FHIR Aggregator Import System

This project launches a HAPI FHIR server and imports public datasets from Google Cloud Storage.

Requirements

• Docker & Docker Compose

Setting Up Docker & Docker Compose

If you are new to Docker, follow these official guides to install and configure Docker and Docker Compose:

• Get Docker
• Install Docker Compose

Once installed, you can verify Docker works by running:

docker --version
docker-compose --version

You should see version information for both.

If you're completely new to Docker, this beginner guide is also helpful:

• Docker Overview

Quick Start

1. Launch the system:

docker-compose up --build

The FHIR server is accessible at:

http://localhost:8080/fhir

Using the Importer Service

The importer code is located in the importer/ directory. It has its own Docker image built using the included importer/Dockerfile. The docker-compose.yml is configured to build the importer from ./importer.

To list available datasets:

docker-compose run importer list
 ✔ Container fhir-aggregator-import-db-1           Running                                                    0.0s 
 ✔ Container fhir-aggregator-import-fhir-server-1  Runnin...                                                  0.0s 
🔍 Discovering datasets...

Available datasets:
- FHIRIZED-1KGENOMES/META (Size: 14.83 MB)
- FHIRIZED-CDA/META (Size: 1920.23 MB)
- FHIRIZED-CELLOSAURUS/META (Size: 2.98 MB)
- FHIRIZED-GDC/META (Size: 5076.96 MB)
- FHIRIZED-GTEX/META (Size: 165.15 MB)
- FHIRIZED-HTAN/META (Size: 1720.20 MB)
- FHIRIZED-ICGC/META (Size: 36.23 MB)
- IG/META (Size: 0.02 MB)

Note: IG/META is an "Implementation Guide" dataset, which used to setup the FHIR server with the necessary resources and profiles. It is not a dataset in the traditional sense.

Import all datasets (skipping legacy datasets by default):

docker-compose run importer import

To import only datasets matching a keyword (e.g., 1KGENOMES):

docker-compose run importer import --only FHIRIZED-1KGENOMES/META

Stopping the System

docker-compose down

To remove persistent data:

docker-compose down -v

Using the FHIR Server

Specify the endpoint:

export FHIR_BASE=http://localhost:8080/fhir

See GraphDefinitions You can interact with the FHIR server using any FHIR client or tools like Postman.

Now that you have the endpoint, if you are comfortable with FHIR, that is all you need. For example:

This query returns the official identifier for all ResearchStudy resources.

• $FHIR_BASE is the environment variable we set earlier, which holds the FHIR server's base URL. It's expanded to the actual URL during execution.
• /ResearchStudy is the FHIR resource type we are interested in (in this case, "ResearchStudy").
• ?_elements=identifier is a FHIR search parameter that limits the returned data to only include the 'identifier' element of the ResearchStudy resources.

Example query:

curl -s $FHIR_BASE'/ResearchStudy?_elements=identifier&identifier.use=official' | jq -rc '.entry[] | [ (.resource.identifier[] | .value), .fullUrl]' | sort

For more see FHIR Aggregator Documentation