@cyanheads/pubmed-mcp-server 2.10.7 → 2.10.9

package/dist/services/ncbi/ncbi-service.js

@@ -39,6 +39,20 @@ function normalizeDiagnosticList(list) {
     }
     return normalized;
 }
+/**
+ * The tracking token each citation is submitted to ECitMatch under — echoed
+ * back verbatim on that citation's response row, and unique within the request.
+ *
+ * `ECitMatchCitation.key` is a caller-supplied label and may repeat, so
+ * reconciling response rows on it collapses two citations onto one row and
+ * hands the second citation's PMID to the first (#113). Distinct caller keys
+ * are used as-is, so a well-formed request is submitted exactly as before; any
+ * repeat switches the whole request to positional tokens.
+ */
+function wireKeysFor(citations) {
+    const keys = citations.map((c) => c.key);
+    return new Set(keys).size === keys.length ? keys : citations.map((_, i) => String(i + 1));
+}
 /** Sentinel reason used when the service-level deadline expires. */
 class NcbiDeadlineExceeded extends Error {
     constructor(deadlineMs) {
@@ -157,10 +171,16 @@ export class NcbiService {
     /**
      * Look up PMIDs from partial citation strings via NCBI ECitMatch.
      * Each citation can include journal, year, volume, first page, and author name.
+     *
+     * Results come back one per submitted citation, in submission order, carrying
+     * the caller's `key`. Correlation runs on the wire key (see
+     * {@link wireKeysFor}), never on `key` itself — that label is caller-supplied
+     * and may repeat. (#113)
      */
     async eCitMatch(citations, options) {
+        const wireKeys = wireKeysFor(citations);
         const bdata = citations
-            .map((c) => `${c.journal ?? ''}|${c.year ?? ''}|${c.volume ?? ''}|${c.firstPage ?? ''}|${c.authorName ?? ''}|${c.key}|`)
+            .map((c, i) => `${c.journal ?? ''}|${c.year ?? ''}|${c.volume ?? ''}|${c.firstPage ?? ''}|${c.authorName ?? ''}|${wireKeys[i]}|`)
             .join('\r');
         const text = await this.performRequest('ecitmatch.cgi', { db: 'pubmed', retmode: 'xml', bdata }, { retmode: 'text', ...(options?.signal && { signal: options.signal }) });
         const parsed = text
@@ -198,15 +218,18 @@ export class NcbiService {
                 ...(rawOutcome && { detail: rawOutcome }),
             };
         });
-        // ECitMatch omits lines for citations it cannot classify. Reconcile against
-        // the submitted citations so every input gets a result row — callers can rely
-        // on results.length === citations.length and correlate by key.
-        const parsedByKey = new Map(parsed.map((r) => [r.key, r]));
-        return citations.map((c) => parsedByKey.get(c.key) ?? {
-            key: c.key,
-            matched: false,
-            pmid: null,
-            status: 'not_found',
+        // ECitMatch omits lines for citations it cannot classify. Reconcile on the
+        // wire key each citation was submitted under — unique within the request, so
+        // one row can never stand in for a second citation — then restore the
+        // caller's label on the way out. Every input gets a result row, so callers
+        // can rely on results.length === citations.length and on results[i]
+        // describing citations[i]. (#54, #113)
+        const parsedByWireKey = new Map(parsed.map((r) => [r.key, r]));
+        return citations.map((c, i) => {
+            const row = parsedByWireKey.get(wireKeys[i] ?? '');
+            return row
+                ? { ...row, key: c.key }
+                : { key: c.key, matched: false, pmid: null, status: 'not_found' };
         });
     }
     /**

package/dist/services/ncbi/ncbi-service.js.map

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package/dist/services/ncbi/parsing/ordered-xml-parser-options.d.ts

@@ -0,0 +1,44 @@
+/**
+ * @fileoverview fast-xml-parser options shared by every JATS parser instance in
+ * this server. PMC EFetch and Europe PMC both serve JATS Z39.96 and both feed
+ * `parsePmcArticle`, so their parsers must agree field-for-field: a divergence
+ * makes the same article render differently depending on which upstream
+ * answered. Dependency-free leaf — it imports a type and nothing else — so any
+ * service can import it without introducing a cycle.
+ * @module src/services/ncbi/parsing/ordered-xml-parser-options
+ */
+/**
+ * NCBI and Europe PMC responses routinely carry numeric character references
+ * for punctuation and diacritics, especially in page ranges and author names.
+ * Keep entity processing enabled, but cap aggregate expansion so a hostile or
+ * malformed payload cannot turn entity resolution into a denial of service. The
+ * ceiling is high enough for trusted bibliographic payloads.
+ */
+export declare const XML_PROCESS_ENTITIES_OPTIONS: {
+    readonly enabled: true;
+    readonly maxTotalExpansions: 100000;
+};
+/**
+ * Options for the JATS mixed-content parsers. `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`, zero-padded pages, and reference
+ * labels like `1.` would otherwise coerce to `Number` (→ `4.002e+29`, `123`,
+ * `1`); every value on this path is `String()`-ed downstream, so coercion is
+ * pure downside. Entity decoding is unaffected (governed by `processEntities` /
+ * `htmlEntities`), so page-range en-dashes still resolve. (#69, #127)
+ */
+export declare const ORDERED_XML_PARSER_OPTIONS: {
+    readonly preserveOrder: true;
+    readonly ignoreAttributes: false;
+    readonly attributeNamePrefix: '@_';
+    readonly parseTagValue: false;
+    readonly trimValues: false;
+    readonly processEntities: {
+        readonly enabled: true;
+        readonly maxTotalExpansions: 100000;
+    };
+    readonly htmlEntities: true;
+};
+//# sourceMappingURL=ordered-xml-parser-options.d.ts.map

package/dist/services/ncbi/parsing/ordered-xml-parser-options.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"ordered-xml-parser-options.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/ordered-xml-parser-options.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAIH;;;;;;GAMG;AACH,eAAO,MAAM,4BAA4B;aACvC,OAAO;aACP,kBAAkB,EAAE,MAAO;CACnB,CAAC;AAEX;;;;;;;;;;GAUG;AACH,eAAO,MAAM,0BAA0B;;;kCAGhB,IAAI;;;;;qCAjBL,MAAO;;;CAsBE,CAAC"}

package/dist/services/ncbi/parsing/ordered-xml-parser-options.js

@@ -0,0 +1,41 @@
+/**
+ * @fileoverview fast-xml-parser options shared by every JATS parser instance in
+ * this server. PMC EFetch and Europe PMC both serve JATS Z39.96 and both feed
+ * `parsePmcArticle`, so their parsers must agree field-for-field: a divergence
+ * makes the same article render differently depending on which upstream
+ * answered. Dependency-free leaf — it imports a type and nothing else — so any
+ * service can import it without introducing a cycle.
+ * @module src/services/ncbi/parsing/ordered-xml-parser-options
+ */
+/**
+ * NCBI and Europe PMC responses routinely carry numeric character references
+ * for punctuation and diacritics, especially in page ranges and author names.
+ * Keep entity processing enabled, but cap aggregate expansion so a hostile or
+ * malformed payload cannot turn entity resolution into a denial of service. The
+ * ceiling is high enough for trusted bibliographic payloads.
+ */
+export const XML_PROCESS_ENTITIES_OPTIONS = {
+    enabled: true,
+    maxTotalExpansions: 100_000,
+};
+/**
+ * Options for the JATS mixed-content parsers. `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`, zero-padded pages, and reference
+ * labels like `1.` would otherwise coerce to `Number` (→ `4.002e+29`, `123`,
+ * `1`); every value on this path is `String()`-ed downstream, so coercion is
+ * pure downside. Entity decoding is unaffected (governed by `processEntities` /
+ * `htmlEntities`), so page-range en-dashes still resolve. (#69, #127)
+ */
+export const ORDERED_XML_PARSER_OPTIONS = {
+    preserveOrder: true,
+    ignoreAttributes: false,
+    attributeNamePrefix: '@_',
+    parseTagValue: false,
+    trimValues: false,
+    processEntities: XML_PROCESS_ENTITIES_OPTIONS,
+    htmlEntities: true,
+};
+//# sourceMappingURL=ordered-xml-parser-options.js.map

package/dist/services/ncbi/parsing/ordered-xml-parser-options.js.map

@@ -0,0 +1 @@
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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts

@@ -7,7 +7,7 @@
  * inline children and drops body sections for markup-heavy articles.
  * @module src/services/ncbi/parsing/pmc-article-parser
  */
-import type { ParsedPmcArticle, ParsedPmcAuthor, ParsedPmcReference, ParsedPmcSection } from '../types.js';
+import type { ParsedPmcArticle, ParsedPmcAuthor, ParsedPmcReference, ParsedPmcSection, ParsedPmcTable } from '../types.js';
 import { type JatsNode } from './pmc-xml-helpers.js';
 /** Extract authors from a single `<contrib-group>` node. Non-author contributors are skipped. */
 export declare function extractJatsAuthors(contribGroup: JatsNode | undefined): ParsedPmcAuthor[];
@@ -19,13 +19,53 @@ export declare function extractJatsAuthors(contribGroup: JatsNode | undefined):
  */
 export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
 /**
- * Extract references from a `<back>` node. Prefers `<mixed-citation>` over
- * `<element-citation>`, descending into `<citation-alternatives>` when a ref
- * carries both forms there rather than as direct children of `<ref>`. Mixed
- * citations are read verbatim; structured element citations are rendered
- * field-by-field with separators (see `renderElementCitation`).
+ * Extract every `<table-wrap>` under `root` in document order — pass the
+ * `<article>` node.
+ *
+ * The walk covers the whole article rather than `<body>` alone: about a quarter
+ * of real tables sit in `<floats-group>`, `<back>/<sec>`, `<table-wrap-group>`
+ * or `<app-group>/<app>`, so a body-scoped extractor drops them. Each table
+ * names the innermost enclosing `<sec>` wherever that sits — a back-matter or
+ * appendix section counts, and naming it is the reader's only positional cue
+ * there. Only a table inside no `<sec>` at all, such as a `<floats-group>`
+ * deposit, carries no section name.
+ *
+ * Only XHTML `<tr>`/`<td>`/`<th>` bodies are read. **Decision, not an
+ * oversight:** across a 283-table survey of open-access records, 276 were XHTML,
+ * 7 were graphic-only deposits and 0 used the CALS `<tgroup>` model. Graphic-only
+ * and CALS bodies therefore take the unextractable path — returned with their
+ * label and caption and a reason — rather than adding a second table model no
+ * observed record needs. Revisit only if CALS shows up in the wild. (#111)
  */
-export declare function extractReferences(back: JatsNode | undefined): ParsedPmcReference[];
+export declare function extractPmcTables(root: JatsNode | undefined): ParsedPmcTable[];
+/**
+ * Widest grid a single table row may occupy, and the ceiling every declared
+ * span is clamped to. Real deposits are far narrower — the widest row observed
+ * across a live sample was 15 columns — so this bounds a malformed or hostile
+ * span rather than limiting any genuine table: `colspan="99999999"` costs a
+ * bounded row instead of an unbounded allocation, and a `rowspan` that large
+ * carries a bounded number of rows down. How many rows a table has is set by its
+ * source `<tr>` elements and needs no cap of its own. (#111)
+ */
+export declare const MAX_TABLE_COLUMNS = 512;
+/**
+ * Extract references from anywhere under `root` — pass the `<article>` node to
+ * cover a whole document, or a `<back>` node to scope the search to it.
+ *
+ * `<ref-list>` placement is not uniform: roughly 60% of Europe PMC deposits nest
+ * it under `body/sec/sec` and the rest put it directly under `<back>`, so a
+ * search scoped to a direct `<back>` child misses the majority. Every
+ * `<ref-list>` descendant is collected in document order instead, and a `<ref>`
+ * id already seen is skipped so a document exposing the same list under both
+ * containers still yields each reference once. (#116)
+ *
+ * Prefers `<mixed-citation>` over `<element-citation>`, descending into
+ * `<citation-alternatives>` when a ref carries both forms there rather than as
+ * direct children of `<ref>`. Both forms are rendered child-by-child so adjacent
+ * elements stay separable (see `renderMixedCitation` and
+ * `renderElementCitation`).
+ */
+export declare function extractReferences(root: JatsNode | undefined): ParsedPmcReference[];
 /**
  * Parse a single JATS `<article>` node (from PMC EFetch via the ordered parser)
  * into a structured `ParsedPmcArticle`. The input node is the element wrapper

package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map

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