/** createTabFile, added by tbh, 01/2009 */
public HashMap<String, Integer> createTabFile(
ExtractBean eb,
long sysTimeBegin,
String generalFileDir,
DatasetBean datasetBean,
int activeStudyId,
int parentStudyId,
String generalFileDirCopy) {
TabReportBean answer = new TabReportBean();
DatasetDAO dsdao = new DatasetDAO(ds);
// create the extract bean here, tbh
eb = dsdao.getDatasetData(eb, activeStudyId, parentStudyId);
eb.getMetadata();
eb.computeReport(answer);
long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
String TXTFileName = datasetBean.getName() + "_tab.xls";
int fId =
this.createFile(
TXTFileName,
generalFileDir,
answer.toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.TXTFILE,
true);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFile(
TXTFileName,
generalFileDirCopy,
answer.toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.TXTFILE,
false);
}
logger.info("created txt file");
// return TXTFileName;
HashMap answerMap = new HashMap<String, Integer>();
answerMap.put(TXTFileName, new Integer(fId));
return answerMap;
}
/** createODMfile, added by tbh, 01/2009 */
public HashMap<String, Integer> createODMFile(
String odmVersion,
long sysTimeBegin,
String generalFileDir,
DatasetBean datasetBean,
StudyBean currentStudy,
String generalFileDirCopy,
ExtractBean eb,
Integer currentStudyId,
Integer parentStudyId,
String studySubjectNumber) {
Integer ssNumber = getStudySubjectNumber(studySubjectNumber);
MetaDataCollector mdc = new MetaDataCollector(ds, datasetBean, currentStudy);
AdminDataCollector adc = new AdminDataCollector(ds, datasetBean, currentStudy);
ClinicalDataCollector cdc = new ClinicalDataCollector(ds, datasetBean, currentStudy);
MetaDataCollector.setTextLength(200);
if (odmVersion != null) {
// by default odmVersion is 1.2
if ("1.3".equals(odmVersion)) {
ODMBean odmb = new ODMBean();
odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 ODM1-3-0.xsd");
ArrayList<String> xmlnsList = new ArrayList<String>();
xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.3\"");
odmb.setXmlnsList(xmlnsList);
odmb.setODMVersion("1.3");
mdc.setODMBean(odmb);
adc.setOdmbean(odmb);
cdc.setODMBean(odmb);
} else if ("oc1.2".equals(odmVersion)) {
ODMBean odmb = new ODMBean();
// odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.2 OpenClinica-ODM1-2-1.xsd");
odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.2 OpenClinica-ODM1-2-1-OC1.xsd");
ArrayList<String> xmlnsList = new ArrayList<String>();
xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.2\"");
xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/openclinica_odm/v1.2\"");
odmb.setXmlnsList(xmlnsList);
odmb.setODMVersion("oc1.2");
mdc.setODMBean(odmb);
adc.setOdmbean(odmb);
cdc.setODMBean(odmb);
} else if ("oc1.3".equals(odmVersion)) {
ODMBean odmb = mdc.getODMBean();
// odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 OpenClinica-ODM1-3-0.xsd");
odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 OpenClinica-ODM1-3-0-OC1.xsd");
ArrayList<String> xmlnsList = new ArrayList<String>();
xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.3\"");
xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/openclinica_odm/v1.3\"");
odmb.setXmlnsList(xmlnsList);
odmb.setODMVersion("oc1.3");
mdc.setODMBean(odmb);
adc.setOdmbean(odmb);
cdc.setODMBean(odmb);
}
}
//////////////////////////////////////////
////////// MetaData Extraction //////////
mdc.collectFileData();
MetaDataReportBean metaReport = new MetaDataReportBean(mdc.getOdmStudyMap());
metaReport.setODMVersion(odmVersion);
metaReport.setOdmBean(mdc.getODMBean());
metaReport.createChunkedOdmXml(Boolean.TRUE);
long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
String ODMXMLFileName = mdc.getODMBean().getFileOID() + ".xml";
int fId =
this.createFileK(
ODMXMLFileName,
generalFileDir,
metaReport.getXmlOutput().toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFileK(
ODMXMLFileName,
generalFileDirCopy,
metaReport.getXmlOutput().toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
}
//////////////////////////////////////////
////////// AdminData Extraction //////////
adc.collectFileData();
AdminDataReportBean adminReport = new AdminDataReportBean(adc.getOdmAdminDataMap());
adminReport.setODMVersion(odmVersion);
adminReport.setOdmBean(mdc.getODMBean());
adminReport.createChunkedOdmXml(Boolean.TRUE);
sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
fId =
this.createFileK(
ODMXMLFileName,
generalFileDir,
adminReport.getXmlOutput().toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFileK(
ODMXMLFileName,
generalFileDirCopy,
adminReport.getXmlOutput().toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
}
//////////////////////////////////////////
////////// ClinicalData Extraction ///////
DatasetDAO dsdao = new DatasetDAO(ds);
String sql = eb.getDataset().getSQLStatement();
String st_sed_in = dsdao.parseSQLDataset(sql, true, true);
String st_itemid_in = dsdao.parseSQLDataset(sql, false, true);
int datasetItemStatusId = eb.getDataset().getDatasetItemStatus().getId();
String ecStatusConstraint = dsdao.getECStatusConstraint(datasetItemStatusId);
String itStatusConstraint = dsdao.getItemDataStatusConstraint(datasetItemStatusId);
Iterator<OdmStudyBase> it = cdc.getStudyBaseMap().values().iterator();
while (it.hasNext()) {
OdmStudyBase u = it.next();
ArrayList newRows =
dsdao.selectStudySubjects(
u.getStudy().getId(),
0,
st_sed_in,
st_itemid_in,
dsdao.genDatabaseDateConstraint(eb),
ecStatusConstraint,
itStatusConstraint);
///////////////
int fromIndex = 0;
boolean firstIteration = true;
while (fromIndex < newRows.size()) {
int toIndex =
fromIndex + ssNumber < newRows.size() ? fromIndex + ssNumber : newRows.size() - 1;
List x = newRows.subList(fromIndex, toIndex + 1);
fromIndex = toIndex + 1;
String studySubjectIds = "";
for (int i = 0; i < x.size(); i++) {
StudySubjectBean sub = new StudySubjectBean();
sub = (StudySubjectBean) x.get(i);
studySubjectIds += "," + sub.getId();
} // for
studySubjectIds = studySubjectIds.replaceFirst(",", "");
ClinicalDataUnit cdata =
new ClinicalDataUnit(
ds,
datasetBean,
cdc.getOdmbean(),
u.getStudy(),
cdc.getCategory(),
studySubjectIds);
cdata.setCategory(cdc.getCategory());
cdata.collectOdmClinicalData();
FullReportBean report = new FullReportBean();
report.setClinicalData(cdata.getOdmClinicalData());
report.setOdmStudyMap(mdc.getOdmStudyMap());
report.setODMVersion(odmVersion);
// report.setOdmStudy(mdc.getOdmStudy());
report.setOdmBean(mdc.getODMBean());
if (firstIteration && fromIndex >= newRows.size()) {
report.createChunkedOdmXml(Boolean.TRUE, true, true);
firstIteration = false;
} else if (firstIteration) {
report.createChunkedOdmXml(Boolean.TRUE, true, false);
firstIteration = false;
} else if (fromIndex >= newRows.size()) {
report.createChunkedOdmXml(Boolean.TRUE, false, true);
} else {
report.createChunkedOdmXml(Boolean.TRUE, false, false);
}
fId =
this.createFileK(
ODMXMLFileName,
generalFileDir,
report.getXmlOutput().toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFileK(
ODMXMLFileName,
generalFileDirCopy,
report.getXmlOutput().toString(),
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
}
}
}
sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
fId =
this.createFileK(
ODMXMLFileName,
generalFileDir,
"</ODM>",
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
true);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFileK(
ODMXMLFileName,
generalFileDirCopy,
"</ODM>",
datasetBean,
sysTimeEnd,
ExportFormatBean.XMLFILE,
false);
}
//////////////////////////////////////////
////////// pre pagination extraction /////
/*
mdc.collectFileData();
adc.collectOdmAdminDataMap();
cdc.collectOdmClinicalDataMap();
FullReportBean report = new FullReportBean();
report.setClinicalDataMap(cdc.getOdmClinicalDataMap());
report.setAdminDataMap(adc.getOdmAdminDataMap());
report.setOdmStudyMap(mdc.getOdmStudyMap());
report.setOdmBean(mdc.getODMBean());
report.setODMVersion(odmVersion);
report.createOdmXml(Boolean.TRUE);
long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
String ODMXMLFileName = mdc.getODMBean().getFileOID() + ".xml";
int fId = this.createFile(ODMXMLFileName, generalFileDir, report.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, true);
if (!"".equals(generalFileDirCopy)) {
int fId2 = this.createFile(ODMXMLFileName, generalFileDirCopy, report.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false);
} */
// return ODMXMLFileName;
HashMap answerMap = new HashMap<String, Integer>();
answerMap.put(ODMXMLFileName, new Integer(fId));
return answerMap;
}
@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);
}
public void processRequest() throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
int studyId = fp.getInt("id");
StudyBean study = (StudyBean) sdao.findByPK(studyId);
// find all sites
ArrayList sites = (ArrayList) sdao.findAllByParent(studyId);
// find all user and roles in the study, include ones in sites
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
ArrayList userRoles = udao.findAllByStudyId(studyId);
// find all subjects in the study, include ones in sites
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
ArrayList subjects = ssdao.findAllByStudy(study);
// find all events in the study, include ones in sites
StudyEventDefinitionDAO sefdao = new StudyEventDefinitionDAO(sm.getDataSource());
ArrayList definitions = sefdao.findAllByStudy(study);
String action = request.getParameter("action");
if (studyId == 0) {
addPageMessage("Please choose a study to restore.");
forwardPage(Page.STUDY_LIST_SERVLET);
} else {
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("studyToRestore", study);
request.setAttribute("sitesToRestore", sites);
request.setAttribute("userRolesToRestore", userRoles);
request.setAttribute("subjectsToRestore", subjects);
request.setAttribute("definitionsToRRestore", definitions);
forwardPage(Page.RESTORE_STUDY);
} else {
logger.info("submit to restore the study");
// change all statuses to unavailable
StudyDAO studao = new StudyDAO(sm.getDataSource());
study.setStatus(Status.AVAILABLE);
study.setUpdater(ub);
study.setUpdatedDate(new Date());
studao.update(study);
// remove all sites
for (int i = 0; i < sites.size(); i++) {
StudyBean site = (StudyBean) sites.get(i);
site.setStatus(Status.AVAILABLE);
site.setUpdater(ub);
site.setUpdatedDate(new Date());
sdao.update(site);
}
// remove all users and roles
for (int i = 0; i < userRoles.size(); i++) {
StudyUserRoleBean role = (StudyUserRoleBean) userRoles.get(i);
role.setStatus(Status.AVAILABLE);
role.setUpdater(ub);
role.setUpdatedDate(new Date());
udao.updateStudyUserRole(role, role.getUserName());
}
// remove all subjects
for (int i = 0; i < subjects.size(); i++) {
StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
subject.setStatus(Status.AVAILABLE);
subject.setUpdater(ub);
subject.setUpdatedDate(new Date());
ssdao.update(subject);
}
// remove all study_group
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
ArrayList groups = sgdao.findAllByStudy(study);
for (int i = 0; i < groups.size(); i++) {
StudyGroupBean group = (StudyGroupBean) groups.get(i);
group.setStatus(Status.AVAILABLE);
group.setUpdater(ub);
group.setUpdatedDate(new Date());
sgdao.update(group);
// all subject_group_map
ArrayList subjectGroupMaps = sgmdao.findAllByStudyGroupId(group.getId());
for (int j = 0; j < subjectGroupMaps.size(); j++) {
SubjectGroupMapBean sgMap = (SubjectGroupMapBean) subjectGroupMaps.get(j);
sgMap.setStatus(Status.AVAILABLE);
sgMap.setUpdater(ub);
sgMap.setUpdatedDate(new Date());
sgmdao.update(sgMap);
}
}
// remove all event definitions and event
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
for (int i = 0; i < definitions.size(); i++) {
StudyEventDefinitionBean definition = (StudyEventDefinitionBean) definitions.get(i);
definition.setStatus(Status.AVAILABLE);
definition.setUpdater(ub);
definition.setUpdatedDate(new Date());
sefdao.update(definition);
ArrayList edcs = (ArrayList) edcdao.findAllByDefinition(definition.getId());
for (int j = 0; j < edcs.size(); j++) {
EventDefinitionCRFBean edc = (EventDefinitionCRFBean) edcs.get(j);
edc.setStatus(Status.AVAILABLE);
edc.setUpdater(ub);
edc.setUpdatedDate(new Date());
edcdao.update(edc);
}
ArrayList events = (ArrayList) sedao.findAllByDefinition(definition.getId());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
for (int j = 0; j < events.size(); j++) {
StudyEventBean event = (StudyEventBean) events.get(j);
event.setStatus(Status.AVAILABLE);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
sedao.update(event);
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
for (int k = 0; k < eventCRFs.size(); k++) {
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
eventCRF.setStatus(Status.AVAILABLE);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
ecdao.update(eventCRF);
ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
for (int a = 0; a < itemDatas.size(); a++) {
ItemDataBean item = (ItemDataBean) itemDatas.get(a);
item.setStatus(Status.AVAILABLE);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
} // for definitions
DatasetDAO datadao = new DatasetDAO(sm.getDataSource());
ArrayList dataset = datadao.findAllByStudyId(study.getId());
for (int i = 0; i < dataset.size(); i++) {
DatasetBean data = (DatasetBean) dataset.get(i);
data.setStatus(Status.AVAILABLE);
data.setUpdater(ub);
data.setUpdatedDate(new Date());
datadao.update(data);
}
addPageMessage("This study has been restored successfully.");
forwardPage(Page.STUDY_LIST_SERVLET);
}
}
}
@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();
}
}