GDI User Portal - Dataset Discovery Service

The GDI User Portal Dataset Discovery Service is a crucial component of the Genomic Data Infrastructure (GDI) project, which aims to facilitate access to genomic, phenotypic, and clinical data across Europe. The GDI project is committed to establishing a federated, sustainable, and secure infrastructure to enable seamless data access. Leveraging the outcomes of the Beyond 1 Million Genomes (B1MG) project, the GDI project is actively realizing the ambitious goals set forth by the 1+Million Genomes (1+MG) initiative.

The GDI User Portal Dataset Discovery Service serves as an interface between User Portal and the data discovery tools. It is developed using Quarkus version 3 and GraalVM for Java 21. This application plays a crucial role in enabling access request integration between the Data User and different Data Authorities.

• Status: 0.0.0
• Related Project: 1+ Million Genomes Project

Installation

Ensure you have Maven and GraalVM installed in your machine. We recommend to use SDKMAN!.

sdk install java 21.0.2-graal
sdk install maven 3.9.6
echo -e "\nexport GRAALVM_HOME=\"$HOME/.sdkman/candidates/java/21.0.2-graal/\"" >> $HOME/.zprofile
echo -e "\nryuk.container.privileged=true" >> $HOME/.testcontainers.properties
echo -e "\nexport TESTCONTAINERS_DOCKER_SOCKET_OVERRIDE=\"${HOME}/.colima/docker.sock\"" >> $HOME/.zprofile
echo -e "\nexport DOCKER_HOST=\"unix:///${HOME}/.colima/docker.sock\"" >> $HOME/.zprofile
echo -e "\nexport TESTCONTAINERS_RYUK_DISABLED=true" >> $HOME/.zprofile

Running the application in dev mode

You can run your application in dev mode that enables live coding using:

mvn compile quarkus:dev

NOTE: Quarkus now ships with a Dev UI, which is available in dev mode only at http://localhost:8080/q/dev/.

Packaging and running the application

The application can be packaged using:

mvn package

It produces the quarkus-run.jar file in the target/quarkus-app/ directory. Be aware that it’s not an über-jar as the dependencies are copied into the target/quarkus-app/lib/ directory.

The application is now runnable using java -jar target/quarkus-app/quarkus-run.jar.

If you want to build an über-jar, execute the following command:

mvn package -Dquarkus.package.type=uber-jar

The application, packaged as an über-jar, is now runnable using java -jar target/*-runner.jar.

Creating a native executable

You can create a native executable using:

mvn package -Dnative

You can then execute your native executable with: ./target/*-runner

If you want to learn more about building native executables, please consult https://quarkus.io/guides/maven-tooling.

Running tests

All tests are automatically executed when you build a new package.

License

• All original source code is licensed under Apache-2.0.
• All documentation is licensed under CC-BY-4.0.
• For more accurate information, check the individual files.