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 [email protected] On Mon, Feb 15, 2016 at 9:45 AM, Jay Urbain <[email protected]> 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 >
