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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: jcasPool problem
Date Thu, 16 Feb 2017 15:41:54 GMT
Hi Alaa,
There is not a need for LVG.  It is supposed to generate lexical variants. https://www.nlm.nih.gov/research/umls/new_users/online_learning/LEX_004.html
Many already exist in the dictionary.  In some tests that I did in the past, using lvg increased
recall about 1%.  If it is preventing you from doing something else (like multithreading),
then that 1 point may not be worth a nightmare of hacks.

-----Original Message-----
From: Alaa al Barari [mailto:alaa.albarari@gmail.com] 
Sent: Thursday, February 16, 2017 8:49 AM
To: dev@ctakes.apache.org
Subject: Re: jcasPool problem

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://urldefense.proofpoint.com/v2/url?u=https-3A__uima.apache.o
> > > rg_d_uimaj-2Dcurrent_tutorials-5Fand-5F&d=DwIBaQ&c=qS4goWBT7poplM6
> > > 9zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4
> > > f7d4gTao&m=-9rqXueVLY9oE2yc4wUow7fQ_NFbjZZ-zXktI4aCGSQ&s=VcmPUAVgs
> > > nx-sPvhmhoRk6pkXYFq7QDY8OPzhUaplpk&e=
> > > 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:3
> > > > 91)
> > > > 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.proc
> > > > ess(
> > > > AnalysisEngineImplBase.java:267) at 
> > > > org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.proc
> > > > ess(
> > > > 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(JavaResourceMethodDispatche
> > > > rPr
> > > > 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.executeFilt
> > > > er(
> > > > DefaultFilterChain.java:288)
> > > > at
> > > > org.glassfish.grizzly.filterchain.DefaultFilterChain.
> executeChainPart(
> > > > 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$Worker.doWor
> > > > k(
> > > > AbstractThreadPool.java:564)
> > > > at
> > > > org.glassfish.grizzly.threadpool.AbstractThreadPool$
> > > > 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.AbstractConceptFactory.
> > > > createConcepts(AbstractConceptFactory.java:37)
> > > > at
> > > > org.apache.ctakes.dictionary.lookup2.concept.UmlsJdbcConceptFactory.
> > > > createConcepts(UmlsJdbcConceptFactory.java:55)
> > > > at
> > > > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.
> > > process(
> > > > AbstractJCasTermAnnotator.java:179)
> > > > at
> > > > org.apache.uima.analysis_component.JCasAnnotator_ImplBase.proces
> > > > s(
> > > > JCasAnnotator_ImplBase.java:48)
> > > > at
> > > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.
> > > > callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:3
> > > > 75)
> > > >
> > >
> > >
> > >
> > > --
> > > with Regards
> > > Shahid Ashraf
> > >
> >
> >
> >
> > --
> > Eng Alaa Al-Barari
> > phone 0599297470
> >
>
>
>
> --
> with Regards
> Shahid Ashraf
>



--
Eng Alaa Al-Barari
phone 0599297470
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