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genopri-shcs/project/PPPClient/src/database/DBconnectorClient.java
09691ea9bb9edowngrade_java6

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DBconnectorClient.java
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package database;
import java.math.BigInteger;
import java.sql.Date;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.logging.Level;
import java.util.logging.Logger;
import crypto.elgamal.PartialSecret;
import framework.ClinicalFactor;
import framework.Marker;
import framework.WeightedMarker;
import framework.test.TestName;
public class DBconnectorClient extends DBConnection {
private static final Logger LOGGER = Logger.getLogger(DBconnectorClient.class.getName());
public DBconnectorClient(DatabaseConfig dbConfig) {
super(dbConfig, DatabaseDriverName.MYSQL);
}
public LinkedList<Integer> getPatients() throws SQLException{
openConnection();
LinkedList<Integer> patients = new LinkedList<Integer>();
preparedStmt = connect.prepareStatement("SELECT ID_p FROM " + database + ".patients");
resultSet = preparedStmt.executeQuery();
while(resultSet.next()){
patients.add(resultSet.getInt("ID_p"));
}
closeConnection();
return patients;
}
public HashMap<String, ArrayList<TestName>> getRelevantTestsByGroup() throws SQLException {
openConnection();
HashMap<String, ArrayList<TestName>> tests = new HashMap<String, ArrayList<TestName>>();
preparedStmt = connect.prepareStatement("SELECT ID_t, name, grp FROM " + database + ".tests WHERE ID_t < 100");
resultSet = preparedStmt.executeQuery();
while(resultSet.next()){
// retrieve current test
int testId = resultSet.getInt("ID_t");
String testName = resultSet.getString("name");
String testGroup = resultSet.getString("grp");
TestName currentTest = new TestName(testId, testName, testGroup);
// add test to hashmap
if (! tests.containsKey(testGroup)) {
tests.put(testGroup, new ArrayList<TestName>());
}
tests.get(testGroup).add(currentTest);
}
closeConnection();
return tests;
}
// @Deprecated
// public HashMap<String, LinkedList<TestName>> getTestsByGroup() throws SQLException {
// openConnection();
//
// HashMap<String, LinkedList<TestName>> tests = new HashMap<>();
//
// preparedStatement = connect.prepareStatement("SELECT ID_t, name, grp FROM " + database + ".tests");
// resultSet = preparedStatement.executeQuery();
// while(resultSet.next()){
// // retrieve current test
// int testId = resultSet.getInt("ID_t");
// String testName = resultSet.getString("name");
// String testGroup = resultSet.getString("grp");
// TestName currentTest = new TestName(testId, testName, testGroup);
//
// // add test to hashmap
// if (! tests.containsKey(testGroup)) {
// tests.put(testGroup, new LinkedList<TestName>());
// }
// tests.get(testGroup).add(currentTest);
// }
//
// closeConnection();
// return tests;
// }
public int getTestID(String desc) throws SQLException{
openConnection();
int ID_t = 0;
preparedStmt = connect.prepareStatement("SELECT ID_t FROM " + database + ".tests where name = ?");
preparedStmt.setString(1, desc);
resultSet = preparedStmt.executeQuery();
if(resultSet.next()){
ID_t = resultSet.getInt("ID_t");
}
closeConnection();
return ID_t;
}
public ArrayList<String> getTestGroup() throws SQLException{
openConnection();
ArrayList<String> groups = new ArrayList<String>();
preparedStmt = connect.prepareStatement("SELECT distinct(grp) as grp FROM " + database + ".tests");
resultSet = preparedStmt.executeQuery();
while(resultSet.next()){
groups.add(resultSet.getString("grp"));
}
closeConnection();
return groups;
}
public ArrayList<WeightedMarker> getMarkers(int ID_t) throws SQLException{
ArrayList<WeightedMarker> markers = new ArrayList<WeightedMarker>();
preparedStmt = connect.prepareStatement("SELECT ID_m, weight FROM " + database + ".m_t WHERE ID_t = ?");
preparedStmt.setInt(1, ID_t);
resultSet = preparedStmt.executeQuery();
while(resultSet.next()){
String markerId = resultSet.getString("ID_m");
double weight = resultSet.getDouble("weight");
markers.add(new WeightedMarker(new Marker(markerId), weight));
}
return markers;
}
public PartialSecret getPrivateKey(int ID_p) throws SQLException{
BigInteger prk = null;
preparedStmt = connect.prepareStatement("SELECT value FROM " + database + ".cryptokeys WHERE ID_p = ? AND isPublic = 0");
preparedStmt.setInt(1, ID_p);
resultSet = preparedStmt.executeQuery();
if(resultSet.next()){
prk = new BigInteger(resultSet.getString("value"));
}
return new PartialSecret(PartialSecret.PART_MU, prk);
}
public void insertMarker(String rs_code, String risk_allele, String ref_allele, int position, double maf, String chr) throws SQLException{
openConnection();
preparedStmt = connect.prepareStatement("SELECT * FROM " + database + ".markers WHERE rs = ?");
preparedStmt.setString(1, rs_code);
resultSet = preparedStmt.executeQuery();
if(!resultSet.next()){
preparedStmt = connect.prepareStatement("INSERT INTO " + database + ".markers (rs,chr,position,risk_allele,ref_allele,maf) VALUES (?,?,?,?,?,?)");
preparedStmt.setString(1, rs_code);
preparedStmt.setString(2, chr);
preparedStmt.setInt(3, position);
preparedStmt.setString(4, risk_allele);
preparedStmt.setString(5, ref_allele);
preparedStmt.setDouble(6, maf);
preparedStmt.executeUpdate();
closeConnection();
}
closeConnection();
}
public void insertKey(int ID_p, String key, boolean flag ) throws SQLException{
openConnection();
preparedStmt = connect.prepareStatement("INSERT INTO " + database + ".cryptokeys (ID_p,value,isPublic) VALUES (?,?,?)");
preparedStmt.setInt(1, ID_p);
preparedStmt.setString(2, key);
preparedStmt.setBoolean(3, flag);
preparedStmt.executeUpdate();
closeConnection();
}
public void insertPatient(int ID_p, String name, String last_name, String sex, Date birthdate) throws SQLException{
openConnection();
preparedStmt = connect.prepareStatement("SELECT * FROM " + database + ".patients WHERE ID_p = ?");
preparedStmt.setInt(1, ID_p);
resultSet = preparedStmt.executeQuery();
if(!resultSet.next()){
preparedStmt = connect.prepareStatement("INSERT INTO " + database + ".patients VALUES (?,?,?,?,?)");
preparedStmt.setInt(1, ID_p);
preparedStmt.setString(2, name);
preparedStmt.setString(3, last_name);
preparedStmt.setString(4, sex);
preparedStmt.setDate(5, birthdate);
preparedStmt.executeUpdate();
}
// closeConnection();
}
public String[] getAlleles(String rs_code) throws SQLException{
String[] result = new String[2];
// openConnection();
preparedStmt = connect.prepareStatement("SELECT risk_allele, ref_allele FROM " + database + ".markers WHERE rs = ?");
preparedStmt.setString(1, rs_code);
resultSet = preparedStmt.executeQuery();
if(resultSet.next()){
result[0] = resultSet.getString("risk_allele");
result[1] = resultSet.getString("ref_allele");
}
return result;
}
public double[] getQuartiles(int id_t) {
openConnection();
double second = 0;
double median = 0;
double third = 0;
try {
preparedStmt = connect
.prepareStatement("SELECT 2nd,median,3rd FROM " + database + ".quartile_dist WHERE ID_t = ?");
preparedStmt.setInt(1, id_t);
resultSet = preparedStmt.executeQuery();
while (resultSet.next()) {
second = resultSet.getDouble("2nd");
median = resultSet.getDouble("median");
third = resultSet.getDouble("3rd");
}
} catch (SQLException e) {
Logger.getLogger(DBconnectorClient.class.getName()).log(Level.SEVERE, null, e);
e.printStackTrace();
}
closeConnection();
double[] result = { second, median, third };
return result;
}
public void insertResult(int id_p, int id_t, double result) {
openConnection();
LOGGER.log(Level.FINER, "putting result");
try {
preparedStmt = connect
.prepareStatement("INSERT INTO " + database + ".results (ID_t, ID_p, result, date) VALUES (?,?,?,?)");
preparedStmt.setInt(1, id_t);
preparedStmt.setInt(2, id_p);
preparedStmt.setDouble(3, result);
preparedStmt.setDate(4, new Date(System.currentTimeMillis()));
preparedStmt.executeUpdate();
} catch (SQLException e) {
Logger.getLogger(DBconnectorClient.class.getName()).log(Level.SEVERE, null, e);
e.printStackTrace();
}
closeConnection();
}
public ArrayList<ClinicalFactor> getCFs(int ID_t) {
ArrayList<ClinicalFactor> cfs = new ArrayList<ClinicalFactor>();
try{
preparedStmt = connect.prepareStatement("SELECT ID_cf, weight FROM " + database + ".cf_t WHERE ID_t = ?");
preparedStmt.setInt(1, ID_t);
resultSet = preparedStmt.executeQuery();
while (resultSet.next()) {
int cfId = resultSet.getInt("ID_cf");
double weight = resultSet.getDouble("weight");
cfs.add(new ClinicalFactor(cfId, weight));
}
}catch(SQLException e) {
Logger.getLogger(DBconnectorClient.class.getName()).log(Level.SEVERE, null, e);
e.printStackTrace();
}
return cfs;
}
}
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