fhir-terminology-runtime 0.1.0

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package/README.md

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+# FHIR Terminology Runtime
+
+> Local FHIR terminology runtime for ValueSet expansion, CodeSystem resolution, and terminology operations  
+> Part of the [FUME](https://github.com/Outburn-IL/fume-community) open-source initiative · Apache 2.0 License
+
+## Overview
+
+`fhir-terminology-runtime` (FTR):
+- Expands ValueSets (compose.include / compose.exclude) using CodeSystems from FHIR packages.
+- Resolves CodeSystems by canonical URL with package-context-aware versioning.
+- Caches expanded ValueSets alongside source packages for performance.
+- Supports implicit code systems (ISO 3166, BCP-47) without external dependencies.
+
+## Why?
+
+Many ValueSets in FHIR packages can be locally expanded given complete CodeSystems. Local expansion:
+- Avoids round-trips to external terminology servers for static, package-defined terminology
+- Provides deterministic, reproducible expansions
+- Works offline and in constrained environments
+- Enables fast terminology operations in data transformation pipelines
+
+FTR supports multiple FHIR versions, package-context-aware resolution, lazy or full-cache modes, and works hand-in-hand with [`fhir-package-explorer`](https://github.com/Outburn-IL/fhir-package-explorer) and [`fhir-package-installer`](https://github.com/Outburn-IL/fhir-package-installer).
+
+## Installation
+
+```
+npm install fhir-terminology-runtime
+```
+
+## Usage
+
+### 1. Create an instance
+
+FTR uses dependency injection - you provide a pre-configured `FhirPackageExplorer` instance. This allows sharing a single FPE instance across multiple modules (e.g., FSG and FTR):
+
+```ts
+import { FhirTerminologyRuntime } from 'fhir-terminology-runtime';
+import { FhirPackageExplorer } from 'fhir-package-explorer';
+
+// Create a single FPE instance
+const fpe = await FhirPackageExplorer.create({
+  context: ['hl7.fhir.us.core@6.1.0'],
+  cachePath: './.fhir-cache',
+  fhirVersion: '4.0.1',
+  skipExamples: true
+});
+
+// Create FTR using the shared FPE
+const ftr = await FhirTerminologyRuntime.create({
+  fpe,
+  cacheMode: 'lazy', // 'lazy' | 'ensure' | 'rebuild' | 'none'
+  fhirVersion: '4.0.1'
+});
+```
+
+Benefits of this approach:
+- ✅ Share a single FPE instance across FSG, FTR, and other modules
+- ✅ Single source of truth for FHIR package configuration
+- ✅ Better resource management and configuration consistency
+- ✅ Explicit dependency management
+
+If a base FHIR package is missing from the package context and dependencies, FPE will add it automatically according to `fhirVersion`.
+
+### 2. Expand a ValueSet
+
+```ts
+const expansion = await ftr.expandValueSet('administrative-gender'); // id | name | canonical URL
+```
+
+The `expandValueSet` method accepts any FSH-style identifier: canonical URL, id or name. It also accepts a resolved metadata object if you already have one.
+
+### 3. Get ValueSet Expansion Count
+
+Get the count of concepts in a ValueSet expansion without loading the full expansion if possible. Results are cached in memory.
+
+```ts
+const result = await ftr.getValueSetExpansionCount('administrative-gender');
+
+if (result.status === 'ok') {
+  console.log(`Count: ${result.count}`);
+} else {
+  console.log(`Could not count: ${result.reason}`);
+}
+```
+
+The result type is:
+```ts
+type CountResult =
+  | { status: 'ok'; count: number }
+  | { status: 'unknown'; reason: 'unexpandable-valueset' | 'unknown-valueset' | 'duplicate-code' };
+```
+
+### 4. Check membership (`inValueSet`)
+
+For fast validation of whether a code is in a ValueSet, use `inValueSet`.
+
+It accepts either:
+- a plain code string (common case; system is implicit), OR
+- a Coding-like object with `{ system, code }`.
+
+```ts
+const r1 = await ftr.inValueSet('A', 'administrative-gender');
+//    ^ MembershipResult
+
+const r2 = await ftr.inValueSet({ system: 'http://hl7.org/fhir/administrative-gender', code: 'male' }, 'administrative-gender');
+```
+
+Return type:
+```ts
+type ConceptProps = {
+  system: string;
+  code: string;
+  display?: string;
+  version?: string;
+};
+
+type MembershipResult =
+  | { status: 'member'; concept: ConceptProps }
+  | { status: 'not-member' }
+  | { status: 'unknown'; reason: UnknownReason };
+```
+
+Unknown reasons:
+- `unknown-valueset`: the ValueSet identifier could not be resolved.
+- `unexpandable-valueset`: the ValueSet could not be expanded locally.
+- `duplicate-code`: returned only for **code-only** lookups when the same code exists under **multiple systems** in the ValueSet (ambiguous without a system).
+
+## Membership caching (`membershipCache`)
+
+`inValueSet` is optimized for very fast repeated lookups and uses multiple caching layers:
+- An in-memory LRU for **small** ValueSets (≤ 50 unique codes), holding up to 100 ValueSets.
+- An in-memory LRU for **per-code** results for larger ValueSets, holding up to 10,000 code lookups.
+- An optional **external async cache** (injectable) used as a fallback and for persistence/distributed caching.
+
+### Configure an external membership cache
+
+Provide a `membershipCache` in `FhirTerminologyRuntime.create(...)`:
+
+```ts
+const ftr = await FhirTerminologyRuntime.create({
+  fpe,
+  cacheMode: 'lazy',
+  fhirVersion: '4.0.1',
+  membershipCache
+});
+```
+
+The external cache is keyed deterministically by ValueSet metadata: `(packageId, packageVersion, filename)`.
+
+Interface (simplified):
+```ts
+type ValueSetDeterministicKey = {
+  packageId: string;
+  packageVersion: string;
+  filename: string;
+};
+
+type MembershipCacheEntry =
+  | { status: 'member'; conceptsBySystem: Record<string, ConceptProps> }
+  | { status: 'not-member' };
+
+interface TerminologyMembershipCache {
+  getCode(vs: ValueSetDeterministicKey, code: string): Promise<MembershipCacheEntry | undefined>;
+  setCode(vs: ValueSetDeterministicKey, code: string, entry: MembershipCacheEntry): Promise<void>;
+
+  // Optional: more efficient priming for large ValueSets
+  bulkSetCodes?(vs: ValueSetDeterministicKey, entries: Array<[string, MembershipCacheEntry]>): Promise<void>;
+}
+```
+
+### What does “prime / priming” mean?
+
+In this codebase, **priming** refers specifically to the optional *external membership cache* behavior.
+
+When FTR says it will **prime** the external cache for a ValueSet, it means:
+- FTR has already built a local membership index for that ValueSet (from its expansion).
+- FTR then **bulk-populates the external cache** with *membership answers for many (often all) codes* in that ValueSet, so future `inValueSet(...)` calls can be answered without re-expanding/re-indexing.
+
+This is different from the normal per-lookup caching that happens during `inValueSet`:
+- **Per-lookup cache sync** (always small): after answering a single code lookup, FTR may write a single `(ValueSetKey, code) -> entry` into the external cache.
+- **Priming** (larger write, optional): FTR writes *many* codes for the same ValueSet in one go (ideally via `bulkSetCodes`).
+
+#### Why prime at all?
+
+Priming is a performance / distribution optimization:
+- Speeds up future lookups for the same ValueSet (especially in fresh processes/containers).
+- Enables sharing membership knowledge across workers if the external cache is shared (Redis, DB, etc.).
+- Reduces repeated “first time” cost where the runtime would otherwise need to expand and index again.
+
+#### What exactly gets written during priming?
+
+Priming writes entries shaped like `MembershipCacheEntry`:
+
+- For each `code` in the ValueSet, FTR writes:
+  - `{ status: 'member', conceptsBySystem: { [systemUrl]: { system, code, display?, version? }, ... } }`
+
+Notes:
+- The external cache entry can store **multiple systems** for the same `code`. This is important because `inValueSet('X', vs)` can be ambiguous when multiple systems contain the same code.
+- FTR does **not** write "unknown" results to the external cache (for example `duplicate-code`), because unknown results often depend on whether the caller provided a system. Instead, FTR stores the raw “member by system(s)” facts.
+
+#### When does priming happen?
+
+Priming happens inside `inValueSet(...)` after FTR has built a local index for that ValueSet.
+
+Current behavior:
+- **Small ValueSets (≤ 50 unique codes)**:
+  - FTR builds an in-memory “small index”.
+  - FTR also primes the external cache “for completeness” because the write is cheap.
+- **Large ValueSets (> 50 unique codes)**:
+  - FTR uses a per-code LRU for in-memory caching.
+  - FTR attempts a one-time priming for that ValueSet so subsequent lookups can hit the external cache.
+
+Important: priming is **best-effort**.
+- If the external cache is unavailable or throws, FTR continues and still answers the lookup from local evaluation.
+- Priming failures do not make `inValueSet` fail.
+
+#### What does “primed” mean?
+
+“Primed” is a state meaning: *“we believe the external cache already contains the bulk membership entries for this ValueSet key.”*
+
+---
+
+## ConceptMap translation (`translateConceptMap`)
+
+FTR can translate codes using `ConceptMap` resources from FHIR packages.
+
+API:
+
+```ts
+const result = await ftr.translateConceptMap('A', 'some-conceptmap');
+
+if (result.status === 'mapped') {
+  console.log(result.targets);
+} else {
+  console.log(result.reason);
+}
+```
+
+Return type:
+
+- `mapped`: one or more targets were found
+- `unmapped`: no targets, with a reason
+
+Input:
+- A code string (common case; source `system` is implicit), or
+- A Coding-like object `{ system, code }`.
+
+Output:
+- Returns a structured result object.
+- When `status === 'mapped'`, `targets` is an array of **full target Codings** (never just a string code).
+- When `status === 'unmapped'`, `reason` explains why no targets were returned.
+
+Unmapped reasons:
+- `code-not-in-conceptmap`: the source code is not present in the ConceptMap.
+- `no-translation`: the source code exists, but no translation exists for the requested source system (or the mapping is empty).
+- `unsupported-equivalence`: a mapping exists, but all targets were ignored because their `equivalence` values are unsupported. In this case, `ignoredEquivalences` is included.
+- `duplicate-code`: returned only for **code-only** lookups when the same code exists under **multiple source systems** in the ConceptMap.
+- `invalid-code`: the input code was empty.
+
+Note: if the ConceptMap identifier cannot be resolved or the ConceptMap cannot be loaded, `translateConceptMap` throws.
+
+### Equivalence handling
+
+Only these `ConceptMap.group.element.target[].equivalence` values are used for translation:
+
+```txt
+equivalent
+equal
+wider
+subsumes
+```
+
+If `equivalence` is missing (allowed in FHIR R3), it is treated as `equivalent`.
+Any other equivalence value is ignored.
+
+### Group flattening
+
+All `ConceptMap.group[]` entries are treated as a single flattened mapping.
+Group boundaries have no semantic meaning for translation in this runtime.
+
+### Server ConceptMaps (optional `fhirClient`)
+
+If you provide a `fhirClient` to `FhirTerminologyRuntime.create(...)`, `translateConceptMap` can resolve ConceptMaps from a FHIR server.
+
+- When `conceptMap` is a string and `packageFilter` is **not** provided, the runtime tries the server first and then falls back to packages.
+- When `packageFilter` is provided, the runtime skips server resolution and uses packages only.
+
+Server resolution attempts (in order):
+- `ConceptMap?url={identifier}`
+- `ConceptMap/{identifier}`
+- `ConceptMap?name={identifier}`
+
+If the server ConceptMaps may change at runtime, you can clear cached server ConceptMaps:
+
+```ts
+await ftr.clearServerConceptMapsFromCache();
+// or clear for a specific server base URL
+await ftr.clearServerConceptMapsFromCache('https://example.org/fhir');
+```
+
+### Translation caching (`conceptMapCache`)
+
+`translateConceptMap` uses multiple caching layers similar to `inValueSet`:
+
+- In-memory LRU for **small** ConceptMaps (≤ 50 unique source codes), holding up to 20 ConceptMaps.
+- In-memory LRU for **hot per-code** translation results, holding up to 1,000 lookups.
+- Optional **external async cache** (injectable) used for cold-start / distributed caching.
+
+Provide a `conceptMapCache` in `FhirTerminologyRuntime.create(...)`:
+
+```ts
+const ftr = await FhirTerminologyRuntime.create({
+  fpe,
+  cacheMode: 'lazy',
+  fhirVersion: '4.0.1',
+  conceptMapCache
+});
+```
+
+The external ConceptMap cache is keyed by a deterministic ConceptMap namespace:
+
+- Package ConceptMaps: `(packageId, packageVersion, filename)`
+- Server ConceptMaps: (keyed by server base URL + ConceptMap URL)
+
+Interface (simplified):
+
+```ts
+type ConceptMapDeterministicKey =
+  | { kind: 'package'; packageId: string; packageVersion: string; filename: string }
+  | { kind: 'server'; serverBaseUrl: string; url: string };
+
+type ConceptMapTranslation = {
+  system: string;
+  code: string;
+  display?: string;
+  version?: string;
+  equivalence: 'equivalent' | 'equal' | 'wider' | 'subsumes';
+};
+
+type ConceptMapCacheEntry =
+  | {
+      status: 'found';
+      bySourceSystem: Record<string, { targets: ConceptMapTranslation[]; ignoredEquivalences?: string[] }>;
+    }
+  | { status: 'not-found' };
+
+interface TerminologyConceptMapCache {
+  getCode(cm: ConceptMapDeterministicKey, code: string): Promise<ConceptMapCacheEntry | undefined>;
+  setCode(cm: ConceptMapDeterministicKey, code: string, entry: ConceptMapCacheEntry): Promise<void>;
+
+  bulkSetCodes?(cm: ConceptMapDeterministicKey, entries: Array<[string, ConceptMapCacheEntry]>): Promise<void>;
+
+  // Required: used for package reinstall / server ConceptMap reload operations
+  clearNamespace(namespacePrefix: string): Promise<void>;
+}
+```
+
+Implementation note for cache authors:
+- FTR provides the `namespacePrefix` string to `clearNamespace(...)`.
+- Your implementation does **not** need to invent prefixes, but it **must** store keys in a way that preserves the prefix so prefix-clearing is possible (for example, avoid hashing the entire key in a way that prevents enumerating/deleting by prefix).
+
+FTR supports two ways to track this state:
+
+1) **Automatic external primed-state (default; no extra methods required)**
+
+FTR automatically tracks whether a ConceptMap has been primed in the external cache using the **same `getCode/setCode` methods you already implement**.
+
+Concretely:
+- After a successful prime, FTR writes a reserved **sentinel entry** under a reserved “code” key.
+- Before priming, FTR checks whether that sentinel entry exists.
+
+This means the “standard cache interface” is just `getCode`/`setCode` (and optionally `bulkSetCodes`). You do **not** need to implement any additional primed-state methods.
+
+What you might see in your cache:
+- FTR may store an extra entry with `code = '__ftr__primed__'` to represent “this ValueSet has been primed”.
+- This entry is internal bookkeeping and is never used as a real terminology code lookup.
+
+Collision note (extremely unlikely): if a ValueSet legitimately contains the code `'__ftr__primed__'`, FTR will avoid using the sentinel mechanism for that ValueSet and will fall back to in-memory priming guards.
+
+2) **In-memory primed-state (fallback)**
+
+If the external cache is unavailable (or throws), FTR uses an in-memory Set (one per process) to avoid re-priming repeatedly within the same runtime instance.
+
+This distinction matters:
+- The in-memory guard prevents repeated priming *only within the current process*.
+- The external primed-state prevents repeated priming across processes and restarts.
+
+#### A concrete mental model
+
+Consider a large ValueSet `VS` and a code lookup `inValueSet('C10', VS)`:
+
+1) FTR tries the in-memory LRUs.
+2) If configured, FTR tries the external cache for `(VS-key, 'C10')`.
+3) If not found, FTR expands/indexes locally, answers the lookup, and then:
+   - **syncs** the single code result to the external cache, and
+   - may **prime** the external cache for `VS` (bulk write) so future codes (`C11`, `C12`, …) can be served externally.
+
+#### Priming is not ValueSet expansion caching
+
+FTR has two separate caching concepts:
+- **Expansion caching**: stores the expanded ValueSet JSON on disk under `.ftr/` alongside packages.
+- **Membership caching**: accelerates `inValueSet` lookups (in-memory LRUs + optional external cache).
+
+“Priming” only refers to the **external membership cache** behavior.
+
+## ValueSet Expansion Details
+
+The expansion engine performs a deterministic local expansion when possible:
+- Supports: `compose.include` (system + all codes, or explicit concept list), `compose.exclude`, and `include.valueSet` recursion (with cycle detection) plus JSON-style set semantics (union of includes, subtraction of excludes, intersection when combining explicit concepts with referenced ValueSets for the same system).
+- Not supported yet: `include.filter` (expansion will throw an error). This intentionally surfaces intensional ValueSets so callers can fallback to an external terminology service if possible.
+- Recursion: `include.valueSet` entries are resolved first in the source package; if not found there, a global context fallback is attempted.
+- Fallback: If local generation fails but the original ValueSet resource contains an `expansion.contains`, that original expansion is returned and cached (no attempt is made to validate staleness).
+- Displays: When an `include.concept` list supplies explicit codes with displays, the associated CodeSystem resource is not loaded (performance optimization).
+
+### CodeSystem Resolution Rules
+
+When expanding ValueSets the runtime resolves referenced CodeSystems by canonical URL (may be a versioned URL):
+1. Attempt resolution within the originating ValueSet's package (exact version context).
+2. If not found, fall back to global [`fhir-package-explorer`](https://github.com/Outburn-IL/fhir-package-explorer) context using semver-aware `resolveMeta` from FPE to pick a single best version (prevents duplicate version conflicts).
+3. Only CodeSystems with `content = 'complete'` are eligible. Any other `content` will throw an expansion error.
+4. CodeSystems themselves are NOT cached by FTR (they live in their package). Only the derived ValueSet expansion result is cached.
+
+### Expansion Caching
+
+Expanded (or fallback) ValueSets are cached in a dedicated `.ftr` directory alongside source packages. Repeated calls reuse the cached expansion unless `cacheMode` is `none`.
+
+## Context
+You must provide an array of FHIR packages in `context`. Any package or its dependencies missing in the local FHIR package cache will be downloaded and installed (by [`fhir-package-installer`](https://github.com/Outburn-IL/fhir-package-installer)).
+
+Supports `<id>#<version>`, `<id>@<version>`, `<id>` (latest version) or a package identifier object e.g:
+```
+{
+    id: 'hl7.fhir.us.core',
+    version: '6.1.0'
+}
+```
+
+## Cache Modes
+
+| Mode      | Behavior                                                                                 |
+|-----------|------------------------------------------------------------------------------------------|
+| `lazy`    | *Default*. Generates and caches expansions on demand.                                    |
+| `ensure`  | Ensures all ValueSets have cached expansions (missing ones are generated).               |
+| `rebuild` | Clears cache and regenerates all expansions from scratch.                                |
+| `none`    | Disables caching completely (expansions computed each call, nothing written).            |
+
+Cached artifacts are stored under:
+
+```
+<cachePath>/<packageId>#<packageVersion>/.ftr/<FTR version>/
+```
+- Filenames mirror originals in `<cachePath>/<packageId>#<packageVersion>/package`.
+- FTR Version directory uses major.minor.x (e.g. `0.1.x`).
+
+**DEVELOPER NOTICE** – Any change that affects expansion generation output MUST increment the minor version so previously cached results are not silently reused.
+
+## Cache Path
+`cachePath` defines the FHIR package cache directory to be used. This is passed through to [`fhir-package-explorer`](https://github.com/Outburn-IL/fhir-package-explorer) and [`fhir-package-installer`](https://github.com/Outburn-IL/fhir-package-installer).  
+If not provided, the default cache location will be used.  
+See: [Package Cache Directory section](https://github.com/Outburn-IL/fhir-package-installer/blob/main/README.md#package-cache-directory) in FPI's readme for details.
+
+## FHIR Version
+
+Specify the default FHIR version with the `fhirVersion` option. This determines which base definitions are used when none are explicitly imported through dependencies.
+If not specified, defaults to `4.0.1` (FHIR R4).
+
+## Roadmap
+- External terminology service support (fallback for intensional ValueSets)
+- ConceptMap lookup and translation operations
+- LMDB-based caching for improved performance
+- `include.filter` support for local logical expansion
+- Terminology validation operations
+- Expansion parameterization (e.g. date constraints, designations)
+
+## License
+
+Apache License 2.0  
+© Outburn Ltd. 2022–2025. All Rights Reserved.