I am not 100% about this terminology but I think the AggregatePlaintextFastUMLSProcessor.xml is just the Uima Descriptor file that describes the default Clinical Pipeline (in ctakes 4.0 this should be the default).
As for the errors, it looks like it is in lvg, which probably can fail and still have the overall pipeline work ok. Honestly I don't know whether it would change the output of the dictionary module. Are you running from the binary download of cTAKES? Or did you download lvg with maven? If the latter you could try removing the ctakes-lvg directory in your maven repo (under ~/.m2/repository) and force maven to re-download. If the former I'm not sure what to recommend. Sorry for the delayed response. Tim ________________________________________ From: Schenk, Gundolf <[email protected]> Sent: Friday, January 12, 2018 5:18 PM To: [email protected] Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL] anyone? On 1/8/18, 11:47 AM, "Schenk, Gundolf" <[email protected]> wrote: 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.
