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Unable to connect to mysql db with JPA (java persistance)

I'm fairly new to Java--though, coming from PHP + JS. I aim to make a CRUD (+MVC) with Java Servlets.
I am using Java EE 7. I based some of my patterns here with this and that (both have the same final files).
So, I am implementing MVC, and I can't seem to make my code to work. JPA seems to be the main issue; I can't fetch anything from the database.
Here's the repository (really small project -- 7~8 classes). Models; DAO.
I had setup controllers.Test(url: /test) to test if I could actually communicate with the database via JPA. However, when I go to /test(controllers.Test), an exception is thrown. The same goes for controllers.NewsEdit(url: /edit).
java.lang.NullPointerException
controllers.Test.doGet(Test.java:36)
javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
When I visit home(url: /; controller.NewsIndex), I receive no exceptions -- I get the homepage, but no data at all. Is there anything I'm doing wrong?
My SQL files are located in the /sql folder. I got persistent.xml on META-INF/.
Any help or reference would be appreciated. Really need to learn it..
Thanks!

Ok,
A lil explanation about NullPointerException.
When the variable (in this case private NewsDAO newsDAO;) hasn't been initialized, that "pointer" is pointing to nothing in memory. Then when you try to call a method, there is nothing there and the NPE happens.
The problem here is that private NewsDAO newsDAO; is not being injected by the container and therefore when you call newsDAO.all(); newDAO is null and throws the exception.
CDI Injection only happens for components managed by the containers. I'm a spring guy so I'm not sure where to go here. Try to figure out if your NewsDAO is being loaded by the container.
Tomcat is a web container... You need a full Application server with an EJB container to run your example. Try to download and run on glassfish, JBoss or any other full app server.
more info here.
http://en.wikipedia.org/wiki/Application_server#Java_application_servers
and
http://www.oracle.com/technetwork/java/javaee/overview/compatibility-jsp-136984.html

How do I test if EJB is running on JBoss AS 7 server

Again, many excellent answers from the fine folks here on SO. I am still unable to connect. But I believe Gimby might have had a good suggestion that there may be something wrong with the server or the beans. According to the log file generated when JBoss started, my beans have been deployed. The administrator of the server is unable to run the admin console for vulnerabilities reasons so there is no way to see if the beans are running. Is there a command line tool that I could point him to for testing? Is there a simple test I could write that would check the beans? I have tried most everything I have found and others have suggested and keep getting various errors. most times being:
javax.naming.CommunicationException: Could not obtain connection to any of these urls: remote://:4647
I've encountered other errors as I have made changes to various files and code but this one is the most frequent. If the call I make to the bean is right, and that is questionable, then how do I tell if the bean is even running or not>

There seems to be some uncleared situations here.
Still I want to ask you, if your bean got a remote interface.
You could use lookup to find your bean on this server.
You also could deploy for example a RESTservice on your jboss server, which look for your bean locally, so you dont have to specify any connection properties, but you would need the jndi name.
Hope this helps a bit, greets Jerome.

JMX Remote Deployment Architecture

I'm reading up on JMX for the first time, and trying to see if its a feasible solution to a problem we're having on production.
We have an architecture that is constantly hitting a remote web service (managed by a different team on their own servers) and requesting data from it (we also cache from this service, but its a sticky problem where caching isn't extremely effective).
We'd like the ability to dynamically turn logging on/off at one specific point in the code, right before we hit the web service, where we can see the exact URLs/queries we're sending to the service. If we just blindly set a logging level and logged all web service requests, we'd have astronomically-large log files.
JMX seems to be the solution, where we control the logging in this section with a managed bean, and then can set that bean's state (setLoggingEnabled(boolean), etc.) remotely via some manager (probably just basic HTML adaptor).
My questions are all deployment-related:
If I write the MBean interface and impl, as well as the agent (which register MBeans and the HTML adaptor with the platform MBean server), do I compile, package & deploy those inside my main web application (WAR), or do they have to compile to their own, say, JAR and sit on the JVM beside my application?
We have a Dev, QA, Demo and Prod envrionment; is it possible to have 1 single HTML adaptor pointing to an MBean server which has different MBeans registered to it, 1 for each environment? It would be nice to have one URL to go to where you can manage beans in different environments
If the answer to my first question above is that the MBean interface, impl and agent all deploy inside your application, then is it possible to have your JMX-enabled application deployed on one server (say, Demo), but to monitor it from another server?
Thanks in advance!

How you package the MBeans is in great part a matter of portability. Will these specific services have any realistic usefulness outside the scope of this webapp ? If not, I would simply declare your webapp "JMX Manageable" and build it in. Otherwise, componentize the MBeans, put them in a jar, put the jar in the WEB-INF/lib and initialize them using a startup servlet configured in your web.xml.
For the single HTML adaptor, yes it is possible. Think of it as having Dev, QA, Demo and Prod MBeanServers, and then one Master MBeanServer. Your HTML Adaptor should render the master. Then you can use the OpenDMK cascading service to register cascades of Dev, QA, Demo and Prod in the Master. Now you will see all 5 MBeanServer's beans in the HTML adaptor display.
Does that answer your third question ?

JMX is a technology used for remote management of your application and for a situation for example when you want to change a configuration without a restart is the most proper use.
But in your case, I don't see why you would need JMX. For example if you use Log4j for your logging you could configure a file watchdog and just change logging to the lowest possible level. I.e. to debug. This does not require a restart and IMHO that should have been your initial design in the first place i.e. work arround loggers and levels. Right now, it is not clear what you mean and what happens with setLoggingEnable.
In any case, the managed bean is supposed to be deployed with your application and if you are using Spring you are in luck since it offers a really nice integration with JMX and you could deploy your spring beans as managed beans.
Finally when you connect to your process you will see the managed beans running for that JVM. So I am not sure what exactly you mean with point 2.
Anyway I hope this helps a little

JMX - MBean automated registration on application deployment

I need some direction with JMX and Java EE.
I am aware (after few weeks of research) that the JMX specification is missing as far as deployment is concerned. There are few vendor specific implementations for what I am looking for but none are cross vendor. I would like to automate the deployment of MBeans and registration with the Server. I need the server to load and register my MBeand when the application is deployed and remove when the application is un-deployed.
I develop with:
NetBean 6.7.1, GlassFish 2.1, Java EE 5, EJB 3
More specific, I need a way to manage timer service runs. My application need to run different archiving agents and batch reporting. I was hoping the JMX will give me remote access to create and manage the timer services and enable the user to create his own schedule. If the JMX is auto registered on application deployment the user can immediately connect and manage the schedule.
On the other hand, how can an EJB connect/access an MBean?
Many thanks in advance.
Gadi.

I investigated JMX and EJB in Glassfish few years ago, so I don't remember all the details. But this might still help.
Glassfish-specific JMX. Glassfish has AMX and custom MBean can be deployed. AFAIK, such beans are meant to monitor the server itself, not to interact closely with a specific application. Such bean can be made persistent, and Glassfish will store their value somewhere across restart. Maybe have a look.
Registration and lookup. You can register MBean anytime from within an application using the MBeanPlatform, or MBeanServer. See this link, I don't remember exactly. You can also lookup other JMX bean and invoke operations on them. The names for the lookup are a bit crazy though. You can register the MBean when the app. starts from within a ServletContextListener.
Classloaders and deployment. The MBeans and the EJB instances are in distinct Classloader. I think you will need to place the .jar with the MBean implementation in the Glassfish deployment directory structure or add it the list of .jar in the classpath via the admin console. You can relatively easily manage to register a bean from within an EJB module, but a bean can not access a EJB easily, at least from my experience.
I managed to use plain JMX to expose statistics from my EJB application, and that worked relatively well. But I don't know if it's adequate to have something more interactive, as in your case where you want to have the EJB change their behavior depending the timer configured with JMX. I fear you will have troubles with this approach.
Hope it helps, despite the vagueness of what I remember.

How do I fix this JBoss EJB client authentication issue?

I have an EJB deployed under JBoss (we're moving a project to it from Weblogic), I can get an EJBHome reference to the EJB via a JNDI lookup.
The login-config.xml application-policy contains several login modules (I don't know if these are ANDs or ORs?) - org.jboss.security.spi.BaseCertLoginModule, LdapLoginModule, RoleMappingLoginModule and ClientLoginModule.
When my client code tries to invoke the create method via reflection, calling invoke, I get an InvocationException which wraps an AccessException, which wraps a final exception of javax.security.auth.login.FailedLoginException: Password Incorrect/Password Required at org.jboss.security.auth.spi.UsernamePasswordLoginModule.login(UsernamePasswordLoginModule.java:213)....
Am I missing some client code to use BaseCertLoginModule, or one of the others in the login-config.xml, instead of UsernamePasswordLoginModule?
Thanks in advance, any suggestions appreciated, apologies for not posting the entire stacktrace but it's on a secured network without internet access.