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Posted to user@ctakes.apache.org by digital girl <cy...@hotmail.com> on 2013/09/30 22:11:15 UTC
RE: Resource Initialization Exception with cTakes 3.1.0
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
Re: Resource Initialization Exception with cTakes 3.1.0
Posted by Pei Chen <ch...@apache.org>.
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 <cy...@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
>
>
Re: Resource Initialization Exception with cTakes 3.1.0 - Resolved!
Posted by samir chabou <sa...@yahoo.com>.
i'm glad that works for you :). I got the help from the others when i need it and i try to shared with the others...
________________________________
From: digital girl <cy...@hotmail.com>
To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Sent: Thursday, October 3, 2013 8:57:07 PM
Subject: RE: Resource Initialization Exception with cTakes 3.1.0 - Resolved!
Samir, you're a genius!!!
I executed the AggregatePlaintextUMLSProcessor and watched the command window since the log files didn't provide any additional details....sure enough there was an 'out of memory' error that appeared. I did what you said about updating the memory min and max to 500m and 1500m (respectively) and reran AggregatePlaintextUMLSProcessor and it loaded!!!
Thanks so much for your help, I really appreciate it man.
Also, thanks to Stamatis, Murali and Pei for their responses.
Now I can focus on learning how this tool works now that it's working. :-)
Regards,
Paula
________________________________
>From samir chabou <sa...@yahoo.com>
Subject Re: Resource Initialization Exception with cTakes 3.1.0
Date Thu, 03 Oct 2013 16:33:31 GMT
if it hangs may be you have a heap size problem. Does the console show any error ?
When you double click on UIMA_CVD--clinical_documents_pipeline.launch can you check if -Xms
and -Xmx set to these values -Xms500M -Xmx1500M"
as shown bellow (the latest line). Also try the analysis engine in the ctakes-core project
the AggregateAE.xml (more simple and does not cause problem of heap)
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
<listEntry value="/ctakes-clinical-pipeline"/>
</listAttribute>
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
<listEntry value="4"/>
</listAttribute>
<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
<mapAttribute key="org.eclipse.debug.core.preferred_launchers">
<mapEntry key="[debug]" value="com.Instantiations.profiler.localJavaApplicationDelegate"/>
</mapAttribute>
<stringAttribute key="org.eclipse.debug.ui.target_debug_perspective" value="perspective_default"/>
<stringAttribute key="org.eclipse.debug.ui.target_run_perspective" value="perspective_default"/>
<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.annot_view.Gladis"/>
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-clinical-pipeline"/>
<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value=""-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties"
-XX:+UseConcMarkSweepGC -Xms500M -Xmx1500M"/>
</launchConfiguration> -------------
From: cybersation@hotmail.com
To: user@ctakes.apache.org
Subject: RE: Resource Initialization Exception with cTakes 3.1.0
Date: Wed, 2 Oct 2013 15:48:58 -0400
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
RE: Resource Initialization Exception with cTakes 3.1.0 - Resolved!
Posted by digital girl <cy...@hotmail.com>.
Samir, you're a genius!!!
I executed the AggregatePlaintextUMLSProcessor and watched the command window since the log files didn't provide any additional details....sure enough there was an 'out of memory' error that appeared. I did what you said about updating the memory min and max to 500m and 1500m (respectively) and reran AggregatePlaintextUMLSProcessor and it loaded!!!
Thanks so much for your help, I really appreciate it man.
Also, thanks to Stamatis, Murali and Pei for their responses.
Now I can focus on learning how this tool works now that it's working. :-)
Regards,
Paula
Fromsamir chabou <sa...@yahoo.com>SubjectRe: Resource Initialization Exception with cTakes 3.1.0DateThu, 03 Oct 2013 16:33:31 GMTif it hangs may be you have a heap size problem. Does the console show any error ?
When you double click on UIMA_CVD--clinical_documents_pipeline.launch can you check if -Xms
and -Xmx set to these values -Xms500M -Xmx1500M"
as shown bellow (the latest line). Also try the analysis engine in the ctakes-core project
the AggregateAE.xml (more simple and does not cause problem of heap)
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
<listEntry value="/ctakes-clinical-pipeline"/>
</listAttribute>
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
<listEntry value="4"/>
</listAttribute>
<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
<mapAttribute key="org.eclipse.debug.core.preferred_launchers">
<mapEntry key="[debug]" value="com.Instantiations.profiler.localJavaApplicationDelegate"/>
</mapAttribute>
<stringAttribute key="org.eclipse.debug.ui.target_debug_perspective" value="perspective_default"/>
<stringAttribute key="org.eclipse.debug.ui.target_run_perspective" value="perspective_default"/>
<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.annot_view.Gladis"/>
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-clinical-pipeline"/>
<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value=""-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties"
-XX:+UseConcMarkSweepGC -Xms500M -Xmx1500M"/>
</launchConfiguration>
------------- From: cybersation@hotmail.com
To: user@ctakes.apache.org
Subject: RE: Resource Initialization Exception with cTakes 3.1.0
Date: Wed, 2 Oct 2013 15:48:58 -0400
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
Re: Resource Initialization Exception with cTakes 3.1.0
Posted by samir chabou <sa...@yahoo.com>.
if it hangs may be you have a heap size problem. Does the console show any error ?
When you double click on UIMA_CVD--clinical_documents_pipeline.launch can you check if -Xms and -Xmx set to these values -Xms500M -Xmx1500M"
as shown bellow (the latest line). Also try the analysis engine in the ctakes-core project the AggregateAE.xml (more simple and does not cause problem of heap)
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
<listEntry value="/ctakes-clinical-pipeline"/>
</listAttribute>
<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
<listEntry value="4"/>
</listAttribute>
<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
<mapAttribute key="org.eclipse.debug.core.preferred_launchers">
<mapEntry key="[debug]" value="com.Instantiations.profiler.localJavaApplicationDelegate"/>
</mapAttribute>
<stringAttribute key="org.eclipse.debug.ui.target_debug_perspective" value="perspective_default"/>
<stringAttribute key="org.eclipse.debug.ui.target_run_perspective" value="perspective_default"/>
<stringAttribute key="org.eclipse.jdt.launching.CLASSPATH_PROVIDER" value="org.eclipse.m2e.launchconfig.classpathProvider"/>
<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="org.apache.uima.tools.annot_view.Gladis"/>
<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="ctakes-clinical-pipeline"/>
<stringAttribute key="org.eclipse.jdt.launching.SOURCE_PATH_PROVIDER" value="org.eclipse.m2e.launchconfig.sourcepathProvider"/>
<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value=""-Djava.util.logging.config.file=${env_var:UIMA_HOME}/Logger.properties" -XX:+UseConcMarkSweepGC -Xms500M -Xmx1500M"/>
</launchConfiguration>
________________________________
From: digital girl <cy...@hotmail.com>
To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Sent: Wednesday, October 2, 2013 3:48:58 PM
Subject: RE: Resource Initialization Exception with cTakes 3.1.0
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
RE: Resource Initialization Exception with cTakes 3.1.0
Posted by digital girl <cy...@hotmail.com>.
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
Re: Resource Initialization Exception with cTakes 3.1.0
Posted by samir chabou <sa...@yahoo.com>.
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 <cy...@hotmail.com>
To: "user@ctakes.apache.org" <us...@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
RE: Resource Initialization Exception with cTakes 3.1.0
Posted by digital girl <cy...@hotmail.com>.
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