feat(#114): fix bundle format

mediator/src/controllers/cht.ts

@@ -22,44 +22,50 @@ export async function createPatient(chtPatientDoc: any) {
 
   const fhirPatient = buildFhirPatientFromCht(chtPatientDoc.doc);
   // create or update in the FHIR Server
-  // note that either way, its a PUT with the id from the patient doc
+  // even for create, sends a PUT request
   return updateFhirResource({ ...fhirPatient, resourceType: 'Patient' });
 }
 
 export async function updatePatientIds(chtFormDoc: any) {
   // first, get the existing patient from fhir server
-  const response = await getFHIRPatientResource(chtFormDoc.openmrs_patient_uuid);
+  const response = await getFHIRPatientResource(chtFormDoc.external_id);
 
   if (response.status != 200) {
     return { status: 500, data: { message: `FHIR responded with ${response.status}`} };
   } else if (response.data.total == 0){
-    return { status: 404, data: { message: `Patient not found`} };
+    // in case the patient is not found, return 200 to prevent retries
+    return { status: 200, data: { message: `Patient not found`} };
   }
 
   const fhirPatient = response.data.entry[0].resource;
   addId(fhirPatient, chtPatientIdentifierType, chtFormDoc.patient_id);
 
   // now, we need to get the actual patient doc from cht...
   const patient_uuid = await getPatientUUIDFromSourceId(chtFormDoc._id);
-  addId(fhirPatient, chtDocumentIdentifierType, patient_uuid);
-
-  return updateFhirResource({ ...fhirPatient, resourceType: 'Patient' });
+  if (patient_uuid){
+    addId(fhirPatient, chtDocumentIdentifierType, patient_uuid);
+    return updateFhirResource({ ...fhirPatient, resourceType: 'Patient' });
+  } else {
+    // in case the patient is not found, return 200 to prevent retries
+    return { status: 200, data: { message: `Patient not found`} };
+  }
 }
 
 export async function createEncounter(chtReport: any) {
   const fhirEncounter = buildFhirEncounterFromCht(chtReport);
+  const response = await updateFhirResource(fhirEncounter);
 
-  const bundle: fhir4.Bundle = {
-    resourceType: 'Bundle',
-    type: 'collection',
-    entry: [fhirEncounter]
+  if (response.status != 200 && response.status != 201){
+    // in case of an error from fhir server, return it to caller
+    return response;
   }
 
   for (const entry of chtReport.observations) {
     if (entry.valueCode || entry.valueString || entry.valueDateTime) {
       const observation = buildFhirObservationFromCht(chtReport.patient_uuid, fhirEncounter, entry);
-      bundle.entry?.push(observation);
+      updateFhirResource(observation);
     }
   }
-  return createFhirResource(bundle);
+
+  return { status: 200, data: {} };
 }

mediator/src/mappers/cht.ts

@@ -72,7 +72,7 @@ export function buildFhirPatientFromCht(chtPatient: any): fhir4.Patient {
     telecom: [phone]
   };
 
-  copyIdToNamedIdentifier(patient, chtDocumentIdentifierType);
+  copyIdToNamedIdentifier(patient, patient, chtDocumentIdentifierType);
 
   return patient;
 }

mediator/src/mappers/openmrs.ts

@@ -25,7 +25,7 @@ const visitType: fhir4.CodeableConcept = {
   text: "Home Visit",
   coding: [{
     system: "http://fhir.openmrs.org/code-system/visit-type",
-    code: "d66e9fe0-7d51-4801-a550-5d462ad1c944",
+    code: "7b0f5697-27e3-40c4-8bae-f4049abfb4ed",
     display: "Home Visit",
   }]
 }
@@ -35,15 +35,22 @@ Build an OpenMRS Visit w/ Visit Note
 From a fhir Encounter
 One CHT encounter will become 2 OpenMRS Encounters
 */
-export function buildOpenMRSVisit(fhirEncounter: fhir4.Encounter): fhir4.Encounter[] {
+export function buildOpenMRSVisit(patientId: string, fhirEncounter: fhir4.Encounter): fhir4.Encounter[] {
   const openMRSVisit = fhirEncounter;
   openMRSVisit.type = [visitType]
-  //openMRSVisit.subject.reference = `Patient/${patient_id}`
+
+  const subjectRef: fhir4.Reference = {
+	  reference: `Patient/${patientId}`,
+    type: "Patient"
+  };
+
+  openMRSVisit.subject = subjectRef;
 
   const visitRef: fhir4.Reference = {
 	  reference: `Encounter/${openMRSVisit.id}`,
     type: "Encounter"
   };
+
   const openMRSVisitNote: fhir4.Encounter = {
     ...openMRSVisit,
     id: randomUUID(),
@@ -82,6 +89,7 @@ export function buildOpenMRSPatient(fhirPatient: fhir4.Patient): fhir4.Patient {
   }
   fhirPatient.name = fhirPatient.name?.map(addId);
   fhirPatient.identifier = fhirPatient.identifier?.map(addId);
+  fhirPatient.telecom = fhirPatient.telecom?.map(addId);
   return fhirPatient;
 }
 

mediator/src/routes/cht.ts

@@ -1,6 +1,7 @@
 import { Router } from 'express';
 import { requestHandler } from '../utils/request';
 import { createPatient, updatePatientIds, createEncounter } from '../controllers/cht'
+import { syncPatients, syncEncountersAndObservations} from '../utils/openmrs_sync'
 
 const router = Router();
 
@@ -21,4 +22,13 @@ router.post(
   requestHandler((req) => createEncounter(req.body))
 );
 
+router.post(
+  '/sync',
+  requestHandler(async (req) => {
+    await syncPatients();
+    syncEncountersAndObservations();
+    return { status: 200, data: {}};
+  })
+);
+
 export default router;

mediator/src/routes/tests/cht.spec.ts

@@ -2,6 +2,9 @@ import request from 'supertest';
 import app from '../../..';
 import { ChtPatientFactory, ChtPregnancyForm } from '../../middlewares/schemas/tests/cht-request-factories';
 import * as fhir from '../../utils/fhir';
+import axios from 'axios';
+
+jest.mock('axios');
 
 describe('POST /cht/patient', () => {
   it('accepts incoming request with valid patient resource', async () => {
@@ -44,6 +47,6 @@ describe('POST /cht/patient', () => {
       resourceType: 'Patient',
     });
     */
-    expect(fhir.createFhirResource).toHaveBeenCalled();
+    expect(fhir.updateFhirResource).toHaveBeenCalled();
   });
 });

mediator/src/utils/cht.ts

@@ -87,7 +87,11 @@ export async function getPatientUUIDFromSourceId(source_id: string) {
   }
 
   const patient = await queryCht(query);
-  return patient.data.docs[0]._id;
+  if ( patient.data.docs && patient.data.docs.length > 0 ){
+    return patient.data.docs[0]._id;
+  } else {
+    return ''
+  }
 }
 
 export async function createChtPatient(fhirPatient: fhir4.Patient) {

mediator/src/utils/fhir.ts

@@ -114,20 +114,24 @@ export async function getFHIRPatients(lastUpdated: Date) {
   );
 }
 
-export function copyIdToNamedIdentifier(resource: fhir4.Patient, fromIDType: fhir4.CodeableConcept){
+export function copyIdToNamedIdentifier(fromResource: any, toResource: fhir4.Patient | fhir4.Encounter, fromIDType: fhir4.CodeableConcept){
   const identifier: fhir4.Identifier = {
     type: fromIDType,
-    value: resource.id
+    value: fromResource.id,
+    use: "secondary"
   };
-  resource.identifier?.push(identifier);
-  return resource;
+  const sameIdType = (id: any) => (id.type.text === fromIDType.text)
+  if (!toResource.identifier?.some(sameIdType)) {
+    toResource.identifier?.push(identifier);
+  }
+  return toResource;
 }
 
-export function getIdType(resource: fhir4.Patient, idType: fhir4.CodeableConcept): string{
+export function getIdType(resource: fhir4.Patient | fhir4.Encounter, idType: fhir4.CodeableConcept): string{
   return resource.identifier?.find((id: any) => id?.type.text == idType.text)?.value || '';
 }
 
-export function addId(resource: fhir4.Patient, idType: fhir4.CodeableConcept, value: string){
+export function addId(resource: fhir4.Patient | fhir4.Encounter, idType: fhir4.CodeableConcept, value: string){
   const identifier: fhir4.Identifier = {
     type: idType,
     value: value
@@ -171,7 +175,7 @@ export async function updateFhirResource(doc: fhir4.Resource) {
       },
     });
 
-    return { status: res.status, data: res.data };
+    return { status: res?.status, data: res?.data };
   } catch (error: any) {
     logger.error(error);
     return { status: error.status, data: error.data };
@@ -184,7 +188,20 @@ export async function getFhirResourcesSince(lastUpdated: Date, resourceType: str
       `${FHIR.url}/${resourceType}/?_lastUpdated=gt${lastUpdated.toISOString()}`,
       axiosOptions
     );
-    return { status: res.status, data: res.data };
+    return { status: res?.status, data: res?.data };
+  } catch (error: any) {
+    logger.error(error);
+    return { status: error.status, data: error.data };
+  }
+}
+
+export async function getFhirResource(id: string, resourceType: string) {
+  try {
+    const res = await axios.get(
+      `${FHIR.url}/${resourceType}/${id}`,
+      axiosOptions
+    );
+    return { status: res?.status, data: res?.data };
   } catch (error: any) {
     logger.error(error);
     return { status: error.status, data: error.data };