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From Alaa al Barari <alaa.albar...@gmail.com>
Subject Re: jcasPool problem
Date Thu, 16 Feb 2017 13:53:31 GMT
one more thing please, from where I can get this fastUMLSAggregate.xml file
?

On Thu, Feb 16, 2017 at 3:48 PM, Alaa al Barari <alaa.albarari@gmail.com>
wrote:

> Thanks I will try that and let you know, is there a need for LVG In fast
> dictionary lookup ? Please correct me If I am wrong but I understand lvg is
> responsible for synonyms .... and hence with fast dictionary there is no
> need for lvg right ?
>
> On Thu, Feb 16, 2017 at 3:42 PM, shahid ashraf <shahid@trialx.com> wrote:
>
>> Yes it worked ... but in multiprocessing ... LVG module gives errors(its
>> should be f9 if you don't use that..)
>> I am using simple fastUMLSAggregate.xml...
>>
>>
>>
>> On Thu, Feb 16, 2017 at 7:10 PM, Alaa al Barari <alaa.albarari@gmail.com>
>> wrote:
>>
>> > Thanks Shahid, when you built the pipline using xml descriptor it
>> worked ?
>> >
>> > whats your xml schema ?
>> >
>> > On Thu, Feb 16, 2017 at 3:22 PM, shahid ashraf <shahid@trialx.com>
>> wrote:
>> >
>> > > Hi
>> > >
>> > > I have tried jcaspool too but it did not worked for me as well (Same
>> > > Error). I did not tried to use after spending some time... not an
>> expert
>> > on
>> > > java... so i just used the Descriptor (XML) based code to build
>> pipeline
>> > > and created a CAS Pool.
>> > > Let me know if you are able to get anything ...
>> > >
>> > > Here is the link from which you can build the descriptor XML based
>> > pipeline
>> > > with CASPool.
>> > >
>> > > https://uima.apache.org/d/uimaj-current/tutorials_and_
>> > > users_guides.html#ugr.tug.applications.multi_threaded
>> > >
>> > >
>> > >
>> > > On Thu, Feb 16, 2017 at 6:03 PM, Alaa al Barari <
>> alaa.albarari@gmail.com
>> > >
>> > > wrote:
>> > >
>> > > > Hi,
>> > > >
>> > > > anyone used jcasPool before ? is it working with you ? any ideas,
>> > > insights
>> > > > ....  I have this issue :
>> > > > aggregateBuilder = Pipeline.getAggregateBuilder();
>> > > > pipeline = aggregateBuilder.createAggregate();
>> > > > jCasPool = new JCasPool(10, pipeline);
>> > > >
>> > > >
>> > > > then
>> > > >
>> > > > JCas jcas = jCasPool.getJCas(0);
>> > > > jcas.setDocumentText(text);
>> > > > pipeline.process(jcas);
>> > > >
>> > > > but it throws the following exception when calling second block of
>> code
>> > > > twice :
>> > > >
>> > > > Info:   Annotator processing failed.
>> > > > Severe:   org.apache.uima.analysis_engine.
>> > AnalysisEngineProcessException
>> > > :
>> > > > Annotator processing failed.
>> > > > at
>> > > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
>> > > > callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391)
>> > > > at
>> > > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
>> > > > processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296)
>> > > > at
>> > > > org.apache.uima.analysis_engine.asb.impl.ASB_impl$
>> > AggregateCasIterator.
>> > > > processUntilNextOutputCas(ASB_impl.java:567)
>> > > > at
>> > > > org.apache.uima.analysis_engine.asb.impl.ASB_impl$
>> > > > AggregateCasIterator.<init>(ASB_impl.java:409)
>> > > > at
>> > > > org.apache.uima.analysis_engine.asb.impl.ASB_impl.
>> > > > process(ASB_impl.java:342)
>> > > > at
>> > > > org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.
>> > > > processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267)
>> > > > at
>> > > > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.
>> process(
>> > > > AnalysisEngineImplBase.java:267)
>> > > > at
>> > > > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.
>> process(
>> > > > AnalysisEngineImplBase.java:280)
>> > > > at com.whatever.getCode(Manager.java:217)
>> > > > at com.whatever.analyzeText(Manager.java:122)
>> > > > at com.whatever.analyzeCode(GenericResource.java:56)
>> > > > at sun.reflect.GeneratedMethodAccessor220.invoke(Unknown Source)
>> > > > at
>> > > > sun.reflect.DelegatingMethodAccessorImpl.invoke(
>> > > > DelegatingMethodAccessorImpl.java:43)
>> > > > at java.lang.reflect.Method.invoke(Method.java:498)
>> > > > at
>> > > > org.glassfish.jersey.server.model.internal.
>> > > ResourceMethodInvocationHandle
>> > > > rFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
>> > > > at
>> > > > org.glassfish.jersey.server.model.internal.
>> > > AbstractJavaResourceMethodDisp
>> > > > atcher.invoke(AbstractJavaResourceMethodDispatcher.java:125)
>> > > > at
>> > > > org.glassfish.jersey.server.model.internal.
>> > > JavaResourceMethodDispatcherPr
>> > > > ovider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherPr
>> > > > ovider.java:152)
>> > > > at
>> > > > org.glassfish.jersey.server.model.internal.
>> > > AbstractJavaResourceMethodDisp
>> > > > atcher.dispatch(AbstractJavaResourceMethodDispatcher.java:91)
>> > > > at
>> > > > org.glassfish.jersey.server.model.ResourceMethodInvoker.
>> > > > invoke(ResourceMethodInvoker.java:346)
>> > > > at
>> > > > org.glassfish.jersey.server.model.ResourceMethodInvoker.
>> > > > apply(ResourceMethodInvoker.java:341)
>> > > > at
>> > > > org.glassfish.jersey.server.model.ResourceMethodInvoker.
>> > > > apply(ResourceMethodInvoker.java:101)
>> > > > at org.glassfish.jersey.server.ServerRuntime$1.run(
>> > > ServerRuntime.java:224)
>> > > > at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
>> > > > at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
>> > > > at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
>> > > > at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
>> > > > at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
>> > > > at
>> > > > org.glassfish.jersey.process.internal.RequestScope.
>> > > > runInScope(RequestScope.java:317)
>> > > > at org.glassfish.jersey.server.ServerRuntime.process(
>> > > > ServerRuntime.java:198)
>> > > > at
>> > > > org.glassfish.jersey.server.ApplicationHandler.handle(
>> > > > ApplicationHandler.java:946)
>> > > > at org.glassfish.jersey.servlet.WebComponent.service(
>> > > > WebComponent.java:323)
>> > > > at
>> > > > org.glassfish.jersey.servlet.ServletContainer.service(
>> > > > ServletContainer.java:372)
>> > > > at
>> > > > org.glassfish.jersey.servlet.ServletContainer.service(
>> > > > ServletContainer.java:335)
>> > > > at
>> > > > org.glassfish.jersey.servlet.ServletContainer.service(
>> > > > ServletContainer.java:218)
>> > > > at
>> > > > org.apache.catalina.core.StandardWrapper.service(
>> > > > StandardWrapper.java:1682)
>> > > > at
>> > > > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(
>> > > > ApplicationFilterChain.java:344)
>> > > > at
>> > > > org.apache.catalina.core.ApplicationFilterChain.doFilter(
>> > > > ApplicationFilterChain.java:214)
>> > > > at com.thetransactioncompany.cors.CORSFilter.doFilter(
>> > > CORSFilter.java:208)
>> > > > at com.thetransactioncompany.cors.CORSFilter.doFilter(
>> > > CORSFilter.java:274)
>> > > > at
>> > > > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(
>> > > > ApplicationFilterChain.java:256)
>> > > > at
>> > > > org.apache.catalina.core.ApplicationFilterChain.doFilter(
>> > > > ApplicationFilterChain.java:214)
>> > > > at
>> > > > org.apache.catalina.core.StandardWrapperValve.invoke(
>> > > > StandardWrapperValve.java:316)
>> > > > at
>> > > > org.apache.catalina.core.StandardContextValve.invoke(
>> > > > StandardContextValve.java:160)
>> > > > at
>> > > > org.apache.catalina.core.StandardPipeline.doInvoke(
>> > > > StandardPipeline.java:734)
>> > > > at
>> > > > org.apache.catalina.core.StandardPipeline.invoke(
>> > > > StandardPipeline.java:673)
>> > > > at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
>> > > > at
>> > > > org.apache.catalina.core.StandardHostValve.invoke(
>> > > > StandardHostValve.java:174)
>> > > > at
>> > > > org.apache.catalina.connector.CoyoteAdapter.doService(
>> > > > CoyoteAdapter.java:357)
>> > > > at
>> > > > org.apache.catalina.connector.CoyoteAdapter.service(
>> > > > CoyoteAdapter.java:260)
>> > > > at
>> > > > com.sun.enterprise.v3.services.impl.ContainerMapper.
>> > > > service(ContainerMapper.java:188)
>> > > > at
>> > > > org.glassfish.grizzly.http.server.HttpHandler.runService(
>> > > > HttpHandler.java:191)
>> > > > at
>> > > > org.glassfish.grizzly.http.server.HttpHandler.doHandle(
>> > > > HttpHandler.java:168)
>> > > > at
>> > > > org.glassfish.grizzly.http.server.HttpServerFilter.
>> > > > handleRead(HttpServerFilter.java:189)
>> > > > at
>> > > > org.glassfish.grizzly.filterchain.ExecutorResolver$
>> > > > 9.execute(ExecutorResolver.java:119)
>> > > > at
>> > > > org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(
>> > > > DefaultFilterChain.java:288)
>> > > > at
>> > > > org.glassfish.grizzly.filterchain.DefaultFilterChain.execute
>> ChainPart(
>> > > > DefaultFilterChain.java:206)
>> > > > at
>> > > > org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(
>> > > > DefaultFilterChain.java:136)
>> > > > at
>> > > > org.glassfish.grizzly.filterchain.DefaultFilterChain.process(
>> > > > DefaultFilterChain.java:114)
>> > > > at
>> > > > org.glassfish.grizzly.ProcessorExecutor.execute(
>> > > ProcessorExecutor.java:77)
>> > > > at
>> > > > org.glassfish.grizzly.nio.transport.TCPNIOTransport.
>> > > > fireIOEvent(TCPNIOTransport.java:838)
>> > > > at
>> > > > org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(
>> > > > AbstractIOStrategy.java:113)
>> > > > at
>> > > > org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(
>> > > > WorkerThreadIOStrategy.java:115)
>> > > > at
>> > > > org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$
>> > > > 100(WorkerThreadIOStrategy.java:55)
>> > > > at
>> > > > org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$
>> > > > WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:135)
>> > > > at
>> > > > org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(
>> > > > AbstractThreadPool.java:564)
>> > > > at
>> > > > org.glassfish.grizzly.threadpool.AbstractThreadPool$
>> > > > Worker.run(AbstractThreadPool.java:544)
>> > > > at java.lang.Thread.run(Thread.java:745)
>> > > > Caused by: java.lang.NullPointerException
>> > > > at com.mysql.jdbc.ResultSetImpl.checkColumnBounds(
>> > > ResultSetImpl.java:766)
>> > > > at com.mysql.jdbc.ResultSetImpl.getStringInternal(
>> > > ResultSetImpl.java:5241)
>> > > > at com.mysql.jdbc.ResultSetImpl.getString(ResultSetImpl.java:5163)
>> > > > at
>> > > > org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory.
>> > > > getStringCodesWithDesc(JdbcConceptFactory.java:409)
>> > > > at
>> > > > org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory.
>> > > > createConcept(JdbcConceptFactory.java:294)
>> > > > at
>> > > > org.apache.ctakes.dictionary.lookup2.concept.AbstractConcept
>> Factory.
>> > > > createConcepts(AbstractConceptFactory.java:37)
>> > > > at
>> > > > org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConcept
>> Factory.
>> > > > createConcepts(UmlsJdbcConceptFactory.java:55)
>> > > > at
>> > > > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.
>> > > process(
>> > > > AbstractJCasTermAnnotator.java:179)
>> > > > 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:375)
>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > with Regards
>> > > Shahid Ashraf
>> > >
>> >
>> >
>> >
>> > --
>> > Eng Alaa Al-Barari
>> > phone 0599297470
>> >
>>
>>
>>
>> --
>> with Regards
>> Shahid Ashraf
>>
>
>
>
> --
> Eng Alaa Al-Barari
> phone 0599297470
>



-- 
Eng Alaa Al-Barari
phone 0599297470

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