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 <[email protected]>
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:[email protected]]
Sent: Thursday, March 13, 2014 11:59 AM
To: [email protected]
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:[email protected]]
Sent: Thursday, March 13, 2014 11:53 AM
To: '[email protected]'
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
