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From Marshall Schor <...@schor.com>
Subject Re: Build Error with Concept Mapper 2.10.2
Date Wed, 26 Feb 2020 14:06:24 GMT
Looking at the stack trace, the error is coming from line 418 in Concept Mapper.

Looking at the code (you can see here
https://svn.apache.org/viewvc/uima/addons/tags/ConceptMapper-2.10.2/src/main/java/org/apache/uima/conceptMapper/ConceptMapper.java?view=markup
)

the code is trying to get the type associated with the result Annotation Name
parameter. 

The "null pointer exception" is thrown when the getType method is passed a null
value.

I'm guessing that your configuration might be missing the parameter setting for
the Result Annotation Name parameter?

-Marshall

On 2/25/2020 1:15 PM, Chinyere O. wrote:
> Hi,
>
> I'm new to UIMA and I'm trying to get the concept mapper to run. I've downloaded the
concept mapper bin file, added all the configuration parameters, and added the jar packages
to the class path. Could someone help me figure out what I'm doing wrong.
>
> Thank you,
> Chinyere
>
> Error Log:
> 08:09:20.573 - 16: org.apache.uima.conceptMapper.Logger.log(46): INFO: ConceptMapper
INFO: Loading Dictionary from file:/C:/Users/Chinyere/eclipse_workspace_2018/NYUW_PathReader/resources/PathologyBiomakers.xml
> 08:09:20.579 - 16: org.apache.uima.conceptMapper.Logger.log(46): INFO: ConceptMapper
INFO: Loading dictionary
> 08:09:20.671 - 16: org.apache.uima.jcas.impl.JCasImpl.reportInitErrors(809): WARNING:
> JCas Type "org.apache.uima.conceptMapper.support.tokenizer.TokenAnnotation" implements
getters and setters for feature "tokenType", but the type system doesnt define that feature.
> JCas Type "org.apache.uima.conceptMapper.support.tokenizer.TokenAnnotation" implements
getters and setters for feature "tokenClass", but the type system doesnt define that feature.
>
> 08:09:20.672 - 16: org.apache.uima.jcas.impl.JCasImpl.reportInitErrors(809): WARNING:
> JCas Type "org.apache.uima.conceptMapper.support.tokenizer.TokenAnnotation" implements
getters and setters for feature "tokenType", but the type system doesnt define that feature.
> JCas Type "org.apache.uima.conceptMapper.support.tokenizer.TokenAnnotation" implements
getters and setters for feature "tokenClass", but the type system doesnt define that feature.
>
> 08:09:20.682 - 16: org.apache.uima.conceptMapper.Logger.log(46): INFO: ConceptMapper
INFO: Finished loading 4 entries
> 08:09:20.682 - 16: org.apache.uima.conceptMapper.Logger.log(46): INFO: ConceptMapper
INFO: ...done loading dictionary from file:/C:/Users/Chinyere/eclipse_workspace_2018/NYUW_PathReader/resources/PathologyBiomakers.xml
> 08:09:27.65 - 16: org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(434):
SEVERE: Exception occurred
> org.apache.uima.analysis_engine.AnalysisEngineProcessException
>                 at org.apache.uima.conceptMapper.ConceptMapper.process(ConceptMapper.java:574)
>                 at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
>                 at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:401)
>                 at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:318)
>                 at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
>                 at org.apache.uima.tools.cvd.MainFrame.internalRunAE(MainFrame.java:1528)
>                 at org.apache.uima.tools.cvd.MainFrame.runAE(MainFrame.java:430)
>                 at org.apache.uima.tools.cvd.control.AnnotatorRerunEventHandler.actionPerformed(AnnotatorRerunEventHandler.java:40)
>                 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$500(Unknown Source)
>                 at java.awt.EventQueue$3.run(Unknown Source)
>                 at java.awt.EventQueue$3.run(Unknown Source)
>                 at java.security.AccessController.doPrivileged(Native Method)
>                 at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown
Source)
>                 at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown
Source)
>                 at java.awt.EventQueue$4.run(Unknown Source)
>                 at java.awt.EventQueue$4.run(Unknown Source)
>                 at java.security.AccessController.doPrivileged(Native Method)
>                 at java.security.ProtectionDomain$JavaSecurityAccessImpl.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)
> Caused by: java.lang.NullPointerException
>                 at org.apache.uima.cas.impl.TypeSystemImpl.ll_getCodeForTypeName(TypeSystemImpl.java:1407)
>                 at org.apache.uima.cas.impl.TypeSystemImpl.getType(TypeSystemImpl.java:612)
>                 at org.apache.uima.conceptMapper.ConceptMapper.typeSystemInit(ConceptMapper.java:418)
>                 at org.apache.uima.conceptMapper.ConceptMapper.process(ConceptMapper.java:503)
>                 ... 45 more
>
> 08:09:27.67 - 16: org.apache.uima.tools.cvd.MainFrame.handleException(527): SEVERE: Exception
occurred
> org.apache.uima.analysis_engine.AnalysisEngineProcessException
>                 at org.apache.uima.conceptMapper.ConceptMapper.process(ConceptMapper.java:574)
>                 at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48)
>                 at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:401)
>                 at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:318)
>                 at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:269)
>                 at org.apache.uima.tools.cvd.MainFrame.internalRunAE(MainFrame.java:1528)
>                 at org.apache.uima.tools.cvd.MainFrame.runAE(MainFrame.java:430)
>                 at org.apache.uima.tools.cvd.control.AnnotatorRerunEventHandler.actionPerformed(AnnotatorRerunEventHandler.java:40)
>                 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$500(Unknown Source)
>                 at java.awt.EventQueue$3.run(Unknown Source)
>                 at java.awt.EventQueue$3.run(Unknown Source)
>                 at java.security.AccessController.doPrivileged(Native Method)
>                 at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown
Source)
>                 at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown
Source)
>                 at java.awt.EventQueue$4.run(Unknown Source)
>                 at java.awt.EventQueue$4.run(Unknown Source)
>                 at java.security.AccessController.doPrivileged(Native Method)
>                 at java.security.ProtectionDomain$JavaSecurityAccessImpl.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)
> Caused by: java.lang.NullPointerException
>                 at org.apache.uima.cas.impl.TypeSystemImpl.ll_getCodeForTypeName(TypeSystemImpl.java:1407)
>                 at org.apache.uima.cas.impl.TypeSystemImpl.getType(TypeSystemImpl.java:612)
>                 at org.apache.uima.conceptMapper.ConceptMapper.typeSystemInit(ConceptMapper.java:418)
>                 at org.apache.uima.conceptMapper.ConceptMapper.process(ConceptMapper.java:503)
>                 ... 45 more
>
>

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