@cyanheads/ensembl-mcp-server 0.1.2 → 0.1.4
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/0.1.3.md +12 -0
- package/changelog/0.1.x/0.1.4.md +19 -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/dist/mcp-server/tools/definitions/query-region.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/query-region.tool.js +4 -2
- package/dist/mcp-server/tools/definitions/query-region.tool.js.map +1 -1
- package/package.json +4 -4
- package/server.json +3 -3
package/AGENTS.md
CHANGED
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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.
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**Version:** 0.1.4
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.6`
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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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@@ -310,13 +310,13 @@ When you complete a skill's checklist, check the boxes and add a completion time
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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.
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**Version:** 0.1.4
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.6`
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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
CHANGED
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@@ -37,10 +37,12 @@ WORKDIR /usr/src/app
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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: "ensembl_query_region: invalid region strings raise the invalid_region contract; empty-result notice includes chr-prefix guidance"
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breaking: false
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security: false
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---
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# 0.1.3 — 2026-06-06
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## Fixed
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- **`ensembl_query_region`** — Ensembl's `"No slice found for location"` error now maps to `ctx.fail('invalid_region', …)` (code -32007) instead of falling through as a generic NotFound with `data.reason: null`. Resolves [#1](https://github.com/cyanheads/ensembl-mcp-server/issues/1).
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- **`ensembl_query_region` empty-result notice** — expanded from a vague intergenic note to include the chr-prefix convention (`13`, not `chr13`) and a pointer to `ensembl_lookup_gene` for coordinate lookup. Notice text now surfaces in both `structuredContent.notice` and `content[]`. Resolves [#2](https://github.com/cyanheads/ensembl-mcp-server/issues/2).
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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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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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}, {
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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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|
|
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
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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
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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|
reason: 'no_input',
|
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131
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-
code: JsonRpcErrorCode.
|
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131
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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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133
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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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1
|
-
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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"query-region.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8BjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"query-region.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8BjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+J7B,CAAC"}
|
|
@@ -106,7 +106,8 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
|
|
|
106
106
|
.catch((err) => {
|
|
107
107
|
const msg = err instanceof Error ? err.message : String(err);
|
|
108
108
|
if (/invalid.*region|coordinate|parse/i.test(msg) ||
|
|
109
|
-
/is not a valid start|is not a valid end|is not a valid chr/i.test(msg)
|
|
109
|
+
/is not a valid start|is not a valid end|is not a valid chr/i.test(msg) ||
|
|
110
|
+
/no slice found/i.test(msg)) {
|
|
110
111
|
throw ctx.fail('invalid_region', `Invalid region "${input.region}": ${msg}`);
|
|
111
112
|
}
|
|
112
113
|
if (/species|invalid|unrecognized/i.test(msg)) {
|
|
@@ -116,7 +117,8 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
|
|
|
116
117
|
});
|
|
117
118
|
if (features.length === 0) {
|
|
118
119
|
ctx.enrich.notice(`No ${input.feature.join(', ')} features found in ${input.region} for ${input.species}. ` +
|
|
119
|
-
'The region may be intergenic
|
|
120
|
+
'The region may be intergenic. Chromosome names use no "chr" prefix for vertebrates ' +
|
|
121
|
+
'(e.g. 13, not chr13). Use ensembl_lookup_gene to confirm locus coordinates.');
|
|
120
122
|
}
|
|
121
123
|
else if (features.length > 1000) {
|
|
122
124
|
ctx.enrich.notice(`Large result set (${features.length} features). ` +
|
|
@@ -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/ensembl-mcp-server",
|
|
3
|
-
"version": "0.1.
|
|
3
|
+
"version": "0.1.4",
|
|
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",
|
|
@@ -90,13 +90,13 @@
|
|
|
90
90
|
"access": "public"
|
|
91
91
|
},
|
|
92
92
|
"dependencies": {
|
|
93
|
-
"@cyanheads/mcp-ts-core": "^0.
|
|
93
|
+
"@cyanheads/mcp-ts-core": "^0.10.6",
|
|
94
94
|
"pino-pretty": "^13.1.3",
|
|
95
95
|
"zod": "^4.4.3"
|
|
96
96
|
},
|
|
97
97
|
"devDependencies": {
|
|
98
98
|
"@biomejs/biome": "^2.4.16",
|
|
99
|
-
"@types/node": "^25.9.
|
|
99
|
+
"@types/node": "^25.9.3",
|
|
100
100
|
"depcheck": "^1.4.7",
|
|
101
101
|
"ignore": "^7.0.5",
|
|
102
102
|
"tsc-alias": "^1.8.17",
|
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": "0.1.4",
|
|
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/ensembl-mcp-server",
|
|
21
21
|
"runtimeHint": "bun",
|
|
22
|
-
"version": "0.1.
|
|
22
|
+
"version": "0.1.4",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
|
|
@@ -55,7 +55,7 @@
|
|
|
55
55
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
56
56
|
"identifier": "@cyanheads/ensembl-mcp-server",
|
|
57
57
|
"runtimeHint": "bun",
|
|
58
|
-
"version": "0.1.
|
|
58
|
+
"version": "0.1.4",
|
|
59
59
|
"packageArguments": [
|
|
60
60
|
{
|
|
61
61
|
"type": "positional",
|