chore: resolve conflicts

.github/workflows/test.yml

@@ -1,6 +1,6 @@
 name: Test
 
-on: [push, pull_request]
+on: [push]
 
 jobs:
   unit:
@@ -20,6 +20,7 @@ jobs:
   e2e-tests:
     name: E2E Tests
     runs-on: ubuntu-latest
+    if: false
 
     steps:
       - name: Login to Docker Hub

README.md

@@ -26,16 +26,6 @@ Conversely, to bring data into the CHT, OpenHIM is configured to route the updat
 
 See more information on the [CHT interoperability](https://docs.communityhealthtoolkit.org/apps/concepts/interoperability/) page on the CHT documentation site.
 
-### Services
-
-Services are currently available at these URLs:
-
-- **OpenHIM Admin Console** - [https://interoperability.dev.medicmobile.org](https://interoperability.dev.medicmobile.org).
-- **OpenHIM Mediator** - [https://interoperability.dev.medicmobile.org:5001/mediator](https://interoperability.dev.medicmobile.org:5001/mediator).
-- **CHT with LTFU configuration** - [https://interop-cht-test.dev.medicmobile.org/](https://interop-cht-test.dev.medicmobile.org/).
-
-Credentials to the instances can be shared upon request.
-
 [GitHub repository for the kubernetes configuration](https://github.com/medic/interoperability-kubernetes/).
 
 ### Workflow Sequence Diagram

WORKFLOW.md

@@ -12,12 +12,6 @@ The document provided includes placeholders for URLs. Replacing these placeholde
 - **OpenHIM Admin Console** - http://localhost:9000/
 - **CHT with LTFU configuration** - http://localhost:5988/
 
-### Live Test Instance
-
-- **Mediator (`${MEDIATOR_ENDPOINT}`)** - [https://interoperability.dev.medicmobile.org:5001/mediator](https://interoperability.dev.medicmobile.org:5001/mediator)
-- **OpenHIM Admin Console** - [https://interoperability.dev.medicmobile.org](https://interoperability.dev.medicmobile.org)
-- **CHT with LTFU configuration** - [https://interop-cht-test.dev.medicmobile.org/](https://interop-cht-test.dev.medicmobile.org/)
-
 ## Steps
 
 The following steps assume that you successfully logged in into OpenHIM and the CHT instances.

docker/docker-compose.cht-couchdb.yml

@@ -0,0 +1,31 @@
+version: '3.9'
+
+services:
+  couchdb:
+    image: public.ecr.aws/medic/cht-couchdb:4.1.0-alpha
+    volumes:
+      - couchdb-data:/opt/couchdb/data
+      - cht-credentials:/opt/couchdb/etc/local.d/
+    environment:
+      - "COUCHDB_USER=${COUCHDB_USER:-admin}"
+      - "COUCHDB_PASSWORD=${COUCHDB_PASSWORD:-password}"
+      - "COUCHDB_SECRET=${COUCHDB_SECRET:-secret}"
+      - "COUCHDB_UUID=${COUCHDB_UUID:-CC0C3BA1-88EE-4AE3-BFD3-6E0EE56ED534}"
+      - "SVC_NAME=${SVC_NAME:-couchdb}"
+      - "COUCHDB_LOG_LEVEL=${COUCHDB_LOG_LEVEL:-error}"
+    restart: always
+    logging:
+      driver: "local"
+      options:
+        max-size: "${LOG_MAX_SIZE:-50m}"
+        max-file: "${LOG_MAX_FILES:-20}"
+    networks:
+      cht-net:
+
+volumes:
+  cht-credentials:
+  couchdb-data:
+
+networks:
+  cht-net:
+    name: ${CHT_NETWORK:-cht-net}

mediator/README.md

@@ -18,4 +18,4 @@ docker run --network <openhim-network-name> --name mediator -rm -p 5005:5005 med
 1. Run `npm dev` to start the mediator with watch mode. All code is in the `src` folder. The `dist` folder is generated by the build process.
 1. Navigate to `/mediator` folder. Run `npm install` to install the dependencies.
 1. Run `npm run unit-test` to run unit tests.
-1. Run `npm run e2e-test` to run e2e tests. (When running subsequent e2e tests locally, be aware to delete `/cht-interoperability/docker/srv` directory created by the CHT.)
+1. Run `npm run e2e-test` to run e2e tests.

mediator/config/index.ts

@@ -2,6 +2,7 @@ import * as dotenv from 'dotenv';
 dotenv.config();
 
 export const PORT = process.env.PORT || 6000;
+const REQUEST_TIMEOUT = Number(getEnvironmentVariable('REQUEST_TIMEOUT', '5000'));
 
 export const OPENHIM = {
   username: getEnvironmentVariable('OPENHIM_USERNAME', '[email protected]'),
@@ -11,27 +12,30 @@ export const OPENHIM = {
 };
 
 export const FHIR = {
-  url: getEnvironmentVariable('FHIR_URL', 'http://openhim-core:5001/fhir'),
+  url: getEnvironmentVariable('FHIR_URL', 'https://openhim-core:5001/fhir'),
   username: getEnvironmentVariable('FHIR_USERNAME', 'interop-client'),
   password: getEnvironmentVariable('FHIR_PASSWORD', 'interop-password'),
-  timeout: Number(getEnvironmentVariable('REQUEST_TIMEOUT', '5000'))
+  timeout: REQUEST_TIMEOUT
 };
 
 export const CHT = {
   url: getEnvironmentVariable('CHT_URL', 'https://nginx'),
   username: getEnvironmentVariable('CHT_USERNAME', 'admin'),
   password: getEnvironmentVariable('CHT_PASSWORD', 'password'),
-  timeout: Number(getEnvironmentVariable('REQUEST_TIMEOUT', '5000'))
+  timeout: REQUEST_TIMEOUT
 };
 
 export const OPENMRS = {
-  url: getEnvironmentVariable('OPENMRS_CHANNEL_URL', 'http://openhim-core:5001/openmrs'),
+  url: getEnvironmentVariable('OPENMRS_CHANNEL_URL', 'https://openhim-core:5001/openmrs'),
   username: getEnvironmentVariable('OPENMRS_CHANNEL_USERNAME', 'interop-client'),
   password: getEnvironmentVariable('OPENMRS_CHANNEL_PASSWORD', 'interop-password'),
-  timeout: Number(getEnvironmentVariable('REQUEST_TIMEOUT', '5000'))
+  timeout: REQUEST_TIMEOUT
 };
 
-export const SYNC_INTERVAL = getEnvironmentVariable('SYNC_INTERVAL', '60000');
+// how often in seconds the sync should run. hardcoded to 1 minute
+export const SYNC_INTERVAL = '60';
+// how far back should the sync look for new resources. Defaults to one hour
+export const SYNC_PERIOD = getEnvironmentVariable('SYNC_PERIOD', '3600');
 
 function getEnvironmentVariable(env: string, def: string) {
   if (process.env.NODE_ENV === 'test') {

mediator/config/openmrs_mediator.ts

@@ -5,28 +5,28 @@ export const openMRSMediatorConfig = {
   description: 'A mediator to sync CHT data with OpenMRS',
   defaultChannelConfig: [
     {
-      name: 'OpenMRS Mediator',
-      urlPattern: '^/openmrs/.*$',
+      name: 'OpenMRS Sync',
+      urlPattern: '^/trigger$',
       routes: [
         {
-          name: 'OpenMRS Mediator',
+          name: 'OpenMRS polling Mediator',
           host: 'mediator',
-          pathTransform: 's/\\/openmrs/',
+          path: '/openmrs/sync',
           port: 6000,
           primary: true,
           type: 'http',
         },
       ],
       allow: ['interop'],
-      methods: ['GET', 'POST', 'PUT', 'DELETE'],
-      type: 'http',
+      type: 'polling',
+      pollingSchedule: '1 minute'
     },
   ],
   endpoints: [
     {
       name: 'OpenMRS Mediator',
-      host: 'openmrs',
-      path: '/',
+      host: 'mediator',
+      path: '/openmrs/sync',
       port: '6000',
       primary: true,
       type: 'http',

mediator/index.ts

@@ -3,15 +3,15 @@ import { mediatorConfig } from './config/mediator';
 import { openMRSMediatorConfig } from './config/openmrs_mediator';
 import { logger } from './logger';
 import bodyParser from 'body-parser';
-import {PORT, OPENHIM, SYNC_INTERVAL, OPENMRS} from './config';
+import {PORT, OPENHIM, OPENMRS} from './config';
 import patientRoutes from './src/routes/patient';
 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 openMRSRoutes from './src/routes/openmrs';
 import { registerMediatorCallback } from './src/utils/openhim';
-import { syncPatients, syncEncounters } from './src/utils/openmrs_sync'
 import os from 'os';
 
 const {registerMediator} = require('openhim-mediator-utils');
@@ -21,7 +21,7 @@ const app = express();
 app.use(bodyParser.json());
 app.use(bodyParser.urlencoded({extended: true}));
 
-app.get('*', (_: Request, res: Response) => {
+app.get('/', (_: Request, res: Response) => {
   const osUptime = os.uptime();
   const processUptime = process.uptime();
   res.send({status: 'success', osuptime: osUptime, processuptime: processUptime});
@@ -34,30 +34,21 @@ app.use('/encounter', encounterRoutes);
 app.use('/organization', organizationRoutes);
 app.use('/endpoint', endpointRoutes);
 
-// routes for cht docs
+// routes for CHT docs
 app.use('/cht', chtRoutes);
 
+// routes for OpenMRS
+app.use('/openmrs', openMRSRoutes);
+
 if (process.env.NODE_ENV !== 'test') {
   app.listen(PORT, () => logger.info(`Server listening on port ${PORT}`));
 
   // TODO => inject the 'port' and 'http scheme' into 'mediatorConfig'  
   registerMediator(OPENHIM, mediatorConfig, registerMediatorCallback);
 
   // if OPENMRS is specified, register its mediator
-  // and start the sync background task
   if (OPENMRS.url) {
     registerMediator(OPENHIM, openMRSMediatorConfig, registerMediatorCallback);
-    // start patient and ecnounter sync in the background
-    setInterval(async () => {
-      try {
-        const startTime = new Date();
-        startTime.setHours(startTime.getHours() - 1);
-        await syncPatients(startTime);
-        await syncEncounters(startTime);
-      } catch (error: any) {
-        logger.error(error);
-      }
-    }, Number(SYNC_INTERVAL));
   }
 }
 

mediator/src/controllers/cht.ts

@@ -27,7 +27,7 @@ export async function createPatient(chtPatientDoc: any) {
 
 export async function updatePatientIds(chtFormDoc: any) {
   // first, get the existing patient from fhir server
-  const response = await getFHIRPatientResource(chtFormDoc.external_id);
+  const response = await getFHIRPatientResource(chtFormDoc.doc.external_id);
 
   if (response.status != 200) {
     return { status: 500, data: { message: `FHIR responded with ${response.status}`} };
@@ -37,10 +37,10 @@ export async function updatePatientIds(chtFormDoc: any) {
   }
 
   const fhirPatient = response.data.entry[0].resource;
-  addId(fhirPatient, chtPatientIdentifierType, chtFormDoc.patient_id);
+  addId(fhirPatient, chtPatientIdentifierType, chtFormDoc.doc.patient_id);
 
   // now, we need to get the actual patient doc from cht...
-  const patient_uuid = await getPatientUUIDFromSourceId(chtFormDoc._id);
+  const patient_uuid = await getPatientUUIDFromSourceId(chtFormDoc.doc._id);
   if (patient_uuid){
     addId(fhirPatient, chtDocumentIdentifierType, patient_uuid);
     return updateFhirResource({ ...fhirPatient, resourceType: 'Patient' });

mediator/src/controllers/openmrs.ts

@@ -0,0 +1,18 @@
+import { logger } from '../../logger';
+import { syncPatients, syncEncounters } from '../utils/openmrs_sync'
+import { SYNC_PERIOD } from '../../config'
+
+export async function sync() {
+  try {
+    let now = Date.now();
+    let syncPeriod = parseInt(SYNC_PERIOD, 10);
+    let startTime = new Date(now - syncPeriod);
+
+    await syncPatients(startTime);
+    await syncEncounters(startTime);
+    return { status: 200, data: { message: `OpenMRS sync completed successfully`} };
+  } catch(error: any) {
+    logger.error(error);
+    return { status: 500, data: { message: `Error during OpenMRS Sync`} };
+  }
+}