@cyanheads/ensembl-mcp-server 0.4.0 → 0.4.1
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 +2 -2
- package/CLAUDE.md +2 -2
- package/Dockerfile +10 -6
- package/LICENSE +1 -1
- package/README.md +2 -2
- package/changelog/0.4.x/0.4.1.md +30 -0
- package/changelog/template.md +5 -3
- package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts +5 -0
- package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-sequence.tool.js +35 -21
- package/dist/mcp-server/tools/definitions/get-sequence.tool.js.map +1 -1
- package/dist/services/ensembl/ensembl-service.d.ts +1 -1
- package/dist/services/ensembl/ensembl-service.d.ts.map +1 -1
- package/dist/services/ensembl/ensembl-service.js +11 -2
- package/dist/services/ensembl/ensembl-service.js.map +1 -1
- package/package.json +9 -7
- package/server.json +3 -3
package/AGENTS.md
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@@ -1,8 +1,8 @@
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# Developer Protocol
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**Server:** ensembl-mcp-server
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**Version:** 0.4.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.
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**Version:** 0.4.1
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.14`
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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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package/CLAUDE.md
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# Developer Protocol
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**Server:** ensembl-mcp-server
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**Version:** 0.4.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.
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**Version:** 0.4.1
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.14`
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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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package/Dockerfile
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# This stage installs all dependencies (including dev), builds the TypeScript
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# source code into JavaScript, and prepares the production assets.
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# ==============================================================================
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FROM oven/bun:1.3 AS build
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FROM oven/bun:1.3.14 AS build
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WORKDIR /usr/src/app
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# Copy dependency manifests for optimized layer caching
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COPY package.json bun.lock ./
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# Install all dependencies (including dev dependencies for building)
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# Install all dependencies (including dev dependencies for building).
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# The BuildKit cache mount persists Bun's global package cache across builds.
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RUN --mount=type=cache,target=/root/.bun/install/cache \
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bun install --frozen-lockfile --ignore-scripts
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# Copy the rest of the source code
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COPY . .
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# application. It uses a slim base image and only includes production
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# dependencies and build artifacts.
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# ==============================================================================
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FROM oven/bun:1.3-slim AS production
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FROM oven/bun:1.3.14-slim AS production
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WORKDIR /usr/src/app
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# Install only production dependencies, ignoring any lifecycle scripts (like 'prepare')
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# that are not needed in the final production image.
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RUN bun
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RUN --mount=type=cache,target=/root/.bun/install/cache \
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bun install --production --frozen-lockfile --ignore-scripts
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# Conditionally install OpenTelemetry optional peer dependencies (Tier 3).
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# These are not bundled by default to keep the base image lean. Enable at build time
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# with: docker build --build-arg OTEL_ENABLED=true
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ARG OTEL_ENABLED=true
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RUN
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RUN --mount=type=cache,target=/root/.bun/install/cache \
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if [ "$OTEL_ENABLED" = "true" ]; then \
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bun add @hono/otel \
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@opentelemetry/instrumentation-http \
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@opentelemetry/exporter-metrics-otlp-http \
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package/LICENSE
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@@ -186,7 +186,7 @@ Apache License
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same "printed page" as the copyright notice for easier
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identification within third-party archives.
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Copyright
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Copyright 2026 Casey Hand @cyanheads
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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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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### Prerequisites
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- [Bun v1.3.
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- [Bun v1.3.14](https://bun.sh/) or higher (or Node.js v24+).
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- No API key required — Ensembl REST is fully public.
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### Installation
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---
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summary: "ensembl_get_sequence forwards expand_5prime/expand_3prime to stable-ID genomic lookups and accepts a bare chr:start-end region when species is set; mcp-ts-core 0.10.10 → 0.10.14 with a Bun supply-chain guard and Dockerfile hardening"
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breaking: false
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security: false
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---
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# 0.4.1 — 2026-07-09
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## Added
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- **`ensembl_get_sequence` accepts a bare `chr:start-end` region when `species` is set** — alongside the existing `species:chr:start-end` form, so region-mode input chains directly from `ensembl_lookup_gene`/`ensembl_query_region` coordinates without repackaging into a server-specific string. A bare region given without `species` throws the new `missing_species` `ValidationError`. ([#14](https://github.com/cyanheads/ensembl-mcp-server/issues/14))
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## Changed
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- **`@cyanheads/mcp-ts-core` maintenance adoption** — 12 skills re-synced to the current framework set; see Dependencies for the version arrow.
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- **Supply-chain guard** — `bunfig.toml` sets `install.minimumReleaseAge` (3 days, `@cyanheads/mcp-ts-core` excluded) and `install.security.scanner = "@socketsecurity/bun-security-scanner"`.
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- **`devcheck.config.json`** outdated-package allowlist adds `@socketsecurity/bun-security-scanner`; `scripts/devcheck.ts`'s outdated check also skips any package held back by the `minimumReleaseAge` guard instead of flagging it as unexpected.
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- **`Dockerfile`** pins `oven/bun:1.3.14` (was floating `1.3`), adds BuildKit cache mounts to both install stages, and runs the build-stage install with `--ignore-scripts`.
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- **`.github/SECURITY.md`** and **`.gitattributes`** added; **`LICENSE`** copyright year 2025 → 2026.
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## Fixed
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- **`ensembl_get_sequence` stable-ID genomic lookups now forward `expand_5prime`/`expand_3prime`** — previously only region-mode requests received these params, so a stable-ID call returned the same sequence length regardless of the requested expansion. `EnsemblService.getSequenceById` now accepts both params and gates them to `type=genomic` (Ensembl ignores them for cdna/cds/protein). ([#13](https://github.com/cyanheads/ensembl-mcp-server/issues/13))
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## Dependencies
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- `@cyanheads/mcp-ts-core` `^0.10.10` → `^0.10.14`
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- `tsc-alias` `^1.8.17` → `^1.9.0`
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- `vitest` `^4.1.9` → `^4.1.10`
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- `@socketsecurity/bun-security-scanner` `^1.1.2` added
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package/changelog/template.md
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# usage. Flagged as `Breaking` in the rollup.
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breaking: false
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# Set `true`
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#
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#
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# Set `true` ONLY for a security fix in THIS project's own source code — a
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# vulnerability or hardening in code you ship. A dependency or transitive CVE
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# bump is routine maintenance, NOT a security release: record it under
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# `## Dependencies` (with the advisory ID) and leave this `false`. When true,
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# pairs with the `## Security` section below and flags `Security` in the rollup.
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security: false
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# Optional free-form notes for maintenance agents processing this release.
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readonly code: JsonRpcErrorCode.ValidationError;
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readonly when: "The requested sequence type is incompatible with the provided ID type.";
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readonly recovery: string;
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}, {
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readonly reason: "missing_species";
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readonly code: JsonRpcErrorCode.ValidationError;
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readonly when: "A bare chr:start-end region was given without a species.";
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readonly recovery: string;
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}], undefined>;
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//# sourceMappingURL=get-sequence.tool.d.ts.map
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{"version":3,"file":"get-sequence.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAKjE,eAAO,MAAM,kBAAkB
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{"version":3,"file":"get-sequence.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAKjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA8L7B,CAAC"}
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'Returns the sequence with its stable ID, molecule type, and character count — large sequences are ' +
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'returned in full but the length is stated so callers can budget context. The type parameter selects ' +
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'which sequence is fetched: genomic (default, includes introns), cdna (spliced transcript), ' +
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'cds (coding sequence only), protein. For region mode, set id to
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'(e.g. homo_sapiens:13:32315086-32400268)
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'cds (coding sequence only), protein. For region mode, set id to a region — either ' +
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'species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end with ' +
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'species set (e.g. id 13:32315086-32400268, species homo_sapiens). Protein sequences require a transcript or ' +
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'protein stable ID (ENST…/ENSP…), not a gene ID — use ensembl_lookup_gene with expand_transcripts=true ' +
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'to get the canonical transcript ID first.',
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annotations: { readOnlyHint: true, openWorldHint: true, idempotentHint: true },
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input: z.object({
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id: z
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.string()
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.describe('Ensembl stable ID (ENSG…, ENST…, ENSP…) or region
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'
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.describe('Ensembl stable ID (ENSG…, ENST…, ENSP…) or a genomic region for region mode. ' +
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'Region accepts species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare ' +
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'chr:start-end (e.g. 13:32315086-32400268) when the species field is set.'),
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type: z
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.optional()
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'Required for
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'Required for a bare chr:start-end region; optional for the species:chr:start-end form ' +
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'(the embedded species is used when the field is omitted). ' +
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'Optional for stable ID lookups — Ensembl infers species from the ID prefix.'),
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expand_5prime: z
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.number()
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'Use ensembl_lookup_gene with expand_transcripts=true to find the canonical transcript ID, ' +
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'then request the protein or cds sequence from that transcript ID.',
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},
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{
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reason: 'missing_species',
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code: JsonRpcErrorCode.ValidationError,
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when: 'A bare chr:start-end region was given without a species.',
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recovery: 'Set species (e.g. homo_sapiens) alongside the chr:start-end region, ' +
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'or use the combined species:chr:start-end id form.',
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},
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],
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async handler(input, ctx) {
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ctx.log.info('Fetching sequence', { id: input.id, type: input.type });
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const service = getEnsemblService();
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//
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// Region mode accepts two id shapes:
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// species:chr:start-end embedded species (e.g. homo_sapiens:13:32315086-32400268)
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// chr:start-end bare region — the species field supplies the species
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// Scaffold/patch names carry dots (e.g. GL000220.1), so the chromosome segment
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// allows "." alongside word characters. Colon count is the discriminant: the two
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// patterns are mutually exclusive (2 colons vs. 1), and a stable ID (ENSG…, no
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// colon) matches neither, routing to stable-ID mode below.
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const isPrefixedRegion = /^[a-z_]+:[\w.]+:\d+-\d+$/i.test(input.id);
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const isBareRegion = /^[\w.]+:\d+-\d+$/.test(input.id);
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if (isPrefixedRegion || isBareRegion) {
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// For the prefixed form the species is the segment before the first colon and
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// the region is everything after it; the bare form takes its species from the
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// species field and uses the whole id as the region.
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const firstColon = input.id.indexOf(':');
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const species = input.species?.trim() || (isPrefixedRegion ? input.id.slice(0, firstColon) : undefined);
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const region = isPrefixedRegion ? input.id.slice(firstColon + 1) : input.id;
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if (!species) {
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throw ctx.fail('missing_species', `Region ${input.id} needs a species — set species (e.g. homo_sapiens) or use the species:chr:start-end id form.`);
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}
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const [speciesFromId, chr, range] = parts;
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const speciesStr = input.species?.trim() || speciesFromId;
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const region = `${chr}:${range}`;
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const seq = await service
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.getSequenceByRegion(
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.getSequenceByRegion(species, region, input.expand_5prime, input.expand_3prime, ctx)
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.catch((err) => {
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const msg = err instanceof Error ? err.message : String(err);
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if (/not found|invalid|no stable id/i.test(msg)) {
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@@ -113,7 +127,7 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
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113
127
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}
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114
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// Stable ID mode
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115
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const seq = await service
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116
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-
.getSequenceById(input.id.trim(), input.type, ctx)
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130
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+
.getSequenceById(input.id.trim(), input.type, input.expand_5prime, input.expand_3prime, ctx)
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117
131
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.catch((err) => {
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118
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const msg = err instanceof Error ? err.message : String(err);
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if (/protein.*gene|cds.*gene|type.*mismatch|incompatible/i.test(msg) ||
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"get-sequence.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.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;AAE1E,MAAM,cAAc,GAAG,CAAC,SAAS,EAAE,MAAM,EAAE,KAAK,EAAE,SAAS,CAAU,CAAC;AAEtE,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,cAAc;IACrB,WAAW,EACT,oGAAoG;QACpG,oGAAoG;QACpG,sGAAsG;QACtG,6FAA6F;QAC7F,
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1
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+
{"version":3,"file":"get-sequence.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.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;AAE1E,MAAM,cAAc,GAAG,CAAC,SAAS,EAAE,MAAM,EAAE,KAAK,EAAE,SAAS,CAAU,CAAC;AAEtE,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,cAAc;IACrB,WAAW,EACT,oGAAoG;QACpG,oGAAoG;QACpG,sGAAsG;QACtG,6FAA6F;QAC7F,oFAAoF;QACpF,8FAA8F;QAC9F,8GAA8G;QAC9G,wGAAwG;QACxG,2CAA2C;IAC7C,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,CACP,+EAA+E;YAC7E,0FAA0F;YAC1F,0EAA0E,CAC7E;QACH,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,cAAc,CAAC;aACpB,OAAO,CAAC,SAAS,CAAC;aAClB,QAAQ,CACP,6BAA6B;YAC3B,yDAAyD;YACzD,yDAAyD;YACzD,iFAAiF;YACjF,4DAA4D,CAC/D;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,0DAA0D;YACxD,wFAAwF;YACxF,4DAA4D;YAC5D,6EAA6E,CAChF;QACH,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,mFAAmF;YACjF,kEAAkE,CACrE;QACH,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,qFAAqF;YACnF,kEAAkE,CACrE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;QACvE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,0DAA0D,CAAC;QACrF,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,QAAQ,CACP,wFAAwF;YACtF,wDAAwD;YACxD,sEAAsE,CACzE;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,CACP,qGAAqG;YACnG,yEAAyE,CAC5E;QACH,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;KAC/F,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,mDAAmD;YACzD,QAAQ,EACN,oEAAoE;gBACpE,wDAAwD;SAC3D;QACD;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,wEAAwE;YAC9E,QAAQ,EACN,kGAAkG;gBAClG,4FAA4F;gBAC5F,mEAAmE;SACtE;QACD;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,sEAAsE;gBACtE,oDAAoD;SACvD;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,mBAAmB,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;QACtE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,qCAAqC;QACrC,sFAAsF;QACtF,iFAAiF;QACjF,+EAA+E;QAC/E,iFAAiF;QACjF,+EAA+E;QAC/E,2DAA2D;QAC3D,MAAM,gBAAgB,GAAG,2BAA2B,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACpE,MAAM,YAAY,GAAG,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAEvD,IAAI,gBAAgB,IAAI,YAAY,EAAE,CAAC;YACrC,8EAA8E;YAC9E,8EAA8E;YAC9E,qDAAqD;YACrD,MAAM,UAAU,GAAG,KAAK,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;YACzC,MAAM,OAAO,GACX,KAAK,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;YAC1F,MAAM,MAAM,GAAG,gBAAgB,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YAC5E,IAAI,CAAC,OAAO,EAAE,CAAC;gBACb,MAAM,GAAG,CAAC,IAAI,CACZ,iBAAiB,EACjB,UAAU,KAAK,CAAC,EAAE,8FAA8F,CACjH,CAAC;YACJ,CAAC;YACD,MAAM,GAAG,GAAG,MAAM,OAAO;iBACtB,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,CAAC,aAAa,EAAE,KAAK,CAAC,aAAa,EAAE,GAAG,CAAC;iBACnF,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,iCAAiC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAChD,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,UAAU,KAAK,CAAC,EAAE,eAAe,GAAG,EAAE,CAAC,CAAC;gBACtE,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,OAAO,GAAG,CAAC;QACb,CAAC;QAED,iBAAiB;QACjB,MAAM,GAAG,GAAG,MAAM,OAAO;aACtB,eAAe,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,aAAa,EAAE,KAAK,CAAC,aAAa,EAAE,GAAG,CAAC;aAC3F,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IACE,sDAAsD,CAAC,IAAI,CAAC,GAAG,CAAC;gBAChE,uCAAuC,CAAC,IAAI,CAAC,GAAG,CAAC;gBACjD,8BAA8B,CAAC,IAAI,CAAC,GAAG,CAAC,EACxC,CAAC;gBACD,MAAM,GAAG,CAAC,IAAI,CACZ,eAAe,EACf,wBAAwB,KAAK,CAAC,IAAI,oEAAoE;oBACpG,8EAA8E,CACjF,CAAC;YACJ,CAAC;YACD,IAAI,yBAAyB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,MAAM,KAAK,CAAC,EAAE,wBAAwB,CAAC,CAAC;YACtE,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QACL,OAAO,GAAG,CAAC;IACb,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,gBAAgB,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QACxC,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC;QAC3D,KAAK,CAAC,IAAI,CAAC,aAAa,MAAM,CAAC,IAAI,kBAAkB,MAAM,CAAC,MAAM,CAAC,cAAc,EAAE,IAAI,IAAI,EAAE,CAAC,CAAC;QAC/F,IAAI,MAAM,CAAC,WAAW;YAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,MAAM,CAAC,WAAW,EAAE,CAAC,CAAC;QAC7E,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,6DAA6D;QAC7D,IAAI,MAAM,CAAC,GAAG,CAAC,MAAM,GAAG,GAAG,EAAE,CAAC;YAC5B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YAClB,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,MAAM,MAAM,CAAC,MAAM,CAAC,cAAc,EAAE,oBAAoB,CAAC,CAAC;YACrE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACpB,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YAClB,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YACvB,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACpB,CAAC;QACD,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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@@ -17,7 +17,7 @@ export declare class EnsemblService {
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17
17
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lookupGenesBatch(ids: string[], expandTranscripts: boolean, ctx: Context): Promise<Map<string, GeneRecord>>;
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18
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lookupSymbolsBatch(symbols: string[], species: string, expandTranscripts: boolean, ctx: Context): Promise<Map<string, GeneRecord>>;
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19
19
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lookupTranscript(id: string, ctx: Context): Promise<TranscriptRecord>;
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20
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-
getSequenceById(id: string, type: string, ctx: Context): Promise<SequenceRecord>;
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20
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+
getSequenceById(id: string, type: string, expand5prime: number, expand3prime: number, ctx: Context): Promise<SequenceRecord>;
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21
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getSequenceByRegion(species: string, region: string, expand5prime: number, expand3prime: number, ctx: Context): Promise<SequenceRecord>;
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22
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queryRegion(species: string, region: string, features: string[], biotype: string | undefined, ctx: Context): Promise<OverlapFeature[]>;
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predictVariantHgvs(notation: string, species: string, ctx: Context): Promise<VepRecord[]>;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"ensembl-service.d.ts","sourceRoot":"","sources":["../../../src/services/ensembl/ensembl-service.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AAGrE,OAAO,KAAK,EAEV,UAAU,EAEV,cAAc,EACd,cAAc,EASd,cAAc,EACd,WAAW,EACX,gBAAgB,EAChB,SAAS,EACT,SAAS,EACV,MAAM,YAAY,CAAC;AAqKpB,qBAAa,cAAc;IACzB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;gBAErB,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,cAAc;YAM1C,SAAS;IAmFvB,OAAO,CAAC,cAAc;IAuBhB,UAAU,CACd,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,EACf,iBAAiB,EAAE,OAAO,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,UAAU,CAAC;IAOhB,cAAc,CAAC,EAAE,EAAE,MAAM,EAAE,iBAAiB,EAAE,OAAO,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,UAAU,CAAC;IAOzF,gBAAgB,CACpB,GAAG,EAAE,MAAM,EAAE,EACb,iBAAiB,EAAE,OAAO,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;IAc7B,kBAAkB,CACtB,OAAO,EAAE,MAAM,EAAE,EACjB,OAAO,EAAE,MAAM,EACf,iBAAiB,EAAE,OAAO,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;IAiB7B,gBAAgB,CAAC,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,gBAAgB,CAAC;IAQrE,eAAe,
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1
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+
{"version":3,"file":"ensembl-service.d.ts","sourceRoot":"","sources":["../../../src/services/ensembl/ensembl-service.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AAGrE,OAAO,KAAK,EAEV,UAAU,EAEV,cAAc,EACd,cAAc,EASd,cAAc,EACd,WAAW,EACX,gBAAgB,EAChB,SAAS,EACT,SAAS,EACV,MAAM,YAAY,CAAC;AAqKpB,qBAAa,cAAc;IACzB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;gBAErB,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,cAAc;YAM1C,SAAS;IAmFvB,OAAO,CAAC,cAAc;IAuBhB,UAAU,CACd,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,EACf,iBAAiB,EAAE,OAAO,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,UAAU,CAAC;IAOhB,cAAc,CAAC,EAAE,EAAE,MAAM,EAAE,iBAAiB,EAAE,OAAO,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,UAAU,CAAC;IAOzF,gBAAgB,CACpB,GAAG,EAAE,MAAM,EAAE,EACb,iBAAiB,EAAE,OAAO,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;IAc7B,kBAAkB,CACtB,OAAO,EAAE,MAAM,EAAE,EACjB,OAAO,EAAE,MAAM,EACf,iBAAiB,EAAE,OAAO,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;IAiB7B,gBAAgB,CAAC,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,gBAAgB,CAAC;IAQrE,eAAe,CACnB,EAAE,EAAE,MAAM,EACV,IAAI,EAAE,MAAM,EACZ,YAAY,EAAE,MAAM,EACpB,YAAY,EAAE,MAAM,EACpB,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,CAAC;IAapB,mBAAmB,CACvB,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,MAAM,EACpB,YAAY,EAAE,MAAM,EACpB,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,CAAC;IAYpB,WAAW,CACf,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,EAAE,EAClB,OAAO,EAAE,MAAM,GAAG,SAAS,EAC3B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,EAAE,CAAC;IAWtB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC;IAOzF,oBAAoB,CACxB,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,EACb,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,EACf,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,SAAS,EAAE,CAAC;IAQjB,gBAAgB,CAAC,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC;IASjF,mBAAmB,CACvB,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,aAAa,EAAE,MAAM,GAAG,SAAS,EACjC,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,CAAC;IAOpB,eAAe,CACnB,EAAE,EAAE,MAAM,EACV,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,aAAa,EAAE,MAAM,GAAG,SAAS,EACjC,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,CAAC;IASpB,YAAY,CAAC,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,SAAS,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC;IAUxF,WAAW,CAAC,QAAQ,EAAE,MAAM,GAAG,SAAS,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,WAAW,EAAE,CAAC;CAMtF;AAMD,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,cAAc,GAAG,IAAI,CAEnF;AAED,wBAAgB,iBAAiB,IAAI,cAAc,CAKlD"}
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@@ -283,8 +283,17 @@ export class EnsemblService {
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283
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return normalizeTranscript(raw);
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284
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}
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285
285
|
// --- Sequence ---
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286
|
-
async getSequenceById(id, type, ctx) {
|
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287
|
-
const
|
|
286
|
+
async getSequenceById(id, type, expand5prime, expand3prime, ctx) {
|
|
287
|
+
const params = [`type=${encodeURIComponent(type)}`];
|
|
288
|
+
// Ensembl only honors expansion when type=genomic; it is meaningless for
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289
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+
// cdna/cds/protein, so gate the params to avoid sending them where the API ignores them.
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290
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+
if (type === 'genomic') {
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291
|
+
if (expand5prime > 0)
|
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292
|
+
params.push(`expand_5prime=${expand5prime}`);
|
|
293
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+
if (expand3prime > 0)
|
|
294
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+
params.push(`expand_3prime=${expand3prime}`);
|
|
295
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+
}
|
|
296
|
+
const path = `/sequence/id/${encodeURIComponent(id)}?${params.join('&')}`;
|
|
288
297
|
const raw = await this.fetchWithRetry(path, ctx);
|
|
289
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|
return normalizeSequence(raw, type);
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290
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|
}
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@@ -1 +1 @@
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1
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-
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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": "0.4.
|
|
3
|
+
"version": "0.4.1",
|
|
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",
|
|
@@ -69,7 +69,7 @@
|
|
|
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69
|
"url": "https://github.com/cyanheads/ensembl-mcp-server/issues"
|
|
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70
|
},
|
|
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71
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"homepage": "https://github.com/cyanheads/ensembl-mcp-server#readme",
|
|
72
|
-
"author": "
|
|
72
|
+
"author": "Casey Hand <casey@caseyjhand.com> (https://caseyjhand.com)",
|
|
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73
|
"funding": [
|
|
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|
{
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|
"type": "github",
|
|
@@ -81,7 +81,7 @@
|
|
|
81
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|
}
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|
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|
],
|
|
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83
|
"license": "Apache-2.0",
|
|
84
|
-
"packageManager": "bun@1.3.
|
|
84
|
+
"packageManager": "bun@1.3.14",
|
|
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85
|
"engines": {
|
|
86
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|
"bun": ">=1.3.0",
|
|
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"node": ">=24.0.0"
|
|
@@ -90,17 +90,19 @@
|
|
|
90
90
|
"access": "public"
|
|
91
91
|
},
|
|
92
92
|
"dependencies": {
|
|
93
|
-
"@cyanheads/mcp-ts-core": "^0.10.
|
|
93
|
+
"@cyanheads/mcp-ts-core": "^0.10.14",
|
|
94
94
|
"pino-pretty": "^13.1.3",
|
|
95
95
|
"zod": "^4.4.3"
|
|
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},
|
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"devDependencies": {
|
|
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98
|
"@biomejs/biome": "^2.5.0",
|
|
99
|
+
"@socketsecurity/bun-security-scanner": "^1.1.2",
|
|
99
100
|
"@types/node": "^26.0.0",
|
|
100
101
|
"depcheck": "^1.4.7",
|
|
101
102
|
"ignore": "^7.0.5",
|
|
102
|
-
"tsc-alias": "^1.
|
|
103
|
+
"tsc-alias": "^1.9.0",
|
|
103
104
|
"typescript": "^6.0.3",
|
|
104
|
-
"vitest": "^4.1.
|
|
105
|
-
}
|
|
105
|
+
"vitest": "^4.1.10"
|
|
106
|
+
},
|
|
107
|
+
"trustedDependencies": ["@socketsecurity/bun-security-scanner"]
|
|
106
108
|
}
|
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": "0.4.
|
|
9
|
+
"version": "0.4.1",
|
|
10
10
|
"remotes": [
|
|
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11
|
{
|
|
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12
|
"type": "streamable-http",
|
|
@@ -19,7 +19,7 @@
|
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/ensembl-mcp-server",
|
|
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21
|
"runtimeHint": "bun",
|
|
22
|
-
"version": "0.4.
|
|
22
|
+
"version": "0.4.1",
|
|
23
23
|
"packageArguments": [
|
|
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|
{
|
|
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25
|
"type": "positional",
|
|
@@ -55,7 +55,7 @@
|
|
|
55
55
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
56
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|
"identifier": "@cyanheads/ensembl-mcp-server",
|
|
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|
"runtimeHint": "bun",
|
|
58
|
-
"version": "0.4.
|
|
58
|
+
"version": "0.4.1",
|
|
59
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|
"packageArguments": [
|
|
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|
{
|
|
61
61
|
"type": "positional",
|