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.albar...@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 <sha...@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.albar...@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 <sha...@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.albar...@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
