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Simple Java app on a Windows Server ... should I use Java EE

I'm gonna be creating a fairly straightforward Java app for my company that will process a csv file nightly. It's going to be running on our existing Small Business Server 2011 box so it definitely needs to run as a service (cause it has to run whether someone is logged into the server or not). Eventually I'd like to add a web component to it so I can view the log files from this app via a browser instead of having to pull them off the server manually.
I'm looking for feedback on what would be the best approach for this project. Should I use Jave SE and use a service wrapper around the created app to turn it into a service. Or should I use Jave EE (which I assume already runs as a service)? I've never used or developed for Java EE, so I'm not sure if this would be the best approach or if it would be overkill. If Jave EE is the best approach any and all information you can share on how to get started with it would be much appreciated.
Thanks,
Harry

For the short term, are you looking for a web interface through which someone uploads (web interface) or some process pushes (web service) a csv file that you then process? If yes, then consider Java EE: servlets, RESTful web services, and such, as others have mentioned.
Otherwise, are you just going to process an existing csv file that's "out on the file system somewhere" on a scheduled basis? If yes then consider timer based Java EE service.
Your production environment's management team might have some insight on what they'd prefer. If they are oriented around a windows management scheme they might be more comfortable with the "native windows" approach to deployment, start, stop, restart, scheduling, etc (i.e. the service-wrapped java program). Another layer of "service management" for just one process may be unnecessary complexity.
Document your setup/configuration/expectations whatever you do.
Longer term, as pointed out by others, your desire for a java-based web monitoring interface will require an app server. Consider your short/longer priorities, schedules to be met, etc. What do you need, when?

Java EE is a set of APIs, including JMS, servlet, JNDI, JDBC, EJBs etc. Consequently by using any one of these APIs you can pretty much claim that you're using Java EE, for what it's worth.
As to your particular problem, I would perhaps develop your program as a simple servlet based app and run it under a small container such as Jetty. That way you have a lightweight container (Jetty) and a fairly trivial program to write that can have a simple front-end for admin/monitoring. Note that the Servlet API forms part of the Java EE spec, so you're Java EE compliant, albeit in a minor fashion.
An alternative to this is (depending on how important that web interface is) is to write the program as a standalone program, and run it as a service using the Java Service Wrapper. At a later date you can then embed Jetty into your program and write your simple servlet-based API to run under the embedded web server. I used this approach on a number of projects and it works very well.

Anything that requires enterprise-level functionality should be done using Java EE:
The Java EE platform is built on top of the Java SE platform. The Java EE platform provides an API and runtime environment for developing and running large-scale, multi-tiered, scalable, reliable, and secure network applications.
http://docs.oracle.com/javaee/6/firstcup/doc/gkhoy.html

Others have explained you what is JavaEE.
Since you say "simple", I guess JSP and Servlets can do the work. You will need a web container like tomcat and that's all(it is easier than having a ejb container + web!). Actually servlets and JSP can do stuff which are not simple too.
If you are willing to use something like sessions, which have great design than Servlet sessions, then you might want to deal with EJB and all.

Unless you're ready to implement a web server yourself from Java SE, you don't have much choice: you'll need some web application framework. It can ba a Java EE web container, or another implementation like Play, for example. But Java SE won't be sufficient.

You may use webservices for instance axis2

What advantages are there on using GWT over a php framework such as Yii

I am about to start developing a private TODO website (that later will be extended to Web applications). I am unsure what framework to use. I have read about GWT and PHP frameworks such as Yii. What advantages do each one have over another.
Background
- experience in Java
- got an apache web host that supports php
Doubts:
Would developing in GWT mean that refactoring would be easier than developing in PHP (especially since you can use Eclipse)
seems like PHP frameworks such as Yii design objects for you once you create database layout ... can this be done with GWT?
Thanks!

One big difference I haven't seen mentioned in the question or answers/comments is that Yii is a server-side framework, which runs entirely on your own/hosted server, whereas GWT compiles to JavaScript, and is therefore runs in the client's browser only. These two offerings (and ideas) serve very different purposes, and can be used together.
When using GWT to build the client, the server can be built using any tool desired, so long as it exposes data to the JS-based client. That can be in the form of JSON or XML, or some other data encoding (GWT's built in RPC, for example, can pass complex object graphs to and from a Java servlet container).
If you were to use them together, Yii could be used to create PHP objects from the database schema/layout, and to build the various rules for authentication/authorization so the client can read and write data. GWT could then be used to build a client which reads and updates that data, making calls to services exposed by Yii/PHP code.

If you like Eclipse you can certainly stay with Eclipse and still develop in PHP. The PHP tools from eclipse.org are very good and the IDE plugin from Aptana is even better.
Regarding Yii vs GWT, it really depends on your language of choice. If you are highly proficient in Java and really like the strong typing of the Java language then GWT is a good choice (although there are certainly other choices that keep you in the Java world such as Tapestry). PHP frameworks vary quite widely in how much they embrace OOP and concepts such as creating your business objects based on your database. Yii definitely stands out as a framework due to the code generation capabilities built in. That will definitely help you if you're getting started with PHP.

Best RIA tools for a Java backend

I've written a java server side application with many classes and EJB's that do things like output RSS information and update a database. I also have a web service connection thorugh SOAP and some basic servlets and xhtml pages that do very simple display of some of the infomration.
What I need now is advice on what a good Java centric approach to building a rich client side experience, and RIA that connected to the server side functionality I've created.
I'm using Glassfish 3.1, and JEE6. I'm considering Java Server Faces but it's more of a framework for developing simple webpages. What I want is a javascript heavy application that runs in the browser, is very graphical with animations and can connect to the services I've created underneath probably through websockets.
I want all of the AJAX, and Javascript support you would expect from a modern RIA experience.
What Java technologies will get me there. Or am I leaving the Java sphear and entering something else. I'm just trying to stay with java as long as possible for this application as an experiment of Java's abilities. So what Java tools are out there for RIA and integrated JavaScript?
Thank you,

For Java definitely the Google Web Toolkit.
You could also look at Vaadin. Unfortunately there isn't really
a good SOAP client for JavaScript but if you had a JSON REST webservice
and are willing to develop in JavaScript I also recommended
to look at frameworks like ExtJS, JavaScriptMVC or Backbone.js.

Java Ajax Framework integration

I'm looking for a java AJAX framework which I can include into my existing webapp. I've found sweetDev RIA . Are there such other frameworks which I could look into it?

I'd take a look at DWR: Direct Web Remoting. It allows you to directly call Java (web services) from JavaScript in a really intuitive way.

Last couple of years, I have been developing rich looking web applications with icefaces. It is pretty cool, ajax is buit-in and it blends very well with jsf. If you use icefaces, javascript is not required anymore. In our web project we use javascript only in couple of places.
Here is an excerpt from icefaces homepage: "As a leading open source Ajax framework, ICEfaces is more than a Ajax JSF component library, it's an J2EE Ajax framework for developing and deploying rich enterprise applications (REAs). With ICEfaces, enterprise Java developers can easily develop rich enterprise applications in Java, not JavaScript."

I suggest ExtJS (with jQuery underneath), but you might prefer GWT. I think it's easier for Java programmers who are seeking to wade slowly into JavaScript waters.

I would really check out extjs.com. It is the most feature complete javascript component library I know of. The components are fast, have beautiful default styling, and the API is very powerful. AJAX support is also excellent. Most of my current web development include extjs in some way.
It's very easy to use this library with java. Most of the time, I just have some server side component that returns data in JSON.
There is also ExtTLD; a tablib wrapper for extjs. I have never used it myself, though.

Google Web Toolkit ( GWT )

you can also use Apache's 'Myfaces' project http://myfaces.apache.org
Its a JSF implementation, and also has components with in built ajax capability.

You can try SweetDevRia, it's possible to add ajax in your application without writing Javascript. You only need to use JSP tags

A "Portlet-Like" java technolgy for a Web app

Do you know a technology which can provide me a portlet-like interface?
But I do not want to use JSR 168/268 portlet specifications and a portlet container.
The reason is: My web app is a product which can be installed on the client's server (it can be weblogic/websphere/tomcat).
Packing the portlets container along with my application to be installed on clients web server is just too much.
Besides, there are a lot of features this technology offers which I don't need. Actually, all I need is the porlets look and feel (dragable and customizable windows,adding and removing windows and so on).
I know there is also the possibility to do it with client technology (like jquery) and that is cool, but I would like to know if there is any kind of java technology out there which will also give me that.
So, if you know something like a struts or a spring-mvc component library which does this job or maybe a third party product, I would like to know.
If you think my whole approach is wrong I would also like to know that.

Take a look at gwtportlets. From their site;
GWT Portlets is a free open source web
framework for building GWT (Google Web
Toolkit) applications. It defines a
very simple & productive, yet powerful
programming model to build good
looking, modular GWT applications.
The programming model is somewhat
similar to writing JSR168 portlets for
a portal server (Liferay, JBoss Portal
etc.). The "portal" is your
application built using the GWT
Portlets framework as a library.
Application functionality is developed
as loosely coupled Portlets each with
an optional server side DataProvider.
Take a look at the demo here

Another suggestion would be JSF 2.0 which provide AJAX support for updating part of the HTML-page out of the box.
Have a look at this series to get an idea of the possibilities:
http://www.ibm.com/developerworks/java/library/j-jsf2fu1/index.html