FHIR Schema Converter

Convert FHIR resource definitions into Postgres views so they can be easily queries using SQL

NB: This is a proof of concept and not currently intended for production use

High-level Architecture

Prerequisites

A docker container with Postgres FHIR database. This includes synthetic data created using Synthea

docker run -d -p 3000:3000 -p 5432:5432 fhirbase/fhirbase:latest

Running the application

sbt run

Verifying results

• Connect to local postgres DB using a SQL client host: localhost database: fhirbase user: postgres pass: postgres

• run query ( is the resource name processed in lower case):

select * from <viewname>

Metabase

Setup

Pre-requisites:

• Docker
• Kitematic

1. Run the Metabase docker container using mounted file storage volume containing the Care Connect Profile Analysis dashboard

docker run -d -p 3001:3000 -v $PWD/metabase-data/metabase.db:/tmp/metabase.db -e "MB_DB_FILE=/tmp/metabase.db" --name metabase metabase/metabase

2. In Kitematic, select the new Metabase container and on the right-hand side of the window there will be a volumes window. Select the suggested mounted storage volume containing the metabase.db folder.

3. In Kitematic, select the Metabase container and then select the settings for this container. Under Network, scroll to the bottom and add a connection for the fhirbase container created in the Pre-Requisites section at the start of this readme. The connection alias should be fhirbase.

4. To log in to the Metabase dashboard, navigate to localhost:3001 in a browser and use the following credentials:

Username: example.user@kainos.com
Password: password1

Making changes to metabase

To save changes made to the metabase database, copy metabase.db folder from docker.

cd metabase-data
docker cp metabase2:/metabase.db ./

Performance Testing

The default Docker container already contains about 1500 patients but to load more data:

1. Clone the Synthea repo and generate an extra 1000 records

git clone https://github.com/synthetichealth/synthea.git
cd synthea

sed -i '' "/exporter\.fhir\.bulk_data = / s/=.*/= true/" src/main/resources/synthea.properties

./gradlew build -x test

#Generate 1000 records in bulk format
./run_synthea -p 1000 -s 100

2. Stop existing Fhirbase container and start with this command to have a shared folder

docker run -v $PWD:/tmp/synthea -d -p 3000:3000 -p 5432:5432 fhirbase/fhirbase:latest

3. Log into docker container

docker ps -a 
<get container id for fhirbase>
docker exec -i -t <container id> /bin/bash

4. Import all the files previously created by Synthea

cd /tmp/synthea/output/fhir

for i in ./*.ndjson; do
 echo $i
 fhirbase --host localhost -p 5432 -d fhirbase -U postgres -W postgres --fhir=3.3.0 load -m insert $i
done