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
