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What is Fumifier?\n2. Feature Highlights\n3. When to Use\n4. Installation\n5. Quick Start\n6. FLASH DSL Overview (Very Brief)\n7. FHIR Integration & Structure Navigation\n8. Diagnostics, Threshold Policy & Verbose Mode\n9. API Reference\n10. Custom Functions & Logging\n11. TypeScript Support\n12. CLI / REPL (future)\n13. Performance Notes\n14. Cached Parsing\n15. Mapping Repository\n16. Syntax Enhancements\n17. Contributing\n18. Acknowledgements\n\n---\n## 1. What is Fumifier?\nFumifier is the executable core of the **FLASH DSL** used in the broader **FUME** toolkit. It allows authors to express rich transformation, mapping, projection and validation logic over JSON (especially FHIR® resources) using a concise expression language inspired by FHIR Shorthand (FSH) and JSONata but extended for:\n- FHIR profile / element introspection\n- Cardinality & primitive handling\n- Pattern / fixed value enforcement\n- Value set binding validation\n- Structured diagnostics with policy‑driven severities\n\nFumifier compiles a FLASH expression string to an executable object, then evaluates it against input JSON, optionally enriched with a FHIR structure navigator.\n\n---\n## 2. Feature Highlights\n- Modern ES Module implementation (Node ≥ 20)\n- **Browser Entry Point** 🌐 **New in v1.4.0** – lightweight parsing-only module for browsers (~103KB vs ~341KB)\n- **Mapping Repository** 📚 **New in v1.8.0** – reusable expression library with caching support\n- **Trailing Semicolons** 📝 **New in v1.7.0** – optional semicolons in inline FLASH rule assignments\n- **Assume Block** 🔄 **New in v1.3.0** – semicolon-separated expressions at root level treated as implicit blocks\n- **Dual Assignment** 🎯 **New in v1.6.0** – support for dual assignment patterns with deferred validation\n- **Auto-Injected Fixed Values** ✨ **New in v1.5.0** – automatic injection of safe fixed-value optional elements\n- **AST Mobility** ⭐ **New in v1.0.0** – serialize/deserialize compiled expressions as JSON\n- Async evaluation pipeline with selective short‑circuiting\n- FLASH blocks & rules lowered into native evaluator stages\n- Tuple streams & ancestry tracking for context‑rich transformations\n- Policy‑driven diagnostics (throw / log / collect / validate levels)\n- Built‑in logging helpers: `$trace`, `$info`, `$warn`\n- Pluggable FHIR Structure Navigator (external package) for resolving StructureDefinition metadata, children, regex constraints, and value set expansions\n- Selective / inhibited validation depending on severity thresholds\n- Verbose evaluation mode returning a full diagnostics report instead of throwing\n- Function chaining (`func1 ~> func2`), partial application, lambdas, higher‑order utilities\n- Deterministic timestamp utilities `$now()`, `$millis()` bound per evaluation invocation\n\n---\n## 3. When to Use\nUse Fumifier when you need:\n- Declarative JSON / FHIR resource transformation & mapping\n- Enriching raw FHIR payloads guided by profiles\n- Validated outputs with controllable strictness\n- Embedding a safe, sandbox‑style expression engine in higher‑level services\n\n---\n## 4. Installation\n```bash\nnpm install fumifier\n```\n\n### Browser Entry Point 🌐 **New in v1.4.0**\n\nFor browser environments or when you only need parsing capabilities without evaluation:\n\n```javascript\n// ES6 modules\nimport { parse, validate, tokenize } from 'fumifier/browser';\n\n// Parse expressions to AST\nconst ast = parse('name.first & \" \" & name.family');\n\n// Validate syntax\nconst result = validate('name.first &');\nconsole.log(result.isValid, result.errors);\n\n// Extract tokens for syntax highlighting  \nconst tokens = tokenize('$patient.name[0].given');\n```\n\nThe browser entry point is **~103KB** (vs ~341KB for the full package) and includes:\n- ✅ Syntax parsing & AST generation\n- ✅ Real-time validation & error recovery\n- ✅ Tokenization for syntax highlighting\n- ✅ Basic FLASH syntax recognition\n- ❌ No expression evaluation or FHIR navigation\n\nSee [BROWSER.md](./BROWSER.md) for complete documentation.\n\nNode requirement: `>= 20` (see `package.json` engines field).\n\n---\n## 5. Quick Start\n```js\nimport fumifier from 'fumifier';\nimport { createNavigator } from '@outburn/structure-navigator'; // example placeholder\n\nconst expr = `\n  /* Simple example */\n  {\n    id: $.id,\n    fullName: $.name.given[0] & ' ' & $.name.family,\n    firstTwoCodes: $.code.coding[0..1].code\n  }\n`;\n\nconst navigator = await createNavigator({ /* supply FHIR package sources */ });\nconst compiled = await fumifier(expr, { navigator });\n\nconst input = {/* FHIR resource JSON */};\nconst output = await compiled.evaluate(input);\nconsole.log(output);\n```\n\nVerbose (never throws controlled diagnostics):\n```js\nconst report = await compiled.evaluateVerbose(input);\nif (!report.ok) {\n  console.warn('Partial/diagnostic status', report.status, report.diagnostics);\n}\n```\n\nCustom thresholds per evaluation:\n```js\nconst output = await compiled.evaluate(input, {\n  throwLevel: 10,     // stricter: throw even on invalid\n  logLevel: 40,       // log fatal/invalid/error/warning\n  collectLevel: 70,   // collect all severities (default)\n  validationLevel: 30 // run validations for severities < 30\n});\n```\n\n---\n## 6. FLASH DSL Overview (Very Brief)\nFLASH extends JSONata‑style expressions with:\n- Flash blocks / rules (prefix `[` lowering to unary nodes) controlling grouped evaluation\n- FHIR element awareness (cardinality shaping, pattern & fixed value injection – some still on roadmap)\n- Enhanced tuple streams for multi‑binding contexts (`@` root, indices, ancestry labels)\n- Policy‑aware validation primitives\n\n(Full language guide forthcoming.)\n\n---\n## 7. FHIR Integration & Structure Navigation\nWhen the supplied expression contains FLASH constructs requiring FHIR knowledge (flagged during parse), a `navigator` must be provided. Fumifier then:\n1. Resolves referenced StructureDefinitions (base + differential)\n2. Caches compiled FHIR regex patterns\n3. Resolves value set expansions (if requested by rules)\n4. Attaches metadata collections onto the evaluation environment via well‑known Symbols.\n\nIf FLASH features are detected but no navigator is passed and recovery is disabled, an `F1000` error is raised.\n\n---\n## 8. Diagnostics, Threshold Policy & Verbose Mode\nSeverity (lower = more critical):\n- fatal(0) < invalid(10) < error(20) < warning(30) < notice(40) < info(50) < debug(60)\n\nThreshold variables (bindings) control behavior:\n- `throwLevel` (default 30): throw when severity < level\n- `logLevel` (40): log when severity < level (to the evaluation-environment logger set via `compiled.setLogger(...)` or `runtimeOptions.logger`)\n- `collectLevel` (70): collect into diagnostics bag when severity < level\n- `validationLevel` (30): run a validation only if its severity < level\n\n`evaluate(...)` throws once a diagnostic meets throw criteria. `evaluateVerbose(...)` never throws; it returns `{ ok, status, result, diagnostics }` where `status` (200/206/422) reflects collected severities.\n\nSee `PolicyThresholds.md` for deeper guidance.\n\n---\n## 9. API Reference\n### `await fumifier(expressionText, options)`\n### `await fumifier(astObject, options)` ⭐ **New in v1.0.0**\nReturns a compiled expression object.\n\nThe fumifier function now accepts either:\n- `expressionText: string` – FLASH/JSONata expression to parse and compile\n- `astObject: Object` – Pre-parsed AST JSON to compile directly (**AST Mobility**)\n\n`options`:\n- `navigator?: FhirStructureNavigator` – required only if FLASH FHIR features are used.\n- `recover?: boolean` – attempt AST recovery on parse/resolution errors, collecting them as AST.errors instead of throwing. This is the recovery mode for parsing, not evaluation.\n- `astCache?: AstCacheInterface` – optional AST cache implementation for parsed expressions. Defaults to shared LRU cache.\n- `mappingCache?: MappingCacheInterface` – optional mapping repository for named expressions with `getKeys()` and `get(key)` methods.\n- `logger?: Logger` – optional logger implementation with `{ debug, info, warn, error }` methods. Defaults to console-based logger.\n- `fhirClient?: FhirClient` – optional FHIR client from `@outburn/fhir-client` for server operations.\n- `bindings?: Record<string, any>` – optional initial variable/function bindings (no signature support for functions).\n\nCompiled object methods:\n- `evaluate(input, bindings?, runtimeOptions?) -> Promise<any>`\n- `evaluateVerbose(input, bindings?, runtimeOptions?) -> Promise<{ ok, status, result, diagnostics }>`\n- `assign(name, value)` – bind a variable permanently to the compiled expression\n- `registerFunction(name, implementation, signature?)` – register custom function with optional JSONata signature\n- `setLogger(logger)` – set logger implementation\n- `setMappingCache(cache)` – set mapping cache implementation\n- `setFhirClient(client)` – set FHIR client for server operations\n- `ast()` – returns internal AST\n- `errors()` – returns compilation errors (if any)\n\n**RuntimeOptions** (third parameter to `evaluate`/`evaluateVerbose`):\n- `logger?: Logger` – override logger for this evaluation only\n- `fhirClient?: FhirClient` – override FHIR client for this evaluation only\n- `mappingCache?: MappingCacheInterface` – override mapping cache for this evaluation only\n\nExample with runtime overrides:\n```js\nconst compiled = await fumifier(expr, {\n  logger: defaultLogger,\n  fhirClient: defaultClient\n});\n\n// Use defaults\nawait compiled.evaluate(input);\n\n// Override for specific evaluation\nawait compiled.evaluate(input, bindings, {\n  logger: requestLogger,\n  fhirClient: tenantClient\n});\n```\n\n### AST Mobility ⭐ **New in v1.0.0**\nFumifier now supports \"AST mobility\" - the ability to serialize and recreate compiled expressions:\n\n```js\n// 1. Create and extract AST\nconst expr1 = await fumifier('$x * 2 + $y');\nconst ast = expr1.ast();\n\n// 2. Serialize AST to JSON\nconst astJson = JSON.stringify(ast);\n\n// 3. Recreate expression from AST\nconst deserializedAst = JSON.parse(astJson);\nconst expr2 = await fumifier(deserializedAst);\n\n// 4. Both expressions work identically\nconst result1 = await expr1.evaluate({}, { x: 5, y: 3 }); // 13\nconst result2 = await expr2.evaluate({}, { x: 5, y: 3 }); // 13\n```\n\n**Use Cases:**\n- Cache compiled expressions as JSON for faster application startup\n- Transfer expressions between processes, services, or storage systems\n- Version control and database storage of transformation logic\n- Hot-reload expressions without re-parsing\n- Expression introspection and analysis tools\n\n### Custom Bindings\nPass `bindings` to `evaluate` to set parameter variables or override thresholds (`throwLevel`, etc.).\n\n### Signatures\nSignatures follow `<argtypes:return>` style. Example: `<s?:u>` means optional string param returning undefined.\n\n---\n## 10. Custom Functions, Logging & FHIR Client\n### Custom Functions\n```js\ncompiled.registerFunction('toUpper', function(v){ return String(v).toUpperCase(); }, '<s:s>');\n```\nWithin a custom function `this` contains `{ environment, input }`.\n\n### Built-in Logging Functions\nBuilt‑in logging helpers produce diagnostics respecting thresholds:\n- `$warn(message)` code `F5320`\n- `$info(message)` code `F5500`\n- `$trace(value?, label, projection?)` code `F5600` – returns original value for chaining\n\n### FHIR Client Functions\nWhen a FHIR client is provided (via `options.fhirClient` or `setFhirClient()`), the following functions become available:\n\n```js\nimport { FhirClient } from '@outburn/fhir-client';\n\nconst client = new FhirClient({\n  baseUrl: 'https://hapi.fhir.org/baseR4',\n  fhirVersion: 'R4'\n});\n\nconst compiled = await fumifier(expr, { fhirClient: client });\n\n// Available functions in expressions:\n// $search(resourceType, params?, options?) -> Bundle or Resource[]\n// $capabilities() -> CapabilityStatement\n// $resourceId(resourceType, params, options?) -> string (resource ID)\n// $searchSingle(resourceTypeOrRef, params?, options?) -> Resource\n// $resolve(resourceTypeOrRef, params?, options?) -> Resource\n// $literal(resourceType, params, options?) -> string (resourceType/id)\n```\n\n**Example expressions:**\n```javascript\n// Search for patients\n$search('Patient', { name: 'John' })\n\n// Get server capabilities\n$capabilities()\n\n// Get resource ID from search\n$resourceId('Patient', { identifier: 'http://system|12345' })\n\n// Resolve single resource by search\n$searchSingle('Patient', { identifier: 'http://system|12345' })\n\n// Resolve by literal reference\n$resolve('Patient/123')\n\n// Get literal reference from search\n$literal('Patient', { identifier: 'http://system|12345' })\n```\n\n**Error Handling:**\nFHIR client operations follow Fumifier's centralized error handling:\n- `F5200`: FHIR client not configured\n- `F5201-F5203`: General FHIR client errors\n- `F5210`: Resource not found (404)\n- `F5211`: Search returned no results\n- `F5212`: Search returned multiple results when one expected\n\n**Runtime Override:**\n```js\n// Per-evaluation FHIR client override (e.g., for multi-tenancy)\nawait compiled.evaluate(input, bindings, {\n  fhirClient: tenantSpecificClient\n});\n```\n\n---\n## 11. TypeScript Support\nTypes are published via `fumifier.d.ts`. (If missing, build pipeline will generate from `fumifier.ts` – ensure the file ships in the package.)\nExample:\n```ts\nimport fumifier, { type FumifierOptions } from 'fumifier';\nconst compiled = await fumifier('$.id', {} as FumifierOptions);\n```\n\n---\n## 12. CLI / REPL (future)\nPlanned: `npx fumifier --expr file.fume --in input.json` for quick invocations & experimentation.\n\n---\n## 13. Performance Notes\n- Avoid extremely large arrays where possible (range operator limited to 1e7 entries)\n- Tail call optimization is implemented for lambdas returning thunks\n- Regex compilation for FHIR primitives cached per compiled expression\n- Parallelizable map phases flagged internally to reduce await churn (best effort)\n\n---\n## 14. Cached Parsing ⭐ **New**\nFumifier now supports caching of parsed expressions to improve performance when the same expressions are used repeatedly:\n\n```javascript\nimport fumifier from 'fumifier';\n\n// Uses default shared LRU cache (128MB limit)\nconst compiled = await fumifier('Patient.name.given');\n\n// Provide custom AST cache implementation\nconst myAstCache = {\n  // identity is an object: { source, version, recover, rootPackages? }\n  async get(identity) { /* your get logic */ },\n  async set(identity, value) { /* your set logic */ }\n};\nconst compiled2 = await fumifier('Patient.name.given', { astCache: myAstCache });\n\n// Cache identities include expression text, recover mode, FHIR context, and fumifier version\n// Concurrent requests for the same expression are deduplicated automatically\n```\n\n**Key Features:**\n- **Default LRU Cache**: Shared across all fumifier instances with memory-based eviction\n- **External Cache Support**: Implement `{ get, set }` interface for Redis, database, etc.\n- **Smart Cache Identities**: Based on expression text, recover mode, FHIR context, and fumifier version\n- **Concurrent Deduplication**: Multiple requests for the same unparsed expression share results\n- **$eval Inheritance**: Expressions evaluated via `$eval()` inherit the parent's AST cache\n\n\n---\n## 15. Mapping Repository 📚 **New in v1.8.0**\nFumifier now supports a mapping repository feature that allows you to create reusable libraries of named expressions:\n\n```javascript\n// Define a mapping cache with reusable expressions\nconst mappingCache = {\n  async getKeys() {\n    return ['greeting', 'formatPatient', 'validateData'];\n  },\n  async get(key) {\n    const mappings = {\n      'greeting': '\"Hello, \" & $',\n      'formatPatient': '{ \"id\": $.id, \"fullName\": $.name.given[0] & \" \" & $.name.family }',\n      'validateData': '$length($) > 0 ? $ : undefined'\n    };\n    return mappings[key];\n  }\n};\n\n// Use mappings in expressions\nconst compiled = await fumifier('$greeting(\"World\")', { mappingCache });\nconst result = await compiled.evaluate({}); // \"Hello, World\"\n\n// FLASH expressions in mappings (requires navigator)\nconst flashMappings = {\n  'createPatient': `\nInstanceOf: Patient\n* id = \"patient-\" & $uuid()\n* active = true\n  `\n};\n\nconst flashCompiled = await fumifier('$createPatient($)', {\n  navigator,\n  mappingCache: { get: async (key) => flashMappings[key], getKeys: async () => Object.keys(flashMappings) }\n});\n```\n\n**Key Features:**\n- **Named Expressions**: Store and reuse complex transformations\n- **Bindings Support**: Pass parameters to mappings: `$myMapping(input, {\"param\": value})`\n- **FLASH Integration**: Use full FLASH syntax in mapping definitions\n- **Error Handling**: Comprehensive error reporting for mapping issues\n- **Caching**: Mappings are compiled and cached for performance\n- **Nested Calls**: Mappings can call other mappings\n- **Override Support**: Bindings can override mapping functions\n\n---\n## 16. Syntax Enhancements ✨ **New Features**\n\n### Trailing Semicolons (v1.7.0)\nFLASH rule assignments now support optional trailing semicolons for improved readability:\n\n```javascript\n// Both syntax styles work identically:\nconst withSemicolons = await fumifier(`\nInstanceOf: Patient\n* id = \"test-patient\";\n* active = true;\n* gender = \"male\";\n`);\n\nconst withoutSemicolons = await fumifier(`\nInstanceOf: Patient  \n* id = \"test-patient\"\n* active = true\n* gender = \"male\"\n`);\n```\n\n### Assume Block Feature (v1.3.0)\nRoot-level expressions separated by semicolons are automatically treated as implicit blocks:\n\n```javascript\n// Multiple expressions at root level\nconst compiled = await fumifier(`\n$x := 5;\n$y := 10;\n$x + $y\n`);\n\nconst result = await compiled.evaluate({}); // 15\n```\n\n### Dual Assignment Patterns (v1.6.0)\nSupport for dual assignment patterns with deferred mandatory validation:\n\n```javascript\n// Multiple rules targeting the same non-repeating parent element\nconst compiled = await fumifier(`\nInstanceOf: MyPatientProfile\n* identifier[NonRepeatingSlice].use = \"usual\"\n* identifier[NonRepeatingSlice].value = \"12345\"\n`);\n```\n\n### Auto-Injected Fixed Values (v1.5.0)\nAutomatic injection of optional elements that are safe to auto-inject when they have fixed values (including both human-readable fields like display text/units, and some semantically meaningful fields that are profile-fixed). Note that mandatory elements with fixed values are always injected, this feature does the same for optional elements if they are regarded safe.\n\n---\n## 17. Contributing\n1. Fork & clone\n2. `npm install`\n3. `npm test` (runs lint + install FSH test package + coverage)\n4. Create feature branch (`feat/...` or `fix/...`)\n5. Add / update tests under `test/`\n6. Run coverage target: `npm run check-coverage`\n7. Open PR with concise description & rationale\n\nCoding standards: ESLint (config in repo) – aim for zero warnings. Commit messages: Conventional style (`feat:`, `fix:`, `chore:`...).\n\nSecurity / PHI: Test data MUST NOT contain real patient information.\n\n\n---\n## 19. License & Attribution\nGNU Affero General Public License v3.0 (see `LICENSE`). Portions adapted from / inspired by JSONata (MIT). Include original JSONata notices where required.\nFHIR® is the registered trademark of HL7 and is used with permission.\n\nIf you redistribute modified sources, retain attribution headers and provide a NOTICE file summarizing third‑party attributions.\n\n---\n## 20. Acknowledgements\n- JSONata project for foundational expression evaluation concepts\n- HL7 & FHIR community\n- Contributors & early adopters of the FUME / FLASH ecosystem\n\n---\n## Minimal Example (Copy/Paste)\n```js\nimport fumifier from 'fumifier';\n\nconst compiled = await fumifier('{ id: $.id, given: $.name.given[0] }');\nconst result = await compiled.evaluate({ id: '123', name: { given: ['Alice'] }});\nconsole.log(result); // { id: '123', given: 'Alice' }\n```\n\n---\nIssues & feedback: please open a GitHub issue once the public repository is live.","readmeFilename":"README.md"}