Merge pull request #10 from mozzy11/isante

update local setup

.gitignore

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

README.md

@@ -43,3 +43,31 @@ Navigate to the `HaitiHealthBox` directory on your machine and run the following
 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:

isanteplus.env

@@ -7,5 +7,5 @@ OMRS_CONFIG_CONNECTION_URL=jdbc:mysql://isanteplus-mysql:3306/openmrs?autoReconn
 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=${IPLUS_DB_PW}
+OMRS_CONFIG_CONNECTION_PASSWORD=mysqlpw
 OMRS_DEV_DEBUG_PORT=1044

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

@@ -1,19 +1,85 @@
 {
-    "Users": [
-      {
-        "groups": [
-          "admin"
-        ],
-        "firstname": "Super",
-        "surname": "User",
-        "email": "root@openhim.org",
-        "passwordAlgorithm": "sha512",
-        "passwordHash": "3ffa5a209fad0151388a1fc0eb2d93cfb95648c38a79ee19b8c19811ee9256a49dfc929afd1f81f35533553044d2fc19921939f9b53ef5024f9ae0486aecca05",
-        "passwordSalt": "b9bce89f512c986981512a91a9eeb5ef",
-        "expiry": null,
-        "locked": false,
-        "tokenType": null,
-        "token": null
-      }
-    ]
+  "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

@@ -15,12 +15,12 @@ spring.jpa.hibernate.ddl-auto=update
 
 org.openelisglobal.fhirstore.uri=http://fhir.openelis.org:8080/fhir/
 
-org.openelisglobal.remote.source.uri=http://fhir.openelis.org.remote: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://fhir.openelis.org.remote:8080/fhir/
+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
@@ -31,5 +31,5 @@ org.openelisglobal.fhir.subscriber.resources=Task,Patient,ServiceRequest,Diagnos
 facilitylist.schedule.fixedRate=864000000
 
 #provider List
-org.openelisglobal.providerlist.fhirstore=http://fhir.openelis.org.remote:8080/fhir/
+org.openelisglobal.providerlist.fhirstore=http://openhim-core:5001/fhir/
 org.openelisglobal.requester.identifier=Practitioner/f9badd80-ab76-11e2-9e96-0800200c9a66