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.albar...@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 <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://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.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: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
