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I2B2QueryResponse.java
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Thu, May 23, 11:24

I2B2QueryResponse.java
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package ch.epfl.lca1.medco.i2b2.crc;
import ch.epfl.lca1.medco.i2b2.I2b2Status;
import ch.epfl.lca1.medco.i2b2.MessagesUtil;
import ch.epfl.lca1.medco.util.Logger;
import ch.epfl.lca1.medco.util.MedCoUtil;
import ch.epfl.lca1.medco.util.XMLUtil;
import ch.epfl.lca1.medco.util.exceptions.I2B2XMLException;
import com.eclipsesource.json.Json;
import com.eclipsesource.json.JsonObject;
import com.eclipsesource.json.JsonValue;
import edu.harvard.i2b2.common.exception.I2B2Exception;
import edu.harvard.i2b2.common.util.jaxb.JAXBUtilException;
import edu.harvard.i2b2.crc.datavo.i2b2message.*;
import edu.harvard.i2b2.crc.datavo.setfinder.query.*;
import org.javatuples.Triplet;
import org.jdom.Document;
import org.jdom.Element;
import org.jdom.JDOMException;
import org.jdom.input.SAXBuilder;
import javax.xml.bind.JAXBContext;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.StringWriter;
import java.nio.charset.Charset;
/**
* Created by misbach on 15.07.17.
*/
public class I2B2QueryResponse extends ResponseMessageType {
private static MedCoUtil util = MedCoUtil.getInstance();
private static MessagesUtil msgUtil = MedCoUtil.getMsgUtil();
private MasterInstanceResultResponseType parsedBody;
private QueryResultInstanceType resultPatientSet;
private QueryResultInstanceType resultPatientCount;
private String encCountResult;
private static edu.harvard.i2b2.crc.datavo.i2b2message.ObjectFactory i2b2OF =
new edu.harvard.i2b2.crc.datavo.i2b2message.ObjectFactory();
private static edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory querySetFinderOF =
new edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory();
// todo: centralize somewhere all hardcoded XML tags
private static final String JSON_RESULT_XML_TAG_START = "<json_results>",
JSON_RESULT_XML_TAG_END = "</json_results>";
public I2b2Status getI2b2Status() throws I2B2XMLException {
return msgUtil.parseStatus(this);
}
/**
* Extract only the first result type (between PATIENT_SET and PATIENT_COUNT_XML) from the results.
* Verficication made by the caller.
*/
private void extractResults() throws I2B2Exception {
// extract instance result and check status
for (QueryResultInstanceType queryResultInstance : parsedBody.getQueryResultInstance()) {
QueryStatusTypeType queryStatus = queryResultInstance.getQueryStatusType();
Logger.info("Status of query " + parsedBody.getQueryMaster().getName() + " is " + queryStatus.getName() + " / " + queryStatus.getStatusTypeId());
if (!queryStatus.getStatusTypeId().trim().equals("3")) {
throw Logger.error(new I2B2Exception("I2b2 query does not have the finished status: " + queryStatus.getName() + " / " + queryStatus.getStatusTypeId()));
}
// result type id = 1 ==> type "PATIENTSET"
// result type id = 4 ==> type "PATIENT_COUNT_XML"
if (resultPatientSet == null && queryResultInstance.getQueryResultType().getResultTypeId().trim().equals("1")) {
resultPatientSet = queryResultInstance;
} else if (resultPatientCount == null && queryResultInstance.getQueryResultType().getResultTypeId().trim().equals("4")) {
resultPatientCount = queryResultInstance;
}
}
}
/**
* Server side constructor
*
* @param queryReqResponse
* @throws I2B2Exception
*/
public I2B2QueryResponse(ResponseMessageType queryReqResponse) throws I2B2Exception {
setMessageBody(queryReqResponse.getMessageBody());
setMessageHeader(queryReqResponse.getMessageHeader());
setRequestHeader(queryReqResponse.getRequestHeader());
setResponseHeader(queryReqResponse.getResponseHeader());
// attempt to bug fix: https://stackoverflow.com/questions/377865/intermittent-classcastexception-from-elementnsimpl-to-own-type-during-unmarshall
synchronized (JAXBContext.class) {
try {
parsedBody = (MasterInstanceResultResponseType) msgUtil.getUnwrapHelper().getObjectByClass(
getMessageBody().getAny(), MasterInstanceResultResponseType.class);
} catch (ClassCastException | JAXBUtilException e) {
throw Logger.error(new I2B2XMLException("JAXB unwrap failed.", e));
}
extractResults();
}
Logger.info("Query " + parsedBody.getQueryMaster().getName() + " result: patient set id = " + getPatientSetId() + ", size = " + getPatientSetSize());
}
public String getPatientSetId() {
return resultPatientSet == null ? null : resultPatientSet.getResultInstanceId();
}
public int getPatientSetSize() {
return resultPatientSet == null ? -1 : resultPatientSet.getSetSize();
}
public int getPatientCount() {
return resultPatientCount == null ? -1 : resultPatientCount.getSetSize();
}
public void resetResultInstanceListToClearCountOnly() {
parsedBody.getQueryResultInstance().clear();
parsedBody.getQueryResultInstance().add(resultPatientCount);
}
public void resetResultInstanceListToEncryptedCountOnly() {
parsedBody.getQueryResultInstance().clear();
// copy most of the fields value from the original count result
QueryResultInstanceType resultInstance = querySetFinderOF.createQueryResultInstanceType();
resultInstance.setResultInstanceId(resultPatientCount.getResultInstanceId());
resultInstance.setQueryInstanceId(resultPatientCount.getQueryInstanceId());
resultInstance.setDescription(resultPatientCount.getDescription());
resultInstance.setQueryResultType(resultPatientCount.getQueryResultType());
resultInstance.setObfuscateMethod(resultPatientCount.getObfuscateMethod());
resultInstance.setStartDate(resultPatientCount.getStartDate());
resultInstance.setEndDate(resultPatientCount.getEndDate());
resultInstance.setQueryStatusType(resultPatientCount.getQueryStatusType());
// override 2 specific fields: set size and message (contains the encrypted count)
XmlValueType xml = querySetFinderOF.createXmlValueType();
resultInstance.setMessage(xml);
resultInstance.setSetSize(-1);
parsedBody.getQueryResultInstance().add(resultInstance);
}
/**
* Sets the encrypted count value both in the class field and into the response XML message.
* The
* @param pubKey
* @param encResult
* @throws I2B2Exception
*/
public void setQueryResults(String pubKey, String encResult, JsonObject times) throws I2B2Exception {
this.encCountResult = encResult;
XmlValueType xml = parsedBody.getQueryResultInstance().get(0).getMessage();
JsonObject jsonResults = Json.object()
.add("pub_key", Json.value(pubKey))
.add("enc_count_result", Json.value(encResult))
.add("times", times);
xml.getContent().add(JSON_RESULT_XML_TAG_START + jsonResults.toString() + JSON_RESULT_XML_TAG_END);
Logger.debug("MedCo results string is " + jsonResults.toString());
Logger.info("Query results set for query " + parsedBody.getQueryMaster().getName());
}
public String getEncCountResult() {
return encCountResult;
}
// todo: put hardcoded xml tags as fields (also in setqueryresults)
public Triplet<String, String, String> getQueryResults() throws I2B2XMLException {
XmlValueType xml = parsedBody.getQueryResultInstance().get(0).getMessage();
if (xml.getContent().size() != 1) {
Logger.warn("Incorrect number of values inside message.");
}
String unescapedResult = XMLUtil.unEscapeXmlValue((String) xml.getContent().get(0));
String jsonResultString = unescapedResult.substring(unescapedResult.indexOf(
JSON_RESULT_XML_TAG_START) + JSON_RESULT_XML_TAG_START.length(),
unescapedResult.lastIndexOf(JSON_RESULT_XML_TAG_END));
JsonObject jsonResult = Json.parse(jsonResultString).asObject();
String pubKey = jsonResult.getString("pub_key", "NOT_FOUND"),
encResult = jsonResult.getString("enc_count_result", "NOT_FOUND");
JsonObject times = jsonResult.get("times").asObject();
return new Triplet<>(pubKey, encResult, times.toString());
}
}

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