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medco-i2b2-cell/src/server/ch/epfl/lca1/medco/i2b2/crc/I2B2QueryRequest.java
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I2B2QueryRequest.java
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package ch.epfl.lca1.medco.i2b2.crc;
import java.util.List;
import ch.epfl.lca1.medco.i2b2.I2b2Status;
import edu.harvard.i2b2.crc.datavo.i2b2message.*;
import edu.harvard.i2b2.crc.datavo.setfinder.query.*;
import ch.epfl.lca1.medco.i2b2.MessagesUtil;
import ch.epfl.lca1.medco.i2b2.pm.UserAuthentication;
import ch.epfl.lca1.medco.util.Logger;
import ch.epfl.lca1.medco.util.MedCoUtil;
import edu.harvard.i2b2.common.exception.I2B2Exception;
import edu.harvard.i2b2.common.util.jaxb.JAXBUtilException;
import edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory;
import org.javatuples.Triplet;
/**
* Represents an I2B2 query request.
* Use for server side:
* Use for client side
*
* @author mickael
*
*/
public class I2B2QueryRequest extends RequestMessageType {
// live references to the 2 elements of the request body
private PsmQryHeaderType queryHeader;
private QueryDefinitionRequestType queryBody;
private UserAuthentication authentication;
private static final String I2B2_RESULT_OPTION_TYPE = "PATIENT_COUNT_XML";
private static MedCoUtil util = MedCoUtil.getInstance();
private static MessagesUtil msgUtil = util.getMsgUtil();
private static edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory querySetFinderOF =
new edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory();
private static edu.harvard.i2b2.crc.datavo.i2b2message.ObjectFactory i2b2OF =
new edu.harvard.i2b2.crc.datavo.i2b2message.ObjectFactory();
/**
* Used on server-side to parse an incoming request.
* Unmashall the query from string.
* Checks type is with query definition. (both in header annnnnnnd for the type of xml for qrequestbody)
*
* @param requestString
* @throws JAXBUtilException if the string could not be parsed / unmashalled
* @throws I2B2Exception if the request is of the wrong type
*/
public I2B2QueryRequest(String requestString) throws I2B2Exception {
try {
// JAXB parsing
RequestMessageType parsedRequest = msgUtil.parseI2b2Request(requestString);
authentication = new UserAuthentication(parsedRequest.getMessageHeader());
setMessageHeader(authentication);
setMessageBody(parsedRequest.getMessageBody());
setRequestHeader(parsedRequest.getRequestHeader());
queryHeader = (PsmQryHeaderType) msgUtil.getUnwrapHelper().getObjectByClass(
getMessageBody().getAny(), PsmQryHeaderType.class);
queryBody = (QueryDefinitionRequestType) msgUtil.getUnwrapHelper().getObjectByClass(
getMessageBody().getAny(), QueryDefinitionRequestType.class);
// check type is query request with query definition
if (!queryHeader.getRequestType().equals(PsmRequestTypeType.CRC_QRY_RUN_QUERY_INSTANCE_FROM_QUERY_DEFINITION)) {
throw new I2B2Exception("Only query from query definition supported, got:" + queryHeader.getRequestType());
}
} catch (ClassCastException | JAXBUtilException e) {
throw Logger.error(new I2B2Exception("JAXB unwrap failed.", e));
}
}
/**
* Used on client-side to create a request.
*/
public I2B2QueryRequest(UserAuthentication auth) {
// authentication
authentication = auth;
setMessageHeader(authentication);
// standard information generated by i2b2 webclient
RequestHeaderType reqHeader = i2b2OF.createRequestHeaderType();
reqHeader.setResultWaittimeMs(util.getI2b2Waittimems());
setRequestHeader(reqHeader);
queryHeader = querySetFinderOF.createPsmQryHeaderType();
queryHeader.setRequestType(PsmRequestTypeType.CRC_QRY_RUN_QUERY_INSTANCE_FROM_QUERY_DEFINITION);
UserType user = querySetFinderOF.createUserType();
user.setGroup(authentication.getSecurity().getDomain());
user.setLogin(authentication.getSecurity().getUsername());
user.setValue(authentication.getSecurity().getUsername());
queryHeader.setUser(user);
queryHeader.setEstimatedTime(0);
// query request = query definition (created later) + result output list
queryBody = querySetFinderOF.createQueryDefinitionRequestType();
// result output
ResultOutputOptionListType outputList = querySetFinderOF.createResultOutputOptionListType();
ResultOutputOptionType resultOption = querySetFinderOF.createResultOutputOptionType();
resultOption.setPriorityIndex(1);
resultOption.setName(I2B2_RESULT_OPTION_TYPE);
outputList.getResultOutput().add(resultOption);
queryBody.setResultOutputList(outputList);
// create the body
BodyType body = i2b2OF.createBodyType();
body.getAny().add(querySetFinderOF.createPsmheader(queryHeader));
body.getAny().add(querySetFinderOF.createRequest(queryBody));
setMessageBody(body);
}
public void setQueryDefinition(String queryName, List<List<String>> itemKeys) {
QueryDefinitionType queryDef = querySetFinderOF.createQueryDefinitionType();
queryDef.setQueryName(queryName);
queryDef.setQueryId(queryName);
queryDef.setQueryDescription("Query generated by the Java client: " + queryName);
queryDef.setSpecificityScale(0);
int panelCount = 0;
for (List<String> panel : itemKeys) {
PanelType panelXml = querySetFinderOF.createPanelType();
panelXml.setPanelNumber(++panelCount);
panelXml.setPanelAccuracyScale(0);
for (String itemKey : panel) {
ItemType itemXml = querySetFinderOF.createItemType();
itemXml.setItemKey(itemKey);
itemXml.setItemIsSynonym(false);
panelXml.getItem().add(itemXml);
}
queryDef.getPanel().add(panelXml);
}
queryBody.setQueryDefinition(queryDef);
}
/**
* Extracts the query definition from the request.
*
* @return the query definition
* @throws JAXBUtilException
*/
public QueryDefinitionType getQueryDefinition() {
return queryBody.getQueryDefinition();
}
/**
* Resets and sets to the provided output types the list of result output type.
*
* @param outputTypeNames
*/
public void setOutputTypes(String[] outputTypeNames) {
List<ResultOutputOptionType> outputsList = queryBody.getResultOutputList().getResultOutput();
outputsList.clear();
for (String outputTypeName : outputTypeNames) {
ResultOutputOptionType outputType = querySetFinderOF.createResultOutputOptionType();
outputType.setName(outputTypeName);
outputsList.add(outputType);
}
}
public String getQueryName() {
return queryBody.getQueryDefinition().getQueryName();
}
public UserAuthentication getUserAuthentication() {
return authentication;
}
}
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