Merge from main repo: HL7 fixes for SimHospital (#2555)

src/examples/lab-integration/read-oru-message.test.ts

@@ -241,7 +241,7 @@ describe('Read from Partner Lab', () => {
 
  // Check that Specimen collection dates have been set
  const checkSpecimen1 = await medplum.readReference(serviceRequest.specimen?.[0] as Reference<Specimen>);
- expect(checkSpecimen1.receivedTime).toBe('2023-02-09T11:43:00.000-05:00');
+ expect(checkSpecimen1.receivedTime).toBe('2023-02-09T16:43:00.000Z');
 
  // Check that a PDF has been uploaded
  expect(createBinarySpy).toHaveBeenCalled();

src/examples/lab-integration/read-oru-message.ts

@@ -6,7 +6,7 @@ import {
  Hl7Message,
  Hl7Segment,
  MedplumClient,
- parseHl7Date,
+ parseHl7DateTime,
  streamToBuffer,
 } from '@medplum/core';
 import {
@@ -103,7 +103,7 @@ export async function processOruMessage(
 ): Promise<void> {
  // Parse the HL7 MSH segment
  // See: https://v2plus.hl7.org/2021Jan/segment-definition/MSH.html
- const messageType = message.get('MSH')?.get(8)?.get(0);
+ const messageType = message.header.getComponent(9, 1);
 
  // Message type should be "ORU"
  if (messageType !== 'ORU') {
@@ -113,7 +113,7 @@ export async function processOruMessage(
 
  // Parse the HL7 PID segment to read the patient id
  // See: https://v2plus.hl7.org/2021Jan/segment-definition/PID.html
- const orderId = message.get('PID')?.get(2)?.toString();
+ const orderId = message.getSegment('PID')?.getComponent(2, 1);
 
  if (!orderId || orderId.length === 0) {
  throw new Error('Missing order id');
@@ -142,8 +142,7 @@ export async function processOruMessage(
 
  // Update the collection date of each specimen associated with the order
  // See: https://v2plus.hl7.org/2021Jan/segment-definition/OBR.html
- const collectionDate = parseHl7Date(message.get('OBR')?.get(14).toString(), {
- seconds: false,
+ const collectionDate = parseHl7DateTime(message.getSegment('OBR')?.getField(14)?.toString(), {
  tzOffset: PARTNER_TIMEZONE,
  });
 
@@ -244,16 +243,17 @@ async function getCancellationReason(
 ): Promise<CodeableConcept | undefined> {
  // Read the first OBR Segment to find the order status
  // See: https://v2plus.hl7.org/2021Jan/segment-definition/OBR.html
- const obrIndex = message.segments.findIndex((segment) => segment.get(0).get(0) === 'OBR');
- const obrStatus = OBSERVATION_STATUS[message.segments[obrIndex]?.get(25).get(0)];
+ const obrIndex = message.segments.findIndex((segment) => segment.name === 'OBR');
+ const obr = message.getSegment(obrIndex);
+ const obrStatus = OBSERVATION_STATUS[obr?.getComponent(25, 1) as string];
 
  const isCancelled = obrStatus === 'cancelled';
 
  // If the order was cancelled, read the following note (NTE) segment to extract the cancellation reason
  // Note: How this cancellation reason is sent will differ across LIS/EHR systems
  if (isCancelled) {
- const obrNote = message.segments[obrIndex + 1];
- const noteText = obrNote.get(3).toString().toUpperCase();
+ const obrNote = message.getSegment(obrIndex + 1) as Hl7Segment;
+ const noteText = obrNote.getField(3).toString().toUpperCase();
  // Create a note on the order to describe the cancellation reason
  if (!serviceRequest.note) {
  serviceRequest.note = [];
@@ -328,18 +328,17 @@ function processObxSegments(
 
  // Loop through all segments, handling observation segments (OBX) and note segments (nte)
  for (const segment of message.segments) {
- // We're starting to process a new observation, so enqueue the previous observation
- if (segment.get(0).toString() === 'OBX') {
+ if (segment.name === 'OBX') {
+  // We're starting to process a new observation, so enqueue the previous observation
  if (prevObservation) {
  observations.push(prevObservation);
  }
 
  prevObservation = processObservation(segment, serviceRequest, performer);
- }
- // Handle associated notes
- // See https://v2plus.hl7.org/2021Jan/segment-definition/NTE.html
- else if (segment.get(0).toString() === 'NTE') {
- const noteText = segment.get(3).toString();
+ } else if (segment.name === 'NTE') {
+ // Handle associated notes
+ // See https://v2plus.hl7.org/2021Jan/segment-definition/NTE.html
+ const noteText = segment.getComponent(3, 1).toString();
 
  if (!prevObservation) {
  console.warn(`Warning: Received the following note with no observation: '${noteText}'`);
@@ -358,6 +357,7 @@ function processObxSegments(
 
  return observations;
 }
+
 /**
  * Convert an OBX segment into a FHIR `Observation` resource. This function handles two different types of OBX messages
  * NM - Numerical Observations
@@ -377,11 +377,11 @@ function processObservation(
 ): Observation | undefined {
  // Convert the reported code into a standard LOINC code
  // Note: The reported coding scheme will vary across labs
- const reportedCode = segment.get(3).get(3);
+ const reportedCode = segment.getComponent(3, 4);
  const code = LOINC_CODES[reportedCode];
 
  if (!code) {
- console.error(`Unrecognized code '${segment.get(3).toString()}'. Skipping....`);
+ console.error(`Unrecognized code '${segment.getField(3)?.toString()}'. Skipping....`);
  return undefined;
  }
 
@@ -390,24 +390,24 @@ function processObservation(
  basedOn: [createReference(serviceRequest)],
  code,
  subject: serviceRequest.subject,
- status: OBSERVATION_STATUS[segment.get(11).get(0)],
- issued: parseHl7Date(segment.get(14)?.get(0)),
+ status: OBSERVATION_STATUS[segment.getComponent(11, 1)],
+ issued: parseHl7DateTime(segment.getComponent(14, 1)),
 
  performer: [createReference(performer)],
  specimen: serviceRequest.specimen?.[0],
  };
 
  // Extract numerical value and units
- const valueType = segment.get(2).get(0);
- const value = segment.get(5).get(0);
- const unit = segment.get(6).get(0);
- const refRange = segment.get(7).get(0);
+ const valueType = segment.getComponent(2, 1);
+ const value = segment.getComponent(5, 1);
+ const unit = segment.getComponent(6, 1);
+ const refRange = segment.getComponent(7, 1);
  let quantity: Quantity | undefined = { unit, system: 'https://unitsofmeasure.org' };
  let interpretation: CodeableConcept | undefined;
 
  if (valueType === 'NM') {
  // If it's a numerical observation, populate a valueQuantity
- interpretation = INTERPRETATION_CODES[segment.get(8).get(0)];
+ interpretation = INTERPRETATION_CODES[segment.getComponent(8, 1)];
  quantity.value = Number.parseFloat(value);
  } else if (valueType === 'ST') {
  // If it's a structured text field, check for the following conditions:
@@ -474,10 +474,10 @@ async function uploadEmbeddedPdfs(
  message: Hl7Message
 ): Promise<Media[]> {
  // Upload PDF reports
- const pdfLines = message.segments.filter((seg) => seg.get(3)?.get(1) === 'PDFBASE64');
+ const pdfLines = message.segments.filter((seg) => seg.getComponent(3, 2) === 'PDFBASE64');
  const media = await Promise.all(
  pdfLines.map(async (segment: Hl7Segment) => {
- const encodedData = segment.get(5).get(4);
+ const encodedData = segment.getComponent(5, 5);
  const decodedData = Buffer.from(encodedData, 'base64');
  return medplum.uploadMedia(decodedData, 'application/pdf', fileName, {
  subject: report.subject,