Re: Build Error with Concept Mapper 2.10.2
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 j
Re: Build Error with Concept Mapper 2.10.2
The two warnings about getters and setters seem to indicate you are using class flies that are out of sync with your current type system. Have you tried to delete and recreate these classes? I occasionally get this error when I re-generate (JCasGen) on top of an existing file, it merges instead of rewrites the file so artifacts from prior type definitions can exist. This can be why the system gets a NPE during execution, your code may be using these features still.
Re: Build Error with Concept Mapper 2.10.2
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. 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.Wind
Build Error with Concept Mapper 2.10.2
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)
