Regarding "really only doing pretty basic syntax level analyses" from http://mail-archives.apache.org/mod_mbox/incubator-ctakes-user/201212.mbox/browser
I think Pete got that impression because the "toy" dictionary included with cTAKES is so small he probably didn't happen to select any words that are in that dictionary. I will update the readme to include a sample sentence that will show NEs being found. The "toy" dictionary included with cTAKES includes the words aspirin, knee, and pain. I will create a JIRA issue now and add the sentence "Patient took aspirin for knee pain" -- James > -----Original Message----- > From: [email protected] > [mailto:ctakes-user-return-42- > [email protected]] On Behalf Of Chen, Pei > Sent: Monday, December 03, 2012 10:09 AM > To: Peter Szolovits > Cc: [email protected] > Subject: RE: Usability issues > > [cc'd ctakes-user@] > Hi Pete, > Thanks for the feedback. > > > 1. Using the CVD engine as suggested in the readme file, I find that > > the interface panel at the bottom left does not get a vertical scroll > > bar even if it expands to have more rows than are visible in the > > panel. Although one can navigate to off-screen entries using the > arrow keys, one can't see the entry. > We'll take a closer look at this. We are reusing UIMA's CVD/CPE; but > this issue may not be a huge issue once we have a ctakes-gui (currently > in sandbox). > > > 2. This level of analysis is really only doing pretty basic syntax > > level analyses. I assume that the UMLS resources also mentioned in > the readme are needed. > > When I try loading the AggregatePlaintextUMLSProcessor.xml, the > > options under the Run menu remain as Run AggregatePlaintextProcessor, > > not AggregatePlaintextUMLSProcessor. > Yes, if you plan to use the UMLS resources (ctakes-resources-3.0.0.zip) > from https://sourceforge.net/projects/ctakesresources/files, you'll need > to download the resources zip file and unpack/add it to the resources > folder. [For licenses reasons.] > > > 3. The other question from the readme is that I'm supposed to provide > > a UMLS username and password. Are there the ones I use to access UMLS > > at NLM/UTS, or something more local. Does cTakes actually > > authenticate against the UMLS servers? If not, then what am I > supposed to use for these? > Correct, you'll need your NLM/UTS username and password. During init of > resources, cTAKES will perform a call to the NLM license validation web > service (as agreed with the NLM). > One can pass the variables (ctakes.umlsuser and ctakes.umlspw) as > JAVA_OPTS, export env variable, or set in the XML file in the ctakes- > dictionary-lookup file. > > > 4. I just tried to increase memory by 4x (-Xms2048M -Xmx4096M) and > > then tried to re-run runctakesCVD.sh. This time, I get a popup in > > Java when I try to load the AggregatePlaintextUMLSProcessor.xml > > saying that there was a resource initialization error, and I should > > take a look at the log file. Alas, I can't find the log file. > The log file if using the CVD is: found in Tools -> View Log file I'll > open a Jira item for the mem setting > (https://issues.apache.org/jira/browse/CTAKES-112). > I *think* this happens when you try to load multiple AE's in the same > CVD (not sure if the CVD cleans up all of the resources.) I think the > temp work around is to close the JVM process and start a new one when > using a new AE (or aggregate AE). > > --Pei > > > -----Original Message----- > > From: Peter Szolovits [mailto:[email protected]] > > Sent: Sunday, December 02, 2012 10:22 AM > > To: Chen, Pei > > Subject: Usability issues > > > > Pei, I'm starting to play with the 3.0 version of UIMA that you > pointed me at. > > I've managed to get it up and running, but have a couple of questions: > > > > 1. Using the CVD engine as suggested in the readme file, I find that > > the interface panel at the bottom left does not get a vertical scroll > > bar even if it expands to have more rows than are visible in the > > panel. Although one can navigate to off-screen entries using the > arrow keys, one can't see the entry. > > > > 2. This level of analysis is really only doing pretty basic syntax > > level analyses. I assume that the UMLS resources also mentioned in > the readme are needed. > > When I try loading the AggregatePlaintextUMLSProcessor.xml, the > > options under the Run menu remain as Run AggregatePlaintextProcessor, > > not AggregatePlaintextUMLSProcessor. However, I do now notice that > > the Java process in loading this resource gives an out of memory error > > (appended below). I'll try with a larger memory footprint. > > > > 3. The other question from the readme is that I'm supposed to provide > > a UMLS username and password. Are there the ones I use to access UMLS > > at NLM/UTS, or something more local. Does cTakes actually > > authenticate against the UMLS servers? If not, then what am I > supposed to use for these? > > > > Thanks. --Pete > > > > Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: > > Java heap space > > at clear.model.OneVsAllModel.loadAux(OneVsAllModel.java:98) > > at clear.model.OneVsAllModel.load(OneVsAllModel.java:88) > > at clear.model.AbstractModel.<init>(AbstractModel.java:58) > > at > > clear.model.AbstractMultiModel.<init>(AbstractMultiModel.java:51) > > at clear.model.OneVsAllModel.<init>(OneVsAllModel.java:56) > > at clear.decode.OneVsAllDecoder.<init>(OneVsAllDecoder.java:52) > > at > > org.apache.ctakes.dependency.parser.ae.ClearParserUtil.createParser(Cl > > ear > > ParserUtil.java:97) > > at > > org.apache.ctakes.dependency.parser.ae.ClearParserDependencyParserAE.i > > nitialize(ClearParserDependencyParserAE.java:143) > > at > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init > > ialize > > AnalysisComponent(PrimitiveAnalysisEngine_impl.java:250) > > at > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.init > > ialize > > (PrimitiveAnalysisEngine_impl.java:156) > > at > > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys > > i > > sEngineFactory_impl.java:94) > > at > > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C > > ompositeResourceFactory_impl.java:62) > > at > > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java: > > 269) > > at > > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework > > .java:387) > > at > > org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java: > > 25 > > 4) > > at > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init > > AS > > B(AggregateAnalysisEngine_impl.java:431) > > at > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init > > ializ > > eAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375) > > at > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.init > > ializ > > e(AggregateAnalysisEngine_impl.java:185) > > at > > org.apache.uima.impl.AnalysisEngineFactory_impl.produceResource(Analys > > i > > sEngineFactory_impl.java:94) > > at > > org.apache.uima.impl.CompositeResourceFactory_impl.produceResource(C > > ompositeResourceFactory_impl.java:62) > > at > > org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java: > > 269) > > at > > org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework > > .java:354) > > at > > org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1484) > > at > > org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:47 > > 7) > > at > > org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerf > > o > > rmed(AnnotatorOpenEventHandler.java:52) > > at > > > javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018) > > at > > javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java > > :2 > > 341) > > at > > javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel. > > java:402) > > at > > javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) > > at javax.swing.AbstractButton.doClick(AbstractButton.java:376) > > at > > > javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) > > at > > com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157) > > Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException > > at > > org.apache.uima.tools.cvd.control.IndexTreeSelectionListener.valueChan > > ge > > d(IndexTreeSelectionListener.java:70) > > at javax.swing.JTree.fireValueChanged(JTree.java:2919) > > at > > > javax.swing.JTree$TreeSelectionRedirector.valueChanged(JTree.java:3378) > > at > > javax.swing.tree.DefaultTreeSelectionModel.fireValueChanged(DefaultTre > > e > > SelectionModel.java:634) > > at > > javax.swing.tree.DefaultTreeSelectionModel.notifyPathChange(DefaultTre > > e > > SelectionModel.java:1092) > > at > > javax.swing.tree.DefaultTreeSelectionModel.setSelectionPaths(DefaultTr > > ee > > SelectionModel.java:293) > > at > > javax.swing.tree.DefaultTreeSelectionModel.setSelectionPath(DefaultTre > > eS > > electionModel.java:187) > > at javax.swing.JTree.setSelectionPath(JTree.java:1631) > > at > > javax.swing.plaf.basic.BasicTreeUI.selectPathForEvent(BasicTreeUI.java > > :2373 > > ) > > at > > javax.swing.plaf.basic.BasicTreeUI$Handler.handleSelection(BasicTreeUI > > .jav > > a:3589) > > at > > > javax.swing.plaf.basic.BasicTreeUI$Handler.mousePressed(BasicTreeUI.java > : > > 3528) > > at > > java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:27 > > 9) > > at java.awt.Component.processMouseEvent(Component.java:6502) > > at > > javax.swing.JComponent.processMouseEvent(JComponent.java:3321) > > at java.awt.Component.processEvent(Component.java:6270) > > at java.awt.Container.processEvent(Container.java:2229) > > at java.awt.Component.dispatchEventImpl(Component.java:4861) > > at java.awt.Container.dispatchEventImpl(Container.java:2287) > > at java.awt.Component.dispatchEvent(Component.java:4687) > > at > > java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832) > > at > > java.awt.LightweightDispatcher.processMouseEvent(Container.java:4489) > > at > > java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422) > > at java.awt.Container.dispatchEventImpl(Container.java:2273) > > at java.awt.Window.dispatchEventImpl(Window.java:2719) > > at java.awt.Component.dispatchEvent(Component.java:4687) > > at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:703) > > at java.awt.EventQueue.access$000(EventQueue.java:102) > > at java.awt.EventQueue$3.run(EventQueue.java:662) > > at java.awt.EventQueue$3.run(EventQueue.java:660) > > at java.security.AccessController.doPrivileged(Native Method) > > at > > java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDom > > ain > > .java:76) > > at > > java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDom > > ain > > .java:87) > > at java.awt.EventQueue$4.run(EventQueue.java:676) > > at java.awt.EventQueue$4.run(EventQueue.java:674) > > at java.security.AccessController.doPrivileged(Native Method) > > at > > java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDom > > ain > > .java:76) > > at java.awt.EventQueue.dispatchEvent(EventQueue.java:673) > > at > > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre > > ad.java:244) > > at > > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.j > > a > > va:163) > > at > > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre > > ad.java:151) > > at > > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:147) > > at > > java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:139) > > at java.awt.EventDispatchThread.run(EventDispatchThread.java:97) > >
