fhir-persistence 0.1.0

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

@@ -0,0 +1,321 @@
+/**
+ * Repository Types & Interfaces
+ *
+ * Defines the contract for FHIR resource persistence operations.
+ * All implementations must support transactional CRUD with versioning.
+ *
+ * Design decisions (from WF-E2E-001 Medplum analysis):
+ * - `id` and `versionId` are UUIDs, generated app-side
+ * - Every write produces a new history entry (new version snapshot)
+ * - Soft delete: `deleted=true`, `content=''`, `__version=-1`
+ * - Optimistic locking via `ifMatch` (versionId comparison)
+ *
+ * @module fhir-persistence/repo
+ */
+/**
+ * Operation context — flows through all CRUD/Search operations.
+ *
+ * S1 (Phase B): Only `project` is used — multi-tenant isolation.
+ * S5 (Phase C): Will extend to use `author`, `accessPolicy`, `superAdmin`.
+ */
+export interface OperationContext {
+    /** Current project ID for multi-tenant scoping. */
+    project?: string;
+    /** The actor performing the operation (User/Bot/ClientApplication reference). */
+    author?: string;
+    /** The AccessPolicy ID bound to this operation. */
+    accessPolicy?: string;
+    /** Whether this is a super-admin operation (bypasses project scoping). */
+    superAdmin?: boolean;
+}
+/**
+ * Platform resource types that require special handling.
+ *
+ * These are MedXAI-defined resources (not part of FHIR R4 base spec).
+ * They participate in multi-tenant isolation via `projectId`.
+ */
+export declare const PLATFORM_RESOURCE_TYPES: ReadonlySet<string>;
+/**
+ * Protected resource types that can only be managed by super-admins or
+ * the system itself. Normal project-scoped operations cannot create/update/delete these.
+ *
+ * Phase B: informational only — enforcement deferred to Phase C (Auth).
+ */
+export declare const PROTECTED_RESOURCE_TYPES: ReadonlySet<string>;
+/**
+ * Resource types that can be managed by project admins (not just super-admins).
+ *
+ * Phase B: informational only — enforcement deferred to Phase C (Auth).
+ */
+export declare const PROJECT_ADMIN_RESOURCE_TYPES: ReadonlySet<string>;
+/**
+ * Minimal FHIR resource shape for persistence operations.
+ *
+ * This is intentionally loose — the repository does not validate
+ * resource structure (that's the validator's job). It only requires
+ * `resourceType` and optionally `id` / `meta`.
+ */
+export interface FhirResource {
+    resourceType: string;
+    id?: string;
+    meta?: FhirMeta;
+    [key: string]: unknown;
+}
+/**
+ * FHIR Meta element (subset used by the repository).
+ */
+export interface FhirMeta {
+    versionId?: string;
+    lastUpdated?: string;
+    source?: string;
+    profile?: string[];
+    [key: string]: unknown;
+}
+/**
+ * A FHIR resource that has been persisted (id and meta are guaranteed).
+ */
+export interface PersistedResource extends FhirResource {
+    id: string;
+    meta: FhirMeta & {
+        versionId: string;
+        lastUpdated: string;
+    };
+}
+/**
+ * Options for `createResource()`.
+ */
+export interface CreateResourceOptions {
+    /**
+     * Pre-assigned UUID for the resource.
+     * Used in batch/transaction operations where the ID is determined
+     * before the create call.
+     */
+    assignedId?: string;
+}
+/**
+ * Options for `updateResource()`.
+ */
+export interface UpdateResourceOptions {
+    /**
+     * Expected versionId for optimistic locking.
+     * If provided and does not match the current versionId,
+     * the update is rejected with `ResourceVersionConflictError`.
+     *
+     * Corresponds to the HTTP `If-Match` header.
+     */
+    ifMatch?: string;
+}
+/**
+ * Options for history queries.
+ */
+export interface HistoryOptions {
+    /**
+     * Only include versions updated after this instant.
+     * Corresponds to the `_since` parameter.
+     */
+    since?: string;
+    /**
+     * Maximum number of entries to return.
+     * Corresponds to the `_count` parameter.
+     */
+    count?: number;
+    /**
+     * Cursor for pagination — the `lastUpdated` value of the last
+     * entry from the previous page. Only entries with `lastUpdated`
+     * strictly before this value are returned.
+     */
+    cursor?: string;
+}
+/**
+ * A single entry in a history result, including delete markers.
+ */
+export interface HistoryEntry {
+    /** The resource (null for delete entries). */
+    resource: PersistedResource | null;
+    /** The versionId for this entry. */
+    versionId: string;
+    /** The timestamp of this version. */
+    lastUpdated: string;
+    /** Whether this entry represents a deletion. */
+    deleted: boolean;
+    /** The resource type (needed for delete entries where resource is null). */
+    resourceType: string;
+    /** The resource id. */
+    id: string;
+}
+/**
+ * Options for search execution.
+ */
+export interface SearchOptions {
+    /** Whether to include total count. */
+    total?: 'none' | 'estimate' | 'accurate';
+}
+/**
+ * Result of a search execution.
+ */
+export interface SearchResult {
+    /** Matched resources. */
+    resources: PersistedResource[];
+    /** Included resources from _include/_revinclude (search.mode = 'include'). */
+    included?: PersistedResource[];
+    /** Total count (only when `total=accurate`). */
+    total?: number;
+}
+/**
+ * FHIR Resource Repository — persistence contract.
+ *
+ * All write operations are transactional (ACID).
+ * All write operations produce a history entry.
+ */
+export interface ResourceRepository {
+    /**
+     * Create a new FHIR resource.
+     *
+     * - Generates `id` (UUID) if not provided via `options.assignedId`
+     * - Generates `meta.versionId` (UUID)
+     * - Sets `meta.lastUpdated` to current time
+     * - Writes to main table + history table in a transaction
+     * - If `context.project` is set, injects projectId into the row
+     *
+     * @returns The persisted resource with populated `id` and `meta`.
+     */
+    createResource<T extends FhirResource>(resource: T, options?: CreateResourceOptions, context?: OperationContext): Promise<T & PersistedResource>;
+    /**
+     * Read a resource by type and ID.
+     *
+     * When `context.project` is set, verifies the resource belongs to that project.
+     *
+     * @throws ResourceNotFoundError if the resource does not exist.
+     * @throws ResourceGoneError if the resource has been deleted.
+     */
+    readResource(resourceType: string, id: string, context?: OperationContext): Promise<PersistedResource>;
+    /**
+     * Update an existing resource.
+     *
+     * - The resource must have `id` set.
+     * - Generates new `meta.versionId` (UUID)
+     * - Sets `meta.lastUpdated` to current time
+     * - Writes to main table (UPSERT) + history table in a transaction
+     * - If `options.ifMatch` is set, performs optimistic locking check
+     * - If `context.project` is set, injects projectId into the row
+     *
+     * @throws ResourceNotFoundError if the resource does not exist.
+     * @throws ResourceGoneError if the resource has been deleted.
+     * @throws ResourceVersionConflictError if `ifMatch` does not match.
+     */
+    updateResource<T extends FhirResource>(resource: T, options?: UpdateResourceOptions, context?: OperationContext): Promise<T & PersistedResource>;
+    /**
+     * Soft-delete a resource.
+     *
+     * - Sets `deleted=true`, `content=''`, `__version=-1`
+     * - Writes a delete history entry
+     *
+     * @throws ResourceNotFoundError if the resource does not exist.
+     * @throws ResourceGoneError if already deleted.
+     */
+    deleteResource(resourceType: string, id: string, context?: OperationContext): Promise<void>;
+    /**
+     * Read the version history of a resource (newest first).
+     */
+    readHistory(resourceType: string, id: string, options?: HistoryOptions): Promise<HistoryEntry[]>;
+    /**
+     * Read type-level history (all changes to a resource type, newest first).
+     */
+    readTypeHistory(resourceType: string, options?: HistoryOptions): Promise<HistoryEntry[]>;
+    /**
+     * Read a specific version of a resource.
+     *
+     * @throws ResourceNotFoundError if the version does not exist.
+     */
+    readVersion(resourceType: string, id: string, versionId: string): Promise<PersistedResource>;
+    /**
+     * Search for resources matching the given search request.
+     *
+     * - Executes parameterized SQL built from the search request
+     * - Optionally returns total count when `options.total === 'accurate'`
+     * - If `context.project` is set, adds projectId filter to the query
+     *
+     * @param request - Parsed FHIR search request.
+     * @param options - Search options (e.g., total mode).
+     * @param context - Operation context for project scoping.
+     * @returns Search result with matched resources and optional total.
+     */
+    searchResources(request: import('../search/types.js').SearchRequest, options?: SearchOptions, context?: OperationContext): Promise<SearchResult>;
+}
+/**
+ * v1 ResourceRow — preserved for backward compatibility with FhirRepository (PG).
+ * @deprecated Use ResourceRowV2 for new code.
+ */
+export interface ResourceRow {
+    [key: string]: unknown;
+    id: string;
+    content: string;
+    lastUpdated: string;
+    deleted: boolean;
+    projectId: string;
+    __version: number;
+    _source?: string;
+    _profile?: string[];
+    compartments?: string[];
+}
+/**
+ * v2 ResourceRow — dialect-neutral, no projectId/__version.
+ *
+ * Changes from v1:
+ * - Removed `projectId` (no multi-tenancy)
+ * - Removed `__version` (schema version tracking)
+ * - Added `versionId` (UUID for ETag / optimistic locking)
+ * - `deleted` is number (0/1) for SQLite compat
+ * - `_profile` is JSON string, not string[]
+ * - `compartments` is JSON string, not string[]
+ */
+export interface ResourceRowV2 {
+    [key: string]: unknown;
+    id: string;
+    versionId: string;
+    content: string;
+    lastUpdated: string;
+    deleted: number;
+    _source?: string | null;
+    _profile?: string | null;
+    compartments?: string | null;
+}
+/**
+ * v1 HistoryRow — preserved for backward compatibility.
+ * @deprecated Use HistoryRowV2 for new code.
+ */
+export interface HistoryRow {
+    [key: string]: unknown;
+    id: string;
+    versionId: string;
+    lastUpdated: string;
+    content: string;
+}
+/**
+ * v2 HistoryRow — includes deleted flag.
+ *
+ * Changes from v1:
+ * - Added `deleted` (0/1) for soft-delete tracking
+ * - `content` preserved even on delete (ADR-08)
+ */
+export interface HistoryRowV2 {
+    [key: string]: unknown;
+    id: string;
+    versionId: string;
+    lastUpdated: string;
+    content: string;
+    deleted: number;
+}
+/**
+ * Schema version constant.
+ *
+ * Tracks the schema migration version (not the resource version).
+ * Incremented when the schema structure changes.
+ * Set to -1 for deleted resources.
+ */
+export declare const SCHEMA_VERSION = 1;
+/**
+ * Schema version for deleted resources.
+ */
+export declare const DELETED_SCHEMA_VERSION = -1;
+//# sourceMappingURL=types.d.ts.map

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

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package/dist/lib/schema/ddl-generator.d.ts

@@ -0,0 +1,81 @@
+/**
+ * DDL Generator
+ *
+ * Converts `ResourceTableSet` / `SchemaDefinition` to SQL DDL strings.
+ * All functions are pure — no database dependency.
+ *
+ * v2 upgrade: Now supports both SQLite and PostgreSQL dialects.
+ * The `dialect` parameter controls type mapping and syntax differences.
+ *
+ * ## Output Format
+ *
+ * - All identifiers are double-quoted for safety
+ * - Uses `CREATE TABLE IF NOT EXISTS` / `CREATE INDEX IF NOT EXISTS`
+ * - Generates all CREATE TABLEs first, then all CREATE INDEXes
+ * - Idempotent — safe to run multiple times
+ *
+ * @module fhir-persistence/schema
+ */
+import type { IndexSchema, MainTableSchema, HistoryTableSchema, ReferencesTableSchema, LookupTableSchema, GlobalLookupTableSchema, ResourceTableSet, SchemaDefinition } from './table-schema.js';
+export type DDLDialect = 'sqlite' | 'postgres';
+/**
+ * Generate a `CREATE TABLE IF NOT EXISTS` statement for a main table.
+ */
+export declare function generateCreateMainTable(table: MainTableSchema, dialect?: DDLDialect): string;
+/**
+ * Generate a `CREATE TABLE IF NOT EXISTS` statement for a history table.
+ *
+ * v2: Handles versionSeq AUTOINCREMENT for SQLite and GENERATED ALWAYS for PG.
+ */
+export declare function generateCreateHistoryTable(table: HistoryTableSchema, dialect?: DDLDialect): string;
+/**
+ * Generate a `CREATE TABLE IF NOT EXISTS` statement for a references table.
+ */
+export declare function generateCreateReferencesTable(table: ReferencesTableSchema, dialect?: DDLDialect): string;
+/**
+ * Generate a `CREATE INDEX IF NOT EXISTS` statement.
+ *
+ * Supports:
+ * - `opClass` — operator class appended to each column key (e.g., `gin_trgm_ops`)
+ * - `expression` — functional expression to index instead of plain columns
+ *   (e.g., `to_tsvector('simple'::regconfig, family)`)
+ */
+export declare function generateCreateIndex(index: IndexSchema, tableName: string, dialect?: DDLDialect): string | null;
+/**
+ * Generate all DDL statements for a single resource type (3 tables + indexes).
+ *
+ * Returns an array of SQL statements in order:
+ * 1. CREATE TABLE for main table
+ * 2. CREATE TABLE for history table
+ * 3. CREATE TABLE for references table
+ * 4. All CREATE INDEX statements
+ */
+export declare function generateResourceDDL(tableSet: ResourceTableSet, dialect?: DDLDialect): string[];
+/**
+ * Generate a `CREATE TABLE IF NOT EXISTS` statement for a lookup sub-table.
+ */
+export declare function generateCreateLookupTable(table: LookupTableSchema, dialect?: DDLDialect): string;
+/**
+ * Generate a `CREATE TABLE IF NOT EXISTS` statement for a global lookup table.
+ */
+export declare function generateCreateGlobalLookupTable(table: GlobalLookupTableSchema, dialect?: DDLDialect): string;
+/**
+ * Generate all DDL statements for a complete schema definition.
+ *
+ * Order:
+ * 1. Global lookup tables (HumanName, Address, ContactPoint, Identifier)
+ * 2. Resource tables (main, history, references)
+ * 3. All indexes (global lookup + resource tables)
+ *
+ * @param schema - The complete schema definition.
+ * @returns Array of SQL DDL statements.
+ */
+export declare function generateSchemaDDL(schema: SchemaDefinition, dialect?: DDLDialect): string[];
+/**
+ * Generate the complete DDL as a single string, with statements
+ * separated by double newlines.
+ *
+ * Includes a header comment with version and generation timestamp.
+ */
+export declare function generateSchemaDDLString(schema: SchemaDefinition, dialect?: DDLDialect): string;
+//# sourceMappingURL=ddl-generator.d.ts.map

package/dist/lib/schema/ddl-generator.d.ts.map

@@ -0,0 +1 @@
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package/dist/lib/schema/index.d.ts

@@ -0,0 +1,8 @@
+/**
+ * Schema module — barrel exports
+ *
+ * @module fhir-persistence/schema
+ */
+export type { SqlColumnType, ColumnSchema, IndexSchema, ConstraintSchema, MainTableSchema, HistoryTableSchema, ReferencesTableSchema, ResourceTableSet, SchemaDefinition, SearchParamMeta, GlobalLookupTableSchema, LookupTableType, } from './table-schema.js';
+export type { DDLDialect } from './ddl-generator.js';
+//# sourceMappingURL=index.d.ts.map

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

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package/dist/lib/schema/table-schema-builder.d.ts

@@ -0,0 +1,66 @@
+/**
+ * Table Schema Builder
+ *
+ * Core of Phase 8. Pure functions that derive `ResourceTableSet`
+ * (3 tables per resource) from `StructureDefinitionRegistry` and
+ * `SearchParameterRegistry`.
+ *
+ * ## Design
+ *
+ * Each FHIR resource type gets:
+ * - **Main table** — fixed columns + search columns
+ * - **History table** — fixed structure (no search columns)
+ * - **References table** — fixed structure with composite PK
+ *
+ * Search columns are generated from `SearchParameterImpl`:
+ * - `column` strategy → one column per param
+ * - `token-column` strategy → three columns per param (__X, __XText, __XSort)
+ * - `lookup-table` strategy → sort column only (__XSort)
+ *
+ * All functions are pure — no global state, no database dependency.
+ *
+ * @module fhir-persistence/schema
+ */
+import type { GlobalLookupTableSchema, ResourceTableSet, SchemaDefinition } from './table-schema.js';
+import type { StructureDefinitionRegistry } from '../registry/structure-definition-registry.js';
+import type { SearchParameterRegistry } from '../registry/search-parameter-registry.js';
+/**
+ * Build the 4 global shared lookup tables matching Medplum's production design.
+ *
+ * These tables are shared across ALL resource types and store decomposed
+ * complex FHIR types for precise search via JOINs:
+ * - `HumanName` — name/given/family from Patient.name, Practitioner.name, etc.
+ * - `Address` — address/city/country/postalCode/state/use
+ * - `ContactPoint` — system/value/use from telecom fields
+ * - `Identifier` — system/value from identifier fields
+ *
+ * Each table has Medplum-style indexes: btree + trigram (gin_trgm_ops)
+ * for efficient prefix, exact, and substring search.
+ */
+export declare function buildGlobalLookupTables(): GlobalLookupTableSchema[];
+/**
+ * Build the complete 3-table schema for a single resource type.
+ *
+ * @param resourceType - The FHIR resource type (e.g., `'Patient'`).
+ * @param sdRegistry - StructureDefinitionRegistry (used to verify the type exists).
+ * @param spRegistry - SearchParameterRegistry (provides search column definitions).
+ * @returns The complete `ResourceTableSet` for the resource type.
+ * @throws Error if the resource type is not found or is abstract.
+ */
+export declare function buildResourceTableSet(resourceType: string, sdRegistry: StructureDefinitionRegistry, spRegistry: SearchParameterRegistry): ResourceTableSet;
+/**
+ * Build table schemas for ALL non-abstract resource types.
+ *
+ * @returns Array of `ResourceTableSet`, one per concrete resource type, sorted alphabetically.
+ */
+export declare function buildAllResourceTableSets(sdRegistry: StructureDefinitionRegistry, spRegistry: SearchParameterRegistry): ResourceTableSet[];
+/**
+ * Build a complete `SchemaDefinition` for all resource types.
+ *
+ * @param sdRegistry - StructureDefinitionRegistry with indexed profiles.
+ * @param spRegistry - SearchParameterRegistry with indexed search params.
+ * @param version - Schema version string (default: `'fhir-r4-v4.0.1'`).
+ * @returns The complete `SchemaDefinition`.
+ */
+export declare function buildSchemaDefinition(sdRegistry: StructureDefinitionRegistry, spRegistry: SearchParameterRegistry, version?: string): SchemaDefinition;
+//# sourceMappingURL=table-schema-builder.d.ts.map

package/dist/lib/schema/table-schema-builder.d.ts.map

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