feat(#114): get observations and patients together with encounters

mediator/src/controllers/cht.ts

@@ -63,7 +63,7 @@ export async function createEncounter(chtReport: any) {
   for (const entry of chtReport.observations) {
     if (entry.valueCode || entry.valueString || entry.valueDateTime) {
       const observation = buildFhirObservationFromCht(chtReport.patient_uuid, fhirEncounter, entry);
-      updateFhirResource(observation);
+      createFhirResource(observation);
     }
   }
 

mediator/src/mappers/cht.ts

@@ -140,3 +140,27 @@ export function buildFhirObservationFromCht(patient_id: string, encounter: fhir4
 
   return observation;
 }
+
+export async function buildChtRecordFromObservations(patient: fhir4.Patient, observations: fhir4.Observation[]) {
+  const patientId = getIdType(patient, chtDocumentIdentifierType);
+
+  const record: any = {
+    _meta: {
+      form: "openmrs_anc"
+    },
+    patient_id: patientId
+  }
+
+  observations.forEach((observation: fhir4.Observation) => {
+    if ( observation?.code?.coding && observation.code.coding.length > 0){
+      const code = observation.code.coding[0].code?.toLowerCase() || '';
+      if (observation.valueCodeableConcept) {
+        record[code] = observation.valueCodeableConcept.text;
+      } else if (observation.valueDateTime) {
+        record[code] = observation.valueDateTime.split('T')[0];
+      }
+    }
+  });
+
+  return record;
+}

mediator/src/middlewares/schemas/encounter.ts

@@ -1,6 +1,7 @@
 import joi from 'joi';
 
 export const EncounterSchema = joi.object({
+  resourceType: joi.string(),
   id: joi.string().uuid(),
   identifier: joi
     .array()

mediator/src/middlewares/schemas/patient.ts

@@ -1,6 +1,7 @@
 import joi from 'joi';
 
 export const PatientSchema = joi.object({
+  resourceType: joi.string(),
   id: joi.string().uuid(),
   identifier: joi
     .array()

mediator/src/middlewares/schemas/tests/fhir-resource-factories.ts

@@ -17,13 +17,15 @@ export const HumanNameFactory = Factory.define('humanName')
   .attr('given', ['John']);
 
 export const PatientFactory = Factory.define('patient')
+  .attr('resourceType', 'Patient')
   .attr('id', randomUUID())
   .attr('identifier', identifier)
   .attr('name', () => [HumanNameFactory.build()])
   .attr('gender', 'male')
   .attr('birthDate', '2000-01-01');
 
 export const EncounterFactory = Factory.define('encounter')
+  .attr('resourceType', 'Encounter')
   .attr('id', randomUUID())
   .attr('identifier', identifier)
   .attr('status', 'planned')

mediator/src/routes/cht.ts

@@ -1,7 +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'
+import { syncPatients, syncEncounters } from '../utils/openmrs_sync'
 
 const router = Router();
 
@@ -25,8 +25,12 @@ router.post(
 router.post(
   '/sync',
   requestHandler(async (req) => {
-    await syncPatients();
-    syncEncountersAndObservations();
+    async function syncAll() {
+      await syncPatients();
+      await syncEncounters();
+    }
+    // dont await, return immediately
+    syncAll();
     return { status: 200, data: {}};
   })
 );

mediator/src/utils/cht.ts

@@ -3,7 +3,8 @@ import { CHT } from '../../config';
 import { generateBasicAuthUrl } from './url';
 import https from 'https';
 import path from 'path';
-import { buildChtPatientFromFhir } from '../mappers/cht';
+import { buildChtPatientFromFhir, buildChtRecordFromObservations } from '../mappers/cht';
+import { logger } from '../../logger';
 
 type CouchDBQuery = {
     selector: Record<string, any>;
@@ -29,7 +30,13 @@ export async function createChtRecord(patientId: string) {
 
   const chtApiUrl = generateChtRecordsApiUrl(CHT.url, CHT.username, CHT.password);
 
-  return await axios.post(chtApiUrl, record, getOptions());
+  try {
+    const res = await axios.post(chtApiUrl, record, getOptions());
+    return { status: res?.status, data: res?.data };
+  } catch (error: any) {
+    logger.error(error);
+    return { status: error.status, data: error.data };
+  }
 }
 
 async function getLocation(fhirPatient: fhir4.Patient) {
@@ -105,47 +112,42 @@ export async function createChtPatient(fhirPatient: fhir4.Patient) {
   return chtRecordsApi(cht_patient);
 }
 
-export async function chtRecordFromObservations(patient_id: string, observations: any) {
-  const record: any = {
-    _meta: {
-      form: "openmrs_anc"
-    },
-    patient_id: patient_id
-  }
-
-  for (const entry of observations.entry) {
-    if (entry.resource.resourceType == 'Observation') {
-      const code:string = entry.resource.code.coding[0].code;
-      if (entry.resource.valueCodeableConcept) {
-        record[code.toLowerCase()] = entry.resource.valueCodeableConcept.text;
-      } else if (entry.resource.valueDateTime) {
-        record[code.toLowerCase()] = entry.resource.valueDateTime.split('T')[0];
-      }
-    }
-  }
-
+export async function chtRecordFromObservations(patient: fhir4.Patient, observations: fhir4.Observation[]) {
+  const record = buildChtRecordFromObservations(patient, observations);
   return chtRecordsApi(record);
 }
 
-export async function updateChtDocument(doc: any, update_object: any) {
-  const chtApiUrl = generateChtDBUrl(CHT.url, CHT.username, CHT.password);
-  const updated_doc = { ...doc, ...update_object }
-  return await axios.put(path.join(chtApiUrl, doc._id), updated_doc, getOptions());
-}
-
 export async function chtRecordsApi(doc: any) {
   const chtApiUrl = generateChtRecordsApiUrl(CHT.url, CHT.username, CHT.password);
-  return await axios.post(chtApiUrl, doc, getOptions());
+  try {
+    const res = await axios.post(chtApiUrl, doc, getOptions());
+    return { status: res?.status, data: res?.data };
+  } catch (error: any) {
+    logger.error(error);
+    return { status: error.status, data: error.data };
+  }
 }
 
 export async function getChtDocumentById(doc_id: string) {
   const chtApiUrl = generateChtDBUrl(CHT.url, CHT.username, CHT.password);
-  return await axios.get(path.join(chtApiUrl, doc_id), getOptions());
+  try {
+    const res = await axios.get(path.join(chtApiUrl, doc_id), getOptions());
+    return { status: res?.status, data: res?.data };
+  } catch (error: any) {
+    logger.error(error);
+    return { status: error.status, data: error.data };
+  }
 }
 
 export async function queryCht(query: any) {
   const chtApiUrl = generateChtDBUrl(CHT.url, CHT.username, CHT.password);
-  return await axios.post(path.join(chtApiUrl, '_find'), query, getOptions());
+  try {
+    const res = await axios.post(path.join(chtApiUrl, '_find'), query, getOptions());
+    return { status: res?.status, data: res?.data };
+  } catch (error: any) {
+    logger.error(error);
+    return { status: error.status, data: error.data };
+  }
 }
 
 export const generateChtRecordsApiUrl = (chtUrl: string, username: string, password: string) => {

mediator/src/utils/fhir.ts

@@ -114,21 +114,21 @@ export async function getFHIRPatients(lastUpdated: Date) {
   );
 }
 
-export function copyIdToNamedIdentifier(fromResource: any, toResource: fhir4.Patient | fhir4.Encounter, fromIDType: fhir4.CodeableConcept){
+export function copyIdToNamedIdentifier(fromResource: any, toResource: fhir4.Patient | fhir4.Encounter, fromIdType: fhir4.CodeableConcept){
   const identifier: fhir4.Identifier = {
-    type: fromIDType,
+    type: fromIdType,
     value: fromResource.id,
     use: "secondary"
   };
-  const sameIdType = (id: any) => (id.type.text === fromIDType.text)
+  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 | fhir4.Encounter, idType: fhir4.CodeableConcept): string{
-  return resource.identifier?.find((id: any) => id?.type.text == idType.text)?.value || '';
+  return resource?.identifier?.find((id: any) => id?.type.text == idType.text)?.value || '';
 }
 
 export function addId(resource: fhir4.Patient | fhir4.Encounter, idType: fhir4.CodeableConcept, value: string){
@@ -140,6 +140,14 @@ export function addId(resource: fhir4.Patient | fhir4.Encounter, idType: fhir4.C
   return resource;
 }
 
+export function replaceReference(resource: any, referenceKey: string, referred: fhir4.Resource) {
+  const newReference: fhir4.Reference = {
+    reference: `${referred.resourceType}/${referred.id}`,
+    type: referred.resourceType
+  }
+  resource[referenceKey] = newReference;
+}
+
 export async function getFHIRLocation(locationId: string) {
   return await axios.get(
     `${FHIR.url}/Patient/?identifier=${locationId}`,
@@ -152,13 +160,7 @@ export async function deleteFhirSubscription(id?: string) {
 
 export async function createFhirResource(doc: fhir4.Resource) {
   try {
-    const res = await axios.post(`${FHIR.url}/${doc.resourceType}`, doc, {
-      auth: {
-        username: FHIR.username,
-        password: FHIR.password,
-      },
-    });
-
+    const res = await axios.post(`${FHIR.url}/${doc.resourceType}`, doc, axiosOptions);
     return { status: res.status, data: res.data };
   } catch (error: any) {
     logger.error(error);
@@ -168,12 +170,7 @@ export async function createFhirResource(doc: fhir4.Resource) {
 
 export async function updateFhirResource(doc: fhir4.Resource) {
   try {
-    const res = await axios.put(`${FHIR.url}/${doc.resourceType}/${doc.id}`, doc, {
-      auth: {
-        username: FHIR.username,
-        password: FHIR.password,
-      },
-    });
+    const res = await axios.put(`${FHIR.url}/${doc.resourceType}/${doc.id}`, doc, axiosOptions); 
 
     return { status: res?.status, data: res?.data };
   } catch (error: any) {
@@ -184,10 +181,12 @@ export async function updateFhirResource(doc: fhir4.Resource) {
 
 export async function getFhirResourcesSince(lastUpdated: Date, resourceType: string) {
   try {
-    const res = await axios.get(
-      `${FHIR.url}/${resourceType}/?_lastUpdated=gt${lastUpdated.toISOString()}`,
-      axiosOptions
-    );
+    let url = `${FHIR.url}/${resourceType}/?_lastUpdated=gt${lastUpdated.toISOString()}`;
+    // for encounters, include related resources
+    if (resourceType === 'Encounter') {
+      url = url + '&_revinclude=Observation:encounter&_include=Encounter:patient';
+    }
+    const res = await axios.get(url, axiosOptions);
     return { status: res?.status, data: res?.data };
   } catch (error: any) {
     logger.error(error);

mediator/src/utils/openmrs.ts

@@ -18,10 +18,12 @@ export async function getOpenMRSPatientResource(patientId: string) {
 
 export async function getOpenMRSResourcesSince(lastUpdated: Date, resourceType: string) {
   try {
-    const res = await axios.get(
-      `${OPENMRS.url}/${resourceType}/?_lastUpdated=gt${lastUpdated.toISOString()}`,
-      axiosOptions
-    );
+    let url = `${OPENMRS.url}/${resourceType}/?_lastUpdated=gt${lastUpdated.toISOString()}`;
+    // for encounters, include related resources
+    if (resourceType === 'Encounter') {
+      url = url + '&_revinclude=Observation:encounter&_include=Encounter:patient';
+    }
+    const res = await axios.get(url, axiosOptions);
     return { status: res.status, data: res.data };
   } catch (error: any) {
     logger.error(error);
@@ -31,13 +33,7 @@ export async function getOpenMRSResourcesSince(lastUpdated: Date, resourceType:
 
 export async function createOpenMRSResource(doc: fhir4.Resource) {
   try {
-    const res = await axios.post(`${OPENMRS.url}/${doc.resourceType}`, doc, {
-      auth: {
-        username: OPENMRS.username,
-        password: OPENMRS.password,
-      },
-    });
-
+    const res = await axios.post(`${OPENMRS.url}/${doc.resourceType}`, doc, axiosOptions);
     return { status: res.status, data: res.data };
   } catch (error: any) {
     logger.error(error);
@@ -47,13 +43,7 @@ export async function createOpenMRSResource(doc: fhir4.Resource) {
 
 export async function updateOpenMRSResource(doc: fhir4.Resource) {
   try {
-    const res = await axios.put(`${OPENMRS.url}/${doc.resourceType}/${doc.id}`, doc, {
-      auth: {
-        username: OPENMRS.username,
-        password: OPENMRS.password,
-      },
-    });
-
+    const res = await axios.post(`${OPENMRS.url}/${doc.resourceType}/${doc.id}`, doc, axiosOptions);
     return { status: res.status, data: res.data };
   } catch (error: any) {
     logger.error(error);