I have embedded a JSCH SSH Java applet in a web page and need to know if it's possible to run a script (of any language like PHP) to automate logging in and running commands. I have heard of expect4j and java robot but cannot see any way to implement it. Keep in mind, I'm not great with Java so I don't know everything about it. Any help is appreciated.
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JSch is an SSH client library, and by itself only allows programmatically steered connections to another server. The user interaction has to be build around it by users of the library.
The JCTerm applet provided on the website also contains a terminal emulator in form of a Java GUI. If you only want to automatically execute some command (and maybe show its output in the web page), you could do everything on the server side, and don't need the applet with its terminal emulator. (You would need either some PHP-Java bridge on the server side or some Java-enabled webserver with a Servlet or similar, though.)
(If the web server would be the same machine as the server you'll run the command on you wouldn't even need the SSH connection, but could execute the stuff directly.)
If the server can't do anything (i.e. a "static server"), an applet is the way to go, yes. You can either modify JCTerm or create a new applet from scratch (using JCTerm's connection code as an example on how to connect to to the server).
If you don't have to fear any malicious users in your LAN (i.e. between web server and user, the SSH server doesn't matter), you can embedd the password (or preferably a private key for public-key authentication) into the applet's jar file, and pass it to the library for connection. (You should also include the server's public key for easier checking.)
Provide the command(s) to a
ChannelExec(instead of aChannelShell), this makes it easier to provide input (if necessary) and capture the output. Pipe the output in a text area, or simply use a green/red label saying if the command was successfully executed.(I might have a look at this in the next days and try to do it. No promise, though.)