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);
        }
    }
}

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);}
    }

}

I don't think reading the executable (a series of binary numbers) will do any good. Also, The class java.lang.ProcessBuilder, in Java 1.5, is used to create operating system processe. Instead you should use the jython API: http://www.jython.org/javadoc/org/python/util/PythonInterpreter.html

Particularly: PyInstance and PythonInterpreter;

Try to use PrecessBuilder -

try{

   String prg = "import sys\nprint int(sys.argv[1])+int(sys.argv[2])\n";
   BufferedWriter out = new BufferedWriter(new FileWriter("test1.py"));
   out.write(prg);
   out.close();
   int number1 = 10;
   int number2 = 32;

   ProcessBuilder pb = new ProcessBuilder("python","test1.py",""+number1,""+number2);
   Process p = pb.start();

   BufferedReader in = new BufferedReader(new InputStreamReader(p.getInputStream()));
   int ret = new Integer(in.readLine()).intValue();
   System.out.println("value is : "+ret);
}catch(Exception e){System.out.println(e);}

See here from more detail.

Make sure you start python unbuffered with -u flag:

Force the binary layer of the stdout and stderr streams (which is available as their buffer attribute) to be unbuffered. The text I/O layer will still be line-buffered if writing to the console, or block-buffered if redirected to a non-interactive file.

Edit

I recommend reviewing the buffering all the same. The python unbuffered is a common one, but you possibly still have some buffering. Make sure you flush java writer, writer.flush().

I haven't found a solution yet, however I've implemented workaround/cleaner solution. I've decided to separate totally java and python code and created microservice for data retrieving. I use flask for rest webservice (followed this tutorial https://docs.dataplicity.com/docs/control-gpios-using-rest-api) and call it directly from java.
Since this does not resolve my initial question I do not mark it as an answer, however it might help someone.