Hi Xiayuan, Caused by: java.io.FileNotFoundException: org/apache/ctakes/dictionary/l ookup/rxnorm_index
Do you have the file the folder in your class path? Normally, it should be inside the resources directory. Note: The RxNorm indexes are UMLS resources and require a separate download. Resources Resources are required to run most of cTAKES. They are available for download from SourceForge: ctakes-resources-3.1.0.zip [1]. Please download, unzip and add/merge the contents to the existing resources directory. Follow the User or Developer Install Guide to direct you through the installation process. [1] http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download --Pei On Mon, Mar 17, 2014 at 5:48 PM, Xiayuan Huang <[email protected]> wrote: > Hello Pei, > > I met the similar exception, I tried to solve it for long but still cnt > figure it out. Could you please have a look? > > > > 3/17/14 4:10:14 PM - 15: org.apache.uima.tools.cvd. > MainFrame.handleException(527): SEVERE: Exception occurred > org.apache.uima.resource.ResourceInitializationException > at org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl. > load(LuceneIndexReaderResourceImpl.java:80) > > 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.initializeAggregateAnalysisEng > ine(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:2018) > at javax.swing.AbstractButton$Handler.actionPerformed( > AbstractButton.java:2341) > at javax.swing.DefaultButtonModel.fireActionPerformed( > DefaultButtonModel.java:402) > at javax.swing.DefaultButtonModel.setPressed( > DefaultButtonModel.java:259) > at javax.swing.AbstractButton.doClick(AbstractButton.java:376) > at javax.swing.plaf.basic.BasicMenuItemUI.doClick( > BasicMenuItemUI.java:833) > at javax.swing.plaf.basic.BasicMenuItemUI$Handler. > mouseReleased(BasicMenuItemUI.java:877) > at java.awt.Component.processMouseEvent(Component.java:6505) > at javax.swing.JComponent.processMouseEvent(JComponent.java:3321) > at java.awt.Component.processEvent(Component.java:6270) > at java.awt.Container.processEvent(Container.java:2229) > at java.awt.Component.dispatchEventImpl(Component.java:4861) > at java.awt.Container.dispatchEventImpl(Container.java:2287) > at java.awt.Component.dispatchEvent(Component.java:4687) > at java.awt.LightweightDispatcher.retargetMouseEvent(Container. > java:4832) > at java.awt.LightweightDispatcher.processMouseEvent(Container. > java:4492) > at java.awt.LightweightDispatcher.dispatchEvent(Container.java: > 4422) > at java.awt.Container.dispatchEventImpl(Container.java:2273) > at java.awt.Window.dispatchEventImpl(Window.java:2719) > at java.awt.Component.dispatchEvent(Component.java:4687) > at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:723) > at java.awt.EventQueue.access$200(EventQueue.java:103) > at java.awt.EventQueue$3.run(EventQueue.java:682) > at java.awt.EventQueue$3.run(EventQueue.java:680) > at java.security.AccessController.doPrivileged(Native Method) > at java.security.ProtectionDomain$1.doIntersectionPrivilege( > ProtectionDomain.java:76) > at java.security.ProtectionDomain$1.doIntersectionPrivilege( > ProtectionDomain.java:87) > at java.awt.EventQueue$4.run(EventQueue.java:696) > at java.awt.EventQueue$4.run(EventQueue.java:694) > at java.security.AccessController.doPrivileged(Native Method) > at java.security.ProtectionDomain$1.doIntersectionPrivilege( > ProtectionDomain.java:76) > at java.awt.EventQueue.dispatchEvent(EventQueue.java:693) > at java.awt.EventDispatchThread.pumpOneEventForFilters( > EventDispatchThread.java:244) > at java.awt.EventDispatchThread.pumpEventsForFilter( > EventDispatchThread.java:163) > at java.awt.EventDispatchThread.pumpEventsForHierarchy( > EventDispatchThread.java:151) > at java.awt.EventDispatchThread.pumpEvents( > EventDispatchThread.java:147) > at java.awt.EventDispatchThread.pumpEvents( > EventDispatchThread.java:139) > at java.awt.EventDispatchThread.run(EventDispatchThread.java:97) > Caused by: java.io.FileNotFoundException: org/apache/ctakes/dictionary/ > lookup/rxnorm_index > at org.apache.ctakes.core.resource.FileLocator. > locateExplicitly(FileLocator.java:93) > at org.apache.ctakes.core.resource.FileLocator. > locateFile(FileLocator.java:68) > at org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl. > load(LuceneIndexReaderResourceImpl.java:58) > ... 58 more > > > > > > On 2014-03-13 11:22, Measure, Alex - BLS wrote: > >> Thanks Pei. I did that previously, but I redid it again per your >> instructions and everything works perfectly now. I must have made an >> error. Thanks! >> >> Alex >> >> -----Original Message----- >> From: Chen, Pei [mailto:[email protected]] >> Sent: Thursday, March 13, 2014 11:59 AM >> To: [email protected] >> Subject: RE: Resource Initialization Exception cTAKES 3.1.1 >> >> From the downloads page, have you tried: >> Resources >> Resources are required to run most of cTAKES. They are available for >> download from SourceForge: ctakes-resources-3.1.0.zip [1]. >> Please download, unzip and add/merge the contents to the existing >> resources directory. Follow the User or Developer Install Guide to >> direct you through the installation process. >> [1] >> http://sourceforge.net/projects/ctakesresources/ >> files/ctakes-resources-3.1.0.zip/download >> >> From: Measure, Alex - BLS [mailto:[email protected]] >> Sent: Thursday, March 13, 2014 11:53 AM >> To: '[email protected]' >> Subject: Resource Initialization Exception cTAKES 3.1.1 >> >> I am trying to resolve a Resource Initialization Exception I am >> receiving while loading the AggregatePlaintextUMLSProcessor, can >> anyone assist me? Details are below: >> >> I am using ctakes-3.1.1 along with ctakes-resources-3.1.0, installed >> per the User Guide on a Windows 7 machine. I have entered my UMLS >> license information in the CVD.bat file and increased the max heap >> size to 4096M (my machine has 8GB of memory). >> >> When I attempt to load the AggregatePlaintextUMLSProcessor in the CVD >> I receive a Resource Initialization Exception. I have no trouble >> loading and running the AggregatePlaintextProcessor. I also have no >> trouble using the AggregatePlaintextUMLSProcessor with an earlier >> version of ctakes, ctakes-3.0-incubating. >> >> If I look at the command prompt as the CVD is attempting to load the >> Processor, it appears to be getting stuck at: >> >> Loading model: >> ............................. >> 13 Mar 2014 11:38:36 INFO Chunker - Chunker model file: >> C:\Users\measure_a\Desktop\apache >> -ctakes-3.1.1\apache-ctakes-3.1.1\resources\org\apache\ >> ctakes\chunker\models\chunker-model >> .zip >> >> >> The full log file is below: >> 3/13/14 11:38:36 AM - 14: >> org.apache.uima.tools.cvd.MainFrame.handleException(527): 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: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$200(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: java.sql.SQLException: File input/output error: >> java.io.IOException: Stream closed >> at org.hsqldb.jdbc.Util.sqlException(Unknown Source) >> at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source) >> at org.hsqldb.jdbcDriver.getConnection(Unknown Source) >> at org.hsqldb.jdbcDriver.connect(Unknown Source) >> at java.sql.DriverManager.getConnection(Unknown Source) >> at java.sql.DriverManager.getConnection(Unknown Source) >> at >> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load( >> JdbcConnectionResourceImpl.java:109) >> ... 58 more >> >> I would greatly appreciate any assistance you might provide. >> >> Alex >> >
