Hi Andrey On CVD the LVG is using the new dbs.. But while i added the ctakes-lvg jar to the multithreaded code(SERVLET) like
mvn install:install-file -Dfile=/Users/shahid/projects/workspace/ctakes/ctakes-lvg/target/ctakes-lvg-3.2.3-SNAPSHOT.jar -DgroupId=org.apache.ctakes -DartifactId=ctakes-lvg -Dversion=3.2.3-SNAPSHOT -Dpackaging=jar -DgeneratePom=true and changed the POM entry in the servlet pom.xml as well like I am getting following errors: Let me know if i you have any input on this .. (seems library issue ...) 13 Feb 2017 15:23:05 INFO JdbcConnectionFactory - Connecting to jdbc:hsqldb:file:org/apache/ctakes/dictionary/lookup/fast/custom_11/custom_11: org.apache.uima.resource.ResourceInitializationException: Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed. (Descriptor: file:/Users/shahid/projects/healthnlp/examples/ctakes-web-client/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.internal.util.ResourcePool.fillPool(ResourcePool.java:246 ) at org.apache.uima.internal.util.ResourcePool.<init>(ResourcePool.java:100) at org.apache.uima.internal.util.AnalysisEnginePool.<init>( AnalysisEnginePool.java:91) at org.apache.uima.analysis_engine.impl.MultiprocessingAnalysisEngine_impl.initialize( MultiprocessingAnalysisEngine_impl.java:118) 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:498) at org.apache.ctakes.web.client.servlet.DemoServlet.init(DemoServlet.java:90 ) at javax.servlet.GenericServlet.init(GenericServlet.java:244) at org.eclipse.jetty.servlet.ServletHolder.initServlet( ServletHolder.java:532) at org.eclipse.jetty.servlet.ServletHolder.doStart(ServletHolder.java:344) at org.eclipse.jetty.util.component.AbstractLifeCycle.start( AbstractLifeCycle.java:64) at org.eclipse.jetty.servlet.ServletHandler.initialize( ServletHandler.java:791) at org.eclipse.jetty.servlet.ServletContextHandler.startContext( ServletContextHandler.java:265) at org.eclipse.jetty.webapp.WebAppContext.startContext( WebAppContext.java:1242) at org.eclipse.jetty.server.handler.ContextHandler.doStart( ContextHandler.java:717) at org.eclipse.jetty.webapp.WebAppContext.doStart(WebAppContext.java:494) at org.eclipse.jetty.util.component.AbstractLifeCycle.start( AbstractLifeCycle.java:64) at org.eclipse.jetty.server.handler.HandlerWrapper.doStart( HandlerWrapper.java:95) at org.eclipse.jetty.server.Server.doStart(Server.java:282) at org.eclipse.jetty.util.component.AbstractLifeCycle.start( AbstractLifeCycle.java:64) at net.sourceforge.eclipsejetty.starter.embedded.JettyEmbeddedAdapter.start( JettyEmbeddedAdapter.java:67) at net.sourceforge.eclipsejetty.starter.common.AbstractJettyLauncherMain.launch( AbstractJettyLauncherMain.java:84) at net.sourceforge.eclipsejetty.starter.embedded.JettyEmbeddedLauncherMain.main( JettyEmbeddedLauncherMain.java:42) 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.JdbcRareWordDictionary at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.initialize( AbstractJCasTermAnnotator.java:117) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initializeAnalysisComponent( PrimitiveAnalysisEngine_impl.java:266) ... 37 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.JdbcRareWordDictionary 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.AbstractJCasTermAnnotator.initialize( AbstractJCasTermAnnotator.java:115) ... 38 more Caused by: java.lang.reflect.InvocationTargetException at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance( NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance( DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescriptorParser.parseDictionary( DictionaryDescriptorParser.java:196) ... 41 more Caused by: java.lang.NoSuchMethodError: org.hsqldb.DatabaseURL.parseURL(Ljava/lang/String;ZZ)Lorg/hsqldb/persist/HsqlProperties; at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source) at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(DriverManager.java:664) at java.sql.DriverManager.getConnection(DriverManager.java:247) 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) ... 46 more On Mon, Feb 13, 2017 at 2:58 PM, Andrey Kurdumov <kant2...@googlemail.com> wrote: > Cool, > .properties file looks ok. You could make database readonly by adding > readonly=true to it if you needed that. > > Did you able to test how LVG 2016/17 working in multithreaded environment? > I did not test like that, because I need LVG for different purposes, so > that's interesting to know how it works. > > 2017-02-13 15:22 GMT+06:00 shahid ashraf <sha...@trialx.com>: > >> >> Thanks Andrey >> >> >> I was able to successfully update the database... and use in dev through >> cvd. >> >> i was using sqltool (which was wrong), i switched to DatabaseManager >> >> *java -cp ~/Downloads/hsqldb_1_8_0_10.jar org.hsqldb.util.DatabaseManager* >> >> *java -cp ~/Downloads/hsqldb-2.3.4/hsqldb/lib/hsqldb.jar >> org.hsqldb.util.DatabaseManager* >> >> After above steps the properties file looks like: >> >> #HSQL Database Engine 2.3.4 >> >> #Mon Feb 13 11:34:05 IST 2017 >> >> version=2.3.4 >> >> modified=no >> >> tx_timestamp=0 >> >> >> >> >> On Mon, Feb 13, 2017 at 1:38 AM, shahid ashraf <sha...@trialx.com> wrote: >> >>> >>> >>> Hi >>> >>> How can i check the above steps are successfully being executed... >>> Currently getting Error.. Have done these steps in dev ctakes... from svn >>> not from your github stuff >>> >>> This is what i did: >>> java -cp ~/Downloads/hsqldb_1_8_0_10.jar org.hsqldb.util.SqlTool >>> --rcfile custom_umls.rc custom_umls >>> >>> SET SCRIPTFORMAT TEXT >>> SHUTDOWN >>> >>> java -jar ~/Downloads/hsqldb-2.3.4/hsqldb/lib/sqltool.jar --rcfile >>> custom_umls.rc custom_umls >>> >>> SHUTDOWN >>> >>> Also sean can't we create a new fast dictionary via dictioanry_gui as >>> 2.3.4 compatible version (any steps to do that) >>> >>> Error Log >>> >>> 12 Feb 2017 22:28:12 INFO JdbcConnectionFactory - Connecting to >>> jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/look >>> up/fast/custom_umls/custom_umls: >>> >>> 12 Feb 2017 22:28:12 FATAL ENGINE - could not reopen database >>> >>> org.hsqldb.HsqlException: wrong database file version >>> >>> at org.hsqldb.error.Error.error(Unknown Source) >>> >>> at org.hsqldb.error.Error.error(Unknown Source) >>> >>> at org.hsqldb.persist.HsqlDatabaseProperties.load(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(DriverManager.java:664) >>> >>> at java.sql.DriverManager.getConnection(DriverManager.java:247) >>> >>> 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:75) >>> >>> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) >>> >>> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Native >>> ConstructorAccessorImpl.java:62) >>> >>> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(De >>> legatingConstructorAccessorImpl.java:45) >>> >>> at java.lang.reflect.Constructor.newInstance(Constructor.java:422) >>> >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDictionary(DictionaryDescriptorParser.java:205) >>> >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDictionaries(DictionaryDescriptorParser.java:165) >>> >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133) >>> >>> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnno >>> tator.initialize(AbstractJCasTermAnnotator.java:115) >>> >>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >>> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) >>> >>> 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(UIMAFram >>> ework.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(AggregateAnalysisEng >>> ine_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(UIMAFram >>> ework.java:354) >>> >>> 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.control.AnnotatorOpenEventHandler. >>> actionPerformed(AnnotatorOpenEventHandler.java:52) >>> >>> at javax.swing.AbstractButton.fireActionPerformed(AbstractButto >>> n.java:2022) >>> >>> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractB >>> utton.java:2346) >>> >>> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBu >>> ttonModel.java:402) >>> >>> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259 >>> ) >>> >>> at javax.swing.AbstractButton.doClick(AbstractButton.java:376) >>> >>> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItem >>> UI.java:833) >>> >>> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) >>> >>> at javax.swing.plaf.basic.BasicMenuItemUI$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(Pro >>> tectionDomain.java:75) >>> >>> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Pro >>> tectionDomain.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(Pro >>> tectionDomain.java:75) >>> >>> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) >>> >>> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDis >>> patchThread.java:201) >>> >>> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispat >>> chThread.java:116) >>> >>> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDis >>> patchThread.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) >>> >>> 12 Feb 2017 22:28:12 FATAL ENGINE - could not reopen database >>> >>> org.hsqldb.HsqlException: wrong database file version >>> >>> at org.hsqldb.error.Error.error(Unknown Source) >>> >>> at org.hsqldb.error.Error.error(Unknown Source) >>> >>> at org.hsqldb.persist.HsqlDatabaseProperties.load(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(DriverManager.java:664) >>> >>> at java.sql.DriverManager.getConnection(DriverManager.java:247) >>> >>> 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:75) >>> >>> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) >>> >>> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Native >>> ConstructorAccessorImpl.java:62) >>> >>> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(De >>> legatingConstructorAccessorImpl.java:45) >>> >>> at java.lang.reflect.Constructor.newInstance(Constructor.java:422) >>> >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDictionary(DictionaryDescriptorParser.java:205) >>> >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDictionaries(DictionaryDescriptorParser.java:165) >>> >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133) >>> >>> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnno >>> tator.initialize(AbstractJCasTermAnnotator.java:115) >>> >>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >>> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) >>> >>> 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(UIMAFram >>> ework.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(AggregateAnalysisEng >>> ine_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(UIMAFram >>> ework.java:354) >>> >>> 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.control.AnnotatorOpenEventHandler. >>> actionPerformed(AnnotatorOpenEventHandler.java:52) >>> >>> at javax.swing.AbstractButton.fireActionPerformed(AbstractButto >>> n.java:2022) >>> >>> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractB >>> utton.java:2346) >>> >>> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBu >>> ttonModel.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(BasicMenuItem >>> UI.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(Pro >>> tectionDomain.java:75) >>> >>> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Pro >>> tectionDomain.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(Pro >>> tectionDomain.java:75) >>> >>> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) >>> >>> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDis >>> patchThread.java:201) >>> >>> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispat >>> chThread.java:116) >>> >>> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDis >>> patchThread.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) >>> >>> >>> 12 Feb 2017 22:28:12 ERROR JdbcConnectionFactory - Could not create >>> Connection with jdbc:hsqldb:file:/Users/shahid >>> /projects/workspace/ctakes/resources/org/apache/ctakes/dicti >>> onary/lookup/fast/custom_umls/custom_umls as sa >>> >>> java.sql.SQLException: wrong database file version >>> >>> 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(DriverManager.java:664) >>> >>> at java.sql.DriverManager.getConnection(DriverManager.java:247) >>> >>> 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:75) >>> >>> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) >>> >>> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Native >>> ConstructorAccessorImpl.java:62) >>> >>> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(De >>> legatingConstructorAccessorImpl.java:45) >>> >>> at java.lang.reflect.Constructor.newInstance(Constructor.java:422) >>> >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDictionary(DictionaryDescriptorParser.java:205) >>> >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDictionaries(DictionaryDescriptorParser.java:165) >>> >>> at org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDe >>> scriptorParser.parseDescriptor(DictionaryDescriptorParser.java:133) >>> >>> at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnno >>> tator.initialize(AbstractJCasTermAnnotator.java:115) >>> >>> at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine >>> _impl.initializeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) >>> >>> 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(UIMAFram >>> ework.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(AggregateAnalysisEng >>> ine_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(UIMAFram >>> ework.java:354) >>> >>> 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.control.AnnotatorOpenEventHandler. >>> actionPerformed(AnnotatorOpenEventHandler.java:52) >>> >>> at javax.swing.AbstractButton.fireActionPerformed(AbstractButto >>> n.java:2022) >>> >>> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractB >>> utton.java:2346) >>> >>> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBu >>> ttonModel.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(BasicMenuItem >>> UI.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(Pro >>> tectionDomain.java:75) >>> >>> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Pro >>> tectionDomain.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(Pro >>> tectionDomain.java:75) >>> >>> at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) >>> >>> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDis >>> patchThread.java:201) >>> >>> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispat >>> chThread.java:116) >>> >>> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDis >>> patchThread.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.hsqldb.HsqlException: wrong database file version >>> >>> at org.hsqldb.error.Error.error(Unknown Source) >>> >>> at org.hsqldb.error.Error.error(Unknown Source) >>> >>> at org.hsqldb.persist.HsqlDatabaseProperties.load(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) >>> >>> ... 72 more >>> >>> >>> >>> On Tue, Jan 31, 2017 at 5:52 PM, Andrey Kurdumov < >>> kant2...@googlemail.com> wrote: >>> >>>> Basically after LVG2016 update you have to store all databases in >>>> HSQLDB 2.3.4 format. Thus you should upgrade data to that format. Other >>>> things exactly the same. I intentionally don't introduce other changes in >>>> the setup so it will be easier to incorporate to existing code. >>>> >>>> Steps to upgrade from HSQLDB 1.8 to 2.3.4 >>>> 1. Open HSQLDB in the HSQLDb manager for version 1.8 (not 2.3.4) >>>> 2. Run following commands: >>>> SET SCRIPTFORMAT TEXT >>>> SHUTDOWN >>>> 3. Close HSQLDB manager >>>> 4. Open database in the HSQLDB Manager for version 2.3.4 >>>> 5. Execute >>>> SHUTDOWN >>>> 6. Now you have database updated. >>>> >>>> LVG 2016 already comes in HSQLDB 2.3.4 format. IIRC you need update >>>> only ctakesnormx database to make pipeline works. >>>> >>>> >>>> I definitely want to have my code support LVG data outside of cTakes >>>> installation and now with latest LVG this is easily possible. Let me know >>>> if you interested in this setup. >>>> >>>> 2017-01-29 22:35 GMT+06:00 shahid ashraf <sha...@trialx.com>: >>>> >>>>> Hi Andrey >>>>> >>>>> It would be good , if you update some steps how to setup new LVG. >>>>> (Have also cloned your repo.) >>>>> >>>>> >>>>> >>>>> >>>>> On Sun, Jan 29, 2017 at 5:59 PM, Andrey Kurdumov < >>>>> kant2...@googlemail.com> wrote: >>>>> >>>>>> I update code in GitHub to include LVG 2017 >>>>>> >>>>>> 2017-01-29 15:29 GMT+06:00 Andrey Kurdumov <kant2...@googlemail.com>: >>>>>> >>>>>> > I ask guy who publish LVG to Maven update to version 2017, so I >>>>>> have to >>>>>> > update my repository with LVG 2017 version. If you interested, I >>>>>> could >>>>>> > update LVG to that version too. Now that's just simple change in >>>>>> pom.xml >>>>>> > >>>>>> > 2017-01-29 14:39 GMT+06:00 Finan, Sean < >>>>>> sean.fi...@childrens.harvard.edu>: >>>>>> > >>>>>> >> Hi Andrey, >>>>>> >> >>>>>> >> You have recently been a great contributor to ctakes , and I really >>>>>> >> appreciate that. You have answered devlist questions and your LVG >>>>>> update >>>>>> >> is a seriously big deal. Because of this, you are probably very >>>>>> interested >>>>>> >> in the upcoming release. You may have read emails that were on >>>>>> the devlist >>>>>> >> these past two days. I would like to assure you that no matter >>>>>> what could >>>>>> >> be read into these emails (ok, I can be a little grouchy before >>>>>> the coffee >>>>>> >> sets in) there are at least a couple of us who really want to get >>>>>> LVG >>>>>> >> updated and will try our best to make certain that the next release >>>>>> >> includes the improvement. We are happy and impressed with your >>>>>> initiative >>>>>> >> and furnishing a fully implemented update, and the 3.2.3 branch >>>>>> made a few >>>>>> >> weeks ago will just not pass muster in our opinion. Ergh, now I >>>>>> sound like >>>>>> >> a politician. That is not intended. I just want you to know that >>>>>> even >>>>>> >> though recent emails may imply that there is an immature power >>>>>> struggle, >>>>>> >> that is not the case. I think that everybody in the ctakes >>>>>> community wants >>>>>> >> to get a release out asap, and everybody wants it to be a quality >>>>>> release. >>>>>> >> Postponing the release a few weeks to get your updates into the >>>>>> codebase >>>>>> >> is, in my opinion, really important. I just want to let you know >>>>>> that in >>>>>> >> case you were aware of the 3.2.3 RC cut made a few weeks ago and >>>>>> worry that >>>>>> >> the update will not get into the official cut. I will do what I >>>>>> can to >>>>>> >> move ctakes into 2017. >>>>>> >> >>>>>> >> Regards, >>>>>> >> Sean >>>>>> >> >>>>>> >> -----Original Message----- >>>>>> >> From: Andrey Kurdumov [mailto:kant2...@googlemail.com] >>>>>> >> Sent: Thursday, January 19, 2017 6:49 AM >>>>>> >> To: cTakes developers list >>>>>> >> Subject: Update LVG to 2016 version >>>>>> >> >>>>>> >> As I promise, I udpate cTakes to support LVG version 2016 year. >>>>>> >> >>>>>> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__github. >>>>>> >> com_kant2002_cTakes&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14J >>>>>> >> ZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao >>>>>> >> &m=RdfyvGDEhgrlIGv4Ue0X6DViLFyykHEokJgGzgoG5Vs&s=IJWxluJDIVh >>>>>> >> ugnzWsfRl0TzL0LWzW6_kunc_GRJVew4&e= >>>>>> >> >>>>>> >> Please take a look. >>>>>> >> In the github following modifications to current version of cTakes >>>>>> >> - Removed two large files to make project fit GitHub restrictions. >>>>>> >> - Some very small cleanup which placed in separate commit. >>>>>> >> - Some fixes to ytex related tests, that's was required for me to >>>>>> pass >>>>>> >> mvn install command. >>>>>> >> >>>>>> >> Assumptions: >>>>>> >> - User should update ctakesnormx and other databases from HSQLdb >>>>>> 1.8 to >>>>>> >> HSQLDB 2.3.4 >>>>>> >> >>>>>> >> I already sign Apache ICLA as user akurdyumov for another project >>>>>> (Apache >>>>>> >> Cordova) so if you want update cTakes to LVG2016 please use my >>>>>> code. If I >>>>>> >> need something else to submit code to cTakes project, let me know. >>>>>> >> >>>>>> > >>>>>> > >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> with Regards >>>>> Shahid Ashraf >>>>> >>>> >>>> >>> >>> >>> -- >>> with Regards >>> Shahid Ashraf >>> >>> >>> >>> -- >>> with Regards >>> Shahid Ashraf >>> >> >> >> >> -- >> with Regards >> Shahid Ashraf >> > > -- with Regards Shahid Ashraf
