Hi Scooter, Glad you managed to get it working. JNI is always a bit painful. Not really familiar with OSGI workings but xom should only be used for writing CML (libiocml) if you’re not writing CML then this module isn’t needed and I would just exclude that.
Things also get fun with jnati if the user doesn’t have a home directory :-). Was actually tempted to patch JNIInChI to allow specification of the repo location (other than ~/.jnati/). It can be done via config files but there’s no way to pass this down to JNATI. Cheers, J On Dec 6, 2014, at 5:46 AM, Scooter Morris <[email protected]> wrote: > Hi all, > I wanted to give an update on my progress. I finally have things > working, but there were a couple of steps: > > 1) I had to add a "BundleSource" to jnati to support the loading from > OSGi bundles. This solved the "Unknown URL protocol: bundle" error. > 2) In my pom file, I had to specifically exclude xerces, xalan, and > xml-apis. Really old versions of these were getting pulled in by xom, > which seem to be a requirement in a couple of cdk modules (for cml?). > Once I did that, the cast failures went away. > > -- scooter > > 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 <[email protected]> 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 >> > > > ------------------------------------------------------------------------------ > 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=164703151&iu=/4140/ostg.clktrk > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------------------ 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=164703151&iu=/4140/ostg.clktrk _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
