Re: Problems building a pipeline with PEAR components

Tue, 26 Jun 2007 04:14:58 -0700

I have to apologize for that long question. My Problem is solved now. The fault was, that I created an initial CAS from my first component that did not had the relevant part of the type system (a did not mention that our real type system comes in 3 parts, to keep the problem simple - but that was too simple I guess). Now I use the complete TypeSystem to create the initial CAS and the NETagger works fine.
btw: Is there a simple way to create a CAS from only a type system descriptor? Currently I am using an analyis engine, to get my initial CAS. 

sorry,
Matthias

P.S. was using UIMA 2.1


Michael Baessler wrote:

Hi Matthias,


there were a lot of changes in the PEAR stuff during the last weeks, 
so to help you with your questions I need to know what UIMA version do 
you use.



I think you have tested the PEAR files standalone and in that scenario 
all works fine, right?


-- Michael

Matthias Muehlhausen wrote:

Hello,


I am currently building a web application (with SpringMVC running in 
tomcat) that should serve to demonstrate the result of the processing 
of each component in this pipeline. Some components do their job, 
while others don't.


These are the facts:

- I am using one TypeSystem that is in the classpath of the main 
application (as a jar).
- Each PEAR component has a type system descriptor, that reside in 
the 'desc' folder and are referenced by the AnalysisEngine 
descriptors. The type system descriptors are all the identical.
- The component that does not work (a NETagger) uses another 
component (utilities) - while the other working components don't 
(!!!) - for getting a special Annotation object (type 'Variation' - a 
bio entity). The call is:

entity = (Entity) AnnotationTools.getAnnotationByName(aJCas, className).

This call gives back null, and throws a 
java.lang.reflect.InvocationTargetException caused by a 
org.apache.uima.cas.CASRuntimeException: JCas type 
"de.julielab.jules.types.Variation" used in Java code,  but was not 
declared in the XML type descriptor.
- I checked if the descriptors are missing that type, but they don't, 
so I assume that the descriptors themselves are OK. Perhaps they have 
a wrong place - but how do I see which descriptor UIMA uses at a time?
- I am installing the PEARs at runtime with the 
PackageInstaller.installPackage(...) method
- The utilities are included in the main application as a jar; they 
don't have any type system descriptors, because they should be used 
independently and they are working in a 'non-PEAR' environement.

-can this have to do something with running it with tomcat?


I already recognized that each PEAR is loaded by a different 
classloader and that this caused that the PEARs itself could not use 
its own TypeSystem-JAR or other JARs that has dublicates in other 
PEARs or the main application (e.g. log4j) - this is some kind of 
mysterious for me - could someone explain why this is so?



So what can I do to get my NETagger running? Could anybody help me. 
Hints and tips are also very welcome. (I'm getting frustrated with 
this f... problem)



I attached a part of the tomcat logging file that shows the 
stacktrace in detail when the above mentiond Exception is thrown.


greetings
Matthias

------------------------------------------------------------------------


829774 [http-8080-Processor25] DEBUG 
de.julielab.jules.ae.netagger.EntityAnnotator  - process(JCas, 
ResultSpecification) -  JNET: processing next document
830295 [http-8080-Processor25] ERROR 
de.julielab.jules.ae.netagger.EntityAnnotator  - addAnnotation(JCas, 
int, int, String)

java.lang.reflect.InvocationTargetException

        at 
sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at 
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) 

        at 
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) 

        at 
java.lang.reflect.Constructor.newInstance(Constructor.java:494)
        at 
de.julielab.jules.utility.AnnotationTools.getAnnotationByClassName(AnnotationTools.java:49) 

        at 
de.julielab.jules.ae.netagger.EntityAnnotator.addAnnotation(EntityAnnotator.java:399) 

        at 
de.julielab.jules.ae.netagger.EntityAnnotator.writeToCAS(EntityAnnotator.java:373) 

        at 
de.julielab.jules.ae.netagger.EntityAnnotator.process(EntityAnnotator.java:235) 

        at 
org.apache.uima.analysis_engine.impl.compatibility.AnnotatorAdapter.process(AnnotatorAdapter.java:146) 

        at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:373) 

        at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:292) 

        at 
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:202) 

        at 
de.julielab.jules.demo.domain.AnalysisComponent.process(AnalysisComponent.java:98) 

        at 
de.julielab.jules.demo.domain.PipelineImpl.process(PipelineImpl.java:366) 

        at 
de.julielab.jules.demo.domain.PipelineFactory.getPipelineInstance(PipelineFactory.java:129) 

        at 
org.apache.jsp.WEB_002dINF.jsp.index_jsp._jspService(index_jsp.java:242)
        at 
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)

        at 
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:334) 

        at 
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
        at 
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)

        at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) 

        at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) 

        at 
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672) 

        at 
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463) 

        at 
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398) 

        at 
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) 

        at 
org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142) 

        at 
org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:243) 

        at 
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1141) 

        at 
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:878) 

        at 
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) 

        at 
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:461) 

        at 
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:416) 


        at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)

        at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) 

        at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) 

        at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) 

        at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178) 

        at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126) 

        at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105) 

        at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107) 

        at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) 

        at 
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869) 

        at 
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664) 

        at 
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) 

        at 
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80) 

        at 
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684) 


        at java.lang.Thread.run(Thread.java:595)

Caused by: org.apache.uima.cas.CASRuntimeException: JCas type 
"de.julielab.jules.types.Variation" used in Java code,  but was not 
declared in the XML type descriptor.

        at org.apache.uima.jcas.impl.JCasImpl.getType(JCasImpl.java:292)
        at org.apache.uima.jcas.cas.TOP.<init>(TOP.java:92)

        at 
org.apache.uima.jcas.cas.AnnotationBase.<init>(AnnotationBase.java:53)
        at 
org.apache.uima.jcas.tcas.Annotation.<init>(Annotation.java:54)

        at de.julielab.jules.types.Annotation.<init>(Annotation.java:41)
        at de.julielab.jules.types.Entity.<init>(Entity.java:42)
        at de.julielab.jules.types.BioEntity.<init>(BioEntity.java:41)
        at de.julielab.jules.types.Variation.<init>(Variation.java:41)
        ... 51 more

26.06.2007 11:57:39 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl 
callAnalysisComponentProcess(397)

SCHWERWIEGEND: Exception occurred

org.apache.uima.analysis_engine.AnalysisEngineProcessException: 
Annotator processing failed.
        at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:384) 

        at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:292) 

        at 
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:202) 

        at 
de.julielab.jules.demo.domain.AnalysisComponent.process(AnalysisComponent.java:98) 

        at 
de.julielab.jules.demo.domain.PipelineImpl.process(PipelineImpl.java:366) 

        at 
de.julielab.jules.demo.domain.PipelineFactory.getPipelineInstance(PipelineFactory.java:129) 

        at 
org.apache.jsp.WEB_002dINF.jsp.index_jsp._jspService(index_jsp.java:242)
        at 
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)

        at 
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:334) 

        at 
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
        at 
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)

        at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) 

        at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) 

        at 
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672) 

        at 
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463) 

        at 
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398) 

        at 
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) 

        at 
org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142) 

        at 
org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:243) 

        at 
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1141) 

        at 
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:878) 

        at 
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) 

        at 
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:461) 

        at 
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:416) 


        at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)

        at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) 

        at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) 

        at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) 

        at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178) 

        at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126) 

        at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105) 

        at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107) 

        at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) 

        at 
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869) 

        at 
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664) 

        at 
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) 

        at 
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80) 

        at 
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684) 


        at java.lang.Thread.run(Thread.java:595)
Caused by: java.lang.NullPointerException

        at 
de.julielab.jules.ae.netagger.EntityAnnotator.addAnnotation(EntityAnnotator.java:424) 

        at 
de.julielab.jules.ae.netagger.EntityAnnotator.writeToCAS(EntityAnnotator.java:373) 

        at 
de.julielab.jules.ae.netagger.EntityAnnotator.process(EntityAnnotator.java:235) 

        at 
org.apache.uima.analysis_engine.impl.compatibility.AnnotatorAdapter.process(AnnotatorAdapter.java:146) 

        at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:373) 


        ... 41 more

830323 [http-8080-Processor25] ERROR 
de.julielab.jules.demo.domain.AnalysisComponent  - process(CAS) 
Analysis Engine Name=Variation Tagger
org.apache.uima.analysis_engine.AnalysisEngineProcessException: 
Annotator processing failed.
        at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:384) 

        at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:292) 

        at 
org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:202) 

        at 
de.julielab.jules.demo.domain.AnalysisComponent.process(AnalysisComponent.java:98) 

        at 
de.julielab.jules.demo.domain.PipelineImpl.process(PipelineImpl.java:366) 

        at 
de.julielab.jules.demo.domain.PipelineFactory.getPipelineInstance(PipelineFactory.java:129) 

        at 
org.apache.jsp.WEB_002dINF.jsp.index_jsp._jspService(index_jsp.java:242)
        at 
org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:97)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)

        at 
org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:334) 

        at 
org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:314)
        at 
org.apache.jasper.servlet.JspServlet.service(JspServlet.java:264)

        at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)

        at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) 

        at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) 

        at 
org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:672) 

        at 
org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:463) 

        at 
org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:398) 

        at 
org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:301) 

        at 
org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:142) 

        at 
org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:243) 

        at 
org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1141) 

        at 
org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:878) 

        at 
org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) 

        at 
org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:461) 

        at 
org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:416) 


        at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)

        at 
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:252) 

        at 
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:173) 

        at 
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) 

        at 
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:178) 

        at 
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:126) 

        at 
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:105) 

        at 
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:107) 

        at 
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:148) 

        at 
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:869) 

        at 
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:664) 

        at 
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:527) 

        at 
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:80) 

        at 
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:684) 


        at java.lang.Thread.run(Thread.java:595)
Caused by: java.lang.NullPointerException

        at 
de.julielab.jules.ae.netagger.EntityAnnotator.addAnnotation(EntityAnnotator.java:424) 

        at 
de.julielab.jules.ae.netagger.EntityAnnotator.writeToCAS(EntityAnnotator.java:373) 

        at 
de.julielab.jules.ae.netagger.EntityAnnotator.process(EntityAnnotator.java:235) 

        at 
org.apache.uima.analysis_engine.impl.compatibility.AnnotatorAdapter.process(AnnotatorAdapter.java:146) 

        at 
org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:373) 


        ... 41 more

  





--
Matthias Mühlhausen
Jena University Language and Information Engineering (JULIE) Lab
Phone: +49-3641-944305
Fax:   +49-3641-944321
email: [EMAIL PROTECTED]
URL:   http://www.coling.uni-jena.de























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