@Override
protected void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
// changes to this servlet, we now look at group name too, tbh 05/2009
String triggerName = fp.getString("tname");
String gName = fp.getString("gname");
String groupName = "";
if (gName.equals("") || gName.equals("0")) {
groupName = TRIGGER_GROUP;
} else { // if (gName.equals("1")) {
groupName = TRIGGER_IMPORT_GROUP;
}
// << tbh 09/03/2009 #4143
scheduler = getScheduler();
Trigger trigger = scheduler.getTrigger(triggerName.trim(), groupName);
// trigger bean is a wrapper for the trigger, to serve as a link btw
// quartz classes and oc classes
// is it really necessary? DRY
if (trigger == null) {
System.out.println("*** reset trigger group name");
groupName = TRIGGER_GROUP;
trigger = scheduler.getTrigger(triggerName.trim(), groupName);
}
// << tbh 09/03/2009 #4143
// above is a hack, if we add more trigger groups this will have
// to be redone
System.out.println("found trigger name: " + triggerName);
System.out.println("found group name: " + groupName);
// System.out.println("found trigger on the other side, full name: " +
// trigger.getFullName());
TriggerBean triggerBean = new TriggerBean();
JobDataMap dataMap = new JobDataMap();
AuditEventDAO auditEventDAO = new AuditEventDAO(sm.getDataSource());
try {
triggerBean.setFullName(trigger.getName());
triggerBean.setPreviousDate(trigger.getPreviousFireTime());
triggerBean.setNextDate(trigger.getNextFireTime());
// >> set active here, tbh 10/08/2009
if (scheduler.getTriggerState(triggerName, groupName) == Trigger.STATE_PAUSED) {
triggerBean.setActive(false);
System.out.println("setting active to false for trigger: " + trigger.getName());
} else {
triggerBean.setActive(true);
System.out.println("setting active to TRUE for trigger: " + trigger.getName());
}
// <<
if (trigger.getDescription() != null) {
triggerBean.setDescription(trigger.getDescription());
}
if (trigger.getJobDataMap().size() > 0) {
dataMap = trigger.getJobDataMap();
String contactEmail = dataMap.getString(ExampleSpringJob.EMAIL);
System.out.println("found email: " + contactEmail);
// String datasetId =
// dataMap.getString(ExampleSpringJob.DATASET_ID);
// int dsId = new Integer(datasetId).intValue();
if (gName.equals("") || gName.equals("0")) {
String tab = dataMap.getString(ExampleSpringJob.TAB);
String cdisc = dataMap.getString(ExampleSpringJob.CDISC);
String spss = dataMap.getString(ExampleSpringJob.SPSS);
String periodToRun = dataMap.getString(ExampleSpringJob.PERIOD);
// int userId = new Integer(userAcctId).intValue();
int dsId = dataMap.getInt(ExampleSpringJob.DATASET_ID);
triggerBean.setCdisc(cdisc);
triggerBean.setSpss(spss);
triggerBean.setTab(tab);
triggerBean.setPeriodToRun(periodToRun);
DatasetDAO datasetDAO = new DatasetDAO(sm.getDataSource());
DatasetBean dataset = (DatasetBean) datasetDAO.findByPK(dsId);
triggerBean.setDataset(dataset);
}
int userId = dataMap.getInt(ExampleSpringJob.USER_ID);
// need to set information, extract bean, user account bean
UserAccountDAO userAccountDAO = new UserAccountDAO(sm.getDataSource());
triggerBean.setContactEmail(contactEmail);
UserAccountBean userAccount = (UserAccountBean) userAccountDAO.findByPK(userId);
triggerBean.setUserAccount(userAccount);
ArrayList<AuditEventBean> triggerLogs =
auditEventDAO.findAllByAuditTable(trigger.getName());
// set the table for the audit event beans here
ArrayList allRows = AuditEventRow.generateRowsFromBeans(triggerLogs);
EntityBeanTable table = fp.getEntityBeanTable();
String[] columns = {
resword.getString("date_and_time"),
resword.getString("action_message"),
resword.getString("entity_operation"),
// resword.getString("study_site"),
// resword.getString("study_subject_ID"),
resword.getString("changes_and_additions"),
resword.getString("actions")
};
table.setColumns(new ArrayList(Arrays.asList(columns)));
table.setAscendingSort(false);
table.hideColumnLink(1);
table.hideColumnLink(3);
table.hideColumnLink(4);
table.setQuery("ViewSingleJob?tname=" + triggerName + "&gname=" + gName, new HashMap());
table.setRows(allRows);
table.computeDisplay();
request.setAttribute("table", table);
}
} catch (NullPointerException e) {
// TODO Auto-generated catch block
System.out.println(" found NPE " + e.getMessage());
e.printStackTrace();
}
// need to show the extract for which this runs, which files, etc
// in other words the job data map
request.setAttribute("triggerBean", triggerBean);
request.setAttribute("groupName", groupName);
forwardPage(Page.VIEW_SINGLE_JOB);
}
@Override
protected void executeInternal(JobExecutionContext context) throws JobExecutionException {
// need to generate a Locale so that user beans and other things will
// generate normally
Locale locale = new Locale("en-US");
ResourceBundleProvider.updateLocale(locale);
ResourceBundle pageMessages = ResourceBundleProvider.getPageMessagesBundle();
// logger.debug("--");
// logger.debug("-- executing a job " + message + " at " + new
// java.util.Date().toString());
JobDataMap dataMap = context.getMergedJobDataMap();
SimpleTrigger trigger = (SimpleTrigger) context.getTrigger();
try {
ApplicationContext appContext =
(ApplicationContext) context.getScheduler().getContext().get("applicationContext");
String studySubjectNumber =
((CoreResources) appContext.getBean("coreResources")).getField("extract.number");
coreResources = (CoreResources) appContext.getBean("coreResources");
ruleSetRuleDao = (RuleSetRuleDao) appContext.getBean("ruleSetRuleDao");
dataSource = (DataSource) appContext.getBean("dataSource");
mailSender = (OpenClinicaMailSender) appContext.getBean("openClinicaMailSender");
AuditEventDAO auditEventDAO = new AuditEventDAO(dataSource);
// Scheduler scheduler = context.getScheduler();
// JobDetail detail = context.getJobDetail();
// jobDetailBean = (JobDetailBean) detail;
/*
* data map here should coincide with the job data map found in
* CreateJobExportServlet, with the following code: jobDataMap = new
* JobDataMap(); jobDataMap.put(DATASET_ID, datasetId);
* jobDataMap.put(PERIOD, period); jobDataMap.put(EMAIL, email);
* jobDataMap.put(TAB, tab); jobDataMap.put(CDISC, cdisc);
* jobDataMap.put(SPSS, spss);
*/
String alertEmail = dataMap.getString(EMAIL);
String localeStr = dataMap.getString(LOCALE);
if (localeStr != null) {
locale = new Locale(localeStr);
ResourceBundleProvider.updateLocale(locale);
pageMessages = ResourceBundleProvider.getPageMessagesBundle();
}
int dsId = dataMap.getInt(DATASET_ID);
String tab = dataMap.getString(TAB);
String cdisc = dataMap.getString(CDISC);
String cdisc12 = dataMap.getString(CDISC12);
if (cdisc12 == null) {
cdisc12 = "0";
}
String cdisc13 = dataMap.getString(CDISC13);
if (cdisc13 == null) {
cdisc13 = "0";
}
String cdisc13oc = dataMap.getString(CDISC13OC);
if (cdisc13oc == null) {
cdisc13oc = "0";
}
String spss = dataMap.getString(SPSS);
int userId = dataMap.getInt(USER_ID);
int studyId = dataMap.getInt(STUDY_ID);
// String datasetId = dataMap.getString(DATASET_ID);
// int dsId = new Integer(datasetId).intValue();
// String userAcctId = dataMap.getString(USER_ID);
// int userId = new Integer(userAcctId).intValue();
// why the flip-flop? if one property is set to 'true' we can
// see jobs in another screen but all properties have to be
// strings
logger.debug("-- found the job: " + dsId + " dataset id");
// for (Iterator it = dataMap.entrySet().iterator(); it.hasNext();)
// {
// java.util.Map.Entry entry = (java.util.Map.Entry) it.next();
// Object key = entry.getKey();
// Object value = entry.getValue();
// // logger.debug("-- found datamap property: " + key.toString() +
// // " : " + value.toString());
// }
HashMap fileName = new HashMap<String, Integer>();
if (dsId > 0) {
// trying to not throw an error if there's no dataset id
DatasetDAO dsdao = new DatasetDAO(dataSource);
DatasetBean datasetBean = (DatasetBean) dsdao.findByPK(dsId);
StudyDAO studyDao = new StudyDAO(dataSource);
UserAccountDAO userAccountDAO = new UserAccountDAO(dataSource);
// hmm, three lines in the if block DRY?
String generalFileDir = "";
String generalFileDirCopy = "";
String exportFilePath = SQLInitServlet.getField("exportFilePath");
String pattern =
"yyyy"
+ File.separator
+ "MM"
+ File.separator
+ "dd"
+ File.separator
+ "HHmmssSSS"
+ File.separator;
SimpleDateFormat sdfDir = new SimpleDateFormat(pattern);
generalFileDir =
DATASET_DIR
+ datasetBean.getId()
+ File.separator
+ sdfDir.format(new java.util.Date());
if (!"".equals(exportFilePath)) {
generalFileDirCopy =
SQLInitServlet.getField("filePath") + exportFilePath + File.separator;
}
// logger.debug("-- created the following dir: " +
// generalFileDir);
long sysTimeBegin = System.currentTimeMillis();
// set up the user bean here, tbh
// logger.debug("-- gen tab file 00");
userBean = (UserAccountBean) userAccountDAO.findByPK(userId);
// needs to also be captured by the servlet, tbh
// logger.debug("-- gen tab file 00");
generateFileService =
new GenerateExtractFileService(dataSource, userBean, coreResources, ruleSetRuleDao);
// logger.debug("-- gen tab file 00");
// tbh #5796 - covers a bug when the user changes studies, 10/2010
StudyBean activeStudy = (StudyBean) studyDao.findByPK(studyId);
StudyBean parentStudy = new StudyBean();
logger.debug(
"active study: " + studyId + " parent study: " + activeStudy.getParentStudyId());
if (activeStudy.getParentStudyId() > 0) {
// StudyDAO sdao = new StudyDAO(sm.getDataSource());
parentStudy = (StudyBean) studyDao.findByPK(activeStudy.getParentStudyId());
} else {
parentStudy = activeStudy;
// covers a bug in tab file creation, tbh 01/2009
}
logger.debug("-- found extract bean ");
ExtractBean eb =
generateFileService.generateExtractBean(datasetBean, activeStudy, parentStudy);
MessageFormat mf = new MessageFormat("");
StringBuffer message = new StringBuffer();
StringBuffer auditMessage = new StringBuffer();
// use resource bundle page messages to generate the email, tbh
// 02/2009
// message.append(pageMessages.getString("html_email_header_1")
// + " " + alertEmail +
// pageMessages.getString("html_email_header_2") + "<br/>");
message.append(
"<p>"
+ pageMessages.getString("email_header_1")
+ " "
+ EmailEngine.getAdminEmail()
+ " "
+ pageMessages.getString("email_header_2")
+ " Job Execution "
+ pageMessages.getString("email_header_3")
+ "</p>");
message.append("<P>Dataset: " + datasetBean.getName() + "</P>");
message.append("<P>Study: " + activeStudy.getName() + "</P>");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_1")
+ datasetBean.getName()
+ pageMessages.getString("html_email_body_2")
+ SQLInitServlet.getField("sysURL")
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// logger.debug("-- gen tab file 00");
if ("1".equals(tab)) {
logger.debug("-- gen tab file 01");
fileName =
generateFileService.createTabFile(
eb,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy.getId(),
parentStudy.getId(),
generalFileDirCopy);
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_tab_delimited"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your tab-delimited file <a href='AccessFile?fileId="
// + getFileIdInt(fileName) + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_tab_delimited")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(cdisc)) {
String odmVersion = "oc1.2";
fileName =
generateFileService.createODMFile(
odmVersion,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy,
generalFileDirCopy,
eb,
activeStudy.getId(),
parentStudy.getId(),
studySubjectNumber,
true,
true,
true,
null);
logger.debug("-- gen odm file");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_odm_12"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your ODM 1.2 w/OpenClinica Extension XML file <a
// href='AccessFile?fileId="
// + getFileIdInt(fileName)
// + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_odm_12")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(cdisc12)) {
String odmVersion = "1.2";
fileName =
generateFileService.createODMFile(
odmVersion,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy,
generalFileDirCopy,
eb,
activeStudy.getId(),
parentStudy.getId(),
studySubjectNumber,
true,
true,
true,
null);
logger.debug("-- gen odm file 1.2 default");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_odm_12_xml"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// // auditMessage.append(
// "You can access your ODM 1.2 XML file <a href='AccessFile?fileId="
// + getFileIdInt(fileName) + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_odm_12_xml")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(cdisc13)) {
String odmVersion = "1.3";
fileName =
generateFileService.createODMFile(
odmVersion,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy,
generalFileDirCopy,
eb,
activeStudy.getId(),
parentStudy.getId(),
studySubjectNumber,
true,
true,
true,
null);
logger.debug("-- gen odm file 1.3");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_odm_13"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your ODM 1.3 XML file <a href='AccessFile?fileId="
// + getFileIdInt(fileName) + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_odm_13")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(cdisc13oc)) {
String odmVersion = "oc1.3";
fileName =
generateFileService.createODMFile(
odmVersion,
sysTimeBegin,
generalFileDir,
datasetBean,
activeStudy,
generalFileDirCopy,
eb,
activeStudy.getId(),
parentStudy.getId(),
studySubjectNumber,
true,
true,
true,
null);
logger.debug("-- gen odm file 1.3 oc");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_odm_13_xml"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your ODM 1.3 w/OpenClinica Extension XML file <a
// href='AccessFile?fileId="
// + getFileIdInt(fileName)
// + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_odm_13_xml")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
if ("1".equals(spss)) {
SPSSReportBean answer = new SPSSReportBean();
fileName =
generateFileService.createSPSSFile(
datasetBean,
eb,
activeStudy,
parentStudy,
sysTimeBegin,
generalFileDir,
answer,
generalFileDirCopy);
logger.debug("-- gen spss file");
message.append(
"<p>"
+ pageMessages.getString("html_email_body_4")
+ " "
+ getFileNameStr(fileName)
+ pageMessages.getString("html_email_body_4_5")
+ SQLInitServlet.getField("sysURL.base")
+ "AccessFile?fileId="
+ getFileIdInt(fileName)
+ pageMessages.getString("html_email_body_3")
+ "</p>");
// MessageFormat mf = new MessageFormat("");
// mf.applyPattern(pageMessages.getString(
// "you_can_access_spss"));
// Object[] arguments = { getFileIdInt(fileName) };
// auditMessage.append(mf.format(arguments));
// auditMessage.append(
// "You can access your SPSS files <a href='AccessFile?fileId="
// + getFileIdInt(fileName) + "'>here</a>.<br/>");
auditMessage.append(
pageMessages.getString("you_can_access_spss")
+ getFileIdInt(fileName)
+ pageMessages.getString("access_end"));
}
// wrap up the message, and send the email
message.append(
"<p>"
+ pageMessages.getString("html_email_body_5")
+ "</P><P>"
+ pageMessages.getString("email_footer"));
try {
mailSender.sendEmail(
alertEmail.trim(),
pageMessages.getString("job_ran_for") + " " + datasetBean.getName(),
message.toString(),
true);
} catch (OpenClinicaSystemException ose) {
// Do Nothing, In the future we might want to have an email
// status added to system.
}
TriggerBean triggerBean = new TriggerBean();
triggerBean.setDataset(datasetBean);
triggerBean.setUserAccount(userBean);
triggerBean.setFullName(trigger.getName());
auditEventDAO.createRowForExtractDataJobSuccess(triggerBean, auditMessage.toString());
} else {
TriggerBean triggerBean = new TriggerBean();
// triggerBean.setDataset(datasetBean);
triggerBean.setUserAccount(userBean);
triggerBean.setFullName(trigger.getName());
auditEventDAO.createRowForExtractDataJobFailure(triggerBean);
// logger.debug("-- made it here for some reason, ds id: "
// + dsId);
}
// logger.debug("-- generated file: " + fileNameStr);
// dataSource.
} catch (Exception e) {
// TODO Auto-generated catch block -- ideally should generate a fail
// msg here, tbh 02/2009
logger.debug("-- found exception: " + e.getMessage());
e.printStackTrace();
}
}
