openGeneMap (db.ts)

Manages SQLite database for gene capsules with schema migrations, indices for failure codes and q-values, and storage for coding pattern strategies and hints.

import Database from 'better-sqlite3';
import * as fs from 'fs';
import * as path from 'path';
import * as os from 'os';

export const HELIX_DIR = path.join(os.homedir(), '.helix');
export const GENE_MAP_DB_PATH = path.join(HELIX_DIR, 'gene-map.db');

/**
 * Create the coding-capsule table if it does not already exist.
 * Idempotent — safe to call on every open.
 */
function ensureSchema(db: Database.Database): void {
  db.exec(`CREATE TABLE IF NOT EXISTS gene_capsules_coding (
    id INTEGER PRIMARY KEY AUTOINCREMENT,
    failure_code TEXT NOT NULL,
    category TEXT NOT NULL DEFAULT 'coding',
    pattern TEXT,
    typical_files TEXT,
    issue_keywords TEXT,
    strategy TEXT NOT NULL,
    hint TEXT NOT NULL,
    example_fix TEXT,
    q_value REAL DEFAULT 0.5,
    success_count INTEGER D

... (truncated -- full source via MCP)