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 <gundolf.sch...@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 <masanz.ja...@gmail.com> > *Reply-To: *"user@ctakes.apache.org" <user@ctakes.apache.org> > *Date: *Wednesday, January 17, 2018 at 5:43 AM > *To: *"user@ctakes.apache.org" <user@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 <gundolf.sch...@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 <masanz.ja...@gmail.com> > *Reply-To: *"user@ctakes.apache.org" <user@ctakes.apache.org> > *Date: *Saturday, January 13, 2018 at 12:09 PM > *To: *"user@ctakes.apache.org" <user@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.mil...@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 <gundolf.sch...@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" <gundolf.sch...@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. > > > > > >
