Stop shipping unshaded fat jars

[ctrueden]

A "fat jar" is a JAR that bundles some or all of its dependencies with it. This may be fine if the dependencies are shaded (i.e., their packages are renamed). But in many cases such as the JRuby and Jython uberjars, at least some of the dependencies are not shaded. This causes problems because there are often then multiple versions of the same library available on the classpath from multiple fat jars. To avoid this problem, the Fiji update site should not include any such unshaded fat jars, but instead ship only individual JAR libraries for all its components.

[fcollman]

The proposed fixed of deleting jruby-complete.jar does not appear to work anymore to fix jython os.path modules.. i am still getting the error after deleting jruby-complete

[ctrueden]

See also Fiji BugZilla bug #741.

[ctrueden]

See also http://thread.gmane.org/gmane.comp.java.imagej/33501

[ctrueden]

As a workaround, you can delete jffi-1.2.7.jar and Jython will work again.

I figured this out as follows:

• Plugins > Utilities > Find Jar for Class
• Paste name of problematic class from the exception: com.kenai.jffi.InvocationBuffer
• Click OK

Note the warning that appears about how the class is present in two different locations.

[ctrueden]

I fixed Jython. And we already split up JRuby. That just leaves Batik, I think!

[ctrueden]

Progress:

• scijava/pom-scijava@11c9596
• fiji/SNT@82ba66f
• trackmate-sc/TrackMate@af5bb36
• fiji/IO@370e18d

Releases coming soon! Then batik will be fixed, and Fiji will no longer ship any uber-JARs.

[ctrueden]

All is complete, and uploaded to the Java-8 update site. However, there is currently a bug in the updater which prevents marking files obsolete on downstream update sites. So, I cannot remove the old batik uber-JAR yet. As soon as we find a workaround, I'll close this issue.

[bramalingam]

@ctrueden : The workflow (of opening an .msr file with the Java8 update site enabled) works without any issues on the Bio-Formats side, on Windows. (This was previously failing due to dependency clashes)

[ctrueden]

@bramalingam Thanks for the feedback. Glad it is working for your needs. I will close this issue now since all is resolved on the coding side. The removal of the batik uber-JAR will take place when we migrate the Java-8 components back to the core Fiji and ImageJ update sites, hopefully soon.