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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
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 12:13:37 GMT
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 "AggregatePlaintextUMLSProcessor.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/AssertionMiniPipelineAnalysisEngine.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.txt
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.initialize(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.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
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.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
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.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
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.initialize(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.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
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.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
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
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