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Ingest broken in the "technology branch", aka 4.2.3 - PrimePush related code needs to be refactored. #2758

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kcondon opened this issue Nov 23, 2015 · 2 comments
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Ingest broken in the "technology branch", aka 4.2.3 - PrimePush related code needs to be refactored. #2758

kcondon opened this issue Nov 23, 2015 · 2 comments
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@kcondon
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Feature: File Upload & Handling Type: Bug a defect
Milestone
4.2.3

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@kcondon
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kcondon commented Nov 23, 2015

Tab. Ingest was not working in the "technology branch" (release 4.2.3) at all, for any files. Because of a version conflict - it was upgrade to PrimeFaces 5.3, yet it was still trying to use the deprecated functionality from the older version of PrimePush.
So the error report below is simply one such example. It was not specific to the particular files used, or the fact that the files were uploaded in a zip file, etc.

This is a child issue of #2730, main PrimeFaces upgrade ticket.

(@landreev, Jan. 8 2016)

Original error report:

Ingest does not appear to be working correctly on the experimental branch:
Ingesting a small collection of tabular files results in files not ingesting, remaining forever with status of ingest in progress, yet dataset is editable and publishable. Also, several related server log errors:

[2015-11-20T17:17:07.724-0500] [glassfish 4.1] [INFO] [] [edu.harvard.iq.dataverse.ingest.IngestServiceBean] [tid: _ThreadID=256 _ThreadName=jk-connector(4)] [timeMillis: 1448057827724] [levelValue: 800] [[
Attempting to ingest 7 tabular data file(s).]]

[2015-11-20T17:17:07.986-0500] [glassfish 4.1] [INFO] [] [edu.harvard.iq.dataverse.ingest.IngestMessageBean] [tid: _ThreadID=218 _ThreadName=p: thread-pool-1; w: 5] [timeMillis: 1448057827986] [levelValue: 800] [[
Start ingest job;]]

[2015-11-20T17:17:08.003-0500] [glassfish 4.1] [WARNING] [AS-EJB-00056] [javax.enterprise.ejb.container] [tid: _ThreadID=218 _ThreadName=p: thread-pool-1; w: 5] [timeMillis: 1448057828003] [levelValue: 900] [[
A system exception occurred during an invocation on EJB IngestServiceBean, method: public boolean edu.harvard.iq.dataverse.ingest.IngestServiceBean.ingestAsTabular(java.lang.Long)]]

[2015-11-20T17:17:08.004-0500] [glassfish 4.1] [WARNING] [] [javax.enterprise.ejb.container] [tid: _ThreadID=218 _ThreadName=p: thread-pool-1; w: 5] [timeMillis: 1448057828004] [levelValue: 900] [[

javax.ejb.EJBException
at com.sun.ejb.containers.EJBContainerTransactionManager.processSystemException(EJBContainerTransactionManager.java:748)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:698)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:503)
at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4566)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2074)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2044)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
at com.sun.proxy.$Proxy616.ingestAsTabular(Unknown Source)
at edu.harvard.iq.dataverse.ingest.EJB31_Generated__IngestServiceBean__Intf____Bean.ingestAsTabular(Unknown Source)
at edu.harvard.iq.dataverse.ingest.IngestMessageBean.onMessage(IngestMessageBean.java:88)
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:497)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4786)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:656)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:73)
at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at sun.reflect.GeneratedMethodAccessor313.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4758)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4746)
at org.glassfish.ejb.mdb.MessageBeanContainer.deliverMessage(MessageBeanContainer.java:1219)
at org.glassfish.ejb.mdb.MessageBeanListenerImpl.deliverMessage(MessageBeanListenerImpl.java:81)
at com.sun.enterprise.connectors.inbound.MessageEndpointInvocationHandler.invoke(MessageEndpointInvocationHandler.java:171)
at com.sun.proxy.$Proxy664.onMessage(Unknown Source)
at com.sun.messaging.jms.ra.OnMessageRunner.run(OnMessageRunner.java:283)
at com.sun.enterprise.connectors.work.OneWork.doWork(OneWork.java:107)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.performWork(ThreadPoolImpl.java:497)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.run(ThreadPoolImpl.java:540)
Caused by: java.lang.NullPointerException
at edu.harvard.iq.dataverse.ingest.IngestServiceBean.ingestAsTabular(IngestServiceBean.java:1370)
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:497)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4786)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:656)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:64)
at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at sun.reflect.GeneratedMethodAccessor313.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at sun.reflect.GeneratedMethodAccessor322.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4758)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4746)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
... 32 more
]]

[2015-11-20T17:17:08.075-0500] [glassfish 4.1] [WARNING] [] [javax.resourceadapter.mqjmsra.inbound.message] [tid: _ThreadID=218 _ThreadName=p: thread-pool-1; w: 5] [timeMillis: 1448057828075] [levelValue: 900] [[
MQJMSRA_MR2001: run:Caught Exception from onMessage():Redelivering:
javax.ejb.EJBException: message-driven bean method public abstract void javax.jms.MessageListener.onMessage(javax.jms.Message) system exception
at org.glassfish.ejb.mdb.MessageBeanContainer.deliverMessage(MessageBeanContainer.java:1254)
at org.glassfish.ejb.mdb.MessageBeanListenerImpl.deliverMessage(MessageBeanListenerImpl.java:81)
at com.sun.enterprise.connectors.inbound.MessageEndpointInvocationHandler.invoke(MessageEndpointInvocationHandler.java:171)
at com.sun.proxy.$Proxy664.onMessage(Unknown Source)
at com.sun.messaging.jms.ra.OnMessageRunner.run(OnMessageRunner.java:283)
at com.sun.enterprise.connectors.work.OneWork.doWork(OneWork.java:107)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.performWork(ThreadPoolImpl.java:497)
at com.sun.corba.ee.impl.threadpool.ThreadPoolImpl$WorkerThread.run(ThreadPoolImpl.java:540)
Caused by: javax.ejb.EJBException
at com.sun.ejb.containers.EJBContainerTransactionManager.processSystemException(EJBContainerTransactionManager.java:748)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:698)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:503)
at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4566)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2074)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2044)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:88)
at com.sun.proxy.$Proxy616.sendFailNotification(Unknown Source)
at edu.harvard.iq.dataverse.ingest.EJB31_Generated__IngestServiceBean__Intf____Bean.sendFailNotification(Unknown Source)
at edu.harvard.iq.dataverse.ingest.IngestMessageBean.onMessage(IngestMessageBean.java:125)
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:497)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4786)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:656)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:73)
at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at sun.reflect.GeneratedMethodAccessor313.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4758)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4746)
at org.glassfish.ejb.mdb.MessageBeanContainer.deliverMessage(MessageBeanContainer.java:1219)
... 7 more
Caused by: java.lang.NullPointerException
at edu.harvard.iq.dataverse.ingest.IngestServiceBean.sendFailNotification(IngestServiceBean.java:1350)
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:497)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:1081)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:1153)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4786)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:656)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
at org.jboss.weld.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:64)
at org.jboss.weld.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at sun.reflect.GeneratedMethodAccessor313.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:608)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at sun.reflect.GeneratedMethodAccessor322.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:883)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:822)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:369)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4758)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4746)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
... 32 more
]]
@kcondon kcondon added this to the 4.2.3 milestone Nov 23, 2015
@landreev landreev changed the title Ingest: When ingesting an assortment of files from a small zip file, ingest does not work, files remain stuck in ingest, dataset still editable. Ingest broken in the "technology branch", aka 4.2.3 - PrimePush related code needs to be refactored. Jan 8, 2016
@landreev landreev assigned kcondon and unassigned landreev Jan 9, 2016
@landreev
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landreev commented Jan 9, 2016

Moving to QA.

TL;DR:
PimeFaces advertised this upgrade of their push/atmosphere technology as a complete and major rewrite. I was hoping it would solve all the problems we've had with its flakiness. But so far I'm not super impressed. I spent a lot of time experimenting with it, and I've already seen it being kinda flaky, just like the old version. By flaky I mean, keeps working, then, after another deployment, starts throwing exceptions in the logs ("connection already opened", every time a dataset page is reloaded). This being totally intermittent. Did some searching, found some people having the same issue; nobody knows why it happens; the only solution - "just keep redeploying until it goes away". More of an annoyance rather than a real issue, but still.
Actual ingest should be working properly though.

(but I keep fantasizing about finding another solution for this that does not require atmosphere at all).

@landreev landreev mentioned this issue Jan 9, 2016
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@kcondon
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kcondon commented Jan 11, 2016

Ingest is now working. There are some logging statements that may need to be cleaned up and as mentioned some errors. Will open new tickets as needed. Closing.

@kcondon kcondon closed this as completed Jan 11, 2016
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