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OpenELIS-OpenMRS Flows

Introduction

Apache camel routes that integrate OpenELIS and OpenMRS.

The integration is incomplete and work is paused until all the prerequisites are implemented on OpenELIS Global.

List of TODOs for OpenELIS Global can be tracked on this public Notion board.

Click here to watch the screen recordings of the OpenMRS-OpenELIS integration.

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Technical Overview

The project is built on top of OpenMRS-EIP core, so the assumption is that you have an existing OpenMRS EIP based application and wish to add to it odoo integration logic. The project contains camel routes that track inserts, updates and delete operations in specific tables in an OpenMRS database to take appropriate action in an odoo system.

If you don't have an existing OpenMRS EIP based application, you will need to first create one as documented here, then add the camel routes provided in this project and application properties.

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Architecture

1. Lab Order Creation in OpenMRS

• When a Lab Order is created in OpenMRS, the following resources are created in OpenELIS (assuming LOINC mapping exists in OpenELIS):
  • Practitioner
  • Patient
  • ServiceRequest
  • Location
  • Task

2. Incoming Order in OpenELIS

• Every x minutes, OpenELIS triggers a workflow to look for Tasks in REQUESTED status.
• The Task resource must have reference to existing ServiceRequest, Practitioner, Location, and Patient resources in the remote FHIR server.
• The Task is converted into an Incoming Order stored in the OpenELIS database and shown in the .

3. Lab Result between OpenELIS and OpenMRS

• A Task is created in OpenMRS to track the Lab Order status in OpenELIS.
• Polling Mechanism:
  • Every y minutes, OpenMRS polls Tasks with REQUESTED or ACCEPTED status.
  • For each Task, the corresponding Task in OpenELIS is fetched.
• Status Update:
  • If the OpenELIS Task status is updated to COMPLETED, the corresponding DiagnosticReport and Observation are fetched from OpenELIS and saved in OpenMRS.
  • The OpenMRS Task status is also updated to COMPLETED.

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Integrations

Integration	Sync	Status	Unit Test
Patient	OpenMRS ⮕ OpenELIS	✅	✅
Lab Order	OpenMRS ⮕ OpenELIS	🚧 Panels not supported	✅
Lab Order Result	OpenELIS ⮕ OpenMRS	✅	✅
Modify Lab Order	OpenMRS ⮕ OpenELIS	❌	❌
Discontinue Lab Order	OpenMRS ⮕ OpenELIS	❌	❌

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Steps to run

OpenELIS

• Disable TLS from FHIR store

  • Remove ./volume/tomcat/hapi_server.xml:/opt/bitnami/tomcat/conf/server.xml from OpenELIS docker-compose.yml

• Update the following configs in common.properties

  org.openelisglobal.fhirstore.uri=http://fhir.openelis.org:8080/fhir/
  
  org.openelisglobal.remote.source.uri=http://fhir.openelis.org:8080/fhir/
  org.openelisglobal.remote.source.updateStatus=true
  org.openelisglobal.remote.source.identifier=Practitioner/671ee2f8-ced1-411f-aadf-d12fe1e6f2ed
  

• Visit Admin tab in OpenELIS https://host/api/OpenELIS-Global/MasterListsPage

• Under Admin->Order Entry Configuration mark external orders config as true

• Under Admin->Test Management->Modify tests select any test and add LOINC code and save. Note LOINC codes can be found under Dictionary tab on a running OpenMRS instance. Example http://localhost/openmrs/dictionary/concept.htm?conceptId=54

• [Optional] Enable SSO

  • Add to build.docker-compose.yml:

  keycloak:
    container_name: keycloak
    image: quay.io/keycloak/keycloak:25.0.1
    ports:
      - 8089:8080
    command: start-dev
    environment:
      KEYCLOAK_ADMIN: admin
      KEYCLOAK_ADMIN_PASSWORD: admin
      KC_HOSTNAME: http://localhost:8089
      KC_HOSTNAME_STRICT: false
      KC_HOSTNAME_STRICT_HTTPS: false
    networks:
      - default 
  

  • Configure OpenELIS in ./volume/properties/common.properties:

  org.itech.login.saml=true
  org.itech.login.saml.metadatalocation=http://keycloak:8080/realms/OpenELIS/protocol/saml/descriptor
  

  • Run docker compose -f build.docker-compose.yml up -d --build
  • Configure keycloak:

    • Login with admin credentials

    • Create Realm -> OpenELIS

    • Create client ->

      type: SAML
      name: OpenELIS-Global_saml
      Client ID: OpenELIS-Global_saml
      Valid redirect URIs: https://localhost/api/OpenELIS-Global/login/saml2/sso/keycloak
      

    • Edit Keys client signature required: off

    • Create User: admin

    • Set password under Credentials tab

    • Restart OpenELIS docker restart openelisglobal-webapp

Wait for it to start up and then access the frontend at https://localhost/login. There should be an SSO Login button, login with admin user (users must exist in OpenELIS and Keycloak currently, admin user exists by default in OEG)

Ozone: eip-openelis-openmrs

Make the following changes in your Ozone Distro.

• Create a file docker-compose-openelis.yml under ozone/run/docker/

  • Add the following configurations

    services:
    
      # OpenMRS - OpenELIS integration service
      eip-openelis-openmrs:
        depends_on:
          openmrs:
            condition: service_healthy
          mysql:
            condition: service_started
        environment:
          - OPENELIS_FHIR_SERVER_URL=http://192.168.29.135:8081 #OpenELIS FHIR server instance
          - OPENELIS_FHIR_USERNAME=admin
          - OPENELIS_FHIR_PASSWORD=adminADMIN!
          - OPENMRS_SERVER_URL=http://openmrs:8080/openmrs #OpenMRS instance
          - OPENMRS_SERVER_USER=${OPENMRS_USER}
          - OPENMRS_SERVER_PASSWORD=${OPENMRS_PASSWORD}
          - OPENMRS_RESULTS_ENCOUNTER_TYPE_UUID=${RESULTS_ENCOUNTER_TYPE_UUID}
          - OPENMRS_IDENTIFIER_TYPE_UUID=${OPENMRS_IDENTIFIER_TYPE_UUID}
          - OPENMRS_CONCEPT_COMPLEX_UUID=${CONCEPT_COMPLEX_UUID}
          - BAHMNI_TEST_ORDER_TYPE_UUID=${BAHMNI_TEST_ORDER_TYPE_UUID}
          - EIP_PROFILE=prod
          - EIP_WATCHED_TABLES=patient,person_name,person_address,patient_identifier,orders,test_order
          - EIP_DB_NAME_OPENELIS=${EIP_DB_NAME_OPENELIS}
          - EIP_DB_USER_OPENELIS=${EIP_DB_USER_OPENELIS}
          - EIP_DB_PASSWORD_OPENELIS=${EIP_DB_PASSWORD_OPENELIS}
          - MYSQL_ADMIN_USER=root
          - MYSQL_ADMIN_USER_PASSWORD=${MYSQL_ROOT_PASSWORD}
          - OPENMRS_DB_HOST=${OPENMRS_DB_HOST}
          - OPENMRS_DB_PORT=${OPENMRS_DB_PORT}
          - OPENMRS_DB_NAME=${OPENMRS_DB_NAME}
          - OPENMRS_DB_USER=${OPENMRS_DB_USER}
          - OPENMRS_DB_PASSWORD=${OPENMRS_DB_PASSWORD}
          - OPENMRS_USER=${OPENMRS_USER}
          - OPENMRS_PASSWORD=${OPENMRS_PASSWORD}
          - EIP_FHIR_RESOURCES=Patient,ServiceRequest
          - EIP_FHIR_SERVER_URL=http://openmrs:8080/openmrs/ws/fhir2/R4
          - EIP_FHIR_USERNAME=${OPENMRS_USER}
          - EIP_FHIR_PASSWORD=${OPENMRS_PASSWORD}
        image: mekomsolutions/eip-client:2.1.0
        networks:
          ozone:
            aliases:
              - eip-client-openelis
        restart: unless-stopped
        volumes:
          - "${DISTRO_PATH}/binaries/eip-openelis-openmrs:/eip-client/routes"
          - eip-home-openelis:/eip-home
    
      mysql:
        environment:
          EIP_DB_NAME_OPENELIS: ${EIP_DB_NAME_OPENELIS}
          EIP_DB_USER_OPENELIS: ${EIP_DB_USER_OPENELIS}
          EIP_DB_PASSWORD_OPENELIS: ${EIP_DB_PASSWORD_OPENELIS}
        volumes:
          - "${SQL_SCRIPTS_PATH}/mysql/eip-openelis-openmrs:/docker-entrypoint-initdb.d/db/eip-openelis-openmrs"
    
    volumes:
      eip-home-openelis: ~
    

• Create a directory eip-openelis-openmrs under ozone/distro/data/mysql with a file create_eip_openelis_openmrs_db.sh

  • Add the following commands

    #!/bin/bash
    
    set -eu
    
    function create_user_and_database() {
    mysql --password=$MYSQL_ROOT_PASSWORD --user=root <<MYSQL_SCRIPT
        CREATE DATABASE $1;
        CREATE USER '$2'@'localhost' IDENTIFIED BY '$3';
        CREATE USER '$2'@'%' IDENTIFIED BY '$3';
        GRANT ALL PRIVILEGES ON $1.* TO '$2'@'localhost';
        GRANT ALL PRIVILEGES ON $1.* TO '$2'@'%';
        FLUSH PRIVILEGES;
    MYSQL_SCRIPT
    }
    
    create_eip_client_user_and_database() {
        local dbName="${1:-}"
        local dbUser="${2:-}"
        local dbUserPassword="${3:-}"
        if [ "${dbName:-}" ] && [ "${dbUser:-}" ] && [ "${dbUserPassword:-}" ]; then
            create_user_and_database "$dbName" "$dbUser" "$dbUserPassword";
        fi
    }
    
    echo "Creating '${EIP_DB_USER_OPENELIS}' user and '${EIP_DB_NAME_OPENELIS}' database..."
    create_eip_client_user_and_database ${EIP_DB_NAME_OPENELIS:-} ${EIP_DB_USER_OPENELIS:-} ${EIP_DB_PASSWORD_OPENELIS:-};

  • Edit ozone/run/docker/scripts/docker-compose-files.txt remove docker-compose-senaite.yml and add docker-compose-openelis.yml

  • Create a directory eip-openelis-openmrs under ozone/distro/binaries/ and paste the eip-openelis-openmrs JAR Example: eip-openelis-openmrs-1.0.0-SNAPSHOT.jar

• After setting up OpenELIS and Ozone distro, start the Ozone environment using ./start.sh command.
• Once the Ozone distro is up and running create a Patient and start a Visit, add a Lab Order Eg. (Red Blood Cell) and save.
• This Lab Order should be visible under Order->Incoming Orders->Search