Re: ctakes ResourceInitializationException
Hi ctakes developers, I'm attempting to set up cTakes 3.2.2 for development in Eclipse Juno IDE for Java EE Developers 4.5, on Max OS X Yosemite 10.10.5. I've followed (to the best of my knowledge) the directions posted here (Developer Install 3.2): https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+Developer+Install+Guide and here (Developer Install 3.0): https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+Developer+Install+Guide I receive a: java.lang.NoClassDefFoundError: org/springframework/validation/DataBinder (see log below). I receive this error whenever I try to load any analysis engine, i.e., Run -> Load AE. Thinking that DataBinder is defined within the springframework, spring-context, I added the following dependency to the pom.xml of ctakes-clinical-pipeline. It had no affect. org.springframework spring-context Any advice or direction is appreciated. Thanks, Jay 2/24/16 8:39:23 PM - 19: org.apache.uima.tools.cvd.MainFrame.handleException(528): SEVERE: org/springframework/validation/DataBinder java.lang.NoClassDefFoundError: org/springframework/validation/DataBinder at org.apache.uima.fit.component.JCasAnnotator_ImplBase.initialize(JCasAnnotator_ImplBase.java:50) at org.apache.ctakes.core.ae.CopyAnnotator.initialize(CopyAnnotator.java:89) 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(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:6535) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6300) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4891) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4713) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525) at
ctakes ResourceInitializationException
Hi, I'm trying to run bin/runctakesCVD.sh. When I try to load the AggregatePlaintextUMLSProcessor.xml, as described in the User install guide ( https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+User+Install+Guide) I receive the ResourceInitializationException (please see details below). It appears that I do not have something set up correctly with the UMLS resources. If I try to run the AggregatePlaintextProcessor, everything seems to work Ok. I get the same error with or without defining my UMLS credentials in runctakesCVD.sh Why is it trying to open a database connection? Any help or direction would be appreciated. Thanks, Jay Environment: OS X Yosemite 10.10.5 Java 1.8 Downloads: apache-ctakes-3.2.2 ctakes-resources-3.2.1.1-bin Copied the resources directory: ditto /Users/jayurbain/Downloads/ctakes-resources-3.2.1.1-bin/resources/* /Users/jayurbain/Dropbox/apache-ctakes-3.2.2/resources Added my UMLS user authentication to runtakesCVD.sh java -Dctakes.umlsuser= -Dctakes.umlspw= Exception: 2/15/16 10:09:10 AM - 15: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Exception occurred org.apache.uima.resource.ResourceInitializationException at org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:130) at org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603) 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: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:6535) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6300) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4891) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4713) 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:2750) at java.awt.Component.dispatchEvent(Component.java:4713) 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
Re: Apache cTAKES - ResourceInitializationException
Pankaj, Caused by: java.lang.NullPointerException* * at java.io.Reader.init(Reader.java:78)* * at java.io.InputStreamReader.init(InputStreamReader.java:72)* My guess is you are trying to read something which is null. Hope it helps. Regards, Harpreet On Wednesday, May 27, 2015, Pankaj Shinde pankaj.shi...@krixi.com wrote: Hi, I want to parse clinical documents using Apache cTAKES. I have a set of clinical documents as plain texts. For this, I am using BagOfCUIsGenerator.java and cTAKES jars. I configured this in IntelliJ IDEA as a java project. When I try to run, I am getting exception and error as follows. Output: *log4j:WARN No appenders could be found for logger (org.springframework.validation.DataBinder).* *log4j:WARN Please initialize the log4j system properly.* *log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.* *Loading configuration.* *Loading feature templates.* *Loading lexica.* *Loading model:* ** *Exception in thread main org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine failed. (Descriptor: file:/D:/Dev/Savy/java_projects/cTakes/desc/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml)* * at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:251)* * at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:155)* * 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.factory.AnalysisEngineFactory.createEngineFromPath(AnalysisEngineFactory.java:773)* * at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.init(BagOfAnnotationsGenerator.java:60)* * at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.init(BagOfAnnotationsGenerator.java:54)* * at BagOfCUIsGenerator.init(BagOfCUIsGenerator.java:21)* * at BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:61)* * at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)* * at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)* * at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)* * at java.lang.reflect.Method.invoke(Method.java:606)* * at com.intellij.rt.execution.application.AppMain.main(AppMain.java:134)* *Caused by: java.lang.NullPointerException* * at java.io.Reader.init(Reader.java:78)* * at java.io.InputStreamReader.init(InputStreamReader.java:72)* * at java.util.Scanner.init(Scanner.java:608)* * at org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor.init(ContextWordWindowExtractor.java:55)* * at org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize_history_extractor(HistoryCleartkAnalysisEngine.java:58)* * at org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize(HistoryCleartkAnalysisEngine.java:49)* * at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:249)* * ... 24 more* *Process finished with exit code 1* Please help. Thanks Pankaj Shinde
Apache cTAKES - ResourceInitializationException
Hi, I want to parse clinical documents using Apache cTAKES. I have a set of clinical documents as plain texts. For this, I am using BagOfCUIsGenerator.java and cTAKES jars. I configured this in IntelliJ IDEA as a java project. When I try to run, I am getting exception and error as follows. Output: *log4j:WARN No appenders could be found for logger (org.springframework.validation.DataBinder).* *log4j:WARN Please initialize the log4j system properly.* *log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.* *Loading configuration.* *Loading feature templates.* *Loading lexica.* *Loading model:* ** *Exception in thread main org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine failed. (Descriptor: file:/D:/Dev/Savy/java_projects/cTakes/desc/ctakes-assertion/desc/analysis_engine/HistoryCleartkAnalysisEngine.xml)* * at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:251)* * at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:155)* * 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.factory.AnalysisEngineFactory.createEngineFromPath(AnalysisEngineFactory.java:773)* * at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.init(BagOfAnnotationsGenerator.java:60)* * at org.apache.ctakes.clinicalpipeline.runtime.BagOfAnnotationsGenerator.init(BagOfAnnotationsGenerator.java:54)* * at BagOfCUIsGenerator.init(BagOfCUIsGenerator.java:21)* * at BagOfCUIsGenerator.main(BagOfCUIsGenerator.java:61)* * at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)* * at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)* * at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)* * at java.lang.reflect.Method.invoke(Method.java:606)* * at com.intellij.rt.execution.application.AppMain.main(AppMain.java:134)* *Caused by: java.lang.NullPointerException* * at java.io.Reader.init(Reader.java:78)* * at java.io.InputStreamReader.init(InputStreamReader.java:72)* * at java.util.Scanner.init(Scanner.java:608)* * at org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor.init(ContextWordWindowExtractor.java:55)* * at org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize_history_extractor(HistoryCleartkAnalysisEngine.java:58)* * at org.apache.ctakes.assertion.medfacts.cleartk.HistoryCleartkAnalysisEngine.initialize(HistoryCleartkAnalysisEngine.java:49)* * at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:249)* * ... 24 more* *Process finished with exit code 1* Please help. Thanks Pankaj Shinde
