void setRollbackOnly() {
try {
transactionManager.setRollbackOnly();
} catch (javax.transaction.SystemException se) {
se.printStackTrace();
}
}
public void onMessage(final Message message) {
try {
// Step 9. We know the client is sending a text message so we cast
TextMessage textMessage = (TextMessage) message;
// Step 10. get the text from the message.
String text = textMessage.getText();
System.out.println("message " + text + " received");
if (!textMessage.getJMSRedelivered()) {
// Step 11. On first delivery get the transaction, take a look, and throw an exception
Transaction tx = tm.getTransaction();
if (tx != null) {
System.out.println("something is wrong, there should be no global transaction: " + tx);
} else {
System.out.println(
"there is no global transaction, although the message delivery is using a local transaction");
System.out.println("let's throw an exception and see what happens");
throw new RuntimeException("DOH!");
}
} else {
// Step 12. Print the message
System.out.println(
"The message was redelivered since the message delivery used a local transaction");
}
} catch (JMSException e) {
e.printStackTrace();
} catch (SystemException e) {
e.printStackTrace();
}
}
public static void main(String[] args) {
UserTransaction ut = null;
try {
boolean abort = false;
System.setProperty(Context.INITIAL_CONTEXT_FACTORY, "weblogic.jndi.WLInitialContextFactory");
System.setProperty(Context.PROVIDER_URL, "t3://localhost:7001");
ut = getUserTransaction();
ut.begin();
MessagePublisher mp =
new MessagePublisher("jms/JTATestJMSConnectionFactory", "jms/JTATestJMSQueue", false);
mp.publishMessage("Hello JMS2");
mp.publishMessage("Hello again JMS2");
new AmitkJTADao("jdbc/JTATestDataSource")
.updateRecord(1, new Date(System.currentTimeMillis()));
if (abort) throw new Exception("Forcefully aborting transaction");
ut.commit();
} catch (Exception e) {
e.printStackTrace();
try {
if (null != ut) ut.rollback();
} catch (SystemException se) {
se.printStackTrace();
} finally {
ut = null;
}
}
}
/*
* (non-Javadoc)
* @see org.mobicents.slee.runtime.transaction.SleeTransactionManager#mandateTransaction()
*/
public void mandateTransaction() throws TransactionRequiredLocalException {
try {
final Transaction tx = getTransaction();
if (tx == null) throw new TransactionRequiredLocalException("Transaction Mandatory");
final int status = tx.getStatus();
if (status != Status.STATUS_ACTIVE && status != Status.STATUS_MARKED_ROLLBACK) {
throw new IllegalStateException("There is no active tx, tx is in state: " + status);
}
} catch (SystemException e) {
throw new SLEEException(e.getMessage(), e);
}
}
void execute(final ActivityHandle handle, final int activityFlags)
throws StartActivityException, SLEEException {
final SleeTransactionManager txManager = sleeContainer.getTransactionManager();
final Runnable runnable =
new Runnable() {
public void run() {
boolean rollback = true;
try {
txManager.begin();
sleeEndpoint._startActivity(handle, activityFlags);
rollback = false;
} catch (NotSupportedException e) {
throw new SLEEException(e.getMessage(), e);
} catch (SystemException e) {
throw new SLEEException(e.getMessage(), e);
} finally {
try {
if (rollback) {
txManager.rollback();
} else {
txManager.commit();
}
} catch (Throwable e) {
throw new SLEEException(e.getMessage(), e);
}
}
}
};
Transaction tx = null;
try {
tx = txManager.getTransaction();
if (tx != null) {
txManager.suspend();
}
runnable.run();
} catch (SystemException e) {
throw new SLEEException(e.getMessage(), e);
} finally {
if (tx != null) {
try {
txManager.resume(tx);
} catch (Throwable e) {
throw new SLEEException(e.getMessage(), e);
}
}
}
}
/** 重载父类方法，设置事务的状态标识为回滚状态 */
public void rollback() throws SQLException {
JDBCTransaction tx = TransactionManager.getTransaction();
try {
if (tx != null) tx.setRollbackOnly();
} catch (IllegalStateException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (SystemException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (Exception e) {
e.printStackTrace();
}
}
public void setRollbackOnly() {
if (transaction == null) {
throw new IllegalStateException("Current thread is not associated with a transaction.");
}
try {
synchronized (this) {
transaction.setRollbackOnly();
}
} catch (SystemException e) {
throw (IllegalStateException)
new IllegalStateException("Failed to set transaction to rollback only: " + e.getMessage())
.initCause(e);
}
}
/**
* Rollback a transaction
*
* @exception SystemException Thrown if an error occurs
*/
public void rollbackTransaction() throws SystemException {
Long key = Long.valueOf(Thread.currentThread().getId());
TransactionImpl tx = txs.get(key);
if (tx != null) {
try {
tx.rollback();
} catch (Throwable t) {
SystemException se = new SystemException("Error during rollback");
se.initCause(t);
throw se;
} finally {
txs.remove(key);
}
} else {
throw new IllegalStateException("No transaction to rollback");
}
}
/**
* Handles the HTTP <code>POST</code> method.
*
* @param request servlet request
* @param response servlet response
* @throws ServletException if a servlet-specific error occurs
* @throws IOException if an I/O error occurs
*/
@Override
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
try {
String showid = request.getParameter("si");
String[] pics;
pics = request.getParameterValues("pics[]");
String[] comms;
comms = request.getParameterValues("comms[]");
utx.begin();
EntityManager em = emf.createEntityManager();
for (int i = 0; i < pics.length; i++) {
Ecpresentations etemp = em.getReference(Ecpresentations.class, showid);
Ecinfo ef = new Ecinfo();
ef.setPicy(pics[i]);
ef.setDetails(comms[i]);
ef.setShowid(etemp);
em.persist(ef);
}
utx.commit();
RequestDispatcher view = request.getRequestDispatcher("addinforeport.jsp");
view.forward(request, response);
em.close();
} catch (NotSupportedException ex) {
ex.printStackTrace();
} catch (SystemException ex) {
ex.printStackTrace();
} catch (RollbackException ex) {
ex.printStackTrace();
} catch (HeuristicMixedException ex) {
ex.printStackTrace();
} catch (HeuristicRollbackException ex) {
ex.printStackTrace();
} catch (SecurityException ex) {
ex.printStackTrace();
} catch (IllegalStateException ex) {
ex.printStackTrace();
}
}
@PostConstruct
private void init() {
try {
userTransaction.begin();
initData();
userTransaction.commit();
} catch (NotSupportedException e) {
e.printStackTrace();
} catch (SystemException e) {
e.printStackTrace();
} catch (HeuristicRollbackException e) {
e.printStackTrace();
} catch (javax.transaction.RollbackException e) {
e.printStackTrace();
} catch (HeuristicMixedException e) {
e.printStackTrace();
}
}
/**
* Example for sending a message fire and forget
*
* @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse response)
*/
protected void doGet(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
final String methodName = "doGet";
// We simply return some text showing what we've done
response.setContentType("text/plain");
PrintWriter out = response.getWriter();
WLMJMSMessageProducer wlmConnection = null;
boolean complete = false;
try {
// Begin a transaction
userTransaction.begin();
// Print the user transaction status
out.println(WLMJMSTranUtils.summarizeUserTranStatus(userTransaction));
// Create our JMS connection/session/producer using the WLM connection logic
// Many fire-and-forget scenarios are for exactly once delivery, where a
// database is updated in the same transaction as sending the request.
// For this reason in this example we begin a transaction and send
// a persistent message.
// As such JDBC operations could be inserted into this sample, and would
// be coordinated in an atomic transaction with sending the request.
//
// If you are instead looking to send nonpersistent messages, such as publishing
// some non-critical state data on a topic, then you should consider
// removing the transaction, changing the transaction
// boolean in the getMessageProducer() call to false, and setting the DeliveryMode
// to NON_PERSISTENT when sending the message.
out.println("JMS destination: " + fireAndForgetTarget);
wlmConnection =
wlmJMSAttach.getMessageProducer(fireAndForgetTarget, true, Session.AUTO_ACKNOWLEDGE);
// TODO: Replace this section with business logic
// We create a temporary queue solely for the purpose of finding out where
// we are connected, as the temporary queue name should show this.
// This is inefficient, so it is for demonstration purposes only.
TemporaryQueue temporaryQueue = wlmConnection.getSession().createTemporaryQueue();
String temporaryQueueName = temporaryQueue.getQueueName();
out.println("Temporary queue showing where we are connected:");
out.println(temporaryQueueName);
temporaryQueue.delete();
String exampleMessageBody =
this.getClass().getName()
+ " (thread \""
+ Thread.currentThread().getName()
+ "\") sending at "
+ new Date();
Message message = wlmConnection.getSession().createTextMessage(exampleMessageBody);
out.println("Sending message \"" + exampleMessageBody + "\"");
// Send the message
wlmConnection
.getProducer()
.send(
message,
DeliveryMode.PERSISTENT, /* We are persistent in this example */
wlmConnection.getProducer().getPriority() /* Default priority */,
0 /* Do not expire */);
out.println("JMSMessageID: " + message.getJMSMessageID());
// Commit the transaction
userTransaction.commit();
// Mark that we're complete, so that we throw any exception seen during cleanup,
// and do not attempt rollback of the transaction
complete = true;
} catch (HeuristicMixedException e) {
if (log.enabled()) log.logExStack(methodName, "Transaction HeuristicMixedException", e);
throw new ServletException("Transaction HeuristicMixedException: " + e.getMessage(), e);
} catch (HeuristicRollbackException e) {
if (log.enabled()) log.logExStack(methodName, "Transaction HeuristicRollbackException", e);
throw new ServletException("Transaction HeuristicRollbackException: " + e.getMessage(), e);
} catch (RollbackException e) {
if (log.enabled()) log.logExStack(methodName, "Transaction RollbackException", e);
throw new ServletException("Transaction RollbackException: " + e.getMessage(), e);
} catch (NotSupportedException e) {
if (log.enabled()) log.logExStack(methodName, "Transaction NotSupportedException", e);
throw new ServletException("Transaction NotSupportedException: " + e.getMessage(), e);
} catch (SystemException e) {
if (log.enabled()) log.logExStack(methodName, "Transaction SystemException", e);
throw new ServletException("Transaction SystemException: " + e.getMessage(), e);
} catch (JMSException e) {
if (log.enabled()) log.logRootExMsg(methodName, "JMSException in business logic", e);
throw new ServletException("JMSException: " + e.getMessage(), e);
} finally {
// Rollback if we didn't complete
if (!complete)
try {
userTransaction.rollback();
} catch (SystemException e) {
// We are already on an exception path, so we should not throw this exception
if (log.enabled()) log.logExStack(methodName, "Exception during rollback", e);
}
// Close off our resources, ensuring we only throw an exception if we completed
// our earlier logic, so we don't override an earlier exception that being thrown.
if (wlmConnection != null)
try {
wlmConnection.close(complete);
} catch (JMSException e) {
throw new ServletException("JMSException on Connection close: " + e.getMessage(), e);
}
}
}
public String execute() {
String rtnVal = SUCCESS;
UserTransaction tx = null;
try {
sampleName = sampleName != null && sampleName.equals("0") ? null : sampleName;
if (jobType != null) {
boolean isProjectRegistration = eventName.equals(Constants.EVENT_PROJECT_REGISTRATION);
boolean isSampleRegistration = eventName.equals(Constants.EVENT_SAMPLE_REGISTRATION);
if (projectName == null
|| projectName.equals("0")
|| eventName == null
|| eventName.equals("0")) throw new Exception("Project or Event type is not selected.");
if (jobType.equals("insert")) { // loads single event
tx = (UserTransaction) new InitialContext().lookup("java:comp/UserTransaction");
tx.begin();
psewt.loadAll(
null,
this.createMultiLoadParameter(projectName, loadingProject, loadingSample, beanList));
this.reset();
} else if (jobType.equals("grid")) { // loads multiple events from grid view
tx = (UserTransaction) new InitialContext().lookup("java:comp/UserTransaction");
tx.begin();
for (GridBean gBean : gridList) {
if (gBean != null) {
if (isProjectRegistration
&& gBean.getProjectName() != null
&& gBean.getProjectPublic() != null) {
loadingProject = new Project();
loadingProject.setProjectName(gBean.getProjectName());
loadingProject.setIsPublic(Integer.valueOf(gBean.getProjectPublic()));
} else if (isSampleRegistration
&& gBean.getSampleName() != null
&& gBean.getSamplePublic() != null) {
loadingSample = new Sample();
loadingSample.setSampleName(gBean.getSampleName());
loadingSample.setParentSampleName(gBean.getParentSampleName());
loadingSample.setIsPublic(Integer.valueOf(gBean.getSamplePublic()));
} else {
if (gBean.getSampleName() != null) {
this.sampleName = gBean.getSampleName();
}
}
List<FileReadAttributeBean> fBeanList = gBean.getBeanList();
if (fBeanList != null && fBeanList.size() > 0) {
psewt.loadAll(
null,
this.createMultiLoadParameter(
projectName, loadingProject, loadingSample, fBeanList));
}
}
}
this.reset();
} else if (jobType.equals("file")) { // loads data from a CSV file to grid view
if (!this.uploadFile.canRead()) {
throw new Exception("Error in reading the file.");
} else {
try {
CSVReader reader = new CSVReader(new FileReader(this.uploadFile));
int lineCount = 0;
List<String> columns = new ArrayList<String>();
String currProjectName = null;
gridList = new ArrayList<GridBean>();
boolean hasSampleName = false;
String[] line;
while ((line = reader.readNext()) != null) {
if (lineCount != 1) {
if (lineCount == 0) {
Collections.addAll(columns, line);
hasSampleName = columns.indexOf("SampleName") >= 0;
} else {
int colIndex = 0;
currProjectName = line[colIndex++];
if (!isProjectRegistration && !currProjectName.equals(this.projectName)) {
throw new Exception(MULTIPLE_SUBJECT_IN_FILE_MESSAGE);
}
GridBean gBean = new GridBean();
gBean.setProjectName(currProjectName);
if (hasSampleName) {
gBean.setSampleName(line[(colIndex++)]);
}
if (isProjectRegistration) {
gBean.setProjectName(currProjectName);
gBean.setProjectPublic(line[(colIndex++)]);
} else if (isSampleRegistration) {
gBean.setParentSampleName(line[(colIndex++)]);
gBean.setSamplePublic(line[(colIndex++)]);
}
gBean.setBeanList(new ArrayList<FileReadAttributeBean>());
for (; colIndex < columns.size(); colIndex++) {
FileReadAttributeBean fBean = new FileReadAttributeBean();
fBean.setProjectName(
isProjectRegistration ? currProjectName : this.projectName);
fBean.setAttributeName(columns.get(colIndex));
fBean.setAttributeValue(line[colIndex]);
gBean.getBeanList().add(fBean);
}
this.gridList.add(gBean);
}
}
lineCount++;
}
jobType = "grid";
} catch (Exception ex) {
throw ex;
}
}
} else if (jobType.equals("template")) { // download template
List<EventMetaAttribute> emaList =
readPersister.getEventMetaAttributes(projectName, eventName);
/*
* removing the sanity check on sample requirement since multiple sample support is in action
* by hkim 5/2/13
ModelValidator validator = new ModelValidator();
validator.validateEventTemplateSanity(emaList, projectName, sampleName, eventName);
*/
TemplatePreProcessingUtils cvsUtils = new TemplatePreProcessingUtils();
String templateType = jobType.substring(jobType.indexOf("_") + 1);
downloadStream =
cvsUtils.buildFileContent(templateType, emaList, projectName, sampleName, eventName);
downloadContentType = templateType.equals("c") ? "csv" : "vnd.ms-excel";
rtnVal = Constants.FILE_DOWNLOAD_MSG;
}
}
} catch (Exception ex) {
logger.error("Exception in EventLoader : " + ex.toString());
ex.printStackTrace();
if (ex.getClass() == ForbiddenResourceException.class) {
addActionError(Constants.DENIED_USER_EDIT_MESSAGE);
return Constants.FORBIDDEN_ACTION_RESPONSE;
} else if (ex.getClass() == ForbiddenResourceException.class) {
addActionError(Constants.DENIED_USER_EDIT_MESSAGE);
return LOGIN;
} else if (ex.getClass() == ParseException.class)
addActionError(Constants.INVALID_DATE_MESSAGE);
else {
addActionError(ex.toString());
}
// deletes uploaded files in event of error
if (loadedFiles != null && loadedFiles.size() > 0) {
for (String filePath : loadedFiles) {
File tempFile = new File(fileStoragePath + filePath);
if (tempFile.exists()) tempFile.delete();
}
}
try {
if (tx != null) tx.rollback();
} catch (SystemException se) {
addActionError(se.toString());
}
rtnVal = ERROR;
} finally {
try {
// get project list for the drop down box
List<String> projectNameList = new ArrayList<String>();
if (projectNames == null || projectNames.equals("")) {
projectNameList.add("ALL");
} else if (projectNames.contains(",")) {
projectNameList.addAll(Arrays.asList(projectNames.split(",")));
} else {
projectNameList.add(projectNames);
}
projectList = readPersister.getProjects(projectNameList);
if (tx != null && tx.getStatus() != Status.STATUS_NO_TRANSACTION) {
tx.commit();
}
if (jobType != null && jobType.equals("grid") && this.uploadFile != null) {
this.uploadFile.delete();
}
} catch (Exception ex) {
ex.printStackTrace();
}
}
return rtnVal;
}
/** @see com.idega.block.importer.business.ImportFileHandler#handleRecords() */
@Override
public boolean handleRecords() {
failedRecords = new ArrayList();
errorLog = new TreeMap();
report = new Report(file.getFile().getName()); // Create a report file.
// It will be located in
// the Report dir
IWTimestamp t = IWTimestamp.RightNow();
t.setAsDate();
today = t.getDate();
t.setDay(1);
firstDayInCurrentMonth = t.getTimestamp();
t.addDays(-1);
lastDayInPreviousMonth = t.getTimestamp();
transaction = this.getSessionContext().getUserTransaction();
Timer clock = new Timer();
clock.start();
try {
// initialize business beans and data homes
communeUserBusiness =
(CommuneUserBusiness) this.getServiceInstance(CommuneUserBusiness.class);
schoolBusiness = (SchoolBusiness) this.getServiceInstance(SchoolBusiness.class);
schoolHome = schoolBusiness.getSchoolHome();
schoolTypeHome = schoolBusiness.getSchoolTypeHome();
schoolYearHome = schoolBusiness.getSchoolYearHome();
schoolClassHome = (SchoolClassHome) this.getIDOHome(SchoolClass.class);
schoolClassMemberHome = (SchoolClassMemberHome) this.getIDOHome(SchoolClassMember.class);
communeHome = (CommuneHome) this.getIDOHome(Commune.class);
studyPathHome = (SchoolStudyPathHome) this.getIDOHome(SchoolStudyPath.class);
placementImportDateHome =
(PlacementImportDateHome) this.getIDOHome(PlacementImportDate.class);
try {
season =
schoolBusiness.getCurrentSchoolSeason(schoolBusiness.getCategoryElementarySchool());
} catch (FinderException e) {
e.printStackTrace();
println("NackaHighSchoolPlacementHandler: School season is not defined.");
return false;
}
transaction.begin();
// iterate through the records and process them
String item;
int count = 0;
boolean failed = false;
while (!(item = (String) file.getNextRecord()).trim().equals("")) {
count++;
if (!processRecord(item, count)) {
failedRecords.add(item);
failed = true;
// break;
}
if ((count % 100) == 0) {
System.out.println(
"NackaHighSchoolHandler processing RECORD ["
+ count
+ "] time: "
+ IWTimestamp.getTimestampRightNow().toString());
}
item = null;
}
if (!failed) {
if (!terminateOldPlacements()) {
failed = true;
}
}
printFailedRecords();
clock.stop();
println("Number of records handled: " + (count - 1));
println(
"Time to handle records: "
+ clock.getTime()
+ " ms OR "
+ ((int) (clock.getTime() / 1000))
+ " s");
// success commit changes
if (!failed) {
transaction.commit();
} else {
transaction.rollback();
}
report.store(false);
return !failed;
} catch (Exception e) {
e.printStackTrace();
try {
transaction.rollback();
} catch (SystemException e2) {
e2.printStackTrace();
}
report.store(false);
return false;
}
}
/**
* 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);
}
}
}
}
}
