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From Marshall Schor <...@schor.com>
Subject Re: Build Error with Concept Mapper 2.10.2
Date Sat, 01 Jun 2019 16:18:07 GMT
This error happens (I'm reading from the stack trace) in

ConceptMapper's typeSystemInit method, on line (ConceptMapper.java:418)

Looking at that line in the source code:
resultAnnotationType = typeSystem.getType(resultAnnotationName);

The NPE is thrown if the value of the string "resultAnnotationName" is null.

This is, according to the source code, set from a "configuration parameter" 
named "ResultingAnnotationName".

So, I'm guessing your setup isn't specifying this configuration parameter.

Let us know if specifying this and related features (see https://uima.apache.org/d/uima-addons-current/ConceptMapper/ConceptMapperAnnotatorUserGuide.html#configParams
) fixes this.

-Marshall Schor


On 5/31/2019 1:27 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 parameter files, and 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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