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owlcollab / owltools

OWLTools
BSD 3-Clause "New" or "Revised" License
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Don't include signature files in owltools-oort-all.jar #306

Closed alexhenrie closed 3 years ago

alexhenrie commented 3 years ago

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 commented 3 years ago

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

alexhenrie commented 3 years ago

@balhoff Could you take a look at this please?

balhoff commented 3 years ago

Thanks! Does this require a release?

alexhenrie commented 3 years ago

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 commented 3 years ago

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

alexhenrie commented 3 years ago

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 commented 3 years ago

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

Thanks, made this change in #309.