@cyanheads/pubmed-mcp-server 2.3.9 → 2.3.10

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Files changed (24) hide show
  1. package/CLAUDE.md +1 -1
  2. package/README.md +1 -1
  3. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  4. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +2 -4
  5. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  6. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  7. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +5 -8
  8. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  9. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +21 -25
  10. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
  11. package/dist/services/ncbi/parsing/pmc-article-parser.js +176 -223
  12. package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
  13. package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts +44 -0
  14. package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map +1 -0
  15. package/dist/services/ncbi/parsing/pmc-xml-helpers.js +86 -0
  16. package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map +1 -0
  17. package/dist/services/ncbi/response-handler.d.ts +12 -0
  18. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  19. package/dist/services/ncbi/response-handler.js +53 -9
  20. package/dist/services/ncbi/response-handler.js.map +1 -1
  21. package/dist/services/ncbi/types.d.ts +6 -124
  22. package/dist/services/ncbi/types.d.ts.map +1 -1
  23. package/package.json +1 -1
  24. package/server.json +3 -3
package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Agent Protocol
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.3.9
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+ **Version:** 2.3.10
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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  > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.3.9-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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+ [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.3.10-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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  [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAsN5B,CAAC"}
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+ {"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAmN5B,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js CHANGED
@@ -114,10 +114,8 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
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  if (!xmlData || !('PubmedArticleSet' in xmlData)) {
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  throw new Error('Invalid EFetch response from NCBI: missing PubmedArticleSet');
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  }
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- if (!xmlData.PubmedArticleSet?.PubmedArticle) {
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- return { articles: [], totalReturned: 0 };
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- }
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- const xmlArticles = ensureArray(xmlData.PubmedArticleSet.PubmedArticle);
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+ const rawArticles = xmlData.PubmedArticleSet?.PubmedArticle;
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+ const xmlArticles = rawArticles ? ensureArray(rawArticles) : [];
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  const articles = xmlArticles
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  .filter((a) => a?.MedlineCitation)
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  .map((a) => {
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map CHANGED
@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAgDjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAiO5B,CAAC"}
1
+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAgDjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA2N5B,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED
@@ -6,7 +6,7 @@
6
6
  import { tool, z } from '@cyanheads/mcp-ts-core';
7
7
  import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
8
8
  import { parsePmcArticle } from '../../../services/ncbi/parsing/pmc-article-parser.js';
9
- import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
9
+ import { findAll, findOne } from '../../../services/ncbi/parsing/pmc-xml-helpers.js';
10
10
  function normalizePmcId(id) {
11
11
  return id.replace(/^PMC/i, '');
12
12
  }
@@ -143,15 +143,12 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
143
143
  else {
144
144
  pmcIds = (input.pmcids ?? []).map(normalizePmcId);
145
145
  }
146
- const xmlData = await getNcbiService().eFetch({ db: 'pmc', id: pmcIds.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: pmcIds.length > 5 });
147
- if (!xmlData || !('pmc-articleset' in xmlData)) {
146
+ const xmlData = await getNcbiService().eFetch({ db: 'pmc', id: pmcIds.join(','), retmode: 'xml' }, { retmode: 'xml', useOrderedParser: true, usePost: pmcIds.length > 5 });
147
+ const articleSet = findOne(xmlData, 'pmc-articleset');
148
+ if (!articleSet) {
148
149
  throw new Error('Invalid PMC EFetch response: missing pmc-articleset');
149
150
  }
150
- const articleSet = xmlData['pmc-articleset'];
151
- if (!articleSet?.article) {
152
- return { articles: [], totalReturned: 0, ...(unavailablePmids && { unavailablePmids }) };
153
- }
154
- let articles = ensureArray(articleSet.article).map(parsePmcArticle);
151
+ let articles = findAll(articleSet, 'article').map(parsePmcArticle);
155
152
  if (input.sections?.length) {
156
153
  const sectionFilter = input.sections;
157
154
  articles = articles.map((a) => ({
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts CHANGED
@@ -1,34 +1,30 @@
1
1
  /**
2
2
  * @fileoverview Parser for PMC full-text articles in JATS XML format.
3
- * Extracts metadata, body sections, and references from PMC EFetch responses.
3
+ * Consumes the ordered tree shape from fast-xml-parser's `preserveOrder: true`
4
+ * mode (see `pmc-xml-helpers.ts`) so that mixed-content elements — `<p>`,
5
+ * `<abstract>`, `<title>` with inline `<italic>`, `<xref>`, `<sup>`, etc. —
6
+ * read back in document order. Parsing in the default object shape scrambles
7
+ * inline children and drops body sections for markup-heavy articles.
4
8
  * @module src/services/ncbi/parsing/pmc-article-parser
5
9
  */
6
- import type { ParsedPmcArticle, ParsedPmcAuthor, ParsedPmcReference, ParsedPmcSection, XmlJatsArticle, XmlJatsBack, XmlJatsBody, XmlJatsContribGroup } from '../types.js';
10
+ import type { ParsedPmcArticle, ParsedPmcAuthor, ParsedPmcReference, ParsedPmcSection } from '../types.js';
11
+ import { type JatsNode } from './pmc-xml-helpers.js';
12
+ /** Extract authors from a single `<contrib-group>` node. Non-author contributors are skipped. */
13
+ export declare function extractJatsAuthors(contribGroup: JatsNode | undefined): ParsedPmcAuthor[];
7
14
  /**
8
- * Recursively extracts plain text content from a JATS XML node.
9
- * Handles mixed content where text and child elements are interleaved.
10
- * fast-xml-parser with `preserveOrder: false` stores text in `#text` and
11
- * child elements as named properties — document order is lost, but all
12
- * text content is preserved.
15
+ * Extract body sections from a `<body>` node, walking children in document order.
16
+ * Consecutive bare `<p>` siblings are collected into an untitled section so
17
+ * articles with mixed structure (direct paragraphs + trailing `<sec>`, common
18
+ * in manuscript-submitted PMC deposits) preserve their main text.
13
19
  */
14
- export declare function extractTextContent(node: unknown): string;
20
+ export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
21
+ /** Extract references from a `<back>` node. Prefers mixed-citation over element-citation. */
22
+ export declare function extractReferences(back: JatsNode | undefined): ParsedPmcReference[];
15
23
  /**
16
- * Extracts authors from JATS contrib-group elements.
17
- * Only includes contributors with contrib-type="author".
24
+ * Parse a single JATS `<article>` node (from PMC EFetch via the ordered parser)
25
+ * into a structured `ParsedPmcArticle`. The input node is the element wrapper
26
+ * itself — `{ article: [...], ':@': { '@_article-type': ... } }` — not the
27
+ * outer `<pmc-articleset>`.
18
28
  */
19
- export declare function extractJatsAuthors(contribGroups: XmlJatsContribGroup | XmlJatsContribGroup[] | undefined): ParsedPmcAuthor[];
20
- /**
21
- * Recursively extracts body sections from JATS sec elements.
22
- */
23
- export declare function extractBodySections(body: XmlJatsBody | undefined): ParsedPmcSection[];
24
- /**
25
- * Extracts references from JATS back matter ref-list.
26
- */
27
- export declare function extractReferences(back: XmlJatsBack | undefined): ParsedPmcReference[];
28
- /**
29
- * Parses a JATS XML article (from PMC EFetch) into a structured ParsedPmcArticle.
30
- * @param xmlArticle - The parsed JATS article object from fast-xml-parser.
31
- * @returns A fully parsed PMC article with metadata, body sections, and optional references.
32
- */
33
- export declare function parsePmcArticle(xmlArticle: XmlJatsArticle): ParsedPmcArticle;
29
+ export declare function parsePmcArticle(articleNode: JatsNode): ParsedPmcArticle;
34
30
  //# sourceMappingURL=pmc-article-parser.d.ts.map
package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map CHANGED
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