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Reader.java
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Wed, Jan 8, 06:26

Reader.java
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package io.hla;
import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.math.BigInteger;
import java.sql.SQLException;
import java.util.ArrayList;
import javax.swing.JTextPane;
import javax.swing.text.BadLocationException;
import javax.swing.text.SimpleAttributeSet;
import javax.swing.text.StyleConstants;
import javax.swing.text.StyledDocument;
import crypto.CryptoException;
import crypto.paillier.PaillierScheme;
import database.DBconnector_server;
public class Reader implements Runnable{
private File input_f;
private BufferedReader br;
private DBconnector_server conn_s;
private String path_gprobs;
private String path_fam;
private JTextPane tp;
private StyledDocument doc;
public Reader(String gprobs, String fam, JTextPane txp){
conn_s = new DBconnector_server();
path_fam = fam;
path_gprobs = gprobs;
tp = txp;
doc = tp.getStyledDocument();
}
// /**
// * @param args
// * @throws IOException
// * @throws CryptoException
// * @throws SQLException
// */
// public static void main(String[] args) throws IOException, SQLException, CryptoException {
//
// Reader r = new Reader("C:\\Users\\raisaro\\Dropbox\\EPFL\\Genomic Privacy\\CHUV\\dataSet\\SHCS693.samples.26-04-13.HLA.bgl.gprobs",
// "C:\\Users\\raisaro\\Dropbox\\EPFL\\Genomic Privacy\\CHUV\\dataSet\\SHCS693.samples.26-04-13.HLA.fam", null);
// // hardcoded paths
// r.run();
// System.out.println("GPROBS file complete");
//
// }
@Override
public void run() {
try{
// conn_s.openConnection();
//check extension file for the FAM file
String[] pathCheck = path_fam.split("\\.");
if(!pathCheck[pathCheck.length-1].equalsIgnoreCase("fam")) {
throw new IOException("Wrong Format for FAM File!");
}
long start = System.currentTimeMillis();
SimpleAttributeSet attribute = new SimpleAttributeSet();
StyleConstants.setForeground(attribute, Color.BLACK);
try {
doc.insertString(doc.getLength(), "Analysing FAM File, please wait..." + "\n\n", attribute);
} catch (BadLocationException e1) {
e1.printStackTrace();
}
input_f = new File(path_fam);
br = new BufferedReader(new FileReader(input_f));
String newline;
ArrayList<Integer> IDs_p = new ArrayList<Integer>();
while((newline = br.readLine()) != null ){
String[] tokens = newline.split(" ");
int pat_id;
try{
pat_id = Integer.parseInt(tokens[0]);
}
catch(Exception e){
String[] subtokens = tokens[0].split("_");
pat_id = Integer.parseInt(subtokens[1]);
}
IDs_p.add(pat_id);
}
//check extension file for the GPROBS file
pathCheck = path_gprobs.split("\\.");
if(!pathCheck[pathCheck.length-1].equalsIgnoreCase("gprobs")) {
throw new IOException("Wrong Format for GPROBS File!");
}
try {
doc.insertString(doc.getLength(), "Parsing GRPOBS File, please wait..." + "\n", attribute);
} catch (BadLocationException e1) {
e1.printStackTrace();
}
input_f = new File(path_gprobs);
br = new BufferedReader(new FileReader(input_f));
double pp = 0d;
double pa = 0d;
// double aa;
ArrayList<String>[] p_hla = new ArrayList[IDs_p.size()];
for(int i = 0; i<IDs_p.size(); i++){
p_hla[i] = new ArrayList<String>();
}
while((newline = br.readLine()) != null){
String[] tokens = newline.split(" ");
for(int i = 0; i<IDs_p.size(); i++){
pp = Double.parseDouble(tokens[i*3+3]);
pa = Double.parseDouble(tokens[i*3+4]);
if(pp>0.8){
p_hla[i].add(tokens[0]);
p_hla[i].add(tokens[0]);
}else if(pa>0.8){
p_hla[i].add(tokens[0]);
}
}
}
BigInteger[] pbk;
PaillierScheme s;
try {
doc.insertString(doc.getLength(), "Encryption of HLA values, please wait..." + "\n", attribute);
} catch (BadLocationException e1) {
e1.printStackTrace();
}
for(int i=0; i<p_hla.length;i++){
String hla_a = "";
String hla_b = "";
String hla_c = "";
for(int j=0; j<p_hla[i].size(); j++){
// System.out.println(p_hla[i].get(j));
String[] tokens = p_hla[i].get(j).split("_");
if(tokens[1].equals("A") && tokens[2].length() == 4)
hla_a = hla_a.concat(tokens[2]).concat(";");
else if(tokens[1].equals("B") && tokens[2].length() == 4)
hla_b = hla_b.concat(tokens[2]).concat(";");
else if(tokens[1].equals("C") && tokens[2].length() == 4)
hla_c = hla_c.concat(tokens[2]).concat(";");
}
pbk = conn_s.getPublicKey(IDs_p.get(i));
s = new PaillierScheme(pbk[0],pbk[1],pbk[2]);
BigInteger[] enc_hla_A = s.encrypt(new BigInteger(hla_a.getBytes()));
BigInteger[] enc_hla_B = s.encrypt(new BigInteger(hla_b.getBytes()));
BigInteger[] enc_hla_C = s.encrypt(new BigInteger(hla_c.getBytes()));
conn_s.insertEncryptedHLA(IDs_p.get(i), enc_hla_A[0], enc_hla_A[1], enc_hla_B[0], enc_hla_B[1], enc_hla_C[0], enc_hla_C[1]);
}
long end = System.currentTimeMillis();
try {
doc.insertString(doc.getLength(), "Parsing GRPOBS File completed!" + "\n\n", attribute);
doc.insertString(doc.getLength(), (end-start) + " ms\n", attribute);
} catch (BadLocationException e1) {
e1.printStackTrace();
}
// conn_s.closeConnection();
}catch(IOException | NumberFormatException | CryptoException e){
e.printStackTrace();
SimpleAttributeSet error = new SimpleAttributeSet();
StyleConstants.setForeground(error, Color.RED);
try {
doc.insertString(doc.getLength(), e.getMessage() + "\n", error);
} catch (BadLocationException e1) {
e1.printStackTrace();
}
} catch (SQLException e) {
e.printStackTrace();
SimpleAttributeSet error = new SimpleAttributeSet();
StyleConstants.setForeground(error, Color.RED);
try {
doc.insertString(doc.getLength(), "No Connection with the Server" + "\n", error);
} catch (BadLocationException e1) {
e1.printStackTrace();
}
}
}
}

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