Have put username and password (umls) in custom.xml as well. Still getting this error: 1/22/17 12:09:18 AM - 14: org.apache.uima.tools.cvd. MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: file:/usr/local/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:/usr/local/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$Handler.actionPerformed( AbstractButton.java:2346) at javax.swing.DefaultButtonModel.fireActionPerformed( DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) at javax.swing.plaf.basic.BasicMenuItemUI$Handler. mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6525) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6290) at java.awt.Container.processEvent(Container.java:2234) at java.awt.Component.dispatchEventImpl(Component.java:4881) at java.awt.Container.dispatchEventImpl(Container.java:2292) at java.awt.Component.dispatchEvent(Component.java:4703) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) at java.awt.Container.dispatchEventImpl(Container.java:2278) at java.awt.Window.dispatchEventImpl(Window.java:2750) at java.awt.Component.dispatchEvent(Component.java:4703) 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$1.doIntersectionPrivilege( ProtectionDomain.java:75) at java.security.ProtectionDomain$1.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$1.doIntersectionPrivilege( ProtectionDomain.java:75) 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 Unknown class org.apache.ctakes.dictionary.lookup2.concept. JdbcConceptFactory 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 Unknown class org.apache.ctakes.dictionary.lookup2.concept. JdbcConceptFactory at org.apache.ctakes.dictionary.lookup2.dictionary. DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser. java:255) at org.apache.ctakes.dictionary.lookup2.dictionary. DictionaryDescriptorParser.parseConceptFactories(DictionaryDescriptorParser. java:226) at org.apache.ctakes.dictionary.lookup2.dictionary. DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser. java:133) at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator. initialize(AbstractJCasTermAnnotator.java:130) ... 56 more Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary. lookup2.concept.JdbcConceptFactory at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:264) at org.apache.ctakes.dictionary.lookup2.dictionary. DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser. java:253) ... 59 more
On Sat, Jan 21, 2017 at 5:36 PM, shahid ashraf <sha...@trialx.com> wrote: > Hi I was able to run and produce the new custom umls files. and where put > under ctakes binary (not dev). > > I changed the name under apache-ctakes-3.2.2/ > desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/ > UmlsLookupAnnotator.xml > > <name>DictionaryDescriptorFile</name> > <description/> > <fileResourceSpecifier> > <fileUrl>file:org/apache/ctakes/dictionary/lookup/fast/ > custom.xml</fileUrl> > > when running AggregatePlantextFastUmlsProcessor.xml I am getting > following error (not when using old org/apache/ctakes/ > dictionary/lookup/fast/cTakesHsql.xml) > > 5: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: > Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae > .DefaultJCasTermAnnotator" failed. (Descriptor: > file:/usr/local/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:/usr/local/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$Handler.actionPerformed( > AbstractButton.java:2346) > at javax.swing.DefaultButtonModel.fireActionPerformed( > DefaultButtonModel.java:402) > at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) > at javax.swing.AbstractButton.doClick(AbstractButton.java:376) > at javax.swing.plaf.basic.BasicMenuItemUI.doClick( > BasicMenuItemUI.java:833) > at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) > at javax.swing.plaf.basic.BasicMenuItemUI$Handler. > mouseReleased(BasicMenuItemUI.java:877) > at java.awt.Component.processMouseEvent(Component.java:6525) > at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) > at java.awt.Component.processEvent(Component.java:6290) > at java.awt.Container.processEvent(Container.java:2234) > at java.awt.Component.dispatchEventImpl(Component.java:4881) > at java.awt.Container.dispatchEventImpl(Container.java:2292) > at java.awt.Component.dispatchEvent(Component.java:4703) > at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) > at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533) > at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) > at java.awt.Container.dispatchEventImpl(Container.java:2278) > at java.awt.Window.dispatchEventImpl(Window.java:2750) > at java.awt.Component.dispatchEvent(Component.java:4703) > 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$1.doIntersectionPrivilege( > ProtectionDomain.java:75) > at java.security.ProtectionDomain$1.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$1.doIntersectionPrivilege( > ProtectionDomain.java:75) > 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 > Unknown class org.apache.ctakes.dictionary.lookup2.concept. > JdbcConceptFactory > 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 > Unknown class org.apache.ctakes.dictionary.lookup2.concept. > JdbcConceptFactory > at org.apache.ctakes.dictionary.lookup2.dictionary. > DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser. > java:255) > at org.apache.ctakes.dictionary.lookup2.dictionary. > DictionaryDescriptorParser.parseConceptFactories( > DictionaryDescriptorParser.java:226) > at org.apache.ctakes.dictionary.lookup2.dictionary. > DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser. > java:133) > at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator. > initialize(AbstractJCasTermAnnotator.java:130) > ... 56 more > Caused by: java.lang.ClassNotFoundException: org.apache.ctakes.dictionary. > lookup2.concept.JdbcConceptFactory > at java.net.URLClassLoader.findClass(URLClassLoader.java:381) > at java.lang.ClassLoader.loadClass(ClassLoader.java:424) > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) > at java.lang.ClassLoader.loadClass(ClassLoader.java:357) > at java.lang.Class.forName0(Native Method) > at java.lang.Class.forName(Class.java:264) > at org.apache.ctakes.dictionary.lookup2.dictionary. > DictionaryDescriptorParser.parseConceptFactory(DictionaryDescriptorParser. > java:253) > ... 59 more > > -- > with Regards > Shahid Ashraf > -- with Regards Shahid Ashraf
