@cyanheads/ensembl-mcp-server 0.4.1 → 0.4.2
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 +1 -1
- package/CLAUDE.md +1 -1
- package/README.md +1 -1
- package/changelog/0.4.x/0.4.2.md +19 -0
- package/dist/mcp-server/resources/definitions/gene.resource.d.ts.map +1 -1
- package/dist/mcp-server/resources/definitions/gene.resource.js +3 -1
- package/dist/mcp-server/resources/definitions/gene.resource.js.map +1 -1
- package/dist/mcp-server/resources/definitions/transcript.resource.d.ts.map +1 -1
- package/dist/mcp-server/resources/definitions/transcript.resource.js +3 -1
- package/dist/mcp-server/resources/definitions/transcript.resource.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts +4 -0
- package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-homology.tool.js +52 -12
- package/dist/mcp-server/tools/definitions/get-homology.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-sequence.tool.js +8 -4
- package/dist/mcp-server/tools/definitions/get-sequence.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-xrefs.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-xrefs.tool.js +3 -1
- package/dist/mcp-server/tools/definitions/get-xrefs.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-gene.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-gene.tool.js +13 -5
- package/dist/mcp-server/tools/definitions/lookup-gene.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/predict-variant.tool.d.ts +8 -0
- package/dist/mcp-server/tools/definitions/predict-variant.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/predict-variant.tool.js +138 -16
- package/dist/mcp-server/tools/definitions/predict-variant.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 +6 -2
- package/dist/mcp-server/tools/definitions/query-region.tool.js.map +1 -1
- package/package.json +1 -1
- 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:** 0.4.
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**Version:** 0.4.2
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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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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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**Version:** 0.4.2
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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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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_predict_variant and ensembl_get_homology cap high-cardinality output (transcript consequences, PubMed IDs, homologs) by default with truthful totals and an uncap escape hatch; every declared ctx.fail site now surfaces a recovery hint"
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breaking: false
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security: false
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---
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# 0.4.2 — 2026-07-09
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## Added
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- **`ensembl_predict_variant`** gains `max_transcript_consequences` (default `10`, sentinel `0` = uncapped) and `max_pubmed_ids_per_variant` (default `10`, sentinel `0` = uncapped) input params, plus `include_all_colocated_pubmed` (default `false`) to bypass the PubMed cap regardless of the limit. Each VEP record gains output field `transcriptConsequencesTotal`; each colocated variant gains `pubmedTotal` — both report the true pre-cap count. ([#15](https://github.com/cyanheads/ensembl-mcp-server/issues/15))
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- **`ensembl_get_homology`** gains `max_results` (default `25`, sentinel `0` = uncapped). ([#15](https://github.com/cyanheads/ensembl-mcp-server/issues/15))
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- **`enrichment.truncated`/`shown`/`cap`** fields added to `ensembl_predict_variant` and `ensembl_get_homology` output, populated whenever a cap trims the response.
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- **Every declared `ctx.fail` site** across 8 tool/resource files (24 call sites — `ensembl_predict_variant`, `ensembl_get_homology`, `ensembl_get_sequence`, `ensembl_get_xrefs`, `ensembl_lookup_gene`, `ensembl_query_region`, and the `gene`/`transcript` resources) now passes `{ ...ctx.recoveryFor(reason) }`, surfacing the tool's declared `recovery` guidance onto `data.recovery.hint` (mirrored into `content[0].text` as `Recovery: …`). ([#16](https://github.com/cyanheads/ensembl-mcp-server/issues/16))
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## Changed
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- **Default output for `ensembl_predict_variant` and `ensembl_get_homology` is now capped** — transcript consequences, per-variant PubMed IDs, and homolog lists trim to their defaults instead of returning every match. A single composed `enrichment.notice` discloses what was omitted and how to retrieve the rest (raise the cap, or set it to `0` / `include_all_colocated_pubmed=true` for the full set).
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- **`ensembl_get_homology`'s `totalCount`** now reports the true available homolog count rather than the returned page length — it can exceed `homologs.length` when the result was capped. ([#15](https://github.com/cyanheads/ensembl-mcp-server/issues/15))
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{"version":3,"file":"gene.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gene.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,mBAAmB;;;;;;;
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{"version":3,"file":"gene.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gene.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,mBAAmB;;;;;;;GA6D9B,CAAC"}
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@@ -33,7 +33,9 @@ export const ensemblGeneResource = resource('ensembl://gene/{id}', {
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const gene = await service.lookupGeneById(params.id, true, ctx).catch((err) => {
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const msg = err instanceof Error ? err.message : String(err);
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if (/not found/i.test(msg)) {
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throw ctx.fail('not_found', `Gene ${params.id} not found in Ensembl
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throw ctx.fail('not_found', `Gene ${params.id} not found in Ensembl.`, {
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...ctx.recoveryFor('not_found'),
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});
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}
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throw err;
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});
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{"version":3,"file":"gene.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gene.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,CAAC,MAAM,mBAAmB,GAAG,QAAQ,CAAC,qBAAqB,EAAE;IACjE,IAAI,EAAE,cAAc;IACpB,WAAW,EACT,yGAAyG;QACzG,uDAAuD;QACvD,0EAA0E;IAC5E,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,CACP,kCAAkC;YAChC,4EAA4E;YAC5E,+CAA+C,CAClD;KACJ,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,8CAA8C;YACpD,QAAQ,EACN,+EAA+E;gBAC/E,qEAAqE;SACxE;KACF;IAED,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,wBAAwB,EAAE,EAAE,EAAE,EAAE,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QAC3D,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,IAAI,GAAG,MAAM,OAAO,CAAC,cAAc,CAAC,MAAM,CAAC,EAAE,EAAE,IAAI,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACrF,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IAAI,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC3B,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,QAAQ,MAAM,CAAC,EAAE,wBAAwB,CAAC,CAAC;
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{"version":3,"file":"gene.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gene.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,CAAC,MAAM,mBAAmB,GAAG,QAAQ,CAAC,qBAAqB,EAAE;IACjE,IAAI,EAAE,cAAc;IACpB,WAAW,EACT,yGAAyG;QACzG,uDAAuD;QACvD,0EAA0E;IAC5E,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,CACP,kCAAkC;YAChC,4EAA4E;YAC5E,+CAA+C,CAClD;KACJ,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,8CAA8C;YACpD,QAAQ,EACN,+EAA+E;gBAC/E,qEAAqE;SACxE;KACF;IAED,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,wBAAwB,EAAE,EAAE,EAAE,EAAE,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QAC3D,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,IAAI,GAAG,MAAM,OAAO,CAAC,cAAc,CAAC,MAAM,CAAC,EAAE,EAAE,IAAI,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACrF,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IAAI,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC3B,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,QAAQ,MAAM,CAAC,EAAE,wBAAwB,EAAE;oBACrE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;iBAChC,CAAC,CAAC;YACL,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QAEH,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,gCAAgC;gBACrC,IAAI,EAAE,sBAAsB;gBAC5B,WAAW,EAAE,kDAAkD;gBAC/D,QAAQ,EAAE,kBAAkB;aAC7B;YACD;gBACE,GAAG,EAAE,gCAAgC;gBACrC,IAAI,EAAE,qBAAqB;gBAC3B,WAAW,EAAE,4BAA4B;gBACzC,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}
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{"version":3,"file":"transcript.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/transcript.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,yBAAyB;;;;;;;
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{"version":3,"file":"transcript.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/transcript.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,yBAAyB;;;;;;;GAuDpC,CAAC"}
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const transcript = await service.lookupTranscript(params.id, ctx).catch((err) => {
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throw ctx.fail('not_found', `Transcript ${params.id} not found in Ensembl
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throw ctx.fail('not_found', `Transcript ${params.id} not found in Ensembl.`, {
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...ctx.recoveryFor('not_found'),
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});
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{"version":3,"file":"transcript.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/transcript.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,CAAC,MAAM,yBAAyB,GAAG,QAAQ,CAAC,2BAA2B,EAAE;IAC7E,IAAI,EAAE,oBAAoB;IAC1B,WAAW,EACT,0FAA0F;QAC1F,+FAA+F;QAC/F,2FAA2F;IAC7F,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,CACP,wCAAwC;YACtC,4EAA4E;YAC5E,+CAA+C,CAClD;KACJ,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,oDAAoD;YAC1D,QAAQ,EACN,+EAA+E;gBAC/E,6EAA6E;SAChF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,8BAA8B,EAAE,EAAE,EAAE,EAAE,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QACjE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,UAAU,GAAG,MAAM,OAAO,CAAC,gBAAgB,CAAC,MAAM,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACvF,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IAAI,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC3B,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,cAAc,MAAM,CAAC,EAAE,wBAAwB,CAAC,CAAC;
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{"version":3,"file":"transcript.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/transcript.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,CAAC,MAAM,yBAAyB,GAAG,QAAQ,CAAC,2BAA2B,EAAE;IAC7E,IAAI,EAAE,oBAAoB;IAC1B,WAAW,EACT,0FAA0F;QAC1F,+FAA+F;QAC/F,2FAA2F;IAC7F,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,CACP,wCAAwC;YACtC,4EAA4E;YAC5E,+CAA+C,CAClD;KACJ,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,oDAAoD;YAC1D,QAAQ,EACN,+EAA+E;gBAC/E,6EAA6E;SAChF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,8BAA8B,EAAE,EAAE,EAAE,EAAE,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QACjE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,UAAU,GAAG,MAAM,OAAO,CAAC,gBAAgB,CAAC,MAAM,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACvF,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IAAI,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC3B,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,cAAc,MAAM,CAAC,EAAE,wBAAwB,EAAE;oBAC3E,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;iBAChC,CAAC,CAAC;YACL,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QAEH,OAAO,UAAU,CAAC;IACpB,CAAC;IAED,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,sCAAsC;gBAC3C,IAAI,EAAE,+CAA+C;gBACrD,WAAW,EAAE,qCAAqC;gBAClD,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}
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@@ -14,6 +14,7 @@ export declare const ensemblGetHomology: import("@cyanheads/mcp-ts-core").ToolDe
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paralogues: "paralogues";
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all: "all";
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}>>;
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max_results: z.ZodDefault<z.ZodNumber>;
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}, z.core.$strip>, z.ZodObject<{
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homologs: z.ZodArray<z.ZodObject<{
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targetId: z.ZodString;
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@@ -44,5 +45,8 @@ export declare const ensemblGetHomology: import("@cyanheads/mcp-ts-core").ToolDe
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readonly recovery: "Provide exactly one: a gene symbol (with optional species) or a stable Ensembl gene ID.";
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}], {
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readonly notice: z.ZodOptional<z.ZodString>;
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readonly truncated: z.ZodOptional<z.ZodBoolean>;
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readonly shown: z.ZodOptional<z.ZodNumber>;
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readonly cap: z.ZodOptional<z.ZodNumber>;
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}>;
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//# sourceMappingURL=get-homology.tool.d.ts.map
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{"version":3,"file":"get-homology.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-homology.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,kBAAkB
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{"version":3,"file":"get-homology.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-homology.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkP7B,CAAC"}
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@@ -73,18 +73,40 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
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'orthologues: genes related by speciation (cross-species equivalents). ' +
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'paralogues: genes related by duplication (within or across species). ' +
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'all: both orthologs and paralogs.'),
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max_results: z
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.number()
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.int()
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.min(0)
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.default(25)
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.describe('Maximum number of homologs to return. Broad orthology queries ' +
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'(e.g. BRCA2 across all species) can return 150+ homologs; the default keeps ' +
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'responses focused. Set to 0 to return every homolog uncapped. ' +
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'totalCount always reports the true number available before this cap.'),
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}),
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output: z.object({
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homologs: z
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.array(HomologyEntrySchema.describe('A single homologous gene with its stable ID, species, homology type, and sequence identity metrics.'))
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.describe('Homologous genes found for the query gene.'
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-
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.describe('Homologous genes found for the query gene, capped to max_results. ' +
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'totalCount reports the full count available before the cap.'),
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totalCount: z
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.number()
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.describe('Total number of homologs available before the max_results cap. ' +
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'Exceeds the returned homologs count when the list was capped.'),
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queryId: z.string().describe('The resolved Ensembl gene ID used for the homology query.'),
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querySpecies: z.string().describe('The source species used for the query.'),
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queryType: z.string().describe('The homology type queried (orthologues, paralogues, or all).'),
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}),
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enrichment: {
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notice: z
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notice: z
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.string()
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.optional()
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.describe('Guidance when no homologs are found or the list was capped.'),
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truncated: z
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.boolean()
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.optional()
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.describe('True when the homolog list was capped at max_results.'),
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shown: z.number().optional().describe('Number of homologs returned after the max_results cap.'),
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cap: z.number().optional().describe('The max_results limit applied to the homolog list.'),
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},
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errors: [
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{
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@@ -117,10 +139,12 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
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});
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const service = getEnsemblService();
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if (!input.symbol?.trim() && !input.id?.trim()) {
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throw ctx.fail('no_input', 'Provide either symbol (with species) or a stable gene ID.'
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throw ctx.fail('no_input', 'Provide either symbol (with species) or a stable gene ID.', {
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...ctx.recoveryFor('no_input'),
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});
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}
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if (input.id?.trim() && input.symbol?.trim()) {
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throw ctx.fail('conflicting_input', 'Provide either symbol or id, not both — they may resolve to different genes.');
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throw ctx.fail('conflicting_input', 'Provide either symbol or id, not both — they may resolve to different genes.', { ...ctx.recoveryFor('conflicting_input') });
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}
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const idTrimmed = input.id?.trim();
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const symbolTrimmed = input.symbol?.trim();
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@@ -132,7 +156,9 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
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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|no valid lookup|page not found/i.test(msg)) {
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throw ctx.fail('not_found', `Gene ID "${idTrimmed}" not found in Ensembl
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throw ctx.fail('not_found', `Gene ID "${idTrimmed}" not found in Ensembl.`, {
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...ctx.recoveryFor('not_found'),
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});
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}
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throw err;
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});
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@@ -148,7 +174,7 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
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const msg = err instanceof Error ? err.message : String(err);
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// Ensembl returns {"error":"<species_name>"} for invalid gene symbols in homology endpoint
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if (/not found|no valid lookup/i.test(msg) || msg === input.species) {
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throw ctx.fail('not_found', `Gene symbol "${submittedSymbol}" not found in ${input.species}
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throw ctx.fail('not_found', `Gene symbol "${submittedSymbol}" not found in ${input.species}.`, { ...ctx.recoveryFor('not_found') });
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}
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throw err;
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});
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@@ -157,15 +183,27 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
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// fall back to the submitted symbol only when the response carried no data entry.
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queryId = result.resolvedQueryId ?? submittedSymbol;
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}
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// Ensembl returns the full homolog set; cap post-fetch so broad orthology
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// queries stay compact by default. totalCount stays the true available count
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// so a caller is never misled about completeness (max_results = 0 disables).
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const availableCount = homologs.length;
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const returned = input.max_results > 0 ? homologs.slice(0, input.max_results) : homologs;
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if (returned.length === 0) {
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ctx.enrich.notice(`No ${input.type} found for "${queryId}" in ${input.species}` +
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(input.target_species ? ` targeting ${input.target_species}` : '') +
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'. Try type=all or remove the target_species filter.');
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}
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else if (returned.length < availableCount) {
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ctx.enrich.truncated({
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shown: returned.length,
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cap: input.max_results,
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guidance: `Showing ${returned.length} of ${availableCount} homologs. ` +
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'Raise max_results (0 returns all) or set target_species to narrow to one species.',
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});
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}
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return {
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homologs,
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totalCount:
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homologs: returned,
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totalCount: availableCount,
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queryId,
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querySpecies: input.species,
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queryType: input.type,
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@@ -174,7 +212,9 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
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format: (result) => {
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const lines = [];
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lines.push(`## Homologs of ${result.queryId} (${result.querySpecies})`);
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const shown = result.homologs.length;
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const foundLabel = result.totalCount > shown ? `${shown} of ${result.totalCount}` : `${result.totalCount}`;
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lines.push(`**Type:** ${result.queryType} | **Found:** ${foundLabel}\n`);
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if (result.homologs.length === 0) {
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lines.push('No homologs found. Try type=all or remove the target_species filter.');
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return [{ type: 'text', text: lines.join('\n') }];
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@@ -1 +1 @@
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-
{"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,qEAAqE;YACrE,6BAA6B,CAChC;QACH,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,iDAAiD;YAC/C,8DAA8D;YAC9D,iCAAiC,CACpC;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,
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|
+
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@@ -1 +1 @@
|
|
|
1
|
-
{"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAoM7B,CAAC"}
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@@ -112,14 +112,16 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
|
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|
112
112
|
const species = input.species?.trim() || (isPrefixedRegion ? input.id.slice(0, firstColon) : undefined);
|
|
113
113
|
const region = isPrefixedRegion ? input.id.slice(firstColon + 1) : input.id;
|
|
114
114
|
if (!species) {
|
|
115
|
-
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
|
|
115
|
+
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.`, { ...ctx.recoveryFor('missing_species') });
|
|
116
116
|
}
|
|
117
117
|
const seq = await service
|
|
118
118
|
.getSequenceByRegion(species, region, input.expand_5prime, input.expand_3prime, ctx)
|
|
119
119
|
.catch((err) => {
|
|
120
120
|
const msg = err instanceof Error ? err.message : String(err);
|
|
121
121
|
if (/not found|invalid|no stable id/i.test(msg)) {
|
|
122
|
-
throw ctx.fail('not_found', `Region ${input.id} not found: ${msg}
|
|
122
|
+
throw ctx.fail('not_found', `Region ${input.id} not found: ${msg}`, {
|
|
123
|
+
...ctx.recoveryFor('not_found'),
|
|
124
|
+
});
|
|
123
125
|
}
|
|
124
126
|
throw err;
|
|
125
127
|
});
|
|
@@ -134,10 +136,12 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
|
|
|
134
136
|
/requesting a gene and type not equal/i.test(msg) ||
|
|
135
137
|
/multiple sequences detected/i.test(msg)) {
|
|
136
138
|
throw ctx.fail('type_mismatch', `Cannot request type "${input.type}" from a gene ID — use a transcript or protein stable ID instead. ` +
|
|
137
|
-
`Call ensembl_lookup_gene with expand_transcripts=true to get transcript IDs
|
|
139
|
+
`Call ensembl_lookup_gene with expand_transcripts=true to get transcript IDs.`, { ...ctx.recoveryFor('type_mismatch') });
|
|
138
140
|
}
|
|
139
141
|
if (/not found|no stable id/i.test(msg)) {
|
|
140
|
-
throw ctx.fail('not_found', `ID ${input.id} not found in Ensembl
|
|
142
|
+
throw ctx.fail('not_found', `ID ${input.id} not found in Ensembl.`, {
|
|
143
|
+
...ctx.recoveryFor('not_found'),
|
|
144
|
+
});
|
|
141
145
|
}
|
|
142
146
|
throw err;
|
|
143
147
|
});
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"get-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;EAqH1B,CAAC"}
|
|
@@ -75,7 +75,9 @@ export const ensemblGetXrefs = tool('ensembl_get_xrefs', {
|
|
|
75
75
|
.catch((err) => {
|
|
76
76
|
const msg = err instanceof Error ? err.message : String(err);
|
|
77
77
|
if (/not found/i.test(msg)) {
|
|
78
|
-
throw ctx.fail('not_found', `ID "${input.id}" not found in Ensembl
|
|
78
|
+
throw ctx.fail('not_found', `ID "${input.id}" not found in Ensembl.`, {
|
|
79
|
+
...ctx.recoveryFor('not_found'),
|
|
80
|
+
});
|
|
79
81
|
}
|
|
80
82
|
throw err;
|
|
81
83
|
});
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.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,eAAe,GAAG,CAAC,CAAC,MAAM,CAAC;IAC/B,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sGAAsG,CACvG;IACH,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;IACtF,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,iFAAiF;QAC/E,+BAA+B,CAClC;IACH,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oFAAoF,CAAC;IACjG,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;CACzF,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,mBAAmB,EAAE;IACvD,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,8FAA8F;QAC9F,kGAAkG;QAClG,8FAA8F;QAC9F,gGAAgG;QAChG,iEAAiE;QACjE,qFAAqF;QACrF,6FAA6F;QAC7F,uCAAuC;IACzC,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,2DAA2D;YACzD,mEAAmE;YACnE,kGAAkG,CACrG;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uEAAuE;YACrE,iEAAiE;YACjE,2DAA2D;YAC3D,gEAAgE;YAChE,+DAA+D,CAClE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,eAAe,CAAC,QAAQ,CACtB,0FAA0F,CAC3F,CACF;aACA,QAAQ,CAAC,uDAAuD,CAAC;QACpE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4CAA4C,CAAC;QAC7E,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;KAC1E,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;KACvF;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iEAAiE;YACvE,QAAQ,EACN,wEAAwE;gBACxE,mFAAmF;SACtF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;QACtE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,KAAK,GAAG,MAAM,OAAO;aACxB,YAAY,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,SAAS,EAAE,GAAG,CAAC;aACrE,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,IAAI,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC3B,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,KAAK,CAAC,EAAE,yBAAyB,CAAC,CAAC;
|
|
1
|
+
{"version":3,"file":"get-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.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,eAAe,GAAG,CAAC,CAAC,MAAM,CAAC;IAC/B,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sGAAsG,CACvG;IACH,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;IACtF,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,iFAAiF;QAC/E,+BAA+B,CAClC;IACH,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oFAAoF,CAAC;IACjG,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;CACzF,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,mBAAmB,EAAE;IACvD,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,8FAA8F;QAC9F,kGAAkG;QAClG,8FAA8F;QAC9F,gGAAgG;QAChG,iEAAiE;QACjE,qFAAqF;QACrF,6FAA6F;QAC7F,uCAAuC;IACzC,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,2DAA2D;YACzD,mEAAmE;YACnE,kGAAkG,CACrG;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uEAAuE;YACrE,iEAAiE;YACjE,2DAA2D;YAC3D,gEAAgE;YAChE,+DAA+D,CAClE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,eAAe,CAAC,QAAQ,CACtB,0FAA0F,CAC3F,CACF;aACA,QAAQ,CAAC,uDAAuD,CAAC;QACpE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4CAA4C,CAAC;QAC7E,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;KAC1E,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;KACvF;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iEAAiE;YACvE,QAAQ,EACN,wEAAwE;gBACxE,mFAAmF;SACtF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;QACtE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,KAAK,GAAG,MAAM,OAAO;aACxB,YAAY,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,SAAS,EAAE,GAAG,CAAC;aACrE,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,IAAI,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC3B,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,KAAK,CAAC,EAAE,yBAAyB,EAAE;oBACpE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;iBAChC,CAAC,CAAC;YACL,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QAEL,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACvB,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,wBAAwB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YAC/E,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,iCAAiC,KAAK,CAAC,EAAE,GAAG,UAAU,IAAI;gBACxD,+DAA+D,CAClE,CAAC;QACJ,CAAC;QACD,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QAE/B,OAAO,EAAE,KAAK,EAAE,UAAU,EAAE,KAAK,CAAC,MAAM,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;IAClE,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,2BAA2B,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC;QAC1D,KAAK,CAAC,IAAI,CAAC,cAAc,MAAM,CAAC,UAAU,IAAI,CAAC,CAAC;QAEhD,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC9B,KAAK,CAAC,IAAI,CAAC,4BAA4B,CAAC,CAAC;YACzC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,oCAAoC;QACpC,MAAM,IAAI,GAAG,IAAI,GAAG,EAA+B,CAAC;QACpD,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YAC7B,MAAM,EAAE,GAAG,CAAC,CAAC,MAAM,IAAI,SAAS,CAAC;YACjC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC;YACpC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC;QACxB,CAAC;QAED,KAAK,MAAM,CAAC,EAAE,EAAE,OAAO,CAAC,IAAI,IAAI,EAAE,CAAC;YACjC,MAAM,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE,aAAa,CAAC;YAC9C,KAAK,CAAC,IAAI,CAAC,OAAO,WAAW,IAAI,EAAE,GAAG,WAAW,IAAI,WAAW,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC7F,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;gBACxB,IAAI,IAAI,GAAG,OAAO,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,SAAS,IAAI,SAAS,IAAI,CAAC;gBAC9D,IAAI,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,SAAS;oBAAE,IAAI,IAAI,KAAK,CAAC,CAAC,SAAS,GAAG,CAAC;gBAC5E,IAAI,CAAC,CAAC,WAAW;oBAAE,IAAI,IAAI,KAAK,CAAC,CAAC,WAAW,EAAE,CAAC;gBAChD,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YACnB,CAAC;YACD,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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@@ -1 +1 @@
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|
1
|
-
{"version":3,"file":"lookup-gene.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-gene.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmEjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
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1
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+
{"version":3,"file":"lookup-gene.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-gene.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmEjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAmQ5B,CAAC"}
|
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@@ -156,7 +156,9 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
|
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156
156
|
input.symbols?.length,
|
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157
157
|
].filter(Boolean).length;
|
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158
158
|
if (inputCount > 1) {
|
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159
|
-
throw ctx.fail('conflicting_input', 'Provide exactly one of: symbol, id, ids, or symbols.'
|
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159
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+
throw ctx.fail('conflicting_input', 'Provide exactly one of: symbol, id, ids, or symbols.', {
|
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160
|
+
...ctx.recoveryFor('conflicting_input'),
|
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161
|
+
});
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160
162
|
}
|
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161
163
|
// --- Batch by IDs ---
|
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162
164
|
if (input.ids?.length) {
|
|
@@ -190,10 +192,12 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
|
|
|
190
192
|
.catch((err) => {
|
|
191
193
|
const msg = err instanceof Error ? err.message : String(err);
|
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192
194
|
if (/not found|no stable id|no results|no valid lookup/i.test(msg)) {
|
|
193
|
-
throw ctx.fail('not_found', `Gene symbol "${input.symbol}" not found in ${speciesStr}
|
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195
|
+
throw ctx.fail('not_found', `Gene symbol "${input.symbol}" not found in ${speciesStr}.`, { ...ctx.recoveryFor('not_found') });
|
|
194
196
|
}
|
|
195
197
|
if (/species|invalid|unrecognized/i.test(msg)) {
|
|
196
|
-
throw ctx.fail('invalid_species', `Species "${speciesStr}" not recognized by Ensembl
|
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198
|
+
throw ctx.fail('invalid_species', `Species "${speciesStr}" not recognized by Ensembl.`, {
|
|
199
|
+
...ctx.recoveryFor('invalid_species'),
|
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200
|
+
});
|
|
197
201
|
}
|
|
198
202
|
throw err;
|
|
199
203
|
});
|
|
@@ -206,13 +210,17 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
|
|
|
206
210
|
.catch((err) => {
|
|
207
211
|
const msg = err instanceof Error ? err.message : String(err);
|
|
208
212
|
if (/not found|no stable id/i.test(msg)) {
|
|
209
|
-
throw ctx.fail('not_found', `Gene ID "${input.id}" not found in Ensembl
|
|
213
|
+
throw ctx.fail('not_found', `Gene ID "${input.id}" not found in Ensembl.`, {
|
|
214
|
+
...ctx.recoveryFor('not_found'),
|
|
215
|
+
});
|
|
210
216
|
}
|
|
211
217
|
throw err;
|
|
212
218
|
});
|
|
213
219
|
return { gene };
|
|
214
220
|
}
|
|
215
|
-
throw ctx.fail('no_input', 'Provide symbol (with species), id, ids, or symbols.'
|
|
221
|
+
throw ctx.fail('no_input', 'Provide symbol (with species), id, ids, or symbols.', {
|
|
222
|
+
...ctx.recoveryFor('no_input'),
|
|
223
|
+
});
|
|
216
224
|
},
|
|
217
225
|
format: (result) => {
|
|
218
226
|
const lines = [];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
{"version":3,"file":"lookup-gene.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-gene.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,uBAAuB,GAAG,CAAC,CAAC,MAAM,CAAC;IACvC,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;IAChE,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;IACvE,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oEAAoE,CAAC;IACjF,WAAW,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,0DAA0D,CAAC;IAC7F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IAC/F,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;IAC3F,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAChF,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;CAC/E,CAAC,CAAC;AAEH,MAAM,gBAAgB,GAAG,CAAC,CAAC,MAAM,CAAC;IAChC,EAAE,EAAE,CAAC;SACF,MAAM,EAAE;SACR,QAAQ,CAAC,2EAA2E,CAAC;IACxF,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,6EAA6E,CAAC;IAC1F,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;IAC9F,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;IACnF,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,yDAAyD,CAAC;IACtE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;IACjF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kDAAkD,CAAC;IACzF,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;IACrF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAChF,YAAY,EAAE,CAAC;SACZ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oFAAoF,CAAC;IACjG,WAAW,EAAE,CAAC;SACX,KAAK,CAAC,uBAAuB,CAAC,QAAQ,CAAC,oCAAoC,CAAC,CAAC;SAC7E,QAAQ,EAAE;SACV,QAAQ,CAAC,gEAAgE,CAAC;CAC9E,CAAC,CAAC;AAEH,MAAM,iBAAiB,GAAG,CAAC,CAAC,MAAM,CAAC;IACjC,6FAA6F;IAC7F,SAAS,EAAE,CAAC;SACT,KAAK,CACJ,CAAC;SACE,MAAM,CAAC,EAAE,CAAC;SACV,WAAW,EAAE;SACb,QAAQ,CAAC,sEAAsE,CAAC,CACpF;SACA,QAAQ,CAAC,8EAA8E,CAAC;IAC3F,MAAM,EAAE,CAAC;SACN,KAAK,CACJ,CAAC;SACE,MAAM,CAAC,EAAE,CAAC;SACV,WAAW,EAAE;SACb,QAAQ,CACP,iGAAiG,CAClG,CACJ;SACA,QAAQ,CAAC,+EAA+E,CAAC;CAC7F,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,qBAAqB,EAAE;IAC3D,KAAK,EAAE,aAAa;IACpB,WAAW,EACT,2FAA2F;QAC3F,sGAAsG;QACtG,oGAAoG;QACpG,mGAAmG;QACnG,mGAAmG;QACnG,kGAAkG;QAClG,iGAAiG;IACnG,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,mDAAmD;YACjD,qEAAqE;YACrE,mCAAmC,CACtC;QACH,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mFAAmF;YACjF,wCAAwC,CAC3C;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,iFAAiF;YAC/E,kDAAkD;YAClD,sFAAsF;YACtF,oDAAoD,CACvD;QACH,GAAG,EAAE,CAAC;aACH,KAAK,CACJ,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mEAAmE,CAAC,CACzF;aACA,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,EAAE;aACV,QAAQ,CACP,4DAA4D;YAC1D,uFAAuF,CAC1F;QACH,OAAO,EAAE,CAAC;aACP,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4DAA4D,CAAC,CAAC;aACxF,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,EAAE;aACV,QAAQ,CACP,uCAAuC;YACrC,qEAAqE;YACrE,uFAAuF,CAC1F;QACH,kBAAkB,EAAE,CAAC;aAClB,OAAO,EAAE;aACT,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,+DAA+D;YAC7D,wEAAwE;YACxE,6CAA6C,CAChD;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,IAAI,EAAE,gBAAgB,CAAC,QAAQ,EAAE,CAAC,QAAQ,CACxC,uDAAuD,CACxD;QACD,KAAK,EAAE,iBAAiB,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAC1C,oDAAoD,CACrD;KACF,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,wDAAwD;YAC9D,QAAQ,EACN,iGAAiG;gBACjG,sGAAsG;SACzG;QACD;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,mDAAmD;YACzD,QAAQ,EACN,6DAA6D;gBAC7D,2FAA2F;SAC9F;QACD;YACE,MAAM,EAAE,UAAU;YAClB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,oDAAoD;YAC1D,QAAQ,EACN,gGAAgG;SACnG;QACD;YACE,MAAM,EAAE,mBAAmB;YAC3B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,4DAA4D;YAClE,QAAQ,EACN,qFAAqF;SACxF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,iBAAiB,EAAE;YAC9B,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,EAAE,EAAE,KAAK,CAAC,EAAE;YACZ,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,SAAS,EAAE,KAAK,CAAC,GAAG,EAAE,MAAM,IAAI,KAAK,CAAC,OAAO,EAAE,MAAM;SACtD,CAAC,CAAC;QACH,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,UAAU,GAAG;YACjB,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE;YACpB,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE;YAChB,KAAK,CAAC,GAAG,EAAE,MAAM;YACjB,KAAK,CAAC,OAAO,EAAE,MAAM;SACtB,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC;QACzB,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;YACnB,MAAM,GAAG,CAAC,IAAI,CAAC,mBAAmB,EAAE,sDAAsD,EAAE;gBAC1F,GAAG,GAAG,CAAC,WAAW,CAAC,mBAAmB,CAAC;aACxC,CAAC,CAAC;QACL,CAAC;QAED,uBAAuB;QACvB,IAAI,KAAK,CAAC,GAAG,EAAE,MAAM,EAAE,CAAC;YACtB,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,gBAAgB,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,kBAAkB,EAAE,GAAG,CAAC,CAAC;YACrF,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;YAC3C,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,CAAC;YACxC,MAAM,MAAM,GAAG,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IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACtB,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC;gBACjC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;oBACvB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;gBAC7C,CAAC;YACH,CAAC;QACH,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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@@ -7,6 +7,9 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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7
7
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export declare const ensemblPredictVariant: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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8
8
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variant: z.ZodString;
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9
9
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species: z.ZodDefault<z.ZodString>;
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10
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+
max_transcript_consequences: z.ZodDefault<z.ZodNumber>;
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11
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+
max_pubmed_ids_per_variant: z.ZodDefault<z.ZodNumber>;
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12
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+
include_all_colocated_pubmed: z.ZodDefault<z.ZodBoolean>;
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10
13
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}, z.core.$strip>, z.ZodObject<{
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11
14
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results: z.ZodArray<z.ZodObject<{
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12
15
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input: z.ZodOptional<z.ZodString>;
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@@ -34,11 +37,13 @@ export declare const ensemblPredictVariant: import("@cyanheads/mcp-ts-core").Too
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34
37
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score: z.ZodNumber;
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35
38
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}, z.core.$strip>>;
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36
39
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}, z.core.$strip>>;
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40
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+
transcriptConsequencesTotal: z.ZodOptional<z.ZodNumber>;
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37
41
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colocatedVariants: z.ZodArray<z.ZodObject<{
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38
42
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id: z.ZodOptional<z.ZodString>;
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39
43
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alleleString: z.ZodOptional<z.ZodString>;
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40
44
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clinicalSignificance: z.ZodOptional<z.ZodArray<z.ZodString>>;
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41
45
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pubmed: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
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46
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+
pubmedTotal: z.ZodOptional<z.ZodNumber>;
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42
47
|
}, z.core.$strip>>;
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|
43
48
|
}, z.core.$strip>>;
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44
49
|
totalCount: z.ZodNumber;
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@@ -54,5 +59,8 @@ export declare const ensemblPredictVariant: import("@cyanheads/mcp-ts-core").Too
|
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|
54
59
|
readonly recovery: string;
|
|
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{"version":3,"file":"predict-variant.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/predict-variant.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;
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{"version":3,"file":"predict-variant.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/predict-variant.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA+HjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyVhC,CAAC"}
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.describe('Maximum PubMed IDs to return per colocated known variant. Well-studied variants (e.g. rs334) ' +
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enrichment: {
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notice: z
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truncated: z
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shown: z
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errors: [
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{
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.catch((err) => {
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throw ctx.fail('invalid_notation', `Invalid region+allele notation "${input.variant}": ${msg}`, { ...ctx.recoveryFor('invalid_notation') });
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});
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}
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});
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const msg = err instanceof Error ? err.message : String(err);
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throw ctx.fail('not_found', `Variant identifier ${input.variant} not found in dbSNP
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});
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}
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if (/invalid|unrecognized|parse|malformed/i.test(msg)) {
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throw ctx.fail('invalid_notation', `Invalid variant identifier "${input.variant}": ${msg}`, { ...ctx.recoveryFor('invalid_notation') });
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}
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});
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.catch((err) => {
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if (/invalid|unrecognized|parse|malformed|hgvs/i.test(msg)) {
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throw ctx.fail('invalid_notation', `Invalid HGVS notation "${input.variant}": ${msg}
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throw ctx.fail('invalid_notation', `Invalid HGVS notation "${input.variant}": ${msg}`, {
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|
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});
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}
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throw ctx.fail('not_found', `Variant ${input.variant} not found.`, {
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});
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}
|
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|
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});
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}
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// VEP returns the full consequence + colocated-variant set; cap post-fetch so common
|
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// calls stay compact by default while the totals stay truthful. A cap of 0 (or
|
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// include_all_colocated_pubmed for the nested PubMed lists) disables it.
|
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const capConsequences = input.max_transcript_consequences > 0;
|
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+
const capPubmed = input.max_pubmed_ids_per_variant > 0 && !input.include_all_colocated_pubmed;
|
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|
+
let consequencesShown = 0;
|
|
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|
+
let consequencesTotal = 0;
|
|
265
|
+
let pubmedCapped = false;
|
|
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|
+
const shaped = results.map((r) => {
|
|
267
|
+
consequencesTotal += r.transcriptConsequences.length;
|
|
268
|
+
const transcriptConsequences = capConsequences
|
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|
+
? r.transcriptConsequences.slice(0, input.max_transcript_consequences)
|
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|
+
: r.transcriptConsequences;
|
|
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|
+
consequencesShown += transcriptConsequences.length;
|
|
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|
+
const colocatedVariants = r.colocatedVariants.map((cv) => {
|
|
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|
+
if (!cv.pubmed)
|
|
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|
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return cv;
|
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|
+
const pubmedTotal = cv.pubmed.length;
|
|
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|
+
const pubmed = capPubmed ? cv.pubmed.slice(0, input.max_pubmed_ids_per_variant) : cv.pubmed;
|
|
277
|
+
if (pubmed.length < pubmedTotal)
|
|
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|
+
pubmedCapped = true;
|
|
279
|
+
return { ...cv, pubmed, pubmedTotal };
|
|
280
|
+
});
|
|
281
|
+
return {
|
|
282
|
+
...r,
|
|
283
|
+
transcriptConsequences,
|
|
284
|
+
transcriptConsequencesTotal: r.transcriptConsequences.length,
|
|
285
|
+
colocatedVariants,
|
|
286
|
+
};
|
|
287
|
+
});
|
|
288
|
+
if (shaped.length === 0) {
|
|
200
289
|
ctx.enrich.notice(`No VEP results for "${input.variant}". ` +
|
|
201
290
|
'Verify the notation format and that the position falls within an annotated region.');
|
|
202
291
|
}
|
|
203
|
-
|
|
204
|
-
|
|
292
|
+
else {
|
|
293
|
+
// Both caps can trip on one call (rs334: 66 consequences and 100+ PubMed IDs).
|
|
294
|
+
// ctx.enrich.notice is last-wins, so compose the omission fragments into ONE string.
|
|
295
|
+
const fragments = [];
|
|
296
|
+
const consequencesOmitted = consequencesTotal - consequencesShown;
|
|
297
|
+
if (consequencesOmitted > 0) {
|
|
298
|
+
fragments.push(`showing ${consequencesShown} of ${consequencesTotal} transcript consequences`);
|
|
299
|
+
}
|
|
300
|
+
if (pubmedCapped) {
|
|
301
|
+
fragments.push(`capped PubMed IDs to ${input.max_pubmed_ids_per_variant} per colocated variant`);
|
|
302
|
+
}
|
|
303
|
+
if (fragments.length > 0) {
|
|
304
|
+
const guidance = `${fragments.join('; ')}. Raise max_transcript_consequences (0 returns all) ` +
|
|
305
|
+
'or set include_all_colocated_pubmed=true for the full detail.';
|
|
306
|
+
if (consequencesOmitted > 0) {
|
|
307
|
+
ctx.enrich.truncated({
|
|
308
|
+
shown: consequencesShown,
|
|
309
|
+
cap: input.max_transcript_consequences,
|
|
310
|
+
guidance,
|
|
311
|
+
});
|
|
312
|
+
}
|
|
313
|
+
else {
|
|
314
|
+
ctx.enrich.notice(guidance);
|
|
315
|
+
}
|
|
316
|
+
}
|
|
317
|
+
}
|
|
318
|
+
ctx.enrich.total(shaped.length);
|
|
319
|
+
return { results: shaped, totalCount: shaped.length };
|
|
205
320
|
},
|
|
206
321
|
format: (result) => {
|
|
207
322
|
const lines = [];
|
|
@@ -228,13 +343,20 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
|
|
|
228
343
|
cvLine += ` — ${cv.clinicalSignificance.join(', ')}`;
|
|
229
344
|
}
|
|
230
345
|
if (cv.pubmed?.length) {
|
|
231
|
-
|
|
346
|
+
const pubmedTotal = cv.pubmedTotal ?? cv.pubmed.length;
|
|
347
|
+
const pubmedSuffix = pubmedTotal > cv.pubmed.length
|
|
348
|
+
? ` (showing ${cv.pubmed.length} of ${pubmedTotal})`
|
|
349
|
+
: '';
|
|
350
|
+
cvLine += ` | PubMed: ${cv.pubmed.join(', ')}${pubmedSuffix}`;
|
|
232
351
|
}
|
|
233
352
|
lines.push(cvLine);
|
|
234
353
|
}
|
|
235
354
|
}
|
|
236
355
|
if (r.transcriptConsequences.length > 0) {
|
|
237
|
-
|
|
356
|
+
const shownTc = r.transcriptConsequences.length;
|
|
357
|
+
const totalTc = r.transcriptConsequencesTotal ?? shownTc;
|
|
358
|
+
const tcCount = totalTc > shownTc ? `${shownTc} of ${totalTc}` : `${shownTc}`;
|
|
359
|
+
lines.push(`\n**Transcript consequences (${tcCount}):**`);
|
|
238
360
|
for (const tc of r.transcriptConsequences) {
|
|
239
361
|
const geneLabel = tc.geneSymbol ?? tc.geneId ?? 'unknown';
|
|
240
362
|
lines.push(`\n#### ${geneLabel} — ${tc.transcriptId ?? 'unknown'}`);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"query-region.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"query-region.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0CjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4K7B,CAAC"}
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|
@@ -122,10 +122,14 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
|
|
|
122
122
|
if (/invalid.*region|coordinate|parse/i.test(msg) ||
|
|
123
123
|
/is not a valid start|is not a valid end|is not a valid chr/i.test(msg) ||
|
|
124
124
|
/no slice found/i.test(msg)) {
|
|
125
|
-
throw ctx.fail('invalid_region', `Invalid region "${input.region}": ${msg}
|
|
125
|
+
throw ctx.fail('invalid_region', `Invalid region "${input.region}": ${msg}`, {
|
|
126
|
+
...ctx.recoveryFor('invalid_region'),
|
|
127
|
+
});
|
|
126
128
|
}
|
|
127
129
|
if (/species|invalid|unrecognized/i.test(msg)) {
|
|
128
|
-
throw ctx.fail('invalid_species', `Species "${input.species}" not recognized
|
|
130
|
+
throw ctx.fail('invalid_species', `Species "${input.species}" not recognized.`, {
|
|
131
|
+
...ctx.recoveryFor('invalid_species'),
|
|
132
|
+
});
|
|
129
133
|
}
|
|
130
134
|
throw err;
|
|
131
135
|
});
|
|
@@ -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": "0.4.
|
|
3
|
+
"version": "0.4.2",
|
|
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",
|
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": "0.4.2",
|
|
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": "0.4.
|
|
22
|
+
"version": "0.4.2",
|
|
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": "0.4.
|
|
58
|
+
"version": "0.4.2",
|
|
59
59
|
"packageArguments": [
|
|
60
60
|
{
|
|
61
61
|
"type": "positional",
|