Module Filter - java.util.Arrays$ArrayList cannot be cast to java.util.Set

Development
1

Hi All,

I created an openmrs module to import new Concepts using a XLS file. I’m getting the follwing error in the controller after Import the xls file ( https://github.com/Guimino/conceptimport.git),

An Internal Error has Occurred java.lang.ClassCastException java.util.Arrays$ArrayList cannot be cast to java.util.Set

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Hide Stack Trace org.hibernate.type.SetType.wrap(SetType.java:61) org.hibernate.event.def.WrapVisitor.processArrayOrNewCollection(WrapVisitor.java:106) org.hibernate.event.def.WrapVisitor.processCollection(WrapVisitor.java:73) org.hibernate.event.def.AbstractVisitor.processValue(AbstractVisitor.java:122) org.hibernate.event.def.WrapVisitor.processValue(WrapVisitor.java:120) org.hibernate.event.def.AbstractVisitor.processEntityPropertyValues(AbstractVisitor.java:77) org.hibernate.event.def.DefaultFlushEntityEventListener.wrapCollections(DefaultFlushEntityEventListener.java:218) org.hibernate.event.def.DefaultFlushEntityEventListener.onFlushEntity(DefaultFlushEntityEventListener.java:152) org.hibernate.event.def.AbstractFlushingEventListener.flushEntities(AbstractFlushingEventListener.java:219) org.hibernate.event.def.AbstractFlushingEventListener.flushEverythingToExecutions(AbstractFlushingEventListener.java:99) org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:50) org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216) org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:383) org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:133) org.springframework.orm.hibernate3.HibernateTransactionManager.doCommit(HibernateTransactionManager.java:657) org.springframework.transaction.support.AbstractPlatformTransactionManager.processCommit(AbstractPlatformTransactionManager.java:755) org.springframework.transaction.support.AbstractPlatformTransactionManager.commit(AbstractPlatformTransactionManager.java:724) org.springframework.transaction.interceptor.TransactionAspectSupport.commitTransactionAfterReturning(TransactionAspectSupport.java:475) org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:270) org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:94) org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) com.sun.proxy.$Proxy1257.createPharmaceuticalFormConcepts(Unknown Source) org.openmrs.module.conceptimport.web.controller.ConceptImportManageController.onSubmit(ConceptImportManageController.java:61) sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) java.lang.reflect.Method.invoke(Method.java:606) org.springframework.web.bind.annotation.support.HandlerMethodInvoker.invokeHandlerMethod(HandlerMethodInvoker.java:176) org.springframework.web.servlet.mvc.annotation.AnnotationMethodHandlerAdapter.invokeHandlerMethod(AnnotationMethodHandlerAdapter.java:440) org.springframework.web.servlet.mvc.annotation.AnnotationMethodHandlerAdapter.handle(AnnotationMethodHandlerAdapter.java:428) org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:925) org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:856) org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:953) org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:855) javax.servlet.http.HttpServlet.service(HttpServlet.java:650) org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:829) javax.servlet.http.HttpServlet.service(HttpServlet.java:731) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) org.openmrs.module.web.filter.ForcePasswordChangeFilter.doFilter(ForcePasswordChangeFilter.java:61) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) org.openmrs.module.web.filter.ModuleFilterChain.doFilter(ModuleFilterChain.java:72) org.openmrs.module.web.filter.ModuleFilter.doFilter(ModuleFilter.java:54) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) org.openmrs.web.filter.OpenmrsFilter.doFilterInternal(OpenmrsFilter.java:109) org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:230) org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) org.openmrs.web.filter.StartupFilter.doFilter(StartupFilter.java:105) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) org.openmrs.web.filter.StartupFilter.doFilter(StartupFilter.java:105) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) org.openmrs.web.filter.StartupFilter.doFilter(StartupFilter.java:105) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88) org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:218) org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110) org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:506) org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169) org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962) org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:452) org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1087) org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637) org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2536) org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2525) java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) java.lang.Thread.run(Thread.java:745) org.openmrs.api.APIException: A user context must first be passed to setUserContext()…use Context.openSession() (and closeSession() to prevent memory leaks!) before using the API at org.openmrs.api.context.Context.getUserContext(Context.java:245) at org.openmrs.api.context.Context.getAuthenticatedUser(Context.java:644) at org.openmrs.aop.AuthorizationAdvice.before(AuthorizationAdvice.java:51) at org.springframework.aop.framework.adapter.MethodBeforeAdviceInterceptor.invoke(MethodBeforeAdviceInterceptor.java:50) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at com.sun.proxy.$Proxy1242.getGlobalProperty(Unknown Source) at org.apache.jsp.WEB_002dINF.view.uncaughtException_jsp._jspService(uncaughtException_jsp.java:551) at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70) at javax.servlet.http.HttpServlet.service(HttpServlet.java:731) at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:439) at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:395) at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:339) at javax.servlet.http.HttpServlet.service(HttpServlet.java:731) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:101) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:101) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:747) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:487) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:410) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:337) at org.springframework.web.servlet.view.InternalResourceView.renderMergedOutputModel(InternalResourceView.java:238) at org.springframework.web.servlet.view.AbstractView.render(AbstractView.java:263) at org.springframework.web.servlet.DispatcherServlet.render(DispatcherServlet.java:1208) at org.springframework.web.servlet.DispatcherServlet.processDispatchResult(DispatcherServlet.java:992) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:939) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:856) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:953) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:855) at javax.servlet.http.HttpServlet.service(HttpServlet.java:650) at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:829) at javax.servlet.http.HttpServlet.service(HttpServlet.java:731) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:101) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:230) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:747) at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:487) at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:410) at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:337) at org.apache.catalina.core.StandardHostValve.custom(StandardHostValve.java:479) at org.apache.catalina.core.StandardHostValve.throwable(StandardHostValve.java:417) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:204) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:452) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1087) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637) at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2536) at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2525) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745)

2

This seems related to some issue where some collection getter on Concept was changed to return a Set instead of a list, i think it’s indexTerms. I believe there is a ticket to fix it to return a list, in the meantime you might want to update your code to expect a Set.

3

Thank you for your quick reply.

That issue of returning a “Set” is solved. The problem now is: If you check the code in the repo: We @steliomo have a class ConceptImportManageController that has a service to import and create Pharmacy concepts: this.importConceptDictionaryService.createPharmaceuticalFormConcepts(concepts);

The process of importing the concepts was giving an error of returning a Set and the tansaction was rolling back. So we added this: this.sessionFactory.getCurrentSession().setFlushMode(FlushMode.MANUAL)

And now the import process finishes but when the request/execution of the service completes and is returning to the controller,

this error appear as you see in the stacktrace

org.openmrs.module.conceptimport.web.controller.ConceptImportManageController.onSubmit(ConceptImportManageController.java:61)

org.openmrs.module.web.filter.ForcePasswordChangeFilter.doFilter(ForcePasswordChangeFilter.java:61)

org.openmrs.module.web.filter.ModuleFilterChain.doFilter(ModuleFilterChain.java:72) org.openmrs.module.web.filter.ModuleFilter.doFilter(ModuleFilter.java:54)

org.openmrs.web.filter.OpenmrsFilter.doFilterInternal(OpenmrsFilter.java:109)

org.openmrs.web.filter.StartupFilter.doFilter(StartupFilter.java:105)

4

The stack trace you shared is not helpful because it looks incomplete, setting the flush mode to manual is never a good work-around for a hibernate related exception you’re encountering. Finding and fixing the issue causing the exception is always the way to go, I guess you should remove it now after all the exception is gone.

5

Hi, I solved it . beyond setting flush mode to manual , after finishing the import I was delivering the flushMode to default value, so I removed this last (I left it manual and it works).

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6

Hi all,

Well I agree with you @wyclif when you say that controlling hibernate session manually is not a good approach but at the same time is some how tricky to deal with special classes in omrs like Obs, Order, Concept and so on. When I got that problem I had no choice. I created a util class to control hibernate Flush Mode.

7

You should not be leaving the hibernate session at manual, you should set it back to the original value and not the ‘default’ value.

What you’re trying to do is a good thing but it’s the way you’re implementing it that I think doesn’t seem exactly correct to me. I understand that you want to do a bulk import and flush to the DB once may be because you don’t want premature flushes to lead to failures due to unmet constraints. But this can lead to running out of memory in case your import is fairly large with all those objects added to the hibernate session, what you want to do is to set the import to manual and then flush manually say every after 100 items are imported, when the entire import is done you MUST set the flush mode back to the ORIGINAL value, it means you would have to cache the original value before setting it to manual and use the cached value to reset it and you want to reset the value in a finally clause.

1 Like