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From WP Roshan <suno...@gmail.com>
Subject Re: Apache cTakes-3.2.3 - Exception in thread "main" java.lang.NoClassDefFoundError: scala/ScalaObject ..... Caused by: java.lang.ClassNotFoundException: scala.ScalaObject
Date Thu, 06 Oct 2016 13:28:30 GMT
Hi Sean,

Thanks for the great information really appreciate that. I'll do what you
have suggested and let the community know If I encounter any issues that'll
help someone who have same issue to solve this.

By the way I would like to add some comment about your comment : - " It
looked to me like you do not want it (you commented it in
AggregatePlainText...)."

I actually didn't commented any lines of "AggregatePlaintextUMLSProcesso
r.xml" file comes with cTakes-3.2.3. instead what I did was un-comment the
commented lines in
https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml
comes as an original Apache repository file and ran the CAS Visual Debugger
and ClinicalPipelineWithUmls.java

I feel like I had miscommunication. but I hope it'll be clear now.


Regards,
Roshan




On Thu, Oct 6, 2016 at 6:28 PM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:

> Hi Roshan,
>
> The Assertion module provides the same attributes as the fully uncommented
> CuisOnly pipeline: polarity, uncertainty, generics and Subject.  The
> CuisOnly pipeline allows you to add them one-by-one using non-Assertion
> entries by uncommenting existing lines.  By default it does none of them,
> just extracts concepts.
>
> You can certainly replace the one-by-one with a single Assertion entry if
> and when you want.  It looked to me like you do not want it (you commented
> it in AggregatePlainText...).
>
> If you do want to use Assertion, you can look here for input and output
> information: https://cwiki.apache.org/confluence/display/CTAKES/
> cTAKES+3.0+-+Assertion
>
> There aren't standard outputs from these pipelines.  To generate .xmi
> files that can be used by the Cas Visual Debugger you have to specify an
> output generator - inaptly referred to as a "Cas Consumer" in the
> Collection Processing Engine (CPE) gui.  For basic usage, go here:
> https://cwiki.apache.org/confluence/display/CTAKES/
> cTAKES+3.1+User+Install+Guide#cTAKES3.1UserInstallGuide-
> CollectionProcessingEngine(CPE)
> Or, you can go straight to the author (uima) documentation here:
> https://uima.apache.org/downloads/releaseDocs/2.1.0-incubating/docs/html/
> tutorials_and_users_guides/tutorials_and_users_guides.html#ugr.tug.cpe
>
> The cas consumer that you want is probably ctakes-core,
> desc/cc/XmiWriterCasConsumer.xml
> However, if you are only interested in concepts, try the
> PrettyTextWriter.  Using this you won't need to navigate the xmi through
> the CVD.  For an example of "pretty" output check:
> http://52.26.219.218:8080/index.jsp
>
>
> There are other ways to do all of this, but for now the above information
> may get you started.
>
> Sean
>
>
> -----Original Message-----
> From: WP Roshan [mailto:sunone5@gmail.com]
> Sent: Thursday, October 06, 2016 8:29 AM
> To: dev@ctakes.apache.org
> Subject: Re: Apache cTakes-3.2.3 - Exception in thread "main" java.lang.NoClassDefFoundError:
> scala/ScalaObject ..... Caused by: java.lang.ClassNotFoundException:
> scala.ScalaObject
>
> Hi Sean,
>
> My goal is concept & concept-text extraction from xmi file. It was
> possible with cTakes-3.1.0 either way - I mean CAS Visual debugger or using
> ClinicalPipelineWithUmls.java.
> But cTakes-3.2.3 is not annotating Concept with "
> AggregatePlaintextUMLSProcessor.xml"
>
> Does "CuisOnlyPlaintextUMLSProcessor" support or will it do Assertion
> Annotation ?
>
> Roshan
>
> On Thu, Oct 6, 2016 at 5:43 PM, Finan, Sean <
> Sean.Finan@childrens.harvard.edu> wrote:
>
> > Hi W.P.,
> >
> > What is your goal for the run?  The easiest thing for you to do might
> > be trying the "CuisOnlyPlaintextUMLSProcessor" pipeline .xml .  That
> > will start you with a fast pipeline that provides cuis from dictionary
> lookup.
> > It has commented lines that you can uncomment, adding one module at a
> > time to see what they do.  With everything uncommented you will get
> > cuis, cuis for variations not in the dictionary (e.g. pluralities),
> > polarity, subject, and flags for generics, history of, and
> > uncertainty.  Once you have this in hand, to get more you can start
> > building out a fresh .xml to fit your desired pipeline.
> >
> > Sean
> >
> > -----Original Message-----
> > From: WP Roshan [mailto:sunone5@gmail.com]
> > Sent: Thursday, October 06, 2016 7:33 AM
> > To: dev@ctakes.apache.org; user@ctakes.apache.org
> > Subject: Apache cTakes-3.2.3 - Exception in thread "main" java.lang.
> NoClassDefFoundError:
> > scala/ScalaObject ..... Caused by: java.lang.ClassNotFoundException:
> > scala.ScalaObject
> >
> > Hi All,
> >
> > I have slightly modified cTakes-3.2.3 "AggregatePlaintextUMLSProcesso
> > r.xml"
> > ,in following location,
> >
> > cTakes-3.2.3\ctakes-clinical-pipeline\desc\analysis_engine\
> > AggregatePlaintextUMLSProcessor.xml
> >
> > Original AggregatePlaintextUMLSProcessor.xml file had following
> > directives but commented. I just comment-off bellow directives because
> > I need to get concept annotated in CAS Visual Debugger (CVD) and as
> > well as producing xmi file running after ClinicalPipelineWithUmls.java
> > file as standalone way.
> >
> > Please note that without any modification to
> > AggregatePlaintextUMLSProcessor.xml
> > file, CAS Visual Debugger (CVD) and ClinicalPipelineWithUmls.java
> > perfectly ran ( independently ) but did not annotated any concept and
> concept types.
> >
> > comment-off around line number 75
> > ------------------------------------------------------------
> > -------------------
> > <delegateAnalysisEngine key="AssertionAnnotator">
> >       <import
> > location="../../../ctakes-assertion/desc/AssertionMiniPipelineAnalysis
> > E
> > ngine.xml"/>
> > </delegateAnalysisEngine>
> >
> >
> > comment-off around line number 161
> > -----------------------------------------------------------
> > <node>AssertionAnnotator</node>
> >
> >
> > comment-off around line number 217
> > -----------------------------------------------------------
> > <type
> > allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.
> > LookupWindowAnnotation</type>
> >
> > But I got following issues when I ran CAS Visual Debugger (CVD) and
> > ClinicalPipelineWithUmls.java independently.
> >
> > ClinicalPipelineWithUmls.java - Error occurred with modified
> > AggregatePlaintextUMLSProcessor.xml
> > ############################################################
> > #########################
> > Started org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls at
> > Thu Oct 06 16:09:33 IST 2016
> > log4j: reset attribute= "false".
> > log4j: Threshold ="null".
> > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > log4j: Setting [ProgressAppender] additivity to [false].
> > log4j: Level value for ProgressAppender is  [INFO].
> > log4j: ProgressAppender level set to INFO
> > log4j: Class name: [org.apache.log4j.ConsoleAppender]
> > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> > log4j: Setting property [conversionPattern] to [%m].
> > log4j: Adding appender named [noEolAppender] to category
> > [ProgressAppender].
> > log4j: Retreiving an instance of org.apache.log4j.Logger.
> > log4j: Setting [ProgressDone] additivity to [false].
> > log4j: Level value for ProgressDone is  [INFO].
> > log4j: ProgressDone level set to INFO
> > log4j: Class name: [org.apache.log4j.ConsoleAppender]
> > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> > log4j: Setting property [conversionPattern] to [%m%n].
> > log4j: Adding appender named [eolAppender] to category [ProgressDone].
> > log4j: Level value for root is  [INFO].
> > log4j: root level set to INFO
> > log4j: Class name: [org.apache.log4j.ConsoleAppender]
> > log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> > log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy
> > HH:mm:ss} %5p %c{1} - %m%n].
> > log4j: Adding appender named [consoleAppender] to category [root].
> > Reading from directory:
> > args[0]=../../../ctakes-clinical-pipeline/data/input/MS-Case-Study-1.t
> > xt
> > Outputting to directory:
> > args[1]=../../../ctakes-clinical-pipeline/data/output/xmi
> > 06 Oct 2016 16:09:35  INFO LvgCmdApiResourceImpl - Loading NLM Norm
> > and Lvg with config file = C:\eclipse-neon-work-space-1\
> > cTakes-3.2.3\ctakes-lvg-res\target\classes\org\apache\
> > ctakes\lvg\data\config\lvg.properties
> > 06 Oct 2016 16:09:35  INFO LvgCmdApiResourceImpl -   config file absolute
> > path =
> > C:\eclipse-neon-work-space-1\cTakes-3.2.3\ctakes-lvg-res\
> > target\classes\org\apache\ctakes\lvg\data\config\lvg.properties
> > 06 Oct 2016 16:09:35  INFO LvgCmdApiResourceImpl - cwd =
> > C:\eclipse-neon-work-space-1\cTakes-3.2.3\ctakes-clinical-pipeline
> > 06 Oct 2016 16:09:35  INFO LvgCmdApiResourceImpl - cd
> > C:\eclipse-neon-work-space-1\cTakes-3.2.3\ctakes-lvg-res\
> > target\classes\org\apache\ctakes\lvg\
> > 06 Oct 2016 16:09:36  INFO LvgCmdApiResourceImpl - cd
> > C:\eclipse-neon-work-space-1\cTakes-3.2.3\ctakes-clinical-pipeline
> > 06 Oct 2016 16:09:36  INFO ClearNLPDependencyParserAE - using Morphy
> > analysis? true Loading configuration.
> > Loading feature templates.
> > Loading lexica.
> > Loading model:
> > ............................................................
> > ............................
> > 06 Oct 2016 16:09:48  INFO Chunker - Chunker model file:
> > org/apache/ctakes/chunker/models/chunker-model.zip
> > 06 Oct 2016 16:09:49  INFO ContextDependentTokenizerAnnotator - Finite
> > state machines loaded.
> > 06 Oct 2016 16:09:49  INFO ConstituencyParser - Initializing parser...
> > 06 Oct 2016 16:09:54  INFO ContextAnnotator - Using left , right scope
> > sizes: 7 , 7
> > 06 Oct 2016 16:09:54  INFO ContextAnnotator - Using scope order:
> > LEFT,RIGHT
> > 06 Oct 2016 16:09:54  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
> > 06 Oct 2016 16:09:54  INFO ContextAnnotator - Using context analyzer:
> > org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
> > 06 Oct 2016 16:09:54  INFO NegationContextAnalyzer -
> > initBoundaryData() called for ContextInitializer
> > 06 Oct 2016 16:09:54  INFO ContextAnnotator - Using context consumer:
> > org.apache.ctakes.necontexts.negation.NegationContextHitConsumer
> > 06 Oct 2016 16:09:54  INFO ContextAnnotator - Using lookup window type:
> > org.apache.ctakes.typesystem.type.textspan.Sentence
> > 06 Oct 2016 16:09:54  INFO ContextAnnotator - Using focus type:
> > org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
> > 06 Oct 2016 16:09:54  INFO ContextAnnotator - Using context type:
> > org.apache.ctakes.typesystem.type.syntax.BaseToken
> > 06 Oct 2016 16:09:54  INFO AssertionAnalysisEngine - scope model file:
> > /C:/eclipse-neon-work-space-1/cTakes-3.2.3/ctakes-assertion-
> > res/target/classes/org/apache/ctakes/assertion/models/scope.model
> > 06 Oct 2016 16:09:54  INFO AssertionAnalysisEngine - cue model file:
> > /C:/eclipse-neon-work-space-1/cTakes-3.2.3/ctakes-assertion-
> > res/target/classes/org/apache/ctakes/assertion/models/cue.model
> > scope model:
> > /C:/eclipse-neon-work-space-1/cTakes-3.2.3/ctakes-assertion-
> > res/target/classes/org/apache/ctakes/assertion/models/scope.model
> > Exception in thread "main" java.lang.NoClassDefFoundError:
> > scala/ScalaObject at java.lang.ClassLoader.defineClass1(Native Method)
> > at java.lang.ClassLoader.defineClass(Unknown Source) at java.security.
> > SecureClassLoader.defineClass(Unknown Source) at
> > java.net.URLClassLoader.defineClass(Unknown
> > Source) at java.net.URLClassLoader.access$100(Unknown Source) 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.mitre.medfacts.i2b2.annotation.ScopeParser.<init>(ScopeParser.java
> > :22)
> > at
> > org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initializ
> > e(
> > AssertionAnalysisEngine.java:121)
> > at
> > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> > initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> > at
> > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> > initialize(PrimitiveAnalysisEngine_impl.java:156)
> > 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:
> > 254)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ASB(
> > AggregateAnalysisEngine_impl.java:431)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:37
> > 5)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > initialize(AggregateAnalysisEngine_impl.java:185)
> > 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:
> > 254)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ASB(
> > AggregateAnalysisEngine_impl.java:431)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:37
> > 5)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > initialize(AggregateAnalysisEngine_impl.java:185)
> > 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:
> > 254)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ASB(
> > AggregateAnalysisEngine_impl.java:431)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:37
> > 5)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > initialize(AggregateAnalysisEngine_impl.java:185)
> > 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.produceResource(UIMAFramework.java:314)
> > at
> > org.apache.uima.UIMAFramework.produceAnalysisEngine(
> > UIMAFramework.java:425)
> > at org.apache.uima.fit.pipeline.JCasIterable.iterator(
> > JCasIterable.java:76)
> > at
> > org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(
> > ClinicalPipelineWithUmls.java:76)
> > Caused by: java.lang.ClassNotFoundException: scala.ScalaObject 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) ... 47 more
> >
> >
> > CAS Visual Debugger (CVD) - Error occured with modified
> > AggregatePlaintextUMLSProcessor.xml
> > ############################################################
> > #######################################
> > 10/6/16 3:58:28 PM - 16:
> > org.apache.uima.tools.cvd.MainFrame.handleException(528): SEVERE:
> > scala/ScalaObject
> > java.lang.NoClassDefFoundError: scala/ScalaObject at
> > java.lang.ClassLoader.defineClass1(Native Method) at
> > java.lang.ClassLoader.defineClass(Unknown Source) at java.security.
> > SecureClassLoader.defineClass(Unknown Source) at
> > java.net.URLClassLoader.defineClass(Unknown
> > Source) at java.net.URLClassLoader.access$100(Unknown Source) 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.mitre.medfacts.i2b2.annotation.ScopeParser.<init>(ScopeParser.java
> > :22)
> > at
> > org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initializ
> > e(
> > AssertionAnalysisEngine.java:121)
> > at
> > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> > initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> > at
> > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> > initialize(PrimitiveAnalysisEngine_impl.java:156)
> > 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:
> > 254)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ASB(
> > AggregateAnalysisEngine_impl.java:431)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:37
> > 5)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > initialize(AggregateAnalysisEngine_impl.java:185)
> > 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:
> > 254)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init
> > ASB(
> > AggregateAnalysisEngine_impl.java:431)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:37
> > 5)
> > at
> > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
> > initialize(AggregateAnalysisEngine_impl.java:185)
> > 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$500(Unknown Source) at
> > java.awt.EventQueue$3.run(Unknown Source) at
> > java.awt.EventQueue$3.run(Unknown
> > Source) at java.security.AccessController.doPrivileged(Native Method)
> > at java.security.ProtectionDomain$JavaSecurityAccessImpl.
> > doIntersectionPrivilege(Unknown
> > Source)
> > at
> > java.security.ProtectionDomain$JavaSecurityAccessImpl.
> > doIntersectionPrivilege(Unknown
> > Source)
> > at java.awt.EventQueue$4.run(Unknown Source) at
> > java.awt.EventQueue$4.run(Unknown
> > Source) at java.security.AccessController.doPrivileged(Native Method)
> > at java.security.ProtectionDomain$JavaSecurityAccessImpl.
> > 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.
> ClassNotFoundException:
> > scala.ScalaObject 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) ... 77 more
> >
> >
> > I added following Scala dependency to
> > cTakes-3.2.3\ctakes-clinical-pipeline\pom.xml
> > cTakes-3.2.3\ctakes-assertion\pom.xml and as well as
> > cTakes-3.2.3\pom.xml file and ran "mvn clean install -U -DskipTests"
> > command and build was success.
> >
> > <!--
> > https://urldefense.proofpoint.com/v2/url?u=https-3A__
> > mvnrepository.com_artifact_org.scala-2Dtools.sbinary_
> > sbinary-5F2.9.0&d=CwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU
> > &r=
> > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=64oaaGH_-
> > 1KVM5eOR6CagMulGLYXMbfL2xdX-vnLwOE&s=BxnFFaQTuH3Qu4LPTR6S9FQjaiN-
> > 8UtfNfRzg3Ln7PU&e=  --> <dependency>
> >   <groupId>org.scala-tools.sbinary</groupId>
> >   <artifactId>sbinary_2.9.0</artifactId>
> >    <version>0.4.0</version>
> > </dependency>
> >
> > But either issues not solved but because of modified
> > AggregatePlaintextUMLSProcessor.xml file. My key requirement is
> > concept annotated in CAS visual debugger & and generated in xmi file
> > when ran after ClinicalPipelineWithUmls.java file.
> >
> > Anyone noted and do have solution for this?
> >
> > W.P.Roshan
> > --
> > SunONE
> >
>
>
>
> --
> SunONE
>



-- 
SunONE

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