npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.3.8 → 2.3.9 - Mend

@cyanheads/pubmed-mcp-server 2.3.8 → 2.3.9

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 (13) hide show

package/CLAUDE.md +1 -1
package/README.md +1 -1
package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +1 -0
package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
package/dist/mcp-server/tools/definitions/search-articles.tool.js +51 -4
package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
package/dist/services/ncbi/parsing/esummary-parser.d.ts.map +1 -1
package/dist/services/ncbi/parsing/esummary-parser.js +19 -4
package/dist/services/ncbi/parsing/esummary-parser.js.map +1 -1
package/dist/services/ncbi/types.d.ts +15 -3
package/dist/services/ncbi/types.d.ts.map +1 -1
package/package.json +1 -1
package/server.json +3 -3

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.3.8
+**Version:** 2.3.9
 **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-2.3.8-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/)
+[![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/)
 [![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/search-articles.tool.d.ts CHANGED Viewed

@@ -75,5 +75,6 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
         pubmedUrl: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
     searchUrl: z.ZodString;
+    notice: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>>;
 //# sourceMappingURL=search-articles.tool.d.ts.map

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;~~AAsCjD~~,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA4Q7B~~,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;AAsEjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAuS7B,CAAC"}

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

@@ -7,6 +7,31 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { sanitization } from '@cyanheads/mcp-ts-core/utils';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
+/**
+ * Accepts empty strings (treated as "no filter" by the handler) or dates in
+ * YYYY, YYYY/MM, or YYYY/MM/DD form with `/`, `-`, or `.` separators.
+ * Catches obvious typos at the edge so they don't degrade silently to 0 results.
+ */
+const DATE_RE = /^$|^\d{4}([/\-.]\d{1,2}([/\-.]\d{1,2})?)?$/;
+/**
+ * Produces an optional human- and agent-readable hint for edge cases where
+ * bare empty arrays leave the caller without enough signal to recover:
+ * - No matches at all (suggest spell-check / removing filters)
+ * - Filters applied but nothing matched (suggest relaxing filters)
+ * - Pagination overshoot (offset ≥ totalFound)
+ */
+function buildNotice(args) {
+    const { totalFound, pmidCount, offset, hasFilters } = args;
+    if (totalFound === 0) {
+        return hasFilters
+            ? 'No results matched your query with the applied filters. Try removing filters (e.g. dateRange, publicationTypes, meshTerms), broadening dates, or verifying author/journal spelling.'
+            : 'No results matched your query. Try running pubmed_spell_check for a suggested correction or broaden the query.';
+    }
+    if (pmidCount === 0 && offset > 0 && offset >= totalFound) {
+        return `Offset ${offset} exceeds totalFound (${totalFound}). Reset offset to 0 or reduce it below ${totalFound} to page through results.`;
+    }
+    return;
+}
 const AppliedFiltersSchema = z.object({
     dateRange: z
         .object({
@@ -52,8 +77,14 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             .describe('Sort order: relevance (default), pub_date (newest first), author, or journal'),
         dateRange: z
             .object({
-            minDate: z.string().describe('Start date (YYYY/MM/DD, YYYY/MM, or YYYY)'),
-            maxDate: z.string().describe('End date (YYYY/MM/DD, YYYY/MM, or YYYY)'),
+            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)'),
+            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)'),
             dateType: z
                 .enum(['pdat', 'mdat', 'edat'])
                 .default('pdat')
@@ -64,10 +95,13 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         publicationTypes: z
             .array(z.string())
             .optional()
-            .describe('Filter by publication type (e.g. "Review", "Clinical Trial", "Meta-Analysis")'),
+            .describe('Filter by publication type (e.g. "Review", "Clinical Trial", "Meta-Analysis"). Multiple values are OR\'d — any match qualifies.'),
         author: z.string().optional().describe('Filter by author name (e.g. "Smith J")'),
         journal: z.string().optional().describe('Filter by journal name'),
-        meshTerms: z.array(z.string()).optional().describe('Filter by MeSH terms'),
+        meshTerms: z
+            .array(z.string())
+            .optional()
+            .describe("Filter by MeSH terms. Multiple terms are AND'd — all must match."),
         language: z.string().optional().describe('Filter by language (e.g. "english")'),
         hasAbstract: z.boolean().optional().describe('Only include articles with abstracts'),
         freeFullText: z.boolean().optional().describe('Only include free full text articles'),
@@ -103,6 +137,10 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         }))
             .describe('Brief summaries (empty array when summaryCount is 0)'),
         searchUrl: z.string().describe('PubMed search URL'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Optional guidance when results are empty or paging overshot — e.g. how to broaden filters or reset offset. Absent on successful result pages.'),
     }),
     async handler(input, ctx) {
         ctx.log.info('Executing pubmed_search', { query: input.query });
@@ -206,6 +244,12 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             totalFound: esResult.count,
             pmidCount: pmids.length,
         });
+        const notice = buildNotice({
+            totalFound: esResult.count,
+            pmidCount: pmids.length,
+            offset: input.offset,
+            hasFilters: Object.keys(appliedFilters).length > 0,
+        });
         return {
             query: input.query,
             effectiveQuery,
@@ -215,6 +259,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             pmids,
             summaries,
             searchUrl,
+            ...(notice && { notice }),
         };
     },
     format: (result) => {
@@ -255,6 +300,8 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
                 lines.push(`- **Species:** ${result.appliedFilters.species}`);
             }
         }
+        if (result.notice)
+            lines.push(`\n> ${result.notice}`);
         if (result.pmids.length > 0)
             lines.push(`\n**PMIDs:** ${result.pmids.join(', ')}`);
         if (result.summaries?.length) {

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

	@@ -1 +1 @@
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package/dist/services/ncbi/parsing/esummary-parser.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,EAKV,cAAc,EACd,kBAAkB,EAClB,cAAc,IAAI,iBAAiB,EAEpC,MAAM,aAAa,CAAC;AAGrB;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,CAAC,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAQ3E;AA8BD;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAajE;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,MAAM,EAChB,aAAa,CAAC,EAAE,cAAc,GAC7B,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CAkC7B;~~AAiPD~~;;;GAGG;AACH,wBAAsB,qBAAqB,CACzC,cAAc,CAAC,EAAE,cAAc,EAC/B,OAAO,CAAC,EAAE,cAAc,GACvB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAiD/B"}
1	+ {"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,EAKV,cAAc,EACd,kBAAkB,EAClB,cAAc,IAAI,iBAAiB,EAEpC,MAAM,aAAa,CAAC;AAGrB;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,CAAC,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAQ3E;AA8BD;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAajE;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,MAAM,EAChB,aAAa,CAAC,EAAE,cAAc,GAC7B,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CAkC7B;AAkQD;;;GAGG;AACH,wBAAsB,qBAAqB,CACzC,cAAc,CAAC,EAAE,cAAc,EAC/B,OAAO,CAAC,EAAE,cAAc,GACvB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAiD/B"}

package/dist/services/ncbi/parsing/esummary-parser.js CHANGED Viewed

@@ -102,6 +102,21 @@ export async function standardizeESummaryDate(dateStr, parentContext) {
     }
     return;
 }
+/**
+ * Returns the id type (e.g. 'doi', 'pmc') from an ESummary ArticleId entry,
+ * normalizing across JSON (`idtype`) and XML (`IdType`) casings.
+ */
+function getArticleIdType(id) {
+    return id.idtype ?? id.IdType;
+}
+/**
+ * Returns the raw value field from an ESummary ArticleId entry,
+ * normalizing across JSON (`value`) and XML (`Value`) casings. The value may
+ * be a string or number — `getText` handles both.
+ */
+function getArticleIdValue(id) {
+    return id.value ?? id.Value;
+}
 function parseESummaryAuthorsFromDocumentSummary(docSummary) {
     const authorsProp = docSummary.Authors;
     if (!authorsProp)
@@ -205,13 +220,13 @@ function parseSingleDocumentSummary(docSummary) {
     }
     let doiValue = getText(docSummary.DOI, undefined);
     if (!doiValue) {
-        const doiEntry = idsArray.find((id) => id.idtype === 'doi');
+        const doiEntry = idsArray.find((id) => getArticleIdType(id) === 'doi');
         if (doiEntry) {
-            doiValue = getText(doiEntry.value, undefined);
+            doiValue = getText(getArticleIdValue(doiEntry), undefined);
         }
     }
-    const pmcEntry = idsArray.find((id) => id.idtype === 'pmc');
-    const pmcIdValue = pmcEntry ? getText(pmcEntry.value, undefined) : undefined;
+    const pmcEntry = idsArray.find((id) => getArticleIdType(id) === 'pmc');
+    const pmcIdValue = pmcEntry ? getText(getArticleIdValue(pmcEntry), undefined) : undefined;
     const title = getText(docSummary.Title);
     const source = getText(docSummary.Source) || getText(docSummary.FullJournalName) || getText(docSummary.SO);
     const rawPubDate = getText(docSummary.PubDate);

package/dist/services/ncbi/parsing/esummary-parser.js.map CHANGED Viewed

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

@@ -282,10 +282,22 @@ export interface ESummaryAuthor {
     clusterid?: string;
     name: string;
 }
+/**
+ * NCBI returns ArticleId entries in two shapes depending on retmode:
+ * - JSON (`retmode=json&version=2.0`): lowercase keys `{ idtype, idtypen, value }`
+ * - XML  (`retmode=xml&version=2.0`):  capitalized child elements parsed as
+ *   `{ IdType, IdTypeN, Value }` by fast-xml-parser.
+ *
+ * Both shapes are supported so callers don't have to care which retmode produced
+ * the summary. Use the helpers in `esummary-parser.ts` to read them safely.
+ */
 export interface ESummaryArticleId {
-    idtype: string;
-    idtypen: number;
-    value: string;
+    IdType?: string;
+    IdTypeN?: number;
+    idtype?: string;
+    idtypen?: number;
+    Value?: string | number;
+    value?: string | number;
     [key: string]: unknown;
 }
 export interface ESummaryHistory {

package/dist/services/ncbi/types.d.ts.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": "2.3.8",
+  "version": "2.3.9",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
   "type": "module",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.3.8",
+  "version": "2.3.9",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.3.8",
+      "version": "2.3.9",
       "packageArguments": [
         {
           "type": "positional",
@@ -60,7 +60,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.3.8",
+      "version": "2.3.9",
       "packageArguments": [
         {
           "type": "positional",