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From Xiayuan Huang <huan...@cs.wisc.edu>
Subject Re: Resource Initialization Exception cTAKES 3.1.1
Date Tue, 18 Mar 2014 15:24:26 GMT
Hi Pei,

I followed the instructions and copied umls resources to my ctakes home 
directory where contains one resources folder. But that exception still 
happens. And another question, how can I enlarge my memory setting in 
order to avoid outofmemory exception.

Thanks
Xiayuan


On 2014-03-18 10:17, Pei Chen wrote:
> Hi Xiayuan,
>  Caused by: java.io.FileNotFoundException:
> org/apache/ctakes/dictionary/lookup/rxnorm_index
> 
> Do you have the file the folder in your class path?
> Normally, it should be inside the resources directory.
> Note: The RxNorm indexes are UMLS resources and require
> a separate download.
> 
> Resources
>  Resources are required to run most of cTAKES. They are available for
> download from SourceForge: ctakes-resources-3.1.0.zip [1].
>  Please download, unzip and add/merge the contents to the existing
> resources directory. Follow the User or Developer Install Guide to
> direct you through the installation process.
> 
> [1] http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download
> [1]
> 
> --Pei
> 
> On Mon, Mar 17, 2014 at 5:48 PM, Xiayuan Huang <huangxy@cs.wisc.edu>
> wrote:
> 
>> Hello Pei,
>> 
>> I met the similar exception, I tried to solve it for long but still
>> cnt figure it out. Could you please have a look?
>> 
>> 3/17/14 4:10:14 PM - 15:
>> org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE:
>> Exception occurred
>> org.apache.uima.resource.ResourceInitializationException
>>         at
>> 
> org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:80)
>> 
>>         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(AbstractButton.java:2018)
>>         at
>> 
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
>>         at
>> 
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
>>         at
>> 
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
>>         at
>> javax.swing.AbstractButton.doClick(AbstractButton.java:376)
>>         at
>> 
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
>>         at
>> 
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
>>         at
>> java.awt.Component.processMouseEvent(Component.java:6505)
>>         at
>> javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
>>         at java.awt.Component.processEvent(Component.java:6270)
>>         at java.awt.Container.processEvent(Container.java:2229)
>>         at
>> java.awt.Component.dispatchEventImpl(Component.java:4861)
>>         at
>> java.awt.Container.dispatchEventImpl(Container.java:2287)
>>         at
>> java.awt.Component.dispatchEvent(Component.java:4687)
>>         at
>> 
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
>>         at
>> 
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
>>         at
>> java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
>>         at
>> java.awt.Container.dispatchEventImpl(Container.java:2273)
>>         at java.awt.Window.dispatchEventImpl(Window.java:2719)
>>         at
>> java.awt.Component.dispatchEvent(Component.java:4687)
>>         at
>> java.awt.EventQueue.dispatchEventImpl(EventQueue.java:723)
>>         at java.awt.EventQueue.access$200(EventQueue.java:103)
>>         at java.awt.EventQueue$3.run(EventQueue.java:682)
>>         at java.awt.EventQueue$3.run(EventQueue.java:680)
>>         at java.security.AccessController.doPrivileged(Native
>> Method)
>>         at
>> 
> java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
>>         at
>> 
> java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
>>         at java.awt.EventQueue$4.run(EventQueue.java:696)
>>         at java.awt.EventQueue$4.run(EventQueue.java:694)
>>         at java.security.AccessController.doPrivileged(Native
>> Method)
>>         at
>> 
> java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
>>         at
>> java.awt.EventQueue.dispatchEvent(EventQueue.java:693)
>>         at
>> 
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:244)
>>         at
>> 
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:163)
>>         at
>> 
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:151)
>>         at
>> 
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:147)
>>         at
>> 
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:139)
>>         at
>> java.awt.EventDispatchThread.run(EventDispatchThread.java:97)
>> Caused by: java.io.FileNotFoundException:
>> org/apache/ctakes/dictionary/lookup/rxnorm_index
>>         at
>> 
> org.apache.ctakes.core.resource.FileLocator.locateExplicitly(FileLocator.java:93)
>>         at
>> 
> org.apache.ctakes.core.resource.FileLocator.locateFile(FileLocator.java:68)
>>         at
>> 
> org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl.load(LuceneIndexReaderResourceImpl.java:58)
>>         ... 58 more
>> 
>> On 2014-03-13 11:22, Measure, Alex - BLS wrote:
>> 
>>> Thanks Pei. I did that previously, but I redid it again per your
>>> instructions and everything works perfectly now. I must have made
>>> an
>>> error. Thanks!
>>> 
>>> Alex
>>> 
>>> -----Original Message-----
>>> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
>>> Sent: Thursday, March 13, 2014 11:59 AM
>>> To: user@ctakes.apache.org
>>> Subject: RE: Resource Initialization Exception cTAKES 3.1.1
>>> 
>>> From the downloads page, have you tried:
>>> Resources
>>> Resources are required to run most of cTAKES. They are available
>>> for
>>> download from SourceForge: ctakes-resources-3.1.0.zip [1].
>>> Please download, unzip and add/merge the contents to the existing
>>> resources directory. Follow the User or Developer Install
>>> Guide to
>>> direct you through the installation process.
>>> [1]
>>> 
>> 
> http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download
>>> [1]
>>> 
>>> From: Measure, Alex - BLS [mailto:Measure.Alex@bls.gov]
>>> Sent: Thursday, March 13, 2014 11:53 AM
>>> To: 'user@ctakes.apache.org'
>>> Subject: Resource Initialization Exception cTAKES 3.1.1
>>> 
>>> I am trying to resolve a Resource Initialization Exception I am
>>> receiving while loading the AggregatePlaintextUMLSProcessor, can
>>> anyone assist me? Details are below:
>>> 
>>> I am using ctakes-3.1.1 along with ctakes-resources-3.1.0,
>>> installed
>>> per the User Guide on a Windows 7 machine. I have entered my UMLS
>>> license information in the CVD.bat file and increased the max
>>> heap
>>> size to 4096M (my machine has 8GB of memory).
>>> 
>>> When I attempt to load the AggregatePlaintextUMLSProcessor in the
>>> CVD
>>> I receive a Resource Initialization Exception. I have no trouble
>>> loading and running the AggregatePlaintextProcessor. I also have
>>> no
>>> trouble using the AggregatePlaintextUMLSProcessor with an earlier
>>> version of ctakes, ctakes-3.0-incubating.
>>> 
>>> If I look at the command prompt as the CVD is attempting to load
>>> the
>>> Processor, it appears to be getting stuck at:
>>> 
>>> Loading model:
>>> .............................
>>> 13 Mar 2014 11:38:36  INFO Chunker - Chunker model file:
>>> C:Usersmeasure_aDesktopapache
>>> 
>> 
> -ctakes-3.1.1apache-ctakes-3.1.1resourcesorgapachectakeschunkermodelschunker-model
>>> .zip
>>> 
>>> The full log file is below:
>>> 3/13/14 11:38:36 AM - 14:
>>> org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE:
>>> Exception occurred
>>> org.apache.uima.resource.ResourceInitializationException
>>>                 at
>>> 
>> 
> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:130)
>>>                 at
>>> 
>> 
> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
>>>                 at
>>> 
>> 
> org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
>>>                 at
>>> 
>> 
> org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
>>>                 at
>>> 
>> 
> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
>>>                 at
>>> 
>> 
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:123)
>>>                 at
>>> 
>> 
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>>                 at
>>> 
>> 
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>>>                 at
>>> 
>> 
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>>                 at
>>> 
>> 
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
>>>                 at
>>> 
>> 
> org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
>>>                 at
>>> 
>> 
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
>>>                 at
>>> 
>> 
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>>                 at
>>> 
>> 
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
>>>                 at
>>> 
>> 
> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(AnalysisEngineFactory_impl.java:94)
>>>                 at
>>> 
>> 
> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(CompositeResourceFactory_impl.java:62)
>>>                 at
>>> 
>> 
> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>>                 at
>>> 
>> 
> org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:354)
>>>                 at
>>> org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
>>>                 at
>>> 
>> 
> org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477)
>>>                 at
>>> 
>> 
> org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
>>>                 at
>>> javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>>>                 at
>>> javax.swing.AbstractButton$Handler.actionPerformed(Unknown
>>> Source)
>>>                 at
>>> javax.swing.DefaultButtonModel.fireActionPerformed(Unknown
>>> Source)
>>>                 at
>>> javax.swing.DefaultButtonModel.setPressed(Unknown Source)
>>>                 at
>>> javax.swing.AbstractButton.doClick(Unknown Source)
>>>                 at
>>> javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
>>>                 at
>>> 
>> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
>>> Source)
>>>                 at
>>> java.awt.Component.processMouseEvent(Unknown Source)
>>>                 at
>>> javax.swing.JComponent.processMouseEvent(Unknown Source)
>>>                 at
>>> java.awt.Component.processEvent(Unknown Source)
>>>                 at
>>> java.awt.Container.processEvent(Unknown Source)
>>>                 at
>>> java.awt.Component.dispatchEventImpl(Unknown Source)
>>>                 at
>>> java.awt.Container.dispatchEventImpl(Unknown Source)
>>>                 at
>>> java.awt.Component.dispatchEvent(Unknown Source)
>>>                 at
>>> java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
>>>                 at
>>> java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
>>>                 at
>>> java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
>>>                 at
>>> java.awt.Container.dispatchEventImpl(Unknown Source)
>>>                 at
>>> java.awt.Window.dispatchEventImpl(Unknown Source)
>>>                 at
>>> java.awt.Component.dispatchEvent(Unknown Source)
>>>                 at
>>> java.awt.EventQueue.dispatchEventImpl(Unknown Source)
>>>                 at
>>> java.awt.EventQueue.access$200(Unknown Source)
>>>                 at
>>> java.awt.EventQueue$3.run(Unknown Source)
>>>                 at
>>> java.awt.EventQueue$3.run(Unknown Source)
>>>                 at
>>> java.security.AccessController.doPrivileged(Native Method)
>>>                 at
>>> java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
>>> Source)
>>>                 at
>>> java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
>>> Source)
>>>                 at
>>> java.awt.EventQueue$4.run(Unknown Source)
>>>                 at
>>> java.awt.EventQueue$4.run(Unknown Source)
>>>                 at
>>> java.security.AccessController.doPrivileged(Native Method)
>>>                 at
>>> java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
>>> Source)
>>>                 at
>>> java.awt.EventQueue.dispatchEvent(Unknown Source)
>>>                 at
>>> java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown
>>> Source)
>>>                 at
>>> java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
>>>                 at
>>> java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown
>>> Source)
>>>                 at
>>> java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>>>                 at
>>> java.awt.EventDispatchThread.pumpEvents(Unknown Source)
>>>                 at
>>> java.awt.EventDispatchThread.run(Unknown Source)
>>> Caused by: java.sql.SQLException: File input/output error:
>>> java.io.IOException: Stream closed
>>>                 at
>>> org.hsqldb.jdbc.Util.sqlException(Unknown Source)
>>>                 at
>>> org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
>>>                 at
>>> org.hsqldb.jdbcDriver.getConnection(Unknown Source)
>>>                 at
>>> org.hsqldb.jdbcDriver.connect(Unknown Source)
>>>                 at
>>> java.sql.DriverManager.getConnection(Unknown Source)
>>>                 at
>>> java.sql.DriverManager.getConnection(Unknown Source)
>>>                 at
>>> 
>> 
> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(JdbcConnectionResourceImpl.java:109)
>>>                 ... 58 more
>>> 
>>> I would greatly appreciate any assistance you might provide.
>>> 
>>> Alex
> 
> 
> 
> Links:
> ------
> [1]
> http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.1.0.zip/download

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