tomdcsmith / eva-ws

European Variation Archive REST web services API

European Variation Archive (EVA)

The European Variation Archive is an open-access database of all types of genetic variation data from all species. The service is available in https://www.ebi.ac.uk/eva

This repository contains the core of the application and the web services.

Build

In order to build EVA, you need to install the Java Development Kit 7 and Maven.

The project dependencies are OpenCGA and Variation-Commons

You can get OpenCGA 0.5.2 from https://github.com/opencb/opencga, branch hotfix/0.5. Please follow the download/compilation instructions there.

You can get Variation-Commons from https://github.com/EBIvariation/variation-commons. This project can be installed with just mvn clean install.

After it has been compiled, if you just want to build the WAR, run mvn package -DskipTests and you should obtain a file to deploy in Tomcat or other Java container.

Testing

The tests implemented so far are integration (not unit) tests, so a working WAR file needs to be created first. The Jetty plugin for Maven has been included to ease the testing process.

1. Fill the datasource information in the file eva-server/src/main/webapp/WEB-INF/jetty-env.xml
2. Build the WAR file as described in the section above
3. Run mvn jetty:run from the eva-server subfolder
4. Run mvn test from the root folder

Enabling OAuth2 Security

In order to enable OAuth2 Security you must enable the oauth2-security profile in the spring-boot application in any way supported by Spring-boot as stated in Spring documentation. In adition, the application requires configuration to point to the public user check endpoints of your OAuth2 compatible authentication service. More information is available in Spring documentation.

When using OAuth2 Security, Swagger UI will be still enabled and public to review the API but no command sent from the UI will be authorized.