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fileMetadataExtractableFromNetcdf causing regression for S3 direct upload #9601

Closed pdurbin closed 1 year ago

pdurbin commented 1 year ago

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 |#]
cmbz commented 1 year ago

Sized as 33 after conversation with Phil