Spike: Java 9 and Java EE 8

[djbrooke]

An investigation about what needs to be done to upgrade our infrastructure to support:

• Java 9
• Java EE 8
• Glassfish 5 (will be handled in Glassfish 5 Upgrade #4248 instead)

Output of this spike will be well-informed items detailing the upgrade steps and things to test.

[pdurbin]

Java 9

I don't believe it makes sense to upgrade to Java 9 at this time. It's only been out for a few weeks so Linux vendors haven't had time to package it as java-1.9.0-openjdk. We want the same easy upgrade that we had from Java 7 to Java 8 where we simply change a single digit in a yum command like we did in 1abbd77 for #2151.

The next question is, "When will we be able to simply run yum install java-1.9.0-openjdk on CentOS and get Java 9? I'm not exactly sure but we can expect java-1.9.0-openjdk to land first in Fedora and then CentOS. According to https://fedoraproject.org//wiki/Changes/Java9TechPreview Java 9 will be part of Fedora 27 and https://bugzilla.redhat.com/show_bug.cgi?id=1447237 appears to be the tracking bug for including it. We've been able to happily run the java-1.8.0-openjdk RPM on CentOS 6 and I'm not sure if that means we'll be able to run java-1.9.0-openjdk on CentOS 6 as well or if we'll need to upgrade to CentOS 7. According to the "Oracle Java SE Support Roadmap" doc at http://www.oracle.com/technetwork/java/eol-135779.html Java 8 will stop receiving security updates in Sep 2018.

[pdurbin]

Glassfish 5

Today at our architecture meeting we talked a bit about Glassfish 5 vs Payara. I believe the primary thing our customers want is security. At @bjonnh said, "I'm annoyed that we have to use horribly old software and be stuck with it." @donsizemore opened #4172 asking about Payara support.

The thing about Payara is that it's updated more regularly than Glassfish. Here's a little chart I made from a spreadsheet I made based on release dates on Wikipedia. Note how regular the Payara releases are:

More regular releases probably means better security, right? I would hope so. Anyway, over at #4172 I'm asking when we should expect Payara 5 because it would be nice to upgrade to the latest major version if we can. As @landreev mentioned in the meeting today, maybe it wouldn't be too tough to support both Glassfish and Payara. I'm not sure. So far I've been hacking a bit on trying to get Dataverse running on Glassfish 5 and I assume that work will carry over fine to Payara 5. I'll push a branch once I have something to show. At a high level, we need to update the following:

• Dataverse installer
• Vagrant files
• Docker files
• Installation Guide
• Dev Guide

We might need to change our Java code itself but I hope not. We'll see.

[pdurbin]

I missed sprint planning yesterday but I heard this issue got moved to the backlog. At standup I mentioned I'd push what I was working on to my fork, which I just did: pdurbin@d757099

[pdurbin]

I just made pull request #4244 for upgrading to Glassfish 5. I'd like to get some Code Review on it so I'll move it to that column at https://waffle.io/IQSS/dataverse

As I indicated above, it's premature to upgrade to Java 9.

I also did not bump the Java EE version from 7 to 8 in pom.xml. Let's do this in small chunks.

Along the way I also fixed #3905 and probably #2443. Basically, I started using the official installer for the first time on a dev environment. Previously I always used some variation of https://github.com/IQSS/dataverse/blob/v4.8.1/scripts/deploy/phoenix.dataverse.org/install which is much smaller and simpler (and Bash instead of Perl). My main objection to the installer originally is that it required root (that's a lot what #2443 is about) but this is no longer the case.

[matthew-a-dunlap]

Java 9: Looks pretty good, I seem to have it mostly running after a few hours today, but we probably don't want to upgrade yet.

Details:

• Tested on Oracle JDK 9.0.1+11 on osx 10.13
• Need Netbeans 9 for Java 9 to compile easily. There is only a developer build of Netbeans 9 and no release date (but active development). May be able to work around this with digging into maven but I did not do this.
• Builds w/o tests after cleaning up a few new ambiguous references (from new classes brought into Java 9)
• Tests have 1 error, the root cause seems to be that MimetypesFileTypeMap() getContentType is not returning right for png. Looking like implementation weirdness from Java 9, for now I'm just leaving it broken.
• Starts with more sql noise than I remember, but its been a while since I deployed from command line (see java 9 sql error.txt).
• Most of the simple dataverse interactions work! Create/delete dataset/dataverse works. Create user works. Uploading data DOES NOT work (see java 9 file upload error.txt).
• TravisCI works fine switching to Java9.
• Glassfish 4.1 itself is unable to detect the JDK version for Java 9. Glassfish needs to be set to explicitly use Java 8.

[matthew-a-dunlap]

Java EE 8: Unsure, blocked by errors still present in Glassfish 5, also facing a number of issues on its own or ones compounded with Glassfish 5.

• Depricated api errors when building, but build does work
• Not supported by Netbeans yet, had to manually switch over Java EE 8 libraries. Different errors have come forth when enabling different Java EE 8 libraries, referred to https://stackoverflow.com/questions/45852077/netbeans-how-to-add-a-javaee-version and http://www.oracle.com/webfolder/technetwork/jsc/xml/ns/javaee/index.html#8
• Error with all enabled: On launch I get the error below. I could try adding and removing parts of Java EE 8 to see what other errors are there but I'm not sure its worth the work. This is especially true because I can't make it much farther as there are Glassfish 5 errors that I cannot pass.
  /dataverse.xhtml @20,83 value="#{DataversePage.dataverse.id}": Target Unreachable, identifier 'DataversePage' resolved to null javax.el.PropertyNotFoundException: /dataverse.xhtml @20,83 value="#{DataversePage.dataverse.id}": Target Unreachable, identifier 'DataversePage' resolved to null
• Error with EE 8 core & servlet 4.0:

Version:1.0 StartHTML:0000000100 EndHTML:0000010413 StartFragment:0000000100 EndFragment:0000010413 [2017-10-31T15:44:54.805-0400] [glassfish 5.0] [WARNING] [] [javax.enterprise.resource.webcontainer.jsf.lifecycle] [tid: _ThreadID=31 _ThreadName=http-listener-1(5)] [timeMillis: 1509479094
805] [levelValue: 900] [[ /dataverse.xhtml @20,83 value="#{DataversePage.dataverse.id}": Target Unreachable, identifier 'DataversePage' resolved to null javax.el.PropertyNotFoundException: /dataverse.xhtml @20,83 value="#{DataversePage.dataverse.id}": Target Unreachable, identifier 'DataversePage' resolved to null

• Error with EE 8 core & JSF 2.3:

Version:1.0 StartHTML:0000000100 EndHTML:0000009302 StartFragment:0000000100 EndFragment:0000009302 java.lang.NullPointerException
       at edu.harvard.iq.dataverse.ControlledVocabularyValueConverter.getAsObject(ControlledVocabularyValueConverter.java:29)
       at com.sun.faces.renderkit.html_basic.MenuRenderer.convertSelectManyValuesForCollection(MenuRenderer.java:457)
       at com.sun.faces.renderkit.html_basic.MenuRenderer.convertSelectManyValuesForModel(MenuRenderer.java:333)
       at com.sun.faces.renderkit.html_basic.MenuRenderer.convertSelectManyValue(MenuRenderer.java:133)
       at com.sun.faces.renderkit.html_basic.MenuRenderer.getConvertedValue(MenuRenderer.java:305)

• Error with EE 8 core only:

Version:1.0 StartHTML:0000000100 EndHTML:0000009302 StartFragment:0000000100 EndFragment:0000009302 java.lang.NullPointerException
       at edu.harvard.iq.dataverse.ControlledVocabularyValueConverter.getAsObject(ControlledVocabularyValueConverter.java:29)
       at com.sun.faces.renderkit.html_basic.MenuRenderer.convertSelectManyValuesForCollection(MenuRenderer.java:457)
       at com.sun.faces.renderkit.html_basic.MenuRenderer.convertSelectManyValuesForModel(MenuRenderer.java:333)
       at com.sun.faces.renderkit.html_basic.MenuRenderer.convertSelectManyValue(MenuRenderer.java:133)
       at com.sun.faces.renderkit.html_basic.MenuRenderer.getConvertedValue(MenuRenderer.java:305)
       at org.primefaces.component.selectmanycheckbox.SelectManyCheckboxRenderer.getConvertedValue(SelectManyCheckboxRenderer.java:40)
...

This is as far as I went, I need a better understanding of which resources we need to upgrade. I can try to fix these first lines of issues and push forward but its hard for me to tell if issues from Glassfish 5 could also be @ play.

[djbrooke]

Thanks @matthew-a-dunlap for creating a well-informed issue for each upgrade. Those are here:

• Java 11 Upgrade (no free security fixes for Oracle Java 8 after January 2019) #4259
• Java EE 8 Upgrade #4260