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 > >
