Hello Parth, I have already done that. After adding the UMLS credentials also, I am getting the error
-Ankit On Fri, Jun 8, 2018 at 11:00 PM, Parth Natu <[email protected]> wrote: > > Hi Ankit, > > Please add the following parameters before the "-cp" in the Java command > in the .sh file. > > > -Dctakes.umlsuser=[username] -Dctakes.umlspw=[password] > > Try executing the same and let me know the results > > Parth > > On Jun 9, 2018 at 7:29 AM, <Ankit Bisht <[email protected]>> > wrote: > > Hello Parth, > > Please find attached the .sh file. The command is: > bin/runctakesCVD.sh -desc desc/ctakes-clinical-pipeline/ > desc/analysis_engine/AggregatePlaintextFastUMLSProcessor.xml > I am following this guide: > https://cwiki.apache.org/confluence/display/CTAKES/ > cTAKES+4.0+User+Install+Guide > -Ankit > > On Fri, Jun 8, 2018 at 12:29 PM, Parth Natu <[email protected]> wrote: > >> >> Hello Ankit, >> Can you attach there edited .sh files and the command that you use to run >> it? >> >> Parth >> >> On Jun 8, 2018 at 9:50 PM, <Ankit Bisht <[email protected]>> >> wrote: >> >> 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.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 >> .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.produceResou >> rce(AnalysisEngineFactory_impl.java:94) >> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe >> source(CompositeResourceFactory_impl.java:62) >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) >> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram >> ework.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(AggregateAnalysisEng >> ine_impl.java:373) >> at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine >> _impl.initialize(AggregateAnalysisEngine_impl.java:186) >> at org.apache.uima.impl.AnalysisEngineFactory_impl.produceResou >> rce(AnalysisEngineFactory_impl.java:94) >> at org.apache.uima.impl.CompositeResourceFactory_impl.produceRe >> source(CompositeResourceFactory_impl.java:62) >> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:279) >> at org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFram >> ework.java:371) >> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484) >> at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFra >> me.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.UmlsJdbcRare >> WordDictionary >> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnno >> tator.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.UmlsJdbcRare >> WordDictionary >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseDictionary(DictionaryDescriptorParser.java:199) >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156) >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128) >> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnno >> tator.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.DictionaryDe >> scriptorParser.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.JdbcConnectionFact >> ory.getConnection(JdbcConnectionFactory.java:84) >> at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWord >> Dictionary.<init>(JdbcRareWordDictionary.java:91) >> at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWord >> Dictionary.<init>(JdbcRareWordDictionary.java:72) >> at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRare >> WordDictionary.<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.JdbcConnectionFact >> ory.getConnection(JdbcConnectionFactory.java:84) >> at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWord >> Dictionary.<init>(JdbcRareWordDictionary.java:91) >> at org.apache.ctakes.dictionary.lookup2.dictionary.JdbcRareWord >> Dictionary.<init>(JdbcRareWordDictionary.java:72) >> at org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRare >> WordDictionary.<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.DictionaryDe >> scriptorParser.parseDictionary(DictionaryDescriptorParser.java:196) >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseDictionaries(DictionaryDescriptorParser.java:156) >> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >> scriptorParser.parseDescriptor(DictionaryDescriptorParser.java:128) >> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnno >> tator.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] >> > 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]> >>> *Date: *Friday, June 8, 2018 at 08:12 >>> *To: *"[email protected]" <[email protected]>, "Schenk, >>> Gundolf" <[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]> 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]> >>> *Reply-To: *"[email protected]" <[email protected]> >>> *Date: *Wednesday, June 6, 2018 at 20:22 >>> *To: *"[email protected]" <[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 >>> >>> >>> >> >> >
