npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.6.2 → 2.6.4 - Mend

@cyanheads/pubmed-mcp-server 2.6.2 → 2.6.4

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 (19) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.6.2
+**Version:** 2.6.4
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
 > **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 Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![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-2.6.2-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-^1.29.0-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) [![Version](https://img.shields.io/badge/Version-2.6.4-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-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
 [![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/)

package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"convert-ids.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAajD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;~~kBA8FzB~~,CAAC"}
1	+ {"version":3,"file":"convert-ids.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAajD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;kBAyGzB,CAAC"}

package/dist/mcp-server/tools/definitions/convert-ids.tool.js CHANGED Viewed

@@ -33,10 +33,19 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
             .array(z
             .object({
             requestedId: z.string().describe('The ID that was submitted'),
-            pmid: z.string().optional().describe('PubMed ID'),
-            pmcid: z.string().optional().describe('PubMed Central ID'),
-            doi: z.string().optional().describe('Digital Object Identifier'),
-            errmsg: z.string().optional().describe('Error message if conversion failed'),
+            pmid: z.string().optional().describe('PubMed ID; absent if no mapping was found'),
+            pmcid: z
+                .string()
+                .optional()
+                .describe('PubMed Central ID; absent if the article has no PMC copy'),
+            doi: z
+                .string()
+                .optional()
+                .describe('Digital Object Identifier; absent if no DOI is on record'),
+            errmsg: z
+                .string()
+                .optional()
+                .describe('Error message if conversion failed. Presence of `errmsg` is the failure signal; absence means the conversion succeeded.'),
         })
             .describe('Per-ID conversion record'))
             .describe('Conversion results, one per input ID'),

package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED Viewed

@@ -144,23 +144,24 @@ const UnavailableSchema = z
     .describe('One PMID that could not be returned with an explanation of why');
 // ─── Tool Definition ─────────────────────────────────────────────────────────
 export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
-    description: 'Fetch full-text articles. Primary source is PubMed Central (structured JATS with sections and references). When a PMID has no PMC copy, transparently falls back to Unpaywall (open-access copies hosted by publishers or institutional repositories) and returns best-effort HTML-as-Markdown or PDF-as-text. Set UNPAYWALL_EMAIL to enable the fallback. Accepts PMC IDs directly or PubMed IDs (auto-resolved via the PMC ID Converter).',
+    description: 'Fetch full-text articles. Primary source is PubMed Central (structured JATS with sections and references). When a PMID has no PMC copy, transparently falls back to Unpaywall (open-access copies hosted by publishers or institutional repositories) and returns best-effort HTML-as-Markdown or PDF-as-text. Set UNPAYWALL_EMAIL to enable the fallback. Provide exactly one of `pmcids` (PMC IDs directly) or `pmids` (PubMed IDs, auto-resolved via the PMC ID Converter) — not both, not neither.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/fetch-fulltext.tool.ts',
-    input: z.object({
+    input: z
+        .object({
         pmcids: z
             .array(z.string())
             .min(1)
             .max(10)
             .optional()
-            .describe('PMC IDs to fetch (e.g. ["PMC9575052"]). Provide this OR pmids, not both.'),
+            .describe('PMC IDs to fetch (e.g. ["PMC9575052"]). Provide exactly one of `pmcids` or `pmids`.'),
         pmids: z
             .array(pmidStringSchema)
             .min(1)
             .max(10)
             .optional()
-            .describe('PubMed IDs. Articles in PMC are returned as structured JATS. Articles not in PMC are retrieved from Unpaywall when UNPAYWALL_EMAIL is set and a DOI is available. Provide this OR pmcids, not both.'),
+            .describe('PubMed IDs. Provide exactly one of `pmcids` or `pmids`. Articles in PMC are returned as structured JATS; articles not in PMC are retrieved from Unpaywall when UNPAYWALL_EMAIL is set and a DOI is available.'),
         includeReferences: z
             .boolean()
             .default(false)
@@ -176,6 +177,9 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
             .array(z.string())
             .optional()
             .describe('Filter to specific sections by title, case-insensitive (e.g. ["Introduction", "Methods", "Results", "Discussion"]). Applies to `source=pmc` results only.'),
+    })
+        .refine((v) => (v.pmcids === undefined) !== (v.pmids === undefined), {
+        message: 'Provide exactly one of `pmcids` or `pmids` (not both, not neither).',
     }),
     output: z.object({
         articles: z.array(ArticleSchema).describe('Full-text articles'),
@@ -187,7 +191,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
         unavailablePmcIds: z
             .array(z.string())
             .optional()
-            .describe('PMC IDs requested directly that returned no data'),
+            .describe('PMC IDs that returned no data, whether requested directly via `pmcids` or resolved from `pmids` via the PMC ID Converter'),
     }),
     async handler(input, ctx) {
         ctx.log.info('Executing pubmed_fetch_fulltext', {
@@ -195,10 +199,6 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
             hasPmids: !!input.pmids,
             idCount: (input.pmcids ?? input.pmids)?.length,
         });
-        if (!input.pmcids && !input.pmids)
-            throw new Error('Either pmcids or pmids must be provided');
-        if (input.pmcids && input.pmids)
-            throw new Error('Provide pmcids or pmids, not both');
         // ── PMID path: resolve to PMC + collect unresolved PMIDs for Unpaywall fallback ──
         let pmcIds = [];
         let fallbackCandidates = [];

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map CHANGED Viewed

	@@ -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;AAYjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;~~kBA4F9B~~,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;AAYjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;kBA6F9B,CAAC"}

package/dist/mcp-server/tools/definitions/format-citations.tool.js CHANGED Viewed

@@ -46,9 +46,6 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
         });
         const raw = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 25, signal: ctx.signal });
         const xmlArticles = ensureArray(raw?.PubmedArticleSet?.PubmedArticle);
-        if (xmlArticles.length === 0) {
-            throw new Error(`No articles found for PMIDs: ${input.pmids.join(', ')}`);
-        }
         const citations = xmlArticles.map((xmlArticle) => {
             const parsed = parseFullArticle(xmlArticle);
             return {
@@ -74,6 +71,9 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
         if (result.unavailablePmids?.length) {
             lines.push(`**Unavailable PMIDs:** ${result.unavailablePmids.join(', ')}`);
         }
+        if (result.totalFormatted === 0) {
+            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.`);
+        }
         for (const entry of result.citations) {
             lines.push(`\n## PMID ${entry.pmid}`);
             if (entry.title)

package/dist/mcp-server/tools/definitions/format-citations.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAsR7B,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-citation.tool.js CHANGED Viewed

@@ -21,7 +21,7 @@ function authorSurnames(authors) {
         .filter((s) => s.length > 0 && s !== 'et');
 }
 export const lookupCitationTool = tool('pubmed_lookup_citation', {
-    description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID. Uses NCBI ECitMatch for deterministic matching — more reliable than searching by citation fields.`,
+    description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID. Uses NCBI ECitMatch for deterministic matching — more reliable than searching by citation fields. Each citation must include at least one bibliographic field (journal, year, volume, firstPage, or authorName); more fields = better match accuracy.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-citation.tool.ts',
@@ -45,7 +45,10 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
                 .optional()
                 .describe('Arbitrary label to track this citation in results. Auto-assigned if omitted.'),
         })
-            .describe('Citation to match against PubMed'))
+            .describe('Citation to match against PubMed. Must include at least one bibliographic field (journal, year, volume, firstPage, or authorName).')
+            .refine((c) => !!(c.journal || c.year || c.volume || c.firstPage || c.authorName), {
+            message: 'Each citation must include at least one bibliographic field (journal, year, volume, firstPage, or authorName).',
+        }))
             .min(1)
             .max(25)
             .describe('Citations to look up. More fields = better match accuracy.'),
@@ -67,7 +70,7 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
             candidatePmids: z
                 .array(z.string().describe('PMID'))
                 .optional()
-                .describe('PMIDs returned for AMBIGUOUS matches — candidate articles needing more citation fields to disambiguate. Parsed from the raw `AMBIGUOUS <csv>` detail string for programmatic consumption.'),
+                .describe('Candidate PMIDs returned when the citation matched ambiguously. Add more bibliographic fields and retry to disambiguate, or fetch each candidate via pubmed_fetch_articles to pick the intended one.'),
             matchedFirstAuthor: z
                 .string()
                 .optional()
@@ -77,12 +80,12 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
                 .object({
                 code: z
                     .enum(['author_mismatch', 'year_mismatch'])
-                    .describe('Machine-readable warning classifier for downstream filtering'),
+                    .describe('Machine-readable warning code'),
                 message: z.string().describe('Human-readable description of the warning'),
             })
                 .describe('Non-fatal warning about the match'))
                 .optional()
-                .describe('Non-fatal warnings about this match. ECitMatch weights journal+volume+page and tolerates author/year disagreement, so a returned PMID may not match the queried author or year — downstream code should key on `code` to decide whether to trust the PMID.'),
+                .describe('Non-fatal warnings about this match. A PMID may be returned even when the queried author or year disagrees with the matched article — verify before treating the PMID as authoritative.'),
         })
             .describe('Per-citation match result'))
             .describe('Match results, one per input citation'),
@@ -94,11 +97,6 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
     }),
     async handler(input, ctx) {
         ctx.log.info('Executing pubmed_lookup_citation', { count: input.citations.length });
-        for (const c of input.citations) {
-            if (!c.journal && !c.year && !c.volume && !c.firstPage && !c.authorName) {
-                throw new Error('Each citation must include at least one bibliographic field (journal, year, volume, firstPage, or authorName).');
-            }
-        }
         const citations = input.citations.map((c, i) => ({
             journal: c.journal,
             year: c.year,

package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA4EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~kBAqT7B~~,CAAC"}
1	+ {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA4EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAuT7B,CAAC"}

package/dist/mcp-server/tools/definitions/search-articles.tool.js CHANGED Viewed

@@ -83,18 +83,18 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             minDate: z
                 .string()
                 .regex(DATE_RE, 'Date must be YYYY, YYYY/MM, or YYYY/MM/DD (/, -, or . separators)')
-                .describe('Start date (YYYY/MM/DD, YYYY/MM, or YYYY)'),
+                .describe('Start date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound'),
             maxDate: z
                 .string()
                 .regex(DATE_RE, 'Date must be YYYY, YYYY/MM, or YYYY/MM/DD (/, -, or . separators)')
-                .describe('End date (YYYY/MM/DD, YYYY/MM, or YYYY)'),
+                .describe('End date (YYYY/MM/DD, YYYY/MM, or YYYY); empty string disables this bound'),
             dateType: z
                 .enum(['pdat', 'mdat', 'edat'])
                 .default('pdat')
                 .describe('Date type: pdat (publication), mdat (modification), edat (entrez)'),
         })
             .optional()
-            .describe('Filter by date range'),
+            .describe('Filter by date range. The filter is applied only when both `minDate` and `maxDate` are non-empty; either one empty disables the entire date range.'),
         publicationTypes: z
             .array(z.string())
             .optional()

package/dist/mcp-server/tools/definitions/search-articles.tool.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.6.2",
+  "version": "2.6.4",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata and open-access full text (PMC + Unpaywall), generate citations, explore MeSH terms, and discover related research.",
   "type": "module",
@@ -19,6 +19,8 @@
     "format": "biome check --write --unsafe",
     "test": "bunx vitest run",
     "lint:mcp": "bun run scripts/lint-mcp.ts",
+    "changelog:build": "bun run scripts/build-changelog.ts",
+    "changelog:check": "bun run scripts/build-changelog.ts --check",
     "publish-mcp": "mcp-publisher login github -token \"$(security find-generic-password -a \"$USER\" -s mcp-publisher-github-pat -w)\" && mcp-publisher publish",
     "dev:stdio": "MCP_TRANSPORT_TYPE=stdio bun --watch src/index.ts",
     "dev:http": "MCP_TRANSPORT_TYPE=http bun --watch src/index.ts",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.6.2",
+  "version": "2.6.4",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.6.2",
+      "version": "2.6.4",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.6.2",
+      "version": "2.6.4",
       "packageArguments": [
         {
           "type": "positional",