On 11/25/2014 12:07 AM, Egon Willighagen wrote: > (Arvid: can you have a glance at this email too, please?) > > Scooter, > > On Tue, Nov 25, 2014 at 3:15 AM, Scooter Morris <scoo...@cgl.ucsf.edu> wrote: >> I'm really struggling with jni-inchi and OSGi. There are two >> problems I keep running into. First, I keep getting a warning: > Yeah, it's an annoying combination... it would be so good for the > InChI if there was a native Java library... > >> 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 > I have seen this before, but don't remember what came out of that... > >> 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? > OSGi bundles have been prepared by Arvid, see [0], and available from: > > https://github.com/bioclipse/bioclipse.core/tree/master/net.bioclipse.target.platform/libs > > I think you need the three jnati jars, the jni-inchi, and > net.bioclipse.sea36.util.config.jar ... OK, I'll give those a try. Are the sources available anywhere for the wrappers? > >> 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 > Ah, there is Xerces again... it seems to me you have more than one > Xerces on your classpath... does your plugin pull in a second copy of > this library? Not explicitly, but I did see that cdk was explicitly loading Xerces using loadClass (!?!) for some reason. It apparently uses SAXParser from xerces explicitly for CMLReader, EventCMLReader, OWLAtomTypeReader, AtomTypeReader, OWLAtomTypeMappingReader, IsotopeReader, and INChIReader. > >> 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. > These Xerces issues have been annoying me for some 15 years now, and > they are hard to fix... > > JNI-InChI should indeed not depend on Xerces... > > I think I remember someone using Maven to show a full dependency tree, > but no idea if a similar thing exists for Eclipse... No idea -- I don't use Eclipse much. All of this is for Cytoscape. > > Egon > > 0.http://www.jcheminf.com/content/5/1/14 > Thanks!
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