hi Pei and Paula, this a description of a problem that i had with the resource zipped file it may probably help ... I got some set up problem first time with the zipped resource file. this is how i proceed : I'm using using eclipse to install cTAKES 3.1. First you have to register in UMLS to get your password and userId in order to use umls2011ab (Pei, is password and userId also need it for user-installation as in developer installation ?) 1) I created a new workspace 1) I followed the installation guide BUT I skipped the step 5 "Unzip the cTAKES resources file into a temporary location and copied". I got some problem of this unziped resource file (i think not sure that the zipped resource file is out of sync) 2) once the installation is finished search for resource rxnorm_index and umls2011ab in the folder of the installation (i found them in .../.m2/repository/...) and I copied them in proper resource path (...ctakes-dictionary-lookup-res/.../dictionary/lookup/)
Thanks Samir ________________________________ From: digital girl <[email protected]> To: "[email protected]" <[email protected]> Sent: Tuesday, October 1, 2013 12:18:14 AM Subject: RE: Resource Initialization Exception with cTakes 3.1.0 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
