Essential Standlone 6.2 Update Plugin Not Working

[smroberts]

Hello

fresh "newbie" install.
Protege launches fine, opened essential_baseline_v62.prj fine, EA plugins visible.
Attempt to perform any update thru Essential Update, I get below error. Duesnt matter what the update is , this error appears instantly. Im not expert but is this a plugin clash with the JVM 1.6 supplied with protege?

Exception in thread "AWT-EventQueue-0" java.lang.LinkageError: JAXB 2.1 API is being loaded from the bootstrap classloader, but this RI (from jar:file:/C:/standalone_essential_v6/Protege_3.5/plugins/com.enterprise_architecture.essential.update/jaxb-impl.jar!/com/sun/xml/bind/v2/model/impl/ModelBuilder.class) needs 2.2 API. Use the endorsed directory mechanism to place jaxb-api.jar in the bootstrap classloader. (See http://java.sun.com/j2se/1.6.0/docs/guide/standards/)
at com.sun.xml.bind.v2.model.impl.ModelBuilder.<clinit>(ModelBuilder.java:177)

[jonathan.carter]

Hi,

Thanks for posting about the JAXB issue that you're seeing.
This is certainly something that we've seen before and I'm pretty sure that it's caused by the Java version that you are using with Protege. Java 1.6 is pretty old now, and I would recommend upgrading the Java that Protege is using to Java 1.8.

We've been running with Java 7 and Java 8 for a number of years now without any problems.
Note that Java 1.7 is listed as a pre-requisite on our download page but I see that the stand-alone install guide needs to be updated still!

That you are using Java 1.6 suggests that you have installed Protege using an installer that includes a bundled Java runtime environment. There are two options here - either:

- re-install Protege, using the Download that does NOT include bundled Java after having installed Java 1.8 Runtime from Oracle. Follow the Protege Installer guidance for selecting the correct Java Runtime.

- Or, install the Java 1.8 and then convert your Protege deployment to use that new Java.

If you're on Windows, the second option might actually not be as complex as it sounds, since the Windows version uses some BAT files to start Protege. Edit the line (9?) that sets the JAVA_PATH variable. Out of the box, this points to the local JRE. Change this to the full path to your newly-installed (or maybe you already have) Java 1.8 runtime. Use quotes around the variable to allow it to use the full path to your jre/bin folder, e.g.:

Code: Select all

set JAVA_PATH="C:\PATH TO MY JAVA\jre\bin"

Whilst you are there, it's worth increasing the MAXIMUM_MEMORY to -Xmx1536M, if you haven't already.

If you're on Windows and start Protege from the Icon, you can still switched the JVM that it is using to be your later Java 1.8 - and you can do this through the user interface. Start Protege and then go to File -> Preferences menu -> Protege.lax. Find the row that contains the property lax.nl.current.vm and update the value to be the path to your installed Java Runtime. Note that even on Windows, you should use the '/' (Unix-style) directory separators in this path
(see attached screenshot).

There is an alternative approach to add the JAXB 2.2 libraries to your Java's endorsed folder. I think it should only be the files 'jaxb-api.jar' and 'jaxb-impl.jar' that are included in the Essential Update tab that need to be copied to <PROTEGE_INSTALL>/jre/lib/endorsed (create 'endorsed' if it is not already there).
Restart Protege and it should use these JARs rather than those included with the Java 1.6 Runtime.

I think the most stable way forward is to be using Java 1.7 or higher, which means that you will need to download a Java Runtime if you don't already have one.

Let me know how you get on

Regards

Jonathan

[smroberts]

Hi, and thanks for coming back.

The version Ive installed is actually the standalone bundle from your site via a link shared to me by Sarah.

So I guess that has the older 1.6 jvm? Anyway all sorted now.

Thanks

Steve

[jonathan.carter]

Thanks for getting back to us.

We don't normally have any trouble with the standalone pack, so this is very useful feedback.

Jonathan