NCBI Entrez MCP Server

# Repository Guidelines This guide helps contributors work efficiently on the Entrez MCP Server (Cloudflare Workers + TypeScript). ## Project Structure & Module Organization - `src/`: TypeScript source. - `src/tools/`: MCP tools (Entrez, PubChem, PMC, BYOK, etc.). - `src/lib/`: shared utilities (parsers, formatters, engines, types). - Entry: `src/index.ts`; auth/crypto helpers in `src/accessAuth.ts`, `src/crypto.ts`. - `dist/`: build output (generated by Wrangler). - Tests/scripts at repo root: `test-*.js`, `quick-start.js`, `generate-kms-key.js`. - Config: `wrangler.jsonc`, `tsconfig.json`, `biome.json`. ## Build, Test, and Development Commands - `npm start` / `npm run dev`: run locally via Wrangler at `http://localhost:8787`. - `npm run build`: production build. - `npm run deploy`: deploy to Cloudflare Workers. - `npm test` / `npm run test-api-key`: run API key rate-limit test. - `npm run test-mcp`: test MCP transports. - `npm run test-all`: run both test suites. - `npm run format`: auto-format with Biome. - `npm run lint:fix`: lint and fix with Biome. - `npm run type-check`: TypeScript type checking. - `npm run cf-typegen`: generate Cloudflare Worker types. ## Coding Style & Naming Conventions - Language: TypeScript, 2-space indent, semicolons optional per Biome. - Naming: `PascalCase` for classes/types (e.g., `ChunkingEngine.ts`), `camelCase` for functions/vars, `kebab-case` for tool file names when multiword. - Use Biome for formatting/linting; keep diffs clean: `npm run format && npm run lint:fix`. ## Testing Guidelines - Tests are node scripts in the repo root (no Jest): - `node test-rate-limits.js`, `node test-mcp-transports.js`, `node test-uservault.js`. - Add lightweight script-style tests near related code or root; name `test-<feature>.js`. - Aim for clear console output; prefer deterministic fixtures. ## Commit & Pull Request Guidelines - Commits: imperative present (“Add…, Refactor…, Fix…”); keep subject concise; include scope when helpful. - PRs: include summary, rationale, linked issues, and testing notes; add screenshots/logs for UX/behavior changes; mention rate-limit or DO schema impacts. ## Security & Config Tips - Never commit secrets. Use BYOK tools or env vars: `NCBI_API_KEY`, `KMS_KEY` (see `API_KEY_SETUP.md`). - Validate locally before deploy: `npm run type-check && npm run test-all`. - For Worker bindings/DO changes, update `wrangler.jsonc` and note migrations in the PR.