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java.lang.reflect.UndeclaredThrowableException when download PLP #2132

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ttemnikova opened this issue Oct 12, 2022 · 1 comment · Fixed by #2135
Closed

java.lang.reflect.UndeclaredThrowableException when download PLP #2132

ttemnikova opened this issue Oct 12, 2022 · 1 comment · Fixed by #2135
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@ssuvorov-fls
Labels
bug
Milestone
v2.12.1

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@ttemnikova
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Expected behavior

A correct .zip is downloaded

Actual behavior

Nothing happens on UI. There is the following error in the server log:

2022-10-12 15:19:25.197 ERROR http-nio-8080-exec-1 org.ohdsi.webapi.util.GenericExceptionMapper - [] - java.lang.reflect.UndeclaredThrowableException
	at com.sun.proxy.$Proxy291.exportAnalysis(Unknown Source)
	at org.ohdsi.webapi.prediction.PredictionController.downloadPackage(PredictionController.java:182)
	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 org.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
	at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:144)
	at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161)
	at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:160)
	at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:99)
	at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:389)
	at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:347)
	at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:102)
	at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:326)
	at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
	at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
	at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
	at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
	at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
	at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
	at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305)
	at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154)
	at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:473)
	at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:427)
	at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:388)
	at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:341)
	at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:228)
	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:52)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
	at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:61)
	at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
	at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
	at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
	at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
	at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
	at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
	at org.ohdsi.webapi.shiro.filters.ResponseNoCacheFilter.doFilter(ResponseNoCacheFilter.java:26)
	at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
	at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
	at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
	at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
	at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
	at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
	at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:118)
	at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
	at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
	at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
	at org.apache.shiro.web.servlet.ProxiedFilterChain.doFilter(ProxiedFilterChain.java:66)
	at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:450)
	at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)
	at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)
	at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)
	at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:387)
	at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
	at org.apache.shiro.web.servlet.AdviceFilter.executeChain(AdviceFilter.java:108)
	at org.apache.shiro.web.servlet.AdviceFilter.doFilterInternal(AdviceFilter.java:137)
	at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
	at org.ohdsi.webapi.shiro.filters.CacheFilter.doFilter(CacheFilter.java:35)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
	at org.ohdsi.webapi.shiro.filters.ExceptionHandlerFilter.doFilter(ExceptionHandlerFilter.java:28)
	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:99)
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
	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.HttpPutFormContentFilter.doFilterInternal(HttpPutFormContentFilter.java:109)
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
	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.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:93)
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
	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:197)
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
	at org.springframework.boot.web.support.ErrorPageFilter.doFilter(ErrorPageFilter.java:128)
	at org.springframework.boot.web.support.ErrorPageFilter.access$000(ErrorPageFilter.java:66)
	at org.springframework.boot.web.support.ErrorPageFilter$1.doFilterInternal(ErrorPageFilter.java:103)
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
	at org.springframework.boot.web.support.ErrorPageFilter.doFilter(ErrorPageFilter.java:121)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:197)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:97)
	at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:543)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:135)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
	at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:698)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:78)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:367)
	at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:639)
	at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:65)
	at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:882)
	at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1693)
	at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
	at org.apache.tomcat.util.threads.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1191)
	at org.apache.tomcat.util.threads.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:659)
	at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
	at java.lang.Thread.run(Thread.java:750)
Caused by: java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.ohdsi.webapi.shiro.management.DataSourceAccessBeanPostProcessor.lambda$postProcessAfterInitialization$1(DataSourceAccessBeanPostProcessor.java:58)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
	... 118 more
Caused by: java.lang.RuntimeException: java.lang.RuntimeException: com.fasterxml.jackson.databind.exc.MismatchedInputException: Cannot deserialize instance of `java.lang.String` out of START_OBJECT token
 at [Source: (String)"{"id":178,"name":"demo go bleed in nsaids","description":null,"version":"v2.7.0","skeletonType":"PatientLevelPredictionStudy","skeletonVersion":"v0.0.1","createdBy":{"id":1023,"name":"eldar.allakhverdiiev@odysseusinc.com","login":"eldar.allakhverdiiev@odysseusinc.com"},"createdDate":1665587586788,"modifiedBy":null,"modifiedDate":null,"cohortDefinitions":[{"id":1245,"name":"demo gi bleed"},{"id":1244,"name":"demo nsaids"}],"conceptSets":[],"conceptSetCrossReference":[],"targetIds":[1244],"outcome"[truncated 8821 chars]; line: 1, column: 166] (through reference chain: org.ohdsi.webapi.prediction.specification.PatientLevelPredictionAnalysisImpl["createdBy"])
	at org.ohdsi.webapi.prediction.PredictionServiceImpl.exportAnalysis(PredictionServiceImpl.java:196)
	at org.ohdsi.webapi.prediction.PredictionServiceImpl.exportAnalysis(PredictionServiceImpl.java:186)
	at org.ohdsi.webapi.prediction.PredictionServiceImpl$$FastClassBySpringCGLIB$$9bddc398.invoke(<generated>)
	at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:736)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:283)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:671)
	at org.ohdsi.webapi.prediction.PredictionServiceImpl$$EnhancerBySpringCGLIB$$a7bc0de3.exportAnalysis(<generated>)
	... 125 more
Caused by: java.lang.RuntimeException: com.fasterxml.jackson.databind.exc.MismatchedInputException: Cannot deserialize instance of `java.lang.String` out of START_OBJECT token
 at [Source: (String)"{"id":178,"name":"demo go bleed in nsaids","description":null,"version":"v2.7.0","skeletonType":"PatientLevelPredictionStudy","skeletonVersion":"v0.0.1","createdBy":{"id":1023,"name":"eldar.allakhverdiiev@odysseusinc.com","login":"eldar.allakhverdiiev@odysseusinc.com"},"createdDate":1665587586788,"modifiedBy":null,"modifiedDate":null,"cohortDefinitions":[{"id":1245,"name":"demo gi bleed"},{"id":1244,"name":"demo nsaids"}],"conceptSets":[],"conceptSetCrossReference":[],"targetIds":[1244],"outcome"[truncated 8821 chars]; line: 1, column: 166] (through reference chain: org.ohdsi.webapi.prediction.specification.PatientLevelPredictionAnalysisImpl["createdBy"])
	at org.ohdsi.analysis.Utils.deserialize(Utils.java:239)
	at org.ohdsi.webapi.prediction.PredictionServiceImpl.exportAnalysis(PredictionServiceImpl.java:194)
	... 136 more
Caused by: com.fasterxml.jackson.databind.exc.MismatchedInputException: Cannot deserialize instance of `java.lang.String` out of START_OBJECT token
 at [Source: (String)"{"id":178,"name":"demo go bleed in nsaids","description":null,"version":"v2.7.0","skeletonType":"PatientLevelPredictionStudy","skeletonVersion":"v0.0.1","createdBy":{"id":1023,"name":"eldar.allakhverdiiev@odysseusinc.com","login":"eldar.allakhverdiiev@odysseusinc.com"},"createdDate":1665587586788,"modifiedBy":null,"modifiedDate":null,"cohortDefinitions":[{"id":1245,"name":"demo gi bleed"},{"id":1244,"name":"demo nsaids"}],"conceptSets":[],"conceptSetCrossReference":[],"targetIds":[1244],"outcome"[truncated 8821 chars]; line: 1, column: 166] (through reference chain: org.ohdsi.webapi.prediction.specification.PatientLevelPredictionAnalysisImpl["createdBy"])
	at com.fasterxml.jackson.databind.exc.MismatchedInputException.from(MismatchedInputException.java:59)
	at com.fasterxml.jackson.databind.DeserializationContext.reportInputMismatch(DeserializationContext.java:1445)
	at com.fasterxml.jackson.databind.DeserializationContext.handleUnexpectedToken(DeserializationContext.java:1219)
	at com.fasterxml.jackson.databind.DeserializationContext.handleUnexpectedToken(DeserializationContext.java:1129)
	at com.fasterxml.jackson.databind.deser.std.StringDeserializer.deserialize(StringDeserializer.java:63)
	at com.fasterxml.jackson.databind.deser.std.StringDeserializer.deserialize(StringDeserializer.java:10)
	at com.fasterxml.jackson.databind.deser.impl.MethodProperty.deserializeAndSet(MethodProperty.java:129)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer.vanillaDeserialize(BeanDeserializer.java:288)
	at com.fasterxml.jackson.databind.deser.BeanDeserializer.deserialize(BeanDeserializer.java:151)
	at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:4218)
	at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3214)
	at com.fasterxml.jackson.databind.ObjectMapper.readValue(ObjectMapper.java:3182)
	at org.ohdsi.analysis.Utils.deserialize(Utils.java:237)
	... 137 more

Steps to reproduce behavior

  1. Login
  2. Create a PLP
  3. Fill in the fields
  4. Save
  5. Go to Utilities tab -> Review & Download -> Download Study Package
  6. Enter an archive name and click Download button
@anton-abushkevich
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anton-abushkevich commented Oct 13, 2022 •
edited

There are unused fields in the PLP/PLE specification: createdBy, createdDate, modifiedBy, modifiedDate. These fields are already on the top level of the analysis object (just like in all other assets - concept sets, cohorts and so on) - so they are redundant in the screcification JSON and only causing problems. I suggest we ignore them on serilization/deserialization.

There was an attempt to fix this on the frontend: OHDSI/Atlas#2761 - but apparently it is not working for old analyses or copies of old analyses, which need to be resaved for fix to work.

anton-abushkevich added a commit that referenced this issue Oct 13, 2022
@anton-abushkevich
java.lang.reflect.UndeclaredThrowableException when download PLP #2132
b21693d
@anton-abushkevich anton-abushkevich mentioned this issue Oct 13, 2022
Merged
@anton-abushkevich anton-abushkevich added this to the v2.12.1 milestone Oct 14, 2022
anton-abushkevich added a commit that referenced this issue Oct 26, 2022
@anton-abushkevich
java.lang.reflect.UndeclaredThrowableException when download PLP #2132…
cfa5583 
… (#2135)
anton-abushkevich added a commit that referenced this issue Oct 26, 2022
@anton-abushkevich
java.lang.reflect.UndeclaredThrowableException when download PLP #2132…
b3a3420 
… (#2135)

(cherry picked from commit cfa5583)
ssuvorov-fls pushed a commit that referenced this issue Jan 20, 2023
@anton-abushkevich @ssuvorov-fls
java.lang.reflect.UndeclaredThrowableException when download PLP #2132…
b5a729b 
… (#2135)

(cherry picked from commit cfa5583)
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java.lang.reflect.UndeclaredThrowableException when download PLP #2132 OHDSI/WebAPI
4 participants
@anton-abushkevich @ssuvorov-fls @alex-odysseus @ttemnikova