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From "James Joseph Masanz (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-413) org.apache.uima.tools.cvd.MainFrame.handleException(526):
Date Mon, 06 Mar 2017 03:22:32 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-413?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15896688#comment-15896688
] 

James Joseph Masanz commented on CTAKES-413:
--------------------------------------------

Several things going on here:
- if you want to use a CPE descriptor like DrugNER_PlainText_CPE.xml, you would need to use
runctakesCPE.bat rather than runctakesCVD.bat 
- However, DrugNER_PlainText_CPE.xml refers to ../analysis_engine/DrugAggregateCDAProcessor.xml,
but that descriptor is not part of cTAKES 3.2.2.
- To use the CPE GUI to see the output of the drug ner pipeline when run against a number
of plaintext files, you could create your own CPE descriptor using these steps
    Use runctakesCPE.bat to start the CPE GUI (the Collection Processing Engine Configurator
window)
    For Collection Reader, you can leave the value that gets filled in (fully qualified FilesInDirectoryCollectionReader.xml)
    For Input Directory, use the Browse button to locate the directory containing your input
files
    In the central pane (Analysis Engines) use the Add button to navigate to desc\ctakes-clinical-pipeline\desc\analysis_engine\AggregatePlaintextFastUMLSProcessor.xml
    In the bottom pane (CAS Consumers) use the Browse button to set  the output directory
    Click the Play button at the bottom

> org.apache.uima.tools.cvd.MainFrame.handleException(526):
> ---------------------------------------------------------
>
>                 Key: CTAKES-413
>                 URL: https://issues.apache.org/jira/browse/CTAKES-413
>             Project: cTAKES
>          Issue Type: Bug
>          Components: ctakes-drug-ner
>    Affects Versions: 3.2.2
>         Environment: java 1.7.0_80  apache uima 2.9.0
>            Reporter: yongliu
>             Fix For: 3.2.2
>
>   Original Estimate: 72h
>  Remaining Estimate: 72h
>
> Using runctakesCVD.bat , with DrugNER_PlainText_CPE.xml:
> F:\ctakes\desc\ctakes-drug-ner\desc\collection_processing_engine
> 02:30:17.619 - 14: org.apache.uima.tools.cvd.MainFrame.handleException(526): ����:
An object of class org.apache.uima.resource.ResourceSpecifier was requested, but the XML input
contained an object of class org.apache.uima.collection.impl.metadata.cpe.CpeDescriptionImpl.
 
> org.apache.uima.util.InvalidXMLException: An object of class org.apache.uima.resource.ResourceSpecifier
was requested, but the XML input contained an object of class org.apache.uima.collection.impl.metadata.cpe.CpeDescriptionImpl.
 
> 	at org.apache.uima.util.impl.XMLParser_impl.parseResourceSpecifier(XMLParser_impl.java:401)
> 	at org.apache.uima.util.impl.XMLParser_impl.parseResourceSpecifier(XMLParser_impl.java:379)
> 	at org.apache.uima.tools.cvd.MainFrame.setupAE(MainFrame.java:1477)
> 	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(Unknown Source)
> 	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
> 	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
> 	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
> 	at javax.swing.AbstractButton.doClick(Unknown Source)
> 	at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
> 	at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)
> 	at java.awt.Component.processMouseEvent(Unknown Source)
> 	at javax.swing.JComponent.processMouseEvent(Unknown Source)
> 	at java.awt.Component.processEvent(Unknown Source)
> 	at java.awt.Container.processEvent(Unknown Source)
> 	at java.awt.Component.dispatchEventImpl(Unknown Source)
> 	at java.awt.Container.dispatchEventImpl(Unknown Source)
> 	at java.awt.Component.dispatchEvent(Unknown Source)
> 	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
> 	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
> 	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
> 	at java.awt.Container.dispatchEventImpl(Unknown Source)
> 	at java.awt.Window.dispatchEventImpl(Unknown Source)
> 	at java.awt.Component.dispatchEvent(Unknown Source)
> 	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
> 	at java.awt.EventQueue.access$300(Unknown Source)
> 	at java.awt.EventQueue$3.run(Unknown Source)
> 	at java.awt.EventQueue$3.run(Unknown Source)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
> 	at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
> 	at java.awt.EventQueue$4.run(Unknown Source)
> 	at java.awt.EventQueue$4.run(Unknown Source)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
> 	at java.awt.EventQueue.dispatchEvent(Unknown Source)
> 	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
> 	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
> 	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
> 	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> 	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> 	at java.awt.EventDispatchThread.run(Unknown Source)



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