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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: smoking status - ctakes-3.2.2 error
Date Tue, 23 Jun 2015 13:56:37 GMT
Justin,
There’s an outstanding Jira item to update the smoking status config[1].
In the interim, you may have to use absolute paths for all of the file references in the smoking
status descriptor xml’s.

--Pei

[1] https://issues.apache.org/jira/browse/CTAKES-363

From: Justin Zhang [mailto:justinzhang.xl@gmail.com]
Sent: Monday, June 22, 2015 3:12 PM
To: user@ctakes.apache.org
Subject: smoking status - ctakes-3.2.2 error

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<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.i2b2.org_NLP_DataSets_Download.php&d=BQMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=eX43uMBIHoGxaLgv5sccMzG8lXanT7JVR2habAts79E&s=bKfvQqf4kjYnVZAKI06ZZZQuitijyp0h4Rkonue52ic&e=>

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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