@cyanheads/openalex-mcp-server 0.6.11 → 0.6.13

package/CLAUDE.md

@@ -1,8 +1,9 @@
 # Agent Protocol
 
 **Server:** openalex-mcp-server
-**Version:** 0.6.10
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
+**Version:** 0.6.13
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.6`
+**Engines:** Bun ≥1.3.0, 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.
 
@@ -10,7 +11,7 @@
 
 ## Domain
 
-[OpenAlex](https://openalex.org) is a fully open catalog of the global research system — 270M+ works, 90M+ authors, 100K+ sources. CC0 data, free API key required.
+[OpenAlex](https://openalex.org) is a fully open catalog of the global research system — 270M+ works, 90M+ authors, 100K+ sources. CC0 data, no API key required (email address optional for polite pool access).
 
 **Entity types:** works, authors, sources, institutions, topics, keywords, publishers, funders. All share a uniform API (list/filter, search, get-by-ID, group-by, autocomplete).
 
@@ -34,21 +35,27 @@ No resources — entity lookups need `select` for payload control, which fits to
 
 | Env Var | Required | Description |
 |:--------|:---------|:------------|
-| `OPENALEX_API_KEY` | Yes | API key from openalex.org |
+| `OPENALEX_API_KEY` | No | Email for the OpenAlex polite pool (10x faster rate limits); omit for anonymous access |
 | `OPENALEX_BASE_URL` | No | Default: `https://api.openalex.org` |
 
 ---
 
 ## 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:
+When the user asks what's next or needs direction, suggest options based on the current project state. Common next steps:
 
-1. **Add tests** — scaffold tests for existing definitions using the `add-test` skill
-2. **Field-test definitions** — exercise tools/resources/prompts with real inputs using the `field-test` skill
-3. **Run `devcheck`** — lint, format, typecheck, and security audit
-4. **Run the `security-pass` skill** — audit handlers for MCP-specific security gaps: output injection, scope blast radius, input sinks, tenant isolation
-5. **Run the `polish-docs-meta` skill** — finalize README, CHANGELOG, metadata, and agent protocol for shipping
-6. **Run the `maintenance` skill** — sync skills and dependencies after framework updates
+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.
 
 ---
 
@@ -135,8 +142,11 @@ 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.signal` | `AbortSignal` for cancellation. Passed to `fetch()` in the OpenAlex service. |
-| `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.list(prefix, { cursor, limit })`. Not currently used but available. |
+| `ctx.progress` | Task progress (present when `task: true`) — `.setTotal(n)`, `.increment()`, `.update(message)`. |
 | `ctx.fail` | Typed throw keyed by a declared `errors[]` contract — `ctx.fail(reason, msg?, data?)`. Auto-populates `data.reason` and resolves `code` from the contract. |
 | `ctx.recoveryFor` | Opt-in resolver returning `{ recovery: { hint } }` for a declared reason. Spread into `data` at throw site to surface contract recovery on the wire. |
 | `ctx.requestId` | Unique request ID. |
@@ -264,13 +274,32 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run build` | Compile TypeScript |
 | `bun run rebuild` | Clean + build |
 | `bun run clean` | Remove build artifacts |
-| `bun run devcheck` | Lint + format + typecheck + security |
+| `bun run devcheck` | Lint + format + typecheck + security + changelog sync |
+| `bun run audit:refresh` | Delete `bun.lock`, reinstall, re-audit. Use when `devcheck` flags a transitive advisory — stale lockfile can mask already-patched deps. If advisory survives, it's real. |
 | `bun run tree` | Generate directory structure doc |
 | `bun run format` | Auto-fix formatting |
 | `bun run lint:mcp` | Validate MCP tool/prompt definitions |
+| `bun run list-skills` | List available skills |
 | `bun run test` | Run tests |
 | `bun run start:stdio` | Production mode (stdio, after `rebuild`) |
 | `bun run start:http` | Production mode (HTTP, after `rebuild`) |
+| `bun run changelog:build` | Regenerate `CHANGELOG.md` from `changelog/*.md` |
+| `bun run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
+| `bun run bundle` | Build and pack as `.mcpb` for one-click Claude Desktop install |
+
+---
+
+## Bundling
+
+`bun run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. MCPB is stdio-only — HTTP deployments are unaffected. Consumers who don't need it can delete `manifest.json` and `.mcpbignore`; `lint:packaging` skips cleanly.
+
+**Adding an env var requires both files:** `server.json` (registry discovery, `environmentVariables[]`) and `manifest.json` (bundle install UX, `mcp_config.env` + `user_config`). `lint:packaging` (run by `devcheck`) verifies the env var names match.
+
+---
+
+## Changelog
+
+Directory-based, grouped by minor series via the `.x` semver-wildcard convention. Source of truth: `changelog/<major.minor>.x/<version>.md` (e.g. `changelog/0.6.x/0.6.12.md`) — one file per release, shipped in the npm package. At release, author the per-version file with a concrete version and date, then run `bun run changelog:build` to regenerate the rollup. `changelog/template.md` is a **pristine format reference** — never edited or moved. `CHANGELOG.md` is a **navigation index** regenerated by `bun run changelog:build` — devcheck hard-fails on drift; never hand-edit it.
 
 ---
 
@@ -304,7 +333,7 @@ import { getOpenAlexService } from '@/services/openalex/openalex-service.js';
 
 ## Checklist
 
-- [ ] Zod schemas: all fields have `.describe()`, only JSON-Schema-serializable types (no `z.custom()`, `z.date()`, `z.transform()`, etc.)
+- [ ] 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`.
 - [ ] `format()` renders every terminal field in `output` — enforced by `format-parity` linter via sentinel injection (locale-aware: digit-group separators stripped before matching)
 - [ ] JSDoc `@fileoverview` + `@module` on every file

package/README.md

@@ -1,12 +1,21 @@
 <div align="center">
   <h1>@cyanheads/openalex-mcp-server</h1>
-  <p><b>Access the OpenAlex academic research catalog - 270M+ publications through MCP. STDIO & Streamable HTTP.</b></p>
-  <p><b>4 Tools &middot; 2 Prompts</b></p>
+  <p><b>Access the OpenAlex academic research catalog - 270M+ publications through MCP. STDIO & Streamable HTTP.</b>
+  <div>4 Tools &bull; 2 Prompts</div>
+  </p>
 </div>
 
 <div align="center">
 
-[![Version](https://img.shields.io/badge/Version-0.6.11-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/)
+[![Version](https://img.shields.io/badge/Version-0.6.13-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/openalex-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/openalex-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/openalex-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-v1.3.0-blueviolet.svg?style=flat-square)](https://bun.sh/)
+
+</div>
+
+<div align="center">
+
+[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/openalex-mcp-server/releases/latest/download/openalex-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=openalex-mcp-server&config=eyJtY3BTZXJ2ZXJzIjp7Im9wZW5hbGV4LW1jcC1zZXJ2ZXIiOnsiY29tbWFuZCI6Im5weCIsImFyZ3MiOlsiLXkiLCJAY3lhbmhlYWRzL29wZW5hbGV4LW1jcC1zZXJ2ZXJAbGF0ZXN0Il0sImVudiI6eyJNQ1BfVFJBTlNQT1JUX1RZUEUiOiJzdGRpbyIsIk1DUF9MT0dfTEVWRUwiOiJpbmZvIn19fX0=) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22openalex-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Fopenalex-mcp-server%40latest%22%5D%2C%22env%22%3A%7B%22MCP_TRANSPORT_TYPE%22%3A%22stdio%22%2C%22MCP_LOG_LEVEL%22%3A%22info%22%7D%7D)
+
+[![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
 
 </div>
 
@@ -73,7 +82,7 @@ One-hop citation graph traversal from a seed work. Wraps the OpenAlex `cites`/`c
 - `cites`: works that cite the seed (incoming citations)
 - `cited_by`: works the seed cites (its reference list)
 - `related_to`: OpenAlex algorithmic "related works" (~8-30 typical, may be empty for less-cited seeds)
-- Accepts OpenAlex IDs, DOIs, PMIDs, PMCIDs as `seed_id`; resolves non-W-IDs via a singleton lookup
+- Accepts OpenAlex IDs, DOIs, PMIDs, PMCIDs as `seed_id`; validates the seed via a singleton `/works/{id}` lookup before walking, so non-existent seeds surface as `NotFound`
 - Stacks with `filters`/`sort`/`select` to narrow the graph (e.g., `publication_year=">2020"`, `is_oa="true"`)
 
 ## Prompts
@@ -164,7 +173,7 @@ bun install
 
 | Variable | Description | Default |
 |:---------|:------------|:--------|
-| `OPENALEX_API_KEY` | **Required.** Email address for the OpenAlex [polite pool](https://docs.openalex.org/how-to-use-the-api/rate-limits-and-authentication#the-polite-pool) (faster rate limits). | — |
+| `OPENALEX_API_KEY` | **Optional.** Email address for the OpenAlex [polite pool](https://docs.openalex.org/how-to-use-the-api/rate-limits-and-authentication#the-polite-pool) (10x faster rate limits). Without it, anonymous rate limits apply. | — |
 | `OPENALEX_BASE_URL` | OpenAlex API base URL. | `https://api.openalex.org` |
 | `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |
 | `MCP_HTTP_PORT` | Port for HTTP server. | `3010` |

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

@@ -4,7 +4,7 @@
  */
 import { z } from '@cyanheads/mcp-ts-core';
 declare const ServerConfigSchema: z.ZodObject<{
-    apiKey: z.ZodString;
+    apiKey: z.ZodDefault<z.ZodString>;
     baseUrl: z.ZodDefault<z.ZodString>;
 }, z.core.$strip>;
 export type ServerConfig = z.infer<typeof ServerConfigSchema>;

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

@@ -1 +1 @@
-{"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,QAAA,MAAM,kBAAkB;;;iBAGtB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CAM9C"}
+{"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,QAAA,MAAM,kBAAkB;;;iBAQtB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CAM9C"}

package/dist/config/server-config.js

@@ -4,7 +4,10 @@
  */
 import { z } from '@cyanheads/mcp-ts-core';
 const ServerConfigSchema = z.object({
-    apiKey: z.string().min(1).describe('OpenAlex API key'),
+    apiKey: z
+        .string()
+        .default('')
+        .describe('OpenAlex API key or mailto email — optional (without: anonymous rate limits; with: polite pool)'),
     baseUrl: z.string().url().default('https://api.openalex.org').describe('OpenAlex API base URL'),
 });
 let _config;

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

@@ -1 +1 @@
-{"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IAClC,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,kBAAkB,CAAC;IACtD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,OAAO,CAAC,0BAA0B,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;CAChG,CAAC,CAAC;AAIH,IAAI,OAAiC,CAAC;AAEtC,MAAM,UAAU,eAAe;IAC7B,OAAO,KAAK,kBAAkB,CAAC,KAAK,CAAC;QACnC,MAAM,EAAE,OAAO,CAAC,GAAG,CAAC,gBAAgB;QACpC,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,iBAAiB;KACvC,CAAC,CAAC;IACH,OAAO,OAAO,CAAC;AACjB,CAAC"}
+{"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IAClC,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,OAAO,CAAC,EAAE,CAAC;SACX,QAAQ,CACP,iGAAiG,CAClG;IACH,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,OAAO,CAAC,0BAA0B,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;CAChG,CAAC,CAAC;AAIH,IAAI,OAAiC,CAAC;AAEtC,MAAM,UAAU,eAAe;IAC7B,OAAO,KAAK,kBAAkB,CAAC,KAAK,CAAC;QACnC,MAAM,EAAE,OAAO,CAAC,GAAG,CAAC,gBAAgB;QACpC,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,iBAAiB;KACvC,CAAC,CAAC;IACH,OAAO,OAAO,CAAC;AACjB,CAAC"}

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

@@ -48,10 +48,15 @@ export declare const getCitationGraphTool: import("@cyanheads/mcp-ts-core").Tool
     readonly code: JsonRpcErrorCode.InvalidParams;
     readonly when: "OpenAlex rejected the seed_id, filter, or sort as malformed (HTTP 400).";
     readonly recovery: "Read the upstream message for the rejected token, then retry with a valid OpenAlex work ID (W…), DOI, or PMID for seed_id, or correct the filter/sort field name it names.";
+}, {
+    readonly reason: "reserved_filter_key";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "filters contains cites/cited_by/related_to — the direction parameter reserves those keys.";
+    readonly recovery: "Remove the reserved key from filters, or restate the relationship through direction.";
 }, {
     readonly reason: "entity_not_found";
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "OpenAlex returned no edges for the seed_id in the requested direction.";
-    readonly recovery: "Verify seed_id resolves to an OpenAlex work via openalex_resolve_name; not all works have related_to entries.";
+    readonly when: "OpenAlex has no work matching the seed_id.";
+    readonly recovery: "Verify seed_id with openalex_resolve_name, or pass a known OpenAlex work ID (W…), DOI, PMID, or PMCID.";
 }]>;
 //# sourceMappingURL=citation-graph.tool.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"citation-graph.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/citation-graph.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAGH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkDjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiL/B,CAAC"}
+{"version":3,"file":"citation-graph.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/citation-graph.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAGH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA+CjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAuM/B,CAAC"}

package/dist/mcp-server/tools/definitions/citation-graph.tool.js

@@ -5,21 +5,17 @@
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { renderEntityRecord } from '../../../mcp-server/tools/render-entity-record.js';
-import { getOpenAlexService, normalizeId } from '../../../services/openalex/openalex-service.js';
-/** Bare or URL-form OpenAlex work ID — the only form `cites`/`cited_by`/`related_to` filters accept. */
-const OPENALEX_WORK_ID_PATTERN = /^(?:https:\/\/openalex\.org\/)?W\d+$/;
+import { getOpenAlexService } from '../../../services/openalex/openalex-service.js';
 const OPENALEX_URL_PREFIX = 'https://openalex.org/';
 /**
- * The `cites`/`cited_by`/`related_to` filters require an OpenAlex W-ID; DOIs and PMIDs
- * are rejected upstream even after `normalizeId` adds a `doi:` prefix (that prefix only
- * works on the `/works/{id}` singleton path). Resolve non-W-IDs via a one-shot singleton
- * lookup so callers can pass any identifier the docs advertise.
+ * Resolve any accepted seed identifier to a bare W-ID and confirm it exists. The graph
+ * filters (`cites`/`cited_by`/`related_to`) themselves don't validate the seed — passing
+ * a non-existent W-ID returns zero edges, indistinguishable from a valid seed with no
+ * citations yet. A singleton `/works/{id}` lookup gates the query so bad seeds surface
+ * as NotFound (bubbles via the service as `entity_not_found`) and good seeds with empty
+ * graphs return honest empty results.
  */
 async function resolveSeedToWorkId(service, seedId, ctx) {
-    const normalized = normalizeId(seedId);
-    if (OPENALEX_WORK_ID_PATTERN.test(normalized)) {
-        return normalized.replace(OPENALEX_URL_PREFIX, '');
-    }
     const lookup = await service.search({ entityType: 'works', id: seedId, select: ['id'] }, ctx);
     const record = lookup.results[0];
     if (!record?.id) {
@@ -28,6 +24,7 @@ async function resolveSeedToWorkId(service, seedId, ctx) {
     return record.id.replace(OPENALEX_URL_PREFIX, '');
 }
 const DIRECTIONS = ['cites', 'cited_by', 'related_to'];
+const RESERVED_FILTER_KEYS = new Set(DIRECTIONS);
 function buildCitationEcho(input) {
     const parts = [`seed_id=${input.seed_id}`, `direction=${input.direction}`];
     if (input.filters && Object.keys(input.filters).length > 0) {
@@ -38,7 +35,7 @@ function buildCitationEcho(input) {
     return parts.join(' | ');
 }
 export const getCitationGraphTool = tool('openalex_get_citation_graph', {
-    description: "Walk the citation graph one hop from a seed work. Direction picks which edge: incoming citations (cites), the seed's own references (cited_by), or OpenAlex's algorithmic related-works (related_to). Thin wrapper over openalex_search_entities scoped to works — exposes the direction explicitly so callers do not have to know the underlying filter names. Results pass through the works schema; combine with filters/sort to narrow further.",
+    description: "Walk the citation graph one hop from a seed work. Direction picks the edge: incoming citations (`cites`), the seed's own references (`cited_by`), or OpenAlex's algorithmically-related works (`related_to`). Results use the works schema; combine with filters/sort to narrow further.",
     sourceUrl: 'https://github.com/cyanheads/openalex-mcp-server/blob/main/src/mcp-server/tools/definitions/citation-graph.tool.ts',
     annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
     errors: [
@@ -67,11 +64,17 @@ export const getCitationGraphTool = tool('openalex_get_citation_graph', {
             when: 'OpenAlex rejected the seed_id, filter, or sort as malformed (HTTP 400).',
             recovery: 'Read the upstream message for the rejected token, then retry with a valid OpenAlex work ID (W…), DOI, or PMID for seed_id, or correct the filter/sort field name it names.',
         },
+        {
+            reason: 'reserved_filter_key',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'filters contains cites/cited_by/related_to — the direction parameter reserves those keys.',
+            recovery: 'Remove the reserved key from filters, or restate the relationship through direction.',
+        },
         {
             reason: 'entity_not_found',
             code: JsonRpcErrorCode.NotFound,
-            when: 'OpenAlex returned no edges for the seed_id in the requested direction.',
-            recovery: 'Verify seed_id resolves to an OpenAlex work via openalex_resolve_name; not all works have related_to entries.',
+            when: 'OpenAlex has no work matching the seed_id.',
+            recovery: 'Verify seed_id with openalex_resolve_name, or pass a known OpenAlex work ID (W…), DOI, PMID, or PMCID.',
         },
     ],
     input: z.object({
@@ -85,7 +88,7 @@ export const getCitationGraphTool = tool('openalex_get_citation_graph', {
         filters: z
             .record(z.string(), z.string())
             .optional()
-            .describe('Additional filters to narrow the graph, same syntax as openalex_search_entities. Example: publication_year=">2020", is_oa="true". The direction filter is added automatically — do not pass cites/cited_by/related_to here.'),
+            .describe('Additional filters to narrow the graph, same syntax as openalex_search_entities. Example: publication_year=">2020", is_oa="true". Do not include cites/cited_by/related_to — those are set by the `direction` parameter.'),
         sort: z
             .string()
             .optional()
@@ -133,6 +136,16 @@ export const getCitationGraphTool = tool('openalex_get_citation_graph', {
             .describe('Works on the citation graph in this direction.'),
     }),
     async handler(input, ctx) {
+        if (input.filters) {
+            const reserved = Object.keys(input.filters).find((key) => RESERVED_FILTER_KEYS.has(key));
+            if (reserved !== undefined) {
+                throw ctx.fail('reserved_filter_key', `${reserved} cannot be passed in filters — direction reserves cites/cited_by/related_to.`, {
+                    ...ctx.recoveryFor('reserved_filter_key'),
+                    reservedKey: reserved,
+                    direction: input.direction,
+                });
+            }
+        }
         const service = getOpenAlexService();
         const workId = await resolveSeedToWorkId(service, input.seed_id, ctx);
         const mergedFilters = {

package/dist/mcp-server/tools/definitions/citation-graph.tool.js.map

@@ -1 +1 @@
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package/dist/services/openalex/openalex-service.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AAoBtD,OAAO,EACL,KAAK,aAAa,EAClB,KAAK,aAAa,EAClB,KAAK,kBAAkB,EACvB,KAAK,kBAAkB,EAIvB,KAAK,YAAY,EACjB,KAAK,YAAY,EAClB,MAAM,YAAY,CAAC;AAcpB;;;;;;;;GAQG;AACH,wBAAgB,WAAW,CAAC,EAAE,EAAE,MAAM,GAAG,MAAM,CA6C9C;AA6SD,cAAM,eAAe;IACnB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IACjC,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAS;;IAQhC,yFAAyF;IACzF,OAAO,CAAC,OAAO;IAoCf,OAAO,CAAC,2BAA2B;IAwCnC,OAAO,CAAC,aAAa;IAqCrB,sEAAsE;IAChE,MAAM,CAAC,MAAM,EAAE,YAAY,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,YAAY,CAAC;IA6EvE,4BAA4B;IACtB,OAAO,CAAC,MAAM,EAAE,aAAa,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,aAAa,CAAC;IAoC1E,oCAAoC;IAC9B,YAAY,CAAC,MAAM,EAAE,kBAAkB,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,kBAAkB,CAAC;CAuB1F;AAID,wBAAgB,mBAAmB,IAAI,IAAI,CAE1C;AAED,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD"}
+{"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AAoBtD,OAAO,EACL,KAAK,aAAa,EAClB,KAAK,aAAa,EAClB,KAAK,kBAAkB,EACvB,KAAK,kBAAkB,EAIvB,KAAK,YAAY,EACjB,KAAK,YAAY,EAClB,MAAM,YAAY,CAAC;AAcpB;;;;;;;;GAQG;AACH,wBAAgB,WAAW,CAAC,EAAE,EAAE,MAAM,GAAG,MAAM,CA6C9C;AA+UD,cAAM,eAAe;IACnB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IACjC,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAS;;IAQhC,yFAAyF;IACzF,OAAO,CAAC,OAAO;IAoCf,OAAO,CAAC,2BAA2B;IA4CnC,OAAO,CAAC,aAAa;IAqCrB,sEAAsE;IAChE,MAAM,CAAC,MAAM,EAAE,YAAY,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,YAAY,CAAC;IA8FvE,4BAA4B;IACtB,OAAO,CAAC,MAAM,EAAE,aAAa,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,aAAa,CAAC;IAoC1E,oCAAoC;IAC9B,YAAY,CAAC,MAAM,EAAE,kBAAkB,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,kBAAkB,CAAC;CAuB1F;AAID,wBAAgB,mBAAmB,IAAI,IAAI,CAE1C;AAED,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD"}

package/dist/services/openalex/openalex-service.js

@@ -281,6 +281,22 @@ function logResponseMetrics(parsed, path, ctx) {
         ...(db !== undefined && { dbResponseTimeMs: db }),
     });
 }
+/**
+ * Permissive extractors for OpenAlex's `error` and `message` fields when the body
+ * is truncated mid-string (framework caps `responseBody` at 500 bytes; OpenAlex
+ * valid-fields listings exceed ~1 KB). The terminator `"|…|$` accepts a closing
+ * quote, the framework's truncation ellipsis, or end of string — so whatever
+ * survived the cap still gets extracted.
+ */
+const TRUNCATED_ERROR_FIELD_RE = /"error"\s*:\s*"((?:[^"\\]|\\.)*?)(?:"|…|$)/;
+const TRUNCATED_MESSAGE_FIELD_RE = /"message"\s*:\s*"((?:[^"\\]|\\.)*?)(?:"|…|$)/;
+/**
+ * Extract OpenAlex's `error` and `message` fields from a response body. JSON.parse
+ * works for un-truncated bodies; falls back to regex so the useful prefix of the
+ * upstream message still reaches the caller when the body was cut mid-string.
+ * `truncated` distinguishes the two paths so downstream sanitization can act only
+ * on bodies that were actually cut.
+ */
 function parseOpenAlexErrorBody(responseBody) {
     if (typeof responseBody !== 'string')
         return null;
@@ -291,12 +307,30 @@ function parseOpenAlexErrorBody(responseBody) {
         return {
             error: typeof parsed.error === 'string' ? parsed.error : undefined,
             message: typeof parsed.message === 'string' ? parsed.message : undefined,
+            truncated: false,
         };
     }
     catch {
-        return null;
+        const error = TRUNCATED_ERROR_FIELD_RE.exec(responseBody)?.[1];
+        const message = TRUNCATED_MESSAGE_FIELD_RE.exec(responseBody)?.[1];
+        if (error === undefined && message === undefined)
+            return null;
+        return { error, message, truncated: true };
     }
 }
+/**
+ * OpenAlex 400 messages append an alphabetically-sorted enumeration of valid field
+ * names ("Valid fields are: a, b, c, ..."). When the response body was truncated
+ * mid-list the surviving prefix misleads agents into believing the early-alphabet
+ * fields are the complete set. Strip the list when truncation occurred — the raw
+ * upstream prefix stays available on `data.upstreamMessage` for debugging.
+ */
+const VALID_FIELDS_BOUNDARY_RE = /\s*Valid fields\b.*/is;
+function stripTruncatedValidFieldsList(message) {
+    if (!VALID_FIELDS_BOUNDARY_RE.test(message))
+        return message;
+    return `${message.replace(VALID_FIELDS_BOUNDARY_RE, '').trim()} (list of valid fields omitted — was truncated upstream; see OpenAlex docs)`;
+}
 function getSearchParamKey(searchMode) {
     switch (searchMode) {
         case 'exact':
@@ -340,7 +374,8 @@ class OpenAlexService {
         const operation = `OpenAlex ${path}`;
         const requestContext = toRequestContext(ctx, operation);
         const url = new URL(`${this.baseUrl}${path}`);
-        url.searchParams.set('mailto', this.apiKey);
+        if (this.apiKey)
+            url.searchParams.set('mailto', this.apiKey);
         for (const [key, value] of Object.entries(params)) {
             if (value)
                 url.searchParams.set(key, value);
@@ -385,8 +420,11 @@ class OpenAlexService {
         }
         const { factory, reason } = normalized;
         const upstream = parseOpenAlexErrorBody(error.data?.responseBody);
-        const message = upstream?.message ??
-            upstream?.error ??
+        const rawMessage = upstream?.message ?? upstream?.error;
+        const sanitizedMessage = rawMessage !== undefined && upstream?.truncated
+            ? stripTruncatedValidFieldsList(rawMessage)
+            : rawMessage;
+        const message = sanitizedMessage ??
             (code === JsonRpcErrorCode.NotFound
                 ? `Entity not found at ${path}`
                 : redactUrlsInMessage(error.message));
@@ -479,10 +517,21 @@ class OpenAlexService {
         if (params.searchMode !== 'semantic' && params.sample === undefined) {
             queryParams.cursor = params.cursor ?? '*';
         }
-        const data = (await this.request(`/${params.entityType}`, queryParams, ctx));
+        const searchRequest = this.request(`/${params.entityType}`, queryParams, ctx);
+        // Sampling: OpenAlex returns the sample size in `meta.count`, not the population
+        // matching the filters. The output schema documents `count` as "Total results
+        // matching the query/filters" — issue a parallel per_page=1 lookup without
+        // `sample` to recover the true population and overwrite `count` with it.
+        let populationRequest;
+        if (params.sample !== undefined) {
+            const { sample: _sample, seed: _seed, ...filterParams } = queryParams;
+            populationRequest = this.request(`/${params.entityType}`, { ...filterParams, per_page: '1', cursor: '*' }, ctx);
+        }
+        const [data, populationData] = await Promise.all([searchRequest, populationRequest]);
         return {
             meta: {
                 ...data.meta,
+                ...(populationData !== undefined && { count: populationData.meta.count }),
                 next_cursor: data.meta.next_cursor ?? null,
             },
             results: normalizeEntityRecords(data.results),

package/dist/services/openalex/openalex-service.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/openalex-mcp-server",
-  "version": "0.6.11",
+  "version": "0.6.13",
   "description": "Access the OpenAlex academic research catalog - 270M+ publications through MCP. STDIO & Streamable HTTP.",
   "mcpName": "io.github.cyanheads/openalex-mcp-server",
   "type": "module",
@@ -18,6 +18,10 @@
     "tree": "bun scripts/tree.ts",
     "format": "biome check --write --unsafe .",
     "lint:mcp": "bun scripts/lint-mcp.ts",
+    "lint:packaging": "bun scripts/lint-packaging.ts",
+    "list-skills": "bun scripts/list-skills.ts",
+    "bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/@cyanheads/openalex-mcp-server.mcpb",
+    "audit:refresh": "rm -f bun.lock && bun install && bun audit",
     "changelog:build": "bun scripts/build-changelog.ts",
     "changelog:check": "bun scripts/build-changelog.ts --check",
     "test": "vitest run",
@@ -68,8 +72,9 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.9.1",
-    "pino-pretty": "^13.1.3"
+    "@cyanheads/mcp-ts-core": "^0.9.6",
+    "pino-pretty": "^13.1.3",
+    "zod": "^4.4.3"
   },
   "devDependencies": {
     "@biomejs/biome": "^2.4.15",

package/server.json

@@ -1,12 +1,12 @@
 {
   "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
   "name": "io.github.cyanheads/openalex-mcp-server",
-  "description": "Access the OpenAlex academic research catalog - 270M+ publications via MCP. STDIO & HTTP.",
+  "description": "Access the OpenAlex academic research catalog — 270M+ publications.",
   "repository": {
     "url": "https://github.com/cyanheads/openalex-mcp-server",
     "source": "github"
   },
-  "version": "0.6.11",
+  "version": "0.6.13",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/openalex-mcp-server",
       "runtimeHint": "node",
-      "version": "0.6.11",
+      "version": "0.6.13",
       "packageArguments": [
         {
           "type": "positional",
@@ -33,9 +33,9 @@
       "environmentVariables": [
         {
           "name": "OPENALEX_API_KEY",
-          "description": "API key from openalex.org (free).",
+          "description": "OpenAlex API key or mailto email \u2014 optional. Without: anonymous rate limits. With: polite pool access.",
           "format": "string",
-          "isRequired": true
+          "isRequired": false
         },
         {
           "name": "OPENALEX_BASE_URL",
@@ -61,7 +61,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/openalex-mcp-server",
       "runtimeHint": "node",
-      "version": "0.6.11",
+      "version": "0.6.13",
       "packageArguments": [
         {
           "type": "positional",
@@ -75,9 +75,9 @@
       "environmentVariables": [
         {
           "name": "OPENALEX_API_KEY",
-          "description": "API key from openalex.org (free).",
+          "description": "OpenAlex API key or mailto email \u2014 optional. Without: anonymous rate limits. With: polite pool access.",
           "format": "string",
-          "isRequired": true
+          "isRequired": false
         },
         {
           "name": "OPENALEX_BASE_URL",