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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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