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From samir chabou <samir...@yahoo.com>
Subject Re: Resource Initialization Exception with cTakes 3.1.0
Date Tue, 01 Oct 2013 14:27:58 GMT
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 <cybersation@hotmail.com>
To: "user@ctakes.apache.org" <user@ctakes.apache.org> 
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: cybersation@hotmail.com
To: user@ctakes.apache.org
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: 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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