The Common Data Model of the FAIR4Health Project is implemented as HL7 FHIR profiles. This project includes the following in 2 main directories:
- The FHIR Implementation Guide containing the FHIR profiles developed to reflect the common data model of the FAIR4Health Project.
- Configuration files for the onFHIR Repository so that onFHIR starts up with the FAIR4Health profiles.
The Common Data Model of the FAIR4Health Project is implemented by utilizing HL7 FHIR profiles.
onFHIR.oi is a high-performance and fully compliant HL7 FHIR Repository. This image makes use of the open source version of the onFHIR Repository.
This image includes an onFHIR.io instance preconfigured with the FAIR4Health Common Data Model profiles.
Latest release can be quickly installed with the following docker run command. Please note that onFHIR.io uses MongoDB as its backend data storage system. onFHIR.io can be started with an embedded MongoDB instance while it can also connect to an existing running MongoDB instance through appropriate configuration parameters (see the Environment Variables).
$ docker run --name f4h-onfhir -e APP_CONF_FILE=fair4health.conf -e LOGBACK_CONF_FILE=logback.xml -e DB_EMBEDDED=true -d fair4health/onfhir:latest
This image can also be run with docker-compose. The following example runs a mongo container and onFHIR is set to not to use an embedded MongoDB instance.
version: '2'
services:
mongo:
image: mongo:4.4
volumes:
- './volumes/mongo:/data/db'
ports:
- 27017:27017
container_name: f4h-mongo
onfhir:
image: fair4health/onfhir:latest
depends_on:
- mongo
environment:
APP_CONF_FILE: 'fair4health.conf'
LOGBACK_CONF_FILE: 'logback.xml'
FHIR_ROOT_URL: 'https://f4h.srdc.com.tr/fhir'
DB_EMBEDDED: 'false'
DB_HOST: 'f4h-mongo:27017'
ports:
- 8080:8080
container_name: f4h-onfhir
The onFHIR image of the FAIR4Health uses several environment variables.
APP_CONF_FILE: This environment variable can be used to provide all configuration parameters through a Typesafe config file. onFHIR Repository provides an example of such a configuration file together with descriptions of the configuration parameters. This image ships with a predefined configuration file regarding the FAIR4Health Common Data Model FHIR profiles which can be found here.
LOGBACK_CONF_FILE: This environment variable can be used to provide a logback configuration file. This image ships with a logback configuration file which can be found here.
SERVER_HOST: Hostname (or IP address) that the onFHIR server will bind. Using 0.0.0.0 will bind the server to both localhost and the IP of the server that you deploy it.
SERVER_PORT: Port number that the onFHIR server will listen.
SERVER_BASE_URI: Base URI for the onFHIR server e.g. With the default configuration, the root path of the FHIR server will be http://localhost:8080/fhir in which /fhir is the SERVER_BASE_URI.
FHIR_INIT: When true, then for every restart of the server, it reads the FHIR configuration files, configure the onFHIR instance accordingly and then setup/update the MongoDB database. This should be true if executed for the first time. When false, then for every restart of the server, it configures the onFHIR instandce by reading the existing configurations from the database, not from the configuration files.
FHIR_ROOT_URL: Root URL for Server Access (this can be different from the SERVER_HOST parameter due to deployment alternatives especially when you are deploying the server behind a proxy). The value of this variable should be the URL which can be used to access to the onFHIR server from outside world so that the Accessible links can be created accordingly.
DB_EMBEDDED: onFHIR server requires a MongoDB instance. The application can be run on an embedded MongoDB instance if no external MondoDB is configured through the DB_HOST variable. If DB_EMBEDDED is true, then the MongoDB instance will be automatically started on the first host:port parameter provided with the DB_HOST environment variable.
DB_HOST: Host and ports for the MongoDB databases (you can use multiple if it is a sharded cluster or replica set). While "localhost:27017" is a valid single instance configuration, you can give "localhost:27019,localhost:27020" to enable the onFHIR server work on multiple MongoDB instances.
DB_NAME: The name of the database to be created for running the onFHIR server.
This research has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824666, FAIR4Health Project (Improving Health Research in EU through FAIR Data).