@cyanheads/ensembl-mcp-server 0.1.3 → 0.1.5
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 +4 -4
- package/CLAUDE.md +4 -4
- package/Dockerfile +5 -0
- package/README.md +1 -1
- package/changelog/0.1.x/0.1.4.md +19 -0
- package/changelog/0.1.x/0.1.5.md +28 -0
- package/dist/index.js +2 -0
- package/dist/index.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/get-homology.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/get-homology.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-gene.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/lookup-gene.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/lookup-gene.tool.js.map +1 -1
- package/package.json +6 -6
- package/server.json +3 -3
package/AGENTS.md
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# Developer Protocol
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**Server:** ensembl-mcp-server
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**Version:** 0.1.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9
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**Version:** 0.1.5
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
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**Engines:** Bun ≥1.3.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
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**Zod:** ^4.4.3
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| `npm run start:http` | Production mode (HTTP) |
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| `npm run changelog:build` | Regenerate `CHANGELOG.md` from `changelog/*.md` |
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| `npm run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
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| `npm run bundle` | Build and
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| `npm run bundle` | Build, pack, and clean a `.mcpb` for one-click Claude Desktop install |
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---
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## Bundling
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`npm run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. MCPB is stdio-only — HTTP and Cloudflare Workers deployments are unaffected. Consumers who don't need it can delete `manifest.json` and `.mcpbignore`; `lint:packaging` skips cleanly.
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`npm run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. The pack step is followed by `scripts/clean-mcpb.ts`, which prunes dev dependencies (`mcpb clean`) and strips dependency-shipped agent docs (`node_modules/**` `skills/`, `.claude/`, `.agents/`, `SKILL.md`) that root-anchored `.mcpbignore` patterns cannot reach. MCPB is stdio-only — HTTP and Cloudflare Workers 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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package/CLAUDE.md
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# Developer Protocol
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**Server:** ensembl-mcp-server
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**Version:** 0.1.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9
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**Version:** 0.1.5
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
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**Engines:** Bun ≥1.3.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
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**Zod:** ^4.4.3
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| `npm run start:http` | Production mode (HTTP) |
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| `npm run changelog:build` | Regenerate `CHANGELOG.md` from `changelog/*.md` |
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| `npm run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
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| `npm run bundle` | Build and
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| `npm run bundle` | Build, pack, and clean a `.mcpb` for one-click Claude Desktop install |
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---
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## Bundling
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`npm run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. MCPB is stdio-only — HTTP and Cloudflare Workers deployments are unaffected. Consumers who don't need it can delete `manifest.json` and `.mcpbignore`; `lint:packaging` skips cleanly.
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`npm run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. The pack step is followed by `scripts/clean-mcpb.ts`, which prunes dev dependencies (`mcpb clean`) and strips dependency-shipped agent docs (`node_modules/**` `skills/`, `.claude/`, `.agents/`, `SKILL.md`) that root-anchored `.mcpbignore` patterns cannot reach. MCPB is stdio-only — HTTP and Cloudflare Workers 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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package/Dockerfile
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ENV NODE_ENV=production
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# OCI image metadata (https://github.com/opencontainers/image-spec/blob/main/annotations.md)
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ARG APP_VERSION
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LABEL org.opencontainers.image.title="@cyanheads/ensembl-mcp-server"
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LABEL org.opencontainers.image.description="Look up genes, fetch sequences, predict variant consequences, find orthologs and cross-database xrefs via Ensembl REST via MCP. STDIO or Streamable HTTP."
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LABEL org.opencontainers.image.source="https://github.com/cyanheads/ensembl-mcp-server"
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LABEL org.opencontainers.image.licenses="Apache-2.0"
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LABEL org.opencontainers.image.version="${APP_VERSION}"
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# Copy dependency manifests
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COPY package.json bun.lock ./
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# Expose the port the server listens on
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EXPOSE ${MCP_HTTP_PORT}
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# Health check using a bun-native fetch (slim image ships no curl/wget)
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HEALTHCHECK --interval=30s --timeout=5s --start-period=10s --retries=3 CMD bun -e "fetch('http://localhost:'+(process.env.MCP_HTTP_PORT??'3010')+'/healthz').then((r)=>process.exit(r.ok?0:1)).catch(()=>process.exit(1))"
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# The command to start the server
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CMD ["bun", "run", "dist/index.js"]
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package/README.md
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<div align="center">
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/ensembl-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/ensembl-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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---
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summary: "mcp-ts-core ^0.9.21 → ^0.10.6; name/title identity in createApp(); Dockerfile healthcheck + APP_VERSION label; bundle script runs clean-mcpb.ts"
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breaking: false
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security: false
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---
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# 0.1.4 — 2026-06-11
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## Changed
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- **`@cyanheads/mcp-ts-core`** `^0.9.21` → `^0.10.6` — framework maintenance adoption.
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- **`createApp()`** — `name` and `title` fields set explicitly to `'ensembl-mcp-server'` for identity consistency across all display surfaces.
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- **`no_input` error contract** — `ensembl_lookup_gene` and `ensembl_get_homology` now declare the missing-input case as `ValidationError` instead of `InvalidParams`, aligning with the framework's baseline validation code.
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- **`Dockerfile`** — added `APP_VERSION` build-arg and `org.opencontainers.image.version` OCI label; added `HEALTHCHECK` using a Bun-native `fetch` to `/healthz` (no curl/wget dependency).
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- **`bundle` script** — now runs `scripts/clean-mcpb.ts` after pack to prune dev deps (`mcpb clean`) and strip dependency-shipped agent docs (`node_modules/**` `skills/`, `.claude/`, `.agents/`, `SKILL.md`) that root-anchored `.mcpbignore` patterns cannot reach.
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- **`lint-packaging.ts`** — added bundle-content and identity guards: `.mcpbignore` anchoring, critical-runtime-path protection, post-bundle agent-doc content check, and `name`/`title`/`display_name` identity alignment.
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- **`check-framework-antipatterns.ts`** — added a `z.coerce.boolean()` env-flag rule (use `z.stringbool()`) and skips matches on comment lines.
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- **`@types/node`** `^25.9.2` → `^25.9.3` (dev dep).
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- **Skills** — synced to framework `^0.10.6` skill set.
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---
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summary: "mcp-ts-core ^0.10.6 → ^0.10.9; new check-dependency-specifiers devcheck gate; plugin-manifest packaging checks; fresh-scaffold/worktree devcheck guards; 14 skills re-synced; biome 2.5 + dep refresh"
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breaking: false
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security: false
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---
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# 0.1.5 — 2026-06-20
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## Added
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- **`scripts/check-dependency-specifiers.ts`** — new `devcheck` step (`Dependency Specifiers`, flag `--no-dep-specifiers`) that hard-fails on floating specifiers (`latest`, `*`, pre-release dist-tags) in `package.json`'s dependency sections and `bun.lock`'s `workspaces` map. Catches `bun update --latest` writing a literal `latest` dist-tag into the lock — correct at write time, then re-resolving past the `package.json` range on the next install. ([#246](https://github.com/cyanheads/mcp-ts-core/issues/246))
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- **Plugin-manifest packaging checks** — `scripts/lint-packaging.ts` now validates `.claude-plugin/plugin.json` and `.codex-plugin/plugin.json` (non-empty descriptions, unscoped machine name in display fields, full `package.json` name in the install arg). Gated by the new `devcheck.config.json` `packaging.pluginManifests` flag; the `devcheck` Packaging gate now runs whenever a plugin manifest is present, not only when `manifest.json` exists. ([#240](https://github.com/cyanheads/mcp-ts-core/issues/240))
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## Changed
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- **`@cyanheads/mcp-ts-core`** `^0.10.6` → `^0.10.9` — framework maintenance adoption.
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- **`.codex-plugin/plugin.json`** — populated the empty `interface.longDescription` with a full server overview (tools, resources, the `ensembl_gene_dossier` prompt, species naming, `ENSEMBL_BASE_URL`).
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- **`scripts/devcheck.ts`** — git-dependent checks (TODOs/FIXMEs, Tracked Secrets, Framework Antipatterns) now skip via a shared `isGitRepo()` guard when `.git` is absent, instead of failing on `git grep`/`git ls-files` exit 128. ([#243](https://github.com/cyanheads/mcp-ts-core/issues/243))
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- **`scripts/build-changelog.ts`** — under `--check`, exits cleanly when no `<major.minor>.x/` version files exist yet (fresh scaffold), rather than throwing. ([#242](https://github.com/cyanheads/mcp-ts-core/issues/242))
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- **`scripts/check-skill-versions.ts`** — skips a `SKILL.md` deleted from the worktree (`existsSync` guard) instead of crashing with ENOENT on maintenance passes that prune an upstream-removed skill. ([#237](https://github.com/cyanheads/mcp-ts-core/issues/237))
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- **`scripts/check-framework-antipatterns.ts`** — self-guards for direct invocation outside a git repo.
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- **Skills** — 14 `SKILL.md` files re-synced to the framework `^0.10.9` set, including seven `metadata.version` bumps propagating body drift ([#238](https://github.com/cyanheads/mcp-ts-core/issues/238)) and the `api-context` `ctx.content` collector reference ([#239](https://github.com/cyanheads/mcp-ts-core/issues/239)).
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### Dependency bumps
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- `@biomejs/biome` `^2.4.16` → `^2.5.0`
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- `@types/node` `^25.9.3` → `^26.0.0`
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- `vitest` `^4.1.8` → `^4.1.9`
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package/dist/index.js
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import { ensemblQueryRegion } from './mcp-server/tools/definitions/query-region.tool.js';
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import { initEnsemblService } from './services/ensembl/ensembl-service.js';
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await createApp({
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name: 'ensembl-mcp-server',
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title: 'ensembl-mcp-server',
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tools: [
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ensemblListSpecies,
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ensemblLookupGene,
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package/dist/index.js.map
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,wBAAwB,EAAE,MAAM,yDAAyD,CAAC;AACnG,OAAO,EAAE,mBAAmB,EAAE,MAAM,qDAAqD,CAAC;AAC1F,OAAO,EAAE,sBAAsB,EAAE,MAAM,wDAAwD,CAAC;AAChG,OAAO,EAAE,yBAAyB,EAAE,MAAM,2DAA2D,CAAC;AACtG,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,eAAe,EAAE,MAAM,kDAAkD,CAAC;AACnF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,iBAAiB,EAAE,MAAM,oDAAoD,CAAC;AACvF,OAAO,EAAE,qBAAqB,EAAE,MAAM,wDAAwD,CAAC;AAC/F,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAE3E,MAAM,SAAS,CAAC;IACd,KAAK,EAAE;QACL,kBAAkB;QAClB,iBAAiB;QACjB,kBAAkB;QAClB,kBAAkB;QAClB,qBAAqB;QACrB,kBAAkB;QAClB,eAAe;KAChB;IACD,SAAS,EAAE,CAAC,mBAAmB,EAAE,yBAAyB,EAAE,sBAAsB,CAAC;IACnF,OAAO,EAAE,CAAC,wBAAwB,CAAC;IACnC,YAAY,EAAE;;;;oHAIoG;IAClH,KAAK,CAAC,IAAI;QACR,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IAChD,CAAC;CACF,CAAC,CAAC"}
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,wBAAwB,EAAE,MAAM,yDAAyD,CAAC;AACnG,OAAO,EAAE,mBAAmB,EAAE,MAAM,qDAAqD,CAAC;AAC1F,OAAO,EAAE,sBAAsB,EAAE,MAAM,wDAAwD,CAAC;AAChG,OAAO,EAAE,yBAAyB,EAAE,MAAM,2DAA2D,CAAC;AACtG,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,eAAe,EAAE,MAAM,kDAAkD,CAAC;AACnF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,iBAAiB,EAAE,MAAM,oDAAoD,CAAC;AACvF,OAAO,EAAE,qBAAqB,EAAE,MAAM,wDAAwD,CAAC;AAC/F,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAE3E,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,KAAK,EAAE;QACL,kBAAkB;QAClB,iBAAiB;QACjB,kBAAkB;QAClB,kBAAkB;QAClB,qBAAqB;QACrB,kBAAkB;QAClB,eAAe;KAChB;IACD,SAAS,EAAE,CAAC,mBAAmB,EAAE,yBAAyB,EAAE,sBAAsB,CAAC;IACnF,OAAO,EAAE,CAAC,wBAAwB,CAAC;IACnC,YAAY,EAAE;;;;oHAIoG;IAClH,KAAK,CAAC,IAAI;QACR,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IAChD,CAAC;CACF,CAAC,CAAC"}
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readonly recovery: string;
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}, {
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readonly reason: "no_input";
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readonly code: JsonRpcErrorCode.
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readonly code: JsonRpcErrorCode.ValidationError;
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readonly when: "Neither symbol nor id was provided.";
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readonly recovery: "Provide either symbol (with species) or a stable Ensembl gene ID.";
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}], {
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code: JsonRpcErrorCode.ValidationError,
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when: 'Neither symbol nor id was provided.',
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recovery: 'Provide either symbol (with species) or a stable Ensembl gene ID.',
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101
|
},
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-homology.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-homology.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAG1E,MAAM,cAAc,GAAG,CAAC,aAAa,EAAE,YAAY,EAAE,KAAK,CAAU,CAAC;AAErE,MAAM,mBAAmB,GAAG,CAAC,CAAC,MAAM,CAAC;IACnC,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iEAAiE,CAAC;IAChG,aAAa,EAAE,CAAC;SACb,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,gEAAgE,CAAC;IAC7E,IAAI,EAAE,CAAC;SACJ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,0EAA0E;QACxE,wDAAwD,CAC3D;IACH,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,wEAAwE;QACtE,kDAAkD,CACrD;IACH,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,iEAAiE;QAC/D,oEAAoE,CACvE;IACH,aAAa,EAAE,CAAC;SACb,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sEAAsE;QACpE,wCAAwC,CAC3C;CACJ,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,mBAAmB;IAC1B,WAAW,EACT,sGAAsG;QACtG,4GAA4G;QAC5G,wGAAwG;QACxG,6FAA6F;QAC7F,0GAA0G;QAC1G,gDAAgD;IAClD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,wDAAwD;YACtD,8DAA8D,CACjE;QACH,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,iDAAiD;YAC/C,8DAA8D;YAC9D,sCAAsC,CACzC;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,OAAO,CAAC,cAAc,CAAC;aACvB,QAAQ,CACP,qFAAqF;YACnF,6EAA6E,CAChF;QACH,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,+EAA+E;YAC7E,wDAAwD;YACxD,oDAAoD,CACvD;QACH,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,cAAc,CAAC;aACpB,OAAO,CAAC,aAAa,CAAC;aACtB,QAAQ,CACP,8BAA8B;YAC5B,wEAAwE;YACxE,uEAAuE;YACvE,mCAAmC,CACtC;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,mBAAmB,CAAC,QAAQ,CAC1B,qGAAqG,CACtG,CACF;aACA,QAAQ,CAAC,4CAA4C,CAAC;QACzD,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;QACrE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2DAA2D,CAAC;QACzF,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC3E,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,8DAA8D,CAAC;KAC/F,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;KAC/E;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,wDAAwD;YAC9D,QAAQ,EACN,oFAAoF;gBACpF,2DAA2D;SAC9D;QACD;YACE,MAAM,EAAE,UAAU;YAClB,IAAI,EAAE,gBAAgB,CAAC,
|
|
1
|
+
{"version":3,"file":"get-homology.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-homology.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAG1E,MAAM,cAAc,GAAG,CAAC,aAAa,EAAE,YAAY,EAAE,KAAK,CAAU,CAAC;AAErE,MAAM,mBAAmB,GAAG,CAAC,CAAC,MAAM,CAAC;IACnC,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iEAAiE,CAAC;IAChG,aAAa,EAAE,CAAC;SACb,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,gEAAgE,CAAC;IAC7E,IAAI,EAAE,CAAC;SACJ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,0EAA0E;QACxE,wDAAwD,CAC3D;IACH,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,wEAAwE;QACtE,kDAAkD,CACrD;IACH,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,iEAAiE;QAC/D,oEAAoE,CACvE;IACH,aAAa,EAAE,CAAC;SACb,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sEAAsE;QACpE,wCAAwC,CAC3C;CACJ,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,mBAAmB;IAC1B,WAAW,EACT,sGAAsG;QACtG,4GAA4G;QAC5G,wGAAwG;QACxG,6FAA6F;QAC7F,0GAA0G;QAC1G,gDAAgD;IAClD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,wDAAwD;YACtD,8DAA8D,CACjE;QACH,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,iDAAiD;YAC/C,8DAA8D;YAC9D,sCAAsC,CACzC;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,OAAO,CAAC,cAAc,CAAC;aACvB,QAAQ,CACP,qFAAqF;YACnF,6EAA6E,CAChF;QACH,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,+EAA+E;YAC7E,wDAAwD;YACxD,oDAAoD,CACvD;QACH,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,cAAc,CAAC;aACpB,OAAO,CAAC,aAAa,CAAC;aACtB,QAAQ,CACP,8BAA8B;YAC5B,wEAAwE;YACxE,uEAAuE;YACvE,mCAAmC,CACtC;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,mBAAmB,CAAC,QAAQ,CAC1B,qGAAqG,CACtG,CACF;aACA,QAAQ,CAAC,4CAA4C,CAAC;QACzD,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;QACrE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2DAA2D,CAAC;QACzF,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC3E,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,8DAA8D,CAAC;KAC/F,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;KAC/E;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,wDAAwD;YAC9D,QAAQ,EACN,oFAAoF;gBACpF,2DAA2D;SAC9D;QACD;YACE,MAAM,EAAE,UAAU;YAClB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,qCAAqC;YAC3C,QAAQ,EAAE,mEAAmE;SAC9E;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kBAAkB,EAAE;YAC/B,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,EAAE,EAAE,KAAK,CAAC,EAAE;YACZ,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,aAAa,EAAE,KAAK,CAAC,cAAc;YACnC,IAAI,EAAE,KAAK,CAAC,IAAI;SACjB,CAAC,CAAC;QACH,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,CAAC,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,EAAE,CAAC;YAC/C,MAAM,GAAG,CAAC,IAAI,CAAC,UAAU,EAAE,2DAA2D,CAAC,CAAC;QAC1F,CAAC;QAED,MAAM,SAAS,GAAG,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,CAAC;QACnC,MAAM,aAAa,GAAG,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC;QAC3C,IAAI,OAAe,CAAC;QACpB,IAAI,QAAyB,CAAC;QAE9B,IAAI,SAAS,EAAE,CAAC;YACd,OAAO,GAAG,SAAS,CAAC;YACpB,QAAQ,GAAG,MAAM,OAAO;iBACrB,eAAe,CAAC,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,cAAc,EAAE,GAAG,CAAC;iBAC9E,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,2CAA2C,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC1D,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,YAAY,OAAO,yBAAyB,CAAC,CAAC;gBAC5E,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;QACP,CAAC;aAAM,CAAC;YACN,OAAO,GAAG,aAAa,IAAI,EAAE,CAAC;YAC9B,QAAQ,GAAG,MAAM,OAAO;iBACrB,mBAAmB,CAAC,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,cAAc,EAAE,GAAG,CAAC;iBAClF,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,2FAA2F;gBAC3F,IAAI,4BAA4B,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,KAAK,KAAK,CAAC,OAAO,EAAE,CAAC;oBACpE,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,gBAAgB,OAAO,kBAAkB,KAAK,CAAC,OAAO,GAAG,CAAC,CAAC;gBACzF,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;QACP,CAAC;QAED,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC1B,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,MAAM,KAAK,CAAC,IAAI,eAAe,OAAO,QAAQ,KAAK,CAAC,OAAO,EAAE;gBAC3D,CAAC,KAAK,CAAC,cAAc,CAAC,CAAC,CAAC,cAAc,KAAK,CAAC,cAAc,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBAClE,qDAAqD,CACxD,CAAC;QACJ,CAAC;QACD,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC;QAElC,OAAO;YACL,QAAQ;YACR,UAAU,EAAE,QAAQ,CAAC,MAAM;YAC3B,OAAO;YACP,YAAY,EAAE,KAAK,CAAC,OAAO;YAC3B,SAAS,EAAE,KAAK,CAAC,IAAI;SACtB,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,kBAAkB,MAAM,CAAC,OAAO,KAAK,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC;QACxE,KAAK,CAAC,IAAI,CAAC,aAAa,MAAM,CAAC,SAAS,iBAAiB,MAAM,CAAC,UAAU,IAAI,CAAC,CAAC;QAEhF,IAAI,MAAM,CAAC,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,KAAK,CAAC,IAAI,CAAC,sEAAsE,CAAC,CAAC;YACnF,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,QAAQ,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;YAChC,IAAI,CAAC,CAAC,aAAa;gBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,aAAa,EAAE,CAAC,CAAC;YACnE,IAAI,CAAC,CAAC,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;YACvD,IAAI,CAAC,CAAC,MAAM,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,yBAAyB,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YAClF,IAAI,CAAC,CAAC,OAAO,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,0BAA0B,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACrF,IAAI,CAAC,CAAC,aAAa;gBAAE,KAAK,CAAC,IAAI,CAAC,6BAA6B,CAAC,CAAC,aAAa,EAAE,CAAC,CAAC;YAChF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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@@ -50,7 +50,7 @@ export declare const ensemblLookupGene: import("@cyanheads/mcp-ts-core").ToolDef
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50
50
|
readonly recovery: string;
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51
51
|
}, {
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readonly reason: "no_input";
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53
|
-
readonly code: JsonRpcErrorCode.
|
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53
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+
readonly code: JsonRpcErrorCode.ValidationError;
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54
|
readonly when: "Neither symbol, id, ids, nor symbols was provided.";
|
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55
55
|
readonly recovery: "Provide exactly one of: symbol (with species), id, ids array, or symbols array (with species).";
|
|
56
56
|
}], undefined>;
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@@ -128,7 +128,7 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
|
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128
128
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},
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{
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reason: 'no_input',
|
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131
|
-
code: JsonRpcErrorCode.
|
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|
+
code: JsonRpcErrorCode.ValidationError,
|
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132
132
|
when: 'Neither symbol, id, ids, nor symbols was provided.',
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recovery: 'Provide exactly one of: symbol (with species), id, ids array, or symbols array (with species).',
|
|
134
134
|
},
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@@ -1 +1 @@
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|
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1
|
-
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/ensembl-mcp-server",
|
|
3
|
-
"version": "0.1.
|
|
3
|
+
"version": "0.1.5",
|
|
4
4
|
"mcpName": "io.github.cyanheads/ensembl-mcp-server",
|
|
5
5
|
"description": "Look up genes, fetch sequences, predict variant consequences, find orthologs and cross-database xrefs via Ensembl REST via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
|
@@ -31,7 +31,7 @@
|
|
|
31
31
|
"format:unsafe": "biome check --write --unsafe .",
|
|
32
32
|
"lint:mcp": "bun run scripts/lint-mcp.ts",
|
|
33
33
|
"lint:packaging": "bun run scripts/lint-packaging.ts",
|
|
34
|
-
"bundle": "
|
|
34
|
+
"bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/ensembl-mcp-server.mcpb && bun run scripts/clean-mcpb.ts dist/ensembl-mcp-server.mcpb",
|
|
35
35
|
"changelog:build": "bun run scripts/build-changelog.ts",
|
|
36
36
|
"changelog:check": "bun run scripts/build-changelog.ts --check",
|
|
37
37
|
"release:github": "bun run scripts/release-github.ts",
|
|
@@ -90,17 +90,17 @@
|
|
|
90
90
|
"access": "public"
|
|
91
91
|
},
|
|
92
92
|
"dependencies": {
|
|
93
|
-
"@cyanheads/mcp-ts-core": "^0.9
|
|
93
|
+
"@cyanheads/mcp-ts-core": "^0.10.9",
|
|
94
94
|
"pino-pretty": "^13.1.3",
|
|
95
95
|
"zod": "^4.4.3"
|
|
96
96
|
},
|
|
97
97
|
"devDependencies": {
|
|
98
|
-
"@biomejs/biome": "^2.
|
|
99
|
-
"@types/node": "^
|
|
98
|
+
"@biomejs/biome": "^2.5.0",
|
|
99
|
+
"@types/node": "^26.0.0",
|
|
100
100
|
"depcheck": "^1.4.7",
|
|
101
101
|
"ignore": "^7.0.5",
|
|
102
102
|
"tsc-alias": "^1.8.17",
|
|
103
103
|
"typescript": "^6.0.3",
|
|
104
|
-
"vitest": "^4.1.
|
|
104
|
+
"vitest": "^4.1.9"
|
|
105
105
|
}
|
|
106
106
|
}
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/ensembl-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "0.1.
|
|
9
|
+
"version": "0.1.5",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
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@@ -19,7 +19,7 @@
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19
19
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"registryBaseUrl": "https://registry.npmjs.org",
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20
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"identifier": "@cyanheads/ensembl-mcp-server",
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"runtimeHint": "bun",
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22
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-
"version": "0.1.
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22
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+
"version": "0.1.5",
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"packageArguments": [
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{
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"type": "positional",
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@@ -55,7 +55,7 @@
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55
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"registryBaseUrl": "https://registry.npmjs.org",
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56
56
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"identifier": "@cyanheads/ensembl-mcp-server",
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"runtimeHint": "bun",
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58
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-
"version": "0.1.
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58
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+
"version": "0.1.5",
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59
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"packageArguments": [
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60
60
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{
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61
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"type": "positional",
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