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Don't include signature files in owltools-oort-all.jar#306

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balhoff merged 1 commit intoowlcollab:masterfrom
alexhenrie:filter-signatures
Oct 16, 2020
Merged

Don't include signature files in owltools-oort-all.jar#306
balhoff merged 1 commit intoowlcollab:masterfrom
alexhenrie:filter-signatures

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@alexhenrie alexhenrie commented Oct 8, 2020

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.

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alexhenrie commented Oct 8, 2020 •
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As a workaround, you could instead run zip OWLTools-Oort/bin/owltools-oort-all.jar -d META-INF/TESTKEY.RSA after ./build.sh.

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alexhenrie commented Oct 16, 2020

@balhoff Could you take a look at this please?

@balhoff balhoff merged commit 0109374 into owlcollab:master Oct 16, 2020
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balhoff commented Oct 16, 2020

Thanks! Does this require a release?

@alexhenrie alexhenrie deleted the filter-signatures branch October 16, 2020 15:34
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alexhenrie commented Oct 16, 2020

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.

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balhoff commented Oct 16, 2020

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

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alexhenrie commented Oct 16, 2020

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.

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balhoff commented Oct 16, 2020

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

Thanks, made this change in #309.

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