Don't include signature files in owltools-oort-all.jar

[alexhenrie]

The problem described in pull request #299 has popped up again:

$ ./OWLTools-Oort/bin/ontology-release-runner
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.SecurityException: Invalid signature file digest for Manifest main attributes
        at sun.security.util.SignatureFileVerifier.processImpl(SignatureFileVerifier.java:330)
        at sun.security.util.SignatureFileVerifier.process(SignatureFileVerifier.java:263)
        at java.util.jar.JarVerifier.processEntry(JarVerifier.java:318)
        at java.util.jar.JarVerifier.update(JarVerifier.java:230)
        at java.util.jar.JarFile.initializeVerifier(JarFile.java:383)
        at java.util.jar.JarFile.ensureInitialization(JarFile.java:617)
        at java.util.jar.JavaUtilJarAccessImpl.ensureInitialization(JavaUtilJarAccessImpl.java:69)
        at sun.misc.URLClassPath$JarLoader$2.getManifest(URLClassPath.java:991)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:451)
        at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:418)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:351)
        at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:495)

Copying the signature filter from OWLTools-Runner/pom.xml to OWLTools-Oort/pom.xml resolves the problem.

[alexhenrie]

As a workaround, you could instead run zip OWLTools-Oort/bin/owltools-oort-all.jar -d META-INF/TESTKEY.RSA after ./build.sh.

[alexhenrie]

@balhoff Could you take a look at this please?

[balhoff]

Thanks! Does this require a release?

[alexhenrie]

Thank you! My lab at the University of Utah has just been cloning the latest version from the Git repository, so we don't need a new release here. I would check to see whether the last prebuilt release has this problem but I get the error "Unable to create the home directory ‘/srv/nfs/share/jenkins’" when I try to visit the download page.

[balhoff]

For the last release we started using the github releases downloads. The Berkeley server is out of commission.

[alexhenrie]

Oh okay. It would be nice to remove the link to the Berkeley server from README.md then. Anyway, it looks like the last release still works fine without any workarounds.

[balhoff]

It would be nice to remove the link to the Berkeley server from README.md then.

Thanks, made this change in #309.