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(MainFrame.java:476 > ) > > at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler. > actionPerformed(AnnotatorOpenEventHandler.java:52) > > at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022 > ) > > at javax.swing.AbstractButton$Handler.actionPerformed(AbstractB > utton.java:2346) > > at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBu > ttonModel.java:402) > > at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) > > at javax.swing.AbstractButton.doClick(AbstractButton.java:376) > > at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833 > ) > > at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) > > at javax.swing.plaf.basic.BasicMenuItemUI$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(MainFrame.java:476 > ) > > at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler. > actionPerformed(AnnotatorOpenEventHandler.java:52) > > at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.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(BasicMenuItemUI.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/dictionary/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(MainFrame.java:476 > ) > > at org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler. > actionPerformed(AnnotatorOpenEventHandler.java:52) > > at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.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(BasicMenuItemUI.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.Finan@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
