gnomad-genetics-mcp-server: Instructions file for Codex

Developer Protocol

Server: gnomad-genetics-mcp-server Version: 0.4.2 Framework: @cyanheads/mcp-ts-core ^0.13.16 Engines: Bun ≥1.4.0, Node ≥24.0.0 MCP SDK: @modelcontextprotocol/server ^2.3.1 Zod: ^4.6.7

Read the framework docs first: node_modules/@cyanheads/mcp-ts-core/CLAUDE.md contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.

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Core Rules

• Logic throws, framework catches. Tool/resource handlers are pure — throw on failure, no try/catch. Plain Error is fine; the framework catches, classifies, and formats. Use error factories (notFound(), validationError(), etc.) when the error code matters.
• Use ctx.log for request-scoped logging. No console calls.
• Use ctx.state for tenant-scoped storage. Never access persistence directly.
• Need input the caller didn't supply? return ctx.requestInput(...) and read ctx.inputs when the handler is re-entered. Never await for user input mid-handler.
• Secrets in env vars only — never hardcoded.
• Cut noise. Add only what earns its place: no speculative generality, no guards for states the framework already prevents (Zod-validated params, classified errors), no abstraction until a third caller proves it, no option nothing sets.
• Close the loop on issues. When implementing work tracked by a GitHub issue, comment on the issue with what landed and close it. Do both — a comment without a close leaves stale issues open; a close without a comment leaves no record of what shipped. The comment is for future readers — state the concrete changes, not the conversation that produced them.

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Patterns

Real definitions from this server, condensed. The full versions live under src/mcp-server/.

Tool (src/mcp-server/tools/definitions/gnomad-get-gene-constraint.tool.ts)

import { tool, z } from '@cyanheads/mcp-ts-core';
import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
import { getGnomadService } from '@/services/gnomad/gnomad-service.js';
import { datasetField, geneField, referenceGenomeField } from '../shared-schemas.js';

export const gnomadGetGeneConstraint = tool('gnomad_get_gene_constraint', {
  title: 'gnomad-genetics-mcp-server: get gene constraint',
  description: 'Fetch gnomAD loss-of-function constraint for a gene — pLI, LOEUF, …',
  annotations: { readOnlyHint: true, openWorldHint: true, idempotentHint: true },
  input: z.object({ gene: geneField, dataset: datasetField, reference_genome: referenceGenomeField }),
  output: z.object({
    gene_id: z.string().describe('Ensembl gene ID resolved for the gene.'),
    symbol: z.string().describe('HGNC gene symbol.'),
    pli: z.number().nullable().describe('pLI — probability of LoF intolerance; >0.9 intolerant.'),
    // … remaining flat constraint fields, all nullable
    constraint_flags: z.array(z.string()).describe('Caveat flags gnomAD attaches to the constraint.'),
  }),
  // Typed error contract — ctx.fail('gene_not_found', …) is type-checked against this union.
  errors: [
    { reason: 'gene_not_found', code: JsonRpcErrorCode.NotFound,
      when: 'No gene matched the symbol or Ensembl ID in this build.',
      recovery: 'Check the symbol spelling or resolve a stable Ensembl gene ID via ensembl_lookup_gene.' },
  ],

  async handler(input, ctx) {
    const svc = getGnomadService();
    const dsCtx = svc.resolveDatasetContext(input.dataset, input.reference_genome);
    const constraint = await svc.getGeneConstraint(input.gene, dsCtx, ctx);
    if (!constraint) throw ctx.fail('gene_not_found', `Gene "${input.gene}" not found.`);
    return constraint;
  },

  // format() populates content[] — the markdown twin of structuredContent.
  // Different clients read different surfaces (Claude Code → structuredContent,
  // Claude Desktop → content[]); both must carry the same data.
  // Enforced at lint time: every field in `output` must appear in the rendered text.
  format: (result) => [{ type: 'text', text: `## ${result.symbol} (${result.gene_id})` }],
});