Hi Ankit, Thanks for the screenshot and the log output. I can only guess: 1) I can see out-of-memory errors. So perhaps you are running low on memory.
2) The other message that caught my attention is the UMLS dictionary. Perhaps something went wrong with the installation fo the metathesaurus. Are you using it? Cheers, Gundolf. From: Ankit Bisht <[email protected]> Date: Friday, June 8, 2018 at 09:20 To: "Schenk, Gundolf" <[email protected]> Cc: "[email protected]" <[email protected]> Subject: Re: Regardng Apache cTakes Hello Gundolf, I have attached the snapshot of the error which I am getting. Also check my log files, this might help: 10:58:42.492 - 1: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae<https://protect2.fireeye.com/url?k=d2cb505296f21a07.d2cb774f-3da4a1b0ae9ebae2&u=http://lookup2.ae>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/C:/Users/ankit/Desktop/apache-ctakes-4.0.0/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<https://protect2.fireeye.com/url?k=d2cb505296f21a07.d2cb774f-3da4a1b0ae9ebae2&u=http://lookup2.ae>.DefaultJCasTermAnnotator" failed. (Descriptor: file:/C:/Users/ankit/Desktop/apache-ctakes-4.0.0/desc/ctakes-dictionary-lookup-fast/desc/analysis_engine/UmlsLookupAnnotator.xml) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:271) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:170) 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:279) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:407) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:256) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:429) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:373) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:186) 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:279) at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:371) 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.CVD.main(CVD.java:164) Caused by: org.apache.uima.resource.ResourceInitializationException: MESSAGE LOCALIZATION FAILED: 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<https://protect2.fireeye.com/url?k=d2cb505296f21a07.d2cb774f-3da4a1b0ae9ebae2&u=http://lookup2.ae>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:131) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) ... 16 more Caused by: org.apache.uima.analysis_engine.annotator.AnnotatorContextException: MESSAGE LOCALIZATION FAILED: 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:199) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128) at org.apache.ctakes.dictionary.lookup2.ae<https://protect2.fireeye.com/url?k=d2cb505296f21a07.d2cb774f-3da4a1b0ae9ebae2&u=http://lookup2.ae>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129) ... 17 more Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:196) ... 20 more Caused by: java.sql.SQLException: error in script file line: 1141005 java.lang.OutOfMemoryError: GC overhead limit exceeded at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:84) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72) at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31) ... 25 more Caused by: org.hsqldb.HsqlException: error in script file line: 1141005 java.lang.OutOfMemoryError: GC overhead limit exceeded at org.hsqldb.error.Error.error(Unknown Source) at org.hsqldb.scriptio.ScriptReaderText.readExistingData(Unknown Source) at org.hsqldb.scriptio.ScriptReaderBase.readAll(Unknown Source) at org.hsqldb.persist.Log.processScript(Unknown Source) at org.hsqldb.persist.Log.open(Unknown Source) at org.hsqldb.persist.Logger.open(Unknown Source) at org.hsqldb.Database.reopen(Unknown Source) at org.hsqldb.Database.open(Unknown Source) at org.hsqldb.DatabaseManager.getDatabase(Unknown Source) at org.hsqldb.DatabaseManager.newSession(Unknown Source) ... 34 more Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded at java.util.Arrays.copyOfRange(Unknown Source) at java.lang.String.<init>(Unknown Source) at java.lang.String.substring(Unknown Source) at org.hsqldb.persist.HsqlDatabaseProperties.isVersion18(Unknown Source) at org.hsqldb.Table.insertFromScript(Unknown Source) at org.hsqldb.scriptio.ScriptReaderText.readExistingData(Unknown Source) at org.hsqldb.scriptio.ScriptReaderBase.readAll(Unknown Source) at org.hsqldb.persist.Log.processScript(Unknown Source) at org.hsqldb.persist.Log.open(Unknown Source) at org.hsqldb.persist.Logger.open(Unknown Source) at org.hsqldb.Database.reopen(Unknown Source) at org.hsqldb.Database.open(Unknown Source) at org.hsqldb.DatabaseManager.getDatabase(Unknown Source) at org.hsqldb.DatabaseManager.newSession(Unknown Source) at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at java.sql.DriverManager.getConnection(Unknown Source) at org.apache.ctakes.dictionary.lookup2.util.JdbcConnectionFactory.getConnection(JdbcConnectionFactory.java:84) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:91) at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWordDictionary.<init>(JdbcRareWordDictionary.java:72) at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary.<init>(UmlsJdbcRareWordDictionary.java:31) at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source) at java.lang.reflect.Constructor.newInstance(Unknown Source) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary(DictionaryDescriptorParser.java:196) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128) at org.apache.ctakes.dictionary.lookup2.ae<https://protect2.fireeye.com/url?k=d2cb505296f21a07.d2cb774f-3da4a1b0ae9ebae2&u=http://lookup2.ae>.AbstractJCasTermAnnotator.initialize(AbstractJCasTermAnnotator.java:129) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:266) -Ankit On Fri, Jun 8, 2018 at 11:24 AM, Schenk, Gundolf <[email protected]<mailto:[email protected]>> wrote: Hi Ankit, I am not sure what is happening. The error message that you posted either indicates that your pipeline is corrupted and then you need to fix that, or the error message contains typos and you have an actual problem with initialization which might be due to missing resources. Please double check and post the exact error message you are getting. Cheers, Gundolf. From: Ankit Bisht <[email protected]<mailto:[email protected]>> Date: Friday, June 8, 2018 at 08:12 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "Schenk, Gundolf" <[email protected]<mailto:[email protected]>> Subject: Re: Regardng Apache cTakes Hello Gundolf, Thanks for replying back. Yes, I follow the cTakes user installation guide. I mean I get the error when I run this command to start ctakes CAS visual debugger : bin\runctakesCVD.bat desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml -Ankit On Thu, Jun 7, 2018 at 12:01 PM, Schenk, Gundolf <[email protected]<mailto:[email protected]>> wrote: Hi Ankit, Have you followed this guide? https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide What exactly do you mean by “open it”? Cheers, Gundolf. From: Ankit Bisht <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Date: Wednesday, June 6, 2018 at 20:22 To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Regardng Apache cTakes Hello, I am trying to use Apache Ctakes. I have installed it but when I am trying to open it, I am getting an error that org.apache.uima.resource.resourceinitializationexception: Initialization of annotator class "org.apached.ctakes.dictionary.lookup2.ae<https://protect2.fireeye.com/url?k=b97dad412ab8c249.b97d8a5c-3a2f789363131c1e&u=http://dictionary.lookup2.ae>.DefaultJCastermAnnotaor" failed Regards Ankit Bisht
