@cyanheads/ensembl-mcp-server 0.1.1

package/dist/mcp-server/tools/definitions/list-species.tool.js

@@ -0,0 +1,105 @@
+/**
+ * @fileoverview Tool to list Ensembl-supported species with display names, assemblies, and taxon IDs.
+ * @module mcp-server/tools/definitions/list-species
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { getEnsemblService } from '../../../services/ensembl/ensembl-service.js';
+const DIVISION_VALUES = [
+    'EnsemblVertebrates',
+    'EnsemblPlants',
+    'EnsemblFungi',
+    'EnsemblMetazoa',
+    'EnsemblProtists',
+];
+const SpeciesItemSchema = z.object({
+    name: z
+        .string()
+        .describe('Ensembl internal species name in lowercase_underscore format (e.g. homo_sapiens, mus_musculus). ' +
+        'This is the value to pass as the species parameter in all other Ensembl tools.'),
+    displayName: z
+        .string()
+        .optional()
+        .describe('Human-readable scientific name (e.g. Homo sapiens).'),
+    commonName: z.string().optional().describe('Common name (e.g. Human, Mouse).'),
+    taxonId: z.string().optional().describe('NCBI taxonomy ID for this species.'),
+    assembly: z.string().optional().describe('Current genome assembly name (e.g. GRCh38).'),
+    division: z
+        .string()
+        .optional()
+        .describe('Ensembl division this species belongs to (e.g. EnsemblVertebrates, EnsemblPlants).'),
+});
+export const ensemblListSpecies = tool('ensembl_list_species', {
+    title: 'List Ensembl Species',
+    description: 'List species supported by Ensembl with display name, common name, assembly, taxon ID, and division. ' +
+        'Required discovery step — species names like homo_sapiens are opaque to non-biologists and are the ' +
+        'input format every other Ensembl tool expects. Filter by division to limit results; use nameContains ' +
+        'to find a species by partial name match. Returns the full species catalog when no filters are applied ' +
+        '(EnsemblVertebrates has ~250 species; all divisions combined have ~1,000+).',
+    annotations: { readOnlyHint: true, openWorldHint: false, idempotentHint: true },
+    input: z.object({
+        division: z
+            .enum(DIVISION_VALUES)
+            .optional()
+            .describe('Filter to a specific Ensembl division. ' +
+            'EnsemblVertebrates includes human, mouse, zebrafish, and other vertebrates. ' +
+            'EnsemblPlants covers crop and model plant genomes. ' +
+            'EnsemblFungi, EnsemblMetazoa, EnsemblProtists cover non-vertebrate model organisms. ' +
+            'Omit to return all divisions.'),
+        nameContains: z
+            .string()
+            .optional()
+            .describe('Case-insensitive substring filter applied locally after fetching. ' +
+            'Matches against species name, display name, and common name. ' +
+            'Example: "sapiens" matches homo_sapiens; "mouse" matches mus_musculus.'),
+    }),
+    output: z.object({
+        species: z
+            .array(SpeciesItemSchema.describe('A single Ensembl species entry.'))
+            .describe('Species matching the filter criteria, sorted by internal name.'),
+        totalCount: z.number().describe('Total number of matching species after local filtering.'),
+    }),
+    enrichment: {
+        notice: z.string().optional().describe('Guidance when the filter matches no species.'),
+    },
+    async handler(input, ctx) {
+        ctx.log.info('Listing species', { division: input.division, nameContains: input.nameContains });
+        const service = getEnsemblService();
+        let species = await service.listSpecies(input.division, ctx);
+        if (input.nameContains?.trim()) {
+            const q = input.nameContains.toLowerCase();
+            const tokens = q.split(/\s+/).filter(Boolean);
+            species = species.filter((s) => {
+                const hay = [s.name, s.displayName, s.commonName].filter(Boolean).join(' ').toLowerCase();
+                return tokens.every((t) => hay.includes(t));
+            });
+            if (species.length === 0) {
+                ctx.enrich.notice(`No species matched "${input.nameContains}". ` +
+                    'Call ensembl_list_species without nameContains to browse all species.');
+            }
+        }
+        species.sort((a, b) => a.name.localeCompare(b.name));
+        ctx.enrich.total(species.length);
+        return { species, totalCount: species.length };
+    },
+    format: (result) => {
+        if (result.species.length === 0) {
+            return [{ type: 'text', text: 'No matching species found.' }];
+        }
+        const lines = [`## Ensembl Species (${result.totalCount} total)\n`];
+        for (const s of result.species) {
+            const label = s.displayName ?? s.name;
+            const common = s.commonName ? ` (${s.commonName})` : '';
+            lines.push(`**${label}**${common}`);
+            lines.push(`- Internal name: \`${s.name}\``);
+            if (s.assembly)
+                lines.push(`- Assembly: ${s.assembly}`);
+            if (s.taxonId)
+                lines.push(`- Taxon ID: ${s.taxonId}`);
+            if (s.division)
+                lines.push(`- Division: ${s.division}`);
+            lines.push('');
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+//# sourceMappingURL=list-species.tool.js.map

package/dist/mcp-server/tools/definitions/list-species.tool.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"list-species.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/list-species.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,eAAe,GAAG;IACtB,oBAAoB;IACpB,eAAe;IACf,cAAc;IACd,gBAAgB;IAChB,iBAAiB;CACT,CAAC;AAEX,MAAM,iBAAiB,GAAG,CAAC,CAAC,MAAM,CAAC;IACjC,IAAI,EAAE,CAAC;SACJ,MAAM,EAAE;SACR,QAAQ,CACP,kGAAkG;QAChG,gFAAgF,CACnF;IACH,WAAW,EAAE,CAAC;SACX,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,qDAAqD,CAAC;IAClE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;IAC9E,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;IAC7E,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;IACvF,QAAQ,EAAE,CAAC;SACR,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oFAAoF,CAAC;CAClG,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,sBAAsB;IAC7B,WAAW,EACT,sGAAsG;QACtG,qGAAqG;QACrG,uGAAuG;QACvG,wGAAwG;QACxG,6EAA6E;IAC/E,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,KAAK,EAAE,cAAc,EAAE,IAAI,EAAE;IAC/E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,QAAQ,EAAE,CAAC;aACR,IAAI,CAAC,eAAe,CAAC;aACrB,QAAQ,EAAE;aACV,QAAQ,CACP,yCAAyC;YACvC,8EAA8E;YAC9E,qDAAqD;YACrD,sFAAsF;YACtF,+BAA+B,CAClC;QACH,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,oEAAoE;YAClE,+DAA+D;YAC/D,wEAAwE,CAC3E;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CAAC,iBAAiB,CAAC,QAAQ,CAAC,iCAAiC,CAAC,CAAC;aACpE,QAAQ,CAAC,gEAAgE,CAAC;QAC7E,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yDAAyD,CAAC;KAC3F,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;KACvF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,iBAAiB,EAAE,EAAE,QAAQ,EAAE,KAAK,CAAC,QAAQ,EAAE,YAAY,EAAE,KAAK,CAAC,YAAY,EAAE,CAAC,CAAC;QAChG,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QACpC,IAAI,OAAO,GAAG,MAAM,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;QAE7D,IAAI,KAAK,CAAC,YAAY,EAAE,IAAI,EAAE,EAAE,CAAC;YAC/B,MAAM,CAAC,GAAG,KAAK,CAAC,YAAY,CAAC,WAAW,EAAE,CAAC;YAC3C,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;YAC9C,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE;gBAC7B,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAC;gBAC1F,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC;YAC9C,CAAC,CAAC,CAAC;YACH,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBACzB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,uBAAuB,KAAK,CAAC,YAAY,KAAK;oBAC5C,uEAAuE,CAC1E,CAAC;YACJ,CAAC;QACH,CAAC;QAED,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;QACrD,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;QAEjC,OAAO,EAAE,OAAO,EAAE,UAAU,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC;IACjD,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,4BAA4B,EAAE,CAAC,CAAC;QAChE,CAAC;QACD,MAAM,KAAK,GAAa,CAAC,uBAAuB,MAAM,CAAC,UAAU,WAAW,CAAC,CAAC;QAC9E,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,MAAM,KAAK,GAAG,CAAC,CAAC,WAAW,IAAI,CAAC,CAAC,IAAI,CAAC;YACtC,MAAM,MAAM,GAAG,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YACxD,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,KAAK,MAAM,EAAE,CAAC,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC;YAC7C,IAAI,CAAC,CAAC,QAAQ;gBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;YACxD,IAAI,CAAC,CAAC,OAAO;gBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;YACtD,IAAI,CAAC,CAAC,QAAQ;gBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;YACxD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,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"}

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

@@ -0,0 +1,57 @@
+/**
+ * @fileoverview Tool to resolve genes by symbol + species or by Ensembl stable ID.
+ * @module mcp-server/tools/definitions/lookup-gene
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const ensemblLookupGene: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    symbol: z.ZodOptional<z.ZodString>;
+    id: z.ZodOptional<z.ZodString>;
+    species: z.ZodOptional<z.ZodString>;
+    ids: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    symbols: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    expand_transcripts: z.ZodDefault<z.ZodBoolean>;
+}, z.core.$strip>, z.ZodObject<{
+    gene: z.ZodOptional<z.ZodObject<{
+        id: z.ZodString;
+        species: z.ZodOptional<z.ZodString>;
+        displayName: z.ZodOptional<z.ZodString>;
+        description: z.ZodOptional<z.ZodString>;
+        biotype: z.ZodOptional<z.ZodString>;
+        chromosome: z.ZodOptional<z.ZodString>;
+        start: z.ZodOptional<z.ZodNumber>;
+        end: z.ZodOptional<z.ZodNumber>;
+        strand: z.ZodOptional<z.ZodNumber>;
+        assemblyName: z.ZodOptional<z.ZodString>;
+        transcripts: z.ZodOptional<z.ZodArray<z.ZodObject<{
+            id: z.ZodString;
+            displayName: z.ZodOptional<z.ZodString>;
+            biotype: z.ZodOptional<z.ZodString>;
+            isCanonical: z.ZodBoolean;
+            start: z.ZodOptional<z.ZodNumber>;
+            end: z.ZodOptional<z.ZodNumber>;
+            strand: z.ZodOptional<z.ZodNumber>;
+            lengthInBp: z.ZodOptional<z.ZodNumber>;
+        }, z.core.$strip>>>;
+    }, z.core.$strip>>;
+    batch: z.ZodOptional<z.ZodObject<{
+        succeeded: z.ZodArray<z.ZodObject<{}, z.core.$loose>>;
+        failed: z.ZodArray<z.ZodObject<{}, z.core.$loose>>;
+    }, z.core.$strip>>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "The gene symbol or stable ID was not found in Ensembl.";
+    readonly recovery: string;
+}, {
+    readonly reason: "invalid_species";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "The species string was not recognized by Ensembl.";
+    readonly recovery: string;
+}, {
+    readonly reason: "no_input";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    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).";
+}], undefined>;
+//# sourceMappingURL=lookup-gene.tool.d.ts.map

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

@@ -0,0 +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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAmO5B,CAAC"}

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

@@ -0,0 +1,254 @@
+/**
+ * @fileoverview Tool to resolve genes by symbol + species or by Ensembl stable ID.
+ * @module mcp-server/tools/definitions/lookup-gene
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { getEnsemblService } from '../../../services/ensembl/ensembl-service.js';
+const TranscriptSummarySchema = z.object({
+    id: z.string().describe('Ensembl transcript stable ID (ENST…).'),
+    displayName: z.string().optional().describe('Transcript display name.'),
+    biotype: z
+        .string()
+        .optional()
+        .describe('Transcript biotype (e.g. protein_coding, lncRNA, retained_intron).'),
+    isCanonical: z.boolean().describe('True when this is the canonical transcript for the gene.'),
+    start: z.number().optional().describe('Transcript start position on the chromosome (1-based).'),
+    end: z.number().optional().describe('Transcript end position on the chromosome (1-based).'),
+    strand: z.number().optional().describe('Strand: 1 for forward, -1 for reverse.'),
+    lengthInBp: z.number().optional().describe('Transcript length in base pairs.'),
+});
+const GeneResultSchema = z.object({
+    id: z
+        .string()
+        .describe('Ensembl gene stable ID (ENSG…). Use this as input to other Ensembl tools.'),
+    species: z
+        .string()
+        .optional()
+        .describe('Species in Ensembl internal format (e.g. homo_sapiens). Echoed from lookup.'),
+    displayName: z.string().optional().describe('Gene symbol or display name (e.g. BRCA2, TP53).'),
+    description: z.string().optional().describe('Brief gene description from Ensembl.'),
+    biotype: z
+        .string()
+        .optional()
+        .describe('Gene biotype (e.g. protein_coding, lncRNA, pseudogene).'),
+    chromosome: z.string().optional().describe('Chromosome or sequence region name.'),
+    start: z.number().optional().describe('Gene start position on the chromosome (1-based).'),
+    end: z.number().optional().describe('Gene end position on the chromosome (1-based).'),
+    strand: z.number().optional().describe('Strand: 1 for forward, -1 for reverse.'),
+    assemblyName: z
+        .string()
+        .optional()
+        .describe('Genome assembly name (e.g. GRCh38). All coordinates are relative to this assembly.'),
+    transcripts: z
+        .array(TranscriptSummarySchema.describe('A single transcript summary entry.'))
+        .optional()
+        .describe('Transcript list. Present only when expand_transcripts is true.'),
+});
+const BatchResultSchema = z.object({
+    // passthrough() — fields rendered via format()'s renderGene helper, not individually listed.
+    succeeded: z
+        .array(z
+        .object({})
+        .passthrough()
+        .describe('A resolved gene record with the same shape as the gene output field.'))
+        .describe('Gene records for IDs/symbols that resolved successfully. Same shape as gene.'),
+    failed: z
+        .array(z
+        .object({})
+        .passthrough()
+        .describe('A failed lookup entry with query (the submitted ID or symbol) and error (reason string) fields.'))
+        .describe('IDs/symbols that could not be resolved, with per-item query and error fields.'),
+});
+export const ensemblLookupGene = tool('ensembl_lookup_gene', {
+    title: 'Lookup Gene',
+    description: 'Resolve a gene by symbol + species (or by stable ID) to its Ensembl ID, genomic location ' +
+        '(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.',
+    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.'),
+        id: z
+            .string()
+            .optional()
+            .describe('Ensembl stable gene ID (e.g. ENSG00000139618 or ENSG00000139618.7 with version). ' +
+            'Species is not required for ID lookup.'),
+        species: z
+            .string()
+            .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. ' +
+            '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.'),
+        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.'),
+        expand_transcripts: z
+            .boolean()
+            .default(false)
+            .describe('When true, include the full transcript list in the response. ' +
+            'Each transcript has its ID, biotype, canonical flag, and coordinates. ' +
+            'Default is false to keep responses compact.'),
+    }),
+    output: z.object({
+        gene: GeneResultSchema.optional().describe('Single gene record. Present for symbol or id lookups.'),
+        batch: BatchResultSchema.optional().describe('Batch results. Present for ids or symbols lookups.'),
+    }),
+    errors: [
+        {
+            reason: 'not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'The gene symbol or stable ID was not found in Ensembl.',
+            recovery: 'Verify the symbol spelling or ID format. Use ensembl_list_species to confirm the species name, ' +
+                'then retry. Stable IDs are versioned (ENSG00000139618.7) — omitting the version resolves to current.',
+        },
+        {
+            reason: 'invalid_species',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'The species string was not recognized by Ensembl.',
+            recovery: 'Call ensembl_list_species to discover valid species names. ' +
+                'Species must be in lowercase_underscore format (homo_sapiens, not Human or Homo Sapiens).',
+        },
+        {
+            reason: 'no_input',
+            code: JsonRpcErrorCode.InvalidParams,
+            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).',
+        },
+    ],
+    async handler(input, ctx) {
+        ctx.log.info('Looking up gene', {
+            symbol: input.symbol,
+            id: input.id,
+            species: input.species,
+            batchSize: input.ids?.length ?? input.symbols?.length,
+        });
+        const service = getEnsemblService();
+        // --- Batch by IDs ---
+        if (input.ids?.length) {
+            const map = await service.lookupGenesBatch(input.ids, input.expand_transcripts, ctx);
+            const succeeded = Array.from(map.values());
+            const resolvedIds = new Set(map.keys());
+            const failed = input.ids
+                .filter((id) => !resolvedIds.has(id))
+                .map((id) => ({ query: id, error: `ID ${id} not found in Ensembl.` }));
+            return { batch: { succeeded, failed } };
+        }
+        // --- Batch by symbols ---
+        if (input.symbols?.length) {
+            const speciesStr = input.species?.trim() || 'homo_sapiens';
+            const map = await service.lookupSymbolsBatch(input.symbols, speciesStr, input.expand_transcripts, ctx);
+            const succeeded = Array.from(map.values());
+            const resolvedSymbols = new Set(map.keys());
+            const failed = input.symbols
+                .filter((s) => !resolvedSymbols.has(s))
+                .map((s) => ({
+                query: s,
+                error: `Symbol ${s} not found in Ensembl for species ${speciesStr}.`,
+            }));
+            return { batch: { succeeded, failed } };
+        }
+        // --- Single symbol ---
+        if (input.symbol?.trim()) {
+            const speciesStr = input.species?.trim() || 'homo_sapiens';
+            const gene = await service
+                .lookupGene(input.symbol.trim(), speciesStr, input.expand_transcripts, ctx)
+                .catch((err) => {
+                const msg = err instanceof Error ? err.message : String(err);
+                if (/not found|no stable id|no results|no valid lookup/i.test(msg)) {
+                    throw ctx.fail('not_found', `Gene symbol "${input.symbol}" not found in ${speciesStr}.`);
+                }
+                if (/species|invalid|unrecognized/i.test(msg)) {
+                    throw ctx.fail('invalid_species', `Species "${speciesStr}" not recognized by Ensembl.`);
+                }
+                throw err;
+            });
+            return { gene };
+        }
+        // --- Single ID ---
+        if (input.id?.trim()) {
+            const gene = await service
+                .lookupGeneById(input.id.trim(), input.expand_transcripts, ctx)
+                .catch((err) => {
+                const msg = err instanceof Error ? err.message : String(err);
+                if (/not found|no stable id/i.test(msg)) {
+                    throw ctx.fail('not_found', `Gene ID "${input.id}" not found in Ensembl.`);
+                }
+                throw err;
+            });
+            return { gene };
+        }
+        throw ctx.fail('no_input', 'Provide symbol (with species), id, ids, or symbols.');
+    },
+    format: (result) => {
+        const lines = [];
+        const renderGene = (g) => {
+            lines.push(`## ${g.displayName ?? g.id}`);
+            lines.push(`**ID:** ${g.id}`);
+            if (g.species)
+                lines.push(`**Species:** ${g.species}`);
+            if (g.biotype)
+                lines.push(`**Biotype:** ${g.biotype}`);
+            if (g.description)
+                lines.push(`**Description:** ${g.description}`);
+            if (g.chromosome)
+                lines.push(`**Chromosome:** ${g.chromosome}`);
+            if (g.start != null)
+                lines.push(`**Start:** ${g.start}`);
+            if (g.end != null)
+                lines.push(`**End:** ${g.end}`);
+            if (g.strand != null)
+                lines.push(`**Strand:** ${g.strand} (${g.strand === -1 ? 'reverse' : 'forward'})`);
+            if (g.assemblyName)
+                lines.push(`**Assembly:** ${g.assemblyName}`);
+            if (g.transcripts?.length) {
+                lines.push(`\n**Transcripts (${g.transcripts.length}):**`);
+                for (const t of g.transcripts) {
+                    const canon = t.isCanonical ? ' ★ canonical' : '';
+                    const loc = t.start != null && t.end != null
+                        ? ` ${t.start}-${t.end}${t.strand != null ? `:${t.strand}` : ''}`
+                        : '';
+                    const len = t.lengthInBp != null ? ` ${t.lengthInBp}bp` : '';
+                    lines.push(`- ${t.id}${t.displayName ? ` (${t.displayName})` : ''}${canon}${t.biotype ? ` [${t.biotype}]` : ''}${loc}${len}`);
+                }
+            }
+        };
+        if (result.gene) {
+            renderGene(result.gene);
+        }
+        else if (result.batch) {
+            const { succeeded, failed } = result.batch;
+            lines.push(`## Batch Lookup Results`);
+            lines.push(`**Succeeded:** ${succeeded.length} | **Failed:** ${failed.length}\n`);
+            for (const g of succeeded) {
+                renderGene(g);
+                lines.push('');
+            }
+            if (failed.length > 0) {
+                lines.push('### Failed lookups');
+                for (const f of failed) {
+                    lines.push(`- **${f.query}:** ${f.error}`);
+                }
+            }
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+//# sourceMappingURL=lookup-gene.tool.js.map

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

@@ -0,0 +1 @@
+{"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,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,+DAA+D,CAClE;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,gFAAgF;YAChF,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,yEAAyE,CAC5E;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,gEAAgE;YAChE,6CAA6C,CAChD;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,aAAa;YACpC,IAAI,EAAE,oDAAoD;YAC1D,QAAQ,EACN,gGAAgG;SACnG;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,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,KAAK,CAAC,GAAG;iBACrB,MAAM,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;iBACpC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,wBAAwB,EAAE,CAAC,CAAC,CAAC;YACzE,OAAO,EAAE,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC;QAC1C,CAAC;QAED,2BAA2B;QAC3B,IAAI,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,CAAC;YAC1B,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,cAAc,CAAC;YAC3D,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,kBAAkB,CAC1C,KAAK,CAAC,OAAO,EACb,UAAU,EACV,KAAK,CAAC,kBAAkB,EACxB,GAAG,CACJ,CAAC;YACF,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;YAC3C,MAAM,eAAe,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,CAAC;YAC5C,MAAM,MAAM,GAAG,KAAK,CAAC,OAAO;iBACzB,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;iBACtC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBACX,KAAK,EAAE,CAAC;gBACR,KAAK,EAAE,UAAU,CAAC,qCAAqC,UAAU,GAAG;aACrE,CAAC,CAAC,CAAC;YACN,OAAO,EAAE,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC;QAC1C,CAAC;QAED,wBAAwB;QACxB,IAAI,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE,CAAC;YACzB,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,cAAc,CAAC;YAC3D,MAAM,IAAI,GAAG,MAAM,OAAO;iBACvB,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,IAAI,EAAE,EAAE,UAAU,EAAE,KAAK,CAAC,kBAAkB,EAAE,GAAG,CAAC;iBAC1E,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,oDAAoD,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACnE,MAAM,GAAG,CAAC,IAAI,CACZ,WAAW,EACX,gBAAgB,KAAK,CAAC,MAAM,kBAAkB,UAAU,GAAG,CAC5D,CAAC;gBACJ,CAAC;gBACD,IAAI,+BAA+B,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC9C,MAAM,GAAG,CAAC,IAAI,CAAC,iBAAiB,EAAE,YAAY,UAAU,8BAA8B,CAAC,CAAC;gBAC1F,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,OAAO,EAAE,IAAI,EAAE,CAAC;QAClB,CAAC;QAED,oBAAoB;QACpB,IAAI,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,EAAE,CAAC;YACrB,MAAM,IAAI,GAAG,MAAM,OAAO;iBACvB,cAAc,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,kBAAkB,EAAE,GAAG,CAAC;iBAC9D,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,yBAAyB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACxC,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,YAAY,KAAK,CAAC,EAAE,yBAAyB,CAAC,CAAC;gBAC7E,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,OAAO,EAAE,IAAI,EAAE,CAAC;QAClB,CAAC;QAED,MAAM,GAAG,CAAC,IAAI,CAAC,UAAU,EAAE,qDAAqD,CAAC,CAAC;IACpF,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAG3B,MAAM,UAAU,GAAG,CAAC,CAAW,EAAE,EAAE;YACjC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,WAAW,IAAI,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC1C,KAAK,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC9B,IAAI,CAAC,CAAC,OAAO;gBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;YACvD,IAAI,CAAC,CAAC,OAAO;gBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;YACvD,IAAI,CAAC,CAAC,WAAW;gBAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC;YACnE,IAAI,CAAC,CAAC,UAAU;gBAAE,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC,UAAU,EAAE,CAAC,CAAC;YAChE,IAAI,CAAC,CAAC,KAAK,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACzD,IAAI,CAAC,CAAC,GAAG,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;YACnD,IAAI,CAAC,CAAC,MAAM,IAAI,IAAI;gBAClB,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC;YACrF,IAAI,CAAC,CAAC,YAAY;gBAAE,KAAK,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC,YAAY,EAAE,CAAC,CAAC;YAClE,IAAI,CAAC,CAAC,WAAW,EAAE,MAAM,EAAE,CAAC;gBAC1B,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,WAAW,CAAC,MAAM,MAAM,CAAC,CAAC;gBAC3D,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,CAAC;oBAC9B,MAAM,KAAK,GAAG,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC;oBAClD,MAAM,GAAG,GACP,CAAC,CAAC,KAAK,IAAI,IAAI,IAAI,CAAC,CAAC,GAAG,IAAI,IAAI;wBAC9B,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,MAAM,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE;wBACjE,CAAC,CAAC,EAAE,CAAC;oBACT,MAAM,GAAG,GAAG,CAAC,CAAC,UAAU,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;oBAC7D,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,WAAW,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,GAAG,GAAG,GAAG,EAAE,CAClH,CAAC;gBACJ,CAAC;YACH,CAAC;QACH,CAAC,CAAC;QAEF,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;YAChB,UAAU,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;QAC1B,CAAC;aAAM,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YACxB,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC;YAC3C,KAAK,CAAC,IAAI,CAAC,yBAAyB,CAAC,CAAC;YACtC,KAAK,CAAC,IAAI,CAAC,kBAAkB,SAAS,CAAC,MAAM,kBAAkB,MAAM,CAAC,MAAM,IAAI,CAAC,CAAC;YAClF,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;gBAC1B,UAAU,CAAC,CAAa,CAAC,CAAC;gBAC1B,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACjB,CAAC;YACD,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"}

package/dist/mcp-server/tools/definitions/predict-variant.tool.d.ts

@@ -0,0 +1,58 @@
+/**
+ * @fileoverview Tool to predict functional consequences of sequence variants using Ensembl VEP.
+ * @module mcp-server/tools/definitions/predict-variant
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const ensemblPredictVariant: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    variant: z.ZodString;
+    species: z.ZodDefault<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    results: z.ZodArray<z.ZodObject<{
+        input: z.ZodOptional<z.ZodString>;
+        chromosome: z.ZodOptional<z.ZodString>;
+        start: z.ZodOptional<z.ZodNumber>;
+        end: z.ZodOptional<z.ZodNumber>;
+        assemblyName: z.ZodOptional<z.ZodString>;
+        mostSevereConsequence: z.ZodOptional<z.ZodString>;
+        transcriptConsequences: z.ZodArray<z.ZodObject<{
+            transcriptId: z.ZodOptional<z.ZodString>;
+            geneId: z.ZodOptional<z.ZodString>;
+            geneSymbol: z.ZodOptional<z.ZodString>;
+            consequenceTerms: z.ZodArray<z.ZodString>;
+            impact: z.ZodOptional<z.ZodString>;
+            biotype: z.ZodOptional<z.ZodString>;
+            hgvsc: z.ZodOptional<z.ZodString>;
+            hgvsp: z.ZodOptional<z.ZodString>;
+            aminoAcids: z.ZodOptional<z.ZodString>;
+            sift: z.ZodOptional<z.ZodObject<{
+                prediction: z.ZodString;
+                score: z.ZodNumber;
+            }, z.core.$strip>>;
+            polyphen: z.ZodOptional<z.ZodObject<{
+                prediction: z.ZodString;
+                score: z.ZodNumber;
+            }, z.core.$strip>>;
+        }, z.core.$strip>>;
+        colocatedVariants: z.ZodArray<z.ZodObject<{
+            id: z.ZodOptional<z.ZodString>;
+            alleleString: z.ZodOptional<z.ZodString>;
+            clinicalSignificance: z.ZodOptional<z.ZodArray<z.ZodString>>;
+            pubmed: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        }, z.core.$strip>>;
+    }, z.core.$strip>>;
+    totalCount: z.ZodNumber;
+}, z.core.$strip>, readonly [{
+    readonly reason: "invalid_notation";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "The variant notation is malformed or cannot be parsed by VEP.";
+    readonly recovery: string;
+}, {
+    readonly reason: "not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "The variant location falls outside any known transcript or assembly region.";
+    readonly recovery: string;
+}], {
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
+//# sourceMappingURL=predict-variant.tool.d.ts.map

package/dist/mcp-server/tools/definitions/predict-variant.tool.d.ts.map

@@ -0,0 +1 @@
+{"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;AA6GjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwMhC,CAAC"}