Develop Reference

Why does the output of my shell script doesn't print in console?

I am trying to print the output of a shell script on the console using java. When I manually run the script, I get
C:/Users/user1/Desktop/shell.sh: line 78: /usr/ucb/ps: No such file or directory
<STATUS>: Probe [ devicename ] is not running!
But, when I try to run it on my Java program, the output is not being printed on the console.
My code is:
ProcessBuilder processBuilder = new ProcessBuilder("C:/Program Files/Git/git-bash.exe","C:/Users/user1/Desktop/shell.sh");
try {
Process process = processBuilder.start();
StringBuilder output = new StringBuilder();
BufferedReader reader = new BufferedReader(
new InputStreamReader(process.getInputStream()));
String line;
while ((line = reader.readLine()) != null) {
output.append(line + "\n");
System.out.println(line);
}
int exitVal = process.waitFor();
if (exitVal == 0) {
System.out.println("Success!");
System.out.println(output);
System.exit(0);
} else {
//abnormal...
}
} catch (IOException e) {
e.printStackTrace();
} catch (InterruptedException e) {
e.printStackTrace();
}
The only output I am getting is "Success". When I debugged my code, I found that the code never enters the condition
while ((line = reader.readLine()) != null)
even though, in the bash terminal, there are lines of output. Why is this happening?
I am stuck at this point and I couldn't find any other explanations for this problem. Kindly help.

You are running git-bash.exe which opens as a windows application. Although Java has access to the stdout/stderr streams of git-bash.exe, these are not necessarily the same as the stdout/err of the internal launch of your shell script within git-bash.exe.
One way to see the stdout/err of your command would be to make a java friendly version of the .sh script which launches your original sh and redirects output to a specific files which you can then access within java afterwards.
ProcessBuilder pb = new ProcessBuilder("C:/Program Files/Git/GIT-BASH.EXE","/c/Users/blah/somescript.sh");
somescript.sh:
#!/bin/sh
runtheoriginalcommand > ~/somepath.out 2> ~/somepath.err
You could also add extra args to wrapper to pass the out/err files to be used so there is no contention with any other launches or hardcoded output files.

How to start Rserve automatically from Java?

I am writing a Java application in IntelliJ IDE. The application used Rserve package to connect to R and perform some functions. When I want to run my code for the first time, I have to launch R in the command line and start the Rserve as a daemon, which looks something like this:
R
library(Rserve)
Rserve()
After doing this, I can easily access all the function in R without any errors. However, since this Java code would be bundled as an executable file, so is there a way that Rserve() is invoked automatically as soon as the code is run so that I have to skip this manual step of starting Rserve using the command line?

Here is the code for the Class I wrote to get Rserve working from Java
public class InvokeRserve {
public static void invoke() {
String s;
try {
// run the Unix ""R CMD RServe --vanilla"" command
// using the Runtime exec method:
Process p = Runtime.getRuntime().exec("R CMD RServe --vanilla");
BufferedReader stdInput = new BufferedReader(new
InputStreamReader(p.getInputStream()));
BufferedReader stdError = new BufferedReader(new
InputStreamReader(p.getErrorStream()));
// read the output from the command
System.out.println("Here is the standard output of the command:\n");
while ((s = stdInput.readLine()) != null) {
System.out.println(s);
}
// read any errors from the attempted command
System.out.println("Here is the standard error of the command (if any):\n");
while ((s = stdError.readLine()) != null) {
System.out.println(s);
}
// System.exit(0);
}
catch (IOException e) {
System.out.println("exception happened - here's what I know: ");
e.printStackTrace();
System.exit(-1);
}
}
}

I know this question has been asked a long back . I think You have the answer. But the below answer may help others. That's why I am posting my answer.
answer:- Instead of going again and again to the R console to start Rserve. One thing you can do is you can write a java program to start Rserve.
Below code you can use in a java program to start Rserve.
https://www.sitepoint.com/community/t/call-linux-command-from-java-application/3751. This is the link where you will get the code to run a linux command from java.I have changed the command only and posting below.
package javaapplication13;
import java.io.*;
public class linux_java {
public static void main(String[] args) {
try {
String command ="R CMD Rserve";
BufferedWriter out = new BufferedWriter(new FileWriter(
new File(
"/home/jayshree/Desktop/testqavhourly.tab"), true));
final Process process = Runtime.getRuntime().exec(command);
BufferedReader buf = new BufferedReader(new InputStreamReader(
process.getInputStream()));
String line;
while ((line = buf.readLine()) != null) {
out.write(line);
out.newLine();
}
buf.close();
out.close();
int returnCode = process.waitFor();
System.out.println("Return code = " + returnCode);
} catch (Exception e) {
e.printStackTrace();
}
}
}

Control a command line program session via Java

I have a computer algebra program (called Reduce) that works in the shell in an interactive manner: launch Reduce in the shell, then you can define variables, compute this and that, and what not. Reduce prints the output into the shell. My idea is that I want to build a frontend for this text-based program that evaluates its output and converts it into a nice LaTeX style formula. For this I want to use Java.
I can start Reduce via exec(). But how can I emulate text input to the opened shell, and how can I read back what Reduce writes into the shell?
Thanks
Jens
Edit 1: Current Code
// get the shell
Runtime rt = Runtime.getRuntime();
// execute reduce
String[] commands = {"D:/Programme/Reduce/reduce.com", "", ""};
Process proc = null;
try {
proc = rt.exec(commands);
} catch (Exception e) {
System.out.println("Error!\n");
}
// get the associated input / output / error streams
BufferedReader stdInput = new BufferedReader(new InputStreamReader(proc.getInputStream()));
BufferedWriter stdOutput = new BufferedWriter(new OutputStreamWriter(proc.getOutputStream()));
BufferedReader stdError = new BufferedReader(new InputStreamReader(proc.getErrorStream()));
// read the output from the command
System.out.println("Here is the standard output of the command:\n");
String s = null;
try {
while ((s = stdInput.readLine()) != null) {
System.out.println(s);
}
} catch (Exception e) {
}
// read any errors from the attempted command
System.out.println("Here is the standard error of the command (if any):\n");
try {
while ((s = stdError.readLine()) != null) {
System.out.println(s);
}
} catch (Exception e) {
}

You need to get the streams associated with the process including the InputStream, OutputStream, and ErrorStream. You then can send messages to the process via the OutputStream and then read info from the process via the InputStream and the ErrorStream.
From some code of mine:
final ProcessBuilder pBuilder = new ProcessBuilder(TEST_PROCESS_ARRAY);
final Process proc = pBuilder.start();
procInputStream = proc.getInputStream();
errorStream = proc.getErrorStream();
errorSBuffer = new StringBuffer();
streamGobblerSb = new StreamGobblerSb(errorStream, "Autoit Error", errorSBuffer);
new Thread(streamGobblerSb).start();
final Scanner scan = new Scanner(procInputStream);

You may want to look into using the Process class.
http://docs.oracle.com/javase/7/docs/api/java/lang/Process.html
I believe you may be able to start the process, and then use getOutputStream() to feed commands into the process.

While this is not strictly an answer, I discovered that it is more convenient for me to stick with PHP's function proc_open(). That way I can include the output directly in the frontend and do not need to worry about the communication between my Java program and the html frontend.
For everybody who wants to stick to the Java method: the article http://www.javaworld.com/javaworld/jw-12-2000/jw-1229-traps.html is a good reference.

How to edit file on console from Java?

I'm trying to edit a file from CLI. I'm executing the nano command (I know that command will always be available); when I execute it, I can see nano's output but I cannot interact with it. How can I pass user input to the command? Do you have a better idea to easily edit a file from within my Java app?
This is my code:
String command = "nano /tmp/163377867.txt ";
try {
Process process = Runtime.getRuntime().exec(command);
InputStream inputStream = process.getInputStream();
InputStreamReader inputStreamReader = new InputStreamReader(inputStream);
BufferedReader bufferedReader = new BufferedReader(inputStreamReader);
String line;
while ((line = bufferedReader.readLine()) != null) {
System.out.println(line);
}
} catch (IOException e) {
e.printStackTrace();
}

The problem with Java's Runtime.exec is that it connects stdin and stdout to "pipes," while many console programs need a TTY device.
One way to solve this problem is to make the Java program's controlling terminal available to the program you execute:
Process proc = Runtime.getRuntime().exec(new String[]{
"sh", "-c", command+" </dev/tty >/dev/tty"});
proc.waitFor(); // wait for user to finish editing the file

Running Python scripts in Java

I'm trying to run a python script during the execution of my java code, because it will depend on the output received from the python script. So far I've tried using jythonc, unfortunately to no success, and now im trying to use the java Runtime and java Process to execute the python script.
Now I've run into a problem when trying to call the python script. I feel as though it doesn't even call the script because it takes less than a couple seconds to get to the next page....
Could the problem be how I am calling the python script?? I am trying to run this through a web application...
Here is some of my code:
String run = "cmd /c python duplicatetestingoriginal.py" ;
boolean isCreated = fwr.writeFile(BugFile, GD, 500, true, 5, "LET");
if(isCreated){
try{
r = Runtime.getRuntime();
p = r.exec(run);
BufferedReader stdInput = new BufferedReader(new InputStreamReader(p.getInputStream()));
BufferedReader stdError = new BufferedReader(new InputStreamReader(p.getErrorStream()));
String line = "";
while ((line = stdInput.readLine()) != null) {
System.out.println(line);
}
while ((line = stdError.readLine()) != null) {
errorW.write(line);
}
int exitVal = p.waitFor();
arrayList = fwr.readResults();
}catch(Exception e){
}
}
else{
// troubleshoot....
}

Instead of String for the command, split it to chunks and make a String[]. No need to state cmd /c, I think.
This is a sample code from my application:
//Running on windows
command = new String[4];
command[0]=directory.getCanonicalPath()+"/data/ExtenalApp.exe"; //extenal commandline app, not placed in path, but in subfolder
command[1]=directory.getCanonicalPath()+"/data/SomeFile.txt"; //file needed for the external app, sent as an argument
command[2]=arg1; //argument for the app
command[3]=arg2; //argument for the app
//Running on Mac
command = new String[6];
command[0]="python";
command[1]=directory.getCanonicalPath()+"/data/wp.py"; //path to the script
command[2]="-F"; //argument/Flag/option
command[3]="--dir="+path; //argument/option
command[4]="--filename="+filename; //argument/option
command[5]=argument; //argument/option
Process process = Runtime.getRuntime().exec(command);
process.waitFor();
process.destroy();
I don't handle the Input/Output streams because the script/app doesn't require input, and outputs only when finished, nothing important. Which might not be the case for you.