fhir-engine 0.4.0 → 0.4.1

package/CHANGELOG.md

@@ -5,6 +5,24 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.4.1] - 2026-03-15
+
+### Fixed
+
+- **`resolvePackages()` — 0 resource types after cache linking** — When the system cache package was installed by third-party tools (e.g. Firely Terminal) that only place `package.json` inside the `package/` subdirectory (not at cache root), `PackageScanner` would discover the package at the wrong depth, causing `PackageLoader` to construct a double-nested `package/package` path → ENOENT → 0 StructureDefinitions loaded → 0 tables created → `no such table: Patient_References`
+- **New helper `ensureCacheRootManifest()`** — Copies `package/package.json` to cache root before creating junction/symlink, ensuring consistent structure regardless of which tool populated the cache
+
+### Changed
+
+- **Test suite expanded** — from 95 to 96 tests:
+  - New test: verify cache root `package.json` exists after resolve (Firely Terminal scenario)
+
+### Notes
+
+- Resolves `FIX_ZERO_RESOURCE_TYPES.md` — Method A fix applied in `fhir-engine`; optional Method B (fhir-definition scanner hardening) deferred to P1
+
+---
+
 ## [0.4.0] - 2026-03-15
 
 ### Added

package/dist/cjs/index.cjs

@@ -246,6 +246,7 @@ async function resolvePackages(config, options) {
       const cachePath = cache.getPath(ig.name, version);
       if (cachePath) {
         logger?.info(`Found ${ig.name}@${version} in system cache, linking...`);
+        ensureCacheRootManifest(cachePath);
         createLink(cachePath, localPath);
         results.push({ name: ig.name, version, path: localPath, source: "cache" });
         continue;
@@ -266,6 +267,7 @@ async function resolvePackages(config, options) {
         errors.push({ name: ig.name, error: `Failed to locate cached package after download` });
         continue;
       }
+      ensureCacheRootManifest(newCachePath);
       createLink(newCachePath, localPath);
       results.push({ name: ig.name, version, path: localPath, source: "download" });
     } catch (err) {
@@ -281,6 +283,13 @@ async function resolvePackages(config, options) {
     errors
   };
 }
+function ensureCacheRootManifest(cachePath) {
+  const rootManifest = (0, import_node_path2.join)(cachePath, "package.json");
+  const nestedManifest = (0, import_node_path2.join)(cachePath, "package", "package.json");
+  if (!(0, import_node_fs2.existsSync)(rootManifest) && (0, import_node_fs2.existsSync)(nestedManifest)) {
+    (0, import_node_fs2.copyFileSync)(nestedManifest, rootManifest);
+  }
+}
 function createLink(target, linkPath) {
   if ((0, import_node_fs2.existsSync)(linkPath)) {
     try {

package/dist/cjs/index.cjs.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/index.ts", "../../src/engine.ts", "../../src/adapter-factory.ts", "../../src/config.ts", "../../src/logger.ts", "../../src/package-resolver.ts"],
-  "sourcesContent": ["// fhir-engine \u2014 public API\n\nexport { createFhirEngine } from './engine.js';\nexport { defineConfig, loadFhirConfig } from './config.js';\nexport { createConsoleLogger } from './logger.js';\nexport { createAdapter } from './adapter-factory.js';\nexport { resolvePackages } from './package-resolver.js';\n\nexport type {\n  FhirEngine,\n  FhirEngineConfig,\n  FhirEnginePlugin,\n  FhirEngineStatus,\n  EngineContext,\n  DatabaseConfig,\n  SqliteDatabaseConfig,\n  SqliteWasmDatabaseConfig,\n  PostgresDatabaseConfig,\n  PackagesConfig,\n  Logger,\n  ResolvePackagesOptions,\n  ResolvedPackage,\n  ResolvePackagesResult,\n} from './types.js';\n\n// Re-export key upstream types for convenience\nexport type { DefinitionRegistry, DefinitionProvider } from 'fhir-definition';\nexport type { FhirRuntimeInstance } from 'fhir-runtime';\nexport type { FhirPersistence, StorageAdapter } from 'fhir-persistence';\n\n// ---------------------------------------------------------------------------\n// Search utilities (from fhir-persistence)\n// ---------------------------------------------------------------------------\n\nexport { parseSearchRequest, executeSearch } from 'fhir-persistence';\nexport type { SearchRequest, SearchResult, SearchOptions } from 'fhir-persistence';\n\n// ---------------------------------------------------------------------------\n// FHIRPath evaluation (from fhir-runtime)\n// ---------------------------------------------------------------------------\n\nexport { evalFhirPath, evalFhirPathBoolean, evalFhirPathString, evalFhirPathTyped } from 'fhir-runtime';\n", "import { loadDefinitionPackages } from 'fhir-definition';\nimport { createRuntime, extractSearchValues, extractAllSearchValues, extractReferences } from 'fhir-runtime';\nimport { FhirDefinitionBridge, FhirRuntimeProvider, FhirSystem, parseSearchRequest, executeSearch } from 'fhir-persistence';\n\nimport { createAdapter } from './adapter-factory.js';\nimport { loadFhirConfig } from './config.js';\nimport { createConsoleLogger } from './logger.js';\nimport { resolvePackages } from './package-resolver.js';\nimport type { EngineContext, FhirEngine, FhirEngineConfig, FhirEnginePlugin, FhirEngineStatus } from './types.js';\n\n/**\n * Resolve the SQL dialect from the database config type.\n */\nfunction resolveDialect(type: FhirEngineConfig['database']['type']): 'sqlite' | 'postgres' {\n  switch (type) {\n    case 'sqlite':\n    case 'sqlite-wasm':\n      return 'sqlite';\n    case 'postgres':\n      return 'postgres';\n  }\n}\n\n/**\n * Validate the engine configuration, throwing on missing required fields.\n */\nfunction validateConfig(config: FhirEngineConfig): void {\n  if (!config.database) {\n    throw new Error('fhir-engine: config.database is required');\n  }\n  if (!config.database.type) {\n    throw new Error('fhir-engine: config.database.type is required (sqlite | sqlite-wasm | postgres)');\n  }\n  if (!config.packages) {\n    throw new Error('fhir-engine: config.packages is required');\n  }\n  if (!config.packages.path) {\n    throw new Error('fhir-engine: config.packages.path is required');\n  }\n}\n\n/**\n * Run a lifecycle hook on all plugins in order.\n * Wraps errors with the plugin name for clear diagnostics.\n */\nasync function runPluginHook(\n  plugins: FhirEnginePlugin[],\n  hook: 'init' | 'start' | 'ready',\n  ctx: EngineContext,\n): Promise<void> {\n  for (const plugin of plugins) {\n    const fn = plugin[hook];\n    if (fn) {\n      try {\n        await fn.call(plugin, ctx);\n      } catch (err) {\n        throw new Error(\n          `fhir-engine: plugin \"${plugin.name}\" failed during ${hook}: ${err instanceof Error ? err.message : String(err)}`,\n          { cause: err },\n        );\n      }\n    }\n  }\n}\n\n/**\n * Create and bootstrap a fully initialized FHIR engine.\n *\n * This is the single entry point for all FHIR applications.\n * It assembles fhir-definition, fhir-runtime, and fhir-persistence\n * into a running system from a single configuration object.\n *\n * @example\n * ```ts\n * const engine = await createFhirEngine({\n *   database: { type: 'sqlite', path: ':memory:' },\n *   packages: { path: './fhir-packages' },\n * });\n *\n * const patient = await engine.persistence.createResource('Patient', {\n *   resourceType: 'Patient',\n *   name: [{ family: 'Smith', given: ['John'] }],\n * });\n *\n * await engine.stop();\n * ```\n */\nexport async function createFhirEngine(config?: FhirEngineConfig): Promise<FhirEngine> {\n  // \u2500\u2500 0. Resolve config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (!config) {\n    config = await loadFhirConfig();\n  }\n  validateConfig(config);\n\n  const logger = config.logger ?? createConsoleLogger();\n  const plugins = config.plugins ?? [];\n  logger.info('Initializing fhir-engine...');\n\n  // \u2500\u2500 1a. Resolve packages (download/link if config.igs is set) \u2500\n  if (config.igs && config.igs.length > 0) {\n    logger.info(`Resolving ${config.igs.length} IG package(s)...`);\n    const resolveResult = await resolvePackages(config, { logger });\n    for (const pkg of resolveResult.packages) {\n      logger.info(`Resolved ${pkg.name}@${pkg.version} (${pkg.source})`);\n    }\n    if (!resolveResult.success) {\n      for (const err of resolveResult.errors) {\n        logger.warn(`Failed to resolve package ${err.name}: ${err.error}`);\n      }\n    }\n  }\n\n  // \u2500\u2500 1b. Load FHIR definitions \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  logger.info(`Loading FHIR packages from: ${config.packages.path}`);\n  const { registry, result } = loadDefinitionPackages(config.packages.path);\n  logger.info(\n    `Loaded ${result.packages.length} package(s): ${result.packages.map((p) => `${p.name}@${p.version}`).join(', ')}`,\n  );\n\n  // \u2500\u2500 2. Create fhir-runtime \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  logger.info('Creating fhir-runtime instance...');\n  const runtime = await createRuntime({ definitions: registry, preloadCore: false });\n\n  // \u2500\u2500 3. Build provider bridges \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const definitionBridge = new FhirDefinitionBridge(registry);\n  const runtimeProvider = new FhirRuntimeProvider({\n    extractSearchValues,\n    extractAllSearchValues,\n    extractReferences,\n  });\n\n  // \u2500\u2500 4. Create storage adapter \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const adapter = createAdapter(config.database, logger);\n\n  // \u2500\u2500 5. Build EngineContext \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const ctx: { -readonly [K in keyof EngineContext]: EngineContext[K] } = {\n    config,\n    definitions: registry,\n    runtime,\n    adapter,\n    persistence: undefined,\n    logger,\n  };\n\n  // \u2500\u2500 6. INIT phase \u2014 plugins run before persistence \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (plugins.length > 0) {\n    logger.info(`Running init for ${plugins.length} plugin(s): ${plugins.map((p) => p.name).join(', ')}`);\n    await runPluginHook(plugins, 'init', ctx);\n  }\n\n  // \u2500\u2500 7. Initialize FhirSystem \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const dialect = resolveDialect(config.database.type);\n  const system = new FhirSystem(adapter, {\n    dialect,\n    runtimeProvider,\n    packageName: config.packageName ?? 'fhir-engine.default',\n    packageVersion: config.packageVersion ?? '1.0.0',\n  });\n\n  logger.info('Initializing persistence system (schema + migration)...');\n  const { persistence, sdRegistry, spRegistry, igResult, resourceTypes } =\n    await system.initialize(definitionBridge);\n\n  logger.info(`Persistence ready \u2014 IG action: ${igResult.action}, ${resourceTypes.length} resource type(s)`);\n\n  // ctx.persistence now available\n  ctx.persistence = persistence;\n\n  // \u2500\u2500 8. START phase \u2014 plugins can access persistence \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (plugins.length > 0) {\n    logger.info(`Running start for ${plugins.length} plugin(s)...`);\n    await runPluginHook(plugins, 'start', ctx);\n  }\n\n  // \u2500\u2500 9. READY phase \u2014 system fully operational \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (plugins.length > 0) {\n    logger.info(`Running ready for ${plugins.length} plugin(s)...`);\n    await runPluginHook(plugins, 'ready', ctx);\n  }\n\n  // \u2500\u2500 10. Return FhirEngine \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  let stopped = false;\n  const startedAt = new Date();\n  const loadedPackages = result.packages.map((p) => `${p.name}@${p.version}`);\n  const fhirVersions = [...new Set(\n    result.packages\n      .map((p) => {\n        if (p.name.includes('.r4.')) return '4.0';\n        if (p.name.includes('.r4b.')) return '4.3';\n        if (p.name.includes('.r5.')) return '5.0';\n        return undefined;\n      })\n      .filter(Boolean),\n  )] as string[];\n\n  const engine: FhirEngine = {\n    definitions: registry,\n    runtime,\n    adapter,\n    persistence,\n    sdRegistry,\n    spRegistry,\n    igResult,\n    resourceTypes,\n    logger,\n    context: ctx as EngineContext,\n\n    async search(resourceType, queryParams, options) {\n      const request = parseSearchRequest(resourceType, queryParams, spRegistry);\n      return executeSearch(adapter, request, spRegistry, options);\n    },\n\n    status(): FhirEngineStatus {\n      return {\n        fhirVersions,\n        loadedPackages,\n        resourceTypes,\n        databaseType: config.database.type,\n        igAction: igResult.action,\n        startedAt,\n        plugins: plugins.map((p) => p.name),\n      };\n    },\n\n    async stop() {\n      if (stopped) return;\n      stopped = true;\n      logger.info('Stopping fhir-engine...');\n\n      // Stop plugins in reverse registration order\n      for (let i = plugins.length - 1; i >= 0; i--) {\n        const plugin = plugins[i];\n        if (plugin.stop) {\n          try {\n            await plugin.stop.call(plugin, ctx as EngineContext);\n          } catch (err) {\n            logger.error(\n              `Plugin \"${plugin.name}\" failed during stop: ${err instanceof Error ? err.message : String(err)}`,\n            );\n          }\n        }\n      }\n\n      await adapter.close();\n      logger.info('fhir-engine stopped.');\n    },\n  };\n\n  logger.info('fhir-engine ready.');\n  return engine;\n}\n", "import { BetterSqlite3Adapter, SQLiteAdapter } from 'fhir-persistence';\nimport type { StorageAdapter } from 'fhir-persistence';\nimport type { DatabaseConfig, Logger } from './types.js';\n\n/**\n * Create a StorageAdapter from the database configuration.\n *\n * Supported adapters:\n * - `sqlite`      \u2192 BetterSqlite3Adapter (native, Node.js / Electron)\n * - `sqlite-wasm` \u2192 SQLiteAdapter (sql.js WASM, browser / cross-platform)\n * - `postgres`    \u2192 not yet available (PostgresAdapter not exported from fhir-persistence)\n */\nexport function createAdapter(config: DatabaseConfig, logger: Logger): StorageAdapter {\n  switch (config.type) {\n    case 'sqlite': {\n      logger.info(`Creating BetterSqlite3Adapter (path: ${config.path})`);\n      return new BetterSqlite3Adapter({\n        path: config.path,\n        wal: config.wal ?? true,\n        busyTimeout: config.busyTimeout ?? 5000,\n      });\n    }\n\n    case 'sqlite-wasm': {\n      logger.info(`Creating SQLiteAdapter (WASM, path: ${config.path})`);\n      return new SQLiteAdapter(config.path);\n    }\n\n    case 'postgres': {\n      throw new Error(\n        'fhir-engine: PostgreSQL adapter is not yet available. ' +\n        'PostgresAdapter is not exported from fhir-persistence v0.1.0. ' +\n        'Use database.type = \"sqlite\" for now.',\n      );\n    }\n\n    default: {\n      const _exhaustive: never = config;\n      throw new Error(`fhir-engine: unknown database type: ${(_exhaustive as DatabaseConfig).type}`);\n    }\n  }\n}\n", "import { existsSync, readFileSync } from 'node:fs';\nimport { resolve, extname } from 'node:path';\nimport { pathToFileURL } from 'node:url';\nimport type { FhirEngineConfig, DatabaseConfig } from './types.js';\n\n// ---------------------------------------------------------------------------\n// defineConfig \u2014 typed identity helper for fhir.config.ts / .js\n// ---------------------------------------------------------------------------\n\n/**\n * Type-safe config helper for `fhir.config.ts` / `fhir.config.js`.\n *\n * @example\n * ```ts\n * // fhir.config.ts\n * import { defineConfig } from 'fhir-engine';\n *\n * export default defineConfig({\n *   database: { type: 'sqlite', path: './fhir.db' },\n *   packages: { path: './fhir-packages' },\n * });\n * ```\n */\nexport function defineConfig(config: FhirEngineConfig): FhirEngineConfig {\n  return config;\n}\n\n// ---------------------------------------------------------------------------\n// Config file discovery order\n// ---------------------------------------------------------------------------\n\nconst CONFIG_FILENAMES = [\n  'fhir.config.ts',\n  'fhir.config.js',\n  'fhir.config.mjs',\n  'fhir.config.json',\n] as const;\n\n// ---------------------------------------------------------------------------\n// loadFhirConfig \u2014 auto-discover and load config\n// ---------------------------------------------------------------------------\n\n/**\n * Load engine configuration from a file.\n *\n * If `configPath` is provided, loads that exact file.\n * Otherwise, searches the current working directory for config files\n * in this order: `fhir.config.ts` \u2192 `fhir.config.js` \u2192 `fhir.config.mjs` \u2192 `fhir.config.json`.\n *\n * Environment variable overrides are applied on top of the loaded config.\n *\n * @param configPath - Explicit path to a config file (optional).\n * @returns The resolved `FhirEngineConfig`.\n */\nexport async function loadFhirConfig(configPath?: string): Promise<FhirEngineConfig> {\n  let resolvedPath: string;\n\n  if (configPath) {\n    resolvedPath = resolve(configPath);\n    if (!existsSync(resolvedPath)) {\n      throw new Error(`fhir-engine: config file not found: ${resolvedPath}`);\n    }\n  } else {\n    const cwd = process.cwd();\n    const found = CONFIG_FILENAMES\n      .map((name) => resolve(cwd, name))\n      .find((p) => existsSync(p));\n    if (!found) {\n      throw new Error(\n        `fhir-engine: no config file found in ${cwd}. ` +\n        `Expected one of: ${CONFIG_FILENAMES.join(', ')}`,\n      );\n    }\n    resolvedPath = found;\n  }\n\n  const config = await loadConfigFile(resolvedPath);\n  return applyEnvOverrides(config);\n}\n\n// ---------------------------------------------------------------------------\n// File loaders\n// ---------------------------------------------------------------------------\n\nasync function loadConfigFile(filePath: string): Promise<FhirEngineConfig> {\n  const ext = extname(filePath);\n\n  if (ext === '.json') {\n    return loadJsonConfig(filePath);\n  }\n\n  if (ext === '.ts' || ext === '.js' || ext === '.mjs') {\n    return loadModuleConfig(filePath);\n  }\n\n  throw new Error(`fhir-engine: unsupported config file extension: ${ext}`);\n}\n\nfunction loadJsonConfig(filePath: string): FhirEngineConfig {\n  try {\n    const raw = readFileSync(filePath, 'utf-8');\n    return JSON.parse(raw) as FhirEngineConfig;\n  } catch (err) {\n    throw new Error(\n      `fhir-engine: failed to parse config file ${filePath}: ${err instanceof Error ? err.message : String(err)}`,\n      { cause: err },\n    );\n  }\n}\n\nasync function loadModuleConfig(filePath: string): Promise<FhirEngineConfig> {\n  try {\n    const fileUrl = pathToFileURL(filePath).href;\n    const mod = await import(fileUrl);\n    const config = mod.default ?? mod;\n\n    if (!config || typeof config !== 'object') {\n      throw new Error('config file must export a FhirEngineConfig object as default export');\n    }\n\n    return config as FhirEngineConfig;\n  } catch (err) {\n    if (err instanceof Error && err.message.includes('must export')) {\n      throw err;\n    }\n    throw new Error(\n      `fhir-engine: failed to load config file ${filePath}: ${err instanceof Error ? err.message : String(err)}`,\n      { cause: err },\n    );\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Environment variable overrides\n// ---------------------------------------------------------------------------\n\nconst VALID_DB_TYPES = ['sqlite', 'sqlite-wasm', 'postgres'] as const;\n\n/**\n * Apply environment variable overrides on top of a loaded config.\n *\n * | Env Variable        | Overrides                        |\n * |---------------------|----------------------------------|\n * | FHIR_DATABASE_TYPE  | config.database.type             |\n * | FHIR_DATABASE_URL   | config.database.path / .url      |\n * | FHIR_PACKAGES_PATH  | config.packages.path             |\n * | FHIR_LOG_LEVEL      | (stored for logger filtering)    |\n */\nexport function applyEnvOverrides(config: FhirEngineConfig): FhirEngineConfig {\n  const result = structuredClone(config);\n\n  const dbType = process.env.FHIR_DATABASE_TYPE;\n  const dbUrl = process.env.FHIR_DATABASE_URL;\n  const pkgPath = process.env.FHIR_PACKAGES_PATH;\n\n  if (dbType) {\n    if (!VALID_DB_TYPES.includes(dbType as typeof VALID_DB_TYPES[number])) {\n      throw new Error(\n        `fhir-engine: FHIR_DATABASE_TYPE must be one of: ${VALID_DB_TYPES.join(', ')}. Got: \"${dbType}\"`,\n      );\n    }\n    // Rebuild database config with overridden type\n    const validType = dbType as DatabaseConfig['type'];\n    if (validType === 'postgres') {\n      result.database = { type: 'postgres', url: (result.database as { url?: string }).url ?? '' };\n    } else if (validType === 'sqlite-wasm') {\n      result.database = { type: 'sqlite-wasm', path: (result.database as { path?: string }).path ?? '' };\n    } else {\n      result.database = { type: 'sqlite', path: (result.database as { path?: string }).path ?? '' };\n    }\n  }\n\n  if (dbUrl) {\n    const type = result.database?.type;\n    if (type === 'postgres') {\n      result.database = { ...result.database, type: 'postgres', url: dbUrl };\n    } else if (type === 'sqlite-wasm') {\n      result.database = { ...result.database, type: 'sqlite-wasm', path: dbUrl };\n    } else {\n      result.database = { ...result.database, type: 'sqlite', path: dbUrl };\n    }\n  }\n\n  if (pkgPath) {\n    result.packages = { ...result.packages, path: pkgPath };\n  }\n\n  return result;\n}\n", "import type { Logger } from './types.js';\n\n/**\n * Default console-based logger.\n */\nexport function createConsoleLogger(): Logger {\n  return {\n    debug: (message: string, ...args: unknown[]) => console.debug(`[fhir-engine] ${message}`, ...args),\n    info: (message: string, ...args: unknown[]) => console.info(`[fhir-engine] ${message}`, ...args),\n    warn: (message: string, ...args: unknown[]) => console.warn(`[fhir-engine] ${message}`, ...args),\n    error: (message: string, ...args: unknown[]) => console.error(`[fhir-engine] ${message}`, ...args),\n  };\n}\n", "import { resolve, join } from 'node:path';\nimport { existsSync, mkdirSync, symlinkSync, readFileSync, lstatSync } from 'node:fs';\nimport { PackageCache, PackageRegistryClient } from 'fhir-definition';\n\nimport type { FhirEngineConfig, ResolvePackagesOptions, ResolvedPackage, ResolvePackagesResult, Logger } from './types.js';\n\n/**\n * Ensure the given directory exists (recursive mkdir).\n */\nfunction ensureDirSync(dir: string): void {\n  if (!existsSync(dir)) {\n    mkdirSync(dir, { recursive: true });\n  }\n}\n\n/**\n * Check if a directory contains a FHIR package manifest.\n * Checks both root/package.json and package/package.json\n * (cached packages store content in a 'package' subdirectory).\n */\nfunction hasManifest(dir: string): boolean {\n  return existsSync(join(dir, 'package.json')) || existsSync(join(dir, 'package', 'package.json'));\n}\n\n/**\n * Read the version from a package.json file.\n * Checks both root and package/ subdirectory.\n * Returns the version string or 'local' if not found.\n */\nfunction readLocalVersion(pkgDir: string): string {\n  for (const candidate of [join(pkgDir, 'package.json'), join(pkgDir, 'package', 'package.json')]) {\n    try {\n      const raw = readFileSync(candidate, 'utf-8');\n      const manifest = JSON.parse(raw);\n      return manifest.version ?? 'local';\n    } catch {\n      // try next candidate\n    }\n  }\n  return 'local';\n}\n\n/**\n * Resolve FHIR packages into a project's packages directory.\n *\n * Resolution order for each package:\n * 1. Already exists in packagesPath \u2192 use as-is (source: 'local')\n * 2. Found in system cache (~/.fhir/packages) \u2192 create symlink/junction (source: 'cache')\n * 3. Download from FHIR Package Registry \u2192 cache \u2192 create symlink (source: 'download')\n *\n * @param config  Engine configuration (uses config.igs and config.packages.path)\n * @param options Override packages list, target path, download policy, or logger\n * @returns       Result with resolved packages and any errors\n *\n * @example\n * ```ts\n * const result = await resolvePackages(config);\n * if (!result.success) {\n *   console.warn('Some packages failed:', result.errors);\n * }\n * ```\n */\nexport async function resolvePackages(\n  config: FhirEngineConfig,\n  options?: ResolvePackagesOptions,\n): Promise<ResolvePackagesResult> {\n  const packagesPath = resolve(options?.packagesPath ?? config.packages.path);\n  const igs = options?.packages ?? config.igs ?? 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+  "sourcesContent": ["// fhir-engine \u2014 public API\n\nexport { createFhirEngine } from './engine.js';\nexport { defineConfig, loadFhirConfig } from './config.js';\nexport { createConsoleLogger } from './logger.js';\nexport { createAdapter } from './adapter-factory.js';\nexport { resolvePackages } from './package-resolver.js';\n\nexport type {\n  FhirEngine,\n  FhirEngineConfig,\n  FhirEnginePlugin,\n  FhirEngineStatus,\n  EngineContext,\n  DatabaseConfig,\n  SqliteDatabaseConfig,\n  SqliteWasmDatabaseConfig,\n  PostgresDatabaseConfig,\n  PackagesConfig,\n  Logger,\n  ResolvePackagesOptions,\n  ResolvedPackage,\n  ResolvePackagesResult,\n} from './types.js';\n\n// Re-export key upstream types for convenience\nexport type { DefinitionRegistry, DefinitionProvider } from 'fhir-definition';\nexport type { FhirRuntimeInstance } from 'fhir-runtime';\nexport type { FhirPersistence, StorageAdapter } from 'fhir-persistence';\n\n// ---------------------------------------------------------------------------\n// Search utilities (from fhir-persistence)\n// ---------------------------------------------------------------------------\n\nexport { parseSearchRequest, executeSearch } from 'fhir-persistence';\nexport type { SearchRequest, SearchResult, SearchOptions } from 'fhir-persistence';\n\n// ---------------------------------------------------------------------------\n// FHIRPath evaluation (from fhir-runtime)\n// ---------------------------------------------------------------------------\n\nexport { evalFhirPath, evalFhirPathBoolean, evalFhirPathString, evalFhirPathTyped } from 'fhir-runtime';\n", "import { loadDefinitionPackages } from 'fhir-definition';\nimport { createRuntime, extractSearchValues, extractAllSearchValues, extractReferences } from 'fhir-runtime';\nimport { FhirDefinitionBridge, FhirRuntimeProvider, FhirSystem, parseSearchRequest, executeSearch } from 'fhir-persistence';\n\nimport { createAdapter } from './adapter-factory.js';\nimport { loadFhirConfig } from './config.js';\nimport { createConsoleLogger } from './logger.js';\nimport { resolvePackages } from './package-resolver.js';\nimport type { EngineContext, FhirEngine, FhirEngineConfig, FhirEnginePlugin, FhirEngineStatus } from './types.js';\n\n/**\n * Resolve the SQL dialect from the database config type.\n */\nfunction resolveDialect(type: FhirEngineConfig['database']['type']): 'sqlite' | 'postgres' {\n  switch (type) {\n    case 'sqlite':\n    case 'sqlite-wasm':\n      return 'sqlite';\n    case 'postgres':\n      return 'postgres';\n  }\n}\n\n/**\n * Validate the engine configuration, throwing on missing required fields.\n */\nfunction validateConfig(config: FhirEngineConfig): void {\n  if (!config.database) {\n    throw new Error('fhir-engine: config.database is required');\n  }\n  if (!config.database.type) {\n    throw new Error('fhir-engine: config.database.type is required (sqlite | sqlite-wasm | postgres)');\n  }\n  if (!config.packages) {\n    throw new Error('fhir-engine: config.packages is required');\n  }\n  if (!config.packages.path) {\n    throw new Error('fhir-engine: config.packages.path is required');\n  }\n}\n\n/**\n * Run a lifecycle hook on all plugins in order.\n * Wraps errors with the plugin name for clear diagnostics.\n */\nasync function runPluginHook(\n  plugins: FhirEnginePlugin[],\n  hook: 'init' | 'start' | 'ready',\n  ctx: EngineContext,\n): Promise<void> {\n  for (const plugin of plugins) {\n    const fn = plugin[hook];\n    if (fn) {\n      try {\n        await fn.call(plugin, ctx);\n      } catch (err) {\n        throw new Error(\n          `fhir-engine: plugin \"${plugin.name}\" failed during ${hook}: ${err instanceof Error ? err.message : String(err)}`,\n          { cause: err },\n        );\n      }\n    }\n  }\n}\n\n/**\n * Create and bootstrap a fully initialized FHIR engine.\n *\n * This is the single entry point for all FHIR applications.\n * It assembles fhir-definition, fhir-runtime, and fhir-persistence\n * into a running system from a single configuration object.\n *\n * @example\n * ```ts\n * const engine = await createFhirEngine({\n *   database: { type: 'sqlite', path: ':memory:' },\n *   packages: { path: './fhir-packages' },\n * });\n *\n * const patient = await engine.persistence.createResource('Patient', {\n *   resourceType: 'Patient',\n *   name: [{ family: 'Smith', given: ['John'] }],\n * });\n *\n * await engine.stop();\n * ```\n */\nexport async function createFhirEngine(config?: FhirEngineConfig): Promise<FhirEngine> {\n  // \u2500\u2500 0. Resolve config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (!config) {\n    config = await loadFhirConfig();\n  }\n  validateConfig(config);\n\n  const logger = config.logger ?? createConsoleLogger();\n  const plugins = config.plugins ?? [];\n  logger.info('Initializing fhir-engine...');\n\n  // \u2500\u2500 1a. Resolve packages (download/link if config.igs is set) \u2500\n  if (config.igs && config.igs.length > 0) {\n    logger.info(`Resolving ${config.igs.length} IG package(s)...`);\n    const resolveResult = await resolvePackages(config, { logger });\n    for (const pkg of resolveResult.packages) {\n      logger.info(`Resolved ${pkg.name}@${pkg.version} (${pkg.source})`);\n    }\n    if (!resolveResult.success) {\n      for (const err of resolveResult.errors) {\n        logger.warn(`Failed to resolve package ${err.name}: ${err.error}`);\n      }\n    }\n  }\n\n  // \u2500\u2500 1b. Load FHIR definitions \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  logger.info(`Loading FHIR packages from: ${config.packages.path}`);\n  const { registry, result } = loadDefinitionPackages(config.packages.path);\n  logger.info(\n    `Loaded ${result.packages.length} package(s): ${result.packages.map((p) => `${p.name}@${p.version}`).join(', ')}`,\n  );\n\n  // \u2500\u2500 2. Create fhir-runtime \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  logger.info('Creating fhir-runtime instance...');\n  const runtime = await createRuntime({ definitions: registry, preloadCore: false });\n\n  // \u2500\u2500 3. Build provider bridges \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const definitionBridge = new FhirDefinitionBridge(registry);\n  const runtimeProvider = new FhirRuntimeProvider({\n    extractSearchValues,\n    extractAllSearchValues,\n    extractReferences,\n  });\n\n  // \u2500\u2500 4. Create storage adapter \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const adapter = createAdapter(config.database, logger);\n\n  // \u2500\u2500 5. Build EngineContext \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const ctx: { -readonly [K in keyof EngineContext]: EngineContext[K] } = {\n    config,\n    definitions: registry,\n    runtime,\n    adapter,\n    persistence: undefined,\n    logger,\n  };\n\n  // \u2500\u2500 6. INIT phase \u2014 plugins run before persistence \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (plugins.length > 0) {\n    logger.info(`Running init for ${plugins.length} plugin(s): ${plugins.map((p) => p.name).join(', ')}`);\n    await runPluginHook(plugins, 'init', ctx);\n  }\n\n  // \u2500\u2500 7. Initialize FhirSystem \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const dialect = resolveDialect(config.database.type);\n  const system = new FhirSystem(adapter, {\n    dialect,\n    runtimeProvider,\n    packageName: config.packageName ?? 'fhir-engine.default',\n    packageVersion: config.packageVersion ?? '1.0.0',\n  });\n\n  logger.info('Initializing persistence system (schema + migration)...');\n  const { persistence, sdRegistry, spRegistry, igResult, resourceTypes } =\n    await system.initialize(definitionBridge);\n\n  logger.info(`Persistence ready \u2014 IG action: ${igResult.action}, ${resourceTypes.length} resource type(s)`);\n\n  // ctx.persistence now available\n  ctx.persistence = persistence;\n\n  // \u2500\u2500 8. START phase \u2014 plugins can access persistence \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (plugins.length > 0) {\n    logger.info(`Running start for ${plugins.length} plugin(s)...`);\n    await runPluginHook(plugins, 'start', ctx);\n  }\n\n  // \u2500\u2500 9. READY phase \u2014 system fully operational \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (plugins.length > 0) {\n    logger.info(`Running ready for ${plugins.length} plugin(s)...`);\n    await runPluginHook(plugins, 'ready', ctx);\n  }\n\n  // \u2500\u2500 10. Return FhirEngine \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  let stopped = false;\n  const startedAt = new Date();\n  const loadedPackages = result.packages.map((p) => `${p.name}@${p.version}`);\n  const fhirVersions = [...new Set(\n    result.packages\n      .map((p) => {\n        if (p.name.includes('.r4.')) return '4.0';\n        if (p.name.includes('.r4b.')) return '4.3';\n        if (p.name.includes('.r5.')) return '5.0';\n        return undefined;\n      })\n      .filter(Boolean),\n  )] as string[];\n\n  const engine: FhirEngine = {\n    definitions: registry,\n    runtime,\n    adapter,\n    persistence,\n    sdRegistry,\n    spRegistry,\n    igResult,\n    resourceTypes,\n    logger,\n    context: ctx as EngineContext,\n\n    async search(resourceType, queryParams, options) {\n      const request = parseSearchRequest(resourceType, queryParams, spRegistry);\n      return executeSearch(adapter, request, spRegistry, options);\n    },\n\n    status(): FhirEngineStatus {\n      return {\n        fhirVersions,\n        loadedPackages,\n        resourceTypes,\n        databaseType: config.database.type,\n        igAction: igResult.action,\n        startedAt,\n        plugins: plugins.map((p) => p.name),\n      };\n    },\n\n    async stop() {\n      if (stopped) return;\n      stopped = true;\n      logger.info('Stopping fhir-engine...');\n\n      // Stop plugins in reverse registration order\n      for (let i = plugins.length - 1; i >= 0; i--) {\n        const plugin = plugins[i];\n        if (plugin.stop) {\n          try {\n            await plugin.stop.call(plugin, ctx as EngineContext);\n          } catch (err) {\n            logger.error(\n              `Plugin \"${plugin.name}\" failed during stop: ${err instanceof Error ? err.message : String(err)}`,\n            );\n          }\n        }\n      }\n\n      await adapter.close();\n      logger.info('fhir-engine stopped.');\n    },\n  };\n\n  logger.info('fhir-engine ready.');\n  return engine;\n}\n", "import { BetterSqlite3Adapter, SQLiteAdapter } from 'fhir-persistence';\nimport type { StorageAdapter } from 'fhir-persistence';\nimport type { DatabaseConfig, Logger } from './types.js';\n\n/**\n * Create a StorageAdapter from the database configuration.\n *\n * Supported adapters:\n * - `sqlite`      \u2192 BetterSqlite3Adapter (native, Node.js / Electron)\n * - `sqlite-wasm` \u2192 SQLiteAdapter (sql.js WASM, browser / cross-platform)\n * - `postgres`    \u2192 not yet available (PostgresAdapter not exported from fhir-persistence)\n */\nexport function createAdapter(config: DatabaseConfig, logger: Logger): StorageAdapter {\n  switch (config.type) {\n    case 'sqlite': {\n      logger.info(`Creating BetterSqlite3Adapter (path: ${config.path})`);\n      return new BetterSqlite3Adapter({\n        path: config.path,\n        wal: config.wal ?? true,\n        busyTimeout: config.busyTimeout ?? 5000,\n      });\n    }\n\n    case 'sqlite-wasm': {\n      logger.info(`Creating SQLiteAdapter (WASM, path: ${config.path})`);\n      return new SQLiteAdapter(config.path);\n    }\n\n    case 'postgres': {\n      throw new Error(\n        'fhir-engine: PostgreSQL adapter is not yet available. ' +\n        'PostgresAdapter is not exported from fhir-persistence v0.1.0. ' +\n        'Use database.type = \"sqlite\" for now.',\n      );\n    }\n\n    default: {\n      const _exhaustive: never = config;\n      throw new Error(`fhir-engine: unknown database type: ${(_exhaustive as DatabaseConfig).type}`);\n    }\n  }\n}\n", "import { existsSync, readFileSync } from 'node:fs';\nimport { resolve, extname } from 'node:path';\nimport { pathToFileURL } from 'node:url';\nimport type { FhirEngineConfig, DatabaseConfig } from './types.js';\n\n// ---------------------------------------------------------------------------\n// defineConfig \u2014 typed identity helper for fhir.config.ts / .js\n// ---------------------------------------------------------------------------\n\n/**\n * Type-safe config helper for `fhir.config.ts` / `fhir.config.js`.\n *\n * @example\n * ```ts\n * // fhir.config.ts\n * import { defineConfig } from 'fhir-engine';\n *\n * export default defineConfig({\n *   database: { type: 'sqlite', path: './fhir.db' },\n *   packages: { path: './fhir-packages' },\n * });\n * ```\n */\nexport function defineConfig(config: FhirEngineConfig): FhirEngineConfig {\n  return config;\n}\n\n// ---------------------------------------------------------------------------\n// Config file discovery order\n// ---------------------------------------------------------------------------\n\nconst CONFIG_FILENAMES = [\n  'fhir.config.ts',\n  'fhir.config.js',\n  'fhir.config.mjs',\n  'fhir.config.json',\n] as const;\n\n// ---------------------------------------------------------------------------\n// loadFhirConfig \u2014 auto-discover and load config\n// ---------------------------------------------------------------------------\n\n/**\n * Load engine configuration from a file.\n *\n * If `configPath` is provided, loads that exact file.\n * Otherwise, searches the current working directory for config files\n * in this order: `fhir.config.ts` \u2192 `fhir.config.js` \u2192 `fhir.config.mjs` \u2192 `fhir.config.json`.\n *\n * Environment variable overrides are applied on top of the loaded config.\n *\n * @param configPath - Explicit path to a config file (optional).\n * @returns The resolved `FhirEngineConfig`.\n */\nexport async function loadFhirConfig(configPath?: string): Promise<FhirEngineConfig> {\n  let resolvedPath: string;\n\n  if (configPath) {\n    resolvedPath = resolve(configPath);\n    if (!existsSync(resolvedPath)) {\n      throw new Error(`fhir-engine: config file not found: ${resolvedPath}`);\n    }\n  } else {\n    const cwd = process.cwd();\n    const found = CONFIG_FILENAMES\n      .map((name) => resolve(cwd, name))\n      .find((p) => existsSync(p));\n    if (!found) {\n      throw new Error(\n        `fhir-engine: no config file found in ${cwd}. ` +\n        `Expected one of: ${CONFIG_FILENAMES.join(', ')}`,\n      );\n    }\n    resolvedPath = found;\n  }\n\n  const config = await loadConfigFile(resolvedPath);\n  return applyEnvOverrides(config);\n}\n\n// ---------------------------------------------------------------------------\n// File loaders\n// ---------------------------------------------------------------------------\n\nasync function loadConfigFile(filePath: string): Promise<FhirEngineConfig> {\n  const ext = extname(filePath);\n\n  if (ext === '.json') {\n    return loadJsonConfig(filePath);\n  }\n\n  if (ext === '.ts' || ext === '.js' || ext === '.mjs') {\n    return loadModuleConfig(filePath);\n  }\n\n  throw new Error(`fhir-engine: unsupported config file extension: ${ext}`);\n}\n\nfunction loadJsonConfig(filePath: string): FhirEngineConfig {\n  try {\n    const raw = readFileSync(filePath, 'utf-8');\n    return JSON.parse(raw) as FhirEngineConfig;\n  } catch (err) {\n    throw new Error(\n      `fhir-engine: failed to parse config file ${filePath}: ${err instanceof Error ? err.message : String(err)}`,\n      { cause: err },\n    );\n  }\n}\n\nasync function loadModuleConfig(filePath: string): Promise<FhirEngineConfig> {\n  try {\n    const fileUrl = pathToFileURL(filePath).href;\n    const mod = await import(fileUrl);\n    const config = mod.default ?? mod;\n\n    if (!config || typeof config !== 'object') {\n      throw new Error('config file must export a FhirEngineConfig object as default export');\n    }\n\n    return config as FhirEngineConfig;\n  } catch (err) {\n    if (err instanceof Error && err.message.includes('must export')) {\n      throw err;\n    }\n    throw new Error(\n      `fhir-engine: failed to load config file ${filePath}: ${err instanceof Error ? err.message : String(err)}`,\n      { cause: err },\n    );\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Environment variable overrides\n// ---------------------------------------------------------------------------\n\nconst VALID_DB_TYPES = ['sqlite', 'sqlite-wasm', 'postgres'] as const;\n\n/**\n * Apply environment variable overrides on top of a loaded config.\n *\n * | Env Variable        | Overrides                        |\n * |---------------------|----------------------------------|\n * | FHIR_DATABASE_TYPE  | config.database.type             |\n * | FHIR_DATABASE_URL   | config.database.path / .url      |\n * | FHIR_PACKAGES_PATH  | config.packages.path             |\n * | FHIR_LOG_LEVEL      | (stored for logger filtering)    |\n */\nexport function applyEnvOverrides(config: FhirEngineConfig): FhirEngineConfig {\n  const result = structuredClone(config);\n\n  const dbType = process.env.FHIR_DATABASE_TYPE;\n  const dbUrl = process.env.FHIR_DATABASE_URL;\n  const pkgPath = process.env.FHIR_PACKAGES_PATH;\n\n  if (dbType) {\n    if (!VALID_DB_TYPES.includes(dbType as typeof VALID_DB_TYPES[number])) {\n      throw new Error(\n        `fhir-engine: FHIR_DATABASE_TYPE must be one of: ${VALID_DB_TYPES.join(', ')}. Got: \"${dbType}\"`,\n      );\n    }\n    // Rebuild database config with overridden type\n    const validType = dbType as DatabaseConfig['type'];\n    if (validType === 'postgres') {\n      result.database = { type: 'postgres', url: (result.database as { url?: string }).url ?? '' };\n    } else if (validType === 'sqlite-wasm') {\n      result.database = { type: 'sqlite-wasm', path: (result.database as { path?: string }).path ?? '' };\n    } else {\n      result.database = { type: 'sqlite', path: (result.database as { path?: string }).path ?? '' };\n    }\n  }\n\n  if (dbUrl) {\n    const type = result.database?.type;\n    if (type === 'postgres') {\n      result.database = { ...result.database, type: 'postgres', url: dbUrl };\n    } else if (type === 'sqlite-wasm') {\n      result.database = { ...result.database, type: 'sqlite-wasm', path: dbUrl };\n    } else {\n      result.database = { ...result.database, type: 'sqlite', path: dbUrl };\n    }\n  }\n\n  if (pkgPath) {\n    result.packages = { ...result.packages, path: pkgPath };\n  }\n\n  return result;\n}\n", "import type { Logger } from './types.js';\n\n/**\n * Default console-based logger.\n */\nexport function createConsoleLogger(): Logger {\n  return {\n    debug: (message: string, ...args: unknown[]) => console.debug(`[fhir-engine] ${message}`, ...args),\n    info: (message: string, ...args: unknown[]) => console.info(`[fhir-engine] ${message}`, ...args),\n    warn: (message: string, ...args: unknown[]) => console.warn(`[fhir-engine] ${message}`, ...args),\n    error: (message: string, ...args: unknown[]) => console.error(`[fhir-engine] ${message}`, ...args),\n  };\n}\n", "import { resolve, join } from 'node:path';\nimport { existsSync, mkdirSync, symlinkSync, readFileSync, lstatSync, copyFileSync } from 'node:fs';\nimport { PackageCache, PackageRegistryClient } from 'fhir-definition';\n\nimport type { FhirEngineConfig, ResolvePackagesOptions, ResolvedPackage, ResolvePackagesResult, Logger } from './types.js';\n\n/**\n * Ensure the given directory exists (recursive mkdir).\n */\nfunction ensureDirSync(dir: string): void {\n  if (!existsSync(dir)) {\n    mkdirSync(dir, { recursive: true });\n  }\n}\n\n/**\n * Check if a directory contains a FHIR package manifest.\n * Checks both root/package.json and package/package.json\n * (cached packages store content in a 'package' subdirectory).\n */\nfunction hasManifest(dir: string): boolean {\n  return existsSync(join(dir, 'package.json')) || existsSync(join(dir, 'package', 'package.json'));\n}\n\n/**\n * Read the version from a package.json file.\n * Checks both root and package/ subdirectory.\n * Returns the version string or 'local' if not found.\n */\nfunction readLocalVersion(pkgDir: string): string {\n  for (const candidate of [join(pkgDir, 'package.json'), join(pkgDir, 'package', 'package.json')]) {\n    try {\n      const raw = readFileSync(candidate, 'utf-8');\n      const manifest = JSON.parse(raw);\n      return manifest.version ?? 'local';\n    } catch {\n      // try next candidate\n    }\n  }\n  return 'local';\n}\n\n/**\n * Resolve FHIR packages into a project's packages directory.\n *\n * Resolution order for each package:\n * 1. Already exists in packagesPath \u2192 use as-is (source: 'local')\n * 2. Found in system cache (~/.fhir/packages) \u2192 create symlink/junction (source: 'cache')\n * 3. Download from FHIR Package Registry \u2192 cache \u2192 create symlink (source: 'download')\n *\n * @param config  Engine configuration (uses config.igs and config.packages.path)\n * @param options Override packages list, target path, download policy, or logger\n * @returns       Result with resolved packages and any errors\n *\n * @example\n * ```ts\n * const result = await resolvePackages(config);\n * if (!result.success) {\n *   console.warn('Some packages failed:', result.errors);\n * }\n * ```\n */\nexport async function resolvePackages(\n  config: FhirEngineConfig,\n  options?: ResolvePackagesOptions,\n): Promise<ResolvePackagesResult> {\n  const packagesPath = resolve(options?.packagesPath ?? config.packages.path);\n  const igs = options?.packages ?? config.igs ?? [];\n  const allowDownload = options?.allowDownload ?? config.packageResolve?.allowDownload ?? true;\n  const logger: Logger | undefined = options?.logger ?? config.logger;\n\n  const cache = new PackageCache();\n  const client = new PackageRegistryClient();\n  const results: ResolvedPackage[] = [];\n  const errors: Array<{ name: string; error: string }> = [];\n\n  ensureDirSync(packagesPath);\n\n  for (const ig of igs) {\n    try {\n      // 1. Already exists locally?\n      const localPath = join(packagesPath, ig.name);\n      if (hasManifest(localPath)) {\n        const localVersion = readLocalVersion(localPath);\n        logger?.debug(`Package ${ig.name} already exists locally at ${localPath}`);\n        results.push({ name: ig.name, version: localVersion, path: localPath, source: 'local' });\n        continue;\n      }\n\n      // 2. Resolve version\n      let version = ig.version ?? 'latest';\n      if (version === 'latest') {\n        if (!allowDownload) {\n          errors.push({\n            name: ig.name,\n            error: `Cannot resolve \"latest\" version for ${ig.name} without network access`,\n          });\n          continue;\n        }\n        logger?.info(`Resolving latest version for ${ig.name}...`);\n        version = await client.getLatestVersion(ig.name);\n        logger?.info(`Latest version for ${ig.name}: ${version}`);\n      }\n\n      // 3. Check system cache\n      const cachePath = cache.getPath(ig.name, version);\n      if (cachePath) {\n        // Cache hit \u2014 create symlink\n        logger?.info(`Found ${ig.name}@${version} in system cache, linking...`);\n        ensureCacheRootManifest(cachePath);\n        createLink(cachePath, localPath);\n        results.push({ name: ig.name, version, path: localPath, source: 'cache' });\n        continue;\n      }\n\n      // 4. Download\n      if (!allowDownload) {\n        errors.push({\n          name: ig.name,\n          error: `Package ${ig.name}@${version} not found in cache, and downloads are disabled`,\n        });\n        continue;\n      }\n\n      logger?.info(`Downloading ${ig.name}@${version} from registry...`);\n      const tarball = await client.download(ig.name, version);\n      cache.put(ig.name, version, tarball);\n      logger?.info(`Downloaded and cached ${ig.name}@${version}`);\n\n      // Create symlink from cache to project packages dir\n      const newCachePath = cache.getPath(ig.name, version);\n      if (!newCachePath) {\n        errors.push({ name: ig.name, error: `Failed to locate cached package after download` });\n        continue;\n      }\n      ensureCacheRootManifest(newCachePath);\n      createLink(newCachePath, localPath);\n      results.push({ name: ig.name, version, path: localPath, source: 'download' });\n    } catch (err) {\n      errors.push({\n        name: ig.name,\n        error: err instanceof Error ? err.message : String(err),\n      });\n    }\n  }\n\n  return {\n    success: errors.length === 0,\n    packages: results,\n    errors,\n  };\n}\n\n/**\n * Ensure the cache root directory has a package.json manifest.\n * Some tools (e.g. Firely Terminal) only place package.json inside the\n * package/ subdirectory. Without a root manifest, PackageScanner discovers\n * the package at the wrong depth, causing PackageLoader to construct a\n * double-nested \"package/package\" path that doesn't exist (\u2192 0 resources).\n */\nfunction ensureCacheRootManifest(cachePath: string): void {\n  const rootManifest = join(cachePath, 'package.json');\n  const nestedManifest = join(cachePath, 'package', 'package.json');\n  if (!existsSync(rootManifest) && existsSync(nestedManifest)) {\n    copyFileSync(nestedManifest, rootManifest);\n  }\n}\n\n/**\n * Create a directory junction (Windows) or symlink (Unix) from target to linkPath.\n * Idempotent \u2014 if link already exists, does nothing.\n */\nfunction createLink(target: string, linkPath: string): void {\n  if (existsSync(linkPath)) {\n    // Already exists (either real dir or symlink) \u2014 skip\n    try {\n      const stat = lstatSync(linkPath);\n      if (stat.isSymbolicLink() || stat.isDirectory()) {\n        return;\n      }\n    } catch {\n      // If stat fails, try to create anyway\n    }\n  }\n  // Use 'junction' on Windows (no admin needed), 'dir' on Unix\n  const linkType = process.platform === 'win32' ? 'junction' : 'dir';\n  symlinkSync(target, linkPath, linkType);\n}\n"],
+  "mappings": 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   "names": ["import_fhir_definition", "import_fhir_persistence", "import_node_path", "import_node_fs", "import_fhir_persistence", "import_fhir_runtime"]
 }

package/dist/esm/index.mjs

@@ -153,7 +153,7 @@ function createConsoleLogger() {
 
 // src/package-resolver.ts
 import { resolve as resolve2, join } from "node:path";
-import { existsSync as existsSync2, mkdirSync, symlinkSync, readFileSync as readFileSync2, lstatSync } from "node:fs";
+import { existsSync as existsSync2, mkdirSync, symlinkSync, readFileSync as readFileSync2, lstatSync, copyFileSync } from "node:fs";
 import { PackageCache, PackageRegistryClient } from "fhir-definition";
 function ensureDirSync(dir) {
   if (!existsSync2(dir)) {
@@ -209,6 +209,7 @@ async function resolvePackages(config, options) {
       const cachePath = cache.getPath(ig.name, version);
       if (cachePath) {
         logger?.info(`Found ${ig.name}@${version} in system cache, linking...`);
+        ensureCacheRootManifest(cachePath);
         createLink(cachePath, localPath);
         results.push({ name: ig.name, version, path: localPath, source: "cache" });
         continue;
@@ -229,6 +230,7 @@ async function resolvePackages(config, options) {
         errors.push({ name: ig.name, error: `Failed to locate cached package after download` });
         continue;
       }
+      ensureCacheRootManifest(newCachePath);
       createLink(newCachePath, localPath);
       results.push({ name: ig.name, version, path: localPath, source: "download" });
     } catch (err) {
@@ -244,6 +246,13 @@ async function resolvePackages(config, options) {
     errors
   };
 }
+function ensureCacheRootManifest(cachePath) {
+  const rootManifest = join(cachePath, "package.json");
+  const nestedManifest = join(cachePath, "package", "package.json");
+  if (!existsSync2(rootManifest) && existsSync2(nestedManifest)) {
+    copyFileSync(nestedManifest, rootManifest);
+  }
+}
 function createLink(target, linkPath) {
   if (existsSync2(linkPath)) {
     try {

package/dist/esm/index.mjs.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../src/engine.ts", "../../src/adapter-factory.ts", "../../src/config.ts", "../../src/logger.ts", "../../src/package-resolver.ts", "../../src/index.ts"],
-  "sourcesContent": ["import { loadDefinitionPackages } from 'fhir-definition';\nimport { createRuntime, extractSearchValues, extractAllSearchValues, extractReferences } from 'fhir-runtime';\nimport { FhirDefinitionBridge, FhirRuntimeProvider, FhirSystem, parseSearchRequest, executeSearch } from 'fhir-persistence';\n\nimport { createAdapter } from './adapter-factory.js';\nimport { loadFhirConfig } from './config.js';\nimport { createConsoleLogger } from './logger.js';\nimport { resolvePackages } from './package-resolver.js';\nimport type { EngineContext, FhirEngine, FhirEngineConfig, FhirEnginePlugin, FhirEngineStatus } from './types.js';\n\n/**\n * Resolve the SQL dialect from the database config type.\n */\nfunction resolveDialect(type: FhirEngineConfig['database']['type']): 'sqlite' | 'postgres' {\n  switch (type) {\n    case 'sqlite':\n    case 'sqlite-wasm':\n      return 'sqlite';\n    case 'postgres':\n      return 'postgres';\n  }\n}\n\n/**\n * Validate the engine configuration, throwing on missing required fields.\n */\nfunction validateConfig(config: FhirEngineConfig): void {\n  if (!config.database) {\n    throw new Error('fhir-engine: config.database is required');\n  }\n  if (!config.database.type) {\n    throw new Error('fhir-engine: config.database.type is required (sqlite | sqlite-wasm | postgres)');\n  }\n  if (!config.packages) {\n    throw new Error('fhir-engine: config.packages is required');\n  }\n  if (!config.packages.path) {\n    throw new Error('fhir-engine: config.packages.path is required');\n  }\n}\n\n/**\n * Run a lifecycle hook on all plugins in order.\n * Wraps errors with the plugin name for clear diagnostics.\n */\nasync function runPluginHook(\n  plugins: FhirEnginePlugin[],\n  hook: 'init' | 'start' | 'ready',\n  ctx: EngineContext,\n): Promise<void> {\n  for (const plugin of plugins) {\n    const fn = plugin[hook];\n    if (fn) {\n      try {\n        await fn.call(plugin, ctx);\n      } catch (err) {\n        throw new Error(\n          `fhir-engine: plugin \"${plugin.name}\" failed during ${hook}: ${err instanceof Error ? err.message : String(err)}`,\n          { cause: err },\n        );\n      }\n    }\n  }\n}\n\n/**\n * Create and bootstrap a fully initialized FHIR engine.\n *\n * This is the single entry point for all FHIR applications.\n * It assembles fhir-definition, fhir-runtime, and fhir-persistence\n * into a running system from a single configuration object.\n *\n * @example\n * ```ts\n * const engine = await createFhirEngine({\n *   database: { type: 'sqlite', path: ':memory:' },\n *   packages: { path: './fhir-packages' },\n * });\n *\n * const patient = await engine.persistence.createResource('Patient', {\n *   resourceType: 'Patient',\n *   name: [{ family: 'Smith', given: ['John'] }],\n * });\n *\n * await engine.stop();\n * ```\n */\nexport async function createFhirEngine(config?: FhirEngineConfig): Promise<FhirEngine> {\n  // \u2500\u2500 0. Resolve config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (!config) {\n    config = await loadFhirConfig();\n  }\n  validateConfig(config);\n\n  const logger = config.logger ?? createConsoleLogger();\n  const plugins = config.plugins ?? [];\n  logger.info('Initializing fhir-engine...');\n\n  // \u2500\u2500 1a. Resolve packages (download/link if config.igs is set) \u2500\n  if (config.igs && config.igs.length > 0) {\n    logger.info(`Resolving ${config.igs.length} IG package(s)...`);\n    const resolveResult = await resolvePackages(config, { logger });\n    for (const pkg of resolveResult.packages) {\n      logger.info(`Resolved ${pkg.name}@${pkg.version} (${pkg.source})`);\n    }\n    if (!resolveResult.success) {\n      for (const err of resolveResult.errors) {\n        logger.warn(`Failed to resolve package ${err.name}: ${err.error}`);\n      }\n    }\n  }\n\n  // \u2500\u2500 1b. Load FHIR definitions \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  logger.info(`Loading FHIR packages from: ${config.packages.path}`);\n  const { registry, result } = loadDefinitionPackages(config.packages.path);\n  logger.info(\n    `Loaded ${result.packages.length} package(s): ${result.packages.map((p) => `${p.name}@${p.version}`).join(', ')}`,\n  );\n\n  // \u2500\u2500 2. Create fhir-runtime \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  logger.info('Creating fhir-runtime instance...');\n  const runtime = await createRuntime({ definitions: registry, preloadCore: false });\n\n  // \u2500\u2500 3. Build provider bridges \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const definitionBridge = new FhirDefinitionBridge(registry);\n  const runtimeProvider = new FhirRuntimeProvider({\n    extractSearchValues,\n    extractAllSearchValues,\n    extractReferences,\n  });\n\n  // \u2500\u2500 4. Create storage adapter \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const adapter = createAdapter(config.database, logger);\n\n  // \u2500\u2500 5. Build EngineContext \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const ctx: { -readonly [K in keyof EngineContext]: EngineContext[K] } = {\n    config,\n    definitions: registry,\n    runtime,\n    adapter,\n    persistence: undefined,\n    logger,\n  };\n\n  // \u2500\u2500 6. INIT phase \u2014 plugins run before persistence \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (plugins.length > 0) {\n    logger.info(`Running init for ${plugins.length} plugin(s): ${plugins.map((p) => p.name).join(', ')}`);\n    await runPluginHook(plugins, 'init', ctx);\n  }\n\n  // \u2500\u2500 7. Initialize FhirSystem \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const dialect = resolveDialect(config.database.type);\n  const system = new FhirSystem(adapter, {\n    dialect,\n    runtimeProvider,\n    packageName: config.packageName ?? 'fhir-engine.default',\n    packageVersion: config.packageVersion ?? '1.0.0',\n  });\n\n  logger.info('Initializing persistence system (schema + migration)...');\n  const { persistence, sdRegistry, spRegistry, igResult, resourceTypes } =\n    await system.initialize(definitionBridge);\n\n  logger.info(`Persistence ready \u2014 IG action: ${igResult.action}, ${resourceTypes.length} resource type(s)`);\n\n  // ctx.persistence now available\n  ctx.persistence = persistence;\n\n  // \u2500\u2500 8. START phase \u2014 plugins can access persistence \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (plugins.length > 0) {\n    logger.info(`Running start for ${plugins.length} plugin(s)...`);\n    await runPluginHook(plugins, 'start', ctx);\n  }\n\n  // \u2500\u2500 9. READY phase \u2014 system fully operational \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (plugins.length > 0) {\n    logger.info(`Running ready for ${plugins.length} plugin(s)...`);\n    await runPluginHook(plugins, 'ready', ctx);\n  }\n\n  // \u2500\u2500 10. Return FhirEngine \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  let stopped = false;\n  const startedAt = new Date();\n  const loadedPackages = result.packages.map((p) => `${p.name}@${p.version}`);\n  const fhirVersions = [...new Set(\n    result.packages\n      .map((p) => {\n        if (p.name.includes('.r4.')) return '4.0';\n        if (p.name.includes('.r4b.')) return '4.3';\n        if (p.name.includes('.r5.')) return '5.0';\n        return undefined;\n      })\n      .filter(Boolean),\n  )] as string[];\n\n  const engine: FhirEngine = {\n    definitions: registry,\n    runtime,\n    adapter,\n    persistence,\n    sdRegistry,\n    spRegistry,\n    igResult,\n    resourceTypes,\n    logger,\n    context: ctx as EngineContext,\n\n    async search(resourceType, queryParams, options) {\n      const request = parseSearchRequest(resourceType, queryParams, spRegistry);\n      return executeSearch(adapter, request, spRegistry, options);\n    },\n\n    status(): FhirEngineStatus {\n      return {\n        fhirVersions,\n        loadedPackages,\n        resourceTypes,\n        databaseType: config.database.type,\n        igAction: igResult.action,\n        startedAt,\n        plugins: plugins.map((p) => p.name),\n      };\n    },\n\n    async stop() {\n      if (stopped) return;\n      stopped = true;\n      logger.info('Stopping fhir-engine...');\n\n      // Stop plugins in reverse registration order\n      for (let i = plugins.length - 1; i >= 0; i--) {\n        const plugin = plugins[i];\n        if (plugin.stop) {\n          try {\n            await plugin.stop.call(plugin, ctx as EngineContext);\n          } catch (err) {\n            logger.error(\n              `Plugin \"${plugin.name}\" failed during stop: ${err instanceof Error ? err.message : String(err)}`,\n            );\n          }\n        }\n      }\n\n      await adapter.close();\n      logger.info('fhir-engine stopped.');\n    },\n  };\n\n  logger.info('fhir-engine ready.');\n  return engine;\n}\n", "import { BetterSqlite3Adapter, SQLiteAdapter } from 'fhir-persistence';\nimport type { StorageAdapter } from 'fhir-persistence';\nimport type { DatabaseConfig, Logger } from './types.js';\n\n/**\n * Create a StorageAdapter from the database configuration.\n *\n * Supported adapters:\n * - `sqlite`      \u2192 BetterSqlite3Adapter (native, Node.js / Electron)\n * - `sqlite-wasm` \u2192 SQLiteAdapter (sql.js WASM, browser / cross-platform)\n * - `postgres`    \u2192 not yet available (PostgresAdapter not exported from fhir-persistence)\n */\nexport function createAdapter(config: DatabaseConfig, logger: Logger): StorageAdapter {\n  switch (config.type) {\n    case 'sqlite': {\n      logger.info(`Creating BetterSqlite3Adapter (path: ${config.path})`);\n      return new BetterSqlite3Adapter({\n        path: config.path,\n        wal: config.wal ?? true,\n        busyTimeout: config.busyTimeout ?? 5000,\n      });\n    }\n\n    case 'sqlite-wasm': {\n      logger.info(`Creating SQLiteAdapter (WASM, path: ${config.path})`);\n      return new SQLiteAdapter(config.path);\n    }\n\n    case 'postgres': {\n      throw new Error(\n        'fhir-engine: PostgreSQL adapter is not yet available. ' +\n        'PostgresAdapter is not exported from fhir-persistence v0.1.0. ' +\n        'Use database.type = \"sqlite\" for now.',\n      );\n    }\n\n    default: {\n      const _exhaustive: never = config;\n      throw new Error(`fhir-engine: unknown database type: ${(_exhaustive as DatabaseConfig).type}`);\n    }\n  }\n}\n", "import { existsSync, readFileSync } from 'node:fs';\nimport { resolve, extname } from 'node:path';\nimport { pathToFileURL } from 'node:url';\nimport type { FhirEngineConfig, DatabaseConfig } from './types.js';\n\n// ---------------------------------------------------------------------------\n// defineConfig \u2014 typed identity helper for fhir.config.ts / .js\n// ---------------------------------------------------------------------------\n\n/**\n * Type-safe config helper for `fhir.config.ts` / `fhir.config.js`.\n *\n * @example\n * ```ts\n * // fhir.config.ts\n * import { defineConfig } from 'fhir-engine';\n *\n * export default defineConfig({\n *   database: { type: 'sqlite', path: './fhir.db' },\n *   packages: { path: './fhir-packages' },\n * });\n * ```\n */\nexport function defineConfig(config: FhirEngineConfig): FhirEngineConfig {\n  return config;\n}\n\n// ---------------------------------------------------------------------------\n// Config file discovery order\n// ---------------------------------------------------------------------------\n\nconst CONFIG_FILENAMES = [\n  'fhir.config.ts',\n  'fhir.config.js',\n  'fhir.config.mjs',\n  'fhir.config.json',\n] as const;\n\n// ---------------------------------------------------------------------------\n// loadFhirConfig \u2014 auto-discover and load config\n// ---------------------------------------------------------------------------\n\n/**\n * Load engine configuration from a file.\n *\n * If `configPath` is provided, loads that exact file.\n * Otherwise, searches the current working directory for config files\n * in this order: `fhir.config.ts` \u2192 `fhir.config.js` \u2192 `fhir.config.mjs` \u2192 `fhir.config.json`.\n *\n * Environment variable overrides are applied on top of the loaded config.\n *\n * @param configPath - Explicit path to a config file (optional).\n * @returns The resolved `FhirEngineConfig`.\n */\nexport async function loadFhirConfig(configPath?: string): Promise<FhirEngineConfig> {\n  let resolvedPath: string;\n\n  if (configPath) {\n    resolvedPath = resolve(configPath);\n    if (!existsSync(resolvedPath)) {\n      throw new Error(`fhir-engine: config file not found: ${resolvedPath}`);\n    }\n  } else {\n    const cwd = process.cwd();\n    const found = CONFIG_FILENAMES\n      .map((name) => resolve(cwd, name))\n      .find((p) => existsSync(p));\n    if (!found) {\n      throw new Error(\n        `fhir-engine: no config file found in ${cwd}. ` +\n        `Expected one of: ${CONFIG_FILENAMES.join(', ')}`,\n      );\n    }\n    resolvedPath = found;\n  }\n\n  const config = await loadConfigFile(resolvedPath);\n  return applyEnvOverrides(config);\n}\n\n// ---------------------------------------------------------------------------\n// File loaders\n// ---------------------------------------------------------------------------\n\nasync function loadConfigFile(filePath: string): Promise<FhirEngineConfig> {\n  const ext = extname(filePath);\n\n  if (ext === '.json') {\n    return loadJsonConfig(filePath);\n  }\n\n  if (ext === '.ts' || ext === '.js' || ext === '.mjs') {\n    return loadModuleConfig(filePath);\n  }\n\n  throw new Error(`fhir-engine: unsupported config file extension: ${ext}`);\n}\n\nfunction loadJsonConfig(filePath: string): FhirEngineConfig {\n  try {\n    const raw = readFileSync(filePath, 'utf-8');\n    return JSON.parse(raw) as FhirEngineConfig;\n  } catch (err) {\n    throw new Error(\n      `fhir-engine: failed to parse config file ${filePath}: ${err instanceof Error ? err.message : String(err)}`,\n      { cause: err },\n    );\n  }\n}\n\nasync function loadModuleConfig(filePath: string): Promise<FhirEngineConfig> {\n  try {\n    const fileUrl = pathToFileURL(filePath).href;\n    const mod = await import(fileUrl);\n    const config = mod.default ?? mod;\n\n    if (!config || typeof config !== 'object') {\n      throw new Error('config file must export a FhirEngineConfig object as default export');\n    }\n\n    return config as FhirEngineConfig;\n  } catch (err) {\n    if (err instanceof Error && err.message.includes('must export')) {\n      throw err;\n    }\n    throw new Error(\n      `fhir-engine: failed to load config file ${filePath}: ${err instanceof Error ? err.message : String(err)}`,\n      { cause: err },\n    );\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Environment variable overrides\n// ---------------------------------------------------------------------------\n\nconst VALID_DB_TYPES = ['sqlite', 'sqlite-wasm', 'postgres'] as const;\n\n/**\n * Apply environment variable overrides on top of a loaded config.\n *\n * | Env Variable        | Overrides                        |\n * |---------------------|----------------------------------|\n * | FHIR_DATABASE_TYPE  | config.database.type             |\n * | FHIR_DATABASE_URL   | config.database.path / .url      |\n * | FHIR_PACKAGES_PATH  | config.packages.path             |\n * | FHIR_LOG_LEVEL      | (stored for logger filtering)    |\n */\nexport function applyEnvOverrides(config: FhirEngineConfig): FhirEngineConfig {\n  const result = structuredClone(config);\n\n  const dbType = process.env.FHIR_DATABASE_TYPE;\n  const dbUrl = process.env.FHIR_DATABASE_URL;\n  const pkgPath = process.env.FHIR_PACKAGES_PATH;\n\n  if (dbType) {\n    if (!VALID_DB_TYPES.includes(dbType as typeof VALID_DB_TYPES[number])) {\n      throw new Error(\n        `fhir-engine: FHIR_DATABASE_TYPE must be one of: ${VALID_DB_TYPES.join(', ')}. Got: \"${dbType}\"`,\n      );\n    }\n    // Rebuild database config with overridden type\n    const validType = dbType as DatabaseConfig['type'];\n    if (validType === 'postgres') {\n      result.database = { type: 'postgres', url: (result.database as { url?: string }).url ?? '' };\n    } else if (validType === 'sqlite-wasm') {\n      result.database = { type: 'sqlite-wasm', path: (result.database as { path?: string }).path ?? '' };\n    } else {\n      result.database = { type: 'sqlite', path: (result.database as { path?: string }).path ?? '' };\n    }\n  }\n\n  if (dbUrl) {\n    const type = result.database?.type;\n    if (type === 'postgres') {\n      result.database = { ...result.database, type: 'postgres', url: dbUrl };\n    } else if (type === 'sqlite-wasm') {\n      result.database = { ...result.database, type: 'sqlite-wasm', path: dbUrl };\n    } else {\n      result.database = { ...result.database, type: 'sqlite', path: dbUrl };\n    }\n  }\n\n  if (pkgPath) {\n    result.packages = { ...result.packages, path: pkgPath };\n  }\n\n  return result;\n}\n", "import type { Logger } from './types.js';\n\n/**\n * Default console-based logger.\n */\nexport function createConsoleLogger(): Logger {\n  return {\n    debug: (message: string, ...args: unknown[]) => console.debug(`[fhir-engine] ${message}`, ...args),\n    info: (message: string, ...args: unknown[]) => console.info(`[fhir-engine] ${message}`, ...args),\n    warn: (message: string, ...args: unknown[]) => console.warn(`[fhir-engine] ${message}`, ...args),\n    error: (message: string, ...args: unknown[]) => console.error(`[fhir-engine] ${message}`, ...args),\n  };\n}\n", "import { resolve, join } from 'node:path';\nimport { existsSync, mkdirSync, symlinkSync, readFileSync, lstatSync } from 'node:fs';\nimport { PackageCache, PackageRegistryClient } from 'fhir-definition';\n\nimport type { FhirEngineConfig, ResolvePackagesOptions, ResolvedPackage, ResolvePackagesResult, Logger } from './types.js';\n\n/**\n * Ensure the given directory exists (recursive mkdir).\n */\nfunction ensureDirSync(dir: string): void {\n  if (!existsSync(dir)) {\n    mkdirSync(dir, { recursive: true });\n  }\n}\n\n/**\n * Check if a directory contains a FHIR package manifest.\n * Checks both root/package.json and package/package.json\n * (cached packages store content in a 'package' subdirectory).\n */\nfunction hasManifest(dir: string): boolean {\n  return existsSync(join(dir, 'package.json')) || existsSync(join(dir, 'package', 'package.json'));\n}\n\n/**\n * Read the version from a package.json file.\n * Checks both root and package/ subdirectory.\n * Returns the version string or 'local' if not found.\n */\nfunction readLocalVersion(pkgDir: string): string {\n  for (const candidate of [join(pkgDir, 'package.json'), join(pkgDir, 'package', 'package.json')]) {\n    try {\n      const raw = readFileSync(candidate, 'utf-8');\n      const manifest = JSON.parse(raw);\n      return manifest.version ?? 'local';\n    } catch {\n      // try next candidate\n    }\n  }\n  return 'local';\n}\n\n/**\n * Resolve FHIR packages into a project's packages directory.\n *\n * Resolution order for each package:\n * 1. Already exists in packagesPath \u2192 use as-is (source: 'local')\n * 2. Found in system cache (~/.fhir/packages) \u2192 create symlink/junction (source: 'cache')\n * 3. Download from FHIR Package Registry \u2192 cache \u2192 create symlink (source: 'download')\n *\n * @param config  Engine configuration (uses config.igs and config.packages.path)\n * @param options Override packages list, target path, download policy, or logger\n * @returns       Result with resolved packages and any errors\n *\n * @example\n * ```ts\n * const result = await resolvePackages(config);\n * if (!result.success) {\n *   console.warn('Some packages failed:', result.errors);\n * }\n * ```\n */\nexport async function resolvePackages(\n  config: FhirEngineConfig,\n  options?: ResolvePackagesOptions,\n): Promise<ResolvePackagesResult> {\n  const packagesPath = resolve(options?.packagesPath ?? config.packages.path);\n  const igs = options?.packages ?? config.igs ?? [];\n  const allowDownload = options?.allowDownload ?? config.packageResolve?.allowDownload ?? true;\n  const logger: Logger | undefined = options?.logger ?? config.logger;\n\n  const cache = new PackageCache();\n  const client = new PackageRegistryClient();\n  const results: ResolvedPackage[] = [];\n  const errors: Array<{ name: string; error: string }> = [];\n\n  ensureDirSync(packagesPath);\n\n  for (const ig of igs) {\n    try {\n      // 1. Already exists locally?\n      const localPath = join(packagesPath, ig.name);\n      if (hasManifest(localPath)) {\n        const localVersion = readLocalVersion(localPath);\n        logger?.debug(`Package ${ig.name} already exists locally at ${localPath}`);\n        results.push({ name: ig.name, version: localVersion, path: localPath, source: 'local' });\n        continue;\n      }\n\n      // 2. Resolve version\n      let version = ig.version ?? 'latest';\n      if (version === 'latest') {\n        if (!allowDownload) {\n          errors.push({\n            name: ig.name,\n            error: `Cannot resolve \"latest\" version for ${ig.name} without network access`,\n          });\n          continue;\n        }\n        logger?.info(`Resolving latest version for ${ig.name}...`);\n        version = await client.getLatestVersion(ig.name);\n        logger?.info(`Latest version for ${ig.name}: ${version}`);\n      }\n\n      // 3. Check system cache\n      const cachePath = cache.getPath(ig.name, version);\n      if (cachePath) {\n        // Cache hit \u2014 create symlink\n        logger?.info(`Found ${ig.name}@${version} in system cache, linking...`);\n        createLink(cachePath, localPath);\n        results.push({ name: ig.name, version, path: localPath, source: 'cache' });\n        continue;\n      }\n\n      // 4. Download\n      if (!allowDownload) {\n        errors.push({\n          name: ig.name,\n          error: `Package ${ig.name}@${version} not found in cache, and downloads are disabled`,\n        });\n        continue;\n      }\n\n      logger?.info(`Downloading ${ig.name}@${version} from registry...`);\n      const tarball = await client.download(ig.name, version);\n      cache.put(ig.name, version, tarball);\n      logger?.info(`Downloaded and cached ${ig.name}@${version}`);\n\n      // Create symlink from cache to project packages dir\n      const newCachePath = cache.getPath(ig.name, version);\n      if (!newCachePath) {\n        errors.push({ name: ig.name, error: `Failed to locate cached package after download` });\n        continue;\n      }\n      createLink(newCachePath, localPath);\n      results.push({ name: ig.name, version, path: localPath, source: 'download' });\n    } catch (err) {\n      errors.push({\n        name: ig.name,\n        error: err instanceof Error ? err.message : String(err),\n      });\n    }\n  }\n\n  return {\n    success: errors.length === 0,\n    packages: results,\n    errors,\n  };\n}\n\n/**\n * Create a directory junction (Windows) or symlink (Unix) from target to linkPath.\n * Idempotent \u2014 if link already exists, does nothing.\n */\nfunction createLink(target: string, linkPath: string): void {\n  if (existsSync(linkPath)) {\n    // Already exists (either real dir or symlink) \u2014 skip\n    try {\n      const stat = lstatSync(linkPath);\n      if (stat.isSymbolicLink() || stat.isDirectory()) {\n        return;\n      }\n    } catch {\n      // If stat fails, try to create anyway\n    }\n  }\n  // Use 'junction' on Windows (no admin needed), 'dir' on Unix\n  const linkType = process.platform === 'win32' ? 'junction' : 'dir';\n  symlinkSync(target, linkPath, linkType);\n}\n", "// fhir-engine \u2014 public API\n\nexport { createFhirEngine } from './engine.js';\nexport { defineConfig, loadFhirConfig } from './config.js';\nexport { createConsoleLogger } from './logger.js';\nexport { createAdapter } from './adapter-factory.js';\nexport { resolvePackages } from './package-resolver.js';\n\nexport type {\n  FhirEngine,\n  FhirEngineConfig,\n  FhirEnginePlugin,\n  FhirEngineStatus,\n  EngineContext,\n  DatabaseConfig,\n  SqliteDatabaseConfig,\n  SqliteWasmDatabaseConfig,\n  PostgresDatabaseConfig,\n  PackagesConfig,\n  Logger,\n  ResolvePackagesOptions,\n  ResolvedPackage,\n  ResolvePackagesResult,\n} from './types.js';\n\n// Re-export key upstream types for convenience\nexport type { DefinitionRegistry, DefinitionProvider } from 'fhir-definition';\nexport type { FhirRuntimeInstance } from 'fhir-runtime';\nexport type { FhirPersistence, StorageAdapter } from 'fhir-persistence';\n\n// ---------------------------------------------------------------------------\n// Search utilities (from fhir-persistence)\n// ---------------------------------------------------------------------------\n\nexport { parseSearchRequest, executeSearch } from 'fhir-persistence';\nexport type { SearchRequest, SearchResult, SearchOptions } from 'fhir-persistence';\n\n// ---------------------------------------------------------------------------\n// FHIRPath evaluation (from fhir-runtime)\n// ---------------------------------------------------------------------------\n\nexport { evalFhirPath, evalFhirPathBoolean, evalFhirPathString, evalFhirPathTyped } from 'fhir-runtime';\n"],
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+  "sourcesContent": ["import { loadDefinitionPackages } from 'fhir-definition';\nimport { createRuntime, extractSearchValues, extractAllSearchValues, extractReferences } from 'fhir-runtime';\nimport { FhirDefinitionBridge, FhirRuntimeProvider, FhirSystem, parseSearchRequest, executeSearch } from 'fhir-persistence';\n\nimport { createAdapter } from './adapter-factory.js';\nimport { loadFhirConfig } from './config.js';\nimport { createConsoleLogger } from './logger.js';\nimport { resolvePackages } from './package-resolver.js';\nimport type { EngineContext, FhirEngine, FhirEngineConfig, FhirEnginePlugin, FhirEngineStatus } from './types.js';\n\n/**\n * Resolve the SQL dialect from the database config type.\n */\nfunction resolveDialect(type: FhirEngineConfig['database']['type']): 'sqlite' | 'postgres' {\n  switch (type) {\n    case 'sqlite':\n    case 'sqlite-wasm':\n      return 'sqlite';\n    case 'postgres':\n      return 'postgres';\n  }\n}\n\n/**\n * Validate the engine configuration, throwing on missing required fields.\n */\nfunction validateConfig(config: FhirEngineConfig): void {\n  if (!config.database) {\n    throw new Error('fhir-engine: config.database is required');\n  }\n  if (!config.database.type) {\n    throw new Error('fhir-engine: config.database.type is required (sqlite | sqlite-wasm | postgres)');\n  }\n  if (!config.packages) {\n    throw new Error('fhir-engine: config.packages is required');\n  }\n  if (!config.packages.path) {\n    throw new Error('fhir-engine: config.packages.path is required');\n  }\n}\n\n/**\n * Run a lifecycle hook on all plugins in order.\n * Wraps errors with the plugin name for clear diagnostics.\n */\nasync function runPluginHook(\n  plugins: FhirEnginePlugin[],\n  hook: 'init' | 'start' | 'ready',\n  ctx: EngineContext,\n): Promise<void> {\n  for (const plugin of plugins) {\n    const fn = plugin[hook];\n    if (fn) {\n      try {\n        await fn.call(plugin, ctx);\n      } catch (err) {\n        throw new Error(\n          `fhir-engine: plugin \"${plugin.name}\" failed during ${hook}: ${err instanceof Error ? err.message : String(err)}`,\n          { cause: err },\n        );\n      }\n    }\n  }\n}\n\n/**\n * Create and bootstrap a fully initialized FHIR engine.\n *\n * This is the single entry point for all FHIR applications.\n * It assembles fhir-definition, fhir-runtime, and fhir-persistence\n * into a running system from a single configuration object.\n *\n * @example\n * ```ts\n * const engine = await createFhirEngine({\n *   database: { type: 'sqlite', path: ':memory:' },\n *   packages: { path: './fhir-packages' },\n * });\n *\n * const patient = await engine.persistence.createResource('Patient', {\n *   resourceType: 'Patient',\n *   name: [{ family: 'Smith', given: ['John'] }],\n * });\n *\n * await engine.stop();\n * ```\n */\nexport async function createFhirEngine(config?: FhirEngineConfig): Promise<FhirEngine> {\n  // \u2500\u2500 0. Resolve config \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (!config) {\n    config = await loadFhirConfig();\n  }\n  validateConfig(config);\n\n  const logger = config.logger ?? createConsoleLogger();\n  const plugins = config.plugins ?? [];\n  logger.info('Initializing fhir-engine...');\n\n  // \u2500\u2500 1a. Resolve packages (download/link if config.igs is set) \u2500\n  if (config.igs && config.igs.length > 0) {\n    logger.info(`Resolving ${config.igs.length} IG package(s)...`);\n    const resolveResult = await resolvePackages(config, { logger });\n    for (const pkg of resolveResult.packages) {\n      logger.info(`Resolved ${pkg.name}@${pkg.version} (${pkg.source})`);\n    }\n    if (!resolveResult.success) {\n      for (const err of resolveResult.errors) {\n        logger.warn(`Failed to resolve package ${err.name}: ${err.error}`);\n      }\n    }\n  }\n\n  // \u2500\u2500 1b. Load FHIR definitions \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  logger.info(`Loading FHIR packages from: ${config.packages.path}`);\n  const { registry, result } = loadDefinitionPackages(config.packages.path);\n  logger.info(\n    `Loaded ${result.packages.length} package(s): ${result.packages.map((p) => `${p.name}@${p.version}`).join(', ')}`,\n  );\n\n  // \u2500\u2500 2. Create fhir-runtime \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  logger.info('Creating fhir-runtime instance...');\n  const runtime = await createRuntime({ definitions: registry, preloadCore: false });\n\n  // \u2500\u2500 3. Build provider bridges \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const definitionBridge = new FhirDefinitionBridge(registry);\n  const runtimeProvider = new FhirRuntimeProvider({\n    extractSearchValues,\n    extractAllSearchValues,\n    extractReferences,\n  });\n\n  // \u2500\u2500 4. Create storage adapter \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const adapter = createAdapter(config.database, logger);\n\n  // \u2500\u2500 5. Build EngineContext \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const ctx: { -readonly [K in keyof EngineContext]: EngineContext[K] } = {\n    config,\n    definitions: registry,\n    runtime,\n    adapter,\n    persistence: undefined,\n    logger,\n  };\n\n  // \u2500\u2500 6. INIT phase \u2014 plugins run before persistence \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (plugins.length > 0) {\n    logger.info(`Running init for ${plugins.length} plugin(s): ${plugins.map((p) => p.name).join(', ')}`);\n    await runPluginHook(plugins, 'init', ctx);\n  }\n\n  // \u2500\u2500 7. Initialize FhirSystem \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  const dialect = resolveDialect(config.database.type);\n  const system = new FhirSystem(adapter, {\n    dialect,\n    runtimeProvider,\n    packageName: config.packageName ?? 'fhir-engine.default',\n    packageVersion: config.packageVersion ?? '1.0.0',\n  });\n\n  logger.info('Initializing persistence system (schema + migration)...');\n  const { persistence, sdRegistry, spRegistry, igResult, resourceTypes } =\n    await system.initialize(definitionBridge);\n\n  logger.info(`Persistence ready \u2014 IG action: ${igResult.action}, ${resourceTypes.length} resource type(s)`);\n\n  // ctx.persistence now available\n  ctx.persistence = persistence;\n\n  // \u2500\u2500 8. START phase \u2014 plugins can access persistence \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (plugins.length > 0) {\n    logger.info(`Running start for ${plugins.length} plugin(s)...`);\n    await runPluginHook(plugins, 'start', ctx);\n  }\n\n  // \u2500\u2500 9. READY phase \u2014 system fully operational \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  if (plugins.length > 0) {\n    logger.info(`Running ready for ${plugins.length} plugin(s)...`);\n    await runPluginHook(plugins, 'ready', ctx);\n  }\n\n  // \u2500\u2500 10. Return FhirEngine \u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\n  let stopped = false;\n  const startedAt = new Date();\n  const loadedPackages = result.packages.map((p) => `${p.name}@${p.version}`);\n  const fhirVersions = [...new Set(\n    result.packages\n      .map((p) => {\n        if (p.name.includes('.r4.')) return '4.0';\n        if (p.name.includes('.r4b.')) return '4.3';\n        if (p.name.includes('.r5.')) return '5.0';\n        return undefined;\n      })\n      .filter(Boolean),\n  )] as string[];\n\n  const engine: FhirEngine = {\n    definitions: registry,\n    runtime,\n    adapter,\n    persistence,\n    sdRegistry,\n    spRegistry,\n    igResult,\n    resourceTypes,\n    logger,\n    context: ctx as EngineContext,\n\n    async search(resourceType, queryParams, options) {\n      const request = parseSearchRequest(resourceType, queryParams, spRegistry);\n      return executeSearch(adapter, request, spRegistry, options);\n    },\n\n    status(): FhirEngineStatus {\n      return {\n        fhirVersions,\n        loadedPackages,\n        resourceTypes,\n        databaseType: config.database.type,\n        igAction: igResult.action,\n        startedAt,\n        plugins: plugins.map((p) => p.name),\n      };\n    },\n\n    async stop() {\n      if (stopped) return;\n      stopped = true;\n      logger.info('Stopping fhir-engine...');\n\n      // Stop plugins in reverse registration order\n      for (let i = plugins.length - 1; i >= 0; i--) {\n        const plugin = plugins[i];\n        if (plugin.stop) {\n          try {\n            await plugin.stop.call(plugin, ctx as EngineContext);\n          } catch (err) {\n            logger.error(\n              `Plugin \"${plugin.name}\" failed during stop: ${err instanceof Error ? err.message : String(err)}`,\n            );\n          }\n        }\n      }\n\n      await adapter.close();\n      logger.info('fhir-engine stopped.');\n    },\n  };\n\n  logger.info('fhir-engine ready.');\n  return engine;\n}\n", "import { BetterSqlite3Adapter, SQLiteAdapter } from 'fhir-persistence';\nimport type { StorageAdapter } from 'fhir-persistence';\nimport type { DatabaseConfig, Logger } from './types.js';\n\n/**\n * Create a StorageAdapter from the database configuration.\n *\n * Supported adapters:\n * - `sqlite`      \u2192 BetterSqlite3Adapter (native, Node.js / Electron)\n * - `sqlite-wasm` \u2192 SQLiteAdapter (sql.js WASM, browser / cross-platform)\n * - `postgres`    \u2192 not yet available (PostgresAdapter not exported from fhir-persistence)\n */\nexport function createAdapter(config: DatabaseConfig, logger: Logger): StorageAdapter {\n  switch (config.type) {\n    case 'sqlite': {\n      logger.info(`Creating BetterSqlite3Adapter (path: ${config.path})`);\n      return new BetterSqlite3Adapter({\n        path: config.path,\n        wal: config.wal ?? true,\n        busyTimeout: config.busyTimeout ?? 5000,\n      });\n    }\n\n    case 'sqlite-wasm': {\n      logger.info(`Creating SQLiteAdapter (WASM, path: ${config.path})`);\n      return new SQLiteAdapter(config.path);\n    }\n\n    case 'postgres': {\n      throw new Error(\n        'fhir-engine: PostgreSQL adapter is not yet available. ' +\n        'PostgresAdapter is not exported from fhir-persistence v0.1.0. ' +\n        'Use database.type = \"sqlite\" for now.',\n      );\n    }\n\n    default: {\n      const _exhaustive: never = config;\n      throw new Error(`fhir-engine: unknown database type: ${(_exhaustive as DatabaseConfig).type}`);\n    }\n  }\n}\n", "import { existsSync, readFileSync } from 'node:fs';\nimport { resolve, extname } from 'node:path';\nimport { pathToFileURL } from 'node:url';\nimport type { FhirEngineConfig, DatabaseConfig } from './types.js';\n\n// ---------------------------------------------------------------------------\n// defineConfig \u2014 typed identity helper for fhir.config.ts / .js\n// ---------------------------------------------------------------------------\n\n/**\n * Type-safe config helper for `fhir.config.ts` / `fhir.config.js`.\n *\n * @example\n * ```ts\n * // fhir.config.ts\n * import { defineConfig } from 'fhir-engine';\n *\n * export default defineConfig({\n *   database: { type: 'sqlite', path: './fhir.db' },\n *   packages: { path: './fhir-packages' },\n * });\n * ```\n */\nexport function defineConfig(config: FhirEngineConfig): FhirEngineConfig {\n  return config;\n}\n\n// ---------------------------------------------------------------------------\n// Config file discovery order\n// ---------------------------------------------------------------------------\n\nconst CONFIG_FILENAMES = [\n  'fhir.config.ts',\n  'fhir.config.js',\n  'fhir.config.mjs',\n  'fhir.config.json',\n] as const;\n\n// ---------------------------------------------------------------------------\n// loadFhirConfig \u2014 auto-discover and load config\n// ---------------------------------------------------------------------------\n\n/**\n * Load engine configuration from a file.\n *\n * If `configPath` is provided, loads that exact file.\n * Otherwise, searches the current working directory for config files\n * in this order: `fhir.config.ts` \u2192 `fhir.config.js` \u2192 `fhir.config.mjs` \u2192 `fhir.config.json`.\n *\n * Environment variable overrides are applied on top of the loaded config.\n *\n * @param configPath - Explicit path to a config file (optional).\n * @returns The resolved `FhirEngineConfig`.\n */\nexport async function loadFhirConfig(configPath?: string): Promise<FhirEngineConfig> {\n  let resolvedPath: string;\n\n  if (configPath) {\n    resolvedPath = resolve(configPath);\n    if (!existsSync(resolvedPath)) {\n      throw new Error(`fhir-engine: config file not found: ${resolvedPath}`);\n    }\n  } else {\n    const cwd = process.cwd();\n    const found = CONFIG_FILENAMES\n      .map((name) => resolve(cwd, name))\n      .find((p) => existsSync(p));\n    if (!found) {\n      throw new Error(\n        `fhir-engine: no config file found in ${cwd}. ` +\n        `Expected one of: ${CONFIG_FILENAMES.join(', ')}`,\n      );\n    }\n    resolvedPath = found;\n  }\n\n  const config = await loadConfigFile(resolvedPath);\n  return applyEnvOverrides(config);\n}\n\n// ---------------------------------------------------------------------------\n// File loaders\n// ---------------------------------------------------------------------------\n\nasync function loadConfigFile(filePath: string): Promise<FhirEngineConfig> {\n  const ext = extname(filePath);\n\n  if (ext === '.json') {\n    return loadJsonConfig(filePath);\n  }\n\n  if (ext === '.ts' || ext === '.js' || ext === '.mjs') {\n    return loadModuleConfig(filePath);\n  }\n\n  throw new Error(`fhir-engine: unsupported config file extension: ${ext}`);\n}\n\nfunction loadJsonConfig(filePath: string): FhirEngineConfig {\n  try {\n    const raw = readFileSync(filePath, 'utf-8');\n    return JSON.parse(raw) as FhirEngineConfig;\n  } catch (err) {\n    throw new Error(\n      `fhir-engine: failed to parse config file ${filePath}: ${err instanceof Error ? err.message : String(err)}`,\n      { cause: err },\n    );\n  }\n}\n\nasync function loadModuleConfig(filePath: string): Promise<FhirEngineConfig> {\n  try {\n    const fileUrl = pathToFileURL(filePath).href;\n    const mod = await import(fileUrl);\n    const config = mod.default ?? mod;\n\n    if (!config || typeof config !== 'object') {\n      throw new Error('config file must export a FhirEngineConfig object as default export');\n    }\n\n    return config as FhirEngineConfig;\n  } catch (err) {\n    if (err instanceof Error && err.message.includes('must export')) {\n      throw err;\n    }\n    throw new Error(\n      `fhir-engine: failed to load config file ${filePath}: ${err instanceof Error ? err.message : String(err)}`,\n      { cause: err },\n    );\n  }\n}\n\n// ---------------------------------------------------------------------------\n// Environment variable overrides\n// ---------------------------------------------------------------------------\n\nconst VALID_DB_TYPES = ['sqlite', 'sqlite-wasm', 'postgres'] as const;\n\n/**\n * Apply environment variable overrides on top of a loaded config.\n *\n * | Env Variable        | Overrides                        |\n * |---------------------|----------------------------------|\n * | FHIR_DATABASE_TYPE  | config.database.type             |\n * | FHIR_DATABASE_URL   | config.database.path / .url      |\n * | FHIR_PACKAGES_PATH  | config.packages.path             |\n * | FHIR_LOG_LEVEL      | (stored for logger filtering)    |\n */\nexport function applyEnvOverrides(config: FhirEngineConfig): FhirEngineConfig {\n  const result = structuredClone(config);\n\n  const dbType = process.env.FHIR_DATABASE_TYPE;\n  const dbUrl = process.env.FHIR_DATABASE_URL;\n  const pkgPath = process.env.FHIR_PACKAGES_PATH;\n\n  if (dbType) {\n    if (!VALID_DB_TYPES.includes(dbType as typeof VALID_DB_TYPES[number])) {\n      throw new Error(\n        `fhir-engine: FHIR_DATABASE_TYPE must be one of: ${VALID_DB_TYPES.join(', ')}. Got: \"${dbType}\"`,\n      );\n    }\n    // Rebuild database config with overridden type\n    const validType = dbType as DatabaseConfig['type'];\n    if (validType === 'postgres') {\n      result.database = { type: 'postgres', url: (result.database as { url?: string }).url ?? '' };\n    } else if (validType === 'sqlite-wasm') {\n      result.database = { type: 'sqlite-wasm', path: (result.database as { path?: string }).path ?? '' };\n    } else {\n      result.database = { type: 'sqlite', path: (result.database as { path?: string }).path ?? '' };\n    }\n  }\n\n  if (dbUrl) {\n    const type = result.database?.type;\n    if (type === 'postgres') {\n      result.database = { ...result.database, type: 'postgres', url: dbUrl };\n    } else if (type === 'sqlite-wasm') {\n      result.database = { ...result.database, type: 'sqlite-wasm', path: dbUrl };\n    } else {\n      result.database = { ...result.database, type: 'sqlite', path: dbUrl };\n    }\n  }\n\n  if (pkgPath) {\n    result.packages = { ...result.packages, path: pkgPath };\n  }\n\n  return result;\n}\n", "import type { Logger } from './types.js';\n\n/**\n * Default console-based logger.\n */\nexport function createConsoleLogger(): Logger {\n  return {\n    debug: (message: string, ...args: unknown[]) => console.debug(`[fhir-engine] ${message}`, ...args),\n    info: (message: string, ...args: unknown[]) => console.info(`[fhir-engine] ${message}`, ...args),\n    warn: (message: string, ...args: unknown[]) => console.warn(`[fhir-engine] ${message}`, ...args),\n    error: (message: string, ...args: unknown[]) => console.error(`[fhir-engine] ${message}`, ...args),\n  };\n}\n", "import { resolve, join } from 'node:path';\nimport { existsSync, mkdirSync, symlinkSync, readFileSync, lstatSync, copyFileSync } from 'node:fs';\nimport { PackageCache, PackageRegistryClient } from 'fhir-definition';\n\nimport type { FhirEngineConfig, ResolvePackagesOptions, ResolvedPackage, ResolvePackagesResult, Logger } from './types.js';\n\n/**\n * Ensure the given directory exists (recursive mkdir).\n */\nfunction ensureDirSync(dir: string): void {\n  if (!existsSync(dir)) {\n    mkdirSync(dir, { recursive: true });\n  }\n}\n\n/**\n * Check if a directory contains a FHIR package manifest.\n * Checks both root/package.json and package/package.json\n * (cached packages store content in a 'package' subdirectory).\n */\nfunction hasManifest(dir: string): boolean {\n  return existsSync(join(dir, 'package.json')) || existsSync(join(dir, 'package', 'package.json'));\n}\n\n/**\n * Read the version from a package.json file.\n * Checks both root and package/ subdirectory.\n * Returns the version string or 'local' if not found.\n */\nfunction readLocalVersion(pkgDir: string): string {\n  for (const candidate of [join(pkgDir, 'package.json'), join(pkgDir, 'package', 'package.json')]) {\n    try {\n      const raw = readFileSync(candidate, 'utf-8');\n      const manifest = JSON.parse(raw);\n      return manifest.version ?? 'local';\n    } catch {\n      // try next candidate\n    }\n  }\n  return 'local';\n}\n\n/**\n * Resolve FHIR packages into a project's packages directory.\n *\n * Resolution order for each package:\n * 1. Already exists in packagesPath \u2192 use as-is (source: 'local')\n * 2. Found in system cache (~/.fhir/packages) \u2192 create symlink/junction (source: 'cache')\n * 3. Download from FHIR Package Registry \u2192 cache \u2192 create symlink (source: 'download')\n *\n * @param config  Engine configuration (uses config.igs and config.packages.path)\n * @param options Override packages list, target path, download policy, or logger\n * @returns       Result with resolved packages and any errors\n *\n * @example\n * ```ts\n * const result = await resolvePackages(config);\n * if (!result.success) {\n *   console.warn('Some packages failed:', result.errors);\n * }\n * ```\n */\nexport async function resolvePackages(\n  config: FhirEngineConfig,\n  options?: ResolvePackagesOptions,\n): Promise<ResolvePackagesResult> {\n  const packagesPath = resolve(options?.packagesPath ?? config.packages.path);\n  const igs = options?.packages ?? config.igs ?? [];\n  const allowDownload = options?.allowDownload ?? config.packageResolve?.allowDownload ?? true;\n  const logger: Logger | undefined = options?.logger ?? config.logger;\n\n  const cache = new PackageCache();\n  const client = new PackageRegistryClient();\n  const results: ResolvedPackage[] = [];\n  const errors: Array<{ name: string; error: string }> = [];\n\n  ensureDirSync(packagesPath);\n\n  for (const ig of igs) {\n    try {\n      // 1. Already exists locally?\n      const localPath = join(packagesPath, ig.name);\n      if (hasManifest(localPath)) {\n        const localVersion = readLocalVersion(localPath);\n        logger?.debug(`Package ${ig.name} already exists locally at ${localPath}`);\n        results.push({ name: ig.name, version: localVersion, path: localPath, source: 'local' });\n        continue;\n      }\n\n      // 2. Resolve version\n      let version = ig.version ?? 'latest';\n      if (version === 'latest') {\n        if (!allowDownload) {\n          errors.push({\n            name: ig.name,\n            error: `Cannot resolve \"latest\" version for ${ig.name} without network access`,\n          });\n          continue;\n        }\n        logger?.info(`Resolving latest version for ${ig.name}...`);\n        version = await client.getLatestVersion(ig.name);\n        logger?.info(`Latest version for ${ig.name}: ${version}`);\n      }\n\n      // 3. Check system cache\n      const cachePath = cache.getPath(ig.name, version);\n      if (cachePath) {\n        // Cache hit \u2014 create symlink\n        logger?.info(`Found ${ig.name}@${version} in system cache, linking...`);\n        ensureCacheRootManifest(cachePath);\n        createLink(cachePath, localPath);\n        results.push({ name: ig.name, version, path: localPath, source: 'cache' });\n        continue;\n      }\n\n      // 4. Download\n      if (!allowDownload) {\n        errors.push({\n          name: ig.name,\n          error: `Package ${ig.name}@${version} not found in cache, and downloads are disabled`,\n        });\n        continue;\n      }\n\n      logger?.info(`Downloading ${ig.name}@${version} from registry...`);\n      const tarball = await client.download(ig.name, version);\n      cache.put(ig.name, version, tarball);\n      logger?.info(`Downloaded and cached ${ig.name}@${version}`);\n\n      // Create symlink from cache to project packages dir\n      const newCachePath = cache.getPath(ig.name, version);\n      if (!newCachePath) {\n        errors.push({ name: ig.name, error: `Failed to locate cached package after download` });\n        continue;\n      }\n      ensureCacheRootManifest(newCachePath);\n      createLink(newCachePath, localPath);\n      results.push({ name: ig.name, version, path: localPath, source: 'download' });\n    } catch (err) {\n      errors.push({\n        name: ig.name,\n        error: err instanceof Error ? err.message : String(err),\n      });\n    }\n  }\n\n  return {\n    success: errors.length === 0,\n    packages: results,\n    errors,\n  };\n}\n\n/**\n * Ensure the cache root directory has a package.json manifest.\n * Some tools (e.g. Firely Terminal) only place package.json inside the\n * package/ subdirectory. Without a root manifest, PackageScanner discovers\n * the package at the wrong depth, causing PackageLoader to construct a\n * double-nested \"package/package\" path that doesn't exist (\u2192 0 resources).\n */\nfunction ensureCacheRootManifest(cachePath: string): void {\n  const rootManifest = join(cachePath, 'package.json');\n  const nestedManifest = join(cachePath, 'package', 'package.json');\n  if (!existsSync(rootManifest) && existsSync(nestedManifest)) {\n    copyFileSync(nestedManifest, rootManifest);\n  }\n}\n\n/**\n * Create a directory junction (Windows) or symlink (Unix) from target to linkPath.\n * Idempotent \u2014 if link already exists, does nothing.\n */\nfunction createLink(target: string, linkPath: string): void {\n  if (existsSync(linkPath)) {\n    // Already exists (either real dir or symlink) \u2014 skip\n    try {\n      const stat = lstatSync(linkPath);\n      if (stat.isSymbolicLink() || stat.isDirectory()) {\n        return;\n      }\n    } catch {\n      // If stat fails, try to create anyway\n    }\n  }\n  // Use 'junction' on Windows (no admin needed), 'dir' on Unix\n  const linkType = process.platform === 'win32' ? 'junction' : 'dir';\n  symlinkSync(target, linkPath, linkType);\n}\n", "// fhir-engine \u2014 public API\n\nexport { createFhirEngine } from './engine.js';\nexport { defineConfig, loadFhirConfig } from './config.js';\nexport { createConsoleLogger } from './logger.js';\nexport { createAdapter } from './adapter-factory.js';\nexport { resolvePackages } from './package-resolver.js';\n\nexport type {\n  FhirEngine,\n  FhirEngineConfig,\n  FhirEnginePlugin,\n  FhirEngineStatus,\n  EngineContext,\n  DatabaseConfig,\n  SqliteDatabaseConfig,\n  SqliteWasmDatabaseConfig,\n  PostgresDatabaseConfig,\n  PackagesConfig,\n  Logger,\n  ResolvePackagesOptions,\n  ResolvedPackage,\n  ResolvePackagesResult,\n} from './types.js';\n\n// Re-export key upstream types for convenience\nexport type { DefinitionRegistry, DefinitionProvider } from 'fhir-definition';\nexport type { FhirRuntimeInstance } from 'fhir-runtime';\nexport type { FhirPersistence, StorageAdapter } from 'fhir-persistence';\n\n// ---------------------------------------------------------------------------\n// Search utilities (from fhir-persistence)\n// ---------------------------------------------------------------------------\n\nexport { parseSearchRequest, executeSearch } from 'fhir-persistence';\nexport type { SearchRequest, SearchResult, SearchOptions } from 'fhir-persistence';\n\n// ---------------------------------------------------------------------------\n// FHIRPath evaluation (from fhir-runtime)\n// ---------------------------------------------------------------------------\n\nexport { evalFhirPath, evalFhirPathBoolean, evalFhirPathString, evalFhirPathTyped } from 'fhir-runtime';\n"],
+  "mappings": 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   "names": ["resolve", "existsSync", "readFileSync", "parseSearchRequest", "executeSearch"]
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "fhir-engine",
-  "version": "0.4.0",
+  "version": "0.4.1",
   "description": "FHIR Engine for healthcare data management",
   "homepage": "https://github.com/medxaidev/fhir-engine#readme",
   "license": "MIT",