Startup NPE on application termination with running jobs

[marikaris]

How to Reproduce

Kill application when still having running jobs
Start again

Expected behavior

Application reindexes failed jobs

Observed behavior

Nullpointer

14:34:01.037 [RMI TCP Connection(2)-127.0.0.1] INFO  o.m.bootstrap.MolgenisBootstrapper - Bootstrapping application ...
14:34:03.896 [RMI TCP Connection(2)-127.0.0.1] ERROR o.s.web.context.ContextLoader - Context initialization failed
java.lang.NullPointerException: null
	at org.molgenis.data.support.EntityTypeUtils.isReferenceType(EntityTypeUtils.java:104)
	at org.molgenis.util.EntityUtils.getTypedValue(EntityUtils.java:40)
	at org.molgenis.data.index.bootstrap.IndexBootstrapper.registerIndexAction(IndexBootstrapper.java:84)
	at java.util.Iterator.forEachRemaining(Iterator.java:116)
	at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
	at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)
	at org.molgenis.data.index.bootstrap.IndexBootstrapper.registerNewIndexActionForDirtyJobs(IndexBootstrapper.java:77)
	at java.util.ArrayList.forEach(ArrayList.java:1249)
	at org.molgenis.data.index.bootstrap.IndexBootstrapper.bootstrap(IndexBootstrapper.java:68)
	at org.molgenis.bootstrap.MolgenisBootstrapper.onApplicationEvent(MolgenisBootstrapper.java:100)
	at org.molgenis.bootstrap.MolgenisBootstrapper.onApplicationEvent(MolgenisBootstrapper.java:26)
	at org.molgenis.bootstrap.MolgenisBootstrapper$$FastClassBySpringCGLIB$$96732c53.invoke(<generated>)
	at org.springframework.cglib.proxy.MethodProxy.invoke(MethodProxy.java:204)
	at org.springframework.aop.framework.CglibAopProxy$CglibMethodInvocation.invokeJoinpoint(CglibAopProxy.java:738)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
	at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99)
	at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:282)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.aspectj.MethodInvocationProceedingJoinPoint.proceed(MethodInvocationProceedingJoinPoint.java:85)
	at org.molgenis.security.core.runas.RunAsSystemAspect.runAsSystem(RunAsSystemAspect.java:44)
	at org.molgenis.security.core.runas.RunAsSystemAspect.aroundAdvice(RunAsSystemAspect.java:23)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.springframework.aop.aspectj.AbstractAspectJAdvice.invokeAdviceMethodWithGivenArgs(AbstractAspectJAdvice.java:629)
	at org.springframework.aop.aspectj.AbstractAspectJAdvice.invokeAdviceMethod(AbstractAspectJAdvice.java:618)
	at org.springframework.aop.aspectj.AspectJAroundAdvice.invoke(AspectJAroundAdvice.java:70)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:168)
	at org.springframework.aop.interceptor.ExposeInvocationInterceptor.invoke(ExposeInvocationInterceptor.java:92)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
	at org.springframework.aop.framework.CglibAopProxy$DynamicAdvisedInterceptor.intercept(CglibAopProxy.java:673)
	at org.molgenis.bootstrap.MolgenisBootstrapper$$EnhancerBySpringCGLIB$$3c8e7d9b.onApplicationEvent(<generated>)
	at org.springframework.context.event.SimpleApplicationEventMulticaster.invokeListener(SimpleApplicationEventMulticaster.java:167)
	at org.springframework.context.event.SimpleApplicationEventMulticaster.multicastEvent(SimpleApplicationEventMulticaster.java:139)
	at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:393)
	at org.springframework.context.support.AbstractApplicationContext.publishEvent(AbstractApplicationContext.java:347)
	at org.springframework.context.support.AbstractApplicationContext.finishRefresh(AbstractApplicationContext.java:883)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:546)
	at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:443)
	at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:325)
	at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:107)
	at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5116)
	at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5634)
	at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
	at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:899)
	at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:875)
	at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
	at org.apache.catalina.startup.HostConfig.manageApp(HostConfig.java:1863)
	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.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
	at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
	at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801)
	at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:618)
	at org.apache.catalina.mbeans.MBeanFactory.createStandardContext(MBeanFactory.java:565)
	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.apache.tomcat.util.modeler.BaseModelMBean.invoke(BaseModelMBean.java:301)
	at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.invoke(DefaultMBeanServerInterceptor.java:819)
	at com.sun.jmx.mbeanserver.JmxMBeanServer.invoke(JmxMBeanServer.java:801)
	at javax.management.remote.rmi.RMIConnectionImpl.doOperation(RMIConnectionImpl.java:1468)
	at javax.management.remote.rmi.RMIConnectionImpl.access$300(RMIConnectionImpl.java:76)
	at javax.management.remote.rmi.RMIConnectionImpl$PrivilegedOperation.run(RMIConnectionImpl.java:1309)
	at javax.management.remote.rmi.RMIConnectionImpl.doPrivilegedOperation(RMIConnectionImpl.java:1401)
	at javax.management.remote.rmi.RMIConnectionImpl.invoke(RMIConnectionImpl.java:829)
	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 sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:346)
	at sun.rmi.transport.Transport$1.run(Transport.java:200)
	at sun.rmi.transport.Transport$1.run(Transport.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.rmi.transport.Transport.serviceCall(Transport.java:196)
	at sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:568)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:826)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.lambda$run$0(TCPTransport.java:683)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:682)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

entityId is null

[dennishendriksen]

Cannot reproduce on master branch:

1. Start application with an empty database
2. Terminate the application during the indexing job that produces lines like:
   07:34:52.109 [pool-7-thread-1] DEBUG o.m.data.jobs.model.JobExecution - progress (6, Indexing sys_ont_OntologyTermHit)
3. Start application

Can reproduce on master branch:

1. Start application with an empty database
2. Import molgenis-platform-integration-tests\src\test\resources\xls\it_emx_datatypes.xlsx
3. Terminate the application during import
4. Start application

[dennishendriksen]

Issue seems related to fix for #6480 in 4e6cc8c.