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Java EE deployment issue

I'm running into some issues in deploying my Java EE application, and could use some advice.
I have 3 components to deploy:
Integration layer (Data): POJOs and CDI Beans - JAR file
Application layer (BL): EJBs, CDI Beans and POJOs - JAR file
Presentation layer: Servlets and such - WAR file
Optimally, I would like to be able to deploy both the integration and application layer JARs in the same Java EE server, but as separate JARs (since I might want to change the hardware configuration later on and separate them into two different servers on two separate machines).
The problem, is that I'm unable to get the CDI injection from the integration layer JAR to the application layer JAR to work. The server says (and probably rightfully so) that it's impossible to resolve the injections.
So far I came up with these possible solutions:
Package the two JARs into a single EAR file (maybe throw in the WAR as well ...), and deploy that
Use JNDI between the different layers (possibly create a CDI producer to do a generic injection based on JNDI names or something like that)
In the integration layer, make the objects being injected into the application layer (the DAOs) EJBs instead of CDI beans
I don't like either of these solutions (especially the last), since they restrict my future deployment options. The second solution does not restrict me, but it might become tedious at some point (when I accumulate a lot of code).
Finally, my question is:
Is there an option I didn't find yet, that would allow me to deploy the two JARs on the same server with the CDI injections working ? Possibly something that would still work if at some point I separate the JARs into different servers ?

Yes, there are other options as well.
Use a java EE container that supports OSGi as well, and use OSGi interface for your deployment dependencies. At least Websphere, Glassfish, JBoss (with jbosgi installed), Jonas support deploying OSGi bundles. This means your modules should be converted into OSGi bundles.
Use a container-specific extension that allows modules to communicate between each other. JBoss as jboss-deployment-structure.xml that you can use to have a dependency to another deployment.
Use a server-provided shared classpath for your dependencies. Wouldn't really recommend this.
My vote would go for OSGi.
None of them will work by themselves however if you deploy packages to different servers. A remote technology like remote EJBs, remote JNDI lookups, Spring remoting, HTTP-based api, CORBA or similar is needed between different servers. In Java EE, EJB is the de-facto standard for this, but Spring remoting is not bad either.
Update: you added that you use TomEE servers. Indeed TomEE won't support the first two options I mentioned. I would use EJB in that case - the fact that you're using EJBs can be abstracted away from the business layer using an EJB delegate, and you could use EJB (stateless session bean) only for the interface part, leaving your DAOs as POJOs.

not sure what your goal is but deploying a war is fine, can even be done manually with these commands:
mkdir -p webapps/myapp/WEB-INF/lib
cp myjar*.jar webapps/myapp/WEB-INF/lib/
If your goal is to be able to split them you can use TomEE skinny war feature.
Create a war with a WEB-INF/jars.txt file.
In this jars.txt put one line by dependency/jar. It can be the path to the jar or maven coordinates.
Once setup it will allow you to change jars one by one then simply restart the server. This is great when several teams work on the same binary.
There are some alternative with TomEE but this one has the advantage to be easy to change to a portable one (war).

Should we use ApacheCXF or EJBs for communicating the logic and web modules?

We are currently developing a web application for college and we would like some advice from a more experienced developer.
We have a backend using Hibernate to operate on a MySQL database. Another project is the web UI that uses the API delivered by the backend (registering user, fetching data associated with certain profiles etc.). We use the JSF framework (RichFaces) for the UI. Everything is built using Maven.
The technology we can't decide on is for the communication between UI and logic modules. The first option is to use ApacheCXF to provide SOAP webservices that UI can be a client of. The second option is to use EJBs to invoke backend methods from the UI module.
What approach is more widely-used? As far as we read on the Web, using EJB is faster than SOAP webservices. On the other hand, we don't have any experience with EJBs using Tomcat (we would prefer using Tomcat since it seems to be a cheaper option, however we don't know what we would have to do in order to use EJBs with Tomcat). Additionally, working with webservices since the beginning will allow us to add support for different platforms (for example, Android).
Another aspect which we are discussing is about how should the application be deployed. The alternatives we have considered right now are:
Deploy it as a single WAR project (which would solve the problem we have about communicating the UI with the backend of our application).
Deploy two WAR projects in the same server using webservices for communication between the projects. (We have a prototype using this approach deployed on a Tomcat server)
Deploy a WAR project and EJB project.
Deploy an EAR project which would contain the references to the WAR and EJB projects. (We have a prototype using this approach deployed on a Glassfish server)
The project right now is starting, so we will only be handling a couple hundreds of users right now. However, if the project succeeds we would need to deal with a couple million of users.
Any advice would be appreciated. Thanks.
Edit: So any advice about how the project should be deployed? Is it necessary to use EAR? Is there any advantage if we deploy the project as an EAR module?
Edit 2: We found the advice we needed on this thread: Deploying java applications (Tomcat/Glassfish)

First things first. I would avoid using Web Services if there's no need for it. If you feel that you might need to call this system from external programs and platforms, then go for it. Even then, I would only use the web service interface for external integration, and still have an internal EJB implementation.
EJBs are awesome for enterprise applications. I would highly recommend that you look into that. They provide support for EJB Pooling, Transactions, Aspect oriented programming, Security, Stateful sessions, Java Messaging, JNDI etc. And you can inject them directly inside a Managed Bean (JSF). You said that you will eventually handle millions of users, so I assume that you will want your application to run as fast as possible, I don't think SOAP web services will be a good fit. Remember that SOAP web services encode messages as text, so if your application will be sending binary files etc, then you'll suffer significant performance issues.
As far as deployment goes I would go with an EAR, or a WAR for the JSF and and EAR backend. you can use Injection to pull the classes you need, even remotely, from multiple web applications and other EAR apps.
I'm not sure why you say Tomcat is Cheaper. Glassfish open source edition is a fully functioning JavaEE6 Server and its free. JBoss is also JavaEE compliant and is free. both of them are used in lots of production environments. I find glassfish to be much more user friendly, and would recommend it to EJB noobs :)
I also started with Tomcat, but now I don't use it at all. why use the servlet container only, when you can have the whole shabang? hope this helps.

we use ApacheCXF at work and its has SOAP and Restful. Reliable and relatively easy to setup. I am not sure why you want to use glassfish maybe it's preference but you can implement your projects in eclipse too. It's really that is up to you and your team and the requirements and skill sets your team may have to build and support, that a side CXF webservice+apache + eclipse with maybe two war files would be a good path.

I wouldn't use web services in this case. You can use managed beans as controllers.
Put the logic into EJBs, views into rich faces and control the flow using managed beans.
If you use maven you can generate a project with the structure of EAR (war for web module and jar for ejbs). I don't remember the name of an archetype but you can find it easily.

How do I programmatically start/stop an EJB

Does anyone know if it's possible to start/stop an EJB within my application code? Eg. I have some MDBs that I wish to selectively start/stop while my application is running? Any ideas? Can this maybe be done via JMX?
Cheers!

The EJB spec has no mechanism to start/stop individual EJBs (or even modules) within an application. It is possible to start/stop applications dynamically using JMX via JSR 77.
(I see you're using the jboss tag. I have no expertise in JBoss, so I don't know if it provides extensions that support what you want to do.)

An EJB is not something that can be "started" or "stopped". Sure, it has a life cycle but that is more concerned with creation, activation, passivation and removal of EJB instances, and it's entirely up to the EJB container to manage the life cycle.
In short: you can't manage an EJB's life cycle programmatically.

Each deployed MDB has a management MBean. The MBean class is org.jboss.ejb3.mdb.MdbDelegateWrapper. The JMX ObjectName varies between versions of JBoss 4, and vary depending on how you deployed them. Assuming you deployed an MDB called MyMDB in a jar called myapp.jar which was in an ear called myapp.ear, the name might be:
jboss.j2ee:ear=myapp.ear,jar=myapp.jar,name=MyMDB,service=EJB3
Older version of JBoss 4 also had a system hashcode in there. And if you're not using EJB3, I think the service will still be there only it will be EJB2.
Anyways, once you find the management bean, you can call the stop and start operations. We use this frequently to pause message delivery.

EJB, spring & hibernate

I've been doing Java standard edition development for awhile, and the frameworks and solutions have been fairly obvious to me (Swing for GUI, etc). I've recently begun the task of building a server for my own needs and to host a web page (things the server will be doing in addition to hosting a web page would include personal SVN hosting and integrating more web functionality into existing and future applications). For coding for only a single computer (that is, distributed computing, etc. is not really a concern)- I'm not entirely certain between Spring, Hibernate and EJB and am not very knowledgeable as to the capabilities of each. Information would be appreciated. I know Spring is an alternative to EJB, and Hibernate is an object-relational mapping library, so does EJB combine the two?

EJB3 in summary consists of 3 bean types; Message Driven Beans, Stateless/Stateful Session Beans and Entity Beans or JPA (Java Persistance Architecture). Hibernate can be used as a JPA provider, but it doesn't have to be used that way.
Spring has functionality that is roughly similar to Message Driven Beans and Stateless/Stateful session beans but it does not have an equivalent to JPA. Instead it allows you to utilize JPA or hibernate directly but if you do combine Spring with JPA you'll need an EJB container.
Another difference is that EJB is provided by 'containers' whereas spring is a framework that can be deployed into a java se application or a java servlet container web application like jetty or tomcat. Its an important distinction to make. Tomcat is not an EJB container, only a servlet container, hence if you were to only use basic tomcat, you couldn't use EJBs but you could use spring by including the required spring jar files in your web application (WEB-INF/lib). In that case you wouldn't use JPA either but you could use hibernate.
Some java servers that ARE EJB containers include weblogic, websphere, jboss, geronimo, and glassfish. Tomcat can become an EJB container if you combine it with OpenEJB.
In an application i'm developing at the moment, I'm using tomcat + openejb so I have an EJB container so I can use JPA with OpenJPA as the persistance provider. I'm using Spring MVC to do the web application development and will most likely use spring security as well down the track. I probably will also use Stateless Session EJBs as well to encapsulate business functionality but i could just as easily use Spring service/dao beans instead of statless session ejbs as well.
Its pretty confusing sometimes to work out what parts of which framework or container you should use and really comes down to either preference or using functionality in one that doesn't exist in the other or ease of use. Another consideration is memory utilization. Some of the ejb containers consume large amounts of memory just starting up with no applications running. This is one reason I ended up using tomcat + openejb. Hope this helps.

Java EE without Application Server

Since EJB 3 we have embeddable EJB containers, JPA implementations can be used without an application server, there is Weld for contexts and dependency injection and so on. Since on many systems is only Tomcat available, I wonder, if Java EE could be used without an application server but with a Servlet container like Tomcat.
What would I have to do to set up an Java environment? What drawbacks do you see?

Note that Tomcat is an Application Server. That said, in October we released Apache TomEE which is Tomcat with the missing JavaEE parts added, then Java EE 6 certified using the official TCK from Oracle.
The stack evolved from what used to be simply called "OpenEJB/Tomcat", which was a useful stack with a bad name :) Commonly overlooked because of the "EJB" part, meanwhile it also delivered Transactions, JMS, WebServices and more to Tomcat. The new name is far better and now it's officially certified like JBoss or GlassFish. We're pretty excited about its future.

If I understand well, you want to use EJB3/JPA within a servlet container.
There are not only stand-alone implementations of JPA, but also embeddable EJB3 container, such as OpenEJB or Glassfish embeddable container. So nothing prevents you from starting such an embeddable container from the Servlet container to use EJB3.
(Note: I don't know all the details about transactions. In a full-blown app. server, you have JTA and a distributed transaction manager. You don't have that in a Servlet container such as Tomcat. JPA works with JTA and plain JDBC, but I don't know exactly how an embeddable container work without JTA. Still, I guess that would work given that such embeddable containers are also meant for unit-testing where I guess there is no JTA distributed transaction manager.)
Another approach would be to use Spring. Spring and EJB3 have indeed become very similar. You can start the Spring DI container within the Servlet container and benefit more or less from the same facilities as EJB3 (declarative transactions, etc.). See this post about Spring vs. EJB3.
All these technologies have become pretty modular, especially with Java EE profiles. You can use Sevlets, EJB3, JMS, JPA, even JTA somehow independently of one other. You can also create an environment where you cherry pick the ones you would like, either with Spring or with Java EE. The question is when does it stop to make sense and rather use an app. server with everything available and easily manageable. I think Servlet/EJB3/JPA is the limit, if more is needed go for an app. server.

You will generally require some kind of container, even if that container doesn't provide Java EE-related services. After all, you do need a long-lived JVM process to host the code that you're executing. Tomcat and Jetty will do the job nicely, and in addition to basic servlet services, provide a few useful extras that will be relevant, like connection pooling.

J2EE without application server was introduced years ago by me (Guy Pardon, from Atomikos), with this seminal article: http://www.onjava.com/pub/a/onjava/2006/02/08/j2ee-without-application-server.html - focused on JMS and JDBC at the time.
In general it's easy to setup thanks to Spring and Hibernate. Actually, I got inspired to do this after doing a Java EE project and being confronted with the XML hell associated with app servers and EJBs. Without application server things suddenly became a lot simpler and more testable.
If you need a Tomcat installation then can be a bit more of a hassle to configure, but recently Atomikos has introduced out-of-the-box Tomcat integration as part of its commercial offering at http://www.atomikos.com.
HTH