TranSMART API library

Overview

The packages in the TranSMART API library depend on Java 11. To add the Nexus repository where the packages are published, add the following to your Maven configuration:

<repositories>
    <repository>
        <id>nl.thehyve.nexus.releases</id>
        <name>The Hyve - Nexus releases repository</name>
        <url>https://repo.thehyve.nl/content/repositories/releases/</url>
    </repository>
</repositories>

This repository contains the following packages:

transmart-common

Data classes, resource specifications and Feign clients for the TranSMART REST API.

<dependency>
    <groupId>org.transmartproject</groupId>
    <artifactId>transmart-common</artifactId>
    <version>0.0.9</version>
</dependency>

transmart-proxy

Proxy server controllers and client services.

<dependency>
    <groupId>org.transmartproject</groupId>
    <artifactId>transmart-proxy</artifactId>
    <version>0.0.9</version>
</dependency>

transmart-proxy-server

Spring Boot application that serves as a TranSMART REST API proxy. See below for instructions on running the proxy server.

Configure Keycloak and TranSMART connection

The transmart-proxy-server uses Keycloak as an identity provider. The following settings need to be configured before running the application.

Property	Description
keycloak.auth-server-url	Keycloak url, e.g, https://keycloak.example.com/auth
keycloak.realm	Keycloak realm.
keycloak.resource	Keycloak client id.
transmart-client.transmart-server-url	The TranSMART server url, e.g., https://transmart-dev.thehyve.net

See application-dev.yml for example configuration.

Run

Make sure you have Maven installed.

# create a jar package
mvn clean package

There should now be a .jar-file in transmart-proxy-server/target/transmart-proxy-server-<version>.jar.

# run the packaged application
java -jar transmart-proxy-server/target/transmart-proxy-server-<version>.jar

There should now be an application running at http://localhost:9050/.

Use

There is a Swagger documentation describing how to use the transmart-proxy API. It is exposed at the application URL, by default: http://localhost:9050/.

Development

Run in development mode

cd transmart-proxy-server
# run the application in development mode
mvn spring-boot:run -Dspring.profiles.active=dev

Install

# install the package locally
mvn clean install

Tests

Run all tests:

mvn test

Acknowledgement

This project was funded by the German Ministry of Education and Research (BMBF) as part of the project DIFUTURE - Data Integration for Future Medicine within the German Medical Informatics Initiative (grant no. 01ZZ1804D).

License

Copyright © 2019 The Hyve B.V.

transmart-lib is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.