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Posted to dev@ctakes.apache.org by shahid ashraf <sh...@trialx.com> on 2017/02/12 20:08:02 UTC
Fwd: Update LVG to 2016 version
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/
lookup/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.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:75)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorA
ccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
tructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDictionary(DictionaryDesc
riptorParser.java:205)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDictionaries(DictionaryDe
scriptorParser.java:165)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDescriptor(DictionaryDesc
riptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.
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(AggregateAnalysisEngine_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$Handler.actionPerformed(Abstra
ctButton.java:2346)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBut
tonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
at javax.swing.plaf.basic.BasicMenuItemUI$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(Protec
tionDomain.java:75)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Protec
tionDomain.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(Protec
tionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDi
spatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispa
tchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDi
spatchThread.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.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:75)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorA
ccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
tructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDictionary(DictionaryDesc
riptorParser.java:205)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDictionaries(DictionaryDe
scriptorParser.java:165)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDescriptor(DictionaryDesc
riptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.
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(AggregateAnalysisEngine_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(Abstra
ctButton.java:2346)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBut
tonModel.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(Protec
tionDomain.java:75)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Protec
tionDomain.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(Protec
tionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDi
spatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispa
tchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDi
spatchThread.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.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:75)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorA
ccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
tructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDictionary(DictionaryDesc
riptorParser.java:205)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDictionaries(DictionaryDe
scriptorParser.java:165)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDescriptor(DictionaryDesc
riptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.
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(AggregateAnalysisEngine_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(Abstra
ctButton.java:2346)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBut
tonModel.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(Protec
tionDomain.java:75)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Protec
tionDomain.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(Protec
tionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDi
spatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispa
tchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDi
spatchThread.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 <ka...@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 <sh...@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 <kant2002@googlemail.com
>> > wrote:
>>
>>> I update code in GitHub to include LVG 2017
>>>
>>> 2017-01-29 15:29 GMT+06:00 Andrey Kurdumov <ka...@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:kant2002@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
Re: Update LVG to 2016 version
Posted by "Taposh D. Roy" <Ta...@kp.org>.
Please unsubscribe me.
Regards,
T
On 2/12/17, 12:08 PM, "shahid ashraf" <sh...@trialx.com> wrote:
Caution: This email came from outside Kaiser Permanente. Do not open attachments or click on links if you do not recognize the sender.
______________________________________________________________________
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/
lookup/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.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:75)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorA
ccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
tructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDictionary(DictionaryDesc
riptorParser.java:205)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDictionaries(DictionaryDe
scriptorParser.java:165)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDescriptor(DictionaryDesc
riptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.
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(AggregateAnalysisEngine_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(Abstra
ctButton.java:2346)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBut
tonModel.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(Protec
tionDomain.java:75)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Protec
tionDomain.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(Protec
tionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDi
spatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispa
tchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDi
spatchThread.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.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:75)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorA
ccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
tructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDictionary(DictionaryDesc
riptorParser.java:205)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDictionaries(DictionaryDe
scriptorParser.java:165)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDescriptor(DictionaryDesc
riptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.
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(AggregateAnalysisEngine_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(Abstra
ctButton.java:2346)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBut
tonModel.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(Protec
tionDomain.java:75)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Protec
tionDomain.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(Protec
tionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDi
spatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispa
tchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDi
spatchThread.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.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:75)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorA
ccessorImpl.java:62)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingCons
tructorAccessorImpl.java:45)
at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDictionary(DictionaryDesc
riptorParser.java:205)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDictionaries(DictionaryDe
scriptorParser.java:165)
at org.apache.ctakes.dictionary.lookup2.dictionary.
DictionaryDescriptorParser.parseDescriptor(DictionaryDesc
riptorParser.java:133)
at org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.
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(AggregateAnalysisEngine_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(Abstra
ctButton.java:2346)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultBut
tonModel.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(Protec
tionDomain.java:75)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Protec
tionDomain.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(Protec
tionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDi
spatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispa
tchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDi
spatchThread.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 <ka...@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 <sh...@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 <kant2002@googlemail.com
>> > wrote:
>>
>>> I update code in GitHub to include LVG 2017
>>>
>>> 2017-01-29 15:29 GMT+06:00 Andrey Kurdumov <ka...@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:kant2002@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
NOTICE TO RECIPIENT: If you are not the intended recipient of this e-mail, you are prohibited from sharing, copying, or otherwise using or disclosing its contents. If you have received this e-mail in error, please notify the sender immediately by reply e-mail and permanently delete this e-mail and any attachments without reading, forwarding or saving them. Thank you.
Re: Update LVG to 2016 version
Posted by shahid ashraf <sh...@trialx.com>.
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 <sh...@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 <ka...@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 <sh...@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 <sh...@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 <
>>>> kant2002@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 <sh...@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 <
>>>>>> kant2002@googlemail.com> wrote:
>>>>>>
>>>>>>> I update code in GitHub to include LVG 2017
>>>>>>>
>>>>>>> 2017-01-29 15:29 GMT+06:00 Andrey Kurdumov <kant2002@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:kant2002@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
Re: Update LVG to 2016 version
Posted by shahid ashraf <sh...@trialx.com>.
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 <ka...@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 <sh...@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 <sh...@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 <
>>> kant2002@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 <sh...@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 <
>>>>> kant2002@googlemail.com> wrote:
>>>>>
>>>>>> I update code in GitHub to include LVG 2017
>>>>>>
>>>>>> 2017-01-29 15:29 GMT+06:00 Andrey Kurdumov <ka...@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:kant2002@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
Re: Update LVG to 2016 version
Posted by Andrey Kurdumov <ka...@googlemail.com>.
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 <sh...@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 <sh...@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 <kant2002@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 <sh...@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 <
>>>> kant2002@googlemail.com> wrote:
>>>>
>>>>> I update code in GitHub to include LVG 2017
>>>>>
>>>>> 2017-01-29 15:29 GMT+06:00 Andrey Kurdumov <ka...@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:kant2002@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
>
Re: Update LVG to 2016 version
Posted by shahid ashraf <sh...@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 <sh...@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 <ka...@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 <sh...@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 <
>>> kant2002@googlemail.com> wrote:
>>>
>>>> I update code in GitHub to include LVG 2017
>>>>
>>>> 2017-01-29 15:29 GMT+06:00 Andrey Kurdumov <ka...@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:kant2002@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