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Posted to user@ctakes.apache.org by "Miller, Timothy" <Ti...@childrens.harvard.edu> on 2018/01/13 13:05:20 UTC
Re: Errors when executing AggregatePlaintextFastUMLSProcessor
[EXTERNAL]
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 <Gu...@ucsf.edu>
Sent: Friday, January 12, 2018 5:18 PM
To: user@ctakes.apache.org
Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
anyone?
On 1/8/18, 11:47 AM, "Schenk, Gundolf" <Gu...@ucsf.edu> 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.
Re: Errors when executing AggregatePlaintextFastUMLSProcessor
[EXTERNAL]
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
I copied the resources yet again and used “overwrite” instead of “merge” this time. Tataa! No more error messages. I feel a bit more confident now about the results and what to expect from the default pipeline. Seems indeed some tweaking is necessary to annotate the father correctly as subject in “father has hx of diabetes” rather than the patient.
Many thanks for your patient help!
Cheers,
Gundolf.
From: James Masanz <ma...@gmail.com>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Thursday, January 18, 2018 at 11:15 AM
To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
I wasn't clear - the names of the directories seem to be confusing things.
The files you mention are in a subdirectory called tables.
The hsql database files are in the HSqlDb subdirectory which was in your list:
drwxr-xr-x 6 gschenk 192 Jan 5 11:28 HSqlDb
In that subdirectory, you should see files with names like lvg2008*
Offhand I'm not sure about the drugner engine is part of the default Clinical Pipeline. I'll have to take a look at that.
On Thu, Jan 18, 2018 at 12:24 PM, Schenk, Gundolf <Gu...@ucsf.edu>> wrote:
Hi James,
Many thanks for the link. It seems like the default Clinical Pipeline does not extract/annotate everything correctly. For example, in "father has hx of diabetes" the pipeline recognizes “diabetes” but does not set the subject attribute to “other” or “father”. Also, I have not seen any annotation from the drugner engine, although I understood that it is part of the default pipeline, is it not?
On my installation I do not have the lvg files that you mention. In /Users/gschenk/NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data I have this structure:
drwxr-xr-x 6 gschenk 192 Jan 5 11:28 HSqlDb
-rw-r--r--@ 1 gschenk 319 Jan 5 11:22 ReadMe.txt
drwxr-xr-x 8 gschenk 256 Jan 5 11:23 Unicode
-rw-rw-r--@ 1 gschenk 264 Jan 5 11:22 build.txt
drwxr-xr-x 7 gschenk 224 Jan 5 11:23 config
drwxr-xr-x 7 gschenk 224 Jan 5 11:23 misc
drwxr-xr-x 12 gschenk 384 Jan 5 11:23 rules
drwxr-xr-x 11 gschenk 352 Jan 16 09:54 tables
-rwxr-xr-x@ 1 gschenk 37 Apr 2 2017 version.txt
and in tables:
-rwxr-xr-x 1 gschenk 2486063 Jan 16 09:54 acronym.data
-rwxr-xr-x 1 gschenk 72583370 Jan 16 09:54 antiNorm.data
-rwxr-xr-x 1 gschenk 31753678 Jan 16 09:54 canonical.data
-rwxr-xr-x 1 gschenk 324456 Jan 16 09:54 derivation.data
-rwxr-xr-x 1 gschenk 156803364 Jan 16 09:54 fruitful.data
-rwxr-xr-x 1 gschenk 74664993 Jan 16 09:54 infl.data
-rwxr-xr-x 1 gschenk 704862 Jan 16 09:54 nominalization.data
-rwxr-xr-x 1 gschenk 83452 Jan 16 09:54 properNoun.data
-rwxr-xr-x 1 gschenk 229622 Jan 16 09:54 synonyms.data
Am I missing something (settings/resources/…)?
Cheers,
Gundolf.
From: James Masanz <ma...@gmail.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Wednesday, January 17, 2018 at 5:43 AM
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
When I run the pipeline I also get 32 IdentifiedAnnotations
On windows, I see these sizes for the lvg database files
922746880 lvg2008.data
104 lvg2008.properties
1312589 lvg2008.script
This might help you get started with the meaning of the annotations:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Assertion
On Tue, Jan 16, 2018 at 2:52 PM, Schenk, Gundolf <Gu...@ucsf.edu>> wrote:
Dear Tim and James,
Many thanks for your replies. I run cTAKES it as a downloaded “binary” from the mac osx Terminal app command line. I don’t use an IDE nor did I install it via maven nor from svn. I have downloaded the resources (again) and merged the lvg and dictionary folders into the designated places. The total size in the lvg subdirectory is 807.3 MB. Is this about the correct size, James? This did not change the errors output.
I am not familiar with UIMA nor do I know much about nlp in general. I noticed that the errors only show when I load the AE xml file visa the CVD interface. Using the pipeline via cmdline no errors are shown. In both cases I get 32 identified annotations. Is this number as expected?
So, I guess the information extraction works to the extent of these annotators capability, and to go further or improve the result I would have to tweak the algorithm somehow. Agreed?
Is there documentation, that describes the meaning of the fields in the resulting xmi file? I would like to use it the xmi file as input for post-processing. Thanks!
Cheers,
Gundolf.
From: James Masanz <ma...@gmail.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, January 13, 2018 at 12:09 PM
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
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 <Ti...@childrens.harvard.edu>> 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 <Gu...@ucsf.edu>>
Sent: Friday, January 12, 2018 5:18 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
anyone?
On 1/8/18, 11:47 AM, "Schenk, Gundolf" <Gu...@ucsf.edu>> 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<https://protect2.fireeye.com/url?k=29542e3c71795085.29542e3c-73f5da448e27151a&u=http://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.
Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
Posted by James Masanz <ma...@gmail.com>.
I wasn't clear - the names of the directories seem to be confusing things.
The files you mention are in a subdirectory called tables.
The hsql database files are in the HSqlDb subdirectory which was in your
list:
drwxr-xr-x 6 gschenk 192 Jan 5 11:28 HSqlDb
In that subdirectory, you should see files with names like lvg2008*
Offhand I'm not sure about the drugner engine is part of the default
Clinical Pipeline. I'll have to take a look at that.
On Thu, Jan 18, 2018 at 12:24 PM, Schenk, Gundolf <Gu...@ucsf.edu>
wrote:
> Hi James,
>
>
>
> Many thanks for the link. It seems like the default Clinical Pipeline does
> not extract/annotate everything correctly. For example, in "father has hx
> of diabetes" the pipeline recognizes “diabetes” but does not set the
> subject attribute to “other” or “father”. Also, I have not seen any
> annotation from the drugner engine, although I understood that it is part
> of the default pipeline, is it not?
>
>
>
> On my installation I do not have the lvg files that you mention. In
> /Users/gschenk/NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data
> I have this structure:
>
> drwxr-xr-x 6 gschenk 192 Jan 5 11:28 HSqlDb
>
> -rw-r--r--@ 1 gschenk 319 Jan 5 11:22 ReadMe.txt
>
> drwxr-xr-x 8 gschenk 256 Jan 5 11:23 Unicode
>
> -rw-rw-r--@ 1 gschenk 264 Jan 5 11:22 build.txt
>
> drwxr-xr-x 7 gschenk 224 Jan 5 11:23 config
>
> drwxr-xr-x 7 gschenk 224 Jan 5 11:23 misc
>
> drwxr-xr-x 12 gschenk 384 Jan 5 11:23 rules
>
> drwxr-xr-x 11 gschenk 352 Jan 16 09:54 tables
>
> -rwxr-xr-x@ 1 gschenk 37 Apr 2 2017 version.txt
>
>
>
> and in tables:
>
> -rwxr-xr-x 1 gschenk 2486063 Jan 16 09:54 acronym.data
>
> -rwxr-xr-x 1 gschenk 72583370 Jan 16 09:54 antiNorm.data
>
> -rwxr-xr-x 1 gschenk 31753678 Jan 16 09:54 canonical.data
>
> -rwxr-xr-x 1 gschenk 324456 Jan 16 09:54 derivation.data
>
> -rwxr-xr-x 1 gschenk 156803364 Jan 16 09:54 fruitful.data
>
> -rwxr-xr-x 1 gschenk 74664993 Jan 16 09:54 infl.data
>
> -rwxr-xr-x 1 gschenk 704862 Jan 16 09:54 nominalization.data
>
> -rwxr-xr-x 1 gschenk 83452 Jan 16 09:54 properNoun.data
>
> -rwxr-xr-x 1 gschenk 229622 Jan 16 09:54 synonyms.data
>
>
>
>
>
> Am I missing something (settings/resources/…)?
>
>
>
>
>
> Cheers,
>
> Gundolf.
>
>
>
>
>
> *From: *James Masanz <ma...@gmail.com>
> *Reply-To: *"user@ctakes.apache.org" <us...@ctakes.apache.org>
> *Date: *Wednesday, January 17, 2018 at 5:43 AM
> *To: *"user@ctakes.apache.org" <us...@ctakes.apache.org>
> *Subject: *Re: Errors when executing AggregatePlaintextFastUMLSProcessor
> [EXTERNAL]
>
>
>
> When I run the pipeline I also get 32 IdentifiedAnnotations
>
>
>
> On windows, I see these sizes for the lvg database files
>
>
>
> 922746880 lvg2008.data
>
> 104 lvg2008.properties
>
> 1312589 lvg2008.script
>
>
>
> This might help you get started with the meaning of the annotations:
>
>
>
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Assertion
>
>
>
>
>
>
>
>
>
> On Tue, Jan 16, 2018 at 2:52 PM, Schenk, Gundolf <Gu...@ucsf.edu>
> wrote:
>
> Dear Tim and James,
>
>
>
> Many thanks for your replies. I run cTAKES it as a downloaded “binary”
> from the mac osx Terminal app command line. I don’t use an IDE nor did I
> install it via maven nor from svn. I have downloaded the resources (again)
> and merged the lvg and dictionary folders into the designated places. The
> total size in the lvg subdirectory is 807.3 MB. Is this about the correct
> size, James? This did not change the errors output.
>
>
>
> I am not familiar with UIMA nor do I know much about nlp in general. I
> noticed that the errors only show when I load the AE xml file visa the CVD
> interface. Using the pipeline via cmdline no errors are shown. In both
> cases I get 32 identified annotations. Is this number as expected?
>
>
>
> So, I guess the information extraction works to the extent of these
> annotators capability, and to go further or improve the result I would have
> to tweak the algorithm somehow. Agreed?
>
>
>
> Is there documentation, that describes the meaning of the fields in the
> resulting xmi file? I would like to use it the xmi file as input for
> post-processing. Thanks!
>
>
>
> Cheers,
>
> Gundolf.
>
>
>
>
>
>
>
> *From: *James Masanz <ma...@gmail.com>
> *Reply-To: *"user@ctakes.apache.org" <us...@ctakes.apache.org>
> *Date: *Saturday, January 13, 2018 at 12:09 PM
> *To: *"user@ctakes.apache.org" <us...@ctakes.apache.org>
> *Subject: *Re: Errors when executing AggregatePlaintextFastUMLSProcessor
> [EXTERNAL]
>
>
>
>
>
> 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 <
> Timothy.Miller@childrens.harvard.edu> 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 <Gu...@ucsf.edu>
> Sent: Friday, January 12, 2018 5:18 PM
> To: user@ctakes.apache.org
> Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor
> [EXTERNAL]
>
> anyone?
>
> On 1/8/18, 11:47 AM, "Schenk, Gundolf" <Gu...@ucsf.edu> 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
> <https://protect2.fireeye.com/url?k=29542e3c71795085.29542e3c-73f5da448e27151a&u=http://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.
>
>
>
>
>
>
Re: Errors when executing AggregatePlaintextFastUMLSProcessor
[EXTERNAL]
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
Hi James,
Many thanks for the link. It seems like the default Clinical Pipeline does not extract/annotate everything correctly. For example, in "father has hx of diabetes" the pipeline recognizes “diabetes” but does not set the subject attribute to “other” or “father”. Also, I have not seen any annotation from the drugner engine, although I understood that it is part of the default pipeline, is it not?
On my installation I do not have the lvg files that you mention. In /Users/gschenk/NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data I have this structure:
drwxr-xr-x 6 gschenk 192 Jan 5 11:28 HSqlDb
-rw-r--r--@ 1 gschenk 319 Jan 5 11:22 ReadMe.txt
drwxr-xr-x 8 gschenk 256 Jan 5 11:23 Unicode
-rw-rw-r--@ 1 gschenk 264 Jan 5 11:22 build.txt
drwxr-xr-x 7 gschenk 224 Jan 5 11:23 config
drwxr-xr-x 7 gschenk 224 Jan 5 11:23 misc
drwxr-xr-x 12 gschenk 384 Jan 5 11:23 rules
drwxr-xr-x 11 gschenk 352 Jan 16 09:54 tables
-rwxr-xr-x@ 1 gschenk 37 Apr 2 2017 version.txt
and in tables:
-rwxr-xr-x 1 gschenk 2486063 Jan 16 09:54 acronym.data
-rwxr-xr-x 1 gschenk 72583370 Jan 16 09:54 antiNorm.data
-rwxr-xr-x 1 gschenk 31753678 Jan 16 09:54 canonical.data
-rwxr-xr-x 1 gschenk 324456 Jan 16 09:54 derivation.data
-rwxr-xr-x 1 gschenk 156803364 Jan 16 09:54 fruitful.data
-rwxr-xr-x 1 gschenk 74664993 Jan 16 09:54 infl.data
-rwxr-xr-x 1 gschenk 704862 Jan 16 09:54 nominalization.data
-rwxr-xr-x 1 gschenk 83452 Jan 16 09:54 properNoun.data
-rwxr-xr-x 1 gschenk 229622 Jan 16 09:54 synonyms.data
Am I missing something (settings/resources/…)?
Cheers,
Gundolf.
From: James Masanz <ma...@gmail.com>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Wednesday, January 17, 2018 at 5:43 AM
To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
When I run the pipeline I also get 32 IdentifiedAnnotations
On windows, I see these sizes for the lvg database files
922746880 lvg2008.data
104 lvg2008.properties
1312589 lvg2008.script
This might help you get started with the meaning of the annotations:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Assertion
On Tue, Jan 16, 2018 at 2:52 PM, Schenk, Gundolf <Gu...@ucsf.edu>> wrote:
Dear Tim and James,
Many thanks for your replies. I run cTAKES it as a downloaded “binary” from the mac osx Terminal app command line. I don’t use an IDE nor did I install it via maven nor from svn. I have downloaded the resources (again) and merged the lvg and dictionary folders into the designated places. The total size in the lvg subdirectory is 807.3 MB. Is this about the correct size, James? This did not change the errors output.
I am not familiar with UIMA nor do I know much about nlp in general. I noticed that the errors only show when I load the AE xml file visa the CVD interface. Using the pipeline via cmdline no errors are shown. In both cases I get 32 identified annotations. Is this number as expected?
So, I guess the information extraction works to the extent of these annotators capability, and to go further or improve the result I would have to tweak the algorithm somehow. Agreed?
Is there documentation, that describes the meaning of the fields in the resulting xmi file? I would like to use it the xmi file as input for post-processing. Thanks!
Cheers,
Gundolf.
From: James Masanz <ma...@gmail.com>>
Reply-To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Date: Saturday, January 13, 2018 at 12:09 PM
To: "user@ctakes.apache.org<ma...@ctakes.apache.org>" <us...@ctakes.apache.org>>
Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
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 <Ti...@childrens.harvard.edu>> 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 <Gu...@ucsf.edu>>
Sent: Friday, January 12, 2018 5:18 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
anyone?
On 1/8/18, 11:47 AM, "Schenk, Gundolf" <Gu...@ucsf.edu>> 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<https://protect2.fireeye.com/url?k=29542e3c71795085.29542e3c-73f5da448e27151a&u=http://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.
Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
Posted by James Masanz <ma...@gmail.com>.
When I run the pipeline I also get 32 IdentifiedAnnotations
On windows, I see these sizes for the lvg database files
922746880 lvg2008.data
104 lvg2008.properties
1312589 lvg2008.script
This might help you get started with the meaning of the annotations:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.0+-+Assertion
On Tue, Jan 16, 2018 at 2:52 PM, Schenk, Gundolf <Gu...@ucsf.edu>
wrote:
> Dear Tim and James,
>
>
>
> Many thanks for your replies. I run cTAKES it as a downloaded “binary”
> from the mac osx Terminal app command line. I don’t use an IDE nor did I
> install it via maven nor from svn. I have downloaded the resources (again)
> and merged the lvg and dictionary folders into the designated places. The
> total size in the lvg subdirectory is 807.3 MB. Is this about the correct
> size, James? This did not change the errors output.
>
>
>
> I am not familiar with UIMA nor do I know much about nlp in general. I
> noticed that the errors only show when I load the AE xml file visa the CVD
> interface. Using the pipeline via cmdline no errors are shown. In both
> cases I get 32 identified annotations. Is this number as expected?
>
>
>
> So, I guess the information extraction works to the extent of these
> annotators capability, and to go further or improve the result I would have
> to tweak the algorithm somehow. Agreed?
>
>
>
> Is there documentation, that describes the meaning of the fields in the
> resulting xmi file? I would like to use it the xmi file as input for
> post-processing. Thanks!
>
>
>
> Cheers,
>
> Gundolf.
>
>
>
>
>
>
>
> *From: *James Masanz <ma...@gmail.com>
> *Reply-To: *"user@ctakes.apache.org" <us...@ctakes.apache.org>
> *Date: *Saturday, January 13, 2018 at 12:09 PM
> *To: *"user@ctakes.apache.org" <us...@ctakes.apache.org>
> *Subject: *Re: Errors when executing AggregatePlaintextFastUMLSProcessor
> [EXTERNAL]
>
>
>
>
>
> 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 <
> Timothy.Miller@childrens.harvard.edu> 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 <Gu...@ucsf.edu>
> Sent: Friday, January 12, 2018 5:18 PM
> To: user@ctakes.apache.org
> Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor
> [EXTERNAL]
>
> anyone?
>
> On 1/8/18, 11:47 AM, "Schenk, Gundolf" <Gu...@ucsf.edu> 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
> <https://protect2.fireeye.com/url?k=29542e3c71795085.29542e3c-73f5da448e27151a&u=http://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.
>
>
>
>
>
Re: Errors when executing AggregatePlaintextFastUMLSProcessor
[EXTERNAL]
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
Dear Tim and James,
Many thanks for your replies. I run cTAKES it as a downloaded “binary” from the mac osx Terminal app command line. I don’t use an IDE nor did I install it via maven nor from svn. I have downloaded the resources (again) and merged the lvg and dictionary folders into the designated places. The total size in the lvg subdirectory is 807.3 MB. Is this about the correct size, James? This did not change the errors output.
I am not familiar with UIMA nor do I know much about nlp in general. I noticed that the errors only show when I load the AE xml file visa the CVD interface. Using the pipeline via cmdline no errors are shown. In both cases I get 32 identified annotations. Is this number as expected?
So, I guess the information extraction works to the extent of these annotators capability, and to go further or improve the result I would have to tweak the algorithm somehow. Agreed?
Is there documentation, that describes the meaning of the fields in the resulting xmi file? I would like to use it the xmi file as input for post-processing. Thanks!
Cheers,
Gundolf.
From: James Masanz <ma...@gmail.com>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Saturday, January 13, 2018 at 12:09 PM
To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
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 <Ti...@childrens.harvard.edu>> 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 <Gu...@ucsf.edu>>
Sent: Friday, January 12, 2018 5:18 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
anyone?
On 1/8/18, 11:47 AM, "Schenk, Gundolf" <Gu...@ucsf.edu>> 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<https://protect2.fireeye.com/url?k=29542e3c71795085.29542e3c-73f5da448e27151a&u=http://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.
Re: Errors when executing AggregatePlaintextFastUMLSProcessor [EXTERNAL]
Posted by James Masanz <ma...@gmail.com>.
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 <
Timothy.Miller@childrens.harvard.edu> 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 <Gu...@ucsf.edu>
> Sent: Friday, January 12, 2018 5:18 PM
> To: user@ctakes.apache.org
> Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor
> [EXTERNAL]
>
> anyone?
>
> On 1/8/18, 11:47 AM, "Schenk, Gundolf" <Gu...@ucsf.edu> 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.
>
>
>
>
>