fhir-persistence 0.1.0

package/dist/lib/store/fhir-store.d.ts

@@ -0,0 +1,44 @@
+/**
+ * FhirStore — v2 CRUD Facade
+ *
+ * Provides create / read / update / delete / history operations
+ * against any StorageAdapter implementation (SQLite, PostgreSQL, etc.).
+ *
+ * Design decisions:
+ * - Uses StorageAdapter interface (not DatabaseClient directly)
+ * - All writes are transactional (BEGIN IMMEDIATE on SQLite)
+ * - Soft delete: deleted=1, content preserved (ADR-08)
+ * - Optimistic locking via versionId (If-Match / ETag)
+ * - History ordered by versionSeq DESC
+ * - No projectId (single-tenant)
+ *
+ * @module fhir-persistence/store
+ */
+import type { StorageAdapter } from '../db/adapter.js';
+import type { FhirResource, PersistedResource, HistoryEntry } from '../repo/types.js';
+import type { ReferenceRowV2 } from '../repo/reference-indexer.js';
+export interface CreateResourceOptions {
+    /** Pre-assigned ID (used in batch/transaction). */
+    assignedId?: string;
+}
+export interface UpdateResourceOptions {
+    /** Expected versionId for optimistic locking (If-Match header). */
+    ifMatch?: string;
+}
+export interface HistoryOptions {
+    since?: string;
+    count?: number;
+    cursor?: string;
+}
+export declare class FhirStore {
+    private readonly adapter;
+    constructor(adapter: StorageAdapter);
+    createResource<T extends FhirResource>(resourceType: string, resource: T, options?: CreateResourceOptions): Promise<T & PersistedResource>;
+    readResource(resourceType: string, id: string): Promise<PersistedResource>;
+    updateResource<T extends FhirResource>(resourceType: string, resource: T, options?: UpdateResourceOptions): Promise<T & PersistedResource>;
+    deleteResource(resourceType: string, id: string): Promise<void>;
+    readVersion(resourceType: string, id: string, versionId: string): Promise<PersistedResource>;
+    readHistory(resourceType: string, id: string, options?: HistoryOptions): Promise<HistoryEntry[]>;
+    writeReferences(resourceType: string, resourceId: string, refs: ReferenceRowV2[]): Promise<void>;
+}
+//# sourceMappingURL=fhir-store.d.ts.map

package/dist/lib/store/fhir-store.d.ts.map

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package/dist/lib/terminology/terminology-code-repo.d.ts

@@ -0,0 +1,61 @@
+/**
+ * Terminology Code Repository
+ *
+ * Persists CodeSystem codes as a display cache in `terminology_codes`.
+ * Provides fast lookup by (system, code) and by code alone.
+ *
+ * Key design decisions:
+ * - Uses StorageAdapter (not DatabaseClient)
+ * - `?` placeholders for SQLite compatibility
+ * - `INSERT OR IGNORE` for idempotent batch inserts
+ * - PRIMARY KEY (system, code) — composite
+ * - INDEX (code) for lookupByCode without system
+ *
+ * @module fhir-persistence/terminology
+ */
+import type { StorageAdapter } from '../db/adapter.js';
+export interface TerminologyCode {
+    /** Code system URI (e.g., "http://loinc.org"). */
+    system: string;
+    /** Code value (e.g., "8480-6"). */
+    code: string;
+    /** Human-readable display text. */
+    display: string;
+}
+export declare class TerminologyCodeRepo {
+    private readonly adapter;
+    constructor(adapter: StorageAdapter);
+    /**
+     * Ensure the terminology_codes table and indexes exist.
+     */
+    ensureTable(): Promise<void>;
+    /**
+     * Batch insert codes. Duplicates are silently ignored (INSERT OR IGNORE).
+     *
+     * @param codes - Array of codes to insert.
+     * @returns Number of codes actually inserted (excluding duplicates).
+     */
+    batchInsert(codes: TerminologyCode[]): Promise<number>;
+    /**
+     * Lookup display text for a specific (system, code) pair.
+     *
+     * @returns Display text, or undefined if not found.
+     */
+    lookup(system: string, code: string): Promise<string | undefined>;
+    /**
+     * Lookup all codes matching a code value (any system).
+     * Useful for code-only search without specifying system.
+     *
+     * @returns Array of matching TerminologyCode entries.
+     */
+    lookupByCode(code: string): Promise<TerminologyCode[]>;
+    /**
+     * Get the total number of codes in the table.
+     */
+    getCodeCount(): Promise<number>;
+    /**
+     * Remove all codes from the table.
+     */
+    clear(): Promise<void>;
+}
+//# sourceMappingURL=terminology-code-repo.d.ts.map

package/dist/lib/terminology/terminology-code-repo.d.ts.map

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package/dist/lib/terminology/valueset-repo.d.ts

@@ -0,0 +1,76 @@
+/**
+ * ValueSet Repository
+ *
+ * Persists FHIR ValueSet resources in `terminology_valuesets`.
+ * Each ValueSet is uniquely identified by (url, version).
+ *
+ * Key design decisions:
+ * - Uses StorageAdapter (not DatabaseClient)
+ * - `?` placeholders for SQLite compatibility
+ * - `INSERT OR REPLACE` for upsert semantics
+ * - PRIMARY KEY (url, version) — composite
+ * - Content stored as JSON text
+ *
+ * @module fhir-persistence/terminology
+ */
+import type { StorageAdapter } from '../db/adapter.js';
+export interface StoredValueSet {
+    /** ValueSet canonical URL (e.g., "http://hl7.org/fhir/ValueSet/observation-codes"). */
+    url: string;
+    /** ValueSet version (e.g., "4.0.1"). */
+    version: string;
+    /** ValueSet name (human-readable). */
+    name: string | null;
+    /** Full ValueSet content as JSON string. */
+    content: string;
+    /** When this record was stored. */
+    storedAt: string;
+}
+export interface ValueSetInput {
+    url: string;
+    version: string;
+    name?: string;
+    content: string;
+}
+export declare class ValueSetRepo {
+    private readonly adapter;
+    constructor(adapter: StorageAdapter);
+    /**
+     * Ensure the terminology_valuesets table exists.
+     */
+    ensureTable(): Promise<void>;
+    /**
+     * Insert or update a ValueSet.
+     * If a ValueSet with the same (url, version) exists, it is replaced.
+     */
+    upsert(input: ValueSetInput): Promise<void>;
+    /**
+     * Get a specific ValueSet by url and version.
+     *
+     * @returns The stored ValueSet, or undefined if not found.
+     */
+    getValueSet(url: string, version: string): Promise<StoredValueSet | undefined>;
+    /**
+     * Get all versions of a ValueSet by URL.
+     *
+     * @returns Array of stored ValueSets, ordered by version.
+     */
+    getByUrl(url: string): Promise<StoredValueSet[]>;
+    /**
+     * Get all stored ValueSets.
+     */
+    getAll(): Promise<StoredValueSet[]>;
+    /**
+     * Remove a specific ValueSet by url and version.
+     */
+    remove(url: string, version: string): Promise<void>;
+    /**
+     * Get the total number of stored ValueSets.
+     */
+    getValueSetCount(): Promise<number>;
+    /**
+     * Remove all stored ValueSets.
+     */
+    clear(): Promise<void>;
+}
+//# sourceMappingURL=valueset-repo.d.ts.map

package/dist/lib/terminology/valueset-repo.d.ts.map

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package/dist/lib/transaction/bundle-processor.d.ts

@@ -0,0 +1,84 @@
+/**
+ * Bundle Processor — v2
+ *
+ * Processes FHIR Bundle resources of type `transaction` and `batch`
+ * using FhirStore + StorageAdapter (not FhirRepository).
+ *
+ * Key differences from v1 (src/repo/bundle-processor.ts):
+ * - Uses `FhirStore` for CRUD (not `FhirRepository`)
+ * - Uses `StorageAdapter.transaction()` for atomic transactions
+ * - `urn:uuid:` carries resourceType via `UrnTarget`
+ * - Batch rejects `urn:uuid:` references (returns 400)
+ * - Supports `If-None-Exist` conditional create
+ * - `?` placeholders (SQLite), `deleted = 0` (INTEGER)
+ *
+ * @module fhir-persistence/transaction
+ */
+import type { FhirResource, PersistedResource } from '../repo/types.js';
+import type { StorageAdapter } from '../db/adapter.js';
+import type { FhirStore } from '../store/fhir-store.js';
+/**
+ * A single entry in a FHIR Bundle.
+ */
+export interface BundleEntry {
+    fullUrl?: string;
+    resource?: FhirResource;
+    request?: {
+        method: 'GET' | 'POST' | 'PUT' | 'DELETE';
+        url: string;
+        /** If-None-Exist header for conditional create. */
+        ifNoneExist?: string;
+    };
+}
+/**
+ * A FHIR Bundle resource.
+ */
+export interface Bundle {
+    resourceType: 'Bundle';
+    type: 'transaction' | 'batch';
+    entry?: BundleEntry[];
+}
+/**
+ * Result entry for a single bundle operation.
+ */
+export interface BundleResponseEntry {
+    resource?: PersistedResource;
+    response: {
+        status: string;
+        location?: string;
+        etag?: string;
+        lastModified?: string;
+        outcome?: {
+            issue: Array<{
+                severity: string;
+                code: string;
+                diagnostics: string;
+            }>;
+        };
+    };
+}
+/**
+ * Result of processing a bundle.
+ */
+export interface BundleResponse {
+    resourceType: 'Bundle';
+    type: 'transaction-response' | 'batch-response';
+    entry: BundleResponseEntry[];
+}
+/**
+ * v2: Process a transaction bundle — all-or-nothing.
+ *
+ * All entries are processed within a single StorageAdapter transaction.
+ * If any entry fails, the entire transaction is rolled back.
+ *
+ * Entry processing order: strict sequential (no reorder).
+ */
+export declare function processTransactionV2(store: FhirStore, adapter: StorageAdapter, bundle: Bundle): Promise<BundleResponse>;
+/**
+ * v2: Process a batch bundle — each entry independently.
+ *
+ * Each entry is processed in its own try/catch.
+ * urn:uuid references are rejected in batch mode (return 400).
+ */
+export declare function processBatchV2(store: FhirStore, bundle: Bundle): Promise<BundleResponse>;
+//# sourceMappingURL=bundle-processor.d.ts.map

package/dist/lib/transaction/bundle-processor.d.ts.map

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package/dist/lib/transaction/urn-resolver.d.ts

@@ -0,0 +1,62 @@
+/**
+ * URN Resolver — v2
+ *
+ * Builds a mapping from `urn:uuid:` references to actual resource IDs,
+ * and deep-resolves those references within FHIR resources.
+ *
+ * Key differences from v1 (src/repo/bundle-processor.ts inline logic):
+ * - Extracted into a dedicated module for testability
+ * - `UrnTarget` carries `resourceType` (not just the string "Type/id")
+ * - `deepResolveUrns` is iterative (no recursion depth limit needed)
+ * - Only replaces `.reference` fields (FHIR Reference type)
+ *
+ * @module fhir-persistence/transaction
+ */
+import type { FhirResource } from '../repo/types.js';
+/**
+ * A resolved URN target with explicit resourceType.
+ */
+export interface UrnTarget {
+    /** The assigned resource ID. */
+    id: string;
+    /** The FHIR resource type (e.g., "Patient"). */
+    resourceType: string;
+}
+/**
+ * A single entry in a FHIR Bundle (minimal shape for URN resolution).
+ */
+export interface BundleEntryForUrn {
+    fullUrl?: string;
+    resource?: FhirResource;
+    request?: {
+        method: string;
+        url: string;
+    };
+}
+/**
+ * Build a mapping from `urn:uuid:` fullUrls to assigned IDs + resourceTypes.
+ *
+ * Only processes POST entries with `urn:uuid:` fullUrl.
+ * Each matching entry gets a newly generated UUID as its assigned ID.
+ *
+ * The returned map has two key formats for each entry:
+ * - `"urn:uuid:<uuid>"` → `UrnTarget` (for fullUrl-based lookup)
+ *
+ * @param entries - Bundle entries to scan.
+ * @returns Map from urn:uuid string to UrnTarget.
+ */
+export declare function buildUrnMap(entries: BundleEntryForUrn[]): Map<string, UrnTarget>;
+/**
+ * Replace `urn:uuid:` references in a resource with actual `Type/id` references.
+ *
+ * Only replaces values in `.reference` fields (FHIR Reference type)
+ * to avoid accidental replacement in narratives or identifiers.
+ *
+ * Uses structured deep-walk (iterative stack, not recursive).
+ *
+ * @param resource - The FHIR resource to resolve (will be cloned).
+ * @param urnMap - Map from urn:uuid strings to UrnTarget.
+ * @returns A new resource with resolved references.
+ */
+export declare function deepResolveUrns<T extends FhirResource>(resource: T, urnMap: Map<string, UrnTarget>): T;
+//# sourceMappingURL=urn-resolver.d.ts.map

package/dist/lib/transaction/urn-resolver.d.ts.map

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package/dist/tsdoc-metadata.json

@@ -0,0 +1,11 @@
+// This file is read by tools that parse documentation comments conforming to the TSDoc standard.
+// It should be published with your NPM package.  It should not be tracked by Git.
+{
+  "tsdocVersion": "0.12",
+  "toolPackages": [
+    {
+      "packageName": "@microsoft/api-extractor",
+      "packageVersion": "7.57.7"
+    }
+  ]
+}

package/package.json

@@ -0,0 +1,87 @@
+{
+  "name": "fhir-persistence",
+  "version": "0.1.0",
+  "description": "Embedded FHIR R4 persistence layer — CRUD, search, indexing, schema migration over SQLite and PostgreSQL",
+  "homepage": "https://github.com/medxaidev/fhir-persistence#readme",
+  "license": "MIT",
+  "author": "Fangjun <fangjun20208@gmail.com>",
+  "keywords": [
+    "fhir",
+    "fhir-r4",
+    "fhir-persistence",
+    "fhir-server",
+    "fhir-search",
+    "hl7",
+    "healthcare",
+    "sqlite",
+    "postgresql",
+    "embedded-database",
+    "schema-migration",
+    "search-indexing",
+    "typescript",
+    "interoperability",
+    "clinical",
+    "ehr"
+  ],
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/medxaidev/fhir-persistence.git"
+  },
+  "bugs": {
+    "url": "https://github.com/medxaidev/fhir-persistence/issues"
+  },
+  "publishConfig": {
+    "access": "public",
+    "registry": "https://registry.npmjs.org/"
+  },
+  "sideEffects": false,
+  "type": "module",
+  "main": "./dist/cjs/index.cjs",
+  "module": "./dist/esm/index.mjs",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    ".": {
+      "import": {
+        "types": "./dist/esm/index.d.ts",
+        "default": "./dist/esm/index.mjs"
+      },
+      "require": {
+        "types": "./dist/cjs/index.d.ts",
+        "default": "./dist/cjs/index.cjs"
+      }
+    },
+    "./package.json": "./package.json"
+  },
+  "files": [
+    "dist",
+    "README.md",
+    "LICENSE",
+    "CHANGELOG.md"
+  ],
+  "scripts": {
+    "clean": "rimraf dist",
+    "build": "npm run clean && tsc && node ./scripts/esbuild.mjs",
+    "test": "vitest run",
+    "prepublishOnly": "npm run test && npm run build"
+  },
+  "dependencies": {
+    "better-sqlite3": "^12.6.2",
+    "fhir-definition": "^0.5.0",
+    "fhir-runtime": "^0.8.1",
+    "sql.js": "^1.14.1"
+  },
+  "devDependencies": {
+    "@microsoft/api-extractor": "^7.57.7",
+    "@types/better-sqlite3": "^7.6.13",
+    "@types/node": "25.2.0",
+    "esbuild": "0.27.2",
+    "rimraf": "6.1.2",
+    "tsx": "4.21.0",
+    "typescript": "5.9.3",
+    "vitest": "4.0.18"
+  },
+  "engines": {
+    "node": ">=18.0.0",
+    "npm": ">=9.0.0"
+  }
+}