use of org.akaza.openclinica.dao.submit.SubjectGroupMapDAO in project OpenClinica by OpenClinica.
the class ListStudySubjectServlet method processRequest.
// >>
// < ResourceBundleresword;
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
locale = LocaleResolver.getLocale(request);
// < resword =
// ResourceBundle.getBundle("org.akaza.openclinica.i18n.words",locale);
// BWP 3098 << close the info side panel and show icons
request.setAttribute("closeInfoShowIcons", true);
// >>
// BWP 3195, 3330 : designed to address pagination issues
String pageNumber = fp.getString(SUBJECT_PAGE_NUMBER);
StringBuilder paginatingQuery = new StringBuilder("");
String filterKeyword = fp.getString(FILTER_KEYWORD);
String tmpSearch = fp.getString(SEARCH_SUBMITTED);
boolean searchSubmitted = !(tmpSearch == null || "".equalsIgnoreCase(tmpSearch)) && !"".equalsIgnoreCase(filterKeyword) && !"+".equalsIgnoreCase(filterKeyword);
if (pageNumber != null && !"".equalsIgnoreCase(pageNumber)) {
int tempNum = 0;
try {
tempNum = Integer.parseInt(pageNumber);
} catch (NumberFormatException nfe) {
// tempNum is already initialized to 0
}
if (tempNum > 0) {
paginatingQuery = new StringBuilder(SUBJECT_PAGE_NUMBER).append("=").append(pageNumber);
paginatingQuery.append("&ebl_paginated=1");
}
}
// URL encode the search keyword, since it will be a parameter in the
// URL
String filterKeywordURLEncode = java.net.URLEncoder.encode(filterKeyword, "UTF-8");
if (searchSubmitted) {
paginatingQuery.append("&ebl_sortColumnInd=0&submitted=1&ebl_sortAscending=1&ebl_filtered=1");
paginatingQuery.append("&").append(FILTER_KEYWORD).append("=").append(filterKeywordURLEncode);
}
request.setAttribute(PAGINATING_QUERY, paginatingQuery.toString());
StudyDAO stdao = new StudyDAO(sm.getDataSource());
StudySubjectDAO sdao = new StudySubjectDAO(sm.getDataSource());
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
// YW << update study parameters of current study.
// "collectDob" and "genderRequired" are set as the same as the parent
// study
// tbh, also add the params "subjectPersonIdRequired",
// "subjectIdGeneration", "subjectIdPrefixSuffix"
int parentStudyId = currentStudy.getParentStudyId();
ArrayList studyGroupClasses = new ArrayList();
ArrayList allDefs = new ArrayList();
// tbh
if (parentStudyId > 0) {
StudyBean parentStudy = (StudyBean) stdao.findByPK(parentStudyId);
studyGroupClasses = sgcdao.findAllActiveByStudy(parentStudy);
allDefs = seddao.findAllActiveByStudy(parentStudy);
} else {
parentStudyId = currentStudy.getId();
studyGroupClasses = sgcdao.findAllActiveByStudy(currentStudy);
allDefs = seddao.findAllActiveByStudy(currentStudy);
}
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
StudyParameterValueBean parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "collectDob");
currentStudy.getStudyParameterConfig().setCollectDob(parentSPV.getValue());
parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "genderRequired");
currentStudy.getStudyParameterConfig().setGenderRequired(parentSPV.getValue());
parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectPersonIdRequired");
currentStudy.getStudyParameterConfig().setSubjectPersonIdRequired(parentSPV.getValue());
parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectIdGeneration");
currentStudy.getStudyParameterConfig().setSubjectIdGeneration(parentSPV.getValue());
parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectIdPrefixSuffix");
currentStudy.getStudyParameterConfig().setSubjectIdPrefixSuffix(parentSPV.getValue());
// for all the study groups for each group class
for (int i = 0; i < studyGroupClasses.size(); i++) {
StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
ArrayList groups = sgdao.findAllByGroupClass(sgc);
sgc.setStudyGroups(groups);
}
request.setAttribute("studyGroupClasses", studyGroupClasses);
// information for the event tabs
session.setAttribute("allDefsArray", allDefs);
session.setAttribute("allDefsNumber", new Integer(allDefs.size()));
session.setAttribute("groupSize", new Integer(studyGroupClasses.size()));
// find all the subjects in current study
ArrayList subjects = sdao.findAllByStudyId(currentStudy.getId());
ArrayList<DisplayStudySubjectBean> displayStudySubs = new ArrayList<DisplayStudySubjectBean>();
// BEGIN LOOPING THROUGH SUBJECTS
for (int i = 0; i < subjects.size(); i++) {
StudySubjectBean studySub = (StudySubjectBean) subjects.get(i);
ArrayList groups = (ArrayList) sgmdao.findAllByStudySubject(studySub.getId());
ArrayList subGClasses = new ArrayList();
for (int j = 0; j < studyGroupClasses.size(); j++) {
StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(j);
boolean hasClass = false;
for (int k = 0; k < groups.size(); k++) {
SubjectGroupMapBean sgmb = (SubjectGroupMapBean) groups.get(k);
if (sgmb.getGroupClassName().equalsIgnoreCase(sgc.getName())) {
subGClasses.add(sgmb);
hasClass = true;
break;
}
}
if (!hasClass) {
subGClasses.add(new SubjectGroupMapBean());
}
}
ArrayList subEvents = new ArrayList();
// find all events order by definition ordinal
ArrayList events = sedao.findAllByStudySubject(studySub);
for (int j = 0; j < allDefs.size(); j++) {
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) allDefs.get(j);
boolean hasDef = false;
// logger.info("...set blank to "+blankid);
for (int k = 0; k < events.size(); k++) {
StudyEventBean se = (StudyEventBean) events.get(k);
if (se.getStudyEventDefinitionId() == sed.getId()) {
se.setStudyEventDefinition(sed);
// logger.info(">>>found assigned id "+sed.getId()+" sed
// name: "+sed.getName()+" "+se.getId());
subEvents.add(se);
hasDef = true;
}
}
if (!hasDef) {
StudyEventBean blank = new StudyEventBean();
blank.setSubjectEventStatus(SubjectEventStatus.NOT_SCHEDULED);
blank.setStudyEventDefinitionId(sed.getId());
// how can we set the following:
// logger.info("...resetting blank id: "+blank.getId()+" to
// "+blankid);
// blank.setId(blankid);
blank.setStudyEventDefinition(sed);
// logger.info(">>>blank id: "+blank.getId());
// logger.info(">>>found unassigned id "+sed.getId()+" sed
// name: "+sed.getName()+" ");
subEvents.add(blank);
}
}
// logger.info("subevents size after all adds: "+subEvents.size());
// reorganize the events and find the repeating ones
// subEvents:[aa bbb cc d ee]
// finalEvents:[a(2) b(3) c(2) d e(2)]
int prevDefId = 0;
int currDefId = 0;
ArrayList finalEvents = new ArrayList();
int repeatingNum = 1;
int count = 0;
StudyEventBean event = new StudyEventBean();
// begin looping through subject events
for (int j = 0; j < subEvents.size(); j++) {
StudyEventBean se = (StudyEventBean) subEvents.get(j);
currDefId = se.getStudyEventDefinitionId();
if (currDefId != prevDefId) {
// find a new event
if (repeatingNum > 1) {
event.setRepeatingNum(repeatingNum);
repeatingNum = 1;
}
// add current event to final
finalEvents.add(se);
event = se;
count++;
// logger.info("event id? "+event.getId());
} else {
// repeating event
repeatingNum++;
event.getRepeatEvents().add(se);
// event.getRepeatEvents().size());
if (j == subEvents.size() - 1) {
event.setRepeatingNum(repeatingNum);
repeatingNum = 1;
}
}
prevDefId = currDefId;
}
// end looping through subject events
DisplayStudySubjectBean dssb = new DisplayStudySubjectBean();
// logger.info("final events size: "+finalEvents.size());
dssb.setStudyEvents(finalEvents);
dssb.setStudySubject(studySub);
dssb.setStudyGroups(subGClasses);
displayStudySubs.add(dssb);
}
// END LOOPING THROUGH SUBJECTS
// Set a subject property to determine whether to show a signed-type
// icon (electronic signature)
// in the JSP view or not
// Get all event crfs by studyevent id; then use
// EventDefinitionCRFDAO.isRequired to
// determine whether any uncompleted CRFs are required.
boolean isRequiredUncomplete = false;
for (DisplayStudySubjectBean subject : displayStudySubs) {
for (Iterator it = subject.getStudyEvents().iterator(); it.hasNext(); ) {
StudyEventBean event = (StudyEventBean) it.next();
if (event.getSubjectEventStatus() != null && event.getSubjectEventStatus().getId() == 3) {
// disallow the subject from signing any studies
subject.setStudySignable(false);
break;
} else {
// determine whether the subject has any required,
// uncompleted event CRFs
isRequiredUncomplete = eventHasRequiredUncompleteCRFs(event);
if (isRequiredUncomplete) {
subject.setStudySignable(false);
break;
}
}
}
}
fp = new FormProcessor(request);
EntityBeanTable table = fp.getEntityBeanTable();
ArrayList allStudyRows = DisplayStudySubjectRow.generateRowsFromBeans(displayStudySubs);
ArrayList columnArray = new ArrayList();
columnArray.add(resword.getString("study_subject_ID"));
columnArray.add(resword.getString("subject_status"));
columnArray.add(resword.getString("OID"));
columnArray.add(resword.getString("gender"));
// new
columnArray.add(resword.getString("secondary_ID"));
for (int i = 0; i < studyGroupClasses.size(); i++) {
StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
columnArray.add(sgc.getName());
}
for (int i = 0; i < allDefs.size(); i++) {
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) allDefs.get(i);
columnArray.add(sed.getName());
}
columnArray.add(resword.getString("actions"));
String[] columns = new String[columnArray.size()];
columnArray.toArray(columns);
// String[] columns = {"ID", "Subject Status", "Gender", "Enrollment
// Date",
// "Study Events", "Actions" };
table.setColumns(new ArrayList(Arrays.asList(columns)));
table.setQuery(getBaseURL(), new HashMap());
table.hideColumnLink(columnArray.size() - 1);
// table.addLink("Enroll a new subject",
// "javascript:leftnavExpand('addSubjectRowExpress');");
table.setRows(allStudyRows);
if (filterKeyword != null && !"".equalsIgnoreCase(filterKeyword)) {
table.setKeywordFilter(filterKeyword);
}
table.computeDisplay();
request.setAttribute("table", table);
// request.setAttribute("subjects", subjects);
String idSetting = currentStudy.getStudyParameterConfig().getSubjectIdGeneration();
// set up auto study subject id
if (idSetting.equals("auto editable") || idSetting.equals("auto non-editable")) {
// Shaoyu Su
// int nextLabel = ssdao.findTheGreatestLabel() + 1;
// request.setAttribute("label", new Integer(nextLabel).toString());
request.setAttribute("label", resword.getString("id_generated_Save_Add"));
}
FormDiscrepancyNotes discNotes = new FormDiscrepancyNotes();
session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
forwardPage(getJSP());
}
use of org.akaza.openclinica.dao.submit.SubjectGroupMapDAO in project OpenClinica by OpenClinica.
the class AddNewSubjectServlet method processRequest.
// YW >>
/*
* (non-Javadoc)
*
* @see org.akaza.openclinica.control.core.SecureController#processRequest()
*/
@Override
protected void processRequest() throws Exception {
checkStudyLocked(Page.LIST_STUDY_SUBJECTS, respage.getString("current_study_locked"));
checkStudyFrozen(Page.LIST_STUDY_SUBJECTS, respage.getString("current_study_frozen"));
StudySubjectDAO ssd = new StudySubjectDAO(sm.getDataSource());
StudyDAO stdao = new StudyDAO(sm.getDataSource());
StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
ArrayList classes = new ArrayList();
panel.setStudyInfoShown(false);
FormProcessor fp = new FormProcessor(request);
FormDiscrepancyNotes discNotes;
SimpleDateFormat sdf = new SimpleDateFormat("MM/dd/yyyy");
// TODO l10n for dates? Note that in some places we hard-code the YOB by
// using "01/01/"+yob,
// not exactly supporting i18n...tbh
// YW << update study parameters of current study.
// "collectDob" and "genderRequired" are set as the same as the parent
// study
int parentStudyId = currentStudy.getParentStudyId();
if (parentStudyId <= 0) {
parentStudyId = currentStudy.getId();
classes = sgcdao.findAllActiveByStudy(currentStudy);
} else {
StudyBean parentStudy = (StudyBean) stdao.findByPK(parentStudyId);
classes = sgcdao.findAllActiveByStudy(parentStudy);
}
StudyParameterValueDAO spvdao = new StudyParameterValueDAO(sm.getDataSource());
StudyParameterValueBean parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "collectDob");
currentStudy.getStudyParameterConfig().setCollectDob(parentSPV.getValue());
parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "genderRequired");
currentStudy.getStudyParameterConfig().setGenderRequired(parentSPV.getValue());
// YW >>
// tbh
StudyParameterValueBean checkPersonId = spvdao.findByHandleAndStudy(parentStudyId, "subjectPersonIdRequired");
currentStudy.getStudyParameterConfig().setSubjectPersonIdRequired(checkPersonId.getValue());
if (!fp.isSubmitted()) {
if (fp.getBoolean("instr")) {
session.removeAttribute(FORM_DISCREPANCY_NOTES_NAME);
forwardPage(Page.INSTRUCTIONS_ENROLL_SUBJECT);
} else {
setUpBeans(classes);
Date today = new Date(System.currentTimeMillis());
String todayFormatted = local_df.format(today);
fp.addPresetValue(INPUT_ENROLLMENT_DATE, todayFormatted);
// YW 10-07-2007 <<
String idSetting = "";
if (currentStudy.getParentStudyId() > 0) {
parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectIdGeneration");
currentStudy.getStudyParameterConfig().setSubjectIdGeneration(parentSPV.getValue());
}
idSetting = currentStudy.getStudyParameterConfig().getSubjectIdGeneration();
// YW >>
logger.info("subject id setting :" + idSetting);
// available ID (label) for now
if (idSetting.equals("auto editable") || idSetting.equals("auto non-editable")) {
// Shaoyu Su
// int nextLabel = ssd.findTheGreatestLabel() + 1;
// fp.addPresetValue(INPUT_LABEL, new Integer(nextLabel).toString());
fp.addPresetValue(INPUT_LABEL, resword.getString("id_generated_Save_Add"));
}
setPresetValues(fp.getPresetValues());
discNotes = new FormDiscrepancyNotes();
session.setAttribute(FORM_DISCREPANCY_NOTES_NAME, discNotes);
forwardPage(Page.ADD_NEW_SUBJECT);
}
} else {
// values in database <subject> table for "add existing subject"
if (!fp.getBoolean(EXISTING_SUB_SHOWN)) {
DOB = fp.getString(INPUT_DOB);
YOB = fp.getString(INPUT_YOB);
GENDER = fp.getString(INPUT_GENDER);
}
// YW >>
discNotes = (FormDiscrepancyNotes) session.getAttribute(FORM_DISCREPANCY_NOTES_NAME);
if (discNotes == null) {
discNotes = new FormDiscrepancyNotes();
}
DiscrepancyValidator v = new DiscrepancyValidator(request, discNotes);
v.addValidation(INPUT_LABEL, Validator.NO_BLANKS);
String subIdSetting = currentStudy.getStudyParameterConfig().getSubjectIdGeneration();
if (!subIdSetting.equalsIgnoreCase("auto non-editable") && !subIdSetting.equalsIgnoreCase("auto editable")) {
v.addValidation(INPUT_LABEL, Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 30);
}
if (currentStudy.getStudyParameterConfig().getSubjectPersonIdRequired().equals("required")) {
v.addValidation(INPUT_UNIQUE_IDENTIFIER, Validator.NO_BLANKS);
}
v.addValidation(INPUT_UNIQUE_IDENTIFIER, Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 255);
if (!StringUtils.isBlank(fp.getString(INPUT_SECONDARY_LABEL))) {
v.addValidation(INPUT_SECONDARY_LABEL, Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 30);
}
String dobSetting = currentStudy.getStudyParameterConfig().getCollectDob();
if (dobSetting.equals("1")) {
// date of birth
v.addValidation(INPUT_DOB, Validator.IS_A_DATE);
if (!StringUtils.isBlank(fp.getString("INPUT_DOB"))) {
v.alwaysExecuteLastValidation(INPUT_DOB);
}
v.addValidation(INPUT_DOB, Validator.DATE_IN_PAST);
} else if (dobSetting.equals("2")) {
// year of birth
v.addValidation(INPUT_YOB, Validator.IS_AN_INTEGER);
v.alwaysExecuteLastValidation(INPUT_YOB);
v.addValidation(INPUT_YOB, Validator.COMPARES_TO_STATIC_VALUE, NumericComparisonOperator.GREATER_THAN_OR_EQUAL_TO, 1000);
// get today's year
Date today = new Date();
Calendar c = Calendar.getInstance();
c.setTime(today);
int currentYear = c.get(Calendar.YEAR);
v.addValidation(INPUT_YOB, Validator.COMPARES_TO_STATIC_VALUE, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, currentYear);
} else {
// DOB not used, added tbh 102007
logger.info("should read this only if DOB not used");
}
ArrayList acceptableGenders = new ArrayList();
acceptableGenders.add("m");
acceptableGenders.add("f");
if (!currentStudy.getStudyParameterConfig().getGenderRequired().equals("false")) {
v.addValidation(INPUT_GENDER, Validator.IS_IN_SET, acceptableGenders);
}
v.addValidation(INPUT_ENROLLMENT_DATE, Validator.IS_A_DATE);
v.alwaysExecuteLastValidation(INPUT_ENROLLMENT_DATE);
v.addValidation(INPUT_ENROLLMENT_DATE, Validator.DATE_IN_PAST);
boolean locationError = false;
if (fp.getBoolean("addWithEvent")) {
v.addValidation(INPUT_EVENT_START_DATE, Validator.IS_A_DATE);
v.alwaysExecuteLastValidation(INPUT_EVENT_START_DATE);
if (currentStudy.getStudyParameterConfig().getEventLocationRequired().equalsIgnoreCase("required")) {
v.addValidation("location", Validator.NO_BLANKS);
locationError = true;
}
}
HashMap errors = v.validate();
SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
// global
String uniqueIdentifier = fp.getString(INPUT_UNIQUE_IDENTIFIER);
// Id
SubjectBean subjectWithSameId = new SubjectBean();
SubjectBean subjectWithSameIdInParent = new SubjectBean();
boolean showExistingRecord = false;
if (!uniqueIdentifier.equals("")) {
boolean subjectWithSameIdInCurrentStudyTree = false;
// checks whether there is a subject with same id inside current
// study/site
subjectWithSameId = sdao.findByUniqueIdentifierAndStudy(uniqueIdentifier, currentStudy.getId());
// tbh
if (subjectWithSameId.isActive()) {
// ||
// subjectWithSameIdInParent.isActive())
// {
Validator.addError(errors, INPUT_UNIQUE_IDENTIFIER, resexception.getString("subject_with_person_ID") + " " + uniqueIdentifier + " " + resexception.getString("is_already_enrolled_in_this_study"));
subjectWithSameIdInCurrentStudyTree = true;
logger.info("just added unique id in study tree");
} else {
// checks whether there is a subject with same id inside
// sites of
// current study
subjectWithSameId = sdao.findByUniqueIdentifierAndParentStudy(uniqueIdentifier, currentStudy.getId());
if (subjectWithSameId.isActive()) {
StudySubjectBean ssub = ssd.findBySubjectIdAndStudy(subjectWithSameId.getId(), currentStudy);
StudyBean site = (StudyBean) stdao.findByPK(ssub.getStudyId());
Validator.addError(errors, INPUT_UNIQUE_IDENTIFIER, resexception.getString("this_subject_person_ID") + " " + uniqueIdentifier + resexception.getString("has_already_enrolled_site") + site.getName() + resexception.getString("of_current_study_need_to_move") + resexception.getString("please_have_user_manage_privileges"));
subjectWithSameIdInCurrentStudyTree = true;
} else {
// check whether there is a subject with same id in the
// parent study
subjectWithSameId = sdao.findByUniqueIdentifierAndStudy(uniqueIdentifier, currentStudy.getParentStudyId());
if (subjectWithSameId.isActive()) {
Validator.addError(errors, INPUT_UNIQUE_IDENTIFIER, resexception.getString("this_subject_with_person_ID") + " " + uniqueIdentifier + resexception.getString("has_already_enrolled_parent_study"));
subjectWithSameIdInCurrentStudyTree = true;
} else {
// YW 11-26-2007 << check whether there is a subject
// with the same id in other sites of the same study
subjectWithSameId = sdao.findByUniqueIdentifierAndParentStudy(uniqueIdentifier, currentStudy.getParentStudyId());
if (subjectWithSameId.isActive()) {
Validator.addError(errors, INPUT_UNIQUE_IDENTIFIER, resexception.getString("this_subject_with_person_ID") + " " + uniqueIdentifier + resexception.getString("has_already_enrolled_site_study"));
subjectWithSameIdInCurrentStudyTree = true;
}
// YW >>
}
}
}
if (!subjectWithSameIdInCurrentStudyTree) {
subjectWithSameId = sdao.findByUniqueIdentifier(uniqueIdentifier);
// found subject with same id in other study
if (subjectWithSameId.isActive()) {
showExistingRecord = true;
}
}
}
// end of the block if(!uniqueIdentifier.equals(""))
String label = fp.getString(INPUT_LABEL);
String personId = fp.getString(INPUT_UNIQUE_IDENTIFIER);
String secondaryLable = fp.getString(INPUT_SECONDARY_LABEL);
// then Study Subject ID should be created when db row is inserted.
if (label.contains("<") || label.contains(">")) {
Validator.addError(errors, INPUT_LABEL, resexception.getString("study_subject_id_can_not_contain_html_lessthan_or_greaterthan_elements"));
}
if (secondaryLable.contains("<") || secondaryLable.contains(">")) {
Validator.addError(errors, INPUT_SECONDARY_LABEL, resexception.getString("secondary_id_can_not_contain_html_lessthan_or_greaterthan_elements"));
}
if (personId.contains("<") || personId.contains(">")) {
Validator.addError(errors, INPUT_UNIQUE_IDENTIFIER, resexception.getString("person_id_can_not_contain_html_lessthan_or_greaterthan_elements"));
}
if (!label.equalsIgnoreCase(resword.getString("id_generated_Save_Add"))) {
StudySubjectBean subjectWithSameLabel = ssd.findByLabelAndStudy(label, currentStudy);
StudySubjectBean subjectWithSameLabelInParent = new StudySubjectBean();
// tbh
if (currentStudy.getParentStudyId() > 0) {
// <
subjectWithSameLabelInParent = ssd.findSameByLabelAndStudy(label, currentStudy.getParentStudyId(), 0);
// --
// blank
// id
// since
// the
// ss
// hasn't
// been
// created
// yet,
// tbh
}
// tbh
if (subjectWithSameLabel.isActive() || subjectWithSameLabelInParent.isActive()) {
Validator.addError(errors, INPUT_LABEL, resexception.getString("another_assigned_this_ID_choose_unique"));
}
}
if (!classes.isEmpty()) {
for (int i = 0; i < classes.size(); i++) {
StudyGroupClassBean sgc = (StudyGroupClassBean) classes.get(i);
int groupId = fp.getInt("studyGroupId" + i);
String notes = fp.getString("notes" + i);
if ("Required".equals(sgc.getSubjectAssignment()) && groupId == 0) {
Validator.addError(errors, "studyGroupId" + i, resexception.getString("group_class_is_required"));
}
if (notes.trim().length() > 255) {
Validator.addError(errors, "notes" + i, resexception.getString("notes_cannot_longer_255"));
}
sgc.setStudyGroupId(groupId);
sgc.setGroupNotes(notes);
}
}
if (!errors.isEmpty()) {
addPageMessage(respage.getString("there_were_some_errors_submission"));
if (locationError) {
addPageMessage(respage.getString("location_blank_error"));
}
setInputMessages(errors);
fp.addPresetValue(INPUT_DOB, fp.getString(INPUT_DOB));
fp.addPresetValue(INPUT_YOB, fp.getString(INPUT_YOB));
fp.addPresetValue(INPUT_GENDER, fp.getString(INPUT_GENDER));
fp.addPresetValue(INPUT_UNIQUE_IDENTIFIER, uniqueIdentifier);
fp.addPresetValue(INPUT_LABEL, label);
fp.addPresetValue(INPUT_SECONDARY_LABEL, fp.getString(INPUT_SECONDARY_LABEL));
fp.addPresetValue(INPUT_ENROLLMENT_DATE, fp.getString(INPUT_ENROLLMENT_DATE));
fp.addPresetValue(INPUT_EVENT_START_DATE, fp.getString(INPUT_EVENT_START_DATE));
fp.addPresetValue(STUDY_EVENT_DEFINITION, fp.getInt(STUDY_EVENT_DEFINITION));
fp.addPresetValue(LOCATION, fp.getString(LOCATION));
fp.addPresetValue(EDIT_DOB, fp.getString(EDIT_DOB));
setPresetValues(fp.getPresetValues());
setUpBeans(classes);
boolean existingSubShown = fp.getBoolean(EXISTING_SUB_SHOWN);
if (!existingSubShown) {
Object isSubjectOverlay = fp.getRequest().getParameter("subjectOverlay");
if (isSubjectOverlay != null) {
int eventId = fp.getInt("studyEventDefinition");
if (eventId < 1) {
Validator.addError(errors, STUDY_EVENT_DEFINITION, resexception.getString("input_not_acceptable_option"));
}
String location = fp.getString(LOCATION);
if (location == null && location.length() == 0) {
Validator.addError(errors, LOCATION, resexception.getString("field_not_blank"));
}
request.setAttribute("showOverlay", true);
forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
} else {
forwardPage(Page.ADD_NEW_SUBJECT);
}
} else {
forwardPage(Page.ADD_EXISTING_SUBJECT);
}
} else {
// no errors
StudySubjectBean studySubject = new StudySubjectBean();
SubjectBean subject = new SubjectBean();
boolean existingSubShown = fp.getBoolean(EXISTING_SUB_SHOWN);
if (showExistingRecord && !existingSubShown) {
needUpdate = false;
subject = subjectWithSameId;
Calendar cal = Calendar.getInstance();
int year = 0;
if (subject.getDateOfBirth() != null) {
cal.setTime(subject.getDateOfBirth());
year = cal.get(Calendar.YEAR);
fp.addPresetValue(INPUT_DOB, local_df.format(subject.getDateOfBirth()));
} else {
fp.addPresetValue(INPUT_DOB, "");
}
if (currentStudy.getStudyParameterConfig().getCollectDob().equals("1") && !subject.isDobCollected()) {
// fp.addPresetValue(EDIT_DOB, "yes");
fp.addPresetValue(INPUT_DOB, fp.getString(INPUT_DOB));
}
// YW << it has been taken off to solve bug0001125
/*
* else { fp.addPresetValue(INPUT_DOB, ""); }
*/
// YW >>
fp.addPresetValue(INPUT_YOB, String.valueOf(year));
if (!currentStudy.getStudyParameterConfig().getGenderRequired().equals("false")) {
fp.addPresetValue(INPUT_GENDER, subject.getGender() + "");
} else {
fp.addPresetValue(INPUT_GENDER, "");
}
// Shaoyu Su: delay setting INPUT_LABEL field
if (!label.equalsIgnoreCase(resword.getString("id_generated_Save_Add"))) {
fp.addPresetValue(INPUT_LABEL, label);
}
fp.addPresetValue(INPUT_SECONDARY_LABEL, fp.getString(INPUT_SECONDARY_LABEL));
fp.addPresetValue(INPUT_ENROLLMENT_DATE, fp.getString(INPUT_ENROLLMENT_DATE));
fp.addPresetValue(INPUT_EVENT_START_DATE, fp.getString(INPUT_EVENT_START_DATE));
// YW >>
fp.addPresetValue(INPUT_UNIQUE_IDENTIFIER, subject.getUniqueIdentifier());
setPresetValues(fp.getPresetValues());
setUpBeans(classes);
// YW <<
int warningCount = 0;
if (currentStudy.getStudyParameterConfig().getGenderRequired().equalsIgnoreCase("true")) {
if (String.valueOf(subjectWithSameId.getGender()).equals(" ")) {
fp.addPresetValue(G_WARNING, "emptytrue");
fp.addPresetValue(INPUT_GENDER, GENDER);
needUpdate = true;
updateSubject = subjectWithSameId;
updateSubject.setGender(GENDER.toCharArray()[0]);
warningCount++;
} else if (!String.valueOf(subjectWithSameId.getGender()).equals(GENDER)) {
fp.addPresetValue(G_WARNING, "true");
warningCount++;
} else {
fp.addPresetValue(G_WARNING, "false");
}
} else {
fp.addPresetValue(G_WARNING, "false");
}
// Current study required DOB
if (currentStudy.getStudyParameterConfig().getCollectDob().equals("1")) {
// date-of-birth in subject table is not completed
if (subjectWithSameId.isDobCollected() == false) {
needUpdate = true;
updateSubject = subjectWithSameId;
updateSubject.setDobCollected(true);
if (subjectWithSameId.getDateOfBirth() == null) {
fp.addPresetValue(INPUT_DOB, DOB);
updateSubject.setDateOfBirth(new Date(DOB));
} else {
String y = String.valueOf(subjectWithSameId.getDateOfBirth()).split("\\-")[0];
String[] d = DOB.split("\\/");
// if year-of-birth in subject table
if (!y.equals("0001")) {
// year, use year-of-birth
if (!y.equals(d[2])) {
fp.addPresetValue(D_WARNING, "dobYearWrong");
fp.addPresetValue(INPUT_DOB, d[0] + "/" + d[1] + "/" + y);
updateSubject.setDateOfBirth(sdf.parse(d[0] + "/" + d[1] + "/" + y));
} else {
fp.addPresetValue(D_WARNING, "dobUsed");
fp.addPresetValue(INPUT_DOB, DOB);
updateSubject.setDateOfBirth(sdf.parse(DOB));
}
} else // date-of-birth is not required in subject
// table
{
fp.addPresetValue(D_WARNING, "emptyD");
fp.addPresetValue(INPUT_DOB, DOB);
updateSubject.setDateOfBirth(sdf.parse(DOB));
}
}
warningCount++;
} else // date-of-birth in subject table but doesn't match DOB
if (!local_df.format(subjectWithSameId.getDateOfBirth()).toString().equals(DOB)) {
// System.out.println("comparing " +
// local_df.format(
// subjectWithSameId.getDateOfBirth()).toString());
fp.addPresetValue(D_WARNING, "currentDOBWrong");
warningCount++;
} else // date-of-birth in subject table matchs DOB
{
fp.addPresetValue(D_WARNING, "false");
}
} else // current Study require YOB
if (currentStudy.getStudyParameterConfig().getCollectDob().equals("2")) {
String y = String.valueOf(subjectWithSameId.getDateOfBirth()).split("\\-")[0];
// year of date-of-birth in subject table is avaible
if (!y.equals("0001")) {
// year in subject table doesn't match YOB,
if (!y.equals(YOB)) {
fp.addPresetValue(Y_WARNING, "yobWrong");
warningCount++;
} else // year in subject table matches YOB
{
fp.addPresetValue(Y_WARNING, "false");
}
} else // year of date-of-birth in the subject talbe is not
// availbe, YOB is used
{
needUpdate = true;
updateSubject = subjectWithSameId;
fp.addPresetValue(Y_WARNING, "yearEmpty");
fp.addPresetValue(INPUT_YOB, YOB);
updateSubject.setDateOfBirth(sdf.parse("01/01/" + YOB));
warningCount++;
}
} else // current study require no DOB, there is no need to check
// date-of-birth in the subject table
{
fp.addPresetValue(Y_WARNING, "false");
}
if (warningCount > 0) {
warningCount = 0;
forwardPage(Page.ADD_EXISTING_SUBJECT);
return;
}
// forwardPage(Page.ADD_EXISTING_SUBJECT);
// return;
// YW >>
}
// to be inserted into both <subject> and <studysubject> tables
if (!showExistingRecord) {
// YW >>
if (!StringUtil.isBlank(fp.getString(INPUT_GENDER))) {
subject.setGender(fp.getString(INPUT_GENDER).charAt(0));
} else {
subject.setGender(' ');
}
subject.setUniqueIdentifier(uniqueIdentifier);
if (currentStudy.getStudyParameterConfig().getCollectDob().equals("1")) {
if (!StringUtil.isBlank(fp.getString(INPUT_DOB))) {
subject.setDateOfBirth(fp.getDate(INPUT_DOB));
subject.setDobCollected(true);
} else {
subject.setDateOfBirth(null);
subject.setDobCollected(false);
}
} else if (currentStudy.getStudyParameterConfig().getCollectDob().equals("2")) {
// generate a fake birthday in 01/01/YYYY format, only
// the year is
// valid
// added the "2" to make sure that 'not used' is kept to
// null, tbh 102007
subject.setDobCollected(false);
int yob = fp.getInt(INPUT_YOB);
Date fakeDate = new Date("01/01/" + yob);
// Calendar fakeCal = Calendar.getInstance();
// fakeCal.set(Calendar.YEAR, yob);
// fakeCal.set(Calendar.MONTH, 1);
// fakeCal.set(Calendar.DAY_OF_MONTH, 1);
// String dobString = "01/01/" + yob;
String dobString = local_df.format(fakeDate);
try {
Date fakeDOB = local_df.parse(dobString);
subject.setDateOfBirth(fakeDOB);
} catch (ParseException pe) {
subject.setDateOfBirth(new Date());
addPageMessage(respage.getString("problem_happened_saving_year"));
}
}
subject.setStatus(Status.AVAILABLE);
subject.setOwner(ub);
subject = sdao.create(subject);
if (!subject.isActive()) {
throw new OpenClinicaException(resexception.getString("could_not_create_subject"), "3");
}
// YW << for showExistingRecord && existingSubShown,
// If input value(s) is(are) different from database,
// warning will be shown.
// If value(s) in database is(are) empty, entered value(s)
// could be used;
// Otherwise, value(s) in database will be used.
// For date-of-birth, if database only has year-of-birth,
// the year in database will be used for year part
} else if (existingSubShown) {
if (!needUpdate) {
subject = subjectWithSameId;
} else {
updateSubject.setUpdater(ub);
updateSubject = (SubjectBean) sdao.update(updateSubject);
if (!updateSubject.isActive()) {
throw new OpenClinicaException("Could not create subject.", "5");
}
subject = updateSubject;
needUpdate = false;
}
}
// YW >>
// enroll the subject in the active study
studySubject.setSubjectId(subject.getId());
studySubject.setStudyId(currentStudy.getId());
studySubject.setLabel(fp.getString(INPUT_LABEL));
studySubject.setSecondaryLabel(fp.getString(INPUT_SECONDARY_LABEL));
studySubject.setStatus(Status.AVAILABLE);
studySubject.setEnrollmentDate(fp.getDate(INPUT_ENROLLMENT_DATE));
if (fp.getBoolean("addWithEvent")) {
studySubject.setEventStartDate(fp.getDate(INPUT_EVENT_START_DATE));
}
studySubject.setOwner(ub);
// Shaoyu Su: prevent same label ("Study Subject ID")
if (fp.getString(INPUT_LABEL).equalsIgnoreCase(resword.getString("id_generated_Save_Add"))) {
synchronized (simpleLockObj) {
int nextLabel = ssd.findTheGreatestLabel() + 1;
studySubject.setLabel(nextLabel + "");
studySubject = ssd.createWithoutGroup(studySubject);
if (showExistingRecord && !existingSubShown) {
fp.addPresetValue(INPUT_LABEL, label);
}
}
} else {
studySubject = ssd.createWithoutGroup(studySubject);
}
if (!classes.isEmpty() && studySubject.isActive()) {
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
for (int i = 0; i < classes.size(); i++) {
StudyGroupClassBean group = (StudyGroupClassBean) classes.get(i);
int studyGroupId = group.getStudyGroupId();
String notes = group.getGroupNotes();
SubjectGroupMapBean map = new SubjectGroupMapBean();
map.setNotes(group.getGroupNotes());
map.setStatus(Status.AVAILABLE);
map.setStudyGroupId(group.getStudyGroupId());
map.setStudySubjectId(studySubject.getId());
map.setStudyGroupClassId(group.getId());
map.setOwner(ub);
if (map.getStudyGroupId() > 0) {
sgmdao.create(map);
}
}
}
if (!studySubject.isActive()) {
throw new OpenClinicaException(resexception.getString("could_not_create_study_subject"), "4");
}
// save discrepancy notes into DB
FormDiscrepancyNotes fdn = (FormDiscrepancyNotes) session.getAttribute(FORM_DISCREPANCY_NOTES_NAME);
DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
String[] subjectFields = { INPUT_DOB, INPUT_YOB, INPUT_GENDER };
for (String element : subjectFields) {
saveFieldNotes(element, fdn, dndao, subject.getId(), "subject", currentStudy);
}
saveFieldNotes(INPUT_ENROLLMENT_DATE, fdn, dndao, studySubject.getId(), "studySub", currentStudy);
request.removeAttribute(FormProcessor.FIELD_SUBMITTED);
request.setAttribute(CreateNewStudyEventServlet.INPUT_STUDY_SUBJECT, studySubject);
request.setAttribute(CreateNewStudyEventServlet.INPUT_REQUEST_STUDY_SUBJECT, "no");
request.setAttribute(FormProcessor.FIELD_SUBMITTED, "0");
addPageMessage(respage.getString("subject_with_unique_identifier") + studySubject.getLabel() + respage.getString("X_was_created_succesfully"));
if (fp.getBoolean("addWithEvent")) {
createStudyEvent(fp, studySubject);
// YW <<
request.setAttribute("id", studySubject.getId() + "");
// String url= response.encodeRedirectURL("ViewStudySubject?id=" + studySubject.getId());
// response.sendRedirect(url);
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
// + studySubject.getId()));
return;
}
String submitEvent = fp.getString(SUBMIT_EVENT_BUTTON);
String submitEnroll = fp.getString(SUBMIT_ENROLL_BUTTON);
String submitDone = fp.getString(SUBMIT_DONE_BUTTON);
session.removeAttribute(FORM_DISCREPANCY_NOTES_NAME);
if (!StringUtil.isBlank(submitEvent)) {
forwardPage(Page.CREATE_NEW_STUDY_EVENT_SERVLET);
} else if (!StringUtil.isBlank(submitEnroll)) {
// NEW MANTIS ISSUE 4770
setUpBeans(classes);
Date today = new Date(System.currentTimeMillis());
String todayFormatted = local_df.format(today);
fp.addPresetValue(INPUT_ENROLLMENT_DATE, todayFormatted);
// YW 10-07-2007 <<
String idSetting = "";
if (currentStudy.getParentStudyId() > 0) {
parentSPV = spvdao.findByHandleAndStudy(parentStudyId, "subjectIdGeneration");
currentStudy.getStudyParameterConfig().setSubjectIdGeneration(parentSPV.getValue());
}
idSetting = currentStudy.getStudyParameterConfig().getSubjectIdGeneration();
// YW >>
logger.info("subject id setting :" + idSetting);
// set up auto study subject id
if (idSetting.equals("auto editable") || idSetting.equals("auto non-editable")) {
// Shaoyu Su
// int nextLabel = ssd.findTheGreatestLabel() + 1;
// fp.addPresetValue(INPUT_LABEL, new Integer(nextLabel).toString());
fp.addPresetValue(INPUT_LABEL, resword.getString("id_generated_Save_Add"));
}
setPresetValues(fp.getPresetValues());
discNotes = new FormDiscrepancyNotes();
session.setAttribute(FORM_DISCREPANCY_NOTES_NAME, discNotes);
// End of 4770
forwardPage(Page.ADD_NEW_SUBJECT);
} else {
// forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
// forwardPage(Page.SUBMIT_DATA_SERVLET);
request.setAttribute("id", studySubject.getId() + "");
// String url=response.encodeRedirectURL("ViewStudySubject?id=" + studySubject.getId());
// response.sendRedirect(url);
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
return;
}
}
// end of no error (errors.isEmpty())
}
// end of fp.isSubmitted()
}
use of org.akaza.openclinica.dao.submit.SubjectGroupMapDAO in project OpenClinica by OpenClinica.
the class ViewSubjectGroupClassServlet method processRequest.
@Override
public void processRequest() throws Exception {
String action = request.getParameter("action");
FormProcessor fp = new FormProcessor(request);
int classId = fp.getInt("id");
if (classId == 0) {
addPageMessage(respage.getString("please_choose_a_subject_group_class_to_view"));
forwardPage(Page.SUBJECT_GROUP_CLASS_LIST_SERVLET);
} else {
StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
StudyDAO studyDao = new StudyDAO(sm.getDataSource());
StudyGroupClassBean sgcb = (StudyGroupClassBean) sgcdao.findByPK(classId);
StudyBean study = (StudyBean) studyDao.findByPK(sgcb.getStudyId());
checkRoleByUserAndStudy(ub, sgcb.getStudyId(), study.getParentStudyId());
// YW 09-19-2007 <<
sgcb.setGroupClassTypeName(GroupClassType.get(sgcb.getGroupClassTypeId()).getName());
// YW >>
ArrayList groups = sgdao.findAllByGroupClass(sgcb);
ArrayList studyGroups = new ArrayList();
for (int i = 0; i < groups.size(); i++) {
StudyGroupBean sg = (StudyGroupBean) groups.get(i);
ArrayList subjectMaps = sgmdao.findAllByStudyGroupClassAndGroup(sgcb.getId(), sg.getId());
sg.setSubjectMaps(subjectMaps);
// YW<<
studyGroups.add(sg);
// YW>>
}
request.setAttribute("group", sgcb);
// request.setAttribute("studyGroups", groups);
request.setAttribute("studyGroups", studyGroups);
forwardPage(Page.VIEW_SUBJECT_GROUP_CLASS);
}
}
use of org.akaza.openclinica.dao.submit.SubjectGroupMapDAO in project OpenClinica by OpenClinica.
the class RemoveStudyServlet method processRequest.
@Override
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(respage.getString("please_choose_a_study_to_remove"));
forwardPage(Page.STUDY_LIST_SERVLET);
} else {
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("studyToRemove", study);
request.setAttribute("sitesToRemove", sites);
request.setAttribute("userRolesToRemove", userRoles);
request.setAttribute("subjectsToRemove", subjects);
request.setAttribute("definitionsToRemove", definitions);
forwardPage(Page.REMOVE_STUDY);
} else {
logger.info("submit to remove the study");
// change all statuses to unavailable
StudyDAO studao = new StudyDAO(sm.getDataSource());
study.setOldStatus(study.getStatus());
study.setStatus(Status.DELETED);
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);
if (!site.getStatus().equals(Status.DELETED)) {
site.setOldStatus(site.getStatus());
site.setStatus(Status.AUTO_DELETED);
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);
logger.info("remove user role" + role.getName());
if (!role.getStatus().equals(Status.DELETED)) {
role.setStatus(Status.AUTO_DELETED);
role.setUpdater(ub);
role.setUpdatedDate(new Date());
udao.updateStudyUserRole(role, role.getUserName());
}
}
// YW << bug fix for that current active study has been deleted
if (study.getId() == currentStudy.getId()) {
currentStudy.setStatus(Status.DELETED);
currentRole.setStatus(Status.DELETED);
} else // (auto-removed)
if (currentStudy.getParentStudyId() == study.getId()) {
currentStudy.setStatus(Status.AUTO_DELETED);
// we may need handle this later?
currentRole.setStatus(Status.DELETED);
}
// remove all subjects
for (int i = 0; i < subjects.size(); i++) {
StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
if (!subject.getStatus().equals(Status.DELETED)) {
subject.setStatus(Status.AUTO_DELETED);
subject.setUpdater(ub);
subject.setUpdatedDate(new Date());
ssdao.update(subject);
}
}
// remove all study_group_class
// changed by jxu on 08-31-06, to fix the problem of no study_id
// in study_group table
StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
// YW 09-27-2007, enable status updating for StudyGroupClassBean
ArrayList groups = sgcdao.findAllByStudy(study);
for (int i = 0; i < groups.size(); i++) {
StudyGroupClassBean group = (StudyGroupClassBean) groups.get(i);
if (!group.getStatus().equals(Status.DELETED)) {
group.setStatus(Status.AUTO_DELETED);
group.setUpdater(ub);
group.setUpdatedDate(new Date());
sgcdao.update(group);
// all subject_group_map
ArrayList subjectGroupMaps = sgmdao.findAllByStudyGroupClassId(group.getId());
for (int j = 0; j < subjectGroupMaps.size(); j++) {
SubjectGroupMapBean sgMap = (SubjectGroupMapBean) subjectGroupMaps.get(j);
if (!sgMap.getStatus().equals(Status.DELETED)) {
sgMap.setStatus(Status.AUTO_DELETED);
sgMap.setUpdater(ub);
sgMap.setUpdatedDate(new Date());
sgmdao.update(sgMap);
}
}
}
}
ArrayList groupClasses = sgcdao.findAllActiveByStudy(study);
for (int i = 0; i < groupClasses.size(); i++) {
StudyGroupClassBean gc = (StudyGroupClassBean) groupClasses.get(i);
if (!gc.getStatus().equals(Status.DELETED)) {
gc.setStatus(Status.AUTO_DELETED);
gc.setUpdater(ub);
gc.setUpdatedDate(new Date());
sgcdao.update(gc);
}
}
// 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);
if (!definition.getStatus().equals(Status.DELETED)) {
definition.setStatus(Status.AUTO_DELETED);
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);
if (!edc.getStatus().equals(Status.DELETED)) {
edc.setStatus(Status.AUTO_DELETED);
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);
if (!event.getStatus().equals(Status.DELETED)) {
event.setStatus(Status.AUTO_DELETED);
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);
if (!eventCRF.getStatus().equals(Status.DELETED)) {
eventCRF.setOldStatus(eventCRF.getStatus());
eventCRF.setStatus(Status.AUTO_DELETED);
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);
if (!item.getStatus().equals(Status.DELETED)) {
item.setOldStatus(item.getStatus());
item.setStatus(Status.AUTO_DELETED);
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);
if (!data.getStatus().equals(Status.DELETED)) {
data.setStatus(Status.AUTO_DELETED);
data.setUpdater(ub);
data.setUpdatedDate(new Date());
datadao.update(data);
}
}
addPageMessage(resexception.getString("this_study_has_been_removed_succesfully"));
forwardPage(Page.STUDY_LIST_SERVLET);
}
}
}
use of org.akaza.openclinica.dao.submit.SubjectGroupMapDAO in project OpenClinica by OpenClinica.
the class RestoreSiteServlet method processRequest.
@Override
public void processRequest() throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
String idString = request.getParameter("id");
logger.info("site id:" + idString);
int siteId = Integer.valueOf(idString.trim()).intValue();
StudyBean study = (StudyBean) sdao.findByPK(siteId);
// find all user and roles
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
ArrayList userRoles = udao.findAllByStudyId(siteId);
// find all subjects
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
ArrayList subjects = ssdao.findAllByStudy(study);
// find all events
StudyEventDefinitionDAO sefdao = new StudyEventDefinitionDAO(sm.getDataSource());
ArrayList definitions = sefdao.findAllByStudy(study);
String action = request.getParameter("action");
if (StringUtil.isBlank(idString)) {
addPageMessage(respage.getString("please_choose_a_site_to_restore"));
forwardPage(Page.SITE_LIST_SERVLET);
} else {
if ("confirm".equalsIgnoreCase(action)) {
// site can be restored when its parent study is not "removed"
// -- YW -6-21-2007
StudyBean parentstudy = (StudyBean) sdao.findByPK(study.getParentStudyId());
if (!"removed".equals(parentstudy.getStatus().getName())) {
request.setAttribute("siteToRestore", study);
request.setAttribute("userRolesToRestore", userRoles);
request.setAttribute("subjectsToRestore", subjects);
// request.setAttribute("definitionsToRestore",
// definitions);
} else {
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("choosen_site_cannot_restored"));
Object[] arguments = { study.getName(), parentstudy.getName() };
addPageMessage(mf.format(arguments));
forwardPage(Page.STUDY_LIST_SERVLET);
}
forwardPage(Page.RESTORE_SITE);
} else {
logger.info("submit to restore the site");
// change all statuses to unavailable
StudyDAO studao = new StudyDAO(sm.getDataSource());
study.setStatus(study.getOldStatus());
study.setUpdater(ub);
study.setUpdatedDate(new Date());
studao.update(study);
// restore all users and roles
for (int i = 0; i < userRoles.size(); i++) {
StudyUserRoleBean role = (StudyUserRoleBean) userRoles.get(i);
if (role.getStatus().equals(Status.AUTO_DELETED)) {
role.setStatus(Status.AVAILABLE);
role.setUpdater(ub);
role.setUpdatedDate(new Date());
// YW << So study_user_role table status_id field can be
// updated
udao.updateStudyUserRole(role, role.getUserName());
}
// YW 06-18-2007 >>
}
// study
if (study.getId() == currentStudy.getId()) {
currentStudy.setStatus(Status.AVAILABLE);
StudyUserRoleBean r = (new UserAccountDAO(sm.getDataSource())).findRoleByUserNameAndStudyId(ub.getName(), currentStudy.getId());
StudyUserRoleBean rInParent = (new UserAccountDAO(sm.getDataSource())).findRoleByUserNameAndStudyId(ub.getName(), currentStudy.getParentStudyId());
// according to logic in SecureController.java: inherited
// role from parent study, pick the higher role
currentRole.setRole(Role.max(r.getRole(), rInParent.getRole()));
}
// YW >>
// restore 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);
if (group.getStatus().equals(Status.AUTO_DELETED)) {
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);
if (sgMap.getStatus().equals(Status.AUTO_DELETED)) {
sgMap.setStatus(Status.AVAILABLE);
sgMap.setUpdater(ub);
sgMap.setUpdatedDate(new Date());
sgmdao.update(sgMap);
}
}
}
}
// restore all events with subjects
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
for (int i = 0; i < subjects.size(); i++) {
StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
if (subject.getStatus().equals(Status.AUTO_DELETED)) {
subject.setStatus(Status.AVAILABLE);
subject.setUpdater(ub);
subject.setUpdatedDate(new Date());
ssdao.update(subject);
ArrayList events = sedao.findAllByStudySubject(subject);
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
for (int j = 0; j < events.size(); j++) {
StudyEventBean event = (StudyEventBean) events.get(j);
if (event.getStatus().equals(Status.AUTO_DELETED)) {
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++) {
// YW << fix broken page for storing site
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
// >> YW
if (eventCRF.getStatus().equals(Status.AUTO_DELETED)) {
eventCRF.setStatus(eventCRF.getOldStatus());
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);
if (item.getStatus().equals(Status.AUTO_DELETED)) {
item.setStatus(item.getOldStatus());
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
}
}
}
}
}
// for subjects
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(respage.getString("this_site_has_been_restored_succesfully"));
String fromListSite = (String) session.getAttribute("fromListSite");
if (fromListSite != null && fromListSite.equals("yes") && currentRole.getRole().equals(Role.STUDYDIRECTOR)) {
session.removeAttribute("fromListSite");
forwardPage(Page.SITE_LIST_SERVLET);
} else {
session.removeAttribute("fromListSite");
if (currentRole.getRole().equals(Role.ADMIN)) {
forwardPage(Page.STUDY_LIST_SERVLET);
} else {
forwardPage(Page.SITE_LIST_SERVLET);
}
}
}
}
}
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