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 "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
