Pass two separate arguments to ProcessBuilder instead of concatenating --arg1 and argumentValue:

ProcessBuilder builder = new ProcessBuilder("C:\\Python33\\python.exe",
                                            "-u",
                                            "C:\\...\\script.py,
                                            "--arg1",
                                            "argumentValue");

Otherwise the program to be executed will see a single argument --arg1 argumentValue that it does not recognise.

Usually when executing commands using ProcessBuilder, PATH variable is not taken into consideration. Your python C:/Machine_Learning/Text_Analysis/Ontology_based.py is directly working in your CMD shell because it can locate the python executable using the PATH variable. Please provide the absolute path to python command in your Java code. In below code replace <Absolute Path to Python> with the path to python command and its libraries. Usually it will something like C:\Python27\python in Windows by default

package text_clustering;

import java.io.*;

public class Similarity {

    /**
     * 
     * @param args
     * 
     */
    public static void main(String[] args){
        try{
            String pythonPath = "C:/Machine_Learning/Text_Analysis/Ontology_based.py";
            //String pythonExe = "C:/Users/AppData/Local/Continuum/Anaconda/python.exe";
            ProcessBuilder pb = new ProcessBuilder(Arrays.asList("<Absolute Path to Python>/python", pythonPath));
            Process p = pb.start();

            BufferedReader bfr = new BufferedReader(new InputStreamReader(p.getInputStream()));
            String line = "";
            System.out.println("Running Python starts: " + line);
            int exitCode = p.waitFor();
            System.out.println("Exit Code : "+exitCode);
            line = bfr.readLine();
            System.out.println("First Line: " + line);
            while ((line = bfr.readLine()) != null){
                System.out.println("Python Output: " + line);


            }

        }catch(Exception e){System.out.println(e);}
    }

}

Just give them as separate strings in the array, instead of combining the last two into "val_31 val_32":

String[] command = {"script.py", "run",
                    "-arg1", "val1", 
                    "-arg2", "val2" ,          
                    "-arg3" , "val_31", "val_32",
       };

Otherwise it will escape the space in between val_31 and val_32 because you are telling it that they're a single parameter. Incidentally, you can also use the varargs constructor and skip having to create an array, if you want:

ProcessBuilder probuilder = new ProcessBuilder( "script.py", "run",
                    "-arg1", "val1", 
                    "-arg2", "val2" ,          
                    "-arg3" , "val_31", "val_32");

You need to specify your python path:

run in your terminal: "which python3"

ProcessBuilder builder = new ProcessBuilder("your/python/path/python3","main.py","-rd ",selectedFile.getAbsolutePath());

You can check the ProcessBuilder documentation over at Sunoracle, but basically, you can run the interpreter for the scripting language and pass the script you want to run to it.

For example, let's say you have a script in /home/myuser/py_script.py, and python is in /usr/bin/

class ProcessRunner
{
    public static void main(String [] args)
    {
        ProcessBuilder pb = new ProcessBuilder("/usr/bin/python", "/home/myuser/py_script.py");
        Process p = pb.start();
    }
}

An extremely basic example, you can get fancier with changing the working directory and change the environment.

You can also construct ProcessBuilder with a String array or a subtype of List<String>. The first item in the list should be the program/executable you want to run, and all the following items are arguments to the program.

String pbCommand[] = { "/usr/bin/python", "/home/myuser/py_script.py" };
ProcessBuilder pb = new ProcessBuilder(pbCommand);
Process p = pb.start();

So if I understand your requirement, you want to invoke a class method in pdfFileScraper.py. The basics of doing this from the shell would be something akin to:

scraper=path/to/pdfFileScraper.py
dir_of_scraper=$(dirname $scraper)
export PYTHONPATH=$dir_of_scraper
python -c 'import pdfFileScraper; pdfFileScraper.ClassInScraper()'

What we do is get the directory of pdfFileScraper, and add it to the PYTHONPATH, then we run python with a command that imports the pdfFileScraper file as a module, which exposes all the methods and classes in the class in the namespace pdfFileScraper, and then construct a class ClassInScraper().

In java, something like:

import java.io.*;
import java.util.*;

public class RunFile {
    public static void main(String args[]) throws Exception {
        File f = new File(args[0]); // .py file (e.g. bob/script.py)

        String dir = f.getParent(); // dir of .py file
        String file = f.getName(); // name of .py file (script.py)
        String module = file.substring(0, file.lastIndexOf('.'));
        String command = "import " + module + "; " + module + "." + args[1];
        List<String> items = Arrays.asList("python", "-c", command);
        ProcessBuilder pb = new ProcessBuilder(items);
        Map<String, String> env = pb.environment();
        env.put("PYTHONPATH", dir);
        pb.redirectErrorStream();
        Process p = pb.start();

        BufferedReader bfr = new BufferedReader(new InputStreamReader(p.getInputStream()));
        String line = "";
        System.out.println("Running Python starts: " + line);
        int exitCode = p.waitFor();
        System.out.println("Exit Code : " + exitCode);
        line = bfr.readLine();
        System.out.println("First Line: " + line);
        while ((line = bfr.readLine()) != null) {
            System.out.println("Python Output: " + line);
        }
    }
}

When you spawn a process from another process, they can only (mostly rather) communicate through their input and output streams. Thus you cannot expect the return value from main33() in python to reach Java, it will end its life within Python runtime environment only. In case you need to send something back to Java process you need to write that to print().

Modified both of your python and java code snippets.

import sys
def main33():
    print("This is what I am looking for")

if __name__ == '__main__':
    globals()[sys.argv[1]]()
    #should be 0 for successful exit
    #however just to demostrate that this value will reach Java in exit code
    sys.exit(220)

public static void main(String[] args) throws Exception {       
        String filePath = "D:\\test\\test.py";      
        ProcessBuilder pb = new ProcessBuilder()
            .command("python", "-u", filePath, "main33");        
        Process p = pb.start(); 
        BufferedReader in = new BufferedReader(
            new InputStreamReader(p.getInputStream()));
        StringBuilder buffer = new StringBuilder();     
        String line = null;
        while ((line = in.readLine()) != null){           
            buffer.append(line);
        }
        int exitCode = p.waitFor();
        System.out.println("Value is: "+buffer.toString());                
        System.out.println("Process exit value:"+exitCode);        
        in.close();
    }