feat(#114): Create OpenMRS Mediator

docker/docker-compose.mediator.yml

@@ -16,6 +16,9 @@ services:
       - "FHIR_URL=${FHIR_URL:-http://openhim-core:5001/fhir}"
       - "FHIR_USERNAME=${FHIR_USERNAME:-interop-client}"
       - "FHIR_PASSWORD=${FHIR_PASSWORD:-interop-password}"
+      - "OPENMRS_URL=${OPENMRS_URL:-http://openhim-core:5001/openmrs}"
+      - "OPENMRS_USERNAME=${OPENMRS_USERNAME:-interop-client}"
+      - "OPENMRS_PASSWORD=${OPENMRS_PASSWORD:-interop-password}"
       - "CHT_URL=${CHT_URL:-https://nginx}"
       - "CHT_USERNAME=${CHT_USERNAME:-admin}"
       - "CHT_PASSWORD=${CHT_PASSWORD:-password}"

docker/docker-compose.openmrs-poller.yml

@@ -0,0 +1,15 @@
+version: '3.9'
+
+services:
+  openmrs-poller:
+    build: ../openmrs-poller
+    container_name: openmrs-poller
+    networks:
+      - cht-net
+    environment:
+      - OPENMRS_URL=${OPENMRS_URL}
+      - OPENMRS_USER=${OPENMRS_USER}
+      - OPENMRS_PASSWORD=${OPENMRS_PASSWORD}
+      - OPENHIM_URL=${OPENHIM_URL}
+      - OPENHIM_USER=${OPENHIM_USER}
+      - OPENHIM_PASSWORD=${OPENHIM_PASSWORD}

docs/sequence-diagram/cht-form-submission.txt

@@ -0,0 +1,31 @@
+title CHT Form Submission
+
+participant CHT
+
+participantgroup 
+participant OpenHIM
+participant Mediator
+participant FHIR Server
+end
+
+participant Requesting System
+autoactivation on
+box over CHT: Form submission in CHT
+box over CHT: Outbound push\nrecognizes a\ntracked form was submitted
+CHT->OpenHIM: Outbound push POSTS Data Record\nDocument to OpenHim
+OpenHIM->Mediator:
+box over Mediator: Mediator creates Encounter FHIR
+box over Mediator: Mediator creates Observation FHIR Resources\nfrom the fields in the data record document
+box over Mediator: Mediator creates Bundle\nfrom Encounter and Observations
+Mediator->FHIR Server: POST Encounter Bundle
+box over FHIR Server: FHIR Server saves\nthe resources in the Bundle
+FHIR Server-->Mediator: FHIR Bundle Response
+Mediator-->OpenHIM: 200 Response (no body)
+OpenHIM-->CHT: 200 Response (no body)
+destroysilent CHT
+box over Requesting System: Any FHIR Compliant Server\nthat has been set up as a client\nin OpenHIM can now request\nEncounter or Observation records from CHT
+Requesting System->OpenHIM: GET FHIR Encounter
+OpenHIM->FHIR Server: GET FHIR Encounter
+FHIR Server-->OpenHIM: FHIR Searchset response
+OpenHIM-->Requesting System: FHIR Searchset Response
+autoactivation off

docs/sequence-diagram/cht-incoming-forms.txt

@@ -0,0 +1,32 @@
+title CHT Incoming Forms
+
+participant Requesting System
+
+participantgroup
+participant OpenHIM
+participant Mediator
+participant FHIR Server
+end
+
+participant CHT
+
+autoactivation on
+box over Requesting System: A FHIR Encounter\nwith Observations is created
+activate Mediator
+Mediator->Requesting System: Mediator GETs FHIR Encounters
+Requesting System-->Mediator: FHIR Searchset Response
+Mediator->Requesting System: Mediator GETs FHIR Observations
+Requesting System-->Mediator: FHIR Searchset Response
+Mediator->FHIR Server: Mediator GETs FHIR Encounters
+FHIR Server-->Mediator: FHIR Searchset Response
+Mediator->FHIR Server: Mediator GETs FHIR Observations
+FHIR Server-->Mediator: FHIR Searchset Response
+box over Mediator: Mediator compares Resources from\nFHIR Server and Requesting System
+box over Mediator: Encounters found in Requesting System but\nnot in Requesting System are sent to CHT
+box over Mediator: Mediator converts FHIR Observations\n for each Encounter into form fields
+Mediator->CHT: Mediator POSTS to the records API
+box over CHT: CHT saves a data_record\nwith the data from the patient\ncreation form
+CHT-->Mediator: CHT Responds with source record id.
+deactivate Mediator
+autoactivation off
+

docs/sequence-diagram/cht-incoming-patients.txt

@@ -0,0 +1,38 @@
+title CHT Incoming Patients
+
+participant Requesting System
+
+participantgroup
+participant OpenHIM
+participant Mediator
+participant FHIR Server
+end
+
+participant CHT
+
+autoactivation on
+box over Requesting System: A FHIR Patient is created
+Mediator->Requesting System: Mediator GETs FHIR Patients
+activate Mediator
+Requesting System-->Mediator: FHIR Searchset Response
+Mediator->FHIR Server: Mediator GETs FHIR Patients
+FHIR Server-->Mediator: FHIR Searchset Response
+box over Mediator: Mediator compares Resources from\nFHIR Server and Requesting System
+box over Mediator: Patients found in FHIR Serverbut\nnot in Requesting System are sent to Requesting System
+Mediator->CHT: Mediator POSTS to the records API
+box over CHT: CHT saves a data_record\nwith the data from the patient\ncreation form
+CHT-->Mediator: CHT Responds with source record id.
+deactivate Mediator
+box over CHT: CHT creates a patient document
+box over CHT: CHT adds parent using place_id
+box over CHT: CHT adds patient_id and other fields with transitions
+CHT->OpenHIM: Outbound push recognizes new patient and sends
+OpenHIM->Mediator: 
+Mediator->FHIR Server: GET FHIR Patient\nusing external_id
+FHIR Server-->Mediator: FHIR Patient
+box over Mediator: Mediator adds CHT and Medic ID
+Mediator->FHIR Server: PUT FHIR Patient\nwith updated ids
+FHIR Server-->Mediator:
+Mediator-->OpenHIM:
+OpenHIM-->CHT:
+autoactivation off

docs/sequence-diagram/cht-outgoing-patients.txt

@@ -0,0 +1,25 @@
+title CHT Outgoing Patients
+
+participant Requesting System
+
+participantgroup 
+participant OpenHIM
+participant Mediator
+participant FHIR Server
+end
+
+autoactivation on
+box over Requesting System: A FHIR Patient is created
+Mediator->Requesting System: Mediator GETs FHIR Patients
+activate Mediator
+Requesting System-->Mediator: FHIR Searchset Response 
+Mediator->FHIR Server: Mediator GETs FHIR Patients
+FHIR Server-->Mediator: FHIR Searchset Response
+box over Mediator: Mediator compares Resources from\nFHIR Server and Requesting System
+box over Mediator: Patients found in FHIR Serverbut\nnot in Requesting System are sent to Requesting System 
+Mediator->Requesting System: Mediator POSTS new Patients
+Requesting System-->Mediator: FHIR Patient Response\n(w/ Requesting System ids)
+Mediator->FHIR Server: Mediator PUTS Patient\nw/ updated ids from requesting System
+FHIR Server-->Mediator:
+deactivate Mediator
+autoactivation off

docs/sequence-diagram/cht-patient-creation.txt

@@ -0,0 +1,29 @@
+title CHT Patient Creation
+
+participant CHT
+
+participantgroup 
+participant OpenHIM
+participant Mediator
+participant FHIR Server
+end
+
+participant Requesting System
+autoactivation on
+box over CHT: Patient is created in CHT
+box over CHT: Outbound push\nrecognizes changes
+CHT->OpenHIM: Outbound push POSTS Patient\nDocument to OpenHim
+OpenHIM->Mediator:
+box over Mediator: Mediator converts Patient\nDocument to FHIR Patient
+Mediator->FHIR Server: POST Patient FHIR
+box over FHIR Server: FHIR Server saves\nthe Patient FHIR
+FHIR Server-->Mediator: FHIR Patient Response
+Mediator-->OpenHIM: 200 Response (no body)
+OpenHIM-->CHT: 200 Response (no body)
+destroysilent CHT
+box over Requesting System: Any FHIR Compliant Server\nthat has been set up as a client\nin OpenHIM can now request\nPatient records from CHT
+Requesting System->OpenHIM: GET FHIR Patient
+OpenHIM->FHIR Server: GET FHIR Patient
+FHIR Server-->OpenHIM: FHIR Searchset response
+OpenHIM-->Requesting System: FHIR Searchset Response
+autoactivation off

mediator/config/index.ts

@@ -22,6 +22,11 @@ export const CHT = {
   password: getEnvironmentVariable('CHT_PASSWORD', 'password'),
 };
 
+export const OPENMRS = {
+  url: getEnvironmentVariable('OPENMRS_URL', 'http://openhim-core:5001/openmrs'),
+  username: getEnvironmentVariable('OPENMRS_USERNAME', 'interop-client'),
+  password: getEnvironmentVariable('OPENMRS_PASSWORD', 'interop-password'),
+};
 
 function getEnvironmentVariable(env: string, def: string) {
   if (process.env.NODE_ENV === 'test') {

mediator/index.ts

@@ -8,6 +8,7 @@ import serviceRequestRoutes from './src/routes/service-request';
 import encounterRoutes from './src/routes/encounter';
 import organizationRoutes from './src/routes/organization';
 import endpointRoutes from './src/routes/endpoint';
+import chtRoutes from './src/routes/cht';
 import { registerMediatorCallback } from './src/utils/openhim';
 import os from 'os';
 
@@ -24,12 +25,16 @@ app.get('*', (_: Request, res: Response) => {
   res.send({status: 'success', osuptime: osUptime, processuptime: processUptime});
 });
 
+// routes for valid fhir resources
 app.use('/patient', patientRoutes);
 app.use('/service-request', serviceRequestRoutes);
 app.use('/encounter', encounterRoutes);
 app.use('/organization', organizationRoutes);
 app.use('/endpoint', endpointRoutes);
 
+// routes for cht docs
+app.use('/cht', chtRoutes);
+
 if (process.env.NODE_ENV !== 'test') {
   app.listen(PORT, () => logger.info(`Server listening on port ${PORT}`));
 

mediator/src/controllers/cht.ts

@@ -0,0 +1,65 @@
+import {
+  createFhirResource,
+  updateFhirResource,
+  getFHIRPatientResource,
+  addId
+} from '../utils/fhir';
+import {
+  buildFhirObservationFromCht,
+  buildFhirEncounterFromCht,
+  buildFhirPatientFromCht,
+  chtPatientIdentifierType,
+  chtDocumentIdentifierType
+} from '../mappers/cht';
+import { getPatientUUIDFromSourceId } from '../utils/cht';
+
+export async function createPatient(chtPatientDoc: any) {
+  // hack for sms forms: if source_id but not _id,
+  // first get patient id from source
+  if (chtPatientDoc.doc.source_id){
+    chtPatientDoc.doc._id = await getPatientUUIDFromSourceId(chtPatientDoc.source_id);
+  }
+
+  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
+  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);
+
+  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`} };
+  }
+
+  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' });
+}
+
+export async function createEncounter(chtReport: any) {
+  const fhirEncounter = buildFhirEncounterFromCht(chtReport);
+
+  const bundle: fhir4.Bundle = {
+    resourceType: 'Bundle',
+    type: 'collection',
+    entry: [fhirEncounter]
+  }
+
+  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);
+    }
+  }
+  return createFhirResource(bundle);
+}