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From "Measure, Alex - BLS" <Measure.A...@bls.gov>
Subject RE: Resource Initialization Exception cTAKES 3.1.1
Date Thu, 13 Mar 2014 16:22:41 GMT
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:Pei.Chen@childrens.harvard.edu] 
Sent: Thursday, March 13, 2014 11:59 AM
To: user@ctakes.apache.org
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:Measure.Alex@bls.gov]
Sent: Thursday, March 13, 2014 11:53 AM
To: 'user@ctakes.apache.org'
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



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