@cyanheads/pubmed-mcp-server 2.5.4 → 2.5.6

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Files changed (13) hide show
  1. package/CLAUDE.md +6 -4
  2. package/README.md +1 -1
  3. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +13 -1
  4. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
  5. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +142 -12
  6. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
  7. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  8. package/dist/services/ncbi/ncbi-service.js +8 -0
  9. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  10. package/dist/services/ncbi/types.d.ts +5 -0
  11. package/dist/services/ncbi/types.d.ts.map +1 -1
  12. package/package.json +2 -2
  13. package/server.json +3 -3
package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Agent Protocol
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.5.4
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+ **Version:** 2.5.6
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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  > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
@@ -19,8 +19,9 @@ When the user asks what to do next, what's left, or needs direction, suggest rel
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  5. **Add tests** — scaffold tests for existing definitions using the `add-test` skill
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  6. **Field-test definitions** — exercise tools/resources/prompts with real inputs using the `field-test` skill, get a report of issues and pain points
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  7. **Run `devcheck`** — lint, format, typecheck, and security audit
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- 8. **Run the `polish-docs-meta` skill** — finalize README, CHANGELOG, metadata, and agent protocol for shipping
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- 9. **Run the `maintenance` skill** — sync skills and dependencies after framework updates
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+ 8. **Run the `security-pass` skill** — audit handlers for MCP-specific security gaps: output injection, scope blast radius, input sinks, tenant isolation
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+ 9. **Run the `polish-docs-meta` skill** — finalize README, CHANGELOG, metadata, and agent protocol for shipping
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+ 10. **Run the `maintenance` skill** — sync skills and dependencies after framework updates
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  Tailor suggestions to what's actually missing or stale — don't recite the full list every time.
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@@ -212,7 +213,7 @@ src/
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  Skills are modular instructions in `skills/` at the project root. Read them directly when a task matches — e.g., `skills/add-tool/SKILL.md` when adding a tool.
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- **Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). This makes skills available as context without needing to reference `skills/` paths manually. After framework updates, re-copy to pick up changes.
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+ **Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). This makes skills available as context without needing to reference `skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
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  Available skills:
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@@ -227,6 +228,7 @@ Available skills:
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  | `add-service` | Scaffold a new service integration |
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  | `add-test` | Scaffold test file for a tool, resource, or service |
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  | `field-test` | Exercise tools/resources/prompts with real inputs, verify behavior, report issues |
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+ | `security-pass` | Audit server for MCP-flavored security gaps: output injection, scope blast radius, input sinks, tenant isolation |
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  | `devcheck` | Lint, format, typecheck, audit |
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  | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
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  | `maintenance` | Investigate changelogs, adopt upstream changes, sync skills after `bun update --latest` |
package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.5.4-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-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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+ [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.5.6-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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  [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts CHANGED
@@ -1,6 +1,8 @@
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  /**
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  * @fileoverview Citation lookup tool. Resolves partial bibliographic references
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- * to PubMed IDs using NCBI's ECitMatch service.
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+ * to PubMed IDs using NCBI's ECitMatch service, then verifies author agreement
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+ * against ESummary to catch cases where ECitMatch's journal+volume+page weighting
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+ * returns a PMID whose author roster doesn't contain the queried author.
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  * @module src/mcp-server/tools/definitions/lookup-citation.tool
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  */
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  import { z } from '@cyanheads/mcp-ts-core';
@@ -24,8 +26,18 @@ export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDe
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  ambiguous: "ambiguous";
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  }>;
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  detail: z.ZodOptional<z.ZodString>;
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+ candidatePmids: z.ZodOptional<z.ZodArray<z.ZodString>>;
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+ matchedFirstAuthor: z.ZodOptional<z.ZodString>;
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+ warnings: z.ZodOptional<z.ZodArray<z.ZodObject<{
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+ code: z.ZodEnum<{
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+ author_mismatch: "author_mismatch";
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+ year_mismatch: "year_mismatch";
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+ }>;
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+ message: z.ZodString;
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+ }, z.core.$strip>>>;
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  }, z.core.$strip>>;
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  totalMatched: z.ZodNumber;
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  totalSubmitted: z.ZodNumber;
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+ totalWarnings: z.ZodNumber;
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  }, z.core.$strip>>;
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  //# sourceMappingURL=lookup-citation.tool.d.ts.map
package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map CHANGED
@@ -1 +1 @@
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;AAUjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;kBA+H7B,CAAC"}
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+ {"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAwR7B,CAAC"}
package/dist/mcp-server/tools/definitions/lookup-citation.tool.js CHANGED
@@ -1,11 +1,25 @@
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  /**
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  * @fileoverview Citation lookup tool. Resolves partial bibliographic references
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- * to PubMed IDs using NCBI's ECitMatch service.
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+ * to PubMed IDs using NCBI's ECitMatch service, then verifies author agreement
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+ * against ESummary to catch cases where ECitMatch's journal+volume+page weighting
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+ * returns a PMID whose author roster doesn't contain the queried author.
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  * @module src/mcp-server/tools/definitions/lookup-citation.tool
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  */
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  import { tool, z } from '@cyanheads/mcp-ts-core';
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  import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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+ import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
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  import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
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+ /** Extract the surname token (first whitespace-separated part) from an author string. */
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+ function surname(name) {
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+ return name.trim().split(/\s+/)[0]?.toLowerCase() ?? '';
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+ }
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+ /** Split a formatted authors string ("Lastname FI, Lastname FI, et al.") into surnames. */
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+ function authorSurnames(authors) {
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+ return authors
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+ .split(', ')
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+ .map((a) => surname(a))
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+ .filter((s) => s.length > 0 && s !== 'et');
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+ }
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  export const lookupCitationTool = tool('pubmed_lookup_citation', {
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  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.`,
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  annotations: { readOnlyHint: true, openWorldHint: true },
@@ -50,11 +64,33 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
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  .string()
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  .optional()
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  .describe('Additional detail returned by ECitMatch for non-exact matches'),
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+ candidatePmids: z
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+ .array(z.string().describe('PMID'))
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+ .optional()
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+ .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.'),
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+ matchedFirstAuthor: z
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+ .string()
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+ .optional()
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+ .describe('First author of the matched article (e.g., "Husain M"). Useful eyeball signal for verifying a match.'),
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+ warnings: z
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+ .array(z
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+ .object({
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+ code: z
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+ .enum(['author_mismatch', 'year_mismatch'])
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+ .describe('Machine-readable warning classifier for downstream filtering'),
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+ message: z.string().describe('Human-readable description of the warning'),
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+ })
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+ .describe('Non-fatal warning about the match'))
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+ .optional()
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+ .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.'),
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  })
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  .describe('Per-citation match result'))
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  .describe('Match results, one per input citation'),
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  totalMatched: z.number().describe('Number of citations with PMID matches'),
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  totalSubmitted: z.number().describe('Number of citations submitted'),
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+ totalWarnings: z
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+ .number()
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+ .describe('Number of matched citations that carry at least one warning'),
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  }),
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  async handler(input, ctx) {
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  ctx.log.info('Executing pubmed_lookup_citation', { count: input.citations.length });
@@ -71,40 +107,134 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
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  authorName: c.authorName,
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  key: c.key ?? String(i + 1),
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  }));
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- const results = await getNcbiService().eCitMatch(citations, { signal: ctx.signal });
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- const mapped = results.map((r) => ({
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- key: r.key,
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- matched: r.matched,
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- status: r.status,
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- ...(r.pmid && { pmid: r.pmid }),
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- ...(r.detail && { detail: r.detail }),
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- }));
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+ const ncbi = getNcbiService();
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+ const results = await ncbi.eCitMatch(citations, { signal: ctx.signal });
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+ const queriedAuthorByKey = new Map();
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+ const queriedYearByKey = new Map();
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+ for (const c of citations) {
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+ if (c.authorName)
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+ queriedAuthorByKey.set(c.key, c.authorName);
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+ if (c.year)
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+ queriedYearByKey.set(c.key, c.year);
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+ }
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+ const matchedPmids = Array.from(new Set(results.filter((r) => r.matched && r.pmid).map((r) => r.pmid)));
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+ const summaryByPmid = new Map();
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+ if (matchedPmids.length > 0) {
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+ const summaryResult = await ncbi.eSummary({ db: 'pubmed', id: matchedPmids.join(',') }, { signal: ctx.signal });
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+ const summaries = await extractBriefSummaries(summaryResult);
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+ for (const s of summaries) {
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+ summaryByPmid.set(s.pmid, {
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+ ...(s.authors && { authors: s.authors }),
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+ ...(s.pubDate && { pubDate: s.pubDate }),
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+ });
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+ }
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+ }
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+ const mapped = results.map((r) => {
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+ const base = {
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+ key: r.key,
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+ matched: r.matched,
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+ status: r.status,
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+ ...(r.pmid && { pmid: r.pmid }),
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+ ...(r.detail && { detail: r.detail }),
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+ ...(r.candidatePmids?.length && { candidatePmids: r.candidatePmids }),
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+ };
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+ if (!r.matched || !r.pmid)
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+ return base;
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+ const summary = summaryByPmid.get(r.pmid);
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+ if (!summary)
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+ return base;
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+ const warnings = [];
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+ const { authors, pubDate } = summary;
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+ if (authors) {
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+ const firstAuthor = authors.split(', ')[0]?.trim();
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+ if (firstAuthor && firstAuthor !== 'et al.')
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+ base.matchedFirstAuthor = firstAuthor;
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+ const queried = queriedAuthorByKey.get(r.key);
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+ if (queried) {
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+ const querySurname = surname(queried);
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+ const articleSurnames = authorSurnames(authors);
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+ if (querySurname && !articleSurnames.includes(querySurname)) {
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+ warnings.push({
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+ code: 'author_mismatch',
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+ message: `Queried author "${queried}" not found in matched article authors (${authors}). ECitMatch weights journal+volume+page and may return a PMID whose authors disagree with the query — verify before using this PMID.`,
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+ });
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+ ctx.log.warning('Citation match returned PMID with author mismatch', {
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+ key: r.key,
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+ pmid: r.pmid,
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+ queriedAuthor: queried,
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+ matchedAuthors: authors,
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+ });
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+ }
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+ }
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+ }
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+ const queriedYear = queriedYearByKey.get(r.key);
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+ if (queriedYear && pubDate) {
172
+ const matchedYear = pubDate.slice(0, 4);
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+ if (/^\d{4}$/.test(matchedYear) && matchedYear !== queriedYear.trim()) {
174
+ warnings.push({
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+ code: 'year_mismatch',
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+ message: `Queried year "${queriedYear}" does not match matched article year "${matchedYear}" (pubDate ${pubDate}). ECitMatch tolerates year disagreement — verify before using this PMID.`,
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+ });
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+ ctx.log.warning('Citation match returned PMID with year mismatch', {
179
+ key: r.key,
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+ pmid: r.pmid,
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+ queriedYear,
182
+ matchedYear,
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+ });
184
+ }
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+ }
186
+ if (warnings.length > 0)
187
+ base.warnings = warnings;
188
+ return base;
189
+ });
82
190
  const totalMatched = mapped.filter((r) => r.matched).length;
191
+ const totalWarnings = mapped.filter((r) => r.warnings?.length).length;
83
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  ctx.log.info('pubmed_lookup_citation completed', {
84
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  totalMatched,
85
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  totalSubmitted: citations.length,
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+ totalWarnings,
86
196
  });
87
- return { results: mapped, totalMatched, totalSubmitted: citations.length };
197
+ return { results: mapped, totalMatched, totalSubmitted: citations.length, totalWarnings };
88
198
  },
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  format: (result) => {
90
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  const lines = [
91
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  `## Citation Lookup Results`,
92
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  `**Matched:** ${result.totalMatched}/${result.totalSubmitted}`,
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  ];
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+ if (result.totalWarnings > 0) {
205
+ lines.push(`**Warnings:** ${result.totalWarnings}`);
206
+ }
94
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  for (const r of result.results) {
95
208
  lines.push(`\n### ${r.key}`);
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  if (r.pmid)
97
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  lines.push(`**PMID:** ${r.pmid}`);
211
+ if (r.matchedFirstAuthor)
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+ lines.push(`**First Author:** ${r.matchedFirstAuthor}`);
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+ if (r.candidatePmids?.length) {
214
+ lines.push(`**Candidate PMIDs:** ${r.candidatePmids.join(', ')}`);
215
+ }
98
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  if (r.detail)
99
217
  lines.push(`**Detail:** ${r.detail}`);
218
+ if (r.warnings?.length) {
219
+ lines.push(`**Warnings:**`);
220
+ for (const w of r.warnings) {
221
+ lines.push(`- [${w.code}] ${w.message}`);
222
+ }
223
+ }
100
224
  if (r.status === 'matched') {
225
+ const mismatches = r.warnings?.map((w) => w.code) ?? [];
226
+ const hasMismatch = mismatches.length > 0;
101
227
  lines.push(`**Status:** Matched`);
102
- lines.push(`**Next Step:** PMID is ready for downstream PubMed fetch or citation tools.`);
228
+ lines.push(hasMismatch
229
+ ? `**Next Step:** ${mismatches.join(' + ')} detected — confirm this PMID is the intended article before citing. ECitMatch weights journal+volume+page and can resolve despite author/year disagreement.`
230
+ : `**Next Step:** PMID is ready for downstream PubMed fetch or citation tools.`);
103
231
  continue;
104
232
  }
105
233
  if (r.status === 'ambiguous') {
106
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  lines.push(`**Status:** Ambiguous`);
107
- lines.push(`**Next Step:** Add more citation fields such as journal, year, volume, firstPage, or authorName, then retry.`);
235
+ lines.push(r.candidatePmids?.length
236
+ ? `**Next Step:** Add more citation fields to disambiguate, or fetch the candidate PMIDs above via pubmed_fetch_articles to pick the intended one manually.`
237
+ : `**Next Step:** Add more citation fields such as journal, year, volume, firstPage, or authorName, then retry.`);
108
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  continue;
109
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  }
110
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  lines.push(`**Status:** No match`);
package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/services/ncbi/ncbi-service.js CHANGED
@@ -137,12 +137,20 @@ export class NcbiService {
137
137
  return { key, matched: true, pmid: rawOutcome, status: 'matched' };
138
138
  }
139
139
  if (rawOutcome.startsWith('AMBIGUOUS')) {
140
+ const csv = /^AMBIGUOUS\s+([\d,\s]+)/.exec(rawOutcome)?.[1];
141
+ const candidatePmids = csv
142
+ ? csv
143
+ .split(',')
144
+ .map((p) => p.trim())
145
+ .filter((p) => /^\d+$/.test(p))
146
+ : undefined;
140
147
  return {
141
148
  key,
142
149
  matched: false,
143
150
  pmid: null,
144
151
  status: 'ambiguous',
145
152
  detail: rawOutcome,
153
+ ...(candidatePmids?.length && { candidatePmids }),
146
154
  };
147
155
  }
148
156
  return {
package/dist/services/ncbi/ncbi-service.js.map CHANGED
@@ -1 +1 @@
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package/dist/services/ncbi/types.d.ts CHANGED
@@ -520,6 +520,11 @@ export interface ECitMatchCitation {
520
520
  }
521
521
  /** Single result from ECitMatch lookup. */
522
522
  export interface ECitMatchResult {
523
+ /**
524
+ * Candidate PMIDs for AMBIGUOUS results, parsed from the `AMBIGUOUS <csv>`
525
+ * detail string. Only present when status is `ambiguous`.
526
+ */
527
+ candidatePmids?: string[];
523
528
  /** Raw non-match detail returned by ECitMatch when present */
524
529
  detail?: string;
525
530
  /** The tracking key from the input citation */
package/dist/services/ncbi/types.d.ts.map CHANGED
@@ -1 +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": "2.5.4",
3
+ "version": "2.5.6",
4
4
  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
5
5
  "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
6
6
  "type": "module",
@@ -68,7 +68,7 @@
68
68
  "access": "public"
69
69
  },
70
70
  "dependencies": {
71
- "@cyanheads/mcp-ts-core": "^0.6.17",
71
+ "@cyanheads/mcp-ts-core": "^0.7.0",
72
72
  "fast-xml-parser": "^5.7.1",
73
73
  "pino-pretty": "^13.1.3",
74
74
  "sanitize-html": "^2.17.3"
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": "2.5.4",
9
+ "version": "2.5.6",
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": "2.5.4",
22
+ "version": "2.5.6",
23
23
  "packageArguments": [
24
24
  {
25
25
  "type": "positional",
@@ -60,7 +60,7 @@
60
60
  "registryBaseUrl": "https://registry.npmjs.org",
61
61
  "identifier": "@cyanheads/pubmed-mcp-server",
62
62
  "runtimeHint": "bun",
63
- "version": "2.5.4",
63
+ "version": "2.5.6",
64
64
  "packageArguments": [
65
65
  {
66
66
  "type": "positional",