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Posted to dev@ctakes.apache.org by Alaa al Barari <al...@gmail.com> on 2017/02/16 12:33:24 UTC
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.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
at
org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:125)
at
org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:152)
at
org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.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.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)
RE: jcasPool problem
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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.albarari@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.Finan@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.albarari@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
Re: jcasPool problem
Posted by Alaa al Barari <al...@gmail.com>.
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.Finan@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.albarari@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.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.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.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)
>
--
Eng Alaa Al-Barari
phone 0599297470
RE: jcasPool problem
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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.albarari@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.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
at
org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:125)
at
org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:152)
at
org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.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.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)
RE: jcasPool problem
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
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 <sh...@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
> <al...@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 <sh...@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
Re: jcasPool problem
Posted by Alaa al Barari <al...@gmail.com>.
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 <al...@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 <sh...@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 <al...@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 <sh...@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.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: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
Re: jcasPool problem
Posted by Alaa al Barari <al...@gmail.com>.
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 <sh...@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 <al...@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 <sh...@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.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: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.
> 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.
> > > 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
Re: jcasPool problem
Posted by shahid ashraf <sh...@trialx.com>.
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 <al...@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 <sh...@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.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: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.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.
> > 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
Re: jcasPool problem
Posted by Alaa al Barari <al...@gmail.com>.
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 <sh...@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 <al...@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.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.
> 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
Re: jcasPool problem
Posted by shahid ashraf <sh...@trialx.com>.
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 <al...@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.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.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