Re: [Cdk-user] jni-inchi and OSGi

[John M. <joh...@gm...>]

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 <sc...@cg...> 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 <sc...@cg...> 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
>> 
> 
> 
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