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From digital girl <cybersat...@hotmail.com>
Subject RE: Resource Initialization Exception with cTakes 3.1.0
Date Wed, 02 Oct 2013 19:48:58 GMT
Hi Samir,
 
Thanks for the prompt reply.  Okay, I reinstalled cTakes 3.1.0 and did not do the full resource
zip file copy,  I just copied over the two directories:  rxnorm_index and umls2011ab.
 
I ran the AggregatePlaintextUMLSProcessor and it didn't load so I checked the log and nothing
appeared so I changed the log setting to show all information and tried again.  I got the
following information in the log which states no errors unlike what got before (see original
email below).  However, I'm still back we I started with not being able to see this thing
in action.  In addition I also tried to use the simplified AggregatePlaintextProcessor and
the application just hangs.  I'm at a complete loss here.  I really would love to work with
cTakes and I'm hoping someone could help me out.
 
---below is information taken from log when running AggregatePlaintextUMLSProcessor.------
10/2/13 3:37:11 PM - 14: org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [AggregateCdaUMLSProcessor] initialization begin
10/2/13 3:37:12 PM - 14: org.apache.uima.analysis_engine.asb.impl.ASB_impl.initialize: CONFIG:
ASB initialization begin
10/2/13 3:37:12 PM - 14: org.apache.uima.analysis_engine.asb.impl.ASB_impl.initialize: CONFIG:
ASB initialization successful
10/2/13 3:37:12 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [ClearNLPDependencyParserAE] initialization begin
10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [TokenizerAnnotatorPTB] initialization begin
10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [ContextDependentTokenizerAnnotator] initialization begin
10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [NegationAnnotator] initialization begin
10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [StatusAnnotator] initialization begin
10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [Sentence Detector annotator] initialization begin
10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [Adjust NP in NP NP to span both] initialization begin
10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [Adjust NP in NP PP NP to span all three] initialization begin
10/2/13 3:37:21 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [POSTagger] initialization begin
10/2/13 3:37:22 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG:
trying Resource class org.apache.uima.resource.impl.DataResource_impl
10/2/13 3:37:22 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [Chunker] initialization begin
10/2/13 3:37:23 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG:
trying Resource class org.apache.uima.resource.impl.DataResource_impl
10/2/13 3:37:23 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG:
trying Resource class org.apache.uima.resource.impl.ConfigurableDataResource_impl
10/2/13 3:37:23 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG:
trying Resource class org.apache.uima.resource.impl.ConfigurableDataResource_impl
10/2/13 3:37:23 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG:
trying Resource class org.apache.uima.resource.impl.ConfigurableDataResource_impl
10/2/13 3:37:23 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [UmlsDictionaryLookupAnnotator] initialization begin
10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [ExtractionPrepAnnotator] initialization begin
10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG:
trying Resource class org.apache.uima.resource.impl.DataResource_impl
10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG:
trying Resource class org.apache.uima.resource.impl.DataResource_impl
10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [CdaCasInitializer] initialization begin
10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [LookupWindowAnnotator] initialization begin
10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.asb.impl.ASB_impl.initialize: CONFIG:
ASB initialization begin
10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.asb.impl.ASB_impl.initialize: CONFIG:
ASB initialization successful
10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [NP to LookupWindow] initialization begin
10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [Maximize Lookup Windows] initialization begin
10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [LookupWindowAnnotator] initialization successful
10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [assertionMiniPipelineAnalysisEngine] initialization begin
10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.asb.impl.ASB_impl.initialize: CONFIG:
ASB initialization begin
10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.asb.impl.ASB_impl.initialize: CONFIG:
ASB initialization successful
10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG:
trying Resource class org.apache.uima.resource.impl.DataResource_impl
10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG:
trying Resource class org.apache.uima.resource.impl.DataResource_impl
10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG:
trying Resource class org.apache.uima.resource.impl.DataResource_impl
10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG:
trying Resource class org.apache.uima.resource.impl.DataResource_impl
10/2/13 3:37:24 PM - 14: org.apache.uima.util.SimpleResourceFactory.produceResource: CONFIG:
trying Resource class org.apache.uima.resource.impl.DataResource_impl
10/2/13 3:37:24 PM - 14: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize:
CONFIG: AnalysisEngine [assertionAnalysisEngine] initialization begin
 
Paula

-----------------------------------------------------------------------------------
 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: 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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