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/AssertionMiniPipelineAnalysisE > 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.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 > -- SunONE
