npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.3.2 → 2.3.4 - Mend

@cyanheads/pubmed-mcp-server 2.3.2 → 2.3.4

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 (26) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.3.2
+**Version:** 2.3.4
 **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-2.3.2-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-^1.27.1-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-2.3.3-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-^6.0.2-3178C6.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/)
@@ -49,6 +49,7 @@ Search PubMed with full NCBI query syntax and filters.
 - Sort by relevance, publication date, author, or journal
 - Pagination via offset for paging through large result sets
 - Optional brief summaries for top N results via ESummary
+- Returns the original query plus the fully applied PubMed query and normalized filter metadata
 ---
@@ -86,6 +87,7 @@ Generate formatted citations for articles.
 - Request multiple styles per article in a single call
 - Hand-rolled formatters — zero external dependencies, fully Workers-compatible
 - Up to 50 articles per request
+- Reports formatted counts and unavailable PMIDs for partial-result handling
 ---
@@ -126,6 +128,7 @@ Resolve partial bibliographic references to PubMed IDs via NCBI ECitMatch.
 - More fields = better match accuracy; at least one field required
 - Batch up to 25 citations per request
 - Deterministic matching — more reliable than free-text search for known references
+- Returns explicit `matched`, `not_found`, and `ambiguous` statuses with recovery detail
 ---
@@ -281,7 +284,7 @@ All configuration is validated at startup via Zod schemas in `src/config/server-
 | `NCBI_API_KEY` | NCBI API key for higher rate limits (10 req/s vs 3 req/s) | none |
 | `NCBI_ADMIN_EMAIL` | Contact email sent with NCBI requests (recommended by NCBI) | none |
 | `NCBI_REQUEST_DELAY_MS` | Delay between NCBI requests in ms | 334 (100 with key) |
-| `NCBI_MAX_RETRIES` | Retry attempts for failed NCBI requests | 3 |
+| `NCBI_MAX_RETRIES` | Retry attempts for failed NCBI requests | 6 |
 | `NCBI_TIMEOUT_MS` | NCBI request timeout in ms | `30000` |
 | `OTEL_ENABLED` | Enable OpenTelemetry | `false` |

package/dist/config/server-config.js CHANGED Viewed

@@ -15,7 +15,7 @@ const ServerConfigSchema = z.object({
     /** Minimum delay between NCBI requests in ms. NCBI requires ~334ms without API key. */
     requestDelayMs: z.coerce.number().min(50).max(5000).default(334).describe('Request delay in ms'),
     /** Maximum retry attempts for failed NCBI requests. */
-    maxRetries: z.coerce.number().min(0).max(10).default(3).describe('Max retry attempts'),
+    maxRetries: z.coerce.number().min(0).max(10).default(6).describe('Max retry attempts'),
     /** Request timeout in ms. */
     timeoutMs: z.coerce
         .number()

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

@@ -18,5 +18,8 @@ export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolD
         title: z.ZodOptional<z.ZodString>;
         citations: z.ZodRecord<z.ZodString, z.ZodString>;
     }, z.core.$strip>>;
+    totalSubmitted: z.ZodNumber;
+    totalFormatted: z.ZodNumber;
+    unavailablePmids: z.ZodOptional<z.ZodArray<z.ZodString>>;
 }, z.core.$strip>>;
 //# sourceMappingURL=format-citations.tool.d.ts.map

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;AAUjD,eAAO,MAAM,mBAAmB~~;;;;;;;;;;;;;;kBAmE9B~~,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;AAUjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;kBAuF9B,CAAC"}

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

@@ -26,6 +26,12 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
             citations: z.record(z.string(), z.string()).describe('Citations keyed by style'),
         }))
             .describe('Citations per article'),
+        totalSubmitted: z.number().describe('Number of PMIDs submitted for citation formatting'),
+        totalFormatted: z.number().describe('Number of PMIDs successfully formatted'),
+        unavailablePmids: z
+            .array(z.string())
+            .optional()
+            .describe('Requested PMIDs that did not return article metadata'),
     }),
     async handler(input, ctx) {
         ctx.log.debug('Fetching articles for citation generation', {
@@ -45,10 +51,23 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
                 citations: formatCitations(parsed, input.styles),
             };
         });
-        return { citations };
+        const returnedPmids = new Set(citations.map((entry) => entry.pmid));
+        const unavailablePmids = input.pmids.filter((pmid) => !returnedPmids.has(pmid));
+        return {
+            citations,
+            totalSubmitted: input.pmids.length,
+            totalFormatted: citations.length,
+            ...(unavailablePmids.length > 0 && { unavailablePmids }),
+        };
     },
     format: (result) => {
-        const lines = ['# PubMed Citations'];
+        const lines = [
+            '# PubMed Citations',
+            `**Formatted:** ${result.totalFormatted}/${result.totalSubmitted}`,
+        ];
+        if (result.unavailablePmids?.length) {
+            lines.push(`**Unavailable PMIDs:** ${result.unavailablePmids.join(', ')}`);
+        }
         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 CHANGED Viewed

@@ -18,6 +18,12 @@ export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDe
         key: z.ZodString;
         pmid: z.ZodOptional<z.ZodString>;
         matched: z.ZodBoolean;
+        status: z.ZodEnum<{
+            matched: "matched";
+            not_found: "not_found";
+            ambiguous: "ambiguous";
+        }>;
+        detail: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
     totalMatched: z.ZodNumber;
     totalSubmitted: z.ZodNumber;

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;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;kBAyH7B,CAAC"}

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

@@ -37,6 +37,13 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
             key: z.string().describe('Citation tracking key'),
             pmid: z.string().optional().describe('Matched PubMed ID'),
             matched: z.boolean().describe('Whether a PMID was found'),
+            status: z
+                .enum(['matched', 'not_found', 'ambiguous'])
+                .describe('Lookup outcome classification for this citation'),
+            detail: z
+                .string()
+                .optional()
+                .describe('Additional detail returned by ECitMatch for non-exact matches'),
         }))
             .describe('Match results, one per input citation'),
         totalMatched: z.number().describe('Number of citations with PMID matches'),
@@ -61,7 +68,9 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
         const mapped = results.map((r) => ({
             key: r.key,
             matched: r.matched,
+            status: r.status,
             ...(r.pmid && { pmid: r.pmid }),
+            ...(r.detail && { detail: r.detail }),
         }));
         const totalMatched = mapped.filter((r) => r.matched).length;
         ctx.log.info('pubmed_lookup_citation completed', {
@@ -74,14 +83,27 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
         const lines = [
             `## Citation Lookup Results`,
             `**Matched:** ${result.totalMatched}/${result.totalSubmitted}`,
-            '',
-            '| Key | PMID | Status |',
-            '|:---|:---|:---|',
         ];
         for (const r of result.results) {
-            const pmid = r.pmid ?? '-';
-            const status = r.matched ? 'Matched' : 'No match';
-            lines.push(`| ${r.key} | ${pmid} | ${status} |`);
+            lines.push(`\n### ${r.key}`);
+            if (r.pmid)
+                lines.push(`**PMID:** ${r.pmid}`);
+            if (r.status === 'matched') {
+                lines.push(`**Status:** Matched`);
+                lines.push(`**Next Step:** PMID is ready for downstream PubMed fetch or citation tools.`);
+                continue;
+            }
+            if (r.status === 'ambiguous') {
+                lines.push(`**Status:** Ambiguous`);
+                if (r.detail)
+                    lines.push(`**Detail:** ${r.detail}`);
+                lines.push(`**Next Step:** Add more citation fields such as journal, year, volume, firstPage, or authorName, then retry.`);
+                continue;
+            }
+            lines.push(`**Status:** No match`);
+            if (r.detail)
+                lines.push(`**Detail:** ${r.detail}`);
+            lines.push(`**Next Step:** Verify the citation details or try pubmed_search_articles.`);
         }
         return [{ type: 'text', text: lines.join('\n') }];
     },

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

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

@@ -37,6 +37,29 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
     summaryCount: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     query: z.ZodString;
+    effectiveQuery: z.ZodString;
+    appliedFilters: z.ZodObject<{
+        dateRange: z.ZodOptional<z.ZodObject<{
+            minDate: z.ZodString;
+            maxDate: z.ZodString;
+            dateType: z.ZodEnum<{
+                pdat: "pdat";
+                mdat: "mdat";
+                edat: "edat";
+            }>;
+        }, z.core.$strip>>;
+        publicationTypes: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        author: z.ZodOptional<z.ZodString>;
+        journal: z.ZodOptional<z.ZodString>;
+        meshTerms: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        language: z.ZodOptional<z.ZodString>;
+        hasAbstract: z.ZodOptional<z.ZodBoolean>;
+        freeFullText: z.ZodOptional<z.ZodBoolean>;
+        species: z.ZodOptional<z.ZodEnum<{
+            humans: "humans";
+            animals: "animals";
+        }>>;
+    }, z.core.$strip>;
     totalFound: z.ZodNumber;
     offset: z.ZodNumber;
     pmids: z.ZodArray<z.ZodString>;

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

	@@ -1 +1 @@
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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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA8Q7B,CAAC"}

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

@@ -7,6 +7,38 @@ 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';
+const AppliedFiltersSchema = z.object({
+    dateRange: z
+        .object({
+        minDate: z.string().describe('Applied minimum date'),
+        maxDate: z.string().describe('Applied maximum date'),
+        dateType: z
+            .enum(['pdat', 'mdat', 'edat'])
+            .describe('Applied date field used for the range filter'),
+    })
+        .optional()
+        .describe('Date range filter applied to the search'),
+    publicationTypes: z
+        .array(z.string())
+        .optional()
+        .describe('Publication type filters applied to the search'),
+    author: z.string().optional().describe('Author filter applied to the search'),
+    journal: z.string().optional().describe('Journal filter applied to the search'),
+    meshTerms: z.array(z.string()).optional().describe('MeSH term filters applied to the search'),
+    language: z.string().optional().describe('Language filter applied to the search'),
+    hasAbstract: z
+        .boolean()
+        .optional()
+        .describe('Whether results were restricted to articles with abstracts'),
+    freeFullText: z
+        .boolean()
+        .optional()
+        .describe('Whether results were restricted to free full-text articles'),
+    species: z
+        .enum(['humans', 'animals'])
+        .optional()
+        .describe('Species filter applied to the search'),
+});
 export const searchArticlesTool = tool('pubmed_search_articles', {
     description: 'Search PubMed with full query syntax, filters, and date ranges. Returns PMIDs and optional brief summaries. ' +
         'Supports field-specific filters (author, journal, MeSH terms), common filters (language, species, free full text), ' +
@@ -52,6 +84,10 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
     }),
     output: z.object({
         query: z.string().describe('Original query'),
+        effectiveQuery: z
+            .string()
+            .describe('Sanitized query sent to PubMed after applying all active filters'),
+        appliedFilters: AppliedFiltersSchema.describe('Normalized filter values that were applied to the PubMed query'),
         totalFound: z.number().describe('Total matching articles'),
         offset: z.number().describe('Result offset used'),
         pmids: z.array(z.string()).describe('PubMed IDs'),
@@ -74,27 +110,41 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         ctx.log.info('Executing pubmed_search', { query: input.query });
         const ncbi = getNcbiService();
         let effectiveQuery = await sanitization.sanitizeString(input.query, { context: 'text' });
+        // Build filters — capture normalized values for both query construction and appliedFilters
+        let normalizedDateRange;
         if (input.dateRange?.minDate && input.dateRange?.maxDate) {
-            const minDate = input.dateRange.minDate.replace(/-/g, '/');
-            const maxDate = input.dateRange.maxDate.replace(/-/g, '/');
-            effectiveQuery += ` AND (${minDate}[${input.dateRange.dateType}] : ${maxDate}[${input.dateRange.dateType}])`;
+            normalizedDateRange = {
+                minDate: input.dateRange.minDate.trim().replace(/[-.]/g, '/'),
+                maxDate: input.dateRange.maxDate.trim().replace(/[-.]/g, '/'),
+                dateType: input.dateRange.dateType,
+            };
+            effectiveQuery += ` AND (${normalizedDateRange.minDate}[${normalizedDateRange.dateType}] : ${normalizedDateRange.maxDate}[${normalizedDateRange.dateType}])`;
         }
+        let sanitizedPubTypes;
         if (input.publicationTypes?.length) {
-            const sanitizedPts = await Promise.all(input.publicationTypes.map((pt) => sanitization.sanitizeString(pt, { context: 'text' })));
-            const ptQuery = sanitizedPts.map((pt) => `"${pt}"[Publication Type]`).join(' OR ');
-            effectiveQuery += ` AND (${ptQuery})`;
+            sanitizedPubTypes = await Promise.all(input.publicationTypes.map((pt) => sanitization.sanitizeString(pt, { context: 'text' })));
+            effectiveQuery += ` AND (${sanitizedPubTypes.map((pt) => `"${pt}"[Publication Type]`).join(' OR ')})`;
+        }
+        let sanitizedAuthor;
+        if (input.author) {
+            sanitizedAuthor = await sanitization.sanitizeString(input.author, { context: 'text' });
+            effectiveQuery += ` AND ${sanitizedAuthor}[Author]`;
+        }
+        let sanitizedJournal;
+        if (input.journal) {
+            sanitizedJournal = await sanitization.sanitizeString(input.journal, { context: 'text' });
+            effectiveQuery += ` AND "${sanitizedJournal}"[Journal]`;
         }
-        if (input.author)
-            effectiveQuery += ` AND ${await sanitization.sanitizeString(input.author, { context: 'text' })}[Author]`;
-        if (input.journal)
-            effectiveQuery += ` AND "${await sanitization.sanitizeString(input.journal, { context: 'text' })}"[Journal]`;
+        let sanitizedMeshTerms;
         if (input.meshTerms?.length) {
-            const sanitizedTerms = await Promise.all(input.meshTerms.map((term) => sanitization.sanitizeString(term, { context: 'text' })));
-            const meshQuery = sanitizedTerms.map((term) => `"${term}"[MeSH Terms]`).join(' AND ');
-            effectiveQuery += ` AND (${meshQuery})`;
+            sanitizedMeshTerms = await Promise.all(input.meshTerms.map((term) => sanitization.sanitizeString(term, { context: 'text' })));
+            effectiveQuery += ` AND (${sanitizedMeshTerms.map((term) => `"${term}"[MeSH Terms]`).join(' AND ')})`;
+        }
+        let sanitizedLanguage;
+        if (input.language) {
+            sanitizedLanguage = await sanitization.sanitizeString(input.language, { context: 'text' });
+            effectiveQuery += ` AND ${sanitizedLanguage}[Language]`;
         }
-        if (input.language)
-            effectiveQuery += ` AND ${await sanitization.sanitizeString(input.language, { context: 'text' })}[Language]`;
         if (input.hasAbstract)
             effectiveQuery += ' AND hasabstract[text word]';
         if (input.freeFullText)
@@ -120,7 +170,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             if (esResult.webEnv && esResult.queryKey) {
                 eSummaryParams.WebEnv = esResult.webEnv;
                 eSummaryParams.query_key = esResult.queryKey;
-                eSummaryParams.retmax = input.summaryCount;
+                eSummaryParams.retmax = Math.min(input.summaryCount, pmids.length);
                 eSummaryParams.retstart = input.offset;
             }
             else {
@@ -143,12 +193,25 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             }
         }
         const searchUrl = `https://pubmed.ncbi.nlm.nih.gov/?term=${encodeURIComponent(effectiveQuery)}`;
+        const appliedFilters = {
+            ...(normalizedDateRange && { dateRange: normalizedDateRange }),
+            ...(sanitizedPubTypes?.length && { publicationTypes: sanitizedPubTypes }),
+            ...(sanitizedAuthor && { author: sanitizedAuthor }),
+            ...(sanitizedJournal && { journal: sanitizedJournal }),
+            ...(sanitizedMeshTerms?.length && { meshTerms: sanitizedMeshTerms }),
+            ...(sanitizedLanguage && { language: sanitizedLanguage }),
+            ...(input.hasAbstract && { hasAbstract: true }),
+            ...(input.freeFullText && { freeFullText: true }),
+            ...(input.species && { species: input.species }),
+        };
         ctx.log.info('pubmed_search completed', {
             totalFound: esResult.count,
             pmidCount: pmids.length,
         });
         return {
             query: input.query,
+            effectiveQuery,
+            appliedFilters,
             totalFound: esResult.count,
             offset: input.offset,
             pmids,
@@ -160,9 +223,40 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         const lines = [
             `## PubMed Search Results`,
             `**Query:** ${result.query}`,
+            `**Effective Query:** ${result.effectiveQuery}`,
             `**Total Found:** ${result.totalFound} | **Returned:** ${result.pmids.length} | **Offset:** ${result.offset}`,
             `**Search URL:** ${result.searchUrl}`,
         ];
+        if (Object.keys(result.appliedFilters).length > 0) {
+            lines.push('\n### Applied Filters');
+            if (result.appliedFilters.dateRange) {
+                lines.push(`- **Date Range (${result.appliedFilters.dateRange.dateType}):** ${result.appliedFilters.dateRange.minDate} to ${result.appliedFilters.dateRange.maxDate}`);
+            }
+            if (result.appliedFilters.publicationTypes?.length) {
+                lines.push(`- **Publication Types:** ${result.appliedFilters.publicationTypes.join(', ')}`);
+            }
+            if (result.appliedFilters.author) {
+                lines.push(`- **Author:** ${result.appliedFilters.author}`);
+            }
+            if (result.appliedFilters.journal) {
+                lines.push(`- **Journal:** ${result.appliedFilters.journal}`);
+            }
+            if (result.appliedFilters.meshTerms?.length) {
+                lines.push(`- **MeSH Terms:** ${result.appliedFilters.meshTerms.join(', ')}`);
+            }
+            if (result.appliedFilters.language) {
+                lines.push(`- **Language:** ${result.appliedFilters.language}`);
+            }
+            if (result.appliedFilters.hasAbstract) {
+                lines.push(`- **Has Abstract:** Yes`);
+            }
+            if (result.appliedFilters.freeFullText) {
+                lines.push(`- **Free Full Text:** Yes`);
+            }
+            if (result.appliedFilters.species) {
+                lines.push(`- **Species:** ${result.appliedFilters.species}`);
+            }
+        }
         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/api-client.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,mBAAmB;IAElD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC;~~IAqClB~~;;;;;OAKG;IACG,mBAAmB,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,MAAM,CAAC;~~IA0ClF~~,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAOlB,OAAO,CAAC,WAAW;CASpB"}
1	+ {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,mBAAmB;IAElD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC;IAyClB;;;;;OAKG;IACG,mBAAmB,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,MAAM,CAAC;IA8ClF,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAOlB,OAAO,CAAC,WAAW;CASpB"}

package/dist/services/ncbi/api-client.js CHANGED Viewed

@@ -32,9 +32,16 @@ export class NcbiApiClient {
                 ? await this.postRequest(url, finalParams)
                 : await this.getRequest(url, finalParams);
             if (!response.ok) {
-                const code = response.status >= 400 && response.status < 500
-                    ? JsonRpcErrorCode.InvalidRequest
-                    : JsonRpcErrorCode.ServiceUnavailable;
+                let code;
+                if (response.status === 429) {
+                    code = JsonRpcErrorCode.RateLimited;
+                }
+                else if (response.status >= 500) {
+                    code = JsonRpcErrorCode.ServiceUnavailable;
+                }
+                else {
+                    code = JsonRpcErrorCode.InvalidRequest;
+                }
                 throw new McpError(code, `NCBI API returned HTTP ${response.status}.`, {
                     endpoint,
                     status: response.status,
@@ -75,9 +82,16 @@ export class NcbiApiClient {
             });
             const body = await response.text();
             if (!response.ok) {
-                const code = response.status >= 400 && response.status < 500
-                    ? JsonRpcErrorCode.InvalidRequest
-                    : JsonRpcErrorCode.ServiceUnavailable;
+                let code;
+                if (response.status === 429) {
+                    code = JsonRpcErrorCode.RateLimited;
+                }
+                else if (response.status >= 500) {
+                    code = JsonRpcErrorCode.ServiceUnavailable;
+                }
+                else {
+                    code = JsonRpcErrorCode.InvalidRequest;
+                }
                 throw new McpError(code, `NCBI API returned HTTP ${response.status}: ${body.substring(0, 300)}`, { url, status: response.status, body: body.substring(0, 500) });
             }
             return body;

package/dist/services/ncbi/api-client.js.map CHANGED Viewed

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

@@ -36,9 +36,14 @@ export declare class NcbiService {
      * Accepts up to 200 IDs in a single request. Only works for articles in PMC.
      */
     idConvert(ids: string[], idtype?: string): Promise<IdConvertRecord[]>;
+    /** Error codes that are transient and worth retrying with backoff. */
+    private static readonly RETRYABLE_CODES;
+    /** Maximum backoff delay per retry (prevents exponential explosion at high retry counts). */
+    private static readonly MAX_BACKOFF_MS;
     /**
-     * Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout).
+     * Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout, RateLimited).
      * Non-transient errors (validation, serialization) fail immediately.
+     * Uses capped exponential backoff with jitter.
      */
     private withRetry;
     /**

package/dist/services/ncbi/ncbi-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAEpB,KAAK,aAAa,EAElB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAEpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;gBAHV,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM;IAG/B,OAAO,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,aAAa,CAAC;IAmB1D,QAAQ,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,cAAc,CAAC;IAQlE,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC;IAMb,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,CAAC,CAAC;IAInE,MAAM,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,YAAY,CAAC;IAsB9D,KAAK,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,OAAO,CAAC;IAIlD;;;OAGG;IACG,SAAS,CAAC,SAAS,EAAE,iBAAiB,EAAE,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA8C3E;;;OAGG;IACG,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA+B3E,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;OAIG;YACW,SAAS;IAoCvB;;;;;OAKG;IACH,OAAO,CAAC,cAAc;CAevB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CAgBtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}

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

@@ -93,11 +93,26 @@ export class NcbiService {
             .map((line) => {
             const parts = line.split('|');
             const key = parts[5]?.trim() ?? '';
-            const pmidField = parts[6]?.trim() ?? '';
-            const pmid = pmidField && !pmidField.startsWith('NOT_FOUND') && !pmidField.startsWith('AMBIGUOUS')
-                ? pmidField
-                : null;
-            return { key, matched: pmid !== null, pmid };
+            const rawOutcome = parts[6]?.trim() ?? '';
+            if (/^\d+$/.test(rawOutcome)) {
+                return { key, matched: true, pmid: rawOutcome, status: 'matched' };
+            }
+            if (rawOutcome.startsWith('AMBIGUOUS')) {
+                return {
+                    key,
+                    matched: false,
+                    pmid: null,
+                    status: 'ambiguous',
+                    detail: rawOutcome,
+                };
+            }
+            return {
+                key,
+                matched: false,
+                pmid: null,
+                status: 'not_found',
+                ...(rawOutcome && { detail: rawOutcome }),
+            };
         });
     }
     /**
@@ -120,9 +135,18 @@ export class NcbiService {
         }
         return parsed.records ?? [];
     }
+    /** Error codes that are transient and worth retrying with backoff. */
+    static RETRYABLE_CODES = new Set([
+        JsonRpcErrorCode.ServiceUnavailable,
+        JsonRpcErrorCode.Timeout,
+        JsonRpcErrorCode.RateLimited,
+    ]);
+    /** Maximum backoff delay per retry (prevents exponential explosion at high retry counts). */
+    static MAX_BACKOFF_MS = 30_000;
     /**
-     * Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout).
+     * Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout, RateLimited).
      * Non-transient errors (validation, serialization) fail immediately.
+     * Uses capped exponential backoff with jitter.
      */
     async withRetry(execute, label) {
         for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
@@ -130,14 +154,13 @@ export class NcbiService {
                 return await execute();
             }
             catch (error) {
-                if (error instanceof McpError) {
-                    if (error.code !== JsonRpcErrorCode.ServiceUnavailable &&
-                        error.code !== JsonRpcErrorCode.Timeout) {
-                        throw error;
-                    }
+                if (error instanceof McpError && !NcbiService.RETRYABLE_CODES.has(error.code)) {
+                    throw error;
                 }
                 if (attempt < this.maxRetries) {
-                    const retryDelay = 1000 * 2 ** attempt; // 1s, 2s, 4s
+                    const baseDelay = Math.min(1000 * 2 ** attempt, NcbiService.MAX_BACKOFF_MS);
+                    const jitter = baseDelay * (0.75 + 0.5 * Math.random()); // ±25%
+                    const retryDelay = Math.round(jitter);
                     logger.warning(`NCBI request to ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, { endpoint: label, attempt: attempt + 1, retryDelay });
                     await new Promise((r) => setTimeout(r, retryDelay));
                     continue;

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

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

@@ -612,12 +612,16 @@ export interface ECitMatchCitation {
 }
 /** Single result from ECitMatch lookup. */
 export interface ECitMatchResult {
+    /** Raw non-match detail returned by ECitMatch when present */
+    detail?: string;
     /** The tracking key from the input citation */
     key: string;
     /** Whether a PMID was found */
     matched: boolean;
     /** Matched PubMed ID, or null if no match */
     pmid: string | null;
+    /** Lookup outcome classification for recovery guidance */
+    status: 'matched' | 'not_found' | 'ambiguous';
 }
 /** Single record from the PMC ID Converter API response. */
 export interface IdConvertRecord {

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": "2.3.2",
+  "version": "2.3.4",
   "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",
@@ -67,28 +67,31 @@
     "access": "public"
   },
   "overrides": {
+    "@hono/node-server": ">=1.19.13",
     "brace-expansion": ">=2.0.3",
     "express-rate-limit": ">=8.2.2",
-    "hono": ">=4.12.7",
+    "hono": ">=4.12.12",
     "path-to-regexp": ">=8.4.0",
     "picomatch": ">=4.0.4",
+    "vite": ">=8.0.8",
     "yaml": ">=2.8.3",
     "lodash": ">=4.17.24"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.2.12",
-    "fast-xml-parser": "^5.5.10",
+    "@cyanheads/mcp-ts-core": "^0.3.4",
+    "fast-xml-parser": "^5.5.11",
     "pino-pretty": "^13.1.3",
     "sanitize-html": "^2.17.2"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.10",
-    "@types/node": "^25.5.2",
+    "@biomejs/biome": "^2.4.11",
+    "@types/node": "^25.6.0",
     "@types/sanitize-html": "^2.16.1",
+    "@vitest/coverage-istanbul": "^4.1.4",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.16",
     "typescript": "^6.0.2",
-    "vitest": "^4.1.2"
+    "vitest": "^4.1.4"
   }
 }

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.3.2",
+  "version": "2.3.4",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.3.2",
+      "version": "2.3.4",
       "packageArguments": [
         {
           "type": "positional",
@@ -60,7 +60,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.3.2",
+      "version": "2.3.4",
       "packageArguments": [
         {
           "type": "positional",