Merge from main repo: Release Version 2.1.4 (#2968)

.turbo/turbo-build.log

@@ -1,4 +1,4 @@
 
-> [email protected].3 build
+> [email protected].4 build
 > tsc
 

package.json

@@ -1,6 +1,6 @@
 {
  "name": "medplum-demo-bots",
- "version": "2.1.3",
+ "version": "2.1.4",
  "description": "Medplum Demo Bots",
  "scripts": {
  "build": "tsc",
@@ -13,11 +13,11 @@
  "author": "Medplum <[email protected]>",
  "license": "Apache-2.0",
  "devDependencies": {
- "@medplum/cli": "2.1.3",
- "@medplum/core": "2.1.3",
- "@medplum/eslint-config": "2.1.3",
- "@medplum/fhirtypes": "2.1.3",
- "@medplum/mock": "2.1.3",
+ "@medplum/cli": "2.1.4",
+ "@medplum/core": "2.1.4",
+ "@medplum/eslint-config": "2.1.4",
+ "@medplum/fhirtypes": "2.1.4",
+ "@medplum/mock": "2.1.4",
  "@types/node": "20.6.2",
  "@types/node-fetch": "2.6.5",
  "@types/ssh2-sftp-client": "9.0.0",

src/candid-health/send-to-candid.test.ts

@@ -1,9 +1,12 @@
 import {
+ CPT,
  createReference,
  getReferenceString,
+ ICD10,
  indexSearchParameterBundle,
  indexStructureDefinitionBundle,
  MedplumClient,
+ SNOMED,
 } from '@medplum/core';
 import { readJson } from '@medplum/definitions';
 import { Bundle, Coverage, Encounter, Patient, SearchParameter } from '@medplum/fhirtypes';
@@ -87,12 +90,12 @@ describe('Candid Health Tests', () => {
  {
  coding: [
  {
- system: 'https://snomed.info/sct',
+ system: SNOMED,
  code: '394701000',
  display: 'Asthma follow-up',
  },
  {
- system: 'https://www.ama-assn.org/go/cpt',
+ system: CPT,
  code: '99213',
  display: 'Established patient office visit, 20-29 minutes',
  },
@@ -128,12 +131,12 @@ describe('Candid Health Tests', () => {
  {
  coding: [
  {
- system: 'https://snomed.info/sct',
+ system: SNOMED,
  code: '195967001',
  display: 'Asthma',
  },
  {
- system: 'https://hl7.org/fhir/sid/icd-10',
+ system: ICD10,
  code: 'J45.5',
  display: 'Severe persistent asthma',
  },

src/candid-health/send-to-candid.ts

@@ -1,4 +1,4 @@
-import { BotEvent, getCodeBySystem, getIdentifier, getReferenceString, MedplumClient } from '@medplum/core';
+import { BotEvent, CPT, getCodeBySystem, getIdentifier, getReferenceString, ICD10, MedplumClient } from '@medplum/core';
 import {
  Address,
  Coverage,
@@ -92,7 +92,7 @@ export async function handler(medplum: MedplumClient, event: BotEvent<Encounter>
  place_of_service_code: '10',
  service_lines: [
  {
- procedure_code: encounter.type?.[0] && getCodeBySystem(encounter.type?.[0], 'https://www.ama-assn.org/go/cpt'),
+ procedure_code: encounter.type?.[0] && getCodeBySystem(encounter.type?.[0], CPT),
  quantity: '1',
  units: 'MJ',
  charge_amount_cents: 10000,
@@ -304,7 +304,7 @@ function convertDiagnoses(encounter: Encounter): any[] {
  }
 
  for (const reason of encounter.reasonCode) {
- const code = reason.coding?.find((c) => c.system === 'https://hl7.org/fhir/sid/icd-10');
+ const code = reason.coding?.find((c) => c.system === ICD10);
  if (code) {
  result.push({
  code_type: 'ABK',

src/finalize-reports.test.ts

@@ -1,4 +1,10 @@
-import { createReference, indexSearchParameterBundle, indexStructureDefinitionBundle } from '@medplum/core';
+import {
+ LOINC,
+ UCUM,
+ createReference,
+ indexSearchParameterBundle,
+ indexStructureDefinitionBundle,
+} from '@medplum/core';
 import { readJson } from '@medplum/definitions';
 import { Bundle, DiagnosticReport, Observation, Patient, SearchParameter } from '@medplum/fhirtypes';
 import { MockClient } from '@medplum/mock';
@@ -38,7 +44,7 @@ describe('Finalize Report', async () => {
  code: {
  coding: [
  {
- system: 'https://loinc.org',
+ system: LOINC,
  code: '39156-5',
  display: 'Body Mass Index',
  },
@@ -48,7 +54,7 @@ describe('Finalize Report', async () => {
  valueQuantity: {
  value: 24.5,
  unit: 'kg/m2',
- system: 'https://unitsofmeasure.org',
+ system: UCUM,
  code: 'kg/m2',
  },
  });
@@ -103,7 +109,7 @@ describe('Finalize Report', async () => {
  code: {
  coding: [
  {
- system: 'https://loinc.org',
+ system: LOINC,
  code: '39156-5',
  display: 'Body Mass Index',
  },
@@ -113,7 +119,7 @@ describe('Finalize Report', async () => {
  valueQuantity: {
  value: 24.5,
  unit: 'kg/m2',
- system: 'https://unitsofmeasure.org',
+ system: UCUM,
  code: 'kg/m2',
  },
  });

src/health-gorilla/receive-from-health-gorilla.ts

@@ -1,6 +1,16 @@
-import { allOk, BotEvent, getIdentifier, getReferenceString, MedplumClient, normalizeErrorString } from '@medplum/core';
+import {
+ allOk,
+ BotEvent,
+ convertContainedResourcesToBundle,
+ getIdentifier,
+ getReferenceString,
+ MedplumClient,
+ normalizeErrorString,
+} from '@medplum/core';
 import {
  Account,
+ Bundle,
+ BundleEntryRequest,
  DiagnosticReport,
  Observation,
  OperationOutcome,
@@ -27,81 +37,122 @@ const HEALTH_GORILLA_SYSTEM = 'https://www.healthgorilla.com';
 
 const referenceMap = new Map<string, string>();
 
+/**
+ * Main entry point for the Health Gorilla webhook bot.
+ *
+ * This bot receives a Health Gorilla resource and syncs it to Medplum.
+ *
+ * Health Gorilla uses "contained resources" to represent related resources.
+ *
+ * In Medplum, we recommend that you use references instead of contained resources,
+ * which is often better for data quality and analytics.
+ *
+ * The majority of this bot is dedicated to rewriting references from Health Gorilla.
+ *
+ * @param medplum The Medplum client.
+ * @param event The Bot execution event with a Health Gorilla resource.
+ * @returns Returns OK OperationOutcome on success, or an error OperationOutcome on failure.
+ */
 export async function handler(
  medplum: MedplumClient,
  event: BotEvent<HealthGorillaResource>
 ): Promise<OperationOutcome> {
- try {
- const resource = event.input;
+ const resource = event.input;
 
- if (resource.contained) {
- for (const containedResource of resource.contained) {
- await syncResource(medplum, containedResource as HealthGorillaResource, true);
- }
+ // Move the Health Gorilla resource ID to an identifier
+ if (resource.id) {
+ const identifiers = resource.identifier ?? [];
+ identifiers.push({ system: HEALTH_GORILLA_SYSTEM, value: resource.id });
+ resource.identifier = identifiers;
+ }
 
- // Remove contained resources before syncing the parent resource
- resource.contained = undefined;
- }
+ // Convert the Health Gorilla resource to a Medplum bundle.
+ // This moves contained resources to separate create/update operations.
+ const healthGorillaBundle = convertContainedResourcesToBundle(resource) as Bundle<HealthGorillaResource>;
+
+ // Touch up the bundle before executing
+ // This adds identifiers and ifNoneExist to the bundle entries
+ touchUpBundle(healthGorillaBundle);
 
- await syncResource(medplum, resource);
+ try {
+ // Rewrite references to other resources
+ // For example, convert references to Patient and Organization resources
+ // from Health Gorilla references to Medplum references
+ await rewriteReferences(medplum, healthGorillaBundle);
+
+ // Execute the bundle
+ const result = await medplum.executeBatch(healthGorillaBundle);
+ for (const entry of result.entry ?? []) {
+ if (entry.response) {
+ console.log(entry.response.status, entry.response.location);
+ }
+ }
  } catch (err) {
  console.log(normalizeErrorString(err));
  }
 
  return allOk;
 }
 
-export async function syncResource<T extends HealthGorillaResource>(
- medplum: MedplumClient,
- healthGorillaResource: T,
- contained = false
-): Promise<void> {
- if (healthGorillaResource.resourceType === 'Account' && !healthGorillaResource.status) {
- // Health Gorilla drops Account.status which is a required field
- healthGorillaResource.status = 'active';
- }
-
- // Rewrite references to other resources
- // For example, convert references to Patient and Organization resources
- // from Health Gorilla references to Medplum references
- await rewriteReferences(medplum, healthGorillaResource);
-
- let existingResource: HealthGorillaResource | undefined = undefined;
- let healthGorillaId: string | undefined = undefined;
+/**
+ * Touches up the bundle before executing.
+ *
+ * As part of the conversion from Health Gorilla to Medplum, we need to add identifiers to the resources,
+ * so that we can connect/reuse resources that already exist in Medplum.
+ *
+ * We also take advantage of the "ifNoneExist" feature of FHIR to avoid creating duplicate resources.
+ *
+ * @param bundle The Health Gorilla bundle.
+ */
+function touchUpBundle(bundle: Bundle<HealthGorillaResource>): void {
+ for (const entry of bundle.entry ?? []) {
+ const resource = entry.resource as HealthGorillaResource;
+ const request = entry.request as BundleEntryRequest;
+
+ if (resource.resourceType === 'Account') {
+ // In Health Gorilla, Account connects a Patient and a payment method
+ // So we use the combination of those references as the Account identifier
+ const identifier = resource.guarantor?.[0]?.party?.reference + '-' + resource?.type?.coding?.[0]?.code;
+ if (!resource.identifier) {
+ resource.identifier = [];
+ }
+ resource.identifier.push({ system: HEALTH_GORILLA_SYSTEM, value: identifier });
+ request.ifNoneExist = 'identifier=' + identifier;
+ }
 
- const mergeResourceTypes: HealthGorillaResourceType[] = ['Account'];
- if (mergeResourceTypes.includes(healthGorillaResource.resourceType)) {
- // For some resource types, we attempt a "merge" operation with existing resources.
- // For other resource types, we always create a new resource.
- healthGorillaId = getHealthGorillaId(healthGorillaResource, contained) as string;
- existingResource = await searchByHealthGorillaId(medplum, healthGorillaResource.resourceType, healthGorillaId);
- }
+ if (resource.resourceType === 'PractitionerRole') {
+ // In Health Gorilla, PractitionerRole connects a Practitioner and an Organization
+ // So we use the combination of those references as the PractitionerRole identifier
+ const identifier = resource.practitioner?.reference + '-' + resource.organization?.reference;
+ if (!resource.identifier) {
+ resource.identifier = [];
+ }
+ resource.identifier.push({ system: HEALTH_GORILLA_SYSTEM, value: identifier });
+ request.ifNoneExist = 'identifier=' + identifier;
+ }
 
- if (existingResource) {
- // Update the existing resource
- const updatedResource = await medplum.updateResource({
- ...healthGorillaResource,
- id: existingResource.id,
- identifier: existingResource.identifier,
- });
- console.log('Updated', updatedResource.resourceType, updatedResource.id);
- if (healthGorillaResource.id) {
- referenceMap.set('#' + healthGorillaResource.id, getReferenceString(updatedResource));
+ if (resource.resourceType === 'RequestGroup' || resource.resourceType === 'DiagnosticReport') {
+ const identifier = getIdentifier(resource, HEALTH_GORILLA_SYSTEM);
+ if (identifier) {
+ request.ifNoneExist = 'identifier=' + identifier;
+ }
  }
- } else {
- // Create a new resource
- const createdResource = await medplum.createResource({
- ...healthGorillaResource,
- id: undefined,
- identifier: [{ system: HEALTH_GORILLA_SYSTEM, value: healthGorillaId }],
- });
- console.log('Created', createdResource.resourceType, createdResource.id);
- if (healthGorillaResource.id) {
- referenceMap.set('#' + healthGorillaResource.id, getReferenceString(createdResource));
+
+ if (resource.resourceType === 'ServiceRequest') {
+ const requisition = resource.requisition?.value;
+ if (requisition) {
+ request.ifNoneExist = 'requisition=' + requisition;
+ }
  }
  }
 }
 
+/**
+ * Rewrites Health Gorilla references to Medplum references.
+ *
+ * @param medplum The Medplum client.
+ * @param value An unknown value.
+ */
 async function rewriteReferences(medplum: MedplumClient, value: unknown): Promise<void> {
  if (!value) {
  return;
@@ -145,17 +196,30 @@ async function rewriteReferencesInObject(medplum: MedplumClient, obj: Record<str
  }
 }
 
-function getHealthGorillaId(resource: HealthGorillaResource, contained: boolean): string | undefined {
- if (!contained && resource.id) {
- return resource.id;
- }
- return getIdentifier(resource, HEALTH_GORILLA_SYSTEM);
-}
-
+/**
+ * Tries to find a Medplum resource by Health Gorilla ID.
+ *
+ * In most cases, this is a matter of search by "identifier" rather than "id".
+ *
+ * There are some special cases where "identifier" is not available.
+ *
+ * @param medplum The Medplum client.
+ * @param resourceType The FHIR resource type.
+ * @param id The Health Gorilla resource ID.
+ * @returns The Medplum resource, or undefined if not found.
+ */
 async function searchByHealthGorillaId(
  medplum: MedplumClient,
  resourceType: HealthGorillaResourceType,
  id: string
 ): Promise<HealthGorillaResource | undefined> {
- return medplum.searchOne(resourceType, { identifier: id });
+ if (resourceType === 'ServiceRequest') {
+ // Special case for ServiceRequest - search by requisition instead of identifier
+ // Because Health Gorilla does not include the identifier
+ const requisition = id.split('-')[0];
+ return medplum.searchOne(resourceType, { requisition });
+ }
+
+ // Default case - search by identifier
+ return medplum.searchOne(resourceType, { identifier: `${HEALTH_GORILLA_SYSTEM}|${id}` });
 }