@cyanheads/pubmed-mcp-server 2.7.11 → 2.8.0

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Files changed (21) hide show
  1. package/AGENTS.md +1 -1
  2. package/CLAUDE.md +1 -1
  3. package/README.md +4 -4
  4. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +3 -1
  5. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  6. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +11 -3
  7. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  8. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +6 -2
  9. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
  10. package/dist/mcp-server/tools/definitions/format-citations.tool.js +17 -9
  11. package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
  12. package/dist/services/ncbi/formatting/citation-formatter.d.ts +16 -2
  13. package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
  14. package/dist/services/ncbi/formatting/citation-formatter.js +102 -2
  15. package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
  16. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +5 -1
  17. package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
  18. package/dist/services/ncbi/parsing/pmc-article-parser.js +11 -2
  19. package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
  20. package/package.json +2 -2
  21. package/server.json +3 -3
package/AGENTS.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:** 2.7.11
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+ **Version:** 2.8.0
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
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  **Engines:** Bun ≥1.3.2, Node ≥24.0.0
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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:** 2.7.11
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+ **Version:** 2.8.0
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
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  **Engines:** Bun ≥1.3.2, Node ≥24.0.0
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package/README.md CHANGED
@@ -9,7 +9,7 @@
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- [![Version](https://img.shields.io/badge/Version-2.7.11-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![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) [![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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+ [![Version](https://img.shields.io/badge/Version-2.8.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![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) [![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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  </div>
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@@ -39,7 +39,7 @@
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  | `pubmed_europepmc_search` | Search Europe PMC for preprints, patents, Agricola, and EPMC-only OA records that don't surface in PubMed. Cursor-based pagination. |
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  | `pubmed_fetch_articles` | Fetch full article metadata by PMIDs — abstract, authors, journal, MeSH terms, grants |
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  | `pubmed_fetch_fulltext` | Fetch full-text articles via a chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall. Accepts PMIDs, PMCIDs, or DOIs. |
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- | `pubmed_format_citations` | Generate formatted citations in APA 7th, MLA 9th, BibTeX, or RIS |
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+ | `pubmed_format_citations` | Generate formatted citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM) |
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  | `pubmed_find_related` | Find similar articles, citing articles, or references for a given PMID |
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  | `pubmed_spell_check` | Spell-check biomedical queries using NCBI's ESpell service |
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  | `pubmed_lookup_mesh` | Search and explore MeSH vocabulary — tree numbers, scope notes, entry terms |
@@ -106,7 +106,7 @@ Search Europe PMC (EBI/EMBL-EBI), a broader open-access biomedical corpus than P
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  Generate formatted citations for articles.
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- - Four citation styles: APA 7th, MLA 9th, BibTeX, RIS
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+ - Five citation styles: APA 7th, MLA 9th, BibTeX, RIS, Vancouver (ICMJE/NLM)
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  - Request multiple styles per article in a single call
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  - Hand-rolled formatters — zero external dependencies, fully Workers-compatible
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  - Up to 50 articles per request
@@ -187,7 +187,7 @@ PubMed-specific:
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  - Complete NCBI E-utilities integration (ESearch, EFetch, ESummary, ELink, ESpell, EInfo, ECitMatch) plus PMC ID Converter
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  - Sequential request queue with configurable delay for NCBI rate limit compliance
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  - NCBI-specific XML parser with `isArray` hints for PubMed's inconsistent XML structure
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- - Hand-rolled citation formatters (APA, MLA, BibTeX, RIS) — zero deps, Workers-compatible
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+ - Hand-rolled citation formatters (APA, MLA, BibTeX, RIS, Vancouver) — zero deps, Workers-compatible
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  Agent-friendly output:
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package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts CHANGED
@@ -104,5 +104,7 @@ export declare const fetchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDef
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  readonly code: JsonRpcErrorCode.SerializationError;
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  readonly when: "NCBI EFetch returned a payload missing the PubmedArticleSet wrapper.";
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  readonly recovery: "Retry once; if it persists, NCBI returned malformed data — try fewer PMIDs at once.";
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- }], undefined>;
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+ }], {
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+ readonly notice: z.ZodOptional<z.ZodString>;
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+ }>;
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  //# sourceMappingURL=fetch-articles.tool.d.ts.map
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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqL5B,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js CHANGED
@@ -121,6 +121,14 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
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  .optional()
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  .describe('PMIDs that returned no article data'),
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  }),
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+ // Recovery guidance when no articles are returned — agent-facing context, surfaced via
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+ // ctx.enrich.notice() to both structuredContent and content[]; absent on success.
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+ enrichment: {
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+ notice: z
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+ .string()
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+ .optional()
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+ .describe('Optional guidance when no articles were returned — points to discovery tools. Absent on successful fetches.'),
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+ },
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  async handler(input, ctx) {
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  ctx.log.info('Executing pubmed_fetch', { pmidCount: input.pmids.length });
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  const xmlData = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 100, signal: ctx.signal });
@@ -150,6 +158,9 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
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  requested: input.pmids.length,
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  returned: articles.length,
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  });
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+ if (articles.length === 0) {
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+ ctx.enrich.notice('No articles were returned. These PMIDs may be invalid, unpublished, or withdrawn. Try pubmed_search_articles to discover valid PMIDs.');
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+ }
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  return {
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  articles,
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  totalReturned: articles.length,
@@ -161,9 +172,6 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
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  if (result.unavailablePmids?.length) {
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  lines.push(`**Unavailable PMIDs:** ${result.unavailablePmids.join(', ')}`);
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  }
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- if (result.totalReturned === 0) {
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- lines.push(`\n> No articles were returned. These PMIDs may be invalid, unpublished, or withdrawn. Try \`pubmed_search_articles\` to discover valid PMIDs.`);
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- }
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  for (const a of result.articles) {
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  lines.push(`\n### ${a.title ?? a.pmid ?? 'Unknown'}`);
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  if (a.authors?.length) {
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map CHANGED
@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts CHANGED
@@ -1,6 +1,6 @@
1
1
  /**
2
2
  * @fileoverview PubMed citation tool — generates formatted citations (APA, MLA,
3
- * BibTeX, RIS) for one or more PubMed articles.
3
+ * BibTeX, RIS, Vancouver) for one or more PubMed articles.
4
4
  * @module src/mcp-server/tools/definitions/format-citations.tool
5
5
  */
6
6
  import { z } from '@cyanheads/mcp-ts-core';
@@ -11,11 +11,13 @@ export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolD
11
11
  mla: "mla";
12
12
  bibtex: "bibtex";
13
13
  ris: "ris";
14
+ vancouver: "vancouver";
14
15
  }>, z.ZodArray<z.ZodEnum<{
15
16
  apa: "apa";
16
17
  mla: "mla";
17
18
  bibtex: "bibtex";
18
19
  ris: "ris";
20
+ vancouver: "vancouver";
19
21
  }>>]>>;
20
22
  }, z.core.$strip>, z.ZodObject<{
21
23
  citations: z.ZodArray<z.ZodObject<{
@@ -56,5 +58,7 @@ export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolD
56
58
  readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
57
59
  readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
58
60
  readonly retryable: false;
59
- }], undefined>;
61
+ }], {
62
+ readonly notice: z.ZodOptional<z.ZodString>;
63
+ }>;
60
64
  //# sourceMappingURL=format-citations.tool.d.ts.map
package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAejD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAyG9B,CAAC"}
1
+ {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAejD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwH9B,CAAC"}
package/dist/mcp-server/tools/definitions/format-citations.tool.js CHANGED
@@ -1,6 +1,6 @@
1
1
  /**
2
2
  * @fileoverview PubMed citation tool — generates formatted citations (APA, MLA,
3
- * BibTeX, RIS) for one or more PubMed articles.
3
+ * BibTeX, RIS, Vancouver) for one or more PubMed articles.
4
4
  * @module src/mcp-server/tools/definitions/format-citations.tool
5
5
  */
6
6
  import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -11,9 +11,9 @@ import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.
11
11
  import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
12
12
  import { conceptMeta, EDAM_DATA_FORMATTING, SCHEMA_CREATIVE_WORK } from './_concepts.js';
13
13
  import { pmidStringSchema } from './_schemas.js';
14
- const CitationStyleEnum = z.enum(['apa', 'mla', 'bibtex', 'ris']);
14
+ const CitationStyleEnum = z.enum(['apa', 'mla', 'bibtex', 'ris', 'vancouver']);
15
15
  export const formatCitationsTool = tool('pubmed_format_citations', {
16
- description: 'Get formatted citations for PubMed articles in one or more styles (apa, mla, bibtex, ris). Pass a single style as a string or multiple as an array.',
16
+ description: 'Get formatted citations for PubMed articles in one or more styles (apa, mla, bibtex, ris, vancouver). Pass a single style as a string or multiple as an array.',
17
17
  annotations: { readOnlyHint: true, openWorldHint: true },
18
18
  _meta: conceptMeta([SCHEMA_CREATIVE_WORK, EDAM_DATA_FORMATTING]),
19
19
  sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/format-citations.tool.ts',
@@ -22,14 +22,14 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
22
22
  pmids: z.array(pmidStringSchema).min(1).max(50).describe('PubMed IDs to cite'),
23
23
  format: z
24
24
  .union([
25
- CitationStyleEnum.describe('Single citation style. One of: apa, mla, bibtex, ris.'),
25
+ CitationStyleEnum.describe('Single citation style. One of: apa, mla, bibtex, ris, vancouver.'),
26
26
  z
27
27
  .array(CitationStyleEnum)
28
28
  .min(1)
29
- .describe('Multiple citation styles to generate. Each entry: apa, mla, bibtex, or ris.'),
29
+ .describe('Multiple citation styles to generate. Each entry: apa, mla, bibtex, ris, or vancouver.'),
30
30
  ])
31
31
  .default('apa')
32
- .describe('Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris.'),
32
+ .describe('Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris, vancouver.'),
33
33
  }),
34
34
  output: z.object({
35
35
  citations: z
@@ -48,6 +48,14 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
48
48
  .optional()
49
49
  .describe('Requested PMIDs that did not return article metadata'),
50
50
  }),
51
+ // Recovery guidance when nothing could be formatted — agent-facing context, surfaced
52
+ // via ctx.enrich.notice() to both structuredContent and content[]; absent on success.
53
+ enrichment: {
54
+ notice: z
55
+ .string()
56
+ .optional()
57
+ .describe('Optional guidance when no citations were produced — points to discovery tools. Absent when at least one citation was produced.'),
58
+ },
51
59
  async handler(input, ctx) {
52
60
  const formats = Array.isArray(input.format) ? input.format : [input.format];
53
61
  ctx.log.debug('Fetching articles for citation generation', {
@@ -66,6 +74,9 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
66
74
  });
67
75
  const returnedPmids = new Set(citations.map((entry) => entry.pmid));
68
76
  const unavailablePmids = input.pmids.filter((pmid) => !returnedPmids.has(pmid));
77
+ if (citations.length === 0) {
78
+ ctx.enrich.notice('No articles were returned for the submitted PMIDs. They may be invalid, unpublished, or withdrawn. Try pubmed_search_articles to discover valid PMIDs, or pubmed_spell_check if these came from a noisy source.');
79
+ }
69
80
  return {
70
81
  citations,
71
82
  totalSubmitted: input.pmids.length,
@@ -81,9 +92,6 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
81
92
  if (result.unavailablePmids?.length) {
82
93
  lines.push(`**Unavailable PMIDs:** ${result.unavailablePmids.join(', ')}`);
83
94
  }
84
- if (result.totalFormatted === 0) {
85
- lines.push(`\n> No articles were returned for the submitted PMIDs. They may be invalid, unpublished, or withdrawn. Try \`pubmed_search_articles\` to discover valid PMIDs, or \`pubmed_spell_check\` if these came from a noisy source.`);
86
- }
87
95
  for (const entry of result.citations) {
88
96
  lines.push(`\n## PMID ${entry.pmid}`);
89
97
  if (entry.title)
package/dist/mcp-server/tools/definitions/format-citations.tool.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAErE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AACzF,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAEjD,MAAM,iBAAiB,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,EAAE,WAAW,CAAC,CAAC,CAAC;AAE/E,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EACT,gKAAgK;IAClK,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,EAAE,oBAAoB,CAAC,CAAC;IAChE,SAAS,EACP,oHAAoH;IAEtH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QAC9E,MAAM,EAAE,CAAC;aACN,KAAK,CAAC;YACL,iBAAiB,CAAC,QAAQ,CACxB,kEAAkE,CACnE;YACD,CAAC;iBACE,KAAK,CAAC,iBAAiB,CAAC;iBACxB,GAAG,CAAC,CAAC,CAAC;iBACN,QAAQ,CACP,wFAAwF,CACzF;SACJ,CAAC;aACD,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,sIAAsI,CACvI;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACjF,CAAC;aACD,QAAQ,CAAC,gCAAgC,CAAC,CAC9C;aACA,QAAQ,CAAC,uBAAuB,CAAC;QACpC,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACxF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7E,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,sDAAsD,CAAC;KACpE,CAAC;IAEF,qFAAqF;IACrF,sFAAsF;IACtF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,gIAAgI,CACjI;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,OAAO,GAAoB,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QAC7F,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,OAAO;SACR,CAAC,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,EAC3D,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM,IAAI,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAC1E,CAAC;QACF,MAAM,WAAW,GAAuB,WAAW,CAAC,GAAG,EAAE,gBAAgB,EAAE,aAAa,CAAC,CAAC;QAE1F,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,EAAE;YAC/C,MAAM,MAAM,GAAG,gBAAgB,CAAC,UAAU,CAAC,CAAC;YAC5C,OAAO;gBACL,IAAI,EAAE,MAAM,CAAC,IAAI;gBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,SAAS,EAAE,eAAe,CAAC,MAAM,EAAE,OAAO,CAAC;aAC5C,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QACpE,MAAM,gBAAgB,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;QAEhF,IAAI,SAAS,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC3B,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,iNAAiN,CAClN,CAAC;QACJ,CAAC;QACD,OAAO;YACL,SAAS;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM;YAClC,cAAc,EAAE,SAAS,CAAC,MAAM;YAChC,GAAG,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,gBAAgB,EAAE,CAAC;SACzD,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,oBAAoB;YACpB,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;SACnE,CAAC;QACF,IAAI,MAAM,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,0BAA0B,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC7E,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,aAAa,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;YACtC,IAAI,KAAK,CAAC,KAAK;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC;YAClD,KAAK,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;gBAChE,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;gBAC3C,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;oBAC1C,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,KAAK,QAAQ,UAAU,CAAC,CAAC;gBACpD,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;gBACvB,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
package/dist/services/ncbi/formatting/citation-formatter.d.ts CHANGED
@@ -1,12 +1,12 @@
1
1
  /**
2
2
  * @fileoverview Hand-rolled citation formatters for PubMed articles.
3
- * Supports APA 7th, MLA 9th, BibTeX, and RIS formats.
3
+ * Supports APA 7th, MLA 9th, BibTeX, RIS, and Vancouver (ICMJE/NLM) formats.
4
4
  * Pure TypeScript, zero dependencies, Workers-compatible.
5
5
  * @module src/services/ncbi/formatting/citation-formatter
6
6
  */
7
7
  import type { ParsedArticle } from '../types.js';
8
8
  /** Supported citation output formats. */
9
- export type CitationStyle = 'apa' | 'mla' | 'bibtex' | 'ris';
9
+ export type CitationStyle = 'apa' | 'mla' | 'bibtex' | 'ris' | 'vancouver';
10
10
  /**
11
11
  * Format a PubMed article as an APA 7th edition citation.
12
12
  *
@@ -46,6 +46,20 @@ export declare function formatBibtex(article: ParsedArticle): string;
46
46
  * Record ends with `ER - ` (trailing spaces per spec).
47
47
  */
48
48
  export declare function formatRis(article: ParsedArticle): string;
49
+ /**
50
+ * Format a PubMed article as a Vancouver (ICMJE/NLM) reference — the numbered
51
+ * style used by NEJM, Lancet, JAMA, BMJ, and most biomedical journals.
52
+ *
53
+ * Pattern (the leading list number is the consumer's responsibility — entries
54
+ * are formatted independently, so this returns the unnumbered reference body):
55
+ * ```
56
+ * Surname AB, Surname CD, et al. Article title. Abbrev J Name. Year;Vol(Issue):Pages. doi: 10.x/y
57
+ * ```
58
+ * Journal name uses the NLM/ISO abbreviation when available; pages are used as
59
+ * PubMed supplies them (often elided, e.g. "583-9"); the DOI carries no trailing
60
+ * period so it stays copy-pasteable.
61
+ */
62
+ export declare function formatVancouver(article: ParsedArticle): string;
49
63
  /**
50
64
  * Format a single article in the requested citation style.
51
65
  * Throws on unsupported style.
package/dist/services/ncbi/formatting/citation-formatter.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"citation-formatter.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/formatting/citation-formatter.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,aAAa,EAAuB,MAAM,aAAa,CAAC;AAEtE,yCAAyC;AACzC,MAAM,MAAM,aAAa,GAAG,KAAK,GAAG,KAAK,GAAG,QAAQ,GAAG,KAAK,CAAC;AAgM7D;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA6CxD;AAMD;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAkDxD;AAMD;;;;;;;;;;;;GAYG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA8E3D;AAMD;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA4FxD;AAMD;;;GAGG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,GAAG,MAAM,CAWnF;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAC7B,OAAO,EAAE,aAAa,EACtB,MAAM,EAAE,aAAa,EAAE,GACtB,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAMxB"}
1
+ {"version":3,"file":"citation-formatter.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/formatting/citation-formatter.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,aAAa,EAAuB,MAAM,aAAa,CAAC;AAEtE,yCAAyC;AACzC,MAAM,MAAM,aAAa,GAAG,KAAK,GAAG,KAAK,GAAG,QAAQ,GAAG,KAAK,GAAG,WAAW,CAAC;AAgM3E;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA6CxD;AAMD;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAkDxD;AAMD;;;;;;;;;;;;GAYG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAkF3D;AAMD;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA4FxD;AA4CD;;;;;;;;;;;;GAYG;AACH,wBAAgB,eAAe,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAuC9D;AAMD;;;GAGG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,GAAG,MAAM,CAanF;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAC7B,OAAO,EAAE,aAAa,EACtB,MAAM,EAAE,aAAa,EAAE,GACtB,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAMxB"}
package/dist/services/ncbi/formatting/citation-formatter.js CHANGED
@@ -1,6 +1,6 @@
1
1
  /**
2
2
  * @fileoverview Hand-rolled citation formatters for PubMed articles.
3
- * Supports APA 7th, MLA 9th, BibTeX, and RIS formats.
3
+ * Supports APA 7th, MLA 9th, BibTeX, RIS, and Vancouver (ICMJE/NLM) formats.
4
4
  * Pure TypeScript, zero dependencies, Workers-compatible.
5
5
  * @module src/services/ncbi/formatting/citation-formatter
6
6
  */
@@ -370,8 +370,12 @@ export function formatBibtex(article) {
370
370
  if (m.descriptorName)
371
371
  keywordSet.add(m.descriptorName);
372
372
  }
373
+ // Brace-wrap each term so MeSH descriptors that carry internal commas in
374
+ // their inverted form (e.g. "Databases, Protein") stay a single keyword —
375
+ // biblatex's comma-separated list parser reads a braced item as one element.
373
376
  if (keywordSet.size > 0) {
374
- fields.push(['keywords', escapeBibtex([...keywordSet].join(', '))]);
377
+ const keywords = [...keywordSet].map((k) => `{${escapeBibtex(k)}}`).join(', ');
378
+ fields.push(['keywords', keywords]);
375
379
  }
376
380
  // Build entry
377
381
  const maxKeyLen = Math.max(...fields.map(([k]) => k.length));
@@ -468,6 +472,100 @@ export function formatRis(article) {
468
472
  return lines.join('\n');
469
473
  }
470
474
  // ---------------------------------------------------------------------------
475
+ // Vancouver (ICMJE / NLM)
476
+ // ---------------------------------------------------------------------------
477
+ /**
478
+ * Format a single author in Vancouver style: `Surname AB` — surname, a space,
479
+ * then initials with no periods or internal spaces. Collective/group authors
480
+ * return their name directly.
481
+ */
482
+ function formatAuthorVancouver(author) {
483
+ if (author.collectiveName)
484
+ return author.collectiveName;
485
+ const last = author.lastName ?? '';
486
+ const initialsSource = author.initials ??
487
+ author.firstName
488
+ ?.split(/[\s-]+/)
489
+ .filter(Boolean)
490
+ .map((part) => part[0])
491
+ .join('');
492
+ // Letters only (Unicode-aware), uppercased, no separators: "AB", not "A. B."
493
+ const initials = initialsSource
494
+ ? Array.from(initialsSource)
495
+ .filter((c) => /\p{L}/u.test(c))
496
+ .join('')
497
+ .toUpperCase()
498
+ : '';
499
+ if (!last)
500
+ return initials;
501
+ if (!initials)
502
+ return last;
503
+ return `${last} ${initials}`;
504
+ }
505
+ /**
506
+ * Format the full author list for Vancouver: list every author for six or
507
+ * fewer; for seven or more, list the first six followed by `et al.` (ICMJE).
508
+ */
509
+ function formatAuthorsVancouver(authors) {
510
+ const names = authors.map(formatAuthorVancouver).filter(Boolean);
511
+ if (names.length === 0)
512
+ return '';
513
+ if (names.length <= 6)
514
+ return names.join(', ');
515
+ return `${names.slice(0, 6).join(', ')}, et al.`;
516
+ }
517
+ /**
518
+ * Format a PubMed article as a Vancouver (ICMJE/NLM) reference — the numbered
519
+ * style used by NEJM, Lancet, JAMA, BMJ, and most biomedical journals.
520
+ *
521
+ * Pattern (the leading list number is the consumer's responsibility — entries
522
+ * are formatted independently, so this returns the unnumbered reference body):
523
+ * ```
524
+ * Surname AB, Surname CD, et al. Article title. Abbrev J Name. Year;Vol(Issue):Pages. doi: 10.x/y
525
+ * ```
526
+ * Journal name uses the NLM/ISO abbreviation when available; pages are used as
527
+ * PubMed supplies them (often elided, e.g. "583-9"); the DOI carries no trailing
528
+ * period so it stays copy-pasteable.
529
+ */
530
+ export function formatVancouver(article) {
531
+ const segments = [];
532
+ // Authors — terminate with a period unless the list already ends in "et al."
533
+ const authorStr = article.authors?.length ? formatAuthorsVancouver(article.authors) : '';
534
+ if (authorStr) {
535
+ segments.push(authorStr.endsWith('.') ? authorStr : `${authorStr}.`);
536
+ }
537
+ // Title — sentence case as supplied, single terminating period
538
+ if (article.title) {
539
+ segments.push(`${article.title.replace(/\.\s*$/, '')}.`);
540
+ }
541
+ // Journal — NLM/ISO abbreviation preferred, full title as fallback
542
+ const journal = article.journalInfo;
543
+ const journalName = journal?.isoAbbreviation ?? journal?.title;
544
+ if (journalName) {
545
+ segments.push(`${journalName.replace(/\.\s*$/, '')}.`);
546
+ }
547
+ // Source — "Year;Volume(Issue):Pages."
548
+ const year = getYear(article);
549
+ let source = year !== 'n.d.' ? year : '';
550
+ if (journal?.volume) {
551
+ source += source ? `;${journal.volume}` : journal.volume;
552
+ if (journal.issue)
553
+ source += `(${journal.issue})`;
554
+ if (journal.pages)
555
+ source += `:${journal.pages}`;
556
+ }
557
+ else if (journal?.pages) {
558
+ source += source ? `:${journal.pages}` : journal.pages;
559
+ }
560
+ if (source)
561
+ segments.push(`${source}.`);
562
+ // DOI — NLM "doi: <doi>" form; no trailing period (would corrupt the DOI)
563
+ if (article.doi) {
564
+ segments.push(`doi: ${article.doi}`);
565
+ }
566
+ return segments.join(' ');
567
+ }
568
+ // ---------------------------------------------------------------------------
471
569
  // Dispatchers
472
570
  // ---------------------------------------------------------------------------
473
571
  /**
@@ -484,6 +582,8 @@ export function formatCitation(article, style) {
484
582
  return formatBibtex(article);
485
583
  case 'ris':
486
584
  return formatRis(article);
585
+ case 'vancouver':
586
+ return formatVancouver(article);
487
587
  }
488
588
  }
489
589
  /**
package/dist/services/ncbi/formatting/citation-formatter.js.map CHANGED
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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts CHANGED
@@ -18,7 +18,11 @@ export declare function extractJatsAuthors(contribGroup: JatsNode | undefined):
18
18
  * in manuscript-submitted PMC deposits) preserve their main text.
19
19
  */
20
20
  export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
21
- /** Extract references from a `<back>` node. Prefers mixed-citation over element-citation. */
21
+ /**
22
+ * Extract references from a `<back>` node. Prefers mixed-citation over
23
+ * element-citation, descending into `<citation-alternatives>` when a ref carries
24
+ * both forms there rather than as direct children of `<ref>`.
25
+ */
22
26
  export declare function extractReferences(back: JatsNode | undefined): ParsedPmcReference[];
23
27
  /**
24
28
  * Parse a single JATS `<article>` node (from PMC EFetch via the ordered parser)
package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AACrB,OAAO,EAKL,KAAK,QAAQ,EAGd,MAAM,sBAAsB,CAAC;AAmB9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;AA2HD;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CA2BlF;AA0BD,6FAA6F;AAC7F,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,CAsBlF;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CA4CvE"}
1
+ {"version":3,"file":"pmc-article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/pmc-article-parser.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EACV,gBAAgB,EAChB,eAAe,EAEf,kBAAkB,EAClB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AACrB,OAAO,EAKL,KAAK,QAAQ,EAGd,MAAM,sBAAsB,CAAC;AAmB9B,iGAAiG;AACjG,wBAAgB,kBAAkB,CAAC,YAAY,EAAE,QAAQ,GAAG,SAAS,GAAG,eAAe,EAAE,CA2BxF;AA2HD;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,gBAAgB,EAAE,CA2BlF;AA0BD;;;;GAIG;AACH,wBAAgB,iBAAiB,CAAC,IAAI,EAAE,QAAQ,GAAG,SAAS,GAAG,kBAAkB,EAAE,CA4BlF;AAID;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,WAAW,EAAE,QAAQ,GAAG,gBAAgB,CA4CvE"}
package/dist/services/ncbi/parsing/pmc-article-parser.js CHANGED
@@ -206,7 +206,11 @@ function extractSection(sec) {
206
206
  };
207
207
  }
208
208
  // ─── References ─────────────────────────────────────────────────────────────
209
- /** Extract references from a `<back>` node. Prefers mixed-citation over element-citation. */
209
+ /**
210
+ * Extract references from a `<back>` node. Prefers mixed-citation over
211
+ * element-citation, descending into `<citation-alternatives>` when a ref carries
212
+ * both forms there rather than as direct children of `<ref>`.
213
+ */
210
214
  export function extractReferences(back) {
211
215
  if (!back)
212
216
  return [];
@@ -215,7 +219,12 @@ export function extractReferences(back) {
215
219
  return [];
216
220
  const results = [];
217
221
  for (const ref of findAll(refList, 'ref')) {
218
- const citationNode = findOne(ref, 'mixed-citation') ?? findOne(ref, 'element-citation');
222
+ // JATS wraps the two citation forms in <citation-alternatives> (the NLM
223
+ // construct carrying both a structured <element-citation> and a readable
224
+ // <mixed-citation>). findOne matches direct children only, so resolve that
225
+ // container first; refs with a direct citation node fall through to `ref`.
226
+ const container = findOne(ref, 'citation-alternatives') ?? ref;
227
+ const citationNode = findOne(container, 'mixed-citation') ?? findOne(container, 'element-citation');
219
228
  if (!citationNode)
220
229
  continue;
221
230
  const citation = textContent(citationNode);
package/dist/services/ncbi/parsing/pmc-article-parser.js.map CHANGED
@@ -1 +1 @@
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubmed-mcp-server",
3
- "version": "2.7.11",
3
+ "version": "2.8.0",
4
4
  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
5
5
  "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
6
6
  "type": "module",
@@ -92,7 +92,7 @@
92
92
  },
93
93
  "devDependencies": {
94
94
  "@biomejs/biome": "^2.4.16",
95
- "@types/node": "^25.9.1",
95
+ "@types/node": "^25.9.2",
96
96
  "@types/sanitize-html": "^2.16.1",
97
97
  "@vitest/coverage-istanbul": "^4.1.8",
98
98
  "depcheck": "^1.4.7",
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/pubmed-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "2.7.11",
9
+ "version": "2.8.0",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
20
20
  "identifier": "@cyanheads/pubmed-mcp-server",
21
21
  "runtimeHint": "bun",
22
- "version": "2.7.11",
22
+ "version": "2.8.0",
23
23
  "packageArguments": [
24
24
  {
25
25
  "type": "positional",
@@ -66,7 +66,7 @@
66
66
  "registryBaseUrl": "https://registry.npmjs.org",
67
67
  "identifier": "@cyanheads/pubmed-mcp-server",
68
68
  "runtimeHint": "bun",
69
- "version": "2.7.11",
69
+ "version": "2.8.0",
70
70
  "packageArguments": [
71
71
  {
72
72
  "type": "positional",