4777 file pg citations layout

[qqmyers]

I think this fix got missed when the IQSS 4777 branch was merged into develop before the change below was merged from my branch in the QDR fork into IQSS-4777.

Related Issues

• connects to RIS and EndNote fixes #5054

Pull Request Checklist

• Unit tests completed
• Integration tests: None
• Deployment requirements, SQL updates, Solr updates, etc.: None
• Documentation completed
• Merged latest from "develop" branch and resolved conflicts

[coveralls]

Coverage decreased (-0.0005%) to 15.558% when pulling ebb319f on 4777-file-pg-citations-layout into c61bba9 on develop.

[djbrooke]

Hi @qqmyers - just to confirm, this is the null description fix?

[qqmyers]

@djbrooke - yes

[djbrooke]

Thanks @qqmyers.

@kcondon - as this heads to QA, note that we talked about this a bit after standup. These changes are just for Endnote and RIS exports, not for the Dataverse page itself.

[kcondon]

@qqmyers This throws an exception when I choose RIS format. Also, can you tell me briefly what this does?
Thanks!

[kcondon]

[2018-09-14T17:47:22.349-0400] [glassfish 4.1] [WARNING] [AS-EJB-00056] [javax.enterprise.ejb.container] [t
id: _ThreadID=54 _ThreadName=jk-connector(3)] [timeMillis: 1536961642349] [levelValue: 900] [[
A system exception occurred during an invocation on EJB FileDownloadServiceBean, method: public void edu.
harvard.iq.dataverse.FileDownloadServiceBean.downloadDatasetCitationXML(edu.harvard.iq.dataverse.Dataset)]]

[2018-09-14T17:47:22.349-0400] [glassfish 4.1] [WARNING] [] [javax.enterprise.ejb.container] [tid: _ThreadI
D=54 _ThreadName=jk-connector(3)] [timeMillis: 1536961642349] [levelValue: 900] [[

javax.ejb.EJBException
at com.sun.ejb.containers.EJBContainerTransactionManager.processSystemException(EJBContainerTransac
tionManager.java:748)
at com.sun.ejb.containers.EJBContainerTransactionManager.completeNewTx(EJBContainerTransactionManag
er.java:698)
at com.sun.ejb.containers.EJBContainerTransactionManager.postInvokeTx(EJBContainerTransactionManage
r.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.ja
va:220)
at com.sun.ejb.containers.EJBLocalObjectInvocationHandlerDelegate.invoke(EJBLocalObjectInvocationHa
ndlerDelegate.java:88)
at com.sun.proxy.$Proxy717.downloadDatasetCitationXML(Unknown Source)
at edu.harvard.iq.dataverse.EJB31_Generated__FileDownloadServiceBean__Intf____Bean.downloadData
setCitationXML(Unknown Source)
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.ELUtil.invokeMethod(ELUtil.java:332)
at javax.el.BeanELResolver.invoke(BeanELResolver.java:537)
at javax.el.CompositeELResolver.invoke(CompositeELResolver.java:256)
at com.sun.el.parser.AstValue.invoke(AstValue.java:283)
at com.sun.el.MethodExpressionImpl.invoke(MethodExpressionImpl.java:304)
at org.jboss.weld.util.el.ForwardingMethodExpression.invoke(ForwardingMethodExpression.java:40)
at org.jboss.weld.el.WeldMethodExpression.invoke(WeldMethodExpression.java:50)
at com.sun.faces.facelets.el.TagMethodExpression.invoke(TagMethodExpression.java:105)
at javax.faces.component.MethodBindingMethodExpressionAdapter.invoke(MethodBindingMethodExpressionAdapter.java:87)
at com.sun.faces.application.ActionListenerImpl.processAction(ActionListenerImpl.java:102)
at javax.faces.component.UICommand.broadcast(UICommand.java:315)
at javax.faces.component.UIViewRoot.broadcastEvents(UIViewRoot.java:790)
at javax.faces.component.UIViewRoot.processApplication(UIViewRoot.java:1282)
at com.sun.faces.lifecycle.InvokeApplicationPhase.execute(InvokeApplicationPhase.java:81)
at com.sun.faces.lifecycle.Phase.doPhase(Phase.java:101)
at com.sun.faces.lifecycle.LifecycleImpl.execute(LifecycleImpl.java:198)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:646)
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:25
6)
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: java.lang.NullPointerException
at edu.harvard.iq.dataverse.DataCitation.flattenHtml(DataCitation.java:634)
at edu.harvard.iq.dataverse.DataCitation.createEndNoteXML(DataCitation.java:498)
at edu.harvard.iq.dataverse.DataCitation.writeAsEndNoteCitation(DataCitation.java:397)
at edu.harvard.iq.dataverse.FileDownloadServiceBean.downloadCitationXML(FileDownloadServiceBean.java:275)
at edu.harvard.iq.dataverse.FileDownloadServiceBean.downloadDatasetCitationXML(FileDownloadServiceBean.java:243)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.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.GeneratedMethodAccessor122.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
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.GeneratedMethodAccessor124.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
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)
... 60 more
]]

[qqmyers]

@kcondon - I think you're running the unpatched code. DataCitation line 634 where the null pointer occurs in your stack trace is now a comment. The change here catches the null pointer (caused by the description being null).

(The flattenHtml method, which should already be in the earlier merged code, just removes most of the allowed html formatting in fields like description so that the citation xml/text is plain text / more readable.)

[kcondon]

@qqmyers I was running the code from this branch and it actually works on code from /develop. I'll try building it again just in case I made mental error ;)