/** 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;
}
public int createFile(
String name,
String dir,
String content,
DatasetBean datasetBean,
long time,
ExportFormatBean efb,
boolean saveToDB) {
ArchivedDatasetFileBean fbFinal = new ArchivedDatasetFileBean();
// >> tbh 04/2010 #4915 replace all names' spaces with underscores
name = name.replaceAll(" ", "_");
fbFinal.setId(0);
try {
File complete = new File(dir);
if (!complete.isDirectory()) {
complete.mkdirs();
}
File newFile = new File(complete, name);
newFile.setLastModified(System.currentTimeMillis());
BufferedWriter w = new BufferedWriter(new FileWriter(newFile));
w.write(content);
w.close();
logger.info("finished writing the text file...");
// now, we write the file to the zip file
FileInputStream is = new FileInputStream(newFile);
ZipOutputStream z =
new ZipOutputStream(new FileOutputStream(new File(complete, name + ".zip")));
logger.info("created zip output stream...");
// we write over the content no matter what
// we then check to make sure there are no duplicates
// TODO need to change the above -- save all content!
// z.write(content);
z.putNextEntry(new java.util.zip.ZipEntry(name));
// int length = (int) newFile.length();
int bytesRead;
byte[] buff = new byte[512];
// read from buffered input stream and put into zip file
// while (-1 != (bytesRead = bis.read(buff, 0, buff.length))) {
while ((bytesRead = is.read(buff)) != -1) {
z.write(buff, 0, bytesRead);
}
logger.info("writing buffer...");
// }
z.closeEntry();
z.finish();
// newFile = new File(complete, name+".zip");
// newFile.setLastModified(System.currentTimeMillis());
//
// BufferedWriter w2 = new BufferedWriter(new FileWriter(newFile));
// w2.write(newOut.toString());
// w2.close();
if (is != null) {
try {
is.close();
} catch (java.io.IOException ie) {
ie.printStackTrace();
}
}
logger.info("finished zipping up file...");
// set up the zip to go into the database
if (saveToDB) {
ArchivedDatasetFileBean fb = new ArchivedDatasetFileBean();
fb.setName(name + ".zip");
// logger.info("ODM filename: " + name + ".zip");
fb.setFileReference(dir + name + ".zip");
// logger.info("ODM fileReference: " + dir + name + ".zip");
// current location of the file on the system
fb.setFileSize((int) newFile.length());
// logger.info("ODM setFileSize: " + (int)newFile.length() );
// set the above to compressed size?
fb.setRunTime((int) time);
// logger.info("ODM setRunTime: " + (int)time );
// need to set this in milliseconds, get it passed from above
// methods?
fb.setDatasetId(datasetBean.getId());
// logger.info("ODM setDatasetid: " + ds.getId() );
fb.setExportFormatBean(efb);
// logger.info("ODM setExportFormatBean: success" );
fb.setExportFormatId(efb.getId());
// logger.info("ODM setExportFormatId: " + efb.getId());
fb.setOwner(userBean);
// logger.info("ODM setOwner: " + sm.getUserBean());
fb.setOwnerId(userBean.getId());
// logger.info("ODM setOwnerId: " + sm.getUserBean().getId() );
fb.setDateCreated(new Date(System.currentTimeMillis()));
boolean write = true;
ArchivedDatasetFileDAO asdfDAO = new ArchivedDatasetFileDAO(ds);
// eliminating all checks so that we create multiple files, tbh 6-7
if (write) {
fbFinal = (ArchivedDatasetFileBean) asdfDAO.create(fb);
} else {
logger.info("duplicate found: " + fb.getName());
}
}
// created in database!
} catch (Exception e) {
logger.warn(e.getMessage());
System.out.println("-- exception thrown at createFile: " + e.getMessage());
logger.info("-- exception thrown at createFile: " + e.getMessage());
e.printStackTrace();
}
return fbFinal.getId();
}
public int createFile(
String zipName,
ArrayList names,
String dir,
ArrayList contents,
DatasetBean datasetBean,
long time,
ExportFormatBean efb,
boolean saveToDB) {
ArchivedDatasetFileBean fbFinal = new ArchivedDatasetFileBean();
// >> tbh #4915
zipName = zipName.replaceAll(" ", "_");
fbFinal.setId(0);
try {
File complete = new File(dir);
if (!complete.isDirectory()) {
complete.mkdirs();
}
int totalSize = 0;
ZipOutputStream z =
new ZipOutputStream(new FileOutputStream(new File(complete, zipName + ".zip")));
FileInputStream is = null;
for (int i = 0; i < names.size(); i++) {
String name = (String) names.get(i);
// >> tbh #4915
name = name.replaceAll(" ", "_");
String content = (String) contents.get(i);
File newFile = new File(complete, name);
// totalSize = totalSize + (int)newFile.length();
newFile.setLastModified(System.currentTimeMillis());
BufferedWriter w = new BufferedWriter(new FileWriter(newFile));
w.write(content);
w.close();
logger.info("finished writing the text file...");
// now, we write the file to the zip file
is = new FileInputStream(newFile);
logger.info("created zip output stream...");
z.putNextEntry(new java.util.zip.ZipEntry(name));
int bytesRead;
byte[] buff = new byte[512];
while ((bytesRead = is.read(buff)) != -1) {
z.write(buff, 0, bytesRead);
totalSize += 512;
}
z.closeEntry();
// A. Hamid. 4910
is.close();
if (CoreResources.getField("dataset_file_delete").equalsIgnoreCase("true")
|| CoreResources.getField("dataset_file_delete").equals("")) {
newFile.delete();
}
}
logger.info("writing buffer...");
// }
z.flush();
z.finish();
z.close();
if (is != null) {
try {
is.close();
} catch (java.io.IOException ie) {
ie.printStackTrace();
}
}
logger.info("finished zipping up file...");
// set up the zip to go into the database
if (saveToDB) {
ArchivedDatasetFileBean fb = new ArchivedDatasetFileBean();
fb.setName(zipName + ".zip");
fb.setFileReference(dir + zipName + ".zip");
// current location of the file on the system
fb.setFileSize(totalSize);
// set the above to compressed size?
fb.setRunTime((int) time);
// need to set this in milliseconds, get it passed from above
// methods?
fb.setDatasetId(datasetBean.getId());
fb.setExportFormatBean(efb);
fb.setExportFormatId(efb.getId());
fb.setOwner(userBean);
fb.setOwnerId(userBean.getId());
fb.setDateCreated(new Date(System.currentTimeMillis()));
boolean write = true;
ArchivedDatasetFileDAO asdfDAO = new ArchivedDatasetFileDAO(ds);
if (write) {
fbFinal = (ArchivedDatasetFileBean) asdfDAO.create(fb);
logger.info("Created ADSFile!: " + fbFinal.getId() + " for " + zipName + ".zip");
} else {
logger.info("duplicate found: " + fb.getName());
}
}
// created in database!
} catch (Exception e) {
logger.warn(e.getMessage());
System.out.println("-- exception at create file: " + e.getMessage());
e.printStackTrace();
}
return fbFinal.getId();
}
/**
* createSPSSFile, added by tbh, 01/2009
*
* @param db
* @param eb
* @param currentstudyid
* @param parentstudy
* @return
*/
public HashMap<String, Integer> createSPSSFile(
DatasetBean db,
ExtractBean eb2,
StudyBean currentStudy,
StudyBean parentStudy,
long sysTimeBegin,
String generalFileDir,
SPSSReportBean answer,
String generalFileDirCopy) {
setUpResourceBundles();
String SPSSFileName = db.getName() + "_data_spss.dat";
String DDLFileName = db.getName() + "_ddl_spss.sps";
String ZIPFileName = db.getName() + "_spss";
SPSSVariableNameValidationBean svnvbean = new SPSSVariableNameValidationBean();
answer.setDatFileName(SPSSFileName);
// DatasetDAO dsdao = new DatasetDAO(ds);
// create the extract bean here, tbh
// ExtractBean eb = this.generateExtractBean(db, currentStudy,
// parentStudy);
// eb = dsdao.getDatasetData(eb, currentStudy.getId(),
// parentStudy.getId());
// eb.getMetadata();
// eb.computeReport(answer);
answer.setItems(eb2.getItemNames()); // set up items here to get
// itemMetadata
// set up response sets for each item here
ItemDAO itemdao = new ItemDAO(ds);
ItemFormMetadataDAO imfdao = new ItemFormMetadataDAO(ds);
ArrayList items = answer.getItems();
for (int i = 0; i < items.size(); i++) {
DisplayItemHeaderBean dih = (DisplayItemHeaderBean) items.get(i);
ItemBean item = dih.getItem();
ArrayList metas = imfdao.findAllByItemId(item.getId());
// for (int h = 0; h < metas.size(); h++) {
// ItemFormMetadataBean ifmb = (ItemFormMetadataBean)
// metas.get(h);
// logger.info("group name found:
// "+ifmb.getGroupLabel());
// }
// logger.info("crf versionname" +
// meta.getCrfVersionName());
item.setItemMetas(metas);
}
HashMap eventDescs = new HashMap<String, String>();
eventDescs = eb2.getEventDescriptions();
eventDescs.put("SubjID", resword.getString("study_subject_ID"));
eventDescs.put("ProtocolID", resword.getString("protocol_ID_site_ID"));
eventDescs.put("DOB", resword.getString("date_of_birth"));
eventDescs.put("YOB", resword.getString("year_of_birth"));
eventDescs.put("Gender", resword.getString("gender"));
answer.setDescriptions(eventDescs);
ArrayList generatedReports = new ArrayList<String>();
try {
// YW <<
generatedReports.add(answer.getMetadataFile(svnvbean, eb2).toString());
generatedReports.add(answer.getDataFile().toString());
// YW >>
} catch (IndexOutOfBoundsException i) {
generatedReports.add(answer.getMetadataFile(svnvbean, eb2).toString());
logger.debug("throw the error here");
}
long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
ArrayList titles = new ArrayList();
// YW <<
titles.add(DDLFileName);
titles.add(SPSSFileName);
// YW >>
// create new createFile method that accepts array lists to
// put into zip files
int fId =
this.createFile(
ZIPFileName,
titles,
generalFileDir,
generatedReports,
db,
sysTimeEnd,
ExportFormatBean.TXTFILE,
true);
if (!"".equals(generalFileDirCopy)) {
int fId2 =
this.createFile(
ZIPFileName,
titles,
generalFileDirCopy,
generatedReports,
db,
sysTimeEnd,
ExportFormatBean.TXTFILE,
false);
}
// return DDLFileName;
HashMap answerMap = new HashMap<String, Integer>();
answerMap.put(DDLFileName, new Integer(fId));
return answerMap;
}
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();
}
}