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genopri-shcs/project/GenomicPrivacy(android)/GenomicPrivacy/src/FrameWork/Patient.java
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Patient.java
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package FrameWork;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.math.BigInteger;
import java.util.ArrayList;
import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import android.os.Environment;
import com.cedarsoftware.util.io.JsonReader;
import com.cedarsoftware.util.io.JsonWriter;
import crypto.CryptoException;
import crypto.Scheme;
public class Patient extends User {
private String name;
private String firstName;
private String birth;
private String vcf;
private JsonReader jsr;
private JsonWriter jsw;
private String[] clinicalFactors;
private User u;
private int id;
public Patient(int id, String name, JsonReader jsr, JsonWriter jsw,
String firstName, String birth, String vcf, String[] clinicalFactors) {
super(id, name, jsr,jsw);
this.id = id;
this.firstName = firstName;
this.birth = birth;
this.vcf = vcf;
this.clinicalFactors = clinicalFactors;
}
@SuppressWarnings("null")
public ClinicalFactorsTable checkClinicalFactors(RequestPatient rp) {
// check wich CF correspond to the disease into the request rp and
// return the result into a array of string
ClinicalFactorsTable cft = null;
// 1: check the corresponding CF of the disease X into rp
JSONObject json = new JSONObject();
try {
json.put("type", Type.CF1);
json.put("id_d", rp.getId_t());
} catch (JSONException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// 2: update the CF with these from the DB (checkbox so 1/0 for each CF)
// this is done in serverSide
// CF).
// 3: wait the table from the server
sendToSPU(json);
json = this.receiveFromSPU();
try {
JSONArray jsonArr = (JSONArray) json.get("clinicalString");
String[] clinicalFactor = new String[jsonArr.length()];
for (int i = 0; i < jsonArr.length(); i++) {
clinicalFactor[i] = jsonArr.getString(i);
}
jsonArr = (JSONArray) json.get("cfChecked");
boolean[] checked = new boolean[jsonArr.length()];
for (int i = 0; i < jsonArr.length(); i++) {
checked[i] = jsonArr.getBoolean(i);
}
jsonArr = (JSONArray) json.get("idCF");
ArrayList<Integer> idCF = new ArrayList<Integer>();
for (int i = 0; i < jsonArr.length(); i++) {
System.out.println(jsonArr.getInt(i));
idCF.add(Integer.parseInt(jsonArr.get(i).toString()));
}
cft = new ClinicalFactorsTable(clinicalFactor, checked, idCF);
} catch (JSONException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// 3:return the CF table to the GUI
return cft;
}
public void sendConsent(RequestPatient rp, boolean consent, ArrayList[] cfs) { // respond
// to
// MU, but
// in our
// case
// respond
// to the
// server
JSONObject json = new JSONObject();
try {
JSONArray idCF = new JSONArray();
JSONArray encCF = new JSONArray();
for (int i = 0; i < cfs[0].size(); i++) {
idCF.put(cfs[0].get(i));
}
BigInteger [][] enCFBig = new BigInteger[cfs[1].size()][2];
for (int i = 0; i < idCF.length(); i++) {
ArrayList<BigInteger[]> a = cfs[1];
BigInteger[] btab = a.get(i);
String s1 = btab[0].toString();
String s2 = btab[1].toString();
json.put("s1"+i,s1);
json.put("s2"+i,s2);
}
json.put("type", Type.CONSENT);
json.put("id_r", rp.getId_r());
json.put("consent", consent);
json.put("encCF",enCFBig);
json.put("idCF", idCF);
json.put("id_p", rp.getId_p());
//json.put("encCF", cfs);
} catch (JSONException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
this.sendToSPU(json);
}
public String getFirstName() {
return firstName;
}
public void setFirstName(String firstName) {
this.firstName = firstName;
}
public String getBirth() {
return birth;
}
public void setBirth(String birth) {
this.birth = birth;
}
public String getVcf() {
return vcf;
}
public void setVcf(String vcf) {
this.vcf = vcf;
}
public String[] getClinicalFactors() {
return clinicalFactors;
}
public void setClinicalFactors(String[] clinicalFactors) {
this.clinicalFactors = clinicalFactors;
}
public ClinicalFactorsTable fullfillClinicalFactors(ClinicalFactorsTable cft) {
// TODO Auto-generated method stub
JSONObject json = new JSONObject();
ArrayList[] al = new ArrayList[1];
JSONArray jsarr = new JSONArray(cft.getIdCF());
al[0] = cft.getIdCF();
try {
json.put("type", Type.CF2);
json.put("id_cfs", jsarr);
json.put("id_p", id);
} catch (JSONException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
System.out.println(json.toString());
sendToSPU(json);
json = receiveFromSPU(); // this is a string
String[] allEncVal = null;
try {
JSONArray jsonArrCFT = json.getJSONArray("cfts");
allEncVal = new String[jsonArrCFT.length()];
for (int i = 0; i < jsonArrCFT.length(); i++) {
allEncVal[i] = jsonArrCFT.getString(i);
}
} catch (JSONException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// load the keys
BigInteger[] keys = loadKeys(); // keys(n,g,h,x) where n,g,h are pubkey
// and x prvkey
Scheme scheme = new Scheme(keys[0], keys[1], keys[2], keys[3]);
// at this point we have a string[] like thise : id_cf, encval1,
// encval2, encval12, encval22 separated by ";"
// for each ID_cf, need to fullfill the table cft
// take the id_cf, decrypte the value, found the position in the table
boolean[] cFchecked = new boolean[cft.getIdCF().size()];
for (int i = 0; i < allEncVal.length; i++) {
if (allEncVal[i] == null) {
cFchecked[i] = false;
} else {
String[] encValString = allEncVal[i].split(";");
int id_cf = Integer.parseInt(encValString[0]);
BigInteger encVal1 = new BigInteger(encValString[1]);
BigInteger encVal2 = new BigInteger(encValString[3]);
BigInteger[] cipher = new BigInteger[2];
cipher[0] = encVal1;
cipher[1] = encVal2;
BigInteger dec = null;
try {
dec = scheme.decrypt(cipher);
} catch (CryptoException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
// dec is the value of the CF corresponding to id_cf
// found the position in the table cft.
for (int j = 0; j < cft.getIdCF().size(); j++) {
// System.out.println("j="+j);
boolean checkVal = false;
if (dec.intValue() == 0) {
checkVal = false;
} else if (dec.intValue() == 1) {
checkVal = true;
} else {
System.out.println("Value of dec not 0 or 1 : " + dec);
}
if (id_cf == cft.getIdCF().get(j)) {
cFchecked[i] = checkVal;
}
}
}
}
cft.setCFchecked(cFchecked);
return cft;
}
public BigInteger[] loadKeys() {
BigInteger[] keys = new BigInteger[4];
// read keys from file
File file = new File(Environment.getExternalStorageDirectory()
.getPath() + "/GenomicPrivacy/P_keys/" + id + "keys.txt");
BufferedReader br = null;
try {
br = new BufferedReader(new FileReader(file));
} catch (FileNotFoundException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
String pr1 = null;
try {
pr1 = br.readLine();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
String pr2 = null;
try {
pr2 = br.readLine();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
BigInteger X1 = new BigInteger(pr1);
BigInteger X2 = new BigInteger(pr2);
BigInteger X = X1.add(X2);
String pb = null;
try {
pb = br.readLine();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
String[] pbi = pb.split(",");
BigInteger N = new BigInteger(pbi[0]);
BigInteger G = new BigInteger(pbi[1]);
BigInteger H = new BigInteger(pbi[2]);
keys[0] = N;
keys[1] = G;
keys[2] = H;
keys[3] = X;
return keys;
}
public ArrayList[] updateCF(ArrayList[] cf) {
ArrayList[] cfarray = new ArrayList[2];
ArrayList<BigInteger[]> encCF = new ArrayList<BigInteger[]>();
// take the new values and encrypt them before sending to server
BigInteger[] keys = loadKeys(); // keys(n,g,h,x) where n,g,h are pubkey
// and x prvkey
Scheme scheme = new Scheme(keys[0], keys[1], keys[2], keys[3]);
for (int i = 0; i < cf[0].size(); i++) {
// int id_cf = (int)cf[0].get(i);
boolean val = (Boolean) cf[1].get(i);
BigInteger bigVal;
// encrypt the val
if (val == true) {
bigVal = BigInteger.valueOf(1);
} else {
bigVal = BigInteger.valueOf(0);
}
BigInteger[] encVal = null;
try {
encVal = scheme.encrypt(bigVal);
} catch (CryptoException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
encCF.add(encVal);
}
cfarray[0] = cf[0];
cfarray[1] = encCF;
return cfarray;
}
}
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