Update to Java 8

[sbliven]

It would be nice to switch EPPIC to Java 8. This can't happen quite yet, but I wanted to start an issue to track progress.

Dependency support:

• BioJava
• GWT (should be in GWT 2.8, currently in beta)
• GXT (4.0 with GWT 2.8)
• Hibernate (Supposedly works with 3., but extended support in 5. through hibernate-java8)

[josemduarte]

Isn't the update of EPPIC to Java 8 independent of the libraries? I mean EPPIC can be in 8 whilst the libraries can still be 7.

[sbliven]

We can try it, but I think that all the reflection that happens in GWT might mean that eppic-wui would actually not work with GWT<2.8. That's certainly easy enough to test.

[josemduarte]

Alright I've tried it out and all works! So I've pushed the commit and a build on dev server.

I've also upgraded the java jdk to 8 in both dev and production servers.

We should check if some of the libraries can be updated to newer versions now that we are on 8.

[josemduarte]

So there seems to be an issue with current hibernate version and java 8. The entity manager is currently broken. We need to upgrade hibernate-entitymanager and perhaps other dependencies.

The issue while running a script in dbtools:

javax.persistence.PersistenceException: Unable to configure EntityManagerFactory
    at org.hibernate.ejb.Ejb3Configuration.configure(Ejb3Configuration.java:375)
    at org.hibernate.ejb.HibernatePersistence.createEntityManagerFactory(HibernatePersistence.java:56)
    at javax.persistence.Persistence.createEntityManagerFactory(Persistence.java:63)
    at eppic.db.tools.DBHandler.<init>(DBHandler.java:86)
    at eppic.db.tools.ClusterCrystalForms.main(ClusterCrystalForms.java:135)
    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 eppic.db.tools.Main.callTheTool(Main.java:23)
    at eppic.db.tools.Main.main(Main.java:13)
Caused by: java.lang.RuntimeException: Error while reading file:/home/spencer/dev/biojava/eppic/eppic-dbtools/target/uber-eppic-dbtools-3.0-SNAPSHOT.jar
    at org.hibernate.ejb.packaging.NativeScanner.getClassesInJar(NativeScanner.java:131)
    at org.hibernate.ejb.Ejb3Configuration.addScannedEntries(Ejb3Configuration.java:475)
    at org.hibernate.ejb.Ejb3Configuration.addMetadataFromScan(Ejb3Configuration.java:465)
    at org.hibernate.ejb.Ejb3Configuration.configure(Ejb3Configuration.java:351)
    ... 10 more
Caused by: java.io.IOException: invalid constant type: 18
    at javassist.bytecode.ConstPool.readOne(ConstPool.java:1027)
    at javassist.bytecode.ConstPool.read(ConstPool.java:970)
    at javassist.bytecode.ConstPool.<init>(ConstPool.java:127)
    at javassist.bytecode.ClassFile.read(ClassFile.java:722)
    at javassist.bytecode.ClassFile.<init>(ClassFile.java:109)
    at org.hibernate.ejb.packaging.AbstractJarVisitor.checkAnnotationMatching(AbstractJarVisitor.java:243)
    at org.hibernate.ejb.packaging.AbstractJarVisitor.executeJavaElementFilter(AbstractJarVisitor.java:209)
    at org.hibernate.ejb.packaging.AbstractJarVisitor.addElement(AbstractJarVisitor.java:170)
    at org.hibernate.ejb.packaging.FileZippedJarVisitor.doProcessElements(FileZippedJarVisitor.java:119)
    at org.hibernate.ejb.packaging.AbstractJarVisitor.getMatchingEntries(AbstractJarVisitor.java:146)
    at org.hibernate.ejb.packaging.NativeScanner.getClassesInJar(NativeScanner.java:128)
    ... 13 more
Unable to configure EntityManagerFactory
Error initializing Entity Manager Factory

A related SO thread:

http://stackoverflow.com/questions/24281235/error-creating-entitymanagerfactory-due-to-error-tying-to-scan-jar-file

[josemduarte]

Now fixed by upgrading hibernate to latest 4 version. I'm still playing with upgrading to 5.

[josemduarte]

I've finally managed to upgrade to hibernate 5 (just merged the branch into master), so now we are in latest and greatest hibernate version.

[sbliven]

Awesome, @josemduarte. Do I need to do anything to migrate my local database, or does this happen automatically?

[josemduarte]

The migration should be automatic. It is controlled by a setting in the persistence.xml file. At the moment it is set to hibernate.hbm2ddl.auto=update which means that the schema will be updated upon start-up.

Hibernate 5 has some more foreign key constraints in the tables so it does need to update those. In the full database in dev server, that took quite a while but in a smaller db it should be pretty fast.

[sbliven]

I'm going to reopen this issue since we can't actually use Java 8 methods in the WUI currently. For this, we need to move to GWT 2.8 and GXT 4.0. I've started a gwt2.8 branch to work on this. Getting the java to compile was fairly straightforward, but I can't get the java to js working yet. It's possible there are still bugs due to the beta.

[josemduarte]

Is GXT 4.0 available in maven central? I couldn't find it

[sbliven]

@josemduarte It's not on maven central, but Sencha host a repo for it. I seem to have forgotten to check in that file originally. The branch should compile now.

[josemduarte]

Cool thanks! Actually I've just checked out branch gwt2.8 and it compiled without problems. I haven't tried running it though.

[sbliven]

I had it running on dev for a while today. It compiles fully, but the pages fail to load. I see one additional javascript error relative to the master branch (some variable is null/undefined), but I haven't been able to debug it. GWT 2.8 is supposed to be much easier to debug, so I'll have to try setting up the embedded mode.

If you try to debug it yourself, I recommend the following modifications. It would be good to set up a dev maven profile for these options:

• In eppic-wui/src/main/java/ch/systemsx/sybit/crkwebui/Crkwebui.gwt.xml, uncomment the user.agent line. This reduces the number of compiled permutations from 42 to 18. I would love to get this down to one permutation but I haven't figured out how.
• In eppic-wui/pom.xml, add the line <style>PRETTY</style> to the configuration section of the gwt-maven-plugin to disable minification

[josemduarte]

GWT 2.8 is supposed to be much easier to debug, so I'll have to try setting up the embedded mode.

That is supposedly the theory, if I understand they introduced the SuperDev mode that makes things easier. A year ago or so we tried to set it up (with 2.7) but we never managed. Perhaps it got easier now.

In any case it would be fantastic to have some debugging capabilities for the client code, for the last year we've had to live without a debug mode.

[sbliven]

How important is it to use BioJava 5? Can we postpone upgrading until 3.1, given these problems?

[josemduarte]

I don't think using BioJava 5 is urgent. Plus it would require a lot of refactoring due to the new protein structure data model. Definitely let's leave BioJava 5 for 3.1.