private String getXMLString(JAXBElement<?> jaxbElement) throws Exception {
JAXBUtil jaxbUtil = new JAXBUtil(new String[] {"edu.harvard.i2b2.core.datavo.pdo"});
StringWriter strWriter = new StringWriter();
jaxbUtil.marshaller(jaxbElement, strWriter);
return strWriter.toString();
}
public static String getAnalysisDefinitionXml(AnalysisDefinitionType analysisDefinition)
throws JAXBUtilException {
StringWriter queryDefWriter = new StringWriter();
edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory of =
new edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory();
JAXBUtil jaxbUtil = CRCJAXBUtil.getAnalysisDefJAXBUtil();
jaxbUtil.marshaller(of.createAnalysisDefinition(analysisDefinition), queryDefWriter);
return queryDefWriter.toString();
}
public String writeContentQueryXML(String queryName, String userId) {
// DTOFactory dtoFactory = new DTOFactory();
// QueryType queryType = new QueryType();
// create header
PsmQryHeaderType headerType = new PsmQryHeaderType();
UserType userType = new UserType();
userType.setLogin(userId);
userType.setValue(userId);
headerType.setUser(userType);
headerType.setRequestType(PsmRequestTypeType.CRC_QRY_RUN_QUERY_INSTANCE_FROM_QUERY_DEFINITION);
// QuerySetType querySetType = new QuerySetType();
// querySetType.getQuery().add(queryType);
RequestHeaderType requestHeader = new RequestHeaderType();
requestHeader.setResultWaittimeMs(180000);
BodyType bodyType = new BodyType();
edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory psmOf =
new edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory();
bodyType.getAny().add(psmOf.createPsmheader(headerType));
MessageHeaderType messageHeader = getMessageHeader();
RequestMessageType requestMessageType = new RequestMessageType();
requestMessageType.setMessageBody(bodyType);
requestMessageType.setMessageHeader(messageHeader);
requestMessageType.setRequestHeader(requestHeader);
// dtoFactory.getRequestMessageType(messageHeader, requestHeader,
// bodyType);
JAXBUtil jaxbUtil = PreviousQueryJAXBUtil.getJAXBUtil();
StringWriter strWriter = new StringWriter();
try {
edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.ObjectFactory of =
new edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.ObjectFactory();
jaxbUtil.marshaller(of.createRequest(requestMessageType), strWriter);
} catch (Exception e) {
e.printStackTrace();
}
System.out.println("Generated content XML request: " + strWriter.toString());
return strWriter.toString();
}
/**
* Function accepts parameter in Map. The patient count will be obfuscated if the user is OBFUS
*/
public void generateResult(Map param) throws CRCTimeOutException, I2B2DAOException {
SetFinderConnection sfConn = (SetFinderConnection) param.get("SetFinderConnection");
SetFinderDAOFactory sfDAOFactory = (SetFinderDAOFactory) param.get("SetFinderDAOFactory");
// String patientSetId = (String)param.get("PatientSetId");
String queryInstanceId = (String) param.get("QueryInstanceId");
String TEMP_DX_TABLE = (String) param.get("TEMP_DX_TABLE");
String resultInstanceId = (String) param.get("ResultInstanceId");
// String itemKey = (String) param.get("ItemKey");
String resultTypeName = (String) param.get("ResultOptionName");
String processTimingFlag = (String) param.get("ProcessTimingFlag");
int obfuscatedRecordCount = (Integer) param.get("ObfuscatedRecordCount");
int transactionTimeout = (Integer) param.get("TransactionTimeout");
TransactionManager tm = (TransactionManager) param.get("TransactionManager");
this.setDbSchemaName(sfDAOFactory.getDataSourceLookup().getFullSchema());
Map ontologyKeyMap = (Map) param.get("setFinderResultOntologyKeyMap");
String serverType = (String) param.get("ServerType");
CallOntologyUtil ontologyUtil = (CallOntologyUtil) param.get("CallOntologyUtil");
List<String> roles = (List<String>) param.get("Roles");
String tempTableName = "";
PreparedStatement stmt = null;
boolean errorFlag = false, timeoutFlag = false;
String itemKey = "";
int actualTotal = 0, obsfcTotal = 0;
boolean obfscDataRoleFlag = false;
try {
LogTimingUtil logTimingUtil = new LogTimingUtil();
logTimingUtil.setStartTime();
obfscDataRoleFlag = checkDataObscRole(sfDAOFactory.getOriginalDataSourceLookup(), roles);
itemKey = getItemKeyFromResultType(sfDAOFactory, resultTypeName);
log.debug("Result type's " + resultTypeName + " item key value " + itemKey);
LogTimingUtil subLogTimingUtil = new LogTimingUtil();
subLogTimingUtil.setStartTime();
ConceptsType conceptsType = ontologyUtil.callGetChildren(itemKey);
if (conceptsType != null && conceptsType.getConcept().size() < 1) {
throw new I2B2DAOException(
"Could not fetch children result type "
+ resultTypeName
+ " item key [ "
+ itemKey
+ " ]");
}
subLogTimingUtil.setEndTime();
if (processTimingFlag != null) {
if (processTimingFlag.trim().equalsIgnoreCase(ProcessTimingReportUtil.DEBUG)) {
ProcessTimingReportUtil ptrUtil =
new ProcessTimingReportUtil(sfDAOFactory.getDataSourceLookup());
ptrUtil.logProcessTimingMessage(
queryInstanceId,
ptrUtil.buildProcessTiming(
subLogTimingUtil,
"BUILD - " + resultTypeName + " : Ontology Call(GetChildren) ",
""));
}
}
String itemCountSql =
" select count(distinct PATIENT_NUM) as item_count from "
+ this.getDbSchemaName()
+ "observation_fact obs_fact "
+ " where obs_fact.patient_num in (select patient_num from "
+ TEMP_DX_TABLE
+ " ) "
+ " and obs_fact.concept_cd in (select concept_cd from "
+ this.getDbSchemaName()
+ "concept_dimension where concept_path like ?)";
ResultType resultType = new ResultType();
resultType.setName(resultTypeName);
stmt = sfConn.prepareStatement(itemCountSql);
CancelStatementRunner csr = new CancelStatementRunner(stmt, transactionTimeout);
Thread csrThread = new Thread(csr);
csrThread.start();
for (ConceptType conceptType : conceptsType.getConcept()) {
String dimCode = this.getDimCodeInSqlFormat(conceptType);
itemCountSql =
" select count(distinct PATIENT_NUM) as item_count from "
+ this.getDbSchemaName()
+ " observation_fact "
+ " where "
+ " patient_num in (select patient_num from "
+ TEMP_DX_TABLE
+ " ) and "
+ conceptType.getFacttablecolumn()
+ " IN (select "
+ conceptType.getFacttablecolumn()
+ " from "
+ getDbSchemaName()
+ conceptType.getTablename()
+ " "
+ " where "
+ conceptType.getColumnname()
+ " "
+ conceptType.getOperator()
+ " "
+ dimCode
+ ")";
stmt = sfConn.prepareStatement(itemCountSql);
// // smuniraju: Currently, in postgres, a timeout value > 0 will result in "setQueryTimeout
// is not yet implemented"
// stmt.setQueryTimeout(transactionTimeout);
int queryTimeout =
(serverType.equalsIgnoreCase(DAOFactoryHelper.POSTGRES)) ? 0 : transactionTimeout;
stmt.setQueryTimeout(queryTimeout);
log.debug("Executing count sql [" + itemCountSql + "]");
//
subLogTimingUtil.setStartTime();
ResultSet resultSet = stmt.executeQuery();
if (csr.getSqlFinishedFlag()) {
timeoutFlag = true;
throw new CRCTimeOutException("The query was canceled.");
}
resultSet.next();
int demoCount = resultSet.getInt("item_count");
subLogTimingUtil.setEndTime();
if (processTimingFlag != null) {
if (processTimingFlag.trim().equalsIgnoreCase(ProcessTimingReportUtil.DEBUG)) {
ProcessTimingReportUtil ptrUtil =
new ProcessTimingReportUtil(sfDAOFactory.getDataSourceLookup());
ptrUtil.logProcessTimingMessage(
queryInstanceId,
ptrUtil.buildProcessTiming(
subLogTimingUtil,
"BUILD - "
+ resultTypeName
+ " : COUNT SQL for "
+ conceptType.getDimcode()
+ " ",
"sql=" + itemCountSql));
}
}
//
actualTotal += demoCount;
if (obfscDataRoleFlag) {
GaussianBoxMuller gaussianBoxMuller = new GaussianBoxMuller();
demoCount = (int) gaussianBoxMuller.getNormalizedValueForCount(demoCount);
obsfcTotal += demoCount;
}
DataType mdataType = new DataType();
mdataType.setValue(String.valueOf(demoCount));
mdataType.setColumn(conceptType.getName());
mdataType.setType("int");
resultType.getData().add(mdataType);
}
csr.setSqlFinishedFlag();
csrThread.interrupt();
stmt.close();
edu.harvard.i2b2.crc.datavo.i2b2result.ObjectFactory of =
new edu.harvard.i2b2.crc.datavo.i2b2result.ObjectFactory();
BodyType bodyType = new BodyType();
bodyType.getAny().add(of.createResult(resultType));
ResultEnvelopeType resultEnvelop = new ResultEnvelopeType();
resultEnvelop.setBody(bodyType);
JAXBUtil jaxbUtil = CRCJAXBUtil.getJAXBUtil();
StringWriter strWriter = new StringWriter();
subLogTimingUtil.setStartTime();
jaxbUtil.marshaller(of.createI2B2ResultEnvelope(resultEnvelop), strWriter);
subLogTimingUtil.setEndTime();
tm.begin();
IXmlResultDao xmlResultDao = sfDAOFactory.getXmlResultDao();
xmlResultDao.createQueryXmlResult(resultInstanceId, strWriter.toString());
//
if (processTimingFlag != null) {
if (!processTimingFlag.trim().equalsIgnoreCase(ProcessTimingReportUtil.NONE)) {
ProcessTimingReportUtil ptrUtil =
new ProcessTimingReportUtil(sfDAOFactory.getDataSourceLookup());
if (processTimingFlag.trim().equalsIgnoreCase(ProcessTimingReportUtil.DEBUG)) {
ptrUtil.logProcessTimingMessage(
queryInstanceId,
ptrUtil.buildProcessTiming(subLogTimingUtil, "JAXB - " + resultTypeName, ""));
}
logTimingUtil.setEndTime();
ptrUtil.logProcessTimingMessage(
queryInstanceId,
ptrUtil.buildProcessTiming(logTimingUtil, "BUILD - " + resultTypeName, ""));
}
}
tm.commit();
} catch (com.microsoft.sqlserver.jdbc.SQLServerException sqlServerEx) {
// if the setQueryTimeout worked, then the message would be timed
// out
if (sqlServerEx.getMessage().indexOf("timed out") > -1) {
timeoutFlag = true;
throw new CRCTimeOutException(sqlServerEx.getMessage(), sqlServerEx);
} else if (sqlServerEx
.getMessage()
.indexOf( // if the stmt.cancel()
// worked, then this
// exception is
// thrown
"The query was canceled.")
> -1) {
timeoutFlag = true;
throw new CRCTimeOutException(sqlServerEx.getMessage(), sqlServerEx);
} else {
errorFlag = true;
log.error("Sqlserver error while executing sql", sqlServerEx);
throw new I2B2DAOException("Sqlserver error while executing sql", sqlServerEx);
}
} catch (SQLException sqlEx) {
// catch oracle query timeout error ORA-01013
if (sqlEx.toString().indexOf("ORA-01013") > -1) {
timeoutFlag = true;
throw new CRCTimeOutException(sqlEx.getMessage(), sqlEx);
}
if (sqlEx.getMessage().indexOf("The query was canceled.") > -1) {
timeoutFlag = true;
throw new CRCTimeOutException(sqlEx.getMessage(), sqlEx);
}
errorFlag = true;
log.error("Error while executing sql", sqlEx);
throw new I2B2DAOException("Error while executing sql", sqlEx);
} catch (Exception sqlEx) {
errorFlag = true;
log.error("QueryResultPatientSetGenerator.generateResult:" + sqlEx.getMessage(), sqlEx);
throw new I2B2DAOException(
"QueryResultPatientSetGenerator.generateResult:" + sqlEx.getMessage(), sqlEx);
} finally {
IQueryResultInstanceDao resultInstanceDao = sfDAOFactory.getPatientSetResultDAO();
if (errorFlag) {
resultInstanceDao.updatePatientSet(
resultInstanceId, QueryStatusTypeId.STATUSTYPE_ID_ERROR, 0);
} else {
// set the setsize and the description of the result instance if
// the user role is obfuscated
if (timeoutFlag == false) { // check if the query completed
try {
tm.begin();
String obfusMethod = "", description = null;
if (obfscDataRoleFlag) {
obfusMethod = IQueryResultInstanceDao.OBSUBTOTAL;
// add () to the result type description
// read the description from result type
} else {
obfuscatedRecordCount = actualTotal;
}
IQueryResultTypeDao resultTypeDao = sfDAOFactory.getQueryResultTypeDao();
List<QtQueryResultType> resultTypeList =
resultTypeDao.getQueryResultTypeByName(resultTypeName);
// add "(Obfuscated)" in the description
// description = resultTypeList.get(0)
// .getDescription()
// + " (Obfuscated) ";
String queryName =
sfDAOFactory
.getQueryMasterDAO()
.getQueryDefinition(
sfDAOFactory
.getQueryInstanceDAO()
.getQueryInstanceByInstanceId(queryInstanceId)
.getQtQueryMaster()
.getQueryMasterId())
.getName();
resultInstanceDao.updatePatientSet(
resultInstanceId,
QueryStatusTypeId.STATUSTYPE_ID_FINISHED,
null,
// obsfcTotal,
obfuscatedRecordCount,
actualTotal,
obfusMethod);
description = resultTypeList.get(0).getDescription() + " for \"" + queryName + "\"";
// set the result instance description
resultInstanceDao.updateResultInstanceDescription(resultInstanceId, description);
tm.commit();
} catch (NotSupportedException e) {
throw new I2B2DAOException(
"Failed to write obfuscated description " + e.getMessage(), e);
} catch (SystemException e) {
throw new I2B2DAOException(
"Failed to write obfuscated description " + e.getMessage(), e);
} catch (SecurityException e) {
throw new I2B2DAOException(
"Failed to write obfuscated description " + e.getMessage(), e);
} catch (IllegalStateException e) {
throw new I2B2DAOException(
"Failed to write obfuscated description " + e.getMessage(), e);
} catch (RollbackException e) {
throw new I2B2DAOException(
"Failed to write obfuscated description " + e.getMessage(), e);
} catch (HeuristicMixedException e) {
throw new I2B2DAOException(
"Failed to write obfuscated description " + e.getMessage(), e);
} catch (HeuristicRollbackException e) {
throw new I2B2DAOException(
"Failed to write obfuscated description " + e.getMessage(), e);
}
}
}
}
}
public String wirteQueryXML() {
DTOFactory dtoFactory = new DTOFactory();
// TimeZone pdt = TimeZone.getTimeZone("EST");
// DatatypeFactory dataTypeFactory = null;
// try {
// dataTypeFactory = DatatypeFactory.newInstance();
// XMLGregorianCalendar xmlCalendar =
// dataTypeFactory.newXMLGregorianCalendarDate(2006, 9, 21, -5*60);
// TimeZone pdt = xmlCalendar.getgetTimezone();
// }
// catch (DatatypeConfigurationException e) {
// e.printStackTrace();
// }
// RequestType requestType = new RequestType();
// requestType.setSpecificityScale(specificity());
QueryDefinitionType queryDefinitionType = new QueryDefinitionType();
QueryDefinitionRequestType queryDefinitionRequestType = new QueryDefinitionRequestType();
for (int i = 0; i < panelCount; i++) {
ConceptTreePanel panel = getTreePanel(i);
ArrayList<QueryConceptTreeNodeData> nodelist = panel.data().getItems();
if ((nodelist != null) && (nodelist.size() > 0)) {
System.out.println(
"Panel: "
+ panel.getGroupName()
+ " Excluded: "
+ ((panel.data().exclude()) ? "yes" : "no"));
PanelType panelType = new PanelType();
panelType.setInvert((panel.data().exclude()) ? 1 : 0);
PanelType.TotalItemOccurrences totalItemOccurrences = new PanelType.TotalItemOccurrences();
totalItemOccurrences.setValue(panel.getOccurrenceTimes());
panelType.setTotalItemOccurrences(totalItemOccurrences);
panelType.setPanelNumber(i + 1);
// if(panel.data().startTime() != -1) {
// panelType.setPanelDateFrom(//dataTypeFactory.
// newXMLGregorianCalendarDate(
// dtoFactory.getXMLGregorianCalendarDate(panel.data().startYear(
// ),
// panel.data().startMonth(), panel.data().startDay()));
// }
// if(panel.data().endTime() != -1) {
// panelType.setPanelDateTo(//dataTypeFactory.
// newXMLGregorianCalendarDate(
// dtoFactory.getXMLGregorianCalendarDate(panel.data().endYear(),
// panel.data().endMonth(), panel.data().endDay()));
// }
for (int j = 0; j < nodelist.size(); j++) {
QueryConceptTreeNodeData node = nodelist.get(j);
System.out.println("\tItem: " + node.fullname());
// create item
ItemType itemType = new ItemType();
// itemType.setConstrainByDate(.setDateFrom(dtoFactory.
// getXMLGregorianCalendarDate(2006,
// 10, 4)));
itemType.setItemKey(node.fullname());
itemType.setItemName(node.name());
// mm removed
// itemType.setItemTable(node.lookuptable());
itemType.setTooltip(node.tooltip());
itemType.setHlevel(Integer.parseInt(node.hlevel()));
itemType.setClazz("ENC");
ConstrainByDate cDate = new ConstrainByDate();
ConstrainDateType constrinDataType = new ConstrainDateType();
constrinDataType.setValue(
dtoFactory.getXMLGregorianCalendarDate(
node.startYear(), node.startMonth(), node.startDay()));
if (node.startTime() != -1) {
cDate.setDateFrom(constrinDataType);
}
if (node.endTime() != -1) {
cDate.setDateTo(constrinDataType);
}
itemType.getConstrainByDate().add(cDate);
panelType.getItem().add(itemType);
}
queryDefinitionType.getPanel().add(panelType);
}
}
// create infotype
InfoType infoType = new InfoType();
infoType.setValue("INFO");
infoType.setUrl("http://www.ibm.com");
// create header
PsmQryHeaderType headerType = new PsmQryHeaderType();
UserType userType = new UserType();
userType.setLogin(UserInfoBean.getInstance().getUserName());
userType.setValue(UserInfoBean.getInstance().getUserName());
headerType.setUser(userType);
headerType.setRequestType(PsmRequestTypeType.CRC_QRY_RUN_QUERY_INSTANCE_FROM_QUERY_DEFINITION);
if (queryName == null) {
queryName =
getTreePanel(0).data().getItems().get(0).name()
+ "_"
+ generateMessageId().substring(0, 4);
}
queryDefinitionType.setQueryName(queryName);
queryDefinitionRequestType.setQueryDefinition(queryDefinitionType);
RequestHeaderType requestHeader = new RequestHeaderType();
requestHeader.setResultWaittimeMs(180000);
BodyType bodyType = new BodyType();
edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory psmOf =
new edu.harvard.i2b2.crcxmljaxb.datavo.psm.query.ObjectFactory();
bodyType.getAny().add(psmOf.createPsmheader(headerType));
bodyType.getAny().add(psmOf.createRequest(queryDefinitionRequestType));
// new QueryToolDTOFactory().buildBodyType(headerType,
// queryDefinitionRequestType, null);
MessageHeaderType messageHeader = getMessageHeader();
RequestMessageType requestMessageType = new RequestMessageType();
requestMessageType.setMessageBody(bodyType);
requestMessageType.setMessageHeader(messageHeader);
requestMessageType.setRequestHeader(requestHeader);
// dtoFactory.getRequestMessageType(messageHeader, requestHeader,
// bodyType);
JAXBUtil jaxbUtil = PreviousQueryJAXBUtil.getJAXBUtil();
StringWriter strWriter = new StringWriter();
try {
edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.ObjectFactory of =
new edu.harvard.i2b2.crcxmljaxb.datavo.i2b2message.ObjectFactory();
jaxbUtil.marshaller(of.createRequest(requestMessageType), strWriter);
} catch (Exception e) {
e.printStackTrace();
}
return strWriter.toString();
}