This is my first question on stackoverflow so I'll try to keep it concise and relevant.
I'm currently creating a Java program that is attempting to call an external program located on the system, in order to do this however I am required to call a shell script that sets up links to the relevant libraries to ensure that the system is linked to these before the external program can be executed.
The issue at hand is that I cannot invoke the shell script through Java, I've researched high and low and am aware that of alternative ways such as the use of the ProcessBuilder class. Unfortunately I'm quite new to the world of trying to invoke command line statements through Java and so I'm stuck for answers.
An example of the code I am using can be found below:
private void analyse_JButtonActionPerformed(java.awt.event.ActionEvent evt) {
// Get project path for copying of Fortran program to folder and execution
String projectPath = Newproject_GUI.getProjectPath();
String sourcePath [] = {"/bin/sh ", "-c ","source ~/set_env_WRF_gnu.sh"} ;
Runtime fortranAnalyser = Runtime.getRuntime();
try {
Process p = fortranAnalyser.exec("cp main.exe " + projectPath);
Process k = fortranAnalyser.exec(sourcePath);
BufferedReader is = new BufferedReader(new InputStreamReader(k.getInputStream()));
String line;
while ((line = is.readLine()) != null) {
System.out.println(line);
}
} catch (IOException ex) {
Logger.getLogger(Analyser_GUI.class.getName()).log(Level.SEVERE, null, ex);
}
}
Process p works fine and does indeed copy main.exe to the intended directory when the method is called. Process k however does not and this is where the issue is.
Thanks in advance.
The issue is "source" is internal command of BASH (you are using "sh" but that is just BASH in the simplified mode). So what you do is:
you spawn new process "sh" and source something there (setting some VARIABLES I guess)
the process ends and all VARIABLES are lost
you spawn another process, but VARIABLES are already gone
I am not sure if you use those variables later on, but according to the script name it is probably setting some. Don't do that like this.
By the way if you only want to execute script in bash, you don't need to source it. To get it's side effects, just execute it with:
String sourcePath [] = {"/bin/sh ", "/home/XYZ/set_env_WRF_gnu.sh"} ;
Please note you cannot use ~ in this case, use Java to get your home dir.
Related
I am trying to run a piece of Python code via a Java application. The command when put directly into Command Prompt cd'd to the working directory runs exactly as intended. However, my attempts to use the Runtime and ProcessBuilder classes in conjunction with the Process class has yielded no sign of correct function which would be the creation of a CSV file for every call of the code.
I am running this program using Intellij on Windows 10. I have added each directory I am using to my environmental PATH variable as well as attempting full paths in my commands and just file names. The only source of life I can find is that if I include a .waitFor() method a .isAlive() method will return true before the .waitFor() method is called.
I have searched through various similar questions and concluded that using a ProcessBuilder object is the best way to go and that the biggest issue is probably the structure of my command. However, I have made many iterations and have found nothing that changes the caught error to anything useful.
Here is the privacy augmented code that I have been running, I wrote out the command in full in the process builder as that is the last iteration I have attempted.
for (int y = 1; y < iterator; y++) {
try {
String command =
"C:\\Users\\myName\\AppData\\Local\\Programs\\Python\\Python37\\python C:\\Users\\myName\\IdeaProjects\\projectApplication\\script.py ";
String pythonInputPath = " C:\\Users\\myName\\IdeaProjects\\projectApplication\\bin\\output" + y + ".wav ";
ProcessBuilder pb = new ProcessBuilder(command+Arrays.toString(pythonCommandString).replaceAll("\\s","")+pythonInputPath+Integer.toString(y));
Process p = pb.start();
//Process checks
System.out.println(p.isAlive());
p.waitFor();
System.out.println(p.isAlive());
//Destroying process once complete to ensure smooth iterations
p.destroy();
} catch (Exception ex) {
System.out.println("Problems with python script execution: " + ex);
}
}
They python code takes in a WAV file (pythonInputPath) that is a product of earlier part of the application, an Integer[] that usually includes ~20 values (pythonCommandString), and a single iteration integer (y).
The first call to .isAlive() is true and the second is false as expected however the script normally creates a CSV that should be output to a bin file that exists in the working director and that fails to occur when running from Java. From other examples I expected using the Process builder as opposed to the Runtime stream to work, however, there is no difference in my implementation.
Do not concatenate the program with its arguments. Quoting Oracle ProcessBuilder docs
Each process builder manages these process attributes: a command, a
list of strings which signifies the external program file to be
invoked and its arguments, if any
and
ProcessBuilder pb = new ProcessBuilder("myCommand", "myArg1", "myArg2");
Just use the constructor you use, but pass each argument as a separate string, otherwise the OS will try to find an application that is named as a whole command line you gave, and obviously there is no such program
I have this program that I am writing that has this method that is supposed to execute a program but does not do anything. The method in question is as follows:
public void findCC_Data(List<String> l7) {
StringBuffer output = new StringBuffer();
Process p;
try {
for(String sql_file: l7) {
String command = "cleartool describe " + sql_file;
p = Runtime.getRuntime().exec(command);
System.out.println("Executing: " + command);
p.waitFor();
BufferedReader reader = new BufferedReader(new InputStreamReader(p.getInputStream()));
String line = "";
while ((line = reader.readLine()) != null) {
output.append(line + "\n");
}
if (reader.readLine() == null) {
System.out.println("'reader.readLine()' is equal to null");
}
}
} catch(Exception e) {
e.printStackTrace();
}
System.out.println(output.toString());
}
Does anyone know why the command does not do anything and the reader.readLine() method always returns null?
I am following a tutorial but using the cleartool program instead of the ping program basically. The tutorial is at this URL:https://www.mkyong.com/java/how-to-execute-shell-command-from-java/
Solution
I had the System.out.println(output.toString()) print statement outside of the for loop instead of inside it. Now when I move the SOP statement inside the loop it prints a million plus lines of information on ClearCase version control stuff. To fix put the SOP with the output.toString() inside the loop in the broken code above.
One possibility for a program in (java, python, bash, ...) to do nothing with ClearCase command is if said cleartool command is run within a dynamic view which has been set (cleartool setview).
As I explained before, the cleartool setview command opens a subshell in which commands are supposed to be run, which is not the case here (the java program runs in the main shell)
The other possible cause is that you are reading stdout, not stderr, and somehow this commands returns an error (maybe its execution path is not correct).
thought it would not matter anyway because a method I call before the one in question is supposed to change directories to the dynamic view. It appears it does not work as expected though because the result of the cleartool pwd command is just my desktop
Yes, each cleartool command operates in its own shell. You must set the right execution folder for each Java Process run("cleartool ...") commands, in order for those cleartool commands to start in the right folder.
See "execute file from defined directory with Runtime.getRuntime().exec", although the answer is a bit dated, and that might have changed with Java8.
As the OP noted, the output.toString() print statement was outside of the for loop instead of inside said loop.
You can see additional example in:
"Capturing stdout when calling Runtime.exec"
"No output from Runtime.getRuntime().exec(“ls”)"
Run your command inside a child shell using sh command and redirect the output to nohup, refer nohup and sh command.
once you have the command executed i.e. "nohup cleartool describe " + sql_file;
you can get the error or details from nohup.out file and confirm if there is an issue in executing the command.
How can I set the focus (e.g. cmd+tab) of an arbitrary application (Java or not) from a Java program, on OSX?
Looking for an answer to this question, I came across this question, but it doesn't really help for OSX.
EDIT: one possibiltiy seems to be to use something like Quicksilver, and a Robot to send it keypresses with modifiers. I'd prefer something more portable, though, that requires less setup to make changes after it's compiled....
You should be able to reactivate an already running app using the open command that comes with OS X:
Runtime.exec("open /path/to/Whichever.app");
(Or some equivalent overload of that function.) This will also open an app if it's not running yet.
Chuck's answer tipped me off to osascript, so I decided to give it a shot straight from the command line. Managed to get it working with Runtime.exec(), osascript, and AppleScript.
Java launches an AppleScript and passes it the application name, using osascript from the command line, via Runtime.exec():
try {
List<String> shellCommandList = new ArrayList<String>();
shellCommandList.add("osascript");
shellCommandList.add("activateApplication.scpt");
shellCommandList.add(appName);
String[] shellCommand = (String[])shellCommandList.toArray(new String[0]);
Process p = Runtime.getRuntime().exec(shellCommand);
// if desired, pipe out the script's output
BufferedReader in = new BufferedReader(new InputStreamReader(p.getInputStream()));
String cmdOutStr = "";
while ((cmdOutStr = in.readLine()) != null) {
System.out.println(cmdOutStr);
}
// if desired, check the script's exit value
int exitValue = p.waitFor();
if (exitValue != 0) {
// TODO: error dialog
System.err.println("Invalid application name: "+ appName);
}
} catch (Exception e) {
e.printStackTrace();
}
And the AppleScript uses a run handler to capture the incoming argument:
on run (arguments)
set appName to (item 1 of arguments)
tell application appName to activate
return 0
end run
You can use the javax.script API to run AppleScripts. So you can write a script along the lines of "tell application "WhateverApp" to activate", filling in your arbitrary application for WhateverApp, and it should do what you want.
I run a bash script from my Java program which takes a chunk of data, manipulates it, and splits it up.
It's not a question of whether the bash script works -- I can see the split files in the directory.
Say the original file was "bigFile" in data/
Then
try
{
Process proc = Runtime.getRuntime().exec("bash " + SCRIPT_DIR + "/" + SPLIT_SCRIPT_NAME + " " + args[_MESSAGES_PER_UPLOAD_] + " " + args[_MAXIMUM_MESSAGES_PER_FEED_] + " " + (60000*Integer.parseInt(args[_DURATION_BEFORE_EACH_UPLOAD_IN_MINUTES_])/Integer.parseInt(args[_DURATION_OF_EACH_FEED_IN_MILLISECONDS_])));
proc.waitFor();
}
catch(IOException e) { error(e); }
String fileNames;
File folder = new File(DATA_DIR);
File[] filesToUpload = folder.listFiles();
for (int i = 0; i < filesToUpload.length; ++i)
if (filesToUpload[i].isFile())
{
fileNames = filesToUpload[i].getName();
System.out.println(fileNames);
}
Will print bigFile, not...
$ ls data/
dataChunk_00000
dataChunk_00001
dataChunk_00002
dataChunk_00003
dataChunk_00004
dataChunk_00005
dataChunk_00006
dataChunk_00007
dataChunk_00008
dataChunk_00009
dataChunk_00010
dataChunk_00011
dataChunk_00012
dataChunk_00013
dataChunk_00014
dataChunk_00015
dataChunk_00016
dataChunk_00017
dataChunk_00018
dataChunk_00019
dataChunk_00020
dataChunk_00021
dataChunk_00022
dataChunk_00023
dataChunk_00024
dataChunk_00025
dataChunk_00026
dataChunk_00027
as it should. I'm guessing this is a compiler optimization or something.
Edit: If somebody could explain to me why proc.waitFor() isn't working and/or a better way to solve this, I'd much appreciate it.
The problem with this is not compiler optimization or anything like that.
Its because you are invoking your script with a "bash" in front of it . This causes the process to fork -- so your bash command returns successfully immediately , but your script continues to run in the background and terminate.
The proc.waitFor() has nothing to wait for, the rest of the java program executes before your file has been "split".
You cannot change the directory with java.
If you want to "simulate" it, all you need to do is set the property "user.dir".
I am guessing that your bash script is performing actions asynchronously from its own process/thread. This means that the script finishes executing before the work is complete. This would still pass the waitFor() check and continue executing the code.
EDIT:
Kal's answer explains this more clearly, and it was posted first. The problem is the fact that you use the bash command to execute the script.
I suspect your arguments aren't all passed to your script.
Put all your arguments in an ArrayList instance, pass the instance to the ProcessBuilder, then call the start method on the builder instance, which returns the proc on which you call waitFor.
Here's sample Scala code to show what I mean (I can port it to Java if you're really interested ;-):
import java.lang.{ Process => JProcess, ProcessBuilder => JProcessBuilder }
import java.util.{ArrayList => JArrayList, List => JList, Map => JMap}
import java.io.{InputStreamReader, BufferedReader}
def call(args: String*) = {
val command: JList[String] = new JArrayList[String]()
args.foreach {arg =>
command.add(arg)
}
//log.debug("argument list: %s", command.toString)
val builder = new JProcessBuilder(command)
val proc: JProcess = builder.start()
proc.waitFor()
val read = new BufferedReader(new InputStreamReader(proc.getInputStream()));
val sb: StringBuffer = new StringBuffer()
while(read.ready()) {
sb.append(read.readLine)
}
// sb now has the output of the called process...
val exitValue: Int = proc.exitValue
// http://stuffthathappens.com/blog/2007/11/28/crash-boom-too-many-open-files/
read.close
proc.destroy
(exitValue, sb.toString) // return it
}
Example call in REPL:
scala> call("date")
res156: (Int, java.lang.String) = (0,Mon 18 Jul 2011 22:29:58 BST)
There are a number of wrong assumptions with this program:
Every time you do 'exec' you fork a new process, with its own environment, current directory, etc. Any change of the current directory would have been local to that process and will not affect the parent (your Java process). In other words, there is no way to change the current path of an application using a command in a sub-process, there is no Java API for that either - if you really need this, you have to use native call.
The 'cd' command on Unix is a real command, you do not need the shell in order to run it (unlike Windows).
When you fork a process, you need to make sure that you drain the stdout and stderr, or it is going to block when the OS buffer gets full (see next)
Process.waitFor() works. Always.
A better way to approach the problem is to read carefully the File API and as much as possible work with absolute paths. The 'current directory' is something very usefull when you are in shell, but for applications it ends up being more confusing, so the sooner you resolve it to absolute path - the better.
I tried to run a shell script from java code, but I am facing problem. The script is in batchstart.sh file -
#!/bin/ksh
export DISPLAY=:0.0
Now the script is run with a dot on the command line -- . batchstart.sh
How do I run it from java? My java code is below. It throws the following exception -
java.io.IOException: .: not found
at java.lang.UNIXProcess.forkAndExec(Native Method)
at java.lang.UNIXProcess.<init>(UNIXProcess.java:102)
at java.lang.ProcessImpl.start(ProcessImpl.java:65)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:451)
at java.lang.Runtime.exec(Runtime.java:591)
at java.lang.Runtime.exec(Runtime.java:429)
at SetDisplay.main(SetDisplay.java:12)
import java.io.*;
public class SetDisplay {
public static void main(String[] args) {
File wd = new File("/myhomedir/");
System.out.println("Working Directory: " +wd);
Process proc = null;
try {
proc = Runtime.getRuntime().exec(". batchstart.sh", null, wd);
} catch (Exception e) {
e.printStackTrace();
}
}
}
How do I make the shell script run ?
I tried the following code as well, but that too doesn't work.
File wd = new File("/bin");
System.out.println(wd);
Process proc = null;
try {
proc = Runtime.getRuntime().exec("/bin/bash", null, wd);
}
catch (IOException e) {
e.printStackTrace();
}
if (proc != null) {
BufferedReader in = new BufferedReader(new InputStreamReader(proc.getInputStream()));
PrintWriter out = new PrintWriter(new BufferedWriter(new OutputStreamWriter(proc.getOutputStream())), true);
out.println("cd /home/");
out.println(". batchstart.sh");
out.println("exit");
try {
String line;
while ((line = in.readLine()) != null) {
System.out.println(line);
}
proc.waitFor();
in.close();
out.close();
proc.destroy();
}
catch (Exception e) {
e.printStackTrace();
}
}
When run from the command line, using a dot at the start of a script indicates that the script should be run in the current environment, instead of spawning a new subshell and using a new copy of the current environment. This allows you to export a new value of an environment variable to be used by commands run later from the same interactive shell.
Obviously, this technique only works if you are running your batchstart.sh script from an actual shell. Java does not know how this mechanism works and so the dot means nothing to it. A script cannot modify the environment of the Java process it was called from.
If your goal is to change the value of the DISPLAY environment variable for other commands run by your Java process, consider using the ProcessBuilder class to specify a new environment for the child process. Java does not contain a built-in way to modify variables in its own environment.
The source command (".") is a shell built-in. You have to explicitly run /bin/ksh, passing your script name as the argument (followed by any script arguments).
You have a larger problem if you need to source the script. That usually means that environment changes happen in the context of the current shell, not a subshell.
This won't work with Java since Java's not a shell. You'll need to figure out how to change the environment with Java.
Of course, if I'm wrong and there's more to that script that just setting DISPLAY, it may work as suggested.
The method you're going to have to use depends on what you're trying to achieve(as in "Are you running other programs using exec() that rely on DISPLAY being set?" or "Does your Java program need DISPLAY to be set?").
If, as you state in your comment, it's only your Java program that needs DISPLAY set, just set it outside before your program runs. Create a cmd (or bash) file which sets the DISPLAY variable then calls the JRE to run your program.
#/bin/ksh
export DISPLAY-:0.0
/usr/bin/jre/java your_program blah.blah.blah
I would also modify your main() to check that it's set to something and exit gracefully if not:
if (System.getenv ("DISPLAY") == null)
// doesn't exist, exit gracefully.
The period "." is a shell built-in, and executes the script "in-place", analogous to #include in C/C++. Using "." outside of a shell-script has no meaning.
If you want to run the script from Java, you have to execute the script interpreter (/bin/ksh):
Runtime.getRuntime().exec("/bin/ksh batchstart.sh", ...)
but note that this is not semantically equivalent, since you're executing batchstart.sh as a sub-process instead of sourcing it.