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From John Green <john.travis.gr...@gmail.com>
Subject Re: YTEX Semantic Sim RESTful
Date Tue, 14 Oct 2014 13:19:46 GMT
Thanks Vijay! You are the best! It now works with
http://localhost:8080/services/rest/similarity?conceptGraph=sct-msh-csp-aod&concept1=C0018787&concept2=C0024109&metrics=LCH,INTRINSIC_LCH
which is the name of the graph it was loading.

Copying beans-kernel-simweb.xml
<https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-ytex-res/src/main/resources/org/apache/ctakes/ytex/web/beans-kernel-simweb.xml>
worked
perfectly, thank you very much for the time you spent on this.

Best,
JG

On Tue, Oct 14, 2014 at 8:58 AM, vijay garla <vngarla@gmail.com> wrote:

> 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.green@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.ebert@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)
> > > >
> > > > ------------------------------
> > > > *Powered by Jetty://*
> > > > ------------------------------
> > > >
> > >
> > >
> >
>

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