(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 ... > 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? > 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... Egon 0.http://www.jcheminf.com/content/5/1/14 -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/EgonWillighagen ------------------------------------------------------------------------------ Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
