Hi Seems the previous error i was missing to use the hsqldb 2.3.4 jar... as clinical_pipeline had transitive dependy to 1.8. So fixed that by including 2.3.4 hsqldb jar.
On Mon, Feb 13, 2017 at 3:25 PM, shahid ashraf <sha...@trialx.com> wrote: > 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(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(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(Resource > Pool.java:246) > > at org.apache.uima.internal.util.ResourcePool.<init>(ResourcePool.java:100 > ) > > at org.apache.uima.internal.util.AnalysisEnginePool.<init>(Anal > ysisEnginePool.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(UIMAFram > ework.java:498) > > at org.apache.ctakes.web.client.servlet.DemoServlet.init(DemoS > ervlet.java:90) > > at javax.servlet.GenericServlet.init(GenericServlet.java:244) > > at org.eclipse.jetty.servlet.ServletHolder.initServlet(Serv > letHolder.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(Serv > letHandler.java:791) > > at org.eclipse.jetty.servlet.ServletContextHandler.startContext( > ServletContextHandler.java:265) > > at org.eclipse.jetty.webapp.WebAppContext.startContext(Web > AppContext.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(DictionaryDesc > riptorParser.java:199) > > at org.apache.ctakes.dictionary.lookup2.dictionary. > DictionaryDescriptorParser.parseDictionaries(DictionaryDe > scriptorParser.java:156) > > at org.apache.ctakes.dictionary.lookup2.dictionary. > DictionaryDescriptorParser.parseDescriptor(DictionaryDesc > riptorParser.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(DictionaryDesc > riptorParser.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 > -- with Regards Shahid Ashraf
