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From Chinyere O. <cjokp...@outlook.com>
Subject Build Error with Concept Mapper 2.10.2
Date Tue, 25 Feb 2020 18:15:01 GMT
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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