PLIR dockerized setup

This project contains the dockerized setup for the PLIR project Proof Of Concept. see PLIR archtecture

Ensure you have Docker and Docker compose installed locally. See Docker Installation Instructions for your environment. If running on Linux, check https://docs.docker.com/compose/install/ to install docker compose.

To run the project , follow the instructions below .

1. Clone the repository locally

    git clone https://github.com/openmrs/openmrs-plir-dockerized-setup.git
   

2. Move to the project root directory and spin up the pre-configured OpenMRS ,OpenHIM ,Hapi-Fhir and the streaming-binlog pipeline instances .

   ./run.sh
   

3. You should be able to acces the OpenMRS ,OpenHIM and Hapi-Fhir instances  at the following urls

Instance	URL	credentials (user : password)
OpenMRS	http://localhost:8080/openmrs	admin : Admin123
OpenHIM	http://localhost:9000	[email protected] : openhim-password
Hapi FHir	http://localhost:8090	hapi : hapi123

Note:

• The OpenMRS Instance is pre-loaded with CIEL and a sample form (HIV_form) to collect TX_PVLS, specific data and also TX_CURR data

• The above script also loads the necesary TX_PVLS,TX_CURR Measure and Library Resources into the Hapi FHir . see the Resources under the resources folder.

• The Openhim instance is pre-configured with the necesary meta-data

Wait for the plir-streaming-pipeline container to start running before adding any data into OpenMRS. The running Pipeline will then listen to any  data changes  added in to OpenMRS and route them to the FHIR server through OpenHIM.

4. Invoke the collect-data FHIR Operation using the GET request below to generate the relevant Dataset for

TX_PVLS:     
        GET: http://localhost:8090/fhir/Measure/TX-PVLS/$collect-data?periodStart=<date>&periodEnd=<date>

 TX_CURR:    
        GET: http://localhost:8090/fhir/Measure/TX-CURR/$collect-data?periodStart=<date>&periodEnd=<date>

5. Invoke the evaluate-measure FHIR Operation using the GET request below for the  indicator calculation based on CQL evaluation

TX_PVLS:     
       GET: http://localhost:8090/fhir/Measure/TX-PVLS/$evaluate-measure?periodStart=<date>&periodEnd=<date>

TX_CURR:      
       GET: http://localhost:8090/fhir/Measure/TX-CURR/$evaluate-measure?periodStart=<date>&periodEnd=<date>      

Note : substitute <date> in the GET request with your actual date parameter .

6.You can use the plir-widget to easily query and visualise the Measure report generated from the HAPI-FHIR server .see widget source code under plir-widget/widget-source

• install the http-server . see inginix (proxy-server) config under plir-widget/config/nginx.conf .

• To run the widget , run the command below from the root directory

      ./run-widget.sh  
  

• you should be able to access the widget at http://localhost:7000/ .

Procede to select the measure TX-PVLS,TX_CURR , select the start date and generate the report using the widget

7. To remove and clean out all created containers and volumes, run

     ./stop.sh
   

Auto Regenerating the TX_PVLS Library resource

In case changes have been made to the Library cql logic at resources/tx_pvls_cql.txt orresources/tx_curr_cql.txt , the TX_PVLS,TX_CURR Library resources at resources/tx_pvls-library.json & resources/tx_curr-library.json can be auto re-generated .

• install the jq library

• run the command below from the root directory

  ./scripts/regenerate_tx_pvls-library.sh or ./scripts/regenerate_tx_curr-library.sh
  

The above script encodes the cql logic into Base64 format and rebuilds the TX_PVLS/TX_CURR Library

AUTOMATED PLIR TESTING

You can run the tests in the CI enviroment .see PLIR CI Automated Testing

To set up a local Testing enviroment , Follow the steps below .

Clone the hie-automation-tests framework that Supports Testing PLIR workflow.

git clone https://github.com/openmrs/hie-automation-tests.git

see more details

Prerequisites

• Python version >= 3.7
• Behave version >= 1.2
• Debezium-FHIR-Analytics component
• OpenMRS
• OpenHIM
• HAPI-FHIR

Configuration

Update the Configuration in the config.json file located under the features/config folder . Only OpenMRS , OpenHIM and HapiFHIR are required

NOTE :The deafult configuration are mapped to the default configuration in the dockerized PLIR setup

See sample observation data Posted to OpenMRS under features/data ie obs1.json ,obs2.json ,obs3.json .In case any values are adjusted in the above sample data, adjust the expected TX_PVLS score (rounded off to two decimal places) ie TX_PVLS-SCORE in the config file

• The Test will work best before you add any data to OpenMRS

Execute the test with the command below, under the root directory,but first ensure the PLIR pipeline is up and running.

behave --no-logcapture --include ./features/PLIR

The tests will

• Post Obs data into OpenMRS
• Track the transactions in OpenHIM
• Check whether the correct TX_PVLS indicator measureScore was calculated in HAPI FHIR
• Check whether the correct TX_CURR indicator measureScore was calculated in HAPI FHIR

Main Repositories

• Hapi FHir for OpenMRS PLIR https://github.com/openmrs/openmrs-contrib-plm-fhir-server
• OpenMRS FHIR Analytics tool https://github.com/GoogleCloudPlatform/openmrs-fhir-analytics