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Revision as of 11:28, December 2, 2013 by JenniferVendetti (talk | contribs) (Building with Eclipse)

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Building with Eclipse

This guide describes one possible approach to configuring the Eclipse Platform for working with the Protege Desktop source code. Feel free to make adjustments to suit your needs.


To follow this guide, you must have the following software tools installed:

Configuring Eclipse

This guide describes two ways of loading the core Protege bundles into Eclipse. The first method includes the Protege source code, which is useful for developers interested in understanding the inner workings of Protege. The second method doesn't include the Protege source code, and is generally sufficient for Protege plug-in developers to write, test, and run plug-ins.

Configure Eclipse with Protege sources

When I first set up eclipse this way, I decided to have the Protege source tree be in a separate but parallel directory to the eclipse workspace. I decided that I like this arrangement because, as you will see, it ensures that the eclipse workspace files don't show up as modifications to the Protege source tree sources.

Start of temporary workaround

When the explanation, client and server projects are checked into maven this step will not be necessary. For now, in some directory other than the protege5 directory that we have been using above perform the following operations:

            git clone
            cd org.protege.explanation
            mvn clean install
            cd ..

            git clone
            cd org.protege.owl.server
            mvn clean install
            cd ..

            git clone
            cd org.protege.editor.owl.client
            mvn clean install
            cd ..

I generally do this in the protege5-workspace directory that I use later.

End of Temporary workaround

The first step in this process is to check-out the Protege sources which may be done as follows:

            git clone protege5

Now we build Protege using the maven command:

    cd protege5
    mvn clean install

This takes a little while to run (about a minute on my computer) so now would be a good time to go get a cup of coffee. By running this, we have built a fully functional copy of Protege (in a directory with a name like protege-distribution/target/protege-distribution-5.0.0-beta-04-bin/Protege) and we have arranged that any generated source directories needed by the build are present.

Now we can set up the projects for eclipse. To do this first download a zip file that contains the eclipse information. This zip file can be found here. Unzip this file into the protege5 directory. Note that in addition to including the usual .project and .classpath files, this zip file also contains the META-INF/MANIFEST.MF files. These manifest files are duplicates of the manifest files that are included in the bundles that are created by the mvn build scripts. On windows machines you might see messages that various directories already exist (e.g. org.protege.common) and asking if you want to merge the contents. This is far from an error in this case and actually may mean that you are putting the files in the right places.

Now we start eclipse to create a workspace. This step can actually be done while the maven install step abbove is running. In my example, I created the workspace in a separate directory, protege5-workspace that is at the same level as the protege5 directory that I just created. In this first run of eclipse, all that I plan to do is to setup a parameter that points to the local maven repository. To do this, click on Window->Preferences (Eclipse->Preferences on a mac), select General->Workspace->Linked Resources and click on the button that defines a new path variable.


In this window configure the M2_REPO variable so that it points to the local maven repository which is usually (always?) located at '.m2/repository' in your home directory. This allows me to set up the eclipse projects so that they do not require pointers to system specific locations. The system specific location of the repository is set once in the eclipse workspace rather than several times in each project.

First you need to import the owl api as an eclipse plugin project. Click on File->Import... and select Plug-in Development->Plug-ins and Fragments.


In the next screen you can set the directory to import from to be



Finally on the next screen, you can select the OWL api for import.


Now we can import the eclipse projects from the protege5 directory. From the file menu click Import, select General/Existing Projects into Workspace, and click next:


In the next screen, make sure that "Select root directory" is selected, browse to the protege5 directory that we were working on before, select the plugins that you want to include and click finish:


The important projects to select are org.protege.common, org.protege.editor.core.application, org.protege.editor.owl and protege-distribution. You may need to wait a moment before looking at the errors because it takes a moment to build. The build progress is displayed in the lower right hand corner. At this point in the "Problems" view there will be a single compilation error:

Access restriction: The method render() from the type RDFRendererBase is not accessible due to restriction on required library org.semanticweb.owl.owlapi/owlapi-distribution.jar

I don't know what this error means yet but it appears to be harmless.

Configure Eclipse without Protege sources

Download Protege 4 or 5 distribution.

File->Import and then Plug-in Development->Plug-ins and Fragments.

Then get org.protege.common.jar and org.protege.editor.core.application.jar bundles from the bundles directory of the Protege distribution. Repeat and get org.semanticweb.owl.owlapi.jar and org.protege.editor.owl from the plugins directory of the distribution.

Running Protege

Run Protege with OSGi Framework launcher

This is the easiest type of runnable to create, run and debug. But there are two issues with this approach. First, if you are running mac os x, it won't work. The Mac has some long standing problems with java and eclipse and there appear to be troubles. But it works just fine on linux and windows. Second, this type of runnable may hide or change issues that would occur when the plugin is run in a true Protege deployment. I don't know exactly what eclipse does to make this type of runnable work but suffice it to say that eclipse is being a bit tricky. It is a good idea to at least occasionally the runnable in a more Protege-like environment such as is created by runnable that I describe in the next section.


  • Create a new OSGi runnable
  • Select all the Workspace plugins that you want.
  • Deselect all the Target Platform plugins
  • Click "Add Required Bundles"

Then add some jvm options to specify a logger and memory such as, for example:

-Declipse.ignoreApp=true -Dosgi.noShutdown=true

This setup is generating an exception for me

org.osgi.framework.BundleException: Could not find bundle: org.eclipse.equinox.console
	at org.eclipse.osgi.framework.internal.core.ConsoleManager.checkForConsoleBundle(
	at org.eclipse.core.runtime.adaptor.EclipseStarter.startup(
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(
	at java.lang.reflect.Method.invoke(
	at org.eclipse.equinox.launcher.Main.invokeFramework(
	at org.eclipse.equinox.launcher.Main.basicRun(
	at org.eclipse.equinox.launcher.Main.main( 

When I tried to fix this I got into some problems but it doesn't seem too important.

On a linux machine this works perfectly but on the mac it failed with the exception

               java.lang.UnsupportedClassVersionError: org/protege/editor/owl/ProtegeOWL : Unsupported major.minor version 51.0

This is a serious problem but if it only happens on the mac it may be irrelevant because historically the macs have been unable to run swing programs in eclipse-OSGi mode even after the bug about the problem was closed.

Run Protege in native mode

In this mode we run protege with the same configuration as is used by the end users of eclipse. In some ways, problems with this runnable are easier to debug than problems with the eclipse method given above because there is no hidden magic. But on the other hand, this approach requires more manual steps between debug steps.

Adding the OWL API

       git clone git://
       cd owlapi
       mvn -Declipse.workspace=../protege5-workspace eclipse:add-maven-repo
       mvn eclipse:clean eclipse:eclipse

Import the Existing projects into workspace.

Adding your own plug-in

Now we assume that a developer wants to introduce a plugin into eclipse. We have determined that this can be done in a reasonable manner without requiring that we commit either the META-INF directory or the libraries used by the plugin to our git repository. Since these files are visible to eclipse, it makes sense that we add an entry for them in the .gitignore file. In fact I would suggest that the .gitignore file contain at least the following entries:


The easy way

In this note, I assume that the plugin is maven project. The simplest way to do this would to use the maven eclipse support that is described here. Unfortuately we have had bad experience with this technique but it is sweet when it works and is worth a try. Essentially the two core commands are

    mvn -Declipse.workspace=<path-to-eclipse-workspace> eclipse:add-maven-repo
    mvn eclipse:eclipse

After these commands the project will be ready to import. Also you can arrange that the project that is created is a plugin project by including the following configuration in the pom.xml file:


But if this doesn't work you can try the approach described below.

A manual method

I will describe how I made this approach work with a particular plugin project. I chose the org.protege.owl.rdf project as this is project that includes some libraries.

Temporary workaround

The org.protege.owl.rdf project still has some remnants from the ant build days and these will probably be removed shortly. In the mean time, I manually removed the lib, META-INF directories and the build.xml file.

End of temporary workaround

The first step is to setup the .gitignore file so that git will ignore files that are only meaningful to an eclipse developer and are not of general interest. I suggest the following configuration:


Now I am ready to start eclipse. In eclipse I create a new plugin project called org.protege.owl.rdf making sure that it is based on the files in the gir project org.protege.owl.rdf that I just checked out. If I checked out the org.protege.owl.rdf file into the protege workspace then this usually simply works. In addition try to remember to set the source path to


or you will have to fix this later.

Now I need to replace the MANIFEST.MF that eclipse created with a project-specific that can be used by eclipse. I first need to build the project with maven

    mvn clean install

and then I extract the MANIFST.MF file from the built artifact:

   jar -xf target/org.protege.owl.rdf-1.0.3-SNAPSHOT.jar META-INF/MANIFEST.MF

You might want to run

   git status

at this point to make sure that there are no other files that eclipse has created or modified. Another common file to get changed or modified is the activator. After doing this I refresh eclipse so that it sees the new manifest.

In many cases you will be done at this point. For the org.protege.owl.rdf project there is one more hurdle (which is why I chose it) because it uses libraries that are included in the jar bundle.

Dealing with libraries

If you have a lot of dependencies, the steps below are more than a bit tedious. Is there a maven-eclipse plugin that can help here?

At this point the org.protege.owl.rdf project still has a bunch of errors (342). These errors are caused because eclipse does not know about the dependency of the org.protege.owl.rdf project on some libraries that it uses, the most obvious of which is the openrdf sesame project. One of the typical errors looks like this:

    BNode cannot be resolved to a type

and if I go to the file where this error occurs and then go to the top of the file to see the imports, I see that eclipse is unable to see the package org.openrdf.

Now, since the project builds properly with the command 'mvn clean install' I know that I have all the needed libraries on my machine. The libraries are in my repository. What I need to do is to make eclipse think that the libraries are in the place that it expects them to be and to add them to my class path. The first step to doing this is to add a linked resource variable that makes it easy to link items in my repository to the eclipse workspace. To do this, click on Window->Preferences (Eclipse->Preferences on a mac), select General->Workspace->Linked Resources and click on the button that defines a new path variable.


In this window configure the M2_REPO variable so that it points to the local maven repository which is usually (always?) located at '.m2/repository' in your home directory. This allows me to set up the eclipse projects so that they do not require pointers to system specific locations. The system specific location of the repository is set once in the eclipse workspace rather than once for each project.

Now I work through the list of dependencies so that I can add them all to eclipse. The first dependency looks like this:


To satisfy this dependency I need to link the appropriate version of the sesame-repository-sail jar file in my repository to the org.protege.owl.rdf project directory and add it to my class path. To do this I perform the following steps:

  1. I select the top directory of the project.
  2. I click File->New->File and I get a dialog.
  3. I make sure that the parent folder is the top level directory of the org.protege.owl.rdf project.
  4. I click on "Advanced" because I want to make a file link and that is advanced.
  5. There is then a checkbox near the bottom of the dialog that says link to the file system and I click on that.
  6. I click on variables which causes a sub-dialog to come up.
  7. In that subdialog I select the M2_REPO variable.
  8. I click extend and I get a file browser dialog where the top of the file tree is given by the location pointed to by my M2_REPO variable. The path that I select in this browser is governed by the fields in the dependency record for sesame-repository-sail that I am trying to incorporate into eclipse. I explore my way to org/openrdf/sesame (which is derived from the group id in the pom.xml dependency). From that subdirectory I open sesame-repository-sail (which comes from the artifactId. From that subdirectory I open the directory 2.7.0 which comes from the version. Finally in that directory I select the jar file and I click ok for the file browser dialog.
  9. I make one more check of the parameters in the "New File" dialog. The parent directory should be the top level directory of the org.protege.owl.rdf project, the filename should be sesame-repository-sail-2.7.0.jar and the text in the text box under "link to the file system" should be M2_REPO/org/openrdf/sesame/sesame-repository-sail/2.7.0/sesame-repository-sail-2.7.0.jar.
  10. I click ok to the new file dialog and I have a link.

After all this work I can look in the "Package Explorer" and see that the sesame-repository-sail-2.7.0.jar file has indeed been linked into the workspace. To add this file to the class path, I right click on the file in the "Package Explorer", move the mouse to "Build Path" and then click on "Add to Build Path".

I then repeat these steps for each of the dependencies in the pom, excluding the core protege plugins and libraries that are imported by the manifest. On the mac I keep getting this error dialog that says it cannot launch all these jars but I think that this can be ignored. I don't know what it is trying to launch and everything appears to be working fine. If all this pointing and clicking is getting you down then it may be possible to avoid some of this by editing the .project file directly and then refreshing the project in eclipse. The specifications of linked resources in the .project file looks like this:


The corresponding entry in the .classpath looks like this:

	<classpathentry kind="lib" path="logback-classic-1.0.12.jar"/>

After doing all this work there were a few dependencies of dependencies that were missing:


I found these by applying advanced unix search tools to the maven repository. One such command was:

          for i in `find . -name "*protege*" -prune -o -name *.jar -print`
               echo $i ; jar -tf $i |grep Sail 

I don't know of a generally accessible way of finding the missing dependencies but I suspect that this problem is rare.

Then eclipse has some problems with the manifest. I suspect that these errors are due to a difference of opinion between eclipse and bnd (the MANIFEST was made by maven which uses bnd). The best solution would be to convince eclipse to ignore these errors. Alternatively I opened the manifest in eclipse and applied all the fixes.

I couldn't try the osgi runnable because I am on a mac. But I will try the project that I made later on a unix machine.