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From shahid ashraf <sha...@trialx.com>
Subject Fwd: Update LVG to 2016 version
Date Sun, 12 Feb 2017 20:08:02 GMT
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 <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 <shahid@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

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