@cyanheads/pubmed-mcp-server 1.3.5 → 1.4.3

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "1.3.5",
-  "description": "A Model Context Protocol (MCP) server enabling AI agents to intelligently search, retrieve, and analyze biomedical literature from PubMed via NCBI E-utilities. Built on the mcp-ts-template for robust, production-ready performance.",
+  "version": "1.4.3",
+  "description": "Production-ready PubMed Model Context Protocol (MCP) server that empowers AI agents and research tools with comprehensive access to PubMed's article database. Enables advanced, automated LLM workflows for searching, retrieving, analyzing, and visualizing biomedical and scientific literature via NCBI E-utilities.",
   "main": "dist/index.js",
   "files": [
     "dist"
@@ -26,36 +26,52 @@
     "start:http": "MCP_LOG_LEVEL=debug MCP_TRANSPORT_TYPE=http node dist/index.js",
     "rebuild": "ts-node --esm scripts/clean.ts && npm run build",
     "docs:generate": "typedoc --tsconfig ./tsconfig.typedoc.json",
+    "lint": "eslint .",
+    "lint:fix": "eslint . --fix",
     "tree": "ts-node --esm scripts/tree.ts",
     "fetch-spec": "ts-node --esm scripts/fetch-openapi-spec.ts",
     "format": "prettier --write \"**/*.{ts,js,json,md,html,css}\"",
-    "inspector": "mcp-inspector --config mcp.json --server pubmed-mcp-server"
+    "inspector": "mcp-inspector --config mcp.json --server pubmed-mcp-server",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "test:coverage": "vitest run --coverage"
   },
   "dependencies": {
-    "@hono/node-server": "^1.15.0",
-    "@modelcontextprotocol/sdk": "^1.17.0",
-    "@types/jsonwebtoken": "^9.0.10",
-    "@types/node": "^24.1.0",
+    "@hono/node-server": "^1.17.1",
+    "@modelcontextprotocol/sdk": "^1.17.2",
+    "@opentelemetry/api": "^1.9.0",
+    "@opentelemetry/auto-instrumentations-node": "^0.62.0",
+    "@opentelemetry/exporter-metrics-otlp-http": "^0.203.0",
+    "@opentelemetry/exporter-trace-otlp-http": "^0.203.0",
+    "@opentelemetry/instrumentation-winston": "^0.48.0",
+    "@opentelemetry/resources": "^2.0.1",
+    "@opentelemetry/sdk-metrics": "^2.0.1",
+    "@opentelemetry/sdk-node": "^0.203.0",
+    "@opentelemetry/sdk-trace-node": "^2.0.1",
+    "@opentelemetry/semantic-conventions": "^1.36.0",
+    "@types/node": "^24.2.1",
     "@types/sanitize-html": "^2.16.0",
     "@types/validator": "13.15.2",
     "axios": "^1.11.0",
     "chart.js": "^4.5.0",
     "chartjs-node-canvas": "^5.0.0",
+    "typescript-eslint": "^8.39.0",
     "chrono-node": "^2.8.3",
     "citation-js": "^0.7.20",
     "dotenv": "^16.6.1",
     "fast-xml-parser": "^5.2.5",
     "hono": "^4.8.4",
     "jose": "^6.0.12",
-    "jsonwebtoken": "^9.0.2",
+    "js-yaml": "^4.1.0",
+    "patch-package": "^8.0.0",
+    "tmp": "^0.2.4",
     "node-cron": "^4.2.1",
-    "openai": "^5.11.0",
+    "openai": "^5.12.2",
     "partial-json": "^0.1.7",
-    "js-yaml": "^4.1.0",
     "sanitize-html": "^2.17.0",
     "tiktoken": "^1.0.21",
     "ts-node": "^10.9.2",
-    "typescript": "^5.8.3",
+    "typescript": "^5.9.2",
     "validator": "13.15.15",
     "winston": "^3.17.0",
     "winston-transport": "^4.9.0",
@@ -65,22 +81,32 @@
     "mcp",
     "model-context-protocol",
     "ai-agent",
+    "llm",
     "llm-integration",
     "pubmed",
+    "pubmed-api",
     "ncbi",
     "e-utilities",
     "biomedical-research",
     "scientific-literature",
-    "api-server",
+    "computational-biology",
     "typescript",
-    "node",
     "ai-tools",
     "bioinformatics",
     "health-tech",
+    "research-automation",
     "literature-search",
-    "pubmed-api"
+    "citation-analysis",
+    "data-visualization",
+    "api-server",
+    "typescript",
+    "nodejs",
+    "ai-tools",
+    "research-agent",
+    "generative-ai"
   ],
-  "author": "cyanheads <casey@caseyjhand.com> (https://github.com/cyanheads/pubmed-mcp-server#readme)",
+  "author": "Casey Hand @cyanheads",
+  "email": "casey@caseyjhand.com",
   "license": "Apache-2.0",
   "funding": [
     {
@@ -98,9 +124,11 @@
   "devDependencies": {
     "@types/js-yaml": "^4.0.9",
     "@types/node-cron": "^3.0.11",
-    "patch-package": "^8.0.0",
+    "eslint": "^9.32.0",
     "prettier": "^3.6.2",
-    "typedoc": "^0.28.8"
+    "typedoc": "^0.28.9",
+    "vite-tsconfig-paths": "^5.1.4",
+    "vitest": "^3.2.4"
   },
   "publishConfig": {
     "access": "public"

package/dist/mcp-server/tools/fetchPubMedContent/index.d.ts

@@ -1,7 +0,0 @@
-/**
- * @fileoverview Barrel file for the fetch_pubmed_content tool.
- * Exports the tool's registration function.
- * @module src/mcp-server/tools/fetchPubMedContent/index
- */
-export { registerFetchPubMedContentTool } from "./registration.js";
-//# sourceMappingURL=index.d.ts.map

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package/dist/mcp-server/tools/fetchPubMedContent/index.js

@@ -1,7 +0,0 @@
-/**
- * @fileoverview Barrel file for the fetch_pubmed_content tool.
- * Exports the tool's registration function.
- * @module src/mcp-server/tools/fetchPubMedContent/index
- */
-export { registerFetchPubMedContentTool } from "./registration.js";
-//# sourceMappingURL=index.js.map

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package/dist/mcp-server/tools/fetchPubMedContent/registration.d.ts

@@ -1,11 +0,0 @@
-/**
- * @fileoverview Registration for the fetch_pubmed_content MCP tool.
- * @module src/mcp-server/tools/fetchPubMedContent/registration
- */
-import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-/**
- * Registers the fetch_pubmed_content tool with the MCP server.
- * @param server - The McpServer instance.
- */
-export declare function registerFetchPubMedContentTool(server: McpServer): Promise<void>;
-//# sourceMappingURL=registration.d.ts.map

package/dist/mcp-server/tools/fetchPubMedContent/registration.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"registration.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/fetchPubMedContent/registration.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAepE;;;GAGG;AACH,wBAAsB,8BAA8B,CAClD,MAAM,EAAE,SAAS,GAChB,OAAO,CAAC,IAAI,CAAC,CAgFf"}

package/dist/mcp-server/tools/fetchPubMedContent/registration.js.map

@@ -1 +0,0 @@
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package/dist/mcp-server/tools/generatePubMedChart/index.d.ts.map

@@ -1 +0,0 @@
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package/dist/mcp-server/tools/generatePubMedChart/index.js.map

@@ -1 +0,0 @@
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package/dist/mcp-server/tools/generatePubMedChart/logic.js.map

@@ -1 +0,0 @@
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package/dist/mcp-server/tools/generatePubMedChart/registration.d.ts

@@ -1,8 +0,0 @@
-/**
- * @fileoverview Registers the 'generate_pubmed_chart' tool with the MCP server.
- * This tool now accepts parameterized input for generating charts.
- * @module src/mcp-server/tools/generatePubMedChart/registration
- */
-import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-export declare function registerGeneratePubMedChartTool(server: McpServer): Promise<void>;
-//# sourceMappingURL=registration.d.ts.map

package/dist/mcp-server/tools/generatePubMedChart/registration.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"registration.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/generatePubMedChart/registration.ts"],"names":[],"mappings":"AAOA,OAAO,EAAE,aAAa,EAAE,QAAQ,EAAE,MAAM,iCAAiC,CAAC;AAC1E,OAAO,EACL,YAAY,EACZ,MAAM,EAEN,qBAAqB,GACtB,MAAM,yBAAyB,CAAC;AACjC,OAAO,EAEL,8BAA8B,EAC9B,wBAAwB,GACzB,MAAM,YAAY,CAAC;AAEpB,MAAM,CAAC,KAAK,UAAU,+BAA+B,CACnD,MAAiB;IAEjB,MAAM,SAAS,GAAG,iCAAiC,CAAC;IACpD,MAAM,QAAQ,GAAG,uBAAuB,CAAC;IACzC,MAAM,eAAe,GACnB,6DAA6D;QAC7D,kGAAkG;QAClG,oDAAoD;QACpD,uDAAuD;QACvD,yFAAyF,CAAC;IAC5F,MAAM,OAAO,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,CAAC,CAAC;IAE1E,MAAM,YAAY,CAAC,QAAQ,CACzB,KAAK,IAAI,EAAE;QACT,MAAM,CAAC,IAAI,CACT,QAAQ,EACR,eAAe,EACf,8BAA8B,CAAC,KAAK,EACpC,KAAK,EACH,KAA+B,EAC/B,kBAAuB,EACE,EAAE;YAC3B,MAAM,WAAW,GACf,qBAAqB,CAAC,oBAAoB,CAAC;gBACzC,eAAe,EAAE,OAAO,CAAC,SAAS;gBAClC,SAAS,EAAE,gCAAgC;gBAC3C,cAAc,EAAE,kBAAkB;gBAClC,KAAK;aACN,CAAC,CAAC;YAEL,IAAI,CAAC;gBACH,MAAM,MAAM,GAAG,MAAM,wBAAwB,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC;gBAClE,OAAO;oBACL,OAAO,EAAE;wBACP;4BACE,IAAI,EAAE,OAAO;4BACb,IAAI,EAAE,MAAM,CAAC,UAAU;4BACvB,QAAQ,EAAE,WAAW;yBACtB;qBACF;oBACD,OAAO,EAAE,KAAK;iBACf,CAAC;YACJ,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,MAAM,YAAY,GAAG,YAAY,CAAC,WAAW,CAAC,KAAK,EAAE;oBACnD,SAAS,EAAE,gCAAgC;oBAC3C,OAAO,EAAE,WAAW;oBACpB,KAAK;oBACL,OAAO,EAAE,KAAK;iBACf,CAAC,CAAC;gBAEH,MAAM,QAAQ,GACZ,YAAY,YAAY,QAAQ;oBAC9B,CAAC,CAAC,YAAY;oBACd,CAAC,CAAC,IAAI,QAAQ,CACV,aAAa,CAAC,cAAc,EAC5B,0DAA0D,EAC1D;wBACE,iBAAiB,EAAE,YAAY,CAAC,IAAI;wBACpC,oBAAoB,EAAE,YAAY,CAAC,OAAO;qBAC3C,CACF,CAAC;gBAER,OAAO;oBACL,OAAO,EAAE;wBACP;4BACE,IAAI,EAAE,MAAM;4BACZ,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;gCACnB,KAAK,EAAE;oCACL,IAAI,EAAE,QAAQ,CAAC,IAAI;oCACnB,OAAO,EAAE,QAAQ,CAAC,OAAO;oCACzB,OAAO,EAAE,QAAQ,CAAC,OAAO;iCAC1B;6BACF,CAAC;yBACH;qBACF;oBACD,OAAO,EAAE,IAAI;iBACd,CAAC;YACJ,CAAC;QACH,CAAC,CACF,CAAC;QACF,MAAM,CAAC,MAAM,CAAC,SAAS,QAAQ,eAAe,EAAE,OAAO,CAAC,CAAC;IAC3D,CAAC,EACD;QACE,SAAS;QACT,OAAO;QACP,SAAS,EAAE,aAAa,CAAC,qBAAqB;QAC9C,QAAQ,EAAE,IAAI;KACf,CACF,CAAC;AACJ,CAAC"}

package/dist/mcp-server/tools/getPubMedArticleConnections/index.d.ts

@@ -1,7 +0,0 @@
-/**
- * @fileoverview Barrel file for the getPubMedArticleConnections tool.
- * Exports the registration function for this tool.
- * @module src/mcp-server/tools/getPubMedArticleConnections/index
- */
-export { registerGetPubMedArticleConnectionsTool } from "./registration.js";
-//# sourceMappingURL=index.d.ts.map

package/dist/mcp-server/tools/getPubMedArticleConnections/index.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/getPubMedArticleConnections/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,uCAAuC,EAAE,MAAM,mBAAmB,CAAC"}

package/dist/mcp-server/tools/getPubMedArticleConnections/index.js

@@ -1,7 +0,0 @@
-/**
- * @fileoverview Barrel file for the getPubMedArticleConnections tool.
- * Exports the registration function for this tool.
- * @module src/mcp-server/tools/getPubMedArticleConnections/index
- */
-export { registerGetPubMedArticleConnectionsTool } from "./registration.js";
-//# sourceMappingURL=index.js.map

package/dist/mcp-server/tools/getPubMedArticleConnections/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/getPubMedArticleConnections/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,uCAAuC,EAAE,MAAM,mBAAmB,CAAC"}

package/dist/mcp-server/tools/getPubMedArticleConnections/logic/citationFormatter.d.ts

@@ -1,10 +0,0 @@
-/**
- * @fileoverview Handles citation formatting for the getPubMedArticleConnections tool.
- * Fetches article details using EFetch and formats them into various citation styles.
- * @module src/mcp-server/tools/getPubMedArticleConnections/logic/citationFormatter
- */
-import { RequestContext } from "../../../../utils/index.js";
-import type { GetPubMedArticleConnectionsInput } from "./index.js";
-import type { ToolOutputData } from "./types.js";
-export declare function handleCitationFormats(input: GetPubMedArticleConnectionsInput, outputData: ToolOutputData, context: RequestContext): Promise<void>;
-//# sourceMappingURL=citationFormatter.d.ts.map

package/dist/mcp-server/tools/getPubMedArticleConnections/logic/citationFormatter.d.ts.map

@@ -1 +0,0 @@
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package/dist/mcp-server/tools/getPubMedArticleConnections/logic/citationFormatter.js.map

@@ -1 +0,0 @@
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package/dist/mcp-server/tools/getPubMedArticleConnections/logic/elinkHandler.d.ts

@@ -1,10 +0,0 @@
-/**
- * @fileoverview Handles ELink requests and enriches results with ESummary data
- * for the getPubMedArticleConnections tool.
- * @module src/mcp-server/tools/getPubMedArticleConnections/logic/elinkHandler
- */
-import { RequestContext } from "../../../../utils/index.js";
-import type { GetPubMedArticleConnectionsInput } from "./index.js";
-import type { ToolOutputData } from "./types.js";
-export declare function handleELinkRelationships(input: GetPubMedArticleConnectionsInput, outputData: ToolOutputData, context: RequestContext): Promise<void>;
-//# sourceMappingURL=elinkHandler.d.ts.map

package/dist/mcp-server/tools/getPubMedArticleConnections/logic/elinkHandler.d.ts.map

@@ -1 +0,0 @@
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package/dist/mcp-server/tools/getPubMedArticleConnections/logic/elinkHandler.js.map

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package/dist/mcp-server/tools/getPubMedArticleConnections/logic/types.js

@@ -1,6 +0,0 @@
-/**
- * @fileoverview Shared type definitions for the getPubMedArticleConnections tool logic.
- * @module src/mcp-server/tools/getPubMedArticleConnections/logic/types
- */
-export {};
-//# sourceMappingURL=types.js.map

package/dist/mcp-server/tools/getPubMedArticleConnections/logic/types.js.map

@@ -1 +0,0 @@
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package/dist/mcp-server/tools/getPubMedArticleConnections/registration.d.ts

@@ -1,12 +0,0 @@
-/**
- * @fileoverview Registers the 'get_pubmed_article_connections' tool with the MCP server.
- * This tool finds articles related to a source PMID or retrieves citation formats.
- * @module src/mcp-server/tools/getPubMedArticleConnections/registration
- */
-import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-/**
- * Registers the 'get_pubmed_article_connections' tool with the given MCP server instance.
- * @param {McpServer} server - The MCP server instance.
- */
-export declare function registerGetPubMedArticleConnectionsTool(server: McpServer): Promise<void>;
-//# sourceMappingURL=registration.d.ts.map

package/dist/mcp-server/tools/getPubMedArticleConnections/registration.d.ts.map

@@ -1 +0,0 @@
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package/dist/mcp-server/tools/getPubMedArticleConnections/registration.js.map

@@ -1 +0,0 @@
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package/dist/mcp-server/tools/searchPubMedArticles/index.d.ts

@@ -1,7 +0,0 @@
-/**
- * @fileoverview Barrel file for the searchPubMedArticles tool.
- * Exports the tool's registration function.
- * @module src/mcp-server/tools/searchPubMedArticles/index
- */
-export { registerSearchPubMedArticlesTool } from "./registration.js";
-//# sourceMappingURL=index.d.ts.map

package/dist/mcp-server/tools/searchPubMedArticles/index.js

@@ -1,7 +0,0 @@
-/**
- * @fileoverview Barrel file for the searchPubMedArticles tool.
- * Exports the tool's registration function.
- * @module src/mcp-server/tools/searchPubMedArticles/index
- */
-export { registerSearchPubMedArticlesTool } from "./registration.js";
-//# sourceMappingURL=index.js.map

package/dist/mcp-server/tools/searchPubMedArticles/registration.d.ts

@@ -1,11 +0,0 @@
-/**
- * @fileoverview Registration for the searchPubMedArticles MCP tool.
- * @module src/mcp-server/tools/searchPubMedArticles/registration
- */
-import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-/**
- * Registers the searchPubMedArticles tool with the MCP server.
- * @param server - The McpServer instance.
- */
-export declare function registerSearchPubMedArticlesTool(server: McpServer): Promise<void>;
-//# sourceMappingURL=registration.d.ts.map