Medplum

// SPDX-FileCopyrightText: Copyright Orangebot, Inc. and Medplum contributors // SPDX-License-Identifier: Apache-2.0 import { ContentType, LOINC, UCUM, createReference, indexSearchParameterBundle, indexStructureDefinitionBundle, } from '@medplum/core'; import type { MedplumClient } from '@medplum/core'; import { SEARCH_PARAMETER_BUNDLE_FILES, readJson } from '@medplum/definitions'; import type { Bundle, DiagnosticReport, Observation, Patient, Practitioner, SearchParameter, ServiceRequest, Specimen, } from '@medplum/fhirtypes'; import { MockClient } from '@medplum/mock'; import * as dotenv from 'dotenv'; import { afterEach, beforeAll, beforeEach, describe, expect, test, vi } from 'vitest'; import { createOruMessage, handler } from './send-oru-message'; dotenv.config({ quiet: true }); const CONNECTION_DETAILS = { SFTP_HOST: { name: 'SFTP_HOST', valueString: 'example.server.transfer.us-east-1.amazonaws.com' }, SFTP_USER: { name: 'SFTP_USER', valueString: 'user' }, SFTP_PRIVATE_KEY: { name: 'SFTP_PRIVATE_KEY', valueString: 'abcd' }, }; // Mock the ssh2-sftp-client vi.mock('ssh2-sftp-client'); describe('Send ORU Message to Partner', () => { beforeAll(() => { // Initialize FHIR structure definitions indexStructureDefinitionBundle(readJson('fhir/r4/profiles-types.json') as Bundle); indexStructureDefinitionBundle(readJson('fhir/r4/profiles-resources.json') as Bundle); for (const filename of SEARCH_PARAMETER_BUNDLE_FILES) { indexSearchParameterBundle(readJson(filename) as Bundle<SearchParameter>); } }); beforeEach(async (ctx: any) => { const medplum = new MockClient(); // Create test patient const patient = await medplum.createResource({ resourceType: 'Patient', name: [ { given: ['Jane'], family: 'Doe', }, ], birthDate: '1985-08-01', address: [ { line: ['123 Main Street'], city: 'Springfield', state: 'MA', postalCode: '12345', }, ], telecom: [ { system: 'phone', use: 'home', value: '(555) 123-4567', }, { system: 'phone', use: 'work', value: '(555) 987-6543', }, ], gender: 'female', identifier: [ { system: 'https://lab.medplum.com/patientId', value: 'PT12345', }, ], }); // Create ordering provider const orderer = await medplum.createResource({ resourceType: 'Practitioner', name: [ { prefix: ['Dr.'], given: ['Robert'], family: 'Johnson', }, ], gender: 'male', identifier: [ { system: 'https://lab.medplum.com/practitionerId', value: 'DR12345', }, ], }); // Create specimen const specimen = await medplum.createResource({ resourceType: 'Specimen', subject: createReference(patient), receivedTime: '2023-04-15T14:30:00Z', collection: { collectedDateTime: '2023-04-15T09:15:00Z', }, type: { coding: [ { system: 'http://snomed.info/sct', code: '119364003', display: 'Serum specimen', }, ], text: 'Serum', }, status: 'available', }); // Create service request (lab order) const serviceRequest = await medplum.createResource({ resourceType: 'ServiceRequest', subject: createReference(patient), requester: createReference(orderer), status: 'active', intent: 'order', authoredOn: '2023-04-14T16:00:00Z', specimen: [createReference(specimen)], identifier: [ { system: 'https://lab.medplum.com/orderId', value: 'ORD98765', }, ], code: { coding: [ { system: 'https://lab.medplum.com/orderCode', code: 'PANEL-CHEM', display: 'Comprehensive Chemistry Panel', }, ], text: 'Comprehensive Chemistry Panel', }, }); // Create observations (lab results) const observations = []; // Glucose observation observations.push( await medplum.createResource({ resourceType: 'Observation', status: 'final', subject: createReference(patient), basedOn: [createReference(serviceRequest)], specimen: createReference(specimen), category: [ { coding: [ { system: 'http://terminology.hl7.org/CodeSystem/observation-category', code: 'laboratory', display: 'Laboratory', }, ], }, ], code: { coding: [ { system: LOINC, code: '2339-0', display: 'Glucose', }, ], text: 'Glucose', }, valueQuantity: { value: 95, unit: 'mg/dL', system: UCUM, code: 'mg/dL', }, referenceRange: [ { low: { value: 70, unit: 'mg/dL', system: UCUM, code: 'mg/dL', }, high: { value: 99, unit: 'mg/dL', system: UCUM, code: 'mg/dL', }, text: '70 - 99 mg/dL', }, ], issued: '2023-04-16T10:00:00Z', }) ); // BUN observation observations.push( await medplum.createResource({ resourceType: 'Observation', status: 'final', subject: createReference(patient), basedOn: [createReference(serviceRequest)], specimen: createReference(specimen), category: [ { coding: [ { system: 'http://terminology.hl7.org/CodeSystem/observation-category', code: 'laboratory', display: 'Laboratory', }, ], }, ], code: { coding: [ { system: LOINC, code: '3094-0', display: 'BUN', }, ], text: 'BUN', }, valueQuantity: { value: 18, unit: 'mg/dL', system: UCUM, code: 'mg/dL', }, referenceRange: [ { low: { value: 7, unit: 'mg/dL', system: UCUM, code: 'mg/dL', }, high: { value: 20, unit: 'mg/dL', system: UCUM, code: 'mg/dL', }, text: '7 - 20 mg/dL', }, ], issued: '2023-04-16T10:00:00Z', }) ); // Cholesterol observation with high value observations.push( await medplum.createResource({ resourceType: 'Observation', status: 'final', subject: createReference(patient), basedOn: [createReference(serviceRequest)], specimen: createReference(specimen), category: [ { coding: [ { system: 'http://terminology.hl7.org/CodeSystem/observation-category', code: 'laboratory', display: 'Laboratory', }, ], }, ], code: { coding: [ { system: LOINC, code: '2093-3', display: 'Cholesterol', }, ], text: 'Cholesterol', }, valueQuantity: { value: 220, unit: 'mg/dL', system: UCUM, code: 'mg/dL', }, interpretation: [ { coding: [ { system: 'http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation', code: 'H', display: 'High', }, ], text: 'High', }, ], referenceRange: [ { high: { value: 200, unit: 'mg/dL', system: UCUM, code: 'mg/dL', }, text: '< 200 mg/dL', }, ], issued: '2023-04-16T10:00:00Z', note: [ { text: 'Levels above 200 mg/dL may indicate increased risk of heart disease.', }, ], }) ); // Create diagnostic report const diagnosticReport = await medplum.createResource({ resourceType: 'DiagnosticReport', status: 'final', code: { coding: [ { system: 'https://lab.medplum.com/orderCode', code: 'PANEL-CHEM', display: 'Comprehensive Chemistry Panel', }, ], text: 'Comprehensive Chemistry Panel', }, subject: createReference(patient), resultsInterpreter: [createReference(orderer)], basedOn: [createReference(serviceRequest)], specimen: [createReference(specimen)], result: observations.map(createReference), issued: '2023-04-16T10:30:00Z', performer: [ { display: 'MEDPLUM_LAB', }, ], note: [ { text: 'Sample processed according to standard protocol.', }, ], }); Object.assign(ctx, { medplum, patient, orderer, specimen, serviceRequest, observations, diagnosticReport, }); }); beforeEach(() => { vi.useFakeTimers(); vi.setSystemTime(new Date('2023-04-16T12:00:00Z')); }); afterEach(() => { vi.useRealTimers(); vi.clearAllMocks(); }); test.skip('Test Connection', async (ctx: any) => { try { await handler(ctx.medplum, { bot: { reference: 'Bot/123' }, input: ctx.order, contentType: 'string', secrets: { ...CONNECTION_DETAILS }, }); } catch { console.error('Here'); } }); test('Create ORU message format', async (ctx: any) => { const diagnosticReport = ctx.diagnosticReport as DiagnosticReport; const patient = ctx.patient as Patient; const serviceRequest = ctx.serviceRequest as ServiceRequest; const observations = ctx.observations as Observation[]; const specimen = ctx.specimen as Specimen; const orderer = ctx.orderer as Practitioner; const oruMessage = await createOruMessage( diagnosticReport, serviceRequest, observations, specimen, patient, orderer ); // Verify message exists expect(oruMessage).toBeDefined(); const messageString = oruMessage?.toString() || ''; expect(messageString).toBe(TEST_MESSAGE); }); test('Create ORU message with child observations', async (ctx: any) => { const medplum = ctx.medplum as MedplumClient; const patient = ctx.patient as Patient; const serviceRequest = ctx.serviceRequest as ServiceRequest; const specimen = ctx.specimen as Specimen; const orderer = ctx.orderer as Practitioner; // Create child observations const childObs1 = await medplum.createResource({ resourceType: 'Observation', status: 'final', subject: createReference(patient), basedOn: [createReference(serviceRequest)], specimen: createReference(specimen), category: [ { coding: [ { system: 'http://terminology.hl7.org/CodeSystem/observation-category', code: 'laboratory', display: 'Laboratory', }, ], }, ], code: { coding: [ { system: LOINC, code: '2339-1', display: 'Glucose Fasting', }, ], text: 'Glucose Fasting', }, valueQuantity: { value: 92, unit: 'mg/dL', system: UCUM, code: 'mg/dL', }, issued: '2023-04-16T10:00:00Z', }); const childObs2 = await medplum.createResource({ resourceType: 'Observation', status: 'final', subject: createReference(patient), basedOn: [createReference(serviceRequest)], specimen: createReference(specimen), category: [ { coding: [ { system: 'http://terminology.hl7.org/CodeSystem/observation-category', code: 'laboratory', display: 'Laboratory', }, ], }, ], code: { coding: [ { system: LOINC, code: '2339-2', display: 'Glucose Post-Meal', }, ], text: 'Glucose Post-Meal', }, valueQuantity: { value: 98, unit: 'mg/dL', system: UCUM, code: 'mg/dL', }, issued: '2023-04-16T10:00:00Z', }); // Create parent observation with child observations const parentObs = await medplum.createResource({ resourceType: 'Observation', status: 'final', subject: createReference(patient), basedOn: [createReference(serviceRequest)], specimen: createReference(specimen), category: [ { coding: [ { system: 'http://terminology.hl7.org/CodeSystem/observation-category', code: 'laboratory', display: 'Laboratory', }, ], }, ], code: { coding: [ { system: LOINC, code: '2339-0', display: 'Glucose Panel', }, ], text: 'Glucose Panel', }, hasMember: [createReference(childObs1), createReference(childObs2)], issued: '2023-04-16T10:00:00Z', }); // Create diagnostic report with parent observation const diagnosticReport = await medplum.createResource({ resourceType: 'DiagnosticReport', status: 'final', code: { coding: [ { system: 'https://lab.medplum.com/orderCode', code: 'PANEL-CHEM', display: 'Comprehensive Chemistry Panel', }, ], text: 'Comprehensive Chemistry Panel', }, subject: createReference(patient), resultsInterpreter: [createReference(orderer)], basedOn: [createReference(serviceRequest)], specimen: [createReference(specimen)], result: [createReference(parentObs)], issued: '2023-04-16T10:30:00Z', performer: [ { display: 'MEDPLUM_LAB', }, ], }); const oruMessage = createOruMessage( diagnosticReport, serviceRequest, [parentObs, childObs1, childObs2], specimen, patient, orderer ); // Verify message exists expect(oruMessage).toBeDefined(); const messageString = oruMessage?.toString() || ''; // Verify that both parent and child observations are in the message expect(messageString).toContain('2339-0^Glucose Panel^http://loinc.org'); expect(messageString).toContain('2339-1^Glucose Fasting^http://loinc.org'); expect(messageString).toContain('2339-2^Glucose Post-Meal^http://loinc.org'); }); test('Create ORU message with PDF attachments', async (ctx: any) => { const medplum = ctx.medplum as MedplumClient; const patient = ctx.patient as Patient; const serviceRequest = ctx.serviceRequest as ServiceRequest; const specimen = ctx.specimen as Specimen; const orderer = ctx.orderer as Practitioner; // Create a simple observation const observation = await medplum.createResource({ resourceType: 'Observation', status: 'final', subject: createReference(patient), basedOn: [createReference(serviceRequest)], specimen: createReference(specimen), category: [ { coding: [ { system: 'http://terminology.hl7.org/CodeSystem/observation-category', code: 'laboratory', display: 'Laboratory', }, ], }, ], code: { coding: [ { system: LOINC, code: '2339-0', display: 'Glucose', }, ], text: 'Glucose', }, valueQuantity: { value: 95, unit: 'mg/dL', system: UCUM, code: 'mg/dL', }, issued: '2023-04-16T10:00:00Z', }); // Create diagnostic report with PDF attachment const diagnosticReport = await medplum.createResource({ resourceType: 'DiagnosticReport', status: 'final', code: { coding: [ { system: 'https://lab.medplum.com/orderCode', code: 'PANEL-CHEM', display: 'Comprehensive Chemistry Panel', }, ], text: 'Comprehensive Chemistry Panel', }, subject: createReference(patient), resultsInterpreter: [createReference(orderer)], basedOn: [createReference(serviceRequest)], specimen: [createReference(specimen)], result: [createReference(observation)], issued: '2023-04-16T10:30:00Z', performer: [ { display: 'MEDPLUM_LAB', }, ], presentedForm: [ { contentType: 'application/pdf', data: 'JVBERi0xLjcKCjEgMCBvYmogICUgZW50cnkgcG9pbnQKPDwKICAvVHlwZSAvQ2F0YWxvZwog', // Sample base64 PDF content title: 'DiagnosticReport-2011e7673174e366cfbb17b3.pdf', }, ], }); const oruMessage = createOruMessage( diagnosticReport, serviceRequest, [observation], specimen, patient, orderer, diagnosticReport.presentedForm ); // Verify message exists expect(oruMessage).toBeDefined(); const messageString = oruMessage?.toString() || ''; // Verify that both the observation and PDF attachment are in the message expect(messageString).toContain('2339-0^Glucose^http://loinc.org'); expect(messageString).toContain( 'OBX|2|ED|PDF^PDFBASE64|1|JVBERi0xLjcKCjEgMCBvYmogICUgZW50cnkgcG9pbnQKPDwKICAvVHlwZSAvQ2F0YWxvZwog' ); }); test('Handle missing related resources', async (ctx: any) => { const medplum = ctx.medplum as MedplumClient; // Create a diagnostic report without proper references const incompleteReport = await medplum.createResource({ resourceType: 'DiagnosticReport', status: 'final', code: { text: 'Incomplete Report', }, subject: { reference: 'Patient/missing-id', }, }); // Should throw an error when trying to process this report await expect( handler(medplum, { bot: { reference: 'Bot/123' }, input: incompleteReport, contentType: ContentType.JSON, secrets: CONNECTION_DETAILS, }) ).rejects.toThrow('Could not find required resources for ORU message'); }); }); const TEST_MESSAGE = `MSH|^~\\&|MEDPLUM_LAB|MEDPLUM_LAB||RECEIVING_FACILITY|20230416120000||ORU^R01|MEDPLUM_1681646400000|P|2.5||||||| PID|1|PT12345|||Doe^Jane^^^||1985-08-01|F|||123 Main Street^^Springfield^MA^12345^||(555) 123-4567|(555) 987-6543|||||| OBR|1|ORD98765||PANEL-CHEM^Comprehensive Chemistry Panel^https://lab.medplum.com/orderCode|||20230415091500|||||||||||||||20230416103000|||F OBX|1|NM|2339-0^Glucose^http://loinc.org||95|mg/dL|70-99||||F|||20230416100000||| OBX|2|NM|3094-0^BUN^http://loinc.org||18|mg/dL|7-20||||F|||20230416100000||| OBX|3|NM|2093-3^Cholesterol^http://loinc.org||220|mg/dL|<200|H|||F|||20230416100000||| NTE|1||Levels above 200 mg/dL may indicate increased risk of heart disease.`;