Develop Reference

How to Migrate WebSphere 6.1 to WebSphere 8.5

I am new to WebSphere. One of the project came to upgrade the existing IBM WebSphere application server 6.1 to WebSphere application server 8.5. Four custom EJB application is running on server. Please guide what the solution to migrate to 8.5 Application Server.

I've handled a few migrations and there are definitely some gotchas to watch out for:
If this is any more critical than a development system, there is a bit of planning you'll need to do. You'll have to bring over any config from the old environment, and you'll have to make sure your applications will work in the new environment.
For the former, WebSphere itself ships with the configuration migration tools, both as command line tools and as a wizard. If you're migrating between installs on the same machine, I would definitely recommend the wizard as it better explains the process and what each setting does. If the installs are on different systems, the command line tools can help with that, but the wizard cannot. The tools to use are both documented at this link although for some reason the article neglects to mention that the wizard is also called migration.sh or migration.bat
If you have a cell topology (a deployment manager managing some number of application servers) you'll migrate the deployment manager first and then the nodes. In that case, the old cell will be disabled, so make sure you take a full backup of the old environment so you can roll back if you have to. The specific procedure for migrating a cell has a good overall order of steps to take, but doesn't mention the wizard. You can replace the "create profile, backup, restore" cycle with the wizard, but the rest of the steps should remain the same.
If it's just a standalone application server, those can usually coexist at the same time so you may be able to keep the old one active while you set the new one up, but I don't think there are any established documentation on how to do that, so to be safe, backup, and plan for some downtime.
Another consideration will be the applications themselves. You will be moving to a new version of WebSphere which supports a new level of Java EE and runs on much newer Java SE, and there are often problems and incompatibilities that come up. For that, I recommend running the binary application scanner with your applications and environment specified and seeing what it reports. If there are any severe issues it flags, it may be worth investigating those before starting the migration to minimize downtime.
Already I can tell that using EJB on WebSphere 6.1, you'll need to make sure that you install the EJBDeploy tool with your WebSphere 8.5 install. It will be automatically used during application deployment. Without that, it's pretty likely the applications won't work because their old EJBs won't deploy. Because of this, I believe you still need to use Java 7 unless you install this fix to get it to run on Java 8. I do not recommend running on Java 6 because that is going out of service by Oracle within a year or so.
So, to summarize:
Use the binary application scanner to see if there are any immediate compatibility issues to start addressing in the applications themselves
Make sure you have the EJBDeploy tool installed along with WebSphere 8.5
Use the migration wizard or command line tools to bring over your configuration and deploy your applications
#Jarid's answer documents everything available relating to WebSphere migration, and is also a good resource.

WebSphere provides an official migration toolkit to assist with the migration process: https://www.ibm.com/developerworks/library/mw-1701-was-migration/index.html

Java EE 6 Application Server for Web Profile with JavaMail

I have a Java EE web application using features from the Java EE 6 web profile + the EJB Timer service and JavaMail. I'm currently using GlassFish 3.1.2 full profile during development, but I want to investigate the alternatives because:
There seems to be a bug with multipart forms in GlassFish 3.1.2 and GlassFish 3.1.1 had other problems hurting me which are fixed in 3.1.2. (catch 22...) That bug is fixed by the jar in the ticket.
There seems to be a lot more options for application servers supporting the "web profile" than the "full profile" and the former is supposed to be so much more lightweight.
I want to choose the best option for deployment
I am currently using the embedded application server feature of GlassFish for tests, so a similar facility for any alternative is desirable. At worst, I can live with stiking to GlassFish embedded for the automated tests.
Is it possible to "add" a JavaMail and EJB Timer Service implementation module to an applicaton server implementing only the web profile? Does it work well? If this is not possible, are there alternatives to using JavaMail and the EJB Timer Service?
Which application servers meeting my requirements can you recommend?
Finally, I considered using the "Asynchronous invocation" feature of EJBs which is not part of EJB lite. If I understood correctly, it is illegal to start threads manually when running in a Java EE container. In that case, how can asynchronous operations be started in the Java EE Web Profile?
I'm still relatively new to the whole Java EE ecosystem and terminology so please don't hesitate to ask me to clarify any parts of my question.
Supporting doc
Java EE 6 web profile vs Full profile
EJB 3.1 vs EJB lite
edit 1
According to the Apache TomEE doc, TomEE, TomEE+ and OpenEJB would fit the bill.
edit 2
Based on the AS 7.1 release notes, this thead and this issue JBoss AS 7.1.0 seems to implement all the features I need.

First of all, I have never used GlassFish so I cannot give you any information about that.
I'm not sure if your application is being build for a true production envrionment but jboss 7.1 does not yet have any official commercial support in case you run into trouble.
Jboss 5.1 optimized for JDK 6 has commercial support via red hat.
That being said, a jboss instance can be fully configured and is very flexible. That means that you can start with the 'web' profile and add/remove services you do not need. (Removing unused services is always advised for production environments.)
Here is a wiki that gives information about slimming a jboss profile in jboss 5. It indicates all steps needed to remove a service.
The slimming operation can also be reversed, so you can add anything you need to a certain profile.
So there are basicly two approaches:
Start with a profile like 'default' or 'all' and start removing services that are not needed for your application
Start with the 'minimal' or 'web' profile and start adding services you are missing for your application. You copy the services from a profile that has it. (I personally prefer this approach)
Adding and removing services can be a work of trial and error though. You need to search the internet for a correct guide for the service you are trying to add or remove. (Tip, always do your operations on a copy of the profile provided by the AS and document each step. That way you can start over if you did something that seems irreversible.)
I hope this is of any help.

tom's right that JBoss AS7 doesn't have commercial support yet. However, it is coming - AS7 is being productised as EAP 6 (annoyingly!), and is going into beta in a few days. The community version has been out for a few months now, and although it does have a lot of rough edges, it basically works pretty well.
AS7 has a much more modular architecture than previous versions. The idea is that you only load the modules you need, which means that although it's a full-profile implementation (as of 7.1), if you only use web profile features, you only pay the runtime cost of a web profile implementation. You still have the bits you don't need sitting on disk, but disk is cheap (7.1.0 is 125 MB all in - hardly huge).
I'm afraid i haven't used any other fully-grown app servers (not in the last decade, at least), and so can't comment on them. I believe Geronimo supports full-profile EE6, so if you don't need commercial support, that might be worth a look.
I have spent some time using Tomcat-based setups. Yes, you can add enough extras to Tomcat to create a sort of 'bionic Tomcat' that is basically an app server, but doing it yourself is work you really shouldn't be doing - pure waste. I haven't used TomEE. I'm not a big fan of Tomcat generally, i have to admit.

As you state, OpenEJB/TomEE definitely fit the bill. Here are some examples you might like based on the things you mention:
TimerService and #Schedule
TimerService and ScheduleExpression
#Asynchronous Methods
To configure your JavaMail resource in your test case, just do like so:
Properties p = new Properties();
p.setProperty("superbizMail", "new://Resource?type=javax.mail.Session");
p.setProperty("superbizMail.mail.smtp.host", "mail.superbiz.org");
p.setProperty("superbizMail.mail.smtp.port", "25");
p.setProperty("superbizMail.mail.transport.protocol", "smtp");
p.setProperty("superbizMail.mail.smtp.auth", "true");
p.setProperty("superbizMail.mail.smtp.user", "someuser");
p.setProperty("superbizMail.password", "mypassword");
EJBContainer.createEJBContainer(p);
Then inject the JavaMail Session into your EJB via:
#Resource
private Session superbizMail;
Behind the scenes the 'superbizMail.' part is shaved off all the properties and the resulting set of properties is passed into javax.mail.Session.getDefaultInstance(Properties props). The resulting Session is what is injected into the #Resource reference

Auto Upgrade for Java EE enterprise applications

Our current process for upgrading the application is to undeploy the current version, and then deploy the newly created EAR process.
I have seen softwares which have an "auto update" functionality (such as Spring Tools Suite). The software downloads the updated files automatically and performs a self upgrade. There is no need to download the complete setup again and uninstall/install the application.
I just wanted to check if anything similar exists for Java EE web applications as well?

Many servers today support hot-deployment, where you deploy the app over the running one.
This of course still needs the functionality to pull the app from somewhere.
In JBoss 4 at least (and I think it is also available in 5), you can tell the deployment scanner to watch multiple directories, so it could monitor e.g. a shared drive and when you put the application there it would see it and pick it up.

The proper way to redeploy code at runtime is to use OSGi. This is a system created to allow automatic dependency resolution. It allows e.g. for you to keep running older code for existing connections, while using the new code for new connections.
It also allows you to link to newer versions of libraries, which are loaded automatically.
See https://docs.jboss.org/author/display/AS7/Helloworld+OSGi+quickstart for a nice quickstart for using OSGi with JBoss 7.

Jetty 8 + EJB 3.1 + JTA + CDI + JPA 2 stack?

Can anyone tell me if it is currently possible to "glue together" a partial Java EE 6 Web Profile over Jetty?
I've found a lot of articles about integrating standalone EJB 3 containers, JTA providers, etc with older Jetty versions, so I wounder if I could make it all work together.
I would like to assemble a Servlet 3.0 + CDI + EJB 3.1 + JTA (if needed, all I really want is declarative transaction management) + JPA 2 environment over Jetty 8 (or Tomcat 7 if no Jetty alternatives are available).
My questions are: Can it be done? Has anyone managed to do that? Any articles about getting OpenEJB, Atomikos, Weld, EclipseLink and Jetty (or any other similar stack) working together? Any magical "do it all" pom.xml files out there?
PS: Yeah, I know I could just use GlassFish (which I like very much). I'm just wondering about how hard would it be to get something similar working with a Servlet Container, and how the two environments would compare in terms of complexity, performance, size, deploying speed, hardware resource consumption, etc.

I'd describe this as still in the early stages, but here is what we have so far:
http://svn.apache.org/repos/asf/openejb/trunk/openejb3/assembly/openejb-jetty/
Note, Apache TomEE lives at a similar path, i.e. 'assembly/openejb-tomcat'. Plan is to call the Jetty version Apache JetSet and have it be fully embeddable. Most people with commit are currently working on getting Apache TomEE to be officially Java EE 6 Web Profile certified. I'd describe that work to be in the late stages. We've a great setup in Amazon EC2 to run the web profile TCK against TomEE using a hundred EC2 t1.micro spot instances. It's pretty sweet. The TCK agreement with Apache and Oracle does not allow us to share access publicly. However, any Apache committer can sign an NDA to get access.
Ok, so I mention all that about TomEE because the plan is once we're done with the Tomcat version, to do it all over again with Jetty (JetSet). Many of us committers, myself and Jonathan Gallimore for example, actually prefer Jetty by a large margin. But as the Tomcat integration code was much further along and had more users, we decided to just finish that one first. There is an incredible amount of work that isn't Tomcat specific that we will be able to leverage in the Jetty version; getting access to the TCK legally, the heaps of code to get it to run, the more heaps of code to get it automated, and numerous integration bits which are generic and not specific to Tomcat.
All that said, there's no reason others have to wait to work on a Jetty version just because most of us are still finishing the Tomcat version. Apache projects should be viewed as individuals working together, not companies like Oracle or Redhat or VMWare. That can be both good and bad. The good part is that if you or anyone else wants to hack on the Jetty version you can do that right now. You'll have to submit patches for awhile till you earn commit, but having someone else do the actual commit command is not that bad. If you start small and stay active and open, it's usually pretty easy to earn commit. The key to getting patches in quickly is a steady stream of small to moderately sized patches. Any step forward or sideways with no steps backward is a good patch in my opinion. As long as people can see where you're going it's good enough. Certainly more Agile than the one-big-patch approach and allows for all the really fun and collaborative magic to happen along the way.
Some threads which would be good places to say hello. Step 1 is just to say hello. No need to have code in hand to talk on the dev list or be taken seriously:
http://openejb.979440.n4.nabble.com/Jetty-Integration-td1457408.html
http://openejb.979440.n4.nabble.com/Jetty-Integration-td2318962.html

Tomcat has that stack implemented in a server called TomEE(formerly TomTom).
These are the components it uses.
Connector Apache Geronimo Connector
CDI Apache OpenWebBeans
EJB Apache OpenEJB
Javamail Apache Geronimo JavaMail
JPA Apache OpenJPA
JSF Apache MyFaces
JSP Apache Tomcat
JSTL Apache Tomcat
JTA Apache Geronimo Transaction
Servlet Apache Tomcat
As far as Jetty I'm not sure. OpenEJB is your only option for EJB outside of a JavaEE6 container(AFAIK) and I'm not sure Jetty is 100% tested with this. For CDI you can always use something like Seam.
In my opinion I believe the Spring framework would be your best option for the Jetty container(that's just my opinion though). In my experience after trying to get Tomcat working with Open EJB, Spring is a lot easier to set up.
You also have to remember Open EJB doesn't implement the entire EJB 3.1 stack at this point.
Also Open EJB is not tested on Tomcat 7 either. So you have to stay with Tomcat 6 if you go that route.

OpenEjb has not released a version with JPA2 support, although their development version supports JPA2 fine AFAIK.
I'm using embedded OpenEjb in Jetty6, because I could not get my app working in newer jetties yet. I think there is work under way to get an OpenEJB tightly integrated with Jetty like TomEE, but that may be some way off..

Geronimo is a complete J2EE stack which runs on top of Jetty.
There's a document on its setup on https://cwiki.apache.org/GMOxDOC30/configuring-virtual-host-in-jetty.html

Recommendations for Test Linux/Web Server Environment using Java

I'm a .NET developer looking do some research on my own time to better familiarize myself with Linux and Java (e.g JSP and Servlets).
My plan is to install Linux on an old PC. Then, install and configure a web server capable of hosting JavaServer Pages and Servlets. I would like to create a small web site with dynamic content being pulled from a database. Again, this site is only intended to be used by me for research and testing.
I have very little experience with Linux and Java. Did a couple projects back in college, but that was over 8 years ago.
Below are the questions I have about configuring a test environment I can use for research and testing.
1) What version of Linux should I install on my old PC?
2) What web server should I install on my Linux machine that can be used to host JavaServer Pages and Servlets?
3) What database should I install on the Linux machine? Since I'm doing this for research, it would be nice to test with a DBMS that is commonly used in the real world.
Thanks,
Chris.

You can use Debian, Tomcat and MySQL.
Debian is a fairly common linux distribution and will work on almost every PC.
Tomcat is a simple servlet container. It's the best choice if the only thing you want to do is servlets and JSP.
MySQL is, well MySQL :)
If you do mind using Linux, you can use Ubuntu which is more user-friendly but not really recommended as a server (at least for the default version).
These applications/distributions are from the most used and with the most active communities.
Resources :
debian.org
tomcat.apache.org
mysql.com
ubuntu.com

Whichever you want :-) At work, for example, our Linux servers run Red Hat Enterprise Linux, which is loosely based on Fedora, so that might be a good distribution to use that might be similar to what you would experience in the 'real world'.
Tomcat or JBoss Application Server would be good app servers to start with. Tomcat is just a servlet container, whereas JBoss supports more of the Java EE technologies. That said, many organisations find that a 'lightweight' app server like Tomcat is perfectly adequate.
MySQL and PostgreSQL are both widely-used open source database servers.

I would install the latest Ubuntu. The most user friendly and should work on your old PC.
I would install Glassfish or JBoss. Glassfish comes with Oracle's Java EE and is the easiest to install. JBoss is more widely used in commercial settings. Better yet, install both and try it on both!
MySQL is easy to install on Linux machines. In fact it's usually installed by default by the distribution.
Good luck! Linux is a great learning experience and a lot of fun!

I'm not a specialist in linux distributions, but as webserver the apache tomcat would be the best choice, I think version 6. The database may be a mysql, but for professional usage with more functionality postgresql will be the best choice.

Slackware. You will get lots of different answers on what distribution to use, and a lot of it is personal preference. I always prefer Slackware for server installations, and install all my software from source. I think of Ubuntu and Redhat more as client/desktop installations. I don't like to rely on packages to keep my servers up-to-date.
Tomcat. You don't need J2EE. Tomcat will do the job nicely.
MySQL. It's quite standard and works well.

1) As you want, but I suggest you a Red-Hat (CentOs for example) or Debian (Ubuntu for example) based distribution. With respectively Yum/RPMs and Aptitude/Synaptic, it will be easier to install Java (even if it is not difficult on other distributions).
2) To serve JSP pages and execute servlets, I suggest you Tomcat. It is much easier to install/configure it than other webservers (JBoss, Websphere, Weblogic, etc.), and you won't need them in a first time (EJB, etc.)
3) As a database, you can use MySQL (very easy to install), or PostgreSQL, or Oracle Express Edition (not Open Source but Free... And Oracle is very often used on big projects). From a Java point of view, it will be very similar (JDBC/Hibernate access to database "hide" the specificity of DB)

I think you are starting in the wrong place.
1.
If you want to try out linux try out linux. You don't need to install it - just download a "live CD". I believe the latest Ubuntu installer comes on a live cd.
2.
If you want to try out java web development you don't need to set up a server just install eclipse for java ee and create a dynamic web project. Then just start developing. Try to find some tutorials, etc. Eclipse can even download a development tomcat from within the ide.
3.
For databases - why not just use the same database you use with .net? I am sure there will be a jdbc driver and the code you write shouldn't be that different from any other database.