/**
* Perform operation for the given request using business class(ejb) and return response
*
* @throws I2B2Exception
* @see edu.harvard.i2b2.crc.delegate.RequestHandler#execute()
*/
public BodyType execute() throws I2B2Exception {
QueryProcessorUtil qpUtil = QueryProcessorUtil.getInstance();
String response = null;
BodyType bodyType = new BodyType();
MasterInstanceResultResponseType masterInstanceResponse = null;
try {
StartAnalysisLocal startAnalysisLocal = qpUtil.getStartAnalysisLocal();
DAOFactoryHelper daoFactoryHelper =
new DAOFactoryHelper(
this.getDataSourceLookup().getDomainId(),
getDataSourceLookup().getProjectPath(),
getDataSourceLookup().getOwnerId());
IDAOFactory daoFactory = daoFactoryHelper.getDAOFactory();
// response = queryManagerLocal.processQuery(requestXml);
masterInstanceResponse = startAnalysisLocal.start(daoFactory, requestXml);
// processQuery(this.getDataSourceLookup(), requestXml);
// masterInstanceResponse.setStatus(this.buildCRCStausType(
// RequestHandlerDelegate.DONE_TYPE, "DONE"));
// response = this.buildResponseMessage(requestXml, bodyType);
} catch (I2B2Exception e) {
masterInstanceResponse = new MasterInstanceResultResponseType();
masterInstanceResponse.setStatus(
this.buildCRCStausType(RequestHandlerDelegate.ERROR_TYPE, e.getMessage()));
} finally {
edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory psmObjFactory =
new edu.harvard.i2b2.crc.datavo.setfinder.query.ObjectFactory();
bodyType.getAny().add(psmObjFactory.createResponse(masterInstanceResponse));
}
return bodyType;
}
private boolean checkDataObscRole(DataSourceLookup originalDataSourceLookup, List<String> roles)
throws I2B2Exception {
boolean noDataAggFlag = false, noDataObfscFlag = false;
String domainId = originalDataSourceLookup.getDomainId();
String projectId = originalDataSourceLookup.getProjectPath();
String userId = originalDataSourceLookup.getOwnerId();
DAOFactoryHelper helper = new DAOFactoryHelper(domainId, projectId, userId);
IDAOFactory daoFactory = helper.getDAOFactory();
AuthrizationHelper authHelper = new AuthrizationHelper(domainId, projectId, userId, daoFactory);
try {
authHelper.checkRoleForProtectionLabel("SETFINDER_QRY_WITHOUT_DATAOBFSC", roles);
} catch (MissingRoleException noRoleEx) {
noDataAggFlag = true;
} catch (I2B2Exception e) {
throw e;
}
try {
authHelper.checkRoleForProtectionLabel("SETFINDER_QRY_WITH_DATAOBFSC", roles);
} catch (MissingRoleException noRoleEx) {
noDataObfscFlag = true;
} catch (I2B2Exception e) {
throw e;
}
if (noDataAggFlag && !noDataObfscFlag) {
return true;
} else {
return false;
}
}
public long getTotal(int maxInputList) throws SQLException, I2B2Exception {
IInputOptionListHandler inputOptionListHandler =
PDOFactory.buildInputListHandler(inputList, dataSourceLookup);
// inputList.getPatientList().setMax(maxInputList);
int minIndex = inputOptionListHandler.getMinIndex();
inputOptionListHandler.setMaxIndex(minIndex + maxInputList);
// iterate the panel and call total
IFactRelatedQueryHandler factRelatedHandler = null;
String countSqlFrom = " ";
String countClause = " COUNT(*) ";
if (dataSourceLookup.getServerType().equalsIgnoreCase(DAOFactoryHelper.ORACLE)
|| dataSourceLookup.getServerType().equalsIgnoreCase(DAOFactoryHelper.POSTGRESQL)) {
factRelatedHandler =
new FactRelatedQueryHandler(dataSourceLookup, inputList, filterList, outputOptionList);
} else if (dataSourceLookup.getServerType().equalsIgnoreCase(DAOFactoryHelper.SQLSERVER)) {
countSqlFrom = "as";
countClause = " COUNT_BIG(*) ";
factRelatedHandler =
new SQLServerFactRelatedQueryHandler(
dataSourceLookup, inputList, filterList, outputOptionList);
}
factRelatedHandler.setProjectParamMap(this.projectParamMap);
factRelatedHandler.setModifierMetadataXmlMap(this.modifierMetadataXmlMap);
FactOutputOptionType factOutputOptionType = new FactOutputOptionType();
factOutputOptionType.setOnlykeys(true);
outputOptionList.setObservationSet(factOutputOptionType);
// outputOptionList.getObservationSet().setOnlykeys(true);
// build sql for all the panel
// DAOFactoryHelper daoFactoryHelper = new DAOFactoryHelper(
// dataSourceLookup);
IPageDao pageTotalDao =
daoFactoryHelper.getDAOFactory().getPatientDataDAOFactory().getPageDAO();
int panelCount = filterList.getPanel().size();
List<String> panelSqlList = new ArrayList<String>(panelCount);
List<Integer> sqlCountList = new ArrayList<Integer>(panelCount);
long totalObservations = 0;
for (PanelType singlePanel : filterList.getPanel()) {
int sqlParamCount = singlePanel.getItem().size();
if (singlePanel.getInvert() == 1) {
sqlParamCount++;
}
sqlCountList.add(sqlParamCount);
String totalSql = pageTotalDao.buildTotalSql(factRelatedHandler, singlePanel);
if (totalSql.trim().length() == 0) {
continue;
}
panelSqlList.add(
"SELECT " + countClause + " from ( " + totalSql + " ) " + countSqlFrom + " totalsql");
}
totalObservations =
pageTotalDao.getTotalForAllPanel(panelSqlList, sqlCountList, inputOptionListHandler);
return totalObservations;
}
public PagingHandler(
DAOFactoryHelper helper,
final InputOptionListType inputList,
final FilterListType filterList,
String pageMethodName)
throws I2B2DAOException {
this.daoFactoryHelper = helper;
this.dataSourceLookup = helper.getDataSourceLookup();
this.inputList = inputList;
this.filterList = filterList;
this.outputOptionList = new OutputOptionListType();
pageMethod = PageMethodFactory.buildPageMethod(pageMethodName);
}
public HashMap getMinPatientIndexAndTheTotal(int maxInputList)
throws SQLException, I2B2Exception {
IInputOptionListHandler inputOptionListHandler =
PDOFactory.buildInputListHandler(inputList, dataSourceLookup);
// inputList.getPatientList().setMax(maxInputList);
inputOptionListHandler.setMaxIndex(maxInputList);
// iterate the panel and call total
IFactRelatedQueryHandler factRelatedHandler = null;
String countSqlFrom = " ";
if (dataSourceLookup.getServerType().equalsIgnoreCase(DAOFactoryHelper.ORACLE)
|| dataSourceLookup.getServerType().equalsIgnoreCase(DAOFactoryHelper.POSTGRESQL)) {
factRelatedHandler =
new FactRelatedQueryHandler(dataSourceLookup, inputList, filterList, outputOptionList);
} else if (dataSourceLookup.getServerType().equalsIgnoreCase(DAOFactoryHelper.SQLSERVER)) {
countSqlFrom = "as";
factRelatedHandler =
new SQLServerFactRelatedQueryHandler(
dataSourceLookup, inputList, filterList, outputOptionList);
}
// set project param
factRelatedHandler.setProjectParamMap(this.projectParamMap);
factRelatedHandler.setModifierMetadataXmlMap(this.modifierMetadataXmlMap);
FactOutputOptionType factOutputOptionType = new FactOutputOptionType();
factOutputOptionType.setOnlykeys(true);
outputOptionList.setObservationSet(factOutputOptionType);
// outputOptionList.getObservationSet().setOnlykeys(true);
// build sql for all the panel
// DAOFactoryHelper daoFactoryHelper = new DAOFactoryHelper(
// dataSourceLookup);
IPageDao pageTotalDao =
daoFactoryHelper.getDAOFactory().getPatientDataDAOFactory().getPageDAO();
int panelCount = filterList.getPanel().size();
List<String> panelMinSqlList = new ArrayList<String>(panelCount);
List<Integer> sqlCountList = new ArrayList<Integer>(panelCount);
long totalObservations = 0;
// things to consider to find the minimum
// a)How to handle the different input list (i.e. enumeration list,table
// or patient_dimension)
String panelSql = "";
for (PanelType singlePanel : filterList.getPanel()) {
int sqlParamCount = singlePanel.getItem().size();
if (singlePanel.getInvert() == 1) {
sqlParamCount++;
}
if (inputOptionListHandler.isCollectionId()) {
sqlParamCount++;
}
sqlCountList.add(sqlParamCount);
panelSql = pageTotalDao.buildTotalSql(factRelatedHandler, singlePanel);
if (panelSql.length() == 0) {
continue;
}
String minSql = inputOptionListHandler.generateMinIndexSql(panelSql);
System.out.println("min sql for panel " + minSql);
panelMinSqlList.add(minSql);
}
return pageTotalDao.getMinIndexAndCountAllPanel(
panelMinSqlList, sqlCountList, inputOptionListHandler);
}