Hi Pei, Thanks for the prompt response. Yes, I do see rxnorm_index and umls2011ab directories in the path that you stated. In addition, I also see assertion_cue_phrase_index, drug_index, Orangebook, snomed-like** directories. Paula
From: [email protected] To: [email protected] Subject: RE: Resource Initialization Exception with cTakes 3.1.0 Date: Mon, 30 Sep 2013 16:11:15 -0400 First of all thanks Stamatis and Murali for the prompt reply. Correction: it was cTakes 3.1.0 that I installed not 3.0.1 (I got the '0' and '1' reversed). I did also extract/copy the resource zip file afterwards which did overwrite some of the resource files that were part of the original cTakes3.1.0 install. I followed the instructions on the user guide install web page precisely, the link below. https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide If you guys can help I'd so much appreciate it. Regards,Paula From: [email protected] To: [email protected] Subject: Resource Initialization Exception with cTakes 3.0.1 Date: Mon, 30 Sep 2013 00:03:22 -0400 Hi, I found a similar email posted on the mailing list archives but the specific errors I got are different. I had installed the user version of cTakes 3.0.1 as well as the resources files stated on the user guide. In addition I have a UMLS license. I get the following error when I try to run the AggregatePlaintextUMLSProcessor. I also tried running just the AggregatePlaintextProcessor but it just states not loaded and nothing shows in the log file. I got the below error from running the UMLS aggregate processor. Please advise on how to resolve. Thanks. Regards, Paula ------------------------- 9/29/13 11:52:46 PM - 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
