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automate java desktop application actions

I developed a java desktop application where the user can manually load a file and press a button to start a simulation process. I want to automate the above two steps so that an external program can iteratively call this desktop application multiple times and run the simulation process without any human intervention every time. Any thoughts on how I can go about doing this?

It depends on which OS you do it.
If OS X, use automator, for Windows you can use winautomation and for Linux use google and search (for example) kde automation.

I know this is an old question. But there is a new solution now,
JAuto: a JVMTI agent that runs in Java VM and expose UI widget attributes such as class names, screen coordinates. You talk to JAuto by sending a command to a named pipe. It responds by writing a file. It lets you control a Java program via bash scripts.
Using an input simulator such as xdotool, you can achieve automation under the Linux X11 settings.
Disclaimer: I'm the author of JAuto.

Controlling applications through Java

I am looking for a way to mimic operating-system (Windows in specific) actions through Java. Preferably, the program should run in the background, but it is not a big deal if it does not. I got the background part covered thanks to this question. I was looking for the following specific features :
Maximizing/Minimizing the currently active window. (Can be any window, not just the Java application window.)
Closing the currently active window.
Open installed programs, and system utilities like the calculator, paint, etc. (I figured out this one from this question.)
Shutdown/Restart (This one's done too, thanks to the question here.)
So, my actual question is:
Is it possible to minimize/maximize or close an application window from a java program? (in Windows)
Example Scenario:
Firstly the java program is started, and it runs either as a background process or as a window. Bottom-line is that it should be able to accept triggers like maybe a keyboard shortcut or microphone input to trigger the action. After that suppose a Chrome window is opened and is currently active. Now on pressing the pre-defined shortcut, the Chrome window will minimize/maximize or close.
If the answer to the question is yes, I could use some pointers to start with my application. Thanks!

What you need is like an OS shell programming interface.
In Java side you will define a few interfaces.
Another Java layer will detect which OS is used and will return an implementation of interface: Windows, Linux, Macosx.
Some functionality you can have with simple bash command: in windows cmd, in linux .. to many. Eg shut down, launch MSPaint, Calculator.
Other functionality you can have it with windows API: you will need to write some JNI functions and call it. eg minimize, maximize. It is possible.
Edit:
I see there is no accepted answer, although it is answered properly.
Here is a C# code which does what you need in Java.
Now you need to migrate this code to Java:
In your java class declare a function:
private native maximizeOrMinimizeWindowWithName(String windowName, boolean maximize);
Compile -it
use Javah.exe - it will generate the necesary .h files
Use a C editor, configure environment, use the generated .h file.
-include windows api headers
-load user32.dll
- do more stuf..
compile your C code to .dll
put the your.dll into your app PATH environment variable. ( windows has the . in path, linux not)
-text, bugfix,
for more info you should see a basic JNI tutorials.
-upvote accept :)

This can be initiated from Java, but not actually implemented in Java. In other words, it will take a lot of platform-specfiic JNI library code to get it working.
Java will give you almost no benefit for your use case; you should avoid it altogether for this project.

You should look into Autohotkey. It's an system dedicated to simulate user programmaticly.
Using AH scripts you can easily access all open windows, installed programs and even control mouse and keyboard.

What does the jp2launcher do in the applet program?

Run a page which contains Java applet, notice that a process called jp2launcher is running. What does this process do?

It is part of the "Next Generation Java Plugin" (aka plugin2), the module responsible for starting the JVM for Applets or JNLP (WebStart). I think it also used to launch Java FX. I think it is used starting with Vista, on XP the java.exe is called directly.
Basically the process responsible for talking to the Browser and starting the Java VM. In case of Firefox that launcher is started instead of the "plugin-container" you see for other plugins (like Acrobat).

Close a running program from java application

I open up an external application from my java application. How can I close this application from the same Java application?
thanks

The best you can do (without venturing into messy/complicated/platform specific stuff) is to call Process.kill() on the Process object you got when you started the external application.
I don't think this is guaranteed to close the application*, and there is a chance that it may cause it to close uncleanly; i.e. without giving the application a chance to save open files, etc.
* Indeed, on *NIX if you started a "setuid root" process from a non-root Java application, and the OS won't let it send any signals to to.

Why don't you have a batch (Windows) or script (*nix) file that start and stops that application, and then run your runtime.exec with the parameter start/stop?
UPDATE:
This may help: http://it.toolbox.com/blogs/database-solutions/kill-a-process-in-windows-bat-19875
Second Update
You can also search by exe name using: 'tasklist ^| findstr /i excel.exe'

On Windows this will fail. It's a top 25 bug (or maybe top 25 rfe), though it really isn't so much Java's fault ... On Windows any children of the parent process will not be killed when parent is killed..... and there are many ways to run afoul of this (cmd /c anything and you will be in game-over-land)

How can I suppress MATLAB's command window when calling it from Java?

I am calling MATLAB with Java but I want to suppress the command window of MATLAB to make users feel that I use only one program which is Java.
In addition I read about something called standalone executable for MATLAB, but it didn't work; will that help me?

Check out the Matlab Engine. The engine runs in the background (without a GUI or visible command-line) and you call it from your code. The examples are in C and Fortran, not Java, unfortunately. I got it working with Python once but I don't recall the details.
Also see: 2 ways to use the engine with Java.
ETA: 'matlab -r "statement"' on the (Windows) command line will execute "statement" in Matlab. My Python hack was putting my Matlab code in a .m file and my data into a text file referenced by the .m file then sending 'matlab -r myFile.m' to the Windows command line. See the matlab Windows command. Again, there's no visible GUI for Matlab this way.

When you say "calling it from Java", are you shelling out to Matlab for batch computations, or do you want to embed a long-lived Matlab session in your process and call M code repeatedly from Java code? What OSes do you want to run on?
Matlab has some deployment tools that let you embed a Matlab interpreter and a collection of Matlab source code inside a host language, such as C/C++ or Java. This is what the "Matlab compiler" is - not a real compiler, but a tool that packages a Matlab runtime along with .m source code in a package that looks like a DLL or application. A Matlab "standalone application" is Matlab code that has been packaged this way along with a thin C wrapper that calls an application entry point in your M code.
The Matlab Java Builder is a similar thing that bundles this deployed Matlab engine inside a Java class. If you want to get a license for it, that could make it easy and cosmetically clean to embed Matlab inside your Java application. This is probably what you want.
These deployed Matlab apps do not have a command window because they're intended to blend in with your application. They live in the same process. And, importantly, they do not require license fees for running the deployed app. Shelling out to regular Matlab requires all users running it to have licenses for Matlab and each toolbox that is used.
If shelling out, the "matlab -nosplash -nodesktop" command line will suppress the GUI on Unix. But on Windows you'll still get a minimal Matlab command window. The "-automation" switch on Windows will at least make it minimized. I don't know a way to suppress it entirely on startup.
However, once Matlab is running, you can take advantage of the fact that the Matlab GUI is itself implemented in Java, and have it hide itself. Get your Matlab session to run this hidematlab() using the "-r" command line switch or a startup.m. Note that this is a hack using undocumented Matlab internals and is surely unsupported by MathWorks.
function hidematlab()
%HIDEMATLAB Hide the main Matlab desktop window (HACK)
dtWin = desktopwindow();
if ~isempty(dtWin)
dtWin.setVisible(0);
end
function out = desktopwindow()
%DESKTOPWINDOW Find the main Matlab desktop window (HACK)
wins = java.awt.Window.getOwnerlessWindows();
out = [];
for i = 1:numel(wins)
if isa(wins(i), 'com.mathworks.mde.desk.MLMainFrame')
out = wins(i);
return;
end
end
Beware of gotchas when shelling out on Windows, where Matlab is inherently a GUI app. If your M code throws errors that bubble up to the top level or segfaults, you may find your Matlab session hung, waiting for nonexistent user input, instead of returning you an error.

I don't know of a way to do what you're asking entirely. If your script does an exit manually instead of naturally terminating, you may be able to start the script so that the window that pops up is minimized.
See Launch Application in a minimized state from Java
Start the script with
matlab -nojvm -nosplash -nodesktop -wait -r script_name
You will want the "-wait", otherwise MATLAB will immediately return.
See How can I stop MATLAB from returning until after a command-line script completes?

matlabcontrol is a Java API which will allow you to interact with a running session of MATLAB. It will launch the session and then you will be able to invoke eval and feval as well as set and get variables. By default the session of MATLAB will be visible, but it can be hidden. On Windows it will not be entirely hidden because that is not supported by MATLAB, but it will be started minimized and no splash screen will be shown. To get started using matlabcontrol, take a look at the walkthrough.