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SecGene/GEN/src/core/edu/harvard/i2b2/gen/util/LaplacianNoiseAdder.java
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LaplacianNoiseAdder.java
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package edu.harvard.i2b2.gen.util;
import java.security.SecureRandom;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.sql.Types;
import java.util.HashSet;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.harvard.i2b2.common.exception.I2B2Exception;
import edu.harvard.i2b2.gen.datavo.gen.GenomicQueryTypeType;
public class LaplacianNoiseAdder {
private static Log log = LogFactory.getLog(LaplacianNoiseAdder.class);
private int mu;
private double epsilon;
private DataSourceUtil dsUtil;
private Connection conn;
private SecureRandom sr;
private long bound;
private PreparedStatement getNoisyCount;
private PreparedStatement getNoisyResult;
private PreparedStatement insertEntry;
public LaplacianNoiseAdder(int mu, long bound, int accessLevel, String patientSet) throws I2B2Exception {
log.debug("INIT : LaplacianNoiseGenerator");
this.mu = mu;
this.sr = null;
this.bound = bound;
// Get epsilon for differential privacy
// Query to execute
// select a.epsilon
// from i2b2gen.gen_user_roles a
// where a.access_level = ?
StringBuilder sb = new StringBuilder();
sb.append("select a.");
sb.append(ConstantLookUp.DS_GEN_GEN_USER_ROLES_EPSILON);
sb.append(" from ");
sb.append(ConstantLookUp.getInstance().getGENSchemaName());
sb.append('.');
sb.append(ConstantLookUp.DS_GEN_GEN_USER_ROLES);
sb.append(" a where a.");
sb.append(ConstantLookUp.DS_GEN_GEN_USER_ROLES_ACCESS_LEVEL);
sb.append('=');
sb.append(accessLevel);
log.info("Query : " + sb.toString());
Statement st = null;
ResultSet queryResult = null;
try {
dsUtil = new DataSourceUtil();
conn = dsUtil.getDataSourceConnection(ConstantLookUp.getInstance().getDSName());
st = conn.createStatement();
queryResult = st.executeQuery(sb.toString());
if (queryResult.next())
epsilon = queryResult.getDouble(1);
} catch (SQLException e) {
// Fail to connect to db
// Set default epsilon
this.epsilon = 0.01;
} finally {
try {
st.close();
} catch (SQLException e) {
// do nothing
}
try {
queryResult.close();
} catch (SQLException e) {
// do nothing
}
}
if (this.epsilon != 0) {
try {
sb.setLength(0);
// Query to execute
// select a.count
// from i2b2gen.gen_noisy_result a
// where a.cipher_id=? and a.degree=? and a.access_level=? and a.patient_set_id=? and a.query_type=?
sb.append("select a.");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_COUNT);
sb.append(" from ");
sb.append(ConstantLookUp.getInstance().getGENSchemaName());
sb.append('.');
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT);
sb.append(" a where a.");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_CIPHER_ID);
sb.append("=? and a.");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_DEGREE);
sb.append("=? and a.");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_ACCESS_LEVEL);
sb.append("=? and a.");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_PATIENT_SET_ID);
sb.append("=? and a.");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_QUERY_TYPE);
sb.append("=?");
this.getNoisyCount = conn.prepareStatement(sb.toString());
getNoisyCount.setInt(3, accessLevel);
if (patientSet.isEmpty())
getNoisyCount.setInt(4, -1);
else
getNoisyCount.setInt(4, Integer.valueOf(patientSet));
sb.setLength(0);
// Query to execute
// select a.result
// from i2b2gen.gen_noisy_result a
// where a.cipher_id=? and a.degree=? and a.access_level=? and a.patient_set_id=? and a.query_type=?
sb.append("select a.");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_RESULT);
sb.append(" from ");
sb.append(ConstantLookUp.getInstance().getGENSchemaName());
sb.append('.');
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT);
sb.append(" a where a.");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_CIPHER_ID);
sb.append("=? and a.");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_DEGREE);
sb.append("=? and a.");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_ACCESS_LEVEL);
sb.append("=? and a.");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_PATIENT_SET_ID);
sb.append("=? and a.");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_QUERY_TYPE);
sb.append("=?");
this.getNoisyResult = conn.prepareStatement(sb.toString());
getNoisyResult.setInt(3, accessLevel);
if (patientSet.isEmpty())
getNoisyResult.setInt(4, -1);
else
getNoisyResult.setInt(4, Integer.valueOf(patientSet));
sb.setLength(0);
// Query to execute
// insert into i2b2gen.gen_noisy_result (cipher_id, degree, access_level, patient_set_id, query_type, count, result)
// values (?, ?, ?, ?, ?, ?, ?)
sb.append("insert into ");
sb.append(ConstantLookUp.getInstance().getGENSchemaName());
sb.append('.');
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT);
sb.append(" (");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_CIPHER_ID);
sb.append(", ");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_DEGREE);
sb.append(", ");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_ACCESS_LEVEL);
sb.append(", ");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_PATIENT_SET_ID);
sb.append(", ");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_QUERY_TYPE);
sb.append(", ");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_COUNT);
sb.append(", ");
sb.append(ConstantLookUp.DS_GEN_GEN_NOISY_RESULT_RESULT);
sb.append(") values (?, ?, ?, ?, ?, ?, ?)");
this.insertEntry = conn.prepareStatement(sb.toString());
insertEntry.setInt(3, accessLevel);
if (patientSet.isEmpty())
insertEntry.setInt(4, -1);
else
insertEntry.setInt(4, Integer.valueOf(patientSet));
} catch (SQLException e) {
log.info("Cannot connect to db");
}
} else {
this.getNoisyCount = null;
this.getNoisyResult = null;
this.insertEntry = null;
}
}
private long getNextLong(double sensitivity) {
log.debug("CALL : getNextLong");
if (epsilon == 0.0){
return 0L;
}
if (sr == null)
sr = new SecureRandom();
long value = bound + 1;
while (Math.abs(value) > bound) {
double u = sr.nextDouble()-0.5D;
value = Math.round(mu - sensitivity/this.epsilon*Math.signum(u)*Math.log(1-2*Math.abs(u)));
}
return value;
}
public long addNoise2Count(long count, long cipherId, HashSet<Integer> degrees, GenomicQueryTypeType qt) throws I2B2Exception {
if (this.epsilon == 0.0)
return count;
ResultSet res = null;
try {
getNoisyCount.setLong(1, cipherId);
getNoisyCount.setString(5, qt.name());
for (Integer d : degrees) {
getNoisyCount.setInt(2, d);
res = getNoisyCount.executeQuery();
if (res.next()) {
long noisyCount = res.getLong(1);
res.close();
return noisyCount;
}
res.close();
}
return count+this.getNextLong(1);
} catch(SQLException e) {
e.printStackTrace();
log.debug("Fail to insert noisy count into db");
} finally {
try {
res.close();
} catch (SQLException e) {
// do nothing
}
}
return count+this.getNextLong(1);
}
public long addNoise2Result(long result, long cipherId, int degree, GenomicQueryTypeType qt, long delta, long modulus, Long count) throws I2B2Exception {
if (this.epsilon == 0.0)
return result;
ResultSet res = null;
try {
getNoisyResult.setLong(1, cipherId);
getNoisyResult.setInt(2, degree);
getNoisyResult.setString(5, qt.name());
res = getNoisyResult.executeQuery();
if (res.next())
return res.getLong(1);
else {
long noisyResult = result+this.getNextLong(1)*delta;
if (noisyResult >= modulus)
noisyResult -= modulus;
else if (noisyResult < 0)
noisyResult += modulus;
insertEntry.setLong(1, cipherId);
insertEntry.setInt(2, degree);
insertEntry.setString(5, qt.name());
if (count == null)
insertEntry.setNull(6, Types.BIGINT);
else
insertEntry.setLong(6, count.longValue());
insertEntry.setLong(7, noisyResult);
insertEntry.execute();
return noisyResult;
}
} catch(SQLException e) {
e.printStackTrace();
log.info("Fail to insert noisy result into db");
} finally {
try {
res.close();
} catch (SQLException e) {
// do nothing
}
}
result += this.getNextLong(1)*delta;
if (result >= modulus)
result -= modulus;
return result;
}
public void close() {
try {
this.getNoisyCount.close();
} catch (SQLException e) {
// do nothing
} catch (NullPointerException e){
// do nothing
}
try {
this.getNoisyResult.close();
} catch (SQLException e) {
// do nothing
} catch (NullPointerException e){
// do nothing
}
try {
this.insertEntry.close();
} catch (SQLException e) {
// do nothing
} catch (NullPointerException e){
// do nothing
}
try {
this.conn.close();
} catch (SQLException e) {
// do nothing
}
}
}
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