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From Tommaso Teofili <tommaso.teof...@gmail.com>
Subject Re: Clerezza and UIMA
Date Wed, 13 Feb 2013 15:41:19 GMT
Hi Greg,

thanks for exploring it further, I'll have a look myself at the bug and let
you know.

Thanks,
Tommaso


2013/2/13 Greg Holmberg <holmberg2066@comcast.net>

> I tried it also with JDK 1.6.0_38 and got the same result.
>
> Further searching on the Clerezza mailing list revealed this issue, which
> I think is the root cause of my problem:
>
> https://issues.apache.org/jira/browse/CLEREZZA-724
>
> The reporter of this issue supplied a patch (to
> ext.com.hp.hpl.jena.tdb/pom.xml), but it hasn't been applied yet.  I will
> get the Clerezza source code, apply the patch, build it, and see if it
> changes anything for me.
>
> Greg
>
> ------------------------------
> *From: *"Greg Holmberg" <holmberg2066@comcast.net>
> *To: *"Tommaso Teofili" <tommaso.teofili@gmail.com>
> *Cc: *"uima user" <user@uima.apache.org>
> *Sent: *Tuesday, February 12, 2013 1:21:56 AM
>
> *Subject: *Re: Clerezza and UIMA
>
> Hi Tom maso--
>
>
> Regarding the classloader, the purpose is to make the UIMAClassLoader the
> default for the thread. The UIMAClassLoader has all the classes in the AE
> Pear (which the boot classloader doesn't have--i.e. they weren't on the
> command-line -cp). Without it being the default for the thread, some
> dynamically loaded classes can't be found. For example, when using the
> Clerezza libs, if I leave out the line that says
> thread.setContextClassLoader(uimaClassLoader), then I get:
>
> org.apache.clerezza.rdf.core.serializedform.UnsupportedSerializationFormatException:
> No serializer available for application/rdf+xml
> at
> org.apache.clerezza.rdf.core.serializedform.Serializer.serialize(Serializer.java:142)
>
>
> I'm guessing that the serializers (implementations of an interface) ARE
> loaded dynamically, and can be found in the
> org.apache.clerezza.rdf.jena.serializer Jar, which is in the Pear file, but
> not on the command line classpath. Somehow, when the above method, called
> from my annotator's process() method somewhere below
> AnalysisEngine.process(), tries to load those classes, it doesn't use the
> UIMA classloader, but rather the thread's context classloader, which falls
> back to the boot loader, which can't find them.
>
> On the other hand, if I do set the thread's context classloader to the
> UIMA classloader, then I get the LinkageError for Xerces:
>
> Exception in thread "TAService Worker 0" java.lang.LinkageError: loader
> constraint violation in interface itable initialization: when resolving
> method
> "org.apache.xerces.dom.ElementImpl.getSchemaTypeInfo()Lorg/w3c/dom/TypeInfo;"
> the class loader (instance of
> org/apache/uima/internal/util/UIMAClassLoader) of the current class,
> org/apache/xerces/dom/ElementImpl, and the class loader (instance of
> <bootloader>) for interface org/w3c/dom/Element have different Class
> objects for the type m/TypeInfo; used in the signature
>
> So it seems I'm damn if I do, damned it I don't. How do I get out of this
> catch-22?
>
> By the way, I'm using Oracle JDK 1.7.0_10, in case that matters. I'll also
> try going back to 1.6.0 tomorrow to see if that makes any difference.
>
>
> Thanks,
>
> Greg
>
>
>
> ----- Original Message -----
> From: "Tommaso Teofili" <tommaso.teofili@gmail.com>
> To: "Greg Holmberg" <holmberg2066@comcast.net>
> Cc: "uima user" <user@uima.apache.org>
> Sent: Monday, February 11, 2013 12:35:56 AM
> Subject: Re: Clerezza and UIMA
>
>
> H Greg,
>
>
> the code you're referring to [1] is used essentially for OSGi deployments,
> where each bundle (the package jars) have their own Classloader and
> essentially that would create issues when trying to instantiate AEs whose
> classes are in different bundles than the one which "contains" the UIMA
> framework.
> The way it works is just that each bundle which needs to use UIMA has to
> declare its UIMA components into an OSGi activator extending the
> UIMABundleActivator and thus implementing the #classRegistered method, see
> an example:
>
>
> @Override
>   protected void classRegistered() {
>     classLoaderRepository.registerComponent(SomeAnnotator.class);
>   }
>
>
> In the code you've shown it seems you're redefining the Classloader
> instance to be used by UIMAFramework and also forcing it into the current
> thread, as far as I have seen this is often done in OSGi deployments but I
> wonder if that's your scenario or not, and if not which container are you
> trying to instantiate UIMA into so that we can better understand what's the
> linkage problem coming from.
>
>
> Regards,
> Tommas
>
>
> [1] :
> http://svn.apache.org/repos/asf/incubator/clerezza/trunk/uima/uima.utils/
>
>
>
> 2013/2/7 Greg Holmberg < holmberg2066@comcast.net >
>
>
>
>
> Hi Tommaso--
>
>
> Sorry for the direct email, but you seem to be the expert on combining
> UIMA and Clerezza.
>
> I'm trying to generate RDF from my UIMA AE. I started with the code in
> RDFCASConsumer.java and modified it to change the directory and file to
> which the RDF is written.
>
> I put this in my AE and deployed it in UIMA, running in my own container.
> This container does this:
>
> AnalysisEngine engine = UIMAFramework.produceAnalysisEngine(...);
> ClassLoader uimaClassLoader =
> engine.getResourceManager().getExtensionClassLoader();
> Thread thread = Thread.currentThread();
> thread.setContextClassLoader(uimaClassLoader);
> engine.process(cas);
>
> When I run I get:
>
> Exception in thread "TAService Worker 0" java.lang.LinkageError: loader
> constraint violation in interface itable initialization: when resolving
> method
> "org.apache.xerces.dom.ElementImpl.getSchemaTypeInfo()Lorg/w3c/dom/TypeInfo;"
> the class loader (instance of
> org/apache/uima/internal/util/UIMAClassLoader) of the current class,
> org/apache/xerces/dom/ElementImpl, and the class loader (instance of
> <bootloader>) for interface org/w3c/dom/Element have different Class
> objects for the type m/TypeInfo; used in the signature
>
>
> I see several issues in Clerezza about UIMA and classloaders, which you
> have resolved. There's even a method that gets the classloader to be used
> for XML parsing.
>
> So it seems like you've probably solved this problem related to Xerces and
> classloaders. However, I can't find any documentation about how to use your
> fix.
>
> Can you tell me what I need to do when creating my analysis engine and
> setting the classloader in order to avoid this LinkageError?
>
> Thanks,
>
>
> Greg Holmberg
>
>
>
>
>
>
>

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