Hey! Thanks a lot for the reply. That totally worked. However, I have run into another problem now. After loading the "AggregatePlainTextUmlsProcessor.xml", when I try to run the it on some text sample I get an error saying
org.apache.uima.analysis_engine.AnalysisEngineProcessException . More > detailed information is in the log file > I have attached the log in the attachments. Please do have a look. Any help will be appreciated. On Wed, Jun 11, 2014 at 7:06 PM, Chen, Pei <[email protected]> wrote: > Abhishek, > > Have you tried some of the suggestions from this thread: > > > http://mail-archives.apache.org/mod_mbox/ctakes-dev/201304.mbox/%3CCD84AD35.169BD%25mcoarr%40mitre.org%3E > > > > > > *From:* Abhishek Raj [mailto:[email protected]] > *Sent:* Wednesday, June 11, 2014 4:17 AM > *To:* [email protected] > *Subject:* Cannot load AggregatePlainTextUmlsProcessor.xml > > > > Hello I installed ctakes following > https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation and > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1+User+Install+Guide > . After installation I ran the CVD for annotation purpose. When I try to > load the AggregatePlainTextUmlsProcessor.xml I get error saying > > org.apache.uima.resource.ResourceInitializationException: > > Initialization of annotator class > > "org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator" > failed. (Descriptor: > file:/home/gamerboy/apache-ctakes-3.1.2-SNAPSHOT/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml) > > > > I am behind a proxy network. Not sure this could be the reason though. > >
11/6/14 9:06:55 PM - 12: org.mitre.medfacts.i2b2.cli.BatchRunner.loadEnabledFeaturesFromFile: INFO: opening enabled features file: /home/gamerboy/intern/ctakesins/apache-ctakes-3.1.2-SNAPSHOT/resources/org/apache/ctakes/assertion/models/featureFile11b 11/6/14 9:06:56 PM - 12: org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources: WARNING: The external resource named assertionModelResourceImpl has been declared multiple times with different definitions. The definition of the resource in component /AssertionAnnotator/assertionAnalysisEngine/ will be used. The definition in component /AssertionAnnotator/conceptConverterAnalysisEngine/ will be ignored. 11/6/14 9:06:56 PM - 12: org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources: WARNING: The external resource named scopeModelResourceImpl has been declared multiple times with different definitions. The definition of the resource in component /AssertionAnnotator/assertionAnalysisEngine/ will be used. The definition in component /AssertionAnnotator/conceptConverterAnalysisEngine/ will be ignored. 11/6/14 9:06:56 PM - 12: org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources: WARNING: The external resource named cueModelResourceImpl has been declared multiple times with different definitions. The definition of the resource in component /AssertionAnnotator/assertionAnalysisEngine/ will be used. The definition in component /AssertionAnnotator/conceptConverterAnalysisEngine/ will be ignored. 11/6/14 9:06:56 PM - 12: org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources: WARNING: The external resource named enabledFeaturesResourceImpl has been declared multiple times with different definitions. The definition of the resource in component /AssertionAnnotator/assertionAnalysisEngine/ will be used. The definition in component /AssertionAnnotator/conceptConverterAnalysisEngine/ will be ignored. 11/6/14 9:07:05 PM - 12: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(407): SEVERE: Exception occurred org.apache.uima.analysis_engine.AnalysisEngineProcessException at org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.process(DictionaryLookupAnnotator.java:128) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267) at org.apache.uima.tools.cvd.MainFrame.internalRunAE(MainFrame.java:1526) at org.apache.uima.tools.cvd.MainFrame.runAE(MainFrame.java:430) at org.apache.uima.tools.cvd.control.AnnotatorRerunEventHandler.actionPerformed(AnnotatorRerunEventHandler.java:40) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6505) at javax.swing.JComponent.processMouseEvent(JComponent.java:3311) at java.awt.Component.processEvent(Component.java:6270) at java.awt.Container.processEvent(Container.java:2229) at java.awt.Component.dispatchEventImpl(Component.java:4861) at java.awt.Container.dispatchEventImpl(Container.java:2287) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422) at java.awt.Container.dispatchEventImpl(Container.java:2273) at java.awt.Window.dispatchEventImpl(Window.java:2719) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:694) at java.awt.EventQueue$3.run(EventQueue.java:692) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87) at java.awt.EventQueue$4.run(EventQueue.java:708) at java.awt.EventQueue$4.run(EventQueue.java:706) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:705) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138) at java.awt.EventDispatchThread.run(EventDispatchThread.java:91) Caused by: org.apache.ctakes.dictionary.lookup.DictionaryException: java.sql.SQLException: Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM @[email protected]_snomed_fword_lookup WHERE fword = ?] at org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl.getEntries(JdbcDictionaryImpl.java:139) at org.apache.ctakes.dictionary.lookup.DictionaryEngine.metaLookup(DictionaryEngine.java:137) at org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl.getFirstTokenHits(FirstTokenPermutationImpl.java:529) at org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl.lookup(FirstTokenPermutationImpl.java:126) at org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.performLookup(DictionaryLookupAnnotator.java:146) at org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.process(DictionaryLookupAnnotator.java:122) ... 49 more Caused by: java.sql.SQLException: Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM @[email protected]_snomed_fword_lookup WHERE fword = ?] at org.hsqldb.jdbc.Util.throwError(Unknown Source) at org.hsqldb.jdbc.jdbcPreparedStatement.<init>(Unknown Source) at org.hsqldb.jdbc.jdbcConnection.prepareStatement(Unknown Source) at org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl.initMetaDataPrepStmt(JdbcDictionaryImpl.java:91) at org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl.getEntries(JdbcDictionaryImpl.java:123) ... 54 more 11/6/14 9:07:05 PM - 12: org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(275): SEVERE: Exception occurred org.apache.uima.analysis_engine.AnalysisEngineProcessException at org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.process(DictionaryLookupAnnotator.java:128) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267) at org.apache.uima.tools.cvd.MainFrame.internalRunAE(MainFrame.java:1526) at org.apache.uima.tools.cvd.MainFrame.runAE(MainFrame.java:430) at org.apache.uima.tools.cvd.control.AnnotatorRerunEventHandler.actionPerformed(AnnotatorRerunEventHandler.java:40) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341) 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 javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6505) at javax.swing.JComponent.processMouseEvent(JComponent.java:3311) at java.awt.Component.processEvent(Component.java:6270) at java.awt.Container.processEvent(Container.java:2229) at java.awt.Component.dispatchEventImpl(Component.java:4861) at java.awt.Container.dispatchEventImpl(Container.java:2287) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422) at java.awt.Container.dispatchEventImpl(Container.java:2273) at java.awt.Window.dispatchEventImpl(Window.java:2719) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:694) at java.awt.EventQueue$3.run(EventQueue.java:692) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87) at java.awt.EventQueue$4.run(EventQueue.java:708) at java.awt.EventQueue$4.run(EventQueue.java:706) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:705) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138) at java.awt.EventDispatchThread.run(EventDispatchThread.java:91) Caused by: org.apache.ctakes.dictionary.lookup.DictionaryException: java.sql.SQLException: Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM @[email protected]_snomed_fword_lookup WHERE fword = ?] at org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl.getEntries(JdbcDictionaryImpl.java:139) at org.apache.ctakes.dictionary.lookup.DictionaryEngine.metaLookup(DictionaryEngine.java:137) at org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl.getFirstTokenHits(FirstTokenPermutationImpl.java:529) at org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl.lookup(FirstTokenPermutationImpl.java:126) at org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.performLookup(DictionaryLookupAnnotator.java:146) at org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.process(DictionaryLookupAnnotator.java:122) ... 49 more Caused by: java.sql.SQLException: Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM @[email protected]_snomed_fword_lookup WHERE fword = ?] at org.hsqldb.jdbc.Util.throwError(Unknown Source) at org.hsqldb.jdbc.jdbcPreparedStatement.<init>(Unknown Source) at org.hsqldb.jdbc.jdbcConnection.prepareStatement(Unknown Source) at org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl.initMetaDataPrepStmt(JdbcDictionaryImpl.java:91) at org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl.getEntries(JdbcDictionaryImpl.java:123) ... 54 more 11/6/14 9:07:05 PM - 12: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Exception occurred org.apache.uima.analysis_engine.AnalysisEngineProcessException at org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.process(DictionaryLookupAnnotator.java:128) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267) at org.apache.uima.tools.cvd.MainFrame.internalRunAE(MainFrame.java:1526) at org.apache.uima.tools.cvd.MainFrame.runAE(MainFrame.java:430) at org.apache.uima.tools.cvd.control.AnnotatorRerunEventHandler.actionPerformed(AnnotatorRerunEventHandler.java:40) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341) 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 javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6505) at javax.swing.JComponent.processMouseEvent(JComponent.java:3311) at java.awt.Component.processEvent(Component.java:6270) at java.awt.Container.processEvent(Container.java:2229) at java.awt.Component.dispatchEventImpl(Component.java:4861) at java.awt.Container.dispatchEventImpl(Container.java:2287) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422) at java.awt.Container.dispatchEventImpl(Container.java:2273) at java.awt.Window.dispatchEventImpl(Window.java:2719) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:694) at java.awt.EventQueue$3.run(EventQueue.java:692) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87) at java.awt.EventQueue$4.run(EventQueue.java:708) at java.awt.EventQueue$4.run(EventQueue.java:706) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:705) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138) at java.awt.EventDispatchThread.run(EventDispatchThread.java:91) Caused by: org.apache.ctakes.dictionary.lookup.DictionaryException: java.sql.SQLException: Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM @[email protected]_snomed_fword_lookup WHERE fword = ?] at org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl.getEntries(JdbcDictionaryImpl.java:139) at org.apache.ctakes.dictionary.lookup.DictionaryEngine.metaLookup(DictionaryEngine.java:137) at org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl.getFirstTokenHits(FirstTokenPermutationImpl.java:529) at org.apache.ctakes.dictionary.lookup.algorithms.FirstTokenPermutationImpl.lookup(FirstTokenPermutationImpl.java:126) at org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.performLookup(DictionaryLookupAnnotator.java:146) at org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator.process(DictionaryLookupAnnotator.java:122) ... 49 more Caused by: java.sql.SQLException: Unexpected token: @ in statement [SELECT tui,cui,tok_str FROM @[email protected]_snomed_fword_lookup WHERE fword = ?] at org.hsqldb.jdbc.Util.throwError(Unknown Source) at org.hsqldb.jdbc.jdbcPreparedStatement.<init>(Unknown Source) at org.hsqldb.jdbc.jdbcConnection.prepareStatement(Unknown Source) at org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl.initMetaDataPrepStmt(JdbcDictionaryImpl.java:91) at org.apache.ctakes.dictionary.lookup.jdbc.JdbcDictionaryImpl.getEntries(JdbcDictionaryImpl.java:123) ... 54 more
