Difference between revisions of "Protege4DevDocs"

Revision as of 10:55, July 29, 2010

Guidelines

Protege 4.1 will be compatible with both Java 5 and Java 6. Unfortunately we need to continue supporting Java 5 because of problems with Java on the older Apple platforms (the PowerPC and 32 bit Macs). If you are writing a plugin and you want to be available on all OS X platforms, then you must use Java 5. Otherwise Java 6 works as long as you understand that you are excluding a subset of the Apple platforms.

Please consider writing any P4 code as a plugin.
If you cannot do this for various reasons, please let us know as we may be able to improve the core design in order to support you.
Protege 4.0 has been written specifically to be modular. It uses the OSGi framework as a plugin infrastructure.

Please share.
It is surprising how many people have written plugins for P4 that we just don't hear about.
If you wish to publish to the community, please see our notes on code contributions.

Using an Integrated Development Environment

Protege 4 OWL editor in Eclipse

• Setting up eclipse with Protege 4.1 (Recommended for Protege 4.1)
  This page gives directions for compiling and running Protege 4.1 using Eclipse's plugin development framework. It includes the OS X workaround as well.
• Setting up IntelliJ IDEA with Protege 4.1 (Recommended for Protege 4.1)
  This page gives directions for compiling and running Protege 4.1 using IDEA's Osmorc plug-in.

Protege 4 OWL editor in a Generic IDE

This section describes how to set up an IDE for plugin development. While we have used eclipse to illustrate these pages, we have tried to describe an approach that is generic and will work for all IDE platforms. We welcome others to add pages above to describe how to get Protege 4 running in their favorite IDE. We describe this in two steps - first the core Protege sources are downloaded and compiled and then a plugin project is created.

• Downloading, compiling and running the core Protege sources. The following links cover much the same ground.
  • Compile and run the Protege-OWL editor in a Generic IDE - this page gives directions for compiling Protege 4.0 sources in Eclipse where all bundles are encapsulated in one Eclipse project. These directions are specific to Protege 4.0 and are not applicable to Protege 4.1. However the ant build steps will probably provide enough hints to put together a generic ide environment for Protege 4.1.

Writing A Plugin

The following links are focussed on the problems of writing a plugin and are not focused on how your build environment should be configured. For information about configuring your build environment go to Using an IDE.

This page gives a quick start to writing a plugin for Protege 4. It starts with a guide to writing the empty (trivial) plugin in five minutes. Then it describes how some additional content can be added to the plugin.

Additional Information

In addition to this there are some other useful sources on plugin development:

• plugin types provides a list of plugin types that you can implement in Protege 4.
• Once you have written a plugin you want people to use it. Some very simple steps allow you to advertise your plugin and enable auto-update.
• A short guide to writing a plug-in to show the class hierarchy. This page is not supported by the Protege team and may indeed not be actively updated any more. It has some very useful information but will quite likely slowly go out of date.

Misc

Protege APIs

Here is a summary of the main parts of the Protege 4 API for gaining access to the model and various utilities.

Also see the javadoc for Protege 4.0 code.

UI components

The Protege core and the OWL editor kit both provide a large number of reuseable components and utilities for generating user interfaces for ontologies.

Updating to Protege 4.1

A short guide to migrating plugins from Protege4.0 to Protege4.1 (in progress).

Building Protege4.1 from scratch using ant

The Protege 4.1 build process has been refactored since Protege 4.0. This means that the locations of the various Protege 4.1 plugins is different than the corresponding locations in Protege 4.0. There are several advantages of the new scheme:

• the build files are independent so that changes to one plugin can be propageted to the distribution by compiling just the plugin rather than the redoing an entire Protege build.
• the build files autodetect the format of the protege distribution. This means that a single build file for the os x application bundle (Protege.app) and a felix based distribution.
• the new build process is much simpler allowing us to more easily update the various components.

Although many readers of this section will not be planning on doing an ant build, these directions clarify the location of the various Protege 4.1 plugins in svn.

First you must set the PROTEGE_HOME environment variable which is described here. Then you can build Protege 4.1 by following the following steps.

1. svn checkout http://smi-protege.stanford.edu/repos/protege/protege4/protege-base/trunk protege-base
2. cd protege-base and ant install and cd ... Warning: this step deletes the existing contents of ${PROTEGE_HOME}.
3. svn checkout http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.common/trunk org.protege.common
4. cd org.protege.common and ant install' and cd ..
5. svn checkout http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.editor.core.application/trunk org.protege.editor.core.application
6. cd org.protege.editor.core.application and ant install and cd ..
7. svn checkout http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.semanticweb.owl.owlapi/trunk org.semanticweb.owl.owlapi
8. cd org.semanticweb.owl.owlapi and ant install and cd ..
9. svn checkout http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.editor.owl/trunk org.protege.editor.owl
10. cd org.protege.editor.owl and ant install and cd ..

This will give a minimal installation and other plugins can be added as desired. Source plugins can be created by adding ant add.source before the ant install step. A full run on an extremely slow machine is shown here.

Note about the trunk (29-July-2010)

Currently the trunk is undergoing a refactor to keep up with the changes being made to the OWLAPI. As a consequence of this, if you build Protege from the trunk, the standard Protege reasoners will not work. There is a toy reasoner that I use for testing purposes but for Pellet, HermiT, FaCT++ you are on your own. Therefore - depending on why you are here - you may want to use a version of Protege before this refactor. If so then replace the org.semanticweb.owl.owlapi and org.protege.editor.owl links above with

       http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.semanticweb.owl.owlapi/branches/2010-07-10-before-owlapi-3.1
       http://smi-protege.stanford.edu/repos/protege/protege4/plugins/org.protege.editor.owl/branches/2010-07-10-before-owlapi-3.1

Note that this is time sensitive information. Hopefully this note will be deleted when the trunk version of Protege 4.1 is released.

Embedded OSGi

For people embedding Protege 4 services inside a non-OSGi based applications here is a short example showing how this can work.

Database Backends

There are now two database backends for the OWL API. Very soon we expect to have a Protege plugin that enables both backend mechanisms. We have put together a document describing how both database backends can be used with the owl api.

Client-Server

You will only find extreme bleeding edge stuff here. I am writing a new page describing how to setup a development environment for the client server.

Troubleshooting

• Troubleshooting class loader issues
• Troubleshooting and fixing problems with the Java 5 compiler