Re: Problems with cTAKES 3.1 installation (in Mac OS X 10.9 and Windows 8)

[Kim Ebert <ki...@perfectsearchcorp.com>]

Hi Javier,

A quick google search indicates that the version of Java you are using
cannot interpret the Java bytecode.

http://stackoverflow.com/questions/10382929/unsupported-major-minor-version-51-0

The error you got on Windows is indicating that it cannot find the
resources for cTakes to load. Make sure the directory that contains this
file is on the classpath.

Caused by:
org.apache.uima.resource.ResourceInitializationException:*Could not
access the resource data at
file:org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml.*

Let me know if you are still having problems.

Thanks,

Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/

On 10/14/2014 09:12 AM, Javier Blasco wrote:
> I have started working on NLP very recently.
> I am trying to install cTAKES (following this guide
> <https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide>)
> but I am stumbling across many problems.
>
> I do manage to lauch the java application but I get several errors
> when I try to load the AE suggested in the CVD example
> (AggregatePlaintextUMLSProcessor.xml).
>
> Below are the errors.
> Thanks a lot in advance!
>
> Regards,
>
> ----
>
> *Mac OS X 10.9*
> Currently I have java version "1.7.0_67"
>
> Exception in thread "AWT-EventQueue-0"
> java.lang.UnsupportedClassVersionError:
> org/apache/ctakes/dependency/parser/ae/ClearNLPDependencyParserAE :
> Unsupported major.minor version 51.0
> at java.lang.ClassLoader.defineClass1(Native Method)
> at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
> at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
> at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
> at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
> at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
> at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
> at java.lang.Class.forName0(Native Method)
> at java.lang.Class.forName(Class.java:171)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:204)
> 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:354)
> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
> at
> org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477)
> at
> org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
> at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
> at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
> at
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
> at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
> at
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
> at
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
> at java.awt.Component.processMouseEvent(Component.java:6414)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)
> at java.awt.Component.processEvent(Component.java:6179)
> at java.awt.Container.processEvent(Container.java:2084)
> at java.awt.Component.dispatchEventImpl(Component.java:4776)
> at java.awt.Container.dispatchEventImpl(Container.java:2142)
> at java.awt.Component.dispatchEvent(Component.java:4604)
> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4209)
> at java.awt.Container.dispatchEventImpl(Container.java:2128)
> at java.awt.Window.dispatchEventImpl(Window.java:2492)
> at java.awt.Component.dispatchEvent(Component.java:4604)
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)
> at java.awt.EventQueue.access$400(EventQueue.java:82)
> at java.awt.EventQueue$2.run(EventQueue.java:676)
> at java.awt.EventQueue$2.run(EventQueue.java:674)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
> at
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)
> at java.awt.EventQueue$3.run(EventQueue.java:690)
> at java.awt.EventQueue$3.run(EventQueue.java:688)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)
> at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
> at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
>
>
> *Windows 7 - **Log file*
> 14/10/14 17:06:11 - 14:
> org.apache.uima.tools.cvd.MainFrame.handleException(527): Grave: Error
> initializing "org.apache.uima.resource.impl.DataResource_impl" from
> descriptor
> file:/C:/Users/USUARIO/Documents/apache-ctakes-3.2.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml.
> org.apache.uima.resource.ResourceInitializationException: Error
> initializing "org.apache.uima.resource.impl.DataResource_impl" from
> descriptor
> file:/C:/Users/USUARIO/Documents/apache-ctakes-3.2.0/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml.
> at
> org.apache.uima.util.SimpleResourceFactory.produceResource(SimpleResourceFactory.java:144)
> 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:243)
> at
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:565)
> at
> org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
> at
> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
> at
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
> at
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
> 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:477)
> 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$000(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$1.doIntersectionPrivilege(Unknown
> Source)
> at java.security.ProtectionDomain$1.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$1.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: org.apache.uima.resource.ResourceInitializationException:
> Could not access the resource data at
> file:org/apache/ctakes/dictionary/lookup/LookupDesc_Db.xml.
> at
> org.apache.uima.resource.impl.DataResource_impl.initialize(DataResource_impl.java:127)
> at
> org.apache.uima.util.SimpleResourceFactory.produceResource(SimpleResourceFactory.java:123)
> ... 61 more
>
> *Windows 7 - output to stdin*
>
> C:\Users\USUARIO\Documents\apache-ctakes-3.2.0>set
> CURRENT_DIR=C:\Users\USUARIO\Documents\apache-ctakes-3.2.0 
>
> C:\Users\USUARIO\Documents\apache-ctakes-3.2.0>if not
> "C:\Users\USUARIO\Documents\apache-ctakes-3.2.0" == "" goto gotHome 
>
> C:\Users\USUARIO\Documents\apache-ctakes-3.2.0>if exist
> "C:\Users\USUARIO\Documents\apache-ctakes-3.2.0\bin\runctakesCVD.bat"
> goto okHome 
>
> C:\Users\USUARIO\Documents\apache-ctakes-3.2.0>cd
> C:\Users\USUARIO\Documents\apache-ctakes-3.2.0 
>
> C:\Users\USUARIO\Documents\apache-ctakes-3.2.0>java
> -Dctakes.umlsuser=*** -Dctakes.umlspw=**** -cp
> "C:\Users\USUARIO\Documents\apache-ctakes-3.2.0/lib/*;C:\Users\USUARIO\Documents\apache-ctakes-3.2.0/desc/;C:\Users\USUARIO\Documents\apache-ctakes-3.2.0/resources/"
> -Dlog4j.configuration=file:/C:\Users\USUARIO\Documents\apache-ctakes-3.2.0/config/log4j.xml
> -Xms512M -Xmx3g org.apache.uima.tools.cvd.CVD 
> log4j: reset attribute= "false".
> log4j: Threshold ="null".
> 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].
> 14 oct 2014 17:06:01  INFO ClearNLPDependencyParserAE - using Morphy
> analysis? true
> Loading configuration.
> Loading feature templates.
> Loading lexica.
> Loading model:
> ........................................................................................
> 14 oct 2014 17:06:09  INFO TokenizerAnnotatorPTB - Initializing
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> 14 oct 2014 17:06:09  INFO ContextDependentTokenizerAnnotator - Finite
> state machines loaded.
> 14 oct 2014 17:06:09  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
> 14 oct 2014 17:06:09  INFO NegationContextAnalyzer -
> initBoundaryData() called for ContextInitializer
> 14 oct 2014 17:06:09  INFO ContextAnnotator - SCOPE ORDER: [1, 3]
> 14 oct 2014 17:06:09  INFO StatusContextAnalyzer - initBoundaryData()
> called for ContextInitializer
> 14 oct 2014 17:06:09  INFO SentenceDetector - Sentence detector model
> file: org/apache/ctakes/core/sentdetect/sd-med-model.zip
> 14 oct 2014 17:06:09  INFO POSTagger - POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
> 14 oct 2014 17:06:10  INFO Chunker - Chunker model file:
> org/apache/ctakes/chunker/models/chunker-model.zip
>
>