi/types.d.ts.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.10.7",
+  "version": "2.10.9",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
   "type": "module",
@@ -81,7 +81,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.12.7",
+    "@cyanheads/mcp-ts-core": "^0.12.8",
     "defuddle": "^0.19.3",
     "fast-xml-parser": "^5.11.1",
     "linkedom": "^0.18.13",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.10.7",
+  "version": "2.10.9",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.7",
+      "version": "2.10.9",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.10.7",
+      "version": "2.10.9",
       "packageArguments": [
         {
           "type": "positional",