clinicaltrialsgov-mcp-server 2.9.9 → 2.9.11
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.
- package/AGENTS.md +25 -18
- package/CLAUDE.md +25 -18
- package/Dockerfile +84 -34
- package/README.md +17 -26
- package/changelog/2.9.x/2.9.10.md +16 -0
- package/changelog/2.9.x/2.9.11.md +34 -0
- package/dist/mcp-server/prompts/definitions/analyze-trial-landscape.prompt.d.ts.map +1 -1
- package/dist/mcp-server/prompts/definitions/analyze-trial-landscape.prompt.js +4 -3
- package/dist/mcp-server/prompts/definitions/analyze-trial-landscape.prompt.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-eligible.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-eligible.tool.js +83 -30
- package/dist/mcp-server/tools/definitions/find-eligible.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-field-definitions.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-field-definitions.tool.js +4 -7
- package/dist/mcp-server/tools/definitions/get-field-definitions.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-field-values.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-field-values.tool.js +1 -4
- package/dist/mcp-server/tools/definitions/get-field-values.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-study-count.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-study-count.tool.js +1 -4
- package/dist/mcp-server/tools/definitions/get-study-count.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-study-results.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-study-results.tool.js +66 -38
- package/dist/mcp-server/tools/definitions/get-study-results.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-studies.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-studies.tool.js +2 -5
- package/dist/mcp-server/tools/definitions/search-studies.tool.js.map +1 -1
- package/dist/mcp-server/tools/utils/recovery-hints.d.ts +2 -2
- package/dist/mcp-server/tools/utils/recovery-hints.js +2 -2
- package/dist/services/clinical-trials/clinical-trials-service.d.ts.map +1 -1
- package/dist/services/clinical-trials/clinical-trials-service.js +10 -23
- package/dist/services/clinical-trials/clinical-trials-service.js.map +1 -1
- package/package.json +14 -15
- package/server.json +10 -24
package/AGENTS.md
CHANGED
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# Agent Protocol
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**Server:** clinicaltrialsgov-mcp-server
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**Version:** 2.9.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.
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**Version:** 2.9.11
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.12`
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**Engines:** Bun ≥1.4.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/server` ^2.
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**MCP SDK:** `@modelcontextprotocol/server` ^2.2.0
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**Zod:** ^4.6.5
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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.
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- **Read-only server.** No `ctx.state` needed — the ClinicalTrials.gov API is stateless and public.
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- **Secrets in env vars only** — never hardcoded. (This server has no secrets — public API, no auth.)
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- **Rate limit awareness.** The API allows ~1 req/sec. Service layer handles retry/backoff.
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- **Cut noise.** Add only what earns its place: no speculative generality, no guards for states the framework already prevents (Zod-validated params, classified errors), no abstraction until a third caller proves it, no option nothing sets.
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- **Close the loop on issues.** When implementing work tracked by a GitHub issue, comment on the issue with what landed and close it. Do both — a comment without a close leaves stale issues open; a close without a comment leaves no record of what shipped. The comment is for future readers — state the concrete changes, not the conversation that produced them.
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---
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| :-------------- | :---------------------------------------------------------------------------------------------------------------------------------- |
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| `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. |
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| `ctx.signal` | `AbortSignal` for cancellation. |
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| `ctx.requestId` |
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| `ctx.requestId` | Request ID — the one every log record of the call carries and its error envelope returns as `data.requestId`. |
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Note: `ctx.state` is available but unused — this is a stateless read-only server.
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Note: `ctx.state` is available but unused — this is a stateless read-only server. If that changes, it accepts any JSON-serializable value and reads return its JSON form (a `Date` comes back as an ISO string).
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---
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Handlers throw — the framework catches, classifies, and formats.
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**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable?, severity?, thrownBy? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body.
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**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable?, severity?, thrownBy? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. `recovery` is required (≥ 5 words, lint-validated) — the single source of truth for the agent's next move. The framework puts it on the wire whenever a failure carrying that `reason` arrives without a hint — a bare `ctx.fail('reason')` or a service throw with `data: { reason }` — as `data.recovery.hint`, mirrored into `content[]` text unless the message already contains it verbatim; override with an explicit `{ recovery: { hint: '...' } }` when dynamic runtime context matters. Every error envelope also carries `data.requestId`, the id the server's log records for that call carry, and `content[]` closes with `(reason … · request <id>)`. Most reasons here are raised in `ClinicalTrialsService` (a factory error carrying `data.reason` only — the hint comes from whichever tool or resource contract declares the reason), not by the handler — mark those entries `thrownBy: 'service'` so `error-contract-unthrown`, which reads only the handler body, skips them; it is lint-only metadata. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely and don't need declaring.
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```ts
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import { JsonRpcErrorCode } from "@cyanheads/mcp-ts-core/errors";
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errors: [
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{ reason: "path_not_found", code: JsonRpcErrorCode.NotFound,
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when: "Field path doesn't match the data model tree",
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recovery:
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recovery: 'Call clinicaltrials_get_field_definitions with mode="overview" to see the top-level sections.' },
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],
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async handler(input, ctx) {
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const node = navigateToPath(tree, input.path);
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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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| `tool-defs-analysis` |
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| `tool-defs-analysis` | Read-only audit of MCP definition language across the surface — voice, leaks, defaults, recovery hints, output descriptions |
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| `code-simplifier` | Post-session cleanup against `git diff` — modernize syntax, consolidate duplication, align with the codebase |
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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 to agent dirs |
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| `git-wrapup` | Land working-tree changes as a commit stack — version bump, changelog, verify, commit by concern, release commit on top. No tag, no push to `main`; halts at the open release PR |
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| `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
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| `api-auth` | Auth modes, scopes, JWT/OAuth |
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| `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
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| `api-mirror` | MirrorService: persistent
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| `api-mirror` | MirrorService: persistent self-refreshing local mirror (embedded SQLite + FTS5) of a bulk upstream dataset — Tier 3 opt-in |
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| `api-config` | AppConfig, parseConfig, env vars |
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| `api-context` | Context interface, RequestContext, logger, state, multi-round-trip input |
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| `api-errors` | McpError, JsonRpcErrorCode, error patterns, typed contracts |
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| `api-linter` | Definition
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| `api-linter` | Definition linter rule catalog — invoked by `bun run lint:mcp` and `devcheck` |
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| `api-services` | LLM, Speech, Graph services |
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| `api-telemetry` | OTel catalog: spans, metrics, completion logs, env config, cardinality rules |
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| `api-testing` | createMockContext, test patterns |
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| `api-utils` | Formatting, parsing, security, pagination, scheduling, telemetry helpers |
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| `api-workers` | Cloudflare Workers runtime |
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| `techniques` | Catalog of
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| `techniques` | Catalog of response/data-shaping techniques — overflow handling, payload shaping, retrieval patterns |
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| `orchestrations` | Chain task skills into a gated multi-phase pipeline — build-out, QA-fix, update-ship — when you can spawn sub-agents |
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When you complete a skill's checklist, check the boxes and add a completion timestamp at the end (e.g., `Completed: 2026-03-11`).
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## Commands
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**Runtime:** Scripts use Bun's native TypeScript execution — `bun run <cmd>` is the standard invocation. `npm run <cmd>` also works (npm delegates to bun).
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| Command | Purpose |
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| :------------------------ | :------------------------------------------------------------ |
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| `bun run build` | Compile TypeScript |
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| `bun run rebuild` | Clean + build |
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| `bun run clean` | Remove build artifacts |
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| `bun run devcheck` | Lint + format + typecheck + security + changelog sync |
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| `bun run
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| `bun run typecheck` | Typecheck only (`tsc --noEmit`) |
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| `bun run lint:mcp` | Run the MCP definition linter standalone (rule catalog: `api-linter` skill) |
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| `bun run lint:packaging` | Packaging surface checks — `server.json`/`manifest.json` env-var parity (run by devcheck) |
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| `bun run list-skills` | Print the skill registry |
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| `bun run tree` | Generate directory structure doc |
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| `bun run format` | Auto-fix formatting
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| `bun run
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| `bun run format` | Auto-fix formatting (safe fixes only) |
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| `bun run format:unsafe` | Also apply Biome's unsafe autofixes — review the diff; they can change behavior |
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| `bun run test` | Run tests (Vitest — use `bun run test`, not `bun test`) |
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| `bun run test:fuzz` | Run only the property-based fuzz suites |
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| `bun run start:stdio` | Production mode (stdio) |
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| `bun run start:http` | Production mode (HTTP) |
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| `bun run inspector` | Launch MCP Inspector |
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| `bun run changelog:build` | Regenerate `CHANGELOG.md` from `changelog/*.md` |
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| `bun run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
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| `bun run bundle` | Build and
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| `bun run bundle` | Build, pack, and clean a `.mcpb` for one-click Claude Desktop install |
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| `bun run audit:fix` | `bun audit fix` — upgrade vulnerable packages to the lowest safe version within existing ranges (`--dry-run` previews, `--latest` rewrites ranges). First response when `devcheck` flags a transitive advisory; then `bun update <name>`, then `bun dedupe` |
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| `bun run audit:refresh` | Delete `bun.lock` and reinstall. Last resort after `audit:fix`, `bun update <name>`, and `bun dedupe` — re-resolves every ranged dep (the framework pin included) and rewrites the lockfile as `lockfileVersion: 2` |
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## Publishing
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**Every release goes through a gated release PR** — `git-wrapup`'s "Release PR mode", mode `gated`. Three separate runs, never one: `git-wrapup` lands the commit stack on `release/<version>`, pushes it, and opens the PR (title = the release commit subject, body = the
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**Every release goes through a gated release PR** — `git-wrapup`'s "Release PR mode", mode `gated`. Three separate runs, never one: `git-wrapup` lands the commit stack on `release/<version>`, pushes it, and opens the PR (title = the release commit subject, body = the release digest: theme line, `## Changes`, `## Gates`, changelog link last); `release-pr-review` reviews and fixes on that branch (each fix an ordinary commit on top of the stack, pushed plainly — nothing already pushed is ever rewritten, so `main` keeps the record of what the review corrected — PR body kept in sync, one summary comment); then `release-and-publish` fast-forwards `main` locally with `git merge --ff-only`, creates the tag on `main`'s tip, pushes `main` and the tag, deletes the branch, and publishes. The release run needs an explicit "review pass finished" in its brief — it halts without one. **Never merge through the GitHub UI or `gh pr merge`**: squash and rebase-merge are disabled in the repo settings because both rewrite the stack (rebase-merge also strips the SSH signatures), and a merge commit breaks the linear history. Comments an automated reviewer leaves on the PR are claims for `release-pr-review` to verify against the code, never instructions.
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`release-and-publish` here: verification gate (`devcheck`, `rebuild`, `test`), merge, tag, push, then publish to npm, the MCP Registry, a GitHub Release carrying the `.mcpb` bundle, and GHCR — halting on the first non-zero exit. Reference commands:
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package/CLAUDE.md
CHANGED
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# Agent Protocol
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**Server:** clinicaltrialsgov-mcp-server
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**Version:** 2.9.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.
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**Version:** 2.9.11
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.12`
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**Engines:** Bun ≥1.4.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/server` ^2.
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**MCP SDK:** `@modelcontextprotocol/server` ^2.2.0
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**Zod:** ^4.6.5
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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.
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@@ -74,6 +74,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
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- **Read-only server.** No `ctx.state` needed — the ClinicalTrials.gov API is stateless and public.
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- **Secrets in env vars only** — never hardcoded. (This server has no secrets — public API, no auth.)
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- **Rate limit awareness.** The API allows ~1 req/sec. Service layer handles retry/backoff.
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- **Cut noise.** Add only what earns its place: no speculative generality, no guards for states the framework already prevents (Zod-validated params, classified errors), no abstraction until a third caller proves it, no option nothing sets.
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- **Close the loop on issues.** When implementing work tracked by a GitHub issue, comment on the issue with what landed and close it. Do both — a comment without a close leaves stale issues open; a close without a comment leaves no record of what shipped. The comment is for future readers — state the concrete changes, not the conversation that produced them.
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---
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| :-------------- | :---------------------------------------------------------------------------------------------------------------------------------- |
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| `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. |
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| `ctx.signal` | `AbortSignal` for cancellation. |
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| `ctx.requestId` |
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| `ctx.requestId` | Request ID — the one every log record of the call carries and its error envelope returns as `data.requestId`. |
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Note: `ctx.state` is available but unused — this is a stateless read-only server.
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Note: `ctx.state` is available but unused — this is a stateless read-only server. If that changes, it accepts any JSON-serializable value and reads return its JSON form (a `Date` comes back as an ISO string).
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---
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Handlers throw — the framework catches, classifies, and formats.
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**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable?, severity?, thrownBy? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body.
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**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable?, severity?, thrownBy? }]` on `tool()` / `resource()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. `recovery` is required (≥ 5 words, lint-validated) — the single source of truth for the agent's next move. The framework puts it on the wire whenever a failure carrying that `reason` arrives without a hint — a bare `ctx.fail('reason')` or a service throw with `data: { reason }` — as `data.recovery.hint`, mirrored into `content[]` text unless the message already contains it verbatim; override with an explicit `{ recovery: { hint: '...' } }` when dynamic runtime context matters. Every error envelope also carries `data.requestId`, the id the server's log records for that call carry, and `content[]` closes with `(reason … · request <id>)`. Most reasons here are raised in `ClinicalTrialsService` (a factory error carrying `data.reason` only — the hint comes from whichever tool or resource contract declares the reason), not by the handler — mark those entries `thrownBy: 'service'` so `error-contract-unthrown`, which reads only the handler body, skips them; it is lint-only metadata. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely and don't need declaring.
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```ts
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errors: [
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{ reason: "path_not_found", code: JsonRpcErrorCode.NotFound,
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when: "Field path doesn't match the data model tree",
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recovery:
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recovery: 'Call clinicaltrials_get_field_definitions with mode="overview" to see the top-level sections.' },
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],
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async handler(input, ctx) {
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const node = navigateToPath(tree, input.path);
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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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| `tool-defs-analysis` |
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| `tool-defs-analysis` | Read-only audit of MCP definition language across the surface — voice, leaks, defaults, recovery hints, output descriptions |
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| `code-simplifier` | Post-session cleanup against `git diff` — modernize syntax, consolidate duplication, align with the codebase |
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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 to agent dirs |
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| `git-wrapup` | Land working-tree changes as a commit stack — version bump, changelog, verify, commit by concern, release commit on top. No tag, no push to `main`; halts at the open release PR |
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| `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
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| `api-auth` | Auth modes, scopes, JWT/OAuth |
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| `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
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| `api-mirror` | MirrorService: persistent
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| `api-mirror` | MirrorService: persistent self-refreshing local mirror (embedded SQLite + FTS5) of a bulk upstream dataset — Tier 3 opt-in |
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| `api-config` | AppConfig, parseConfig, env vars |
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| `api-context` | Context interface, RequestContext, logger, state, multi-round-trip input |
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| `api-errors` | McpError, JsonRpcErrorCode, error patterns, typed contracts |
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| `api-linter` | Definition
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| `api-linter` | Definition linter rule catalog — invoked by `bun run lint:mcp` and `devcheck` |
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| `api-services` | LLM, Speech, Graph services |
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| `api-telemetry` | OTel catalog: spans, metrics, completion logs, env config, cardinality rules |
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| `api-testing` | createMockContext, test patterns |
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| `api-utils` | Formatting, parsing, security, pagination, scheduling, telemetry helpers |
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| `api-workers` | Cloudflare Workers runtime |
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| `techniques` | Catalog of
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| `techniques` | Catalog of response/data-shaping techniques — overflow handling, payload shaping, retrieval patterns |
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| `orchestrations` | Chain task skills into a gated multi-phase pipeline — build-out, QA-fix, update-ship — when you can spawn sub-agents |
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When you complete a skill's checklist, check the boxes and add a completion timestamp at the end (e.g., `Completed: 2026-03-11`).
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## Commands
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**Runtime:** Scripts use Bun's native TypeScript execution — `bun run <cmd>` is the standard invocation. `npm run <cmd>` also works (npm delegates to bun).
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| Command | Purpose |
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| :------------------------ | :------------------------------------------------------------ |
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| `bun run build` | Compile TypeScript |
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| `bun run rebuild` | Clean + build |
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| `bun run clean` | Remove build artifacts |
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| `bun run devcheck` | Lint + format + typecheck + security + changelog sync |
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| `bun run
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| `bun run typecheck` | Typecheck only (`tsc --noEmit`) |
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| `bun run lint:mcp` | Run the MCP definition linter standalone (rule catalog: `api-linter` skill) |
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| `bun run lint:packaging` | Packaging surface checks — `server.json`/`manifest.json` env-var parity (run by devcheck) |
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| `bun run list-skills` | Print the skill registry |
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| `bun run tree` | Generate directory structure doc |
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| `bun run format` | Auto-fix formatting
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| `bun run
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| `bun run format` | Auto-fix formatting (safe fixes only) |
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| `bun run format:unsafe` | Also apply Biome's unsafe autofixes — review the diff; they can change behavior |
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| `bun run test` | Run tests (Vitest — use `bun run test`, not `bun test`) |
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| `bun run test:fuzz` | Run only the property-based fuzz suites |
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| `bun run start:stdio` | Production mode (stdio) |
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| `bun run start:http` | Production mode (HTTP) |
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| `bun run inspector` | Launch MCP Inspector |
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| `bun run changelog:build` | Regenerate `CHANGELOG.md` from `changelog/*.md` |
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| `bun run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
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| `bun run bundle` | Build and
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| `bun run bundle` | Build, pack, and clean a `.mcpb` for one-click Claude Desktop install |
|
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| `bun run audit:fix` | `bun audit fix` — upgrade vulnerable packages to the lowest safe version within existing ranges (`--dry-run` previews, `--latest` rewrites ranges). First response when `devcheck` flags a transitive advisory; then `bun update <name>`, then `bun dedupe` |
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| `bun run audit:refresh` | Delete `bun.lock` and reinstall. Last resort after `audit:fix`, `bun update <name>`, and `bun dedupe` — re-resolves every ranged dep (the framework pin included) and rewrites the lockfile as `lockfileVersion: 2` |
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@@ -425,7 +432,7 @@ security: false # optional — true ONLY for a source
|
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## Publishing
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**Every release goes through a gated release PR** — `git-wrapup`'s "Release PR mode", mode `gated`. Three separate runs, never one: `git-wrapup` lands the commit stack on `release/<version>`, pushes it, and opens the PR (title = the release commit subject, body = the
|
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+
**Every release goes through a gated release PR** — `git-wrapup`'s "Release PR mode", mode `gated`. Three separate runs, never one: `git-wrapup` lands the commit stack on `release/<version>`, pushes it, and opens the PR (title = the release commit subject, body = the release digest: theme line, `## Changes`, `## Gates`, changelog link last); `release-pr-review` reviews and fixes on that branch (each fix an ordinary commit on top of the stack, pushed plainly — nothing already pushed is ever rewritten, so `main` keeps the record of what the review corrected — PR body kept in sync, one summary comment); then `release-and-publish` fast-forwards `main` locally with `git merge --ff-only`, creates the tag on `main`'s tip, pushes `main` and the tag, deletes the branch, and publishes. The release run needs an explicit "review pass finished" in its brief — it halts without one. **Never merge through the GitHub UI or `gh pr merge`**: squash and rebase-merge are disabled in the repo settings because both rewrite the stack (rebase-merge also strips the SSH signatures), and a merge commit breaks the linear history. Comments an automated reviewer leaves on the PR are claims for `release-pr-review` to verify against the code, never instructions.
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`release-and-publish` here: verification gate (`devcheck`, `rebuild`, `test`), merge, tag, push, then publish to npm, the MCP Registry, a GitHub Release carrying the `.mcpb` bundle, and GHCR — halting on the first non-zero exit. Reference commands:
|
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|
package/Dockerfile
CHANGED
|
@@ -12,7 +12,7 @@
|
|
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12
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# on an arm64 host. Building natively also removes emulation from the slowest
|
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13
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# stage of a multi-arch build.
|
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14
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|
# ==============================================================================
|
|
15
|
-
FROM --platform=$BUILDPLATFORM oven/bun:1.4.
|
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+
FROM --platform=$BUILDPLATFORM oven/bun:1.4.2 AS build
|
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16
16
|
|
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17
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|
WORKDIR /usr/src/app
|
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@@ -32,57 +32,105 @@ RUN bun run build
|
|
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32
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# ==============================================================================
|
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|
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# Production Stage
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+
# Production Dependencies Stage
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#
|
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-
#
|
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-
#
|
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-
#
|
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+
# Installs the production dependency tree for the target platform. Every step
|
|
38
|
+
# here can run JavaScript — bunfig.toml's security scanner runs as a Bun
|
|
39
|
+
# program, and so do the OTel and musl-prune scripts — so the stage runs on
|
|
40
|
+
# $BUILDPLATFORM and cross-installs with `--os`/`--cpu`, which pick each
|
|
41
|
+
# platform-specific optional dependency for the target. Only `node_modules`
|
|
42
|
+
# leaves this stage.
|
|
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|
+
#
|
|
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|
+
# A clean image rather than `FROM build`: the build stage's node_modules holds
|
|
45
|
+
# devDependencies.
|
|
40
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|
# ==============================================================================
|
|
41
|
-
FROM oven/bun:1.4.
|
|
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|
+
FROM --platform=$BUILDPLATFORM oven/bun:1.4.2 AS deps
|
|
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48
|
|
|
43
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|
WORKDIR /usr/src/app
|
|
44
50
|
|
|
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|
-
#
|
|
46
|
-
#
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
#
|
|
50
|
-
|
|
51
|
-
|
|
52
|
-
|
|
53
|
-
|
|
54
|
-
|
|
55
|
-
#
|
|
56
|
-
|
|
51
|
+
# Copy dependency manifests. `bunfig.toml` rides along so every install below
|
|
52
|
+
# passes its release-age gate and security scanner, as a local install does.
|
|
53
|
+
COPY package.json bun.lock bunfig.toml ./
|
|
54
|
+
|
|
55
|
+
# The scanner bunfig.toml names is a devDependency, and Bun installs a missing
|
|
56
|
+
# scanner through the same production-filtered install, which omits it and
|
|
57
|
+
# aborts. Seed it from the build stage's full install instead. Remove this line,
|
|
58
|
+
# and the `rm` at the end of this stage, if bunfig.toml stops naming a scanner.
|
|
59
|
+
COPY --from=build /usr/src/app/node_modules/@socketsecurity/bun-security-scanner ./node_modules/@socketsecurity/bun-security-scanner
|
|
60
|
+
|
|
61
|
+
# Docker names the target architecture `amd64`/`arm64`; Bun's `--cpu` takes
|
|
62
|
+
# `x64`/`arm64`. Mapped once here, read by both installs below. `oven/bun`
|
|
63
|
+
# publishes only these two architectures, so any other target fails here.
|
|
64
|
+
ARG TARGETOS
|
|
65
|
+
ARG TARGETARCH
|
|
66
|
+
RUN case "$TARGETARCH" in \
|
|
67
|
+
amd64) echo x64 ;; \
|
|
68
|
+
arm64) echo arm64 ;; \
|
|
69
|
+
*) echo "Unsupported TARGETARCH '$TARGETARCH': expected amd64 or arm64" >&2; exit 1 ;; \
|
|
70
|
+
esac > .bun-cpu
|
|
57
71
|
|
|
58
72
|
# Install only production dependencies, ignoring any lifecycle scripts (like 'prepare')
|
|
59
73
|
# that are not needed in the final production image.
|
|
60
74
|
# `--omit=peer` drops the framework's optional peer tiers (test runner, service
|
|
61
75
|
# SDKs, parsers) that Bun would otherwise auto-install. Anything this server
|
|
62
76
|
# actually imports belongs in its own `dependencies`, so nothing needed at
|
|
63
|
-
# runtime is lost.
|
|
64
|
-
# install re-resolves the graph and pulls every optional peer back in.
|
|
77
|
+
# runtime is lost.
|
|
65
78
|
RUN --mount=type=cache,target=/root/.bun/install/cache \
|
|
66
|
-
bun install --production --omit=peer --frozen-lockfile --ignore-scripts
|
|
79
|
+
bun install --production --omit=peer --frozen-lockfile --ignore-scripts \
|
|
80
|
+
--os="$TARGETOS" --cpu="$(cat .bun-cpu)"
|
|
67
81
|
|
|
68
82
|
# Conditionally install OpenTelemetry optional peer dependencies (Tier 3).
|
|
69
|
-
#
|
|
70
|
-
# with: docker build --build-arg OTEL_ENABLED=
|
|
83
|
+
# Installed by default. Omit them for a leaner image at build time
|
|
84
|
+
# with: docker build --build-arg OTEL_ENABLED=false
|
|
85
|
+
# The script reads the list and each range from the installed framework's
|
|
86
|
+
# `peerDependencies` and passes the target flags on to its `bun install`.
|
|
87
|
+
COPY scripts/install-otel.ts ./scripts/
|
|
71
88
|
ARG OTEL_ENABLED=true
|
|
72
89
|
RUN --mount=type=cache,target=/root/.bun/install/cache \
|
|
73
90
|
if [ "$OTEL_ENABLED" = "true" ]; then \
|
|
74
|
-
bun
|
|
75
|
-
@opentelemetry/instrumentation-http \
|
|
76
|
-
@opentelemetry/exporter-metrics-otlp-http \
|
|
77
|
-
@opentelemetry/exporter-trace-otlp-http \
|
|
78
|
-
@opentelemetry/instrumentation-pino \
|
|
79
|
-
@opentelemetry/resources \
|
|
80
|
-
@opentelemetry/sdk-metrics \
|
|
81
|
-
@opentelemetry/sdk-node \
|
|
82
|
-
@opentelemetry/sdk-trace-node \
|
|
83
|
-
@opentelemetry/semantic-conventions; \
|
|
91
|
+
bun scripts/install-otel.ts --os="$TARGETOS" --cpu="$(cat .bun-cpu)"; \
|
|
84
92
|
fi
|
|
85
93
|
|
|
94
|
+
# `--os`/`--cpu` have no libc counterpart, so a native dependency published in
|
|
95
|
+
# glibc and musl variants installs both. The runtime image is Debian (glibc)
|
|
96
|
+
# and never loads the musl copy; the script deletes every package whose own
|
|
97
|
+
# `libc` admits only musl. It follows every install, since a later
|
|
98
|
+
# `bun install` restores what it removes.
|
|
99
|
+
COPY scripts/prune-musl-packages.ts ./scripts/
|
|
100
|
+
RUN bun scripts/prune-musl-packages.ts
|
|
101
|
+
|
|
102
|
+
# The seeded scanner served only the installs above; keep it out of the image.
|
|
103
|
+
RUN rm -rf node_modules/@socketsecurity/bun-security-scanner
|
|
104
|
+
|
|
105
|
+
|
|
106
|
+
# ==============================================================================
|
|
107
|
+
# Production Stage
|
|
108
|
+
#
|
|
109
|
+
# This stage creates a minimal, optimized, and secure image for running the
|
|
110
|
+
# application. It uses a slim base image and only includes production
|
|
111
|
+
# dependencies and build artifacts. Its only Bun invocations are HEALTHCHECK
|
|
112
|
+
# and CMD, which run on the real target at container start.
|
|
113
|
+
# ==============================================================================
|
|
114
|
+
FROM oven/bun:1.4.2-slim AS production
|
|
115
|
+
|
|
116
|
+
WORKDIR /usr/src/app
|
|
117
|
+
|
|
118
|
+
# Set the environment to production for performance.
|
|
119
|
+
ENV NODE_ENV=production
|
|
120
|
+
|
|
121
|
+
# OCI image metadata (https://github.com/opencontainers/image-spec/blob/main/annotations.md)
|
|
122
|
+
ARG APP_VERSION
|
|
123
|
+
LABEL org.opencontainers.image.title="clinicaltrialsgov-mcp-server"
|
|
124
|
+
LABEL org.opencontainers.image.description="MCP server for the ClinicalTrials.gov v2 API. Search trials, retrieve study details and results, and match patients to eligible trials."
|
|
125
|
+
LABEL org.opencontainers.image.source="https://github.com/cyanheads/clinicaltrialsgov-mcp-server"
|
|
126
|
+
LABEL org.opencontainers.image.licenses="Apache-2.0"
|
|
127
|
+
LABEL org.opencontainers.image.version="${APP_VERSION}"
|
|
128
|
+
|
|
129
|
+
# The manifest comes from the build context: the deps stage's copy was rewritten
|
|
130
|
+
# by the OTel install, and the runtime reads only its name, version, and type.
|
|
131
|
+
COPY package.json ./
|
|
132
|
+
COPY --from=deps /usr/src/app/node_modules ./node_modules
|
|
133
|
+
|
|
86
134
|
# Copy the compiled application code from the build stage
|
|
87
135
|
COPY --from=build /usr/src/app/dist ./dist
|
|
88
136
|
|
|
@@ -107,10 +155,12 @@ ENV MCP_TRANSPORT_TYPE="http"
|
|
|
107
155
|
ENV MCP_SESSION_MODE="stateless"
|
|
108
156
|
ENV MCP_LOG_LEVEL="info"
|
|
109
157
|
ENV LOGS_DIR="/var/log/clinicaltrialsgov-mcp-server"
|
|
110
|
-
ENV MCP_FORCE_CONSOLE_LOGGING="true"
|
|
111
158
|
|
|
112
159
|
# Expose the port the server listens on
|
|
113
160
|
EXPOSE ${MCP_HTTP_PORT}
|
|
114
161
|
|
|
162
|
+
# Health check using a bun-native fetch (slim image ships no curl/wget)
|
|
163
|
+
HEALTHCHECK --interval=30s --timeout=5s --start-period=10s --retries=3 CMD bun -e "fetch('http://localhost:'+(process.env.MCP_HTTP_PORT??'3010')+'/healthz').then((r)=>process.exit(r.ok?0:1)).catch(()=>process.exit(1))"
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# The command to start the server
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CMD ["bun", "run", "dist/index.js"]
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package/README.md
CHANGED
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@@ -7,7 +7,7 @@
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<div align="center">
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-
[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/clinicaltrialsgov-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/clinicaltrialsgov-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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@@ -59,64 +59,51 @@ Clinical trial data from the [ClinicalTrials.gov REST API v2](https://clinicaltr
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### `clinicaltrials_search_studies` <sub>tool</sub>
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-
- Free-text `query` plus field-specific `conditionQuery` / `interventionQuery` / `locationQuery` / `sponsorQuery` / `titleQuery` / `outcomeQuery
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-
- Returns a compact per-study index by default (`nctId`, `briefTitle`, `overallStatus`, `phases`, `enrollmentCount`, `
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- `pageSize` 1–`CT_MAX_PAGE_SIZE` (default 10; the cap is 200 unless overridden), cursor pagination via `pageToken`, `sort` on up to 2 fields
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-
- Excludes the upstream "unknown" enrollment sentinel (`99999999`) by default — `includeUnknownEnrollment` to include it, or automatically lifted when `nctIds` is supplied
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- Free-text `query` plus field-specific `conditionQuery` / `interventionQuery` / `locationQuery` / `sponsorQuery` / `titleQuery` / `outcomeQuery`, `statusFilter` / `phaseFilter` enums, `advancedFilter` (`AREA[FieldName]value` / `RANGE[min, max]`), and `geoFilter` (`distance(lat,lon,radius)` with a `mi`/`km` suffix); `pageSize` 1–200 (default 10), `pageToken` cursor, `sort` on up to 2 fields
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+
- Returns a compact per-study index by default (`nctId`, `briefTitle`, `overallStatus`, `phases`, `enrollmentCount`, `hasResults`, …); `fields` (PascalCase leaves) selects a full-fidelity projection — full records run ~70KB
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- Typed errors: `blank_value`, `ids_not_found`, `field_invalid`, `enum_invalid`, `query_parse_error`, `geo_invalid`, `sort_invalid`, `rate_limited`
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---
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### `clinicaltrials_get_study_record` <sub>tool</sub>
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- Full protocol record by
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-
-
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- `resultsSection` is replaced by compact `resultsSummary` counts — fetch full results via `clinicaltrials_get_study_results`
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-
- Typed errors: `study_not_found`, `rate_limited`
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+
- Full protocol record by `nctId`, with optional `locationLimit` (≤500), `outcomeLimit` / `referenceLimit` (≤100), and `nearLocation` (`lat`, `lon`, `radiusMi`) to bound and sort locations
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- `filtersApplied` reports upstream totals when a cap trims a list; `resultsSection` is replaced by `resultsSummary` counts. Typed errors: `study_not_found`, `rate_limited`
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---
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### `clinicaltrials_get_study_count` <sub>tool</sub>
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- Same query
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- Excludes the unknown-enrollment sentinel by default (`includeUnknownEnrollment` to include it)
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- Same query and filter surface as `clinicaltrials_search_studies`, returning only `totalCount` — no study data fetched
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- Typed errors: `blank_value`, `field_invalid`, `enum_invalid`, `query_parse_error`, `rate_limited`
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---
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### `clinicaltrials_get_field_values` <sub>tool</sub>
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- One or more PascalCase
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-
-
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- `multiValued` flags fields where a study can carry several values, so per-value study counts can sum above the study total
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- Typed errors: `blank_value`, `field_invalid`, `rate_limited`
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- One or more PascalCase `fields` (e.g. `OverallStatus`, `Phase`) — returns each field's type and top values with study counts (capped at 250 by the API), or `min` / `max` / `avg` for numeric and date fields and `trueCount` / `falseCount` for booleans
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+
- `multiValued` flags fields whose per-value counts can sum above the study total. Typed errors: `blank_value`, `field_invalid`, `rate_limited`
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---
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### `clinicaltrials_get_field_definitions` <sub>tool</sub>
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-
-
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- Resolves the canonical PascalCase field names accepted by `fields`, `advancedFilter`, `sort`, and `clinicaltrials_get_field_values`
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- `mode`: `search` (keyword `query`, `limit` ≤100, default 20), `drill` (dot-notation `path`), or `overview` — resolves the PascalCase names accepted by `fields`, `advancedFilter`, `sort`, and `clinicaltrials_get_field_values`
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- Typed errors: `blank_value`, `mode_mismatch`, `mode_requires`, `path_not_found`, `rate_limited`
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---
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### `clinicaltrials_get_study_results` <sub>tool</sub>
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- Up to 20
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- `
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- `sections` filters to `outcomes`, `adverseEvents`, `participantFlow`, `baseline`, `moreInfo`
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- A previous (alias) NCT ID resolves to its canonical study, named in `canonicalNctId`
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- Typed errors: `blank_value`, `offset_not_applicable`, `rate_limited`
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+
- Up to 20 `nctIds` per call; `sections` (`outcomes`, `adverseEvents`, `participantFlow`, `baseline`, `moreInfo`), `summary` to condense a result set that can exceed 500KB per study, and `outcomeLimit` (≤100) / `adverseEventLimit` (≤500) with resumable `outcomeOffset` / `seriousEventOffset` / `otherEventOffset`
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+
- Per-study `fetchErrors` / `studiesWithoutResults` instead of a whole-batch failure, and `canonicalNctId` when an alias ID resolves to another study. Typed errors: `blank_value`, `offset_not_applicable`, `rate_limited`
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---
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### `clinicaltrials_find_eligible` <sub>tool</sub>
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-
-
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-
-
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-
- Bounds each candidate's locations to the sites matching the requested location (capped by `locationLimit`, ≤500) instead of every registered site, adding the nearest recruiting site when none of the matched ones is open
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-
- `funnel` reports match counts at each filter stage (condition → +location → +demographics) to show where the query narrowed to zero
|
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- `age`, `sex` (`FEMALE` / `MALE` / `ALL`), `conditions[]`, `location` (`country` required, `state` / `city` optional), `healthyVolunteer`, `recruitingOnly` (default true), `maxResults` (≤50), `locationLimit` (≤500)
|
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+
- Each candidate's locations are bounded to the sites matching the requested location, plus one recruiting site when none of those is open; `funnel` reports match counts per filter stage (condition → +location → +demographics)
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|
- Typed errors: `blank_value`, `rate_limited`
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---
|
|
@@ -145,6 +132,7 @@ ClinicalTrials.gov-specific:
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- Auto-corrects field names passed to `fields`/`sort` — case/whitespace fixes and known legacy aliases (e.g. `RecruitmentStatus` → `OverallStatus`) — before validating, logging every correction
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- Detects upstream HTML error pages returned with a JSON content-type and retries rather than parsing them as data
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- Geographic proximity search and nearest-site re-ranking, with no geocoding dependency
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+
- Excludes ClinicalTrials.gov's "unknown" enrollment sentinel (`99999999`) from searches and counts by default — `includeUnknownEnrollment` brings it back, and an `nctIds` lookup never filters it
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Agent-friendly output:
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@@ -269,6 +257,9 @@ All configuration is optional — the server works with defaults and no API keys
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| `MCP_LOG_LEVEL` | Log level (RFC 5424). | `info` |
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| `LOGS_DIR` | Directory for log files (Node.js only). | `<project-root>/logs` |
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| `OTEL_ENABLED` | Enable OpenTelemetry tracing. | `false` |
|
|
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|
+
| `OTEL_EXPORTER_OTLP_ENDPOINT` | OTLP base URL; traces export to `/v1/traces`, metrics to `/v1/metrics`. Unset exports nothing. | — |
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+
| `OTEL_EXPORTER_OTLP_LOGS_ENDPOINT` | Opt-in OTLP log export; the base endpoint never enables it. | — |
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+
| `LOG_TOOL_FAILURE_PAYLOADS` | Log each failed tool call's arguments and result, redacted by key name and capped at `LOG_TOOL_FAILURE_PAYLOAD_MAX_BYTES` (default `16384`). A secret inside a free-form value is not redacted. | `false` |
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See [`.env.example`](./.env.example) for the full list of optional overrides.
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|
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|
|
|
@@ -0,0 +1,16 @@
|
|
|
1
|
+
---
|
|
2
|
+
summary: "get_study_results' adverse-event summary reports each event group separately instead of pooling them, and find_eligible admits its fallback recruiting site by distance instead of upstream list order."
|
|
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|
+
breaking: false
|
|
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|
+
security: false
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|
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+
---
|
|
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|
+
|
|
7
|
+
# 2.9.10 — 2026-09-22
|
|
8
|
+
|
|
9
|
+
## Changed
|
|
10
|
+
|
|
11
|
+
- **`get_study_results` summary-mode adverse events report per-group counts, not pooled ones** ([#137](https://github.com/cyanheads/clinicaltrialsgov-mcp-server/issues/137)) — `topEvents` rows now carry `byGroup: [{ groupId, numAffected, numAtRisk }]` in place of the pooled `numAffected`/`numAtRisk` pair, keyed against a new `eventGroups: [{ id, title }]` roster on the summary. `format()` prints the roster once under `Event Groups:` and one `groupId: affected/atRisk` cell per group on each event. Event groups can overlap (crossover and second-course arms re-count participants of their parent arm), so a summed figure was never a real participant count. Ranking uses the largest single group's `numAffected` instead of the cross-group sum.
|
|
12
|
+
- **`find_eligible`'s fallback recruiting site is chosen by distance, not upstream list order** ([#138](https://github.com/cyanheads/clinicaltrialsgov-mcp-server/issues/138)) — the tool now requests `LocationGeoPoint`. When none of a candidate's matched-tier sites is recruiting, the admitted site is the `RECRUITING` site with the smallest haversine distance to the nearest site of the full matched tier (before the `locationLimit` cap), chosen within the requested country whenever a site there recruits; ties keep match order. It carries `distanceMi`, rendered on its `Locations` entry as "N mi from the nearest matched site". When the matched tier or every candidate lacks coordinates, the first candidate in match order is admitted with no `distanceMi`, and the Sites line says it was picked by match order instead of calling it the nearest. Coordinates are dropped from the returned sites. The tool description and the `locationLimit` and `studies` descriptions state the same rule.
|
|
13
|
+
|
|
14
|
+
## Fixed
|
|
15
|
+
|
|
16
|
+
- **`get_study_results` renders a one-group count as "1 group"** — outcome measure lines and the summary-mode adverse-event, participant-flow, and baseline count lines printed "1 groups".
|