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From Pei Chen <chen...@apache.org>
Subject Re: Resource Initialization Exception with cTakes 3.1.0
Date Mon, 30 Sep 2013 20:18:47 GMT
Hi Paula,
Could you do a directory listing on:
$CTAKES_HOME/resources/org/apache/ctakes/dictionary/lookup?
Do you see
rxnorm_index and umls2011ab
?
--Pei


On Mon, Sep 30, 2013 at 4:11 PM, digital girl <cybersation@hotmail.com>wrote:

> 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: cybersation@hotmail.com
> To: user@ctakes.apache.org
> 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
>
>

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