>From this line in the error message "SET TABLE PUBLIC.LEXSYNONYM INDEX '202240 202240 0 0 5056'" it appears you might not have the full LVG database installed, which is an optional step of installing cTAKES.
If I'm right about that and if you are running within an IDE, you can try to merge resources from https://sourceforge.net/projects/ctakesresources/files/ctakes-resources-4.0-bin.zip/download into the relevant subproject. In your case (lvg) this would mean merging the contents of resources\org\apache\ctakes\lvg\ from that zip into ctakes-lvg-res\src\main\resources\org\apache\ctakes\lvg If you are running from the binary downloads, try merging the contents of resources\org\apache\ctakes\lvg\ from that zip into the resources directory, which in your case looks like it is: /Users/gschenk/NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg One way to see if you have the full LVG is to look at the sizes of the files in /Users/gschenk/NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg If you have the full LVG database, the files in that directory will be more than a GB in total. As Tim mentioned, if LVG fails, the rest of the pipeline will run. The LVG component of cTAKES was written to improve recall but it's not clear if it is necessary any more, or under which circumstances it is more or less likely to be worth including in a pipeline. some of the differences between the Default Clinical Pipeline and the running the pipeline defined by AggregatePlaintextFastUMLSProcessor.xml are: - the Default Clinical Pipeline uses piper files to define which components are run. The main one is DefaultFastPipeline.piper, which then references others. - The fixedFlow element of AggregatePlaintextFastUMLSProcessor lists which components, including the LvgAnnotator, are run when you use AggregatePlaintextFastUMLSProcessor.xml for getting started with cTAKES, especially if you are running the code from the trunk of SVN, I recommend using piper files. Piper files are not a generic UIMA concept, they are specific to cTAKES. For people planning to use UIMA-AS rather than just UIMA, I'd recommend learning to use the XML descriptors which you will want to understand when reading the UMA-AS documentation. -- James On Sat, Jan 13, 2018 at 8:05 AM, Miller, Timothy < [email protected]> wrote: > 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.initializeAggregateAnalysisEng > ine(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.initializeAggregateAnalysisEng > ine(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.initializeAggregateAnalysisEng > ine(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. > > > > >
