Develop Reference

Executing a command using JSch

I'm using JSch to automate remotely launching a python script from a background Java process.
Modifying the Shell.java example included in the JSch package, I've successfully installed JSch, connected to my Pi, and even commented out the user/domain/password/host key checking prompt boxes in favor of storing these values directly in my Java code.
After my java code logs into the remote Pi, I'd like it to send something like
sudo nohup python2 myFoo.py & disown
to the terminal.
In the Shell.java example I'm modifying, I see lines of code redirecting the input and output streams of the channel object to System.in and System.out but I'd like to simply manually inject that above line into the remote terminal and disconnect.
Why/my goal:
I have a small mesh network of Pi's running a script for most of the day.
I'd like to eliminate downtime, but the code sometimes stops working after looping for 3-4 days straight, (sometimes as long as a week straight before the code bugs out and stops).
The script running on each node updates a mySQL database with a "last check in" field.
I'm hoping to write a small background program in Java that will run indefinitely on my server, checking the "last check in" for each station every now and then, and if it notices a node go down, remotely ssh into it and sudo reboot now, wait about 60-100 seconds, then sudo nohup python2 myFoo.py & disown

You have picked a wrong example. The "shell" channel is for implementing an interactive shell session, not for automating a command execution.
Use the "exec" channel, see the Exec.java example.
Channel channel=session.openChannel("exec");
((ChannelExec)channel).setCommand(command);
channel.connect();
...
For a full code, see How to read JSch command output? – Which shows how to correctly read both standard and error output simultaneously, to allow command to complete and to collect all output including the errors.

How to view a runnable .jar's output via SSH client

I have a .jar runnable running on my server. When I run the file locally I am able to see its output via my IDE. Similarly I can connect via SSH and run the file and see the output, but when I close the session the JAR exits.
Is there any way to have my application continuously running and then tapping into the java applications output using a terminal service like SSH without having to stop/start the application.
Any help would be appreciated.

You can use either screen or nohup
What is happening is that when you close your SSH session, there is a hangup call made to the program.
You could use nohup. Nohup stands for "no hangup"
nohup java -jar myJar.jar > outputFile.txt
That would run the program in the backround and send all output to outputFile.txt. When you end your session it will continue running. You must use a kill command to kill it.
The second option is you could use screen which essentually creates a detachable "ghost session". When you run screen it looks like you are in a different ssh session. Then when you detach from screen, the processes continues in the backround. When you exit your ssh session, screen continues to run.
You simply ssh back into the server, and re-attach to your screen session, and like magic, your program is still running with all relevent output. A simple read on the man page should catch you up on how to do this.
man screen
Lastly, I decided to add this third option, not because its viable, but simply so you can understand that it is an option. (Some people would claim this is the only REAL option as it is what your SUPPOSED to do. Frankly I couldn't care less and think you should do whatever is the easiest to get to your goal.)
You can also edit your program to swallow the hangup signal. The program would then always run in the backround. You can then use
java -jar myJar.jar & > outputFile.com
The & tells the command to start a new process (aka run in the backround) and the > sends the output to a file. This is how normal server applications like tomcat or spring boot work. They simply swallow the hangup call.

How is interacting with a prompt of a third party command line program different from a Windows Command prompt?

I was recently trying to make a Swing GUI to send and receive commands from a third party command line program. I used the same procedure as used and working for Command Prompt, i.e., ProcessBuilder class to execute and then used BufferedReader to read responses from the program. I can surely mention it again that I could read some response, at least, from the Windows command prompt(sometimes I needed to use a Scanner in stead). When I used the same on this command line program,
It didn't show up
It didn't respond to either BufferedReader or Scanner.
I searched the internet and found a monotonous reply from it that executing the same procedure on them both is not the same thing because they are not the same things. I have not been able to complete my project till now, but I can sleep a little more at ease if I get to know what is the difference between them, their execution, aren't they same, is there any way in which we can actually bring them together and that my problem can be solved?

Most likely the program starts its own shell and does no longer interact with the original one. (You would notice this if the program opens a new window)
Or the program needs some specific library to be present to be able to interact with a shell (readline seems to be the case here) and that is not present in your Java Environment.
As a quick hack you might try to start bash (or cmd) that then starts the tool. bash and cmd have readline library. I don't have a windows ready here but as a guess just try to call your program like cmd urjtag.exe instead of just urjtag.exe that way you start a cmd process (with that you can interact) and that cmd starts the urjtag.exe where you already know that it can interact with.
Either way the problem lies in the way the program you want to call interacts with the shell and you should ask the authors of the program how it does and how you can connect to it.

From the UrJTAG documentation:
JTAG (IEEE 1149.1) is a serial interface for testing devices with
integrated circuits.
and
UrJTAG is a software package which enables working with JTAG-aware
(IEEE 1149.1) hardware devices (parts) and boards through a JTAG
adapter.
It is not a command prompt.
It is not meant to be used as a command prompt for generic programs.
So, as other monotonous responses have already told you, it and the windows command prompt are not the same thing, even though you seem to think they are. It has a very specific use-case as described in the documentation.
The windows command prompt is a special program which invokes specific executables and passes command line arguments to them in a specific way.
The java.exe executable is designed to understand this kind of invocation.
Since the UrJTAG executable it is not a generic command prompt, it doesn't do what the windows command prompt does, and so will not work for running Java programs like you want.

About program running independent from command line under unix

I am writing a java program that runs under unix.
It would like run forever. But when I start it from command line, I have to leave that window open always until the program stop.
Could anyone give me some idea about how can i run it at back end? Just start it from command line then I could close that command line.
Thank you very much.

If you don't want to "daemonize" it you can just use nohup:
$ nohup your-program &
$ exit
and your-program will continue to run in the background until it finishes.

You're asking about making your program a "daemon". Check out these links about daemonizing java programs, and this one about daemonizing any process in linux.

...Another option is to use the "screen" utility. Its a little tricky if you've never used it, but you can do things like launch a job in a terminal at work and easily reconnect to the same terminal from anywhere else to check on the status of the job. I use it for connecting to servers where I run long-running jobs. Without using screen my process would die if my local machine crashes, or the power goes out, or fire, etc.

Pass a command to program running in detachtty

I've got a Java command-line application that I start with detachtty /var/run/handle /path/to/script. I can bring it to the foreground by running attachtty /var/run/handle. When active, the application displays a log of things it has printed out, and a line to input commands. Is there a way I could write a shell script that would send it a command, wait a short while, and then echo out whatever new characters attachtty would have printed to the screen?