fhir-persistence 0.1.0

package/dist/lib/registry/search-parameter-registry.d.ts

@@ -0,0 +1,175 @@
+/**
+ * SearchParameter Registry
+ *
+ * Indexes FHIR SearchParameter definitions and determines the physical
+ * storage strategy for each parameter. Drives search column generation
+ * in `TableSchemaBuilder`.
+ *
+ * ## Strategy Mapping (from WF-MIG-003)
+ *
+ * | SearchParam.type | Strategy       | Column Type                          |
+ * |------------------|----------------|--------------------------------------|
+ * | date             | column         | TIMESTAMPTZ (or DATE)                |
+ * | string           | column         | TEXT                                 |
+ * | reference        | column         | TEXT                                 |
+ * | number           | column         | DOUBLE PRECISION                     |
+ * | quantity         | column         | DOUBLE PRECISION                     |
+ * | uri              | column         | TEXT                                 |
+ * | boolean          | column         | BOOLEAN (not used in practice)       |
+ * | token            | token-column   | UUID[] + TEXT[] + TEXT (3 cols)       |
+ * | special          | skipped        | —                                    |
+ * | composite        | skipped        | —                                    |
+ *
+ * Lookup-table strategy is determined by matching specific search param
+ * codes (name, address, etc.) — generates a sort column only in the
+ * main table; actual data is written by the Repository layer (Phase 9).
+ *
+ * @module fhir-persistence/registry
+ */
+import type { SqlColumnType } from '../schema/table-schema.js';
+/**
+ * FHIR SearchParameter type codes.
+ */
+export type SearchParamType = 'number' | 'date' | 'string' | 'token' | 'reference' | 'composite' | 'quantity' | 'uri' | 'special';
+/**
+ * Physical storage strategy for a search parameter.
+ *
+ * - `column` — single column in the main table
+ * - `token-column` — three columns (UUID[], TEXT[], TEXT) for token search
+ * - `lookup-table` — separate lookup table; only a sort column in main table
+ */
+export type SearchStrategy = 'column' | 'token-column' | 'lookup-table';
+/**
+ * Column type for search parameter columns.
+ */
+export type SearchColumnType = SqlColumnType;
+/**
+ * Resolved implementation details for a single search parameter
+ * on a specific resource type.
+ */
+export interface SearchParameterImpl {
+    /** SearchParameter.code (e.g., `'birthdate'`). */
+    code: string;
+    /** FHIR search parameter type. */
+    type: SearchParamType;
+    /** Resource types this parameter applies to. */
+    resourceTypes: string[];
+    /** FHIRPath expression for value extraction. */
+    expression: string;
+    /** Physical storage strategy. */
+    strategy: SearchStrategy;
+    /** Column name in the main table (for `column` strategy). */
+    columnName: string;
+    /** PostgreSQL column type (for `column` strategy). */
+    columnType: SearchColumnType;
+    /** Whether the column stores an array of values. */
+    array: boolean;
+}
+/**
+ * Raw FHIR SearchParameter shape (subset of fields we need).
+ */
+export interface SearchParameterResource {
+    resourceType: 'SearchParameter';
+    code: string;
+    type: SearchParamType;
+    base: string[];
+    expression?: string;
+    url?: string;
+    name?: string;
+    target?: string[];
+}
+/**
+ * Shape of a FHIR Bundle containing SearchParameter entries.
+ */
+export interface SearchParameterBundle {
+    resourceType: 'Bundle';
+    entry?: Array<{
+        resource?: SearchParameterResource;
+    }>;
+}
+/**
+ * Indexes SearchParameter definitions by resource type.
+ *
+ * ## Usage
+ *
+ * ```typescript
+ * const registry = new SearchParameterRegistry();
+ * const bundle = JSON.parse(fs.readFileSync('search-parameters.json', 'utf8'));
+ * registry.indexBundle(bundle);
+ *
+ * const patientParams = registry.getForResource('Patient');
+ * ```
+ */
+export declare class SearchParameterRegistry {
+    /**
+     * Map from resource type → Map from param code → SearchParameterImpl.
+     */
+    private readonly byResource;
+    /**
+     * Total number of indexed implementations (across all resource types).
+     */
+    private _totalCount;
+    /**
+     * Number of skipped parameters (composite, special, ignored).
+     */
+    private _skippedCount;
+    /**
+     * Index all SearchParameter entries from a FHIR Bundle.
+     *
+     * Skips entries that are:
+     * - Not a SearchParameter resource
+     * - Of type `composite` or `special`
+     * - In the ignored list (`_id`, `_lastUpdated`, etc.)
+     *
+     * @returns Stats about the indexing operation.
+     */
+    indexBundle(bundle: SearchParameterBundle): {
+        indexed: number;
+        skipped: number;
+    };
+    /**
+     * Index a single SearchParameterImpl directly.
+     *
+     * Useful for adding platform-specific or custom search parameters.
+     */
+    indexImpl(resourceType: string, impl: SearchParameterImpl): void;
+    /**
+     * Get all search parameter implementations for a resource type.
+     *
+     * @returns Array of SearchParameterImpl, sorted by code for deterministic output.
+     */
+    getForResource(resourceType: string): SearchParameterImpl[];
+    /**
+     * Get a specific search parameter implementation for a resource type.
+     */
+    getImpl(resourceType: string, code: string): SearchParameterImpl | undefined;
+    /**
+     * Check if a resource type has any indexed search parameters.
+     */
+    hasResource(resourceType: string): boolean;
+    /**
+     * Get all resource types that have indexed search parameters.
+     */
+    getResourceTypes(): string[];
+    /**
+     * Get the total number of indexed implementations.
+     */
+    get totalCount(): number;
+    /**
+     * Get the number of skipped parameters.
+     */
+    get skippedCount(): number;
+    /**
+     * Get the number of resource types with indexed parameters.
+     */
+    get resourceTypeCount(): number;
+    /**
+     * Remove all indexed parameters.
+     */
+    clear(): void;
+    /**
+     * Build a SearchParameterImpl from a raw SearchParameter resource.
+     */
+    private buildImpl;
+}
+//# sourceMappingURL=search-parameter-registry.d.ts.map

package/dist/lib/registry/search-parameter-registry.d.ts.map

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package/dist/lib/registry/structure-definition-registry.d.ts

@@ -0,0 +1,93 @@
+/**
+ * StructureDefinition Registry
+ *
+ * Indexes `CanonicalProfile[]` by resource type for fast lookup.
+ * MedXAI equivalent of Medplum's `indexStructureDefinitionBundle()` →
+ * `DATA_TYPES`, but as an injectable instance (no global state).
+ *
+ * Used by `TableSchemaBuilder` to determine which resource types
+ * need tables and to access element definitions for search column
+ * generation.
+ *
+ * @module fhir-persistence/registry
+ */
+/**
+ * Minimal CanonicalProfile shape (replaces @medxai/fhir-core dependency).
+ */
+export interface CanonicalProfile {
+    url: string;
+    name: string;
+    kind: 'resource' | 'complex-type' | 'primitive-type' | 'logical';
+    type: string;
+    abstract: boolean;
+    elements: Map<string, unknown>;
+}
+/**
+ * Indexes CanonicalProfile instances by their `type` field for O(1) lookup.
+ *
+ * ## Usage
+ *
+ * ```typescript
+ * const registry = new StructureDefinitionRegistry();
+ * const profiles = loadBundleFromFile('profiles-resources.json').profiles;
+ * registry.indexAll(profiles);
+ *
+ * const patient = registry.get('Patient');
+ * const tableTypes = registry.getTableResourceTypes(); // ~140+ types
+ * ```
+ */
+export declare class StructureDefinitionRegistry {
+    private readonly profiles;
+    /**
+     * Index a single CanonicalProfile by its `type` field.
+     *
+     * If a profile with the same type already exists, it is overwritten
+     * (later definitions override earlier ones, matching BundleLoader
+     * merge semantics).
+     */
+    index(profile: CanonicalProfile): void;
+    /**
+     * Index multiple CanonicalProfiles.
+     *
+     * Profiles are indexed in order; later entries override earlier
+     * ones with the same type.
+     */
+    indexAll(profiles: readonly CanonicalProfile[]): void;
+    /**
+     * Get a profile by resource type name.
+     *
+     * @param resourceType - The FHIR resource type (e.g., `'Patient'`).
+     * @returns The CanonicalProfile, or `undefined` if not indexed.
+     */
+    get(resourceType: string): CanonicalProfile | undefined;
+    /**
+     * Check if a resource type is indexed.
+     */
+    has(resourceType: string): boolean;
+    /**
+     * Get all resource types that should have database tables.
+     *
+     * Returns types where `kind === 'resource'` AND `abstract === false`.
+     * This excludes:
+     * - Abstract types (Resource, DomainResource)
+     * - Complex types (HumanName, Address)
+     * - Primitive types (string, boolean)
+     * - Logical models
+     *
+     * Results are sorted alphabetically for deterministic output.
+     */
+    getTableResourceTypes(): string[];
+    /**
+     * Get all indexed type names (regardless of kind or abstract).
+     */
+    getAllTypes(): string[];
+    /**
+     * Get the number of indexed profiles.
+     */
+    get size(): number;
+    /**
+     * Remove all indexed profiles.
+     */
+    clear(): void;
+}
+//# sourceMappingURL=structure-definition-registry.d.ts.map

package/dist/lib/registry/structure-definition-registry.d.ts.map

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package/dist/lib/repo/errors.d.ts

@@ -0,0 +1,61 @@
+/**
+ * Repository Error Hierarchy
+ *
+ * Maps to standard FHIR/HTTP error semantics:
+ * - 404 Not Found → ResourceNotFoundError
+ * - 410 Gone → ResourceGoneError
+ * - 412 Precondition Failed → ResourceVersionConflictError
+ *
+ * @module fhir-persistence/repo
+ */
+/**
+ * Base class for all repository errors.
+ */
+export declare class RepositoryError extends Error {
+    readonly name: string;
+    constructor(message: string);
+}
+/**
+ * Resource not found (HTTP 404).
+ */
+export declare class ResourceNotFoundError extends RepositoryError {
+    readonly name = "ResourceNotFoundError";
+    readonly resourceType: string;
+    readonly resourceId: string;
+    constructor(resourceType: string, id: string);
+}
+/**
+ * Resource has been deleted (HTTP 410 Gone).
+ */
+export declare class ResourceGoneError extends RepositoryError {
+    readonly name = "ResourceGoneError";
+    readonly resourceType: string;
+    readonly resourceId: string;
+    constructor(resourceType: string, id: string);
+}
+/**
+ * Multiple matches found for conditional operation (HTTP 412 Precondition Failed).
+ *
+ * Thrown when a conditional update/delete matches more than one resource.
+ */
+export declare class PreconditionFailedError extends RepositoryError {
+    readonly name = "PreconditionFailedError";
+    readonly resourceType: string;
+    readonly matchCount: number;
+    constructor(resourceType: string, matchCount: number);
+}
+/**
+ * Optimistic locking conflict (HTTP 412 Precondition Failed).
+ *
+ * Thrown when `ifMatch` (expected versionId) does not match
+ * the current versionId of the resource.
+ */
+export declare class ResourceVersionConflictError extends RepositoryError {
+    readonly name = "ResourceVersionConflictError";
+    readonly resourceType: string;
+    readonly resourceId: string;
+    readonly expectedVersion: string;
+    readonly actualVersion: string;
+    constructor(resourceType: string, id: string, expectedVersion: string, actualVersion: string);
+}
+//# sourceMappingURL=errors.d.ts.map

package/dist/lib/repo/errors.d.ts.map

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package/dist/lib/repo/history-bundle.d.ts

@@ -0,0 +1,78 @@
+/**
+ * History Bundle Builder
+ *
+ * Constructs FHIR R4 Bundle of type `history` from `HistoryEntry[]`.
+ * Pure function — no database dependency.
+ *
+ * FHIR R4 History Bundle spec:
+ * - `Bundle.type` = `"history"`
+ * - Each entry has `request` (method + URL) and `response` (status + etag)
+ * - Delete entries have `request.method = "DELETE"` and no `resource`
+ * - Entries ordered newest first
+ *
+ * @module fhir-persistence/repo
+ */
+import type { HistoryEntry } from './types.js';
+/**
+ * A FHIR R4 Bundle (minimal shape for history).
+ */
+export interface HistoryBundle {
+    resourceType: 'Bundle';
+    id: string;
+    type: 'history';
+    total: number;
+    link?: BundleLink[];
+    entry?: HistoryBundleEntry[];
+}
+export interface BundleLink {
+    relation: string;
+    url: string;
+}
+export interface HistoryBundleEntry {
+    fullUrl?: string;
+    resource?: Record<string, unknown>;
+    request: {
+        method: string;
+        url: string;
+    };
+    response: {
+        status: string;
+        etag?: string;
+        lastModified?: string;
+    };
+}
+/**
+ * Options for building a history bundle.
+ */
+export interface BuildHistoryBundleOptions {
+    /** Base URL for fullUrl construction (e.g., `"http://localhost:3000/fhir/R4"`). */
+    baseUrl?: string;
+    /** Total count of matching entries (may differ from entries.length if paginated). */
+    total?: number;
+    /** Self link URL. */
+    selfUrl?: string;
+    /** Next page link URL. */
+    nextUrl?: string;
+}
+/**
+ * Build a FHIR R4 history Bundle from HistoryEntry[].
+ *
+ * @param entries - History entries (newest first).
+ * @param options - Optional bundle metadata.
+ * @returns A FHIR R4 Bundle of type `history`.
+ */
+export declare function buildHistoryBundle(entries: HistoryEntry[], options?: BuildHistoryBundleOptions): HistoryBundle;
+/**
+ * Determine the HTTP method for a history entry.
+ *
+ * Heuristic: if the entry is the first version (oldest) for a resource,
+ * it's a POST (create). Otherwise it's a PUT (update).
+ * Delete entries are always DELETE.
+ *
+ * For simplicity, we check if this is the first entry in the history
+ * by comparing with the resource's creation time. Since we don't have
+ * that info here, we use a simple heuristic: POST for the first entry
+ * in the array (oldest), PUT for the rest.
+ */
+export declare function determineMethod(entries: HistoryEntry[], index: number): string;
+//# sourceMappingURL=history-bundle.d.ts.map

package/dist/lib/repo/history-bundle.d.ts.map

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package/dist/lib/repo/index.d.ts

@@ -0,0 +1,17 @@
+/**
+ * Repository module — Public API (v2)
+ *
+ * @module fhir-persistence/repo
+ */
+export type { FhirResource, FhirMeta, PersistedResource, ResourceRepository, CreateResourceOptions, UpdateResourceOptions, HistoryOptions, HistoryEntry, SearchOptions, SearchResult, ResourceRow, HistoryRow, OperationContext, } from './types.js';
+export { SCHEMA_VERSION, DELETED_SCHEMA_VERSION, PLATFORM_RESOURCE_TYPES, PROTECTED_RESOURCE_TYPES, PROJECT_ADMIN_RESOURCE_TYPES, } from './types.js';
+export { RepositoryError, ResourceNotFoundError, ResourceGoneError, ResourceVersionConflictError, } from './errors.js';
+export { buildResourceRow, buildResourceRowWithSearch, buildDeleteRow, buildHistoryRow, buildDeleteHistoryRow, } from './row-builder.js';
+export type { ReferenceRow } from './reference-indexer.js';
+export { extractReferences } from './reference-indexer.js';
+export type { SearchColumnValues } from './row-indexer.js';
+export { buildSearchColumns, buildMetadataColumns, hashToken, extractPropertyPath, getNestedValues, } from './row-indexer.js';
+export { buildUpsertSQL, buildInsertSQL, buildSelectByIdSQL, buildSelectHistorySQL, buildSelectVersionSQL, buildInstanceHistorySQL, buildTypeHistorySQL, } from './sql-builder.js';
+export type { HistoryBundle, HistoryBundleEntry, BundleLink, BuildHistoryBundleOptions, } from './history-bundle.js';
+export { buildHistoryBundle } from './history-bundle.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/lib/repo/index.d.ts.map

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package/dist/lib/repo/indexing-pipeline.d.ts

@@ -0,0 +1,108 @@
+/**
+ * Indexing Pipeline — v2
+ *
+ * Unified orchestrator that combines three indexing concerns into
+ * a single `indexResource()` call:
+ *
+ * 1. **Search columns** — Extract values from resource JSON via
+ *    `buildSearchColumns()` and merge into the main table row.
+ * 2. **References** — Extract outgoing references via
+ *    `extractReferencesV2()` and write to `{RT}_References` table.
+ * 3. **Lookup tables** — Extract HumanName/Address/ContactPoint/Identifier
+ *    rows via `buildLookupTableRows()` and write to global lookup tables.
+ *
+ * Design decisions:
+ * - Accepts SearchParameterImpl[] (resolved by caller from registry)
+ * - All writes use StorageAdapter v2 (? placeholders)
+ * - Replace strategy for references and lookup rows (delete + insert)
+ * - Search columns are returned (not written) — caller merges into main row
+ * - Pipeline is stateless; dependencies injected via constructor
+ *
+ * @module fhir-persistence/repo
+ */
+import type { StorageAdapter } from '../db/adapter.js';
+import type { SearchParameterImpl } from '../registry/search-parameter-registry.js';
+import type { FhirResource } from './types.js';
+import type { SearchColumnValues, LookupTableRow } from './row-indexer.js';
+import type { ReferenceRowV2 } from './reference-indexer.js';
+import { LookupTableWriter } from './lookup-table-writer.js';
+import type { RuntimeProvider } from '../providers/runtime-provider.js';
+/**
+ * Result of indexing a single resource.
+ */
+export interface IndexResult {
+    /** Search column values to merge into the main table row. */
+    searchColumns: SearchColumnValues;
+    /** Reference rows written to {RT}_References table. */
+    referenceCount: number;
+    /** Lookup table rows written to global lookup tables. */
+    lookupRowCount: number;
+}
+/**
+ * Options for the indexing pipeline.
+ */
+export interface IndexingPipelineOptions {
+    /** Enable lookup table writes (default: true). */
+    enableLookupTables?: boolean;
+    /** Enable reference indexing (default: true). */
+    enableReferences?: boolean;
+    /** Optional RuntimeProvider for FHIRPath-driven extraction (B3). */
+    runtimeProvider?: RuntimeProvider;
+}
+export declare class IndexingPipeline {
+    private readonly adapter;
+    private readonly lookupWriter;
+    private readonly options;
+    private readonly runtimeProvider;
+    constructor(adapter: StorageAdapter, options?: IndexingPipelineOptions);
+    /**
+     * Index a resource: extract search columns, write references, write lookup rows.
+     *
+     * @param resourceType - The FHIR resource type (e.g., "Patient").
+     * @param resource - The FHIR resource (must have `id`).
+     * @param impls - SearchParameterImpl list for this resource type.
+     * @returns IndexResult with search columns and write counts.
+     */
+    indexResource(resourceType: string, resource: FhirResource, impls: SearchParameterImpl[]): Promise<IndexResult>;
+    /**
+     * Remove all index data for a deleted resource.
+     *
+     * @param resourceType - The FHIR resource type.
+     * @param resourceId - The resource ID.
+     */
+    deleteIndex(resourceType: string, resourceId: string): Promise<void>;
+    /**
+     * Extract search column values without writing references or lookup rows.
+     * Useful for re-indexing or testing.
+     */
+    extractSearchColumns(resource: FhirResource, impls: SearchParameterImpl[]): SearchColumnValues;
+    /**
+     * Extract reference rows without writing them.
+     * Useful for re-indexing or testing.
+     */
+    extractReferences(resource: FhirResource, impls: SearchParameterImpl[]): ReferenceRowV2[];
+    /**
+     * Extract lookup table rows without writing them.
+     * Useful for re-indexing or testing.
+     */
+    extractLookupRows(resource: FhirResource, impls: SearchParameterImpl[]): LookupTableRow[];
+    /**
+     * Get the underlying LookupTableWriter for direct access.
+     */
+    getLookupWriter(): LookupTableWriter;
+    private writeReferences;
+    private writeLookupRows;
+    /**
+     * Convert SearchParameterImpl[] to SearchParameterDef[] for RuntimeProvider.
+     */
+    private implsToDefs;
+    /**
+     * Extract search column values via RuntimeProvider.
+     */
+    private extractViaRuntime;
+    /**
+     * Extract references via RuntimeProvider → ReferenceRowV2[].
+     */
+    private extractRefsViaRuntime;
+}
+//# sourceMappingURL=indexing-pipeline.d.ts.map

package/dist/lib/repo/indexing-pipeline.d.ts.map

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package/dist/lib/repo/lookup-table-writer.d.ts

@@ -0,0 +1,46 @@
+/**
+ * Lookup Table Writer — v2
+ *
+ * Manages the 4 global lookup tables (HumanName, Address, ContactPoint, Identifier)
+ * using StorageAdapter v2. Handles DDL creation, row insertion (replace strategy),
+ * and deletion.
+ *
+ * Design decisions:
+ * - Uses StorageAdapter interface (not DatabaseClient directly)
+ * - All writes use `?` placeholders (SQLite-compatible, rewritten for PG)
+ * - Replace strategy: DELETE existing rows for resourceId, then INSERT new ones
+ * - Each lookup table has a `resourceId` column + type-specific columns
+ * - Batch insert per table type for efficiency
+ *
+ * @module fhir-persistence/repo
+ */
+import type { StorageAdapter } from '../db/adapter.js';
+import type { LookupTableRow } from './row-indexer.js';
+export declare class LookupTableWriter {
+    private readonly adapter;
+    private initialized;
+    constructor(adapter: StorageAdapter);
+    /**
+     * Create all 4 lookup tables + indexes if they don't exist.
+     */
+    ensureTables(): Promise<void>;
+    /**
+     * Write lookup table rows for a resource (replace strategy).
+     *
+     * 1. Deletes all existing rows for the resourceId across all 4 tables
+     * 2. Inserts new rows grouped by table type
+     *
+     * @param resourceId - The resource ID to index.
+     * @param rows - LookupTableRow[] from `buildLookupTableRows()`.
+     */
+    writeRows(resourceId: string, rows: LookupTableRow[]): Promise<void>;
+    /**
+     * Delete all lookup table rows for a given resourceId.
+     */
+    deleteRows(resourceId: string): Promise<void>;
+    /**
+     * Get all lookup rows for a given resourceId and table type.
+     */
+    getRows<T = Record<string, unknown>>(table: string, resourceId: string): Promise<T[]>;
+}
+//# sourceMappingURL=lookup-table-writer.d.ts.map

package/dist/lib/repo/lookup-table-writer.d.ts.map

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package/dist/lib/repo/reference-indexer.d.ts

@@ -0,0 +1,56 @@
+/**
+ * Reference Indexer
+ *
+ * Extracts outgoing reference relationships from FHIR resource JSON
+ * and produces rows for the `{ResourceType}_References` table.
+ *
+ * Used by `FhirRepository` on create/update to populate the references
+ * table, which is required for `_revinclude` support.
+ *
+ * @module fhir-persistence/repo
+ */
+import type { SearchParameterImpl } from '../registry/search-parameter-registry.js';
+import type { FhirResource } from './types.js';
+/**
+ * A single row for the `{ResourceType}_References` table.
+ */
+export interface ReferenceRow {
+    /** The source resource ID. */
+    resourceId: string;
+    /** The target resource ID (extracted from the reference string). */
+    targetId: string;
+    /** The search parameter code (e.g., "subject", "patient"). */
+    code: string;
+}
+/**
+ * v2: A row for the `{ResourceType}_References` table.
+ * Adds targetType and referenceRaw for more precise reference queries.
+ */
+export interface ReferenceRowV2 {
+    /** The source resource ID. */
+    resourceId: string;
+    /** The target resource type (e.g., "Patient"). */
+    targetType: string;
+    /** The target resource ID. */
+    targetId: string;
+    /** The search parameter code (e.g., "subject"). */
+    code: string;
+    /** The original reference string, or null. */
+    referenceRaw: string | null;
+}
+/**
+ * Extract all outgoing reference rows from a FHIR resource.
+ *
+ * Iterates over all reference-type search parameters and extracts
+ * target resource IDs from the resource JSON.
+ *
+ * @param resource - The FHIR resource (must have `id`).
+ * @param impls - SearchParameterImpl list for this resource type.
+ * @returns Array of ReferenceRow ready for SQL insertion.
+ */
+export declare function extractReferences(resource: FhirResource, impls: SearchParameterImpl[]): ReferenceRow[];
+/**
+ * v2: Extract all outgoing reference rows with targetType + referenceRaw.
+ */
+export declare function extractReferencesV2(resource: FhirResource, impls: SearchParameterImpl[]): ReferenceRowV2[];
+//# sourceMappingURL=reference-indexer.d.ts.map