Hi John, Looking at the code, that error is due to the concept graph 'umls' not being loaded. by default, ytex is configured to use the sct-rxnorm concept graph.
Can you see if this works: http://localhost:8080/services/rest/similarity?conceptGraph=sct-rxnorm&concept1=C0018787&concept2=C0024109&metrics=LCH,INTRINSIC_LCH To set the concept graph name set the ytex.conceptGraphName in resources/org/apache/ctakes/ytex/ytex.properties If not, there may be an issue in a config file; if you get another NPE, please * copy https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-kernel-simweb.xml to CTAKES_HOME/resources/org/apache/ctakes/ytex/web/ * copy https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-distribution/src/main/bin/ytexweb.bat to CTAKES_HOME/bin HTH! Vijay On Tue, Oct 14, 2014 at 1:51 PM, John Green <john.travis.gr...@gmail.com> wrote: > Good idea Kim! Unfortunately, that wasn't it. Ill admit, though, I hadnt > looked at that variable yet. > > Thanks for your help, > JG > > On Mon, Oct 13, 2014 at 6:28 PM, Kim Ebert < > kim.eb...@perfectsearchcorp.com> > wrote: > > > 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) > > > > > > ------------------------------ > > > 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