// src/utils/validation.ts
import { z } from 'zod';
/**
* Zod validation schemas for AlphaGenome MCP Server inputs
*/
// ============================================================================
// Base Validation Schemas
// ============================================================================
// Chromosome validation
const chromosomeSchema = z
.string()
.regex(
/^chr([1-9]|1[0-9]|2[0-2]|X|Y)$/,
'Invalid chromosome format (use chr1-chr22, chrX, chrY)'
);
// Nucleotide validation (case-insensitive, converts to uppercase)
const nucleotideSchema = z
.string()
.regex(/^[ATGCatgc]+$/, 'Invalid nucleotide (use A, T, G, C only)')
.transform((s) => s.toUpperCase());
// Positive integer validation
const positiveIntSchema = z.number().int().positive('Position must be a positive integer');
// ============================================================================
// Variant Prediction Validation
// ============================================================================
export const variantPredictionSchema = z
.object({
chromosome: chromosomeSchema,
position: positiveIntSchema,
ref: nucleotideSchema,
alt: nucleotideSchema,
output_types: z
.array(
z.enum([
'rna_seq',
'cage',
'splice',
'histone',
'tf_binding',
'dnase',
'atac',
'contact_map',
])
)
.optional(),
tissue_type: z.string().optional(),
})
.refine((data) => data.ref !== data.alt, {
message: 'Reference and alternate alleles must be different',
});
// ============================================================================
// Region Analysis Validation
// ============================================================================
export const regionAnalysisSchema = z
.object({
chromosome: chromosomeSchema,
start: positiveIntSchema,
end: positiveIntSchema,
analysis_types: z
.array(z.enum(['promoter', 'enhancer', 'silencer', 'tf_binding', 'chromatin_state']))
.optional(),
resolution: z.enum(['base', 'window']).optional(),
})
.refine((data) => data.end > data.start, {
message: 'End position must be greater than start position',
})
.refine((data) => data.end - data.start >= 1000, {
message: 'Region must be at least 1kb (1,000 bp)',
})
.refine((data) => data.end - data.start <= 1000000, {
message: 'Region must be at most 1Mb (1,000,000 bp)',
});
// ============================================================================
// Batch Scoring Validation
// ============================================================================
export const batchScoreSchema = z.object({
variants: z
.array(
z.object({
chromosome: chromosomeSchema,
position: positiveIntSchema,
ref: nucleotideSchema,
alt: nucleotideSchema,
variant_id: z.string().optional(),
})
)
.min(1, 'At least one variant is required')
.max(100, 'Maximum 100 variants allowed'),
scoring_metric: z.enum(['rna_seq', 'splice', 'regulatory_impact', 'combined']),
top_n: z.number().int().min(1).max(100).optional().default(10),
include_interpretation: z.boolean().optional().default(false),
});
// ============================================================================
// Validation Helper Function
// ============================================================================
/**
* Validate input data against a Zod schema
* @param schema - Zod schema to validate against
* @param data - Data to validate
* @returns Validated and typed data
* @throws ValidationError with detailed error messages
*/
export function validateInput<T>(schema: z.ZodSchema<T>, data: unknown): T {
try {
return schema.parse(data);
} catch (error) {
if (error instanceof z.ZodError) {
const messages = error.errors.map((e) => {
const path = e.path.length > 0 ? `${e.path.join('.')}: ` : '';
return `${path}${e.message}`;
});
throw new Error(`Validation error:\n${messages.join('\n')}`);
}
throw error;
}
}
/**
* Safe validation that returns result object instead of throwing
* @param schema - Zod schema to validate against
* @param data - Data to validate
* @returns Object with success flag and either data or error
*/
export function safeValidateInput<T>(
schema: z.ZodSchema<T>,
data: unknown
): { success: true; data: T } | { success: false; error: string } {
try {
const validated = schema.parse(data);
return { success: true, data: validated };
} catch (error) {
if (error instanceof z.ZodError) {
const messages = error.errors.map((e) => {
const path = e.path.length > 0 ? `${e.path.join('.')}: ` : '';
return `${path}${e.message}`;
});
return { success: false, error: messages.join('\n') };
}
return { success: false, error: 'Unknown validation error' };
}
}
