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Posted to dev@ctakes.apache.org by Andrey Kurdumov <ka...@googlemail.com> on 2017/01/19 11:48:37 UTC
Update LVG to 2016 version
As I promise, I udpate cTakes to support LVG version 2016 year.
https://github.com/kant2002/cTakes
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.
RE: Update LVG to 2016 version
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Andrey,
I won't have time to test this until next week or maybe even after that. If there are no showstoppers then you have done the community a great favor! Others and I have wanted to update LVG and hsqldb for so, so long. I hope that somebody out there can have a look at this as I would really like to get it into the upcoming release!
Cheers!
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_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=RdfyvGDEhgrlIGv4Ue0X6DViLFyykHEokJgGzgoG5Vs&s=IJWxluJDIVhugnzWsfRl0TzL0LWzW6_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.
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
Fwd: Update LVG to 2016 version
Posted by shahid ashraf <sh...@trialx.com>.
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 Andrey Kurdumov <ka...@googlemail.com>.
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 <ka...@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
>
Re: Update LVG to 2016 version
Posted by 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 <ka...@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
Re: Update LVG to 2016 version
Posted by Andrey Kurdumov <ka...@googlemail.com>.
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 <Se...@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.
>>
>
>
Re: Update LVG to 2016 version
Posted by 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 <Se...@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_
> 3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> RdfyvGDEhgrlIGv4Ue0X6DViLFyykHEokJgGzgoG5Vs&s=
> IJWxluJDIVhugnzWsfRl0TzL0LWzW6_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.
>
RE: Update LVG to 2016 version
Posted by "Finan, Sean" <Se...@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_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=RdfyvGDEhgrlIGv4Ue0X6DViLFyykHEokJgGzgoG5Vs&s=IJWxluJDIVhugnzWsfRl0TzL0LWzW6_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.