Merge pull request #10 from mozzy11/isante

update local setup

.github/workflows/main.yml

@@ -0,0 +1,61 @@
+name: CI
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  release:
+    types: [published]
+  workflow_dispatch:
+env:
+  IPLUS_DB_PW: mysqlpw
+jobs:
+  CI:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v1
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Pull containers
+        run: docker-compose pull
+      
+      - name: Cache containers
+        uses: satackey/action-docker-layer-caching@v0.0.11
+        continue-on-error: true
+
+      - name: Start all containers
+        run: docker-compose up -d
+      
+      - name: Sleep for 120 seconds
+        run: sleep 120
+        shell: bash
+
+      - name: Display docker logs for openhim config
+        run: docker-compose logs openhim-config
+
+      - name: Show docker logs for isanteplus
+        run: docker logs isanteplus
+
+      - name: Wait For OpenMRS
+        run: docker-compose -f test.docker-compose.yml up --exit-code-from wait wait
+
+      - name: Restart streaming pipeline
+        run: docker-compose up -d --force-recreate streaming-pipeline
+      
+      - name: Sleep for 30 seconds
+        run: sleep 30
+        shell: bash
+      
+      - name: Run Basic API Tests (https://www.postman.com/itechuw/workspace/haiti-sedish/collection/1525496-192e3c9f-caea-4056-8077-b67af442f01c)
+        env:
+          POSTMAN_COLLECTION: https://www.getpostman.com/collections/22647ce67595a103f9c1
+        run: docker-compose -f test.docker-compose.yml up --exit-code-from newman newman
+               
+      - name: Run iSantePlus QA Framework (https://github.com/IsantePlus/isanteplus-qaframework)
+        run: docker-compose -f test.docker-compose.yml up --exit-code-from qa qa
+        continue-on-error: false
+      

.gitignore

@@ -0,0 +1,3 @@
+volume/.DS_Store
+volume/isanteplus/.DS_Store
+*/.DS_Store

.postman/env.json

@@ -0,0 +1,11 @@
+{
+	"name": "ci",
+	"values": [
+		{
+			"key": "isanteplus-url",
+			"value": "http://isanteplus:8080",
+			"enabled": true
+		}
+	],
+	"_postman_variable_scope": "environment"
+}

README.md

@@ -1,2 +1,73 @@
 # HaitiHealthBox
 An all-inclusive health information system setup for health facilities in Haiti
+
+# Setup Instructions
+
+## Step One: Install Docker
+See https://docs.docker.com/engine/install/
+
+Test to make sure both of these commands work:
+```sh
+docker -v
+docker compose version
+```
+
+**Note: If your docker version does not support the `docker compose` syntax, 
+install `docker-compose` using the instructions here: https://docs.docker.com/compose/install/**
+
+
+## Step Two: Get HaitiHealthBox from GitHub
+
+Run the following command:
+```sh
+git clone https://github.com/I-TECH-UW/HaitiHealthBox.git
+```
+
+If you want to use a specific version from the [version list](https://github.com/I-TECH-UW/HaitiHealthBox/releases), you can check out the corresponding tag. For example, to use version `0.0.0-alpha`, run:
+```sh
+git checkout v0.0.0-alpha
+```
+
+Otherwise, you can use the latest `main` branch that is the default. 
+
+## Step Three: Set some configurations
+Set some temporary variables to store your desired iSantePlus Database and iSantePlus admin passwords:
+
+```sh
+export IPLUS_ADMIN_PW=<your-password>
+export IPLUS_DB_PW=<your-password>
+```
+## Step Four: Boot up Docker Enviornment
+Navigate to the `HaitiHealthBox` directory on your machine and run the following command:
+```sh
+docker-compose up -d
+```
+
+## Local setup
+
+Spin up the services
+
+```
+docker-compose -f docker-compose.local.yml up -d
+```
+
+Acces the services at 
+
+| Instance  |     URL       | credentials (user : password)|
+|---------- |:-------------:|------:                       |
+| Isanteplus   |  https://localhost/openmrs/login.htm  | admin : Admin123 |
+| OpenHIM   |    https://localhost/  |  root@openhim.org : admin |
+| OpenELIS | https://localhost/OpenELIS-Global/ |    admin : adminADMIN!| 
+
+## Instructions 
+1. Add the necesary Lab Unit permisions to the User      
+Go To `Admin -> User Management -> Select User -> Under "Roles" ,Choose "ALL Lab Units" and select  "All Permissions"`
+
+2. Enable Importing electronic orders       
+Go To `Admin -> Order Entry Configuration -> Select "external orders" -> Click "Modify" -> select "True"`
+
+3. Add the Right Test Catalogue ie tests with `Loinc Codes`
+
+see [more](https://i-tech-uw.github.io/healthinformationexchange/lis-workflows/lis-workflows.html#tutorial-lab-order-communication-between-openmrs-and-openelis) for the EMR-LIS communication
+
+

docker-compose.local.yml

@@ -0,0 +1,227 @@
+version: "3.8"
+
+services:
+  ###
+  # reverse proxy
+  ###
+  nginx:
+    image: nginx:latest
+    container_name: nginx
+    restart: always
+    ports:
+      - 80:80
+      - 443:443
+    volumes:
+      - certs-vol:/etc/nginx/certs/
+      - keys-vol:/etc/nginx/keys/
+      - ./volume/nginix/nginx.conf:/etc/nginx/conf.d/default.conf
+    depends_on:
+      - certs 
+     
+
+  ##
+  #iSantePlus Server
+  ##
+  isanteplus:
+    container_name: isanteplus
+    hostname: isanteplus
+    image: ghcr.io/isanteplus/docker-isanteplus-server:v2.3.7
+    restart: unless-stopped
+    env_file:
+      - ./isanteplus.env
+    volumes:
+      - /openmrs/data
+      - ./volume/isanteplus/custom_modules:/custom_modules
+    # ports:
+    #   - 8081:8080  
+    logging:
+      driver: "json-file"
+      options:
+        max-size: "10m"
+
+ 
+
+  isanteplus-mysql:
+    image: ghcr.io/isanteplus/docker-isanteplus-db:v2.2.1
+    command: mysqld --character-set-server=utf8 --collation-server=utf8_general_ci --sql_mode=""
+    restart: unless-stopped
+    container_name: isanteplus-mysql
+    hostname: isanteplus-mysql
+    healthcheck:
+      test: "exit 0"
+    environment:
+      - MYSQL_DATABASE=openmrs
+      - MYSQL_ROOT_PASSWORD=debezium
+      - MYSQL_USER=mysqluser
+      - MYSQL_PASSWORD=mysqlpw
+      - MYSQL_ROOT_HOST=% # Allow docker containers to connect to mysql
+    volumes:
+     # - ./mysql.cnf:/etc/mysql/conf.d/custom.cnf # mysql config preconfigured to allow binlog/debezium
+      - /var/lib/mysql
+   
+  
+  # streaming-pipeline: 
+  #   image: ghcr.io/i-tech-uw/openmrs-fhir-analytics/streaming-binlog:latest
+  #   container_name: streaming-pipeline
+  #   healthcheck:
+  #     test: "exit 0"
+  #   volumes:
+  #     - ./configs/streaming-pipeline/config.json:/deployments/config.json
+  #     # data is the directory which you want to persist the generated parquet files
+  #     # - ./configs/streaming-pipeline/parquet:/tmp
+  #   environment:
+  #     - OPENMRS_URL=http://isanteplus:8080/openmrs
+  #     - OPENMRS_USERNAME=admin
+  #     - OPENMRS_PASSWORD=${IPLUS_ADMIN_PW-Admin123}
+  #     - SINK_URL=https://openhim-ssl.sedish-haiti.org/SHR/fhir
+  #     - SINK_USERNAME=${OPENHIM_STREAMING_CLIENT-streaming}
+  #     - SINK_PASSWORD=${OPENHIM_STREAMING_PW-streaming}
+  #     - JDBC_FETCH_SIZE=10000
+  #     - JDBC_MAX_POOL_SIZE=50
+  #     - JDBC_INITIAL_POOL_SIZE=10
+  #     - JDBC_DRIVER_CLASS=com.mysql.cj.jdbc.Driver
+  #     # the 2 variable below should be same as volume mappings above
+  #     - PARQUET_PATH=
+  #     - FHIR_DEBEZIUM_CONFIG_PATH=/deployments/config.json
+  ###
+  # OpenHIM
+  ###
+  openhim-core:
+    container_name: openhim-core
+    hostname: openhim-core
+    image: jembi/openhim-core:v7.1.0
+    restart: unless-stopped
+    environment:
+      mongo_url: "mongodb://mongo-db/openhim"
+      mongo_atnaUrl: "mongodb://mongo-db/openhim"
+      NODE_ENV: "development"
+  
+    ports:
+    #   - 5000
+    #   - 5001
+      - 8080:8080
+
+
+  openhim-console:
+    container_name: openhim-console
+    hostname: openhim-console
+    image: jembi/openhim-console:v1.15.0
+    restart: unless-stopped
+    volumes:
+      - ./volume/openhim/console.json:/usr/share/nginx/html/config/default.json
+    healthcheck:
+      test: "curl -sS http://openhim-console || exit 1"
+      interval: 10s
+      timeout: 60s
+      retries: 3
+    # ports: 
+    #   - 3000:80
+
+
+  # Loads Default OpenHIM Config
+  openhim-config:
+    container_name: openhim-config
+    image: ghcr.io/i-tech-uw/openhim-config:v0.0.0
+    volumes:
+      - ./volume/openhim/initial-config.json:/app/test-openhim-config.json
+
+  mongo-db:
+    container_name: mongo-db
+    image: mongo:3.4
+    volumes:
+      - /data/db
+    restart: unless-stopped
+ 
+  ####
+  # OpenELIS
+  ####
+  certs:
+    container_name: oe-certs
+    image: ghcr.io/i-tech-uw/certgen:main
+    restart: always
+    environment:
+      - KEYSTORE_PW="kspass"
+      - TRUSTSTORE_PW="tspass"
+    volumes:
+      - cert-volume:/etc/openelis-global
+      - keys-vol:/etc/ssl/private/
+      - certs-vol:/etc/ssl/certs/
+
+
+  database:
+    container_name: openelisglobal-database
+    image: postgres:9.5
+    # ports:
+    #   - "15432:5432"
+    restart: always
+    env_file:
+      - ./volume/database/database.env
+    volumes:
+      # preserves the database between containers
+      - db-data:/var/lib/postgresql/data
+        # files here will run on install
+      - ./volume/database/dbInit:/docker-entrypoint-initdb.d
+
+    healthcheck:
+      test: ["CMD", "pg_isready", "-q", "-d", "clinlims", "-U", "clinlims"]
+      timeout: 45s
+      interval: 10s
+      retries: 10
+
+  oe.openelis.org:
+    container_name: openelisglobal-webapp
+    image: ghcr.io/i-tech-uw/openelis-global-2:2.7.3.2
+    depends_on:
+      - database
+    # ports:
+    #   - "8095:8080"
+    #   - "8443:8443"
+    restart: always
+    environment:
+      - TZ=Africa/Nairobi
+        # context.xml doesn't seem to be able to pick up environment variables directly, so we are passing them in as CATALINA_OPTS
+      - CATALINA_OPTS= -Ddatasource.url=jdbc:postgresql://database:5432/clinlims -Ddatasource.username=clinlims -Ddatasource.password=clinlims
+    volumes:
+      - cert-volume:/etc/openelis-global
+      # -  openelis-plugins-data:/var/lib/openelis-global/plugins
+      - ./volume/tomcat/oe_server.xml:/usr/local/tomcat/conf/server.xml
+    secrets:
+      - source: datasource.password
+      - source: common.properties
+
+
+  fhir.openelis.org:
+    container_name: external-fhir-api
+    image: hapiproject/hapi:v5.5.1
+    # ports:
+    # - "8081:8080"
+    restart: always
+    environment:
+      - hapi.fhir.auto_create_placeholder_reference_targets=true
+      - hapi.fhir.allow_placeholder_references=true
+      - hapi.fhir.allow_external_references=true
+  
+
+  fhir.openelis.org.remote:
+    container_name: openelis-remote-source
+    image: hapiproject/hapi:v5.5.1
+    # ports:
+    #   - "8081:8080"
+    restart: always
+    environment:
+      - hapi.fhir.auto_create_placeholder_reference_targets=true
+      - hapi.fhir.allow_placeholder_references=true
+      - hapi.fhir.allow_external_references=true
+  
+
+secrets:
+  datasource.password:
+    file: ./volume/properties/datasource.password
+  common.properties:
+    file: ./volume/properties/common.properties
+
+volumes:
+  db-data:
+  cert-volume:
+  certs-vol:
+  keys-vol:

docker-compose.yml

@@ -8,33 +8,35 @@ services:
     image: traefik:v2.6.1
     container_name: traefik
     ports:
-      - '80:80'
-      - '443:443'
-      - '8080:8080'
+      - "80:80"
+      - "443:443"
     volumes:
-      - ./certs/:/etc/certs/       
+      - ./certs/:/etc/certs/
       - /var/run/docker.sock:/var/run/docker.sock
-      - ./configs/conf.yaml:/conf/conf.yaml  
-      - ./configs/traefik.yaml:/etc/traefik/traefik.yaml
-    
+      - ./volume/traefik/conf.yaml:/conf/conf.yaml
+      - ./volume/traefik/traefik.yaml:/etc/traefik/traefik.yaml
+
   ###
   # iSantePlus Server
   ###
   isanteplus:
     container_name: isanteplus
     hostname: isanteplus
-    image: ghcr.io/isanteplus/docker-isanteplus-server:v2.3.0
+    image: ghcr.io/isanteplus/docker-isanteplus-server:v2.3.7
     restart: unless-stopped
     env_file:
       - ./isanteplus.env
     volumes:
       - /openmrs/data
       - ./custom_modules:/custom_modules
-      - ./dist:/openmrs/data/frontend
     logging:
       driver: "json-file"
       options:
         max-size: "10m"
+    ports:
+      - 8080:8080
+    networks:
+      - local_facility
 
   isanteplus-mysql:
     image: ghcr.io/isanteplus/docker-isanteplus-db:v2.2.1
@@ -48,14 +50,37 @@ services:
       - MYSQL_DATABASE=openmrs
       - MYSQL_ROOT_PASSWORD=debezium
       - MYSQL_USER=mysqluser
-      - MYSQL_PASSWORD=mysqlpw
+      - MYSQL_PASSWORD=${IPLUS_DB_PW-mysqlpw}
       - MYSQL_ROOT_HOST=% # Allow docker containers to connect to mysql
     volumes:
       - ./mysql.cnf:/etc/mysql/conf.d/custom.cnf # mysql config preconfigured to allow binlog/debezium
       - /var/lib/mysql
-    ports:
-    - "3306:3306"
-
+    networks:
+      - local_facility
+  
+  streaming-pipeline: 
+    image: ghcr.io/i-tech-uw/openmrs-fhir-analytics/streaming-binlog:latest
+    container_name: streaming-pipeline
+    healthcheck:
+      test: "exit 0"
+    volumes:
+      - ./configs/streaming-pipeline/config.json:/deployments/config.json
+      # data is the directory which you want to persist the generated parquet files
+      # - ./configs/streaming-pipeline/parquet:/tmp
+    environment:
+      - OPENMRS_URL=http://isanteplus:8080/openmrs
+      - OPENMRS_USERNAME=admin
+      - OPENMRS_PASSWORD=${IPLUS_ADMIN_PW-Admin123}
+      - SINK_URL=https://openhim-ssl.sedish-haiti.org/SHR/fhir
+      - SINK_USERNAME=${OPENHIM_STREAMING_CLIENT-streaming}
+      - SINK_PASSWORD=${OPENHIM_STREAMING_PW-streaming}
+      - JDBC_FETCH_SIZE=10000
+      - JDBC_MAX_POOL_SIZE=50
+      - JDBC_INITIAL_POOL_SIZE=10
+      - JDBC_DRIVER_CLASS=com.mysql.cj.jdbc.Driver
+      # the 2 variable below should be same as volume mappings above
+      - PARQUET_PATH=
+      - FHIR_DEBEZIUM_CONFIG_PATH=/deployments/config.json
   ###
   # OpenHIM
   ###
@@ -73,35 +98,38 @@ services:
       interval: 20s
       timeout: 20s
       retries: 2
-    networks:
-      - hie
     volumes:
       - ./configs/openhim/healthcheck.js:/healthcheck.js
-
+    ports:
+      - 5000
+      - 5001
+      - 8090:8080
+    networks:
+      - local_facility
   openhim-console:
     container_name: openhim-console
     hostname: openhim-console
     image: jembi/openhim-console:latest
     restart: unless-stopped
     volumes:
-      - ./configs/openhim-console/default.json:/usr/share/nginx/html/config/default.json
+      - ./volume/openhim/console.json:/usr/share/nginx/html/config/default.json
     healthcheck:
       test: "curl -sS http://openhim-console || exit 1"
       interval: 10s
       timeout: 60s
       retries: 3
+    ports: 
+      - 3000:80
     networks:
-      - hie
-
+      - local_facility
   # Loads Default OpenHIM Config
   openhim-config:
     container_name: openhim-config
     image: ghcr.io/i-tech-uw/openhim-config:v0.0.0
     volumes:
-      - ./configs/openhim/test-openhim-config.json:/app/test-openhim-config.json
+      - ./volume/openhim/initial-config.json:/app/test-openhim-config.json
     networks:
-      - hie
-
+      - local_facility
   mongo-db:
     container_name: mongo-db
     image: mongo:3.4
@@ -109,4 +137,100 @@ services:
       - /data/db
     restart: unless-stopped
     networks:
-      - hie
+      - local_facility
+  ####
+  # OpenELIS
+  ####
+  certs:
+    container_name: oe-certs
+    image: ghcr.io/i-tech-uw/certgen:main
+    restart: always
+    environment:
+      - KEYSTORE_PW="kspass"
+      - TRUSTSTORE_PW="tspass"
+    volumes:
+      - cert-volume:/etc/openelis-global
+    networks:
+      - local_facility
+  database:
+    container_name: openelisglobal-database
+    image: postgres:9.5
+    ports:
+      - "15432:5432"
+    restart: always
+    env_file:
+      - ./volume/database/database.env
+    volumes:
+      # preserves the database between containers
+      - db-data:/var/lib/postgresql/data
+        # files here will run on install
+      - ./volume/database/dbInit:/docker-entrypoint-initdb.d
+    networks:
+      - local_facility
+    healthcheck:
+      test: ["CMD", "pg_isready", "-q", "-d", "clinlims", "-U", "clinlims"]
+      timeout: 45s
+      interval: 10s
+      retries: 10
+
+  oe.openelis.org:
+    container_name: openelisglobal-webapp
+    image: ghcr.io/i-tech-uw/openelis-global-2:develop
+    depends_on:
+      - database
+    ports:
+      - "8095:8080"
+      - "8443:8443"
+    restart: always
+    environment:
+      - TZ=Africa/Nairobi
+        # context.xml doesn't seem to be able to pick up environment variables directly, so we are passing them in as CATALINA_OPTS
+      - CATALINA_OPTS= -Ddatasource.url=jdbc:postgresql://database:5432/clinlims -Ddatasource.username=clinlims -Ddatasource.password=clinlims
+    volumes:
+      - cert-volume:/etc/openelis-global
+      # -  openelis-plugins-data:/var/lib/openelis-global/plugins
+      - ./volume/tomcat/oe_server.xml:/usr/local/tomcat/conf/server.xml
+    secrets:
+      - source: datasource.password
+      - source: common.properties
+    networks:
+      - local_facility
+
+  fhir.openelis.org:
+    container_name: external-fhir-api
+    image: hapiproject/hapi:v5.5.1
+    # ports:
+    # - "8081:8080"
+    restart: always
+    environment:
+      - hapi.fhir.auto_create_placeholder_reference_targets=true
+      - hapi.fhir.allow_placeholder_references=true
+      - hapi.fhir.allow_external_references=true
+    networks:
+      - local_facility
+
+  fhir.openelis.org.remote:
+    container_name: openelis-remote-source
+    image: hapiproject/hapi:v5.5.1
+    ports:
+      - "8081:8080"
+    restart: always
+    environment:
+      - hapi.fhir.auto_create_placeholder_reference_targets=true
+      - hapi.fhir.allow_placeholder_references=true
+      - hapi.fhir.allow_external_references=true
+    networks:
+      - local_facility
+
+secrets:
+  datasource.password:
+    file: ./volume/properties/datasource.password
+  common.properties:
+    file: ./volume/properties/common.properties
+
+volumes:
+  db-data:
+  cert-volume:
+
+networks:
+  local_facility:

isanteplus.env

@@ -0,0 +1,11 @@
+OMRS_JAVA_MEMORY_OPTS="-Xmx8192m -Xms4096m -XX:NewSize=512m"
+OMRS_CONFIG_CONNECTION_SERVER=isanteplus-mysql
+OMRS_CONFIG_CREATE_DATABASE_USER=false
+OMRS_CONFIG_CREATE_TABLES=false
+OMRS_CONFIG_ADD_DEMO_DATA=false
+OMRS_CONFIG_CONNECTION_URL=jdbc:mysql://isanteplus-mysql:3306/openmrs?autoReconnect=true
+OMRS_CONFIG_HAS_CURRENT_OPENMRS_DATABASE=true
+OMRS_JAVA_SERVER_OPTS="-Dfile.encoding=UTF-8 -server -Djava.security.egd=file:/dev/./urandom -Djava.awt.headless=true -Djava.awt.headlesslib=true"
+OMRS_CONFIG_CONNECTION_USERNAME=mysqluser
+OMRS_CONFIG_CONNECTION_PASSWORD=mysqlpw
+OMRS_DEV_DEBUG_PORT=1044

test.docker-compose.yml

@@ -0,0 +1,48 @@
+version: "3.8"
+
+services:  
+  # QA Framework
+  qa:
+    image: ghcr.io/isanteplus/isanteplus-qaframework:latest
+    container_name: qa
+    environment:
+      - ISANTEPLUS_URL=http://isanteplus:8080/openmrs
+      - ISANTEPLUS_USER=admin
+      - ISANTEPLUS_PW=Admin123
+      - REMOTE_URL_CHROME=http://chrome:4444/wd/hub
+      - TEST_OPTIONS="-Dcucumber.filter.tags=@login"
+    networks:
+      - local_facility
+
+  chrome:
+    image: selenium/standalone-chrome:latest
+    hostname: chrome
+    container_name: chrome
+    ports:
+      - "4444:4444"
+      - "7900:7900"
+    networks:
+      - local_facility
+  # Newman Tests
+  newman:
+    image: postman/newman
+    volumes:
+      - ./.postman:/.postman
+    entrypoint: newman run $POSTMAN_COLLECTION -e /.postman/env.json --insecure --timeout-request 20000 --delay-request 1000
+    networks:
+      - local_facility
+
+  wait:
+    container_name: wait
+    image: ghcr.io/i-tech-uw/wait-for-openmrs-action:v0.4.0 
+    command:
+    - "http://isanteplus:8080/openmrs"
+    - "20" 
+    - "10000"
+    networks:
+      - local_facility
+
+networks:
+  local_facility:
+    external: true
+    name: haitihealthbox_local_facility

volume/database/database.env

@@ -0,0 +1,4 @@
+POSTGRES_USER=postgres
+POSTGRES_PASSWORD=admin
+POSTGRES_DB=clinlims
+POSTGRES_INITDB_ARGS="--auth-host=md5"

volume/database/dbInit/1-pgsqlPermissions.sql

@@ -0,0 +1,4 @@
+
+CREATE USER clinlims PASSWORD 'clinlims';
+CREATE USER admin SUPERUSER PASSWORD 'cPATaahXJlSj';
+ALTER DATABASE clinlims OWNER TO clinlims;

volume/database/dbInit/siteInfo.sql

@@ -0,0 +1,6 @@
+DELETE from clinlims.site_information where name = 'siteNumber';
+INSERT INTO clinlims.site_information( id, lastupdated, "name", description, "value") VALUES ( nextval('clinlims.site_information_seq'), now(), 'siteNumber', 'The site number of the this lab', 'DEV01' );
+
+DELETE from clinlims.site_information where name = 'Accession number prefix';
+INSERT INTO clinlims.site_information( id, lastupdated, "name", description, "value") VALUES ( nextval('clinlims.site_information_seq'), now(), 'Accession number prefix', 'Prefix for SITEYEARNUM format.  Can not be changed if there are samples', 'DEV01' );
+

volume/nginix/nginx.conf

@@ -0,0 +1,32 @@
+server {
+    listen 80;
+    server_name localhost;
+    return 301 https://localhost$request_uri;
+}
+
+server {
+
+  listen 443 ssl;
+  server_name localhost;
+    
+  ssl_certificate /etc/nginx/certs/apache-selfsigned.crt;
+  ssl_certificate_key /etc/nginx/keys/apache-selfsigned.key;
+  
+  proxy_set_header X-Forwarded-For $proxy_protocol_addr; # To forward the original client's IP address 
+  proxy_set_header X-Forwarded-Proto $scheme; # to forward the  original protocol (HTTP or HTTPS)
+  proxy_set_header Host $host; # to forward the original host requested by the client
+      
+  absolute_redirect off;
+     
+  location /openmrs {
+      proxy_pass http://isanteplus:8080;
+  }
+
+  location /OpenELIS-Global {
+      proxy_pass https://oe.openelis.org:8443;
+  }
+
+  location / {
+      proxy_pass http://openhim-console;
+  }
+}

volume/openhim/console.json

@@ -0,0 +1,13 @@
+{
+    "version": "1.10.0",
+    "minimumCoreVersion": "3.4.0",
+    "protocol": "https",
+    "host": "localhost",
+    "port": 8080,
+    "title": "Admin Console",
+    "footerTitle": "OpenHIM Administration Console",
+    "footerPoweredBy": "<a href='http://openhim.org/' target='_blank'>Powered by OpenHIM</a>",
+    "loginBanner": "",
+    "mediatorLastHeartbeatWarningSeconds": 60,
+    "mediatorLastHeartbeatDangerSeconds": 120
+  }

volume/openhim/initial-config.json

@@ -0,0 +1,85 @@
+{
+  "Users": [
+    {
+      "groups": [
+        "admin"
+      ],
+      "firstname": "Super",
+      "surname": "User",
+      "email": "root@openhim.org",
+      "passwordAlgorithm": "sha512",
+      "passwordHash": "e12ea7a5468925ab2b6d839e5b0566c8d8e68d9dd48241282ec1c448c0b11386b499be64011c88060b241ed5a143fea90992dabb0d91a334daecd96e20156c24",
+      "passwordSalt": "5f49ab7df7fac0fd7860d3b1be95cbf4",
+      "expiry": null,
+      "locked": false,
+      "tokenType": null,
+      "token": null
+    }
+  ],
+  "Clients": [],
+  "Channels": [
+    {
+      "methods": [
+        "GET",
+        "POST",
+        "DELETE",
+        "PUT",
+        "OPTIONS",
+        "HEAD",
+        "TRACE",
+        "CONNECT",
+        "PATCH"
+      ],
+      "type": "http",
+      "allow": [],
+      "whitelist": [],
+      "authType": "public",
+      "matchContentTypes": [],
+      "properties": [],
+      "txViewAcl": [],
+      "txViewFullAcl": [],
+      "txRerunAcl": [],
+      "status": "enabled",
+      "rewriteUrls": false,
+      "addAutoRewriteRules": true,
+      "autoRetryEnabled": false,
+      "autoRetryPeriodMinutes": 60,
+      "routes": [
+        {
+          "type": "http",
+          "status": "enabled",
+          "forwardAuthHeader": false,
+          "name": "Central FHIR server",
+          "secured": false,
+          "host": "fhir.openelis.org.remote",
+          "port": 8080,
+          "path": "",
+          "pathTransform": "",
+          "primary": true,
+          "username": "",
+          "password": ""
+        }
+      ],
+      "requestBody": true,
+      "responseBody": true,
+      "rewriteUrlsConfig": [],
+      "name": "central fhir server",
+      "description": "Access to the central FHIR server",
+      "pollingSchedule": null,
+      "matchContentRegex": null,
+      "matchContentXpath": null,
+      "matchContentValue": null,
+      "matchContentJson": null,
+      "urlPattern": "^/fhir/.*$",
+      "tcpHost": null,
+      "tcpPort": null,
+      "updatedBy": {
+        "id": "6374bbabba26d10013784480",
+        "name": "Super User"
+      },
+      "alerts": []
+    }
+  ],
+  "Mediators": [],
+  "ContactGroups": []
+}

volume/properties/common.properties

@@ -0,0 +1,35 @@
+server.ssl.key-store = file:/etc/openelis-global/keystore
+server.ssl.key-store-password = kspass
+server.ssl.key-password = kspass
+server.ssl.trust-store= file:/etc/openelis-global/truststore
+server.ssl.trust-store-password=tspass
+
+#/usr/local/tomcat/webapps/OpenELIS-Global/certs
+encryption.general.password=kspass
+
+spring.datasource.driver=org.postgresql.Driver
+spring.datasource.url= jdbc:postgresql://172.17.0.1:5432/clinlims?currentSchema=clinlims
+spring.datasource.username=clinlims
+spring.datasource.password=MIvfOkcLgzPA
+spring.jpa.hibernate.ddl-auto=update
+
+org.openelisglobal.fhirstore.uri=http://fhir.openelis.org:8080/fhir/
+
+org.openelisglobal.remote.source.uri=http://openhim-core:5001/fhir/
+org.openelisglobal.remote.source.updateStatus=true
+org.openelisglobal.remote.source.identifier=Practitioner/f9badd80-ab76-11e2-9e96-0800200c9a66
+org.openelisglobal.task.useBasedOn=true
+
+org.openelisglobal.fhir.subscriber=http://openhim-core:5001/fhir/
+org.openelisglobal.fhir.subscriber.resources=Task,Patient,ServiceRequest,DiagnosticReport,Observation,Specimen,Practitioner,Encounter
+
+#org.openelisglobal.facilitylist.fhirstore = http://localhost:4000/fhir/DEFAULT
+# org.openelisglobal.facilitylist.authurl= http://localhost:4000/auth/token
+# org.openelisglobal.facilitylist.username= root@gofr.org
+# org.openelisglobal.facilitylist.password= gofr
+# org.openelisglobal.facilitylist.auth= token
+facilitylist.schedule.fixedRate=864000000
+
+#provider List
+org.openelisglobal.providerlist.fhirstore=http://openhim-core:5001/fhir/
+org.openelisglobal.requester.identifier=Practitioner/f9badd80-ab76-11e2-9e96-0800200c9a66

volume/properties/datasource.password

@@ -0,0 +1 @@
+clinlims

volume/tomcat/oe_server.xml

@@ -0,0 +1,167 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  Licensed to the Apache Software Foundation (ASF) under one or more
+  contributor license agreements.  See the NOTICE file distributed with
+  this work for additional information regarding copyright ownership.
+  The ASF licenses this file to You under the Apache License, Version 2.0
+  (the "License"); you may not use this file except in compliance with
+  the License.  You may obtain a copy of the License at
+
+      http://www.apache.org/licenses/LICENSE-2.0
+
+  Unless required by applicable law or agreed to in writing, software
+  distributed under the License is distributed on an "AS IS" BASIS,
+  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+  See the License for the specific language governing permissions and
+  limitations under the License.
+-->
+<!-- Note:  A "Server" is not itself a "Container", so you may not
+     define subcomponents such as "Valves" at this level.
+     Documentation at /docs/config/server.html
+ -->
+<Server port="-1" shutdown="SHUTDOWN">
+  <Listener className="org.apache.catalina.startup.VersionLoggerListener" />
+  <!-- Security listener. Documentation at /docs/config/listeners.html
+  <Listener className="org.apache.catalina.security.SecurityListener" />
+  -->
+  <!--APR library loader. Documentation at /docs/apr.html -->
+  <!--<Listener className="org.apache.catalina.core.AprLifecycleListener" SSLEngine="on" />-->
+  <!-- Prevent memory leaks due to use of particular java/javax APIs-->
+  <Listener className="org.apache.catalina.core.JreMemoryLeakPreventionListener" />
+  <Listener className="org.apache.catalina.mbeans.GlobalResourcesLifecycleListener" />
+  <Listener className="org.apache.catalina.core.ThreadLocalLeakPreventionListener" />
+
+  <!-- Global JNDI resources
+       Documentation at /docs/jndi-resources-howto.html
+  -->
+  <GlobalNamingResources>
+    <!-- Editable user database that can also be used by
+         UserDatabaseRealm to authenticate users
+    -->
+    <Resource name="UserDatabase" auth="Container"
+              type="org.apache.catalina.UserDatabase"
+              description="User database that can be updated and saved"
+              factory="org.apache.catalina.users.MemoryUserDatabaseFactory"
+              pathname="conf/tomcat-users.xml" />
+  </GlobalNamingResources>
+
+  <!-- A "Service" is a collection of one or more "Connectors" that share
+       a single "Container" Note:  A "Service" is not itself a "Container",
+       so you may not define subcomponents such as "Valves" at this level.
+       Documentation at /docs/config/service.html
+   -->
+  <Service name="Catalina">
+
+    <!--The connectors can use a shared executor, you can define one or more named thread pools-->
+    <!--
+    <Executor name="tomcatThreadPool" namePrefix="catalina-exec-"
+        maxThreads="150" minSpareThreads="4"/>
+    -->
+
+
+    <Connector port="8443" minProcessors="5" maxProcessors="75" 
+               enableLookups="true" disableUploadTimeout="true"
+               acceptCount="100" debug="0" scheme="https" secure="true"
+               sslProtocol="TLS" SSLEnabled="true" 
+               keystoreFile="/etc/openelis-global/keystore" keystoreType="PKCS12" keystorePass="kspass"
+               truststoreFile="/etc/openelis-global/truststore" truststoreType="PKCS12" truststorePass="tspass"
+               URIEncoding="UTF-8" />
+               
+    <!-- A "Connector" using the shared thread pool-->
+    <!--
+    <Connector executor="tomcatThreadPool"
+               port="8080" protocol="HTTP/1.1"
+               connectionTimeout="20000"
+               redirectPort="8443" />
+    -->
+    <!-- Define a SSL/TLS HTTP/1.1 Connector on port 8443
+         This connector uses the NIO implementation. The default
+         SSLImplementation will depend on the presence of the APR/native
+         library and the useOpenSSL attribute of the
+         AprLifecycleListener.
+         Either JSSE or OpenSSL style configuration may be used regardless of
+         the SSLImplementation selected. JSSE style configuration is used below.
+    -->
+    <!--
+    <Connector port="8443" protocol="org.apache.coyote.http11.Http11NioProtocol"
+               maxThreads="150" SSLEnabled="true">
+        <SSLHostConfig>
+            <Certificate certificateKeystoreFile="conf/localhost-rsa.jks"
+                         type="RSA" />
+        </SSLHostConfig>
+    </Connector>
+    -->
+    <!-- Define a SSL/TLS HTTP/1.1 Connector on port 8443 with HTTP/2
+         This connector uses the APR/native implementation which always uses
+         OpenSSL for TLS.
+         Either JSSE or OpenSSL style configuration may be used. OpenSSL style
+         configuration is used below.
+    -->
+    <!--
+    <Connector port="8443" protocol="org.apache.coyote.http11.Http11AprProtocol"
+               maxThreads="150" SSLEnabled="true" >
+        <UpgradeProtocol className="org.apache.coyote.http2.Http2Protocol" />
+        <SSLHostConfig>
+            <Certificate certificateKeyFile="conf/localhost-rsa-key.pem"
+                         certificateFile="conf/localhost-rsa-cert.pem"
+                         certificateChainFile="conf/localhost-rsa-chain.pem"
+                         type="RSA" />
+        </SSLHostConfig>
+    </Connector>
+    -->
+
+    <!-- Define an AJP 1.3 Connector on port 8009 -->
+    <!-- 
+    <Connector port="8009" protocol="AJP/1.3" redirectPort="8443" />
+    -->
+
+
+    <!-- An Engine represents the entry point (within Catalina) that processes
+         every request.  The Engine implementation for Tomcat stand alone
+         analyzes the HTTP headers included with the request, and passes them
+         on to the appropriate Host (virtual host).
+         Documentation at /docs/config/engine.html -->
+
+    <!-- You should set jvmRoute to support load-balancing via AJP ie :
+    <Engine name="Catalina" defaultHost="localhost" jvmRoute="jvm1">
+    -->
+    <Engine name="Catalina" defaultHost="localhost">
+
+      <!--For clustering, please take a look at documentation at:
+          /docs/cluster-howto.html  (simple how to)
+          /docs/config/cluster.html (reference documentation) -->
+      <!--
+      <Cluster className="org.apache.catalina.ha.tcp.SimpleTcpCluster"/>
+      -->
+
+      <!-- Use the LockOutRealm to prevent attempts to guess user passwords
+           via a brute-force attack -->
+<!--       <Realm className="org.apache.catalina.realm.LockOutRealm"> -->
+        <!-- This Realm uses the UserDatabase configured in the global JNDI
+             resources under the key "UserDatabase".  Any edits
+             that are performed against this UserDatabase are immediately
+             available for use by the Realm.  -->
+<!--         <Realm className="org.apache.catalina.realm.UserDatabaseRealm" -->
+<!--                resourceName="UserDatabase"/> -->
+<!--       </Realm> -->
+
+      <Host name="localhost"  appBase="webapps"
+            unpackWARs="true" autoDeploy="true">
+            
+        <!-- SingleSignOn valve, share authentication between web applications
+             Documentation at: /docs/config/valve.html -->
+        <!--
+        <Valve className="org.apache.catalina.authenticator.SingleSignOn" />
+        -->
+
+        <!-- Access log processes all example.
+             Documentation at: /docs/config/valve.html
+             Note: The pattern used is equivalent to using pattern="common" -->
+<!--         <Valve className="org.apache.catalina.valves.AccessLogValve" directory="logs" -->
+<!--                prefix="localhost_access_log" suffix=".txt" -->
+<!--                pattern="%h %l %u %t &quot;%r&quot; %s %b" /> -->
+
+      </Host>
+    </Engine>
+  </Service>
+</Server>