Merge branch 'CU-86bygcqxd_Images-Placement-for-DataStore-Dashboards-…

…Monitoring' of github.com:jembi/platform into CU-86bygcqxd_Images-Placement-for-DataStore-Dashboards-Monitoring

.env.cluster

@@ -88,18 +88,18 @@ GF_SERVER_DOMAIN=grafana.domain
 KC_POSTGRES_REPLICA_SET=pgpool-1:5432,pgpool-2:5432,pgpool-3:5432
 
 # Client Registry - JeMPI
-JEMPI_WEB_INSTANCES=3
+JEMPI_WEB_INSTANCES=1
 REACT_APP_JEMPI_BASE_API_HOST=https://jempi-api.domain
 REACT_APP_JEMPI_BASE_API_PORT=50000
 JEMPI_SESSION_SECURE=true
-JEMPI_REPMGR_PARTNER_NODES=jempi-postgresql-01,jempi-postgresql-02,jempi-postgresql-03
+JEMPI_REPMGR_PARTNER_NODES=jempi-postgresql-01
 JEMPI_ASYNC_RECEIVER_INSTANCES=1
 JEMPI_SYNC_RECEIVER_INSTANCES=1
 JEMPI_PRE_PROCESSOR_INSTANCES=1
 JEMPI_CONTROLLER_INSTANCES=1
 JEMPI_EM_CALCULATOR_INSTANCES=1
 JEMPI_LINKER_INSTANCES=1
-JEMPI_API_INSTANCES=3
+JEMPI_API_INSTANCES=1
 
 # Resource limits
 OPENHIM_MEMORY_LIMIT=4G

.github/workflows/docker-publish.yml

@@ -11,25 +11,33 @@ jobs:
   build-and-push:
     runs-on: ubuntu-20.04
     steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v3
 
       - name: Login to DockerHub
-        uses: docker/login-action@v1
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build and push tag
         if: ${{ github.ref_name != 'main' }}
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
+          platforms: linux/amd64,linux/arm64
           push: true
           tags: jembi/platform:${{ github.ref_name }}
 
       - name: Build and push latest
         if: ${{ github.ref_name == 'main' }}
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v5
         with:
+          platforms: linux/amd64,linux/arm64
           push: true
           tags: jembi/platform:latest

Dockerfile

@@ -1,4 +1,4 @@
-FROM openhie/package-base:2.3.1
+FROM openhie/package-base:2.3.2
 
 # Install yq
 RUN curl -L https://github.com/mikefarah/yq/releases/download/v4.23.1/yq_linux_amd64 -o /usr/bin/yq

README.md

@@ -71,6 +71,13 @@ Each service's resource allocations can be piped into their .yml file through en
 - Take note to not allocate less memory to ELK Stack services than their JVM heap sizes.
 - Exit code 137 indicates an out-of-memory failure. When running into this, it means that the service has been allocated too little memory.
 
+## Build multi-platform docker images
+It's essential to make sure that any docker image should be available for multiple platforms : AMD, ARM, ... (not only linux, but MacOS as well). To do so you can follow the steps below :
+1. Create your own custom builder by running `docker buildx create --name mycustombuilder --driver docker-container --bootstrap`
+2. Ask docker to use this new builder for future builds by running `docker buildx use mycustombuilder`
+3. Inspect buildx to see if docker has indeed switched builders to the new one you asked it to use by running `docker buildx inspect`
+4. Then you can perform the build and push, for example : `docker buildx build --platform linux/amd64,linux/arm64 --push -t jembi/hapi:v7.0.3-wget  .`
+
 ## Tests
 
 Tests are located in `/test`

client-registry-jempi/docker-compose.api.yml

@@ -33,6 +33,7 @@ services:
       reverse-proxy:
       kafka:
       default:
+      jempi:
 
 
   jempi-api-kc:
@@ -77,6 +78,7 @@ services:
       reverse-proxy:
       kafka:
       default:
+      jempi:
 
 
 volumes:
@@ -87,6 +89,9 @@ networks:
   reverse-proxy:
     name: reverse-proxy_public
     external: true
+  jempi:
+    name: jempi_public
+    external: true
   kafka:
     name: kafka_public
     external: true

client-registry-jempi/docker-compose.combined-cluster.yml

@@ -6,7 +6,13 @@ services:
       placement:
         constraints:
           - "node.labels.name==node-1"
-
+
+  jempi-bootstrapper:
+    deploy:
+      placement:
+        constraints:
+          - "node.labels.name==node-1"
+
   jempi-postgresql-02:
     image: bitnami/postgresql-repmgr:15.2.0
     environment:
@@ -36,6 +42,8 @@ services:
     configs:
       - target: /docker-entrypoint-initdb.d/jempi_psql_init_db.sql
         source: jempi_psql_init_db.sql
+    networks:
+      jempi:
 
   jempi-postgresql-03:
     image: bitnami/postgresql-repmgr:15.2.0
@@ -66,7 +74,14 @@ services:
     configs:
       - target: /docker-entrypoint-initdb.d/jempi_psql_init_db.sql
         source: jempi_psql_init_db.sql
+    networks:
+      jempi:
 
 volumes:
   jempi-psql-02-data:
   jempi-psql-03-data:
+
+networks:
+  jempi:
+    name: jempi_public
+    external: true

client-registry-jempi/docker-compose.combined.yml

@@ -19,6 +19,7 @@ services:
     networks:
       kafka:
       default:
+      jempi:
 
 
   jempi-etl:
@@ -37,6 +38,7 @@ services:
     networks:
       kafka:
       default:
+      jempi:
 
 
   jempi-controller:
@@ -70,6 +72,7 @@ services:
     networks:
       kafka:
       default:
+      jempi:
 
 
   jempi-linker:
@@ -104,6 +107,7 @@ services:
     networks:
       kafka:
       default:
+      jempi:
 
   jempi-bootstrapper:
     image: jembi/jempi-bootstrapper:${JEMPI_BOOTSTRAPPER_IMAGE_TAG}
@@ -124,6 +128,7 @@ services:
     networks:
       kafka:
       default:
+      jempi:
 
   jempi-postgresql-01:
     image: bitnami/postgresql-repmgr:15.2.0
@@ -151,6 +156,8 @@ services:
     configs:
       - target: /docker-entrypoint-initdb.d/jempi_psql_init_db.sql
         source: jempi_psql_init_db.sql
+    networks:
+      jempi:
 
 volumes:
   jempi-psql-01-data:
@@ -161,7 +168,10 @@ networks:
   kafka:
     name: kafka_public
     external: true
-  defualt:
+  default:
+  jempi:
+    name: jempi_public
+    external: true
 
 
 configs:

client-registry-jempi/docker-compose.dgraph-zero-cluster.yml

@@ -7,7 +7,9 @@ services:
         constraints:
           - node.labels.name == node-1
     command: dgraph zero --my=jempi-zero-01:5080 --replicas 3 --bindall --raft "idx=1"
-
+    networks:
+      jempi:
+
   jempi-zero-02:
     image: dgraph/dgraph:v22.0.0
     volumes:
@@ -25,6 +27,8 @@ services:
       restart_policy:
         condition: on-failure
     command: dgraph zero --my=jempi-zero-02:5080 --replicas 3 --peer=jempi-zero-01:5080 --raft "idx=2"
+    networks:
+      jempi:
 
   jempi-zero-03:
     image: dgraph/dgraph:v22.0.0
@@ -43,7 +47,14 @@ services:
       restart_policy:
         condition: on-failure
     command: dgraph zero --my=jempi-zero-03:5080 --replicas 3 --peer=jempi-zero-01:5080 --raft "idx=3"
+    networks:
+      jempi:
 
 volumes:
   jempi-zero-02-data:
   jempi-zero-03-data:
+
+networks:
+  jempi:
+    name: jempi_public
+    external: true

client-registry-jempi/docker-compose.dgraph-zero.yml

@@ -15,6 +15,13 @@ services:
       restart_policy:
         condition: on-failure
     command: dgraph zero --my=jempi-zero-01:5080 --replicas 1
+    networks:
+      jempi:
 
 volumes:
   jempi-zero-01-data:
+
+networks:
+  jempi:
+    name: jempi_public
+    external: true

client-registry-jempi/docker-compose.dgraph.yml

@@ -16,6 +16,8 @@ services:
       restart_policy:
         condition: on-failure
     command: dgraph alpha --my=jempi-alpha-01:7080 --zero=jempi-zero-01:5080 --security whitelist=0.0.0.0/0 --telemetry "sentry=false;"
+    networks:
+      jempi:
 
   jempi-alpha-02:
     image: dgraph/dgraph:v22.0.0
@@ -32,6 +34,8 @@ services:
       restart_policy:
         condition: on-failure
     command: dgraph alpha --my=jempi-alpha-02:7081 --zero=jempi-zero-01:5080 --security whitelist=0.0.0.0/0 -o 1 --telemetry "sentry=false;"
+    networks:
+      jempi:
 
   jempi-alpha-03:
     image: dgraph/dgraph:v22.0.0
@@ -48,6 +52,8 @@ services:
       restart_policy:
         condition: on-failure
     command: dgraph alpha --my=jempi-alpha-03:7082 --zero=jempi-zero-01:5080 --security whitelist=0.0.0.0/0 -o 2 --telemetry "sentry=false;"
+    networks:
+      jempi:
 
   jempi-ratel:
     image: dgraph/ratel:v21.03.2
@@ -61,8 +67,15 @@ services:
       restart_policy:
         condition: on-failure
     command: dgraph-ratel
+    networks:
+      jempi:
 
 volumes:
   jempi-alpha-01-data:
   jempi-alpha-02-data:
   jempi-alpha-03-data:
+
+networks:
+  jempi:
+    name: jempi_public
+    external: true

client-registry-jempi/importer/mapping-mediator/searchAll.json

@@ -9,7 +9,7 @@
   },
   "inputTransforms": {
     "total": "$count(lookupRequests.jempiSearchAll.data.goldenRecords)",
-    "entry": "$map(lookupRequests.jempiSearchAll.data.goldenRecords, function($v) {{'fullUrl': 'Patient/' & $v.goldenId, 'resource': {'resourceType': 'Patient','id': $v.goldenId,'name': {'given': [$v.demographicData.givenName],'family': $v.demographicData.familyName},'address': [{'city': $v.demographicData.city}],'birthDate': $v.demographicData.dob,'telecom': [{'value': $v.demographicData.phoneNumber,'system': 'phone'}],'identifier': [{'system': $v.sourceId.facility,'value': $v.sourceId.patient},{'system': 'NationalID','value': $v.demographicData.nationalId}],'gender': $v.demographicData.gender}}})"
+    "entry": "$append([], $map(lookupRequests.jempiSearchAll.data.goldenRecords, function($v) {{'fullUrl': 'Patient/' & $v.goldenId, 'resource': {'resourceType': 'Patient','id': $v.goldenId,'name': {'given': [$v.demographicData.givenName],'family': $v.demographicData.familyName},'address': [{'city': $v.demographicData.city}],'birthDate': $v.demographicData.dob,'telecom': [{'value': $v.demographicData.phoneNumber,'system': 'phone'}],'identifier': [{'system': $v.sourceId.facility,'value': $v.sourceId.patient},{'system': 'NationalID','value': $v.demographicData.nationalId}],'gender': $v.demographicData.gender}}}))"
   },
   "inputMapping": {
     "constants.resourceType": "resourceType",

config.yaml

@@ -24,6 +24,7 @@ packages:
   - identity-access-manager-keycloak
   - openhim-mapping-mediator
   - database-postgres
+  - reprocess-mediator
   - fhir-ig-importer
 
 profiles:
@@ -43,6 +44,8 @@ profiles:
       - openhim-mapping-mediator
       - kafka-mapper-consumer
       - kafka-unbundler-consumer
+      - fhir-ig-importer
+      - reprocess-mediator
     envFiles:
       - cdr-dw.env
 

documentation/recipes/README.md

@@ -1,13 +1,12 @@
+
 ---
 description: Pre-defined recipes for common use cases
 ---
 
 # 📜 Recipes
 
-OpenHIM platform comes bundles with a set of generic packages that can be deployed and configured to support a number of different use cases. To help users of OpenHIM Platform get started with something they can make use of immediately, a number of default OpenHIM Platform reciepes are provided. These help you get started with everything you need setup and configured for a particular use case.
-
-We current support the following default recipes:
-
+OpenHIM platform comes bundled with a set of generic packages that can be deployed and configured to support a number of different use cases. To help users of OpenHIM Platform get started with something they can make use of immediately, a number of default OpenHIM Platform recipes are provided. These help you get started with everything you need setup and configured for a particular use case.
 
+We currently support the following default recipes:
 
 <table data-view="cards"><thead><tr><th align="center"></th><th></th><th data-hidden></th><th data-hidden data-card-target data-type="content-ref"></th></tr></thead><tbody><tr><td align="center"><strong>Central Data Repository with Data Warehouse</strong></td><td>A FHIR-based Shared Health record linked to an MPI for linking and matching patient demographics and a default reporting pipeline to transform and visualise FHIR data.</td><td></td><td><a href="central-data-repository-with-data-warehousing.md">central-data-repository-with-data-warehousing.md</a></td></tr><tr><td align="center"><strong>Central Data Repository</strong></td><td>A FHIR-based Shared Health record linked to an MPI for linking and matching patient demographics. No reporting is include but all FHIR data is pushed to Kafka for external system to use.</td><td></td><td><a href="central-data-repository-no-reporting.md">central-data-repository-no-reporting.md</a></td></tr><tr><td align="center"><strong>Master Patient Index</strong></td><td>A master patient index setup using JeMPI. it also includes OpenHIM as the API gateway providing security, a mapping mediator to allow FHIR-based communication with JeMPI and Keycloak to support user management.</td><td></td><td><a href="master-patient-index.md">master-patient-index.md</a></td></tr></tbody></table>

fhir-ig-importer/docker-compose.dev.yml

@@ -10,5 +10,5 @@ services:
   fhir-ig-importer-ui:
     ports:
       - target: 8080
-        published: 3000
+        published: 3334
         mode: host

fhir-ig-importer/docker-compose.yml

@@ -6,6 +6,7 @@ services:
     networks:
       hapi-fhir:
       openhim:
+      default:
     environment:
       HAPI_FHIR_BASE_URL: ${HAPI_FHIR_BASE_URL}
       HAPI_FHIR_INSTANCES: ${HAPI_FHIR_INSTANCES}
@@ -27,4 +28,5 @@ networks:
   openhim:
     name: openhim_public
     external: true
+  default:
 

fhir-ig-importer/importer/docker-compose.config.yml

@@ -18,6 +18,8 @@ services:
         target: /openhimConfig.js
       - source: fhir-ig-importer-config-importer-openhim-import.json
         target: /openhim-import.json
+      - source: fhir-ig-importer-config-importer-ig-importer-app.json
+        target: /ig-importer-app.json
     deploy:
       replicas: 1
       restart_policy:
@@ -34,8 +36,14 @@ configs:
     name: fhir-ig-importer-config-importer-openhim-import.json-${fhir_ig_importer_config_importer_openhim_import_js_DIGEST:?err}
     labels:
       name: fhir-ig-importer
+  fhir-ig-importer-config-importer-ig-importer-app.json:
+    file: ./volume/ig-importer-app.json
+    name: fhir-ig-importer-config-importer-ig-importer-app.json-${fhir_ig_importer_config_importer_ig_importer_app_DIGEST:?err}
+    labels:
+      name: fhir-ig-importer
 
 networks:
   openhim:
     name: openhim_public
     external: true
+  default:

fhir-ig-importer/importer/volume/ig-importer-app.json

@@ -0,0 +1,11 @@
+{
+  "name": "FHIR IG Importer",
+  "description": "FHIR IG microfrontend app",
+  "category": "HIE Configuration",
+  "type": "esmodule",
+  "url": "http://localhost:3334/jembi-fhir-ig-importer.js",
+  "showInPortal": true,
+  "showInSideBar": true,
+  "access_roles": ["admin"],
+  "icon": "https://fonts.gstatic.com/s/i/materialicons/medical_information/v1/24px.svg"
+}