Develop Reference

Having a hard time with linux command calls in Java with exec()

I'm trying to use Runtime.getRuntime().exec() to call a program as if it was called from the terminal, but it just crashes with a fatal error after reading the first file.
In the terminal I run the command like so:
mace4 -c -f inputFile.in > outputFile.out
It works as expected, reading from the first file and outputting in the second one.
In Java I try to run it this way:
String args[] = new String[]{"mace4", "-c", "-f", inputFileName ,">",outputFileName};
try {
String s;
Process proc = Runtime.getRuntime().exec(args, null, new File("/home/user/workDirectory/"));
BufferedReader br = new BufferedReader(
new InputStreamReader(proc.getInputStream()));
while ((s = br.readLine()) != null)
System.out.println("line: " + s);
proc.waitFor();
proc.destroy();
As soon as the program reaches the end of the first file, it throws this:
Fatal error: read_all_input, file > not found
The program is quite old and I can't seem to find a way to get a more detailed error out of it..
I tried calling it with these arguments {"sh or bash", "-c", "mace4", "-c", "-f", inputFileName ,">",outputFileName} which makes the program run and then freeze (or at least nothing appears in the console)..
Am I calling the terminal command wrong and if yes what should I change?
PS: this is my first question here, if I missed anything, I'm sorry..

It looks like you're trying to use the Bash output redirection operator >. This redirects the output of the program you're running to a file (or another program)
This answer explains how to do this using ProcessBuilder which should work for what you're trying to do here.
For example:
ProcessBuilder pb = new ProcessBuilder("mace4", "-c", "-f", inputFileName);
pb.redirectOutput(new File(outputFileName));
Process p = pb.start();

run a .sh file using java

I want to run a .sh file using java. I want a terminal to be opened and then I can execute another commands in the same terminal and finally destroy it.
I already used ProcessBuilder but I could not accomplish this.
My piece of code:
ProcessBuilder pb = new ProcessBuilder("/home/omar/ros_ws/baxter2.sh");
Process p = pb.start();
This method used to work in another code, but I don't know why it's not working in mine.
Thanks in advance

How do you know that it doesn't execute? Maybe you just aren't seeing its result. You should get p.getInputStream() after executing and print in your console, like:
BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()));
String line = null;
while ((line = reader.readLine()) != null)
{
System.out.println(line);
}
Also if you're using jdk 7+, try:
pb.redirectOutput(Redirect.INHERIT);
pb.redirectError(Redirect.INHERIT);
Process p = pb.start();

Does your program output an error, or is your program not interacting with the file?
I would suggest trying the directory method within ProcessBuilder.
Process p = null;
ProcessBuilder pb = new ProcessBuilder("baxter2.sh");
pb.directory("/home/omar/ros_ws");
p = pb.start();
If this doesn't work, you should also look into user permissions for the file that you're trying to access.

I think you should grant the .sh file the executable permission to the OS user used to run the java program by using the below command.
chmod u+x baxter2.sh

Run consecutive Commands Linux with java runtime exec

I need to run two commands Linux using java code like this:
Runtime rt = Runtime.getRuntime();
Process pr=rt.exec("su - test");
String line=null;
BufferedReader input = new BufferedReader(new InputStreamReader(pr.getInputStream()));
while((line=input.readLine()) != null) {
System.out.println(line);
}
pr = rt.exec("whoami");
input = new BufferedReader(new InputStreamReader(pr.getInputStream()));
line=null;
while((line=input.readLine()) != null) {
System.out.println(line);
}
int exitVal = pr.waitFor();
System.out.println("Exited with error code "+exitVal);
} catch(Exception e) {
System.out.println(e.toString());
e.printStackTrace();
}
The problem is the output of the second command ("whoami") doesn't display the current user which used on the first command ("su - test")!
Is there any problem on this code please?

In the general case, you need to run the commands in a shell. Something like this:
Process pr = rt.exec(new String[]{"/bin/sh", "-c", "cd /tmp ; ls"});
But in this case that's not going to work, because su is itself creating an interactive subshell. You can do this though:
Process pr = rt.exec(new String[]{"su", "-c", "whoami", "-", "test"});
or
Process pr = rt.exec(new String[]{"su", "test", "-c", "whoami"});
Another alternative is to use sudo instead of su; e.g.
Process pr = rt.exec(new String[]{"sudo", "-u", "test", "whoami"});
Note: while none of the above actually require this, it is a good idea to assemble the "command line" as an array of Strings, rather than getting exec to do the "parsing". (The problem is that execs splitter does not understand shell quoting.)

As stated in the Javadoc for Runtime.exec():
Executes the specified string command in a separate process.
each time you execute a command via exec() it will be executed in a separate subprocess. This also means that the effect of su ceases to exist immediately upon return, and that's why the whoami command will be executed in another subprocess, again using the user that initially launched the program.
su test -c whoami
will give you the result you want.

If you want to run multiple commands in a way the commands would execute in a subshell if need be see the response here
How can I run multiple commands in just one cmd windows in Java? (using ProcessBuilder to simulate a shell)

Linux shell commands behave strange with Runtime.exec() (screen command)

I am sitting here since at least allways on a problem that really beats me down!
I'm writing on a simple and small java program that easily passes any command to a (linux) screen session.
Shell command: bash -c "screen -p 0 -S sessionname -X eval 'stuff \"some command\"\015'"
When I enter this in the command shell, it all works fine!
But if I let a Java programm do this, nothing happens at all! Not even a message or error or hint! Simply nothing!
I let the program echo the generated screen command and if I take that output and paste it into the shell, it works.
Here is my Java code:
static public void screenCmd() throws IOException
{
String command = "bash -c \"screen -p 0 -S screenname -X eval 'stuff \\\"cmd\\\"\\015'\"";
System.out.println("debug: '" + command + "'"); //output would work
//when copy and paste it to the shell
InputStreamReader isr = new InputStreamReader(
Runtime.getRuntime().exec(command).getInputStream()
);
//for debug output
BufferedReader br = new BufferedReader(isr);
String line = "";
while ((line = br.readLine()) != null)
System.out.println(line);
}
The funniest thing is, that all the other shell commands are working.
I tried Java to exec tail, whomi, cp, ls, ... without any problem. Why not screen?
The Java program is started by the same user who started the screen session.
If somebody has an even small idea please report! I am driving insane here!
p.s.: The screen session also runs a java program! (could that be part of the problem?)
Thanks.

I'd recommend that you try the more modern ProcessBuilder class.
And read these:
Five Common java.lang.Process Pitfalls
When Runtime.exec() won't
From Runtime.exec() to ProcessBuilder

The real problem is the way the command line is parsed: Java's Runtime.exec doesn't follow the same quoting rules as Bash. You should use the array version of the API instead:
String[] command = {"bash", "-c",
"screen -p 0 -S screenname -X eval 'stuff \\\"cmd\\\"\\015'"};
Runtime.getRuntime().exec(command);
You can reduce some of the quoting mess if you exec screen directly without going through bash:
String[] command = {"screen", "-p", "0",
"-S", "10624.pts-2.koivu", "-X", "eval", "stuff \"cmd\"\\015"};

Unix Script not working in Java Process Runtime.exec()

I am developing an application in Spring Web MVC where i need to execute some of the linux script..
I am using tomcat version 5.5 for running my project in linux..
My code is looking like this :
Process proc = runtime.exec("sudo cp /var/tmp/mailserverfiles/editinterface.txt /etc/sysconfig/network-scripts/editinterface.txt");
InputStream inputstream = proc.getInputStream();
InputStreamReader inputstreamreader = new InputStreamReader(inputstream);
BufferedReader bufferedreader = new BufferedReader(inputstreamreader);
String line;
while ((line = bufferedreader.readLine()) != null) {
System.out.println("\nOUTPUT = " + line);
}
System.out.print("\nbefore execute6");
try {
if (proc.waitFor() != 0) {
System.err.println("\nexit value = " + proc.exitValue());
}
} catch (InterruptedException e) {
System.err.println("\nERROR = " + e);
}
Here i want to cp a particular file from one location to another using linux script..
But when i am executing this part, i am getting
exit value = 1
as a output.. I have also tried to put this script into .sh file and try to execute that shell script here from Java Code, but i am getting same result..
Can anybody tell me, what should be the reason for this ?
Thanks in advance..

I would guess that sudo is expecting an interactive terminal in order to ask for a password. Since there is no interactive terminal, it prints an error message to stderr and exits with an exit code of 1. You are not reading the error stream, so you won't see any message that it might print.
You will definitely want to read the error stream in any case. Doing so now will help you diagnose what is going wrong at this point.

I assume the user that Tomcat is running under has unrestricted access to sudo? And that it's not being prompted for a password?

It is possible that your search path is weird and that "cp" and "sudo" are not found when you try to execute the command.
Here are some things you could try to track down your problem(s):
Try running the "cp" command without "sudo".
Try giving the full pathname of the command(s). This will avoid search path problems.
By default "sudo" logs failed commands using syslog(3). See if you can find traces in the corresponding logfiles.

Assuming you can run your command from a command line, logged in as the tomcat user - try
ProcessBuilder pb = new ProcessBuilder("/usr/bin/sudo", "cp",
"/var/tmp/mailserverfiles/editinterface.txt",
"/etc/sysconfig/network-scripts/editinterface.txt");
pb.redirectErrorStream(true);
Process proc = pb.start();
... rest of code as before
if things still fail, start debugging. strace should be helpful. e.g. run this shell script
from your java application, and figure out where things fail in the /tmp/trace.txt file:
#!/bin/sh
strace -f sudo cp /var/tmp/mailserverfiles/editinterface.txt /etc/sysconfig/network-scripts/editinterface.txt >/tmp/trace.txt 2>&1

Whilst not directly answering your question, the following will help. You need to read stdout and stderr (to capture all process output), and do this concurrently to prevent blocking of the spawned process. See this answer for more info.