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Posted to dev@ctakes.apache.org by Jay Urbain <ja...@gmail.com> on 2016/02/15 15:45:15 UTC
ctakes resource exception
Hi,
I'm trying to run bin/runctakesCVD.sh. When I try to load the
AggregatePlaintextFastUMLSProcessor.xml, as described in the User install
guide (
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+User+Install+Guide)
I receive the ResourceInitializationException (please see details below).
It appears that I do not have something set up correctly with the UMLS
resources. If I try to run the AggregatePlaintextProcessor, everything
seems to work Ok.
Any help or direction would be appreciated.
Thanks,
Jay
Environment:
OS X Yosemite 10.10.5
Java 1.8
Downloads:
apache-ctakes-3.2.2
ctakes-resources-3.2.1.1-bin
Copied the resources directory:
ditto /Users/jayurbain/Downloads/ctakes-resources-3.2.1.1-bin/resources/*
/Users/jayurbain/Dropbox/apache-ctakes-3.2.2/resources
Added my UMLS user authentication to runtakesCVD.sh
java -Dctakes.umlsuser=<YOUR_UMLS_ID_HERE>
-Dctakes.umlspw=<YOUR_UMLS_PASSSWORD_HERE>
Exception:
2/15/16 8:34:25 AM - 15:
org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
Initialization of annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor:
file:/Users/jayurbain/Dropbox/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
org.apache.uima.resource.ResourceInitializationException: Initialization of
annotator class
"org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
(Descriptor:
file:/Users/jayurbain/Dropbox/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
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:476)
at
org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
at java.awt.Component.processMouseEvent(Component.java:6535)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6300)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4891)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
at java.awt.Container.dispatchEventImpl(Container.java:2280)
at java.awt.Window.dispatchEventImpl(Window.java:2750)
at java.awt.Component.dispatchEvent(Component.java:4713)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
Caused by: org.apache.uima.resource.ResourceInitializationException:
EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
Can't find resource for bundle java.util.PropertyResourceBundle, key Could
not construct
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
at
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
... 55 more
Caused by:
org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
Can't find resource for bundle java.util.PropertyResourceBundle, key Could
not construct
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:203)
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:160)
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:131)
at
org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
... 56 more
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at
org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:200)
... 59 more
Caused by: java.sql.SQLException: No Hsql DB exists at Url
at
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:109)
at
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:60)
at
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:93)
at
org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:75)
at
org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
... 64 more
Caused by: java.io.FileNotFoundException: No File exists at
resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx.script
at
org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
at
org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:106)
... 68 more
Re: ctakes resource exception
Posted by Pei Chen <pe...@wiredinformatics.com>.
Jay,
Did you also download and unzip the dictionary itself?
UMLS® Dictionary
Zipped copy of the cTAKES™ UMLS® dictionary. Please refer to the TODO :
Should write a separate page that outlines what the dictionaries are,
licensing, and where/how to get them on the net, where to install them
locally, and how to configure user/pass Dictionary Install Guide
<https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Dictionary+Lookup>
for assistance. Install fast version if only running ctakes-fast.
All Versions
<http://sourceforge.net/projects/ctakesresources/files/ctakes-resources-3.2.1.1-bin.zip/download>
Fast
Version
<http://sourceforge.net/projects/ctakesresources/files/ctakessnorx-3.2.1.1.zip/download>
Pei Chen
Wired Informatics <http://www.wiredinformatics.com>
265 Franklin St Ste 1702
Boston, MA 02110
tel: (617) 433-7544
Pei.Chen@wiredinformatics.com
On Mon, Feb 15, 2016 at 9:45 AM, Jay Urbain <ja...@gmail.com> wrote:
> Hi,
>
> I'm trying to run bin/runctakesCVD.sh. When I try to load the
> AggregatePlaintextFastUMLSProcessor.xml, as described in the User install
> guide (
>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+User+Install+Guide
> )
> I receive the ResourceInitializationException (please see details below).
>
> It appears that I do not have something set up correctly with the UMLS
> resources. If I try to run the AggregatePlaintextProcessor, everything
> seems to work Ok.
>
> Any help or direction would be appreciated.
>
> Thanks,
> Jay
>
> Environment:
> OS X Yosemite 10.10.5
> Java 1.8
>
> Downloads:
> apache-ctakes-3.2.2
> ctakes-resources-3.2.1.1-bin
>
> Copied the resources directory:
> ditto /Users/jayurbain/Downloads/ctakes-resources-3.2.1.1-bin/resources/*
> /Users/jayurbain/Dropbox/apache-ctakes-3.2.2/resources
>
> Added my UMLS user authentication to runtakesCVD.sh
> java -Dctakes.umlsuser=<YOUR_UMLS_ID_HERE>
> -Dctakes.umlspw=<YOUR_UMLS_PASSSWORD_HERE>
>
> Exception:
>
> 2/15/16 8:34:25 AM - 15:
> org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE:
> Initialization of annotator class
> "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
> (Descriptor:
>
> file:/Users/jayurbain/Dropbox/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
> org.apache.uima.resource.ResourceInitializationException: Initialization of
> annotator class
> "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.
> (Descriptor:
>
> file:/Users/jayurbain/Dropbox/apache-ctakes-3.2.2/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml)
> at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:252)
> at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:156)
> 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:476)
> at
>
> org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
> at
>
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
> at
>
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
> at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
> at
>
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
> at java.awt.Component.processMouseEvent(Component.java:6535)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
> at java.awt.Component.processEvent(Component.java:6300)
> at java.awt.Container.processEvent(Container.java:2236)
> at java.awt.Component.dispatchEventImpl(Component.java:4891)
> at java.awt.Container.dispatchEventImpl(Container.java:2294)
> at java.awt.Component.dispatchEvent(Component.java:4713)
> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525)
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
> at java.awt.Container.dispatchEventImpl(Container.java:2280)
> at java.awt.Window.dispatchEventImpl(Window.java:2750)
> at java.awt.Component.dispatchEvent(Component.java:4713)
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
> at java.awt.EventQueue.access$500(EventQueue.java:97)
> at java.awt.EventQueue$3.run(EventQueue.java:709)
> at java.awt.EventQueue$3.run(EventQueue.java:703)
> at java.security.AccessController.doPrivileged(Native Method)
> at
>
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
> at
>
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
> at java.awt.EventQueue$4.run(EventQueue.java:731)
> at java.awt.EventQueue$4.run(EventQueue.java:729)
> at java.security.AccessController.doPrivileged(Native Method)
> at
>
> java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
> at
>
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
> at
>
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
> at
>
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
> Caused by: org.apache.uima.resource.ResourceInitializationException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key Could
> not construct
> org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
> at
>
> org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:132)
> at
>
> org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250)
> ... 55 more
> Caused by:
> org.apache.uima.analysis_engine.annotator.AnnotatorContextException:
> EXCEPTION MESSAGE LOCALIZATION FAILED: java.util.MissingResourceException:
> Can't find resource for bundle java.util.PropertyResourceBundle, key Could
> not construct
> org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary
> at
>
> org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:203)
> at
>
> org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:160)
> at
>
> org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:131)
> at
>
> org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:130)
> ... 56 more
> Caused by: java.lang.reflect.InvocationTargetException
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
> at
>
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
> at
>
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
> at
>
> org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:200)
> ... 59 more
> Caused by: java.sql.SQLException: No Hsql DB exists at Url
> at
>
> org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:109)
> at
>
> org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:60)
> at
>
> org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:93)
> at
>
> org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:75)
> at
>
> org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31)
> ... 64 more
> Caused by: java.io.FileNotFoundException: No File exists at
>
> resources/org/apache/ctakes/dictionary/lookup/fast/ctakessnorx/ctakessnorx.script
> at
>
> org.apache.ctakes.core.resource.FileLocator.getFullPath(FileLocator.java:162)
> at
>
> org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnectionUrl(JdbcConnectionFactory.java:106)
> ... 68 more
>