@cyanheads/openalex-mcp-server 0.7.11 → 0.7.13
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 +16 -13
- package/CLAUDE.md +16 -13
- package/README.md +9 -8
- package/changelog/0.7.x/0.7.12.md +13 -0
- package/changelog/0.7.x/0.7.13.md +22 -0
- package/changelog/template.md +7 -24
- package/dist/config/server-config.d.ts.map +1 -1
- package/dist/config/server-config.js +5 -4
- package/dist/config/server-config.js.map +1 -1
- package/dist/mcp-server/tools/definitions/citation-graph.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/citation-graph.tool.js +2 -2
- package/dist/mcp-server/tools/definitions/citation-graph.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/resolve-name.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/resolve-name.tool.js +9 -4
- package/dist/mcp-server/tools/definitions/resolve-name.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-entities.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/search-entities.tool.js.map +1 -1
- package/dist/services/openalex/openalex-service.d.ts +10 -0
- package/dist/services/openalex/openalex-service.d.ts.map +1 -1
- package/dist/services/openalex/openalex-service.js +38 -0
- package/dist/services/openalex/openalex-service.js.map +1 -1
- package/package.json +8 -7
- package/server.json +3 -3
package/AGENTS.md
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@@ -1,11 +1,11 @@
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# Developer Protocol
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**Server:** openalex-mcp-server
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**Version:** 0.7.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.
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**Engines:** Bun ≥1.
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**Version:** 0.7.13
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.0`
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**Engines:** Bun ≥1.4.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
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**Zod:** ^4.
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**Zod:** ^4.6.1
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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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## Skills
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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.
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Skills are modular instructions in `framework-skills/` at the project root. Read them directly when a task matches — e.g., `framework-skills/add-tool/SKILL.md` when adding a tool.
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**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).
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**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 `framework-skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
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Available skills:
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@@ -256,8 +256,9 @@ Available skills:
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| `code-simplifier` | Post-session cleanup against `git diff` — modernize syntax, consolidate duplication, align with the codebase |
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| `techniques` | Reusable response/data-shaping patterns — overflow handling, payload shaping, retrieval |
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| `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
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| `git-wrapup` |
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| `release-
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| `git-wrapup` | Prepare the version, changelog, verification, and commit stack. |
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| `release-pr-review` | Review an open release PR when the project opts into release PR mode. |
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| `release-and-publish` | Tag + push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup`. |
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| `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
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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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| `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` |
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@@ -275,7 +276,7 @@ Available skills:
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| `api-workers` | Cloudflare Workers runtime |
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| `api-mirror` | MirrorService: persistent local SQLite mirror of a bulk upstream dataset — Tier 3 opt-in |
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**Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
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**Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `framework-skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
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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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@@ -289,7 +290,8 @@ When you complete a skill's checklist, check the boxes and add a completion time
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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 audit:
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| `bun run audit:fix` | Run `bun audit fix` to upgrade vulnerable packages within existing ranges. |
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| `bun run audit:refresh` | Delete `bun.lock` and reinstall; last resort after `audit:fix`, targeted updates, and `bun dedupe`. |
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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 lint:mcp` | Validate MCP tool/prompt definitions |
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@@ -309,6 +311,7 @@ When you complete a skill's checklist, check the boxes and add a completion time
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`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.
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**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.
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Every bundle option must be wired as `${user_config.<option>}`; optional strings need a default. Claude plugins use the same options under `userConfig`, while Codex forwards user variables through `env_vars`. Never overwrite a user's exported value with an empty plugin `env` entry.
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---
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@@ -361,7 +364,7 @@ import { getOpenAlexService } from '@/services/openalex/openalex-service.js';
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- [ ] OpenAlex wrapping: tests include at least one sparse payload case with omitted upstream fields
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- [ ] Registered in `createApp()` arrays (directly or via barrel exports)
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- [ ] Tests use `createMockContext()` from `@cyanheads/mcp-ts-core/testing`
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- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` =
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- [ ] `.codex-plugin/mcp.json` updated — server name key
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- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry
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- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = the unscoped repo name; `interface.shortDescription` from `package.json` description
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- [ ] `.codex-plugin/mcp.json` updated — server name key is the unscoped repo name; user-supplied variables are listed in `env_vars`
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- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry keyed by the unscoped repo name; user-supplied variables are declared under `userConfig` and referenced as `${user_config.<option>}`
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- [ ] `bun run devcheck` passes
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package/CLAUDE.md
CHANGED
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@@ -1,11 +1,11 @@
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# Developer Protocol
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**Server:** openalex-mcp-server
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**Version:** 0.7.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.
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**Engines:** Bun ≥1.
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**Version:** 0.7.13
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.0`
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**Engines:** Bun ≥1.4.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
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**Zod:** ^4.
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**Zod:** ^4.6.1
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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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@@ -234,9 +234,9 @@ src/
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## Skills
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237
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-
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.
|
|
237
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+
Skills are modular instructions in `framework-skills/` at the project root. Read them directly when a task matches — e.g., `framework-skills/add-tool/SKILL.md` when adding a tool.
|
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238
238
|
|
|
239
|
-
**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).
|
|
239
|
+
**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 `framework-skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
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Available skills:
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242
242
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@@ -256,8 +256,9 @@ Available skills:
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256
256
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| `code-simplifier` | Post-session cleanup against `git diff` — modernize syntax, consolidate duplication, align with the codebase |
|
|
257
257
|
| `techniques` | Reusable response/data-shaping patterns — overflow handling, payload shaping, retrieval |
|
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258
258
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| `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
|
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| `git-wrapup` |
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| `release-
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| `git-wrapup` | Prepare the version, changelog, verification, and commit stack. |
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260
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| `release-pr-review` | Review an open release PR when the project opts into release PR mode. |
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| `release-and-publish` | Tag + push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup`. |
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| `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
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262
263
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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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263
264
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| `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` |
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@@ -275,7 +276,7 @@ Available skills:
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| `api-workers` | Cloudflare Workers runtime |
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277
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| `api-mirror` | MirrorService: persistent local SQLite mirror of a bulk upstream dataset — Tier 3 opt-in |
|
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277
278
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278
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-
**Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
|
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279
|
+
**Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `framework-skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
|
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281
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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`).
|
|
281
282
|
|
|
@@ -289,7 +290,8 @@ When you complete a skill's checklist, check the boxes and add a completion time
|
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| `bun run rebuild` | Clean + build |
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290
291
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| `bun run clean` | Remove build artifacts |
|
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291
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| `bun run devcheck` | Lint + format + typecheck + security + changelog sync |
|
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292
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-
| `bun run audit:
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293
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+
| `bun run audit:fix` | Run `bun audit fix` to upgrade vulnerable packages within existing ranges. |
|
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294
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| `bun run audit:refresh` | Delete `bun.lock` and reinstall; last resort after `audit:fix`, targeted updates, and `bun dedupe`. |
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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 lint:mcp` | Validate MCP tool/prompt definitions |
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@@ -309,6 +311,7 @@ When you complete a skill's checklist, check the boxes and add a completion time
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`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.
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**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.
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+
Every bundle option must be wired as `${user_config.<option>}`; optional strings need a default. Claude plugins use the same options under `userConfig`, while Codex forwards user variables through `env_vars`. Never overwrite a user's exported value with an empty plugin `env` entry.
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---
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@@ -361,7 +364,7 @@ import { getOpenAlexService } from '@/services/openalex/openalex-service.js';
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- [ ] OpenAlex wrapping: tests include at least one sparse payload case with omitted upstream fields
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362
365
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- [ ] Registered in `createApp()` arrays (directly or via barrel exports)
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363
366
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- [ ] Tests use `createMockContext()` from `@cyanheads/mcp-ts-core/testing`
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364
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-
- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` =
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- [ ] `.codex-plugin/mcp.json` updated — server name key
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- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry
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- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = the unscoped repo name; `interface.shortDescription` from `package.json` description
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- [ ] `.codex-plugin/mcp.json` updated — server name key is the unscoped repo name; user-supplied variables are listed in `env_vars`
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- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry keyed by the unscoped repo name; user-supplied variables are declared under `userConfig` and referenced as `${user_config.<option>}`
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- [ ] `bun run devcheck` passes
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package/README.md
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<div align="center">
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/openalex-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/openalex-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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| `openalex_search_entities` | Search, filter, sort, or retrieve by ID across all 8 entity types. |
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| `openalex_analyze_trends` | Group-by aggregation for trend and distribution analysis. |
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| `openalex_resolve_name` | Resolve a name or an identifier (DOI, ORCID, ROR, PMID,
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| `openalex_resolve_name` | Resolve a name or an identifier (DOI, ORCID, ROR, PMID, ISSN, OpenAlex ID) to an OpenAlex ID. |
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| `openalex_get_citation_graph` | Walk the citation graph one hop from a seed work: cites, cited_by, or related_to. |
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| `openalex_describe_fields` | List valid filter, group_by, and select field names for an entity type — call before building a query to avoid invalid-field errors. |
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Primary discovery and lookup tool. Covers all OpenAlex entity types (works, authors, sources, institutions, topics, keywords, publishers, funders).
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- Retrieve a single entity by ID (OpenAlex ID, DOI, ORCID, ROR, PMID,
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- Retrieve a single entity by ID (OpenAlex ID, DOI, ORCID, ROR, PMID, ISSN), bare or in URL form, with the scheme prefix accepted in any case. A PMCID is recognized as well, bare or as a PubMed Central URL, but OpenAlex indexes no PMCIDs, so it resolves nothing — pass the work's PMID or DOI instead. `id` takes precedence: search criteria passed alongside it are not applied, and the response says which ones were dropped rather than echoing them back as though they ran. The search-only validations (semantic page cap, `sample` with `cursor`, `seed` without `sample`) are skipped too — a lookup is never rejected over parameters it ignores
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- Keyword search with boolean operators, quoted phrases, wildcards, and fuzzy matching
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- Exact and AI semantic search modes
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- Rich filter syntax: AND across fields, OR within fields (`us|gb`), NOT (`!us`), ranges (`2020-2024`), comparisons (`>100`)
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The front door for turning anything you have into an OpenAlex ID. **Always use this before filtering by entity** — names are ambiguous, IDs are not.
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- A name or partial name runs an autocomplete search: up to 10 matches with disambiguation hints, ~200ms
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- An identifier resolves deterministically to the single record it addresses — OpenAlex ID, DOI, ORCID, ROR, PMID,
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+
- An identifier resolves deterministically to the single record it addresses — OpenAlex ID, DOI, ORCID, ROR, PMID, or ISSN, bare or in URL form, with the scheme prefix accepted in any case. No `entity_type` needed: the identifier determines its own
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+
- A PMCID is recognized, bare or as a PubMed Central URL, but OpenAlex indexes no PMCIDs, so it resolves nothing — the empty result says so and points at converting it to a PMID or DOI
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- An identifier that matches nothing returns an empty result naming the scheme, not name-search advice
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- Optional entity type filter and field-level filters, applied to name queries
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- `cites`: works that cite the seed (incoming citations)
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- `cited_by`: works the seed cites (its reference list)
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- `related_to`: OpenAlex algorithmic "related works" (~8-30 typical, may be empty for less-cited seeds)
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- Accepts OpenAlex IDs, DOIs, PMIDs
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+
- Accepts OpenAlex IDs, DOIs, and PMIDs as `seed_id`, bare or in URL form; validates the seed via a singleton `/works/{id}` lookup before walking, so non-existent seeds surface as `NotFound`. A PMCID seed is recognized but OpenAlex indexes no PMCIDs, so it resolves nothing — the `NotFound` says so and points at converting it to a PMID or DOI
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- Stacks with `filters`/`sort`/`select` to narrow the graph (e.g., `publication_year=">2020"`, `is_oa="true"`)
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---
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@@ -118,7 +119,7 @@ Built on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core):
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OpenAlex-specific:
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-
- Typed API client with automatic ID normalization (DOI, ORCID, ROR, PMID, PMCID, ISSN, OpenAlex URLs)
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+
- Typed API client with automatic ID normalization (DOI, ORCID, ROR, PMID, PMCID, ISSN, OpenAlex and PubMed/PubMed Central URLs). A PMCID normalizes but resolves nothing — OpenAlex indexes none — so use the work's PMID or DOI
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- Abstract reconstruction from inverted indices — plaintext instead of OpenAlex's position-keyed encoding
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- HTTP status codes mapped to specific MCP error classes (400 → InvalidParams, 422 → ValidationError, 429 → RateLimited, etc.) with upstream messages surfaced
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- Every API-calling tool reports what the call spent against the OpenAlex daily budget and what is left of it, so a paginated sweep can be priced before it runs instead of ending in a 429. An account holding prepaid balance sees that too, since it keeps serving once the day's allowance is gone
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@@ -164,7 +165,7 @@ Add to your MCP client config (e.g., `claude_desktop_config.json`):
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### Prerequisites
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-
- [Bun v1.
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+
- [Bun v1.4.0](https://bun.sh/) or higher (for development)
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### Installation
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@@ -242,7 +243,7 @@ See [`CLAUDE.md`](./CLAUDE.md) for development guidelines and architectural rule
|
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## Contributing
|
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-
Issues
|
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|
+
Issues are welcome. Run checks before submitting:
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|
```sh
|
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bun run devcheck
|
|
@@ -0,0 +1,13 @@
|
|
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1
|
+
---
|
|
2
|
+
summary: "PMCID is now recognized as a PubMed Central URL too, and every PMCID miss says OpenAlex indexes none and points at converting to a PMID or DOI instead of the generic verify-the-ID advice."
|
|
3
|
+
breaking: false
|
|
4
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+
security: false
|
|
5
|
+
---
|
|
6
|
+
|
|
7
|
+
# 0.7.12 — 2026-09-08
|
|
8
|
+
|
|
9
|
+
## Fixed
|
|
10
|
+
|
|
11
|
+
- **`normalizeId()` gains a PubMed Central URL branch** (#67) — `https://pmc.ncbi.nlm.nih.gov/articles/PMC…/` and the legacy `https://www.ncbi.nlm.nih.gov/pmc/articles/PMC…/` now normalize to `pmcid:PMC…` like the bare form, instead of being forwarded verbatim as a work ID, across `openalex_search_entities` (`id`), `openalex_resolve_name` (`query`), and `openalex_get_citation_graph` (`seed_id`).
|
|
12
|
+
- **A `pmcid:`-scheme 404 now carries a PMCID-specific recovery hint** (#67) — OpenAlex indexes no PMCIDs, so the shared 404 mapping and the `resolve_name` miss notice now say to convert to a PMID or DOI instead of the generic "verify the ID format" text, which could never help a well-formed PMCID.
|
|
13
|
+
- Tool descriptions and README bullets no longer present PMCID as an identifier that resolves — it's recognized, bare or as a PubMed Central URL, but resolves nothing.
|
|
@@ -0,0 +1,22 @@
|
|
|
1
|
+
---
|
|
2
|
+
summary: "Framework adoption and plugin configuration"
|
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3
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+
breaking: false
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|
4
|
+
security: false
|
|
5
|
+
---
|
|
6
|
+
|
|
7
|
+
# 0.7.13 — 2026-09-13
|
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8
|
+
|
|
9
|
+
## Changed
|
|
10
|
+
|
|
11
|
+
- **Plugin configuration** now exposes the OpenAlex API key, mailto, base URL, and log level through Claude Code user settings and Codex environment forwarding; the MCPB manifest wires the same options into its server environment.
|
|
12
|
+
- **HTTP links** no longer duplicate the trailing slash in `MCP_PUBLIC_URL`, and the landing-page curl example uses a compatible initialization handshake (framework fixes from 0.12.8 and 0.12.9).
|
|
13
|
+
- **Environment parsing** treats empty strings and whole-value `${…}` placeholders as unset, so optional OpenAlex settings remain absent and defaulted settings use their schema defaults.
|
|
14
|
+
- **Framework skills and maintenance tooling** now use the `framework-skills/` layout and current scaffold checks, packaging validation, issue forms, and contributor guidance; development requires Bun 1.4.0 or newer.
|
|
15
|
+
|
|
16
|
+
## Dependencies
|
|
17
|
+
|
|
18
|
+
- `@cyanheads/mcp-ts-core` ^0.12.7 → ^0.13.0
|
|
19
|
+
- `zod` ^4.5.4 → ^4.6.1
|
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20
|
+
- `@biomejs/biome` ^2.5.12 → ^2.5.13
|
|
21
|
+
- `@types/node` ^26.4.1 → ^26.5.1
|
|
22
|
+
- `ignore` ^7.0.8 → ^7.0.9
|
package/changelog/template.md
CHANGED
|
@@ -117,30 +117,13 @@ security: false
|
|
|
117
117
|
in that unrelated item's metadata.
|
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118
118
|
|
|
119
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|
TAG ANNOTATIONS — the annotated tag body renders as the GitHub Release body
|
|
120
|
-
via `gh release create --notes-from-tag`.
|
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121
|
-
|
|
122
|
-
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-
|
|
124
|
-
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|
-
|
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126
|
-
|
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|
-
Dependency bumps: ← section header
|
|
128
|
-
← blank line
|
|
129
|
-
- `@cyanheads/mcp-ts-core` ^0.9.1 → ^0.9.6 ← bullet
|
|
130
|
-
← blank line
|
|
131
|
-
Changed: ← only sections with entries
|
|
132
|
-
← blank line
|
|
133
|
-
- `format()` output includes `query` in text mode
|
|
134
|
-
← blank line
|
|
135
|
-
Added:
|
|
136
|
-
← blank line
|
|
137
|
-
- `manifest.json` scaffolded for MCPB bundle support
|
|
138
|
-
- Install badges (Claude Desktop, Cursor, VS Code)
|
|
139
|
-
← blank line
|
|
140
|
-
<N> tests pass; `bun run devcheck` clean. ← footer
|
|
141
|
-
|
|
142
|
-
Never a flat comma-separated string. Always structured markdown with
|
|
143
|
-
sections. The tag must scan well as a rendered GitHub Release page.
|
|
120
|
+
via `gh release create --notes-from-tag`. It is a condensed digest of this
|
|
121
|
+
entry, never a copy, and its format is owned by the `release-and-publish`
|
|
122
|
+
skill (step 4, "Create the annotated tag"): the entry's `summary:` as the
|
|
123
|
+
theme line without the version, flat headline bullets — no Keep-a-Changelog
|
|
124
|
+
section headers, no gates line — at most one deps line, issue backlinks,
|
|
125
|
+
and the changelog link last. In release-PR mode the `git-wrapup` skill
|
|
126
|
+
authors that digest as the PR body's `## Changes` and the tag copies it.
|
|
144
127
|
-->
|
|
145
128
|
|
|
146
129
|
## Added
|
|
@@ -1 +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;
|
|
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;AAG3C,QAAA,MAAM,kBAAkB;;;;iBActB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CAO9C"}
|
|
@@ -3,6 +3,7 @@
|
|
|
3
3
|
* @module config/server-config
|
|
4
4
|
*/
|
|
5
5
|
import { z } from '@cyanheads/mcp-ts-core';
|
|
6
|
+
import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
|
|
6
7
|
const ServerConfigSchema = z.object({
|
|
7
8
|
apiKey: z
|
|
8
9
|
.string()
|
|
@@ -16,10 +17,10 @@ const ServerConfigSchema = z.object({
|
|
|
16
17
|
});
|
|
17
18
|
let _config;
|
|
18
19
|
export function getServerConfig() {
|
|
19
|
-
_config ??= ServerConfigSchema
|
|
20
|
-
apiKey:
|
|
21
|
-
mailto:
|
|
22
|
-
baseUrl:
|
|
20
|
+
_config ??= parseEnvConfig(ServerConfigSchema, {
|
|
21
|
+
apiKey: 'OPENALEX_API_KEY',
|
|
22
|
+
mailto: 'OPENALEX_MAILTO',
|
|
23
|
+
baseUrl: 'OPENALEX_BASE_URL',
|
|
23
24
|
});
|
|
24
25
|
return _config;
|
|
25
26
|
}
|
|
@@ -1 +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;
|
|
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;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AAE/D,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IAClC,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,OAAO,CAAC,EAAE,CAAC;SACX,QAAQ,CACP,sMAAsM,CACvM;IACH,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,OAAO,CAAC,EAAE,CAAC;SACX,QAAQ,CACP,yKAAyK,CAC1K;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,cAAc,CAAC,kBAAkB,EAAE;QAC7C,MAAM,EAAE,kBAAkB;QAC1B,MAAM,EAAE,iBAAiB;QACzB,OAAO,EAAE,mBAAmB;KAC7B,CAAC,CAAC;IACH,OAAO,OAAO,CAAC;AACjB,CAAC"}
|
|
@@ -94,7 +94,7 @@ export declare const getCitationGraphTool: import("@cyanheads/mcp-ts-core").Tool
|
|
|
94
94
|
readonly reason: "entity_not_found";
|
|
95
95
|
readonly code: JsonRpcErrorCode.NotFound;
|
|
96
96
|
readonly when: "OpenAlex has no work matching the seed_id.";
|
|
97
|
-
readonly recovery: "Verify seed_id with openalex_resolve_name, or pass a known OpenAlex work ID (W…), DOI, PMID, or
|
|
97
|
+
readonly recovery: "Verify seed_id with openalex_resolve_name, or pass a known OpenAlex work ID (W…), DOI, or PMID. OpenAlex indexes no PMCIDs, so convert a PMCID to a PMID or DOI before passing it.";
|
|
98
98
|
}], {
|
|
99
99
|
readonly echo: z.ZodString;
|
|
100
100
|
readonly totalCount: z.ZodNumber;
|
|
@@ -120,14 +120,14 @@ export const getCitationGraphTool = tool('openalex_get_citation_graph', {
|
|
|
120
120
|
reason: 'entity_not_found',
|
|
121
121
|
code: JsonRpcErrorCode.NotFound,
|
|
122
122
|
when: 'OpenAlex has no work matching the seed_id.',
|
|
123
|
-
recovery: 'Verify seed_id with openalex_resolve_name, or pass a known OpenAlex work ID (W…), DOI, PMID, or
|
|
123
|
+
recovery: 'Verify seed_id with openalex_resolve_name, or pass a known OpenAlex work ID (W…), DOI, or PMID. OpenAlex indexes no PMCIDs, so convert a PMCID to a PMID or DOI before passing it.',
|
|
124
124
|
},
|
|
125
125
|
],
|
|
126
126
|
input: z.object({
|
|
127
127
|
seed_id: z
|
|
128
128
|
.string()
|
|
129
129
|
.min(1)
|
|
130
|
-
.describe('Seed work identifier. Accepts OpenAlex ID ("W2741809807"), DOI ("10.1038/nature12373" or full URL), PMID ("12345678" or "https://pubmed.ncbi.nlm.nih.gov/12345678"), or
|
|
130
|
+
.describe('Seed work identifier. Accepts OpenAlex ID ("W2741809807"), DOI ("10.1038/nature12373" or full URL), or PMID ("12345678" or "https://pubmed.ncbi.nlm.nih.gov/12345678"). A PMCID is recognized too, bare or as a PubMed Central URL, but OpenAlex indexes no PMCIDs, so it resolves nothing — pass the work\'s PMID or DOI instead. Use openalex_resolve_name first if you only have a title.'),
|
|
131
131
|
direction: z
|
|
132
132
|
.enum(DIRECTIONS)
|
|
133
133
|
.describe('"cites": works that cite seed_id (incoming citations). "cited_by": works that seed_id cites (its reference list). "related_to": OpenAlex algorithmically-related works (~8-30 typical, may be empty for less-cited seeds).'),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
{"version":3,"file":"resolve-name.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/resolve-name.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AASjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA0Q1B,CAAC"}
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@@ -6,10 +6,10 @@
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6
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import { tool, z } from '@cyanheads/mcp-ts-core';
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7
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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import { renderBudgetTrailer } from '../render-budget.js';
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9
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-
import { getOpenAlexService, inferIdentifier } from '../../../services/openalex/openalex-service.js';
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9
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+
import { getOpenAlexService, inferIdentifier, PMCID_NOT_INDEXED_HINT, } from '../../../services/openalex/openalex-service.js';
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10
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import { ENTITY_TYPES } from '../../../services/openalex/types.js';
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export const resolveNameTool = tool('openalex_resolve_name', {
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-
description:
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+
description: "Resolve a name or an identifier to an OpenAlex ID. ALWAYS use this before filtering by entity — names are ambiguous, IDs are not. A name returns up to 10 autocomplete matches with disambiguation hints. An identifier — OpenAlex ID, DOI, ORCID, ROR, PMID, or ISSN, bare or in URL form — resolves directly to the one record it addresses, and needs no entity_type. A PMCID is recognized as well, bare or as a PubMed Central URL, but OpenAlex indexes no PMCIDs, so it resolves nothing — pass the work's PMID or DOI instead.",
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sourceUrl: 'https://github.com/cyanheads/openalex-mcp-server/blob/main/src/mcp-server/tools/definitions/resolve-name.tool.ts',
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annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
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errors: [
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@@ -92,7 +92,7 @@ export const resolveNameTool = tool('openalex_resolve_name', {
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query: z
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.string()
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94
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.min(1)
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95
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-
.describe('Name or partial name to resolve. Also accepts an identifier, bare or in URL form — OpenAlex ID ("W2741809807", "F4320332161"), DOI ("10.1038/nature12373"), ORCID ("0000-0002-1825-0097"), ROR ("https://ror.org/00hx57361"), PMID ("12345678" or "https://pubmed.ncbi.nlm.nih.gov/12345678"),
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95
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+
.describe('Name or partial name to resolve. Also accepts an identifier, bare or in URL form — OpenAlex ID ("W2741809807", "F4320332161"), DOI ("10.1038/nature12373"), ORCID ("0000-0002-1825-0097"), ROR ("https://ror.org/00hx57361"), PMID ("12345678" or "https://pubmed.ncbi.nlm.nih.gov/12345678"), ISSN ("1234-5678") — which resolves straight to that one record instead of running a name search. A PMCID ("PMC1234567" or a PubMed Central URL) is recognized but OpenAlex indexes no PMCIDs, so it resolves nothing — pass the work\'s PMID or DOI instead.'),
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filters: z
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.record(z.string(), z.string())
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.optional()
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@@ -191,7 +191,12 @@ export const resolveNameTool = tool('openalex_resolve_name', {
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notices.push(`Resolved "${input.query}" by ${scheme} — it identifies one ${entity} directly, so ${ignored.join(' and ')} did not apply.`);
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}
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if (result.results.length === 0) {
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-
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+
// A PMCID is the one identifier whose miss says nothing about the identifier: it is
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// well formed and OpenAlex still holds no record for it, so "check it for a typo"
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196
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// sends the caller to re-check something that was never wrong.
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+
notices.push(identifier.scheme === 'pmcid'
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+
? `No ${entity} in OpenAlex for PMCID "${input.query}". ${PMCID_NOT_INDEXED_HINT}`
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199
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+
: `No ${entity} in OpenAlex for ${scheme} "${input.query}". An identifier either resolves or does not — check it for a typo, or search for the entity by name instead.`);
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}
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196
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}
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197
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else if (result.results.length === 0) {
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"resolve-name.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/resolve-name.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,mBAAmB,EAAE,MAAM,qCAAqC,CAAC;AAC1E,OAAO,
|
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1
|
+
{"version":3,"file":"resolve-name.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/resolve-name.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,mBAAmB,EAAE,MAAM,qCAAqC,CAAC;AAC1E,OAAO,EACL,kBAAkB,EAClB,eAAe,EACf,sBAAsB,GACvB,MAAM,yCAAyC,CAAC;AACjD,OAAO,EAAE,YAAY,EAAE,MAAM,8BAA8B,CAAC;AAE5D,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,uBAAuB,EAAE;IAC3D,WAAW,EACT,wgBAAwgB;IAC1gB,SAAS,EACP,kHAAkH;IACpH,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAC9E,MAAM,EAAE;QACN;YACE,MAAM,EAAE,cAAc;YACtB,IAAI,EAAE,gBAAgB,CAAC,WAAW;YAClC,IAAI,EAAE,8FAA8F;YACpG,SAAS,EAAE,IAAI;YACf,QAAQ,EACN,sFAAsF;SACzF;QACD;YACE,MAAM,EAAE,2BAA2B;YACnC,IAAI,EAAE,gBAAgB,CAAC,WAAW;YAClC,IAAI,EAAE,sDAAsD;YAC5D,SAAS,EAAE,KAAK;YAChB,QAAQ,EACN,6NAA6N;SAChO;QACD;YACE,MAAM,EAAE,kBAAkB;YAC1B,IAAI,EAAE,gBAAgB,CAAC,OAAO;YAC9B,IAAI,EAAE,uDAAuD;YAC7D,SAAS,EAAE,IAAI;YACf,QAAQ,EACN,kHAAkH;SACrH;QACD;YACE,MAAM,EAAE,sBAAsB;YAC9B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;YACzC,IAAI,EAAE,6HAA6H;YACnI,SAAS,EAAE,IAAI;YACf,QAAQ,EACN,uFAAuF;SAC1F;QACD;YACE,MAAM,EAAE,uBAAuB;YAC/B,IAAI,EAAE,gBAAgB,CAAC,YAAY;YACnC,IAAI,EAAE,2CAA2C;YACjD,QAAQ,EACN,uHAAuH;SAC1H;QACD;YACE,MAAM,EAAE,oBAAoB;YAC5B,IAAI,EAAE,gBAAgB,CAAC,SAAS;YAChC,IAAI,EAAE,oDAAoD;YAC1D,QAAQ,EAAE,yEAAyE;SACpF;QACD;YACE,MAAM,EAAE,uBAAuB;YAC/B,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,wFAAwF;YAC9F,QAAQ,EACN,mIAAmI;SACtI;QACD;YACE,MAAM,EAAE,yBAAyB;YACjC,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,sFAAsF;YAC5F,QAAQ,EACN,0LAA0L;SAC7L;QACD;YACE,MAAM,EAAE,2BAA2B;YACnC,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,mHAAmH;YACzH,QAAQ,EACN,8IAA8I;SACjJ;QACD;YACE,MAAM,EAAE,+BAA+B;YACvC,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,sGAAsG;YAC5G,QAAQ,EACN,gKAAgK;SACnK;QACD;YACE,MAAM,EAAE,4BAA4B;YACpC,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,gFAAgF;YACtF,QAAQ,EACN,kGAAkG;SACrG;KACF;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,WAAW,EAAE,CAAC;aACX,IAAI,CAAC,YAAY,CAAC;aAClB,QAAQ,EAAE;aACV,QAAQ,CACP,qLAAqL,CACtL;QACH,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,8hBAA8hB,CAC/hB;QACH,OAAO,EAAE,CAAC;aACP,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC;aAC9B,QAAQ,EAAE;aACV,QAAQ,CACP,8LAA8L,CAC/L;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,cAAc,CAAC;YACvC,WAAW,EAAE,CAAC;iBACX,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,gDAAgD,CAAC;YAC7D,YAAY,EAAE,CAAC;iBACZ,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,oLAAoL,CACrL;YACH,WAAW,EAAE,CAAC;iBACX,MAAM,EAAE;iBACR,QAAQ,CACP,6FAA6F,CAC9F;YACH,cAAc,EAAE,CAAC;iBACd,MAAM,EAAE;iBACR,QAAQ,CAAC,0DAA0D,CAAC;YACvE,WAAW,EAAE,CAAC;iBACX,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,8CAA8C,CAAC;YAC3D,IAAI,EAAE,CAAC;iBACJ,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,4OAA4O,CAC7O;SACJ,CAAC;aACD,QAAQ,CACP,wGAAwG,CACzG,CACJ;aACA,QAAQ,CAAC,iCAAiC,CAAC;KAC/C,CAAC;IAEF,qFAAqF;IACrF,2FAA2F;IAC3F,uFAAuF;IACvF,qFAAqF;IACrF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,gMAAgM,CACjM;QACH,MAAM,EAAE,CAAC;aACN,MAAM,CAAC;YACN,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,CACP,gKAAgK,CACjK;YACH,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;YACzF,eAAe,EAAE,CAAC;iBACf,MAAM,EAAE;iBACR,QAAQ,CAAC,wDAAwD,CAAC;YACrE,mBAAmB,EAAE,CAAC;iBACnB,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,mQAAmQ,CACpQ;SACJ,CAAC;aACD,QAAQ,EAAE;aACV,QAAQ,CACP,oNAAoN,CACrN;KACJ;IAED,iBAAiB,EAAE;QACjB,MAAM,EAAE,EAAE,MAAM,EAAE,mBAAmB,EAAE;KACxC;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,OAAO,GAAG,kBAAkB,EAAE,CAAC;QACrC,wFAAwF;QACxF,0FAA0F;QAC1F,uFAAuF;QACvF,MAAM,UAAU,GAAG,eAAe,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC;QAEhD,MAAM,MAAM,GAAG,UAAU;YACvB,CAAC,CAAC,MAAM,OAAO,CAAC,iBAAiB,CAAC,UAAU,EAAE,GAAG,CAAC;YAClD,CAAC,CAAC,MAAM,OAAO,CAAC,YAAY,CACxB;gBACE,UAAU,EAAE,KAAK,CAAC,WAAW;gBAC7B,KAAK,EAAE,KAAK,CAAC,KAAK;gBAClB,OAAO,EAAE,KAAK,CAAC,OAAO;aACvB,EACD,GAAG,CACJ,CAAC;QAEN,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE;YAC5B,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,UAAU,EAAE,UAAU,EAAE,UAAU,IAAI,KAAK,CAAC,WAAW,IAAI,KAAK;YAChE,WAAW,EAAE,UAAU,CAAC,CAAC,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,cAAc;YAC5D,UAAU,EAAE,MAAM,CAAC,OAAO,CAAC,MAAM;SAClC,CAAC,CAAC;QAEH,MAAM,OAAO,GAAa,EAAE,CAAC;QAC7B,IAAI,UAAU,EAAE,CAAC;YACf,MAAM,MAAM,GACV,UAAU,CAAC,MAAM,KAAK,UAAU,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,UAAU,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC;YACrF,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,CAAC,OAAO,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;YACvD,MAAM,OAAO,GAAa,EAAE,CAAC;YAC7B,IAAI,KAAK,CAAC,WAAW,IAAI,KAAK,CAAC,WAAW,KAAK,UAAU,CAAC,UAAU,EAAE,CAAC;gBACrE,OAAO,CAAC,IAAI,CAAC,gBAAgB,KAAK,CAAC,WAAW,GAAG,CAAC,CAAC;YACrD,CAAC;YACD,IAAI,KAAK,CAAC,OAAO,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,MAAM,GAAG,CAAC;gBAAE,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;YACpF,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACvB,OAAO,CAAC,IAAI,CACV,aAAa,KAAK,CAAC,KAAK,QAAQ,MAAM,wBAAwB,MAAM,iBAAiB,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,iBAAiB,CAC5H,CAAC;YACJ,CAAC;YACD,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAChC,oFAAoF;gBACpF,kFAAkF;gBAClF,+DAA+D;gBAC/D,OAAO,CAAC,IAAI,CACV,UAAU,CAAC,MAAM,KAAK,OAAO;oBAC3B,CAAC,CAAC,MAAM,MAAM,2BAA2B,KAAK,CAAC,KAAK,MAAM,sBAAsB,EAAE;oBAClF,CAAC,CAAC,MAAM,MAAM,oBAAoB,MAAM,KAAK,KAAK,CAAC,KAAK,+GAA+G,CAC1K,CAAC;YACJ,CAAC;QACH,CAAC;aAAM,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACvC,OAAO,CAAC,IAAI,CACV,mBAAmB,KAAK,CAAC,KAAK,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,UAAU,KAAK,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,2FAA2F,CACpL,CAAC;QACJ,CAAC;QACD,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC;YAAE,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;QAE7D,OAAO,MAAM,CAAC;IAChB,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,mBAAmB,EAAE,CAAC,CAAC;QACvD,CAAC;QACD,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,YAAY,IAAI,YAAY,OAAO,CAAC,CAAC,WAAW,GAAG,CAAC,CAAC;YACvE,MAAM,OAAO,GAAa,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YACjC,IAAI,CAAC,CAAC,WAAW;gBAAE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC;YAC/C,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,cAAc,YAAY,CAAC,CAAC;YAC9C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,WAAW,KAAK,IAAI,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,WAAW,QAAQ,CAAC,CAAC;YAC9E,IAAI,CAAC,CAAC,IAAI;gBAAE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;YACjC,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;IAC9D,CAAC;CACF,CAAC,CAAC"}
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@@ -161,7 +161,7 @@ export const searchEntitiesTool = tool('openalex_search_entities', {
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161
161
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id: z
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162
162
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.string()
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163
163
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.optional()
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164
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-
.describe('Retrieve a single entity by ID. Supports: OpenAlex ID ("W2741809807"), DOI ("10.1038/nature12373"), ORCID ("0000-0002-1825-0097"), ROR ("https://ror.org/00hx57361"), PMID ("12345678" or "https://pubmed.ncbi.nlm.nih.gov/12345678"),
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+
.describe('Retrieve a single entity by ID. Supports: OpenAlex ID ("W2741809807"), DOI ("10.1038/nature12373"), ORCID ("0000-0002-1825-0097"), ROR ("https://ror.org/00hx57361"), PMID ("12345678" or "https://pubmed.ncbi.nlm.nih.gov/12345678"), ISSN ("1234-5678"). A PMCID is recognized too, bare ("PMC1234567") or as a PubMed Central URL, but OpenAlex indexes no PMCIDs, so it resolves nothing — pass the work\'s PMID or DOI instead. When provided, `query`, `search_mode`, `filters`, `sort`, `sample`, and `seed` are not applied — the returned record is the entity at that ID regardless of them, and the response `notice` names any you passed. `select` still applies: the curated per-entity-type default is returned unless you pass `select` (use `["*"]` for the complete record). To filter, drop `id` and search. Use openalex_resolve_name to find the ID if unknown.'),
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query: z
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.string()
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.optional()
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@@ -1 +1 @@
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1
|
-
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@@ -4,6 +4,14 @@
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4
4
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*/
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5
5
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import type { Context } from '@cyanheads/mcp-ts-core';
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6
6
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import { type AnalyzeParams, type AnalyzeResult, type AutocompleteParams, type AutocompleteRecord, type AutocompleteResult, type EntityRecord, type EntityType, type SearchParams, type SearchResult } from './types.js';
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7
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+
/**
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8
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+
* Recovery for a PMCID that reached OpenAlex and came back with nothing. OpenAlex indexes no
|
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9
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+
* PMCIDs — `has_pmcid:true` matches zero works and a work's `ids` object never carries the key —
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10
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+
* so a PMCID cannot resolve however well formed it is, and the generic "verify the ID format"
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11
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+
* advice sends the caller back to retry an identifier that can never work. Shared by the 404
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12
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+
* mapping here and the `openalex_resolve_name` miss notice so both say the same thing.
|
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13
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+
*/
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14
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+
export declare const PMCID_NOT_INDEXED_HINT = "OpenAlex indexes no PMCIDs, so a PMCID resolves nothing however it is written. Convert it to a PMID or DOI \u2014 the NCBI ID Converter (https://www.ncbi.nlm.nih.gov/pmc/tools/idconv/) does this \u2014 and retry with that identifier.";
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7
15
|
/**
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8
16
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* Detect ID format and return the API path segment.
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9
17
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* "10.1038/nature12373" → "doi:10.1038/nature12373"
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@@ -13,6 +21,8 @@ import { type AnalyzeParams, type AnalyzeResult, type AutocompleteParams, type A
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13
21
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* "https://ror.org/00hx57361" → "ror:https://ror.org/00hx57361"
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14
22
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* "013meh722" → "ror:013meh722"
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15
23
|
* "PMC1234567" → "pmcid:PMC1234567"
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24
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+
* "https://pmc.ncbi.nlm.nih.gov/articles/PMC1234567/" → "pmcid:PMC1234567"
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25
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+
* "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234567/" → "pmcid:PMC1234567"
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16
26
|
* "https://pubmed.ncbi.nlm.nih.gov/21491125" → "pmid:21491125"
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17
27
|
* "PMID:21491125" → "pmid:21491125"
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18
28
|
* "W2741809807" → "W2741809807"
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@@ -1 +1 @@
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1
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-
{"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;AAsBtD,OAAO,EACL,KAAK,aAAa,EAClB,KAAK,aAAa,EAClB,KAAK,kBAAkB,EACvB,KAAK,kBAAkB,EACvB,KAAK,kBAAkB,EAGvB,KAAK,YAAY,EACjB,KAAK,UAAU,EACf,KAAK,YAAY,EACjB,KAAK,YAAY,EAClB,MAAM,YAAY,CAAC;
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1
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+
{"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;AAsBtD,OAAO,EACL,KAAK,aAAa,EAClB,KAAK,aAAa,EAClB,KAAK,kBAAkB,EACvB,KAAK,kBAAkB,EACvB,KAAK,kBAAkB,EAGvB,KAAK,YAAY,EACjB,KAAK,UAAU,EACf,KAAK,YAAY,EACjB,KAAK,YAAY,EAClB,MAAM,YAAY,CAAC;AAiFpB;;;;;;GAMG;AACH,eAAO,MAAM,sBAAsB,8OACgM,CAAC;AAgBpO;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,WAAW,CAAC,EAAE,EAAE,MAAM,GAAG,MAAM,CAgF9C;AAsBD,8FAA8F;AAC9F,MAAM,WAAW,kBAAkB;IACjC,UAAU,EAAE,UAAU,CAAC;IACvB,gGAAgG;IAChG,EAAE,EAAE,MAAM,CAAC;IACX,mFAAmF;IACnF,MAAM,EAAE,MAAM,CAAC;CAChB;AAED;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,KAAK,EAAE,MAAM,GAAG,kBAAkB,GAAG,SAAS,CAa7E;AAuJD;;;;;GAKG;AACH,wBAAgB,oBAAoB,CAClC,UAAU,EAAE,UAAU,EACtB,MAAM,EAAE,YAAY,GACnB,kBAAkB,CAUpB;AAmeD,cAAM,eAAe;IACnB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IACjC,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAS;IAChC,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAS;IAEhC,cAKC;IAED,yFAAyF;IACzF,OAAO,CAAC,OAAO;IAgDf,OAAO,CAAC,2BAA2B;IA2EnC,OAAO,CAAC,aAAa;IAqCrB,sEAAsE;IAChE,MAAM,CAAC,MAAM,EAAE,YAAY,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,YAAY,CAAC,CA0FtE;IAED,4BAA4B;IACtB,OAAO,CAAC,MAAM,EAAE,aAAa,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,aAAa,CAAC,CAkDzE;IAED;;;;;;;;;;;;OAYG;IACG,iBAAiB,CACrB,UAAU,EAAE,kBAAkB,EAC9B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,kBAAkB,CAAC,CAkB7B;IAED,oCAAoC;IAC9B,YAAY,CAAC,MAAM,EAAE,kBAAkB,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,kBAAkB,CAAC,CAsBxF;CACF;AAID,wBAAgB,mBAAmB,IAAI,IAAI,CAE1C;AAED,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED;;;;;GAKG;AACH,wBAAgB,eAAe,IAAI,MAAM,CAAC,UAAU,EAAE;IAAE,MAAM,EAAE,MAAM,EAAE,CAAC;IAAC,MAAM,EAAE,MAAM,EAAE,CAAA;CAAE,CAAC,CAE5F"}
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@@ -71,6 +71,22 @@ const BARE_ROR_PATTERN = /^0[0-9a-hj-km-np-tv-z]{6}\d{2}$/;
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71
71
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* host is anchored on both ends so a look-alike domain can never be read as PubMed.
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72
72
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*/
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73
73
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const PUBMED_URL_PATTERN = /^https?:\/\/(?:www\.)?pubmed\.ncbi\.nlm\.nih\.gov\/(\d+)\/?$/i;
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74
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+
/**
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75
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+
* A PubMed Central article URL — the current `pmc.ncbi.nlm.nih.gov/articles/…` host and the
|
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76
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+
* legacy `ncbi.nlm.nih.gov/pmc/articles/…` path alike. The article segment is a PMCID, so the
|
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77
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+
* URL carries exactly the same meaning as the bare form; normalizing it is what makes the two
|
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78
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+
* fail identically instead of the URL being forwarded verbatim as a work ID. As with PubMed,
|
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79
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+
* the host is anchored on both ends so a look-alike domain can never be read as PubMed Central.
|
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80
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+
*/
|
|
81
|
+
const PMC_URL_PATTERN = /^https?:\/\/(?:www\.)?(?:pmc\.ncbi\.nlm\.nih\.gov|ncbi\.nlm\.nih\.gov\/pmc)\/articles\/(PMC\d+)\/?$/i;
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82
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+
/**
|
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83
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+
* Recovery for a PMCID that reached OpenAlex and came back with nothing. OpenAlex indexes no
|
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84
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+
* PMCIDs — `has_pmcid:true` matches zero works and a work's `ids` object never carries the key —
|
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85
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+
* so a PMCID cannot resolve however well formed it is, and the generic "verify the ID format"
|
|
86
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+
* advice sends the caller back to retry an identifier that can never work. Shared by the 404
|
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87
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+
* mapping here and the `openalex_resolve_name` miss notice so both say the same thing.
|
|
88
|
+
*/
|
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89
|
+
export const PMCID_NOT_INDEXED_HINT = 'OpenAlex indexes no PMCIDs, so a PMCID resolves nothing however it is written. Convert it to a PMID or DOI — the NCBI ID Converter (https://www.ncbi.nlm.nih.gov/pmc/tools/idconv/) does this — and retry with that identifier.';
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74
90
|
/**
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|
75
91
|
* Prefix `normalizeId()` emits → the single entity type that identifier scheme addresses.
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|
76
92
|
* Every external scheme OpenAlex indexes belongs to exactly one entity type, which is what
|
|
@@ -93,6 +109,8 @@ const ENTITY_TYPE_BY_ID_PREFIX = {
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|
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93
109
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* "https://ror.org/00hx57361" → "ror:https://ror.org/00hx57361"
|
|
94
110
|
* "013meh722" → "ror:013meh722"
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95
111
|
* "PMC1234567" → "pmcid:PMC1234567"
|
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112
|
+
* "https://pmc.ncbi.nlm.nih.gov/articles/PMC1234567/" → "pmcid:PMC1234567"
|
|
113
|
+
* "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1234567/" → "pmcid:PMC1234567"
|
|
96
114
|
* "https://pubmed.ncbi.nlm.nih.gov/21491125" → "pmid:21491125"
|
|
97
115
|
* "PMID:21491125" → "pmid:21491125"
|
|
98
116
|
* "W2741809807" → "W2741809807"
|
|
@@ -145,6 +163,12 @@ export function normalizeId(id) {
|
|
|
145
163
|
if (pubmedPmid) {
|
|
146
164
|
return `pmid:${pubmedPmid}`;
|
|
147
165
|
}
|
|
166
|
+
// PubMed Central URL → the bare PMCID form, matching the `PMC\d+` branch above. Placed with
|
|
167
|
+
// the PubMed URL branch, after the shape-matching ones, for the same reason.
|
|
168
|
+
const pmcId = PMC_URL_PATTERN.exec(trimmed)?.[1];
|
|
169
|
+
if (pmcId) {
|
|
170
|
+
return `pmcid:${pmcId}`;
|
|
171
|
+
}
|
|
148
172
|
// Already prefixed — OpenAlex's bare external-ID schemes are case-sensitive, so a caller's
|
|
149
173
|
// `PMID:`/`DOI:` spelling 404s. Fold a recognized scheme to lower case and leave the value
|
|
150
174
|
// exactly as given: DOIs and ORCIDs carry meaningful casing that is the caller's to set.
|
|
@@ -674,6 +698,14 @@ function resolveThrowReason(code, mappedReason, rawMessage) {
|
|
|
674
698
|
return classifyRateLimitReason(rawMessage);
|
|
675
699
|
return mappedReason;
|
|
676
700
|
}
|
|
701
|
+
/**
|
|
702
|
+
* Is this request path a by-ID lookup for a `pmcid:`-scheme identifier? `normalizeId()` folds a
|
|
703
|
+
* recognized scheme to lower case, so `pmcid:` is the exact prefix every PMCID lookup arrives
|
|
704
|
+
* with, bare form and PubMed Central URL alike.
|
|
705
|
+
*/
|
|
706
|
+
function isPmcidLookup(path) {
|
|
707
|
+
return path.split('/')[2]?.startsWith('pmcid:') ?? false;
|
|
708
|
+
}
|
|
677
709
|
/**
|
|
678
710
|
* Domain-language replacement for the framework's fetch-plumbing message on the failures
|
|
679
711
|
* that never carry an HTTP status. `fetch GET <url> timed out.` describes this client, not
|
|
@@ -874,6 +906,12 @@ class OpenAlexService {
|
|
|
874
906
|
path,
|
|
875
907
|
reason,
|
|
876
908
|
...ctx.recoveryFor(reason),
|
|
909
|
+
// A PMCID lookup that 404s is not a miss to verify and retry — OpenAlex indexes no
|
|
910
|
+
// PMCIDs, so every tool's generic "verify the ID" recovery hands back the one instruction
|
|
911
|
+
// that cannot help. Substituted here, where all three ID-accepting tools inherit it.
|
|
912
|
+
...(code === JsonRpcErrorCode.NotFound && isPmcidLookup(path)
|
|
913
|
+
? { recovery: { hint: PMCID_NOT_INDEXED_HINT } }
|
|
914
|
+
: {}),
|
|
877
915
|
// `RateLimited` sits in the framework's transient set, so `withRetry` would spend the
|
|
878
916
|
// full attempt budget against a budget wall that stays up until the daily reset. This
|
|
879
917
|
// flag is the framework's per-error opt-out from that loop; the contract's own
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/openalex-mcp-server",
|
|
3
|
-
"version": "0.7.
|
|
3
|
+
"version": "0.7.13",
|
|
4
4
|
"description": "Access the OpenAlex academic research catalog - 270M+ publications through MCP. STDIO & Streamable HTTP.",
|
|
5
5
|
"mcpName": "io.github.cyanheads/openalex-mcp-server",
|
|
6
6
|
"type": "module",
|
|
@@ -33,6 +33,7 @@
|
|
|
33
33
|
"bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/openalex-mcp-server.mcpb && bun run scripts/clean-mcpb.ts dist/openalex-mcp-server.mcpb",
|
|
34
34
|
"generate:field-catalog": "bun scripts/generate-field-catalog.ts",
|
|
35
35
|
"audit:refresh": "rm -f bun.lock && bun install && bun audit",
|
|
36
|
+
"audit:fix": "bun audit fix",
|
|
36
37
|
"changelog:build": "bun scripts/build-changelog.ts",
|
|
37
38
|
"changelog:check": "bun scripts/build-changelog.ts --check",
|
|
38
39
|
"test": "vitest run",
|
|
@@ -80,7 +81,7 @@
|
|
|
80
81
|
"license": "Apache-2.0",
|
|
81
82
|
"engines": {
|
|
82
83
|
"node": ">=24.0.0",
|
|
83
|
-
"bun": ">=1.
|
|
84
|
+
"bun": ">=1.4.0"
|
|
84
85
|
},
|
|
85
86
|
"packageManager": "bun@1.4.0",
|
|
86
87
|
"publishConfig": {
|
|
@@ -88,16 +89,16 @@
|
|
|
88
89
|
},
|
|
89
90
|
"trustedDependencies": ["@socketsecurity/bun-security-scanner"],
|
|
90
91
|
"dependencies": {
|
|
91
|
-
"@cyanheads/mcp-ts-core": "^0.
|
|
92
|
+
"@cyanheads/mcp-ts-core": "^0.13.0",
|
|
92
93
|
"pino-pretty": "^13.1.3",
|
|
93
|
-
"zod": "^4.
|
|
94
|
+
"zod": "^4.6.1"
|
|
94
95
|
},
|
|
95
96
|
"devDependencies": {
|
|
96
|
-
"@biomejs/biome": "^2.5.
|
|
97
|
+
"@biomejs/biome": "^2.5.13",
|
|
97
98
|
"@socketsecurity/bun-security-scanner": "^1.1.2",
|
|
98
|
-
"@types/node": "^26.
|
|
99
|
+
"@types/node": "^26.5.1",
|
|
99
100
|
"depcheck": "^1.4.7",
|
|
100
|
-
"ignore": "^7.0.
|
|
101
|
+
"ignore": "^7.0.9",
|
|
101
102
|
"tsc-alias": "^1.9.4",
|
|
102
103
|
"typescript": "^7.0.2",
|
|
103
104
|
"vitest": "^5.0.0"
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/openalex-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "0.7.
|
|
9
|
+
"version": "0.7.13",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
|
|
@@ -19,7 +19,7 @@
|
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/openalex-mcp-server",
|
|
21
21
|
"runtimeHint": "node",
|
|
22
|
-
"version": "0.7.
|
|
22
|
+
"version": "0.7.13",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
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@@ -67,7 +67,7 @@
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67
67
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"registryBaseUrl": "https://registry.npmjs.org",
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68
68
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"identifier": "@cyanheads/openalex-mcp-server",
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69
69
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"runtimeHint": "node",
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70
|
-
"version": "0.7.
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70
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+
"version": "0.7.13",
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71
71
|
"packageArguments": [
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72
72
|
{
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73
73
|
"type": "positional",
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