Medplum

// SPDX-FileCopyrightText: Copyright Orangebot, Inc. and Medplum contributors // SPDX-License-Identifier: Apache-2.0 import { ContentType } from '@medplum/core'; import type { BulkDataExportOutput, Group, Patient } from '@medplum/fhirtypes'; import express from 'express'; import request from 'supertest'; import { initApp, shutdownApp } from '../../app'; import { getConfig, loadTestConfig } from '../../config/loader'; import type { FileSystemStorage } from '../../storage/filesystem'; import { getBinaryStorage } from '../../storage/loader'; import { createTestProject, initTestAuth, waitForAsyncJob, withTestContext } from '../../test.setup'; import { getSystemRepo } from '../repo'; import { groupExportResources } from './groupexport'; import { BulkExporter } from './utils/bulkexporter'; describe('Group Export', () => { const app = express(); const systemRepo = getSystemRepo(); let accessToken: string; beforeAll(async () => { const config = await loadTestConfig(); await initApp(app, config); accessToken = await initTestAuth(); }); afterAll(async () => { await shutdownApp(); }); test('Export Group', async () => { // Create first patient const res1 = await request(app) .post(`/fhir/R4/Patient`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Patient', name: [{ given: ['Alice'], family: 'Smith' }], address: [{ use: 'home', line: ['123 Main St'], city: 'Anywhere', state: 'CA', postalCode: '90210' }], telecom: [ { system: 'phone', value: '555-555-5555' }, { system: 'email', value: 'alice@example.com' }, ], }); expect(res1.status).toBe(201); // Create second patient const res2 = await request(app) .post(`/fhir/R4/Patient`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Patient', name: [{ given: ['Bob'], family: 'Jones' }], address: [{ use: 'home', line: ['456 Happy St'], city: 'Anywhere', state: 'CA', postalCode: '90210' }], telecom: [ { system: 'phone', value: '555-555-1234' }, { system: 'email', value: 'bob@example.com' }, ], }); expect(res2.status).toBe(201); // Create observation const res3 = await request(app) .post(`/fhir/R4/Observation`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Observation', status: 'final', code: { text: 'test' }, subject: { reference: `Patient/${res1.body.id}` }, }); expect(res3.status).toBe(201); // Create device const res4 = await request(app) .post(`/fhir/R4/Device`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Device', }); expect(res4.status).toBe(201); // Create a group const res5 = await request(app) .post(`/fhir/R4/Group`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Group', type: 'person', actual: true, member: [ { entity: { reference: `Patient/${res1.body.id}` } }, { entity: { reference: `Patient/${res2.body.id}` } }, { entity: { reference: `Device/${res4.body.id}` } }, ], }); expect(res5.status).toBe(201); // Start the export const res6 = await request(app) .get(`/fhir/R4/Group/${res5.body.id}/$export`) .set('Authorization', 'Bearer ' + accessToken); expect(res6.status).toBe(202); expect(res6.headers['content-location']).toBeDefined(); // Check the export status const contentLocation = new URL(res6.headers['content-location']); await waitForAsyncJob(res6.headers['content-location'], app, accessToken); const contentLocationRes = await request(app) .get(contentLocation.pathname) .set('Authorization', 'Bearer ' + accessToken); expect(contentLocationRes.status).toBe(200); const output = contentLocationRes.body.output as BulkDataExportOutput[]; expect(output).toHaveLength(4); expect(output.some((o) => o.type === 'Patient')).toBeTruthy(); expect(output.some((o) => o.type === 'Device')).toBeTruthy(); expect(output.some((o) => o.type === 'Observation')).toBeTruthy(); expect(output.some((o) => o.type === 'Group')).toBeTruthy(); expect(output[0].url.startsWith(getConfig().storageBaseUrl)).toBeTruthy(); }); test('Since filter', async () => { const now = new Date(); // 7 days ago const before = new Date(now.getTime() - 1000 * 60 * 60 * 24 * 7); // 3 days ago const since = new Date(now.getTime() - 1000 * 60 * 60 * 24 * 3); // Create patient const res1 = await request(app) .post(`/fhir/R4/Patient`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Patient', name: [{ given: ['Alice'], family: 'Smith' }], address: [{ use: 'home', line: ['123 Main St'], city: 'Anywhere', state: 'CA', postalCode: '90210' }], telecom: [ { system: 'phone', value: '555-555-5555' }, { system: 'email', value: 'alice@example.com' }, ], }); expect(res1.status).toBe(201); // Create observation // (Use extended mode to get the project metadata) const res2 = await request(app) .post(`/fhir/R4/Observation`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .set('X-Medplum', 'extended') .send({ resourceType: 'Observation', status: 'final', code: { text: 'test' }, subject: { reference: `Patient/${res1.body.id}` }, }); expect(res2.status).toBe(201); // Create observation "3 days ago" // (Use systemRepo to set meta.lastUpdated) await withTestContext(() => systemRepo.createResource({ ...res2.body, id: undefined, meta: { ...res2.body.meta, lastUpdated: before.toISOString(), versionId: undefined, }, }) ); // Create group const res4 = await request(app) .post(`/fhir/R4/Group`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Group', type: 'person', actual: true, member: [{ entity: { reference: `Patient/${res1.body.id}` } }], }); expect(res4.status).toBe(201); // Start the export with the "_since" filter const res5 = await request(app) .get(`/fhir/R4/Group/${res4.body.id}/$export?_since=${encodeURIComponent(since.toISOString())}`) .set('Authorization', 'Bearer ' + accessToken); expect(res5.status).toBe(202); expect(res5.headers['content-location']).toBeDefined(); // Check the export status const contentLocation = new URL(res5.headers['content-location']); await waitForAsyncJob(res5.headers['content-location'], app, accessToken); const contentLocationRes = await request(app) .get(contentLocation.pathname) .set('Authorization', 'Bearer ' + accessToken); expect(contentLocationRes.status).toBe(200); const output = contentLocationRes.body.output as BulkDataExportOutput[]; expect(output).toHaveLength(3); expect(output.some((o) => o.type === 'Patient')).toBeTruthy(); expect(output.some((o) => o.type === 'Observation')).toBeTruthy(); // Get the export content const outputLocation = new URL(output.find((o) => o.type === 'Observation')?.url as string); const outputContent = (getBinaryStorage() as FileSystemStorage).readFileByUrlForTests(outputLocation); expect(outputContent).toBeDefined(); // Output format is "ndjson", new line delimited JSON // However, we only expect one Observation, so we can parse it as JSON expect(outputContent.trim().split('\n')).toHaveLength(1); expect(JSON.parse(outputContent).id).toStrictEqual(res2.body.id); }); test('Type filter', async () => { // Create patient const res1 = await request(app) .post(`/fhir/R4/Patient`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Patient', name: [{ given: ['Alice'], family: 'Smith' }], address: [{ use: 'home', line: ['123 Main St'], city: 'Anywhere', state: 'CA', postalCode: '90210' }], telecom: [ { system: 'phone', value: '555-555-5555' }, { system: 'email', value: 'alice@example.com' }, ], }); expect(res1.status).toBe(201); // Create observation // (Use extended mode to get the project metadata) const res2 = await request(app) .post(`/fhir/R4/Observation`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .set('X-Medplum', 'extended') .send({ resourceType: 'Observation', status: 'final', code: { text: 'test' }, subject: { reference: `Patient/${res1.body.id}` }, }); expect(res2.status).toBe(201); // Create group const res3 = await request(app) .post(`/fhir/R4/Group`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Group', type: 'person', actual: true, member: [{ entity: { reference: `Patient/${res1.body.id}` } }], }); expect(res3.status).toBe(201); // Start the export with the "_type" filter const res4 = await request(app) .get(`/fhir/R4/Group/${res3.body.id}/$export?_type=Patient`) .set('Authorization', 'Bearer ' + accessToken); expect(res4.status).toBe(202); expect(res4.headers['content-location']).toBeDefined(); // Check the export status const contentLocation = new URL(res4.headers['content-location']); await waitForAsyncJob(res4.headers['content-location'], app, accessToken); const contentLocationRes = await request(app) .get(contentLocation.pathname) .set('Authorization', 'Bearer ' + accessToken); expect(contentLocationRes.status).toBe(200); const output = contentLocationRes.body.output as BulkDataExportOutput[]; expect(output.some((o) => o.type === 'Patient')).toBeTruthy(); expect(output.some((o) => o.type === 'Observation')).not.toBeTruthy(); }); test('status accepted with error', async () => { // Create group const groupRes = await request(app) .post(`/fhir/R4/Group`) .set('Authorization', 'Bearer ' + accessToken) .set('Content-Type', ContentType.FHIR_JSON) .send({ resourceType: 'Group', type: 'person', actual: true, member: [{ entity: { reference: `Patient/1234` } }], }); expect(groupRes.status).toBe(201); const res4 = await request(app) .get(`/fhir/R4/Group/${groupRes.body.id}/$export`) .set('Authorization', 'Bearer ' + accessToken); expect(res4.status).toBe(202); expect(res4.headers['content-location']).toBeDefined(); await waitForAsyncJob(res4.headers['content-location'], app, accessToken); }); test('groupExportResources without members', async () => { const { project } = await createTestProject(); expect(project).toBeDefined(); const exporter = new BulkExporter(systemRepo); const exportWriteResourceSpy = jest.spyOn(exporter, 'writeResource'); const group: Group = await systemRepo.createResource<Group>({ resourceType: 'Group', type: 'person', actual: true, }); await exporter.start('http://example.com'); await groupExportResources(systemRepo, exporter, project, group); const bulkDataExport = await exporter.close(project); expect(bulkDataExport.status).toBe('completed'); expect(exportWriteResourceSpy).toHaveBeenCalledTimes(0); }); test('groupExportResources members without reference', async () => { const { project } = await createTestProject(); expect(project).toBeDefined(); const exporter = new BulkExporter(systemRepo); const patient: Patient = await systemRepo.createResource<Patient>({ resourceType: 'Patient', name: [{ given: ['Alice'], family: 'Smith' }], address: [{ use: 'home', line: ['123 Main St'], city: 'Anywhere', state: 'CA', postalCode: '90210' }], telecom: [ { system: 'phone', value: '555-555-5555' }, { system: 'email', value: 'alice@example.com' }, ], }); const group: Group = await systemRepo.createResource<Group>({ resourceType: 'Group', type: 'person', actual: true, member: [{ entity: { reference: '' } }, { entity: { reference: `Patient/${patient.id}` } }], }); await exporter.start('http://example.com'); await groupExportResources(systemRepo, exporter, project, group); const bulkDataExport = await exporter.close(project); expect(bulkDataExport.status).toBe('completed'); }); });