Hi,
I am new to cTAKES (and NLP) and I am trying to extract clinically relevant
information from electronic freetext records.
I am running the default Clinical Pipeline. But I have a few general questions
for understanding and for some error output I am seeing.
1) what is the difference between the Clinical Pipeline and the processor
(AggregatePlaintextFastUMLSProcessor.xml)?
2) when running AggregatePlaintextFastUMLSProcessor.xml on the
dr_nutritious_1.txt example via the CVD gui I only see 32 IdentifiedAnnotations
but I get a couple of error messages. Could anyone help me get started, please?
Here are the error/warn messages:
[…]
08 Jan 2018 10:06:22 INFO POSTagger - POS tagger model file:
org/apache/ctakes/postagger/models/mayo-pos.zip
08 Jan 2018 10:06:23 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg
with config file =
/Users/gschenk/NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data/config/lvg.properties
08 Jan 2018 10:06:23 INFO LvgCmdApiResourceImpl - config file absolute path
=
/Users/gschenk/NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data/config/lvg.properties
08 Jan 2018 10:06:23 INFO LvgCmdApiResourceImpl - cwd =
/Users/gschenk/NotesProcessing/apache-ctakes-4.0.0
08 Jan 2018 10:06:23 INFO LvgCmdApiResourceImpl - cd
/Users/gschenk/NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/
08 Jan 2018 10:06:23 INFO ENGINE - open start - state not modified
08 Jan 2018 10:06:23 INFO ENGINE - dataFileCache open start
08 Jan 2018 10:06:23 WARN ENGINE - failed to read a byte array
java.io.EOFException
at org.hsqldb.persist.RAFile.read(Unknown Source)
at org.hsqldb.persist.DataFileCache.readObject(Unknown Source)
at org.hsqldb.persist.DataFileCache.getFromFile(Unknown Source)
at org.hsqldb.persist.DataFileCache.get(Unknown Source)
at org.hsqldb.persist.RowStoreAVLDisk.get(Unknown Source)
at org.hsqldb.persist.RowStoreAVLDisk.setAccessor(Unknown Source)
at org.hsqldb.Table.setIndexRoots(Unknown Source)
at org.hsqldb.Table.setIndexRoots(Unknown Source)
at org.hsqldb.StatementCommand.getResult(Unknown Source)
at org.hsqldb.StatementCommand.execute(Unknown Source)
at org.hsqldb.Session.executeCompiledStatement(Unknown Source)
at org.hsqldb.scriptio.ScriptReaderText.readDDL(Unknown Source)
at org.hsqldb.scriptio.ScriptReaderBase.readAll(Unknown Source)
at org.hsqldb.persist.Log.processScript(Unknown Source)
at org.hsqldb.persist.Log.open(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/java.sql.DriverManager.getConnection(DriverManager.java:678)
at java.sql/java.sql.DriverManager.getConnection(DriverManager.java:229)
at gov.nih.nlm.nls.lvg.Db.DbBase.OpenConnection(DbBase.java:38)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.InitDbAndTrie(LvgCmdApi.java:1529)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.Init(LvgCmdApi.java:1469)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.<init>(LvgCmdApi.java:84)
at
org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:89)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:628)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:464)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:193)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:131)
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.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:371)
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.LoadRecentDescFileEventHandler.actionPerformed(LoadRecentDescFileEventHandler.java:41)
at
java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967)
at
java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308)
at
java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405)
at
java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
at
java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:369)
at
java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:980)
at
java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
at
java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1024)
at
java.desktop/java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:297)
at
java.desktop/java.awt.Component.processMouseEvent(Component.java:6578)
at
java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3343)
at java.desktop/java.awt.Component.processEvent(Component.java:6343)
at java.desktop/java.awt.Container.processEvent(Container.java:2259)
at
java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4961)
at
java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2317)
at java.desktop/java.awt.Component.dispatchEvent(Component.java:4793)
at
java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at
java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4539)
at
java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4480)
at
java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2303)
at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2758)
at java.desktop/java.awt.Component.dispatchEvent(Component.java:4793)
at
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:766)
at java.desktop/java.awt.EventQueue.access$500(EventQueue.java:97)
at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:717)
at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:711)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
at
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:99)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:739)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:737)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:736)
at
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:199)
at
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at
java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at
java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
08 Jan 2018 10:06:23 FATAL ENGINE - DataFileCache.readObject 202240
java.io.EOFException
at org.hsqldb.persist.RAFile.read(Unknown Source)
at org.hsqldb.persist.DataFileCache.readObject(Unknown Source)
at org.hsqldb.persist.DataFileCache.getFromFile(Unknown Source)
at org.hsqldb.persist.DataFileCache.get(Unknown Source)
at org.hsqldb.persist.RowStoreAVLDisk.get(Unknown Source)
at org.hsqldb.persist.RowStoreAVLDisk.setAccessor(Unknown Source)
at org.hsqldb.Table.setIndexRoots(Unknown Source)
at org.hsqldb.Table.setIndexRoots(Unknown Source)
at org.hsqldb.StatementCommand.getResult(Unknown Source)
at org.hsqldb.StatementCommand.execute(Unknown Source)
at org.hsqldb.Session.executeCompiledStatement(Unknown Source)
at org.hsqldb.scriptio.ScriptReaderText.readDDL(Unknown Source)
at org.hsqldb.scriptio.ScriptReaderBase.readAll(Unknown Source)
at org.hsqldb.persist.Log.processScript(Unknown Source)
at org.hsqldb.persist.Log.open(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/java.sql.DriverManager.getConnection(DriverManager.java:678)
at java.sql/java.sql.DriverManager.getConnection(DriverManager.java:229)
at gov.nih.nlm.nls.lvg.Db.DbBase.OpenConnection(DbBase.java:38)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.InitDbAndTrie(LvgCmdApi.java:1529)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.Init(LvgCmdApi.java:1469)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.<init>(LvgCmdApi.java:84)
at
org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:89)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:628)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:464)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:193)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:131)
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.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:371)
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.LoadRecentDescFileEventHandler.actionPerformed(LoadRecentDescFileEventHandler.java:41)
at
java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967)
at
java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308)
at
java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405)
at
java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
at
java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:369)
at
java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:980)
at
java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
at
java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1024)
at
java.desktop/java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:297)
at
java.desktop/java.awt.Component.processMouseEvent(Component.java:6578)
at
java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3343)
at java.desktop/java.awt.Component.processEvent(Component.java:6343)
at java.desktop/java.awt.Container.processEvent(Container.java:2259)
at
java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4961)
at
java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2317)
at java.desktop/java.awt.Component.dispatchEvent(Component.java:4793)
at
java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at
java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4539)
at
java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4480)
at
java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2303)
at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2758)
at java.desktop/java.awt.Component.dispatchEvent(Component.java:4793)
at
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:766)
at java.desktop/java.awt.EventQueue.access$500(EventQueue.java:97)
at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:717)
at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:711)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
at
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:99)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:739)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:737)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:736)
at
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:199)
at
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at
java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at
java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
08 Jan 2018 10:06:23 FATAL ENGINE -
/Users/gschenk/NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008.data
getFromFile failed 202240
org.hsqldb.HsqlException: java.io.EOFException
at org.hsqldb.error.Error.error(Unknown Source)
at org.hsqldb.persist.DataFileCache.readObject(Unknown Source)
at org.hsqldb.persist.DataFileCache.getFromFile(Unknown Source)
at org.hsqldb.persist.DataFileCache.get(Unknown Source)
at org.hsqldb.persist.RowStoreAVLDisk.get(Unknown Source)
at org.hsqldb.persist.RowStoreAVLDisk.setAccessor(Unknown Source)
at org.hsqldb.Table.setIndexRoots(Unknown Source)
at org.hsqldb.Table.setIndexRoots(Unknown Source)
at org.hsqldb.StatementCommand.getResult(Unknown Source)
at org.hsqldb.StatementCommand.execute(Unknown Source)
at org.hsqldb.Session.executeCompiledStatement(Unknown Source)
at org.hsqldb.scriptio.ScriptReaderText.readDDL(Unknown Source)
at org.hsqldb.scriptio.ScriptReaderBase.readAll(Unknown Source)
at org.hsqldb.persist.Log.processScript(Unknown Source)
at org.hsqldb.persist.Log.open(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/java.sql.DriverManager.getConnection(DriverManager.java:678)
at java.sql/java.sql.DriverManager.getConnection(DriverManager.java:229)
at gov.nih.nlm.nls.lvg.Db.DbBase.OpenConnection(DbBase.java:38)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.InitDbAndTrie(LvgCmdApi.java:1529)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.Init(LvgCmdApi.java:1469)
at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.<init>(LvgCmdApi.java:84)
at
org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(LvgCmdApiResourceImpl.java:89)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:628)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:464)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:193)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.initialize(AnalysisEngineImplBase.java:157)
at
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.java:131)
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.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:371)
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.LoadRecentDescFileEventHandler.actionPerformed(LoadRecentDescFileEventHandler.java:41)
at
java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1967)
at
java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2308)
at
java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405)
at
java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262)
at
java.desktop/javax.swing.AbstractButton.doClick(AbstractButton.java:369)
at
java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:980)
at
java.desktop/com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
at
java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1024)
at
java.desktop/java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:297)
at
java.desktop/java.awt.Component.processMouseEvent(Component.java:6578)
at
java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3343)
at java.desktop/java.awt.Component.processEvent(Component.java:6343)
at java.desktop/java.awt.Container.processEvent(Container.java:2259)
at
java.desktop/java.awt.Component.dispatchEventImpl(Component.java:4961)
at
java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2317)
at java.desktop/java.awt.Component.dispatchEvent(Component.java:4793)
at
java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at
java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4539)
at
java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4480)
at
java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2303)
at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2758)
at java.desktop/java.awt.Component.dispatchEvent(Component.java:4793)
at
java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:766)
at java.desktop/java.awt.EventQueue.access$500(EventQueue.java:97)
at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:717)
at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:711)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
at
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:99)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:739)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:737)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at
java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:736)
at
java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:199)
at
java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
at
java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
at
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
at
java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at
java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
Caused by: java.io.EOFException
at org.hsqldb.persist.RAFile.read(Unknown Source)
... 89 more
08 Jan 2018 10:06:23 WARN ENGINE - java.io.EOFException in statement [SET
TABLE PUBLIC.LEXSYNONYM INDEX '202240 202240 0 0 5056']
org.hsqldb.HsqlException: java.io.EOFException
at org.hsqldb.error.Error.error(Unknown Source)
[…]
... 89 more
08 Jan 2018 10:06:23 WARN ENGINE - Script processing failure
org.hsqldb.HsqlException: error in script file line: 49
/Users/gschenk/NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008
java.io.EOFException in statement [SET TABLE PUBLIC.LEXSYNONYM INDEX '202240
202240 0 0 5056']
at org.hsqldb.error.Error.error(Unknown Source)
[…]
... 79 more
Caused by: java.io.EOFException
at org.hsqldb.persist.RAFile.read(Unknown Source)
... 89 more
08 Jan 2018 10:06:23 INFO ENGINE - Database closed
08 Jan 2018 10:06:23 FATAL ENGINE - could not reopen database
org.hsqldb.HsqlException: error in script file line: 49
/Users/gschenk/NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008
java.io.EOFException in statement [SET TABLE PUBLIC.LEXSYNONYM INDEX '202240
202240 0 0 5056']
[…]
Caused by: org.hsqldb.HsqlException: java.io.EOFException
at org.hsqldb.error.Error.error(Unknown Source)
at org.hsqldb.persist.DataFileCache.readObject(Unknown Source)
at org.hsqldb.persist.DataFileCache.getFromFile(Unknown Source)
at org.hsqldb.persist.DataFileCache.get(Unknown Source)
at org.hsqldb.persist.RowStoreAVLDisk.get(Unknown Source)
at org.hsqldb.persist.RowStoreAVLDisk.setAccessor(Unknown Source)
at org.hsqldb.Table.setIndexRoots(Unknown Source)
at org.hsqldb.Table.setIndexRoots(Unknown Source)
at org.hsqldb.StatementCommand.getResult(Unknown Source)
at org.hsqldb.StatementCommand.execute(Unknown Source)
at org.hsqldb.Session.executeCompiledStatement(Unknown Source)
... 79 more
Caused by: java.io.EOFException
at org.hsqldb.persist.RAFile.read(Unknown Source)
... 89 more
08 Jan 2018 10:06:23 INFO ENGINE - open start - state not modified
08 Jan 2018 10:06:23 INFO ENGINE - dataFileCache open start
08 Jan 2018 10:06:27 FATAL ENGINE - DataFileCache.readObject 202240
java.lang.OutOfMemoryError: Java heap space
at org.hsqldb.rowio.RowInputBase.resetRow(Unknown Source)
[…]
... 80 more
Caused by: java.io.EOFException
at org.hsqldb.persist.RAFile.read(Unknown Source)
... 90 more
08 Jan 2018 10:06:31 INFO LvgCmdApiResourceImpl - cd
/Users/gschenk/NotesProcessing/apache-ctakes-4.0.0
08 Jan 2018 10:06:31 INFO DrugMentionAnnotator - Finite state machines loaded.
08 Jan 2018 10:06:33 INFO ClearNLPDependencyParserAE - using Morphy analysis?
true
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
........................................................................................
Loading configuration.
Loading feature templates.
Loading model:
.
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
...
[…]
Loading configuration.
Loading feature templates.
Loading lexica.
Loading model:
................................
Loading model:
.............................
08 Jan 2018 10:06:39 INFO ConstituencyParser - Initializing parser...
08 Jan 2018 10:06:57 INFO SentenceDetector - Starting processing.
08 Jan 2018 10:06:57 INFO TokenizerAnnotatorPTB - process(JCas) in
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
08 Jan 2018 10:06:57 INFO LvgAnnotator - process(JCas)
08 Jan 2018 10:06:57 INFO ContextDependentTokenizerAnnotator - process(JCas)
08 Jan 2018 10:06:57 INFO POSTagger - process(JCas)
08 Jan 2018 10:06:57 INFO Chunker - process(JCas)
08 Jan 2018 10:06:57 INFO ChunkAdjuster - process(JCas)
08 Jan 2018 10:06:57 INFO ChunkAdjuster - process(JCas)
08 Jan 2018 10:06:57 INFO AbstractJCasTermAnnotator - Starting processing
08 Jan 2018 10:06:57 INFO AbstractJCasTermAnnotator - Finished processing
08 Jan 2018 10:06:57 INFO DrugMentionAnnotator - process(JCas)
08 Jan 2018 10:06:57 WARN DocumentIDAnnotationUtil - Unable to find
DocumentIDAnnotation
08 Jan 2018 10:06:57 INFO MaxentParserWrapper - Started processing:
UnknownDocument1
08 Jan 2018 10:06:58 INFO MaxentParserWrapper - Done parsing: UnknownDocument1
Creating extents.
Initializing text frame.
Setting size
Packing frame.
Showing frame.
Done.
Creating extents.
Initializing text frame.
Setting size
Packing frame.
Showing frame.
Done.
There are a ton of more error messages. I am not sure what to look out for. Or
how to approach this efficiently. Seems like the LVG is not working and perhaps
some memory problem. Any help is appreciated.
Thanks,
Gundolf.
