@omniradiology/omnirad 0.1.3

package/db/index.ts

@@ -0,0 +1,350 @@
+import Database from "better-sqlite3";
+import { drizzle } from "drizzle-orm/better-sqlite3";
+import * as schema from "./schema";
+import path from "path";
+import fs from "fs";
+
+// Ensure the data directory exists
+const dataDir = path.join(process.cwd(), "data");
+if (!fs.existsSync(dataDir)) {
+    fs.mkdirSync(dataDir, { recursive: true });
+}
+
+const dbPath = path.join(dataDir, "omnirad.db");
+
+// Singleton pattern - reuse connection across hot reloads in dev
+const globalForDb = globalThis as unknown as {
+    __omniradDb: ReturnType<typeof drizzle> | undefined;
+    __omniradSqlite: Database.Database | undefined;
+};
+
+if (!globalForDb.__omniradSqlite) {
+    globalForDb.__omniradSqlite = new Database(dbPath);
+    globalForDb.__omniradSqlite.pragma("journal_mode = WAL");
+    globalForDb.__omniradSqlite.pragma("foreign_keys = ON");
+    globalForDb.__omniradSqlite.pragma("busy_timeout = 5000"); // 5 seconds to wait for lock
+
+    // Auto-create tables if they don't exist
+    // Wrap in try/catch to avoid build-time crashes if another worker is creating them
+    try {
+        globalForDb.__omniradSqlite.exec(`
+        CREATE TABLE IF NOT EXISTS patients (
+            id TEXT PRIMARY KEY,
+            patient_id_number TEXT,
+            patient_name TEXT NOT NULL,
+            date_of_birth TEXT,
+            age INTEGER,
+            gender TEXT,
+            mobile TEXT,
+            address TEXT,
+            contact_info TEXT,
+            notes TEXT,
+            created_at TEXT NOT NULL,
+            updated_at TEXT
+        );
+
+        CREATE TABLE IF NOT EXISTS reports (
+            id TEXT PRIMARY KEY,
+            patient_id TEXT REFERENCES patients(id) ON DELETE CASCADE,
+            patient_name TEXT,
+            modality TEXT,
+            urgency TEXT,
+            report_status TEXT DEFAULT 'Pending',
+            report_data TEXT NOT NULL,
+            image_data TEXT,
+            created_at TEXT NOT NULL
+        );
+
+        CREATE TABLE IF NOT EXISTS config (
+            id INTEGER PRIMARY KEY DEFAULT 1,
+            n8n_webhook_url TEXT DEFAULT '',
+            supabase_url TEXT DEFAULT '',
+            supabase_anon_key TEXT DEFAULT ''
+        );
+
+        CREATE TABLE IF NOT EXISTS profile (
+            id INTEGER PRIMARY KEY DEFAULT 1,
+            full_name TEXT DEFAULT '',
+            role TEXT DEFAULT '',
+            hospital_name TEXT DEFAULT '',
+            department TEXT DEFAULT ''
+        );
+
+        CREATE TABLE IF NOT EXISTS appearance (
+            id INTEGER PRIMARY KEY DEFAULT 1,
+            theme TEXT DEFAULT 'dark',
+            template TEXT DEFAULT 'standard',
+            hospital_name TEXT DEFAULT '',
+            logo TEXT DEFAULT ''
+        );
+
+        CREATE TABLE IF NOT EXISTS users (
+            id TEXT PRIMARY KEY,
+            full_name TEXT NOT NULL,
+            username TEXT NOT NULL UNIQUE,
+            email TEXT NOT NULL UNIQUE,
+            password_hash TEXT NOT NULL,
+            role TEXT DEFAULT 'User',
+            created_at TEXT NOT NULL
+        );
+
+        CREATE TABLE IF NOT EXISTS sessions (
+            id TEXT PRIMARY KEY,
+            user_id TEXT NOT NULL,
+            expires_at INTEGER NOT NULL,
+            FOREIGN KEY (user_id) REFERENCES users(id)
+        );
+
+        CREATE TABLE IF NOT EXISTS ai_configurations (
+            id TEXT PRIMARY KEY,
+            provider_type TEXT NOT NULL,
+            provider_name TEXT NOT NULL,
+            api_endpoint_url TEXT,
+            api_secret_key TEXT,
+            model_name TEXT NOT NULL,
+            is_active INTEGER DEFAULT 0,
+            is_vision_capable INTEGER DEFAULT 0,
+            max_tokens INTEGER DEFAULT 4096,
+            temperature REAL DEFAULT 0.3,
+            timeout_seconds INTEGER DEFAULT 120,
+            created_at TEXT NOT NULL,
+            updated_at TEXT
+        );
+
+        CREATE TABLE IF NOT EXISTS segmentation_configurations (
+            id TEXT PRIMARY KEY,
+            deployment_mode TEXT,
+            provider_name TEXT,
+            model_name TEXT,
+            model_type TEXT DEFAULT 'medsam3',
+            base_url TEXT,
+            health_endpoint TEXT,
+            predict_endpoint TEXT,
+            api_secret_key TEXT,
+            timeout_seconds INTEGER,
+            supports_contours INTEGER,
+            supports_3d INTEGER,
+            returns_mask INTEGER,
+            returns_box INTEGER,
+            is_active INTEGER,
+            created_at TEXT,
+            updated_at TEXT
+        );
+
+        CREATE TABLE IF NOT EXISTS prompt_templates (
+            id TEXT PRIMARY KEY,
+            name TEXT NOT NULL,
+            template TEXT NOT NULL,
+            is_active INTEGER DEFAULT 0,
+            created_at TEXT NOT NULL,
+            updated_at TEXT
+        );
+
+        CREATE TABLE IF NOT EXISTS report_generation_logs (
+            id TEXT PRIMARY KEY,
+            report_id TEXT,
+            ai_config_id TEXT,
+            model_used TEXT,
+            prompt_template_id TEXT,
+            raw_llm_response TEXT,
+            parsed_successfully INTEGER,
+            retry_count INTEGER,
+            generation_time_ms INTEGER,
+            error_message TEXT,
+            created_at TEXT NOT NULL,
+            FOREIGN KEY (ai_config_id) REFERENCES ai_configurations(id)
+        );
+
+        CREATE TABLE IF NOT EXISTS chat_messages (
+            id INTEGER PRIMARY KEY AUTOINCREMENT,
+            session_id TEXT NOT NULL,
+            role TEXT NOT NULL,
+            content TEXT NOT NULL,
+            viewer_actions TEXT,
+            references_data TEXT,
+            patient_id TEXT,
+            created_at TEXT DEFAULT CURRENT_TIMESTAMP
+        );
+
+        CREATE TABLE IF NOT EXISTS compliance_settings (
+            id INTEGER PRIMARY KEY DEFAULT 1,
+            data_retention_days INTEGER DEFAULT 2555,
+            audit_retention_days INTEGER DEFAULT 2555,
+            session_timeout_minutes INTEGER DEFAULT 15,
+            idle_timeout_minutes INTEGER DEFAULT 30,
+            enable_gdpr_export INTEGER DEFAULT 1,
+            enable_gdpr_anonymize INTEGER DEFAULT 1,
+            enable_gdpr_restriction INTEGER DEFAULT 1,
+            legal_basis TEXT DEFAULT 'legitimate_interest',
+            privacy_policy_url TEXT,
+            dpo_contact_email TEXT,
+            updated_at TEXT
+        );
+
+        CREATE TABLE IF NOT EXISTS fhir_integration_config (
+            id INTEGER PRIMARY KEY DEFAULT 1,
+            enabled INTEGER DEFAULT 0,
+            public_base_url TEXT DEFAULT '',
+            auth_mode TEXT DEFAULT 'bearer_token',
+            inbound_service_request_enabled INTEGER DEFAULT 0,
+            outbound_read_enabled INTEGER DEFAULT 1,
+            external_fhir_base_url TEXT DEFAULT '',
+            external_fhir_auth_type TEXT DEFAULT 'none',
+            external_fhir_client_id TEXT DEFAULT '',
+            external_fhir_client_secret TEXT,
+            external_fhir_bearer_token TEXT,
+            api_token_hash TEXT,
+            created_at TEXT,
+            updated_at TEXT
+        );
+
+        CREATE TABLE IF NOT EXISTS worklist_orders (
+            id TEXT PRIMARY KEY,
+            source_system TEXT DEFAULT 'FHIR',
+            fhir_service_request_id TEXT,
+            patient_id TEXT REFERENCES patients(id) ON DELETE CASCADE,
+            patient_name TEXT,
+            patient_identifier TEXT,
+            status TEXT DEFAULT 'active',
+            intent TEXT DEFAULT 'order',
+            priority TEXT DEFAULT 'routine',
+            urgency TEXT DEFAULT 'Routine',
+            modality TEXT,
+            requested_procedure TEXT,
+            reason TEXT,
+            authored_on TEXT,
+            requester_display TEXT,
+            raw_fhir TEXT,
+            created_at TEXT NOT NULL,
+            updated_at TEXT
+        );
+
+        CREATE TABLE IF NOT EXISTS patient_privacy_controls (
+            id TEXT PRIMARY KEY,
+            patient_id TEXT NOT NULL REFERENCES patients(id) ON DELETE CASCADE,
+            restriction TEXT,
+            consent_status TEXT,
+            anonymized_at TEXT,
+            anonymized_by TEXT,
+            last_exported_at TEXT,
+            last_exported_by TEXT,
+            created_at TEXT NOT NULL,
+            updated_at TEXT
+        );
+    `);
+
+        // ─── Migrations for existing databases ──────────────────────────────
+        // Add patient_id column to reports if it doesn't already exist
+        try {
+            const cols = globalForDb.__omniradSqlite!.pragma('table_info(reports)') as any[];
+            const hasPatientId = cols.some((c: any) => c.name === 'patient_id');
+            if (!hasPatientId) {
+                globalForDb.__omniradSqlite!.exec(`ALTER TABLE reports ADD COLUMN patient_id TEXT REFERENCES patients(id) ON DELETE CASCADE;`);
+                console.log('[OmniRad Db] Migrated: Added patient_id column to reports table.');
+            }
+        } catch (migErr) {
+            console.warn('[OmniRad Db] Migration check for patient_id skipped:', migErr);
+        }
+
+        // Add age column to patients if it doesn't already exist
+        try {
+            const cols = globalForDb.__omniradSqlite!.pragma('table_info(patients)') as any[];
+            const hasAge = cols.some((c: any) => c.name === 'age');
+            if (!hasAge) {
+                globalForDb.__omniradSqlite!.exec(`ALTER TABLE patients ADD COLUMN age INTEGER;`);
+                console.log('[OmniRad Db] Migrated: Added age column to patients table.');
+            }
+        } catch (migErr) {
+            console.warn('[OmniRad Db] Migration check for patients age skipped:', migErr);
+        }
+
+        // Add mobile and address columns to patients if they don't already exist
+        try {
+            const cols = globalForDb.__omniradSqlite!.pragma('table_info(patients)') as any[];
+            if (!cols.some((c: any) => c.name === 'mobile')) {
+                globalForDb.__omniradSqlite!.exec(`ALTER TABLE patients ADD COLUMN mobile TEXT;`);
+                console.log('[OmniRad Db] Migrated: Added mobile column to patients table.');
+            }
+            if (!cols.some((c: any) => c.name === 'address')) {
+                globalForDb.__omniradSqlite!.exec(`ALTER TABLE patients ADD COLUMN address TEXT;`);
+                console.log('[OmniRad Db] Migrated: Added address column to patients table.');
+            }
+        } catch (migErr) {
+            console.warn('[OmniRad Db] Migration check for patients mobile/address skipped:', migErr);
+        }
+
+        // Also ensure position column exists on users (from a prior migration)
+        try {
+            const userCols = globalForDb.__omniradSqlite!.pragma('table_info(users)') as any[];
+            const hasPosition = userCols.some((c: any) => c.name === 'position');
+            if (!hasPosition) {
+                globalForDb.__omniradSqlite!.exec(`ALTER TABLE users ADD COLUMN position TEXT DEFAULT '';`);
+            }
+        } catch (migErr) { /* ignore */ }
+
+        // Ensure PACS columns exist on reports (from a prior migration)
+        try {
+            const repCols = globalForDb.__omniradSqlite!.pragma('table_info(reports)') as any[];
+            const hasPacsStudy = repCols.some((c: any) => c.name === 'pacs_study_uid');
+            if (!hasPacsStudy) {
+                globalForDb.__omniradSqlite!.exec(`
+                    ALTER TABLE reports ADD COLUMN pacs_study_uid TEXT;
+                    ALTER TABLE reports ADD COLUMN pacs_series_uid TEXT;
+                    ALTER TABLE reports ADD COLUMN pacs_source TEXT;
+                `);
+            }
+        } catch (migErr) { /* ignore */ }
+
+        // Ensure PACS columns exist on the config table (migration for databases created before PACS support)
+        try {
+            const cfgCols = globalForDb.__omniradSqlite!.pragma('table_info(config)') as any[];
+            const addIfMissing = (col: string, def: string) => {
+                if (!cfgCols.some((c: any) => c.name === col)) {
+                    globalForDb.__omniradSqlite!.exec(`ALTER TABLE config ADD COLUMN ${col} TEXT DEFAULT '${def}';`);
+                    console.log(`[OmniRad Db] Migrated: Added ${col} column to config table.`);
+                }
+            };
+            addIfMissing('pacs_orthanc_url', '');
+            addIfMissing('pacs_auth_type', 'none');
+            addIfMissing('pacs_username', '');
+            addIfMissing('pacs_password', '');
+            addIfMissing('pacs_bearer_token', '');
+            addIfMissing('pacs_ae_title', '');
+        } catch (migErr) {
+            console.warn('[OmniRad Db] Migration check for config PACS columns skipped:', migErr);
+        }
+
+        // Add purpose, langsmith_api_key, langsmith_project columns to ai_configurations
+        try {
+            const aiCols = globalForDb.__omniradSqlite!.pragma('table_info(ai_configurations)') as any[];
+            if (!aiCols.some((c: any) => c.name === 'purpose')) {
+                globalForDb.__omniradSqlite!.exec(`ALTER TABLE ai_configurations ADD COLUMN purpose TEXT DEFAULT 'report_generation';`);
+                console.log('[OmniRad Db] Migrated: Added purpose column to ai_configurations table.');
+            }
+            if (!aiCols.some((c: any) => c.name === 'langsmith_api_key')) {
+                globalForDb.__omniradSqlite!.exec(`ALTER TABLE ai_configurations ADD COLUMN langsmith_api_key TEXT;`);
+                console.log('[OmniRad Db] Migrated: Added langsmith_api_key column to ai_configurations table.');
+            }
+            if (!aiCols.some((c: any) => c.name === 'langsmith_project')) {
+                globalForDb.__omniradSqlite!.exec(`ALTER TABLE ai_configurations ADD COLUMN langsmith_project TEXT;`);
+                console.log('[OmniRad Db] Migrated: Added langsmith_project column to ai_configurations table.');
+            }
+        } catch (migErr) {
+            console.warn('[OmniRad Db] Migration check for ai_configurations copilot columns skipped:', migErr);
+        }
+
+    } catch (e: any) {
+        if (e.code === 'SQLITE_BUSY') {
+            console.warn('[OmniRad Db] SQLite is busy during auto-creation (another worker might be creating tables). Ignoring.');
+        } else {
+            console.error('[OmniRad Db] Error auto-creating tables:', e);
+        }
+    }
+}
+
+if (!globalForDb.__omniradDb) {
+    globalForDb.__omniradDb = drizzle(globalForDb.__omniradSqlite!, { schema });
+}
+
+export const db = globalForDb.__omniradDb;
+export const sqlite = globalForDb.__omniradSqlite!;

package/db/migrations/0000_odd_quasimodo.sql

@@ -0,0 +1,117 @@
+CREATE TABLE `ai_configurations` (
+	`id` text PRIMARY KEY NOT NULL,
+	`provider_type` text NOT NULL,
+	`provider_name` text NOT NULL,
+	`api_endpoint_url` text,
+	`api_secret_key` text,
+	`model_name` text NOT NULL,
+	`is_active` integer DEFAULT false,
+	`is_vision_capable` integer DEFAULT false,
+	`max_tokens` integer DEFAULT 4096,
+	`temperature` real DEFAULT 0.3,
+	`timeout_seconds` integer DEFAULT 120,
+	`created_at` text NOT NULL,
+	`updated_at` text
+);
+--> statement-breakpoint
+CREATE TABLE `appearance` (
+	`id` integer PRIMARY KEY DEFAULT 1 NOT NULL,
+	`theme` text DEFAULT 'dark',
+	`template` text DEFAULT 'standard',
+	`hospital_name` text DEFAULT '',
+	`logo` text DEFAULT ''
+);
+--> statement-breakpoint
+CREATE TABLE `config` (
+	`id` integer PRIMARY KEY DEFAULT 1 NOT NULL,
+	`n8n_webhook_url` text DEFAULT '',
+	`supabase_url` text DEFAULT '',
+	`supabase_anon_key` text DEFAULT '',
+	`pacs_orthanc_url` text DEFAULT '',
+	`pacs_auth_type` text DEFAULT 'none',
+	`pacs_username` text DEFAULT '',
+	`pacs_password` text DEFAULT '',
+	`pacs_bearer_token` text DEFAULT '',
+	`pacs_ae_title` text DEFAULT ''
+);
+--> statement-breakpoint
+CREATE TABLE `patients` (
+	`id` text PRIMARY KEY NOT NULL,
+	`patient_id_number` text,
+	`patient_name` text NOT NULL,
+	`date_of_birth` text,
+	`gender` text,
+	`contact_info` text,
+	`notes` text,
+	`created_at` text NOT NULL,
+	`updated_at` text
+);
+--> statement-breakpoint
+CREATE TABLE `profile` (
+	`id` integer PRIMARY KEY DEFAULT 1 NOT NULL,
+	`full_name` text DEFAULT '',
+	`role` text DEFAULT '',
+	`hospital_name` text DEFAULT '',
+	`department` text DEFAULT ''
+);
+--> statement-breakpoint
+CREATE TABLE `prompt_templates` (
+	`id` text PRIMARY KEY NOT NULL,
+	`name` text NOT NULL,
+	`template` text NOT NULL,
+	`is_active` integer DEFAULT false,
+	`created_at` text NOT NULL,
+	`updated_at` text
+);
+--> statement-breakpoint
+CREATE TABLE `report_generation_logs` (
+	`id` text PRIMARY KEY NOT NULL,
+	`report_id` text,
+	`ai_config_id` text,
+	`model_used` text,
+	`prompt_template_id` text,
+	`raw_llm_response` text,
+	`parsed_successfully` integer,
+	`retry_count` integer,
+	`generation_time_ms` integer,
+	`error_message` text,
+	`created_at` text NOT NULL,
+	FOREIGN KEY (`ai_config_id`) REFERENCES `ai_configurations`(`id`) ON UPDATE no action ON DELETE no action
+);
+--> statement-breakpoint
+CREATE TABLE `reports` (
+	`id` text PRIMARY KEY NOT NULL,
+	`patient_id` text,
+	`patient_name` text,
+	`modality` text,
+	`urgency` text,
+	`report_status` text DEFAULT 'Pending',
+	`report_data` text NOT NULL,
+	`image_data` text,
+	`pacs_study_uid` text,
+	`pacs_series_uid` text,
+	`pacs_source` text,
+	`created_at` text NOT NULL,
+	FOREIGN KEY (`patient_id`) REFERENCES `patients`(`id`) ON UPDATE no action ON DELETE cascade
+);
+--> statement-breakpoint
+CREATE TABLE `sessions` (
+	`id` text PRIMARY KEY NOT NULL,
+	`user_id` text NOT NULL,
+	`expires_at` integer NOT NULL,
+	FOREIGN KEY (`user_id`) REFERENCES `users`(`id`) ON UPDATE no action ON DELETE no action
+);
+--> statement-breakpoint
+CREATE TABLE `users` (
+	`id` text PRIMARY KEY NOT NULL,
+	`full_name` text NOT NULL,
+	`username` text NOT NULL,
+	`email` text NOT NULL,
+	`password_hash` text NOT NULL,
+	`role` text DEFAULT 'User',
+	`position` text DEFAULT '',
+	`created_at` text NOT NULL
+);
+--> statement-breakpoint
+CREATE UNIQUE INDEX `users_username_unique` ON `users` (`username`);--> statement-breakpoint
+CREATE UNIQUE INDEX `users_email_unique` ON `users` (`email`);