npm - @cyanheads/ensembl-mcp-server - Versions diffs - 0.4.1 → 0.4.3 - Mend

@cyanheads/ensembl-mcp-server 0.4.1 → 0.4.3

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 (47) hide show

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

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

@@ -7,6 +7,9 @@ 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>;
+    max_transcript_consequences: z.ZodDefault<z.ZodNumber>;
+    max_pubmed_ids_per_variant: z.ZodDefault<z.ZodNumber>;
+    include_all_colocated_pubmed: z.ZodDefault<z.ZodBoolean>;
 }, z.core.$strip>, z.ZodObject<{
     results: z.ZodArray<z.ZodObject<{
         input: z.ZodOptional<z.ZodString>;
@@ -34,11 +37,13 @@ export declare const ensemblPredictVariant: import("@cyanheads/mcp-ts-core").Too
                 score: z.ZodNumber;
             }, z.core.$strip>>;
         }, z.core.$strip>>;
+        transcriptConsequencesTotal: z.ZodOptional<z.ZodNumber>;
         colocatedVariants: z.ZodArray<z.ZodObject<{
             id: z.ZodOptional<z.ZodString>;
             alleleString: z.ZodOptional<z.ZodString>;
             clinicalSignificance: z.ZodOptional<z.ZodArray<z.ZodString>>;
             pubmed: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+            pubmedTotal: z.ZodOptional<z.ZodNumber>;
         }, z.core.$strip>>;
     }, z.core.$strip>>;
     totalCount: z.ZodNumber;
@@ -54,5 +59,8 @@ export declare const ensemblPredictVariant: import("@cyanheads/mcp-ts-core").Too
     readonly recovery: string;
 }], {
     readonly notice: z.ZodOptional<z.ZodString>;
+    readonly truncated: z.ZodOptional<z.ZodBoolean>;
+    readonly shown: z.ZodOptional<z.ZodNumber>;
+    readonly cap: z.ZodOptional<z.ZodNumber>;
 }>;
 //# sourceMappingURL=predict-variant.tool.d.ts.map

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

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/predict-variant.tool.js CHANGED Viewed

@@ -65,7 +65,13 @@ const ColocatedVariantSchema = z.object({
     pubmed: z
         .array(z.number().describe('A PubMed ID for literature citing this variant.'))
         .optional()
-        .describe('PubMed IDs for literature associated with this variant.'),
+        .describe('PubMed IDs for literature associated with this variant, capped to ' +
+        'max_pubmed_ids_per_variant. pubmedTotal reports the full count when the list was capped.'),
+    pubmedTotal: z
+        .number()
+        .optional()
+        .describe('Total PubMed IDs available for this variant before the max_pubmed_ids_per_variant cap. ' +
+        'Equals the returned pubmed length when the list was not capped.'),
 });
 const VepResultSchema = z.object({
     input: z.string().optional().describe('The input variant notation as submitted to VEP.'),
@@ -80,8 +86,14 @@ const VepResultSchema = z.object({
         '(e.g. stop_gained, missense_variant, synonymous_variant).'),
     transcriptConsequences: z
         .array(TranscriptConsequenceSchema.describe('Consequence details for one affected transcript, including impact, HGVS notation, and pathogenicity scores.'))
-        .describe('Per-transcript consequence details. High-impact variants may affect many transcripts; ' +
-        'focus on canonical transcripts (isCanonical from ensembl_lookup_gene) for primary effect.'),
+        .describe('Per-transcript consequence details, capped to max_transcript_consequences. High-impact ' +
+        'variants may affect many transcripts; focus on canonical transcripts (isCanonical from ' +
+        'ensembl_lookup_gene) for primary effect. transcriptConsequencesTotal reports the full count.'),
+    transcriptConsequencesTotal: z
+        .number()
+        .optional()
+        .describe('Total transcript consequences available before the max_transcript_consequences cap. ' +
+        'Equals the returned transcriptConsequences length when not capped.'),
     colocatedVariants: z
         .array(ColocatedVariantSchema.describe('A known variant at the same genomic position from public databases (dbSNP, ClinVar).'))
         .describe('Known variants at the same position from public databases (dbSNP, ClinVar). ' +
@@ -96,7 +108,11 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
         'impact level (HIGH/MODERATE/LOW/MODIFIER), and any colocated known variants with clinical significance. ' +
         'HGVS input: provide the full notation including transcript version for best results. ' +
         'Region+allele input: Ensembl normalizes chromosome names and canonical vertebrate output omits the chr ' +
-        'prefix (a chr-prefixed name is also accepted).',
+        'prefix (a chr-prefixed name is also accepted). ' +
+        'By default the response caps transcript consequences (max_transcript_consequences) and per-variant ' +
+        'PubMed IDs (max_pubmed_ids_per_variant) to keep large VEP results compact — well-studied variants ' +
+        'like rs334 otherwise carry 60+ consequences and 100+ citations. Truthful totals are always reported; ' +
+        'set a cap to 0 (or include_all_colocated_pubmed=true) to retrieve the full set.',
     annotations: { readOnlyHint: true, openWorldHint: true, idempotentHint: true },
     input: z.object({
         variant: z
@@ -115,6 +131,29 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
             .describe('Species in Ensembl internal format. Default is homo_sapiens. ' +
             'For non-human variants, set the appropriate species ' +
             '(e.g. mus_musculus for mouse). Use ensembl_list_species to discover valid values.'),
+        max_transcript_consequences: z
+            .number()
+            .int()
+            .min(0)
+            .default(10)
+            .describe('Maximum transcript consequences to return per VEP record. High-impact variants can affect ' +
+            '60+ transcripts; the default keeps the response focused on the top consequences. ' +
+            'Set to 0 to return every transcript consequence uncapped. ' +
+            'transcriptConsequencesTotal on each record always reports the true pre-cap count.'),
+        max_pubmed_ids_per_variant: z
+            .number()
+            .int()
+            .min(0)
+            .default(10)
+            .describe('Maximum PubMed IDs to return per colocated known variant. Well-studied variants (e.g. rs334) ' +
+            'cite 100+ papers; the default trims each list. Set to 0 to return every PubMed ID uncapped. ' +
+            'pubmedTotal on each colocated variant reports the true pre-cap count. ' +
+            'Ignored when include_all_colocated_pubmed is true.'),
+        include_all_colocated_pubmed: z
+            .boolean()
+            .default(false)
+            .describe('When true, return every PubMed ID for each colocated variant, overriding ' +
+            'max_pubmed_ids_per_variant. Default false to keep responses compact.'),
     }),
     output: z.object({
         results: z
@@ -124,7 +163,19 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
         totalCount: z.number().describe('Number of VEP consequence records returned.'),
     }),
     enrichment: {
-        notice: z.string().optional().describe('Guidance when no results are returned.'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Guidance when no results are returned or when caps omitted detail.'),
+        truncated: z
+            .boolean()
+            .optional()
+            .describe('True when transcript consequences were capped at max_transcript_consequences.'),
+        shown: z
+            .number()
+            .optional()
+            .describe('Total transcript consequences returned across all records after the cap.'),
+        cap: z.number().optional().describe('The max_transcript_consequences limit applied.'),
     },
     errors: [
         {
@@ -159,10 +210,12 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
                 .catch((err) => {
                 const msg = err instanceof Error ? err.message : String(err);
                 if (/invalid|unrecognized|parse|malformed/i.test(msg)) {
-                    throw ctx.fail('invalid_notation', `Invalid region+allele notation "${input.variant}": ${msg}`);
+                    throw ctx.fail('invalid_notation', `Invalid region+allele notation "${input.variant}": ${msg}`, { ...ctx.recoveryFor('invalid_notation') });
                 }
                 if (/not found|outside/i.test(msg)) {
-                    throw ctx.fail('not_found', `Variant location not found: ${msg}`);
+                    throw ctx.fail('not_found', `Variant location not found: ${msg}`, {
+                        ...ctx.recoveryFor('not_found'),
+                    });
                 }
                 throw err;
             });
@@ -174,10 +227,12 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
                 const msg = err instanceof Error ? err.message : String(err);
                 // A well-formed rsID that dbSNP does not know reports "No variant found with ID …".
                 if (/not found|no variant|unknown variant/i.test(msg)) {
-                    throw ctx.fail('not_found', `Variant identifier ${input.variant} not found in dbSNP.`);
+                    throw ctx.fail('not_found', `Variant identifier ${input.variant} not found in dbSNP.`, {
+                        ...ctx.recoveryFor('not_found'),
+                    });
                 }
                 if (/invalid|unrecognized|parse|malformed/i.test(msg)) {
-                    throw ctx.fail('invalid_notation', `Invalid variant identifier "${input.variant}": ${msg}`);
+                    throw ctx.fail('invalid_notation', `Invalid variant identifier "${input.variant}": ${msg}`, { ...ctx.recoveryFor('invalid_notation') });
                 }
                 throw err;
             });
@@ -188,20 +243,80 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
                 .catch((err) => {
                 const msg = err instanceof Error ? err.message : String(err);
                 if (/invalid|unrecognized|parse|malformed|hgvs/i.test(msg)) {
-                    throw ctx.fail('invalid_notation', `Invalid HGVS notation "${input.variant}": ${msg}`);
+                    throw ctx.fail('invalid_notation', `Invalid HGVS notation "${input.variant}": ${msg}`, {
+                        ...ctx.recoveryFor('invalid_notation'),
+                    });
                 }
                 if (/not found/i.test(msg)) {
-                    throw ctx.fail('not_found', `Variant ${input.variant} not found.`);
+                    throw ctx.fail('not_found', `Variant ${input.variant} not found.`, {
+                        ...ctx.recoveryFor('not_found'),
+                    });
                 }
                 throw err;
             });
         }
-        if (results.length === 0) {
+        // VEP returns the full consequence + colocated-variant set; cap post-fetch so common
+        // calls stay compact by default while the totals stay truthful. A cap of 0 (or
+        // include_all_colocated_pubmed for the nested PubMed lists) disables it.
+        const capConsequences = input.max_transcript_consequences > 0;
+        const capPubmed = input.max_pubmed_ids_per_variant > 0 && !input.include_all_colocated_pubmed;
+        let consequencesShown = 0;
+        let consequencesTotal = 0;
+        let pubmedCapped = false;
+        const shaped = results.map((r) => {
+            consequencesTotal += r.transcriptConsequences.length;
+            const transcriptConsequences = capConsequences
+                ? r.transcriptConsequences.slice(0, input.max_transcript_consequences)
+                : r.transcriptConsequences;
+            consequencesShown += transcriptConsequences.length;
+            const colocatedVariants = r.colocatedVariants.map((cv) => {
+                if (!cv.pubmed)
+                    return cv;
+                const pubmedTotal = cv.pubmed.length;
+                const pubmed = capPubmed ? cv.pubmed.slice(0, input.max_pubmed_ids_per_variant) : cv.pubmed;
+                if (pubmed.length < pubmedTotal)
+                    pubmedCapped = true;
+                return { ...cv, pubmed, pubmedTotal };
+            });
+            return {
+                ...r,
+                transcriptConsequences,
+                transcriptConsequencesTotal: r.transcriptConsequences.length,
+                colocatedVariants,
+            };
+        });
+        if (shaped.length === 0) {
             ctx.enrich.notice(`No VEP results for "${input.variant}". ` +
                 'Verify the notation format and that the position falls within an annotated region.');
         }
-        ctx.enrich.total(results.length);
-        return { results, totalCount: results.length };
+        else {
+            // Both caps can trip on one call (rs334: 66 consequences and 100+ PubMed IDs).
+            // ctx.enrich.notice is last-wins, so compose the omission fragments into ONE string.
+            const fragments = [];
+            const consequencesOmitted = consequencesTotal - consequencesShown;
+            if (consequencesOmitted > 0) {
+                fragments.push(`showing ${consequencesShown} of ${consequencesTotal} transcript consequences`);
+            }
+            if (pubmedCapped) {
+                fragments.push(`capped PubMed IDs to ${input.max_pubmed_ids_per_variant} per colocated variant`);
+            }
+            if (fragments.length > 0) {
+                const guidance = `${fragments.join('; ')}. Raise max_transcript_consequences (0 returns all) ` +
+                    'or set include_all_colocated_pubmed=true for the full detail.';
+                if (consequencesOmitted > 0) {
+                    ctx.enrich.truncated({
+                        shown: consequencesShown,
+                        cap: input.max_transcript_consequences,
+                        guidance,
+                    });
+                }
+                else {
+                    ctx.enrich.notice(guidance);
+                }
+            }
+        }
+        ctx.enrich.total(shaped.length);
+        return { results: shaped, totalCount: shaped.length };
     },
     format: (result) => {
         const lines = [];
@@ -228,13 +343,20 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
                         cvLine += ` — ${cv.clinicalSignificance.join(', ')}`;
                     }
                     if (cv.pubmed?.length) {
-                        cvLine += ` | PubMed: ${cv.pubmed.join(', ')}`;
+                        const pubmedTotal = cv.pubmedTotal ?? cv.pubmed.length;
+                        const pubmedSuffix = pubmedTotal > cv.pubmed.length
+                            ? ` (showing ${cv.pubmed.length} of ${pubmedTotal})`
+                            : '';
+                        cvLine += ` | PubMed: ${cv.pubmed.join(', ')}${pubmedSuffix}`;
                     }
                     lines.push(cvLine);
                 }
             }
             if (r.transcriptConsequences.length > 0) {
-                lines.push(`\n**Transcript consequences (${r.transcriptConsequences.length}):**`);
+                const shownTc = r.transcriptConsequences.length;
+                const totalTc = r.transcriptConsequencesTotal ?? shownTc;
+                const tcCount = totalTc > shownTc ? `${shownTc} of ${totalTc}` : `${shownTc}`;
+                lines.push(`\n**Transcript consequences (${tcCount}):**`);
                 for (const tc of r.transcriptConsequences) {
                     const geneLabel = tc.geneSymbol ?? tc.geneId ?? 'unknown';
                     lines.push(`\n#### ${geneLabel} — ${tc.transcriptId ?? 'unknown'}`);

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package/dist/mcp-server/tools/definitions/query-region.tool.d.ts CHANGED Viewed

@@ -10,9 +10,9 @@ export declare const ensemblQueryRegion: import("@cyanheads/mcp-ts-core").ToolDe
     feature: z.ZodDefault<z.ZodArray<z.ZodEnum<{
         exon: "exon";
         gene: "gene";
+        regulatory: "regulatory";
         transcript: "transcript";
         variation: "variation";
-        regulatory: "regulatory";
     }>>>;
     biotype: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>, z.ZodObject<{

package/dist/mcp-server/tools/definitions/query-region.tool.d.ts.map CHANGED Viewed

	@@ -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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EAwK7B~~,CAAC"}
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"}

package/dist/mcp-server/tools/definitions/query-region.tool.js CHANGED Viewed

@@ -122,10 +122,14 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
             if (/invalid.*region|coordinate|parse/i.test(msg) ||
                 /is not a valid start|is not a valid end|is not a valid chr/i.test(msg) ||
                 /no slice found/i.test(msg)) {
-                throw ctx.fail('invalid_region', `Invalid region "${input.region}": ${msg}`);
+                throw ctx.fail('invalid_region', `Invalid region "${input.region}": ${msg}`, {
+                    ...ctx.recoveryFor('invalid_region'),
+                });
             }
             if (/species|invalid|unrecognized/i.test(msg)) {
-                throw ctx.fail('invalid_species', `Species "${input.species}" not recognized.`);
+                throw ctx.fail('invalid_species', `Species "${input.species}" not recognized.`, {
+                    ...ctx.recoveryFor('invalid_species'),
+                });
             }
             throw err;
         });

package/dist/mcp-server/tools/definitions/query-region.tool.js.map CHANGED Viewed

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

@@ -227,7 +227,7 @@ export class EnsemblService {
         const operation = `EnsemblService.fetch:${path.split('?')[0]}`;
         const reqCtx = requestContextService.createRequestContext({
             operation,
-            parentContext: { requestId: ctx.requestId },
+            parentContext: ctx,
         });
         return withRetry(() => this.fetchJson(path, ctx, options), {
             operation,

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

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

@@ -1,8 +1,8 @@
 {
   "name": "@cyanheads/ensembl-mcp-server",
-  "version": "0.4.1",
+  "version": "0.4.3",
   "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.",
+  "description": "Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross-database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP.",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -81,7 +81,7 @@
     }
   ],
   "license": "Apache-2.0",
-  "packageManager": "bun@1.3.14",
+  "packageManager": "bun@1.4.0",
   "engines": {
     "bun": ">=1.3.0",
     "node": ">=24.0.0"
@@ -90,19 +90,19 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.10.14",
+    "@cyanheads/mcp-ts-core": "^0.12.3",
     "pino-pretty": "^13.1.3",
     "zod": "^4.4.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.5.0",
+    "@biomejs/biome": "^2.5.9",
     "@socketsecurity/bun-security-scanner": "^1.1.2",
-    "@types/node": "^26.0.0",
+    "@types/node": "^26.2.0",
     "depcheck": "^1.4.7",
-    "ignore": "^7.0.5",
-    "tsc-alias": "^1.9.0",
-    "typescript": "^6.0.3",
-    "vitest": "^4.1.10"
+    "ignore": "^7.0.6",
+    "tsc-alias": "^1.9.2",
+    "typescript": "^7.0.2",
+    "vitest": "^4.1.11"
   },
   "trustedDependencies": ["@socketsecurity/bun-security-scanner"]
 }