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Openmrs ELT Pipeline

The goal of this tool is to provide batch abd near-realtime transformation of OpenMRS data for analytics or data science workflows. This project demonstrates how to perform batch and streaming process for generating flat_obs i.e Extract part of the ELT.

  • Batch - Data is extracted from OpenMRS and stored in delta lake (tables).
  • Streaming - incremental updates are captured then streamed to the delta tables

Getting started

1. Install Requirements

pip install pyspark:2.5.4
pip install kazoo

2. Deploy the debezium/kafka cluster (OpenMRS CDC) demonstrated in CDC

Use version .9 of debezium, version 1.0 doesn't support python API

3. Rename config/config.example.json to config/config.json

set parameters appropriately, should work using default settings

4. Check if all the MySQL views are created - if not create all mysql views by executing mysql scripts in /views folder.

mysql db_name < views/*.sql

5. Execute the batch job as demonstrated below

python3 batch_job.py

6. Execute the streaming job - use Airflow to Schedule

Before executing this script, please ensure you deploy debezium/kafka cluster (OpenMRS CDC) correctly demonstrated in CDC

python3 streaming_job.py

Alternatively, you can checkout example of streaming job demonstrated in Jupyter notebook