Thank you Bandeep and Tomasz, this seems to have solved the issue! Not all of the files were merged (old and new) together.
One last question, if you don’t mind. Despite this fix, I still cannot get the Negation AE to run. The log file is below. It looks like its asking me to modify the XML code; is that correct, and if so, where/how do I do that? Thanks in advance, I appreciate your help. 9/27/16 3:35:00 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: JCas type "org.apache.ctakes.typesystem.type.textspan.Sentence" used in Java code, but was not declared in the XML type descriptor. org.apache.uima.analysis_engine.AnalysisEngineProcessException: JCas type "org.apache.ctakes.typesystem.type.textspan.Sentence" used in Java code, but was not declared in the XML type descriptor. at org.apache.ctakes.necontexts.ContextAnnotator.process(ContextAnnotator.java:245) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267) at org.apache.uima.tools.cvd.MainFrame.internalRunAE(MainFrame.java:1526) at org.apache.uima.tools.cvd.MainFrame.runAE(MainFrame.java:429) at org.apache.uima.tools.cvd.control.AnnotatorRerunEventHandler.actionPerformed(AnnotatorRerunEventHandler.java:40) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6533) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: org.apache.uima.cas.CASRuntimeException: JCas type "org.apache.ctakes.typesystem.type.textspan.Sentence" used in Java code, but was not declared in the XML type descriptor. at org.apache.uima.jcas.impl.JCasImpl.getType(JCasImpl.java:412) at org.apache.uima.jcas.impl.JCasImpl.getCasType(JCasImpl.java:436) at org.apache.uima.jcas.impl.JCasImpl.getAnnotationIndex(JCasImpl.java:1531) at org.apache.ctakes.necontexts.ContextAnnotator.process(ContextAnnotator.java:221) ... 46 more From: Bandeep Singh <bsi...@phemi.com<mailto:bsi...@phemi.com>> Reply-To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> Date: Tuesday, September 27, 2016 at 3:27 PM To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> Subject: Re: Trouble loading AE So, from the logs it appears that model.jar is missing "Caused by: java.io.FileNotFoundException: /org/apache/ctakes/assertion/models/historyOf/model.jar " Again, i thing when you copy the resource folder from your temp folder into the ctakes folder , you are replacing(rather than merging) the complete resource folder that already contains assertion models. Please check in the resource folder (which you pasted inside you ctakes), if it contains assertion folder or not. I Think that where the problem is On Tue, Sep 27, 2016 at 3:11 PM, Gianfrancesco, Milena <milena.gianfrance...@ucsf.edu<mailto:milena.gianfrance...@ucsf.edu>> wrote: Here is the log file: 9/27/16 3:11:19 PM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine" failed. (Descriptor: file:/Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/desc/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml) org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine" failed. (Descriptor: file:/Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/desc/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252) 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:476) at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6533) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) Caused by: org.apache.uima.resource.ResourceInitializationException at org.cleartk.ml<http://org.cleartk.ml>.CleartkAnnotator.initialize(CleartkAnnotator.java:137) at org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine.initialize(AssertionCleartkAnalysisEngine.java:192) at org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize(HistoryCleartkAnalysisEngine.java:46) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) ... 55 more Caused by: java.io.FileNotFoundException: /org/apache/ctakes/assertion/models/historyOf/model.jar (No such file or directory) at java.io.FileInputStream.open0(Native Method) at java.io.FileInputStream.open(FileInputStream.java:195) at java.io.FileInputStream.<init>(FileInputStream.java:138) at java.io.FileInputStream.<init>(FileInputStream.java:93) at org.cleartk.ml.jar.GenericJarClassifierFactory.createClassifier(GenericJarClassifierFactory.java:69) at org.cleartk.ml.jar.JarClassifierFactory.createClassifier(JarClassifierFactory.java:35) at org.cleartk.ml<http://org.cleartk.ml>.CleartkAnnotator.initialize(CleartkAnnotator.java:135) ... 58 more From: Milena Gianfrancesco <milena.gianfrance...@ucsf.edu<mailto:milena.gianfrance...@ucsf.edu>> Date: Tuesday, September 27, 2016 at 2:12 PM To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> Subject: Re: Trouble loading AE Thank you both. I just deleted everything and redownloaded in order to make sure all files were transferred properly. I downloaded ctakes version 3.2.2, and resources version 3.2.1.1. As outlined in the User Guide, I moved the temp resources download to the apache folder, overwriting the previous resources folder. I confirmed that there is a folder /apache-ctakes-3.2.2/resources/org/apache/ctakes/dictionary/lookup/fast When trying to load an UMLS AE (Aggregate Plain Text), this that I get the error message: “org.apache.uima.resource.ResourceInitializationException: initialization of annotator class “org.apache.ctakes.assertio.medfacts.cleartk.HistoryCleartkAnalysisEngine” failed.” Here is the terminal output: 27 Sep 2016 13:58:32 INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip 27 Sep 2016 13:58:33 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded. 27 Sep 2016 13:58:33 INFO ConstituencyParser - Initializing parser... SFGH-0H0DHJW-DT:apache-ctakes-3.2.2 mgianfrancesco$ bin/runctakesCVD.sh 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]. 27 Sep 2016 14:03:29 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg with config file = /Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties 27 Sep 2016 14:03:30 INFO LvgCmdApiResourceImpl - config file absolute path = /Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/data/config/lvg.properties 27 Sep 2016 14:03:30 INFO LvgCmdApiResourceImpl - cwd = /Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2 27 Sep 2016 14:03:30 INFO LvgCmdApiResourceImpl - cd /Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2/resources/org/apache/ctakes/lvg/ 27 Sep 2016 14:03:30 INFO LvgCmdApiResourceImpl - cd /Users/mgianfrancesco/Desktop/apache-ctakes-3.2.2 27 Sep 2016 14:03:30 INFO ClearNLPDependencyParserAE - using Morphy analysis? true Loading configuration. Loading feature templates. Loading lexica. Loading model: ........................................................................................ 27 Sep 2016 14:03:42 INFO Chunker - Chunker model file: org/apache/ctakes/chunker/models/chunker-model.zip 27 Sep 2016 14:03:44 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded. 27 Sep 2016 14:03:44 INFO ConstituencyParser - Initializing parser... From: Bandeep Singh <bsi...@phemi.com<mailto:bsi...@phemi.com>> Reply-To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> Date: Tuesday, September 27, 2016 at 1:21 PM To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> Subject: Re: Trouble loading AE If you are trying to run the AggregatePlaintextFastUMLSProcessor.xml as described by the User guide , my best guess is that you are missing the folder /apache-ctakes-3.2.2/resources/org/apache/ctakes/dictionary/fast On Tue, Sep 27, 2016 at 1:09 PM, Bandeep Singh <bsi...@phemi.com<mailto:bsi...@phemi.com>> wrote: Can you share the complete stack trace (error logs). And may be we will know what is going on. On Tue, Sep 27, 2016 at 12:47 PM, Gianfrancesco, Milena <milena.gianfrance...@ucsf.edu<mailto:milena.gianfrance...@ucsf.edu>> wrote: Thanks, yes, so I am getting this error message in response to loading the AE even though resources have been downloaded as specified in the User Manuel. Any other thoughts as to why this may be occurring? Do any of the files within the resources folder need to be modified before loading? From: Bandeep Singh <bsi...@phemi.com<mailto:bsi...@phemi.com>> Reply-To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> Date: Tuesday, September 27, 2016 at 11:55 AM To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> Subject: Re: Trouble loading AE Hi Milena, I am referring to the same resources mentioned in the User Install Guide doc. -Bandeep On Tue, Sep 27, 2016 at 11:05 AM, Gianfrancesco, Milena <milena.gianfrance...@ucsf.edu<mailto:milena.gianfrance...@ucsf.edu>> wrote: Hi Bandeep, I downloaded resources as instructed in the User Install Guide and copied them into the resources folder. Is that what you are referring to? Or it there another set of UMLS resources to be downloaded? There didn’t appear to be so in the link. Thanks From: Bandeep Singh <bsi...@phemi.com<mailto:bsi...@phemi.com>> Reply-To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> Date: Wednesday, September 21, 2016 at 3:54 PM To: "user@ctakes.apache.org<mailto:user@ctakes.apache.org>" <user@ctakes.apache.org<mailto:user@ctakes.apache.org>> Subject: Re: Trouble loading AE Hi, Glad that it worked ! I think resources are missing in your cTakes installation. Did you download the UMLS resources separately from https://sourceforge.net/projects/ctakesresources/files/?source=navbar And You have to put these resources under org/apache/ctakes/dictionary/ Hope that Helps ! Bandeep On Wed, Sep 21, 2016 at 3:45 PM, Gianfrancesco, Milena <milena.gianfrance...@ucsf.edu<mailto:milena.gianfrance...@ucsf.edu>> wrote: Thanks, Bandeep. That seems to have solved that issue, but now when I try to load AE I get an error message popup that states: "org.apache.uima.resource.ResourceInitializationException". I'm not sure what this means? It only happens when I try to load the AEs that utilize UMLS. Thanks in advance. ________________________________ From: Bandeep Singh [bsi...@phemi.com<mailto:bsi...@phemi.com>] Sent: Tuesday, September 13, 2016 5:24 PM To: user@ctakes.apache.org<mailto:user@ctakes.apache.org> Subject: Re: Trouble loading AE Hi Milena, It looks like a classic example of Java version mismatch. One of the dependencies of cTakes is Java 8 Please make sure you have JAVA SDK installed and not JRE. I have OpenJDK 8 running on my system and cTakes runs fine on my system. -Bandeep On Tue, Sep 13, 2016 at 2:32 PM, Gianfrancesco, Milena <milena.gianfrance...@ucsf.edu<mailto:milena.gianfrance...@ucsf.edu>> wrote: Hello, I have just installed cTakes and followed instructions in the 3.2 User Install Guide. However, I am unable to load an AE. I have a UMLS user name and password, and have updated the appropriate scripts as outlined in the User Guide, yet I get this error when trying to load any AE (even the non-UMLS ones): 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) …… + more I have double checked that I have the latest Java software. Any idea what could be causing this error? Thank you! Milena
