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From Erik Fäßler <erik.faess...@uni-jena.de>
Subject Re: Build Error with Concept Mapper 2.10.2
Date Sat, 01 Jun 2019 11:22:03 GMT
Hey,

it is an NPE in the type system where it tries to get the internal code of a type for its
name.
One parameter of the ConceptMapper is that name of type that should be created for matches.
Did you set this parameter? Because I think this exception could be explained by the type
name being omitted, thus, being null.

Just a guess, of course :-)

Best,

Erik

> On 31. May 2019, at 19:27, Chinyere O. <cjokpara@outlook.com> 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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