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Keyboard/Mouse Robot not working when focused on a certain application

So I am trying to use a robot (either keypress or mouse) to simulate some tests on an application. However, this program isn't allowing me to do so and I'm pretty sure it is a security feature. The application I am using is TEMS Investigation and I am trying to simulate a record and stop recording for some automated tests I have. The program I am using to automate these tests can not access TEMS so there is no way for me to do this without a Robot. So my questions are:
1) How can I override whatever it is that is preventing me from using my robot.
2) Would this be considered illegal if I did? I don't need to break any laws...I just want to get my testing done! lol
I can't even runs something as simple as:
Robot r = new Robot();
r.keyPress(KeyEvent.VK_F2);
r.keyRelease(KeyEvent.VK_F2);
It will run, as I have downloaded some software to tell me what keys I am pressing....just wont be recognized while the TEMS application has focus.
Update: I found out using Notepad I can't use any keys (like "ALT +
F") to perform any menu options. It doesn't even pull up the "File"
menu. I am able to simulate typing in text, just not the context menu.
What was really weird is that I can't even use mouseMove() while TEMS
has the focus

It sounds like your runtime has no knowledge of the TEMS app. If you start it in your java code it should work. For example the following:
Runtime.getRuntime().exec("notepad");
robot.keyPress(KeyEvent.VK_J);
Will bring up notepad and type in the letter J. Try exec-ing TEMS and then send the key press.
And no, it's not illegal.
UPDATE:
To open the file menu in notepad, you would do the following:
robot.keyPress(KeyEvent.VK_ALT);
robot.keyPress(KeyEvent.VK_F);
The two keys must be pressed together before a robot.keyRelease.

How do I create a gui for java that acts like a console

I created a text-based game similar to Zork and I need a gui to run it outside of Eclipse. I want to run it as a jar. (by the way I'm on a mac if that changes anything). I only need an output field and an input field. What would be the easiest way to achieve this?
And how much of my code would I need to change? (I used System.out.print for output and a Scanner for input)

If you want to crate GUI like console the simple way to do it is to add textarea component to your frame or or panel that has scroll bars through the viewport. Create a stream that feeds the component with text. Then simply redirect standard output to that stream. Finish. Start your GUI and enjoy the console.

If you don't want to run this on a terminal, you should probably use Swing with a JTextArea in which you append all the messages to the user, and a simple JTextField for the user to enter his commands.
Here's a quick example of JTextArea so you get an idea. You'll need to read more about events on Swing to make things like reacting to the user pressing the ENTER key to read the contents of the text field and run the game logic.
Note that the screenshot on the example above uses the "Metal" look and feel, but it should look much closer to a native application on the Mac.

Capturing events in X11 even after the loss of focus

I am trying to develop an application which responds to multiple digital pens (IRIS Pens) so that if any of the pen writes on paper; I relay the output to a single screen. Thus making a multi-input whiteboard for myself.
In Ubuntu these pens are recognized as mouse and thus can be handled in a similar manner as mouse events are handled.
So now what I plan to do is to handle these events in C/C++ using XLib and pass these events to a Java Swing application using JNI callback. I am able to do this but when the X11 window looses focus no events are transferred to the Swing frame. I also tried to use the root window in X11 but it does not seem to work.
Any help would be really appreciated. Thanking you in advance.

How about maximizing the C/X11 window in front of the Java one, and making it transparent? You should be able to see the Java window while still focusing on the C/X11 one.
Since you are using Ubuntu, you can achieve this using the "Opacity, brightness and saturation" plugin for Compiz. It is in the compiz-plugins-main package, and you can activate it with Compiz Settings Manager (from the compizconfig-settings-manager package). When you activate the plugin, alt+wheel is bound by default to change the transparency of the focused window.

Try reading the mouse directly. I don't remember the exact location, but you should find it in something like '/dev/input/mouseX', where X is the number of your device, ranging from 0 to n-1 devices..
When you read the packet, your application should block until the mouse moves and then your read function will return a raw mouse packet which describes the delta (which is probably more useful then the screen coordinates, in your case) and the mouse button statuses.
The raw packet can be decoded as described here: http://www.computer-engineering.org/ps2mouse/

Create a modal dialog and set it to XmDIALOG_SYSTEM_MODAL (the actual name of the property depends on your toolkit: Motif, Gtk, Qt, ...). Dialogs like this block the whole display and can never loose focus.
The drawback is of course that you can't do anything else while this dialog is on the screen.
This entry in the X11 FAQ might help.

How to copy text from a browser with Java?

Is there a way to copy text from a browser to my Java app ?
For example, at the left side of my screen I open a browser to point to a URL and shows the content of that page, it might be in a frame or CSS or simple html, on the right side of the screen I open a Java Swing application. I'm interested in certain parts of the browser window that shows some text, and I want my Java app [ without me doing anything ] to copy and paste the text into itself, can it be done ?
I know I can use JEditorPane or JTextPane and set it with an HTMLEditorKit, then load the text into the pane, but if the page uses Frames or some other complex ways, the text I get from the Pane is not what I see on the page, so I don't want to do it by loading the URL into my Java app, instead, I wonder if it can be done in the way I mentioned above ?

I think you're looking at the problem from the wrong angle. If what you want is to harvest a website, I suggest you have a look at the awesome library web-harvest. With a little Xpath wizardry you can get everything you want.
Doing what you describe would imply inter-process communication that seems like an overkill. There are more ways to download a web-page content than the browser.

You may try the following depending on your needs.
With java.awt.Robot you can either 1) Take an screenshot if what you neeed is the content ( without the text, just an image of the browser content ) or 2) Move your self into the browser and programatically press: CTRL-A + CTRL-C and return back to your swing app focus and programatically press: CTRL-V ( or CMD or whatever makes sense in your OS )
But again, this might or not work, depending on what you need.

I know a tool but i am not sure it meet your needs. Have you heard about selenium? http://seleniumhq.org/ It can replicate actions taken by the user in a browser and then manipulate them ussing java code. Have a look at the link it may be handy.

Using java.awt.Robot & a TextField will get the job done, not sure if there is any other way. Have robot press ctrl+a then ctrl+c, bring TextField into focus, and finally have robot press ctrl+v. Now from here you can create a button.setOnAction to save the TextField text into a string. Or you can use a change listener on the TextField setOnKeyReleased to do the same.

Inject a keystroke in java

I'm looking for a way to inject a keystroke into the OS keyboard input buffer,
like when you click a button the program inserts one (or more) keyboard strokes. I wanted to do this in java because I want to run this in (win,linux and osx). I guess that I'll have to make use of the JNI, do anyone have some ideas?
Thanks all stackoverflowers ;)

My guess is that the java.awt.Robot class will do this for you:
new Robot().keyPress(...);
http://download.oracle.com/javase/6/docs/api/java/awt/Robot.html#keyPress(int)
java.awt.Robot "is used to generate native system input events for the purposes of test automation, self-running demos, and other applications where control of the mouse and keyboard is needed."

Check java Robot . I believe this is what you are looking for.
Also check this out. Example