#!/usr/bin/env node
import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
import { z } from 'zod';
import { getDocumentation } from './tools/get-documentation.js';
import { generatePedigree } from './tools/generate-pedigree.js';
const GeneTestSchema = z.object({
type: z.enum(['-', 'S', 'T']),
result: z.enum(['-', 'P', 'N']),
});
// Condition schema per Bennett 2008 NSGC standard (free text)
const ConditionSchema = z.object({
name: z
.string()
.describe(
'Condition/disease name (free text): "Breast cancer", "Huntington\'s disease", "Type 2 diabetes"',
),
age: z.number().optional().describe('Age at diagnosis/onset'),
});
// Use passthrough() to allow arbitrary gene test properties
const IndividualSchema = z
.object({
name: z
.string()
.max(7, 'name exceeds 7 char limit')
.describe('Unique identifier (max 7 chars)'),
sex: z.enum(['M', 'F', 'U']).describe('M=male, F=female, U=unknown'),
display_name: z
.string()
.max(13, 'display_name exceeds 13 char limit')
.optional()
.describe('Human-readable name (max 13 chars)'),
top_level: z
.boolean()
.optional()
.describe(
'ONLY for founders with NO known parents. Siblings without partners still need mother/father refs.',
),
proband: z.boolean().optional().describe('True for the index case'),
mother: z
.string()
.optional()
.describe(
'Reference to mother name. Siblings share same mother/father.',
),
father: z
.string()
.optional()
.describe(
'Reference to father name. Siblings share same mother/father.',
),
age: z.number().optional().describe('Current age'),
yob: z.number().optional().describe('Year of birth'),
status: z.number().optional().describe('0=alive, 1=deceased'),
mztwin: z
.string()
.optional()
.describe('Monozygotic twin marker (same value = identical twins)'),
dztwin: z
.string()
.optional()
.describe('Dizygotic twin marker (same value = fraternal twins)'),
ashkenazi: z.number().optional().describe('0=no, 1=Ashkenazi ancestry'),
noparents: z
.boolean()
.optional()
.describe(
'Shows adoption brackets [ ]. Use for adopted individuals.',
),
// Bennett 2008 standard: conditions as free text
conditions: z
.array(ConditionSchema)
.optional()
.describe(
'ONLY way to get colored fills. Array of conditions/diseases (free text). Gene tests alone do NOT color symbols.',
),
// Bennett standard indicators
carrier: z
.boolean()
.optional()
.describe('Carrier status (dot in center)'),
pregnant: z
.boolean()
.optional()
.describe('Pregnancy (P inside symbol)'),
terminated: z
.boolean()
.optional()
.describe(
'PREGNANCY LOSS ONLY (stillbirth/miscarriage). Shows small triangle. NEVER use for living individuals!',
),
divorced: z
.boolean()
.optional()
.describe('Divorced/separated (hash marks on partnership line)'),
// Gene tests (pattern: {gene}_gene_test)
brca1_gene_test: GeneTestSchema.optional(),
brca2_gene_test: GeneTestSchema.optional(),
palb2_gene_test: GeneTestSchema.optional(),
atm_gene_test: GeneTestSchema.optional(),
chek2_gene_test: GeneTestSchema.optional(),
})
.passthrough();
const server = new McpServer({
name: 'pedigree-mcp',
version: '1.0.0',
});
// Tool 1: Get Documentation
server.tool(
'get_pedigree_documentation',
'Returns comprehensive documentation for the pedigree data format. ALWAYS call this first before generating a pedigree to understand the required data structure, properties, and examples.',
{},
async () => {
const documentation = getDocumentation();
return {
content: [
{
type: 'text',
text: documentation,
},
],
};
},
);
// Tool 2: Generate Pedigree
server.tool(
'generate_pedigree',
'Generates a pedigree tree (Bennett 2008 standard) in PNG or SVG format. IMPORTANT: Use mother/father for ALL individuals with known parents - siblings share same parents. Only use top_level:true for founders with NO known parents.',
{
dataset: z
.array(IndividualSchema)
.describe('Array of family members in pedigreejs format'),
width: z
.number()
.optional()
.default(800)
.describe('Image width in pixels'),
height: z
.number()
.optional()
.default(600)
.describe('Image height in pixels'),
symbol_size: z
.number()
.optional()
.default(35)
.describe('Size of individual symbols'),
background: z
.string()
.optional()
.default('#ffffff')
.describe('Background color'),
labels: z
.array(z.enum(['age', 'yob']))
.optional()
.default(['age'])
.describe(
'Which demographics to show: age, yob, or both. Condition and gene test labels are always shown automatically.',
),
format: z
.enum(['png', 'svg'])
.optional()
.default('png')
.describe(
'Output format: png (base64 image, default) or svg (XML text)',
),
},
async params => {
const result = await generatePedigree({
dataset: params.dataset as any,
width: params.width,
height: params.height,
symbol_size: params.symbol_size,
background: params.background,
labels: params.labels,
format: params.format,
});
const formatText = params.format === 'svg' ? 'SVG' : 'PNG';
if (params.format === 'svg') {
return {
content: [
{
type: 'text',
text: `Pedigree generated successfully (${formatText} format)!\nIndividuals: ${result.metadata.individual_count}\nGenerations: ${result.metadata.generation_count}\nDimensions: ${result.metadata.width}x${result.metadata.height}px`,
},
{
type: 'text',
text: result.svg_string!,
},
],
};
} else {
return {
content: [
{
type: 'text',
text: `Pedigree generated successfully (${formatText} format)!\nIndividuals: ${result.metadata.individual_count}\nGenerations: ${result.metadata.generation_count}\nDimensions: ${result.metadata.width}x${result.metadata.height}px`,
},
{
type: 'image',
data: result.image_base64!,
mimeType: 'image/png',
},
],
};
}
},
);
async function main() {
const transport = new StdioServerTransport();
await server.connect(transport);
console.error('Pedigree MCP server started');
}
main().catch(console.error);
