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fileMetadataExtractableFromNetcdf causing regression for S3 direct upload #9601

Closed
pdurbin opened this issue May 19, 2023 · 1 comment · Fixed by #9611
Closed

fileMetadataExtractableFromNetcdf causing regression for S3 direct upload #9601

pdurbin opened this issue May 19, 2023 · 1 comment · Fixed by #9611
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Size: 30 A percentage of a sprint. 21 hours. (formerly size:33)
Milestone
5.14

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@pdurbin
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pdurbin commented May 19, 2023

The fileMetadataExtractableFromNetcdf method I added in this pull request...

... is causing a regression when S3 direct upload is enabled. Here's how the UI looks.

Screen Shot 2023-05-19 at 11 36 08 AM

Stacktrace

[#|2023-05-19T15:32:22.537+0000|WARNING|Payara 5.2022.4|edu.harvard.iq.dataverse.dataaccess.DataAccess|_ThreadID=96;_ThreadName=http-thread-pool::http-listener-1(2);_TimeMillis=1684510342537;_LevelValue=900;|
Could not find storage driver for: local|#]

[#|2023-05-19T15:33:19.639+0000|WARNING|Payara 5.2022.4|edu.harvard.iq.dataverse.dataaccess.DataAccess|_ThreadID=98;_ThreadName=http-thread-pool::http-listener-1(4);_TimeMillis=1684510399639;_LevelValue=900;|
Could not find storage driver for: local|#]

[#|2023-05-19T15:33:45.613+0000|WARNING|Payara 5.2022.4|javax.enterprise.ejb.container|_ThreadID=99;_ThreadName=http-thread-pool::http-listener-1(5);_TimeMillis=1684510425613;_LevelValue=900;_MessageID=AS-EJB-00056;|
A system exception occurred during an invocation on EJB IngestServiceBean, method: public java.util.List edu.harvard.iq.dataverse.ingest.IngestServiceBean.saveAndAddFilesToDataset(edu.harvard.iq.dataverse.DatasetVersion,java.util.List,edu.harvard.iq.dataverse.DataFile,boolean)|#]

[#|2023-05-19T15:33:45.614+0000|WARNING|Payara 5.2022.4|javax.enterprise.ejb.container|_ThreadID=99;_ThreadName=http-thread-pool::http-listener-1(5);_TimeMillis=1684510425614;_LevelValue=900;|
javax.ejb.EJBException
at com.sun.ejb.containers.EJBContainerTransactionManager.processSystemException(EJBContainerTransactionManager.java:723)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:652)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:482)
at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4601)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2134)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2104)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:90)
at com.sun.proxy.$Proxy377.saveAndAddFilesToDataset(Unknown Source)
at edu.harvard.iq.dataverse.ingest.EJB31_Generated__IngestServiceBean__Intf____Bean.saveAndAddFilesToDataset(Unknown Source)
at edu.harvard.iq.dataverse.EditDatafilesPage.save(EditDatafilesPage.java:1067)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.el.util.ReflectionUtil.invokeMethod(ReflectionUtil.java:163)
at com.sun.el.parser.AstValue.invoke(AstValue.java:261)
at com.sun.el.MethodExpressionImpl.invoke(MethodExpressionImpl.java:237)
at org.jboss.weld.module.web.util.el.ForwardingMethodExpression.invoke(ForwardingMethodExpression.java:40)
at org.jboss.weld.module.web.el.WeldMethodExpression.invoke(WeldMethodExpression.java:50)
at com.sun.faces.facelets.el.TagMethodExpression.invoke(TagMethodExpression.java:65)
at com.sun.faces.application.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:66)
at com.sun.faces.application.ActionListenerImpl.getNavigationOutcome(ActionListenerImpl.java:82)
at com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:71)
at javax.faces.component.UICommand.broadcast(UICommand.java:222)
at javax.faces.component.UIViewRoot.broadcastEvents(UIViewRoot.java:847)
at javax.faces.component.UIViewRoot.processApplication(UIViewRoot.java:1396)
at com.sun.faces.lifecycle.InvokeApplicationPhase.execute(InvokeApplicationPhase.java:58)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:76)
at com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:177)
at javax.faces.webapp.FacesServlet.executeLifecyle(FacesServlet.java:707)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:451)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1637)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:331)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:282)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:257)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:167)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:757)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:577)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:158)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:372)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:239)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:520)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:217)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:182)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:156)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:201)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:95)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:260)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:177)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:109)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:88)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:53)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:524)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:89)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:94)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:33)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:114)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:569)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:549)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.lang.NullPointerException
at edu.harvard.iq.dataverse.dataaccess.S3AccessIO.getMainFileKey(S3AccessIO.java:828)
at edu.harvard.iq.dataverse.dataaccess.S3AccessIO.getMainFileKey(S3AccessIO.java:818)
at edu.harvard.iq.dataverse.dataaccess.S3AccessIO.open(S3AccessIO.java:210)
at edu.harvard.iq.dataverse.ingest.IngestServiceBean.fileMetadataExtractableFromNetcdf(IngestServiceBean.java:1200)
at edu.harvard.iq.dataverse.ingest.IngestServiceBean.saveAndAddFilesToDataset(IngestServiceBean.java:372)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:588)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:408)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4835)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:665)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:834)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:615)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at jdk.internal.reflect.GeneratedMethodAccessor220.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:615)
at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:72)
at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at jdk.internal.reflect.GeneratedMethodAccessor140.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:375)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4807)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4795)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
... 61 more
|#]

[#|2023-05-19T15:33:45.618+0000|WARNING|Payara 5.2022.4|javax.enterprise.resource.webcontainer.jsf.lifecycle|_ThreadID=99;_ThreadName=http-thread-pool::http-listener-1(5);_TimeMillis=1684510425618;_LevelValue=900;|
#{EditDatafilesPage.save}: javax.ejb.EJBException
javax.faces.FacesException: #{EditDatafilesPage.save}: javax.ejb.EJBException
at com.sun.faces.application.ActionListenerImpl.getNavigationOutcome(ActionListenerImpl.java:96)
at com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:71)
at javax.faces.component.UICommand.broadcast(UICommand.java:222)
at javax.faces.component.UIViewRoot.broadcastEvents(UIViewRoot.java:847)
at javax.faces.component.UIViewRoot.processApplication(UIViewRoot.java:1396)
at com.sun.faces.lifecycle.InvokeApplicationPhase.execute(InvokeApplicationPhase.java:58)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:76)
at com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:177)
at javax.faces.webapp.FacesServlet.executeLifecyle(FacesServlet.java:707)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:451)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1637)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:331)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:282)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:257)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:167)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:757)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:577)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:158)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:372)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:239)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:520)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:217)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:182)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:156)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:201)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:95)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:260)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:177)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:109)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:88)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:53)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:524)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:89)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:94)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:33)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:114)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:569)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:549)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: javax.faces.el.EvaluationException: javax.ejb.EJBException
at com.sun.faces.application.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:76)
at com.sun.faces.application.ActionListenerImpl.getNavigationOutcome(ActionListenerImpl.java:82)
... 45 more
Caused by: javax.ejb.EJBException
at com.sun.ejb.containers.EJBContainerTransactionManager.processSystemException(EJBContainerTransactionManager.java:723)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:652)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:482)
at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4601)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2134)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2104)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:90)
at com.sun.proxy.$Proxy377.saveAndAddFilesToDataset(Unknown Source)
at edu.harvard.iq.dataverse.ingest.EJB31_Generated__IngestServiceBean__Intf____Bean.saveAndAddFilesToDataset(Unknown Source)
at edu.harvard.iq.dataverse.EditDatafilesPage.save(EditDatafilesPage.java:1067)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.el.util.ReflectionUtil.invokeMethod(ReflectionUtil.java:163)
at com.sun.el.parser.AstValue.invoke(AstValue.java:261)
at com.sun.el.MethodExpressionImpl.invoke(MethodExpressionImpl.java:237)
at org.jboss.weld.module.web.util.el.ForwardingMethodExpression.invoke(ForwardingMethodExpression.java:40)
at org.jboss.weld.module.web.el.WeldMethodExpression.invoke(WeldMethodExpression.java:50)
at com.sun.faces.facelets.el.TagMethodExpression.invoke(TagMethodExpression.java:65)
at com.sun.faces.application.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:66)
... 46 more
Caused by: java.lang.NullPointerException
at edu.harvard.iq.dataverse.dataaccess.S3AccessIO.getMainFileKey(S3AccessIO.java:828)
at edu.harvard.iq.dataverse.dataaccess.S3AccessIO.getMainFileKey(S3AccessIO.java:818)
at edu.harvard.iq.dataverse.dataaccess.S3AccessIO.open(S3AccessIO.java:210)
at edu.harvard.iq.dataverse.ingest.IngestServiceBean.fileMetadataExtractableFromNetcdf(IngestServiceBean.java:1200)
at edu.harvard.iq.dataverse.ingest.IngestServiceBean.saveAndAddFilesToDataset(IngestServiceBean.java:372)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:588)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:408)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4835)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:665)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:834)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:615)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at jdk.internal.reflect.GeneratedMethodAccessor220.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:615)
at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:72)
at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at jdk.internal.reflect.GeneratedMethodAccessor140.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:375)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4807)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4795)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
... 61 more
|#]

[#|2023-05-19T15:33:45.623+0000|SEVERE|Payara 5.2022.4|javax.enterprise.resource.webcontainer.jsf.context|_ThreadID=99;_ThreadName=http-thread-pool::http-listener-1(5);_TimeMillis=1684510425623;_LevelValue=1000;|
javax.faces.el.EvaluationException: javax.ejb.EJBException
at com.sun.faces.application.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:76)
at com.sun.faces.application.ActionListenerImpl.getNavigationOutcome(ActionListenerImpl.java:82)
at com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:71)
at javax.faces.component.UICommand.broadcast(UICommand.java:222)
at javax.faces.component.UIViewRoot.broadcastEvents(UIViewRoot.java:847)
at javax.faces.component.UIViewRoot.processApplication(UIViewRoot.java:1396)
at com.sun.faces.lifecycle.InvokeApplicationPhase.execute(InvokeApplicationPhase.java:58)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:76)
at com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:177)
at javax.faces.webapp.FacesServlet.executeLifecyle(FacesServlet.java:707)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:451)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1637)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:331)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:282)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:253)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:211)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:257)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:167)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:757)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:577)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:158)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:372)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:239)
at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:520)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:217)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:182)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:156)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:201)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:95)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:260)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:177)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:109)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:88)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:53)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:524)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:89)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:94)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:33)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:114)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:569)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:549)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: javax.ejb.EJBException
at com.sun.ejb.containers.EJBContainerTransactionManager.processSystemException(EJBContainerTransactionManager.java:723)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManager.java:652)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManager.java:482)
at com.sun.ejb.containers.BaseContainer.postInvokeTx(BaseContainer.java:4601)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2134)
at com.sun.ejb.containers.BaseContainer.postInvoke(BaseContainer.java:2104)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:220)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHandlerDelegate.java:90)
at com.sun.proxy.$Proxy377.saveAndAddFilesToDataset(Unknown Source)
at edu.harvard.iq.dataverse.ingest.EJB31_Generated__IngestServiceBean__Intf____Bean.saveAndAddFilesToDataset(Unknown Source)
at edu.harvard.iq.dataverse.EditDatafilesPage.save(EditDatafilesPage.java:1067)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.el.util.ReflectionUtil.invokeMethod(ReflectionUtil.java:163)
at com.sun.el.parser.AstValue.invoke(AstValue.java:261)
at com.sun.el.MethodExpressionImpl.invoke(MethodExpressionImpl.java:237)
at org.jboss.weld.module.web.util.el.ForwardingMethodExpression.invoke(ForwardingMethodExpression.java:40)
at org.jboss.weld.module.web.el.WeldMethodExpression.invoke(WeldMethodExpression.java:50)
at com.sun.faces.facelets.el.TagMethodExpression.invoke(TagMethodExpression.java:65)
at com.sun.faces.application.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:66)
... 46 more
Caused by: java.lang.NullPointerException
at edu.harvard.iq.dataverse.dataaccess.S3AccessIO.getMainFileKey(S3AccessIO.java:828)
at edu.harvard.iq.dataverse.dataaccess.S3AccessIO.getMainFileKey(S3AccessIO.java:818)
at edu.harvard.iq.dataverse.dataaccess.S3AccessIO.open(S3AccessIO.java:210)
at edu.harvard.iq.dataverse.ingest.IngestServiceBean.fileMetadataExtractableFromNetcdf(IngestServiceBean.java:1200)
at edu.harvard.iq.dataverse.ingest.IngestServiceBean.saveAndAddFilesToDataset(IngestServiceBean.java:372)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.glassfish.ejb.security.application.EJBSecurityManager.runMethod(EJBSecurityManager.java:588)
at org.glassfish.ejb.security.application.EJBSecurityManager.invoke(EJBSecurityManager.java:408)
at com.sun.ejb.containers.BaseContainer.invokeBeanMethod(BaseContainer.java:4835)
at com.sun.ejb.EjbInvocation.invokeBeanMethod(EjbInvocation.java:665)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:834)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:615)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.doCall(SystemInterceptorProxy.java:163)
at com.sun.ejb.containers.interceptors.SystemInterceptorProxy.aroundInvoke(SystemInterceptorProxy.java:140)
at jdk.internal.reflect.GeneratedMethodAccessor220.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.EjbInvocation.proceed(EjbInvocation.java:615)
at org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:72)
at org.jboss.weld.module.ejb.SessionBeanInterceptor.aroundInvoke(SessionBeanInterceptor.java:52)
at jdk.internal.reflect.GeneratedMethodAccessor140.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.sun.ejb.containers.interceptors.AroundInvokeInterceptor.intercept(InterceptorManager.java:888)
at com.sun.ejb.containers.interceptors.AroundInvokeChainImpl.invokeNext(InterceptorManager.java:833)
at com.sun.ejb.containers.interceptors.InterceptorManager.intercept(InterceptorManager.java:375)
at com.sun.ejb.containers.BaseContainer.__intercept(BaseContainer.java:4807)
at com.sun.ejb.containers.BaseContainer.intercept(BaseContainer.java:4795)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandler.invoke(EJBLocalObjectInvocationHandler.java:212)
... 61 more
|#]
@pdurbin pdurbin added this to the 5.14 milestone May 19, 2023
@pdurbin pdurbin self-assigned this May 19, 2023
@pdurbin pdurbin mentioned this issue May 19, 2023
Merged
pdurbin added a commit that referenced this issue May 19, 2023
@pdurbin
catch ex to prevent NPE on save in GUI #9601
550483f 
Tested with a NetCDF file and S3 direct upload enabled.
qqmyers added a commit to GlobalDataverseCommunityConsortium/dataverse that referenced this issue May 19, 2023
@qqmyers
fix for IQSS#9601
57e984b
@cmbz cmbz added the Size: 30 A percentage of a sprint. 21 hours. (formerly size:33) label May 22, 2023
@cmbz
Copy link

cmbz commented May 22, 2023

Sized as 33 after conversation with Phil

pdurbin added a commit that referenced this issue May 23, 2023
@pdurbin
disable NetCDF metadata extraction for S3 direct upload #9601
6838fdf
pdurbin added a commit that referenced this issue May 23, 2023
@pdurbin
set expectations about S3 direct upload behavior #9601
046a049
@pdurbin pdurbin mentioned this issue May 23, 2023
Closed
pdurbin added a commit that referenced this issue May 23, 2023
@pdurbin
fix S3 direct upload NPE and keep NetCDF metadata extraction #9601
cf2088d 
Note that the NcML aux file is not created when S3 direct upload is
enabled.
@pdurbin pdurbin removed their assignment May 23, 2023
@pdurbin pdurbin mentioned this issue May 23, 2023
Merged
pdurbin added a commit that referenced this issue May 24, 2023
@pdurbin
set expectations about S3 direct upload behavior #9601
8f83738
@pdurbin pdurbin self-assigned this May 24, 2023
pdurbin added a commit that referenced this issue May 24, 2023
@pdurbin
switch to mime type check #9601
505e8f2
pdurbin added a commit that referenced this issue May 25, 2023
@pdurbin
add dataverse.netcdf.geo-extract-s3-direct-upload config #9601
18076ed 
By default, keep S3 direct upload fast. Don't download NetCDF or HDF5
files to try to pull geospatial metadata out of them when S3 direct
upload is configured. If you really want this, add this setting and make
it true.
@pdurbin pdurbin removed their assignment May 25, 2023
pdurbin added a commit that referenced this issue May 25, 2023
@pdurbin
turn down logging #9601
5a0bf24
pdurbin added a commit that referenced this issue May 26, 2023
@pdurbin
set expectations about NcML files (modern only) #9153 #9601
2d6564a
qqmyers added a commit to GlobalDataverseCommunityConsortium/dataverse that referenced this issue May 30, 2023
@qqmyers
fix for IQSS#9601
bdce3b4
pdurbin added a commit that referenced this issue Jun 15, 2023
@pdurbin
Merge branch 'develop' into 9601-keep-features #9601
1b6f4b2 
Conflicts:
doc/sphinx-guides/source/installation/config.rst
src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceBean.java
pdurbin added a commit that referenced this issue Jul 10, 2023
@pdurbin
Merge branch 'develop' into 9601-keep-features #9601
bbea224
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Size: 30 A percentage of a sprint. 21 hours. (formerly size:33)
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@pdurbin @cmbz