Java Swing executing gFortran code - java

I was wondering is there anyway for Java / Swing code to execute gFortran program on ubuntu/linux platform?
Anyone has some idea on how this could be done ?

One thing you could do is to run a separate program using Runtime to start a Process consisting of your fortran code. The following is an example of this:
Runtime rt = Runtime.getRuntime();
try {
String[] env = {"/path/to/program"};
Process proc = rt.exec("your_program", env);
System.out.println("return value: " + proc.waitFor());
}
catch (Exception ex) {
System.err.println(ex);
}
The above code will execute /path/to/program/your_program and wait for it to finish and then read off the return code.
Alternatively, you could write some information to stdout and read that from your java program:
import java.io.*;
...
Runtime rt = Runtime.getRuntime();
try {
String[] env = {"/path/to/program"};
Process proc = rt.exec("your_program", env);
System.out.println("return value: " + proc.waitFor());
InputStream stream = proc.getInputStream();
BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
while (reader.ready()) {
// Do something with the data here.
System.out.println(reader.readLine());
}
}
catch (Exception ex) {
System.err.println(ex);
}
If you need to supply the external program with arguments you pass them as an array of strings. As an example, if I wanted to run ls -lh /etc/ that is what the following code does:
String[] cmd = {"ls", "-lh", "/etc/"};
String[] env = {"/bin/"};
Process proc = rt.exec(cmd, env);
You could also try using Java Native Interface to communicate with C/C++ code which can interface with fortran.

Related

How to run .sh file, using process builder?

I already create the .sh file, and the inside is:
sudo iptables --flush
sudo iptables -A INPUT -m mac --mac-source 00:00:00:00:00:00 -j DROP
It works normally when I run it on the terminal, but when I use processbuilder, it didn't do anything. No error, but didn't happen anything, this is the code on my java:
Process pb = new ProcessBuilder("/bin/bash","/my/file.sh").start();
I already looking for the answer, but I still failed to run the .sh file, even I do the same thing with people that already done it.
Sorry if this is a bad question, thank you.
Are you sure that the bash is not run? Do you checked the Process object returned by the startmethod? You can get the output value, the output stream, etc. from this objects.
Check your streams and exitvalue for errors... sudo is probably the problem here.
Not necessarily the best code but it gets the job done. Executes a process, takes the process.streams and prints them to System.out. Might helpt to find out what the issue actually is atlest.
ProcessBuilder pb = new ProcessBuilder(args);
pb.redirectErrorStream(true);
final Process proc = pb.start();
final StringBuilder builder = new StringBuilder("Process output");
final Thread logThread = new Thread() {
#Override
public void run() {
InputStream is = proc.getInputStream();
BufferedReader reader = new BufferedReader(new InputStreamReader(is));
try {
String line;
do {
line = reader.readLine();
builder.append("");
builder.append(line == null ? "" : line);
builder.append("<br/>");
} while(line != null);
} catch (IOException e) {
builder.append("Exception! ").append(e.getMessage());
} finally {
try {
reader.close();
} catch (IOException e) {
builder.append("Exception! ").append(e.getMessage());
}
}
}
};
logThread.start();
int retVal = proc.waitFor();
System.out.println(builder.toString());
From Java API Runtime : http://docs.oracle.com/javase/7/docs/api/java/lang/Runtime.html
// Java runtime
Runtime runtime = Runtime.getRuntime();
// Command
String[] command = {"/bin/bash", "/my/file.sh"};
// Process
Process process = runtime.exec(command);
Also you should be careful with sudo commands that may ask for root password.

Running simple CECopy in CMD using Java

I am trying to run a simple "cecopy" in java. I call "cmd.exe" and pass the command through. It creates the directories but doesnt carry out the copy.
Below is the command I am using, set as a string in java:
String cmd = "mkdir \"C:\\\\Dominos\\\\DATFiles\" >> log.txt\n"
+ "\n" +
"cecopy \"dev:\\Application\\\\MCL\\\\Projects\\\\Default\\\\aa.dat\" \"C:\\\\Dominos\\\\DATFiles\");
Below is how I am calling command prompt to execute the DOS statement:
Runtime rt = Runtime.getRuntime();
try {
Process p = rt.exec("cmd.exe /c" + cmd); // Call CMD
p.waitFor(); // Wait till CMD finishes
} catch (InterruptedException | IOException ex) {
Logger.getLogger(readData.class.getName()).log(Level.SEVERE, null, ex);
}
Any help?
Thanks in advance!
You can use process builder. It handles commands with arguments neatly.
ProcessBuilder processBuilder = new ProcessBuilder();
p.command("cmd_to_run", "args_if_any");
p.start();

Get content from outputstream

I am using a really old Java version and i am missing a lot of classes. The system runs on an embedded platform. There is a class to execute system commands, but the output from the command is discarded. Is there anyway to cache or get this output another way?
There is another java application that is not coded by us that we interact with. This application starts a test and output the results in the shell. We are not able to edit the source code of that application.
Any suggestions?
You can check ProcessBuilder to run system commands.
ProcessBuilder pb = new ProcessBuilder("myCommand", "myArg1", "myArg2");
Map env = pb.environment();
env.put("VAR1", "myValue");
env.remove("OTHERVAR");
env.put("VAR2", env.get("VAR1") + "suffix");
pb.directory(new File("myDir"));
File log = new File("log");
pb.redirectErrorStream(true);
pb.redirectOutput(Redirect.appendTo(log));
Process p = pb.start();
If the external app will run inside the same process, you can try to redirect System.out (using System.setOut()) before the call to the external application.
Depending on how desperate you are, you can manipulate the standard output of the launched process by adding a "shim" class. Basically, create your own class with a main method which redirects stdout to your desired location (like some known file).
public class HackMain {
public static void main(String[] args) {
// ... use reflection to hack System.out ...
// invoke "real" main
RealMainClass.main(args);
}
}
Then add a jar with this class to the invoked process command line and call it instead like java -cp <other_jars>:<hack_jar> HackMain [<args> ...].
If you're using a shell wrapper and you have access to the file system you can try to redirect the output of your command to a file and read it from there:
Ish.execute(fancyCommand + " > myfile.tmp");
InputStream is = null;
StringBuilder sb = new StringBuilder();
try {
is = new BufferedInputStream(new FileInputStream("/path/to/myfile.tmp"));
int c;
while ((c = is.read()) != -1){
sb.append((char)c);
}
} catch (IOException ioex) {
ioex.printStackTrace();
} finally {
if (is != null) {
try {
is.close();
} catch (Exception ignore) {
}
}
}

Not able to execute sort command using Runtime or ProcessBuilder

I am trying to execute this command sort --field-separator="," --key=2 /home/dummy/Desktop/sample.csv" -o /home/dummy/Desktop/sample_temp.csv using Java Runtime and ProcessBuilder.
Manually I am able to execute this command in linux, but using Runtime or ProcessBuilder, this command does not execute. It returns with an error code = 2.
Edit:
If I am trying to execute 'ls' command in linux through Java, I get the list of files in the current directory. But, If I try to execute the command 'ls | grep a', an IOException is thrown with error code=2.
Here is the snippet:
public static void main(String[] args) throws IOException {
InputStream is = null;
ByteArrayOutputStream baos = null;
ProcessBuilder pb = new ProcessBuilder("ls | grep a");
try {
Process prs = pb.start();
is = prs.getInputStream();
byte[] b = new byte[1024];
int size = 0;
baos = new ByteArrayOutputStream();
while((size = is.read(b)) != -1){
baos.write(b, 0, size);
}
System.out.println(new String(baos.toByteArray()));
}
catch (IOException e)
{
e.printStackTrace();
}
finally
{
try {
if(is != null) is.close();
if(baos != null) baos.close();
} catch (Exception ex){}
}
}
There could be a range of issue with your code. Hence you did not supply your code I can only guess.
The output file needs to be already created
The ',' field separator does not need the quotes around it (see code below)
So after these 2 issues (both making the program exit with '2'), this code actually works:
import java.io.IOException;
import java.util.Arrays;
public class Test {
public static void main(String[] args) throws IOException, InterruptedException {
ProcessBuilder pb = new ProcessBuilder(Arrays.asList("sort", "--field-separator=,", "--key=2", "/tmp/sample.csv", "-o",
"/tmp/sample_temp.csv"));
Process p = pb.start();
int returnCode = p.waitFor();
System.out.println(returnCode);
}
}
Will print '0' and will sort the file correctly.
For the 'ls | grep' issue, read this great article: http://www.javaworld.com/article/2071275/core-javahen-runtime-exec---won-t/core-java/when-runtime-exec---won-t.html
The article basically explains that the Runtime.exec (and the ProcessBuilder wrapper) is for running processes and not a Shell (the ls | grep you are trying are actually 2 processes in Linux communicating with each other thru stdout/in).
I am able to execute that manually. And error code 2 means Misuse of Shell BuiltIns
I see in your example you are only invoking "ls", not "/usr/bin/ls" (or something like that).
When you execute manually you have the luxury of PATH environment variable which is not availabled to the process you create.
Use "which ls" to discover the location of 'ls' on your target system. For your code to be portable you will have to make it a configurable option.
this is the way to execute any bash commands like sort, ls, cat (with sub-options). Please find the snippet:
private String executeCommand(String command) {
StringBuffer output = new StringBuffer();
Process p;
try {
p = Runtime.getRuntime().exec("script.sh");
p.waitFor();
BufferedReader reader =
new BufferedReader(new InputStreamReader(p.getInputStream()));
String line = "";
while ((line = reader.readLine())!= null) {
output.append(line + "\n");
}
} catch (Exception e) {
e.printStackTrace();
}
return output.toString();
}
In the exec() method, I passed a shell script which contains the bash command within it. That linux command will be executed and you can carry on with the next task. Hope this was helpful.

How to run Unix shell script from Java code?

It is quite simple to run a Unix command from Java.
Runtime.getRuntime().exec(myCommand);
But is it possible to run a Unix shell script from Java code? If yes, would it be a good practice to run a shell script from within Java code?
You should really look at Process Builder. It is really built for this kind of thing.
ProcessBuilder pb = new ProcessBuilder("myshellScript.sh", "myArg1", "myArg2");
Map<String, String> env = pb.environment();
env.put("VAR1", "myValue");
env.remove("OTHERVAR");
env.put("VAR2", env.get("VAR1") + "suffix");
pb.directory(new File("myDir"));
Process p = pb.start();
You can use Apache Commons exec library also.
Example :
package testShellScript;
import java.io.IOException;
import org.apache.commons.exec.CommandLine;
import org.apache.commons.exec.DefaultExecutor;
import org.apache.commons.exec.ExecuteException;
public class TestScript {
int iExitValue;
String sCommandString;
public void runScript(String command){
sCommandString = command;
CommandLine oCmdLine = CommandLine.parse(sCommandString);
DefaultExecutor oDefaultExecutor = new DefaultExecutor();
oDefaultExecutor.setExitValue(0);
try {
iExitValue = oDefaultExecutor.execute(oCmdLine);
} catch (ExecuteException e) {
System.err.println("Execution failed.");
e.printStackTrace();
} catch (IOException e) {
System.err.println("permission denied.");
e.printStackTrace();
}
}
public static void main(String args[]){
TestScript testScript = new TestScript();
testScript.runScript("sh /root/Desktop/testScript.sh");
}
}
For further reference, An example is given on Apache Doc also.
I think you have answered your own question with
Runtime.getRuntime().exec(myShellScript);
As to whether it is good practice... what are you trying to do with a shell script that you cannot do with Java?
I would say that it is not in the spirit of Java to run a shell script from Java. Java is meant to be cross platform, and running a shell script would limit its use to just UNIX.
With that said, it's definitely possible to run a shell script from within Java. You'd use exactly the same syntax you listed (I haven't tried it myself, but try executing the shell script directly, and if that doesn't work, execute the shell itself, passing the script in as a command line parameter).
Yes it is possible to do so. This worked out for me.
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import org.omg.CORBA.portable.InputStream;
public static void readBashScript() {
try {
Process proc = Runtime.getRuntime().exec("/home/destino/workspace/JavaProject/listing.sh /"); //Whatever you want to execute
BufferedReader read = new BufferedReader(new InputStreamReader(
proc.getInputStream()));
try {
proc.waitFor();
} catch (InterruptedException e) {
System.out.println(e.getMessage());
}
while (read.ready()) {
System.out.println(read.readLine());
}
} catch (IOException e) {
System.out.println(e.getMessage());
}
}
Here is my example. Hope it make sense.
public static void excuteCommand(String filePath) throws IOException{
File file = new File(filePath);
if(!file.isFile()){
throw new IllegalArgumentException("The file " + filePath + " does not exist");
}
if(isLinux()){
Runtime.getRuntime().exec(new String[] {"/bin/sh", "-c", filePath}, null);
}else if(isWindows()){
Runtime.getRuntime().exec("cmd /c start " + filePath);
}
}
public static boolean isLinux(){
String os = System.getProperty("os.name");
return os.toLowerCase().indexOf("linux") >= 0;
}
public static boolean isWindows(){
String os = System.getProperty("os.name");
return os.toLowerCase().indexOf("windows") >= 0;
}
Yes, it is possible and you have answered it! About good practises, I think it is better to launch commands from files and not directly from your code. So you have to make Java execute the list of commands (or one command) in an existing .bat, .sh , .ksh ... files.
Here is an example of executing a list of commands in a file MyFile.sh:
String[] cmd = { "sh", "MyFile.sh", "\pathOfTheFile"};
Runtime.getRuntime().exec(cmd);
To avoid having to hardcode an absolute path, you can use the following method that will find and execute your script if it is in your root directory.
public static void runScript() throws IOException, InterruptedException {
ProcessBuilder processBuilder = new ProcessBuilder("./nameOfScript.sh");
//Sets the source and destination for subprocess standard I/O to be the same as those of the current Java process.
processBuilder.inheritIO();
Process process = processBuilder.start();
int exitValue = process.waitFor();
if (exitValue != 0) {
// check for errors
new BufferedInputStream(process.getErrorStream());
throw new RuntimeException("execution of script failed!");
}
}
As for me all things must be simple.
For running script just need to execute
new ProcessBuilder("pathToYourShellScript").start();
The ZT Process Executor library is an alternative to Apache Commons Exec. It has functionality to run commands, capturing their output, setting timeouts, etc.
I have not used it yet, but it looks reasonably well-documented.
An example from the documentation: Executing a command, pumping the stderr to a logger, returning the output as UTF8 string.
String output = new ProcessExecutor().command("java", "-version")
.redirectError(Slf4jStream.of(getClass()).asInfo())
.readOutput(true).execute()
.outputUTF8();
Its documentation lists the following advantages over Commons Exec:
Improved handling of streams
Reading/writing to streams
Redirecting stderr to stdout
Improved handling of timeouts
Improved checking of exit codes
Improved API
One liners for quite complex use cases
One liners to get process output into a String
Access to the Process object available
Support for async processes ( Future )
Improved logging with SLF4J API
Support for multiple processes
This is a late answer. However, I thought of putting the struggle I had to bear to get a shell script to be executed from a Spring-Boot application for future developers.
I was working in Spring-Boot and I was not able to find the file to be executed from my Java application and it was throwing FileNotFoundFoundException. I had to keep the file in the resources directory and had to set the file to be scanned in pom.xml while the application was being started like the following.
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
<includes>
<include>**/*.xml</include>
<include>**/*.properties</include>
<include>**/*.sh</include>
</includes>
</resource>
</resources>
After that I was having trouble executing the file and it was returning error code = 13, Permission Denied. Then I had to make the file executable by running this command - chmod u+x myShellScript.sh
Finally, I could execute the file using the following code snippet.
public void runScript() {
ProcessBuilder pb = new ProcessBuilder("src/main/resources/myFile.sh");
try {
Process p;
p = pb.start();
} catch (IOException e) {
e.printStackTrace();
}
}
Hope that solves someone's problem.
Here is an example how to run an Unix bash or Windows bat/cmd script from Java. Arguments can be passed on the script and output received from the script. The method accepts arbitrary number of arguments.
public static void runScript(String path, String... args) {
try {
String[] cmd = new String[args.length + 1];
cmd[0] = path;
int count = 0;
for (String s : args) {
cmd[++count] = args[count - 1];
}
Process process = Runtime.getRuntime().exec(cmd);
BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(process.getInputStream()));
try {
process.waitFor();
} catch (Exception ex) {
System.out.println(ex.getMessage());
}
while (bufferedReader.ready()) {
System.out.println("Received from script: " + bufferedReader.readLine());
}
} catch (Exception ex) {
System.out.println(ex.getMessage());
System.exit(1);
}
}
When running on Unix/Linux, the path must be Unix-like (with '/' as separator), when running on Windows - use '\'. Hier is an example of a bash script (test.sh) that receives arbitrary number of arguments and doubles every argument:
#!/bin/bash
counter=0
while [ $# -gt 0 ]
do
echo argument $((counter +=1)): $1
echo doubling argument $((counter)): $(($1+$1))
shift
done
When calling
runScript("path_to_script/test.sh", "1", "2")
on Unix/Linux, the output is:
Received from script: argument 1: 1
Received from script: doubling argument 1: 2
Received from script: argument 2: 2
Received from script: doubling argument 2: 4
Hier is a simple cmd Windows script test.cmd that counts number of input arguments:
#echo off
set a=0
for %%x in (%*) do Set /A a+=1
echo %a% arguments received
When calling the script on Windows
runScript("path_to_script\\test.cmd", "1", "2", "3")
The output is
Received from script: 3 arguments received
It is possible, just exec it as any other program. Just make sure your script has the proper #! (she-bang) line as the first line of the script, and make sure there are execute permissions on the file.
For example, if it is a bash script put #!/bin/bash at the top of the script, also chmod +x .
Also as for if it's good practice, no it's not, especially for Java, but if it saves you a lot of time porting a large script over, and you're not getting paid extra to do it ;) save your time, exec the script, and put the porting to Java on your long-term todo list.
I think with
System.getProperty("os.name");
Checking the operating system on can manage the shell/bash scrips if such are supported.
if there is need to make the code portable.
String scriptName = PATH+"/myScript.sh";
String commands[] = new String[]{scriptName,"myArg1", "myArg2"};
Runtime rt = Runtime.getRuntime();
Process process = null;
try{
process = rt.exec(commands);
process.waitFor();
}catch(Exception e){
e.printStackTrace();
}
Just the same thing that Solaris 5.10 it works like this ./batchstart.sh there is a trick I donĀ“t know if your OS accept it use \\. batchstart.sh instead. This double slash may help.
for linux use
public static void runShell(String directory, String command, String[] args, Map<String, String> environment)
{
try
{
if(directory.trim().equals(""))
directory = "/";
String[] cmd = new String[args.length + 1];
cmd[0] = command;
int count = 1;
for(String s : args)
{
cmd[count] = s;
count++;
}
ProcessBuilder pb = new ProcessBuilder(cmd);
Map<String, String> env = pb.environment();
for(String s : environment.keySet())
env.put(s, environment.get(s));
pb.directory(new File(directory));
Process process = pb.start();
BufferedReader inputReader = new BufferedReader(new InputStreamReader(process.getInputStream()));
BufferedWriter outputReader = new BufferedWriter(new OutputStreamWriter(process.getOutputStream()));
BufferedReader errReader = new BufferedReader(new InputStreamReader(process.getErrorStream()));
int exitValue = process.waitFor();
if(exitValue != 0) // has errors
{
while(errReader.ready())
{
LogClass.log("ErrShell: " + errReader.readLine(), LogClass.LogMode.LogAll);
}
}
else
{
while(inputReader.ready())
{
LogClass.log("Shell Result : " + inputReader.readLine(), LogClass.LogMode.LogAll);
}
}
}
catch(Exception e)
{
LogClass.log("Err: RunShell, " + e.toString(), LogClass.LogMode.LogAll);
}
}
public static void runShell(String path, String command, String[] args)
{
try
{
String[] cmd = new String[args.length + 1];
if(!path.trim().isEmpty())
cmd[0] = path + "/" + command;
else
cmd[0] = command;
int count = 1;
for(String s : args)
{
cmd[count] = s;
count++;
}
Process process = Runtime.getRuntime().exec(cmd);
BufferedReader inputReader = new BufferedReader(new InputStreamReader(process.getInputStream()));
BufferedWriter outputReader = new BufferedWriter(new OutputStreamWriter(process.getOutputStream()));
BufferedReader errReader = new BufferedReader(new InputStreamReader(process.getErrorStream()));
int exitValue = process.waitFor();
if(exitValue != 0) // has errors
{
while(errReader.ready())
{
LogClass.log("ErrShell: " + errReader.readLine(), LogClass.LogMode.LogAll);
}
}
else
{
while(inputReader.ready())
{
LogClass.log("Shell Result: " + inputReader.readLine(), LogClass.LogMode.LogAll);
}
}
}
catch(Exception e)
{
LogClass.log("Err: RunShell, " + e.toString(), LogClass.LogMode.LogAll);
}
}
and for usage;
ShellAssistance.runShell("", "pg_dump", new String[]{"-U", "aliAdmin", "-f", "/home/Backup.sql", "StoresAssistanceDB"});
OR
ShellAssistance.runShell("", "pg_dump", new String[]{"-U", "aliAdmin", "-f", "/home/Backup.sql", "StoresAssistanceDB"}, new Hashmap<>());

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