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Posted to user@ctakes.apache.org by John Green <jo...@gmail.com> on 2014/10/13 17:29:13 UTC
YTEX Semantic Sim RESTful
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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Re: YTEX Semantic Sim RESTful
Posted by John Green <jo...@gmail.com>.
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 <vn...@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 <jo...@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://*
> > > > ------------------------------
> > > >
> > >
> > >
> >
>
Re: YTEX Semantic Sim RESTful
Posted by vijay garla <vn...@gmail.com>.
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 <jo...@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$3.run(QueuedThreadPool.java:532)
> > > at java.lang.Thread.run(Thread.java:745)
> > >
> > > ------------------------------
> > > *Powered by Jetty://*
> > > ------------------------------
> > >
> >
> >
>
Re: YTEX Semantic Sim RESTful
Posted by John Green <jo...@gmail.com>.
Good idea Kim! Unfortunately, that wasn't it. Ill admit, though, I hadnt
looked at that variable yet.
Thanks for your help,
JG
On Mon, Oct 13, 2014 at 6:28 PM, Kim Ebert <ki...@perfectsearchcorp.com>
wrote:
> Perhaps your JVM is running out of heap? I've noticed that when I run
> out of heap, cTakes tends to behave erratically.
>
> Kim Ebert
> 1.801.669.7342
> Perfect Search Corp
> http://www.perfectsearchcorp.com/
>
> On 10/13/2014 09:29 AM, John Green wrote:
> > I've been putting off debugging this as it was a piece of this app Im
> > working on, but one that fit in down the road in development. Development
> > has progressed, and here I am. I have posted this one before, was hoping
> to
> > find fresh help.
> >
> > When running ytex.sh in a distro installed at something like
> > ./ctakes3.2.0/apache-ctakes-3.1.2-SNAPSHOT/bin$ 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$3.run(QueuedThreadPool.java:532)
> > at java.lang.Thread.run(Thread.java:745)
> >
> > ------------------------------
> > *Powered by Jetty://*
> > ------------------------------
> >
>
>
Re: YTEX Semantic Sim RESTful
Posted by Kim Ebert <ki...@perfectsearchcorp.com>.
Perhaps your JVM is running out of heap? I've noticed that when I run
out of heap, cTakes tends to behave erratically.
Kim Ebert
1.801.669.7342
Perfect Search Corp
http://www.perfectsearchcorp.com/
On 10/13/2014 09:29 AM, John Green wrote:
> I've been putting off debugging this as it was a piece of this app Im
> working on, but one that fit in down the road in development. Development
> has progressed, and here I am. I have posted this one before, was hoping to
> find fresh help.
>
> When running ytex.sh in a distro installed at something like
> ./ctakes3.2.0/apache-ctakes-3.1.2-SNAPSHOT/bin$ 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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