Return-Path: X-Original-To: archive-asf-public-internal@cust-asf2.ponee.io Delivered-To: archive-asf-public-internal@cust-asf2.ponee.io Received: from cust-asf.ponee.io (cust-asf.ponee.io [163.172.22.183]) by cust-asf2.ponee.io (Postfix) with ESMTP id 2F67E200BA7 for ; Thu, 6 Oct 2016 13:33:38 +0200 (CEST) Received: by cust-asf.ponee.io (Postfix) id 2DD4B160AE0; Thu, 6 Oct 2016 11:33:38 +0000 (UTC) Delivered-To: archive-asf-public@cust-asf.ponee.io Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by cust-asf.ponee.io (Postfix) with SMTP id 2ACE0160AAD for ; Thu, 6 Oct 2016 13:33:36 +0200 (CEST) Received: (qmail 64178 invoked by uid 500); 6 Oct 2016 11:33:35 -0000 Mailing-List: contact user-help@ctakes.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: user@ctakes.apache.org Delivered-To: mailing list user@ctakes.apache.org Received: (qmail 64154 invoked by uid 99); 6 Oct 2016 11:33:34 -0000 Received: from pnap-us-west-generic-nat.apache.org (HELO spamd4-us-west.apache.org) (209.188.14.142) by apache.org (qpsmtpd/0.29) with ESMTP; Thu, 06 Oct 2016 11:33:34 +0000 Received: from localhost (localhost [127.0.0.1]) by spamd4-us-west.apache.org (ASF Mail Server at spamd4-us-west.apache.org) with ESMTP id 672CCC059C; Thu, 6 Oct 2016 11:33:34 +0000 (UTC) X-Virus-Scanned: Debian amavisd-new at spamd4-us-west.apache.org X-Spam-Flag: NO X-Spam-Score: 2.629 X-Spam-Level: ** X-Spam-Status: No, score=2.629 tagged_above=-999 required=6.31 tests=[DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, FREEMAIL_ENVFROM_END_DIGIT=0.25, HTML_MESSAGE=2, RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H3=-0.01, RCVD_IN_MSPIKE_WL=-0.01, RCVD_IN_SORBS_SPAM=0.5, SPF_PASS=-0.001] autolearn=disabled Authentication-Results: spamd4-us-west.apache.org (amavisd-new); dkim=pass (2048-bit key) header.d=gmail.com Received: from mx2-lw-eu.apache.org ([10.40.0.8]) by localhost (spamd4-us-west.apache.org [10.40.0.11]) (amavisd-new, port 10024) with ESMTP id RBO6FiBi0TJV; Thu, 6 Oct 2016 11:33:26 +0000 (UTC) Received: from mail-yw0-f182.google.com (mail-yw0-f182.google.com [209.85.161.182]) by mx2-lw-eu.apache.org (ASF Mail Server at mx2-lw-eu.apache.org) with ESMTPS id E72215FB80; Thu, 6 Oct 2016 11:33:25 +0000 (UTC) Received: by mail-yw0-f182.google.com with SMTP id u124so10854155ywg.3; Thu, 06 Oct 2016 04:33:25 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113; h=mime-version:from:date:message-id:subject:to; bh=jQFObj5WOCcVFz11Kyrnte75zYMVB4pqM5LR1IXHSrI=; b=QTQyP5x2/0vcYIccNE3o4XGWHDXmpKU3zAtuAgM9bKfXBcha9eHPTCn7Iw+rrRmLu4 +uppllx89OPtBB8Xpi5YKIHxt1tKFIt4X5kczzzLeps1EXiCW/6IGPHrrwPct/biXxCz QddUZrRawGy3L4ScPSIxHPYZoV4Rp61VEgGlF9F4WN/MsXwXWjsHmhaiWsThj3MO2DQQ ZX1uQ0jyQxNHXwHVaRyqXeCbbNk2gQBuv1hLvfm0BLUfFhd3xFX978NuLcGek0PaAjK6 8lvYfo1Jvuu9BZkLERiHmf4+axP8hBsRSxFLpdLWGHvN2KZepi1ebMB+2390PolsnTTT ewxA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:mime-version:from:date:message-id:subject:to; bh=jQFObj5WOCcVFz11Kyrnte75zYMVB4pqM5LR1IXHSrI=; b=QqyTkYfbPU/ZPJEkCUE/K5ZKtUOSRbdmNBa+IjSjV1e9ChZBDfcZw3ftVPubWFbu0m oilnjXR4vtYGrFKB5wvUOXwWyhI1qaZkFlHs7IZ/c1/JSmvBTwB69Rl8lwe2Qzp2idUs inuAwt6gvtireUNZAPy0o3pUykHONtTI7RkSdPF8o9SRpBfIs4gQSuKJYez1XPO8S1UB wNP+DrLL8pszIHg2JTWraFgXxS2EErhfzbcmyVXOZ/oF3WElynNngKCGexlO72wQ9DAF fKbOiTa1wEi6tMxJZSWi9LG4BjGGSbGKEml+cIoM86xRqyzSNd4tjjC8jYy6d2PHpS0S Yl9w== X-Gm-Message-State: AA6/9RkwDi0O+VFK4sGnYBdesmM4BERRScdhCC60ZzBGf+2SX4h/YbV7taAmnWGshTirfEu2s3bZ4YjL5HK6XQ== X-Received: by 10.13.194.70 with SMTP id e67mr9842961ywd.133.1475753604548; Thu, 06 Oct 2016 04:33:24 -0700 (PDT) MIME-Version: 1.0 Received: by 10.37.161.194 with HTTP; Thu, 6 Oct 2016 04:33:24 -0700 (PDT) From: WP Roshan Date: Thu, 6 Oct 2016 17:03:24 +0530 Message-ID: Subject: Apache cTakes-3.2.3 - Exception in thread "main" java.lang.NoClassDefFoundError: scala/ScalaObject ..... Caused by: java.lang.ClassNotFoundException: scala.ScalaObject To: dev@ctakes.apache.org, user@ctakes.apache.org Content-Type: multipart/alternative; boundary=001a114f5006600bc4053e30a97d archived-at: Thu, 06 Oct 2016 11:33:38 -0000 --001a114f5006600bc4053e30a97d Content-Type: text/plain; charset=UTF-8 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 ------------------------------------------------------------------------------- comment-off around line number 161 ----------------------------------------------------------- AssertionAnnotator comment-off around line number 217 ----------------------------------------------------------- edu.mayo.bmi.uima.lookup.type.LookupWindowAnnotation 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.(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.(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. org.scala-tools.sbinary sbinary_2.9.0 0.4.0 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 --001a114f5006600bc4053e30a97d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Hi All,

I have slightly = modified cTakes-3.2.3 "AggregatePlaintextUMLSProcessor.xml" ,in f= ollowing location,=C2=A0

cTakes-3.2.3\ctakes-= clinical-pipeline\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml<= /div>

Original AggregatePlaintextUMLSProcessor.xml= =C2=A0file had following directives but commented. I just comment-off bello= w directives because I need to get concept annotated in CAS Visual Debugger= (CVD) and as well as producing xmi file running after ClinicalPipelineWith= Umls.java file as standalone way.

Please note that= without any modification to AggregatePlaintextUMLSProcessor.xml file, CAS = Visual Debugger (CVD) and ClinicalPipelineWithUmls.java perfectly ran ( ind= ependently ) but did not annotated any concept and concept types.

comment-off around line number 75
---------------= ----------------------------------------------------------------
=
<delegateAnalysisEngine key=3D"AssertionAnnotator">
=C2=A0 =C2=A0 =C2=A0 <import location=3D"../../../ctakes-as= sertion/desc/AssertionMiniPipelineAnalysisEngine.xml"/>
&= lt;/delegateAnalysisEngine>


comment-off around line number 161
----------------------------= -------------------------------
<node>AssertionAnnotator<= ;/node>


comment= -off around line number 217
-------------------------------------= ----------------------
<type allAnnotatorFeatures=3D&quo= t;true">edu.mayo.bmi.uima.lookup.type.LookupWindowAnnotation</ty= pe>

But I got following issues when I ran C= AS Visual Debugger (CVD) and ClinicalPipelineWithUmls.java independently.

ClinicalPipelineWithUmls.java=C2=A0- Error occ= urred with modified AggregatePlaintextUMLSProcessor.xml
#########= ###########################################################################= #
Started org.apache.ctakes.clinicalpipeline.ClinicalPipelineWith= Umls at Thu Oct 06 16:09:33 IST 2016
log4j: reset attribute=3D &q= uot;false".
log4j: Threshold =3D"null".
= log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: = Setting [ProgressAppender] additivity to [false].
log4j: Level va= lue for ProgressAppender is =C2=A0[INFO].
log4j: ProgressAppender= level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAp= pender]
log4j: Parsing layout of class: "org.apache.log4j.Pa= tternLayout"
log4j: Setting property [conversionPattern] to = [%m].
log4j: Adding appender named [noEolAppender] to category [P= rogressAppender].
log4j: Retreiving an instance of org.apache.log= 4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is =C2=A0[INFO].
log= 4j: ProgressDone level set to INFO
log4j: Class name: [org.apache= .log4j.ConsoleAppender]
log4j: Parsing layout of class: "org= .apache.log4j.PatternLayout"
log4j: Setting property [conver= sionPattern] to [%m%n].
log4j: Adding appender named [eolAppender= ] to category [ProgressDone].
log4j: Level value for root is =C2= =A0[INFO].
log4j: root level set to INFO
log4j: Class n= ame: [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 [roo= t].
Reading from directory: args[0]=3D../../../ctakes-clinical-pi= peline/data/input/MS-Case-Study-1.txt
Outputting to directory: ar= gs[1]=3D../../../ctakes-clinical-pipeline/data/output/xmi
06 Oct = 2016 16:09:35 =C2=A0INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg w= ith config file =3D C:\eclipse-neon-work-space-1\cTakes-3.2.3\ctakes-lvg-re= s\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties
06 Oct 2016 16:09:35 =C2=A0INFO LvgCmdApiResourceImpl - =C2=A0 config file= absolute path =3D 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 =C2=A0INFO LvgCmdApiResourceImpl - cwd =3D C:\eclipse-= neon-work-space-1\cTakes-3.2.3\ctakes-clinical-pipeline
06 Oct 20= 16 16:09:35 =C2=A0INFO LvgCmdApiResourceImpl - cd C:\eclipse-neon-work-spac= e-1\cTakes-3.2.3\ctakes-lvg-res\target\classes\org\apache\ctakes\lvg\
=
06 Oct 2016 16:09:36 =C2=A0INFO LvgCmdApiResourceImpl - cd C:\eclipse-= neon-work-space-1\cTakes-3.2.3\ctakes-clinical-pipeline
06 Oct 20= 16 16:09:36 =C2=A0INFO ClearNLPDependencyParserAE - using Morphy analysis? = true
Loading configuration.
Loading feature templates.<= /div>
Loading lexica.
Loading model:
..............= ..........................................................................<= /div>
06 Oct 2016 16:09:48 =C2=A0INFO Chunker - Chunker model file: org= /apache/ctakes/chunker/models/chunker-model.zip
06 Oct 2016 16:09= :49 =C2=A0INFO ContextDependentTokenizerAnnotator - Finite state machines l= oaded.
06 Oct 2016 16:09:49 =C2=A0INFO ConstituencyParser - Initi= alizing parser...
06 Oct 2016 16:09:54 =C2=A0INFO ContextAnnotato= r - Using left , right scope sizes: 7 , 7
06 Oct 2016 16:09:54 = =C2=A0INFO ContextAnnotator - Using scope order: LEFT,RIGHT
06 Oc= t 2016 16:09:54 =C2=A0INFO ContextAnnotator - SCOPE ORDER: [1, 3]
06 Oct 2016 16:09:54 =C2=A0INFO ContextAnnotator - Using context analyzer:= org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
06= Oct 2016 16:09:54 =C2=A0INFO NegationContextAnalyzer - initBoundaryData() = called for ContextInitializer
06 Oct 2016 16:09:54 =C2=A0INFO Con= textAnnotator - Using context consumer: org.apache.ctakes.necontexts.negati= on.NegationContextHitConsumer
06 Oct 2016 16:09:54 =C2=A0INFO Con= textAnnotator - Using lookup window type: org.apache.ctakes.typesystem.type= .textspan.Sentence
06 Oct 2016 16:09:54 =C2=A0INFO ContextAnnotat= or - Using focus type: org.apache.ctakes.typesystem.type.textsem.Identified= Annotation
06 Oct 2016 16:09:54 =C2=A0INFO ContextAnnotator - Usi= ng context type: org.apache.ctakes.typesystem.type.syntax.BaseToken
06 Oct 2016 16:09:54 =C2=A0INFO AssertionAnalysisEngine - scope model fi= le: /C:/eclipse-neon-work-space-1/cTakes-3.2.3/ctakes-assertion-res/target/= classes/org/apache/ctakes/assertion/models/scope.model
06 Oct 201= 6 16:09:54 =C2=A0INFO AssertionAnalysisEngine - cue model file: /C:/eclipse= -neon-work-space-1/cTakes-3.2.3/ctakes-assertion-res/target/classes/org/apa= che/ctakes/assertion/models/cue.model
scope model: /C:/eclipse-ne= on-work-space-1/cTakes-3.2.3/ctakes-assertion-res/target/classes/org/apache= /ctakes/assertion/models/scope.model
Exception in thread "ma= in" java.lang.NoClassDefFoundError: scala/ScalaObject
at java.la= ng.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.d= efineClass(Unknown Source)
at java.security.SecureClassLoader.defineC= lass(Unknown Source)
at java.net.URLClassLoader.defineClass(Unknown= Source)
at java.net.URLClassLoader.access$100(Unknown Source)
<= div> = at java.net.URLClassLoader$1.run(Unknown Source)
at java.net.URLClass= Loader$1.run(Unknown Source)
at java.security.AccessController.doPriv= ileged(Native Method)
at java.net.URLClassLoader.findClass(Unknown S= ource)
at java.lang.ClassLoader.loadClass(Unknown Source)
<= span class=3D"gmail-Apple-tab-span" style=3D"white-space:pre"> at su= n.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang= .ClassLoader.loadClass(Unknown Source)
at org.mitre.medfacts.i2b2.ann= otation.ScopeParser.<init>(ScopeParser.java:22)
at org.apache.c= takes.assertion.medfacts.AssertionAnalysisEngine.initialize(AssertionAnalys= isEngine.java:121)
at org.apache.uima.analysis_engine.impl.PrimitiveA= nalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl= .java:250)
at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisE= ngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at org.a= pache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFa= ctory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_= impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.ap= ache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
<= span class=3D"gmail-Apple-tab-span" style=3D"white-space:pre"> at or= g.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.ja= va:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngi= ne_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.apache.= uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateA= nalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apache.u= ima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateA= nalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFa= ctory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org= .apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeRe= sourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceR= esource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.prod= uceAnalysisEngine(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(AggregateAnalysi= sEngine_impl.java:431)
at org.apache.uima.analysis_engine.impl.Aggreg= ateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisE= ngine_impl.java:375)
at org.apache.uima.analysis_engine.impl.Aggreg= ateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Anal= ysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeReso= urceFactory_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.Aggregate= AnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at= org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initiali= zeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
= at o= rg.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize= (AggregateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.Analy= sisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(= CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramewo= rk.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFra= mework.produceResource(UIMAFramework.java:314)
at org.apache.uima.UIM= AFramework.produceAnalysisEngine(UIMAFramework.java:425)
at org.apach= e.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:76)
<= span class=3D"gmail-Apple-tab-span" style=3D"white-space:pre"> at or= g.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipe= lineWithUmls.java:76)
Caused by: java.lang.ClassNotFoundException= : scala.ScalaObject
at java.net.URLClassLoader.findClass(Unknown Sour= ce)
at java.lang.ClassLoader.loadClass(Unknown Source)
at sun.m= isc.Launcher$AppClassLoader.loadClass(Unknown Source)
at java.lang.Cl= assLoader.loadClass(Unknown Source)
... 47 more

<= div>
CAS Visual Debugger (CVD) - Error occured with modified = AggregatePlaintextUMLSProcessor.xml
#############################= ######################################################################
10/6/16 3:58:28 PM - 16: org.apache.uima.tools.cvd.MainFrame.handleEx= ception(528): SEVERE: scala/ScalaObject
java.lang.NoClassDefFound= Error: scala/ScalaObject
at java.lang.ClassLoader.defineClass1(Native= Method)
at java.lang.ClassLoader.defineClass(Unknown Source)
a= t java.security.SecureClassLoader.defineClass(Unknown Source)
at java= .net.URLClassLoader.defineClass(Unknown Source)
at java.net.URLClassL= oader.access$100(Unknown Source)
at java.net.URLClassLoader$1.run(Unk= nown Source)
at java.net.URLClassLoader$1.run(Unknown Source)
a= t java.security.AccessController.doPrivileged(Native Method)
at java.= net.URLClassLoader.findClass(Unknown Source)
at java.lang.ClassLoader= .loadClass(Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadCl= ass(Unknown Source)
at java.lang.ClassLoader.loadClass(Unknown Source= )
= at org.mitre.medfacts.i2b2.annotation.ScopeParser.<init>(Scop= eParser.java:22)
at org.apache.ctakes.assertion.medfacts.AssertionAna= lysisEngine.initialize(AssertionAnalysisEngine.java:121)
at org.apach= e.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysis= Component(PrimitiveAnalysisEngine_impl.java:250)
at org.apache.uima.a= nalysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalys= isEngine_impl.java:156)
at org.apache.uima.impl.AnalysisEngineFactory= _impl.produceResource(AnalysisEngineFactory_impl.java:94)
at org.apac= he.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourc= eFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResour= ce(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceAn= alysisEngine(UIMAFramework.java:387)
at org.apache.uima.analysis_engi= ne.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at org.apache.uima.anal= ysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngi= ne_impl.java:431)
at org.apache.uima.analysis_engine.impl.AggregateAn= alysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine= _impl.java:375)
at org.apache.uima.analysis_engine.impl.AggregateAnal= ysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at = org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEng= ineFactory_impl.java:94)
at org.apache.uima.impl.CompositeResourceFac= tory_impl.produceResource(CompositeResourceFactory_impl.java:62)
= at o= rg.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
<= div> = at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:3= 87)
at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_im= pl.java:254)
at org.apache.uima.analysis_engine.impl.AggregateAnalysi= sEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at org.ap= ache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggre= gateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at org.apac= he.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(Aggreg= ateAnalysisEngine_impl.java:185)
at org.apache.uima.impl.AnalysisEngi= neFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at= org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(Composi= teResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.prod= uceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.= produceAnalysisEngine(UIMAFramework.java:354)
at org.apache.uima.tool= s.cvd.MainFrame.setupAE(MainFrame.java:1484)
at org.apache.uima.tools= .cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
at org.apache.u= ima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOp= enEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerfo= rmed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPe= rformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionP= erformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed= (Unknown Source)
at javax.swing.AbstractButton.doClick(Unknown Source= )
= at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknow= n Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at jav= a.awt.Component.processEvent(Unknown Source)
at java.awt.Container.pr= ocessEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Un= known Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)=
= at java.awt.Component.dispatchEvent(Unknown Source)
at java.aw= t.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.aw= t.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt= .LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Con= tainer.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchE= ventImpl(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.Eve= ntQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown So= urce)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectio= nPrivilege(Unknown Source)
at java.security.ProtectionDomain$JavaSecu= rityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.Ev= entQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown S= ource)
at java.security.AccessController.doPrivileged(Native Method)<= /div>
<= /span>at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersecti= onPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unkn= own Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Un= known Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unk= nown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(U= nknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Sou= rce)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
=
at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: j= ava.lang.ClassNotFoundException: scala.ScalaObject
at java.net.URLCla= ssLoader.findClass(Unknown Source)
at java.lang.ClassLoader.loadClass= (Unknown Source)
at sun.misc.Launcher$AppClassLoader.loadClass(Unknow= n Source)
at java.lang.ClassLoader.loadClass(Unknown Source)
..= . 77 more


I added follow= ing Scala dependency to=C2=A0
cTakes-3.2.3\ctakes-clinical-pipeli= ne\pom.xml
cTakes-3.2.3\ctakes-assertion\pom.xml and as well = as=C2=A0cTakes-3.2.3\pom.xml file and ran "mvn clean install -U -Dskip= Tests" command and build was success.

<dependency>
=C2=A0 <= groupId>org.scala-tools.sbinary</groupId>
=C2=A0 <art= ifactId>sbinary_2.9.0</artifactId>
=C2=A0 =C2=A0<vers= ion>0.4.0</version>
</dependency>

But either issues not solved but because of modified A= ggregatePlaintextUMLSProcessor.xml file. My key requirement is concept anno= tated in CAS visual debugger & and generated in xmi file when ran after= =C2=A0ClinicalPipelineWithUmls.java file.

Anyone n= oted and do have solution for this?

W.P.Roshan
= --=C2=A0=C2=A0
SunONE
--001a114f5006600bc4053e30a97d--