Merge pull request #261 from jembi/recipes

Add default recipes

.env.cluster

@@ -82,7 +82,8 @@ GF_SERVER_DOMAIN=grafana.domain
 
 # Client Registry - JeMPI
 JEMPI_WEB_INSTANCES=3
-REACT_APP_JEMPI_BASE_URL=https://jempi-api.domain/JeMPI
+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_ASYNC_RECEIVER_INSTANCES=1

.github/workflows/main.yaml

@@ -9,25 +9,19 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v2
 
-    - name: Set up Go
-      uses: actions/setup-go@v2
-      with:
-        go-version: 1.17
+      # replaces latest with the version of the release in the config.yaml file
+      - name: Set version
+        run: |
+          sed -i "s/latest/${{ github.event.release.tag_name }}/g" config.yaml
 
-    - name: Build Releases
-      run: ./get-cli.sh
-
-    - name: Test binaries
-      run: ./instant-linux help
-
-    - name: Release
-      uses: softprops/action-gh-release@v1
-      with:
-        files: |
-          ./instant-linux
-          ./instant-macos
-          ./instant.exe
-          ./config.yml
-          ./banner.txt
+      - name: Release
+        uses: softprops/action-gh-release@v1
+        with:
+          files: |
+            ./config.yml
+            ./banner.txt
+            ./cdr-dw.env
+            ./cdr.env
+            ./mpi.env

analytics-datastore-clickhouse/importer/config/clickhouseTables.js

@@ -1,22 +1,52 @@
-const CLUSTERED_MODE = process.env.CLUSTERED_MODE || 'true';
+const CLUSTERED_MODE = process.env.CLUSTERED_MODE || "false";
 
 const queries =
-  Boolean(CLUSTERED_MODE) === true
+  CLUSTERED_MODE === "true"
     ? [
-        `CREATE TABLE default_table(
-			createdAt Date,
-			updatedAt Date
-		) 
-		ENGINE=MergeTree
-		ORDER BY tuple();`,
+        `CREATE TABLE patient_example ON CLUSTER '{cluster}' (
+					id String,
+					version String NULL,
+					inserted_at DateTime DEFAULT now(),
+					last_updated Date NULL,
+					goldenId String,
+					patientGivenName String,
+					patientFamilyName String,
+				) 
+				ENGINE = ReplicatedMergeTree('/clickhouse/tables/{cluster}/{shard}/{table}', '{replica}')
+				ORDER BY tuple();`,
+        `CREATE TABLE observation_example ON CLUSTER '{cluster}' (
+					id String,
+					version String NULL,
+					inserted_at DateTime DEFAULT now(),
+					last_updated Date NULL,
+					observationValue Double,
+					patientId String,
+				) 
+				ENGINE = ReplicatedMergeTree('/clickhouse/tables/{cluster}/{shard}/{table}', '{replica}')
+				ORDER BY tuple();`,
       ]
-    : [
-        `CREATE TABLE default.default_table ON CLUSTER '{cluster}' (
-			createdAt Date,
-			updatedAt Date
-		)
-		ENGINE = ReplicatedMergeTree('/clickhouse/tables/{cluster}/{shard}/{table}', '{replica}')
-		ORDER BY tuple();`,
+	: [
+        `CREATE TABLE patient_example(
+					id String,
+					version String NULL,
+					inserted_at DateTime DEFAULT now(),
+					last_updated Date NULL,
+					goldenId String,
+					patientGivenName String,
+					patientFamilyName String,
+				) 
+				ENGINE=MergeTree
+				ORDER BY tuple();`,
+        `CREATE TABLE observation_example(
+					id String,
+					version String NULL,
+					inserted_at DateTime DEFAULT now(),
+					last_updated Date NULL,
+					observationValue Double,
+					patientId String,
+				) 
+				ENGINE=MergeTree
+				ORDER BY tuple();`,
       ];
 
 module.exports = queries;

cdr-dw.env

@@ -0,0 +1,20 @@
+# General
+CLUSTERED_MODE=false
+
+# Log
+DEBUG=0
+BASHLOG_FILE=0
+BASHLOG_FILE_PATH=platform.log
+
+# Message Bus - Kafka
+#  !NOTE: Topics should comma seperated, optional include partion and repliction values
+#   e.g. <topic>:<partions>:<replicationFactor> -> test:3:2 (defaults to <topics>:3:1)
+KAFKA_TOPICS=2xx,2xx-async,errors,reprocess,3xx,patient,observation,JeMPI-audit-trail
+
+# SSO
+KC_OPENHIM_SSO_ENABLED=true
+OPENHIM_CONSOLE_SHOW_LOGIN=false
+KC_JEMPI_SSO_ENABLED=true
+REACT_APP_JEMPI_BASE_API_PORT=50001
+KC_SUPERSET_SSO_ENABLED=true
+KC_GRAFANA_SSO_ENABLED=true

cdr.env

@@ -0,0 +1,19 @@
+# General
+CLUSTERED_MODE=false
+
+# Log
+DEBUG=0
+BASHLOG_FILE=0
+BASHLOG_FILE_PATH=platform.log
+
+# Message Bus - Kafka
+#  !NOTE: Topics should comma seperated, optional include partion and repliction values
+#   e.g. <topic>:<partions>:<replicationFactor> -> test:3:2 (defaults to <topics>:3:1)
+KAFKA_TOPICS=2xx,2xx-async,errors,reprocess,3xx,patient,observation,JeMPI-audit-trail
+
+# SSO
+KC_OPENHIM_SSO_ENABLED=true
+OPENHIM_CONSOLE_SHOW_LOGIN=false
+KC_JEMPI_SSO_ENABLED=true
+REACT_APP_JEMPI_BASE_API_PORT=50001
+KC_GRAFANA_SSO_ENABLED=true

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

@@ -6,3 +6,9 @@ services:
       - published: 50000
         target: 50000
         mode: host
+
+  jempi-api-kc:
+    ports:
+      - published: 50001
+        target: 50000
+        mode: host

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

@@ -4,16 +4,59 @@ services:
   jempi-api:
     image: jembi/jempi-api:${JEMPI_API_IMAGE_TAG}
     environment:
-      POSTGRESQL_USER: ${POSTGRESQL_USERNAME} 
-      POSTGRESQL_PASSWORD: ${POSTGRESQL_PASSWORD} 
+      LOG4J2_LEVEL: ${LOG4J2_LEVEL}
+      POSTGRESQL_IP: ${JEMPI_REPMGR_PRIMARY_HOST}
+      POSTGRESQL_PORT: 5432
       POSTGRESQL_DATABASE: ${POSTGRESQL_DATABASE}
+      POSTGRESQL_USER: ${POSTGRESQL_USERNAME}
+      POSTGRESQL_PASSWORD: ${POSTGRESQL_PASSWORD}
       KAFKA_BOOTSTRAP_SERVERS: ${KAFKA_HOSTS}
       KAFKA_APPLICATION_ID: ${KAFKA_APPLICATION_ID_API}
       DGRAPH_HOSTS: ${DGRAPH_HOSTS}
       DGRAPH_PORTS: ${DGRAPH_PORTS}
-      HTTP_SERVER_PORT: ${HTTP_SERVER_PORT}
+      API_HTTP_PORT: 50000
+      LINKER_IP: jempi-linker
+      LINKER_HTTP_PORT: 50000
+    volumes:
+      - "jempi-shared-data:/app/csv"
+    deploy:
+      replicas: ${JEMPI_API_INSTANCES}
+      resources:
+        limits:
+          memory: ${JEMPI_API_MEMORY_LIMIT}
+        reservations:
+          memory: ${JEMPI_API_MEMORY_RESERVE}
+    networks:
+      reverse-proxy:
+      kafka:
+      default:
+
+
+  jempi-api-kc:
+    image: jembi/jempi-api-kc:${JEMPI_API_KC_IMAGE_TAG}
+    environment:
       LOG4J2_LEVEL: ${LOG4J2_LEVEL}
-      LINKER_HOST: ${LINKER_HOST}
+      KC_REALM_NAME: ${KC_REALM_NAME}
+      KC_API_URL: ${KC_API_URL}
+      KC_JEMPI_CLIENT_ID: ${KC_JEMPI_CLIENT_ID}
+      KC_JEMPI_CLIENT_SECRET: ${KC_JEMPI_CLIENT_SECRET}
+      KC_JEMPI_ROOT_URL: ${KC_JEMPI_ROOT_URL}
+      KC_FRONTEND_URL: ${KC_FRONTEND_URL}
+      JEMPI_SESSION_SECRET: ${JEMPI_SESSION_SECRET}
+      JEMPI_SESSION_SECURE: ${JEMPI_SESSION_SECURE}
+      JEMPI_SESSION_DOMAIN_NAME: ${JEMPI_SESSION_DOMAIN_NAME}
+      POSTGRESQL_IP: ${JEMPI_REPMGR_PRIMARY_HOST}
+      POSTGRESQL_PORT: 5432
+      POSTGRESQL_DATABASE: ${POSTGRESQL_DATABASE}
+      POSTGRESQL_USER: ${POSTGRESQL_USERNAME}
+      POSTGRESQL_PASSWORD: ${POSTGRESQL_PASSWORD}
+      KAFKA_BOOTSTRAP_SERVERS: ${KAFKA_HOSTS}
+      KAFKA_APPLICATION_ID: ${KAFKA_APPLICATION_ID_API}
+      DGRAPH_HOSTS: ${DGRAPH_HOSTS}
+      DGRAPH_PORTS: ${DGRAPH_PORTS}
+      API_KC_HTTP_PORT: 50000
+      LINKER_IP: jempi-linker
+      LINKER_HTTP_PORT: 50000
     volumes:
       - "jempi-shared-data:/app/csv"
     deploy:
@@ -28,8 +71,10 @@ services:
       kafka:
       default:
 
+
 volumes:
-  jempi-shared-data: 
+  jempi-shared-data:
+
 
 networks:
   reverse-proxy:

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

@@ -4,7 +4,7 @@ services:
   jempi-async-receiver:
     image: jembi/jempi-async-receiver:${JEMPI_ASYNC_RECEIVER_IMAGE_TAG}
     environment:
-      LOG4J2_LEVEL: ${LOG4J2_LEVEL} 
+      LOG4J2_LEVEL: ${LOG4J2_LEVEL}
       KAFKA_BOOTSTRAP_SERVERS: ${KAFKA_HOSTS}
       KAFKA_CLIENT_ID: ${KAFKA_CLIENT_ID_ASYNC}
     volumes:
@@ -20,10 +20,11 @@ services:
       kafka:
       default:
 
+
   jempi-etl:
     image: jembi/jempi-etl:${JEMPI_ETL_IMAGE_TAG}
     environment:
-      LOG4J2_LEVEL: ${LOG4J2_LEVEL} 
+      LOG4J2_LEVEL: ${LOG4J2_LEVEL}
       KAFKA_BOOTSTRAP_SERVERS: ${KAFKA_HOSTS}
       KAFKA_APPLICATION_ID: ${KAFKA_APPLICATION_ID_ETL}
     deploy:
@@ -37,19 +38,24 @@ services:
       kafka:
       default:
 
+
   jempi-controller:
     image: jembi/jempi-controller:${JEMPI_CONTROLLER_IMAGE_TAG}
     environment:
-      POSTGRESQL_USER: ${POSTGRESQL_USERNAME} 
-      POSTGRESQL_PASSWORD: ${POSTGRESQL_PASSWORD} 
+      LOG4J2_LEVEL: ${LOG4J2_LEVEL}
+      POSTGRESQL_IP: ${JEMPI_REPMGR_PRIMARY_HOST}
+      POSTGRESQL_PORT: 5432
       POSTGRESQL_DATABASE: ${POSTGRESQL_DATABASE}
-      POSTGRESQL_HOST: ${POSTGRESQL_HOST}
+      POSTGRESQL_USER: ${POSTGRESQL_USERNAME}
+      POSTGRESQL_PASSWORD: ${POSTGRESQL_PASSWORD}
       KAFKA_BOOTSTRAP_SERVERS: ${KAFKA_HOSTS}
       KAFKA_APPLICATION_ID: ${KAFKA_APPLICATION_ID_CTRL}
       KAFKA_CLIENT_ID: ${KAFKA_CLIENT_ID_CTRL}
-      HTTP_SERVER_PORT: ${HTTP_SERVER_PORT}
-      LOG4J2_LEVEL: ${LOG4J2_LEVEL}
-      LINKER_HOST: ${LINKER_HOST}
+      CONTROLLER_HTTP_PORT: 50000
+      API_IP: jempi-api
+      API_HTTP_PORT: 50000
+      LINKER_IP: jempi-linker
+      LINKER_HTTP_PORT: 50000
     deploy:
       replicas: ${JEMPI_CONTROLLER_INSTANCES}
       resources:
@@ -61,20 +67,25 @@ services:
       kafka:
       default:
 
+
   jempi-linker:
     image: jembi/jempi-linker:${JEMPI_LINKER_IMAGE_TAG}
     environment:
-      POSTGRESQL_USER: ${POSTGRESQL_USERNAME} 
-      POSTGRESQL_PASSWORD: ${POSTGRESQL_PASSWORD} 
+      LOG4J2_LEVEL: ${LOG4J2_LEVEL}
+      POSTGRESQL_IP: ${JEMPI_REPMGR_PRIMARY_HOST}
+      POSTGRESQL_PORT: 5432
       POSTGRESQL_DATABASE: ${POSTGRESQL_DATABASE}
+      POSTGRESQL_USER: ${POSTGRESQL_USERNAME}
+      POSTGRESQL_PASSWORD: ${POSTGRESQL_PASSWORD}
       KAFKA_BOOTSTRAP_SERVERS: ${KAFKA_HOSTS}
       KAFKA_APPLICATION_ID_INTERACTIONS: ${KAFKA_APPLICATION_ID_INTERACTIONS}
       KAFKA_APPLICATION_ID_MU: ${KAFKA_APPLICATION_ID_MU}
       KAFKA_CLIENT_ID_NOTIFICATIONS: ${KAFKA_CLIENT_ID_NOTIFICATIONS}
       DGRAPH_HOSTS: ${DGRAPH_HOSTS}
       DGRAPH_PORTS: ${DGRAPH_PORTS}
-      HTTP_SERVER_PORT: ${HTTP_SERVER_PORT}
-      LOG4J2_LEVEL: ${LOG4J2_LEVEL}
+      LINKER_HTTP_PORT: 50000
+      API_IP: jempi-api
+      API_HTTP_PORT: 50000
       LINKER_MATCH_THRESHOLD: ${LINKER_MATCH_THRESHOLD}
       LINKER_MATCH_THRESHOLD_MARGIN: ${LINKER_MATCH_THRESHOLD_MARGIN}
     deploy:
@@ -88,6 +99,7 @@ services:
       kafka:
       default:
 
+
   jempi-postgresql-01:
     image: bitnami/postgresql-repmgr:15.2.0
     environment:
@@ -114,17 +126,19 @@ services:
     configs:
       - target: /docker-entrypoint-initdb.d/jempi_psql_init_db.sql
         source: jempi_psql_init_db.sql
-  
+
 volumes:
   jempi-psql-01-data:
   jempi-shared-data:
 
+
 networks:
   kafka:
     name: kafka_public
     external: true
   defualt:
 
+
 configs:
   jempi_psql_init_db.sql:
     file: ./importer/jempi_psql_init_db.sql

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

@@ -4,11 +4,15 @@ services:
   jempi-web:
     image: jembi/jempi-web:${JEMPI_WEB_VERSION}
     environment:
-      REACT_APP_JEMPI_BASE_URL: ${REACT_APP_JEMPI_BASE_URL}
-      REACT_APP_MOCK_BACKEND: ${REACT_APP_MOCK_BACKEND}
-      REACT_APP_KC_FRONTEND_URL: ${KC_FRONTEND_URL}
-      REACT_APP_KC_REALM_NAME: ${KC_REALM_NAME}
-      REACT_APP_KC_JEMPI_CLIENT_ID: ${KC_JEMPI_CLIENT_ID}
+      REACT_APP_JEMPI_BASE_API_HOST: ${REACT_APP_JEMPI_BASE_API_HOST}
+      REACT_APP_JEMPI_BASE_API_PORT: ${REACT_APP_JEMPI_BASE_API_PORT}
+      REACT_APP_ENABLE_SSO: ${KC_JEMPI_SSO_ENABLED}
+      REACT_APP_MAX_UPLOAD_CSV_SIZE_IN_MEGABYTES: 128
+      NODE_ENV: production
+      KC_FRONTEND_URL: ${KC_FRONTEND_URL}
+      KC_REALM_NAME: ${KC_REALM_NAME}
+      KC_JEMPI_CLIENT_ID: ${KC_JEMPI_CLIENT_ID}
+      REACT_APP_SHOW_BRAND_LOGO: "false"
     deploy:
       replicas: ${JEMPI_WEB_INSTANCES}
       placement:
@@ -23,6 +27,7 @@ services:
       keycloak:
       default:
 
+
 networks:
   reverse-proxy:
     name: reverse-proxy_public