use of org.akaza.openclinica.bean.core.Status in project OpenClinica by OpenClinica.
the class RestoreEventCRFServlet method processRequest.
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
// eventCRFId
int eventCRFId = fp.getInt("id");
// studySubjectId
int studySubId = fp.getInt("studySubId");
checkStudyLocked("ViewStudySubject?id" + studySubId, respage.getString("current_study_locked"));
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
StudyDAO sdao = new StudyDAO(sm.getDataSource());
if (eventCRFId == 0) {
addPageMessage(respage.getString("please_choose_an_event_CRF_to_restore"));
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
} else {
EventCRFBean eventCRF = (EventCRFBean) ecdao.findByPK(eventCRFId);
StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
// YW 11-07-2007, an event CRF could not be restored if its study
// subject has been removed
Status s = studySub.getStatus();
if ("removed".equalsIgnoreCase(s.getName()) || "auto-removed".equalsIgnoreCase(s.getName())) {
addPageMessage(resword.getString("event_CRF") + resterm.getString("could_not_be") + resterm.getString("restored") + "." + respage.getString("study_subject_has_been_deleted"));
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
}
// YW
request.setAttribute("studySub", studySub);
// construct info needed on view event crf page
CRFDAO cdao = new CRFDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
int crfVersionId = eventCRF.getCRFVersionId();
CRFBean cb = cdao.findByVersionId(crfVersionId);
eventCRF.setCrf(cb);
CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(crfVersionId);
eventCRF.setCrfVersion(cvb);
// then get the definition so we can call
// DisplayEventCRFBean.setFlags
int studyEventId = eventCRF.getStudyEventId();
StudyEventBean event = (StudyEventBean) sedao.findByPK(studyEventId);
int studyEventDefinitionId = sedao.getDefinitionIdFromStudyEventId(studyEventId);
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(studyEventDefinitionId);
event.setStudyEventDefinition(sed);
request.setAttribute("event", event);
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyBean study = (StudyBean) sdao.findByPK(studySub.getStudyId());
EventDefinitionCRFBean edc = edcdao.findByStudyEventDefinitionIdAndCRFId(study, studyEventDefinitionId, cb.getId());
DisplayEventCRFBean dec = new DisplayEventCRFBean();
dec.setEventCRF(eventCRF);
dec.setFlags(eventCRF, ub, currentRole, edc.isDoubleEntry());
// find all item data
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
ArrayList itemData = iddao.findAllByEventCRFId(eventCRF.getId());
request.setAttribute("items", itemData);
String action = request.getParameter("action");
if ("confirm".equalsIgnoreCase(action)) {
if (!eventCRF.getStatus().equals(Status.DELETED) && !eventCRF.getStatus().equals(Status.AUTO_DELETED)) {
addPageMessage(respage.getString("this_event_CRF_avilable_for_study") + " " + " " + respage.getString("please_contact_sysadmin_for_more_information"));
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
return;
}
request.setAttribute("displayEventCRF", dec);
forwardPage(Page.RESTORE_EVENT_CRF);
} else {
logger.info("submit to restore the event CRF from study");
eventCRF.setStatus(Status.AVAILABLE);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
ecdao.update(eventCRF);
// restore all the item data
for (int a = 0; a < itemData.size(); a++) {
ItemDataBean item = (ItemDataBean) itemData.get(a);
if (item.getStatus().equals(Status.AUTO_DELETED)) {
item.setStatus(Status.AVAILABLE);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
String emailBody = respage.getString("the_event_CRF") + cb.getName() + " " + respage.getString("has_been_restored_to_the_event") + " " + event.getStudyEventDefinition().getName() + ".";
addPageMessage(emailBody);
sendEmail(emailBody);
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
}
}
}
use of org.akaza.openclinica.bean.core.Status in project OpenClinica by OpenClinica.
the class RestoreStudyEventServlet method processRequest.
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
// studyEventId
int studyEventId = fp.getInt("id");
// studySubjectId
int studySubId = fp.getInt("studySubId");
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
if (studyEventId == 0) {
addPageMessage(respage.getString("please_choose_a_SE_to_restore"));
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
} else {
StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
// YW 11-07-2007, a study event could not be restored if its study
// subject has been removed
Status s = studySub.getStatus();
if ("removed".equalsIgnoreCase(s.getName()) || "auto-removed".equalsIgnoreCase(s.getName())) {
addPageMessage(resword.getString("study_event") + resterm.getString("could_not_be") + resterm.getString("restored") + "." + respage.getString("study_subject_has_been_deleted"));
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
}
// YW
StudyEventBean event = (StudyEventBean) sedao.findByPK(studyEventId);
request.setAttribute("studySub", studySub);
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(event.getStudyEventDefinitionId());
event.setStudyEventDefinition(sed);
StudyDAO studydao = new StudyDAO(sm.getDataSource());
StudyBean study = (StudyBean) studydao.findByPK(studySub.getStudyId());
request.setAttribute("study", study);
String action = request.getParameter("action");
if ("confirm".equalsIgnoreCase(action)) {
if (event.getStatus().equals(Status.AVAILABLE)) {
addPageMessage(respage.getString("this_event_is_already_available_for_study") + " " + respage.getString("please_contact_sysadmin_for_more_information"));
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
return;
}
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
// find all crfs in the definition
ArrayList eventDefinitionCRFs = (ArrayList) edcdao.findAllByEventDefinitionId(study, sed.getId());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
// construct info needed on view study event page
DisplayStudyEventBean de = new DisplayStudyEventBean();
de.setStudyEvent(event);
de.setDisplayEventCRFs(getDisplayEventCRFs(eventCRFs, eventDefinitionCRFs));
request.setAttribute("displayEvent", de);
forwardPage(Page.RESTORE_STUDY_EVENT);
} else {
logger.info("submit to restore the event to study");
// restore event to study
event.setStatus(Status.AVAILABLE);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
sedao.update(event);
// restore event crfs
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
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);
if (eventCRF.getStatus().equals(Status.AUTO_DELETED)) {
eventCRF.setStatus(Status.AVAILABLE);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
ecdao.update(eventCRF);
// remove all the item data
ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
for (int a = 0; a < itemDatas.size(); a++) {
ItemDataBean item = (ItemDataBean) itemDatas.get(a);
if (item.getStatus().equals(Status.AUTO_DELETED)) {
item.setStatus(Status.AVAILABLE);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
}
String emailBody = respage.getString("the_event") + event.getStudyEventDefinition().getName() + " " + respage.getString("has_been_restored_to_the_study") + " " + study.getName() + ".";
addPageMessage(emailBody);
// sendEmail(emailBody);
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
}
}
}
use of org.akaza.openclinica.bean.core.Status in project OpenClinica by OpenClinica.
the class DataEntryServlet method markCRFComplete.
/**
* The following methods are for 'mark CRF complete'
* @param request TODO
*
* @return
*/
protected boolean markCRFComplete(HttpServletRequest request) throws Exception {
locale = LocaleResolver.getLocale(request);
HttpSession session = request.getSession();
UserAccountBean ub = (UserAccountBean) request.getSession().getAttribute(USER_BEAN_NAME);
EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) request.getAttribute(EVENT_DEF_CRF_BEAN);
EventCRFDAO ecdao = new EventCRFDAO(getDataSource());
ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale);
// < respage =
// ResourceBundle.getBundle("org.akaza.openclinica.i18n.page_messages",
// locale);
// < restext =
// ResourceBundle.getBundle("org.akaza.openclinica.i18n.notes",locale);
// <
// resexception=ResourceBundle.getBundle(
// "org.akaza.openclinica.i18n.exceptions",locale);
getEventCRFBean(request);
getEventDefinitionCRFBean(request);
DataEntryStage stage = ecb.getStage();
// request.setAttribute(TableOfContentsServlet.INPUT_EVENT_CRF_BEAN,
// ecb);
// request.setAttribute(INPUT_EVENT_CRF_ID, new Integer(ecb.getId()));
LOGGER.trace("inout_event_crf_id:" + ecb.getId());
if (stage.equals(DataEntryStage.UNCOMPLETED) || stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) || stage.equals(DataEntryStage.LOCKED)) {
addPageMessage(respage.getString("not_mark_CRF_complete1"), request);
return false;
}
if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
if (!edcb.isDoubleEntry()) {
addPageMessage(respage.getString("not_mark_CRF_complete2"), request);
return false;
}
}
if (isEachRequiredFieldFillout(request) == false) {
addPageMessage(respage.getString("not_mark_CRF_complete4"), request);
return false;
}
/*
* if (ecb.getInterviewerName().trim().equals("")) { throw new InconsistentStateException(errorPage, "You may not mark this Event CRF complete, because
* the interviewer name is blank."); }
*/
Status newStatus = ecb.getStatus();
boolean ide = true;
if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY) && edcb.isDoubleEntry()) {
newStatus = Status.PENDING;
ecb.setUpdaterId(ub.getId());
ecb.setUpdater(ub);
ecb.setUpdatedDate(new Date());
ecb.setDateCompleted(new Date());
} else if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY) && !edcb.isDoubleEntry()) {
newStatus = Status.UNAVAILABLE;
ecb.setUpdaterId(ub.getId());
ecb.setUpdater(ub);
ecb.setUpdatedDate(new Date());
ecb.setDateCompleted(new Date());
ecb.setDateValidateCompleted(new Date());
} else if (stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) && edcb.isDoubleEntry()) {
newStatus = Status.UNAVAILABLE;
ecb.setUpdaterId(ub.getId());
ecb.setUpdater(ub);
ecb.setUpdatedDate(new Date());
ecb.setDateCompleted(new Date());
ecb.setDateValidateCompleted(new Date());
ide = false;
} else if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
newStatus = Status.UNAVAILABLE;
ecb.setDateValidateCompleted(new Date());
ecb.setUpdaterId(ub.getId());
ecb.setUpdater(ub);
ide = false;
}
// create them
if (!isEachSectionReviewedOnce(request)) {
boolean canSave = saveItemsToMarkComplete(newStatus, request);
if (canSave == false) {
addPageMessage(respage.getString("not_mark_CRF_complete3"), request);
return false;
}
}
ecb.setStatus(newStatus);
/*
* Marking the data entry as signed if the corresponding EventDefinitionCRF is being enabled for electronic signature.
*/
if (edcb.isElectronicSignature()) {
ecb.setElectronicSignatureStatus(true);
}
ecb = (EventCRFBean) ecdao.update(ecb);
// note the below statement only updates the DATES, not the STATUS
ecdao.markComplete(ecb, ide);
// update all the items' status to complete
iddao.updateStatusByEventCRF(ecb, newStatus);
// change status for study event
StudyEventDAO sedao = new StudyEventDAO(getDataSource());
StudyEventBean seb = (StudyEventBean) sedao.findByPK(ecb.getStudyEventId());
seb.setUpdatedDate(new Date());
seb.setUpdater(ub);
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(getDataSource());
ArrayList allCRFs = ecdao.findAllByStudyEventAndStatus(seb, Status.UNAVAILABLE);
StudyBean study = (StudyBean) session.getAttribute("study");
ArrayList allEDCs = (ArrayList) edcdao.findAllActiveByEventDefinitionId(study, seb.getStudyEventDefinitionId());
CRFVersionDAO crfversionDao = new CRFVersionDAO(getDataSource());
boolean eventCompleted = true;
boolean allRequired = true;
//JN Adding another flag
boolean allCrfsCompleted = false;
int allEDCsize = allEDCs.size();
ArrayList nonRequiredCrfIds = new ArrayList();
ArrayList requiredCrfIds = new ArrayList();
if (allCRFs.size() == allEDCs.size()) {
// was
//JN: all crfs are completed and then set the subject event status as complete
seb.setSubjectEventStatus(SubjectEventStatus.COMPLETED);
}
seb = (StudyEventBean) sedao.update(seb);
request.setAttribute(INPUT_EVENT_CRF, ecb);
request.setAttribute(EVENT_DEF_CRF_BEAN, edcb);
return true;
}
use of org.akaza.openclinica.bean.core.Status in project OpenClinica by OpenClinica.
the class ImportSpringJob method processData.
/*
* processData, a method which should take in all XML files, check to see if they were imported previously, ? insert
* them into the database if not, and return a message which will go to audit and to the end user.
*/
private ArrayList<String> processData(File[] dest, DataSource dataSource, ResourceBundle respage, ResourceBundle resword, UserAccountBean ub, StudyBean studyBean, File destDirectory, TriggerBean triggerBean, RuleSetServiceInterface ruleSetService) throws Exception {
StringBuffer msg = new StringBuffer();
StringBuffer auditMsg = new StringBuffer();
Mapping myMap = new Mapping();
String propertiesPath = CoreResources.PROPERTIES_DIR;
new File(propertiesPath + File.separator + "ODM1-3-0.xsd");
File xsdFile2 = new File(propertiesPath + File.separator + "ODM1-2-1.xsd");
// @pgawade 18-April-2011 Fix for issue 8394
String ODM_MAPPING_DIR_path = CoreResources.ODM_MAPPING_DIR;
myMap.loadMapping(ODM_MAPPING_DIR_path + File.separator + "cd_odm_mapping.xml");
Unmarshaller um1 = new Unmarshaller(myMap);
ODMContainer odmContainer = new ODMContainer();
// File("log.txt")));
for (File f : dest) {
// >> tbh
boolean fail = false;
// all whitespace, one or more times
String regex = "\\s+";
// replace with underscores
String replacement = "_";
String pattern = "yyyy" + File.separator + "MM" + File.separator + "dd" + File.separator + "HHmmssSSS" + File.separator;
SimpleDateFormat sdfDir = new SimpleDateFormat(pattern);
String generalFileDir = sdfDir.format(new java.util.Date());
File logDestDirectory = new File(destDirectory + File.separator + generalFileDir + f.getName().replaceAll(regex, replacement) + ".log.txt");
if (!logDestDirectory.isDirectory()) {
logger.debug("creating new dir: " + logDestDirectory.getAbsolutePath());
logDestDirectory.mkdirs();
}
File newFile = new File(logDestDirectory, "log.txt");
// FileOutputStream out = new FileOutputStream(new
// File(logDestDirectory, "log.txt"));
// BufferedWriter out = null;
// wrap the below in a try-catch?
BufferedWriter out = new BufferedWriter(new FileWriter(newFile));
// << tbh 06/2010
if (f != null) {
String firstLine = "<P>" + f.getName() + ": ";
msg.append(firstLine);
out.write(firstLine);
auditMsg.append(firstLine);
} else {
msg.append("<P>" + respage.getString("unreadable_file") + ": ");
out.write("<P>" + respage.getString("unreadable_file") + ": ");
auditMsg.append("<P>" + respage.getString("unreadable_file") + ": ");
}
try {
// schemaValidator.validateAgainstSchema(f, xsdFile);
odmContainer = (ODMContainer) um1.unmarshal(new FileReader(f));
logger.debug("Found crf data container for study oid: " + odmContainer.getCrfDataPostImportContainer().getStudyOID());
logger.debug("found length of subject list: " + odmContainer.getCrfDataPostImportContainer().getSubjectData().size());
} catch (Exception me1) {
// fail against one, try another
try {
schemaValidator.validateAgainstSchema(f, xsdFile2);
// for backwards compatibility, we also try to validate vs
// 1.2.1 ODM 06/2008
odmContainer = (ODMContainer) um1.unmarshal(new FileReader(f));
} catch (Exception me2) {
// not sure if we want to report me2
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_xml_is_not_well_formed"));
Object[] arguments = { me1.getMessage() };
msg.append(mf.format(arguments) + "<br/>");
auditMsg.append(mf.format(arguments) + "<br/>");
// break here with an exception
logger.error("found an error with XML: " + msg.toString());
// continue looping
continue;
}
}
// next: check, then import
List<String> errors = getImportCRFDataService(dataSource).validateStudyMetadata(odmContainer, studyBean.getId());
// the user could be in any study ...
if (errors != null) {
if (errors.size() > 0) {
out.write("<P>Errors:<br/>");
for (String error : errors) {
out.write(error + "<br/>");
}
out.write("</P>");
// fail = true;
// forwardPage(Page.IMPORT_CRF_DATA);
// break here with an exception
// throw new Exception("Your XML in the file " + f.getName()
// + " was well formed, but generated metadata errors: " +
// errors.toString());
// msg.append("Your XML in the file " + f.getName() +
// " was well formed, but generated metadata errors: " +
// errors.toString());
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_xml_in_the_file"));
Object[] arguments = { f.getName(), errors.size() };
auditMsg.append(mf.format(arguments) + "<br/>");
msg.append(mf.format(arguments) + "<br/>");
auditMsg.append("You can see the log file <a href='" + SQLInitServlet.getField("sysURL.base") + "ViewLogMessage?n=" + generalFileDir + f.getName() + "&tn=" + triggerBean.getName() + "&gn=1'>here</a>.<br/>");
msg.append("You can see the log file <a href='" + SQLInitServlet.getField("sysURL.base") + "ViewLogMessage?n=" + generalFileDir + f.getName() + "&tn=" + triggerBean.getName() + "&gn=1'>here</a>.<br/>");
// auditMsg.append("Your XML in the file " + f.getName() +
// " was well formed, but generated " + errors.size() +
// " metadata errors." + "<br/>");
out.close();
continue;
} else {
msg.append(respage.getString("passed_study_check") + "<br/>");
msg.append(respage.getString("passed_oid_metadata_check") + "<br/>");
auditMsg.append(respage.getString("passed_study_check") + "<br/>");
auditMsg.append(respage.getString("passed_oid_metadata_check") + "<br/>");
}
}
ImportCRFInfoContainer importCrfInfo = new ImportCRFInfoContainer(odmContainer, dataSource);
// validation errors, the same as in the ImportCRFDataServlet. DRY?
List<EventCRFBean> eventCRFBeans = getImportCRFDataService(dataSource).fetchEventCRFBeans(odmContainer, ub);
ArrayList<Integer> permittedEventCRFIds = new ArrayList<Integer>();
Boolean eventCRFStatusesValid = getImportCRFDataService(dataSource).eventCRFStatusesValid(odmContainer, ub);
List<DisplayItemBeanWrapper> displayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
HashMap<String, String> totalValidationErrors = new HashMap<String, String>();
HashMap<String, String> hardValidationErrors = new HashMap<String, String>();
// The following map is used for setting the EventCRF status post import.
HashMap<Integer, String> importedCRFStatuses = getImportCRFDataService(dataSource).fetchEventCRFStatuses(odmContainer);
// -- does the event already exist? if not, fail
if (eventCRFBeans == null) {
fail = true;
msg.append(respage.getString("no_event_status_matching"));
out.write(respage.getString("no_event_status_matching"));
out.close();
continue;
} else if (!eventCRFBeans.isEmpty()) {
logger.debug("found a list of eventCRFBeans: " + eventCRFBeans.toString());
for (EventCRFBean eventCRFBean : eventCRFBeans) {
DataEntryStage dataEntryStage = eventCRFBean.getStage();
Status eventCRFStatus = eventCRFBean.getStatus();
logger.debug("Event CRF Bean: id " + eventCRFBean.getId() + ", data entry stage " + dataEntryStage.getName() + ", status " + eventCRFStatus.getName());
if (eventCRFStatus.equals(Status.AVAILABLE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
permittedEventCRFIds.add(new Integer(eventCRFBean.getId()));
} else {
// break out here with an exception
// throw new
// Exception("Your listed Event CRF in the file " +
// f.getName() +
// " does not exist, or has already been locked for import."
// );
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_listed_crf_in_the_file"));
Object[] arguments = { f.getName() };
msg.append(mf.format(arguments) + "<br/>");
auditMsg.append(mf.format(arguments) + "<br/>");
out.write(mf.format(arguments) + "<br/>");
out.close();
continue;
}
}
if (eventCRFBeans.size() >= permittedEventCRFIds.size()) {
msg.append(respage.getString("passed_event_crf_status_check") + "<br/>");
auditMsg.append(respage.getString("passed_event_crf_status_check") + "<br/>");
} else {
fail = true;
msg.append(respage.getString("the_event_crf_not_correct_status") + "<br/>");
auditMsg.append(respage.getString("the_event_crf_not_correct_status") + "<br/>");
}
// create a 'fake' request to generate the validation errors
// here, tbh 05/2009
MockHttpServletRequest request = new MockHttpServletRequest();
// Locale locale = new Locale("en-US");
request.addPreferredLocale(locale);
try {
List<DisplayItemBeanWrapper> tempDisplayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
tempDisplayItemBeanWrappers = getImportCRFDataService(dataSource).lookupValidationErrors(request, odmContainer, ub, totalValidationErrors, hardValidationErrors, permittedEventCRFIds);
logger.debug("size of total validation errors: " + totalValidationErrors.size());
displayItemBeanWrappers.addAll(tempDisplayItemBeanWrappers);
} catch (NullPointerException npe1) {
// what if you have 2 event crfs but the third is a fake?
npe1.printStackTrace();
fail = true;
logger.debug("threw a NPE after calling lookup validation errors");
msg.append(respage.getString("an_error_was_thrown_while_validation_errors") + "<br/>");
auditMsg.append(respage.getString("an_error_was_thrown_while_validation_errors") + "<br/>");
out.write(respage.getString("an_error_was_thrown_while_validation_errors") + "<br/>");
logger.debug("=== threw the null pointer, import ===");
} catch (OpenClinicaException oce1) {
fail = true;
logger.error("threw an OCE after calling lookup validation errors " + oce1.getOpenClinicaMessage());
msg.append(oce1.getOpenClinicaMessage() + "<br/>");
// auditMsg.append(oce1.getOpenClinicaMessage() + "<br/>");
out.write(oce1.getOpenClinicaMessage() + "<br/>");
}
} else if (!eventCRFStatusesValid) {
fail = true;
msg.append(respage.getString("the_event_crf_not_correct_status"));
out.write(respage.getString("the_event_crf_not_correct_status"));
out.close();
continue;
} else {
// fail = true;
// break here with an exception
msg.append(respage.getString("no_event_crfs_matching_the_xml_metadata") + "<br/>");
// auditMsg.append(respage.getString("no_event_crfs_matching_the_xml_metadata")
// + "<br/>");
out.write(respage.getString("no_event_crfs_matching_the_xml_metadata") + "<br/>");
// throw new Exception(msg.toString());
out.close();
continue;
}
ArrayList<SubjectDataBean> subjectData = odmContainer.getCrfDataPostImportContainer().getSubjectData();
if (!hardValidationErrors.isEmpty()) {
String messageHardVals = triggerService.generateHardValidationErrorMessage(subjectData, hardValidationErrors, false);
// byte[] messageHardValsBytes = messageHardVals.getBytes();
out.write(messageHardVals);
msg.append(respage.getString("file_generated_hard_validation_error"));
// here we create a file and append the data, tbh 06/2010
fail = true;
} else {
if (!totalValidationErrors.isEmpty()) {
String totalValErrors = triggerService.generateHardValidationErrorMessage(subjectData, totalValidationErrors, false);
out.write(totalValErrors);
// here we also append data to the file, tbh 06/2010
}
String validMsgs = triggerService.generateValidMessage(subjectData, totalValidationErrors);
out.write(validMsgs);
// third place to append data to the file? tbh 06/2010
}
// << tbh 05/2010, bug #5110, leave off the detailed reports
out.close();
if (fail) {
// forwardPage(Page.IMPORT_CRF_DATA);
// break here with an exception
// throw new Exception("Problems encountered with file " +
// f.getName() + ": " + msg.toString());
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("problems_encountered_with_file"));
Object[] arguments = { f.getName(), msg.toString() };
msg = new StringBuffer(mf.format(arguments) + "<br/>");
out.close();
auditMsg.append("You can see the log file <a href='" + SQLInitServlet.getField("sysURL.base") + "ViewLogMessage?n=" + generalFileDir + f.getName() + "&tn=" + triggerBean.getName() + "&gn=1'>here</a>.<br/>");
msg.append("You can see the log file <a href='" + SQLInitServlet.getField("sysURL.base") + "ViewLogMessage?n=" + generalFileDir + f.getName() + "&tn=" + triggerBean.getName() + "&gn=1'>here</a>.<br/>");
// ": " + msg.toString() + "<br/>");
continue;
} else {
msg.append(respage.getString("passing_crf_edit_checks") + "<br/>");
auditMsg.append(respage.getString("passing_crf_edit_checks") + "<br/>");
// session.setAttribute("importedData",
// displayItemBeanWrappers);
// session.setAttribute("validationErrors",
// totalValidationErrors);
// session.setAttribute("hardValidationErrors",
// hardValidationErrors);
// above are to be sent to the user, but what kind of message
// can we make of them here?
// if hard validation errors are present, we only generate one
// table
// otherwise, we generate the other two: validation errors and
// valid data
logger.debug("found total validation errors: " + totalValidationErrors.size());
SummaryStatsBean ssBean = getImportCRFDataService(dataSource).generateSummaryStatsBean(odmContainer, displayItemBeanWrappers, importCrfInfo);
// msg.append("===+");
// the above is a special key that we will use to split the
// message into two parts
// a shorter version for the audit and
// a longer version for the email
msg.append(triggerService.generateSummaryStatsMessage(ssBean, respage) + "<br/>");
// session.setAttribute("summaryStats", ssBean);
// will have to set hard edit checks here as well
// session.setAttribute("subjectData",
// ArrayList<SubjectDataBean> subjectData =
// odmContainer.getCrfDataPostImportContainer().getSubjectData();
// forwardPage(Page.VERIFY_IMPORT_SERVLET);
// instead of forwarding, go ahead and save it all, sending a
// message at the end
msg.append(triggerService.generateSkippedCRFMessage(importCrfInfo, resword) + "<br/>");
// setup ruleSets to run if applicable
List<ImportDataRuleRunnerContainer> containers = this.ruleRunSetup(dataSource, studyBean, ub, ruleSetService, odmContainer);
CrfBusinessLogicHelper crfBusinessLogicHelper = new CrfBusinessLogicHelper(dataSource);
for (DisplayItemBeanWrapper wrapper : displayItemBeanWrappers) {
boolean resetSDV = false;
int eventCrfBeanId = -1;
EventCRFBean eventCrfBean = new EventCRFBean();
logger.debug("right before we check to make sure it is savable: " + wrapper.isSavable());
if (wrapper.isSavable()) {
ArrayList<Integer> eventCrfInts = new ArrayList<Integer>();
logger.debug("wrapper problems found : " + wrapper.getValidationErrors().toString());
itemDataDao.setFormatDates(false);
for (DisplayItemBean displayItemBean : wrapper.getDisplayItemBeans()) {
eventCrfBeanId = displayItemBean.getData().getEventCRFId();
eventCrfBean = (EventCRFBean) eventCrfDao.findByPK(eventCrfBeanId);
logger.debug("found value here: " + displayItemBean.getData().getValue());
logger.debug("found status here: " + eventCrfBean.getStatus().getName());
ItemDataBean itemDataBean = new ItemDataBean();
itemDataBean = itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(displayItemBean.getItem().getId(), eventCrfBean.getId(), displayItemBean.getData().getOrdinal());
if (wrapper.isOverwrite() && itemDataBean.getStatus() != null) {
logger.debug("just tried to find item data bean on item name " + displayItemBean.getItem().getName());
if (!itemDataBean.getValue().equals(displayItemBean.getData().getValue()))
resetSDV = true;
itemDataBean.setUpdatedDate(new Date());
itemDataBean.setUpdater(ub);
itemDataBean.setValue(displayItemBean.getData().getValue());
// set status?
itemDataDao.update(itemDataBean);
logger.debug("updated: " + itemDataBean.getItemId());
// need to set pk here in order to create dn
displayItemBean.getData().setId(itemDataBean.getId());
} else {
resetSDV = true;
itemDataDao.create(displayItemBean.getData());
logger.debug("created: " + displayItemBean.getData().getItemId());
ItemDataBean itemDataBean2 = itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(displayItemBean.getItem().getId(), eventCrfBean.getId(), displayItemBean.getData().getOrdinal());
logger.debug("found: id " + itemDataBean2.getId() + " name " + itemDataBean2.getName());
displayItemBean.getData().setId(itemDataBean2.getId());
}
ItemDAO idao = new ItemDAO(dataSource);
ItemBean ibean = (ItemBean) idao.findByPK(displayItemBean.getData().getItemId());
logger.debug("*** checking for validation errors: " + ibean.getName());
String itemOid = displayItemBean.getItem().getOid() + "_" + wrapper.getStudyEventRepeatKey() + "_" + displayItemBean.getData().getOrdinal() + "_" + wrapper.getStudySubjectOid();
if (wrapper.getValidationErrors().containsKey(itemOid)) {
ArrayList messageList = (ArrayList) wrapper.getValidationErrors().get(itemOid);
for (int iter = 0; iter < messageList.size(); iter++) {
String message = (String) messageList.get(iter);
DiscrepancyNoteBean parentDn = createDiscrepancyNote(ibean, message, eventCrfBean, displayItemBean, null, ub, dataSource, studyBean);
createDiscrepancyNote(ibean, message, eventCrfBean, displayItemBean, parentDn.getId(), ub, dataSource, studyBean);
logger.debug("*** created disc note with message: " + message);
// displayItemBean);
}
}
// Update CRF status
if (!eventCrfInts.contains(new Integer(eventCrfBean.getId()))) {
String eventCRFStatus = importedCRFStatuses.get(new Integer(eventCrfBean.getId()));
if (eventCRFStatus != null && eventCRFStatus.equals(DataEntryStage.INITIAL_DATA_ENTRY.getName()) && eventCrfBean.getStatus().isAvailable()) {
crfBusinessLogicHelper.markCRFStarted(eventCrfBean, ub);
} else {
crfBusinessLogicHelper.markCRFComplete(eventCrfBean, ub);
}
logger.debug("*** just updated event crf bean: " + eventCrfBean.getId());
eventCrfInts.add(new Integer(eventCrfBean.getId()));
}
}
itemDataDao.setFormatDates(true);
// Reset the SDV status if item data has been changed or added
if (eventCrfBean != null && resetSDV)
eventCrfDao.setSDVStatus(false, ub.getId(), eventCrfBean.getId());
}
}
// msg.append("===+");
msg.append(respage.getString("data_has_been_successfully_import") + "<br/>");
auditMsg.append(respage.getString("data_has_been_successfully_import") + "<br/>");
// MessageFormat mf = new MessageFormat("");
String linkMessage = respage.getString("you_can_review_the_data") + SQLInitServlet.getField("sysURL.base") + respage.getString("you_can_review_the_data_2") + SQLInitServlet.getField("sysURL.base") + respage.getString("you_can_review_the_data_3") + generalFileDir + f.getName() + "&tn=" + triggerBean.getFullName() + "&gn=1" + respage.getString("you_can_review_the_data_4") + "<br/>";
// mf.applyPattern(respage.getString("you_can_review_the_data"));
// Object[] arguments = {
// SQLInitServlet.getField("sysURL.base"),
// SQLInitServlet.getField("sysURL.base"), f.getName() };
msg.append(linkMessage);
auditMsg.append(linkMessage);
// was here but is now moved up, tbh
// String finalLine =
// "<p>You can review the entered data <a href='" +
// SQLInitServlet.getField("sysURL.base") +
// "ListStudySubjects'>here</a>.";
// >> tbh additional message
// "you can review the validation messages here" <-- where
// 'here' is a link to view an external file
// i.e. /ViewExternal?n=file_name.txt
// << tbh 06/2010
// msg.append(finalLine);
// auditMsg.append(finalLine);
auditMsg.append(this.runRules(studyBean, ub, containers, ruleSetService, ExecutionMode.SAVE));
}
}
// end for loop
// is the writer still not closed? try to close it
ArrayList<String> retList = new ArrayList<String>();
retList.add(msg.toString());
retList.add(auditMsg.toString());
// msg.toString();
return retList;
}
use of org.akaza.openclinica.bean.core.Status in project OpenClinica by OpenClinica.
the class CrfBusinessLogicHelper method markCRFStarted.
/**
* The following methods are for 'mark CRF complete' Note that we will also wrap Study Event status changes in this
* code, possibly split out in a later release, tbh 06/2008
*
* @return
*/
public boolean markCRFStarted(EventCRFBean ecb, UserAccountBean ub) throws Exception {
EventCRFDAO eventCrfDao = new EventCRFDAO(ds);
StudyDAO sdao = new StudyDAO(ds);
StudyBean study = sdao.findByStudySubjectId(ecb.getStudySubjectId());
EventDefinitionCRFBean edcb = getEventDefinitionCrfByStudyEventAndCrfVersion(ecb, study);
StudyEventDefinitionDAO studyEventDefinitionDao = new StudyEventDefinitionDAO(ds);
StudyEventDefinitionBean sedBean = (StudyEventDefinitionBean) studyEventDefinitionDao.findByPK(edcb.getStudyEventDefinitionId());
CRFDAO crfDao = new CRFDAO(ds);
ArrayList crfs = (ArrayList) crfDao.findAllActiveByDefinition(sedBean);
sedBean.setCrfs(crfs);
logger.debug("inout_event_crf_id:" + ecb.getId());
logger.debug("inout_study_event_def_id:" + sedBean.getId());
Status newStatus = Status.AVAILABLE;
DataEntryStage newStage = ecb.getStage();
ecb.setUpdater(ub);
ecb.setUpdatedDate(new Date());
ecb.setStatus(newStatus);
ecb.setStage(newStage);
ecb = (EventCRFBean) eventCrfDao.update(ecb);
logger.debug("just updated event crf id: " + ecb.getId());
StudyEventDAO sedao = new StudyEventDAO(ds);
StudyEventBean seb = (StudyEventBean) sedao.findByPK(ecb.getStudyEventId());
if (seb.getSubjectEventStatus().isScheduled() || seb.getSubjectEventStatus().isNotScheduled() || seb.getSubjectEventStatus().isDE_Started()) {
// change status for study event
seb.setUpdatedDate(new Date());
seb.setUpdater(ub);
seb.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED);
seb = (StudyEventBean) sedao.update(seb);
}
return true;
}
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