TracNav(MolgenisGuide)?

WARNING: Helios is currently not yet recommended following a series of problems. We recomment MolgenisOnEclipse Galileo. See FAQ

How to develop MOLGENIS on Eclipse/Helios?

We assume you installed:

• Java JDK >= 1.6
• MySQL or other supported database
• Apache Tomcat 6.0 or other supported web engine

1. Install eclipse helios

• Download from

​http://www.eclipse.org/downloads/packages/eclipse-ide-java-ee-developers/heliossr1

• Unzip to a directory of your choice
• Start it
  • Choose a sensible name for your workspace directory

2. install SVN plugin 'subclipse'

Within Eclipse

• go to help -> install new software
• Choose: 'Add' and add new url ​http://subclipse.tigris.org/update_1.6.x
• Type in search box 'required'
• Tick boxes marked with 'required'
• Install

You can also use subversive but there is a consensus in the MOLGENIS team that subclipse is better behaved

3. install freemarker plugin 'Freemarker IDE'

Within Eclipse:

• go to help -> install new software
• Choose: 'Add' and add new url ​http://download.jboss.org/jbosstools/updates/JBossTools-3.1.1.GA/
• Type in search box: 'Freemarker'
• Tick box: Freemarker IDE (not SDK)
• Install

4. checkout molgenis projects

Within Eclipse

• go to Window->Open perspective->Other
• Choose: SVN Repository exploring
• Eclipse may ask you which SVN engine to use, choose SVN kit.
• Right-click on SVN repositories and add new repository
  • URL: ​http://www.molgenis.org/svn
• Browse to molgenis/trunk
  • right-click and choose 'check out'.
• Browse to <yourproject>/trunk
  • right-click and choose 'check out'.

In your workspace you now have two projects

• molgenis - has the generator
• your project - all software specific to your MOLGENIS instance.

5. Develop

From now on development is like on Galileo.

FAQ

Q1: how to add/manage J2EE dependencies

• In Eclipse Galileo there was a seperate entry for this in the project 'properties'.
• In Eclipse Helios this renamed to 'Deployment Assembly'. Here you can also choose other projects to be included.

Q2: I get 404 errors when starting the server

This may happen if Eclipse destroys your WebContent/WEB-INF/web.xml to default.

To solve this:

• right-click WebContent/WEB-INF/web.xml
• update to SVN.
• delete your web server from the 'Servers' pane
• run on server again.

Note: Check your context.xml as well (WebContext?/META-INF/context.xml) and make sure the resource is not "out of sync". If it is, do a refresh on this file.

Q3: I get a very long 'loading web service DOM'

We found this is cause by the jst.web facet being set to 2.5 which is obviously a conflict with the 2.4 servlet api Molgenis is using.

Inside your project change the version of jst.web to 2.4 in .settings/org.eclipse.wst.common.project.facet.core.xml