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Java/JavaFX ProcessHandle possibly not finding all processes (Linux/Debian)

I've a JavaFX application where I've a list of a bunch of script files. Once the application loads, it reads it and and checks which ones are running.
To do that I use a ProcessHandle, as mentioned in various examples here on StackOverflow and other guides/tutorials on the internet.
The problem is, it never finds any of them. There for I programmatically started one, which I know for a fact that it will be running, via Process process = new ProcessBuilder("/path/to/file/my_script.sh").start(); - and it won't find this one either.
Contents of my_script.sh:
#!/bin/bash
echo "Wait for 5 seconds"
sleep 5
echo "Completed"
Java code:
// List of PIDs which correspond to the processes shown after "INFO COMMAND:"
System.out.println("ALL PROCESSES: " + ProcessHandle.allProcesses().toList());
Optional<ProcessHandle> scriptProcessHandle = ProcessHandle.allProcesses().filter(processHandle -> {
System.out.println("INFO COMMAND: " + processHandle.info().command());
Optional<String> processOptional = processHandle.info().command();
return processOptional.isPresent() && processOptional.get().equals("my_script.sh");
}).findFirst();
System.out.println("Script process handle is present: " + scriptProcessHandle.isPresent());
if (scriptProcessHandle.isPresent()) { // Always false
// Do stuff
}
Thanks to the good old fashioned System.out.println(), I noticed that I get this in my output console every time:
ALL PROCESSES: [1, 2, 28, 85, 128, 6944, 21174, 29029, 29071]
INFO COMMAND: Optional[/usr/bin/bwrap]
INFO COMMAND: Optional[/usr/bin/bash]
INFO COMMAND: Optional[/app/idea-IC/jbr/bin/java]
INFO COMMAND: Optional[/app/idea-IC/bin/fsnotifier]
INFO COMMAND: Optional[/home/username/.jdks/openjdk-17.0.2/bin/java]
INFO COMMAND: Optional[/usr/bin/bash]
INFO COMMAND: Optional[/home/username/.jdks/openjdk-17.0.2/bin/java]
INFO COMMAND: Optional[/home/username/.jdks/openjdk-17.0.2/bin/java]
INFO COMMAND: Optional[/usr/bin/bash]
Script process handle is present: false
The first line in the Javadoc of ProcessHandle.allProcess() reads:
Returns a snapshot of all processes visible to the current process.
So how come I can't see the rest of the operating system's processes?
I'm looking for a non-os-dependent solution, if possible. Why? For better portability and hopefully less maintenance in the future.
Notes:
A popular solution for GNU/Linux seems to be to check the proc entries, but I don't know if that would work for at least the majority of the most popular distributions - if it doesn't, adding support for them in a different way, would create more testing and maintenance workload.
I'm aware of ps, windir, tasklist.exe possible solutions (worst comes to worst).
I found the JavaSysMon library but it seems dead and unfortunately:
CPU speed on Linux only reports correct values for Intel CPUs
Edit 1:
I'm on Pop_OS! and installed IntelliJ via the PopShop as flatpak.
In order to start it as root as suggested by mr mcwolf, I went to /home/username/.local/share/flatpak/app/com.jetbrains.IntelliJ-IDEA-Community/x86_64/stable/active/export/bin and found com.jetbrains.IntelliJ-IDEA-Community file.
When I run sudo ./com.jetbrains.IntelliJ-IDEA-Community or sudo /usr/bin/flatpak run --branch=stable --arch=x86_64 com.jetbrains.IntelliJ-IDEA-Community in my terminal, I get error: app/com.jetbrains.IntelliJ-IDEA-Community/x86_64/stable not installed
So I opened the file and ran its contents:
exec /usr/bin/flatpak run --branch=stable --arch=x86_64 com.jetbrains.IntelliJ-IDEA-Community "$#"
This opens IntelliJ, but not as root, so instead I ran:
exec sudo /usr/bin/flatpak run --branch=stable --arch=x86_64 com.jetbrains.IntelliJ-IDEA-Community "$#"
Which prompts for a password and when I write it in, the terminal crashes.
Edit 1.1:
(╯°□°）╯︵ ┻━┻ "flatpak run" is not intended to be ran with sudo
Edit 2:
As mr mcwolf said, I downloaded the IntelliJ from the official website, extracted it and ran the idea.sh as root.
Now a lot more processes are shown. 1/3 of them show up as INFO COMMAND: Optional.empty.
scriptProcessHandle.isPresent() is still unfortunately returning false. I searched through them and my_script.sh is nowhere to be found. I also tried processOptional.isPresent() && processOptional.get().equals("/absolute/path/to/my_script.sh") but I still get false on isPresent() and it's not in the list of shown processes.
Though the last sentence might be a different problem. I'll do more digging.
Edit 3:
Combining .commandLine() and .contains() (instead of .equals()) solves the problem mentioned in "Edit 2".
Optional<ProcessHandle> scriptProcessHandle = ProcessHandle.allProcesses().filter(processHandle -> {
System.out.println("INFO COMMAND LINE: " + processHandle.info().commandLine());
Optional<String> processOptional = processHandle.info().commandLine();
return processOptional.isPresent() && processOptional.get().contains("/absolute/path/to/my_script.sh");
}).findFirst();
System.out.println("Script process handle is present: " + scriptProcessHandle.isPresent());
if (scriptProcessHandle.isPresent()) { // Returns true
// Do stuff
}
.commandLine() also shows script arguments, so that must be kept in mind.

Python 2.7 subprocess call method not working to run java command

I am trying to use a python script to manipulate the input files for my java program. The way I am doing it is I am generating the file name and passing it to subprocess.call() method to execute. Here is my program:
def execJava(self):
self.thisCmd="pause"
call(self.javaCmd,shell=True)
call(self.pauseCmd,shell=True)
Where,
self.javaCmd = 'java -ea -esa -Xfuture -Xss64m -classpath "C:\FVSDK_9_1_1\lib\x86_64\msc_12.0-sse2_crtdll\*" -Djava.library.path="C:\FVSDK_9_1_1\lib\x86_64\msc_12.0-sse2_crtdll;C:\FVSDK_9_1_1\lib\x86_64\share" com.cognitec.jfrsdk.examples.MatchFIRAgainstGallery C:\FVSDK_9_1_1\etc\frsdk.cfg 0 .\tmp\frsdk-scratch\probe_1.fir .\tmp\test\*'
Yes, it's a long complex java instruction but when I run it in the command prompt it works fine. Only when I pass it as a string it doesn't run and returns:
Exception in thread "main" java.lang.Error
After some exploration into the problem, I have discovered that it is due to \x, \t in the instruction, so it is executing
.\tmp\test\*
as
mp est\*
as it replaces \t with tab space while executing. I have looked up quite a bit and didn't find any solution. Any help is much appreciated.

Use forward slashes "/" instead of back slashes "\" for your paths.

Jsch sftp exception : file not found (even if the file exists)

I'm writing a jython code which use Jsch to run some shell instructions on a remote machine. I need to wait a specific shell instruction has finished before continuing the exectuion of the jython code on my local machine (=need to synchronize shell code on a remote machine).
To do that, when the specific shell instruction has finished i create a text file in the remote machine. Then in my jython code I open an sftp channel and try periodically to get the file (using the sftp.exception and a "while true" loop). The code wait until the file is downloaded.
My problem is that even when the file is created, the jsch function "get" doesn't manage to download the file and keep sending "sftp.exception : no such file or directory" .That makes me locked up in an infinite loop.
Here is my code :
#We generate the info files for each class of the classlist
for classname in classlist:
print ("Generating information file (format : .out) for the class %s " % (classname))
#We open a shell channel and run the commands "windchill shell" and then "InfoReport.sh classname".
channel_generate = gl_session.openChannel('shell')
ops = channel_generate.getOutputStream()
ps = PrintStream(ops, True)
channel_generate.connect()
ps.println("windchill shell")
ps.println('rm ' + self.wt_home + '/tmp/' + classname + '.txt')
#The following instruction is the one i need to synchronize
ps.println(self.wt_home + '/bin/' + self.command + " " + classname)
#I create a file to detect the end of the previous instruction
ps.println('echo ok > ' + self.wt_home + '/tmp/' + classname)
ps.println('exit')
ps.close()
#Here we wait until the synchro file is created.
#We connect an sftp server and test every 4 seconds if we can retrieve the file.
channel_synchro = gl_session.openChannel('ftp')
channel_synchro.connect()
#This loop is broken when the get is successful
while True:
try:
channel_synchro.get(self.wt_home + '/tmp/' + classname,'/home/dev/temp')
break
except jsch.SftpException:
time.sleep(4)
#Disconnect and close de sftp channel
channel_synchro.disconnect()
channel_synchro.close()
#Disconnect and close the shell channel
channel_generate.disconnect()
channel_generate.close()
I have tried different solutions : other type of loops, create a new channel in each iteration of the "while true" loop, i have thought about user rights problem, i have checked if the paths are exact and they are, i have checked if the sftp function of my machine works and it works.
Nothing works, i'm still not able to solve this problem

Issue starting cmd.exe twice in a row

I am trying to automate some processes that were build in ancient times, for the sake of avoiding repetitive actions. It is required that the processes are started with one batch and stopped with another (this can not be changed btw).
So i made a commandline tool to do this (and many other repetitive stuff) and I have modelled a command that starts the 'startbatch' and a command that start the 'stopbatch'. Both commands work fine separatly (as I tested them separatly) but there seems to be a problem when i want execute them one after another (in the correct order ofcourse). I get the following error in new cmd.exe window:
The process cannot access the file because it is being used by another process.
the code that i am using to start the batches looks like this:
public void startBatchInDev(String company){
String startBatchFolder = locations.getLocationFor("startbatch");
try{
Runtime runtime = Runtime.getRuntime();
runtime.exec("cmd.exe /C cd \"" + startBatchFolder + "\" & start cmd.exe /k \"" + BATCHSTART + company.toLowerCase()+ "-dev" + BATCH_SUFFIX + "\"");
}
catch(IOException ioe){
ioe.printStackTrace();
}
}
public void stopBatchInDev(String company){
String startBatchFolder = locations.getLocationFor("startbatch");
try{
Runtime runtime = Runtime.getRuntime();
runtime.exec("cmd.exe /C cd \"" + startBatchFolder + "\" & start cmd.exe /k \"" + BATCHSTOP + company.toLowerCase()+ "-dev" + BATCH_SUFFIX + "\"");
}
catch(IOException ioe){
ioe.printStackTrace();
}
}
The names of the batchfiles are concatenated, but they are OK once the application is running.
The error message is quite clear, some file is locked and I can't access it because of it. Some googling confirms my suspicion, but I can't seem to find a solution for this. The hits in google are all about obvious uses of files, like an obvious shared resource. But in my case, i am not working on the same batch file. The stop and start batch are two different files. So I am actually starting to think that it might be the cmd.exe file that is being locked by windows...
So this question is actually two questions:
- what is the exact cause of the described problem?
- how do i programmatically fix this (if possible)?
thanks in advance!

So, basically, bat is not so great :-(
I was able to repro this from java, but I also found that this script:
#echo off
echo STOP
echo STOP >> E:\tmp\java\logfile.txt
C:\cygwin\bin\sleep.exe 1
echo STOP1 >> E:\tmp\java\logfile.txt
C:\cygwin\bin\sleep.exe 1
echo STOP2 >> E:\tmp\java\logfile.txt
When run twice like this:
start test.bat && start test.bat
Will fail with one or more messages like:
The process cannot access the file because it is being used by another process.
The reason is that " >> " redirection opens the file for Read/Write access but only FILE_SHARE_READ sharing. If two different programs attempt to open the file this way, one of them fails.
So, you cannot have two different batch files running at the same time and logging to the same file

Compiling a class using Java code using process

I have this piece of code that compiles a class called tspClassName, when I compile using this code:
Process compileProc = null;
try {
compileProc = Runtime.getRuntime().exec("javac -classpath ."
+ File.separator + "src" + File.separator
+ File.separator + "generated." + tspClassName + ".java -d ." + File.separator + "bin");
// catch exception
if (compileProc.exitValue() != 0)
{
System.out.println("Compile exit status: "
+ compileProc.exitValue());
System.err.println("Compile error:" +
compileProc.getErrorStream());
it outputs this:
"Compile exit status: 2
Compile error:java.io.FileInputStream#17182c1"
The class tspClassName.java compiles without errors otherwise, so I am guessing it has to do with the path,and in my eclipse project, the tspClassName.java resides in package homework4.generated inside src, is there something wrong with the path that I use in the code?
thanks

Your Java code runs a command that looks something like this:
javac -classpath ./src//generated.ClassName.java -d ./bin
I don't think that's what you want. I think you need to change your Java code so it maybe generates something like:
javac -classpath . src/generated/ClassName.java -d ./bin
^
Note the space after the classpath (".").

You can use the javax.tools.JavaCompiler or JCI that wrap this functionality.

I recommend doing something like this:
String command = String.format(
"javac -classpath . src%1$sgenerated%1$s%2$s.java -d .%1$sbin",
File.separator,
tspClassName
);
LOG("Executing " + command);
//... exec(command) etc
... where LOG is whatever your logging framework uses to log the command to be executed. This will help debugging immensely, since it was pointed out that the command you built is ill-constructed.
Alternately you can also build the string using replace
String command =
"javac -classpath . src/generated/ClassName.java -d ./bin"
.replace("/", File.separator)
.replace("ClassName", tspClassName);
This is perhaps more readable.
On draining Process streams
OP's comment suggests that waitFor() never returns. This is likely caused by compilation errors/warnings in javac process.
From the API:
Because some native platforms only provide limited buffer size for standard input and output streams, failure to promptly write the input stream or read the output stream of the subprocess may cause the subprocess to block, and even deadlock.
You need to continuously drain the Process.getOutputStream() et.al.
See also
Java Puzzlers, Puzzle 82: Beer Blast
Related questions
Draining standard error in Java

I think the proper way to do this kind of work is programatically using the javax.tools API, not an external process:
JavaCompiler compiler = ToolProvider.getSystemJavaCompiler()
Reference:
ToolProvider.getSystemJavaCompiler()

The problem could be with the file location instead of using single value parameter for exec()
try 3 parameter method which has the command, environment and location as parameters which helps us to move to the specified location and execute the command
check 6 and 8 methods for reference
http://docs.oracle.com/javase/7/docs/api/java/lang/Runtime.html
Process compile = Runtime.getRuntime().exec("javac "+fname,null,new File(dir));

firstly you should use apache exec library if you want to use processes like that. Apache exec library makes things very easy.
Secondly you should print your std output and std error streams of your process which you are executing. Without them its no way to know whats being executed and what's it doing.
Thirdly, try to print the full cmd line which the process is executing. Copy that cmd line and try to run it manually. Most of the time you would find your issues this way.
And finally if your aim is just to compile a class / generate or modify a class file at runtime give this a good read and try. It has examples too. You could also try code generation / class manipulation libraries like BCEL, JavaAssist etc.
Best of luck.