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MedCoQuery.java
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Mon, Dec 2, 19:58

MedCoQuery.java
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/*
* Copyright (c) 2006-2007 Massachusetts General Hospital
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the i2b2 Software License v1.0
* which accompanies this distribution.
*
* Contributors:
* Rajesh Kuttan
*/
package ch.epfl.lca1.medco;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import ch.epfl.lca1.medco.dao.MedCoDatabase;
import ch.epfl.lca1.medco.i2b2.crc.I2B2CRCCell;
import ch.epfl.lca1.medco.i2b2.crc.I2B2QueryResponse;
import ch.epfl.lca1.medco.unlynx.UnlynxClient;
import ch.epfl.lca1.medco.unlynx.UnlynxQuery;
import ch.epfl.lca1.medco.unlynx.UnlynxQueryResult;
import ch.epfl.lca1.medco.util.Logger;
import ch.epfl.lca1.medco.util.MedCoUtil;
import ch.epfl.lca1.medco.util.StopWatch;
import ch.epfl.lca1.medco.util.exceptions.MedCoException;
import ch.epfl.lca1.medco.i2b2.crc.I2B2QueryRequest;
//
import edu.harvard.i2b2.common.exception.I2B2Exception;
import edu.harvard.i2b2.common.util.jaxb.JAXBUtilException;
import edu.harvard.i2b2.crc.datavo.setfinder.query.PanelType;
import edu.harvard.i2b2.crc.datavo.setfinder.query.QueryDefinitionRequestType;
import edu.harvard.i2b2.crc.datavo.setfinder.query.QueryDefinitionType;
import org.javatuples.Pair;
//todo doc: https://github.com/chb/shrine/tree/master/doc
/**
* Represents a query to MedCo.
* From the XML query (in CRC format), parse to extract the sensitive attributes,
* make query to CRC for non-sensitive attributes, get the patient set from CRC,
* query the cothority with the patient sets and sensitive attributes and answer.
*
* Setfinder query request delegate class $Id: QueryRequestDelegate.java,v 1.17
* 2008/05/08 15:13:45 rk903 Exp $
*
* @author rkuttan
*/
public class MedCoQuery {
private static final String QUERY_ITEM_KEY_ENC_PREFIX = "MEDCO_ENC:",
QUERY_ITEM_KEY_GEN_PREFIX = "MEDCO_GEN:";
/** The original request from client. **/
private I2B2QueryRequest queryRequest;
/** The original XML request from client (a query definition) extracted as XML. **/
private QueryDefinitionRequestType originalRequestXml;
private I2B2CRCCell crcCell;
private MedCoDatabase medcoDao;
public MedCoQuery(I2B2QueryRequest request) throws I2B2Exception {
this.queryRequest = request;
crcCell = new I2B2CRCCell(request.getUserAuthentication());
medcoDao = new MedCoDatabase();
}
/**
*
* @return the query answer in CRC XML format.
* @throws JAXBUtilException
*/
// todo: handle cases: only clear no encrypt / only encrypt no clear
public I2B2QueryResponse executeQuery(int resultMode, String clientPubKey, long timoutSeconds) throws MedCoException, I2B2Exception {
// retrieve the encrypted query terms
StopWatch.steps.start("Query parsing/splitting");
Pair<List<String>, String> encryptedItemsAndPredicate = extractEncryptedQueryTermsAndPredicate();
List<String> encryptedItems = encryptedItemsAndPredicate.getValue0();
String predicate = encryptedItemsAndPredicate.getValue1();
StopWatch.steps.stop();
// make query to i2b2 with the leftovers clear query terms, creates patient set on server side
StopWatch.steps.start("Clear query: i2b2 query");
I2B2QueryResponse clearResponse = crcCell.queryClearTerms(queryRequest);
StopWatch.steps.stop();
// predicate empty: means that there is no encrypted query terms, we can stop here the processing
if (predicate.isEmpty()) {
clearResponse.resetResultInstanceListToClearCountOnly();
clearResponse.setQueryResults("", "", StopWatch.generateAllCsvReports(null));
Logger.info("Query clear only successful (" + queryRequest.getQueryName() + ").");
return clearResponse;
}
StopWatch.steps.start("Clear query: patient set retrieval");
List<String> clearPatientSet = crcCell.queryForPatientSet(clearResponse.getPatientSetId());
StopWatch.steps.stop();
// retrieve encrypted data of the patients
StopWatch.steps.start("Patient set encrypted data retrieval");
List<List<String>> patientsEncData = medcoDao.getPatientsData(clearPatientSet);
//List<List<String>> patientsEncData = new ArrayList<>();
//List<String> tempTest = new ArrayList<>();
//tempTest.add("ZwneoQQyvDUckDcxlOvS+1IvDckXgw7n13IpznyAcHaU6r3uHuSZOXFHUHxhqINh0q6PFj9htw4Ogrt0TR7b5w=="); //todo: change me for 6/9/10!
//patientsEncData.add(tempTest);
StopWatch.steps.stop();
// query unlynx
StopWatch.steps.start("Unlynx query");
UnlynxQuery unlynxQuery = new UnlynxQuery(
queryRequest.getQueryName(),
predicate,
encryptedItems,
patientsEncData,
clientPubKey,
resultMode,
timoutSeconds
);
UnlynxClient unlynxClient = UnlynxClient.executeQuery(unlynxQuery);
unlynxClient.waitForCompletion();
UnlynxQueryResult queryResult = unlynxClient.getQueryResult();
if (unlynxClient.getQueryState() == UnlynxClient.QueryState.COMPLETED) {
Logger.info("MedCo query successful (" + queryRequest.getQueryName() + ").");
} else {
throw Logger.error(new MedCoException("Error during MedCo query: " + queryResult.getErrorMessage()));
}
StopWatch.steps.stop();
StopWatch.overall.stop();
clearResponse.resetResultInstanceListToEncryptedCountOnly();
clearResponse.setQueryResults(clientPubKey, queryResult.getEncResultB64(), StopWatch.generateAllCsvReports(queryResult.getTimes()));
return clearResponse;
}
/**
* Extracts from the i2b2 query the sensitive / encrypted items.
*
* They are the items with a non standard name of "MEDCO_ENC" or "MEDCO_GEN"
* enforce that panel are exclusive!! at least for now
*
// from panel - items to
// (exists(v0, r) || exists(v1, r)) &amp;&amp; (exists(v2, r) || exists(v3, r)) &amp;&amp; exists(v4, r)
* todo: must be modified if invertion implementation
*
* @throws MedCoException if a panel contains mixed clear and encrypted query terms
*/
private Pair<List<String>, String> extractEncryptedQueryTermsAndPredicate() throws MedCoException {
QueryDefinitionType qd = queryRequest.getQueryDefinition();
StringWriter predicateSw = new StringWriter();
List<String> extractedItems = new ArrayList<>();
int encTermCount = 0;
// regex that matches with encrypted query terms
Pattern medcoKeyRegex = Pattern.compile("^(\\s*)(" + QUERY_ITEM_KEY_ENC_PREFIX + "|" + QUERY_ITEM_KEY_GEN_PREFIX + ")(.*)");
// iter on the panels
for (int p = 0 ; p < qd.getPanel().size() ; p++) {
boolean panelIsEnc = false, panelIsClear = false;
PanelType panel = qd.getPanel().get(p);
// iter on the items
int nbItems = panel.getItem().size();
for (int i = 0 ; i < nbItems ; i++) {
// check if item is clear or encrypted, extract and generate predicate if yes
Matcher medcoKeyMatcher = medcoKeyRegex.matcher(panel.getItem().get(i).getItemKey());
if (medcoKeyMatcher.matches()) {
if (i == 0) {
predicateSw.append("(");
}
extractedItems.add(medcoKeyMatcher.group(3));
predicateSw.append("exists(v" + encTermCount++ + ", r)");
if (i < nbItems - 1) {
predicateSw.append(" || ");
} else if (i == nbItems - 1) {
predicateSw.append(")");
if (p < qd.getPanel().size() - 1) {
predicateSw.append(" &amp;&amp; ");
}
}
Logger.debug("Extracted item " + extractedItems.get(extractedItems.size() - 1));
panelIsEnc = true;
} else {
panelIsClear = true;
}
// enforce that a panel can only be one type
if (panelIsClear && panelIsEnc) {
throw Logger.error(new MedCoException("Encountered panel with mixed clear and encrypted query terms: not allowed."));
}
}
// remove panel and log
if (panelIsEnc) {
qd.getPanel().remove(panel);
p--;
Logger.debug("Encountered encrypted panel, removed");
} else if (panelIsClear) {
Logger.debug("Encountered clear panel");
} else {
Logger.warn("Encountered empty panel in query " + qd.getQueryName());
}
}
String predicate = predicateSw.toString();
Logger.info("Extracted " + extractedItems.size() + " encrypted query terms and generated unlynx predicate with " +
encTermCount + " terms: " + predicate + " for query " + queryRequest.getQueryName());
return new Pair<>(extractedItems, predicate);
}
}

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