Hi all,
A quick update. Turns out that cdk has a dependency on xalan and
xerces comes from xom <http://www.xom.nu/> 1.2.5, which pulls in both of
these. xom is used by cdk-qsar, cdk-qsarmolecular, and cdk-dict. Not
sure how necessary xom is, but that's the source of the hard dependency
that's bringing in the apache xml packages.
-- scooter
On 11/25/2014 08:22 AM, Scooter Morris wrote:
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 ...
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!
-- scooter
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