You are viewing a plain text version of this content. The canonical link for it is here.
Posted to user@ctakes.apache.org by WP Roshan <su...@gmail.com> on 2016/10/06 11:33:24 UTC
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://mvnrepository.com/artifact/org.scala-tools.sbinary/sbinary_2.9.0 -->
<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
RE: Apache cTakes-3.2.3 - Exception in thread "main"
java.lang.NoClassDefFoundError: scala/ScalaObject ..... Caused by:
java.lang.ClassNotFoundException: scala.ScalaObject
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Ah, uncommented Assertion ... maybe I misread.
Assertion was commented for release 3.2.1 and replaced with individual engines for Generic, History, Polarity, Subject, and Uncertainty from Cleartk. It looks like this didn't make it into the release notes - sorry about that. Again, this was a replacement - the same functionality still exists, but we favored the cleartk solutions for (I think) speed and similar accuracy. Assertion was left commented in case anybody wanted to test backwards functionality. If you want to do that you should comment the following cleartk lines.
Sean
-----Original Message-----
From: WP Roshan [mailto:sunone5@gmail.com]
Sent: Thursday, October 06, 2016 9:29 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,
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://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_trunk_ctakes-2Dclinical-2Dpipeline_desc_analysis-5Fengine_AggregatePlaintextUMLSProcessor.xml&d=CwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nCyxC3bK1JwXOPno_KJMfXkiA2HNiP3bs_BsTnl9DTM&s=SiEDKygCD5kLW3hQU564Vx1IvuY0RIKDdtHxlSpP67M&e=
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.Finan@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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
> confluence_display_CTAKES_&d=CwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS
> dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nCyxC3bK1J
> wXOPno_KJMfXkiA2HNiP3bs_BsTnl9DTM&s=qi_gw-QTgL9D5VpWb6YhV9Qo-fzj9ZGL-p
> OYsXNKmSc&e=
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
> confluence_display_CTAKES_&d=CwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS
> dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nCyxC3bK1J
> wXOPno_KJMfXkiA2HNiP3bs_BsTnl9DTM&s=qi_gw-QTgL9D5VpWb6YhV9Qo-fzj9ZGL-p
> OYsXNKmSc&e=
> cTAKES+3.1+User+Install+Guide#cTAKES3.1UserInstallGuide-
> CollectionProcessingEngine(CPE)
> Or, you can go straight to the author (uima) documentation here:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__uima.apache.org_d
> ownloads_releaseDocs_2.1.0-2Dincubating_docs_html_&d=CwIBaQ&c=qS4goWBT
> 7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpK
> Gd4f7d4gTao&m=nCyxC3bK1JwXOPno_KJMfXkiA2HNiP3bs_BsTnl9DTM&s=yUgz9gPsl0
> zWCgV1GsyfdaL_gyG-WQw9-FJVuDv3Izs&e=
> 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:
> https://urldefense.proofpoint.com/v2/url?u=http-3A__52.26.219.218-3A80
> 80_index.jsp&d=CwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=
> fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=nCyxC3bK1JwXOPno_KJMfXki
> A2HNiP3bs_BsTnl9DTM&s=bapOsyq__zkPtHGKG11w98csqdyzQ67KuqRgB_GSm2Q&e=
>
>
> 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:sunone5@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.Finan@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:sunone5@gmail.com]
> > Sent: Thursday, October 06, 2016 7:33 AM
> > To: dev@ctakes.apache.org; user@ctakes.apache.org
> > Subject: Apache cTakes-3.2.3 - Exception in thread "main" java.lang.
> NoClassDefFoundError:
> > scala/ScalaObject ..... Caused by: java.lang.ClassNotFoundException:
> > scala.ScalaObject
> >
> > Hi All,
> >
> > I have slightly modified cTakes-3.2.3
> > "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/AssertionMiniPipelineAnalys
> > is
> > 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.ja
> > va
> > :22)
> > at
> > org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initial
> > iz
> > 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.in
> > it
> > 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.in
> > it
> > 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.in
> > it
> > 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.ja
> > va
> > :22)
> > at
> > org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initial
> > iz
> > 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.in
> > it
> > 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.in
> > it
> > 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_3xhKwEW14JZMSdioCoppxe
> > FU
> > &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
Re: Apache cTakes-3.2.3 - Exception in thread "main"
java.lang.NoClassDefFoundError: scala/ScalaObject ..... Caused by:
java.lang.ClassNotFoundException: scala.ScalaObject
Posted by WP Roshan <su...@gmail.com>.
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.Finan@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:sunone5@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.Finan@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:sunone5@gmail.com]
> > Sent: Thursday, October 06, 2016 7:33 AM
> > To: dev@ctakes.apache.org; user@ctakes.apache.org
> > Subject: Apache cTakes-3.2.3 - Exception in thread "main" java.lang.
> NoClassDefFoundError:
> > scala/ScalaObject ..... Caused by: java.lang.ClassNotFoundException:
> > scala.ScalaObject
> >
> > Hi All,
> >
> > I have slightly modified cTakes-3.2.3 "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
RE: Apache cTakes-3.2.3 - Exception in thread "main"
java.lang.NoClassDefFoundError: scala/ScalaObject ..... Caused by:
java.lang.ClassNotFoundException: scala.ScalaObject
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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:sunone5@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.Finan@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:sunone5@gmail.com]
> Sent: Thursday, October 06, 2016 7:33 AM
> To: dev@ctakes.apache.org; user@ctakes.apache.org
> Subject: Apache cTakes-3.2.3 - Exception in thread "main" java.lang.NoClassDefFoundError:
> scala/ScalaObject ..... Caused by: java.lang.ClassNotFoundException:
> scala.ScalaObject
>
> Hi All,
>
> I have slightly modified cTakes-3.2.3 "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
Re: Apache cTakes-3.2.3 - Exception in thread "main"
java.lang.NoClassDefFoundError: scala/ScalaObject ..... Caused by:
java.lang.ClassNotFoundException: scala.ScalaObject
Posted by WP Roshan <su...@gmail.com>.
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.Finan@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:sunone5@gmail.com]
> Sent: Thursday, October 06, 2016 7:33 AM
> To: dev@ctakes.apache.org; user@ctakes.apache.org
> Subject: Apache cTakes-3.2.3 - Exception in thread "main" java.lang.NoClassDefFoundError:
> scala/ScalaObject ..... Caused by: java.lang.ClassNotFoundException:
> scala.ScalaObject
>
> Hi All,
>
> I have slightly modified cTakes-3.2.3 "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
RE: Apache cTakes-3.2.3 - Exception in thread "main"
java.lang.NoClassDefFoundError: scala/ScalaObject ..... Caused by:
java.lang.ClassNotFoundException: scala.ScalaObject
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi W.P.,
What is your goal for the run? The easiest thing for you to do might be trying the "CuisOnlyPlaintextUMLSProcessor" pipeline .xml . That will start you with a fast pipeline that provides cuis from dictionary lookup. It has commented lines that you can uncomment, adding one module at a time to see what they do. With everything uncommented you will get cuis, cuis for variations not in the dictionary (e.g. pluralities), polarity, subject, and flags for generics, history of, and uncertainty. Once you have this in hand, to get more you can start building out a fresh .xml to fit your desired pipeline.
Sean
-----Original Message-----
From: WP Roshan [mailto:sunone5@gmail.com]
Sent: Thursday, October 06, 2016 7:33 AM
To: dev@ctakes.apache.org; user@ctakes.apache.org
Subject: Apache cTakes-3.2.3 - Exception in thread "main" java.lang.NoClassDefFoundError: scala/ScalaObject ..... Caused by: java.lang.ClassNotFoundException: scala.ScalaObject
Hi All,
I have slightly modified cTakes-3.2.3 "AggregatePlaintextUMLSProcessor.xml"
,in following location,
cTakes-3.2.3\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextUMLSProcessor.xml
Original AggregatePlaintextUMLSProcessor.xml file had following directives but commented. I just comment-off bellow directives because I need to get concept annotated in CAS Visual Debugger (CVD) and as well as producing xmi file running after ClinicalPipelineWithUmls.java file as standalone way.
Please note that without any modification to AggregatePlaintextUMLSProcessor.xml file, CAS Visual Debugger (CVD) and ClinicalPipelineWithUmls.java perfectly ran ( independently ) but did not annotated any concept and concept types.
comment-off around line number 75
-------------------------------------------------------------------------------
<delegateAnalysisEngine key="AssertionAnnotator">
<import
location="../../../ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml"/>
</delegateAnalysisEngine>
comment-off around line number 161
-----------------------------------------------------------
<node>AssertionAnnotator</node>
comment-off around line number 217
-----------------------------------------------------------
<type
allAnnotatorFeatures="true">edu.mayo.bmi.uima.lookup.type.LookupWindowAnnotation</type>
But I got following issues when I ran CAS Visual Debugger (CVD) and ClinicalPipelineWithUmls.java independently.
ClinicalPipelineWithUmls.java - Error occurred with modified AggregatePlaintextUMLSProcessor.xml
#####################################################################################
Started org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls at Thu Oct 06 16:09:33 IST 2016
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressAppender] additivity to [false].
log4j: Level value for ProgressAppender is [INFO].
log4j: ProgressAppender level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
Reading from directory:
args[0]=../../../ctakes-clinical-pipeline/data/input/MS-Case-Study-1.txt
Outputting to directory:
args[1]=../../../ctakes-clinical-pipeline/data/output/xmi
06 Oct 2016 16:09:35 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg with config file = C:\eclipse-neon-work-space-1\cTakes-3.2.3\ctakes-lvg-res\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties
06 Oct 2016 16:09:35 INFO LvgCmdApiResourceImpl - config file absolute
path =
C:\eclipse-neon-work-space-1\cTakes-3.2.3\ctakes-lvg-res\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties
06 Oct 2016 16:09:35 INFO LvgCmdApiResourceImpl - cwd = C:\eclipse-neon-work-space-1\cTakes-3.2.3\ctakes-clinical-pipeline
06 Oct 2016 16:09:35 INFO LvgCmdApiResourceImpl - cd C:\eclipse-neon-work-space-1\cTakes-3.2.3\ctakes-lvg-res\target\classes\org\apache\ctakes\lvg\
06 Oct 2016 16:09:36 INFO LvgCmdApiResourceImpl - cd C:\eclipse-neon-work-space-1\cTakes-3.2.3\ctakes-clinical-pipeline
06 Oct 2016 16:09:36 INFO ClearNLPDependencyParserAE - using Morphy analysis? true Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
06 Oct 2016 16:09:48 INFO Chunker - Chunker model file:
org/apache/ctakes/chunker/models/chunker-model.zip
06 Oct 2016 16:09:49 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded.
06 Oct 2016 16:09:49 INFO ConstituencyParser - Initializing parser...
06 Oct 2016 16:09:54 INFO ContextAnnotator - Using left , right scope
sizes: 7 , 7
06 Oct 2016 16:09:54 INFO ContextAnnotator - Using scope order: LEFT,RIGHT
06 Oct 2016 16:09:54 INFO ContextAnnotator - SCOPE ORDER: [1, 3]
06 Oct 2016 16:09:54 INFO ContextAnnotator - Using context analyzer:
org.apache.ctakes.necontexts.negation.NegationContextAnalyzer
06 Oct 2016 16:09:54 INFO NegationContextAnalyzer - initBoundaryData() called for ContextInitializer
06 Oct 2016 16:09:54 INFO ContextAnnotator - Using context consumer:
org.apache.ctakes.necontexts.negation.NegationContextHitConsumer
06 Oct 2016 16:09:54 INFO ContextAnnotator - Using lookup window type:
org.apache.ctakes.typesystem.type.textspan.Sentence
06 Oct 2016 16:09:54 INFO ContextAnnotator - Using focus type:
org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation
06 Oct 2016 16:09:54 INFO ContextAnnotator - Using context type:
org.apache.ctakes.typesystem.type.syntax.BaseToken
06 Oct 2016 16:09:54 INFO AssertionAnalysisEngine - scope model file:
/C:/eclipse-neon-work-space-1/cTakes-3.2.3/ctakes-assertion-res/target/classes/org/apache/ctakes/assertion/models/scope.model
06 Oct 2016 16:09:54 INFO AssertionAnalysisEngine - cue model file:
/C:/eclipse-neon-work-space-1/cTakes-3.2.3/ctakes-assertion-res/target/classes/org/apache/ctakes/assertion/models/cue.model
scope model:
/C:/eclipse-neon-work-space-1/cTakes-3.2.3/ctakes-assertion-res/target/classes/org/apache/ctakes/assertion/models/scope.model
Exception in thread "main" java.lang.NoClassDefFoundError: scala/ScalaObject at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(Unknown Source) at java.security.SecureClassLoader.defineClass(Unknown Source) at java.net.URLClassLoader.defineClass(Unknown Source) at java.net.URLClassLoader.access$100(Unknown Source) at java.net.URLClassLoader$1.run(Unknown Source) at java.net.URLClassLoader$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at
org.mitre.medfacts.i2b2.annotation.ScopeParser.<init>(ScopeParser.java:22)
at
org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initialize(AssertionAnalysisEngine.java:121)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at org.apache.uima.fit.pipeline.JCasIterable.iterator(JCasIterable.java:76)
at
org.apache.ctakes.clinicalpipeline.ClinicalPipelineWithUmls.main(ClinicalPipelineWithUmls.java:76)
Caused by: java.lang.ClassNotFoundException: scala.ScalaObject at java.net.URLClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) ... 47 more
CAS Visual Debugger (CVD) - Error occured with modified AggregatePlaintextUMLSProcessor.xml
###################################################################################################
10/6/16 3:58:28 PM - 16:
org.apache.uima.tools.cvd.MainFrame.handleException(528): SEVERE:
scala/ScalaObject
java.lang.NoClassDefFoundError: scala/ScalaObject at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(Unknown Source) at java.security.SecureClassLoader.defineClass(Unknown Source) at java.net.URLClassLoader.defineClass(Unknown Source) at java.net.URLClassLoader.access$100(Unknown Source) at java.net.URLClassLoader$1.run(Unknown Source) at java.net.URLClassLoader$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at
org.mitre.medfacts.i2b2.annotation.ScopeParser.<init>(ScopeParser.java:22)
at
org.apache.ctakes.assertion.medfacts.AssertionAnalysisEngine.initialize(AssertionAnalysisEngine.java:121)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
at
org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
at
org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
at
org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
Source)
at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown
Source)
at
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown
Source)
at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown
Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Caused by: java.lang.ClassNotFoundException: scala.ScalaObject at java.net.URLClassLoader.findClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) at java.lang.ClassLoader.loadClass(Unknown Source) ... 77 more
I added following Scala dependency to
cTakes-3.2.3\ctakes-clinical-pipeline\pom.xml
cTakes-3.2.3\ctakes-assertion\pom.xml and as well as cTakes-3.2.3\pom.xml file and ran "mvn clean install -U -DskipTests" command and build was success.
<!--
https://urldefense.proofpoint.com/v2/url?u=https-3A__mvnrepository.com_artifact_org.scala-2Dtools.sbinary_sbinary-5F2.9.0&d=CwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=64oaaGH_-1KVM5eOR6CagMulGLYXMbfL2xdX-vnLwOE&s=BxnFFaQTuH3Qu4LPTR6S9FQjaiN-8UtfNfRzg3Ln7PU&e= --> <dependency>
<groupId>org.scala-tools.sbinary</groupId>
<artifactId>sbinary_2.9.0</artifactId>
<version>0.4.0</version>
</dependency>
But either issues not solved but because of modified AggregatePlaintextUMLSProcessor.xml file. My key requirement is concept annotated in CAS visual debugger & and generated in xmi file when ran after ClinicalPipelineWithUmls.java file.
Anyone noted and do have solution for this?
W.P.Roshan
--
SunONE