Getting Started (Docker version)

This tutorial explains how to run Fhirbase using Docker Container Platform.

Installing Docker

Please follow Official Docker installation guide. There are handy installers for all major operating systems.

Running Fhirbase Web Demo

Fhirbase Docker image comes with PostgreSQL instance and already prepared database with Synthea data loaded in it.

docker pull fhirbase/fhirbase:latest

When image is downloaded, type following command to start web demo:

docker run --rm -p 3000:3000 fhirbase/fhirbase:latest

When you'll see an message that web server was started on port 3000, point your browser to the http://localhost:3000, and you'll see the Fhirbase demo page.

To stop webserver, press Ctrl+C.

Creating and Initializing Database

To be able to invoke Fhirbase commands, start container in demonised (-d) mode:

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

Docker will respond with ID of newly created container, a long hash string like 34b55aae4b2538b3a51b87a125bba93f667dc5ddf67aec95d0cb6da6b953993e. Copy this ID to the clipboard. Now we're ready to get Bash shell inside running container. Do following command and paste ID from the clipboard instead of ID placeholder:

docker exec -it [container ID from previous step] /bin/bash

If you see an [email protected]:/$ bash prompt, you can use psql command to create a new database. After invoking psql command your terminal should look like this:

[email protected]:/$ psql
psql (10.5 (Debian 10.5-1.pgdg90+1))
Type "help" for help.
​
postgres=#

Type CREATE DABATASE fb; statement into the prompt and press Enter. Do not forget to put semicolon at the end of the statement. fb here is the name of new database, you can change it to anything you want, but don't forget to change it in all command examples in this tutorial as well.

If PostgreSQL responded with CREATE DATABASE, your new database is created and now you can quit psql with typing \q and pressing Enter.

Now we need to initialize newly created database with FHIR schema to store data in. We will use fhirbase init command for that:

fhirbase -d fb --fhir=3.0.1 init

In this command -d fb specifies name of the database (don't forget to change it if you named database differently in previous step). --fhir=3.0.1 sets a FHIR version you're going to use.

If Fhirbase did not return any error, your database was properly initialized with FHIR schema.

Loading FHIR Data into the Database

To import data into newly created database, use fhirbase load command. Fhirbade Docker image comes with sample NDJSON file containing 127454 Synthea-generated FHIR resources. This bundle is located at /bundle.ndjson.gzip. Invoke following command to load it:

fhirbase -d fb --fhir=3.0.1 load /bundle.ndjson.gzip

Usually it takes about 30 seconds to load this bundle.

Querying FHIR data with SQL

Now we're ready to query our FHIR database with SQL. Let's start psql providing database name:

psql -d fb

You should get fb=# prompt. Copy-and-paste examples below to see some trivial SQL magic.

Most popular given names

SELECT COUNT(*), resource#>>'{name,0,given,0}'
FROM patient
GROUP BY resource#>>'{name,0,given,0}'
ORDER BY COUNT(*) DESC;

Accessing FHIR elements

SELECT resource->'name', resource->'birthDate' 
FROM patient
LIMIT 10;

Searching Patient by name

SELECT id, resource->'name'
FROM patient
WHERE resource#>>'{name,0,given}' ilike '%alec%';