use of org.akaza.openclinica.dao.managestudy.StudyGroupClassDAO in project OpenClinica by OpenClinica.
the class ListEventsForSubjectServlet method processRequest.
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
// checks which module the requests are from
String module = fp.getString(MODULE);
request.setAttribute(MODULE, module);
String pageNumber = fp.getString(ListStudySubjectServlet.SUBJECT_PAGE_NUMBER);
String filterKeyword = fp.getString(ListStudySubjectServlet.FILTER_KEYWORD);
String tmpSearch = fp.getString(ListStudySubjectServlet.SEARCH_SUBMITTED);
boolean searchSubmitted = !(tmpSearch == null || "".equalsIgnoreCase(tmpSearch)) && !"".equalsIgnoreCase(filterKeyword);
SubjectMatrixUtil matrixUtil = new SubjectMatrixUtil();
String query = matrixUtil.createPaginatingQuery(pageNumber);
StringBuilder extendedQuery = new StringBuilder(query);
// 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) {
extendedQuery.append("&ebl_sortColumnInd=0&submitted=1&ebl_sortAscending=1&ebl_filtered=1");
extendedQuery.append("&").append(ListStudySubjectServlet.FILTER_KEYWORD).append("=").append(filterKeywordURLEncode);
}
request.setAttribute(ListStudySubjectServlet.PAGINATING_QUERY, extendedQuery.toString());
int definitionId = fp.getInt("defId");
int tabId = fp.getInt("tab");
if (definitionId <= 0) {
addPageMessage(respage.getString("please_choose_an_ED_ta_to_vies_details"));
forwardPage(Page.LIST_STUDY_SUBJECTS);
return;
}
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(definitionId);
StudySubjectDAO sdao = new StudySubjectDAO(sm.getDataSource());
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
CRFDAO crfdao = new CRFDAO(sm.getDataSource());
// find all the groups in the current study
ArrayList studyGroupClasses = sgcdao.findAllActiveByStudy(currentStudy);
// information for the event tabs
ArrayList allDefs = seddao.findAllActiveByStudy(currentStudy);
boolean isASite = false;
if (currentStudy.getParentStudyId() > 0) {
StudyDAO stdao = new StudyDAO(sm.getDataSource());
StudyBean parent = (StudyBean) stdao.findByPK(currentStudy.getParentStudyId());
allDefs = seddao.findAllActiveByStudy(parent);
}
ArrayList eventDefinitionCRFs = (ArrayList) edcdao.findAllActiveByEventDefinitionId(this.currentStudy, definitionId);
for (int i = 0; i < eventDefinitionCRFs.size(); i++) {
EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(i);
CRFBean crf = (CRFBean) crfdao.findByPK(edc.getCrfId());
edc.setCrf(crf);
}
request.setAttribute("studyGroupClasses", studyGroupClasses);
request.setAttribute("allDefsArray", allDefs);
request.setAttribute("allDefsNumber", new Integer(allDefs.size()));
request.setAttribute("groupSize", new Integer(studyGroupClasses.size()));
request.setAttribute("eventDefCRFSize", new Integer(eventDefinitionCRFs.size()));
request.setAttribute("tabId", new Integer(tabId));
request.setAttribute("studyEventDef", sed);
request.setAttribute("eventDefCRFs", eventDefinitionCRFs);
// find all the subjects in current study
ArrayList subjects = sdao.findAllByStudyId(currentStudy.getId());
ArrayList displayStudySubs = new ArrayList();
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());
}
}
// find all eventcrfs for each event, for each event tab
ArrayList displaySubjectEvents = new ArrayList();
ArrayList<DisplayStudyEventBean> displayEvents = new ArrayList<DisplayStudyEventBean>();
ArrayList events = sedao.findAllByStudySubjectAndDefinition(studySub, sed);
for (int k = 0; k < events.size(); k++) {
StudyEventBean seb = (StudyEventBean) events.get(k);
DisplayStudyEventBean dseb = ListStudySubjectServlet.getDisplayStudyEventsForStudySubject(studySub, seb, sm.getDataSource(), ub, currentRole, this.currentStudy);
// ArrayList eventCRFs = ecdao.findAllByStudyEvent(seb);
// ArrayList al =
// ViewStudySubjectServlet.getUncompletedCRFs(sm.getDataSource(),
// eventDefinitionCRFs, eventCRFs);
// dseb.getUncompletedCRFs().add(al);
displayEvents.add(dseb);
}
ArrayList al = new ArrayList();
for (int k = 0; k < displayEvents.size(); k++) {
DisplayStudyEventBean dseb = displayEvents.get(k);
ArrayList eventCRFs = dseb.getDisplayEventCRFs();
for (int a = 0; a < eventDefinitionCRFs.size(); a++) {
EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(a);
int crfId = edc.getCrfId();
boolean hasCRF = false;
for (int b = 0; b < eventCRFs.size(); b++) {
DisplayEventCRFBean decb = (DisplayEventCRFBean) eventCRFs.get(b);
// decb.getStage().getName() );
if (decb.getEventCRF().getCrf().getId() == crfId) {
dseb.getAllEventCRFs().add(decb);
// logger.info("hasCRf" + crfId +
// decb.getEventCRF().getCrf().getName());
hasCRF = true;
break;
}
}
if (hasCRF == false) {
DisplayEventCRFBean db = new DisplayEventCRFBean();
db.setEventDefinitionCRF(edc);
db.getEventDefinitionCRF().setCrf(edc.getCrf());
dseb.getAllEventCRFs().add(db);
// logger.info("noCRf" + crfId);
}
}
// Issue 3212 BWP <<
if (currentStudy.getParentStudyId() > 0) {
// check each eventDefCRFBean and set its isHidden property
// to true, if its
// persistent/database-derived hideCrf is true (domain rule:
// hide the CRF from users logged into a site)
HideCRFManager hideCRFManager = HideCRFManager.createHideCRFManager();
hideCRFManager.optionallyCheckHideCRFProperty(dseb);
// remove a DisplayEventCRFBean from a DisplayStudyEventBean
// in the list
// if it contains a hidden CRF in its event definition
hideCRFManager.removeHiddenEventCRF(dseb);
// generate a boolean request attribute indicating whether
// any of the CRFs
// should be hidden
boolean hideCRFs = hideCRFManager.studyEventHasAHideCRFProperty(dseb);
request.setAttribute("hideCRFs", hideCRFs);
}
// >>
}
DisplayStudySubjectBean dssb = new DisplayStudySubjectBean();
dssb.setStudySubject(studySub);
dssb.setStudyGroups(subGClasses);
dssb.setStudyEvents(displayEvents);
if (definitionId > 0) {
dssb.setSedId(definitionId);
} else {
dssb.setSedId(-1);
}
displayStudySubs.add(dssb);
}
EntityBeanTable table = fp.getEntityBeanTable();
ArrayList allStudyRows = DisplayStudySubjectEventsRow.generateRowsFromBeans(displayStudySubs);
ArrayList columnArray = new ArrayList();
columnArray.add(resword.getString("ID"));
columnArray.add(resword.getString("subject_status"));
columnArray.add(resword.getString("gender"));
for (int i = 0; i < studyGroupClasses.size(); i++) {
StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
columnArray.add(sgc.getName());
}
// columnArray.add("Event Sequence");
columnArray.add(resword.getString("event_status"));
columnArray.add(resword.getString("event_date"));
// Issue 3212 BWP <<
HideCRFManager hideCRFMgr = HideCRFManager.createHideCRFManager();
hideCRFMgr.hideSpecifiedEventCRFDefBeans(eventDefinitionCRFs);
for (int i = 0; i < eventDefinitionCRFs.size(); i++) {
EventDefinitionCRFBean edc = (EventDefinitionCRFBean) eventDefinitionCRFs.get(i);
// Issue 3212 BWP <<
if (!(currentStudy.getParentStudyId() > 0)) {
columnArray.add(edc.getCrf().getName());
} else {
if (!edc.isHideCrf()) {
columnArray.add(edc.getCrf().getName());
}
}
// >>
}
columnArray.add(resword.getString("actions"));
String[] columns = new String[columnArray.size()];
columnArray.toArray(columns);
table.setColumns(new ArrayList(Arrays.asList(columns)));
table.setQuery("ListEventsForSubject?module=" + module + "&defId=" + definitionId + "&tab=" + tabId, new HashMap());
table.hideColumnLink(columnArray.size() - 1);
// if(currentStudy.getStatus().isAvailable()){
// table.addLink(resword.getString("add_new_subject"), "AddNewSubject");
// }
table.setRows(allStudyRows);
if (filterKeyword != null && !"".equalsIgnoreCase(filterKeyword)) {
table.setKeywordFilter(filterKeyword);
}
table.computeDisplay();
request.setAttribute("table", table);
forwardPage(Page.LIST_EVENTS_FOR_SUBJECT);
}
use of org.akaza.openclinica.dao.managestudy.StudyGroupClassDAO in project OpenClinica by OpenClinica.
the class ListDiscNotesSubjectServlet method processRequest.
// < ResourceBundleresexception,respage;
@Override
protected void processRequest() throws Exception {
String module = request.getParameter("module");
String moduleStr = "manage";
if (module != null && module.trim().length() > 0) {
if ("submit".equals(module)) {
request.setAttribute("module", "submit");
moduleStr = "submit";
} else if ("admin".equals(module)) {
request.setAttribute("module", "admin");
moduleStr = "admin";
} else {
request.setAttribute("module", "manage");
}
}
// << tbh 02/2010 filter out the entire module parameter to catch injections
// BWP 3098>> close the info side panel and show icons
request.setAttribute("closeInfoShowIcons", true);
// <<
// Determine whether to limit the displayed DN's to a certain DN type
int resolutionStatus = 0;
try {
resolutionStatus = Integer.parseInt(request.getParameter("resolutionStatus"));
} catch (NumberFormatException nfe) {
// Show all DN's
resolutionStatus = -1;
}
// Determine whether we already have a collection of resolutionStatus
// Ids, and if not
// create a new attribute. If there is no resolution status, then the
// Set object should be cleared,
// because we do not have to save a set of filter IDs.
boolean hasAResolutionStatus = resolutionStatus >= 1 && resolutionStatus <= 5;
Set<Integer> resolutionStatusIds = (HashSet) session.getAttribute(RESOLUTION_STATUS);
// remove the session if there is no resolution status
if (!hasAResolutionStatus && resolutionStatusIds != null) {
session.removeAttribute(RESOLUTION_STATUS);
resolutionStatusIds = null;
}
if (hasAResolutionStatus) {
if (resolutionStatusIds == null) {
resolutionStatusIds = new HashSet<Integer>();
}
resolutionStatusIds.add(resolutionStatus);
session.setAttribute(RESOLUTION_STATUS, resolutionStatusIds);
}
int discNoteType = 0;
try {
discNoteType = Integer.parseInt(request.getParameter("type"));
} catch (NumberFormatException nfe) {
// Show all DN's
discNoteType = -1;
}
request.setAttribute(DISCREPANCY_NOTE_TYPE, discNoteType);
DiscrepancyNoteUtil discNoteUtil = new DiscrepancyNoteUtil();
// Generate a summary of how we are filtering;
Map<String, List<String>> filterSummary = discNoteUtil.generateFilterSummary(discNoteType, resolutionStatusIds);
if (!filterSummary.isEmpty()) {
request.setAttribute(FILTER_SUMMARY, filterSummary);
}
locale = LocaleResolver.getLocale(request);
StudyBean sbean = (StudyBean) session.getAttribute("study");
//List<DiscrepancyNoteBean> allDiscNotes = discNoteUtil.getThreadedDNotesForStudy(sbean, resolutionStatusIds, sm.getDataSource(), discNoteType, true);
//Map stats = discNoteUtil.generateDiscNoteSummary(allDiscNotes);
Map stats = discNoteUtil.generateDiscNoteSummaryRefactored(sm.getDataSource(), currentStudy, resolutionStatusIds, discNoteType);
request.setAttribute("summaryMap", stats);
Set mapKeys = stats.keySet();
request.setAttribute("mapKeys", mapKeys);
// < resword =
// ResourceBundle.getBundle("org.akaza.openclinica.i18n.words",locale);
StudyDAO studyDAO = 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());
EventCRFDAO edao = new EventCRFDAO(sm.getDataSource());
EventDefinitionCRFDAO eddao = new EventDefinitionCRFDAO(sm.getDataSource());
SubjectDAO subdao = new SubjectDAO(sm.getDataSource());
DiscrepancyNoteDAO dnDAO = new DiscrepancyNoteDAO(sm.getDataSource());
ListDiscNotesSubjectTableFactory factory = new ListDiscNotesSubjectTableFactory(ResourceBundleProvider.getTermsBundle(locale));
factory.setStudyEventDefinitionDao(seddao);
factory.setSubjectDAO(subdao);
factory.setStudySubjectDAO(sdao);
factory.setStudyEventDAO(sedao);
factory.setStudyBean(currentStudy);
factory.setStudyGroupClassDAO(sgcdao);
factory.setSubjectGroupMapDAO(sgmdao);
factory.setStudyDAO(studyDAO);
factory.setCurrentRole(currentRole);
factory.setCurrentUser(ub);
factory.setEventCRFDAO(edao);
factory.setEventDefintionCRFDAO(eddao);
factory.setStudyGroupDAO(sgdao);
factory.setDiscrepancyNoteDAO(dnDAO);
factory.setModule(moduleStr);
factory.setDiscNoteType(discNoteType);
// factory.setStudyHasDiscNotes(allDiscNotes != null &&
// !allDiscNotes.isEmpty());
factory.setResolutionStatus(resolutionStatus);
factory.setResolutionStatusIds(resolutionStatusIds);
factory.setResword(ResourceBundleProvider.getWordsBundle(locale));
String listDiscNotesHtml = factory.createTable(request, response).render();
request.setAttribute("listDiscNotesHtml", listDiscNotesHtml);
forwardPage(getJSP());
}
use of org.akaza.openclinica.dao.managestudy.StudyGroupClassDAO in project OpenClinica by OpenClinica.
the class CreateSubjectGroupClassServlet method submitGroup.
/**
* Saves study group information into database
*
* @throws OpenClinicaException
*/
private void submitGroup() throws OpenClinicaException, IOException {
StudyGroupClassBean group = (StudyGroupClassBean) session.getAttribute("group");
ArrayList studyGroups = (ArrayList) session.getAttribute("studyGroups");
StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
group.setStudyId(currentStudy.getId());
group.setOwner(ub);
group.setStatus(Status.AVAILABLE);
group = (StudyGroupClassBean) sgcdao.create(group);
if (!group.isActive()) {
addPageMessage(respage.getString("the_subject_group_class_not_created_database"));
} else {
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
for (int i = 0; i < studyGroups.size(); i++) {
StudyGroupBean sg = (StudyGroupBean) studyGroups.get(i);
sg.setStudyGroupClassId(group.getId());
sg.setOwner(ub);
sg.setStatus(Status.AVAILABLE);
sgdao.create(sg);
}
addPageMessage(respage.getString("the_subject_group_class_created_succesfully"));
}
ArrayList pageMessages = (ArrayList) request.getAttribute(PAGE_MESSAGE);
session.setAttribute("pageMessages", pageMessages);
response.sendRedirect(request.getContextPath() + Page.MANAGE_STUDY_MODULE.getFileName());
}
use of org.akaza.openclinica.dao.managestudy.StudyGroupClassDAO in project OpenClinica by OpenClinica.
the class CoreSecureController method getStudyGroupClassesByCurrentStudy.
public ArrayList getStudyGroupClassesByCurrentStudy(HttpServletRequest request) {
StudyDAO studyDAO = new StudyDAO(getDataSource());
StudyGroupClassDAO studyGroupClassDAO = new StudyGroupClassDAO(getDataSource());
StudyGroupDAO studyGroupDAO = new StudyGroupDAO(getDataSource());
StudyBean currentStudy = (StudyBean) request.getSession().getAttribute("study");
int parentStudyId = currentStudy.getParentStudyId();
ArrayList studyGroupClasses = new ArrayList();
if (parentStudyId > 0) {
StudyBean parentStudy = (StudyBean) studyDAO.findByPK(parentStudyId);
studyGroupClasses = studyGroupClassDAO.findAllActiveByStudy(parentStudy);
} else {
parentStudyId = currentStudy.getId();
studyGroupClasses = studyGroupClassDAO.findAllActiveByStudy(currentStudy);
}
for (int i = 0; i < studyGroupClasses.size(); i++) {
StudyGroupClassBean sgc = (StudyGroupClassBean) studyGroupClasses.get(i);
ArrayList groups = studyGroupDAO.findAllByGroupClass(sgc);
sgc.setStudyGroups(groups);
}
return studyGroupClasses;
}
use of org.akaza.openclinica.dao.managestudy.StudyGroupClassDAO in project OpenClinica by OpenClinica.
the class EditSelectedServlet method processRequest.
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
boolean selectAll = fp.getBoolean("all");
boolean selectAllItemsGroupsAttrs = fp.getBoolean("allAttrsAndItems");
// BWP 3095: Only show a "select all items" like on a side info panel if
// it
// is not part of the EditSelected-related JSP>>
request.setAttribute("EditSelectedSubmitted", true);
// <<
ItemDAO idao = new ItemDAO(sm.getDataSource());
// CRFDAO crfdao = new CRFDAO(sm.getDataSource());
ItemFormMetadataDAO imfdao = new ItemFormMetadataDAO(sm.getDataSource());
CRFDAO crfdao = new CRFDAO(sm.getDataSource());
DatasetBean db = (DatasetBean) session.getAttribute("newDataset");
if (db == null) {
db = new DatasetBean();
session.setAttribute("newDataset", db);
}
// << tbh
// HashMap eventlist = (HashMap) request.getAttribute("eventlist");
// if (eventlist == null) {
// System.out.println("TTTTT found the second hashmap!");
HashMap eventlist = (LinkedHashMap) session.getAttribute("eventsForCreateDataset");
// }
ArrayList<String> ids = CreateDatasetServlet.allSedItemIdsInStudy(eventlist, crfdao, idao);
// >> tbh 11/09, need to fill in a session variable
if (selectAll) {
logger.info("select all..........");
db = selectAll(db);
MessageFormat msg = new MessageFormat("");
msg.setLocale(locale);
msg.applyPattern(respage.getString("choose_include_all_items_dataset"));
Object[] arguments = { ids.size() };
addPageMessage(msg.format(arguments));
// addPageMessage("You choose to include all items in current study
// for the dataset, " +db.getItemIds().size() + " items total.");
}
if (selectAllItemsGroupsAttrs) {
logger.info("select everything....");
db = selectAll(db);
db.setShowCRFcompletionDate(true);
db.setShowCRFinterviewerDate(true);
db.setShowCRFinterviewerName(true);
db.setShowCRFstatus(true);
db.setShowCRFversion(true);
db.setShowEventEnd(true);
db.setShowEventEndTime(true);
db.setShowEventLocation(true);
db.setShowEventStart(true);
db.setShowEventStartTime(true);
db.setShowEventStatus(true);
db.setShowSubjectAgeAtEvent(true);
db.setShowSubjectDob(true);
db.setShowSubjectGender(true);
db.setShowSubjectGroupInformation(true);
db.setShowSubjectStatus(true);
db.setShowSubjectUniqueIdentifier(true);
// select all groups
ArrayList sgclasses = (ArrayList) session.getAttribute("allSelectedGroups");
//
ArrayList newsgclasses = new ArrayList();
StudyDAO studydao = new StudyDAO(sm.getDataSource());
StudyGroupClassDAO sgclassdao = new StudyGroupClassDAO(sm.getDataSource());
StudyBean theStudy = (StudyBean) studydao.findByPK(sm.getUserBean().getActiveStudyId());
sgclasses = sgclassdao.findAllActiveByStudy(theStudy);
for (int i = 0; i < sgclasses.size(); i++) {
StudyGroupClassBean sgclass = (StudyGroupClassBean) sgclasses.get(i);
sgclass.setSelected(true);
newsgclasses.add(sgclass);
}
session.setAttribute("allSelectedGroups", newsgclasses);
request.setAttribute("allSelectedGroups", newsgclasses);
}
session.setAttribute("newDataset", db);
HashMap events = (HashMap) session.getAttribute(CreateDatasetServlet.EVENTS_FOR_CREATE_DATASET);
if (events == null) {
events = new HashMap();
}
ArrayList allSelectItems = selectAll ? selectAll(events, crfdao, idao) : ViewSelectedServlet.getAllSelected(db, idao, imfdao);
// >> tbh
session.setAttribute("numberOfStudyItems", new Integer(ids.size()).toString());
// << tbh 11/2009
session.setAttribute("allSelectedItems", allSelectItems);
setUpStudyGroups();
forwardPage(Page.CREATE_DATASET_VIEW_SELECTED);
}
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