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UnlynxQuery.java
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Sat, Nov 30, 16:51

UnlynxQuery.java
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package ch.epfl.lca1.medco.unlynx;
import java.util.List;
/**
* Container class for an Unlynx query.
* Given java type input, format into an Unlynx XML Query.
*/
public class UnlynxQuery {
/** Name / ID of the query. */
private String queryId;
/** Predicate to be queried. */
private String predicate;
/** Ordered list of the encrypted where values of the query. */
private List<String> encWhereValuesB64;
/** List of patients, each patients having rows of encrypted (and base64 encoded) data. */
private List<List<String>> encPatientsDataB64;
/** Public key of the client, encoded in base64. */
private String clientPublicKeyB64;
/** Result mode of the query (0: 1 result / DP, 1: all DP have same aggregation). */
private int resultMode;
/** Maximum time (in second) the query should run. */
private long timeoutSeconds;
// TODO: easier constructor
//public UnlynxQuery(I2B2QueryRequest i2b2Query) {
//this(i2b2Query.getName(), i2b2Query.generateUnlynxPredicate)
//this.encWhereValues = encWhereValues;
//this.aggregatingAttributes = "s1";
//this.countFlag = "false";
//}
/**
* Default constructor, filling all fields of the query.
*
* @param queryId the name of the query
* @param predicate the predicate
* @param encWhereValuesB64 the encrypted where values (base64 encoded)
* @param encPatientsDataB64 the encrypted patients data (base64 encoded)
* @param clientPublicKeyB64 the public key of the querier (base64 encoded)
* @param resultMode the result mode of the query (0 or 1)
* @param timeoutSeconds the maximum waiting time in seconds for the query
*/
public UnlynxQuery(String queryId, String predicate, List<String> encWhereValuesB64, List<List<String>> encPatientsDataB64,
String clientPublicKeyB64, int resultMode, long timeoutSeconds) {
this.queryId = queryId;
this.predicate = predicate;
this.encWhereValuesB64 = encWhereValuesB64;
this.encPatientsDataB64 = encPatientsDataB64;
this.clientPublicKeyB64 = clientPublicKeyB64;
this.resultMode = resultMode;
this.timeoutSeconds = timeoutSeconds;
}
/**
* Constructs from the encrypted where query values the string with the appropriate Unlynx format.
*
* @return unlynx - i2b2 formatted where query values.
*/
private String formatEncWhereValues() {
StringBuilder sb = new StringBuilder();
sb.append("{");
for (int i = 0 ; i < encWhereValuesB64.size() ; i++) {
sb.append("w" + (i+1) + ", ");
sb.append(encWhereValuesB64.get(i));
if (i < encWhereValuesB64.size() - 1) {
sb.append(", ");
}
}
sb.append("}");
return sb.toString();
}
/**
* Construct a string containing the query in XML format.
* Example:
*
* {@code
<medco_query>
<id>query ID</id>
<predicate>some predicate</predicate>
<enc_where_values>encrypted where query values</enc_where_values>
<enc_patients_data>
<patient>
<enc_data>enc</enc_data>
<enc_data>enc</enc_data>
<enc_data>enc</enc_data>
</patient>
<patient>
<enc_data>enc</enc_data>
<enc_data>enc</enc_data>
<enc_data>enc</enc_data>
</patient>
</enc_patients_data>
<client_public_key>base64 encoded key</client_public_key>
<result_mode> result mode (0 or 1)</result_mode>
</medco_query>
* }
*
* @return query in Unlynx-I2b2 XML format
*/
String toUnlynxI2b2XML() {
StringBuilder sb = new StringBuilder();
sb.append("<medco_query>\n");
sb.append("<id>" + getQueryID() + "</id>\n");
sb.append("<predicate>" + getPredicate() + "</predicate>\n");
sb.append("<enc_where_values>" + formatEncWhereValues() + "</enc_where_values>\n");
sb.append("<enc_patients_data>\n");
for (List<String> patientData : encPatientsDataB64) {
sb.append("<patient>\n");
for (String dataB64 : patientData) {
sb.append("<enc_data>" + dataB64 + "</enc_data>\n");
}
sb.append("</patient>\n");
}
sb.append("</enc_patients_data>\n");
sb.append("<client_public_key>" + getClientPublicKeyB64() + "</client_public_key>\n");
sb.append("<result_mode>" + getResultMode() + "</result_mode>\n");
sb.append("</medco_query>\n");
return sb.toString();
}
@Override
public String toString() {
return toUnlynxI2b2XML();
}
/**
* @return the query ID
*/
public String getQueryID() {
return queryId;
}
/**
* @return the predicate
*/
public String getPredicate() {
return predicate;
}
/**
* @return the encrypted where values
*/
public List<String> getEncWhereValues() {
return encWhereValuesB64;
}
/**
* @return the encrypted patients data
*/
public List<List<String>> getEncPatientsData() {
return encPatientsDataB64;
}
/**
* @return the querier's public key
*/
public String getClientPublicKeyB64() {
return clientPublicKeyB64;
}
/**
* @return the desired result mode of the query
*/
public int getResultMode() {
return resultMode;
}
/**
* @return the maximum waiting time in seconds to wait for the query execution
*/
public long getTimeoutSeconds() {
return timeoutSeconds;
}
}

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