@cyanheads/pubmed-mcp-server 2.4.1 → 2.5.1

package/CLAUDE.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.4.1
+**Version:** 2.5.0
 **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.
@@ -221,6 +221,7 @@ Available skills:
 | `setup` | Post-init project orientation |
 | `design-mcp-server` | Design tool surface, resources, and services for a new server |
 | `add-tool` | Scaffold a new tool definition |
+| `add-app-tool` | Scaffold an MCP App tool + paired UI resource |
 | `add-resource` | Scaffold a new resource definition |
 | `add-prompt` | Scaffold a new prompt definition |
 | `add-service` | Scaffold a new service integration |
@@ -228,11 +229,12 @@ Available skills:
 | `field-test` | Exercise tools/resources/prompts with real inputs, verify behavior, report issues |
 | `devcheck` | Lint, format, typecheck, audit |
 | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
-| `maintenance` | Sync skills and dependencies after updates |
+| `maintenance` | Investigate changelogs, adopt upstream changes, sync skills after `bun update --latest` |
 | `api-auth` | Auth modes, scopes, JWT/OAuth |
 | `api-config` | AppConfig, parseConfig, env vars |
 | `api-context` | Context interface, logger, state, progress |
 | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
+| `api-linter` | Definition lint rules reference (`format-parity`, `schema-*`, `server-json-*`, …) |
 | `api-services` | LLM, Speech, Graph services |
 | `api-testing` | createMockContext, test patterns |
 | `api-utils` | Formatting, parsing, security, pagination, scheduling |

package/README.md

@@ -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-2.4.1-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-2.5.1-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/)
 
@@ -285,7 +285,8 @@ All configuration is validated at startup via Zod schemas in `src/config/server-
 | `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 | 6 |
-| `NCBI_TIMEOUT_MS` | NCBI request timeout in ms | `30000` |
+| `NCBI_TIMEOUT_MS` | Per-request HTTP timeout in ms | `30000` |
+| `NCBI_TOTAL_DEADLINE_MS` | Total deadline across all retry attempts for one NCBI call, in ms | `60000` |
 | `OTEL_ENABLED` | Enable OpenTelemetry | `false` |
 
 ## Running the server

package/dist/config/server-config.d.ts

@@ -12,6 +12,7 @@ declare const ServerConfigSchema: z.ZodObject<{
     requestDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     maxRetries: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     timeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    totalDeadlineMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
 }, z.core.$strip>;
 export type ServerConfig = z.infer<typeof ServerConfigSchema>;
 export declare function getServerConfig(): ServerConfig;

package/dist/config/server-config.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAU3C,QAAA,MAAM,kBAAkB;;;;;;;;iBAkBtB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CAsB9C"}

package/dist/config/server-config.js

@@ -23,7 +23,13 @@ const ServerConfigSchema = z.object({
         .min(1000)
         .max(120000)
         .default(30000)
-        .describe('Request timeout in ms'),
+        .describe('Per-request HTTP timeout in ms'),
+    totalDeadlineMs: z.coerce
+        .number()
+        .min(5000)
+        .max(600000)
+        .default(60000)
+        .describe('Total deadline across all retry attempts for one NCBI call, in ms'),
 });
 let _config;
 export function getServerConfig() {
@@ -35,6 +41,7 @@ export function getServerConfig() {
             requestDelayMs: 'NCBI_REQUEST_DELAY_MS',
             maxRetries: 'NCBI_MAX_RETRIES',
             timeoutMs: 'NCBI_TIMEOUT_MS',
+            totalDeadlineMs: 'NCBI_TOTAL_DEADLINE_MS',
         });
         /**
          * An API key raises NCBI's rate ceiling from ~3 req/s to ~10 req/s. If the

package/dist/config/server-config.js.map

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package/dist/index.js

@@ -30,6 +30,28 @@ await createApp({
     ],
     resources: [databaseInfoResource],
     prompts: [researchPlanPrompt],
+    landing: {
+        tagline: 'Search PubMed, fetch articles, generate citations, explore MeSH terms, and discover related research.',
+        repoRoot: 'https://github.com/cyanheads/pubmed-mcp-server',
+        links: [
+            { label: 'PubMed', href: 'https://pubmed.ncbi.nlm.nih.gov/', external: true },
+            {
+                label: 'E-utilities docs',
+                href: 'https://www.ncbi.nlm.nih.gov/books/NBK25501/',
+                external: true,
+            },
+            {
+                label: 'Get an NCBI API key',
+                href: 'https://www.ncbi.nlm.nih.gov/account/settings/',
+                external: true,
+            },
+            { label: 'MeSH Browser', href: 'https://meshb.nlm.nih.gov/', external: true },
+        ],
+        envExample: {
+            NCBI_API_KEY: 'your-ncbi-api-key',
+            NCBI_ADMIN_EMAIL: 'you@example.com',
+        },
+    },
     setup() {
         initNcbiService();
     },

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/mcp-server/resources/definitions/database-info.resource.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"database-info.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/database-info.resource.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkBrD,eAAO,MAAM,oBAAoB;;;;;;;;;;kBA+C/B,CAAC"}

package/dist/mcp-server/resources/definitions/database-info.resource.js

@@ -27,7 +27,7 @@ export const databaseInfoResource = resource('pubmed://database/info', {
     output: OutputSchema,
     async handler(_params, ctx) {
         ctx.log.info('Fetching PubMed database info');
-        const raw = (await getNcbiService().eInfo({ db: 'pubmed' }));
+        const raw = (await getNcbiService().eInfo({ db: 'pubmed' }, { signal: ctx.signal }));
         const eInfoResult = (raw.eInfoResult ?? raw);
         const dbInfo = (eInfoResult.DbInfo ?? eInfoResult);
         const dbName = getText(dbInfo.DbName, 'pubmed');

package/dist/mcp-server/resources/definitions/database-info.resource.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/_concepts.d.ts

@@ -0,0 +1,41 @@
+/**
+ * @fileoverview Ontology-backed semantic concept identifiers attached to each
+ * tool's `_meta['io.mcpmed/concepts']` field. Each constant is a stable URI
+ * from an established vocabulary (Schema.org or EDAM) paired with a human
+ * label — no free-text placeholders.
+ *
+ * This implements the semantic concept mapping proposed in MCPmed
+ * (Flotho et al., Briefings in Bioinformatics, 2026; doi:10.1093/bib/bbag076)
+ * with resolvable URIs rather than the placeholder strings used in that paper's
+ * reference implementations.
+ *
+ * Namespacing: the `io.mcpmed/concepts` key is a proposal for MCPmed-aligned
+ * servers. If MCPmed standardizes a different key, this is a single rename.
+ *
+ * @module src/mcp-server/tools/definitions/_concepts
+ */
+/** A single ontology-backed concept tag. */
+export interface ConceptTag {
+    readonly id: string;
+    readonly label: string;
+}
+export declare const SCHEMA_SEARCH_ACTION: ConceptTag;
+export declare const SCHEMA_SCHOLARLY_ARTICLE: ConceptTag;
+export declare const SCHEMA_CREATIVE_WORK: ConceptTag;
+export declare const SCHEMA_DEFINED_TERM: ConceptTag;
+export declare const SCHEMA_DEFINED_TERM_SET: ConceptTag;
+export declare const EDAM_DATABASE_SEARCH: ConceptTag;
+export declare const EDAM_DATA_RETRIEVAL: ConceptTag;
+export declare const EDAM_ID_MAPPING: ConceptTag;
+export declare const EDAM_DATA_FORMATTING: ConceptTag;
+export declare const EDAM_ONTOLOGY_TERMINOLOGY: ConceptTag;
+export declare const EDAM_PUBMED_ID: ConceptTag;
+export declare const EDAM_ACCESSION: ConceptTag;
+/**
+ * Builds the `_meta` payload emitted alongside each tool definition.
+ * Kept as a helper so the key namespace is declared exactly once.
+ */
+export declare function conceptMeta(concepts: readonly ConceptTag[]): {
+    'io.mcpmed/concepts': readonly ConceptTag[];
+};
+//# sourceMappingURL=_concepts.d.ts.map

package/dist/mcp-server/tools/definitions/_concepts.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/_concepts.js

@@ -0,0 +1,74 @@
+/**
+ * @fileoverview Ontology-backed semantic concept identifiers attached to each
+ * tool's `_meta['io.mcpmed/concepts']` field. Each constant is a stable URI
+ * from an established vocabulary (Schema.org or EDAM) paired with a human
+ * label — no free-text placeholders.
+ *
+ * This implements the semantic concept mapping proposed in MCPmed
+ * (Flotho et al., Briefings in Bioinformatics, 2026; doi:10.1093/bib/bbag076)
+ * with resolvable URIs rather than the placeholder strings used in that paper's
+ * reference implementations.
+ *
+ * Namespacing: the `io.mcpmed/concepts` key is a proposal for MCPmed-aligned
+ * servers. If MCPmed standardizes a different key, this is a single rename.
+ *
+ * @module src/mcp-server/tools/definitions/_concepts
+ */
+// Schema.org — generic web entities and actions.
+export const SCHEMA_SEARCH_ACTION = {
+    id: 'https://schema.org/SearchAction',
+    label: 'Search action',
+};
+export const SCHEMA_SCHOLARLY_ARTICLE = {
+    id: 'https://schema.org/ScholarlyArticle',
+    label: 'Scholarly article',
+};
+export const SCHEMA_CREATIVE_WORK = {
+    id: 'https://schema.org/CreativeWork',
+    label: 'Creative work',
+};
+export const SCHEMA_DEFINED_TERM = {
+    id: 'https://schema.org/DefinedTerm',
+    label: 'Defined term',
+};
+export const SCHEMA_DEFINED_TERM_SET = {
+    id: 'https://schema.org/DefinedTermSet',
+    label: 'Defined term set',
+};
+// EDAM ontology — bioinformatics operations, data, and topics.
+export const EDAM_DATABASE_SEARCH = {
+    id: 'https://edamontology.org/operation_2421',
+    label: 'Database search',
+};
+export const EDAM_DATA_RETRIEVAL = {
+    id: 'https://edamontology.org/operation_2422',
+    label: 'Data retrieval',
+};
+export const EDAM_ID_MAPPING = {
+    id: 'https://edamontology.org/operation_3282',
+    label: 'ID mapping',
+};
+export const EDAM_DATA_FORMATTING = {
+    id: 'https://edamontology.org/operation_0335',
+    label: 'Data formatting',
+};
+export const EDAM_ONTOLOGY_TERMINOLOGY = {
+    id: 'https://edamontology.org/topic_0089',
+    label: 'Ontology and terminology',
+};
+export const EDAM_PUBMED_ID = {
+    id: 'https://edamontology.org/data_1187',
+    label: 'PubMed ID',
+};
+export const EDAM_ACCESSION = {
+    id: 'https://edamontology.org/data_2091',
+    label: 'Accession',
+};
+/**
+ * Builds the `_meta` payload emitted alongside each tool definition.
+ * Kept as a helper so the key namespace is declared exactly once.
+ */
+export function conceptMeta(concepts) {
+    return { 'io.mcpmed/concepts': concepts };
+}
+//# sourceMappingURL=_concepts.js.map

package/dist/mcp-server/tools/definitions/_concepts.js.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map

@@ -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;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;kBA4EzB,CAAC"}
+{"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;AAIjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;kBA+EzB,CAAC"}

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

@@ -5,9 +5,12 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
+import { conceptMeta, EDAM_ACCESSION, EDAM_ID_MAPPING } from './_concepts.js';
 export const convertIdsTool = tool('pubmed_convert_ids', {
     description: `Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Uses the NCBI PMC ID Converter API — only resolves articles indexed in PubMed Central. For articles not in PMC, use pubmed_search_articles instead.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
+    _meta: conceptMeta([EDAM_ID_MAPPING, EDAM_ACCESSION]),
+    sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/convert-ids.tool.ts',
     input: z.object({
         ids: z
             .array(z.string().min(1))
@@ -36,7 +39,7 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
             count: input.ids.length,
             idtype: input.idtype,
         });
-        const raw = await getNcbiService().idConvert(input.ids, input.idtype);
+        const raw = await getNcbiService().idConvert(input.ids, input.idtype, { signal: ctx.signal });
         // NCBI returns pmid as a number in JSON — coerce all ID fields to strings
         const records = raw.map((r) => ({
             requestedId: String(r['requested-id']),

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

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

@@ -1 +1 @@
-{"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAOjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAyP5B,CAAC"}
+{"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAajD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA4P5B,CAAC"}

package/dist/mcp-server/tools/definitions/fetch-articles.tool.js

@@ -7,10 +7,13 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.js';
 import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
+import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
 export const fetchArticlesTool = tool('pubmed_fetch_articles', {
     description: 'Fetch full article metadata by PubMed IDs. Returns detailed article information including abstract, authors, journal, MeSH terms.',
     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/fetch-articles.tool.ts',
     input: z.object({
         pmids: z.array(pmidStringSchema).min(1).max(200).describe('PubMed IDs to fetch'),
         includeMesh: z.boolean().default(true).describe('Include MeSH terms'),
@@ -111,7 +114,7 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
     }),
     async handler(input, ctx) {
         ctx.log.info('Executing pubmed_fetch', { pmidCount: input.pmids.length });
-        const xmlData = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 100 });
+        const xmlData = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 100, signal: ctx.signal });
         if (!xmlData || !('PubmedArticleSet' in xmlData)) {
             throw new Error('Invalid EFetch response from NCBI: missing PubmedArticleSet');
         }

package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map

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

@@ -1 +1 @@
-{"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAiDjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAmO5B,CAAC"}
+{"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmDjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA2O5B,CAAC"}

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

@@ -7,12 +7,13 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { parsePmcArticle } from '../../../services/ncbi/parsing/pmc-article-parser.js';
 import { findAll, findOne } from '../../../services/ncbi/parsing/pmc-xml-helpers.js';
+import { conceptMeta, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
 function normalizePmcId(id) {
     return id.replace(/^PMC/i, '');
 }
-async function resolvePmidsToPmcIds(pmids) {
-    const records = await getNcbiService().idConvert(pmids, 'pmid');
+async function resolvePmidsToPmcIds(pmids, signal) {
+    const records = await getNcbiService().idConvert(pmids, 'pmid', signal ? { signal } : undefined);
     const resolved = new Map();
     for (const record of records) {
         if (record.pmid !== undefined && record.pmcid) {
@@ -40,6 +41,8 @@ const SectionSchema = z.object({
 export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
     description: 'Fetch full-text articles from PubMed Central (PMC). Returns complete article body text, sections, and references for open-access articles. Accepts PMC IDs directly or PubMed IDs (auto-resolved via the PMC ID Converter).',
     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({
         pmcids: z
             .array(z.string())
@@ -133,7 +136,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
         let pmcIds;
         let unavailablePmids;
         if (input.pmids) {
-            const resolution = await resolvePmidsToPmcIds(input.pmids);
+            const resolution = await resolvePmidsToPmcIds(input.pmids, ctx.signal);
             if (resolution.resolved.size === 0) {
                 return { articles: [], totalReturned: 0, unavailablePmids: input.pmids };
             }
@@ -144,7 +147,12 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
         else {
             pmcIds = (input.pmcids ?? []).map(normalizePmcId);
         }
-        const xmlData = await getNcbiService().eFetch({ db: 'pmc', id: pmcIds.join(','), retmode: 'xml' }, { retmode: 'xml', useOrderedParser: true, usePost: pmcIds.length > 5 });
+        const xmlData = await getNcbiService().eFetch({ db: 'pmc', id: pmcIds.join(','), retmode: 'xml' }, {
+            retmode: 'xml',
+            useOrderedParser: true,
+            usePost: pmcIds.length > 5,
+            signal: ctx.signal,
+        });
         const articleSet = findOne(xmlData, 'pmc-articleset');
         if (!articleSet) {
             throw new Error('Invalid PMC EFetch response: missing pmc-articleset');

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

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;kBA8J1B,CAAC"}
+{"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;kBAoK1B,CAAC"}

package/dist/mcp-server/tools/definitions/find-related.tool.js

@@ -7,6 +7,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
 import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
+import { conceptMeta, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
 function extractValue(field) {
     if (field === undefined || field === null)
@@ -19,6 +20,8 @@ function extractValue(field) {
 export const findRelatedTool = tool('pubmed_find_related', {
     description: 'Find articles related to a source article — similar content, citing articles, or references.',
     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/find-related.tool.ts',
     input: z.object({
         pmid: pmidStringSchema.describe('Source PubMed ID'),
         relationship: z
@@ -70,7 +73,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
                 eLinkParams.linkname = 'pubmed_pubmed_refs';
                 break;
         }
-        const eLinkResult = (await ncbi.eLink(eLinkParams));
+        const eLinkResult = (await ncbi.eLink(eLinkParams, { signal: ctx.signal }));
         const eLinkResultsArray = ensureArray(eLinkResult?.eLinkResult);
         const firstResult = eLinkResultsArray[0];
         if (firstResult?.ERROR) {
@@ -111,7 +114,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
         const summaryResult = await ncbi.eSummary({
             db: 'pubmed',
             id: pmidsToEnrich.map((p) => p.pmid).join(','),
-        });
+        }, { signal: ctx.signal });
         const briefSummaries = await extractBriefSummaries(summaryResult);
         const summaryMap = new Map(briefSummaries.map((bs) => [bs.pmid, bs]));
         const articles = pmidsToEnrich.map((p) => {