[[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