There isn't really a difference between cas and jcas. Uima was originally started in C++, and when they started to move into java they wrapped the cas in a jcas object.
-----Original Message----- From: Alaa al Barari [mailto:alaa.albar...@gmail.com] Sent: Sunday, February 19, 2017 8:00 AM To: dev@ctakes.apache.org Subject: Re: jcasPool problem Thanks Sean, I will try that, whats the difference between cas and jcas ? On Thu, Feb 16, 2017 at 6:14 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Alaa, > > I have no idea what is causing your error using caspool. Ctakes and > uima both suffer from a lack of descriptive error output. > > Here is something that was used a while ago for testing. The trick is > that the cas pool is just used for storage of reusable cas objects. > The Java ExecutorService handles the actual thread maintenance. > caspool is like jcaspool. > > public class ParallelXcasDeserializer { > > static private final Logger LOGGER = Logger.getLogger( > "ParallelXcasDeserializer" ); > static private final int PROCESS_COUNT = 10; > static private final CasPool CAS_POOL = createCasPool( > PROCESS_COUNT ); > > static private CasPool createCasPool( final int processCount ) { > try { > final AnalysisEngineDescription fastPipelineDesc = > ClinicalPipelineFactory.getFastPipeline(); > final AnalysisEngine fastPipeline = > AnalysisEngineFactory.createEngine( > fastPipelineDesc ); > return new CasPool( processCount, fastPipeline ); > } catch ( UIMAException | MalformedURLException multE ) { > LOGGER.error( multE.getMessage() ); > } > return null; > } > > static private final class XCasDeserializer implements Runnable { > private final String _xcasFilePath; > private XCasDeserializer( final String xcasFilePath ) { > _xcasFilePath = xcasFilePath; > } > @Override > public void run() { > final CAS cas = CAS_POOL.getCas(); > try ( InputStream xCasStream = new FileInputStream( > _xcasFilePath > ) ) { > XCASDeserializer.deserialize( xCasStream, cas ); > final JCas jCas = cas.getJCas(); > OntologyConceptUtil.getCuis( jCas ).forEach( LOGGER::info ); > } catch ( IOException | SAXException | CASException multE ) { > LOGGER.error( multE.getMessage() ); > } > CAS_POOL.releaseCas( cas ); > } > } > > public static void main( final String... args ) { > if ( CAS_POOL == null ) { > LOGGER.error( "Couldn't create CAS Pool, exiting" ); > System.exit( 1 ); > } > final Path inputDir = Paths.get( args[ 0 ] ); > final ExecutorService executor = Executors.newFixedThreadPool( > PROCESS_COUNT ); > try ( DirectoryStream<Path> filePaths = > Files.newDirectoryStream( inputDir ) ) { > for ( Path filePath : filePaths ) { > executor.execute( new XCasDeserializer( > filePath.toString() ) ); > } > } catch ( IOException ioE ) { > LOGGER.error( ioE.getMessage() ); > } > executor.shutdown(); > } > > } > > -----Original Message----- > From: Alaa al Barari [mailto:alaa.albar...@gmail.com] > Sent: Thursday, February 16, 2017 7:33 AM > To: dev@ctakes.apache.org > Subject: jcasPool problem > > 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.ResourceMethodInvocationHan > dle > rFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81) > at > org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodD > isp > atcher.invoke(AbstractJavaResourceMethodDispatcher.java:125) > at > org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatche > rPr > ovider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherPr > ovider.java:152) > at > org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodD > isp > 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.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$Worker.doWork( > AbstractThreadPool.java:564) > at > org.glassfish.grizzly.threadpool.AbstractThreadPool$ > 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.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.proc > ess( > 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) > -- Eng Alaa Al-Barari phone 0599297470
