fhir-persistence 0.3.0 → 0.4.0

package/CHANGELOG.md

@@ -5,6 +5,29 @@ 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).
 
+## [0.4.0] - 2025-03-15
+
+### Fixed
+
+#### PostgreSQL DDL Compatibility (Phase D)
+
+- **`migration-runner.ts`** — Tracking table `_migrations` now uses `TIMESTAMPTZ NOT NULL DEFAULT CURRENT_TIMESTAMP` on PostgreSQL instead of SQLite-only `datetime('now')`
+- **`package-registry-repo.ts`** — `_packages` and `_schema_version` tables use dialect-aware timestamp defaults; `INSERT OR REPLACE` replaced with `INSERT ... ON CONFLICT ... DO UPDATE` on PostgreSQL
+- **`reindex-scheduler.ts`** — `_reindex_jobs` table uses `SERIAL PRIMARY KEY` on PostgreSQL instead of `AUTOINCREMENT`; `datetime('now')` replaced with `CURRENT_TIMESTAMP`
+- **`valueset-repo.ts`** — `terminology_valuesets` table uses dialect-aware timestamp defaults; `INSERT OR REPLACE` replaced with `INSERT ... ON CONFLICT ... DO UPDATE` on PostgreSQL
+- **`lookup-table-writer.ts`** — 4 global lookup tables (`HumanName`, `Address`, `ContactPoint`, `Identifier`) use `SERIAL PRIMARY KEY` on PostgreSQL instead of `AUTOINCREMENT`
+
+### Changed
+
+- **`ig-persistence-manager.ts`** — Now passes `dialect` to `PackageRegistryRepo`, `MigrationRunnerV2`, and `ReindexScheduler` constructors
+- **`indexing-pipeline.ts`** — `IndexingPipelineOptions` accepts `dialect` parameter, passed to `LookupTableWriter`
+- **`fhir-system.ts`** — Passes `dialect` through to `IndexingPipeline` via `FhirPersistence` options
+- All new `dialect` parameters default to `'sqlite'` — fully backward-compatible
+
+### Test Coverage
+
+- **1014 total tests** (1006 passing, 8 skipped) across 56 test files — no regressions
+
 ## [0.3.0] - 2025-03-15
 
 ### Added

package/README.md

@@ -5,7 +5,7 @@ Embedded FHIR R4 persistence layer — CRUD, search, indexing, and schema migrat
 [![npm version](https://img.shields.io/npm/v/fhir-persistence)](https://www.npmjs.com/package/fhir-persistence)
 [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](./LICENSE)
 
-> **v0.3.0** — Dual-backend validated: 1014 tests across SQLite and PostgreSQL
+> **v0.4.0** — Full PostgreSQL DDL compatibility for all system and lookup tables
 
 ## Features
 

package/dist/cjs/index.cjs

@@ -6560,16 +6560,18 @@ var FhirStore = class {
 var import_node_crypto5 = require("node:crypto");
 
 // src/repo/lookup-table-writer.ts
-var LOOKUP_TABLE_DDL = {
-  HumanName: `CREATE TABLE IF NOT EXISTS "HumanName" (
-  "id" INTEGER PRIMARY KEY AUTOINCREMENT,
+function buildLookupTableDDL(dialect) {
+  const pk = dialect === "postgres" ? '"id" SERIAL PRIMARY KEY' : '"id" INTEGER PRIMARY KEY AUTOINCREMENT';
+  return {
+    HumanName: `CREATE TABLE IF NOT EXISTS "HumanName" (
+  ${pk},
   "resourceId" TEXT NOT NULL,
   "name" TEXT,
   "given" TEXT,
   "family" TEXT
 )`,
-  Address: `CREATE TABLE IF NOT EXISTS "Address" (
-  "id" INTEGER PRIMARY KEY AUTOINCREMENT,
+    Address: `CREATE TABLE IF NOT EXISTS "Address" (
+  ${pk},
   "resourceId" TEXT NOT NULL,
   "address" TEXT,
   "city" TEXT,
@@ -6578,20 +6580,21 @@ var LOOKUP_TABLE_DDL = {
   "state" TEXT,
   "use" TEXT
 )`,
-  ContactPoint: `CREATE TABLE IF NOT EXISTS "ContactPoint" (
-  "id" INTEGER PRIMARY KEY AUTOINCREMENT,
+    ContactPoint: `CREATE TABLE IF NOT EXISTS "ContactPoint" (
+  ${pk},
   "resourceId" TEXT NOT NULL,
   "system" TEXT,
   "value" TEXT,
   "use" TEXT
 )`,
-  Identifier: `CREATE TABLE IF NOT EXISTS "Identifier" (
-  "id" INTEGER PRIMARY KEY AUTOINCREMENT,
+    Identifier: `CREATE TABLE IF NOT EXISTS "Identifier" (
+  ${pk},
   "resourceId" TEXT NOT NULL,
   "system" TEXT,
   "value" TEXT
 )`
-};
+  };
+}
 var LOOKUP_TABLE_INDEXES = {
   HumanName: [
     'CREATE INDEX IF NOT EXISTS "HumanName_resourceId_idx" ON "HumanName" ("resourceId")',
@@ -6617,10 +6620,12 @@ var LOOKUP_COLUMNS = {
   Identifier: ["resourceId", "system", "value"]
 };
 var LookupTableWriter = class {
-  constructor(adapter) {
+  constructor(adapter, dialect = "sqlite") {
     this.adapter = adapter;
+    this.ddl = buildLookupTableDDL(dialect);
   }
   initialized = false;
+  ddl;
   // ---------------------------------------------------------------------------
   // DDL
   // ---------------------------------------------------------------------------
@@ -6629,8 +6634,8 @@ var LookupTableWriter = class {
    */
   async ensureTables() {
     if (this.initialized) return;
-    for (const table of Object.keys(LOOKUP_TABLE_DDL)) {
-      await this.adapter.execute(LOOKUP_TABLE_DDL[table]);
+    for (const table of Object.keys(this.ddl)) {
+      await this.adapter.execute(this.ddl[table]);
       for (const idx of LOOKUP_TABLE_INDEXES[table]) {
         await this.adapter.execute(idx);
       }
@@ -6679,7 +6684,7 @@ var LookupTableWriter = class {
    */
   async deleteRows(resourceId) {
     await this.ensureTables();
-    for (const table of Object.keys(LOOKUP_TABLE_DDL)) {
+    for (const table of Object.keys(this.ddl)) {
       await this.adapter.execute(
         `DELETE FROM "${table}" WHERE "resourceId" = ?`,
         [resourceId]
@@ -6705,7 +6710,7 @@ var LookupTableWriter = class {
 var IndexingPipeline = class {
   constructor(adapter, options) {
     this.adapter = adapter;
-    this.lookupWriter = new LookupTableWriter(adapter);
+    this.lookupWriter = new LookupTableWriter(adapter, options?.dialect ?? "sqlite");
     this.runtimeProvider = options?.runtimeProvider;
     this.options = {
       enableLookupTables: options?.enableLookupTables ?? true,
@@ -7403,35 +7408,43 @@ function mapColumnTypeForDialect(type, dialect) {
 
 // src/registry/package-registry-repo.ts
 var PACKAGES_TABLE = "_packages";
-var CREATE_PACKAGES_TABLE = `
+var SCHEMA_VERSION_TABLE = "_schema_version";
+function createPackagesTableDDL(dialect) {
+  const ts = dialect === "postgres" ? "TIMESTAMPTZ NOT NULL DEFAULT CURRENT_TIMESTAMP" : "TEXT NOT NULL DEFAULT (datetime('now'))";
+  return `
 CREATE TABLE IF NOT EXISTS "${PACKAGES_TABLE}" (
   "name" TEXT NOT NULL,
   "version" TEXT NOT NULL,
   "checksum" TEXT NOT NULL,
   "schemaSnapshot" TEXT,
-  "installedAt" TEXT NOT NULL DEFAULT (datetime('now')),
+  "installedAt" ${ts},
   "status" TEXT NOT NULL DEFAULT 'active',
   PRIMARY KEY ("name", "version")
 );
 `;
-var SCHEMA_VERSION_TABLE = "_schema_version";
-var CREATE_SCHEMA_VERSION_TABLE = `
+}
+function createSchemaVersionTableDDL(dialect) {
+  const ts = dialect === "postgres" ? "TIMESTAMPTZ NOT NULL DEFAULT CURRENT_TIMESTAMP" : "TEXT NOT NULL DEFAULT (datetime('now'))";
+  return `
 CREATE TABLE IF NOT EXISTS "${SCHEMA_VERSION_TABLE}" (
   "version" INTEGER NOT NULL PRIMARY KEY,
   "packageList" TEXT NOT NULL,
   "description" TEXT NOT NULL DEFAULT '',
-  "appliedAt" TEXT NOT NULL DEFAULT (datetime('now'))
+  "appliedAt" ${ts}
 );
 `;
+}
 var PackageRegistryRepo = class {
-  constructor(adapter) {
+  constructor(adapter, dialect = "sqlite") {
     this.adapter = adapter;
+    this.dialect = dialect;
   }
+  dialect;
   /**
    * Ensure the packages tracking table exists.
    */
   async ensureTable() {
-    await this.adapter.execute(CREATE_PACKAGES_TABLE);
+    await this.adapter.execute(createPackagesTableDDL(this.dialect));
   }
   /**
    * Get the active version of a package by name.
@@ -7476,7 +7489,7 @@ var PackageRegistryRepo = class {
       [pkg.name]
     );
     await this.adapter.execute(
-      `INSERT OR REPLACE INTO "${PACKAGES_TABLE}" ("name", "version", "checksum", "schemaSnapshot", "status") VALUES (?, ?, ?, ?, 'active')`,
+      this.upsertSQL(),
       [pkg.name, pkg.version, pkg.checksum, pkg.schemaSnapshot ?? null]
     );
     await this.recordSchemaVersion(description ?? `Register ${pkg.name}@${pkg.version}`);
@@ -7493,10 +7506,19 @@ var PackageRegistryRepo = class {
       [pkg.name]
     );
     await this.adapter.execute(
-      `INSERT OR REPLACE INTO "${PACKAGES_TABLE}" ("name", "version", "checksum", "schemaSnapshot", "status") VALUES (?, ?, ?, ?, 'active')`,
+      this.upsertSQL(),
       [pkg.name, pkg.version, pkg.checksum, pkg.schemaSnapshot ?? null]
     );
   }
+  /**
+   * Generate dialect-aware UPSERT SQL.
+   */
+  upsertSQL() {
+    if (this.dialect === "postgres") {
+      return `INSERT INTO "${PACKAGES_TABLE}" ("name", "version", "checksum", "schemaSnapshot", "status") VALUES (?, ?, ?, ?, 'active') ON CONFLICT ("name", "version") DO UPDATE SET "checksum" = EXCLUDED."checksum", "schemaSnapshot" = EXCLUDED."schemaSnapshot", "status" = 'active'`;
+    }
+    return `INSERT OR REPLACE INTO "${PACKAGES_TABLE}" ("name", "version", "checksum", "schemaSnapshot", "status") VALUES (?, ?, ?, ?, 'active')`;
+  }
   /**
    * Remove all versions of a package.
    */
@@ -7528,7 +7550,7 @@ var PackageRegistryRepo = class {
    * Ensure the schema version table exists.
    */
   async ensureSchemaVersionTable() {
-    await this.adapter.execute(CREATE_SCHEMA_VERSION_TABLE);
+    await this.adapter.execute(createSchemaVersionTableDDL(this.dialect));
   }
   /**
    * Record a schema version with the current active package list.
@@ -7578,12 +7600,25 @@ CREATE TABLE IF NOT EXISTS "${TRACKING_TABLE_V2}" (
   "applied_at" TEXT NOT NULL DEFAULT (datetime('now'))
 );
 `;
+var CREATE_TRACKING_TABLE_V2_POSTGRES = `
+CREATE TABLE IF NOT EXISTS "${TRACKING_TABLE_V2}" (
+  "version" INTEGER PRIMARY KEY,
+  "description" TEXT NOT NULL,
+  "type" TEXT NOT NULL DEFAULT 'file',
+  "applied_at" TIMESTAMPTZ NOT NULL DEFAULT CURRENT_TIMESTAMP
+);
+`;
+function createTrackingDDL(dialect) {
+  return dialect === "postgres" ? CREATE_TRACKING_TABLE_V2_POSTGRES : CREATE_TRACKING_TABLE_V2_SQLITE;
+}
 var MigrationRunnerV2 = class {
   adapter;
   migrations;
-  constructor(adapter, migrations = []) {
+  dialect;
+  constructor(adapter, migrations = [], dialect = "sqlite") {
     this.adapter = adapter;
     this.migrations = [...migrations].sort((a, b) => a.version - b.version);
+    this.dialect = dialect;
   }
   // ---------------------------------------------------------------------------
   // Public API
@@ -7592,7 +7627,7 @@ var MigrationRunnerV2 = class {
    * Ensure the tracking table exists.
    */
   async ensureTrackingTable() {
-    await this.adapter.execute(CREATE_TRACKING_TABLE_V2_SQLITE);
+    await this.adapter.execute(createTrackingDDL(this.dialect));
   }
   /**
    * Apply all pending migrations (or up to a target version).
@@ -7768,7 +7803,23 @@ var MigrationRunnerV2 = class {
 
 // src/migration/reindex-scheduler.ts
 var REINDEX_JOBS_TABLE = "_reindex_jobs";
-var CREATE_REINDEX_JOBS_TABLE = `
+function createReindexJobsTableDDL(dialect) {
+  if (dialect === "postgres") {
+    return `
+CREATE TABLE IF NOT EXISTS "${REINDEX_JOBS_TABLE}" (
+  "id" SERIAL PRIMARY KEY,
+  "resourceType" TEXT NOT NULL,
+  "searchParamCode" TEXT NOT NULL,
+  "expression" TEXT NOT NULL,
+  "status" TEXT NOT NULL DEFAULT 'pending',
+  "cursor" TEXT,
+  "processedCount" INTEGER NOT NULL DEFAULT 0,
+  "createdAt" TIMESTAMPTZ NOT NULL DEFAULT CURRENT_TIMESTAMP,
+  "updatedAt" TIMESTAMPTZ NOT NULL DEFAULT CURRENT_TIMESTAMP
+);
+`;
+  }
+  return `
 CREATE TABLE IF NOT EXISTS "${REINDEX_JOBS_TABLE}" (
   "id" INTEGER PRIMARY KEY AUTOINCREMENT,
   "resourceType" TEXT NOT NULL,
@@ -7781,15 +7832,21 @@ CREATE TABLE IF NOT EXISTS "${REINDEX_JOBS_TABLE}" (
   "updatedAt" TEXT NOT NULL DEFAULT (datetime('now'))
 );
 `;
+}
+function nowExpression(dialect) {
+  return dialect === "postgres" ? "CURRENT_TIMESTAMP" : "datetime('now')";
+}
 var ReindexScheduler = class {
-  constructor(adapter) {
+  constructor(adapter, dialect = "sqlite") {
     this.adapter = adapter;
+    this.dialect = dialect;
   }
+  dialect;
   /**
    * Ensure the reindex jobs table exists.
    */
   async ensureTable() {
-    await this.adapter.execute(CREATE_REINDEX_JOBS_TABLE);
+    await this.adapter.execute(createReindexJobsTableDDL(this.dialect));
   }
   /**
    * Schedule reindex jobs from REINDEX deltas.
@@ -7856,7 +7913,7 @@ var ReindexScheduler = class {
       sets.push('"processedCount" = ?');
       values.push(update.processedCount);
     }
-    sets.push(`"updatedAt" = datetime('now')`);
+    sets.push(`"updatedAt" = ${nowExpression(this.dialect)}`);
     values.push(id);
     await this.adapter.execute(
       `UPDATE "${REINDEX_JOBS_TABLE}" SET ${sets.join(", ")} WHERE "id" = ?`,
@@ -7889,9 +7946,9 @@ var IGPersistenceManager = class {
   reindexScheduler;
   constructor(adapter, dialect = "sqlite") {
     this.dialect = dialect;
-    this.packageRepo = new PackageRegistryRepo(adapter);
-    this.migrationRunner = new MigrationRunnerV2(adapter);
-    this.reindexScheduler = new ReindexScheduler(adapter);
+    this.packageRepo = new PackageRegistryRepo(adapter, dialect);
+    this.migrationRunner = new MigrationRunnerV2(adapter, [], dialect);
+    this.reindexScheduler = new ReindexScheduler(adapter, dialect);
   }
   /**
    * Initialize an IG package — the main entry point.
@@ -8072,25 +8129,30 @@ var TerminologyCodeRepo = class {
 
 // src/terminology/valueset-repo.ts
 var VALUESETS_TABLE = "terminology_valuesets";
-var CREATE_VALUESETS_TABLE = `
+function createValuesetsTableDDL(dialect) {
+  const ts = dialect === "postgres" ? "TIMESTAMPTZ NOT NULL DEFAULT CURRENT_TIMESTAMP" : "TEXT NOT NULL DEFAULT (datetime('now'))";
+  return `
 CREATE TABLE IF NOT EXISTS "${VALUESETS_TABLE}" (
   "url" TEXT NOT NULL,
   "version" TEXT NOT NULL,
   "name" TEXT,
   "content" TEXT NOT NULL,
-  "storedAt" TEXT NOT NULL DEFAULT (datetime('now')),
+  "storedAt" ${ts},
   PRIMARY KEY ("url", "version")
 );
 `;
+}
 var ValueSetRepo = class {
-  constructor(adapter) {
+  constructor(adapter, dialect = "sqlite") {
     this.adapter = adapter;
+    this.dialect = dialect;
   }
+  dialect;
   /**
    * Ensure the terminology_valuesets table exists.
    */
   async ensureTable() {
-    await this.adapter.execute(CREATE_VALUESETS_TABLE);
+    await this.adapter.execute(createValuesetsTableDDL(this.dialect));
   }
   /**
    * Insert or update a ValueSet.
@@ -8098,10 +8160,8 @@ var ValueSetRepo = class {
    */
   async upsert(input) {
     await this.ensureTable();
-    await this.adapter.execute(
-      `INSERT OR REPLACE INTO "${VALUESETS_TABLE}" ("url", "version", "name", "content") VALUES (?, ?, ?, ?)`,
-      [input.url, input.version, input.name ?? null, input.content]
-    );
+    const sql = this.dialect === "postgres" ? `INSERT INTO "${VALUESETS_TABLE}" ("url", "version", "name", "content") VALUES (?, ?, ?, ?) ON CONFLICT ("url", "version") DO UPDATE SET "name" = EXCLUDED."name", "content" = EXCLUDED."content"` : `INSERT OR REPLACE INTO "${VALUESETS_TABLE}" ("url", "version", "name", "content") VALUES (?, ?, ?, ?)`;
+    await this.adapter.execute(sql, [input.url, input.version, input.name ?? null, input.content]);
   }
   /**
    * Get a specific ValueSet by url and version.
@@ -8560,7 +8620,8 @@ var FhirSystem = class {
       indexing: {
         enableLookupTables: this.options.enableLookupTables,
         enableReferences: this.options.enableReferences,
-        runtimeProvider: this.options.runtimeProvider
+        runtimeProvider: this.options.runtimeProvider,
+        dialect: this.dialect
       }
     });
     return {