ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Zakir Saifi <zakir.sa...@raxa.com>
Subject Re: Analysis Engine Process Exception while querying ctakes Service frequently
Date Wed, 06 Mar 2019 09:36:46 GMT
Hi @Satyananda Sahu
Could you elaborate about how r*esetting the annotators and process engine*?.
I currently releasing the JCas pool after each rest call and in case of an
exception, I am also releasing the JCas.

Here is my code. Post construct work only for the First time. Then the
subsequent Rest calls process JCas and release after the use.

@PostConstruct
    public void init() throws ServletException {
        LOGGER.info("Initializing analysis engine and jcas pool");
        try {
            final File inputFile    = FileLocator.getFile(PIPER_FILE_PATH);
            PiperFileReader reader  = new
PiperFileReader(inputFile.getAbsolutePath());
            PipelineBuilder builder = reader.getBuilder();
            AnalysisEngineDescription analysisEngineDesc =
builder.getAnalysisEngineDesc();
            engine =
UIMAFramework.produceAnalysisEngine(analysisEngineDesc);
            pool = new JCasPool(300, engine);
        } catch (Exception e) {
            e.printStackTrace();
            throw new ServletException(e);
        }
    }

@RequestMapping(value = "/analyze", method = RequestMethod.POST)
   @ResponseBody
   public Map<String, List<String>> getAnalyzedJSON(@RequestBody String
analysisText) throws ServletException, IOException {
       Map<String, List<String>> resultMap = null;
       if (analysisText != null && analysisText.trim().length() > 0) {
           JCas jcas = pool.getJCas(-1);
           try {
               jcas.setDocumentText(analysisText);
               engine. .process(jcas);
               resultMap = formatResults(jcas);
           } catch (Exception e) {
               e.printStackTrace();
               throw new ServletException(e);
           } finally {
                pool.releaseJCas(jcas); //Releasing JCas
           }
       }
        return resultMap;
   }



On Wed, Mar 6, 2019 at 12:42 PM satyananda sahu <satyananda123@gmail.com>
wrote:

> Reset the annotators and process engine for each call and it should work
> for you.
>
> Thanks,
> Satya
>
> On Tue, Mar 5, 2019 at 3:12 PM Zakir Saifi <zakir.saifi@raxa.com> wrote:
>
> > Hi all,
> >
> > I using Ctakes Rest Service(a Rest Server based on Apache Ctakes) for
> > benchmarking using *Apache Jmeter*. As I have to use it as Rest Server to
> > processing many clinical Text
> >
> > My Configuration for BenchMarking are as follows:
> > I am creating 10 users(threads) each with Ramp up period (*10s*). *That
> > means 1 user is created after every 1 second. *
> > I have loop count of *5* (Number of iteration)
> > There is a time delay of *500ms* between each subsequent Request ( To
> > simulate requests as in real-time scenarios, real-users give delays
> between
> > doing different actions.)
> > I am also changing the *data* with each request by using data from CSV
> > file.
> >
> > I am getting following exceptions for most* of the requests* that comes
> to
> > Ctakes Rest Sever
> >
> > Exception1
> > org.apache.uima.analysis_engine.s: 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
> >
> >
> org.apache.ctakes.rest.service.CtakesRestController.getAnalyzedJSON(CtakesRestController.java:95)
> > at sun.reflect.GeneratedMethodAccessor157.invoke(Unknown Source)
> > at
> >
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> > at java.lang.reflect.Method.invoke(Method.java:498)
> > at
> >
> >
> org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)
> > at
> >
> >
> org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:133)
> > at
> >
> >
> org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:97)
> > at
> >
> >
> org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:827)
> > at
> >
> >
> org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:738)
> > at
> >
> >
> org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
> > at
> >
> >
> org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:967)
> > at
> >
> >
> org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:901)
> > at
> >
> >
> org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
> > at
> >
> >
> org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:872)
> > at javax.servlet.http.HttpServlet.service(HttpServlet.java:661)
> > at
> >
> >
> org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
> > at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
> > at
> >
> >
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
> > at
> >
> >
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
> > at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
> > at
> >
> >
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
> > at
> >
> >
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
> > at
> >
> >
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
> > at
> >
> >
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
> > at
> >
> >
> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
> > at
> >
> >
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
> > at
> >
> >
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
> > at
> >
> >
> org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
> > at
> >
> >
> org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
> > at
> >
> >
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
> > at
> >
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
> > at
> >
> org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)
> > at
> >
> >
> org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
> > at
> >
> >
> org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806)
> > at
> > org.apache.tomcat.util.net
> > .NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498)
> > at
> > org.apache.tomcat.util.net
> > .SocketProcessorBase.run(SocketProcessorBase.java:49)
> > at
> >
> >
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
> > at
> >
> >
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
> > at
> >
> >
> org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
> > at java.lang.Thread.run(Thread.java:748)
> > Caused by: java.lang.NullPointerException
> >
> > Exception2
> > 05-Mar-2019 08:45:32.274 SEVERE [http-nio-8089-exec-3]
> >
> >
> org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(275)
> > Exception occurred
> >  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
> >
> >
> org.apache.ctakes.rest.service.CtakesRestController.getAnalyzedJSON(CtakesRestController.java:95)
> > at sun.reflect.GeneratedMethodAccessor157.invoke(Unknown Source)
> > at
> >
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> > at java.lang.reflect.Method.invoke(Method.java:498)
> > at
> >
> >
> org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:205)
> > at
> >
> >
> org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:133)
> > at
> >
> >
> org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:97)
> > at
> >
> >
> org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:827)
> > at
> >
> >
> org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:738)
> > at
> >
> >
> org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
> > at
> >
> >
> org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:967)
> > at
> >
> >
> org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:901)
> > at
> >
> >
> org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
> > at
> >
> >
> org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:872)
> > at javax.servlet.http.HttpServlet.service(HttpServlet.java:661)
> > at
> >
> >
> org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
> > at javax.servlet.http.HttpServlet.service(HttpServlet.java:742)
> > at
> >
> >
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
> > at
> >
> >
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
> > at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
> > at
> >
> >
> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
> > at
> >
> >
> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
> > at
> >
> >
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)
> > at
> >
> >
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
> > at
> >
> >
> org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493)
> > at
> >
> >
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)
> > at
> >
> >
> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81)
> > at
> >
> >
> org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
> > at
> >
> >
> org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:650)
> > at
> >
> >
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)
> > at
> >
> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342)
> > at
> >
> org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800)
> > at
> >
> >
> org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
> > at
> >
> >
> org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806)
> > at
> > org.apache.tomcat.util.net
> > .NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498)
> > at
> > org.apache.tomcat.util.net
> > .SocketProcessorBase.run(SocketProcessorBase.java:49)
> > at
> >
> >
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
> > at
> >
> >
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
> > at
> >
> >
> org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
> > at java.lang.Thread.run(Thread.java:748)
> > Caused by: java.lang.NullPointerException
> >
> >
> > I have recently changed the *minimum span detection to 1 *and also not
> > excluding any exclusion tags in my Piper files. Since then I am seeing
> this
> > errors coming more frequently. I don't think these errors are associated
> > with any particular type of data to goes to ctakes Service.Because if I
> > increase the time between the subsequent user creation and Time delay
> > between the subsequent call, I am not getting any exception.
> >
> > I am currently running *Ctakes Rest Server* war in a Docker Container
> > having tomcat image with JVM Maximum Memory of* 3 GB.*  Anyone have idea
> > why I am getting these exception on heavy load??
> >
> >
> >
> >
> > Regards
> > Zakir Saifi
> >
>


-- 
Regards
Zakir Saifi
(Software Developer at Raxa)

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message