Tutorial · Set Up Local Test Servers for Analytics

Overview​

Before running the FHIR Data Pipes extraction and transformation pipelines, you need a FHIR source server populated with clinical data.

This tutorial guides you through starting local containerized FHIR servers (HAPI FHIR with PostgreSQL or OpenMRS with MySQL) using Docker Compose, and uploading synthetic patient datasets.

Prerequisites​

• Docker and Docker Compose installed
• Python 3.8 or higher with pip and virtual environment tools
• Git installed and repository cloned locally

Step 1 · Clone the repository and create network​

Clone the fhir-data-pipes repository and create the shared Docker network.

git clone https://github.com/ohs-foundation/fhir-data-pipes.git
cd fhir-data-pipes
docker network create cloudbuild

Step 2 · Start a FHIR source server​

Choose one of the following source server options.

Option A · HAPI FHIR server with PostgreSQL​

Launch a HAPI FHIR R4 server backed by a PostgreSQL database container.

docker compose -f ./docker/hapi-compose.yml up --force-recreate -d

The server base URL is available at http://localhost:8091/fhir.

Option B · OpenMRS Reference Application with MySQL​

Launch OpenMRS preloaded with the FHIR2 module.

docker compose -f ./docker/openmrs-compose.yml up --force-recreate -d

The OpenMRS FHIR endpoint is available at http://localhost:8099/openmrs/ws/fhir2/R4, and the web interface is at http://localhost:8099/openmrs/ with credentials admin / Admin123.

Step 3 · Upload synthetic clinical data​

Install the Python uploader dependencies inside a virtual environment.

python3 -m venv venv
source venv/bin/activate
pip install -r ./synthea-hiv/uploader/requirements.txt

Run the uploader script to load synthetic HIV cohort data into the HAPI FHIR server.

python3 ./synthea-hiv/uploader/main.py HAPI http://localhost:8091/fhir \
  --input_dir ./synthea-hiv/sample_data \
  --cores 4

Step 4 · (Optional) Start a sink FHIR server​

If you plan to test streaming transformed resources to a downstream FHIR server rather than flat database tables or Parquet files, start the destination container.

docker compose -f ./docker/sink-compose.yml up --force-recreate -d

The destination endpoint is available at http://localhost:8098/fhir.

Where to go next​

• Run the full pipeline in Single Machine Analytics Deployment.
• Manage pipeline batches in Try Pipelines Controller with HAPI FHIR.