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 <[email protected]>
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 <[email protected]>
> *Reply-To: *"[email protected]" <[email protected]>
> *Date: *Saturday, January 13, 2018 at 12:09 PM
> *To: *"[email protected]" <[email protected]>
> *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 <
> [email protected]> wrote:
>
> I am not 100% about this terminology but I think the
> AggregatePlaintextFastUMLSProcessor.xml is just the Uima Descriptor file
> that describes the default Clinical Pipeline (in ctakes 4.0 this should be
> the default).
>
> As for the errors, it looks like it is in lvg, which probably can fail and
> still have the overall pipeline work ok. Honestly I don't know whether it
> would change the output of the dictionary module.
>
> Are you running from the binary download of cTAKES? Or did you download
> lvg with maven? If the latter you could try removing the ctakes-lvg
> directory in your maven repo (under ~/.m2/repository) and force maven to
> re-download. If the former I'm not sure what to recommend.
>
> Sorry for the delayed response.
>
> Tim
>
>
> ________________________________________
> From: Schenk, Gundolf <[email protected]>
> Sent: Friday, January 12, 2018 5:18 PM
> To: [email protected]
> Subject: Re: Errors when executing AggregatePlaintextFastUMLSProcessor
> [EXTERNAL]
>
> anyone?
>
> On 1/8/18, 11:47 AM, "Schenk, Gundolf" <[email protected]> wrote:
>
> Hi,
>
> I am new to cTAKES (and NLP) and I am trying to extract clinically
> relevant information from electronic freetext records.
> I am running the default Clinical Pipeline. But I have a few general
> questions for understanding and for some error output I am seeing.
>
> 1) what is the difference between the Clinical Pipeline and the
> processor (AggregatePlaintextFastUMLSProcessor.xml)?
>
> 2) when running AggregatePlaintextFastUMLSProcessor.xml on the
> dr_nutritious_1.txt example via the CVD gui I only see 32
> IdentifiedAnnotations but I get a couple of error messages. Could anyone
> help me get started, please?
> Here are the error/warn messages:
> […]
> 08 Jan 2018 10:06:22 INFO POSTagger - POS tagger model file:
> org/apache/ctakes/postagger/models/mayo-pos.zip
> 08 Jan 2018 10:06:23 INFO LvgCmdApiResourceImpl - Loading NLM Norm
> and Lvg with config file = /Users/gschenk/NotesProcessing/apache-ctakes-
> 4.0.0/resources/org/apache/ctakes/lvg/data/config/lvg.properties
> 08 Jan 2018 10:06:23 INFO LvgCmdApiResourceImpl - config file
> absolute path = /Users/gschenk/NotesProcessing/apache-ctakes-
> 4.0.0/resources/org/apache/ctakes/lvg/data/config/lvg.properties
> 08 Jan 2018 10:06:23 INFO LvgCmdApiResourceImpl - cwd =
> /Users/gschenk/NotesProcessing/apache-ctakes-4.0.0
> 08 Jan 2018 10:06:23 INFO LvgCmdApiResourceImpl - cd /Users/gschenk/
> NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/
> 08 Jan 2018 10:06:23 INFO ENGINE - open start - state not modified
> 08 Jan 2018 10:06:23 INFO ENGINE - dataFileCache open start
> 08 Jan 2018 10:06:23 WARN ENGINE - failed to read a byte array
> java.io.EOFException
> at org.hsqldb.persist.RAFile.read(Unknown Source)
> at org.hsqldb.persist.DataFileCache.readObject(Unknown Source)
> at org.hsqldb.persist.DataFileCache.getFromFile(Unknown Source)
> at org.hsqldb.persist.DataFileCache.get(Unknown Source)
> at org.hsqldb.persist.RowStoreAVLDisk.get(Unknown Source)
> at org.hsqldb.persist.RowStoreAVLDisk.setAccessor(Unknown Source)
> at org.hsqldb.Table.setIndexRoots(Unknown Source)
> at org.hsqldb.Table.setIndexRoots(Unknown Source)
> at org.hsqldb.StatementCommand.getResult(Unknown Source)
> at org.hsqldb.StatementCommand.execute(Unknown Source)
> at org.hsqldb.Session.executeCompiledStatement(Unknown Source)
> at org.hsqldb.scriptio.ScriptReaderText.readDDL(Unknown Source)
> at org.hsqldb.scriptio.ScriptReaderBase.readAll(Unknown Source)
> at org.hsqldb.persist.Log.processScript(Unknown Source)
> at org.hsqldb.persist.Log.open(Unknown Source)
> at org.hsqldb.persist.Logger.open(Unknown Source)
> at org.hsqldb.Database.reopen(Unknown Source)
> at org.hsqldb.Database.open(Unknown Source)
> at org.hsqldb.DatabaseManager.getDatabase(Unknown Source)
> at org.hsqldb.DatabaseManager.newSession(Unknown Source)
> at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source)
> at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source)
> at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source)
> at java.sql/java.sql.DriverManager.getConnection(
> DriverManager.java:678)
> at java.sql/java.sql.DriverManager.getConnection(
> DriverManager.java:229)
> at gov.nih.nlm.nls.lvg.Db.DbBase.OpenConnection(DbBase.java:38)
> at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.InitDbAndTrie(
> LvgCmdApi.java:1529)
> at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.Init(LvgCmdApi.java:1469)
> at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.<init>(LvgCmdApi.java:84)
> at org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(
> LvgCmdApiResourceImpl.java:89)
> at org.apache.uima.resource.impl.ResourceManager_impl.
> registerResource(ResourceManager_impl.java:628)
> at org.apache.uima.resource.impl.ResourceManager_impl.
> initializeExternalResources(ResourceManager_impl.java:464)
> at org.apache.uima.resource.Resource_ImplBase.initialize(
> Resource_ImplBase.java:193)
> at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.
> initialize(AnalysisEngineImplBase.java:157)
> at org.apache.uima.analysis_engine.impl.
> PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.
> java:131)
> at org.apache.uima.impl.AnalysisEngineFactory_impl.
> produceResource(AnalysisEngineFactory_impl.java:94)
> at org.apache.uima.impl.CompositeResourceFactory_impl.
> produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
> java:279)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(
> UIMAFramework.java:407)
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.
> setup(ASB_impl.java:256)
> at org.apache.uima.analysis_engine.impl.
> AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.
> java:429)
> at org.apache.uima.analysis_engine.impl.
> AggregateAnalysisEngine_impl.initializeAggregateAnalysisEng
> ine(AggregateAnalysisEngine_impl.java:373)
> at org.apache.uima.analysis_engine.impl.
> AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.
> java:186)
> at org.apache.uima.impl.AnalysisEngineFactory_impl.
> produceResource(AnalysisEngineFactory_impl.java:94)
> at org.apache.uima.impl.CompositeResourceFactory_impl.
> produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
> java:279)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(
> UIMAFramework.java:371)
> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.
> java:1484)
> at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(
> MainFrame.java:476)
> at org.apache.uima.tools.cvd.control.
> LoadRecentDescFileEventHandler.actionPerformed(
> LoadRecentDescFileEventHandler.java:41)
> at java.desktop/javax.swing.AbstractButton.fireActionPerformed(
> AbstractButton.java:1967)
> at java.desktop/javax.swing.AbstractButton$Handler.
> actionPerformed(AbstractButton.java:2308)
> at java.desktop/javax.swing.DefaultButtonModel.
> fireActionPerformed(DefaultButtonModel.java:405)
> at java.desktop/javax.swing.DefaultButtonModel.setPressed(
> DefaultButtonModel.java:262)
> at java.desktop/javax.swing.AbstractButton.doClick(
> AbstractButton.java:369)
> at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(
> BasicMenuItemUI.java:980)
> at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(
> AquaMenuItemUI.java:157)
> at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.
> mouseReleased(BasicMenuItemUI.java:1024)
> at java.desktop/java.awt.AWTEventMulticaster.mouseReleased(
> AWTEventMulticaster.java:297)
> at java.desktop/java.awt.Component.processMouseEvent(
> Component.java:6578)
> at java.desktop/javax.swing.JComponent.processMouseEvent(
> JComponent.java:3343)
> at java.desktop/java.awt.Component.processEvent(
> Component.java:6343)
> at java.desktop/java.awt.Container.processEvent(
> Container.java:2259)
> at java.desktop/java.awt.Component.dispatchEventImpl(
> Component.java:4961)
> at java.desktop/java.awt.Container.dispatchEventImpl(
> Container.java:2317)
> at java.desktop/java.awt.Component.dispatchEvent(
> Component.java:4793)
> at java.desktop/java.awt.LightweightDispatcher.
> retargetMouseEvent(Container.java:4904)
> at java.desktop/java.awt.LightweightDispatcher.
> processMouseEvent(Container.java:4539)
> at java.desktop/java.awt.LightweightDispatcher.
> dispatchEvent(Container.java:4480)
> at java.desktop/java.awt.Container.dispatchEventImpl(
> Container.java:2303)
> at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:
> 2758)
> at java.desktop/java.awt.Component.dispatchEvent(
> Component.java:4793)
> at java.desktop/java.awt.EventQueue.dispatchEventImpl(
> EventQueue.java:766)
> at java.desktop/java.awt.EventQueue.access$500(EventQueue.java:97)
> at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:717)
> at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:711)
> at java.base/java.security.AccessController.doPrivileged(Native
> Method)
> at java.base/java.security.ProtectionDomain$
> JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
> at java.base/java.security.ProtectionDomain$
> JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:99)
> at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:739)
> at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:737)
> at java.base/java.security.AccessController.doPrivileged(Native
> Method)
> at java.base/java.security.ProtectionDomain$
> JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
> at java.desktop/java.awt.EventQueue.dispatchEvent(
> EventQueue.java:736)
> at java.desktop/java.awt.EventDispatchThread.
> pumpOneEventForFilters(EventDispatchThread.java:199)
> at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(
> EventDispatchThread.java:124)
> at java.desktop/java.awt.EventDispatchThread.
> pumpEventsForHierarchy(EventDispatchThread.java:113)
> at java.desktop/java.awt.EventDispatchThread.pumpEvents(
> EventDispatchThread.java:109)
> at java.desktop/java.awt.EventDispatchThread.pumpEvents(
> EventDispatchThread.java:101)
> at java.desktop/java.awt.EventDispatchThread.run(
> EventDispatchThread.java:90)
> 08 Jan 2018 10:06:23 FATAL ENGINE - DataFileCache.readObject 202240
> java.io.EOFException
> at org.hsqldb.persist.RAFile.read(Unknown Source)
> at org.hsqldb.persist.DataFileCache.readObject(Unknown Source)
> at org.hsqldb.persist.DataFileCache.getFromFile(Unknown Source)
> at org.hsqldb.persist.DataFileCache.get(Unknown Source)
> at org.hsqldb.persist.RowStoreAVLDisk.get(Unknown Source)
> at org.hsqldb.persist.RowStoreAVLDisk.setAccessor(Unknown Source)
> at org.hsqldb.Table.setIndexRoots(Unknown Source)
> at org.hsqldb.Table.setIndexRoots(Unknown Source)
> at org.hsqldb.StatementCommand.getResult(Unknown Source)
> at org.hsqldb.StatementCommand.execute(Unknown Source)
> at org.hsqldb.Session.executeCompiledStatement(Unknown Source)
> at org.hsqldb.scriptio.ScriptReaderText.readDDL(Unknown Source)
> at org.hsqldb.scriptio.ScriptReaderBase.readAll(Unknown Source)
> at org.hsqldb.persist.Log.processScript(Unknown Source)
> at org.hsqldb.persist.Log.open(Unknown Source)
> at org.hsqldb.persist.Logger.open(Unknown Source)
> at org.hsqldb.Database.reopen(Unknown Source)
> at org.hsqldb.Database.open(Unknown Source)
> at org.hsqldb.DatabaseManager.getDatabase(Unknown Source)
> at org.hsqldb.DatabaseManager.newSession(Unknown Source)
> at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source)
> at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source)
> at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source)
> at java.sql/java.sql.DriverManager.getConnection(
> DriverManager.java:678)
> at java.sql/java.sql.DriverManager.getConnection(
> DriverManager.java:229)
> at gov.nih.nlm.nls.lvg.Db.DbBase.OpenConnection(DbBase.java:38)
> at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.InitDbAndTrie(
> LvgCmdApi.java:1529)
> at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.Init(LvgCmdApi.java:1469)
> at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.<init>(LvgCmdApi.java:84)
> at org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(
> LvgCmdApiResourceImpl.java:89)
> at org.apache.uima.resource.impl.ResourceManager_impl.
> registerResource(ResourceManager_impl.java:628)
> at org.apache.uima.resource.impl.ResourceManager_impl.
> initializeExternalResources(ResourceManager_impl.java:464)
> at org.apache.uima.resource.Resource_ImplBase.initialize(
> Resource_ImplBase.java:193)
> at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.
> initialize(AnalysisEngineImplBase.java:157)
> at org.apache.uima.analysis_engine.impl.
> PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.
> java:131)
> at org.apache.uima.impl.AnalysisEngineFactory_impl.
> produceResource(AnalysisEngineFactory_impl.java:94)
> at org.apache.uima.impl.CompositeResourceFactory_impl.
> produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
> java:279)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(
> UIMAFramework.java:407)
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.
> setup(ASB_impl.java:256)
> at org.apache.uima.analysis_engine.impl.
> AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.
> java:429)
> at org.apache.uima.analysis_engine.impl.
> AggregateAnalysisEngine_impl.initializeAggregateAnalysisEng
> ine(AggregateAnalysisEngine_impl.java:373)
> at org.apache.uima.analysis_engine.impl.
> AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.
> java:186)
> at org.apache.uima.impl.AnalysisEngineFactory_impl.
> produceResource(AnalysisEngineFactory_impl.java:94)
> at org.apache.uima.impl.CompositeResourceFactory_impl.
> produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
> java:279)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(
> UIMAFramework.java:371)
> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.
> java:1484)
> at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(
> MainFrame.java:476)
> at org.apache.uima.tools.cvd.control.
> LoadRecentDescFileEventHandler.actionPerformed(
> LoadRecentDescFileEventHandler.java:41)
> at java.desktop/javax.swing.AbstractButton.fireActionPerformed(
> AbstractButton.java:1967)
> at java.desktop/javax.swing.AbstractButton$Handler.
> actionPerformed(AbstractButton.java:2308)
> at java.desktop/javax.swing.DefaultButtonModel.
> fireActionPerformed(DefaultButtonModel.java:405)
> at java.desktop/javax.swing.DefaultButtonModel.setPressed(
> DefaultButtonModel.java:262)
> at java.desktop/javax.swing.AbstractButton.doClick(
> AbstractButton.java:369)
> at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(
> BasicMenuItemUI.java:980)
> at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(
> AquaMenuItemUI.java:157)
> at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.
> mouseReleased(BasicMenuItemUI.java:1024)
> at java.desktop/java.awt.AWTEventMulticaster.mouseReleased(
> AWTEventMulticaster.java:297)
> at java.desktop/java.awt.Component.processMouseEvent(
> Component.java:6578)
> at java.desktop/javax.swing.JComponent.processMouseEvent(
> JComponent.java:3343)
> at java.desktop/java.awt.Component.processEvent(
> Component.java:6343)
> at java.desktop/java.awt.Container.processEvent(
> Container.java:2259)
> at java.desktop/java.awt.Component.dispatchEventImpl(
> Component.java:4961)
> at java.desktop/java.awt.Container.dispatchEventImpl(
> Container.java:2317)
> at java.desktop/java.awt.Component.dispatchEvent(
> Component.java:4793)
> at java.desktop/java.awt.LightweightDispatcher.
> retargetMouseEvent(Container.java:4904)
> at java.desktop/java.awt.LightweightDispatcher.
> processMouseEvent(Container.java:4539)
> at java.desktop/java.awt.LightweightDispatcher.
> dispatchEvent(Container.java:4480)
> at java.desktop/java.awt.Container.dispatchEventImpl(
> Container.java:2303)
> at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:
> 2758)
> at java.desktop/java.awt.Component.dispatchEvent(
> Component.java:4793)
> at java.desktop/java.awt.EventQueue.dispatchEventImpl(
> EventQueue.java:766)
> at java.desktop/java.awt.EventQueue.access$500(EventQueue.java:97)
> at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:717)
> at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:711)
> at java.base/java.security.AccessController.doPrivileged(Native
> Method)
> at java.base/java.security.ProtectionDomain$
> JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
> at java.base/java.security.ProtectionDomain$
> JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:99)
> at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:739)
> at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:737)
> at java.base/java.security.AccessController.doPrivileged(Native
> Method)
> at java.base/java.security.ProtectionDomain$
> JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
> at java.desktop/java.awt.EventQueue.dispatchEvent(
> EventQueue.java:736)
> at java.desktop/java.awt.EventDispatchThread.
> pumpOneEventForFilters(EventDispatchThread.java:199)
> at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(
> EventDispatchThread.java:124)
> at java.desktop/java.awt.EventDispatchThread.
> pumpEventsForHierarchy(EventDispatchThread.java:113)
> at java.desktop/java.awt.EventDispatchThread.pumpEvents(
> EventDispatchThread.java:109)
> at java.desktop/java.awt.EventDispatchThread.pumpEvents(
> EventDispatchThread.java:101)
> at java.desktop/java.awt.EventDispatchThread.run(
> EventDispatchThread.java:90)
> 08 Jan 2018 10:06:23 FATAL ENGINE - /Users/gschenk/
> NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/
> ctakes/lvg/data/HSqlDb/lvg2008.data getFromFile failed 202240
> org.hsqldb.HsqlException: java.io.EOFException
> at org.hsqldb.error.Error.error(Unknown Source)
> at org.hsqldb.persist.DataFileCache.readObject(Unknown Source)
> at org.hsqldb.persist.DataFileCache.getFromFile(Unknown Source)
> at org.hsqldb.persist.DataFileCache.get(Unknown Source)
> at org.hsqldb.persist.RowStoreAVLDisk.get(Unknown Source)
> at org.hsqldb.persist.RowStoreAVLDisk.setAccessor(Unknown Source)
> at org.hsqldb.Table.setIndexRoots(Unknown Source)
> at org.hsqldb.Table.setIndexRoots(Unknown Source)
> at org.hsqldb.StatementCommand.getResult(Unknown Source)
> at org.hsqldb.StatementCommand.execute(Unknown Source)
> at org.hsqldb.Session.executeCompiledStatement(Unknown Source)
> at org.hsqldb.scriptio.ScriptReaderText.readDDL(Unknown Source)
> at org.hsqldb.scriptio.ScriptReaderBase.readAll(Unknown Source)
> at org.hsqldb.persist.Log.processScript(Unknown Source)
> at org.hsqldb.persist.Log.open(Unknown Source)
> at org.hsqldb.persist.Logger.open(Unknown Source)
> at org.hsqldb.Database.reopen(Unknown Source)
> at org.hsqldb.Database.open(Unknown Source)
> at org.hsqldb.DatabaseManager.getDatabase(Unknown Source)
> at org.hsqldb.DatabaseManager.newSession(Unknown Source)
> at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source)
> at org.hsqldb.jdbc.JDBCDriver.getConnection(Unknown Source)
> at org.hsqldb.jdbc.JDBCDriver.connect(Unknown Source)
> at java.sql/java.sql.DriverManager.getConnection(
> DriverManager.java:678)
> at java.sql/java.sql.DriverManager.getConnection(
> DriverManager.java:229)
> at gov.nih.nlm.nls.lvg.Db.DbBase.OpenConnection(DbBase.java:38)
> at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.InitDbAndTrie(
> LvgCmdApi.java:1529)
> at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.Init(LvgCmdApi.java:1469)
> at gov.nih.nlm.nls.lvg.Api.LvgCmdApi.<init>(LvgCmdApi.java:84)
> at org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl.load(
> LvgCmdApiResourceImpl.java:89)
> at org.apache.uima.resource.impl.ResourceManager_impl.
> registerResource(ResourceManager_impl.java:628)
> at org.apache.uima.resource.impl.ResourceManager_impl.
> initializeExternalResources(ResourceManager_impl.java:464)
> at org.apache.uima.resource.Resource_ImplBase.initialize(
> Resource_ImplBase.java:193)
> at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.
> initialize(AnalysisEngineImplBase.java:157)
> at org.apache.uima.analysis_engine.impl.
> PrimitiveAnalysisEngine_impl.initialize(PrimitiveAnalysisEngine_impl.
> java:131)
> at org.apache.uima.impl.AnalysisEngineFactory_impl.
> produceResource(AnalysisEngineFactory_impl.java:94)
> at org.apache.uima.impl.CompositeResourceFactory_impl.
> produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
> java:279)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(
> UIMAFramework.java:407)
> at org.apache.uima.analysis_engine.asb.impl.ASB_impl.
> setup(ASB_impl.java:256)
> at org.apache.uima.analysis_engine.impl.
> AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.
> java:429)
> at org.apache.uima.analysis_engine.impl.
> AggregateAnalysisEngine_impl.initializeAggregateAnalysisEng
> ine(AggregateAnalysisEngine_impl.java:373)
> at org.apache.uima.analysis_engine.impl.
> AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.
> java:186)
> at org.apache.uima.impl.AnalysisEngineFactory_impl.
> produceResource(AnalysisEngineFactory_impl.java:94)
> at org.apache.uima.impl.CompositeResourceFactory_impl.
> produceResource(CompositeResourceFactory_impl.java:62)
> at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.
> java:279)
> at org.apache.uima.UIMAFramework.produceAnalysisEngine(
> UIMAFramework.java:371)
> at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.
> java:1484)
> at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(
> MainFrame.java:476)
> at org.apache.uima.tools.cvd.control.
> LoadRecentDescFileEventHandler.actionPerformed(
> LoadRecentDescFileEventHandler.java:41)
> at java.desktop/javax.swing.AbstractButton.fireActionPerformed(
> AbstractButton.java:1967)
> at java.desktop/javax.swing.AbstractButton$Handler.
> actionPerformed(AbstractButton.java:2308)
> at java.desktop/javax.swing.DefaultButtonModel.
> fireActionPerformed(DefaultButtonModel.java:405)
> at java.desktop/javax.swing.DefaultButtonModel.setPressed(
> DefaultButtonModel.java:262)
> at java.desktop/javax.swing.AbstractButton.doClick(
> AbstractButton.java:369)
> at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI.doClick(
> BasicMenuItemUI.java:980)
> at java.desktop/com.apple.laf.AquaMenuItemUI.doClick(
> AquaMenuItemUI.java:157)
> at java.desktop/javax.swing.plaf.basic.BasicMenuItemUI$Handler.
> mouseReleased(BasicMenuItemUI.java:1024)
> at java.desktop/java.awt.AWTEventMulticaster.mouseReleased(
> AWTEventMulticaster.java:297)
> at java.desktop/java.awt.Component.processMouseEvent(
> Component.java:6578)
> at java.desktop/javax.swing.JComponent.processMouseEvent(
> JComponent.java:3343)
> at java.desktop/java.awt.Component.processEvent(
> Component.java:6343)
> at java.desktop/java.awt.Container.processEvent(
> Container.java:2259)
> at java.desktop/java.awt.Component.dispatchEventImpl(
> Component.java:4961)
> at java.desktop/java.awt.Container.dispatchEventImpl(
> Container.java:2317)
> at java.desktop/java.awt.Component.dispatchEvent(
> Component.java:4793)
> at java.desktop/java.awt.LightweightDispatcher.
> retargetMouseEvent(Container.java:4904)
> at java.desktop/java.awt.LightweightDispatcher.
> processMouseEvent(Container.java:4539)
> at java.desktop/java.awt.LightweightDispatcher.
> dispatchEvent(Container.java:4480)
> at java.desktop/java.awt.Container.dispatchEventImpl(
> Container.java:2303)
> at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:
> 2758)
> at java.desktop/java.awt.Component.dispatchEvent(
> Component.java:4793)
> at java.desktop/java.awt.EventQueue.dispatchEventImpl(
> EventQueue.java:766)
> at java.desktop/java.awt.EventQueue.access$500(EventQueue.java:97)
> at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:717)
> at java.desktop/java.awt.EventQueue$3.run(EventQueue.java:711)
> at java.base/java.security.AccessController.doPrivileged(Native
> Method)
> at java.base/java.security.ProtectionDomain$
> JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
> at java.base/java.security.ProtectionDomain$
> JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:99)
> at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:739)
> at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:737)
> at java.base/java.security.AccessController.doPrivileged(Native
> Method)
> at java.base/java.security.ProtectionDomain$
> JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:89)
> at java.desktop/java.awt.EventQueue.dispatchEvent(
> EventQueue.java:736)
> at java.desktop/java.awt.EventDispatchThread.
> pumpOneEventForFilters(EventDispatchThread.java:199)
> at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(
> EventDispatchThread.java:124)
> at java.desktop/java.awt.EventDispatchThread.
> pumpEventsForHierarchy(EventDispatchThread.java:113)
> at java.desktop/java.awt.EventDispatchThread.pumpEvents(
> EventDispatchThread.java:109)
> at java.desktop/java.awt.EventDispatchThread.pumpEvents(
> EventDispatchThread.java:101)
> at java.desktop/java.awt.EventDispatchThread.run(
> EventDispatchThread.java:90)
> Caused by: java.io.EOFException
> at org.hsqldb.persist.RAFile.read(Unknown Source)
> ... 89 more
> 08 Jan 2018 10:06:23 WARN ENGINE - java.io.EOFException in statement
> [SET TABLE PUBLIC.LEXSYNONYM INDEX '202240 202240 0 0 5056']
> org.hsqldb.HsqlException: java.io.EOFException
> at org.hsqldb.error.Error.error(Unknown Source)
> […]
> ... 89 more
> 08 Jan 2018 10:06:23 WARN ENGINE - Script processing failure
> org.hsqldb.HsqlException: error in script file line: 49 /Users/gschenk/
> NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008
> java.io.EOFException in statement [SET TABLE PUBLIC.LEXSYNONYM INDEX
> '202240 202240 0 0 5056']
> at org.hsqldb.error.Error.error(Unknown Source)
> […]
> ... 79 more
> Caused by: java.io.EOFException
> at org.hsqldb.persist.RAFile.read(Unknown Source)
> ... 89 more
> 08 Jan 2018 10:06:23 INFO ENGINE - Database closed
> 08 Jan 2018 10:06:23 FATAL ENGINE - could not reopen database
> org.hsqldb.HsqlException: error in script file line: 49 /Users/gschenk/
> NotesProcessing/apache-ctakes-4.0.0/resources/org/apache/ctakes/lvg/data/HSqlDb/lvg2008
> java.io.EOFException in statement [SET TABLE PUBLIC.LEXSYNONYM INDEX
> '202240 202240 0 0 5056']
> […]
> Caused by: org.hsqldb.HsqlException: java.io.EOFException
> at org.hsqldb.error.Error.error(Unknown Source)
> at org.hsqldb.persist.DataFileCache.readObject(Unknown Source)
> at org.hsqldb.persist.DataFileCache.getFromFile(Unknown Source)
> at org.hsqldb.persist.DataFileCache.get(Unknown Source)
> at org.hsqldb.persist.RowStoreAVLDisk.get(Unknown Source)
> at org.hsqldb.persist.RowStoreAVLDisk.setAccessor(Unknown Source)
> at org.hsqldb.Table.setIndexRoots(Unknown Source)
> at org.hsqldb.Table.setIndexRoots(Unknown Source)
> at org.hsqldb.StatementCommand.getResult(Unknown Source)
> at org.hsqldb.StatementCommand.execute(Unknown Source)
> at org.hsqldb.Session.executeCompiledStatement(Unknown Source)
> ... 79 more
> Caused by: java.io.EOFException
> at org.hsqldb.persist.RAFile.read(Unknown Source)
> ... 89 more
> 08 Jan 2018 10:06:23 INFO ENGINE - open start - state not modified
> 08 Jan 2018 10:06:23 INFO ENGINE - dataFileCache open start
> 08 Jan 2018 10:06:27 FATAL ENGINE - DataFileCache.readObject 202240
> java.lang.OutOfMemoryError: Java heap space
> at org.hsqldb.rowio.RowInputBase.resetRow(Unknown Source)
> […]
> ... 80 more
> Caused by: java.io.EOFException
> at org.hsqldb.persist.RAFile.read(Unknown Source)
> ... 90 more
> 08 Jan 2018 10:06:31 INFO LvgCmdApiResourceImpl - cd /Users/gschenk/
> NotesProcessing/apache-ctakes-4.0.0
> 08 Jan 2018 10:06:31 INFO DrugMentionAnnotator - Finite state
> machines loaded.
> 08 Jan 2018 10:06:33 INFO ClearNLPDependencyParserAE - using Morphy
> analysis? true
> Loading configuration.
> Loading feature templates.
> Loading lexica.
> Loading model:
> ............................................................
> ............................
> Loading configuration.
> Loading feature templates.
> Loading model:
> .
> Loading configuration.
> Loading feature templates.
> Loading lexica.
> Loading model:
> ...
> […]
> Loading configuration.
> Loading feature templates.
> Loading lexica.
> Loading model:
> ................................
> Loading model:
> .............................
> 08 Jan 2018 10:06:39 INFO ConstituencyParser - Initializing parser...
> 08 Jan 2018 10:06:57 INFO SentenceDetector - Starting processing.
> 08 Jan 2018 10:06:57 INFO TokenizerAnnotatorPTB - process(JCas) in
> org.apache.ctakes.core.ae
> <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.
>
>
>
>
>
