@cyanheads/pubmed-mcp-server 2.7.7 → 2.7.8

package/AGENTS.md

@@ -0,0 +1,365 @@
+# Agent Protocol
+
+**Server:** @cyanheads/pubmed-mcp-server
+**Version:** 2.7.8
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.16`
+**Engines:** Bun ≥1.3.2, Node ≥24.0.0
+
+> **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.
+
+---
+
+## What's Next?
+
+When the user asks what to do next, what's left, or needs direction, suggest relevant options based on the current project state:
+
+1. **Re-run the `setup` skill** — ensures CLAUDE.md, skills, structure, and metadata are populated and up to date with the current codebase
+2. **Run the `design-mcp-server` skill** — if the tool/resource surface hasn't been mapped yet, work through domain design
+3. **Add tools/resources/prompts** — scaffold new definitions using the `add-tool`, `add-app-tool`, `add-resource`, `add-prompt` skills
+4. **Add services** — scaffold domain service integrations using the `add-service` skill
+5. **Add tests** — scaffold tests for existing definitions using the `add-test` skill
+6. **Field-test definitions** — exercise tools/resources/prompts with real inputs using the `field-test` skill, get a report of issues and pain points
+7. **Run `devcheck`** — lint, format, typecheck, and security audit
+8. **Run the `security-pass` skill** — audit handlers for MCP-specific security gaps: output injection, scope blast radius, input sinks, tenant isolation
+9. **Run the `polish-docs-meta` skill** — finalize README, CHANGELOG, metadata, and agent protocol for shipping
+10. **Run the `maintenance` skill** — investigate changelogs, adopt upstream changes, and sync skills after `bun update --latest`
+
+Tailor suggestions to what's actually missing or stale — don't recite the full list every time.
+
+---
+
+## Core Rules
+
+- **Logic throws, framework catches.** Tool/resource handlers are pure — throw on failure, no `try/catch`. Plain `Error` is fine; the framework catches, classifies, and formats. Use error factories (`notFound()`, `validationError()`, etc.) when the error code matters.
+- **Use `ctx.log`** for request-scoped logging. No `console` calls.
+- **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
+- **Check `ctx.elicit` / `ctx.sample`** for presence before calling.
+- **Secrets in env vars only** — never hardcoded.
+- **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.
+
+---
+
+## Patterns
+
+### Tool
+
+```ts
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { getNcbiService } from '@/services/ncbi/ncbi-service.js';
+
+export const spellCheckTool = tool('pubmed_spell_check', {
+  description: "Spell-check a query and get NCBI's suggested correction.",
+  annotations: { readOnlyHint: true, openWorldHint: true },
+
+  input: z.object({
+    query: z.string().min(2).describe('PubMed search query to spell-check'),
+  }),
+
+  output: z.object({
+    original: z.string().describe('Original query'),
+    corrected: z.string().describe('Corrected query (same as original if no suggestion)'),
+    hasSuggestion: z.boolean().describe('Whether NCBI suggested a correction'),
+  }),
+
+  async handler(input, ctx) {
+    ctx.log.info('Executing pubmed_spell_check tool', { query: input.query });
+    const result = await getNcbiService().eSpell({ db: 'pubmed', term: input.query });
+    return { original: result.original, corrected: result.corrected, hasSuggestion: result.hasSuggestion };
+  },
+
+  format: (result) => {
+    if (result.hasSuggestion) {
+      return [{ type: 'text', text: `**Suggested correction:** "${result.corrected}" (original: "${result.original}")` }];
+    }
+    return [{ type: 'text', text: `No spelling corrections suggested for: "${result.original}"` }];
+  },
+});
+```
+
+### Resource
+
+```ts
+import { resource, z } from '@cyanheads/mcp-ts-core';
+import { getNcbiService } from '@/services/ncbi/ncbi-service.js';
+
+export const databaseInfoResource = resource('pubmed://database/info', {
+  name: 'database-info',
+  title: 'PubMed Database Info',
+  description: 'PubMed database metadata including field list, last update date, and record count.',
+  mimeType: 'application/json',
+  params: z.object({}),
+  output: OutputSchema,
+
+  async handler(_params, ctx) {
+    ctx.log.info('Fetching PubMed database info');
+    const raw = await getNcbiService().eInfo({ db: 'pubmed' });
+    // ... parse XML response ...
+    return { dbName, description, count, lastUpdate, fields };
+  },
+
+  list: () => ({
+    resources: [{ uri: 'pubmed://database/info', name: 'PubMed Database Info' }],
+  }),
+});
+```
+
+### Server config
+
+```ts
+// src/config/server-config.ts — lazy-parsed, separate from framework config
+import { z } from '@cyanheads/mcp-ts-core';
+import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
+
+const emptyAsUndefined = (v: unknown) => (v === '' ? undefined : v);
+
+const ServerConfigSchema = z.object({
+  apiKey: z.preprocess(emptyAsUndefined, z.string().optional()).describe('NCBI API key'),
+  toolIdentifier: z.string().default('pubmed-mcp-server').describe('NCBI tool identifier'),
+  adminEmail: z.preprocess(emptyAsUndefined, z.email().optional()).describe('Admin contact email'),
+  requestDelayMs: z.coerce.number().min(50).max(5000).default(334).describe('Request delay in ms'),
+  maxRetries: z.coerce.number().min(0).max(10).default(6).describe('Max retry attempts'),
+  timeoutMs: z.coerce.number().min(1000).max(120000).default(30000).describe('Request timeout in ms'),
+});
+
+let _config: z.infer<typeof ServerConfigSchema> | undefined;
+export function getServerConfig(): z.infer<typeof ServerConfigSchema> {
+  _config ??= parseEnvConfig(ServerConfigSchema, {
+    apiKey: 'NCBI_API_KEY',
+    toolIdentifier: 'NCBI_TOOL_IDENTIFIER',
+    adminEmail: 'NCBI_ADMIN_EMAIL',
+    requestDelayMs: 'NCBI_REQUEST_DELAY_MS',
+    maxRetries: 'NCBI_MAX_RETRIES',
+    timeoutMs: 'NCBI_TIMEOUT_MS',
+  });
+  return _config;
+}
+```
+
+`parseEnvConfig` maps Zod schema paths → env var names so validation errors name the actual variable (`NCBI_REQUEST_DELAY_MS` must be a number) rather than the internal path (`requestDelayMs: expected number`).
+
+---
+
+## Context
+
+Handlers receive a unified `ctx` object. Key properties:
+
+| Property | Description |
+|:---------|:------------|
+| `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. |
+| `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
+| `ctx.elicit` | Ask user for structured input. **Check for presence first:** `if (ctx.elicit) { ... }` |
+| `ctx.sample` | Request LLM completion from the client. **Check for presence first:** `if (ctx.sample) { ... }` |
+| `ctx.progress` | Task progress (present when `task: true`) — `.setTotal(n)`, `.increment()`, `.update(message)`. |
+| `ctx.recoveryFor(reason)` | Typed lookup of the contract `recovery` for a declared reason. Returns `{ recovery: { hint } }` for known reasons, `{}` otherwise. Spread into `ctx.fail` data to mirror the contract hint into `content[]`. |
+| `ctx.signal` | `AbortSignal` for cancellation. |
+| `ctx.requestId` | Unique request ID. |
+| `ctx.tenantId` | Tenant ID from JWT, `'default'` for stdio or HTTP+`MCP_AUTH_MODE=none`. |
+
+---
+
+## Errors
+
+Handlers throw — the framework catches, classifies, and formats.
+
+**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` 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. The `recovery` field is required (≥ 5 words, lint-validated) — it's the single source of truth for the recovery hint. Spread `ctx.recoveryFor('reason')` into `data` to mirror the contract recovery onto the wire (the framework mirrors `data.recovery.hint` into `content[]` text); pass an explicit `recovery: { hint: '...' }` when runtime context matters. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`) bubble freely and don't need declaring.
+
+```ts
+errors: [
+  { reason: 'no_match', code: JsonRpcErrorCode.NotFound,
+    when: 'No requested PMID returned data',
+    recovery: 'Try pubmed_search_articles to discover valid PMIDs first.' },
+],
+async handler(input, ctx) {
+  const articles = await ncbi.fetch(input.pmids);
+  if (articles.length === 0) {
+    // Static contract recovery
+    throw ctx.fail('no_match', `None of ${input.pmids.length} PMIDs returned data`, {
+      ...ctx.recoveryFor('no_match'),
+    });
+  }
+  return { articles };
+}
+```
+
+**Fallback (no contract entry fits):** error factories or plain `Error`.
+
+```ts
+// Error factories — explicit code, concise
+import { notFound, serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
+throw notFound('Item not found', { itemId });
+throw serviceUnavailable('API unavailable', { url }, { cause: err });
+throw serializationError('Invalid XML response', { endpoint });
+
+// Plain Error — framework auto-classifies from message patterns
+throw new Error('Item not found');           // → NotFound
+throw new Error('Invalid query format');     // → ValidationError
+
+// McpError — full control when the code is dynamic
+import { McpError, JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+throw new McpError(JsonRpcErrorCode.DatabaseError, 'Connection failed', { pool: 'primary' });
+```
+
+For HTTP responses, prefer `httpErrorFromResponse(response, { service, data })` from `/utils` over hand-rolled status ladders — covers the full 4xx/5xx → `JsonRpcErrorCode` table and captures body + `Retry-After`.
+
+**Service-layer:** services don't have `ctx.fail`. To carry a contract `reason` from a service throw, pass `data: { reason: 'X' }` to the factory — the auto-classifier preserves `data` on the wire so clients see the same `error.data.reason` they'd see from `ctx.fail`.
+
+See framework CLAUDE.md and the `api-errors` skill for the full auto-classification table, all factories, and the contract reference.
+
+---
+
+## Structure
+
+```text
+src/
+  index.ts                              # createApp() entry point
+  config/
+    server-config.ts                    # NCBI-specific env vars (Zod schema)
+  services/
+    ncbi/
+      ncbi-service.ts                   # NCBI E-utilities service (init/accessor)
+      api-client.ts                     # HTTP client for NCBI API
+      request-queue.ts                  # Rate-limited request queue
+      response-handler.ts              # XML response parsing
+      types.ts                          # NCBI/PubMed domain types
+      parsing/                          # XML parsers (article, esummary, PMC)
+      formatting/                       # Citation formatter (APA, MLA, BibTeX, RIS)
+  mcp-server/
+    tools/definitions/                  # 9 tool definitions (*.tool.ts)
+    resources/definitions/              # database-info.resource.ts
+    prompts/definitions/                # research-plan.prompt.ts
+```
+
+---
+
+## Naming
+
+| What | Convention | Example |
+|:-----|:-----------|:--------|
+| Files | kebab-case with suffix | `search-articles.tool.ts` |
+| Tool/resource/prompt names | snake_case | `pubmed_search_articles` |
+| Directories | kebab-case | `src/services/ncbi/` |
+| Descriptions | Single string or template literal, no `+` concatenation | `'Search PubMed with full query syntax.'` |
+
+---
+
+## Skills
+
+Skills are modular instructions in `skills/` at the project root. Read them directly when a task matches — e.g., `skills/add-tool/SKILL.md` when adding a tool.
+
+**Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). This makes skills available as context without needing to reference `skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
+
+Available skills:
+
+| Skill | Purpose |
+|:------|:--------|
+| `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 |
+| `add-test` | Scaffold test file for a tool, resource, or service |
+| `field-test` | Exercise tools/resources/prompts with real inputs, verify behavior, report issues |
+| `tool-defs-analysis` | Read-only audit of definition language: voice, leaks, defaults, recovery hints, examples |
+| `security-pass` | Audit server for MCP-flavored security gaps: output injection, scope blast radius, input sinks, tenant isolation |
+| `code-simplifier` | Post-session cleanup against `git diff` — modernize syntax, consolidate duplication, align with the codebase |
+| `devcheck` | Lint, format, typecheck, audit |
+| `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
+| `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
+| `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
+| `release-and-publish` | Push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
+| `api-auth` | Auth modes, scopes, JWT/OAuth |
+| `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
+| `api-config` | AppConfig, parseConfig, env vars |
+| `api-context` | Context interface, logger, state, progress |
+| `api-errors` | McpError, JsonRpcErrorCode, error patterns |
+| `api-linter` | Definition linter rule catalog — invoked by `bun run lint:mcp` and `devcheck` |
+| `api-services` | LLM, Speech, Graph services |
+| `api-telemetry` | OTel catalog: spans, metrics, completion logs, env config, cardinality rules |
+| `api-testing` | createMockContext, test patterns |
+| `api-utils` | Formatting, parsing, security, pagination, scheduling, telemetry helpers |
+| `api-workers` | Cloudflare Workers runtime |
+| `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
+| `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
+
+When you complete a skill's checklist, check the boxes and add a completion timestamp at the end (e.g., `Completed: 2026-03-11`).
+
+---
+
+## Commands
+
+| Command | Purpose |
+|:--------|:--------|
+| `bun run build` | Compile TypeScript |
+| `bun run rebuild` | Clean + build |
+| `bun run clean` | Remove build artifacts |
+| `bun run devcheck` | Lint + format + typecheck + security + packaging alignment |
+| `bun run audit:refresh` | Delete `bun.lock`, reinstall, and re-run `bun audit`. Use when `devcheck` flags a transitive advisory — `bun update` is sticky on transitive resolutions, so the advisory may be a stale-lockfile false positive. If it survives the refresh, it's real. |
+| `bun run tree` | Generate directory structure doc |
+| `bun run format` | Auto-fix formatting |
+| `bun run test` | Run tests |
+| `bun run lint:mcp` | Validate MCP definitions against spec |
+| `bun run lint:packaging` | Validate env var alignment between `manifest.json` and `server.json` (skipped cleanly when `manifest.json` is absent) |
+| `bun run list-skills` | List skills in `skills/` with name + description |
+| `bun run bundle` | Build and pack as `dist/pubmed-mcp-server.mcpb` for one-click Claude Desktop install |
+| `bun run start:stdio` | Production mode (stdio) |
+| `bun run start:http` | Production mode (HTTP) |
+
+---
+
+## Bundling
+
+`bun run bundle` produces `dist/pubmed-mcp-server.mcpb` for one-click install in Claude Desktop. MCPB is stdio-only — HTTP and Docker deployments are unaffected. The `release-and-publish` skill attaches the bundle to the GitHub Release at a stable `releases/latest/download/pubmed-mcp-server.mcpb` URL that powers the README install badge.
+
+**Adding an env var requires both files**: `server.json` stdio `environmentVariables[]` (registry discovery) and `manifest.json` `mcp_config.env` (bundle install UX, plus `user_config` if user-prompted). `bun run lint:packaging` (run by `devcheck`) verifies the env var names align.
+
+---
+
+## Publishing
+
+Run the `release-and-publish` skill after git wrapup — it runs the verification gate (`devcheck`, `rebuild`, `test`), pushes commits and tags, and publishes to npm, the MCP Registry, GHCR, and attaches the `.mcpb` bundle to the GitHub Release, halting on the first failure. For reference, the underlying commands are:
+
+```bash
+bun publish --access public
+
+docker buildx build --platform linux/amd64,linux/arm64 \
+  -t ghcr.io/cyanheads/pubmed-mcp-server:<version> \
+  -t ghcr.io/cyanheads/pubmed-mcp-server:latest \
+  --push .
+
+mcp-publisher publish
+```
+
+---
+
+## Imports
+
+```ts
+// Framework — z is re-exported, no separate zod import needed
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { McpError, JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+
+// Server's own code — via path alias
+import { getNcbiService } from '@/services/ncbi/ncbi-service.js';
+```
+
+---
+
+## Checklist
+
+- [ ] Zod schemas: all fields have `.describe()`, only JSON-Schema-serializable types (no `z.custom()`, `z.date()`, `z.transform()`, `z.bigint()`, `z.symbol()`, `z.void()`, `z.map()`, `z.set()`, `z.function()`, `z.nan()`)
+- [ ] Optional nested objects: handler guards for empty inner values from form-based clients (`if (input.obj?.field && ...)`, not just `if (input.obj)`). When regex/length constraints matter, use `z.union([z.literal(''), z.string().regex(...).describe(...)])` — literal variants are exempt from `describe-on-fields`.
+- [ ] JSDoc `@fileoverview` + `@module` on every file
+- [ ] `ctx.log` for logging, `ctx.state` for storage
+- [ ] Handlers throw on failure — error factories or plain `Error`, no try/catch
+- [ ] `format()` renders all data the LLM needs — different clients forward different surfaces (Claude Code → `structuredContent`, Claude Desktop → `content[]`); both must carry the same data
+- [ ] NCBI wrapping: raw/domain/output schemas reviewed against real upstream sparsity/nullability before finalizing required vs optional fields
+- [ ] NCBI wrapping: normalization and `format()` preserve uncertainty; do not fabricate facts from missing upstream data
+- [ ] NCBI wrapping: tests include at least one sparse payload case with omitted upstream fields
+- [ ] Registered in `createApp()` arrays (directly or via barrel exports)
+- [ ] Tests use `createMockContext()` from `@cyanheads/mcp-ts-core/testing`
+- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = package name; `interface.shortDescription` from `package.json` description
+- [ ] `.codex-plugin/mcp.json` updated — server name key matches `package.json` name; env vars added for any required API keys
+- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry with server name key, env vars for any required API keys
+- [ ] `bun run devcheck` passes

package/CLAUDE.md

@@ -1,8 +1,8 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.7.7
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.13`
+**Version:** 2.7.8
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.16`
 **Engines:** Bun ≥1.3.2, Node ≥24.0.0
 
 > **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.

package/README.md

@@ -9,7 +9,7 @@
 
 
 
-[![Version](https://img.shields.io/badge/Version-2.7.7-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-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) [![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/)
+[![Version](https://img.shields.io/badge/Version-2.7.8-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-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) [![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/)
 
 </div>
 

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

@@ -51,5 +51,5 @@ export declare const convertIdsTool: import("@cyanheads/mcp-ts-core").ToolDefini
     readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
     readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
     readonly retryable: false;
-}]>;
+}], undefined>;
 //# sourceMappingURL=convert-ids.tool.d.ts.map

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

@@ -1 +1 @@
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+{"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;AAcjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA2GzB,CAAC"}

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

@@ -104,5 +104,5 @@ export declare const fetchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDef
     readonly code: JsonRpcErrorCode.SerializationError;
     readonly when: "NCBI EFetch returned a payload missing the PubmedArticleSet wrapper.";
     readonly recovery: "Retry once; if it persists, NCBI returned malformed data — try fewer PMIDs at once.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=fetch-articles.tool.d.ts.map

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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0K5B,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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA0K5B,CAAC"}

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

@@ -186,5 +186,5 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
     readonly when: "Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).";
     readonly recovery: "Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.";
     readonly retryable: false;
-}]>;
+}], undefined>;
 //# sourceMappingURL=fetch-fulltext.tool.d.ts.map

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;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoR/D,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAgd5B,CAAC"}
+{"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoR/D,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAgd5B,CAAC"}

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

@@ -26,8 +26,6 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
         source: z.ZodOptional<z.ZodString>;
         pubDate: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
-    totalFound: z.ZodNumber;
-    notice: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>, readonly [{
     readonly reason: "queue_full";
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
@@ -58,5 +56,8 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
     readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
     readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
     readonly retryable: false;
-}]>;
+}], {
+    readonly totalFound: z.ZodNumber;
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
 //# sourceMappingURL=find-related.tool.d.ts.map

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;AAqCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2L1B,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;AAqCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsM1B,CAAC"}

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

@@ -47,12 +47,22 @@ export const findRelatedTool = tool('pubmed_find_related', {
         })
             .describe('Related article with enriched summary'))
             .describe('Related articles'),
+    }),
+    // Result-set context the agent reasons with — the pre-truncation match count and
+    // recovery guidance (invalid source PMID, or references for a non-PMC source).
+    // Surfaced via ctx.enrich(...) to structuredContent and content[]; out of the return.
+    enrichment: {
         totalFound: z.number().describe('Total related articles found before truncation'),
         notice: z
             .string()
             .optional()
             .describe('Optional guidance when results are empty — e.g. invalid source PMID, or references requested for a non-PMC source. Absent on successful result pages.'),
-    }),
+    },
+    // content[] trailer presentation for the enrichment block. totalFound is scalar —
+    // a label restores the human-readable key; notice renders as a blockquote kind-tag.
+    enrichmentTrailer: {
+        totalFound: { label: 'Total Found' },
+    },
     async handler(input, ctx) {
         const ncbi = getNcbiService();
         ctx.log.debug('Finding related articles', {
@@ -90,6 +100,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
             }
         }
         const totalFound = foundPmids.length;
+        ctx.enrich({ totalFound });
         if (foundPmids.length === 0) {
             // ELink returns an empty LinkSet for both invalid source PMIDs and valid
             // PMIDs that simply have no related articles, so a single ESummary on the
@@ -129,12 +140,12 @@ export const findRelatedTool = tool('pubmed_find_related', {
                     ? `No reference list found in PMC for PMID ${input.pmid} (PMCID ${sourcePmcId}).`
                     : `Reference lists require the source article to be indexed in PMC. PMID ${input.pmid} has no PMCID — references unavailable. Use pubmed_fetch_articles to inspect the article record, or try relationship: "similar" / "cited_by".`;
             }
+            if (notice)
+                ctx.enrich.notice(notice);
             return {
                 sourcePmid: input.pmid,
                 relationship: input.relationship,
                 articles: [],
-                totalFound: 0,
-                ...(notice && { notice }),
             };
         }
         const pmidsToEnrich = foundPmids.slice(0, input.maxResults);
@@ -154,18 +165,15 @@ export const findRelatedTool = tool('pubmed_find_related', {
                 pubDate: details?.pubDate,
             };
         });
-        return { sourcePmid: input.pmid, relationship: input.relationship, articles, totalFound };
+        return { sourcePmid: input.pmid, relationship: input.relationship, articles };
     },
     format: (result) => {
         const lines = [
             `# Related Articles for PMID ${result.sourcePmid}`,
-            `**Relationship:** ${result.relationship} | **Found:** ${result.totalFound}`,
+            `**Relationship:** ${result.relationship}`,
         ];
-        if (result.notice)
-            lines.push(`\n> ${result.notice}`);
         if (result.articles.length === 0) {
-            if (!result.notice)
-                lines.push('No related articles found.');
+            lines.push('No related articles found.');
         }
         else {
             for (const a of result.articles) {

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

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package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts

@@ -56,5 +56,5 @@ export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolD
     readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
     readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
     readonly retryable: false;
-}]>;
+}], undefined>;
 //# sourceMappingURL=format-citations.tool.d.ts.map

package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAejD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyG9B,CAAC"}
+{"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAejD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAyG9B,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts

@@ -69,5 +69,5 @@ export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDe
     readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
     readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
     readonly retryable: false;
-}]>;
+}], undefined>;
 //# sourceMappingURL=lookup-citation.tool.d.ts.map

package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAyBjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAwR7B,CAAC"}
+{"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAyBjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAwR7B,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts

@@ -17,7 +17,6 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
         scopeNote: z.ZodOptional<z.ZodString>;
         entryTerms: z.ZodOptional<z.ZodArray<z.ZodString>>;
     }, z.core.$strip>>;
-    notice: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>, readonly [{
     readonly reason: "queue_full";
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
@@ -48,5 +47,7 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
     readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
     readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
     readonly retryable: false;
-}]>;
+}], {
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
 //# sourceMappingURL=lookup-mesh.tool.d.ts.map

package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAqFjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0GzB,CAAC"}
+{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAqFjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6GzB,CAAC"}