Smart EHR MCP Server

import { Database } from 'bun:sqlite'; import { ProcessedAttachment } from './types'; import { ClientFullEHR, ClientProcessedAttachment } from '../clientTypes'; /** * Populates a SQLite database with data from a FullEHR object. * Creates necessary tables and indexes for efficient querying. * * @param fullEhr - The FullEHR object containing FHIR resources and attachments * @param db - An open SQLite database connection * @returns The same database instance after population */ export async function ehrToSqlite(fullEhr: ClientFullEHR, db: Database): Promise<Database> { console.log("[DB:POPULATE] Starting database population from FullEHR"); try { // Begin a transaction for better performance db.exec('BEGIN TRANSACTION;'); // Create tables if they don't exist db.exec(` CREATE TABLE IF NOT EXISTS fhir_resources ( resource_type TEXT NOT NULL, resource_id TEXT NOT NULL, json TEXT NOT NULL, PRIMARY KEY (resource_type, resource_id) ); CREATE TABLE IF NOT EXISTS fhir_attachments ( id INTEGER PRIMARY KEY AUTOINCREMENT, resource_type TEXT NOT NULL, resource_id TEXT NOT NULL, path TEXT NOT NULL, content_type TEXT NOT NULL, json TEXT NOT NULL, content_raw BLOB, content_plaintext TEXT, FOREIGN KEY (resource_type, resource_id) REFERENCES fhir_resources(resource_type, resource_id) ); CREATE INDEX IF NOT EXISTS idx_fhir_resources_type ON fhir_resources(resource_type); CREATE INDEX IF NOT EXISTS idx_fhir_attachments_resource ON fhir_attachments(resource_type, resource_id); `); // Prepare statements for better performance const insertResourceStmt = db.prepare( 'INSERT OR REPLACE INTO fhir_resources (resource_type, resource_id, json) VALUES (?, ?, ?)' ); const insertAttachmentStmt = db.prepare( 'INSERT INTO fhir_attachments (resource_type, resource_id, path, content_type, json, content_raw, content_plaintext) VALUES (?, ?, ?, ?, ?, ?, ?)' ); // Insert FHIR resources let resourceCount = 0; for (const [resourceType, resources] of Object.entries(fullEhr.fhir)) { for (const resource of resources) { if (resource && resource.id) { insertResourceStmt.run(resourceType, resource.id, JSON.stringify(resource)); resourceCount++; } } } console.log(`[DB:POPULATE] Inserted ${resourceCount} FHIR resources`); // Insert attachments if (fullEhr.attachments && fullEhr.attachments.length > 0) { let attachmentCount = 0; for (const attachment of fullEhr.attachments) { insertAttachmentStmt.run( attachment.resourceType, attachment.resourceId, attachment.path, attachment.contentType, attachment.json, attachment.contentBase64, attachment.contentPlaintext ); attachmentCount++; } console.log(`[DB:POPULATE] Inserted ${attachmentCount} attachments`); } else { console.log('[DB:POPULATE] No attachments to insert'); } // Commit transaction db.exec('COMMIT;'); console.log("[DB:POPULATE] Database population completed successfully"); return db; } catch (error) { // Rollback on error try { db.exec('ROLLBACK;'); } catch (rollbackError) { console.error('[DB:POPULATE] Error during rollback:', rollbackError); } console.error('[DB:POPULATE] Error populating database:', error); throw error; } } interface ResourceRow { resource_type: string; json: string; } interface AttachmentRow { resource_type: string; resource_id: string; path: string; content_type: string; json: string; content_raw: ArrayBuffer | null; content_plaintext: string | null; } /** * Reconstructs a FullEHR object from a SQLite database. * Retrieves all FHIR resources and attachments. * * @param db - An open SQLite database connection * @returns A Promise resolving to a FullEHR object */ export async function sqliteToEhr(db: Database): Promise<ClientFullEHR> { // console.log("[DB:RECONSTRUCT] Reconstructing FullEHR from database"); try { // Initialize the FullEHR structure const fhir: Record<string, any[]> = {}; // Fetch all resources grouped by type const resourcesQuery = db.query<ResourceRow, []>(` SELECT resource_type, json FROM fhir_resources ORDER BY resource_type `); for (const row of resourcesQuery.all()) { const resourceType = row.resource_type; const content = JSON.parse(row.json); if (!fhir[resourceType]) { fhir[resourceType] = []; } fhir[resourceType].push(content); } // Fetch all attachments const attachmentsQuery = db.query<AttachmentRow, []>(` SELECT resource_type, resource_id, path, content_type, json, content_raw, content_plaintext FROM fhir_attachments `); const attachments: ClientProcessedAttachment[] = attachmentsQuery.all().map(row => ({ resourceType: row.resource_type, resourceId: row.resource_id, path: row.path, contentType: row.content_type, json: row.json, contentBase64: row.content_raw ? Buffer.from(row.content_raw).toString('base64') : null, contentPlaintext: row.content_plaintext })); const resourceCount = Object.values(fhir).reduce((sum, arr) => sum + arr.length, 0); // console.log(`[DB:RECONSTRUCT] Reconstructed ${resourceCount} resources and ${attachments.length} attachments`); return { fhir, attachments }; } catch (error) { console.error('[DB:RECONSTRUCT] Error reconstructing FullEHR from database:', error); throw error; } }