Tips for developer to configure/deploy Eclipse + Virgo

Last Update: July 29th 2017

This section provides tips to solve some problems regarding Geppetto deploying in a Virgo Server (with Eclipse). These tips summarizes the experience of some Geppetto developers. Some may work on your environment and configuration, some don’t. You will have to identify which one makes sense for you so some software developer skills are required. Unfortunately, sometimes to configure a Virgo Server with Geppetto properly requires some knowledge, a lof of common sense and a little bit of magic. If you have any other tip which can be useful for someone else, don’t hesitate on adding it to the list.

  • Three wise tools.

    • mvn clean || Eclipse command: Run as -> mvn clean
    • mvn install || Eclipse command: Run as -> mvn install
    • mvn update || Eclipse command: Maven -> Update Project

    These three comands are the key tools you will be using during the configuration phase. Usually a mvn install from the org.geppetto project will be enough but sometimes you have to mvn clean/install each project independently. If you don’t manage to mvn install all the projects from org.geppetto root project, try to mvn clean/install the one that is causing the error. Regarding the third command, tipically a maven project has a folder structure like this:


    However, sometimes this folder structure is “corrupted”. Therefore, some compilation errors, which make no sense (Eclipse is complaining about a file although the file is in the right path), are reported. Execute a Maven Update to the project and then mvn clean/ install. After executing a mvn update, remember to unclick the Maven Project Builder (Eclipse command: Right click Project -> Properties -> Builders -> Unclick Maven Project Builder). Otherwise it can slow down and, eventually, crash your Eclipse.

  • In the Virgo server there are four folders to focus on if you are having problems:

    • pickup: if you are not using any IDE you need to have a Otherwise, the file can’t be here.
    • serviceability/log/log.log: If you have any problem have a look at the logs file and try to figure out what is failing
    • stage: If you are using an IDE the geppetto bundles will be deployed here. If you are having some problems and you do not know what to do, sometimes it is a good option to delete the content of this folder. It will be regenerated next time the server is started. However, you may need to delete the Virgo server from Eclipse and create it again adding all the bundles. If you are not using Eclipse, this folder shouldn’t have any bundles and they have to be placed in the repository/usr as .jar and .war files
    • repository/usr: If using an IDE, this folder contains all the .jar dependencies from the different bundles (a script can be found in org.geppetto which copies these files into the Geppetto server). If any library is added or changed, mvn install the geppetto projects and copy the files again.
  • If you have are starting your Virgo Server for the first time and it is not working try to have a look at the Geppetto folder permissions.

  • When starting the Virgo server, the Eclipse console shows information about the process. Every time a new module is deployed properly a message like this one is displayed:

    Installed bundle 'org.geppetto.model.neuroml' version '0.3.6'.
    Starting bundle 'org.geppetto.model.neuroml' version '0.3.6'.
    Started bundle 'org.geppetto.model.neuroml' version '0.3.6'.

    However if the module hasn’t been deployed properly the version you will see is 0.0.0 Double check any compilation or configuration error with the project or the dependencies. Execute mvn install to the project. This command can be executed while the server running.

  • From time to time, the Eclipse Virgo connector doesn’t copy some resources properly. Everything seems to run properly but some actions are not working fine. You will have to copy the resources files into the server (virgo/stage/[projectname]). This error could be tricky to solve as the symptons can be totally diferent depending on the resource that hasn’t been copied to the server. Note that although the resources are located at /src/main/resources in your project folder, in the Virgo Server they can be found in virgo/stage/[projectname] folder outside any subfolders.


    • There is no connection between the client and the server. For instance, you can’t see the geppetto version in the console when the main page is loaded. Also if you try to load a simulation it keeps loading forever. -> The spring configuration (META-INF/spring) in the org.geppetto.frontend resources hasn’t been copied in the server.
    • When executing aspect.getModel() an exception is raised. In the log you will see a trace that says “FileNotFound” -> You will have to copy the main/resources files of the org.geppetto.model.neuroml project.
  • Maven libraries that are downloaded when a mvn install is executed for the first time or after a mvn clean, are stored typically in a folder called .m2 inside your home folder. If the version of any library changes maven automatically download it again. However, if the lib content has changed but the lib version remains the same, you will have to remove the lib in .m2 manually. Note that this is a very uncommon case.

  • You cannot deploy org.geppetto.frontend on your server. This can be due to an Eclipse distribution that is missing some components. From update site, install the below item:

    Web, XML, Java EE and OSGi Enterprise Development -> Eclipse Java EE Developer Tools