npm - @cyanheads/ensembl-mcp-server - Versions diffs - 0.1.5 → 0.2.0 - Mend

@cyanheads/ensembl-mcp-server 0.1.5 → 0.2.0

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.

Files changed (22) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** ensembl-mcp-server
-**Version:** 0.1.5
+**Version:** 0.2.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
@@ -55,7 +55,7 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
   description: 'Resolve a gene by symbol + species or by Ensembl stable ID.',
   annotations: { readOnlyHint: true, openWorldHint: true },
   input: z.object({
-    symbol: z.string().optional().describe('Gene symbol (e.g. BRCA2, TP53). Requires species.'),
+    symbol: z.string().optional().describe('Gene symbol (e.g. BRCA2, TP53). Species defaults to homo_sapiens.'),
     id: z.string().optional().describe('Ensembl stable ID (ENSG…).'),
     species: z.string().default('homo_sapiens').describe('Species in Ensembl format.'),
   }),

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** ensembl-mcp-server
-**Version:** 0.1.5
+**Version:** 0.2.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
@@ -55,7 +55,7 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
   description: 'Resolve a gene by symbol + species or by Ensembl stable ID.',
   annotations: { readOnlyHint: true, openWorldHint: true },
   input: z.object({
-    symbol: z.string().optional().describe('Gene symbol (e.g. BRCA2, TP53). Requires species.'),
+    symbol: z.string().optional().describe('Gene symbol (e.g. BRCA2, TP53). Species defaults to homo_sapiens.'),
     id: z.string().optional().describe('Ensembl stable ID (ENSG…).'),
     species: z.string().default('homo_sapiens').describe('Species in Ensembl format.'),
   }),

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.1.5-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/ensembl-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/ensembl-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/ensembl-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.11-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.2.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/ensembl-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/ensembl-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/ensembl-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.11-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>

package/changelog/0.2.x/0.2.0.md ADDED Viewed

@@ -0,0 +1,13 @@
+---
+summary: "Breaking: ensembl_get_sequence output field lengthInBp → length (unit-aware); ensembl_get_homology and ensembl_lookup_gene now reject more than one of symbol/id/ids/symbols; symbol descriptions corrected to state species defaults to homo_sapiens"
+breaking: true
+security: false
+---
+# 0.2.0 — 2026-06-21
+## Changed
+- **`ensembl_get_sequence` output field `lengthInBp` → `length`** — the field carries the residue count for `type: protein`, where "bp" was wrong; renamed to the unit-neutral `length`. `format()` now labels the value by molecule type (`residues` for protein, `bp` for genomic/cdna/cds) instead of the ambiguous `bp/aa`. Nucleotide-type counts are unchanged; transcript `lengthInBp` fields (genuine base pairs) are untouched. ([#4](https://github.com/cyanheads/ensembl-mcp-server/issues/4))
+- **`ensembl_get_homology` and `ensembl_lookup_gene` reject conflicting inputs** — a call providing more than one of `symbol`, `id`, `ids`, or `symbols` now fails with a `conflicting_input` `ValidationError`. Previously both tools silently resolved by an undocumented precedence (homology let `id` win; lookup ordered ids → symbols → symbol → id), contradicting the "cannot be combined" descriptions. ([#5](https://github.com/cyanheads/ensembl-mcp-server/issues/5))
+- **`symbol` / `species` descriptions corrected** — across both tools' `symbol`, `species`, and `symbols` fields, the `ensembl_lookup_gene` top-level description, and the synced `CLAUDE.md`/`AGENTS.md` example, the wording no longer claims species is required for a symbol lookup; each states species defaults to `homo_sapiens` (override for other organisms). ([#5](https://github.com/cyanheads/ensembl-mcp-server/issues/5))

package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts CHANGED Viewed

@@ -37,6 +37,11 @@ export declare const ensemblGetHomology: import("@cyanheads/mcp-ts-core").ToolDe
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "Neither symbol nor id was provided.";
     readonly recovery: "Provide either symbol (with species) or a stable Ensembl gene ID.";
+}, {
+    readonly reason: "conflicting_input";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "Both symbol and id were provided.";
+    readonly recovery: "Provide exactly one: a gene symbol (with optional species) or a stable Ensembl gene ID.";
 }], {
     readonly notice: z.ZodOptional<z.ZodString>;
 }>;

package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAuL7B,CAAC"}

package/dist/mcp-server/tools/definitions/get-homology.tool.js CHANGED Viewed

@@ -47,13 +47,14 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
             .string()
             .optional()
             .describe('Gene symbol in the source species (e.g. BRCA2, TP53). ' +
-            'Requires species to be set. Cannot be used together with id.'),
+            'Species defaults to homo_sapiens; set species for other organisms. ' +
+            'Cannot be combined with id.'),
         id: z
             .string()
             .optional()
             .describe('Ensembl stable gene ID (e.g. ENSG00000139618). ' +
             'Use ensembl_lookup_gene to get the stable ID from a symbol. ' +
-            'Cannot be used together with symbol.'),
+            'Cannot be combined with symbol.'),
         species: z
             .string()
             .default('homo_sapiens')
@@ -99,6 +100,12 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
             when: 'Neither symbol nor id was provided.',
             recovery: 'Provide either symbol (with species) or a stable Ensembl gene ID.',
         },
+        {
+            reason: 'conflicting_input',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'Both symbol and id were provided.',
+            recovery: 'Provide exactly one: a gene symbol (with optional species) or a stable Ensembl gene ID.',
+        },
     ],
     async handler(input, ctx) {
         ctx.log.info('Getting homologs', {
@@ -112,6 +119,9 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
         if (!input.symbol?.trim() && !input.id?.trim()) {
             throw ctx.fail('no_input', 'Provide either symbol (with species) or a stable gene ID.');
         }
+        if (input.id?.trim() && input.symbol?.trim()) {
+            throw ctx.fail('conflicting_input', 'Provide either symbol or id, not both — they may resolve to different genes.');
+        }
         const idTrimmed = input.id?.trim();
         const symbolTrimmed = input.symbol?.trim();
         let queryId;

package/dist/mcp-server/tools/definitions/get-homology.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts CHANGED Viewed

@@ -19,7 +19,7 @@ export declare const ensemblGetSequence: import("@cyanheads/mcp-ts-core").ToolDe
     id: z.ZodString;
     type: z.ZodString;
     seq: z.ZodString;
-    lengthInBp: z.ZodNumber;
+    length: z.ZodNumber;
     description: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>, readonly [{
     readonly reason: "not_found";

package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts.map CHANGED Viewed

	@@ -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;;;;;;;;;;;;;;;;;;;;;;;;;;;~~cA+K7B~~,CAAC"}
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;;;;;;;;;;;;;;;;;;;;;;;;;;;cA8K7B,CAAC"}

package/dist/mcp-server/tools/definitions/get-sequence.tool.js CHANGED Viewed

@@ -60,9 +60,9 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
             .describe('The full sequence. DNA sequences use IUPAC nucleotide codes (ACGT + ambiguity codes). ' +
             'Protein sequences use single-letter amino acid codes. ' +
             'Large genomic sequences (e.g. 85 kb for BRCA2) are returned in full.'),
-        lengthInBp: z
+        length: z
             .number()
-            .describe('Sequence length in characters (nucleotides or amino acids). ' +
+            .describe('Sequence length in characters — nucleotides for genomic/cdna/cds, amino-acid residues for protein. ' +
             'Use this to budget context window usage before processing the sequence.'),
         description: z.string().optional().describe('Sequence description from Ensembl, if provided.'),
     }),
@@ -132,7 +132,8 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
     format: (result) => {
         const lines = [];
         lines.push(`## Sequence: ${result.id}`);
-        lines.push(`**Type:** ${result.type} | **Length:** ${result.lengthInBp.toLocaleString()} bp/aa`);
+        const unit = result.type === 'protein' ? 'residues' : 'bp';
+        lines.push(`**Type:** ${result.type} | **Length:** ${result.length.toLocaleString()} ${unit}`);
         if (result.description)
             lines.push(`**Description:** ${result.description}`);
         lines.push('');
@@ -140,7 +141,7 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
         if (result.seq.length > 200) {
             lines.push('```');
             lines.push(result.seq.slice(0, 200));
-            lines.push(`… (${result.lengthInBp.toLocaleString()} total characters)`);
+            lines.push(`… (${result.length.toLocaleString()} total characters)`);
             lines.push('```');
         }
         else {

package/dist/mcp-server/tools/definitions/get-sequence.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/lookup-gene.tool.d.ts CHANGED Viewed

@@ -53,5 +53,10 @@ export declare const ensemblLookupGene: import("@cyanheads/mcp-ts-core").ToolDef
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "Neither symbol, id, ids, nor symbols was provided.";
     readonly recovery: "Provide exactly one of: symbol (with species), id, ids array, or symbols array (with species).";
+}, {
+    readonly reason: "conflicting_input";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "More than one of symbol, id, ids, or symbols was provided.";
+    readonly recovery: "Provide exactly one input: a symbol, a stable id, an ids array, or a symbols array.";
 }], undefined>;
 //# sourceMappingURL=lookup-gene.tool.d.ts.map

package/dist/mcp-server/tools/definitions/lookup-gene.tool.d.ts.map CHANGED Viewed

	@@ -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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAsP5B,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-gene.tool.js CHANGED Viewed

@@ -66,15 +66,17 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
         '(chr:start-end:strand), biotype, description, and transcript list. Entry point for most workflows — ' +
         'the stable ID and coordinates returned here are inputs to other tools. Accepts both symbol lookup ' +
         '(BRCA2 + homo_sapiens) and direct ID lookup (ENSG00000139618). Supports batch lookup of up to 20 ' +
-        'IDs or symbols in one call via the ids or symbols field. For symbol lookup, species is required; ' +
-        'for ID lookup, species is not needed. Use ensembl_list_species to discover valid species names.',
+        'IDs or symbols in one call via the ids or symbols field. Provide exactly one of symbol, id, ids, ' +
+        'or symbols. For symbol lookups species defaults to homo_sapiens (override for other organisms); ' +
+        'for ID lookups species is not needed. Use ensembl_list_species to discover valid species names.',
     annotations: { readOnlyHint: true, openWorldHint: true, idempotentHint: true },
     input: z.object({
         symbol: z
             .string()
             .optional()
             .describe('Gene symbol to look up (e.g. BRCA2, TP53, EGFR). ' +
-            'Requires species to be set. Case-insensitive in most species.'),
+            'Species defaults to homo_sapiens; set species for other organisms. ' +
+            'Case-insensitive in most species.'),
         id: z
             .string()
             .optional()
@@ -85,21 +87,21 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
             .optional()
             .describe('Species in Ensembl internal format: lowercase scientific name with underscores ' +
             '(e.g. homo_sapiens, mus_musculus, danio_rerio). ' +
-            'Required when using symbol. Default is homo_sapiens for symbol-based lookups. ' +
+            'Optional for symbol lookups — defaults to homo_sapiens; set it for other organisms. ' +
             'Use ensembl_list_species to discover valid values.'),
         ids: z
             .array(z.string().describe('An Ensembl stable gene or transcript ID to resolve in this batch.'))
             .max(20)
             .optional()
             .describe('Batch lookup: up to 20 Ensembl stable IDs (ENSG…, ENST…). ' +
-            'Returns a succeeded/failed split. Cannot be combined with symbol or id.'),
+            'Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols.'),
         symbols: z
             .array(z.string().describe('A gene symbol to resolve in this batch (e.g. BRCA2, TP53).'))
             .max(20)
             .optional()
             .describe('Batch lookup: up to 20 gene symbols. ' +
-            'Requires species to be set. Returns a succeeded/failed split. ' +
-            'Cannot be combined with symbol, id, or ids.'),
+            'Species defaults to homo_sapiens; set species for other organisms. ' +
+            'Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols.'),
         expand_transcripts: z
             .boolean()
             .default(false)
@@ -132,6 +134,12 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
             when: 'Neither symbol, id, ids, nor symbols was provided.',
             recovery: 'Provide exactly one of: symbol (with species), id, ids array, or symbols array (with species).',
         },
+        {
+            reason: 'conflicting_input',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'More than one of symbol, id, ids, or symbols was provided.',
+            recovery: 'Provide exactly one input: a symbol, a stable id, an ids array, or a symbols array.',
+        },
     ],
     async handler(input, ctx) {
         ctx.log.info('Looking up gene', {
@@ -141,6 +149,15 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
             batchSize: input.ids?.length ?? input.symbols?.length,
         });
         const service = getEnsemblService();
+        const inputCount = [
+            input.symbol?.trim(),
+            input.id?.trim(),
+            input.ids?.length,
+            input.symbols?.length,
+        ].filter(Boolean).length;
+        if (inputCount > 1) {
+            throw ctx.fail('conflicting_input', 'Provide exactly one of: symbol, id, ids, or symbols.');
+        }
         // --- Batch by IDs ---
         if (input.ids?.length) {
             const map = await service.lookupGenesBatch(input.ids, input.expand_transcripts, ctx);

package/dist/mcp-server/tools/definitions/lookup-gene.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ensembl/ensembl-service.js CHANGED Viewed

@@ -55,7 +55,7 @@ function normalizeSequence(raw, type) {
         id: raw.id,
         type,
         seq: raw.seq,
-        lengthInBp: raw.seq.length,
+        length: raw.seq.length,
         ...(raw.desc && { description: raw.desc }),
     };
 }

package/dist/services/ensembl/ensembl-service.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/services/ensembl/types.d.ts CHANGED Viewed

@@ -212,7 +212,7 @@ export type SequenceRecord = {
     id: string;
     type: string;
     seq: string;
-    lengthInBp: number;
+    length: number;
     description?: string;
 };
 export type OverlapFeature = {

package/dist/services/ensembl/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/ensembl-mcp-server",
-  "version": "0.1.5",
+  "version": "0.2.0",
   "mcpName": "io.github.cyanheads/ensembl-mcp-server",
   "description": "Look up genes, fetch sequences, predict variant consequences, find orthologs and cross-database xrefs via Ensembl REST via MCP. STDIO or Streamable HTTP.",
   "type": "module",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/ensembl-mcp-server",
     "source": "github"
   },
-  "version": "0.1.5",
+  "version": "0.2.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/ensembl-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.1.5",
+      "version": "0.2.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -55,7 +55,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/ensembl-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.1.5",
+      "version": "0.2.0",
       "packageArguments": [
         {
           "type": "positional",