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From Pei Chen <chen...@apache.org>
Subject Re: Resource Initialization Exception cTAKES 3.1.1
Date Tue, 18 Mar 2014 15:17:21 GMT
Hi Xiayuan,
Caused by: java.io.FileNotFoundException: org/apache/ctakes/dictionary/l
ookup/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
--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.initializeAggregateAnalysisEng
> ine(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
>>
>> From: Measure, Alex - BLS [mailto:Measure.Alex@bls.gov]
>> Sent: Thursday, March 13, 2014 11:53 AM
>> To: 'user@ctakes.apache.org'
>> Subject: Resource Initialization Exception cTAKES 3.1.1
>>
>> I am trying to resolve a Resource Initialization Exception I am
>> receiving while loading the AggregatePlaintextUMLSProcessor, can
>> anyone assist me? Details are below:
>>
>> I am using ctakes-3.1.1 along with ctakes-resources-3.1.0, installed
>> per the User Guide on a Windows 7 machine. I have entered my UMLS
>> license information in the CVD.bat file and increased the max heap
>> size to 4096M (my machine has 8GB of memory).
>>
>> When I attempt to load the AggregatePlaintextUMLSProcessor in the CVD
>> I receive a Resource Initialization Exception. I have no trouble
>> loading and running the AggregatePlaintextProcessor. I also have no
>> trouble using the AggregatePlaintextUMLSProcessor with an earlier
>> version of ctakes, ctakes-3.0-incubating.
>>
>> If I look at the command prompt as the CVD is attempting to load the
>> Processor, it appears to be getting stuck at:
>>
>> Loading model:
>> .............................
>> 13 Mar 2014 11:38:36  INFO Chunker - Chunker model file:
>> C:\Users\measure_a\Desktop\apache
>> -ctakes-3.1.1\apache-ctakes-3.1.1\resources\org\apache\
>> ctakes\chunker\models\chunker-model
>> .zip
>>
>>
>> The full log file is below:
>> 3/13/14 11:38:36 AM - 14:
>> org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE:
>> Exception occurred
>> org.apache.uima.resource.ResourceInitializationException
>>                 at
>> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(
>> JdbcConnectionResourceImpl.java:130)
>>                 at
>> org.apache.uima.resource.impl.ResourceManager_impl.registerResource(
>> ResourceManager_impl.java:603)
>>                 at
>> org.apache.uima.resource.impl.ResourceManager_impl.
>> initializeExternalResources(ResourceManager_impl.java:442)
>>                 at
>> org.apache.uima.resource.Resource_ImplBase.initialize(
>> Resource_ImplBase.java:153)
>>                 at
>> org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(
>> AnalysisEngineImplBase.java:157)
>>                 at
>> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
>> initialize(PrimitiveAnalysisEngine_impl.java:123)
>>                 at
>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(
>> AnalysisEngineFactory_impl.java:94)
>>                 at
>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(
>> CompositeResourceFactory_impl.java:62)
>>                 at
>> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>                 at
>> org.apache.uima.UIMAFramework.produceAnalysisEngine(
>> UIMAFramework.java:387)
>>                 at
>> org.apache.uima.analysis_engine.asb.impl.ASB_impl.
>> setup(ASB_impl.java:254)
>>                 at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
>> initASB(AggregateAnalysisEngine_impl.java:431)
>>                 at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
>> initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
>>                 at
>> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
>> initialize(AggregateAnalysisEngine_impl.java:185)
>>                 at
>> org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(
>> AnalysisEngineFactory_impl.java:94)
>>                 at
>> org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(
>> CompositeResourceFactory_impl.java:62)
>>                 at
>> org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:269)
>>                 at
>> org.apache.uima.UIMAFramework.produceAnalysisEngine(
>> UIMAFramework.java:354)
>>                 at
>> org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484)
>>                 at
>> org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:477)
>>                 at
>> org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.
>> actionPerformed(AnnotatorOpenEventHandler.java:52)
>>                 at
>> javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
>>                 at
>> javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
>>                 at
>> javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
>>                 at javax.swing.DefaultButtonModel.setPressed(Unknown
>> Source)
>>                 at javax.swing.AbstractButton.doClick(Unknown Source)
>>                 at
>> javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
>>                 at
>> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown
>> Source)
>>                 at java.awt.Component.processMouseEvent(Unknown Source)
>>                 at javax.swing.JComponent.processMouseEvent(Unknown
>> Source)
>>                 at java.awt.Component.processEvent(Unknown Source)
>>                 at java.awt.Container.processEvent(Unknown Source)
>>                 at java.awt.Component.dispatchEventImpl(Unknown Source)
>>                 at java.awt.Container.dispatchEventImpl(Unknown Source)
>>                 at java.awt.Component.dispatchEvent(Unknown Source)
>>                 at
>> java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
>>                 at
>> java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
>>                 at java.awt.LightweightDispatcher.dispatchEvent(Unknown
>> Source)
>>                 at java.awt.Container.dispatchEventImpl(Unknown Source)
>>                 at java.awt.Window.dispatchEventImpl(Unknown Source)
>>                 at java.awt.Component.dispatchEvent(Unknown Source)
>>                 at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
>>                 at java.awt.EventQueue.access$200(Unknown Source)
>>                 at java.awt.EventQueue$3.run(Unknown Source)
>>                 at java.awt.EventQueue$3.run(Unknown Source)
>>                 at java.security.AccessController.doPrivileged(Native
>> Method)
>>                 at
>> java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
>> Source)
>>                 at
>> java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
>> Source)
>>                 at java.awt.EventQueue$4.run(Unknown Source)
>>                 at java.awt.EventQueue$4.run(Unknown Source)
>>                 at java.security.AccessController.doPrivileged(Native
>> Method)
>>                 at
>> java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown
>> Source)
>>                 at java.awt.EventQueue.dispatchEvent(Unknown Source)
>>                 at
>> java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
>>                 at
>> java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
>>                 at
>> java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
>>                 at java.awt.EventDispatchThread.pumpEvents(Unknown
>> Source)
>>                 at java.awt.EventDispatchThread.pumpEvents(Unknown
>> Source)
>>                 at java.awt.EventDispatchThread.run(Unknown Source)
>> Caused by: java.sql.SQLException: File input/output error:
>> java.io.IOException: Stream closed
>>                 at org.hsqldb.jdbc.Util.sqlException(Unknown Source)
>>                 at org.hsqldb.jdbc.jdbcConnection.<init>(Unknown Source)
>>                 at org.hsqldb.jdbcDriver.getConnection(Unknown Source)
>>                 at org.hsqldb.jdbcDriver.connect(Unknown Source)
>>                 at java.sql.DriverManager.getConnection(Unknown Source)
>>                 at java.sql.DriverManager.getConnection(Unknown Source)
>>                 at
>> org.apache.ctakes.core.resource.JdbcConnectionResourceImpl.load(
>> JdbcConnectionResourceImpl.java:109)
>>                 ... 58 more
>>
>> I would greatly appreciate any assistance you might provide.
>>
>> Alex
>>
>

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