Glassfish 5 Upgrade

[djbrooke]

Spun out of #4217. We are more confident with a Glassfish upgrade than we are with Java EE8/Java 9 upgrades. We'll plan to take Glassfish to conclusion and leave the spike as a separate issue.

[djbrooke]

@pameyer - please feel free to drop notes of the issue re: login that you experienced.

[pameyer]

quick check of this branch w\ glassfish5 + apache. curl on top-level url worked as expected (redirect to login page); using a browser triggered a glassfish exception (and failed to allow login).

[2017-10-31T15:13:58.494+0000] [glassfish 5.0] [WARNING] [] [org.glassfish.grizzly.filterchain.DefaultFilterChain] [tid: _ThreadID=50 _ThreadName=jk-connector(2)] [timeMillis: 1509462838494] [levelValue: 900] [[ GRIZZLY0013: Exception during FilterChain execution java.lang.NullPointerException at org.glassfish.grizzly.http.ajp.AjpHandlerFilter.encodeHttpPacket(AjpHandlerFilter.java:282) at org.glassfish.grizzly.http.ajp.AjpHandlerFilter.handleWrite(AjpHandlerFilter.java:245) at org.glassfish.grizzly.filterchain.ExecutorResolver$8.execute(ExecutorResolver.java:111) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284) at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201) at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133) at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112) at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77) at org.glassfish.grizzly.filterchain.FilterChainContext.write(FilterChainContext.java:890) at org.glassfish.grizzly.filterchain.FilterChainContext.write(FilterChainContext.java:858) at org.glassfish.grizzly.http.io.OutputBuffer.flushBuffer(OutputBuffer.java:1092) at org.glassfish.grizzly.http.io.OutputBuffer.flushBinaryBuffers(OutputBuffer.java:1066) at org.glassfish.grizzly.http.io.OutputBuffer.flushAllBuffers(OutputBuffer.java:1036) at org.glassfish.grizzly.http.io.OutputBuffer.close(OutputBuffer.java:754) at org.apache.catalina.connector.OutputBuffer.close(OutputBuffer.java:244) at org.apache.catalina.connector.CoyoteOutputStream.close(CoyoteOutputStream.java:179) at java.nio.channels.Channels$WritableByteChannelImpl.implCloseChannel(Channels.java:469) at java.nio.channels.spi.AbstractInterruptibleChannel.close(AbstractInterruptibleChannel.java:115) at com.sun.faces.application.resource.ResourceHandlerImpl.handleResourceRequest(ResourceHandlerImpl.java:365) at javax.faces.application.ResourceHandlerWrapper.handleResourceRequest(ResourceHandlerWrapper.java:178) at org.primefaces.application.resource.PrimeResourceHandler.handleResourceRequest(PrimeResourceHandler.java:87) at javax.faces.webapp.FacesServlet.service(FacesServlet.java:667) at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1580) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:338) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.glassfish.tyrus.servlet.TyrusServletFilter.doFilter(TyrusServletFilter.java:305) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:250) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:205) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:250) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:256) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160) at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:652) at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:591) at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:155) at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:371) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:238) at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:463) at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:168) at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:206) at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:180) at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:242) 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:539) 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$Worker.doWork(AbstractThreadPool.java:593) at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:573) at java.lang.Thread.run(Thread.java:748) ]]

[matthew-a-dunlap]

I have spent about a day on this and made little progress aside from gaining background knowledge and identifying some errors.

Works: Login & accountRegistration

Broken:

1. Dataverse cannot be published, as the DvObject id is being set to null by some process
2. Search only works with a fix to stop some process from setting the active page to 0. Issue seems similar to the one above. Error attached from when setPage() is removed to show error trace.
3. Dataverse cannot be created, a warning is thrown in the logs and the returned page renders all hidden sections in a broken way.
4. Dataset cannot be created, ControlledVocabularyValueConverter errors out because injected DatasetFieldServiceBean is null.

1. Dataverse cannot be published.txt
2. Search starts with page == 0.txt
3. Dataverse cannot be created.txt
4. Dataset cannot be created.txt

[pdurbin]

Huh, this is interesting, from 2.Search.starts.with.page.0.txt above: javax.el.PropertyNotWritableException: The class 'edu.harvard.iq.dataverse.search.SearchIncludeFragment' does not have a writable property 'page'. at javax.el.BeanELResolver.setValue(BeanELResolver.java:433) . My related commit: 6f72baa

I don't know what to say about the other errors. I was able to create dataverses and datasets via API on Glassfish 5. I didn't test JSF much.

[matthew-a-dunlap]

@pdurbin That log message is the one from when I removed the getPage() setter. Was an easy way to get a useful stack trace (the trace when it errored on page == 0 hid a lot).