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From digital paula <cybersat...@hotmail.com>
Subject RE: Question on Regular Expression Annotator - Last issue resolved, on to next and likely last issue with this addon :-)
Date Thu, 31 Oct 2013 04:19:32 GMT
Hi Again,
 
Ok so I didn't exactly resolve the last issue I just put the concepts file into the UIMA examples
folder....as a sort of workaround.  I did reset the data path to the regular expression project
in the xml descriptor but it didn't get picked up during execution.
 
I executed the Document Analyzer and it became abundantly clear that the issue I had earlier
with the dependencies in Maven was not resolved via quick fix in Eclipse.   
 
I installed the latest XMLBeans and did a SCOMP to generate the JAR in the Regular Annotator
project from the XMLSchema.xsd and added itto project classpath.     The error I got when
trying to execute Document Analyzer was this:
 
Caused by: java.lang.ClassNotFoundException: schemaorg_apache_xmlbeans.system.s4DE0C4BDB0BE7CAF27A97C2453FE4641.TypeSystemHolder
 
What the program is looking for is this:
path\target\generated-classes\xmlbeans\schemaorg_apache_xmlbeans\system\s4DE0C4BDB0BE7CAF27A97C2453FE4641
 
but the JAR has a different string of numeric/chars in the last part of the path.   Please
see attached for illustration.
 
Stepping through the code this time didn't help at all.  
 
Would appreciate any assistance on this.   I tried generating the JAR file on all the historical
XML Beans XMLSchema.xsd file and some of them were equal to each other but none of them matched
the generation I need:....system\s4DE0C4....
 
Regards,
Paula
 
Oh, by the way the last post was actually my first post but not sure why it got posted so
late and out of sequence.
 
------Complete Java Error ---------------------------
Exception in thread "AWT-EventQueue-0" java.lang.ExceptionInInitializerError

 
	at org.apache.incubator.uima.regex.ConceptSetDocument$Factory.parse(ConceptSetDocument.java:163)

	at org.apache.uima.annotator.regex.impl.ConceptFileParser_impl.parseConceptFile(ConceptFileParser_impl.java:66)

	at org.apache.uima.annotator.regex.impl.RegExAnnotator.initialize(RegExAnnotator.java:139)

	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)

	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:158)

	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)

	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)

	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)

	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)

	at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)

	at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)

	at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)

 


	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)

	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)

	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)

	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)

	at javax.swing.AbstractButton.doClick(Unknown Source)

	at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)

	at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)

	at java.awt.Component.processMouseEvent(Unknown Source)

	at javax.swing.JComponent.processMouseEvent(Unknown Source)

	at java.awt.Component.processEvent(Unknown Source)

	at java.awt.Container.processEvent(Unknown Source)

	at java.awt.Component.dispatchEventImpl(Unknown Source)

	at java.awt.Container.dispatchEventImpl(Unknown Source)

	at java.awt.Component.dispatchEvent(Unknown Source)

	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)

	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)

	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)

	at java.awt.Container.dispatchEventImpl(Unknown Source)

	at java.awt.Window.dispatchEventImpl(Unknown Source)

	at java.awt.Component.dispatchEvent(Unknown Source)

	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)

	at java.awt.EventQueue.access$200(Unknown Source)

	at java.awt.EventQueue$3.run(Unknown Source)

	at java.awt.EventQueue$3.run(Unknown Source)

 
	at java.security.AccessController.doPrivileged(Native Method) 
 


	at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)

	at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)

	at java.awt.EventQueue$4.run(Unknown Source)

	at java.awt.EventQueue$4.run(Unknown Source)

 
	at java.security.AccessController.doPrivileged(Native Method) 
 


	at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)

	at java.awt.EventQueue.dispatchEvent(Unknown Source)

	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)

	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)

	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)

	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)

	at java.awt.EventDispatchThread.run(Unknown Source)

 
Caused by: java.lang.RuntimeException: Cannot load SchemaTypeSystem. Unable to load class
with name schemaorg_apache_xmlbeans.system.s4DE0C4BDB0BE7CAF27A97C2453FE4641.TypeSystemHolder.
Make sure the generated binary files are on the classpath.

	at org.apache.xmlbeans.XmlBeans.typeSystemForClassLoader(XmlBeans.java:783)

	at org.apache.incubator.uima.regex.ConceptSetDocument.<clinit>(ConceptSetDocument.java:20)

 


	... 50 more

 
Caused by: java.lang.ClassNotFoundException: schemaorg_apache_xmlbeans.system.s4DE0C4BDB0BE7CAF27A97C2453FE4641.TypeSystemHolder

 


	at java.net.URLClassLoader$1.run(Unknown Source)

	at java.net.URLClassLoader$1.run(Unknown Source)

 
	at java.security.AccessController.doPrivileged(Native Method) 
 


	at java.net.URLClassLoader.findClass(Unknown Source)

	at java.lang.ClassLoader.loadClass(Unknown Source)

	at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)

	at java.lang.ClassLoader.loadClass(Unknown Source)

 
	at org.apache.xmlbeans.XmlBeans.typeSystemForClassLoader(XmlBeans.java:769) 
 


	... 51 more> From: cybersation@hotmail.com
> To: user@uima.apache.org
> Subject: RE: Question on Regular Expression Annotator - Current Issue almost resolved
> Date: Wed, 30 Oct 2013 00:52:49 -0400
> 
> All,
>  
> Please disregard previous post.   I stepped through the code and see what the problem
is, the dataPathElements is storing the path to the UIMA examples and not the RegExpressionAnnotator
project.   I should be able to correct it.
>  
> Marshall, I do appreciate your help with getting me set up with the correct install.
 
>  
> Regards,
> Paula
>  
> > From: cybersation@hotmail.com
> > To: user@uima.apache.org
> > Subject: RE: Question on Regular Expression Annotator - Previous issue resolved,
on to next issue :-)
> > Date: Tue, 29 Oct 2013 22:08:36 -0400
> > 
> > Marshall et al,
> >  
> > I was able to solve the problem, just applied the quick fixes in eclipse.  Apparently
it's a common problem with Maven dependency plugin:
> > http://www.journaldev.com/503/how-to-fix-maven-dependency-plugin-goals-copy-dependencies-unpack-is-not-supported-by-m2e-in-eclipse
> >  
> > The only problem I have now is executing the regular expression annotator, the concepts
file is not being found.     I tested the reg expression annotator in the document analyzer
tool.   I checked and I do see that it's in the resource directory.  I've tried specifically
typing in the path(resources/concepts.xml) on the parameter settings tab in the descriptor
file but the concepts file is just not being picked up.   
> >  
> > Thanks and appreciate anyone's help on this.
> >  
> > Regards,
> > Paula
> >  
> >  
> > Here's the specific error from below:  Caused by: org.apache.uima.annotator.regex.impl.RegexAnnotatorConfigException:
"The resource file concepts.xml could not be found."
> >  
> > -----the entire error-----------------------------------------org.apache.uima.resource.ResourceInitializationException:
Initialization of annotator class "org.apache.uima.annotator.regex.impl.RegExAnnotator" failed.
 (Descriptor: file:/C:/Users/SemanticPrincess/UIMAWorkspaceJuno/RegularExpressionAnnotator/desc/RegExAnnotator.xml)
> > 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:254)
> > 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:158)
> > 	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> > 	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> > 	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> > 	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> > 	at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:255)
> > 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429)
> > 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373)
> > 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186)
> > 	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> > 	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> > 	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> > 	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
> > 	at org.apache.uima.tools.docanalyzer.DocumentAnalyzer.runProcessingThread(DocumentAnalyzer.java:1223)
> > 	at org.apache.uima.tools.docanalyzer.DocumentAnalyzer$ProcessingThread.run(DocumentAnalyzer.java:1332)
> > Caused by: org.apache.uima.annotator.regex.impl.RegexAnnotatorConfigException: "The
resource file resources/concepts.xml could not be found."
> > 	at org.apache.uima.annotator.regex.impl.RegExAnnotator.initialize(RegExAnnotator.java:127)
> > 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> > 	... 15 more
> > org.apache.uima.resource.ResourceInitializationException: Initialization of annotator
class "org.apache.uima.annotator.regex.impl.RegExAnnotator" failed.  (Descriptor: file:/C:/Users/SemanticPrincess/UIMAWorkspaceJuno/RegularExpressionAnnotator/desc/RegExAnnotator.xml)
> > 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:254)
> > 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:158)
> > 	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> > 	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> > 	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> > 	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
> > 	at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:255)
> > 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429)
> > 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373)
> > 	at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186)
> > 	at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
> > 	at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
> > 	at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
> > 	at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
> > 	at org.apache.uima.tools.docanalyzer.DocumentAnalyzer.runProcessingThread(DocumentAnalyzer.java:1223)
> > 	at org.apache.uima.tools.docanalyzer.DocumentAnalyzer$ProcessingThread.run(DocumentAnalyzer.java:1332)
> > Caused by: org.apache.uima.annotator.regex.impl.RegexAnnotatorConfigException: "The
resource file concepts.xml could not be found."
> > 	at org.apache.uima.annotator.regex.impl.RegExAnnotator.initialize(RegExAnnotator.java:127)
> > 	at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> > 	... 15 more
> >    
> >  
> >  
> > 
> >  
> > From: cybersation@hotmail.com
> > To: user@uima.apache.org
> > Subject: FW: Question on Regular Expression Annotator - please disregard previous
post this one is correct
> > Date: Tue, 29 Oct 2013 12:42:11 -0400
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > Hi Marshall,
> > First of all thanks for your prompt response.  Per your recommendation, I did the
tag check out using the link you provided but ran into an error on the maven install with
the 'import maven projects' screen please see attached image.   There was an error with the
'uima-build-helper-maven-plugin'.  I continued with install to resolve later.    After installation
there was a problem with the POM file.  I opened up the POM file, the overview page  states
an error with the "maven-dependency-plugin(goals "copy-dependencies", "unpack") is not supported
by m2e".     The second problem (from description section of eclipse project) states that
"plugin execution not covered by  lifecycle configuration org.apache.uima:uima-build-helper-maven-plugin:2:parse-date-time(execution:
setbuildYear and buildMonth, phase:validate)"
> > I do appreciate your personal assistance with this.     In the meantime, I'll be
reading up on the differences between trunks, tags and branches.  :-)
> > Regards,Paula
> > > Date: Tue, 29 Oct 2013 10:15:35 -0400
> > > From: msa@schor.com
> > > To: user@uima.apache.org
> > > Subject: Re: Question on Regular Expression Annotator - please disregard previous
post this one is correct
> > > 
> > > Hi,
> > > 
> > > It looks like you're working with the "trunk" level of the source.
> > > 
> > > The trunk level sometimes doesn't build, as people are working on it...
> > > 
> > > If you want to build a "released" level, just check out a tag, rather than
the
> > > trunk.  For instance, you could check out of SVN the last release tag, here:
> > > https://svn.apache.org/repos/asf/uima/addons/tags/uima-addons-2.3.1/RegularExpressionAnnotator
> > > 
> > > If you want to work with the trunk, you will need to check out, also, the project:
> > > uima-addons-parent, and build it using "mvn install".  This will create the
> > > missing 2.3.2-SNAPSHOT version of this artifact in your local Maven .m2
> > > repository, and that will fix the problem of it not being found...
> > > 
> > > Cheers. -Marshall
> > > 
> > > On 10/28/2013 10:30 PM, digital paula wrote:
> > > > Hi again,
> > > > When I did a maven install via Eclipse it resolved the issues that I had
in my previous post.   The only error that I have now is with the build.  
> > > > In the POM file there's a problem with this part:  <parent>    <groupId>org.apache.uima</groupId>
   <artifactId>uima-addons-parent</artifactId>    <version>2.3.2-SNAPSHOT</version>
   <relativePath>../uima-addons-parent</relativePath>  </parent>  It states
on the overview tab the following Project build error:  "Non-resolvable parent POM: could
not find artifact org.apac
> > > > Project build error: Non-resolvable parent POM: Could not find artifact
org.apache.uima:uima-addons-parent:pom:2.3.2-SNAPSHOT and 'parent.relativePath' points at
wrong local POM
> > > > I did find a similar problem on the user archives that with the parent
POM but it was for the simple server addon:http://mail-archives.apache.org/mod_mbox/uima-user/201206.mbox/browser
> > > > Would appreciate any help on this. 
> > > > Thanks.
> > > > Regards,Paula
> > > > From: cybersation@hotmail.com
> > > > To: user@uima.apache.org
> > > > Subject: Question on Regular Expression Annotator
> > > > Date: Mon, 28 Oct 2013 12:59:11 -0400
> > > >
> > > >
> > > >
> > > >
> > > > Hi,
> > > >  
> > > > I had completed most of the tutorials on UIMA Framework (though I wasn't
able to do the semantic search due to it not being open source anymore and removed from the
uimaj-examples folder :-(  I came across a reference to the Lemur Project while researching
alternatives and after an evening trying to get it working just ended up scrapping it all
together.  I was able to install the PEAR via the PEAR installation tool but when testing
it crashed due to unable to resolve  references to org.ibm.apache  that no longer existed
so I imported project into Eclipse and changed the references in the java file to java.org.apache
and still ran into problems with the CVD tool, the  indriCASconsumer descriptor was not finding
the java class.   I'm going to look into Solr next since I see it's a more recent semantic
search tool.
> > > >  
> > > > In the meantime, I am trying to work with the regular expression annotator
add on.  I had installed the regular expression annotator via SVN within Eclipse as a separate
project.   http://svn.apache.org/repos/asf/uima/addons/trunk/RegularExpressionAnnotator/
> > > >  
> > > > The problem I had first off was that the reference in each java file was
'package org.apache.uima.annotator.regex' but the build path for the directories was main.java.org.apache.uima.annotator.regex
in the project.  This was resolved by the quick fix in java to change all the package names
in the files to have the correct package name of  main.java.org.apache.uima.annotator.regex.
 
> > > >  
> > > > In addition, I just manually changed the import names such as:  'import
org.apache.uima.annotator.regex.Position' to 
> > > > 'import main.java.org.apache.uima.annotator.regex.Position'
> > > >  
> > > > However I ran into a bit of a snag when I came across these to imports
in the java file ConceptFileParser_Imp.java
> > > > I don't know how to resolve the error (the imports are not resolved) 
since I don't see incubator anywhere in the project and I'm not expert enough at Java to resolve
the second one:
> > > > import org.apache.incubator.uima.regex.AnnotationDocument;
> > > > import org.apache.xmlbeans.XmlError;
> > > >  
> > > > Would appreciate any help. 
> > > >  
> > > > Thanks.
> > > >  
> > > > Regards,
> > > > Paula
> > > >  
> > > >
> > > >  
> > > >  
> > > >  
> > > >  
> > > >  
> > > >  
> > > >  
> > > >  
> > > >  
> > > >  
> > > >  
> > > >  		 	   		   		 	   		  
> > > 
> >  		 	   		   		 	   		   		 	   		  
>  		 	   		  
 		 	   		  
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