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.fi...@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:suno...@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.fi...@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:suno...@gmail.com] > > Sent: Thursday, October 06, 2016 7:33 AM > > To: dev@ctakes.apache.org; u...@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
