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From Justin Zhang <justinzhang...@gmail.com>
Subject smoking status - ctakes-3.2.2 error
Date Mon, 22 Jun 2015 19:11:42 GMT
Hi All,

Any one have run "smoking status pipeline" successfully.
I am using Mac machine to run ctakes version3.2.2

1. Start from terminal to run $CTAKES_HOME/bin/runctakesCVD.sh
      cd $CTAKES_HOME

   java -Dctakes.umlsuser=userid -Dctakes.umlspw=password -cp
$CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/*
-Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g
org.apache.uima.tools.cvd.CVD "$@"

2. Open text file (xml file) I loaded smoking training set (xml format)
requested from i2b2 https://www.i2b2.org/NLP/DataSets/Download.php

3. Load AE
ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE_CDA.xml

   I got the following error "analysis_engine.SentenceAdjuster" was found
in the class path or data path

Caused by: org.apache.uima.util.InvalidXMLException: An import could not be
resolved.  No .xml file with name "analysis_engine.SentenceAdjuster" was
found in the class path or data path. (Descriptor:
file:/Users/justin/vdec_work/ctakes/apache-ctakes-3.2.2/desc/ctakes-smoking-status/desc/analysis_engine/SimulatedProdSmokingTAE_CDA.xml)
at
org.apache.uima.resource.metadata.impl.Import_impl.findAbsoluteUrl(Import_impl.java:107)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:798)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:765)
at
org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngineDescription_impl.java:193)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:147)
... 47 more

4. I added class path in runctakesCVD.sh

    java -Dctakes.umlsuser=userid -Dctakes.umlspw=password -cp
$CTAKES_HOME/desc/ctakes-smoking-status/desc/::$CTAKES_HOME/desc/:$CTAKES_HOME/resources/:$CTAKES_HOME/lib/*
-Dlog4j.configuration=file:$CTAKES_HOME/config/log4j.xml -Xms512M -Xmx3g
org.apache.uima.tools.cvd.CVD "$@"

5. Open same xml file and load the same *CDA.xml annotator engine.

    "SentenceAdjuster" error gone, but got the other error "URI is not
hierarchical"

org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: URI is
not hierarchical
java.lang.IllegalArgumentException: URI is not hierarchical
at java.io.File.<init>(File.java:418)
at
org.apache.ctakes.core.resource.FileResourceImpl.load(FileResourceImpl.java:44)
at
org.apache.uima.resource.impl.ResourceManager_impl.registerResource(ResourceManager_impl.java:603)
at
org.apache.uima.resource.impl.ResourceManager_impl.initializeExternalResources(ResourceManager_impl.java:442)
at
org.apache.uima.resource.Resource_ImplBase.initialize(Resource_ImplBase.java:153)
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:123)
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:269)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:387)
at
org.apache.uima.analysis_engine.asb.impl.ASB_impl.setup(ASB_impl.java:254)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initASB(AggregateAnalysisEngine_impl.java:431)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initializeAggregateAnalysisEngine(AggregateAnalysisEngine_impl.java:375)
at
org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:185)
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:269)
at org.apache.uima.UIMAFramework.produceResource(UIMAFramework.java:314)
at
org.apache.uima.UIMAFramework.produceAnalysisEngine(UIMAFramework.java:425)
at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1486)
at org.apache.uima.tools.cvd.MainFrame.loadAEDescriptor(MainFrame.java:476)
at
org.apache.uima.tools.cvd.control.AnnotatorOpenEventHandler.actionPerformed(AnnotatorOpenEventHandler.java:52)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)
at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:157)
at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)
at java.awt.Component.processMouseEvent(Component.java:6525)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6290)
at java.awt.Container.processEvent(Container.java:2234)
at java.awt.Component.dispatchEventImpl(Component.java:4881)
at java.awt.Container.dispatchEventImpl(Container.java:2292)
at java.awt.Component.dispatchEvent(Component.java:4703)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
at java.awt.Container.dispatchEventImpl(Container.java:2278)
at java.awt.Window.dispatchEventImpl(Window.java:2750)
at java.awt.Component.dispatchEvent(Component.java:4703)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

6. I also tried plained text Annotator "SimulatedProdSmokingTAE.xml", and
got the same error.

Any one could help!

Thanks a lot,


-- 
Justin

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