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
