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converting ejb project from websphere to glassfish 2.0

Hi I have a project in which the coding is on java and this code is using swing, ejb and ibm's websphere coz it was coded in 2001 by someone , so i have to convert it for using it on glassfish 2.0 . The problem is that in this code using the api of ibm's websphere is used like
com.ibm.ejs.util.Uuid;
com.ibm.ivj.ejb.runtime.AbstractAccessBean;
com.ibm.ivj.ejb.runtime.AbstractSessionAccessBean;
com.ibm.etools.ejb.client.runtime.AbstractEJBFactory;
com.ibm.ejs.container.EJSWrapper;
com.ibm.ejs.container.*;
com.ibm.ejs.persistence.EJSJDBCPersister;
com.ibm.websphere.cpi.PersisterHome
com.ibm.ejs.container.*;
com.ibm.ejs.container.*;
com.ibm.ivj.ejb.associations.interfaces.Link;
com.ibm.ivj.ejb.runtime.AbstractAccessBean;
com.ibm.ivj.ejb.runtime.AbstractSessionAccessBean;
com.ibm.xml.parsers.SAXParser;
COM.ibm.db2.jdbc.DB2BaseDataSource;
COM.ibm.db2.jdbc.DB2DataSource;
I don't want to use websphere and also not found any jar file to import that classes on glassfish so please suggest me how to convert it.

The classes you mention are generated by WSAD (WebSphere Application Developer, which is ancestor of RAD) during 'generate deployment and rmic code' phase of build process. You can also tell this from the class names, which probably have funny prefixes and suffixes attached original bean name and reside in the same package. So, developer did not write these classes himself, they are generated for WebSphere, and they shall be omitted (cleaned up from project) before migrating to an application server from another vendor. On how to get rid of these classes you may find instructions at tech note below.
EJBDeploy generation and deletion of stubs, ties and generated deploy code
I would say that you have a pair of problems here, because most probably Enterprise Java spec that was used is not currently supported by new servers (it is probably 1.2 as it is very old). So you must first perform a specification level migration, then application server migration.
For specification level migration (i.e. Java EE 1.2 to 1.4 at least) I would say your best bet would be to use RAD (Rational Application Developer), which can perform specification migration by using simple wizards. You may find information about how to perform this migration at article below.
Migrating the specification level of J2EE projects
Once you upgrade spec level it will be easier to migrate your project to another server because as the spec level increases, effort for server to server migration decreases. At this point what you shall do basically is prepare application server specific deployment descriptors for your target server (Glassfish), for which you shall check glassfish website. A good entry point would be Glassfish migration wiki, and Glassfish verification tool (I can't put links to these because I don't enough reputation to post more than two link at the moment :)

I don't know of any "simple" way to convert such projects. You will end up having to manually change all relevant parts to the updated spec. I assume you are not really willing to upgrade to GF 2.0? You should at least move to 2.1. I highly recommend to move to 3.1.

How to start a Java EE 6 project in Eclipse

I have recently begun learning Java EE 6 after doing Java SE for some years now (together with other languages). I have bought different books about Maven, EJB, JSF, Glassfish and so on (not read them all yet though), and I feel absolutely overwhelmed of the complexity of just making a project.
How would I start a project from "scratch" (Not copying a from an example in the book) in eclipse? I can choose from Dynamic Web project, Maven project, EJB project, EAR application etc. Which should I use if I want to make an application that has EJB/JPA and JSF inside (web application)?
I know about the Standard Maven Directory Layout and archetypes, however I do not know which to choose if this is the way to do it. Of course, I understand that there are many ways of doing it and it is dependent on what I will use it for, but I am learning Java EE 6 so I want to at least have some knowledge of how to set up a basic project as well.
I am also rather overwhelmed by the POM file. How do I know which dependencies I need just to get started with a web application? Or is this included in the correct archetype (if I find one?)
I am using Glassfish as application server, Eclipse, EJB, JPA and JSF. Currently learning from book examples only.

Well, a complete answer to your question would pretty much need an entire book on it's own, but here's some pointers.
The notion of Java EE applications represents any kind of Java application that uses one or more of the Java EE APIs implementation and needs a Java EE application server to run. Java APIs are those such: Servlet,JSP, EJB, JPA, etc. Implementations of these APIs are usually provided by the application Server (like Tomcat has servlet and JSP implementations, Glassfish has those as well plus EJB, etc). There are, let's say non-application server Java EE APIs implementations like Hibernate's implementation of JPA. So in short if you use some of these APIs implementations in your app and deploy it into some application server like Tomcat, Glassfish, JBoss AS, etc, you have a Java EE application.
I've told you all this because in reality, most of the project management tools (like Eclipse, Maven, etc) use these subdivisions like Web-Application, EJB Module, Dynamic Web Project etc, as a custom denomination that establishes the ball park of what set of Java EE APIs your application will use. I.E. a Web Application or Dynamic Web Project will more likely use Servlet and JSP APIs, an EJB Module will (duh) use the EJB APIs and so on. These are, as I said, ball park denominations. A Dynamic Web Application can use EJB or JPA as well, it's not like it's written in stone.
When you use either of these tools such as Eclipse or Maven, to start one of these above mentioned, denominated projects, such as a Dynamic Web Project in Elcipse or a Standard Web Application with Maven, that respective tool will add the common sense dependencies to your template project (like Servlet and JSP in this case), and then let you handle it from here.
The idea here is to understand each type of template of your chosen tool before you use it at the start of your project. Like if you decide to use Eclipse and start with a Dynamic Web Project, you should check out what exactly Eclipse asks of you and does when you do that (it will ask you for the location of a locally installed Java EE application server from where it will pull in such dependencies as a Servlet Implemnentation and a JSP implementation amongs others). Or if you chose Maven, and start a standard web project, you should check out what dependencies it adds to your project via the pom.xml file, what the basic functions of THAT pom.xml file are, etc. You should also check out how each of these tools deploys your application when you tell it to do that, does it use some hot deploy feature of your Java EE server, does it need credentials to access that server first etc.
My brief advice is to start with the very basic example: Install a Tomcat (version 7 is recommended), start Eclipse for Java EE Development, add that Tomcat installation to your Eclipse config, start a Dynamic Web project that uses that Tomcat as Application server, and just do some basic servlets and JSP pages, then use Eclipse to deploy that sucker to tomcat and run it. Then you can branch off to more advanced stuff, like doing the same thing with Maven, integrating a Maven project with Eclipse, adding some more Java EE Stuff (like a JPA Implenentation), etc etc.

http://blogs.oracle.com/arungupta/entry/web_app_development_using_java provides a complete explanation of how to create a Java EE 6 project using Eclipse and GlassFish.
Alternatively, you can also NetBeans to create a Java EE 6 project as explained at:
http://blogs.oracle.com/arungupta/entry/screencast_37_java_ee_6

I can choose from Dynamic Web project, Maven project, EJB project,
EAR application etc. Which should I use if I want to make an
application that has EJB/JPA and JSF inside (web application)?
Before EJB 3.1 spec it was not possible to deploy EJBs in war files, but now, you can. So for a quick prototype you can use a war file rather than an ear file if that's all you require and you are more familiar with it. Of course you can also deploy it in an .ear file.
I believe the Dynamic Web project in Eclipse generates a .war file that you can deploy in your AS.
If you are using Maven, you can also create your project with Maven beforehand, and then import using Maven (via M2Eclipse plugin). This works pretty well for me. Then, with the Glassfish Maven plugin, you can deploy your app to Glassfish via command line.
I am also rather overwhelmed by the POM file. How do I know which
dependencies I need just to get started with a web application? Or is
this included in the correct archetype (if I find one?)
You need the Java EE dependencies at least in a "provided" scope as the server will probably provide these for you. This way they will be available for you in compilation mode. For instance, the one for the JBoss Java EE 5 stack is as follows (not sure about the GlassFissh dependency, but the important stuff is not to include the library in your .ear / .war in order to avoid library conflicts):
<dependency>
<groupId>org.apache.openejb</groupId>
<artifactId>javaee-api</artifactId>
<version>5.0-1</version>
<scope>provided</scope>
</dependency>
Added: As you said, this can be overwhelming at the start, I think this is a good resource on how to setup a Glassfish / Java EE project. Pick the bits you are interested on and good luck.

The first thing I'd ask you is why you're learning so many technologies. If your purpose is getting a job, in my experience, there's a trend in companies away from Java EE and towards simpler solutions. For example, application servers are overkill for most organizations and Tomcat (or another web server) with helper technologies like Spring and standalone JMS servers replacing full-featured and much more complex Java EE servers.
I think you'd be better served focusing on core concepts and simpler technologies as you get started and staying away from IDEs, complex builds, EARs, etc. Instead, start with one or two technologies (e.g. a hello Tomcat app with a simple Ant build) and gradually add each technology in as you find the need. Better yet if you have a real world problem to solve, even if it doesn't pay.
Most companies (at least those with a technical clue) would rather hire a programmer who understands what value a technology like JSF adds and at what cost of complexity than someone with a lot of acronyms on their resume.

How to start a new web app project in Eclipse with Maven?
Just type "archetype:generate" and select JSF + EJB/JPA if available.
This one seems fine: 360: remote ->
org.jboss.weld.archetypes:weld-jsf-jee (Weld archetype for creating a
Java EE 6 application using JSF 2.0, CDI 1.0, EJB 3.1 and JPA 2.0
(persistence unit included))
The Appfuse are quite more complete and may embed stuff you will never
use and that you will have to remove.
After that mvn eclipse:eclipse to be able to load the project in eclipse.

Tomcat7 Alternative

I have never used something different than tomcat. For my current university project I programmed a WebApplication with JSF and Java EE 6. I have to hand it in installed on a VM with Ubuntu OS.
My fellow student told me that Tomcat7 is not released for Ubuntu (or is it?) and tomcat 6 doesn't provide Java EE 6 capabilities.
So I want to ask you if there is an appropriate alternative? Maybe something that doesn't have to require a lot of induction for a tomcat user.
Thank you for your help

I don't think Tomcat is release for anything.
They just put out a release, and V7.0 (I think as of 7.0.6) has now been declared production ready.
So just create your VM with Ubuntu, install Java, download Tomcat, unzip the bundle and install your application.

try the new Jboss, it`s really easy to use, almost the same from tomcat, and they should have for ubuntu( the new version) because they are from red hat too!
EDIT:
To clarify my statement before, Jboss it`s as easy as tomcat to deploy a simple J2EE app.

Glassfish is a well-known free open-source Java application server, but it's a bit more full featured than Tomcat and thus potentially more complicated (it has a full Java EE stack).
Jetty is more like Tomcat in that it's primarily a servlet container, you can take a look at that as well. Some projects (such as Grails) have switched from using Jetty to Tomcat for various reasons, but it may work for your needs.

I would go with Jetty, which damn fast and light.
But it does not support Java EE natively.
What are good alternatives? Glassfish/JBoss.

sun's application server?

in a tutorial they asked me to install the application server which could be downloaded from their site.
what do they mean with application server?
the link they provided: http://java.sun.com/javaee/downloads/index.jsp
i mean come on sun, all these names. jdk then j2ee..and when i wanna download j2se it says jdk6. r they insane? a lot of people are wondering what is what...they just dont know how to name things.
however, back to the question. so with application they mean java ee server?
i've got a mac and people say java is already installed. what is installed exactly? the j2ee or j2se? do i have do download j2ee? Java is just killing me...
EDIT: read something about that the application server is a name for ee server. and there are many ee servers like tomcat, jetty and glassfish. and i know these sometimes are called servlet containers.
so that makes application server = ee server = servlet container?
and jdk = j2se? so j2ee != jdk?

Sun's Application Server has been superseded by the community app server, GlassFish.
The JavaEE download page only has two JavaEE6 download links and both contain versions GlassFish v3. Chances are you only need the web profile, but download the full version if you aren't sure.
Note that GlassFish is just the reference Application Server. You also have other Application servers, such as Apache Geronimo and Oracle Weblogic... as well as ones that are just servlet containers, like Apache Tomcat and Jetty. These types should correspond to GlassFish's normal and web profiles respectively.
These other servers only require a JRE to run applications, or the JDK to develop for them.
Side Note: GlassFish v3 is the only JavaEE 6-compliant server... JavaEE 6 is brand new. The others should be JavaEE 5 compliant.
Also, JavaEE is the new name for J2EE, as sun tries to move away from the Java 2 name.

What do they mean with application server? The link they provided: http://java.sun.com/javaee/downloads/index.jsp
An application server is a component-based middleware used in server centric N-tier architecture. It manages the life-cycle of components deployed on it, it provides services for state maintenance, data access (with pooling of resources), security, clustering and fail-over.
AFAIK, one of the first application server (as just defined above) was ATG Dynamo. Other proprietary application servers include BroadVision, ColdFusion, etc. But none of them really survived to the advent of Java application servers (understand application servers based on the standards defined by Java EE and the Java language).
I mean come on sun, all these names. (...)
Wikipedia does a pretty good job at defining what Java SE is:
Java Platform, Standard Edition or Java SE is a widely used platform for programming in the Java language. It is the Java Platform used to deploy portable applications for general use. In practical terms, Java SE consists of a virtual machine, which must be used to run Java programs, together with a set of libraries (or "packages") needed to allow the use of file systems, networks, graphical interfaces, and so on, from within those programs.
The JRE (Java Runtime Environment) provides the virtual machine and the set of libraries i.e. everything you need to run Java software. The JDK (Java Development Kit) provides a JRE plus a compiler (javac) and some other tools i.e. everything you need to run and develop Java software.
Java EE is a specification (more precisely, a set of specifications) built on top of the libraries provided by Java SE and is more server-side oriented. Implementations of this specification are provided by Java application servers: GlassFish is Sun's implementation, JBoss is RedHat's implementation, WebLogic is BEA Oracle's implementation, WebSphere is IBM's implementation, etc.
Regarding the versions and nomenclature, yes, Sun is crazy. It was an horrible mistake to introduce this "Java 2 Platform, Standard Edition" naming when the version 1.2 came out. I can imagine how confusing this is. But, again, Wikipedia does a great job at clarifying this in the section Nomenclature, standards and specifications:
Java SE was known as Java 2 Platform, Standard Edition or J2SE from version 1.2 until version 1.5. The "SE" is used to distinguish the base platform from Java EE and Java ME. The "2" was originally intended to emphasize the major changes introduced in version 1.2, but was removed in version 1.6. The naming convention has been changed several times over the Java version history. (...)
This should make things more clear.
(...) however, back to the question. so with application server they mean java ee server?
Yes, this is what they mean or, more precisely, they mean Sun GlassFish Enterprise Server (previously named Sun Java System Application Server). Source: http://developers.sun.com/appserver/.
I've got a mac and people say java is already installed. what is installed exactly? the j2ee or j2se? do i have do download j2ee? Java is just killing me...
A JRE or a JDK (if javac available, it's a JDK), so only the Java SE part. And actually, if you are still following me, you don't download Java EE, you download something providing an implementation of it (i.e. an application server).
(...) so that makes application server = ee server = servlet container?
No. To simplify, a Java EE server = Servlet container + EJB Container. Some server are only Servlet container (like Tomcat, Jetty), they don't provide the EJB container part and thus don't fully implement the Java EE specification and can't be considered as full Java EE servers.
and jdk = j2se? so j2ee != jdk?
I hope I covered this with my answer.

In order to run you Java EE applications you need an application server.
The link you provided is to download GlassFish that is one application server.
There are others application servers like Apache Tomcat, Jboss.
JDK stands for Java Development Kit
You need this to develop Java applications.
JRE stands for Java Runtime Environment
You need this to run Java applications.

GlassFish with the Java EE SDK (provided on the link you gave) is what you need. Java EE server = application server.
What is installed on your Mac by default is probably only a JRE (runtime environment) and not a JDK (development kit). Which means, you can run Java apps but not develop. By downloading GlassFish with the Java EE SDK, you'll get the full-blown SDK you need and a server to deploy on.
Hope that helps.

Java SOAP Server that can be deployed in Tomcat, JBoss, Geronimo, etc. etc. etc

I'm hoping to create a Java SOAP server which I can deploy in Tomcat, or in JBoss, or in Geronimo, or in XYZ, etc. etc. etc.
Bottom line, it should have the least dependencies possible. I'm trying to avoid libraries outside of what's included in a standard java distro because of licensing/packaging/reusability issues.
Can any provide a link to where I should start looking, or some example code?

Java 1.6 introduced the possibility to create standard SOAP webservices with the standard JDK.
There are many examples on the web, for example http://weblogs.java.net/blog/2006/12/12/webservices-jdk-6
IDEs like NetBeans also call the necessary tools (apt) automatically which makes it very easy to get started.
However I did not research how well this will work across all available containers.

Apache Axis2 (http://ws.apache.org/axis2/) should provide what you're looking for, or JAX-WS (https://jax-ws.dev.java.net/) if you want more lightweight.

Wow.
http://www.w3.org/TR/soap/
There's the standard. You will be spending a lot of time on this project. You'll need to also check out the HTTP and XML specs to build those components.
Ignoring XFire and Axis2 is an very very expensive choice...

I recently used Metro 1.4 for this (an open source glassfish component) which implements the standard approach for web services.
Drop in the jars in a Java 5 web container, annotate your class and method with standard #tags, and let Metro do the rest.
I have been very pleased with performance in a Jetty container.

If you use Spring web service module you don't need Axis or XFire. I think it's a good way to go if you're already using Spring.