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SecGene/GEN/src/core/edu/harvard/i2b2/gen/callable/unphased/FrequencyHomozygousReference.java
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FrequencyHomozygousReference.java
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package edu.harvard.i2b2.gen.callable.unphased;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Set;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import edu.harvard.i2b2.common.exception.I2B2Exception;
import edu.harvard.i2b2.gen.callable.QueryCallable;
import edu.harvard.i2b2.gen.data.QueryResult;
import edu.harvard.i2b2.gen.datavo.gen.GenomicQueryTypeType;
import edu.harvard.i2b2.gen.encoding.unphased.AlternativeEncoding;
import edu.harvard.i2b2.gen.encoding.unphased.RegularEncoding;
import edu.harvard.i2b2.gen.util.ConstantLookUp;
public class FrequencyHomozygousReference extends QueryCallable {
private static Log log = LogFactory.getLog(FrequencyHomozygousReference.class);
public FrequencyHomozygousReference(Set<Integer> degrees, long cid, String patientSet, int accessLevel) {
super(degrees, cid, patientSet, accessLevel);
log.debug("INIT : FrequencyHomozygousReference");
}
@Override
public QueryResult call() {
StringBuilder sb = new StringBuilder();
// *---Query to execute---*
// select a.no_calls, a.cipher_gt1, a.cipher_gt2, a.cipher_gt3
// from i2b2gen.gen_encrypted_genotypes a
// where a.cipher_id = ? and a.pid_gen in (select b.pid_gen
// from i2b2gen.gen_patient_mapping b
// where b.pid_i2b2 in (select c.patient_num
// from i2b2demodata.qt_patient_set_collection c
// where c.result_instance_id = ?)
// and not exists (select *
// from i2b2gen.gen_filter_patient_set d
//
// *---Similar query (no 'in')---*
// select a.no_calls, a.cipher_gt1, a.cipher_gt2, , a.cipher_gt3
// from i2b2gen.gen_encrypted_genotypes a, i2b2gen.gen_patient_mapping b, i2b2demodata.qt_patient_set_collection c
// where a.pid_gen=b.pid_gen and b.pid_i2b2=c.patient_num and a.cipher_id=? and c.result_instance_id=? and not exists (select *
// from i2b2gen.gen_filter_patient_set d
// where d.access_level=? and d.patient_group=b.patient_group))
try {
sb.append("select a.");
sb.append(ConstantLookUp.DS_GEN_GEN_ENCRYPTED_GENOTYPES_NO_CALLS);
sb.append(", a.");
sb.append(ConstantLookUp.DS_GEN_GEN_ENCRYPTED_GENOTYPES_CIPHER_GT1);
sb.append(", a.");
sb.append(ConstantLookUp.DS_GEN_GEN_ENCRYPTED_GENOTYPES_CIPHER_GT2);
sb.append(", a.");
sb.append(ConstantLookUp.DS_GEN_GEN_ENCRYPTED_GENOTYPES_CIPHER_GT3);
sb.append(" from ");
sb.append(ConstantLookUp.getInstance().getGENSchemaName());
sb.append('.');
sb.append(ConstantLookUp.DS_GEN_GEN_ENCRYPTED_GENOTYPES);
sb.append(" a where a.");
sb.append(ConstantLookUp.DS_GEN_GEN_ENCRYPTED_GENOTYPES_CIPHER_ID);
sb.append('=');
sb.append(cid);
sb.append(" and a.");
sb.append(ConstantLookUp.DS_GEN_GEN_ENCRYPTED_GENOTYPES_PID_GEN);
sb.append(" in (select b.");
sb.append(ConstantLookUp.DS_GEN_GEN_PATIENT_MAPPING_PID_GEN);
sb.append(" from ");
sb.append(ConstantLookUp.getInstance().getGENSchemaName());
sb.append('.');
sb.append(ConstantLookUp.DS_GEN_GEN_PATIENT_MAPPING);
sb.append(" b where ");
if (!patientSet.isEmpty()) {
sb.append("b.");
sb.append(ConstantLookUp.DS_GEN_GEN_PATIENT_MAPPING_PID_I2B2);
sb.append(" in (select c.");
sb.append(ConstantLookUp.DS_CRC_QT_PATIENT_SET_COLLECTION_PATIENT_NUM);
sb.append(" from ");
sb.append(ConstantLookUp.getInstance().getCRCSchemaName());
sb.append('.');
sb.append(ConstantLookUp.DS_CRC_QT_PATIENT_SET_COLLECTION);
sb.append(" c where c.");
sb.append(ConstantLookUp.DS_CRC_QT_PATIENT_SET_COLLECTION_RESULT_INSTANCE_ID);
sb.append('=');
sb.append(patientSet);
sb.append(") and ");
}
sb.append("not exists (select * from ");
sb.append(ConstantLookUp.getInstance().getGENSchemaName());
sb.append('.');
sb.append(ConstantLookUp.DS_GEN_GEN_FILTER_PATIENT_SET);
sb.append(" d where d.");
sb.append(ConstantLookUp.DS_GEN_GEN_FILTER_PATIENT_SET_ACCESS_LEVEL);
sb.append('=');
sb.append(this.accessLevel);
sb.append(" and d.");
sb.append(ConstantLookUp.DS_GEN_GEN_FILTER_PATIENT_SET_PATIENT_GROUP);
sb.append("=b.");
sb.append(ConstantLookUp.DS_GEN_GEN_PATIENT_MAPPING_PATIENT_GROUP);
sb.append("))");
log.info("Query : " + sb.toString());
Connection conn = null;
Statement st = null;
ResultSet res = null;
try {
conn = dsUtil.getDataSourceConnection(ConstantLookUp.getInstance().getDSName());
st = conn.createStatement();
res = st.executeQuery(sb.toString());
//######-----REGULAR ENCODING-----######
RegularEncoding regular= new RegularEncoding(res);
int arraySize = regular.getArraySize();
regular.setGt1(new long[arraySize]);
regular.setGt2(new long[arraySize]);
regular.setModulus2();
long[] sumAllSameNoCalls = new long[arraySize+1];
HashSet<Integer> zeros = new HashSet<Integer>();
//######--------------------------######
//######-----ALTERNATIVE ENCODING-----######
AlternativeEncoding alternative = new AlternativeEncoding(res);
alternative.setGt1(new long[arraySize]);
alternative.setGt2(new long[arraySize]);
alternative.setGt3(new long[arraySize]);
alternative.setModulus2();
alternative.setModulus3();
alternative.setModulus4();
long[] sumAllNumerator = new long[arraySize];
long[] sumAllDenominator = new long[arraySize];
//######--------------------------######
HashMap<HashSet<Integer>,long[]> sumByDegrees = new HashMap<HashSet<Integer>,long[]>();
sumByDegrees.put(new HashSet<Integer>(degrees), new long[arraySize*2+1]);
long modulus = regular.getModulus();
long tm = System.currentTimeMillis();
while (res.next()) {
byte[] bytes = res.getBytes(1);
if (bytes!=null){ //REGULAR ENCODING
regular.frequencyHomozygousReference(sumByDegrees, degrees, zeros, sumAllSameNoCalls);
regular.setUsed(true);
zeros.clear();
} else { //ALTERNATIVE ENCODING
alternative.frequencyHomozygousReference(sumAllNumerator,sumAllDenominator);
alternative.setUsed(true);
}
}
for (long[] v : sumByDegrees.values()) {
if(regular.isUsed()){
for (int i=0;i<arraySize;i++) {
v[i] = modulus-v[i]-sumAllSameNoCalls[i];
if (v[i] < 0)
v[i] += modulus;
}
v[arraySize] += sumAllSameNoCalls[arraySize];
}
if(alternative.isUsed()){
for (int i=0;i<arraySize;i++) {
v[i] += sumAllNumerator[i];
if (v[i] >= modulus)
v[i] -= modulus;
}
for (int i=arraySize+1,j=0;i<arraySize*2+1;i++,j++) {
v[i] += sumAllDenominator[j];
if (v[i] >= modulus)
v[i] -= modulus;
}
}
}
log.info("HOMOMORPHIC ADDITIONS : " + (System.currentTimeMillis()-tm) + " ms");
return new QueryResult(this.cid, sumByDegrees, GenomicQueryTypeType.HOMOZYGOUS_REFERENCE_FREQUENCY);
} catch (SQLException e) {
// Fail to connect to db
} finally {
try {
conn.close();
} catch (SQLException e) {
// do nothing
}
try {
st.close();
} catch (SQLException e) {
// do nothing
}
try {
res.close();
} catch (SQLException e) {
// do nothing
}
}
} catch (I2B2Exception ie) {
// fail to build query
}
return null;
}
}
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