This needs to be generalized for all O2 / O3 deployments, this is a POC based on OpenMRS 2.8 in Cote d’Ivoire
OPENMRS CONNECTION TO HAPI FHIR SERVER
IMPLEMENTERS GUIDE
Draft
Prepared byI-TECH DIGI and ITECH-CIV July 2024
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Welcome to the OpenMRS Connection to HAPI FHIR Server Implementers Implementer's Guide. This guide is designed to assist you in setting up the project within your environment, providing detailed instructions and resources to ensure a smooth and efficient implementation process. It includes the steps required to set up the project locally, such as creating a project directory, cloning the repository, configuring necessary files, and starting the project using Docker. These foundational steps are crucial for ensuring that your implementation is set up correctly from the beginningprovides a step-by-step approach for implementers to establish a connection between OpenMRS and a HAPI FHIR server, facilitating seamless data exchange. It covers essential setup processes, configuration, and deployment strategies applicable to OpenMRS 2.x (O2) and OpenMRS 3.x (O3) environments.
INTENDED AUDIENCE
This guide is intended for implementers responsible for implementing and managing an OpenMRS Health Information Exchange implementation. It assumes a basic understanding of Docker, Git, and web-based application management. Whether you are setting up a new instance or integrating an existing implementation, this guide provides the necessary steps to ensure a successful implementation.
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HOW TO SET UP THE PROJECT LOCALLY
Create a Project Directory:
Create a directory for the project on your local machine.
Navigate to the created directory.
Clone the Repository:
Open Visual Studio Code (VS Code) within the project directory.
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To get started with setting up the project locally, create a directory for the project on your local machine and change directory to the created project.
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To begin with, a secure shell is established to the OpenMRS instance server test1.chis.org. Therefore an implementer is required to set up a public key for SSH connection to the instance. The illustration below shows the private and public SSH keys. The command cat id_rsa.pub will display the public SSH key. The key is used to authenticate on the remote instance.
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Upon successful setup of the public SSH on the remote instance. The instance is accessed on the Visual Studio Code. Click to open a remote window.
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Click on Connect to Host
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Click
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Click on the instance to connect.
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Upon successful connection to the instance. Click on a new terminal.
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HOW TO STARTUP THE SIGDEP3 EMR REMOTELY
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Note: Notice the port on which the SPARK database should be exposed
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Change directory into the project by executing the command; cd code/SIGDEP-3-Docker-Setup
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Startup the project by executing the command; docker compose -f docker-compose-remote-traefick.yml up
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Startup project
The project will be started successfully.
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Expose the apache spark db Apache Spark database port 10001 by clicking on the port tab
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Click on Forward a port and add the port.The port will be forwarded successfully.
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The configurations for the SPARK database used for visualization of data is displayed as shown
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HOW TO DISPLAY DATA ON APACHE HIVE DATABASE MANAGEMENT SYSTEM
In In this section the Apache Hive database management system will be set up. The dbms will pull flat data that will be used for visualization. This guide provides steps on installation of the dbms.
Upon installation of the dbms database management system click to startup
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Startup DBeaverNote: you might be required to download SQLite driver files
Click on New database connection
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Enter the localhost and the port number as exposed on the remote instance forwarded ports. Click on the finish button.
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Upon successful connection click on the default drop-down menu
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To view data, click on the default menu item then click on tables. The tables are displayed.
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Click on tables under defaults
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Run an incremental within the data pipeline.
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To view the flattened tables from patient resources, click on View. In this illustration patient_flat_2 is clicked. Notice the patient created under the local instance is displayed.
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GETTING STARTED: DATA VISUALIZATION