Hi all,
I'm really struggling with jni-inchi and OSGi. There are two
problems I keep running into. First, I keep getting a warning:
WARN net.sf.jnati.deploy.repository.ClasspathRepository - Unknown URL
protocol: bundle
a little debugging and I can see that it's coming from:
TRACE net.sf.jnati.deploy.repository.ClasspathRepository - Manifest
location:
bundle://108.1:46/META-INF/jniinchi/1.03_1/LINUX-AMD64/MANIFEST.xml
So, jnati can't figure out what to do with the bundle URL. I know that
some work went into making p2 bundles of jni-inchi, but since I'm
working in Cytoscape, that doesn't help me much. Are the sources
available for those?
The second problem is probably not really jni-inchi related, but any
suggestions would be appreciated. Once things fail over to my local
cache, I get a class cast exception:
DEBUG net.sf.jnati.deploy.repository.LocalRepository - Artefact path:
/home/scooter/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64
INFO net.sf.jnati.deploy.artefact.ManifestReader - Reading manifest
pool-19-thread-1 WARN [edu.ucsf.rbvi.chemViz2.internal.model.Compound] -
Structure generation failed:
org.apache.xerces.jaxp.DocumentBuilderFactoryImpl cannot be cast to
javax.xml.parsers.DocumentBuilderFactory
java.lang.ClassCastException:
org.apache.xerces.jaxp.DocumentBuilderFactoryImpl cannot be cast to
javax.xml.parsers.DocumentBuilderFactory
at javax.xml.parsers.DocumentBuilderFactory.newInstance(Unknown Source)
at
net.sf.jnati.deploy.artefact.ManifestReader.read(ManifestReader.java:50)
at
net.sf.jnati.deploy.source.ArtefactSource.loadManifest(ArtefactSource.java:43)
at
net.sf.jnati.deploy.NativeArtefactLocator.findArtefactInLocalRepository(NativeArtefactLocator.java:147)
at
net.sf.jnati.deploy.NativeArtefactLocator.getArtefact(NativeArtefactLocator.java:66)
at
net.sf.jnati.deploy.NativeLibraryLoader.loadLibrary(NativeLibraryLoader.java:48)
at
net.sf.jnati.deploy.NativeLibraryLoader.loadLibrary(NativeLibraryLoader.java:42)
at
net.sf.jnati.deploy.NativeLibraryLoader.loadLibrary(NativeLibraryLoader.java:38)
at net.sf.jniinchi.JniInchiWrapper.loadLibrary(JniInchiWrapper.java:87)
at
org.openscience.cdk.inchi.InChIGeneratorFactory.<init>(InChIGeneratorFactory.java:88)
at
org.openscience.cdk.inchi.InChIGeneratorFactory.getInstance(InChIGeneratorFactory.java:107)
I've tried several workarounds, but nothing has really fixed things
yet. Looking at the manifest file for my app, xalan gets pulled in from
somewhere, but I can't figure out who's pulling it in. As near as I can
tell, nothing in cdk or jni-inchi, or my app uses it.
Thanks in advance!
-- scooter
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