Overhead IO : The cryptic case of the extra bytes

[john price]

Could resist the title sorry. Anyway, down to business. I wrote up a simple encoder/decoder program. For some reason, the decryption information always comes back with extra information. A sample of the program running is below. If I open the output file, it always contains some unreadable binary data, sometimes with extra spaces. The words show up fine, but there is extra data. Should I be using "ByteArrayOutputStream"?
If I print it out to the system, it shows up with extra spaces with every line, with no visible extra binary data. Please look at the bottom to see the weird results.
Here it is running :

cc11rocks@cc11rocks-1005HA ~/Desktop $ java EncryptTest 
Enter the 16 or 32 character password: qwertyuiopasdfgh
Thanks for the password!
Enter the file name to be encrypted: simple
Thanks for the file!
Enter the encrypted file name: simpleNotWorking
Thanks for the file name!
File Exists
Hello
This
Is
Wrote
Wrote
cc11rocks@cc11rocks-1005HA ~/Desktop $ java DecryptTest 
Enter the 16 or 32 character password: qwertyuiopasdfgh 
Thanks for the password!
Enter the file name to be decrypted: simpleNotWorking
Thanks for the file!
Enter the decrypted file name(output file) : output.ShouldBeWorking
Thanks for the file name!
Hello











This












Is
cc11rocks@cc11rocks-1005HA ~/Desktop $ 

I can edit out the unnecessary stuff if you want, but the code is relatively short so I won't bother unless you ask me too.

import java.security.*;
import javax.crypto.*;
import javax.crypto.spec.*;
import java.io.*;
import java.util.*;

public class EncryptTest {
String code, file, fileOut;
	public static void main(String[] args) throws Exception {
	EncryptTest tester = new EncryptTest();
	tester.start();
	}
	public void start () {
	System.out.print("Enter the 16 or 32 character password: ");

      BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
      
      try {
         code = br.readLine();
      } 
      catch (Exception ioe) {
      ioe.printStackTrace();
      }
	if (code.length() == 16 || code.length() == 32) {
      System.out.println("Thanks for the password!");
      }
      else {
      System.out.println("Password is not 16 or 32 characters long. Please restart the program manually");
      System.exit(2);
      }
      System.out.print("Enter the file name to be encrypted: ");
      BufferedReader br2 = new BufferedReader(new InputStreamReader(System.in));
      try {
      file = br2.readLine();
      }
      catch (Exception someEx) {
      someEx.printStackTrace();
      }
      System.out.println("Thanks for the file!");
      System.out.print("Enter the encrypted file name: ");
      BufferedReader br3 = new BufferedReader(new InputStreamReader(System.in));
      try {
      fileOut = br3.readLine();
      }
      catch (Exception someEx2) {
      someEx2.printStackTrace();
      }
      System.out.println("Thanks for the file name!");
	boolean exists = (new File(file)).exists();
	if (exists) {
		if (new File(file).isDirectory()) {
		System.out.println("This is a directory. Please restart the program and enter a file name.");
		}
		else {
		System.out.println("File Exists");
		}
	} 
	else {
	System.out.println("File was not found. Please restart the program");
	}
	ArrayList<String> strings = new ArrayList<String>();
	try {
        BufferedReader bufferedReader = new BufferedReader(new FileReader(file));
        String line = null;
        while ((line = bufferedReader.readLine()) != null) {
            strings.add(line);
        }
        bufferedReader.close();
        }
        catch (Exception t) {
        t.printStackTrace();
        }
        for (String test : strings) {
        System.out.println(test);
        }
        String[] args = strings.toArray(new String[strings.size()]);
		for (String lines : args) {
				if (lines == args[0]) {
					createFile(lines);
				}
				else {
					addToFile(lines);
				}
			
		}
	}
	public void createFile (String toEncode) {
	try {
	SecretKeySpec skeySpec = new SecretKeySpec(code.getBytes("UTF-8"), "AES");
		Cipher cipher = Cipher.getInstance("AES");
		cipher.init(Cipher.ENCRYPT_MODE, skeySpec);
		byte[] encrypted = cipher.doFinal(toEncode.getBytes("UTF-8"));
			OutputStream out = new FileOutputStream(fileOut);
			out.write(encrypted);
			out.close();
		}
		catch (Exception e){
			System.err.println("Error: " + e.getMessage());
		}
	}
	public void addToFile(String toEncode) {
	try {
	SecretKeySpec skeySpec = new SecretKeySpec(code.getBytes("UTF-8"), "AES");
		Cipher cipher = Cipher.getInstance("AES");
		cipher.init(Cipher.ENCRYPT_MODE, skeySpec);
		byte[] encrypted = cipher.doFinal(toEncode.getBytes("UTF-8"));
		byte[] spacer = cipher.doFinal(System.getProperty("line.separator").getBytes("UTF-8"));
			OutputStream out = new FileOutputStream(fileOut, true);
			out.write(spacer);
			System.out.println("Wrote");
			out.write(encrypted);
			out.close();
		}
		catch (Exception e){
			System.err.println("Error: " + e.getMessage());
		}
	}
}

import java.security.*;
import javax.crypto.*;
import javax.crypto.spec.*;
import java.io.*;
   
public class DecryptTest {
String code, file, fileOut;
	public static void main(String[] args) throws Exception {
	DecryptTest startItUP = new DecryptTest();
	startItUP.start();
	}
	public void start() throws Exception {
	System.out.print("Enter the 16 or 32 character password: ");

      BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
      
      try {
         code = br.readLine();
      } 
      catch (Exception ioe) {
      ioe.printStackTrace();
      }
	if (code.length() == 16 || code.length() == 32) {
      System.out.println("Thanks for the password!");
      }
      else {
      System.out.println("Password is not 16 or 32 characters long. Please restart the program manually");
      System.exit(2);
      }
      System.out.print("Enter the file name to be decrypted: ");
      BufferedReader br2 = new BufferedReader(new InputStreamReader(System.in));
      try {
      file = br2.readLine();
      }
      catch (Exception someEx) {
      someEx.printStackTrace();
      }
      System.out.println("Thanks for the file!");
      System.out.print("Enter the decrypted file name(output file) : ");
      BufferedReader br3 = new BufferedReader(new InputStreamReader(System.in));
      try {
      fileOut = br3.readLine();
      }
      catch (Exception someEx2) {
      someEx2.printStackTrace();
      }
      System.out.println("Thanks for the file name!");
		Cipher cipher = Cipher.getInstance("AES");
		SecretKeySpec skeySpec = new SecretKeySpec(code.getBytes("UTF-8"), "AES");
		cipher.init(Cipher.DECRYPT_MODE, skeySpec);
		InputStream in = new FileInputStream(new File(file));
		byte[] encrypted = new byte[(int)new File(file).length()];
		in.read(encrypted);
		in.close();
		byte[] original = cipher.doFinal(encrypted);
		String originalString = new String(original, "UTF-8");
		System.out.println(originalString);
		FileWriter output = new FileWriter(new File(fileOut));
		output.write(originalString);
		output.close();
	}
}

Here is the contents of "simple"

Hello
This
Is

Here is the contents of output.ShouldBeWorking :


Thank you very much. I hope you all have a very Merry Christmas and a Happy New Year
John Price

[Ireneusz Kordal]

Hi,

encrypt each line using cipher.update method instead of cipher.doFinal.
Call doFinal only on the last line (chunk of data).
Cipher.doFinal finishes the encryption - and probably fills the remaining space of a block by nulls or something else
(AES is a block encryption algorithm, as wiki says -> webpage it uses fixed 128-bits data block).
But update method appends the encrypted chunk to the block and continues the encryption.
Your encrypted file consist of several finished blocks of data created by doFinal , but you are reading this file by one call do doFinish.

Regards

[john price]

What do I use to start the output? If I put doFinal for the first line, it prints out a blank line and then just the first line. If I put update for the first line, it produces an empty file. If you are wondering what I am saying, look below (I did change it to make it easier and less lines of code) :

String[] args = strings.toArray(new String[strings.size()]);
		for (String lines : args) {
				if (lines == args[0]) {
					algorithm(lines, false, false, true); //toEncode, append, lastLine, firstLine
				}
				else {
					int tell = strings.indexOf(lines);
					System.out.println(tell);
					if (args[tell] + 1 != null) { //if "lines" isn't the last line...
					algorithm(lines, true, false, false); //toEncode, append, lastLine, firstLine
					}
					else {
					algorithm(lines, true, true, false); //toEncode, append, lastLine, firstLine
					}
				}
			
		}
	}
	public void algorithm (String toEncode, boolean append, boolean lastLine, boolean firstLine) {
	try {
		SecretKeySpec skeySpec = new SecretKeySpec(code.getBytes("UTF-8"), "AES");
		Cipher cipher = Cipher.getInstance("AES");
		cipher.init(Cipher.ENCRYPT_MODE, skeySpec);
		byte[] spacer = cipher.update(System.getProperty("line.separator").getBytes("UTF-8"));
		OutputStream out = new FileOutputStream(fileOut, append);
		if (!lastLine) {
		
		if (firstLine) {
		byte[] encrypted = cipher.doFinal(toEncode.getBytes("UTF-8")); //doFinal produces one blank line, followed by the first line only, and update produces nothing
		out.write(encrypted);
		out.close();
		}
		else {
		byte[] encrypted = cipher.update(toEncode.getBytes("UTF-8"));
		out.write(spacer);
		out.write(encrypted);
		out.close();
		}
		}
		else {
		byte[] encrypted = cipher.doFinal(toEncode.getBytes("UTF-8"));
		out.write(spacer);
		out.write(encrypted);
		out.close();
		}
	}
	catch (Exception ex) {
	ex.printStackTrace();
	}
	}

Thanks,
John Price

[Ireneusz Kordal]

Hi,

You don' need to bother with reading data byte by byte, with buffers, separators etc.
use CipherInputStream and CipherOutputStream instead.

       // encrypt the text and save to a file
       String code = "abcdefghabcdefgh";
        SecretKeySpec skeySpec = new SecretKeySpec(code.getBytes("UTF-8"), "AES");
        Cipher cipher = Cipher.getInstance("AES");
        cipher.init(Cipher.ENCRYPT_MODE, skeySpec);

        CipherOutputStream cos = new CipherOutputStream(new FileOutputStream("/tmp/file.cr"), cipher);
        PrintWriter prt = new PrintWriter(new OutputStreamWriter( cos, "utf-8"));

        prt.println("This");
        prt.println("is\na\ntest\n");
        prt.close();


        // print the decrypted text on the console
        skeySpec = new SecretKeySpec(code.getBytes("UTF-8"), "AES");
        cipher = Cipher.getInstance("AES");
        cipher.init(Cipher.DECRYPT_MODE, skeySpec);
        CipherInputStream cis = new CipherInputStream(new FileInputStream("/tmp/file.cr"), cipher);
        BufferedReader bufread = new BufferedReader( new InputStreamReader(cis, "utf-8") );
        
        String str;
        while( null != ( str = bufread.readLine())){
            System.out.println(str);
        }
        bufread.close();
        
        
        // save the decrypted text to the file
        skeySpec = new SecretKeySpec(code.getBytes("UTF-8"), "AES");
        cipher = Cipher.getInstance("AES");
        cipher.init(Cipher.DECRYPT_MODE, skeySpec);
        cis = new CipherInputStream(new FileInputStream("/tmp/file.cr"), cipher);
        Reader reader = new InputStreamReader(cis, "utf-8");
        Writer writer = new OutputStreamWriter( new FileOutputStream("/tmp/file.txt"), "utf-8");
        
        char buffer[] = new char[256];
        int count;
        while( (count = reader.read(buffer)) > 0 ){
            writer.write(buffer, 0, count);
        }
        reader.close();
        writer.close();

[john price]

I believe this is my last issue. I can't seem to properly read the lines in. It's reading the proper amount of lines (3 for the test case), but it's reading each line in as "null". Thank you very much for your suggestion Ireneusz Kordal. I tried it without reading a file in (the information being retrieved from the CLI), and it worked 100%. I then tried reading a file in, but my logic below if faulty somewhere. Everything else seems to work fine. Thanks very much. I hope you all had a great Christmas and have a happy new year!

private String getText() {
       	try {
       		System.out.println(file); //Outputting correct value
        	BufferedReader bufferedReader = new BufferedReader(new FileReader(file));
        	String line;
        	int numberOfLine = 0;
        	while ((line = bufferedReader.readLine()) != null) {
        	numberOfLine++;
        	}
        	data = new String[numberOfLine];
        	int i;
        	for (i = 0; i < numberOfLine; i++) {
        	data[i] = bufferedReader.readLine();
        	}
        }
        catch (Exception stupid) {
        	stupid.printStackTrace(); //No Errors
        }
        System.out.println(i); //Outputting correct value;
        StringBuffer oneString = new StringBuffer("");
        for (String oneIsLonly : data) {
        System.out.println(oneIsLonly); //Output "null" each for each line
        oneString.append("\n" + oneIsLonly);
        }
        return new String(oneString);
       	}

Thank you very much,
John Price

[Rob Spoor]

bufferedReader.readLine() moves the file position forward. Once it starts returning null it will return null forever. Use a List<String> instead of a String instead, and store the Strings as you encounter them:

private String getText() {
    try {
        System.out.println(file); //Outputting correct value
        BufferedReader bufferedReader = new BufferedReader(new FileReader(file));
        String line;
        int numberOfLine = 0;
        // data is no longer a String[] but a List<String>
        data = new ArrayList<String>();
        while ((line = bufferedReader.readLine()) != null) {
            numberOfLine++;
            data.add(line);
        }
    }
    catch (Exception stupid) {
        stupid.printStackTrace(); //No Errors
    }
    //StringBuffer oneString = new StringBuffer("");
    StringBuilder oneString = new StringBuilder(); // StringBuilder instead of StringBuffer, no initial content
    for (String oneIsLonly : data) {
        System.out.println(oneIsLonly); //Output what you expect now
        oneString.append("\n").append(oneIsLonly); // don't use + with StringBuffer / StringBuilder
    }
    //return new String(oneString);
    return oneString.toString(); // slightly better
}

You can (and should) even integrate the StringBuilder part into the first while loop.

[Paul Clapham]

Well, yeah. First you read all of the lines in from the BufferedReader, until it returns null. But you don't do anything with those lines. Then you call nextLine() again that same number of times, which of course continues to return null each time because you already read of the lines in the first loop. And this time you store the nulls in an array.

So what's that all about? Why not just read the lines and put them into a List? That would be much simpler and it might actually work.

[john price]

Thank you guys very much. I appreciate all the work that you did for me. I want to shout out a special thanks to Ireneusz Kordal for helping me out on this particular thread very much. Thank you Rob Spoor and Paul Clapham also! I will be separating this into separate programs for my integration with one of my projects, but here is the final test project that I have edited :

import java.security.*;
import javax.crypto.*;
import javax.crypto.spec.*;
import java.io.*;
import java.util.*;
public class Encrypt_Program {
SecretKeySpec skeySpec;
String code, file, fileOut;

       // encrypt the text and save to a file
       public static void main(String[] args) {
       Encrypt_Program encoder = new Encrypt_Program();
       encoder.encryptAndDecrypt();
       }
       	private String getText() {
       	ArrayList<String> info = new ArrayList<String>();
       	try {
       		System.out.println(file);
        	BufferedReader bufferedReader = new BufferedReader(new FileReader(file));
        	String line;
        	while ((line = bufferedReader.readLine()) != null) {
        	info.add(line);
        	}
        }
        catch (Exception stupid) {
        	stupid.printStackTrace();
        }
        StringBuilder oneString = new StringBuilder("");
        for (String oneIsLonly : info) {
        System.out.println(oneIsLonly);
        if (oneString.toString().equals("")) {
        oneString.append(oneIsLonly);
        }
        else {
        oneString.append("\n" + oneIsLonly);
        }
        }
        return new String(oneString);
       	}
	private void getInfo() {
	System.out.print("Enter the 16 or 32 character password: ");

      	BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
      
      	try {
        	code = br.readLine();
      	} 
      	catch (Exception ioe) {
      		ioe.printStackTrace();
      	}
	if (code.length() == 16 || code.length() == 32) {
     		System.out.println("Thanks for the password!");
      	}
      	else {
      		System.out.println("Password is not 16 or 32 characters long. Please restart the program manually");
      		System.exit(2);
      	}
      	System.out.print("Enter the file name to be encrypted: ");
      	BufferedReader br2 = new BufferedReader(new InputStreamReader(System.in));
      	try {
      		file = br2.readLine();
      	}
      	catch (Exception someEx) {
      		someEx.printStackTrace();
      	}
      	System.out.println("Thanks for the file!");
      	System.out.print("Enter the encrypted file name: ");
      	BufferedReader br3 = new BufferedReader(new InputStreamReader(System.in));
      	try {
      		fileOut = br3.readLine();
      	}
      	catch (Exception someEx2) {
      		someEx2.printStackTrace();
      	}
      	System.out.println("Thanks for the file name!");
	boolean exists = (new File(file)).exists();
	if (exists) {
		if (new File(file).isDirectory()) {
			System.out.println("This is a directory. Please restart the program and enter a file name.");
		}
		else {
			System.out.println("File Exists");
		}
	} 
	else {
		System.out.println("File was not found. Please restart the program");
	}
	}
	private void encryptAndDecrypt() {
	try {
	Cipher cipher = Cipher.getInstance("AES");
	getInfo();
	
	skeySpec = new SecretKeySpec(code.getBytes("UTF-8"), "AES");
	cipher.init(Cipher.ENCRYPT_MODE, skeySpec);

	CipherOutputStream cos = new CipherOutputStream(new FileOutputStream("temp.encrypted"), cipher);
	PrintWriter prt = new PrintWriter(new OutputStreamWriter(cos, "UTF-8"));
	prt.println(getText());
	prt.close();
        // print the decrypted text on the console
        cipher.init(Cipher.DECRYPT_MODE, skeySpec);
        CipherInputStream cis = new CipherInputStream(new FileInputStream("temp.encrypted"), cipher);
        BufferedReader bufread = new BufferedReader(new InputStreamReader(cis, "UTF-8") );
        
        String str;
        while(null != ( str = bufread.readLine())){
            System.out.println(str);
        }
        bufread.close();
        
        
        // save the decrypted text to the file
        skeySpec = new SecretKeySpec(code.getBytes("UTF-8"), "AES");
        cipher = Cipher.getInstance("AES");
        cipher.init(Cipher.DECRYPT_MODE, skeySpec);
        cis = new CipherInputStream(new FileInputStream("temp.encrypted"), cipher);
        Reader reader = new InputStreamReader(cis, "utf-8");
        Writer writer = new OutputStreamWriter(new FileOutputStream(fileOut), "UTF-8");
        
        char buffer[] = new char[256];
        int count;
        while( (count = reader.read(buffer)) > 0 ){
            writer.write(buffer, 0, count);
        }
        reader.close();
        writer.close();
        }
	catch (Exception ex) {
	ex.printStackTrace();
	}
        }
}

Happy new year,
John Price