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IHTSDO / snowstorm

Scalable SNOMED CT Terminology Server using Elasticsearch
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FHIR valuesets not accessible #213

Closed kaboyles closed 3 years ago

kaboyles commented 3 years ago

Hello,

Our customer is unable to access the FHIR valuesets in our test snowstorm server.

Several calls to the API's, regardless of method answers:

{ "resourceType": "OperationOutcome", "issue": [ { "severity": "error", "code": "processing", "diagnostics": "Failed to call access method: java.lang.NullPointerException" } ] }

It works in our production and qa environments.

Any hints?

Thanks, Kim

pgwilliams commented 3 years ago

Hi Kim When you try try the call they're making yourself, do you see the same thing? What shows up in the logs? We've made a lot of updates to the FHIR API in the last week or so, could you also confirm what version you're running? Thanks!

pgwilliams commented 3 years ago

But in any event, if anyone is seeing a NullPointerException then that's a fault with our code. We should be detecting whatever the problem is and replying with some informative error about the cause. Hence assigning the 'bug' label here.

kaboyles commented 3 years ago

Yes, I see the same....Logs coming.

Tannjorn commented 3 years ago

I have some more info that might help, while we are waiting for our supplier to get the logs.

We have three "identical" servers with slightly different content. But there is one major difference at the time of update, the server which is now sending a NullPointerException had a few ValueSets in place. There others had none.

kaboyles commented 3 years ago

Snowstorm version 5.0.6 for all three servers.

pgwilliams commented 3 years ago

Great. If you can get me the call that is being made, that would help also. Thanks!

Tannjorn commented 3 years ago

Yes, all servers are 5.0.6. Would you think a patch/upgrade could help? Is there a newer version available?

Anyway. You can use this https://test.terminologi.ehelse.no/fhir/ValueSet in a browser. I have used the same in Postman, test.terminologi.ehelse.no/fhir as the baseUrl and ValueSet as the only additional function. I have also tried with further queries like trying to expand a specific set, but the error remains the same.

Our two other base URLs are terminologi.ehelse.no and qa.terminologi.ehelse.no.

Trying to use the functions CodeSystem or Translate works fine on all servers.

pgwilliams commented 3 years ago

Oh you're seeing the error even on the basic type url for all ValueSets? Yes there is a newer version available (6.0.0 available on Master to build but not yet published as a Jar), but we didn't change anything in the rendering of ValueSets so I wouldn't expect it to fix the issue. I think the code must be expecting one or more fields to be populated in your VS and they haven't been. This explains when you only see it in your test server. So if you can get me that Exception stack trace from the logs then I can tell you which field it is and you can re-create that ValueSet to fix the problem. I will also fix the code to do something more helpful in this situation!

Zawaken commented 3 years ago

Here's the exception stack we see in the logs. Let me know if you need any more info.



ca.uhn.fhir.rest.server.exceptions.InternalErrorException: Failed to call access method: java.lang.NullPointerException
        at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:244)
        at ca.uhn.fhir.rest.server.method.SearchMethodBinding.invokeServer(SearchMethodBinding.java:256)
        at ca.uhn.fhir.rest.server.method.SearchMethodBinding.invokeServer(SearchMethodBinding.java:49)
        at ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding.doInvokeServer(BaseResourceReturningMethodBinding.java:247)
        at ca.uhn.fhir.rest.server.method.BaseResourceReturningMethodBinding.invokeServer(BaseResourceReturningMethodBinding.java:384)
        at ca.uhn.fhir.rest.server.RestfulServer.handleRequest(RestfulServer.java:1002)
        at ca.uhn.fhir.rest.server.RestfulServer.doGet(RestfulServer.java:336)
        at ca.uhn.fhir.rest.server.RestfulServer.service(RestfulServer.java:1695)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:733)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:53)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
        at io.kaicode.rest.util.branchpathrewrite.BranchPathUriRewriteFilter.doFilter(BranchPathUriRewriteFilter.java:50)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
        at org.snomed.snowstorm.rest.security.RequestHeaderAuthenticationDecoratorWithRequiredRole.doFilterInternal(RequestHeaderAuthenticationDecoratorWithRequiredRole.java:43)
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:103)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:320)
        at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:118)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
        at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:137)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
        at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
        at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:158)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
        at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:63)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
        at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:116)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
        at org.springframework.security.web.header.HeaderWriterFilter.doHeadersAfter(HeaderWriterFilter.java:92)
        at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:77)
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
        at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:105)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
        at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:56)
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119)
        at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:334)
        at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:215)
        at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:178)
        at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:358)
        at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:271)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
        at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:100)
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
        at org.springframework.web.filter.FormContentFilter.doFilterInternal(FormContentFilter.java:93)
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
        at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:201)
        at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:119)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:202)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96)
        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:541)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:139)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:74)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)
        at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:373)
        at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65)
        at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:868)
        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1589)
        at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.lang.Thread.run(Thread.java:748)
Caused by: java.lang.reflect.InvocationTargetException: null
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at ca.uhn.fhir.rest.server.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:239)
        ... 79 common frames omitted
Caused by: java.lang.NullPointerException: null
        at org.snomed.snowstorm.fhir.domain.ValueSetWrapper.getValueSet(ValueSetWrapper.java:50)
        at org.snomed.snowstorm.fhir.services.FHIRValueSetProvider.lambda$findValuesets$0(FHIRValueSetProvider.java:157)
        at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
        at java.util.ArrayList$Itr.forEachRemaining(ArrayList.java:901)
        at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
        at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
        at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:566)
        at org.snomed.snowstorm.fhir.services.FHIRValueSetProvider.findValuesets(FHIRValueSetProvider.java:159)
        ... 84 common frames omitted```
pgwilliams commented 3 years ago

Sweet, thank you so much for that log I see the problem. I'll see how quickly I can get a fix into the build.

FYI @kaicode

pgwilliams commented 3 years ago

Would you be able to try installing this release and let me know how it goes please? https://github.com/IHTSDO/snowstorm/releases/tag/5.1.1

We're also publishing 6.0.1 in the next week or so. That build will not include this fix so you'll want to skip that one and we'll see about a 6.0.2 at some point that will include this particular fix.

kaboyles commented 3 years ago

Patch seems to be working at initial glance/internally. Thanks!! Tannjorn can update more on what the customer is seeing.

Tannjorn commented 3 years ago

This issue can now be closed, as further testing has confirmed that all is good.

pgwilliams commented 3 years ago

Thanks for confirming @kaboyles & @Tannjorn !