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From Jay Urbain <jay.urb...@gmail.com>
Subject ctakes resource exception
Date Mon, 15 Feb 2016 14:45:15 GMT
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

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