Example 41 with CRFVersionBean
use of org.akaza.openclinica.bean.submit.CRFVersionBean in project OpenClinica by OpenClinica.
the class DataEntryServlet method processRequest.
@Override
protected void processRequest(HttpServletRequest request, HttpServletResponse response) throws Exception {
//JN:The following were the the global variables, moved as local.
locale = LocaleResolver.getLocale(request);
EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
SectionBean sb = (SectionBean) request.getAttribute(SECTION_BEAN);
ItemDataDAO iddao = new ItemDataDAO(getDataSource(), locale);
HttpSession session = request.getSession();
StudyBean currentStudy = (StudyBean) session.getAttribute("study");
StudyUserRoleBean currentRole = (StudyUserRoleBean) session.getAttribute("userRole");
SectionDAO sdao = new SectionDAO(getDataSource());
/**
* Determines whether the form was submitted. Calculated once in processRequest. The reason we don't use the normal means to determine if the form was
* submitted (ie FormProcessor.isSubmitted) is because when we use forwardPage, Java confuses the inputs from the just-processed form with the inputs for
* the forwarded-to page. This is a problem since frequently we're forwarding from one (submitted) section to the next (unsubmitted) section. If we use the
* normal means, Java will always think that the unsubmitted section is, in fact, submitted. This member is guaranteed to be calculated before
* shouldLoadDBValues() is called.
*/
boolean isSubmitted = false;
boolean hasGroup = false;
EventCRFDAO ecdao = null;
FormProcessor fp = new FormProcessor(request);
logMe("Enterting DataEntry Servlet" + System.currentTimeMillis());
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(getDataSource());
FormDiscrepancyNotes discNotes;
panel.setStudyInfoShown(false);
String age = "";
UserAccountBean ub = (UserAccountBean) request.getSession().getAttribute(USER_BEAN_NAME);
String instantAtt = CV_INSTANT_META + ecb.getCRFVersionId();
//for 11958: repeating groups rows appear if validation returns to the same section
int isFirstTimeOnSection = fp.getInt("isFirstTimeOnSection");
request.setAttribute("isFirstTimeOnSection", isFirstTimeOnSection + "");
if (getCrfLocker().isLocked(ecb.getId())) {
int userId = getCrfLocker().getLockOwner(ecb.getId());
UserAccountDAO udao = new UserAccountDAO(getDataSource());
UserAccountBean ubean = (UserAccountBean) udao.findByPK(userId);
if (ubean.getId() != ub.getId()) {
addPageMessage(resword.getString("CRF_unavailable") + " " + ubean.getName() + " " + resword.getString("Currently_entering_data") + " " + resword.getString("Leave_the_CRF"), request);
forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET, request, response);
}
} else {
getCrfLocker().lock(ecb.getId(), ub.getId());
}
if (!ecb.isActive()) {
throw new InconsistentStateException(Page.LIST_STUDY_SUBJECTS_SERVLET, resexception.getString("event_not_exists"));
}
logMe("Enterting DataEntry Get the status/number of item discrepancy notes" + System.currentTimeMillis());
// Get the status/number of item discrepancy notes
DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(getDataSource());
ArrayList<DiscrepancyNoteBean> allNotes = new ArrayList<DiscrepancyNoteBean>();
List<DiscrepancyNoteBean> eventCrfNotes = new ArrayList<DiscrepancyNoteBean>();
List<DiscrepancyNoteThread> noteThreads = new ArrayList<DiscrepancyNoteThread>();
// BWP: this try block is not necessary try {
dndao = new DiscrepancyNoteDAO(getDataSource());
allNotes = dndao.findAllTopNotesByEventCRF(ecb.getId());
eventCrfNotes = dndao.findOnlyParentEventCRFDNotesFromEventCRF(ecb);
if (!eventCrfNotes.isEmpty()) {
allNotes.addAll(eventCrfNotes);
}
logMe("Entering DataEntry Create disc note threads out of the various notes" + System.currentTimeMillis());
// Create disc note threads out of the various notes
DiscrepancyNoteUtil dNoteUtil = new DiscrepancyNoteUtil();
noteThreads = dNoteUtil.createThreadsOfParents(allNotes, getDataSource(), currentStudy, null, -1, true);
// variables that provide values for the CRF discrepancy note header
int updatedNum = 0;
int openNum = 0;
int closedNum = 0;
int resolvedNum = 0;
int notAppNum = 0;
DiscrepancyNoteBean tempBean;
for (DiscrepancyNoteThread dnThread : noteThreads) {
/*
* 3014: do not count parent beans, only the last child disc note of the thread.
*/
tempBean = dnThread.getLinkedNoteList().getLast();
if (tempBean != null) {
if (ResolutionStatus.UPDATED.equals(tempBean.getResStatus())) {
updatedNum++;
} else if (ResolutionStatus.OPEN.equals(tempBean.getResStatus())) {
openNum++;
} else if (ResolutionStatus.CLOSED.equals(tempBean.getResStatus())) {
// if (dn.getParentDnId() > 0){
closedNum++;
// }
} else if (ResolutionStatus.RESOLVED.equals(tempBean.getResStatus())) {
// if (dn.getParentDnId() > 0){
resolvedNum++;
// }
} else if (ResolutionStatus.NOT_APPLICABLE.equals(tempBean.getResStatus())) {
notAppNum++;
}
}
}
logMe("Entering DataEntry Create disc note threads out of the various notes DONE" + System.currentTimeMillis());
request.setAttribute("updatedNum", updatedNum + "");
request.setAttribute("openNum", openNum + "");
request.setAttribute("closedNum", closedNum + "");
request.setAttribute("resolvedNum", resolvedNum + "");
request.setAttribute("notAppNum", notAppNum + "");
String fromViewNotes = fp.getString("fromViewNotes");
if (fromViewNotes != null && "1".equals(fromViewNotes)) {
request.setAttribute("fromViewNotes", fromViewNotes);
}
logMe("Entering Create studySubjDao.. ++++stuff" + System.currentTimeMillis());
StudySubjectDAO ssdao = new StudySubjectDAO(getDataSource());
StudySubjectBean ssb = (StudySubjectBean) ssdao.findByPK(ecb.getStudySubjectId());
// YW 11-07-2007, data entry could not be performed if its study subject
// has been removed.
// Notice: ViewSectionDataEntryServelet, ViewSectionDataEntryPreview,
// PrintCRFServlet and PrintDataEntryServlet, have theirs own
// processRequest
Status s = ssb.getStatus();
if ("removed".equalsIgnoreCase(s.getName()) || "auto-removed".equalsIgnoreCase(s.getName())) {
addPageMessage(respage.getString("you_may_not_perform_data_entry_on_a_CRF") + respage.getString("study_subject_has_been_deleted"), request);
request.setAttribute("id", new Integer(ecb.getStudySubjectId()).toString());
session.removeAttribute(instantAtt);
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET, request, response);
}
// YW >>
HashMap<String, String> newUploadedFiles = (HashMap<String, String>) session.getAttribute("newUploadedFiles");
if (newUploadedFiles == null) {
newUploadedFiles = new HashMap<String, String>();
}
request.setAttribute("newUploadedFiles", newUploadedFiles);
if (!fp.getString("exitTo").equals("")) {
request.setAttribute("exitTo", fp.getString("exitTo"));
}
//some EVENT CRF CHECK
logMe("Entering some EVENT CRF CHECK" + System.currentTimeMillis());
if (!fp.getString(GO_EXIT).equals("")) {
session.removeAttribute(GROUP_HAS_DATA);
session.removeAttribute("to_create_crf");
session.removeAttribute("mayProcessUploading");
//Removing the user and EventCRF from the locked CRF List
if (getCrfLocker().isLocked(ecb.getId()) && getCrfLocker().getLockOwner(ecb.getId()) == ub.getId())
getCrfLocker().unlock(ecb.getId());
if (newUploadedFiles.size() > 0) {
if (this.unloadFiles(newUploadedFiles)) {
} else {
String missed = "";
Iterator iter = newUploadedFiles.keySet().iterator();
while (iter.hasNext()) {
missed += " " + newUploadedFiles.get(iter.next());
}
addPageMessage(respage.getString("uploaded_files_not_deleted_or_not_exist") + ": " + missed, request);
}
}
session.removeAttribute("newUploadedFiles");
addPageMessage(respage.getString("exit_without_saving"), request);
// another servlet
if (fromViewNotes != null && "1".equals(fromViewNotes)) {
String viewNotesURL = (String) session.getAttribute("viewNotesURL");
if (viewNotesURL != null && viewNotesURL.length() > 0) {
response.sendRedirect(response.encodeRedirectURL(viewNotesURL));
}
return;
}
String fromResolvingNotes = fp.getString("fromResolvingNotes", true);
String winLocation = (String) session.getAttribute(ViewNotesServlet.WIN_LOCATION);
session.removeAttribute(instantAtt);
if (!StringUtil.isBlank(fromResolvingNotes) && !StringUtil.isBlank(winLocation)) {
response.sendRedirect(response.encodeRedirectURL(winLocation));
} else {
if (!fp.getString("exitTo").equals("")) {
response.sendRedirect(response.encodeRedirectURL(fp.getString("exitTo")));
} else
response.sendRedirect(response.encodeRedirectURL("ListStudySubjects"));
}
// forwardPage(Page.SUBMIT_DATA_SERVLET);
return;
}
logMe("Entering some EVENT CRF CHECK DONE" + System.currentTimeMillis());
// checks if the section has items in item group
// for repeating items
// hasGroup = getInputBeans();
hasGroup = checkGroups(fp, ecb);
Boolean b = (Boolean) request.getAttribute(INPUT_IGNORE_PARAMETERS);
isSubmitted = fp.isSubmitted() && b == null;
// variable is used for fetching any null values like "not applicable"
int eventDefinitionCRFId = 0;
if (fp != null) {
eventDefinitionCRFId = fp.getInt("eventDefinitionCRFId");
}
StudyBean study = (StudyBean) session.getAttribute("study");
// constructs the list of items used on UI
// tbh>>
// logger.trace("trying event def crf id: "+eventDefinitionCRFId);
logMe("Entering some EVENT DEF CRF CHECK " + System.currentTimeMillis());
if (eventDefinitionCRFId <= 0) {
// TODO we have to get that id before we can continue
EventDefinitionCRFBean edcBean = edcdao.findByStudyEventIdAndCRFVersionId(study, ecb.getStudyEventId(), ecb.getCRFVersionId());
eventDefinitionCRFId = edcBean.getId();
}
logMe("Entering some EVENT DEF CRF CHECK DONE " + System.currentTimeMillis());
logMe("Entering some Study EVENT DEF CRF CHECK " + System.currentTimeMillis());
StudyEventDAO seDao = new StudyEventDAO(getDataSource());
EventDefinitionCRFBean edcBean = (EventDefinitionCRFBean) edcdao.findByPK(eventDefinitionCRFId);
EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) edcdao.findByPK(eventDefinitionCRFId);
//JN:Putting the event_def_crf_bean in the request attribute.
request.setAttribute(EVENT_DEF_CRF_BEAN, edcb);
StudyEventBean studyEventBean = (StudyEventBean) seDao.findByPK(ecb.getStudyEventId());
edcBean.setId(eventDefinitionCRFId);
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(getDataSource());
StudyEventDefinitionBean studyEventDefinition = (StudyEventDefinitionBean) seddao.findByPK(edcBean.getStudyEventDefinitionId());
CRFVersionDAO cvdao = new CRFVersionDAO(getDataSource());
CRFVersionBean crfVersionBean = (CRFVersionBean) cvdao.findByPK(ecb.getCRFVersionId());
Phase phase2 = Phase.INITIAL_DATA_ENTRY;
if (getServletPage(request).startsWith(Page.DOUBLE_DATA_ENTRY_SERVLET.getFileName())) {
phase2 = Phase.DOUBLE_DATA_ENTRY;
} else if (getServletPage(request).startsWith(Page.ADMIN_EDIT_SERVLET.getFileName())) {
phase2 = Phase.ADMIN_EDITING;
}
logMe("Entering ruleSets::: CreateAndInitializeRuleSet:::" + Thread.currentThread());
logMe("Entering ruleSets::: CreateAndInitializeRuleSet:::" + Thread.currentThread() + "currentStudy?" + currentStudy + "studyEventDefinition" + studyEventDefinition + "crfVersionBean" + crfVersionBean + "studyEventBean" + studyEventBean + "ecb" + ecb);
// List<RuleSetBean> ruleSets = createAndInitializeRuleSet(currentStudy, studyEventDefinition, crfVersionBean, studyEventBean, ecb, true, request, response);
// boolean shouldRunRules = getRuleSetService(request).shouldRunRulesForRuleSets(ruleSets, phase2);
logMe("Entering getDisplayBean:::::Thread::::" + Thread.currentThread());
DisplaySectionBean section = getDisplayBean(hasGroup, false, request, isSubmitted);
//hasSCDItem has been initialized in getDisplayBean() which is online above
VariableSubstitutionHelper.replaceVariables(section, study, ssb, studyEventDefinition, studyEventBean, dataSource);
if (section.getSection().hasSCDItem()) {
SimpleConditionalDisplayService cds0 = (SimpleConditionalDisplayService) SpringServletAccess.getApplicationContext(getServletContext()).getBean("simpleConditionalDisplayService");
section = cds0.initConditionalDisplays(section);
}
logMe("Entering Find out the id of the section's first field " + System.currentTimeMillis());
// 2790: Find out the id of the section's first field
String firstFieldId = getSectionFirstFieldId(section.getSection().getId());
request.setAttribute("formFirstField", firstFieldId);
// logger.trace("now trying event def crf id: "+eventDefinitionCRFId);
// above is necessary to give us null values during DDE
// ironically, this only covers vertical null value result sets
// horizontal ones are covered in FormBeanUtil, tbh 112007
logMe("Entering displayItemWithGroups " + System.currentTimeMillis());
//@pgawade 30-May-2012 Fix for issue 13963 - added an extra parameter 'isSubmitted' to method createItemWithGroups
List<DisplayItemWithGroupBean> displayItemWithGroups = createItemWithGroups(section, hasGroup, eventDefinitionCRFId, request, isSubmitted);
logMe("Entering displayItemWithGroups end " + System.currentTimeMillis());
this.getItemMetadataService().updateGroupDynamicsInSection(displayItemWithGroups, section.getSection().getId(), ecb);
section.setDisplayItemGroups(displayItemWithGroups);
DisplayTableOfContentsBean toc = TableOfContentsServlet.getDisplayBeanWithShownSections(getDataSource(), (DisplayTableOfContentsBean) request.getAttribute(TOC_DISPLAY), (DynamicsMetadataService) SpringServletAccess.getApplicationContext(getServletContext()).getBean("dynamicsMetadataService"));
request.setAttribute(TOC_DISPLAY, toc);
LinkedList<Integer> sectionIdsInToc = TableOfContentsServlet.sectionIdsInToc(toc);
// why do we get previousSec and nextSec here, rather than in
// getDisplayBeans?
// so that we can use them in forwarding the user to the previous/next
// section
// if the validation was successful
logMe("Entering displayItemWithGroups sdao.findPrevious " + System.currentTimeMillis());
int sIndex = TableOfContentsServlet.sectionIndexInToc(section.getSection(), toc, sectionIdsInToc);
SectionBean previousSec = this.prevSection(section.getSection(), ecb, toc, sIndex);
logMe("Entering displayItemWithGroups sdao.findPrevious end " + System.currentTimeMillis());
SectionBean nextSec = this.nextSection(section.getSection(), ecb, toc, sIndex);
section.setFirstSection(!previousSec.isActive());
section.setLastSection(!nextSec.isActive());
// this is for generating side info panel
// and the information panel under the Title
SubjectDAO subjectDao = new SubjectDAO(getDataSource());
StudyDAO studydao = new StudyDAO(getDataSource());
SubjectBean subject = (SubjectBean) subjectDao.findByPK(ssb.getSubjectId());
// Get the study then the parent study
logMe("Entering Get the study then the parent study " + System.currentTimeMillis());
if (study.getParentStudyId() > 0) {
// this is a site,find parent
StudyBean parentStudy = (StudyBean) studydao.findByPK(study.getParentStudyId());
request.setAttribute("studyTitle", parentStudy.getName());
request.setAttribute("siteTitle", study.getName());
} else {
request.setAttribute("studyTitle", study.getName());
}
logMe("Entering Get the study then the parent study end " + System.currentTimeMillis());
// Let us process the age
if (currentStudy.getStudyParameterConfig().getCollectDob().equals("1")) {
// YW 11-16-2007 erollment-date is used for calculating age.
Date enrollmentDate = ssb.getEnrollmentDate();
age = Utils.getInstacne().processAge(enrollmentDate, subject.getDateOfBirth());
}
//ArrayList beans = ViewStudySubjectServlet.getDisplayStudyEventsForStudySubject(ssb, getDataSource(), ub, currentRole);
request.setAttribute("studySubject", ssb);
request.setAttribute("subject", subject);
//request.setAttribute("beans", beans);
request.setAttribute("eventCRF", ecb);
request.setAttribute("age", age);
request.setAttribute("decryptedPassword", ((SecurityManager) SpringServletAccess.getApplicationContext(getServletContext()).getBean("securityManager")).encrytPassword("root", getUserDetails()));
// set up interviewer name and date
fp.addPresetValue(INPUT_INTERVIEWER, ecb.getInterviewerName());
if (ecb.getDateInterviewed() != null) {
DateFormat local_df = new SimpleDateFormat(resformat.getString("date_format_string"), ResourceBundleProvider.getLocale());
String idateFormatted = local_df.format(ecb.getDateInterviewed());
fp.addPresetValue(INPUT_INTERVIEW_DATE, idateFormatted);
} else {
fp.addPresetValue(INPUT_INTERVIEW_DATE, "");
}
setPresetValues(fp.getPresetValues(), request);
logMe("Entering Checks !submitted " + System.currentTimeMillis());
if (!isSubmitted) {
// TODO: prevent data enterer from seeing results of first round of
// data
// entry, if this is second round
// FLAG--SLOW HERE WHEN LOADING
logMe("Entering Checks !submitted entered " + System.currentTimeMillis());
long t = System.currentTimeMillis();
request.setAttribute(BEAN_DISPLAY, section);
request.setAttribute(BEAN_ANNOTATIONS, getEventCRFAnnotations(request));
session.setAttribute("shouldRunValidation", null);
session.setAttribute("rulesErrors", null);
session.setAttribute(DataEntryServlet.NOTE_SUBMITTED, null);
discNotes = new FormDiscrepancyNotes();
// discNotes = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
// if (discNotes == null) {
// discNotes = new FormDiscrepancyNotes();
// }
// << tbh 01/2010
section = populateNotesWithDBNoteCounts(discNotes, section, request);
populateInstantOnChange(request.getSession(), ecb, section);
LOGGER.debug("+++ just ran populateNotes, printing field notes: " + discNotes.getFieldNotes().toString());
LOGGER.debug("found disc notes: " + discNotes.getNumExistingFieldNotes().toString());
session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
if (section.getSection().hasSCDItem()) {
section = SCDItemDisplayInfo.generateSCDDisplayInfo(section, this.getServletPage(request).equals(Page.INITIAL_DATA_ENTRY) || this.getServletPage(request).equals(Page.ADMIN_EDIT_SERVLET) && !this.isAdminForcedReasonForChange(request));
}
int keyId = ecb.getId();
session.removeAttribute(DoubleDataEntryServlet.COUNT_VALIDATE + keyId);
setUpPanel(section);
if (newUploadedFiles.size() > 0) {
if (this.unloadFiles(newUploadedFiles)) {
} else {
String missed = "";
Iterator iter = newUploadedFiles.keySet().iterator();
while (iter.hasNext()) {
missed += " " + newUploadedFiles.get(iter.next());
}
addPageMessage(respage.getString("uploaded_files_not_deleted_or_not_exist") + ": " + missed, request);
}
}
logMe("Entering Checks !submitted entered end forwarding page " + System.currentTimeMillis());
logMe("Time Took for this block" + (System.currentTimeMillis() - t));
forwardPage(getJSPPage(), request, response);
return;
} else {
logMe("Entering Checks !submitted not entered " + System.currentTimeMillis());
//
// VALIDATION / LOADING DATA
//
// If validation is required for this round, we will go through
// each item and add an appropriate validation to the Validator
//
// Otherwise, we will just load the data into the DisplayItemBean
// so that we can write to the database later.
//
// Validation is required if two conditions are met:
// 1. The user clicked a "Save" button, not a "Confirm" button
// 2. In this type of data entry servlet, when the user clicks
// a Save button, the inputs are validated
//
boolean validate = fp.getBoolean(INPUT_CHECK_INPUTS) && validateInputOnFirstRound();
// did the user click a "Save" button?
// is validation required in this type of servlet when the user
// clicks
// "Save"?
// We can conclude that the user is trying to save data; therefore,
// set a request
// attribute indicating that default values for items shouldn't be
// displayed
// in the application UI that will subsequently be displayed
// TODO: find a better, less random place for this
// session.setAttribute(HAS_DATA_FLAG, true);
// section.setCheckInputs(fp.getBoolean(INPUT_CHECK_INPUTS));
errors = new HashMap();
// ArrayList items = section.getItems();
discNotes = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
if (discNotes == null) {
discNotes = new FormDiscrepancyNotes();
}
// populateNotesWithDBNoteCounts(discNotes, section);
// all items- inlcude items in item groups and other single items
List<DisplayItemWithGroupBean> allItems = section.getDisplayItemGroups();
String attachedFilePath = Utils.getAttachedFilePath(currentStudy);
DiscrepancyValidator v = new DiscrepancyValidator(request, discNotes);
RuleValidator ruleValidator = new RuleValidator(request);
LOGGER.debug("SZE 1 :: " + allItems.size());
logMe("Looping inside !submitted " + System.currentTimeMillis());
for (int i = 0; i < allItems.size(); i++) {
LOGGER.trace("===itering through items: " + i);
DisplayItemWithGroupBean diwg = allItems.get(i);
if (diwg.isInGroup()) {
// for the items in groups
DisplayItemGroupBean dgb = diwg.getItemGroup();
List<DisplayItemGroupBean> dbGroups = diwg.getDbItemGroups();
//dbGroups = diwg.getItemGroups();
List<DisplayItemGroupBean> formGroups = new ArrayList<DisplayItemGroupBean>();
LOGGER.debug("got db item group size " + dbGroups.size());
if (validate) {
// int manualGroups = getManualRows(dbGroups2);
// logger.debug("+++ found manual rows from db group 2: " + manualGroups);
LOGGER.debug("===IF VALIDATE NOT A SINGLE ITEM: got to this part in the validation loop: " + dgb.getGroupMetaBean().getName());
// TODO next marker tbh 112007
// formGroups = validateDisplayItemGroupBean(v,
// dgb,dbGroups, formGroups,
// ruleValidator,groupOrdinalPLusItemOid);
formGroups = validateDisplayItemGroupBean(v, dgb, dbGroups, formGroups, request, response);
LOGGER.debug("form group size after validation " + formGroups.size());
} else {
LOGGER.debug("+++ELSE NOT A SINGLE ITEM: got to this part in the validation loop: " + dgb.getGroupMetaBean().getName());
formGroups = loadFormValueForItemGroup(dgb, dbGroups, formGroups, eventDefinitionCRFId, request);
LOGGER.debug("form group size without validation " + formGroups.size());
}
diwg.setItemGroup(dgb);
diwg.setItemGroups(formGroups);
allItems.set(i, diwg);
} else {
// other single items
DisplayItemBean dib = diwg.getSingleItem();
// dib = (DisplayItemBean) allItems.get(i);
if (validate) {
// generate input name here?
// DisplayItemGroupBean dgb = diwg.getItemGroup();
String itemName = getInputName(dib);
// no Item group for single item, so just use blank
// string as parameter for inputName
// this
dib = validateDisplayItemBean(v, dib, "", request);
// should be
// used,
// otherwise,
// DDE not
// working-jxu
LOGGER.debug("&&& found name: " + itemName);
LOGGER.debug("input VALIDATE " + itemName + ": " + fp.getString(itemName));
// dib.loadFormValue(fp.getString(itemName));
LOGGER.debug("input " + itemName + " has a response set of " + dib.getMetadata().getResponseSet().getOptions().size() + " options");
} else {
String itemName = getInputName(dib);
LOGGER.debug("input NONVALIDATE " + itemName + ": " + fp.getString(itemName));
// dib.loadFormValue(itemName);
dib = loadFormValue(dib, request);
// String itemName = getInputName(dib);
// dib = loadFormValue(itemName);
}
ArrayList children = dib.getChildren();
for (int j = 0; j < children.size(); j++) {
DisplayItemBean child = (DisplayItemBean) children.get(j);
// DisplayItemGroupBean dgb = diwg.getItemGroup();
String itemName = getInputName(child);
child.loadFormValue(fp.getString(itemName));
if (validate) {
// child = validateDisplayItemBean(v, child,
// itemName, ruleValidator, groupOrdinalPLusItemOid,
// false);
child = validateDisplayItemBean(v, child, itemName, request);
// was null changed value 092007 tbh
} else {
// child.loadFormValue(itemName);
child = loadFormValue(child, request);
}
LOGGER.debug("Checking child value for " + itemName + ": " + child.getData().getValue());
children.set(j, child);
}
dib.setChildren(children);
diwg.setSingleItem(runDynamicsItemCheck(dib, null, request));
// logger.trace("just set single item on line 447:
// "+dib.getData().getValue());
// items.set(i, dib);
LOGGER.debug(" I : " + i);
allItems.set(i, diwg);
}
}
logMe("Loop ended " + System.currentTimeMillis());
//JN: This is the list that contains all the scd-shown items.
List<ItemBean> itemBeansWithSCDShown = new ArrayList<ItemBean>();
if (validate && section.getSection().hasSCDItem()) {
logMe(" Validate and Loop " + System.currentTimeMillis());
for (int i = 0; i < allItems.size(); ++i) {
DisplayItemBean dib = allItems.get(i).getSingleItem();
ItemFormMetadataBean ifmb = dib.getMetadata();
if (ifmb.getParentId() == 0) {
if (dib.getScdData().getScdSetsForControl().size() > 0) {
//for control item
//dib has to loadFormValue first. Here loadFormValue has been done in validateDisplayItemBean(v, dib, "")
section.setShowSCDItemIds(SimpleConditionalDisplayService.conditionalDisplayToBeShown(dib, section.getShowSCDItemIds()));
}
if (dib.getScdData().getScdItemMetadataBean().getScdItemFormMetadataId() > 0) {
//for scd item
//a control item is always before its scd item
dib.setIsSCDtoBeShown(section.getShowSCDItemIds().contains(dib.getMetadata().getItemId()));
if (dib.getIsSCDtoBeShown())
itemBeansWithSCDShown.add(dib.getItem());
validateSCDItemBean(v, dib);
}
ArrayList<DisplayItemBean> children = dib.getChildren();
for (int j = 0; j < children.size(); j++) {
DisplayItemBean child = children.get(j);
if (child.getScdData().getScdSetsForControl().size() > 0) {
//for control item
//dib has to loadFormValue first. Here loadFormValue has been done in validateDisplayItemBean(v, dib, "")
section.setShowSCDItemIds(SimpleConditionalDisplayService.conditionalDisplayToBeShown(child, section.getShowSCDItemIds()));
}
if (child.getScdData().getScdItemMetadataBean().getScdItemFormMetadataId() > 0) {
//for scd item
//a control item is always before its scd item
child.setIsSCDtoBeShown(section.getShowSCDItemIds().contains(child.getMetadata().getItemId()));
if (child.getIsSCDtoBeShown())
itemBeansWithSCDShown.add(dib.getItem());
validateSCDItemBean(v, child);
}
}
}
}
logMe(" Validate and Loop end " + System.currentTimeMillis());
}
logMe(" Validate and Loop end " + System.currentTimeMillis());
//JN:calling again here, for the items with simple conditional display and rules.
List<RuleSetBean> ruleSets = createAndInitializeRuleSet(currentStudy, studyEventDefinition, crfVersionBean, studyEventBean, ecb, true, request, response, itemBeansWithSCDShown);
boolean shouldRunRules = getRuleSetService(request).shouldRunRulesForRuleSets(ruleSets, phase2);
// this.getItemMetadataService().resetItemCounter();
HashMap<String, ArrayList<String>> groupOrdinalPLusItemOid = null;
groupOrdinalPLusItemOid = runRules(allItems, ruleSets, true, shouldRunRules, MessageType.ERROR, phase2, ecb, request);
logMe("allItems Loop begin " + System.currentTimeMillis());
for (int i = 0; i < allItems.size(); i++) {
DisplayItemWithGroupBean diwg = allItems.get(i);
if (diwg.isInGroup()) {
// for the items in groups
DisplayItemGroupBean dgb = diwg.getItemGroup();
List<DisplayItemGroupBean> dbGroups = diwg.getDbItemGroups();
//dbGroups = diwg.getItemGroups();
// tbh 01/2010 change the group list?
List<DisplayItemGroupBean> formGroups = new ArrayList<DisplayItemGroupBean>();
// items again?
if (validate) {
// int manualGroups = getManualRows(dbGroups2);
// logger.debug("+++ found manual rows for db group2: " + manualGroups);
formGroups = validateDisplayItemGroupBean(v, dgb, dbGroups, formGroups, ruleValidator, groupOrdinalPLusItemOid, request, response);
// formGroups = validateDisplayItemGroupBean(v, dgb,
// dbGroups, formGroups);
LOGGER.debug("*** form group size after validation " + formGroups.size());
}
diwg.setItemGroup(dgb);
diwg.setItemGroups(formGroups);
allItems.set(i, diwg);
} else {
// other single items
DisplayItemBean dib = diwg.getSingleItem();
// dib = (DisplayItemBean) allItems.get(i);
if (validate) {
String itemName = getInputName(dib);
//
dib = validateDisplayItemBean(v, dib, "", ruleValidator, groupOrdinalPLusItemOid, false, null, request);
// / dib = validateDisplayItemBean(v, dib, "");// this
}
ArrayList children = dib.getChildren();
for (int j = 0; j < children.size(); j++) {
DisplayItemBean child = (DisplayItemBean) children.get(j);
// DisplayItemGroupBean dgb = diwg.getItemGroup();
String itemName = getInputName(child);
child.loadFormValue(fp.getString(itemName));
if (validate) {
child = validateDisplayItemBean(v, child, "", ruleValidator, groupOrdinalPLusItemOid, false, null, request);
// child = validateDisplayItemBean(v, child,
// itemName);
}
children.set(j, child);
LOGGER.debug(" J (children): " + j);
}
dib.setChildren(children);
diwg.setSingleItem(runDynamicsItemCheck(dib, null, request));
LOGGER.debug(" I : " + i);
allItems.set(i, diwg);
}
}
logMe("allItems Loop end " + System.currentTimeMillis());
// YW, 2-1-2008 <<
// A map from item name to item bean object.
HashMap<String, ItemBean> scoreItems = new HashMap<String, ItemBean>();
HashMap<String, String> scoreItemdata = new HashMap<String, String>();
HashMap<String, ItemDataBean> oldItemdata = prepareSectionItemdataObject(sb.getId(), request);
// hold all item names of changed ItemBean in current section
TreeSet<String> changedItems = new TreeSet<String>();
// holds complete disply item beans for checking against 'request
// for change' restriction
ArrayList<DisplayItemBean> changedItemsList = new ArrayList<DisplayItemBean>();
// key is repeating item name, value is its display item group bean
HashMap<String, DisplayItemGroupBean> changedItemsMap = new HashMap<String, DisplayItemGroupBean>();
// key is itemid, value is set of itemdata-ordinal
HashMap<Integer, TreeSet<Integer>> itemOrdinals = prepareItemdataOrdinals(request);
// prepare item data for scoring
updateDataOrdinals(allItems);
section.setDisplayItemGroups(allItems);
scoreItems = prepareScoreItems(request);
scoreItemdata = prepareScoreItemdata(request);
logMe("allItems 2 Loop begin " + System.currentTimeMillis());
for (int i = 0; i < allItems.size(); i++) {
DisplayItemWithGroupBean diwb = allItems.get(i);
if (diwb.isInGroup()) {
// for the items in groups
DisplayItemGroupBean digb = diwb.getItemGroup();
List<DisplayItemGroupBean> dbGroups = diwb.getDbItemGroups();
for (int j = 0; j < dbGroups.size(); j++) {
DisplayItemGroupBean displayGroup = dbGroups.get(j);
List<DisplayItemBean> items = displayGroup.getItems();
if ("remove".equalsIgnoreCase(displayGroup.getEditFlag())) {
for (DisplayItemBean displayItem : items) {
if (displayItem.getMetadata().isShowItem() && digb.getGroupMetaBean().isShowGroup()) {
int itemId = displayItem.getItem().getId();
int ordinal = displayItem.getData().getOrdinal();
if (itemOrdinals.containsKey(itemId)) {
itemOrdinals.get(itemId).remove(ordinal);
}
if (scoreItemdata.containsKey(itemId + "_" + ordinal)) {
scoreItemdata.remove(itemId + "_" + ordinal);
}
changedItems.add(displayItem.getItem().getName());
changedItemsList.add(displayItem);
String formName = displayItem.getItem().getName();
// logger.debug("SET: formName:" + formName);
if (displayGroup.isAuto()) {
formName = getGroupItemInputName(displayGroup, displayGroup.getFormInputOrdinal(), displayItem);
LOGGER.debug("GET: changed formName to " + formName);
} else {
formName = getGroupItemManualInputName(displayGroup, displayGroup.getFormInputOrdinal(), displayItem);
LOGGER.debug("GET-MANUAL: changed formName to " + formName);
}
changedItemsMap.put(formName, displayGroup);
LOGGER.debug("adding to changed items map: " + formName);
}
}
}
}
List<DisplayItemGroupBean> dgbs = diwb.getItemGroups();
int groupsize = dgbs.size();
HashMap<Integer, Integer> maxOrdinals = new HashMap<Integer, Integer>();
boolean first = true;
for (int j = 0; j < dgbs.size(); j++) {
DisplayItemGroupBean displayGroup = dgbs.get(j);
List<DisplayItemBean> items = displayGroup.getItems();
boolean isAdd = "add".equalsIgnoreCase(displayGroup.getEditFlag()) ? true : false;
for (DisplayItemBean displayItem : items) {
ItemBean ib = displayItem.getItem();
String itemName = ib.getName();
int itemId = ib.getId();
if (first) {
maxOrdinals.put(itemId, iddao.getMaxOrdinalForGroup(ecb, sb, displayGroup.getItemGroupBean()));
}
ItemDataBean idb = displayItem.getData();
String value = idb.getValue();
scoreItems.put(itemName, ib);
int ordinal = displayItem.getData().getOrdinal();
if (isAdd && scoreItemdata.containsKey(itemId + "_" + ordinal)) {
int formMax = 1;
if (maxOrdinals.containsKey(itemId)) {
formMax = maxOrdinals.get(itemId);
}
int dbMax = iddao.getMaxOrdinalForGroup(ecb, sb, displayGroup.getItemGroupBean());
ordinal = ordinal >= dbMax ? formMax + 1 : ordinal;
maxOrdinals.put(itemId, ordinal);
displayItem.getData().setOrdinal(ordinal);
scoreItemdata.put(itemId + "_" + ordinal, value);
} else {
scoreItemdata.put(itemId + "_" + ordinal, value);
}
if (itemOrdinals.containsKey(itemId)) {
itemOrdinals.get(itemId).add(ordinal);
} else {
TreeSet<Integer> ordinalSet = new TreeSet<Integer>();
ordinalSet.add(ordinal);
itemOrdinals.put(itemId, ordinalSet);
}
if (isChanged(displayItem, oldItemdata, attachedFilePath)) {
changedItems.add(itemName);
changedItemsList.add(displayItem);
String formName = displayItem.getItem().getName();
// logger.debug("SET: formName:" + formName);
if (displayGroup.isAuto()) {
formName = getGroupItemInputName(displayGroup, displayGroup.getFormInputOrdinal(), displayItem);
LOGGER.debug("RESET: formName group-item-input:" + formName);
} else {
formName = getGroupItemManualInputName(displayGroup, displayGroup.getFormInputOrdinal(), displayItem);
LOGGER.debug("RESET: formName group-item-input-manual:" + formName);
}
changedItemsMap.put(formName, displayGroup);
LOGGER.debug("adding to changed items map: " + formName);
}
}
first = false;
}
} else {
DisplayItemBean dib = diwb.getSingleItem();
ItemBean ib = dib.getItem();
ItemDataBean idb = dib.getData();
int itemId = ib.getId();
String itemName = ib.getName();
String value = idb.getValue();
scoreItems.put(itemName, ib);
// for items which are not in any group, their ordinal is
// set as 1
TreeSet<Integer> ordinalset = new TreeSet<Integer>();
ordinalset.add(1);
itemOrdinals.put(itemId, ordinalset);
scoreItemdata.put(itemId + "_" + 1, value);
if (isChanged(idb, oldItemdata, dib, attachedFilePath)) {
changedItems.add(itemName);
changedItemsList.add(dib);
// changedItemsMap.put(dib.getItem().getName(), new
// DisplayItemGroupBean());
}
ArrayList children = dib.getChildren();
for (int j = 0; j < children.size(); j++) {
DisplayItemBean child = (DisplayItemBean) children.get(j);
ItemBean cib = child.getItem();
scoreItems.put(cib.getName(), cib);
TreeSet<Integer> cordinalset = new TreeSet<Integer>();
cordinalset.add(1);
itemOrdinals.put(itemId, cordinalset);
scoreItemdata.put(cib.getId() + "_" + 1, child.getData().getValue());
if (isChanged(child.getData(), oldItemdata, child, attachedFilePath)) {
changedItems.add(itemName);
changedItemsList.add(child);
// changedItemsMap.put(itemName, new
// DisplayItemGroupBean());
}
}
}
}
logMe("allItems 2 Loop end " + System.currentTimeMillis());
// do calculation for 'calculation' and 'group-calculation' type
// items
// and write the result in DisplayItemBean's ItemDateBean - data
ScoreItemValidator sv = new ScoreItemValidator(request, discNotes);
// *** doing calc here, load it where? ***
SessionManager sm = (SessionManager) request.getSession().getAttribute("sm");
ScoreCalculator sc = new ScoreCalculator(sm, ecb, ub);
logMe("allItems 3 Loop begin " + System.currentTimeMillis());
for (int i = 0; i < allItems.size(); i++) {
DisplayItemWithGroupBean diwb = allItems.get(i);
if (diwb.isInGroup()) {
List<DisplayItemGroupBean> dgbs = diwb.getItemGroups();
for (int j = 0; j < dgbs.size(); j++) {
DisplayItemGroupBean displayGroup = dgbs.get(j);
List<DisplayItemBean> items = displayGroup.getItems();
for (DisplayItemBean displayItem : items) {
ItemFormMetadataBean ifmb = displayItem.getMetadata();
int responseTypeId = ifmb.getResponseSet().getResponseTypeId();
if (responseTypeId == 8 || responseTypeId == 9) {
StringBuffer err = new StringBuffer();
ResponseOptionBean robBean = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0);
String value = "";
String inputName = "";
// getFormInputOrdinal() here, tbh 06/2009
if (displayGroup.isAuto()) {
inputName = getGroupItemInputName(displayGroup, displayGroup.getFormInputOrdinal(), displayItem);
LOGGER.debug("returning input name: " + inputName);
} else {
inputName = getGroupItemManualInputName(displayGroup, displayGroup.getFormInputOrdinal(), displayItem);
LOGGER.debug("returning input name: " + inputName);
}
if (robBean.getValue().startsWith("func: getexternalvalue") || robBean.getValue().startsWith("func: getExternalValue")) {
value = fp.getString(inputName);
LOGGER.debug("*** just set " + fp.getString(inputName) + " for line 815 " + displayItem.getItem().getName() + " with input name " + inputName);
} else {
value = sc.doCalculation(displayItem, scoreItems, scoreItemdata, itemOrdinals, err, displayItem.getData().getOrdinal());
}
displayItem.loadFormValue(value);
if (isChanged(displayItem, oldItemdata, attachedFilePath)) {
changedItems.add(displayItem.getItem().getName());
changedItemsList.add(displayItem);
}
request.setAttribute(inputName, value);
if (validate) {
displayItem = validateCalcTypeDisplayItemBean(sv, displayItem, inputName, request);
if (err.length() > 0) {
Validation validation = new Validation(Validator.CALCULATION_FAILED);
validation.setErrorMessage(err.toString());
sv.addValidation(inputName, validation);
}
}
}
}
}
} else {
DisplayItemBean dib = diwb.getSingleItem();
ItemFormMetadataBean ifmb = dib.getMetadata();
int responseTypeId = ifmb.getResponseSet().getResponseTypeId();
if (responseTypeId == 8 || responseTypeId == 9) {
StringBuffer err = new StringBuffer();
ResponseOptionBean robBean = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0);
String value = "";
if (robBean.getValue().startsWith("func: getexternalvalue") || robBean.getValue().startsWith("func: getExternalValue")) {
String itemName = getInputName(dib);
value = fp.getString(itemName);
LOGGER.debug("just set " + fp.getString(itemName) + " for " + dib.getItem().getName());
LOGGER.debug("found in fp: " + fp.getString(dib.getItem().getName()));
// logger.debug("scoreitemdata: " +
// scoreItemdata.toString());
} else {
value = sc.doCalculation(dib, scoreItems, scoreItemdata, itemOrdinals, err, 1);
}
dib.loadFormValue(value);
if (isChanged(dib.getData(), oldItemdata, dib, attachedFilePath)) {
changedItems.add(dib.getItem().getName());
changedItemsList.add(dib);
// changedItemsMap.put(dib.getItem().getName(), new
// DisplayItemGroupBean());
}
String inputName = getInputName(dib);
request.setAttribute(inputName, value);
if (validate) {
dib = validateCalcTypeDisplayItemBean(sv, dib, "", request);
if (err.length() > 0) {
Validation validation = new Validation(Validator.CALCULATION_FAILED);
validation.setErrorMessage(err.toString());
sv.addValidation(inputName, validation);
}
}
}
ArrayList children = dib.getChildren();
for (int j = 0; j < children.size(); j++) {
DisplayItemBean child = (DisplayItemBean) children.get(j);
ItemFormMetadataBean cifmb = child.getMetadata();
int resTypeId = cifmb.getResponseSet().getResponseTypeId();
if (resTypeId == 8 || resTypeId == 9) {
StringBuffer cerr = new StringBuffer();
child.getDbData().setValue(child.getData().getValue());
ResponseOptionBean crobBean = (ResponseOptionBean) cifmb.getResponseSet().getOptions().get(0);
String cvalue = "";
if (crobBean.getValue().startsWith("func: getexternalvalue") || crobBean.getValue().startsWith("func: getExternalValue")) {
String itemName = getInputName(child);
cvalue = fp.getString(itemName);
LOGGER.debug("just set " + fp.getString(itemName) + " for " + child.getItem().getName());
} else {
cvalue = sc.doCalculation(child, scoreItems, scoreItemdata, itemOrdinals, cerr, 1);
}
child.loadFormValue(cvalue);
if (isChanged(child.getData(), oldItemdata, child, attachedFilePath)) {
changedItems.add(child.getItem().getName());
changedItemsList.add(child);
// changedItemsMap.put(child.getItem().getName(),
// new DisplayItemGroupBean());
}
String cinputName = getInputName(child);
request.setAttribute(cinputName, cvalue);
if (validate) {
child = validateCalcTypeDisplayItemBean(sv, child, "", request);
if (cerr.length() > 0) {
Validation cvalidation = new Validation(Validator.CALCULATION_FAILED);
cvalidation.setErrorMessage(cerr.toString());
sv.addValidation(cinputName, cvalidation);
}
}
}
children.set(j, child);
}
}
}
logMe("allItems 3 Loop end " + System.currentTimeMillis());
// YW >>
// we have to do this since we loaded all the form values into the
// display
// item beans above
// section.setItems(items);
// setting this AFTER we populate notes - will that make a difference?
section.setDisplayItemGroups(allItems);
// logger.debug("+++ try to populate notes");
section = populateNotesWithDBNoteCounts(discNotes, section, request);
populateInstantOnChange(request.getSession(), ecb, section);
if (currentStudy.getStudyParameterConfig().getInterviewerNameRequired().equals("yes")) {
v.addValidation(INPUT_INTERVIEWER, Validator.NO_BLANKS);
}
if (currentStudy.getStudyParameterConfig().getInterviewDateRequired().equals("yes")) {
v.addValidation(INPUT_INTERVIEW_DATE, Validator.NO_BLANKS);
}
if (!StringUtil.isBlank(fp.getString(INPUT_INTERVIEW_DATE))) {
v.addValidation(INPUT_INTERVIEW_DATE, Validator.IS_A_DATE);
v.alwaysExecuteLastValidation(INPUT_INTERVIEW_DATE);
}
if (section.getSection().hasSCDItem()) {
section = SCDItemDisplayInfo.generateSCDDisplayInfo(section, this.getServletPage(request).equals(Page.INITIAL_DATA_ENTRY) || this.getServletPage(request).equals(Page.ADMIN_EDIT_SERVLET) && !this.isAdminForcedReasonForChange(request));
}
// logger.debug("about to validate: " + v.getKeySet());
errors = v.validate();
// tbh >>
if (this.isAdminForcedReasonForChange(request) && this.isAdministrativeEditing() && errors.isEmpty()) {
// "You have changed data after this CRF was marked complete. "
// +
// "You must provide a Reason For Change discrepancy note for this item before you can save this updated information."
String error = respage.getString("reason_for_change_error");
// "Please enter a reason for change discrepancy note before saving."
// ;
int nonforcedChanges = 0;
// items map
if (changedItemsList.size() > 0) {
LOGGER.debug("found admin force reason for change: changed items " + changedItems.toString() + " and changed items list: " + changedItemsList.toString() + " changed items map: " + changedItemsMap.toString());
logMe("DisplayItemBean Loop begin " + System.currentTimeMillis());
for (DisplayItemBean displayItem : changedItemsList) {
String formName = getInputName(displayItem);
ItemDataBean idb = displayItem.getData();
ItemBean item_bean = displayItem.getItem();
ItemFormMetadataBean ifmb = displayItem.getMetadata();
LOGGER.debug("-- found group label " + ifmb.getGroupLabel());
if (!ifmb.getGroupLabel().equalsIgnoreCase("Ungrouped") && !ifmb.getGroupLabel().equalsIgnoreCase("")) {
// << tbh 11/2009 sometimes the group label is blank instead of ungrouped???
Iterator iter = changedItemsMap.entrySet().iterator();
while (iter.hasNext()) {
Map.Entry<String, DisplayItemGroupBean> pairs = (Map.Entry) iter.next();
String formName2 = pairs.getKey();
DisplayItemGroupBean dgb = pairs.getValue();
// logger.debug("found auto: " +
// dgb.isAuto());
String testFormName = "";
if (dgb.isAuto()) {
// testFormName = getGroupItemInputName(dgb, dgb.getFormInputOrdinal(), getManualRows(dgbs), displayItem);
testFormName = getGroupItemInputName(dgb, dgb.getFormInputOrdinal(), displayItem);
} else {
testFormName = getGroupItemManualInputName(dgb, dgb.getFormInputOrdinal(), displayItem);
}
LOGGER.debug("found test form name: " + testFormName);
// if our test is the same with both the display
// item and the display group ...
// logger.debug("comparing " +
// testFormName + " and " + formName2);
int existingNotes = dndao.findNumExistingNotesForItem(idb.getId());
if (testFormName.equals(formName2)) {
formName = formName2;
this.setReasonForChangeError(ecb, item_bean, idb, formName, error, request);
changedItemsMap.remove(formName2);
LOGGER.debug("form name changed: " + formName);
break;
// .., send it as the form name
}
// ... otherwise, don't touch it
// how to tell vs. manual and just plain input?
}
} else {
this.setReasonForChangeError(ecb, item_bean, idb, formName, error, request);
LOGGER.debug("form name added: " + formName);
}
}
logMe("DisplayItemBean Loop end " + System.currentTimeMillis());
}
if (nonforcedChanges > 0) {
// do smething here?
}
}
LOGGER.debug("errors here: " + errors.toString());
// <<
logMe("error check Loop begin " + System.currentTimeMillis());
if (errors.isEmpty() && shouldRunRules) {
LOGGER.debug("Errors was empty");
if (session.getAttribute("rulesErrors") != null) {
// rules have already generated errors, Let's compare old
// error list with new
// error list, if lists not same show errors.
HashMap h = ruleValidator.validate();
Set<String> a = (Set<String>) session.getAttribute("rulesErrors");
Set<String> ba = h.keySet();
Boolean showErrors = false;
for (Object key : ba) {
if (!a.contains(key)) {
showErrors = true;
}
}
if (showErrors) {
errors = h;
if (errors.size() > 0) {
session.setAttribute("shouldRunValidation", "1");
session.setAttribute("rulesErrors", errors.keySet());
} else {
session.setAttribute("shouldRunValidation", null);
session.setAttribute("rulesErrors", null);
}
} else {
session.setAttribute("shouldRunValidation", null);
session.setAttribute("rulesErrors", null);
}
} else if (session.getAttribute("shouldRunValidation") != null && session.getAttribute("shouldRunValidation").toString().equals("1")) {
session.setAttribute("shouldRunValidation", null);
session.setAttribute("rulesErrors", null);
} else {
errors = ruleValidator.validate();
if (errors.size() > 0) {
session.setAttribute("shouldRunValidation", "1");
session.setAttribute("rulesErrors", errors.keySet());
}
}
}
if (!errors.isEmpty()) {
LOGGER.debug("threw an error with data entry...");
// copying below three lines, tbh 03/2010
String[] textFields = { INPUT_INTERVIEWER, INPUT_INTERVIEW_DATE };
fp.setCurrentStringValuesAsPreset(textFields);
setPresetValues(fp.getPresetValues(), request);
// YW, 2-4-2008 <<
logMe("!errors if Loop begin " + System.currentTimeMillis());
HashMap<String, ArrayList<String>> siErrors = sv.validate();
if (siErrors != null && !siErrors.isEmpty()) {
Iterator iter = siErrors.keySet().iterator();
while (iter.hasNext()) {
String fieldName = iter.next().toString();
errors.put(fieldName, siErrors.get(fieldName));
}
}
// we should 'shift' the names here, tbh 02/2010
// need: total number of rows, manual rows, all row names
// plus: error names
Iterator iter2 = errors.keySet().iterator();
while (iter2.hasNext()) {
String fieldName = iter2.next().toString();
LOGGER.debug("found error " + fieldName);
}
// for (int i = 0; i < allItems.size(); i++) {
// DisplayItemWithGroupBean diwb = allItems.get(i);
//
// if (diwb.isInGroup()) {
// List<DisplayItemGroupBean> dgbs = diwb.getItemGroups();
// logger.debug("found manual rows " + getManualRows(dgbs) + " and total rows " + dgbs.size() + " from ordinal " + diwb.getOrdinal());
// }
// }
errors = reshuffleErrorGroupNamesKK(errors, allItems, request);
reshuffleReasonForChangeHashAndDiscrepancyNotes(allItems, request, ecb);
// reset manual rows, so that we can catch errors correctly
// but it needs to be set per block of repeating items? what if there are two or more?
/*
int manualRows = 0; // getManualRows(formGroups);
for (int i = 0; i < allItems.size(); i++) {
DisplayItemWithGroupBean diwb = allItems.get(i);
if (diwb.isInGroup()) {
List<DisplayItemGroupBean> dgbs = diwb.getItemGroups();
manualRows = getManualRows(dgbs);
}
}
*/
//request.setAttribute("manualRows", new Integer(manualRows));
Iterator iter3 = errors.keySet().iterator();
while (iter3.hasNext()) {
String fieldName = iter3.next().toString();
LOGGER.debug("found error after shuffle " + fieldName);
}
//Mantis Issue: 8116. Parsist the markComplete chebox on error
request.setAttribute("markComplete", fp.getString(INPUT_MARK_COMPLETE));
// << tbh, 02/2010
// YW >>
// copied
request.setAttribute(BEAN_DISPLAY, section);
request.setAttribute(BEAN_ANNOTATIONS, fp.getString(INPUT_ANNOTATIONS));
setInputMessages(errors, request);
addPageMessage(respage.getString("errors_in_submission_see_below"), request);
request.setAttribute("hasError", "true");
// addPageMessage("To override these errors and keep the data as
// you
// entered it, click one of the \"Confirm\" buttons. ");
// if (section.isCheckInputs()) {
// addPageMessage("Please notice that you must enter data for
// the
// <b>required</b> entries.");
// }
// we do not save any DNs if we get here, so we have to set it back into session...
session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
// << tbh 01/2010
setUpPanel(section);
forwardPage(getJSPPage(), request, response);
} else {
//reshuffleReasonForChangeHashAndDiscrepancyNotes( allItems, request, ecb);
LOGGER.debug("Do we hit this in save ?????");
logMe("Do we hit this in save ???? " + System.currentTimeMillis());
boolean success = true;
boolean temp = true;
// save interviewer name and date into DB
ecb.setInterviewerName(fp.getString(INPUT_INTERVIEWER));
if (!StringUtil.isBlank(fp.getString(INPUT_INTERVIEW_DATE))) {
ecb.setDateInterviewed(fp.getDate(INPUT_INTERVIEW_DATE));
} else {
ecb.setDateInterviewed(null);
}
if (ecdao == null) {
ecdao = new EventCRFDAO(getDataSource());
}
// set validator id for DDE
DataEntryStage stage = ecb.getStage();
if (stage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
ecb.setValidatorId(ub.getId());
}
// for Administrative editing
if (studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.SIGNED) && changedItemsList.size() > 0) {
studyEventBean.setSubjectEventStatus(SubjectEventStatus.COMPLETED);
studyEventBean.setUpdater(ub);
studyEventBean.setUpdatedDate(new Date());
seDao.update(studyEventBean);
}
// If the Study Subject's Satus is signed and we save a section
// , change status to available
LOGGER.debug("Status of Study Subject {}", ssb.getStatus().getName());
if (ssb.getStatus() == Status.SIGNED && changedItemsList.size() > 0) {
LOGGER.debug("Status of Study Subject is Signed we are updating");
StudySubjectDAO studySubjectDao = new StudySubjectDAO(getDataSource());
ssb.setStatus(Status.AVAILABLE);
ssb.setUpdater(ub);
ssb.setUpdatedDate(new Date());
studySubjectDao.update(ssb);
}
if (ecb.isSdvStatus() && changedItemsList.size() > 0) {
LOGGER.debug("Status of Study Subject is SDV we are updating");
StudySubjectDAO studySubjectDao = new StudySubjectDAO(getDataSource());
ssb.setStatus(Status.AVAILABLE);
ssb.setUpdater(ub);
ssb.setUpdatedDate(new Date());
studySubjectDao.update(ssb);
ecb.setSdvStatus(false);
ecb.setSdvUpdateId(ub.getId());
}
ecb = (EventCRFBean) ecdao.update(ecb);
// save discrepancy notes into DB
FormDiscrepancyNotes fdn = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
dndao = new DiscrepancyNoteDAO(getDataSource());
AddNewSubjectServlet.saveFieldNotes(INPUT_INTERVIEWER, fdn, dndao, ecb.getId(), "EventCRF", currentStudy);
AddNewSubjectServlet.saveFieldNotes(INPUT_INTERVIEW_DATE, fdn, dndao, ecb.getId(), "EventCRF", currentStudy);
// items = section.getItems();
allItems = section.getDisplayItemGroups();
int nextOrdinal = 0;
LOGGER.debug("all items before saving into DB" + allItems.size());
this.output(allItems);
//TODO:Seems longer here, check this
logMe("DisplayItemWithGroupBean allitems4 " + System.currentTimeMillis());
for (int i = 0; i < allItems.size(); i++) {
DisplayItemWithGroupBean diwb = allItems.get(i);
// from executing writeToDB.
if (diwb.isInGroup()) {
List<DisplayItemGroupBean> dgbs = diwb.getItemGroups();
// using the above gets us the correct number of manual groups, tbh 01/2010
List<DisplayItemGroupBean> dbGroups = diwb.getDbItemGroups();
LOGGER.debug("item group size: " + dgbs.size());
LOGGER.debug("item db-group size: " + dbGroups.size());
for (int j = 0; j < dgbs.size(); j++) {
DisplayItemGroupBean displayGroup = dgbs.get(j);
List<DisplayItemBean> items = displayGroup.getItems();
// this ordinal will only useful to create a new
// item data
// update an item data won't touch its ordinal
// int nextOrdinal = iddao.getMaxOrdinalForGroup(ecb, sb, displayGroup.getItemGroupBean()) + 1;
// Determine if any items in this group have data. If so we need to undelete and previously deleted items.
boolean undelete = false;
for (DisplayItemBean displayItem : items) {
String currItemVal = displayItem.getData().getValue();
if (currItemVal != null && !currItemVal.equals("")) {
undelete = true;
break;
}
}
for (DisplayItemBean displayItem : items) {
String fileName = this.addAttachedFilePath(displayItem, attachedFilePath);
boolean writeDN = true;
displayItem.setEditFlag(displayGroup.getEditFlag());
LOGGER.debug("group item value: " + displayItem.getData().getValue());
// if ("add".equalsIgnoreCase(displayItem.getEditFlag()) && fileName.length() > 0 && !newUploadedFiles.containsKey(fileName)) {
// displayItem.getData().setValue("");
// }
//15350, this particular logic, takes into consideration that a DN is created properly as long as the item data record exists and it fails to get created when it doesnt.
//so, we are expanding the logic from writeToDb method to avoid creating duplicate records.
writeDN = writeDN(displayItem);
//pulling from dataset instead of database and correcting the flawed logic of using the database ordinals as max ordinal...
nextOrdinal = displayItem.getData().getOrdinal();
temp = writeToDB(displayItem, iddao, nextOrdinal, request);
LOGGER.debug("just executed writeToDB - 1");
LOGGER.debug("next ordinal: " + nextOrdinal);
// Undelete item if any item in the repeating group has data.
if (undelete && displayItem.getDbData() != null && displayItem.getDbData().isDeleted()) {
iddao.undelete(displayItem.getDbData().getId(), ub.getId());
}
if (temp && newUploadedFiles.containsKey(fileName)) {
newUploadedFiles.remove(fileName);
}
// maybe put ordinal in the place of j? maybe subtract max rows from next ordinal if j is gt
// next ordinal?
String inputName = getGroupItemInputName(displayGroup, j, displayItem);
// String inputName2 = getGroupItemManualInputName(displayGroup, j, displayItem);
if (!displayGroup.isAuto()) {
LOGGER.trace("not auto");
inputName = this.getGroupItemManualInputName(displayGroup, j, displayItem);
}
//htaycher last DN is not stored for new rows
// if (j == dgbs.size() - 1) {
// // LAST ONE
// logger.trace("last one");
// int ordinal = j - this.getManualRows(dgbs);
// logger.debug("+++ found manual rows from line 1326: " + ordinal);
// inputName = getGroupItemInputName(displayGroup, ordinal, displayItem);
// }
// logger.trace("&&& we get previous looking at input name: " + inputName + " " + inputName2);
LOGGER.trace("&&& we get previous looking at input name: " + inputName);
// input name 2 removed from below
inputName = displayItem.getFieldName();
if (writeDN) {
AddNewSubjectServlet.saveFieldNotes(inputName, fdn, dndao, displayItem.getData().getId(), "itemData", currentStudy, ecb.getId());
}
success = success && temp;
}
}
for (int j = 0; j < dbGroups.size(); j++) {
DisplayItemGroupBean displayGroup = dbGroups.get(j);
//JN: Since remove button is gone, the following code can be commented out, however it needs to be tested? Can be tackled when handling discrepancy note w/repeating groups issues.
if ("remove".equalsIgnoreCase(displayGroup.getEditFlag())) {
List<DisplayItemBean> items = displayGroup.getItems();
for (DisplayItemBean displayItem : items) {
String fileName = this.addAttachedFilePath(displayItem, attachedFilePath);
displayItem.setEditFlag(displayGroup.getEditFlag());
LOGGER.debug("group item value: " + displayItem.getData().getValue());
// if ("add".equalsIgnoreCase(displayItem.getEditFlag()) && fileName.length() > 0 && !newUploadedFiles.containsKey(fileName)) {
// displayItem.getData().setValue("");
// }
temp = writeToDB(displayItem, iddao, 0, request);
LOGGER.debug("just executed writeToDB - 2");
if (temp && newUploadedFiles.containsKey(fileName)) {
newUploadedFiles.remove(fileName);
}
// just use 0 here since update doesn't
// touch ordinal
success = success && temp;
}
}
}
} else {
DisplayItemBean dib = diwb.getSingleItem();
// TODO work on this line
// this.addAttachedFilePath(dib, attachedFilePath);
String fileName = addAttachedFilePath(dib, attachedFilePath);
boolean writeDN = writeDN(dib);
temp = writeToDB(dib, iddao, 1, request);
LOGGER.debug("just executed writeToDB - 3");
if (temp && (newUploadedFiles.containsKey(dib.getItem().getId() + "") || newUploadedFiles.containsKey(fileName))) {
// so newUploadedFiles will contain only failed file
// items;
newUploadedFiles.remove(dib.getItem().getId() + "");
newUploadedFiles.remove(fileName);
}
String inputName = getInputName(dib);
LOGGER.trace("3 - found input name: " + inputName);
if (writeDN)
AddNewSubjectServlet.saveFieldNotes(inputName, fdn, dndao, dib.getData().getId(), "itemData", currentStudy, ecb.getId());
success = success && temp;
ArrayList childItems = dib.getChildren();
for (int j = 0; j < childItems.size(); j++) {
DisplayItemBean child = (DisplayItemBean) childItems.get(j);
this.addAttachedFilePath(child, attachedFilePath);
writeDN = writeDN(child);
temp = writeToDB(child, iddao, 1, request);
LOGGER.debug("just executed writeToDB - 4");
if (temp && newUploadedFiles.containsKey(child.getItem().getId() + "")) {
// so newUploadedFiles will contain only failed
// file items;
newUploadedFiles.remove(child.getItem().getId() + "");
}
inputName = getInputName(child);
if (writeDN)
AddNewSubjectServlet.saveFieldNotes(inputName, fdn, dndao, child.getData().getId(), "itemData", currentStudy, ecb.getId());
success = success && temp;
}
}
}
logMe("DisplayItemWithGroupBean allitems4 end " + System.currentTimeMillis());
LOGGER.debug("running rules: " + phase2.name());
List<Integer> prevShownDynItemDataIds = shouldRunRules ? this.getItemMetadataService().getDynamicsItemFormMetadataDao().findShowItemDataIdsInSection(section.getSection().getId(), ecb.getCRFVersionId(), ecb.getId()) : new ArrayList<Integer>();
logMe("DisplayItemWithGroupBean dryrun start" + System.currentTimeMillis());
HashMap<String, ArrayList<String>> rulesPostDryRun = runRules(allItems, ruleSets, false, shouldRunRules, MessageType.WARNING, phase2, ecb, request);
HashMap<String, ArrayList<String>> errorsPostDryRun = new HashMap<String, ArrayList<String>>();
// additional step needed, run rules and see if any items are 'shown' AFTER saving data
logMe("DisplayItemWithGroupBean dryrun end" + System.currentTimeMillis());
boolean inSameSection = false;
logMe("DisplayItemWithGroupBean allitems4 " + System.currentTimeMillis());
if (!rulesPostDryRun.isEmpty()) {
// in same section?
// iterate through the OIDs and see if any of them belong to this section
Iterator iter3 = rulesPostDryRun.keySet().iterator();
while (iter3.hasNext()) {
String fieldName = iter3.next().toString();
LOGGER.debug("found oid after post dry run " + fieldName);
// set up a listing of OIDs in the section
// BUT: Oids can have the group name in them.
int ordinal = -1;
String newFieldName = fieldName;
String[] fieldNames = fieldName.split("\\.");
if (fieldNames.length == 2) {
newFieldName = fieldNames[1];
// check items in item groups here?
if (fieldNames[0].contains("[")) {
int p1 = fieldNames[0].indexOf("[");
int p2 = fieldNames[0].indexOf("]");
try {
ordinal = Integer.valueOf(fieldNames[0].substring(p1 + 1, p2));
} catch (NumberFormatException e) {
ordinal = -1;
}
fieldNames[0] = fieldNames[0].substring(0, p1);
}
}
List<DisplayItemWithGroupBean> displayGroupsWithItems = section.getDisplayItemGroups();
//ArrayList<DisplayItemBean> displayItems = section.getItems();
for (int i = 0; i < displayGroupsWithItems.size(); i++) {
DisplayItemWithGroupBean itemWithGroup = displayGroupsWithItems.get(i);
if (itemWithGroup.isInGroup()) {
LOGGER.debug("found group: " + fieldNames[0]);
// do something there
List<DisplayItemGroupBean> digbs = itemWithGroup.getItemGroups();
LOGGER.debug("digbs size: " + digbs.size());
for (int j = 0; j < digbs.size(); j++) {
DisplayItemGroupBean displayGroup = digbs.get(j);
if (displayGroup.getItemGroupBean().getOid().equals(fieldNames[0]) && displayGroup.getOrdinal() == ordinal - 1) {
List<DisplayItemBean> items = displayGroup.getItems();
for (int k = 0; k < items.size(); k++) {
DisplayItemBean dib = items.get(k);
if (dib.getItem().getOid().equals(newFieldName)) {
//inSameSection = true;
if (!dib.getMetadata().isShowItem()) {
LOGGER.debug("found item in group " + this.getGroupItemInputName(displayGroup, j, dib) + " vs. " + fieldName + " and is show item: " + dib.getMetadata().isShowItem());
dib.getMetadata().setShowItem(true);
}
if (prevShownDynItemDataIds == null || !prevShownDynItemDataIds.contains(dib.getData().getId())) {
inSameSection = true;
errorsPostDryRun.put(this.getGroupItemInputName(displayGroup, j, dib), rulesPostDryRun.get(fieldName));
}
}
items.set(k, dib);
}
displayGroup.setItems(items);
digbs.set(j, displayGroup);
}
}
itemWithGroup.setItemGroups(digbs);
} else {
DisplayItemBean displayItemBean = itemWithGroup.getSingleItem();
ItemBean itemBean = displayItemBean.getItem();
if (newFieldName.equals(itemBean.getOid())) {
//System.out.println("check run dynamics item check " + runDynamicsItemCheck(displayItemBean).getMetadata().isShowItem());
if (!displayItemBean.getMetadata().isShowItem()) {
// double check there?
LOGGER.debug("found item " + this.getInputName(displayItemBean) + " vs. " + fieldName + " and is show item: " + displayItemBean.getMetadata().isShowItem());
// if is repeating, use the other input name? no
displayItemBean.getMetadata().setShowItem(true);
if (prevShownDynItemDataIds == null || !prevShownDynItemDataIds.contains(displayItemBean.getData().getId())) {
inSameSection = true;
errorsPostDryRun.put(this.getInputName(displayItemBean), rulesPostDryRun.get(fieldName));
}
}
}
itemWithGroup.setSingleItem(displayItemBean);
}
displayGroupsWithItems.set(i, itemWithGroup);
}
logMe("DisplayItemWithGroupBean allitems4 end,begin" + System.currentTimeMillis());
// check groups
//List<DisplayItemGroupBean> itemGroups = new ArrayList<DisplayItemGroupBean>();
//itemGroups = section.getDisplayFormGroups();
// But in jsp: section.displayItemGroups.itemGroup.groupMetaBean.showGroup
List<DisplayItemWithGroupBean> itemGroups = section.getDisplayItemGroups();
// List<DisplayItemGroupBean> newItemGroups = new ArrayList<DisplayItemGroupBean>();
for (DisplayItemWithGroupBean itemGroup : itemGroups) {
DisplayItemGroupBean displayGroup = itemGroup.getItemGroup();
if (newFieldName.equals(displayGroup.getItemGroupBean().getOid())) {
if (!displayGroup.getGroupMetaBean().isShowGroup()) {
inSameSection = true;
LOGGER.debug("found itemgroup " + displayGroup.getItemGroupBean().getOid() + " vs. " + fieldName + " and is show item: " + displayGroup.getGroupMetaBean().isShowGroup());
// hmmm how to set highlighting for a group?
errorsPostDryRun.put(displayGroup.getItemGroupBean().getOid(), rulesPostDryRun.get(fieldName));
displayGroup.getGroupMetaBean().setShowGroup(true);
// add necessary rows to the display group here????
// we have to set the items in the itemGroup for the displayGroup
loadItemsWithGroupRows(itemGroup, sb, edcb, ecb, request);
}
}
// newItemGroups.add(displayGroup);
}
logMe("DisplayItemWithGroupBean allitems4 end,end" + System.currentTimeMillis());
// trying to reset the display form groups here, tbh
// section.setItems(displayItems);
section.setDisplayItemGroups(displayGroupsWithItems);
populateInstantOnChange(request.getSession(), ecb, section);
// section.setDisplayFormGroups(newDisplayBean.getDisplayFormGroups());
}
//
this.getItemMetadataService().updateGroupDynamicsInSection(displayItemWithGroups, section.getSection().getId(), ecb);
toc = TableOfContentsServlet.getDisplayBeanWithShownSections(getDataSource(), (DisplayTableOfContentsBean) request.getAttribute(TOC_DISPLAY), (DynamicsMetadataService) SpringServletAccess.getApplicationContext(getServletContext()).getBean("dynamicsMetadataService"));
request.setAttribute(TOC_DISPLAY, toc);
sectionIdsInToc = TableOfContentsServlet.sectionIdsInToc(toc);
sIndex = TableOfContentsServlet.sectionIndexInToc(section.getSection(), toc, sectionIdsInToc);
previousSec = this.prevSection(section.getSection(), ecb, toc, sIndex);
nextSec = this.nextSection(section.getSection(), ecb, toc, sIndex);
section.setFirstSection(!previousSec.isActive());
section.setLastSection(!nextSec.isActive());
//
// we need the following for repeating groups, tbh
// >> tbh 06/2010
// List<DisplayItemWithGroupBean> displayItemWithGroups2 = createItemWithGroups(section, hasGroup, eventDefinitionCRFId);
// section.setDisplayItemGroups(displayItemWithGroups2);
// if so, stay at this section
LOGGER.debug(" in same section: " + inSameSection);
if (inSameSection) {
// copy of one line from early on around line 400, forcing a re-show of the items
// section = getDisplayBean(hasGroup, true);// include all items, tbh
// below a copy of three lines from the if errors = true line, tbh 03/2010
String[] textFields = { INPUT_INTERVIEWER, INPUT_INTERVIEW_DATE };
fp.setCurrentStringValuesAsPreset(textFields);
setPresetValues(fp.getPresetValues(), request);
// below essetially a copy except for rulesPostDryRun
request.setAttribute(BEAN_DISPLAY, section);
request.setAttribute(BEAN_ANNOTATIONS, fp.getString(INPUT_ANNOTATIONS));
setInputMessages(errorsPostDryRun, request);
addPageMessage(respage.getString("your_answers_activated_hidden_items"), request);
request.setAttribute("hasError", "true");
request.setAttribute("hasShown", "true");
session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
setUpPanel(section);
forwardPage(getJSPPage(), request, response);
}
}
if (!inSameSection) {
// else if not in same section, progress as usual
/*
toc =
TableOfContentsServlet.getDisplayBeanWithShownSections(getDataSource(), (DisplayTableOfContentsBean) request.getAttribute(TOC_DISPLAY),
(DynamicsMetadataService) SpringServletAccess.getApplicationContext(getServletContext()).getBean("dynamicsMetadataService"));
request.setAttribute(TOC_DISPLAY, toc);
sectionIdsInToc = TableOfContentsServlet.sectionIdsInToc(toc);
sIndex = TableOfContentsServlet.sectionIndexInToc(section.getSection(), toc, sectionIdsInToc);
previousSec = this.prevSection(section.getSection(), ecb, toc, sIndex);
nextSec = this.nextSection(section.getSection(), ecb, toc, sIndex);
section.setFirstSection(!previousSec.isActive());
section.setLastSection(!nextSec.isActive());
*/
// can we just forward page or do we actually need an ELSE here?
// yes, we do. tbh 05/03/2010
ArrayList<String> updateFailedItems = sc.redoCalculations(scoreItems, scoreItemdata, changedItems, itemOrdinals, sb.getId());
success = updateFailedItems.size() > 0 ? false : true;
// now check if CRF is marked complete
boolean markComplete = fp.getString(INPUT_MARK_COMPLETE).equals(VALUE_YES);
// if the CRF was marked
boolean markSuccessfully = false;
// successfully
if (markComplete && section.isLastSection()) {
LOGGER.debug("need to mark CRF as complete");
markSuccessfully = markCRFComplete(request);
LOGGER.debug("...marked CRF as complete: " + markSuccessfully);
if (!markSuccessfully) {
request.setAttribute(BEAN_DISPLAY, section);
request.setAttribute(BEAN_ANNOTATIONS, fp.getString(INPUT_ANNOTATIONS));
setUpPanel(section);
forwardPage(getJSPPage(), request, response);
return;
}
}
// now write the event crf bean to the database
String annotations = fp.getString(INPUT_ANNOTATIONS);
setEventCRFAnnotations(annotations, request);
Date now = new Date();
ecb.setUpdatedDate(now);
ecb.setUpdater(ub);
ecb = (EventCRFBean) ecdao.update(ecb);
success = success && ecb.isActive();
StudyEventDAO sedao = new StudyEventDAO(getDataSource());
StudyEventBean seb = (StudyEventBean) sedao.findByPK(ecb.getStudyEventId());
seb.setUpdatedDate(now);
seb.setUpdater(ub);
seb = (StudyEventBean) sedao.update(seb);
success = success && seb.isActive();
request.setAttribute(INPUT_IGNORE_PARAMETERS, Boolean.TRUE);
if (newUploadedFiles.size() > 0) {
if (this.unloadFiles(newUploadedFiles)) {
} else {
String missed = "";
Iterator iter = newUploadedFiles.keySet().iterator();
while (iter.hasNext()) {
missed += " " + newUploadedFiles.get(iter.next());
}
addPageMessage(respage.getString("uploaded_files_not_deleted_or_not_exist") + ": " + missed, request);
}
}
if (!success) {
// YW, 3-6-2008 <<
if (updateFailedItems.size() > 0) {
String mess = "";
for (String ss : updateFailedItems) {
mess += ss + ", ";
}
mess = mess.substring(0, mess.length() - 2);
addPageMessage(resexception.getString("item_save_failed_because_database_error") + mess, request);
} else {
// YW>>
addPageMessage(resexception.getString("database_error"), request);
}
request.setAttribute(BEAN_DISPLAY, section);
session.removeAttribute(GROUP_HAS_DATA);
session.removeAttribute(HAS_DATA_FLAG);
session.removeAttribute(DDE_PROGESS);
session.removeAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
LOGGER.debug("try to remove to_create_crf");
session.removeAttribute("to_create_crf");
session.removeAttribute(instantAtt);
// forwardPage(Page.SUBMIT_DATA_SERVLET);
forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET, request, response);
// >> changed tbh, 06/2009
} else {
boolean forwardingSucceeded = false;
if (!fp.getString(GO_PREVIOUS).equals("")) {
if (previousSec.isActive()) {
forwardingSucceeded = true;
request.setAttribute(INPUT_EVENT_CRF, ecb);
request.setAttribute(INPUT_SECTION, previousSec);
int tabNum = 0;
if (fp.getString("tab") == null) {
tabNum = 1;
} else {
tabNum = fp.getInt("tab");
}
request.setAttribute("tab", new Integer(tabNum - 1).toString());
// forwardPage(getServletPage(request), request, response);
getServletContext().getRequestDispatcher(getServletPage(request)).forward(request, response);
}
} else if (!fp.getString(GO_NEXT).equals("")) {
if (nextSec.isActive()) {
forwardingSucceeded = true;
request.setAttribute(INPUT_EVENT_CRF, ecb);
request.setAttribute(INPUT_SECTION, nextSec);
int tabNum = 0;
if (fp.getString("tab") == null) {
tabNum = 1;
} else {
tabNum = fp.getInt("tab");
}
request.setAttribute("tab", new Integer(tabNum + 1).toString());
getServletContext().getRequestDispatcher(getServletPage(request)).forward(request, response);
//forwardPage(getServletPage(request), request, response);
}
}
if (!forwardingSucceeded) {
// ecb);
if (markSuccessfully) {
addPageMessage(respage.getString("data_saved_CRF_marked_complete"), request);
session.removeAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
session.removeAttribute(GROUP_HAS_DATA);
session.removeAttribute(HAS_DATA_FLAG);
session.removeAttribute(DDE_PROGESS);
session.removeAttribute("to_create_crf");
request.setAttribute("eventId", new Integer(ecb.getStudyEventId()).toString());
forwardPage(Page.ENTER_DATA_FOR_STUDY_EVENT_SERVLET, request, response);
} else {
// use clicked 'save'
addPageMessage(respage.getString("data_saved_continue_entering_edit_later"), request);
request.setAttribute(INPUT_EVENT_CRF, ecb);
request.setAttribute(INPUT_EVENT_CRF_ID, new Integer(ecb.getId()).toString());
// is not the last section
if (!section.isLastSection()) {
request.setAttribute(INPUT_SECTION, nextSec);
request.setAttribute(INPUT_SECTION_ID, new Integer(nextSec.getId()).toString());
session.removeAttribute("mayProcessUploading");
} else if (section.isLastSection()) {
//JN ADDED TO avoid return down
// already the last section, should go back to
// view event page
session.removeAttribute(GROUP_HAS_DATA);
session.removeAttribute(HAS_DATA_FLAG);
session.removeAttribute(DDE_PROGESS);
session.removeAttribute("to_create_crf");
session.removeAttribute("mayProcessUploading");
request.setAttribute("eventId", new Integer(ecb.getStudyEventId()).toString());
if (fromViewNotes != null && "1".equals(fromViewNotes)) {
String viewNotesPageFileName = (String) session.getAttribute("viewNotesPageFileName");
session.removeAttribute("viewNotesPageFileName");
session.removeAttribute("viewNotesURL");
if (viewNotesPageFileName != null && viewNotesPageFileName.length() > 0) {
// forwardPage(Page.setNewPage(viewNotesPageFileName, "View Notes"), request, response);
getServletContext().getRequestDispatcher(viewNotesPageFileName).forward(request, response);
}
}
session.removeAttribute(instantAtt);
forwardPage(Page.ENTER_DATA_FOR_STUDY_EVENT_SERVLET, request, response);
return;
}
int tabNum = 0;
if (fp.getString("tab") == null) {
tabNum = 1;
} else {
tabNum = fp.getInt("tab");
}
if (!section.isLastSection()) {
request.setAttribute("tab", new Integer(tabNum + 1).toString());
}
// forwardPage(getServletPage(request), request, response);
getServletContext().getRequestDispatcher(getServletPage(request)).forward(request, response);
}
// session.removeAttribute(AddNewSubjectServlet.
// FORM_DISCREPANCY_NOTES_NAME);
// forwardPage(Page.SUBMIT_DATA_SERVLET);
}
}
}
// end of if-block for dynamic rules not in same section, tbh 05/2010
}
// end of save
}
}
Also used :
DisplayItemBean(org.akaza.openclinica.bean.submit.DisplayItemBean)
ItemBean(org.akaza.openclinica.bean.submit.ItemBean)
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
StudyEventDefinitionBean(org.akaza.openclinica.bean.managestudy.StudyEventDefinitionBean)
StudyEventBean(org.akaza.openclinica.bean.managestudy.StudyEventBean)
EventCRFBean(org.akaza.openclinica.bean.submit.EventCRFBean)
ItemDataBean(org.akaza.openclinica.bean.submit.ItemDataBean)
TreeSet(java.util.TreeSet)
StudyEventDAO(org.akaza.openclinica.dao.managestudy.StudyEventDAO)
ScoreCalculator(org.akaza.openclinica.logic.score.ScoreCalculator)
DiscrepancyNoteUtil(org.akaza.openclinica.service.DiscrepancyNoteUtil)
DynamicsMetadataService(org.akaza.openclinica.service.crfdata.DynamicsMetadataService)
StudyDAO(org.akaza.openclinica.dao.managestudy.StudyDAO)
Status(org.akaza.openclinica.bean.core.Status)
ResolutionStatus(org.akaza.openclinica.bean.core.ResolutionStatus)
SubjectEventStatus(org.akaza.openclinica.bean.core.SubjectEventStatus)
Validation(org.akaza.openclinica.control.form.Validation)
DiscrepancyNoteDAO(org.akaza.openclinica.dao.managestudy.DiscrepancyNoteDAO)
CRFVersionDAO(org.akaza.openclinica.dao.submit.CRFVersionDAO)
FormDiscrepancyNotes(org.akaza.openclinica.control.form.FormDiscrepancyNotes)
FormProcessor(org.akaza.openclinica.control.form.FormProcessor)
DisplayItemWithGroupBean(org.akaza.openclinica.bean.submit.DisplayItemWithGroupBean)
StudyBean(org.akaza.openclinica.bean.managestudy.StudyBean)
EventDefinitionCRFDAO(org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO)
UserAccountDAO(org.akaza.openclinica.dao.login.UserAccountDAO)
InconsistentStateException(org.akaza.openclinica.web.InconsistentStateException)
DataEntryStage(org.akaza.openclinica.bean.core.DataEntryStage)
SectionBean(org.akaza.openclinica.bean.submit.SectionBean)
DisplaySectionBean(org.akaza.openclinica.bean.submit.DisplaySectionBean)
SubjectBean(org.akaza.openclinica.bean.submit.SubjectBean)
StudySubjectBean(org.akaza.openclinica.bean.managestudy.StudySubjectBean)
ScoreItemValidator(org.akaza.openclinica.control.form.ScoreItemValidator)
StudySubjectBean(org.akaza.openclinica.bean.managestudy.StudySubjectBean)
StudyEventDefinitionDAO(org.akaza.openclinica.dao.managestudy.StudyEventDefinitionDAO)
DiscrepancyNoteBean(org.akaza.openclinica.bean.managestudy.DiscrepancyNoteBean)
EventDefinitionCRFBean(org.akaza.openclinica.bean.managestudy.EventDefinitionCRFBean)
Map(java.util.Map)
HashMap(java.util.HashMap)
SectionDAO(org.akaza.openclinica.dao.submit.SectionDAO)
Phase(org.akaza.openclinica.domain.rule.action.RuleActionRunBean.Phase)
Set(java.util.Set)
TreeSet(java.util.TreeSet)
StudySubjectDAO(org.akaza.openclinica.dao.managestudy.StudySubjectDAO)
SubjectDAO(org.akaza.openclinica.dao.submit.SubjectDAO)
ItemDataDAO(org.akaza.openclinica.dao.submit.ItemDataDAO)
UserAccountBean(org.akaza.openclinica.bean.login.UserAccountBean)
Iterator(java.util.Iterator)
DisplayItemBean(org.akaza.openclinica.bean.submit.DisplayItemBean)
EventCRFDAO(org.akaza.openclinica.dao.submit.EventCRFDAO)
DiscrepancyNoteThread(org.akaza.openclinica.service.DiscrepancyNoteThread)
DisplayItemGroupBean(org.akaza.openclinica.bean.submit.DisplayItemGroupBean)
HttpSession(javax.servlet.http.HttpSession)
SessionManager(org.akaza.openclinica.core.SessionManager)
StudyUserRoleBean(org.akaza.openclinica.bean.login.StudyUserRoleBean)
DisplayTableOfContentsBean(org.akaza.openclinica.bean.submit.DisplayTableOfContentsBean)
StudySubjectDAO(org.akaza.openclinica.dao.managestudy.StudySubjectDAO)
ResponseOptionBean(org.akaza.openclinica.bean.submit.ResponseOptionBean)
Date(java.util.Date)
DisplaySectionBean(org.akaza.openclinica.bean.submit.DisplaySectionBean)
DiscrepancyValidator(org.akaza.openclinica.control.form.DiscrepancyValidator)
SimpleConditionalDisplayService(org.akaza.openclinica.service.crfdata.SimpleConditionalDisplayService)
SimpleDateFormat(java.text.SimpleDateFormat)
DateFormat(java.text.DateFormat)
CRFVersionBean(org.akaza.openclinica.bean.submit.CRFVersionBean)
SimpleDateFormat(java.text.SimpleDateFormat)
DynamicsItemFormMetadataBean(org.akaza.openclinica.domain.crfdata.DynamicsItemFormMetadataBean)
ItemFormMetadataBean(org.akaza.openclinica.bean.submit.ItemFormMetadataBean)
RuleSetBean(org.akaza.openclinica.domain.rule.RuleSetBean)
RuleValidator(org.akaza.openclinica.control.form.RuleValidator)
Example 42 with CRFVersionBean
use of org.akaza.openclinica.bean.submit.CRFVersionBean in project OpenClinica by OpenClinica.
the class DataEntryServlet method getDisplayBean.
/**
* Retrieve the DisplaySectionBean which will be used to display the Event CRF Section on the JSP, and also is used to controll processRequest.
* @param request TODO
* @param isSubmitted TODO
*/
protected DisplaySectionBean getDisplayBean(boolean hasGroup, boolean includeUngroupedItems, HttpServletRequest request, boolean isSubmitted) throws Exception {
DisplaySectionBean section = new DisplaySectionBean();
FormProcessor fp = new FormProcessor(request);
HttpSession session = request.getSession();
Locale loc = this.locale == null ? LocaleResolver.getLocale(request) : this.locale;
StudyBean study = (StudyBean) session.getAttribute("study");
SessionManager sm = (SessionManager) request.getSession().getAttribute("sm");
EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
SectionBean sb = (SectionBean) request.getAttribute(SECTION_BEAN);
EventDefinitionCRFBean edcb = (EventDefinitionCRFBean) request.getAttribute(EVENT_DEF_CRF_BEAN);
SectionDAO sdao;
// Find out whether there are ungrouped items in this section
boolean hasUngroupedItems = false;
int eventDefinitionCRFId = fp.getInt("eventDefinitionCRFId");
if (eventDefinitionCRFId <= 0) {
// TODO: this block of code repeats
// many times, need to clean up
//synchronized(this)
{
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(getDataSource());
EventDefinitionCRFBean edcBean = edcdao.findByStudyEventIdAndCRFVersionId(study, ecb.getStudyEventId(), ecb.getCRFVersionId());
eventDefinitionCRFId = edcBean.getId();
}
}
LOGGER.trace("eventDefinitionCRFId " + eventDefinitionCRFId);
// Use this class to find out whether there are ungrouped items in this
// section
FormBeanUtil formBeanUtil = new FormBeanUtil();
List<DisplayItemGroupBean> itemGroups = new ArrayList<DisplayItemGroupBean>();
if (hasGroup) {
DisplaySectionBean newDisplayBean = new DisplaySectionBean();
if (includeUngroupedItems) {
// Null values: this method adds null values to the
// displayitembeans
newDisplayBean = formBeanUtil.createDisplaySectionBWithFormGroups(sb.getId(), ecb.getCRFVersionId(), getDataSource(), eventDefinitionCRFId, ecb, getServletContext());
} else {
newDisplayBean = formBeanUtil.createDisplaySectionWithItemGroups(study, sb.getId(), ecb, ecb.getStudyEventId(), sm, eventDefinitionCRFId, getServletContext());
}
itemGroups = newDisplayBean.getDisplayFormGroups();
// setDataForDisplayItemGroups(itemGroups, sb,ecb,sm);
LOGGER.trace("found item group size: " + itemGroups.size() + " and to string: " + itemGroups.toString());
section.setDisplayFormGroups(itemGroups);
}
// Find out whether any display items are *not* grouped; see issue 1689
hasUngroupedItems = formBeanUtil.sectionHasUngroupedItems(getDataSource(), sb.getId(), itemGroups);
sdao = new SectionDAO(getDataSource());
//
sb.setHasSCDItem(hasUngroupedItems ? sdao.hasSCDItem(sb.getId()) : false);
section.setEventCRF(ecb);
if (sb.getParentId() > 0) {
SectionBean parent = (SectionBean) sdao.findByPK(sb.getParentId());
sb.setParent(parent);
}
section.setSection(sb);
CRFVersionDAO cvdao = new CRFVersionDAO(getDataSource());
CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(ecb.getCRFVersionId());
section.setCrfVersion(cvb);
CRFDAO cdao = new CRFDAO(getDataSource());
CRFBean cb = (CRFBean) cdao.findByPK(cvb.getCrfId());
section.setCrf(cb);
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(getDataSource());
// EventDefinitionCRFBean edcb =
// edcdao.findByStudyEventIdAndCRFVersionId(study,
// ecb.getStudyEventId(), cvb.getId());
section.setEventDefinitionCRF(edcb);
// setup DAO's here to avoid creating too many objects
ItemDAO idao = new ItemDAO(getDataSource());
ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(getDataSource());
ItemDataDAO iddao = new ItemDataDAO(getDataSource(), loc);
// Use itemGroups to determine if there are any ungrouped items
// get all the parent display item beans not in group
logMe("Entering getParentDisplayItems::: Thread is? " + Thread.currentThread());
ArrayList displayItems = getParentDisplayItems(hasGroup, sb, edcb, idao, ifmdao, iddao, hasUngroupedItems, request);
logMe("Entering getParentDisplayItems::: Done and Thread is? " + Thread.currentThread());
LOGGER.debug("just ran get parent display, has group " + hasGroup + " has ungrouped " + hasUngroupedItems);
// now sort them by ordinal,
//JN: Commenting out this logic, its wrong and will give erroneous results.
Collections.sort(displayItems);
// now get the child DisplayItemBeans
for (int i = 0; i < displayItems.size(); i++) {
DisplayItemBean dib = (DisplayItemBean) displayItems.get(i);
dib.setChildren(getChildrenDisplayItems(dib, edcb, request));
//
if (ecb.getStage() == DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE || ecb.getStage() == DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) {
if (shouldLoadDBValues(dib) && !isSubmitted) {
dib.loadDBValue();
}
} else {
if (shouldLoadDBValues(dib)) {
LOGGER.trace("should load db values is true, set value");
dib.loadDBValue();
LOGGER.trace("just got data loaded: " + dib.getData().getValue());
}
}
displayItems.set(i, dib);
}
section.setItems(displayItems);
return section;
}
Also used :
Locale(java.util.Locale)
ItemDAO(org.akaza.openclinica.dao.submit.ItemDAO)
ArrayList(java.util.ArrayList)
ItemDataDAO(org.akaza.openclinica.dao.submit.ItemDataDAO)
EventCRFBean(org.akaza.openclinica.bean.submit.EventCRFBean)
DisplayItemBean(org.akaza.openclinica.bean.submit.DisplayItemBean)
ItemFormMetadataDAO(org.akaza.openclinica.dao.submit.ItemFormMetadataDAO)
DisplayItemGroupBean(org.akaza.openclinica.bean.submit.DisplayItemGroupBean)
EventDefinitionCRFDAO(org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO)
EventCRFDAO(org.akaza.openclinica.dao.submit.EventCRFDAO)
CRFDAO(org.akaza.openclinica.dao.admin.CRFDAO)
CRFVersionDAO(org.akaza.openclinica.dao.submit.CRFVersionDAO)
FormBeanUtil(org.akaza.openclinica.view.form.FormBeanUtil)
FormProcessor(org.akaza.openclinica.control.form.FormProcessor)
HttpSession(javax.servlet.http.HttpSession)
SessionManager(org.akaza.openclinica.core.SessionManager)
StudyBean(org.akaza.openclinica.bean.managestudy.StudyBean)
EventDefinitionCRFDAO(org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO)
EventDefinitionCRFBean(org.akaza.openclinica.bean.managestudy.EventDefinitionCRFBean)
CRFBean(org.akaza.openclinica.bean.admin.CRFBean)
EventCRFBean(org.akaza.openclinica.bean.submit.EventCRFBean)
DisplaySectionBean(org.akaza.openclinica.bean.submit.DisplaySectionBean)
SectionBean(org.akaza.openclinica.bean.submit.SectionBean)
DisplaySectionBean(org.akaza.openclinica.bean.submit.DisplaySectionBean)
CRFVersionBean(org.akaza.openclinica.bean.submit.CRFVersionBean)
EventDefinitionCRFBean(org.akaza.openclinica.bean.managestudy.EventDefinitionCRFBean)
SectionDAO(org.akaza.openclinica.dao.submit.SectionDAO)
Example 43 with CRFVersionBean
use of org.akaza.openclinica.bean.submit.CRFVersionBean in project OpenClinica by OpenClinica.
the class ImportCRFDataServlet method processRequest.
@Override
public void processRequest() throws Exception {
resetPanel();
panel.setStudyInfoShown(false);
panel.setOrderedData(true);
FormProcessor fp = new FormProcessor(request);
// checks which module the requests are from
String module = fp.getString(MODULE);
// keep the module in the session
session.setAttribute(MODULE, module);
String action = request.getParameter("action");
CRFVersionBean version = (CRFVersionBean) session.getAttribute("version");
File xsdFile = new File(SpringServletAccess.getPropertiesDir(context) + "ODM1-3-0.xsd");
File xsdFile2 = new File(SpringServletAccess.getPropertiesDir(context) + "ODM1-2-1.xsd");
if (StringUtil.isBlank(action)) {
logger.info("action is blank");
request.setAttribute("version", version);
forwardPage(Page.IMPORT_CRF_DATA);
}
if ("confirm".equalsIgnoreCase(action)) {
String dir = SQLInitServlet.getField("filePath");
if (!new File(dir).exists()) {
logger.info("The filePath in datainfo.properties is invalid " + dir);
addPageMessage(respage.getString("filepath_you_defined_not_seem_valid"));
forwardPage(Page.IMPORT_CRF_DATA);
}
// All the uploaded files will be saved in filePath/crf/original/
String theDir = dir + "crf" + File.separator + "original" + File.separator;
if (!new File(theDir).isDirectory()) {
new File(theDir).mkdirs();
logger.info("Made the directory " + theDir);
}
// MultipartRequest multi = new MultipartRequest(request, theDir, 50 * 1024 * 1024);
File f = null;
try {
f = uploadFile(theDir, version);
} catch (Exception e) {
logger.warn("*** Found exception during file upload***");
e.printStackTrace();
}
if (f == null) {
forwardPage(Page.IMPORT_CRF_DATA);
}
// TODO
// validation steps
// 1. valid xml - validated by file uploader below
// LocalConfiguration config = LocalConfiguration.getInstance();
// config.getProperties().setProperty(
// "org.exolab.castor.parser.namespaces",
// "true");
// config
// .getProperties()
// .setProperty("org.exolab.castor.sax.features",
// "http://xml.org/sax/features/validation,
// http://apache.org/xml/features/validation/schema,
// http://apache.org/xml/features/validation/schema-full-checking");
// // above sets to validate against namespace
Mapping myMap = new Mapping();
// @pgawade 18-April-2011 Fix for issue 8394
String ODM_MAPPING_DIRPath = CoreResources.ODM_MAPPING_DIR;
myMap.loadMapping(ODM_MAPPING_DIRPath + File.separator + "cd_odm_mapping.xml");
Unmarshaller um1 = new Unmarshaller(myMap);
// um1.addNamespaceToPackageMapping("http://www.openclinica.org/ns/odm_ext_v130/v3.1", "OpenClinica");
// um1.addNamespaceToPackageMapping("http://www.cdisc.org/ns/odm/v1.3"
// ,
// "ODMContainer");
boolean fail = false;
ODMContainer odmContainer = new ODMContainer();
session.removeAttribute("odmContainer");
try {
// schemaValidator.validateAgainstSchema(f, xsdFile);
// utf-8 compliance, tbh 06/2009
InputStreamReader isr = new InputStreamReader(new FileInputStream(f), "UTF-8");
odmContainer = (ODMContainer) um1.unmarshal(isr);
logger.debug("Found crf data container for study oid: " + odmContainer.getCrfDataPostImportContainer().getStudyOID());
logger.debug("found length of subject list: " + odmContainer.getCrfDataPostImportContainer().getSubjectData().size());
// 2. validates against ODM 1.3
// check it all below, throw an exception and route to a
// different
// page if not working
// TODO this block of code needs the xerces serializer in order
// to
// work
// StringWriter myWriter = new StringWriter();
// Marshaller m1 = new Marshaller(myWriter);
//
// m1.setProperty("org.exolab.castor.parser.namespaces",
// "true");
// m1
// .setProperty("org.exolab.castor.sax.features",
// "http://xml.org/sax/features/validation,
// http://apache.org/xml/features/validation/schema,
// http://apache.org/xml/features/validation/schema-full-checking
// ");
//
// m1.setMapping(myMap);
// m1.setNamespaceMapping("",
// "http://www.cdisc.org/ns/odm/v1.3");
// m1.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3
// ODM1-3.xsd");
// m1.marshal(odmContainer);
// if you havent thrown it, you wont throw it here
addPageMessage(respage.getString("passed_xml_validation"));
} catch (Exception me1) {
me1.printStackTrace();
// expanding it to all exceptions, but hoping to catch Marshal
// Exception or SAX Exceptions
logger.info("found exception with xml transform");
//
logger.info("trying 1.2.1");
try {
schemaValidator.validateAgainstSchema(f, xsdFile2);
// for backwards compatibility, we also try to validate vs
// 1.2.1 ODM 06/2008
InputStreamReader isr = new InputStreamReader(new FileInputStream(f), "UTF-8");
odmContainer = (ODMContainer) um1.unmarshal(isr);
} 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() };
addPageMessage(mf.format(arguments));
//
// addPageMessage("Your XML is not well-formed, and does not
// comply with the ODM 1.3 Schema. Please check it, and try
// again. It returned the message: "
// + me1.getMessage());
// me1.printStackTrace();
forwardPage(Page.IMPORT_CRF_DATA);
// you can't really wait to forward because then you throw
// NPEs
// in the next few parts of the code
}
}
// TODO need to output further here
// 2.a. is the study the same one that the user is in right now?
// 3. validates against study metadata
// 3.a. is that study subject in that study?
// 3.b. is that study event def in that study?
// 3.c. is that site in that study?
// 3.d. is that crf version in that study event def?
// 3.e. are those item groups in that crf version?
// 3.f. are those items in that item group?
List<String> errors = getImportCRFDataService().validateStudyMetadata(odmContainer, ub.getActiveStudyId());
if (errors != null) {
// add to session
// forward to another page
logger.info(errors.toString());
for (String error : errors) {
addPageMessage(error);
}
if (errors.size() > 0) {
// fail = true;
forwardPage(Page.IMPORT_CRF_DATA);
} else {
addPageMessage(respage.getString("passed_study_check"));
addPageMessage(respage.getString("passed_oid_metadata_check"));
}
}
logger.debug("passed error check");
// TODO ADD many validation steps before we get to the
// session-setting below
// 4. is the event in the correct status to accept data import?
// -- scheduled, data entry started, completed
// (and the event should already be created)
// (and the event should be independent, ie not affected by other
// events)
Boolean eventCRFStatusesValid = getImportCRFDataService().eventCRFStatusesValid(odmContainer, ub);
ImportCRFInfoContainer importCrfInfo = new ImportCRFInfoContainer(odmContainer, sm.getDataSource());
// The eventCRFBeans list omits EventCRFs that don't match UpsertOn rules. If EventCRF did not exist and
// doesn't match upsert, it won't be created.
List<EventCRFBean> eventCRFBeans = getImportCRFDataService().fetchEventCRFBeans(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().fetchEventCRFStatuses(odmContainer);
// method in the ImportCRFDataService is modified for this fix.
if (eventCRFBeans == null) {
fail = true;
addPageMessage(respage.getString("no_event_status_matching"));
} else {
ArrayList<Integer> permittedEventCRFIds = new ArrayList<Integer>();
logger.info("found a list of eventCRFBeans: " + eventCRFBeans.toString());
// List<DisplayItemBeanWrapper> displayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
// HashMap<String, String> totalValidationErrors = new
// HashMap<String, String>();
// HashMap<String, String> hardValidationErrors = new
// HashMap<String, String>();
logger.debug("found event crfs " + eventCRFBeans.size());
// -- does the event already exist? if not, fail
if (!eventCRFBeans.isEmpty()) {
for (EventCRFBean eventCRFBean : eventCRFBeans) {
DataEntryStage dataEntryStage = eventCRFBean.getStage();
Status eventCRFStatus = eventCRFBean.getStatus();
logger.info("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)) {
// actually want the negative
// was status == available and the stage questions, but
// when you are at 'data entry complete' your status is
// set to 'unavailable'.
// >> tbh 09/2008
// HOWEVER, when one event crf is removed and the rest
// are good, what happens???
// need to create a list and inform that one is blocked
// and the rest are not...
//
permittedEventCRFIds.add(new Integer(eventCRFBean.getId()));
} else {
// fail = true;
// addPageMessage(respage.getString(
// "the_event_crf_not_correct_status"));
// forwardPage(Page.IMPORT_CRF_DATA);
}
}
// did we exclude all the event CRFs? if not, pass, else fail
if (eventCRFBeans.size() >= permittedEventCRFIds.size()) {
addPageMessage(respage.getString("passed_event_crf_status_check"));
} else {
fail = true;
addPageMessage(respage.getString("the_event_crf_not_correct_status"));
}
try {
List<DisplayItemBeanWrapper> tempDisplayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
tempDisplayItemBeanWrappers = getImportCRFDataService().lookupValidationErrors(request, odmContainer, ub, totalValidationErrors, hardValidationErrors, permittedEventCRFIds);
logger.debug("generated display item bean wrappers " + tempDisplayItemBeanWrappers.size());
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?
fail = true;
logger.debug("threw a NPE after calling lookup validation errors");
System.out.println(ExceptionUtils.getStackTrace(npe1));
addPageMessage(respage.getString("an_error_was_thrown_while_validation_errors"));
// npe1.printStackTrace();
} catch (OpenClinicaException oce1) {
fail = true;
logger.debug("threw an OCE after calling lookup validation errors " + oce1.getOpenClinicaMessage());
addPageMessage(oce1.getOpenClinicaMessage());
}
} else if (!eventCRFStatusesValid) {
fail = true;
addPageMessage(respage.getString("the_event_crf_not_correct_status"));
} else {
fail = true;
addPageMessage(respage.getString("no_event_crfs_matching_the_xml_metadata"));
}
// for (HashMap<String, String> crfData : importedData) {
// DisplayItemBeanWrapper displayItemBeanWrapper =
// testing(request,
// crfData);
// displayItemBeanWrappers.add(displayItemBeanWrapper);
// errors = displayItemBeanWrapper.getValidationErrors();
//
// }
}
if (fail) {
logger.debug("failed here - forwarding...");
forwardPage(Page.IMPORT_CRF_DATA);
} else {
addPageMessage(respage.getString("passing_crf_edit_checks"));
session.setAttribute("odmContainer", odmContainer);
session.setAttribute("importedData", displayItemBeanWrappers);
session.setAttribute("validationErrors", totalValidationErrors);
session.setAttribute("hardValidationErrors", hardValidationErrors);
session.setAttribute("importedCRFStatuses", importedCRFStatuses);
session.setAttribute("importCrfInfo", importCrfInfo);
// above are updated 'statically' by the method that originally
// generated the wrappers; soon the only thing we will use
// wrappers for is the 'overwrite' flag
logger.debug("+++ content of total validation errors: " + totalValidationErrors.toString());
SummaryStatsBean ssBean = getImportCRFDataService().generateSummaryStatsBean(odmContainer, displayItemBeanWrappers, importCrfInfo);
session.setAttribute("summaryStats", ssBean);
// will have to set hard edit checks here as well
session.setAttribute("subjectData", odmContainer.getCrfDataPostImportContainer().getSubjectData());
forwardPage(Page.VERIFY_IMPORT_SERVLET);
}
// }
}
}
Also used :
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
Mapping(org.exolab.castor.mapping.Mapping)
SummaryStatsBean(org.akaza.openclinica.bean.submit.crfdata.SummaryStatsBean)
OpenClinicaException(org.akaza.openclinica.exception.OpenClinicaException)
ODMContainer(org.akaza.openclinica.bean.submit.crfdata.ODMContainer)
EventCRFBean(org.akaza.openclinica.bean.submit.EventCRFBean)
Unmarshaller(org.exolab.castor.xml.Unmarshaller)
DisplayItemBeanWrapper(org.akaza.openclinica.bean.submit.DisplayItemBeanWrapper)
Status(org.akaza.openclinica.bean.core.Status)
InputStreamReader(java.io.InputStreamReader)
MessageFormat(java.text.MessageFormat)
FormProcessor(org.akaza.openclinica.control.form.FormProcessor)
OpenClinicaException(org.akaza.openclinica.exception.OpenClinicaException)
InsufficientPermissionException(org.akaza.openclinica.web.InsufficientPermissionException)
FileInputStream(java.io.FileInputStream)
DataEntryStage(org.akaza.openclinica.bean.core.DataEntryStage)
CRFVersionBean(org.akaza.openclinica.bean.submit.CRFVersionBean)
File(java.io.File)
Example 44 with CRFVersionBean
use of org.akaza.openclinica.bean.submit.CRFVersionBean in project OpenClinica by OpenClinica.
the class ViewDiscrepancyNoteServlet method processRequest.
@Override
@SuppressWarnings("unchecked")
protected void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
int eventCRFId = fp.getInt(CreateDiscrepancyNoteServlet.EVENT_CRF_ID);
request.setAttribute(CreateDiscrepancyNoteServlet.EVENT_CRF_ID, new Integer(eventCRFId));
request.setAttribute(DIS_TYPES, DiscrepancyNoteType.list);
if (currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2) || currentRole.getRole().equals(Role.INVESTIGATOR)) {
ArrayList<ResolutionStatus> resStatuses = new ArrayList();
resStatuses.add(ResolutionStatus.UPDATED);
resStatuses.add(ResolutionStatus.RESOLVED);
request.setAttribute(RES_STATUSES, resStatuses);
// it's for parentDNId is null or 0
request.setAttribute(WHICH_RES_STATUSES, "22");
ArrayList<ResolutionStatus> resStatuses2 = new ArrayList<ResolutionStatus>();
resStatuses2.add(ResolutionStatus.OPEN);
resStatuses2.add(ResolutionStatus.RESOLVED);
request.setAttribute(RES_STATUSES2, resStatuses2);
List<DiscrepancyNoteType> types2 = new ArrayList<DiscrepancyNoteType>(DiscrepancyNoteType.list);
types2.remove(DiscrepancyNoteType.QUERY);
request.setAttribute(DIS_TYPES2, types2);
} else if (currentRole.getRole().equals(Role.MONITOR)) {
ArrayList<ResolutionStatus> resStatuses = new ArrayList();
resStatuses.add(ResolutionStatus.OPEN);
resStatuses.add(ResolutionStatus.UPDATED);
resStatuses.add(ResolutionStatus.CLOSED);
request.setAttribute(RES_STATUSES, resStatuses);
request.setAttribute(WHICH_RES_STATUSES, "1");
ArrayList<DiscrepancyNoteType> types2 = new ArrayList<DiscrepancyNoteType>();
types2.add(DiscrepancyNoteType.QUERY);
request.setAttribute(DIS_TYPES2, types2);
} else {
// Role.STUDYDIRECTOR Role.COORDINATOR
List<ResolutionStatus> resStatuses = new ArrayList<ResolutionStatus>(ResolutionStatus.list);
resStatuses.remove(ResolutionStatus.NOT_APPLICABLE);
request.setAttribute(RES_STATUSES, resStatuses);
;
// it's for parentDNId is null or 0 and FVC
request.setAttribute(WHICH_RES_STATUSES, "2");
ArrayList<ResolutionStatus> resStatuses2 = new ArrayList<ResolutionStatus>();
resStatuses2.add(ResolutionStatus.OPEN);
resStatuses2.add(ResolutionStatus.RESOLVED);
request.setAttribute(RES_STATUSES2, resStatuses2);
}
// logic from CreateDiscrepancyNoteServlet
request.setAttribute("unlock", "0");
fp.getBoolean(IS_REASON_FOR_CHANGE);
fp.getBoolean(ERROR_FLAG);
String monitor = fp.getString("monitor");
// } else if ("1".equalsIgnoreCase(monitor)) {// change to allow user to
if ("1".equalsIgnoreCase(monitor)) {
// change to allow user to
// enter note for all items,
// not just blank items
request.setAttribute(CAN_MONITOR, "1");
request.setAttribute("monitor", monitor);
} else {
request.setAttribute(CAN_MONITOR, "0");
}
Boolean fromBox = fp.getBoolean(FROM_BOX);
if (fromBox == null || !fromBox) {
session.removeAttribute(BOX_TO_SHOW);
session.removeAttribute(BOX_DN_MAP);
session.removeAttribute(AUTOVIEWS);
}
Boolean refresh = fp.getBoolean("refresh");
request.setAttribute("refresh", refresh + "");
String ypos = fp.getString("y");
if (ypos == null || ypos.length() == 0) {
ypos = "0";
}
request.setAttribute("y", ypos);
DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
int entityId = fp.getInt(ENTITY_ID, true);
String name = fp.getString(ENTITY_TYPE, true);
String column = fp.getString(ENTITY_COLUMN, true);
String field = fp.getString(ENTITY_FIELD, true);
String isLocked = fp.getString(LOCKED_FLAG);
if (!StringUtil.isBlank(isLocked) && "yes".equalsIgnoreCase(isLocked)) {
request.setAttribute(LOCKED_FLAG, "yes");
} else {
request.setAttribute(LOCKED_FLAG, "no");
}
DateFormat dateFormatter = DateFormat.getDateInstance(DateFormat.DEFAULT, locale);
int subjectId = fp.getInt(CreateDiscrepancyNoteServlet.SUBJECT_ID, true);
int itemId = fp.getInt(CreateDiscrepancyNoteServlet.ITEM_ID, true);
StudySubjectBean ssub = new StudySubjectBean();
if (subjectId > 0) {
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
ssub = (StudySubjectBean) ssdao.findByPK(subjectId);
request.setAttribute("noteSubject", ssub);
}
ItemBean item = new ItemBean();
if (itemId > 0) {
ItemDAO idao = new ItemDAO(sm.getDataSource());
item = (ItemBean) idao.findByPK(itemId);
request.setAttribute("item", item);
request.setAttribute("entityName", item.getName());
}
ItemDataBean itemData = new ItemDataBean();
SimpleDateFormat sdf = new SimpleDateFormat("dd-MMM-yyyy");
int preUserId = 0;
if (!StringUtil.isBlank(name)) {
if ("itemData".equalsIgnoreCase(name)) {
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
itemData = (ItemDataBean) iddao.findByPK(entityId);
request.setAttribute("entityValue", itemData.getValue());
request.setAttribute("entityName", item.getName());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
EventCRFBean ec = (EventCRFBean) ecdao.findByPK(itemData.getEventCRFId());
preUserId = ec.getOwnerId() > 0 ? ec.getOwnerId() : 0;
request.setAttribute("entityCreatedDate", sdf.format(ec.getCreatedDate()));
StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
StudyEventBean se = (StudyEventBean) sed.findByPK(ec.getStudyEventId());
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
se.setName(sedb.getName());
request.setAttribute("studyEvent", se);
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
CRFVersionBean cv = (CRFVersionBean) cvdao.findByPK(ec.getCRFVersionId());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
CRFBean crf = (CRFBean) cdao.findByPK(cv.getCrfId());
request.setAttribute("crf", crf);
} else if ("studySub".equalsIgnoreCase(name)) {
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
ssub = (StudySubjectBean) ssdao.findByPK(entityId);
SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
SubjectBean sub = (SubjectBean) sdao.findByPK(ssub.getSubjectId());
request.setAttribute("noteSubject", ssub);
if (!StringUtil.isBlank(column)) {
if ("enrollment_date".equalsIgnoreCase(column)) {
if (ssub.getEnrollmentDate() != null) {
request.setAttribute("entityValue", dateFormatter.format(ssub.getEnrollmentDate()));
}
request.setAttribute("entityName", resword.getString("enrollment_date"));
} else if ("gender".equalsIgnoreCase(column)) {
request.setAttribute("entityValue", sub.getGender() + "");
request.setAttribute("entityName", resword.getString("gender"));
} else if ("date_of_birth".equalsIgnoreCase(column)) {
if (sub.getDateOfBirth() != null) {
request.setAttribute("entityValue", dateFormatter.format(sub.getDateOfBirth()));
}
request.setAttribute("entityName", resword.getString("date_of_birth"));
} else if ("unique_identifier".equalsIgnoreCase(column)) {
if (sub.getUniqueIdentifier() != null) {
request.setAttribute("entityValue", sub.getUniqueIdentifier());
}
request.setAttribute("entityName", resword.getString("unique_identifier"));
}
}
preUserId = ssub.getOwnerId() > 0 ? ssub.getOwnerId() : 0;
request.setAttribute("entityCreatedDate", sdf.format(ssub.getCreatedDate()));
} else if ("subject".equalsIgnoreCase(name)) {
SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
SubjectBean sub = (SubjectBean) sdao.findByPK(entityId);
// be caution: here for subject, noteSubject is SubjectBean and
// label is unique_identifier
sub.setLabel(sub.getUniqueIdentifier());
request.setAttribute("noteSubject", sub);
if (!StringUtil.isBlank(column)) {
if ("gender".equalsIgnoreCase(column)) {
request.setAttribute("entityValue", ssub.getGender() + "");
request.setAttribute("entityName", resword.getString("gender"));
} else if ("date_of_birth".equalsIgnoreCase(column)) {
if (sub.getDateOfBirth() != null) {
request.setAttribute("entityValue", dateFormatter.format(sub.getDateOfBirth()));
}
request.setAttribute("entityName", resword.getString("date_of_birth"));
} else if ("unique_identifier".equalsIgnoreCase(column)) {
request.setAttribute("entityValue", sub.getUniqueIdentifier());
request.setAttribute("entityName", resword.getString("unique_identifier"));
}
}
preUserId = sub.getOwnerId() > 0 ? sub.getOwnerId() : 0;
request.setAttribute("entityCreatedDate", sdf.format(sub.getCreatedDate()));
} else if ("studyEvent".equalsIgnoreCase(name)) {
StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
StudyEventBean se = (StudyEventBean) sed.findByPK(entityId);
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(se.getStudyEventDefinitionId());
se.setName(sedb.getName());
request.setAttribute("studyEvent", se);
request.setAttribute("noteSubject", new StudySubjectDAO(sm.getDataSource()).findByPK(se.getStudySubjectId()));
if (!StringUtil.isBlank(column)) {
if ("location".equalsIgnoreCase(column)) {
request.setAttribute("entityValue", se.getLocation());
request.setAttribute("entityName", resword.getString("location"));
} else if ("start_date".equalsIgnoreCase(column)) {
if (se.getDateStarted() != null) {
request.setAttribute("entityValue", dateFormatter.format(se.getDateStarted()));
}
request.setAttribute("entityName", resword.getString("start_date"));
} else if ("end_date".equalsIgnoreCase(column)) {
if (se.getDateEnded() != null) {
request.setAttribute("entityValue", dateFormatter.format(se.getDateEnded()));
}
request.setAttribute("entityName", resword.getString("end_date"));
}
}
preUserId = se.getOwnerId() > 0 ? se.getOwnerId() : 0;
request.setAttribute("entityCreatedDate", sdf.format(se.getCreatedDate()));
} else if ("eventCrf".equalsIgnoreCase(name)) {
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
EventCRFBean ec = (EventCRFBean) ecdao.findByPK(entityId);
if (!StringUtil.isBlank(column)) {
if ("date_interviewed".equals(column)) {
if (ec.getDateInterviewed() != null) {
request.setAttribute("entityValue", dateFormatter.format(ec.getDateInterviewed()));
}
request.setAttribute("entityName", resword.getString("date_interviewed"));
} else if ("interviewer_name".equals(column)) {
request.setAttribute("entityValue", ec.getInterviewerName());
request.setAttribute("entityName", resword.getString("interviewer_name"));
}
}
setupStudyEventCRFAttributes(ec);
preUserId = ec.getOwnerId() > 0 ? ec.getOwnerId() : 0;
request.setAttribute("entityCreatedDate", sdf.format(ec.getCreatedDate()));
}
}
boolean writeToDB = fp.getBoolean(CreateDiscrepancyNoteServlet.WRITE_TO_DB, true);
HashMap<Integer, Integer> autoviews = (HashMap<Integer, Integer>) session.getAttribute(AUTOVIEWS);
autoviews = autoviews == null ? new HashMap<Integer, Integer>() : autoviews;
HashMap<Integer, DiscrepancyNoteBean> boxDNMap = (HashMap<Integer, DiscrepancyNoteBean>) session.getAttribute(BOX_DN_MAP);
if (boxDNMap == null || !boxDNMap.containsKey(0)) {
boxDNMap = new HashMap<Integer, DiscrepancyNoteBean>();
// initialize dn for a new thread
DiscrepancyNoteBean dnb = new DiscrepancyNoteBean();
if (currentRole.getRole().equals(Role.RESEARCHASSISTANT) || currentRole.getRole().equals(Role.RESEARCHASSISTANT2) || currentRole.getRole().equals(Role.INVESTIGATOR)) {
dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.ANNOTATION.getId());
dnb.setResolutionStatusId(ResolutionStatus.NOT_APPLICABLE.getId());
autoviews.put(0, 0);
// request.setAttribute("autoView", "0");
} else {
dnb.setDiscrepancyNoteTypeId(DiscrepancyNoteType.QUERY.getId());
dnb.setAssignedUserId(preUserId);
autoviews.put(0, 1);
// request.setAttribute("autoView", "1");
}
boxDNMap.put(0, dnb);
} else if (boxDNMap.containsKey(0)) {
int dnTypeId = boxDNMap.get(0).getDiscrepancyNoteTypeId();
autoviews.put(0, dnTypeId == 3 ? 1 : 0);
}
if (boxDNMap.containsKey(0)) {
int dnTypeId0 = boxDNMap.get(0).getDiscrepancyNoteTypeId();
if (dnTypeId0 == 2 || dnTypeId0 == 4) {
request.setAttribute("typeID0", dnTypeId0 + "");
}
}
// request.setAttribute("enterData", enterData);
request.setAttribute("monitor", monitor);
request.setAttribute(ENTITY_ID, entityId + "");
request.setAttribute(ENTITY_TYPE, name);
request.setAttribute(ENTITY_FIELD, field);
request.setAttribute(ENTITY_COLUMN, column);
request.setAttribute(CreateDiscrepancyNoteServlet.WRITE_TO_DB, writeToDB ? "1" : "0");
ArrayList notes = (ArrayList) dndao.findAllByEntityAndColumn(name, entityId, column);
if (notes.size() > 0) {
notes.get(0);
// @pgawade 21-May-2011 Corrected the condition to throw no access
// error
StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
int parentStudyForNoteSub = 0;
// @pgawade #9801: 07-June-2011 corrected the way to get study
// subject id associated with discrepancy note
// int noteSubId = note.getOwnerId();
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
// StudySubjectBean notessub = (StudySubjectBean)
// ssdao.findByPK(noteSubId);
StudySubjectBean notessub = (StudySubjectBean) ssdao.findByPK(subjectId);
StudyBean studyBeanSub = (StudyBean) studyDAO.findByPK(notessub.getStudyId());
if (null != studyBeanSub) {
parentStudyForNoteSub = studyBeanSub.getParentStudyId();
}
if (notessub.getStudyId() != currentStudy.getId() && currentStudy.getId() != parentStudyForNoteSub) {
addPageMessage(noAccessMessage);
throw new InsufficientPermissionException(Page.MENU_SERVLET, exceptionName, "1");
}
}
FormDiscrepancyNotes newNotes = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
Map<Integer, DiscrepancyNoteBean> noteTree = new LinkedHashMap<Integer, DiscrepancyNoteBean>();
String session_key = eventCRFId + "_" + field;
ArrayList newFieldNotes = null;
if (newNotes != null && (!newNotes.getNotes(field).isEmpty() || !newNotes.getNotes(session_key).isEmpty())) {
newFieldNotes = newNotes.getNotes(field);
if (newFieldNotes == null || newFieldNotes.size() == 0) {
newFieldNotes = newNotes.getNotes(session_key);
}
// System.out.println("how many notes:" + newFieldNotes.size());
for (int i = 0; i < newFieldNotes.size(); i++) {
DiscrepancyNoteBean note = (DiscrepancyNoteBean) newFieldNotes.get(i);
note.setLastUpdator(ub);
note.setLastDateUpdated(new Date());
note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
note.setResStatus(ResolutionStatus.get(note.getResolutionStatusId()));
note.setSaved(false);
if (itemId > 0) {
note.setEntityName(item.getName());
note.setEntityValue(itemData.getValue());
}
note.setSubjectName(ssub.getName());
note.setEntityType(name);
int pId = note.getParentDnId();
if (pId == 0) {
// we can only keep one unsaved note because
// note.id == 0
noteTree.put(note.getId(), note);
}
}
for (int i = 0; i < newFieldNotes.size(); i++) {
DiscrepancyNoteBean note = (DiscrepancyNoteBean) newFieldNotes.get(i);
int pId = note.getParentDnId();
if (pId > 0) {
note.setSaved(false);
note.setLastUpdator(ub);
note.setLastDateUpdated(new Date());
note.setEntityName(item.getName());
note.setSubjectName(ssub.getName());
note.setEntityType(name);
note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
note.setResStatus(ResolutionStatus.get(note.getResolutionStatusId()));
DiscrepancyNoteBean parent = noteTree.get(new Integer(pId));
if (parent != null) {
parent.getChildren().add(note);
}
}
}
}
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
HashMap<Integer, String> fvcInitAssigns = new HashMap<Integer, String>();
for (int i = 0; i < notes.size(); i++) {
DiscrepancyNoteBean note = (DiscrepancyNoteBean) notes.get(i);
note.setColumn(column);
note.setEntityId(entityId);
note.setEntityType(name);
note.setField(field);
Date lastUpdatedDate = note.getCreatedDate();
UserAccountBean lastUpdator = (UserAccountBean) udao.findByPK(note.getOwnerId());
note.setLastUpdator(lastUpdator);
note.setLastDateUpdated(lastUpdatedDate);
int pId = note.getParentDnId();
note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
note.setResStatus(ResolutionStatus.get(note.getResolutionStatusId()));
if (pId == 0) {
noteTree.put(new Integer(note.getId()), note);
}
}
for (int i = 0; i < notes.size(); i++) {
DiscrepancyNoteBean note = (DiscrepancyNoteBean) notes.get(i);
int pId = note.getParentDnId();
if (itemId > 0) {
note.setEntityName(item.getName());
note.setEntityValue(itemData.getValue());
}
note.setSubjectName(ssub.getName());
note.setEntityType(name);
Date lastUpdatedDate = note.getCreatedDate();
UserAccountBean lastUpdator = (UserAccountBean) udao.findByPK(note.getOwnerId());
note.setLastUpdator(lastUpdator);
note.setLastDateUpdated(lastUpdatedDate);
note.setDisType(DiscrepancyNoteType.get(note.getDiscrepancyNoteTypeId()));
note.setResStatus(ResolutionStatus.get(note.getResolutionStatusId()));
if (pId > 0) {
DiscrepancyNoteBean parent = noteTree.get(new Integer(pId));
if (parent != null) {
parent.getChildren().add(note);
if (!note.getCreatedDate().before(parent.getLastDateUpdated())) {
parent.setLastDateUpdated(note.getCreatedDate());
}
if (note.getDiscrepancyNoteTypeId() == 1 && note.getAssignedUserId() > 0) {
int ownerId = note.getOwnerId();
if (fvcInitAssigns.containsKey(pId)) {
String f = fvcInitAssigns.get(pId);
String fn = note.getId() + "." + ownerId;
if (fn.compareTo(f) < 0) {
fvcInitAssigns.put(pId, fn);
}
} else {
fvcInitAssigns.put(pId, note.getId() + "." + ownerId);
}
}
}
}
}
Set parents = noteTree.keySet();
Iterator it = parents.iterator();
while (it.hasNext()) {
Integer key = (Integer) it.next();
DiscrepancyNoteBean note = noteTree.get(key);
note.setNumChildren(note.getChildren().size());
note.setEntityType(name);
if (!boxDNMap.containsKey(key)) {
DiscrepancyNoteBean dn = new DiscrepancyNoteBean();
dn.setId(key);
int dnTypeId = note.getDiscrepancyNoteTypeId();
dn.setDiscrepancyNoteTypeId(dnTypeId);
if (dnTypeId == 3) {
// JsonQuery
dn.setAssignedUserId(note.getOwnerId());
} else if (dnTypeId == 1) {
// FVC
if (fvcInitAssigns.containsKey(key)) {
String[] s = fvcInitAssigns.get(key).split("\\.");
int i = Integer.parseInt(s.length == 2 ? s[1].trim() : "0");
dn.setAssignedUserId(i);
}
}
Role r = currentRole.getRole();
// currentStudy.getId() != currentStudy.getParentStudyId()) {
if (r.equals(Role.RESEARCHASSISTANT) || r.equals(Role.RESEARCHASSISTANT2) || r.equals(Role.INVESTIGATOR)) {
if (dn.getDiscrepancyNoteTypeId() == DiscrepancyNoteType.QUERY.getId() && note.getResStatus().getId() == ResolutionStatus.UPDATED.getId()) {
dn.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
} else {
dn.setResolutionStatusId(ResolutionStatus.RESOLVED.getId());
}
if (dn.getAssignedUserId() > 0) {
autoviews.put(key, 1);
} else {
autoviews.put(key, 0);
}
// copied from CreateDiscrepancyNoteServlet
// request.setAttribute("autoView", "0");
// hide the panel, tbh
} else {
if (note.getResStatus().getId() == ResolutionStatus.RESOLVED.getId()) {
dn.setResolutionStatusId(ResolutionStatus.CLOSED.getId());
} else if (note.getResStatus().getId() == ResolutionStatus.CLOSED.getId()) {
dn.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
} else if (r.equals(Role.MONITOR)) {
dn.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
} else if (dn.getDiscrepancyNoteTypeId() == 1) {
dn.setResolutionStatusId(ResolutionStatus.RESOLVED.getId());
} else {
dn.setResolutionStatusId(ResolutionStatus.UPDATED.getId());
}
autoviews.put(key, 1);
if (dn.getAssignedUserId() > 0) {
} else {
dn.setAssignedUserId(preUserId);
}
}
boxDNMap.put(key, dn);
}
}
session.setAttribute(BOX_DN_MAP, boxDNMap);
session.setAttribute(AUTOVIEWS, autoviews);
// noteTree is a Hashmap mapping note id to a parent note, with all the
// child notes
// stored in the children List.
// BWP 3029>>make sure the parent note has an updated resolution status
// and
// updated date
fixStatusUpdatedDate(noteTree);
request.setAttribute(DIS_NOTES, noteTree);
// copied from CreatediscrepancyNoteServlet generateUserAccounts
StudyDAO studyDAO = new StudyDAO(sm.getDataSource());
StudyBean subjectStudy = studyDAO.findByStudySubjectId(subjectId);
int studyId = currentStudy.getId();
ArrayList<UserAccountBean> userAccounts = new ArrayList();
if (currentStudy.getParentStudyId() > 0) {
userAccounts = udao.findAllUsersByStudyOrSite(studyId, currentStudy.getParentStudyId(), subjectId);
} else if (subjectStudy.getParentStudyId() > 0) {
userAccounts = udao.findAllUsersByStudyOrSite(subjectStudy.getId(), subjectStudy.getParentStudyId(), subjectId);
} else {
userAccounts = udao.findAllUsersByStudyOrSite(studyId, 0, subjectId);
}
request.setAttribute(USER_ACCOUNTS, userAccounts);
request.setAttribute(VIEW_DN_LINK, this.getPageServletFileName());
// audit log items (from ViewItemAuditLogServlet.java)
AuditDAO adao = new AuditDAO(sm.getDataSource());
if (name.equalsIgnoreCase("studysub")) {
name = "study_subject";
} else if (name.equalsIgnoreCase("eventcrf")) {
name = "event_crf";
} else if (name.equalsIgnoreCase("studyevent")) {
name = "study_event";
} else if (name.equalsIgnoreCase("itemdata")) {
name = "item_data";
}
ArrayList itemAuditEvents = adao.findItemAuditEvents(entityId, name);
request.setAttribute("itemAudits", itemAuditEvents);
forwardPage(Page.VIEW_DISCREPANCY_NOTE);
}
Also used :
ItemBean(org.akaza.openclinica.bean.submit.ItemBean)
ItemDAO(org.akaza.openclinica.dao.submit.ItemDAO)
HashMap(java.util.HashMap)
LinkedHashMap(java.util.LinkedHashMap)
ArrayList(java.util.ArrayList)
StudyEventDefinitionBean(org.akaza.openclinica.bean.managestudy.StudyEventDefinitionBean)
StudyEventBean(org.akaza.openclinica.bean.managestudy.StudyEventBean)
LinkedHashMap(java.util.LinkedHashMap)
ResolutionStatus(org.akaza.openclinica.bean.core.ResolutionStatus)
EventCRFBean(org.akaza.openclinica.bean.submit.EventCRFBean)
ItemDataBean(org.akaza.openclinica.bean.submit.ItemDataBean)
StudyEventDAO(org.akaza.openclinica.dao.managestudy.StudyEventDAO)
ArrayList(java.util.ArrayList)
List(java.util.List)
StudyDAO(org.akaza.openclinica.dao.managestudy.StudyDAO)
DiscrepancyNoteDAO(org.akaza.openclinica.dao.managestudy.DiscrepancyNoteDAO)
EventCRFDAO(org.akaza.openclinica.dao.submit.EventCRFDAO)
CRFDAO(org.akaza.openclinica.dao.admin.CRFDAO)
CRFVersionDAO(org.akaza.openclinica.dao.submit.CRFVersionDAO)
FormDiscrepancyNotes(org.akaza.openclinica.control.form.FormDiscrepancyNotes)
FormProcessor(org.akaza.openclinica.control.form.FormProcessor)
StudyBean(org.akaza.openclinica.bean.managestudy.StudyBean)
UserAccountDAO(org.akaza.openclinica.dao.login.UserAccountDAO)
EventCRFBean(org.akaza.openclinica.bean.submit.EventCRFBean)
CRFBean(org.akaza.openclinica.bean.admin.CRFBean)
Role(org.akaza.openclinica.bean.core.Role)
SubjectBean(org.akaza.openclinica.bean.submit.SubjectBean)
StudySubjectBean(org.akaza.openclinica.bean.managestudy.StudySubjectBean)
StudySubjectBean(org.akaza.openclinica.bean.managestudy.StudySubjectBean)
StudyEventDefinitionDAO(org.akaza.openclinica.dao.managestudy.StudyEventDefinitionDAO)
DiscrepancyNoteBean(org.akaza.openclinica.bean.managestudy.DiscrepancyNoteBean)
Set(java.util.Set)
StudySubjectDAO(org.akaza.openclinica.dao.managestudy.StudySubjectDAO)
SubjectDAO(org.akaza.openclinica.dao.submit.SubjectDAO)
InsufficientPermissionException(org.akaza.openclinica.web.InsufficientPermissionException)
ItemDataDAO(org.akaza.openclinica.dao.submit.ItemDataDAO)
AuditDAO(org.akaza.openclinica.dao.admin.AuditDAO)
DiscrepancyNoteType(org.akaza.openclinica.bean.core.DiscrepancyNoteType)
UserAccountBean(org.akaza.openclinica.bean.login.UserAccountBean)
Iterator(java.util.Iterator)
EventCRFDAO(org.akaza.openclinica.dao.submit.EventCRFDAO)
StudySubjectDAO(org.akaza.openclinica.dao.managestudy.StudySubjectDAO)
Date(java.util.Date)
SimpleDateFormat(java.text.SimpleDateFormat)
DateFormat(java.text.DateFormat)
CRFVersionBean(org.akaza.openclinica.bean.submit.CRFVersionBean)
SimpleDateFormat(java.text.SimpleDateFormat)
Example 45 with CRFVersionBean
use of org.akaza.openclinica.bean.submit.CRFVersionBean in project OpenClinica by OpenClinica.
the class UrlRewriteServlet method getOpenClinicaResourceFromURL.
/**
* Method to parse the request URL parameters and get the respective
* database identifiers
*
* @param URLPath
* - example "S_CPCS/320999/SE_CPCS%5B1%5D/F_CPCS_1"
* @param queryString
* - example
* "format=html&mode=view&tabId=1&exitTo=ViewStudySubject"
* @return
*/
public OpenClinicaResource getOpenClinicaResourceFromURL(String URLPath) /*
* ,
* String
* queryString
*/
{
OpenClinicaResource openClinicaResource = new OpenClinicaResource();
if ((null != URLPath) && (!URLPath.equals(""))) {
if (URLPath.contains("/")) {
String[] tokens = URLPath.split("/");
if (tokens.length != 0) {
String URLParamValue = "";
StudyDAO stdao = new StudyDAO(getDataSource());
StudySubjectDAO ssubdao = new StudySubjectDAO(getDataSource());
StudyEventDefinitionDAO sedefdao = new StudyEventDefinitionDAO(getDataSource());
CRFDAO crfdao = new CRFDAO(getDataSource());
CRFVersionDAO crfvdao = new CRFVersionDAO(getDataSource());
ItemDAO idao = new ItemDAO(getDataSource());
ItemGroupDAO igdao = new ItemGroupDAO(getDataSource());
StudyEventDAO sedao = new StudyEventDAO(getDataSource());
StudyBean study = null;
StudySubjectBean subject = null;
StudyEventDefinitionBean sed = null;
CRFBean c = null;
CRFVersionBean cv = null;
ItemBean item = null;
ItemGroupBean ig = null;
StudyEventBean studyEvent = null;
Integer studySubjectId = 0;
Integer eventDefId = 0;
Integer eventRepeatKey = 0;
for (int i = 0; i < tokens.length; i++) {
// when interpreting these request URL parameters, the
// assumption is that the position of
// each type of parameters will be fixed. Meaning, study
// OID is always going to be at the start
// followed by StudySubjectKey followed by study event
// definition OID followed by
// study event repeat key followed by form OID followed
// by item group OID followed by
// item group repeat key followed by item OID
// It can also be done based on the start of OID value
// (example study OID presently
// starts with 'S_' but we will have to change it if we
// change the method of generating
// oID values in future.
URLParamValue = tokens[i].trim();
//System.out.println("URLParamValue::"+URLParamValue);
logger.info("URLPAramValue::" + URLParamValue);
if ((null != URLParamValue) && (!URLParamValue.equals(""))) {
switch(i) {
case 0:
{
// study OID
study = stdao.findByOid(URLParamValue);
//validate study OID
if (study == null) {
openClinicaResource.setInValid(true);
openClinicaResource.getMessages().add(resexception.getString("invalid_study_oid"));
return openClinicaResource;
} else {
openClinicaResource.setStudyOID(URLParamValue);
if (null != study) {
openClinicaResource.setStudyID(study.getId());
}
}
break;
}
case 1:
{
// StudySubjectKey
subject = ssubdao.findByOidAndStudy(URLParamValue, study.getId());
//validate subject OID
if (subject == null) {
openClinicaResource.setInValid(true);
openClinicaResource.getMessages().add(resexception.getString("invalid_subject_oid"));
return openClinicaResource;
} else {
openClinicaResource.setStudySubjectOID(URLParamValue);
if (null != subject) {
studySubjectId = subject.getId();
openClinicaResource.setStudySubjectID(studySubjectId);
}
}
break;
}
case 2:
{
// study event definition OID
// separate study event OID and study event
// repeat key
String seoid = "";
String eventOrdinal = "";
if (URLParamValue.contains("%5B") && URLParamValue.contains("%5D")) {
seoid = URLParamValue.substring(0, URLParamValue.indexOf("%5B"));
openClinicaResource.setStudyEventDefOID(seoid);
eventOrdinal = URLParamValue.substring(URLParamValue.indexOf("%5B") + 3, URLParamValue.indexOf("%5D"));
} else if (URLParamValue.contains("[") && URLParamValue.contains("]")) {
seoid = URLParamValue.substring(0, URLParamValue.indexOf("["));
logger.info("seoid" + seoid);
openClinicaResource.setStudyEventDefOID(seoid);
eventOrdinal = URLParamValue.substring(URLParamValue.indexOf("[") + 1, URLParamValue.indexOf("]"));
logger.info("eventOrdinal::" + eventOrdinal);
} else {
//event ordinal not specified
openClinicaResource.setInValid(true);
openClinicaResource.getMessages().add(resexception.getString("event_ordinal_not_specified"));
return openClinicaResource;
}
if ((null != seoid) && (null != study)) {
sed = sedefdao.findByOidAndStudy(seoid, study.getId(), study.getParentStudyId());
//validate study event oid
if (null == sed) {
openClinicaResource.setInValid(true);
openClinicaResource.getMessages().add(resexception.getString("invalid_event_oid"));
return openClinicaResource;
} else {
eventDefId = sed.getId();
openClinicaResource.setStudyEventDefID(eventDefId);
}
}
if (null != eventRepeatKey) {
eventRepeatKey = Integer.parseInt(eventOrdinal.trim());
//validate the event ordinal specified exists in database
studyEvent = (StudyEventBean) sedao.findByStudySubjectIdAndDefinitionIdAndOrdinal(subject.getId(), sed.getId(), eventRepeatKey);
//this method return new StudyEvent (not null) even if no studyEvent can be found
if (null == studyEvent || studyEvent.getId() == 0) {
openClinicaResource.setInValid(true);
openClinicaResource.getMessages().add(resexception.getString("invalid_event_ordinal"));
return openClinicaResource;
} else {
openClinicaResource.setStudyEventRepeatKey(eventRepeatKey);
}
}
break;
}
case 3:
{
// form OID
openClinicaResource.setFormVersionOID(URLParamValue);
//validate the crf version oid
cv = crfvdao.findByOid(URLParamValue);
if (cv == null) {
openClinicaResource.setInValid(true);
openClinicaResource.getMessages().add(resexception.getString("invalid_crf_oid"));
return openClinicaResource;
} else {
openClinicaResource.setFormVersionID(cv.getId());
//validate if crf is removed
if (cv.getStatus().equals(Status.DELETED)) {
openClinicaResource.setInValid(true);
openClinicaResource.getMessages().add(resexception.getString("removed_crf"));
return openClinicaResource;
} else {
if (null != study) {
// cv =
// crfvdao.findByCrfVersionOidAndStudy(URLParamValue,
// study.getId());
// if (null != cv) {
// openClinicaResource.setFormVersionID(cv.getId());
// openClinicaResource.setFormID(cv.getCrfId());
// }
HashMap studySubjectCRFDataDetails = sedao.getStudySubjectCRFData(study, studySubjectId, eventDefId, URLParamValue, eventRepeatKey);
if ((null != studySubjectCRFDataDetails) && (studySubjectCRFDataDetails.size() != 0)) {
if (studySubjectCRFDataDetails.containsKey("event_crf_id")) {
openClinicaResource.setEventCrfId((Integer) studySubjectCRFDataDetails.get("event_crf_id"));
}
if (studySubjectCRFDataDetails.containsKey("event_definition_crf_id")) {
openClinicaResource.setEventDefinitionCrfId((Integer) studySubjectCRFDataDetails.get("event_definition_crf_id"));
}
if (studySubjectCRFDataDetails.containsKey("study_event_id")) {
openClinicaResource.setStudyEventId((Integer) studySubjectCRFDataDetails.get("study_event_id"));
}
} else {
//no data was found in the database for the combination of parameters in the RESTful URL. There are 2 possible reasons:
//a. The data entry is not started yet for this event CRF. As of OpenClinica 3.1.3 we have not implemented the
// RESTful URL functionality in this case.
//b. The form version OID entered in the URL could be different than the one used in the data entry
openClinicaResource.setInValid(true);
openClinicaResource.getMessages().add(resexception.getString("either_no_data_for_crf_or_data_entry_not_started"));
return openClinicaResource;
}
}
}
}
break;
}
case 4:
{
// item group OID
// separate item group OID and item group
// repeat key
String igoid = "";
String igRepeatKey = "";
if (URLParamValue.contains("[")) {
igoid = URLParamValue.substring(1, URLParamValue.indexOf("["));
igRepeatKey = URLParamValue.substring(URLParamValue.indexOf("["), URLParamValue.indexOf("}]"));
}
if ((null != igoid) && (null != cv)) {
ig = igdao.findByOidAndCrf(URLParamValue, cv.getCrfId());
if (null != ig) {
openClinicaResource.setItemGroupID(ig.getId());
}
}
if (null != igRepeatKey) {
openClinicaResource.setItemGroupRepeatKey(Integer.parseInt(igRepeatKey));
}
break;
}
case 5:
{
// item = idao.find
break;
}
}
// switch end
}
}
}
}
}
return openClinicaResource;
}
Also used :
CRFDAO(org.akaza.openclinica.dao.admin.CRFDAO)
ItemBean(org.akaza.openclinica.bean.submit.ItemBean)
CRFVersionDAO(org.akaza.openclinica.dao.submit.CRFVersionDAO)
ItemDAO(org.akaza.openclinica.dao.submit.ItemDAO)
HashMap(java.util.HashMap)
StudyBean(org.akaza.openclinica.bean.managestudy.StudyBean)
ItemGroupDAO(org.akaza.openclinica.dao.submit.ItemGroupDAO)
StudyEventDefinitionBean(org.akaza.openclinica.bean.managestudy.StudyEventDefinitionBean)
StudyEventBean(org.akaza.openclinica.bean.managestudy.StudyEventBean)
StudySubjectDAO(org.akaza.openclinica.dao.managestudy.StudySubjectDAO)
CRFBean(org.akaza.openclinica.bean.admin.CRFBean)
StudyEventDefinitionDAO(org.akaza.openclinica.dao.managestudy.StudyEventDefinitionDAO)
StudySubjectBean(org.akaza.openclinica.bean.managestudy.StudySubjectBean)
StudyEventDAO(org.akaza.openclinica.dao.managestudy.StudyEventDAO)
CRFVersionBean(org.akaza.openclinica.bean.submit.CRFVersionBean)
ItemGroupBean(org.akaza.openclinica.bean.submit.ItemGroupBean)
StudyDAO(org.akaza.openclinica.dao.managestudy.StudyDAO)
Aggregations
CRFVersionBean (org.akaza.openclinica.bean.submit.CRFVersionBean)100
ArrayList (java.util.ArrayList)70
CRFVersionDAO (org.akaza.openclinica.dao.submit.CRFVersionDAO)61
CRFBean (org.akaza.openclinica.bean.admin.CRFBean)54
EventCRFBean (org.akaza.openclinica.bean.submit.EventCRFBean)53
CRFDAO (org.akaza.openclinica.dao.admin.CRFDAO)46
EventDefinitionCRFBean (org.akaza.openclinica.bean.managestudy.EventDefinitionCRFBean)44
HashMap (java.util.HashMap)38
StudyEventDefinitionBean (org.akaza.openclinica.bean.managestudy.StudyEventDefinitionBean)37
FormProcessor (org.akaza.openclinica.control.form.FormProcessor)36
EventCRFDAO (org.akaza.openclinica.dao.submit.EventCRFDAO)36
EventDefinitionCRFDAO (org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO)33
StudyEventDefinitionDAO (org.akaza.openclinica.dao.managestudy.StudyEventDefinitionDAO)32
StudyBean (org.akaza.openclinica.bean.managestudy.StudyBean)30
StudyEventBean (org.akaza.openclinica.bean.managestudy.StudyEventBean)30
StudyEventDAO (org.akaza.openclinica.dao.managestudy.StudyEventDAO)29
StudyDAO (org.akaza.openclinica.dao.managestudy.StudyDAO)25
StudySubjectBean (org.akaza.openclinica.bean.managestudy.StudySubjectBean)22
Iterator (java.util.Iterator)20
SectionBean (org.akaza.openclinica.bean.submit.SectionBean)20
