Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

DatasetPage.jsonLd java.lang.NullPointerException #5141

Closed
lmaylein opened this issue Oct 5, 2018 · 4 comments
Closed

DatasetPage.jsonLd java.lang.NullPointerException #5141

lmaylein opened this issue Oct 5, 2018 · 4 comments

Comments

@lmaylein
Copy link
Contributor

lmaylein commented Oct 5, 2018

After upgrading from 4.8.6 to 4.9.4 we get the following error for each dataset:

[2018-10-05T12:10:51.663+0200] [glassfish 4.1] [SEVERE] [] [javax.enterprise.resource.webcontainer.jsf.application] [tid: _ThreadID=52 _ThreadName=jk-connector(2)] [timeMillis: 15387342516
63] [levelValue: 1000] [[
  Error Rendering View[/dataset.xhtml]
javax.el.ELException: /dataset.xhtml @39,66 value="#{DatasetPage.jsonLd}": java.lang.NullPointerException
        at com.sun.faces.facelets.el.TagValueExpression.getValue(TagValueExpression.java:114)
        at javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:194)
        at javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:182)
        at javax.faces.component.UIOutput.getValue(UIOutput.java:174)
        at com.sun.faces.renderkit.html_basic.HtmlBasicInputRenderer.getValue(HtmlBasicInputRenderer.java:205)
        at com.sun.faces.renderkit.html_basic.HtmlBasicRenderer.getCurrentValue(HtmlBasicRenderer.java:355)
        at com.sun.faces.renderkit.html_basic.HtmlBasicRenderer.encodeEnd(HtmlBasicRenderer.java:164)
        at javax.faces.component.UIComponentBase.encodeEnd(UIComponentBase.java:919)
        at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1863)
        at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1859)
        at org.primefaces.renderkit.HeadRenderer.encodeBegin(HeadRenderer.java:62)
        at javax.faces.component.UIComponentBase.encodeBegin(UIComponentBase.java:864)
        at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1854)
        at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1859)
        at com.sun.faces.application.view.FaceletViewHandlingStrategy.renderView(FaceletViewHandlingStrategy.java:456)
        at com.sun.faces.application.view.MultiViewHandler.renderView(MultiViewHandler.java:133)
        at javax.faces.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:337)
        at org.ocpsoft.rewrite.faces.RewriteViewHandler.renderView(RewriteViewHandler.java:196)
        at javax.faces.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:337)
        at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:120)
        at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
        at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:219)
        at javax.faces.webapp.FacesServlet.service(FacesServlet.java:647)
        at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:295)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
        at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
        at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
        at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
        at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:415)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:282)
        at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
        at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
        at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201)
        at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175)
        at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
        at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
       at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
        at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
        at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561)
        at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
        at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
        at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
        at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
        at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565)
        at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545)
        at java.lang.Thread.run(Thread.java:748)
Caused by: javax.el.ELException: java.lang.NullPointerException
        at javax.el.BeanELResolver.getValue(BeanELResolver.java:368)
        at com.sun.faces.el.DemuxCompositeELResolver._getValue(DemuxCompositeELResolver.java:176)
        at com.sun.faces.el.DemuxCompositeELResolver.getValue(DemuxCompositeELResolver.java:203)
        at com.sun.el.parser.AstValue.getValue(AstValue.java:140)
        at com.sun.el.parser.AstValue.getValue(AstValue.java:204)
        at com.sun.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:226)
        at org.jboss.weld.el.WeldValueExpression.getValue(WeldValueExpression.java:50)
        at com.sun.faces.facelets.el.TagValueExpression.getValue(TagValueExpression.java:109)
        ... 58 more
Caused by: java.lang.NullPointerException
        at edu.harvard.iq.dataverse.export.ExportService.cacheExport(ExportService.java:282)
        at edu.harvard.iq.dataverse.export.ExportService.exportFormat(ExportService.java:214)
        at edu.harvard.iq.dataverse.export.ExportService.getExport(ExportService.java:100)
        at edu.harvard.iq.dataverse.export.ExportService.getExportAsString(ExportService.java:119)
        at edu.harvard.iq.dataverse.DatasetPage.getJsonLd(DatasetPage.java:4328)
        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 javax.el.BeanELResolver.getValue(BeanELResolver.java:363)
        ... 65 more
]]
@pdurbin
Copy link
Member

pdurbin commented Oct 5, 2018

@lmaylein hi https://github.com/IQSS/dataverse/blob/v4.9.4/src/main/java/edu/harvard/iq/dataverse/export/ExportService.java#L282 seems to indicate that a temp file may not have been created. Is there any more to the stack trace?

@lmaylein
Copy link
Contributor Author

lmaylein commented Oct 5, 2018

Yes, there is more (see above).

Ok. I've tested the migration without the files mounted (but the temp directory is available).

As part of the upgrade procedure we change the virtual machine. I could not switch
the file partition (mounted via NFS) unless #5142 is solved.

[2018-10-05T12:27:08.264+0200] [glassfish 4.1] [WARNING] [] [javax.enterprise.web] [tid: _ThreadID=52 _ThreadName=jk-connector(5)] [timeMillis: 1538735228264] [levelValue: 900] [[
  StandardWrapperValve[Faces Servlet]: Servlet.service() for servlet Faces Servlet threw exception
java.lang.NullPointerException
        at edu.harvard.iq.dataverse.export.ExportService.cacheExport(ExportService.java:282)
        at edu.harvard.iq.dataverse.export.ExportService.exportFormat(ExportService.java:214)
        at edu.harvard.iq.dataverse.export.ExportService.getExport(ExportService.java:100)
        at edu.harvard.iq.dataverse.export.ExportService.getExportAsString(ExportService.java:119)
        at edu.harvard.iq.dataverse.DatasetPage.getJsonLd(DatasetPage.java:4328)
        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 javax.el.BeanELResolver.getValue(BeanELResolver.java:363)
        at com.sun.faces.el.DemuxCompositeELResolver._getValue(DemuxCompositeELResolver.java:176)
        at com.sun.faces.el.DemuxCompositeELResolver.getValue(DemuxCompositeELResolver.java:203)
        at com.sun.el.parser.AstValue.getValue(AstValue.java:140)
        at com.sun.el.parser.AstValue.getValue(AstValue.java:204)
        at com.sun.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:226)
        at org.jboss.weld.el.WeldValueExpression.getValue(WeldValueExpression.java:50)
        at com.sun.faces.facelets.el.TagValueExpression.getValue(TagValueExpression.java:109)
        at javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:194)
        at javax.faces.component.ComponentStateHelper.eval(ComponentStateHelper.java:182)
        at javax.faces.component.UIOutput.getValue(UIOutput.java:174)
        at com.sun.faces.renderkit.html_basic.HtmlBasicInputRenderer.getValue(HtmlBasicInputRenderer.java:205)
        at com.sun.faces.renderkit.html_basic.HtmlBasicRenderer.getCurrentValue(HtmlBasicRenderer.java:355)
        at com.sun.faces.renderkit.html_basic.HtmlBasicRenderer.encodeEnd(HtmlBasicRenderer.java:164)
        at javax.faces.component.UIComponentBase.encodeEnd(UIComponentBase.java:919)
        at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1863)
        at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1859)
        at org.primefaces.renderkit.HeadRenderer.encodeBegin(HeadRenderer.java:62)
        at javax.faces.component.UIComponentBase.encodeBegin(UIComponentBase.java:864)
        at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1854)
        at javax.faces.component.UIComponent.encodeAll(UIComponent.java:1859)
        at com.sun.faces.application.view.FaceletViewHandlingStrategy.renderView(FaceletViewHandlingStrategy.java:456)
        at com.sun.faces.application.view.MultiViewHandler.renderView(MultiViewHandler.java:133)
        at javax.faces.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:337)
        at org.ocpsoft.rewrite.faces.RewriteViewHandler.renderView(RewriteViewHandler.java:196)
        at javax.faces.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:337)
        at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:120)
        at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
        at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:219)
        at javax.faces.webapp.FacesServlet.service(FacesServlet.java:647)
        at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:295)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
        at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
        at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
        at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
        at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:415)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:282)
        at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
        at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
        at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201)
        at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175)
        at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
        at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
        at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
        at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
        at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561)
        at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
        at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
        at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
        at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
        at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565)
        at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545)
        at java.lang.Thread.run(Thread.java:748)
]]

@pdurbin
Copy link
Member

pdurbin commented Oct 5, 2018

As part of the upgrade procedure we change the virtual machine. I could not switch
the file partition (mounted via NFS)

Ok, the error makes sense, then. Dataverse is trying to write the "export" formats to the directory where files for the dataset are stored. For example: /usr/local/glassfish4/glassfish/domains/domain1/files/10.5072/FK2/HCPTZG/export_schema.org.cached

@lmaylein
Copy link
Contributor Author

lmaylein commented Oct 5, 2018

Yes, you are right. If if fake the corresponding directory, everything is okay.
Thanks.

@lmaylein lmaylein closed this as completed Oct 5, 2018
@lmaylein lmaylein mentioned this issue Oct 5, 2018
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@pdurbin @lmaylein