Perhaps your JVM is running out of heap? I've noticed that when I run out of heap, cTakes tends to behave erratically.
Kim Ebert 1.801.669.7342 Perfect Search Corp http://www.perfectsearchcorp.com/ On 10/13/2014 09:29 AM, John Green wrote: > I've been putting off debugging this as it was a piece of this app Im > working on, but one that fit in down the road in development. Development > has progressed, and here I am. I have posted this one before, was hoping to > find fresh help. > > When running ytex.sh in a distro installed at something like > ./ctakes3.2.0/apache-ctakes-3.1.2-SNAPSHOT/bin$ under Ubuntu 14 and trying > to access the restful interface per the docs on a query like such as > http://localhost:8080/similarity?conceptGraph=umls&concept1=C0018787&concept2=C0024109&metrics=LCH,INTRINSIC_LCH > the query fails with a 500 (see below). > > Of note, the http://localhost:8080/semanticSim.jsf works just fine. > > Am I missing something simple? > > Thanks for any and all help, > Best, > JG > > 500 error: > HTTP ERROR 500 > > Problem accessing /services/rest/similarity. Reason: > > Server Error > > Caused by: > > java.lang.RuntimeException: org.apache.cxf.interceptor.Fault > at > org.apache.cxf.interceptor.AbstractFaultChainInitiatorObserver.onMessage(AbstractFaultChainInitiatorObserver.java:116) > at > org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:333) > at > org.apache.cxf.transport.ChainInitiationObserver.onMessage(ChainInitiationObserver.java:121) > at > org.apache.cxf.transport.http.AbstractHTTPDestination.invoke(AbstractHTTPDestination.java:239) > at > org.apache.cxf.transport.servlet.ServletController.invokeDestination(ServletController.java:248) > at > org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:222) > at > org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:153) > at > org.apache.cxf.transport.servlet.CXFNonSpringServlet.invoke(CXFNonSpringServlet.java:167) > at > org.apache.cxf.transport.servlet.AbstractHTTPServlet.handleRequest(AbstractHTTPServlet.java:286) > at > org.apache.cxf.transport.servlet.AbstractHTTPServlet.doGet(AbstractHTTPServlet.java:211) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:687) > at > org.apache.cxf.transport.servlet.AbstractHTTPServlet.service(AbstractHTTPServlet.java:262) > at > org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:698) > at > org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:526) > at > org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:138) > at > org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:568) > at > org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:221) > at > org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1105) > at > org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:453) > at > org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:183) > at > org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1039) > at > org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) > at > org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:201) > at > org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:109) > at > org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) > at org.eclipse.jetty.server.Server.handle(Server.java:445) > at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:277) > at > org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:216) > at > org.eclipse.jetty.io.AbstractConnection$1.run(AbstractConnection.java:505) > at > org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:601) > at > org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:532) > at java.lang.Thread.run(Thread.java:745) > Caused by: org.apache.cxf.interceptor.Fault > at > org.apache.cxf.service.invoker.AbstractInvoker.createFault(AbstractInvoker.java:162) > at > org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:128) > at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:205) > at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:102) > at > org.apache.cxf.interceptor.ServiceInvokerInterceptor$1.run(ServiceInvokerInterceptor.java:58) > at > org.apache.cxf.interceptor.ServiceInvokerInterceptor.handleMessage(ServiceInvokerInterceptor.java:94) > at > org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:272) > ... 30 more > Caused by: java.lang.NullPointerException > at > org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl.getConceptSimilarityService(ConceptSimilarityWebServiceImpl.java:53) > at > org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl.similarity(ConceptSimilarityWebServiceImpl.java:36) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:606) > at > org.apache.cxf.service.invoker.AbstractInvoker.performInvocation(AbstractInvoker.java:180) > at > org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:96) > ... 35 more > > Caused by: > > org.apache.cxf.interceptor.Fault > at > org.apache.cxf.service.invoker.AbstractInvoker.createFault(AbstractInvoker.java:162) > at > org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:128) > at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:205) > at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:102) > at > org.apache.cxf.interceptor.ServiceInvokerInterceptor$1.run(ServiceInvokerInterceptor.java:58) > at > org.apache.cxf.interceptor.ServiceInvokerInterceptor.handleMessage(ServiceInvokerInterceptor.java:94) > at > org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:272) > at > org.apache.cxf.transport.ChainInitiationObserver.onMessage(ChainInitiationObserver.java:121) > at > org.apache.cxf.transport.http.AbstractHTTPDestination.invoke(AbstractHTTPDestination.java:239) > at > org.apache.cxf.transport.servlet.ServletController.invokeDestination(ServletController.java:248) > at > org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:222) > at > org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:153) > at > org.apache.cxf.transport.servlet.CXFNonSpringServlet.invoke(CXFNonSpringServlet.java:167) > at > org.apache.cxf.transport.servlet.AbstractHTTPServlet.handleRequest(AbstractHTTPServlet.java:286) > at > org.apache.cxf.transport.servlet.AbstractHTTPServlet.doGet(AbstractHTTPServlet.java:211) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:687) > at > org.apache.cxf.transport.servlet.AbstractHTTPServlet.service(AbstractHTTPServlet.java:262) > at > org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:698) > at > org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:526) > at > org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:138) > at > org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:568) > at > org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:221) > at > org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1105) > at > org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:453) > at > org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:183) > at > org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1039) > at > org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) > at > org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:201) > at > org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:109) > at > org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) > at org.eclipse.jetty.server.Server.handle(Server.java:445) > at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:277) > at > org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:216) > at > org.eclipse.jetty.io.AbstractConnection$1.run(AbstractConnection.java:505) > at > org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:601) > at > org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:532) > at java.lang.Thread.run(Thread.java:745) > Caused by: java.lang.NullPointerException > at > org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl.getConceptSimilarityService(ConceptSimilarityWebServiceImpl.java:53) > at > org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl.similarity(ConceptSimilarityWebServiceImpl.java:36) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:606) > at > org.apache.cxf.service.invoker.AbstractInvoker.performInvocation(AbstractInvoker.java:180) > at > org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:96) > ... 35 more > > Caused by: > > java.lang.NullPointerException > at > org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl.getConceptSimilarityService(ConceptSimilarityWebServiceImpl.java:53) > at > org.apache.ctakes.ytex.ws.ConceptSimilarityWebServiceImpl.similarity(ConceptSimilarityWebServiceImpl.java:36) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:606) > at > org.apache.cxf.service.invoker.AbstractInvoker.performInvocation(AbstractInvoker.java:180) > at > org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:96) > at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:205) > at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:102) > at > org.apache.cxf.interceptor.ServiceInvokerInterceptor$1.run(ServiceInvokerInterceptor.java:58) > at > org.apache.cxf.interceptor.ServiceInvokerInterceptor.handleMessage(ServiceInvokerInterceptor.java:94) > at > org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:272) > at > org.apache.cxf.transport.ChainInitiationObserver.onMessage(ChainInitiationObserver.java:121) > at > org.apache.cxf.transport.http.AbstractHTTPDestination.invoke(AbstractHTTPDestination.java:239) > at > org.apache.cxf.transport.servlet.ServletController.invokeDestination(ServletController.java:248) > at > org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:222) > at > org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:153) > at > org.apache.cxf.transport.servlet.CXFNonSpringServlet.invoke(CXFNonSpringServlet.java:167) > at > org.apache.cxf.transport.servlet.AbstractHTTPServlet.handleRequest(AbstractHTTPServlet.java:286) > at > org.apache.cxf.transport.servlet.AbstractHTTPServlet.doGet(AbstractHTTPServlet.java:211) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:687) > at > org.apache.cxf.transport.servlet.AbstractHTTPServlet.service(AbstractHTTPServlet.java:262) > at > org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:698) > at > org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:526) > at > org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:138) > at > org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:568) > at > org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:221) > at > org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1105) > at > org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:453) > at > org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:183) > at > org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1039) > at > org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:136) > at > org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:201) > at > org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:109) > at > org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) > at org.eclipse.jetty.server.Server.handle(Server.java:445) > at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:277) > at > org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:216) > at > org.eclipse.jetty.io.AbstractConnection$1.run(AbstractConnection.java:505) > at > org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:601) > at > org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:532) > at java.lang.Thread.run(Thread.java:745) > > ------------------------------ > *Powered by Jetty://* > ------------------------------ >
