Using an IDE (Intellij)

A rough guide on how to develop MOLGENIS in IntelliJ IDEA is described below. This was created using IntelliJ IDEA Ultimate. Most of the time we use the latest IntelliJ version.

Set the maven home dir in IntelliJ

  • Open Preferences, Build Execution Deployment, Maven

  • Set the home dir to where your >= 3.6.0 maven installation lives.

Get the MOLGENIS sourcecode

  • File, New, Project from version control, Git (or Github)

  • Pick for the repository URL.

  • In the Event log: Non-managed pom.xml file found. Choose "Add as Maven Project". (You'll also see 'JPA framework is detected'. Ignore that.)

You now should have a Project called 'molgenis' with a module for each maven module.

Set the project JDK

Open File, Project Structure. For the entire project:

  • (Add and) select Java 11 JDK.

  • Set language level to Java 11.

Create maven run configuration

For normal operation, IntelliJ can compile the sources for you. But some classes get generated so you'll need to run the maven build at least once.

  • Run, Edit Configurations...

  • Press +, add new maven run config, call it molgenis [clean install]

  • Set the project location as run directory

  • Command line is clean install

  • In the tool bar, select the molgenis[clean install] configuration and press the play button.

    MOLGENIS now should compile and test.

Build in IntelliJ

Build, Make project should work fine now and spew out no errors, only warnings.

Java Code Style settings

We format our code according to the Google Java Format. You can run the formatter in maven using target fmt:format. Maven will invoke fmt:check at build time and fail if the code isn't formatted properly.

Git commit hook

If you miss the reformat checkbox, you can configure a git commit hook in the folder where you checked out the molgenis repository. Add a file called .git/hooks/pre-commit with the following contents:

mvn fmt:format

Use MOLGENIS file-templates

  • Make sure that your .idea project folder lives inside your 'molgenis' git project root! Only then will we be able to auto-share templates.

  • Goto 'New / Edit file templates' and switch from 'Default' to 'Project'-scope.

  • Restart IntelliJ after setting the .idea directory and changing the settings


Adds two file templates for creating Package and EntityType classes. The templates can be accessed from the 'New' menu, when right-clicking a java package:

When choosing EntityType and filling out the form...

... a file is created with the necessary boilerplate:

package org.molgenis.test;

import org.springframework.stereotype.Component;

import static java.util.Objects.requireNonNull;
import static;
import static;
import static org.molgenis.test.PigeonEncounterMetadata.ID;
import static org.molgenis.test.InterestingDataPackage.PACKAGE_INTERESTING_DATA;

public class PigeonEncounterMetadata extends SystemEntityType
    private static final String SIMPLE_NAME = "PigeonEncounter";

    public static final String ID = "id";

    private final InterestingDataPackage interestingDataPackage;

    public PigeonEncounterMetadata(InterestingDataPackage interestingDataPackage)
        this.interestingDataPackage = requireNonNull(interestingDataPackage);

    public void init()

        setLabel("Pigeon Encounter");
        //TODO setDescription("");

        addAttribute(ID, ROLE_ID).setLabel("Identifier");

public class PigeonEncounter extends StaticEntity
    public PigeonEncounter(Entity entity)

    public PigeonEncounter(EntityType entityType)

    public PigeonEncounter(String id, EntityType entityType)

    public void setId(String id)
        set(ID, id);

    public String getId()
        return getString(ID);

public class PigeonEncounterFactory extends AbstractSystemEntityFactory<PigeonEncounter, PigeonEncounterMetadata, String>
    PigeonEncounterFactory(PigeonEncounterMetadata pigeonEncounterMetadata, EntityPopulator entityPopulator)
        super(PigeonEncounter.class, pigeonEncounterMetadata, entityPopulator);

Sadly, it's not possible to generate multiple files from one template, so the Metadata and Factory classes have to be manually moved to separate files. (Tip: Set your cursor to the class name and use Refactor > Move... or press F6)

Deploy the backend services

Check: deploy backend services

Deploy / Run in Tomcat server

  • Run, Edit configurations..., +, Tomcat, Local.

  • Call it molgenis-app [exploded]

  • (Add and) select your Tomcat installation

  • Remove any JVM options that are MOLGENIS specific. These will override the environment variables below.

  • In the "Open browser" change the URL to http://localhost (this will open a browser and serve the frontend of MOLGENIS).

  • The tomcat-port needs to point at 8080. This is also defined in the .env.

  • Select the 'Startup/Connection' tab.

  • Copy the content of molgenis-app/dev-env/intellij-tomcat-env and paste it into 'Pass environment variables'.

  • Copy and paste the following three variables in the Environment variables area and select 'Pass environment variables'.

    Fill in your home-directory and email address.

    molgenis.home=**your own version of the data dir****your own email address**
    audit.log.path=**path to where you want to store the audit log file**

    Note: If you want to see the audit log in Kibana in the dev stack, the audit.log.path must be <molgenis_git_root>/molgenis-app/dev-env/logs/audit.log

  • Deployment: Select + -> artifact -> molgenis-app:war exploded

  • Application context: Select /

  • Go back to the first tab, you should now have more options in the update and frame deactivation pulldowns.

  • Select On Update: Redeploy, don't ask (This is the action that will triggered when you press the blue reload button in the run view)

  • Select On frame deactivation: Update resources (This is the action that will be triggered whenever you tab out of IntelliJ)

    (If you get update classes and resources to work, let us know!!)

  • Select the OpenJDK 11 JRE in the 'JRE' property

  • Select your favorite browser in the pulldown.

  • Save the configuration

  • In the tool bar, select the molgenis-app [exploded] configuration and press the play button.

This'll build and deploy MOLGENIS to tomcat and open it in the browser. Whenever you tab from MOLGENIS to the browser, all modified resources will be copied to the deployed exploded war. A browser reload should display the changes.

MULTIPLE RUN CONFIGURATIONS When you have 2 run configurations (e.g. run in debug and run normally) you need to apply the configuration displayed above.

In some cases IntelliJ might not pick up all changes in the file system made during the build process. This may result in an error referencing a missing jar file. This can be fixed by selecting the 'Synchronize MOLGENIS' option from the project action menu.


See also the MOLGENIS Security settings

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