@Override
protected DisplayItemBean validateCalcTypeDisplayItemBean(
ScoreItemValidator sv, DisplayItemBean dib, String inputName, HttpServletRequest request) {
org.akaza.openclinica.bean.core.ResponseType rt =
dib.getMetadata().getResponseSet().getResponseType();
ItemDataDAO iddao = new ItemDataDAO(getDataSource());
boolean isSingleItem = false;
HttpSession session = request.getSession();
if (StringUtil.isBlank(inputName)) { // for single items
inputName = getInputName(dib);
isSingleItem = true;
}
EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
// we only give warning to user if data entered in DDE is different from
// IDE when the first
// time user hits 'save'
int keyId = ecb.getId();
Integer validationCount = (Integer) session.getAttribute(COUNT_VALIDATE + keyId);
ItemDataBean valueToCompare = new ItemDataBean();
if (isSingleItem) {
int idId = dib.getData().getId();
if (idId > 0) {
valueToCompare = (ItemDataBean) iddao.findByPK(idId);
}
} else {
valueToCompare = dib.getDbData();
}
if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.CALCULATION)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.GROUP_CALCULATION)) {
boolean showOriginalItem =
getItemMetadataService().isShown(dib.getItem().getId(), ecb, valueToCompare);
boolean showItem = dib.getMetadata().isShowItem();
boolean showDuplicateItem =
getItemMetadataService()
.hasPassedDDE(
dib.getMetadata(),
ecb,
valueToCompare); // .isShown(dib.getItem().getId(), ecb, dib.getDbData());
if (showOriginalItem && showDuplicateItem || showItem) {
dib = validateDisplayItemBeanText(sv, dib, inputName, request);
}
if (showOriginalItem && showDuplicateItem || showItem) {
sv.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, false);
sv.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ valueToCompare.getValue()
+ " "
+ respage.getString("from_initial_data_entry"));
}
}
return dib;
}
public ArrayList<ItemBean> findAllWithItemDataByCRFVersionId(int crfVersionId, int eventCRFId) {
this.unsetTypeExpected();
this.setTypeExpected(1, TypeNames.STRING); // (item)name
this.setTypeExpected(2, TypeNames.INT); // ordinal
this.setTypeExpected(3, TypeNames.STRING); // oc_oid
this.setTypeExpected(4, TypeNames.INT); // item_data_id
this.setTypeExpected(5, TypeNames.INT); // item_id
this.setTypeExpected(6, TypeNames.STRING); // (item)value
ArrayList<ItemBean> answer = new ArrayList<ItemBean>();
HashMap variables = new HashMap();
variables.put(new Integer(1), new Integer(crfVersionId));
variables.put(new Integer(2), new Integer(eventCRFId));
String sql = digester.getQuery("findAllWithItemDataByCRFVersionId");
ArrayList rows = super.select(sql, variables);
Iterator it = rows.iterator();
int cur_item_id = 0;
ItemBean item_bean = null;
ItemDataBean item_data_bean = null;
while (it.hasNext()) {
HashMap row = (HashMap) it.next();
Integer id = (Integer) row.get("item_id");
if (cur_item_id != id.intValue()) {
item_bean = new ItemBean();
answer.add(item_bean);
cur_item_id = id.intValue();
item_bean.setId(cur_item_id);
item_bean.setName((String) row.get("name"));
item_bean.setOid((String) row.get("oc_oid"));
}
item_data_bean = new ItemDataBean();
item_data_bean.setValue((String) row.get("value"));
item_data_bean.setOrdinal(((Integer) row.get("ordinal")).intValue());
item_data_bean.setId(((Integer) row.get("item_data_id")).intValue());
item_data_bean.setItemId(cur_item_id);
item_bean.addItemDataElement(item_data_bean);
}
return answer;
}
public EntityBean update(EntityBean eb) {
ItemDataBean idb = (ItemDataBean) eb;
idb.setActive(false);
HashMap variables = new HashMap();
variables.put(new Integer(1), new Integer(idb.getEventCRFId()));
variables.put(new Integer(2), new Integer(idb.getItemId()));
variables.put(new Integer(3), new Integer(idb.getStatus().getId()));
variables.put(new Integer(4), idb.getValue());
variables.put(new Integer(5), new Integer(idb.getUpdaterId()));
variables.put(new Integer(6), new Integer(idb.getId()));
this.execute(digester.getQuery("update"), variables);
if (isQuerySuccessful()) {
idb.setActive(true);
}
return idb;
}
public Object getEntityFromHashMap(HashMap hm) {
ItemDataBean eb = new ItemDataBean();
this.setEntityAuditInformation(eb, hm);
eb.setId(((Integer) hm.get("item_data_id")).intValue());
eb.setEventCRFId(((Integer) hm.get("event_crf_id")).intValue());
eb.setItemId(((Integer) hm.get("item_id")).intValue());
eb.setValue((String) hm.get("value"));
eb.setStatus(Status.get(((Integer) hm.get("status_id")).intValue()));
return eb;
}
public EntityBean create(EntityBean eb) {
ItemDataBean idb = (ItemDataBean) eb;
HashMap variables = new HashMap();
variables.put(new Integer(1), new Integer(idb.getEventCRFId()));
variables.put(new Integer(2), new Integer(idb.getItemId()));
variables.put(new Integer(3), new Integer(idb.getStatus().getId()));
variables.put(new Integer(4), idb.getValue());
variables.put(new Integer(5), new Integer(idb.getOwnerId()));
this.execute(digester.getQuery("create"), variables);
if (isQuerySuccessful()) {
idb.setId(getCurrentPK());
}
return idb;
}
@Override
public void processRequest() throws Exception {
SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
int subjectId = fp.getInt("id");
String action = fp.getString("action");
if (subjectId == 0 || StringUtil.isBlank(action)) {
addPageMessage(respage.getString("please_choose_a_subject_to_remove"));
forwardPage(Page.SUBJECT_LIST_SERVLET);
} else {
SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
// find all study subjects
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
ArrayList studySubs = ssdao.findAllBySubjectId(subjectId);
// find study events
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
ArrayList events = sedao.findAllBySubjectId(subjectId);
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("subjectToRemove", subject);
request.setAttribute("studySubs", studySubs);
request.setAttribute("events", events);
forwardPage(Page.REMOVE_SUBJECT);
} else {
logger.info("submit to remove the subject");
// change all statuses to deleted
subject.setStatus(Status.DELETED);
subject.setUpdater(ub);
subject.setUpdatedDate(new Date());
sdao.update(subject);
// remove subject references from study
for (int i = 0; i < studySubs.size(); i++) {
StudySubjectBean studySub = (StudySubjectBean) studySubs.get(i);
if (!studySub.getStatus().equals(Status.DELETED)) {
studySub.setStatus(Status.AUTO_DELETED);
studySub.setUpdater(ub);
studySub.setUpdatedDate(new Date());
ssdao.update(studySub);
}
}
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
for (int j = 0; j < events.size(); j++) {
StudyEventBean event = (StudyEventBean) events.get(j);
if (!event.getStatus().equals(Status.DELETED)) {
event.setStatus(Status.AUTO_DELETED);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
sedao.update(event);
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
for (int k = 0; k < eventCRFs.size(); k++) {
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
if (!eventCRF.getStatus().equals(Status.DELETED)) {
eventCRF.setStatus(Status.AUTO_DELETED);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
ecdao.update(eventCRF);
// remove all the item data
ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
for (int a = 0; a < itemDatas.size(); a++) {
ItemDataBean item = (ItemDataBean) itemDatas.get(a);
if (!item.getStatus().equals(Status.DELETED)) {
item.setStatus(Status.AUTO_DELETED);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
}
}
}
String emailBody =
respage.getString("the_subject")
+ " "
+ respage.getString("has_been_removed_succesfully");
addPageMessage(emailBody);
// sendEmail(emailBody);
forwardPage(Page.SUBJECT_LIST_SERVLET);
}
}
}
@Override
@SuppressWarnings(value = "unchecked")
public void processRequest() throws Exception {
ItemDataDAO itemDataDao = new ItemDataDAO(sm.getDataSource());
EventCRFDAO eventCrfDao = new EventCRFDAO(sm.getDataSource());
CrfBusinessLogicHelper crfBusinessLogicHelper = new CrfBusinessLogicHelper(sm.getDataSource());
String action = request.getParameter("action");
FormProcessor fp = new FormProcessor(request);
// checks which module the requests are from
String module = fp.getString(MODULE);
request.setAttribute(MODULE, module);
resetPanel();
panel.setStudyInfoShown(false);
panel.setOrderedData(true);
setToPanel(resword.getString("create_CRF"), respage.getString("br_create_new_CRF_entering"));
setToPanel(
resword.getString("create_CRF_version"), respage.getString("br_create_new_CRF_uploading"));
setToPanel(
resword.getString("revise_CRF_version"), respage.getString("br_if_you_owner_CRF_version"));
setToPanel(
resword.getString("CRF_spreadsheet_template"),
respage.getString("br_download_blank_CRF_spreadsheet_from"));
setToPanel(
resword.getString("example_CRF_br_spreadsheets"),
respage.getString("br_download_example_CRF_instructions_from"));
if ("confirm".equalsIgnoreCase(action)) {
List<DisplayItemBeanWrapper> displayItemBeanWrappers =
(List<DisplayItemBeanWrapper>) session.getAttribute("importedData");
logger.info("Size of displayItemBeanWrappers : " + displayItemBeanWrappers.size());
forwardPage(Page.VERIFY_IMPORT_CRF_DATA);
}
if ("save".equalsIgnoreCase(action)) {
List<DisplayItemBeanWrapper> displayItemBeanWrappers =
(List<DisplayItemBeanWrapper>) session.getAttribute("importedData");
// System.out.println("Size of displayItemBeanWrappers : " + displayItemBeanWrappers.size());
for (DisplayItemBeanWrapper wrapper : displayItemBeanWrappers) {
int eventCrfBeanId = -1;
EventCRFBean eventCrfBean = new EventCRFBean();
// TODO : tom , the wrapper object has all the necessary data -
// as you see we check the
// is to see if this data is Savable if it is then we go ahead
// and save it. if not we discard.
// So the change needs to happen here , instead of discarding we
// need to file discrepancy notes
// and save the data. If you look in the
// Page.VERIFY_IMPORT_CRF_DATA jsp file you can see how I am
// pulling the errors. and use that in the same way.
logger.info("right before we check to make sure it is savable: " + wrapper.isSavable());
if (wrapper.isSavable()) {
ArrayList<Integer> eventCrfInts = new ArrayList<Integer>();
// based on the use case: "If any of the data does not meet
// validations specified in the CRF
// Template, a discrepancy note is automatically logged.
// The DN will have a type of Failed Validation Check, and
// a message of Failed Validation check."
// System.out.println("wrapper problems found : " +
// wrapper.getValidationErrors().toString());
for (DisplayItemBean displayItemBean : wrapper.getDisplayItemBeans()) {
eventCrfBeanId = displayItemBean.getData().getEventCRFId();
eventCrfBean = (EventCRFBean) eventCrfDao.findByPK(eventCrfBeanId);
logger.info("found value here: " + displayItemBean.getData().getValue());
logger.info("found status here: " + eventCrfBean.getStatus().getName());
// System.out.println("found event crf bean name here: "
// +
// eventCrfBean.getEventName()+" id "+eventCrfBean.getId
// ());
// SO, items can be created in a wrapper which is set to
// overwrite
// we get around this by checking the bean first, to
// make sure it's not null
ItemDataBean itemDataBean = new ItemDataBean();
itemDataBean =
itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(
displayItemBean.getItem().getId(),
eventCrfBean.getId(),
displayItemBean.getData().getOrdinal());
if (wrapper.isOverwrite() && itemDataBean.getStatus() != null) {
// ItemDataBean itemDataBean = new ItemDataBean();
// itemDataBean =
// itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(
// displayItemBean.getItem().getId(),
// eventCrfBean.getId(), displayItemBean
// .getData().getOrdinal());
// itemDataBean =
// itemDataDao.findByEventCRFIdAndItemName(
// eventCrfBean,
// displayItemBean.getItem().getName());
logger.info(
"just tried to find item data bean on item name "
+ displayItemBean.getItem().getName());
itemDataBean.setUpdatedDate(new Date());
itemDataBean.setUpdater(ub);
itemDataBean.setValue(displayItemBean.getData().getValue());
// set status?
itemDataDao.update(itemDataBean);
logger.info("updated: " + itemDataBean.getItemId());
// need to set pk here in order to create dn
displayItemBean.getData().setId(itemDataBean.getId());
} else {
itemDataDao.create(displayItemBean.getData());
logger.info(
"created: "
+ displayItemBean.getData().getItemId()
+ "event CRF ID = "
+ eventCrfBean.getId()
+ "CRF VERSION ID ="
+ eventCrfBean.getCRFVersionId());
// does this dao function work for repeating
// events/groups?
// ItemDataBean itemDataBean =
// itemDataDao.findByEventCRFIdAndItemName(
// eventCrfBean,
// displayItemBean.getItem().getName());
ItemDataBean itemDataBean2 =
itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(
displayItemBean.getItem().getId(),
eventCrfBean.getId(),
displayItemBean.getData().getOrdinal());
logger.info(
"found: id " + itemDataBean2.getId() + " name " + itemDataBean2.getName());
displayItemBean.getData().setId(itemDataBean2.getId());
}
// logger.info("created item data bean:
// "+displayItemBean.getData().getId());
// logger.info("created:
// "+displayItemBean.getData().getName());
// logger.info("continued:
// "+displayItemBean.getData().getItemId());
ItemDAO idao = new ItemDAO(sm.getDataSource());
ItemBean ibean = (ItemBean) idao.findByPK(displayItemBean.getData().getItemId());
// logger.info("continued2: getName " +
// ibean.getName());
// System.out.println("*** checking for validation errors: " + ibean.getName());
String itemOid =
displayItemBean.getItem().getOid()
+ "_"
+ wrapper.getStudyEventRepeatKey()
+ "_"
+ displayItemBean.getData().getOrdinal()
+ "_"
+ wrapper.getStudySubjectOid();
if (wrapper.getValidationErrors().containsKey(itemOid)) {
ArrayList messageList = (ArrayList) wrapper.getValidationErrors().get(itemOid);
// if
// (wrapper.getValidationErrors().containsKey(ibean
// .getName())) {
// ArrayList messageList = (ArrayList)
// wrapper.getValidationErrors
// ().get(ibean.getName());
// could be more then one will have to iterate
// could it be more than one? tbh 08/2008
for (int iter = 0; iter < messageList.size(); iter++) {
String message = (String) messageList.get(iter);
DiscrepancyNoteBean parentDn =
ImportSpringJob.createDiscrepancyNote(
ibean,
message,
eventCrfBean,
displayItemBean,
null,
ub,
sm.getDataSource(),
currentStudy);
ImportSpringJob.createDiscrepancyNote(
ibean,
message,
eventCrfBean,
displayItemBean,
parentDn.getId(),
ub,
sm.getDataSource(),
currentStudy);
// System.out.println("*** created disc note with message: " + message);
// displayItemBean);
}
}
// logger.info("created:
// "+displayItemBean.getDbData().getName());
if (!eventCrfInts.contains(new Integer(eventCrfBean.getId()))) {
crfBusinessLogicHelper.markCRFComplete(eventCrfBean, ub);
// System.out.println("*** just updated event crf bean: " + eventCrfBean.getId());
eventCrfInts.add(new Integer(eventCrfBean.getId()));
}
}
// end of item datas, tbh
// crfBusinessLogicHelper.markCRFComplete(eventCrfBean, ub);
// System .out.println("*** just updated event crf bean: "+
// eventCrfBean.getId());
// need to update the study event status as well, tbh
// crfBusinessLogicHelper.updateStudyEvent(eventCrfBean,
// ub);
// above should do it for us, tbh 08/2008
}
}
addPageMessage(respage.getString("data_has_been_successfully_import"));
// forwardPage(Page.SUBMIT_DATA_SERVLET);
forwardPage(Page.LIST_STUDY_SUBJECTS_SERVLET);
// replaced tbh, 06/2009
}
}
@Override
public void processRequest() throws Exception {
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
int versionId = fp.getInt("id", true);
String module = fp.getString("module");
request.setAttribute("module", module);
String action = fp.getString("action");
if (versionId == 0) {
addPageMessage(respage.getString("please_choose_a_CRF_version_to_remove"));
forwardPage(Page.CRF_LIST_SERVLET);
} else {
if (StringUtil.isBlank(action)) {
addPageMessage(respage.getString("no_action_specified"));
forwardPage(Page.CRF_LIST_SERVLET);
return;
}
CRFVersionBean version = (CRFVersionBean) cvdao.findByPK(versionId);
SectionDAO secdao = new SectionDAO(sm.getDataSource());
EventCRFDAO evdao = new EventCRFDAO(sm.getDataSource());
// find all event crfs by version id
ArrayList eventCRFs = evdao.findUndeletedWithStudySubjectsByCRFVersion(versionId);
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("versionToRemove", version);
request.setAttribute("eventCRFs", eventCRFs);
forwardPage(Page.REMOVE_CRF_VERSION);
} else {
logger.info("submit to remove the crf version");
// version
version.setStatus(Status.DELETED);
version.setUpdater(ub);
version.setUpdatedDate(new Date());
cvdao.update(version);
// added below tbh 092007, seems that we don't remove the event
// crfs in the second pass
for (int ii = 0; ii < eventCRFs.size(); ii++) {
EventCRFBean ecbean = (EventCRFBean) eventCRFs.get(ii);
ecbean.setStatus(Status.AUTO_DELETED);
ecbean.setUpdater(ub);
ecbean.setUpdatedDate(new Date());
evdao.update(ecbean);
}
// added above tbh 092007, to fix task
// all sections
ArrayList sections = secdao.findAllByCRFVersionId(version.getId());
for (int j = 0; j < sections.size(); j++) {
SectionBean section = (SectionBean) sections.get(j);
if (!section.getStatus().equals(Status.DELETED)) {
section.setStatus(Status.AUTO_DELETED);
section.setUpdater(ub);
section.setUpdatedDate(new Date());
secdao.update(section);
}
}
// all item data related to event crfs
ItemDataDAO idao = new ItemDataDAO(sm.getDataSource());
for (int i = 0; i < eventCRFs.size(); i++) {
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(i);
if (!eventCRF.getStatus().equals(Status.DELETED)) {
eventCRF.setStatus(Status.AUTO_DELETED);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
evdao.update(eventCRF);
ArrayList items = idao.findAllByEventCRFId(eventCRF.getId());
for (int j = 0; j < items.size(); j++) {
ItemDataBean item = (ItemDataBean) items.get(j);
if (!item.getStatus().equals(Status.DELETED)) {
item.setStatus(Status.AUTO_DELETED);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
idao.update(item);
}
}
}
}
addPageMessage(
respage.getString("the_CRF")
+ version.getName()
+ " "
+ respage.getString("has_been_removed_succesfully"));
forwardPage(Page.CRF_LIST_SERVLET);
}
}
}
/*
* (non-Javadoc)
*
* @see org.akaza.openclinica.control.core.SecureController#processRequest()
*/
@Override
protected void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
int noteId = fp.getInt(INPUT_NOTE_ID);
String module = (String) session.getAttribute("module");
// Integer subjectId = (Integer) session.getAttribute("subjectId");
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(sm.getDataSource());
DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
dndao.setFetchMapping(true);
// check that the note exists
DiscrepancyNoteBean discrepancyNoteBean = (DiscrepancyNoteBean) dndao.findByPK(noteId);
if (!discrepancyNoteBean.isActive()) {
throw new InconsistentStateException(
Page.MANAGE_STUDY_SERVLET,
resexception.getString("you_are_trying_resolve_discrepancy_not_exist"));
}
// check that the note has not already been closed
ArrayList children = dndao.findAllByParent(discrepancyNoteBean);
discrepancyNoteBean.setChildren(children);
// This logic has been reverted, issue-7459
// if (parentNoteIsClosed(discrepancyNoteBean)) {
// throw new InconsistentStateException(Page.VIEW_DISCREPANCY_NOTES_IN_STUDY_SERVLET,
// respage
// .getString("the_discrepancy_choose_has_been_closed_resolved_create_new"));
// }
// all clear, send the user to the resolved screen
String entityType = discrepancyNoteBean.getEntityType().toLowerCase();
discrepancyNoteBean.setResStatus(
ResolutionStatus.get(discrepancyNoteBean.getResolutionStatusId()));
discrepancyNoteBean.setDisType(
DiscrepancyNoteType.get(discrepancyNoteBean.getDiscrepancyNoteTypeId()));
// BWP 03/17/2009 3166: if it's not an ItemData type note, redirect
// Monitors to View Subject or
// View Study Events <<
if (currentRole.getRole().equals(Role.MONITOR)
&& !"itemdata".equalsIgnoreCase(entityType)
&& !"eventcrf".equalsIgnoreCase(entityType)) {
redirectMonitor(module, discrepancyNoteBean);
return;
}
// >>
// If Study is Frozen or Locked
if (currentStudy.getStatus().isFrozen()
&& !"itemdata".equalsIgnoreCase(entityType)
&& !"eventcrf".equalsIgnoreCase(entityType)) {
redirectMonitor(module, discrepancyNoteBean);
return;
}
boolean toView = false;
boolean isCompleted = false;
if ("itemdata".equalsIgnoreCase(entityType)) {
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
ItemDataBean idb = (ItemDataBean) iddao.findByPK(discrepancyNoteBean.getEntityId());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
EventCRFBean ecb = (EventCRFBean) ecdao.findByPK(idb.getEventCRFId());
StudySubjectBean studySubjectBean =
(StudySubjectBean) studySubjectDAO.findByPK(ecb.getStudySubjectId());
discrepancyNoteBean.setSubjectId(studySubjectBean.getId());
discrepancyNoteBean.setItemId(idb.getItemId());
if (ecb.getStatus().equals(Status.UNAVAILABLE)) {
isCompleted = true;
}
toView = true; // we want to go to view note page if the note is
// for item data
}
// logger.info("set up pop up url: " + createNoteURL);
// System.out.println("set up pop up url: " + createNoteURL);
boolean goNext =
prepareRequestForResolution(
request, sm.getDataSource(), currentStudy, discrepancyNoteBean, isCompleted);
Page p = getPageForForwarding(discrepancyNoteBean, isCompleted);
// logger.info("found page for forwarding: " + p.getFileName());
if (p == null) {
throw new InconsistentStateException(
Page.VIEW_DISCREPANCY_NOTES_IN_STUDY_SERVLET,
resexception.getString("the_discrepancy_note_triying_resolve_has_invalid_type"));
} else {
if (p.getFileName().contains("?")) {
if (!p.getFileName().contains("fromViewNotes=1")) {
p.setFileName(p.getFileName() + "&fromViewNotes=1");
}
} else {
p.setFileName(p.getFileName() + "?fromViewNotes=1");
}
String createNoteURL =
CreateDiscrepancyNoteServlet.getAddChildURL(
discrepancyNoteBean, ResolutionStatus.CLOSED, true);
setPopUpURL(createNoteURL);
}
if (!goNext) {
setPopUpURL("");
addPageMessage(
respage.getString("you_may_not_perform_admin_edit_on_CRF_not_completed_by_user"));
p = Page.VIEW_DISCREPANCY_NOTES_IN_STUDY_SERVLET;
}
forwardPage(p);
}
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
int studySubId = fp.getInt(STUDY_SUB_ID, true);
int eventCRFId = fp.getInt(EVENT_CRF_ID);
String action = request.getParameter("action");
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
StudyDAO sdao = new StudyDAO(sm.getDataSource());
if (eventCRFId == 0) {
addPageMessage(respage.getString("please_choose_an_event_CRF_to_delete"));
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
} else {
EventCRFBean eventCRF = (EventCRFBean) ecdao.findByPK(eventCRFId);
StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
request.setAttribute("studySub", studySub);
// construct info needed on view event crf page
CRFDAO cdao = new CRFDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
int crfVersionId = eventCRF.getCRFVersionId();
CRFBean cb = cdao.findByVersionId(crfVersionId);
eventCRF.setCrf(cb);
CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(crfVersionId);
eventCRF.setCrfVersion(cvb);
// then get the definition so we can call
// DisplayEventCRFBean.setFlags
int studyEventId = eventCRF.getStudyEventId();
StudyEventBean event = (StudyEventBean) sedao.findByPK(studyEventId);
int studyEventDefinitionId = sedao.getDefinitionIdFromStudyEventId(studyEventId);
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyEventDefinitionBean sed =
(StudyEventDefinitionBean) seddao.findByPK(studyEventDefinitionId);
event.setStudyEventDefinition(sed);
request.setAttribute("event", event);
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyBean study = (StudyBean) sdao.findByPK(studySub.getStudyId());
EventDefinitionCRFBean edc =
edcdao.findByStudyEventDefinitionIdAndCRFId(study, studyEventDefinitionId, cb.getId());
DisplayEventCRFBean dec = new DisplayEventCRFBean();
dec.setEventCRF(eventCRF);
dec.setFlags(eventCRF, ub, currentRole, edc.isDoubleEntry());
// find all item data
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
dnDao = new DiscrepancyNoteDAO(sm.getDataSource());
ArrayList<ItemDataBean> itemData = iddao.findAllByEventCRFId(eventCRF.getId());
request.setAttribute("items", itemData);
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("displayEventCRF", dec);
forwardPage(Page.DELETE_EVENT_CRF);
} else {
logger.info("submit to delete the event CRF from event");
// OC-6303 Deleting Event CRF resets Show / Hide logic
// delete records from DynamicItemForm and DynamicItemGroup
getDynamicsItemFormMetadataDao().delete(eventCRFId);
getDynamicsItemGroupMetadataDao().delete(eventCRFId);
eventCRF.setOldStatus(eventCRF.getStatus());
eventCRF.setStatus(Status.RESET);
eventCRF.setUpdater(ub);
ecdao.update(eventCRF);
for (ItemDataBean itemdata : itemData) {
// OC-6343 Rule behaviour must be reset if an Event CRF is deleted
// delete the records from ruleActionRunLogDao
getRuleActionRunLogDao().delete(itemdata.getId());
// OC-6344 Notes & Discrepancies must be set to "closed" when event CRF is deleted
// parentDiscrepancyNoteList is the list of the parent DNs records only
ArrayList<DiscrepancyNoteBean> parentDiscrepancyNoteList =
getDnDao().findParentNotesOnlyByItemData(itemdata.getId());
for (DiscrepancyNoteBean parentDiscrepancyNote : parentDiscrepancyNoteList) {
if (parentDiscrepancyNote.getResolutionStatusId()
!= 4) { // if the DN's resolution status is not set to Closed
String description = resword.getString("dn_auto-closed_description");
String detailedNotes = resword.getString("dn_auto_closed_detailed_notes");
// create new DN record , new DN Map record , also update the parent record
createDiscrepancyNoteBean(
description, detailedNotes, itemdata.getId(), study, ub, parentDiscrepancyNote);
}
}
iddao = new ItemDataDAO(sm.getDataSource());
ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
ItemDataBean idBean = (ItemDataBean) iddao.findByPK(itemdata.getId());
ItemFormMetadataBean ifmBean =
ifmdao.findByItemIdAndCRFVersionId(idBean.getItemId(), crfVersionId);
// Updating Dn_item_data_map actovated column into false for the existing DNs
ArrayList<DiscrepancyNoteBean> dnBeans =
getDnDao().findExistingNotesForItemData(itemdata.getId());
if (dnBeans.size() != 0) {
DiscrepancyNoteBean dnBean = new DiscrepancyNoteBean();
dnBean.setEntityId(itemdata.getId());
dnBean.setActivated(false);
getDnDao().updateDnMapActivation(dnBean);
}
// Default Values are not addressed
itemdata.setValue("");
itemdata.setOldStatus(itemdata.getStatus());
itemdata.setOwner(ub);
itemdata.setStatus(Status.AVAILABLE);
itemdata.setUpdater(ub);
iddao.updateUser(itemdata);
iddao.update(itemdata);
}
// OC-6291 event_crf status change
eventCRF.setOldStatus(eventCRF.getStatus());
eventCRF.setStatus(Status.AVAILABLE);
eventCRF.setUpdater(ub);
ecdao.update(eventCRF);
if (event.getSubjectEventStatus().isCompleted()
|| event.getSubjectEventStatus().isSigned()) {
event.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED);
event.setUpdater(ub);
sedao = new StudyEventDAO(sm.getDataSource());
sedao.update(event);
}
String emailBody =
respage.getString("the_event_CRF")
+ cb.getName()
+ respage.getString("has_been_deleted_from_the_event")
+ event.getStudyEventDefinition().getName()
+ ". "
+ respage.getString("has_been_deleted_from_the_event_cont");
addPageMessage(emailBody);
// sendEmail(emailBody);
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
}
}
}
private ItemDataBean copyItemDataBean(ItemDataBean src) {
ItemDataBean result = new ItemDataBean();
result.setEventCRFId(src.getEventCRFId());
result.setItemId(src.getItemId());
result.setValue(src.getValue());
result.setOrdinal(src.getOrdinal());
result.setSelected(src.isSelected());
result.setAuditLog(src.isAuditLog());
result.setCreatedDate(src.getCreatedDate());
result.setUpdatedDate(src.getUpdatedDate());
result.setOwner(src.getOwner());
result.setOwnerId(src.getOwnerId());
result.setUpdater(src.getUpdater());
result.setUpdaterId(src.getUpdaterId());
result.setStatus(src.getStatus());
return result;
}
@Override
protected DisplayItemBean validateDisplayItemBean(
DiscrepancyValidator v, DisplayItemBean dib, String inputName, HttpServletRequest request) {
org.akaza.openclinica.bean.core.ResponseType rt =
dib.getMetadata().getResponseSet().getResponseType();
HttpSession session = request.getSession();
EventCRFBean ecb = (EventCRFBean) request.getAttribute(INPUT_EVENT_CRF);
boolean isSingleItem = false;
if (StringUtil.isBlank(inputName)) { // for single items
inputName = getInputName(dib);
isSingleItem = true;
}
// we only give warning to user if data entered in DDE is different from
// IDE when the first
// time user hits 'save'
int keyId = ecb.getId();
Integer validationCount = (Integer) session.getAttribute(COUNT_VALIDATE + keyId);
// @pgawade 12-Aug-2011 issue 10601:
// 1. Moved the call to loadFormValue method setting values
// from form here. It was at the end
// of this method before that is after validations and so an extra
// validation for checking value entered
// against the data type was getting implemented for non-repeating group
// items.
// 2. Copying the form data into new object for non repeating items to
// pass to validation
// for matching IDE and DDE values. Id same reference is used, the way
// code here was written, it affetcs
// the value used in validation of data entered in DDE against the
// related data type
ItemDataBean valueToCompareTmp = dib.getData();
ItemDataBean valueToCompare = copyItemDataBean(valueToCompareTmp);
if (!isSingleItem) {
valueToCompare = dib.getDbData();
}
// only load form value when an item is not in a group,
// if in group, the value is already loaded
// see formGroups = loadFormValueForItemGroup(digb,digbs,formGroups);
if (isSingleItem) {
dib = loadFormValue(dib, request);
}
boolean showOriginalItem =
getItemMetadataService()
.isShown(dib.getItem().getId(), ecb, valueToCompare); // was dib.getData()
boolean showItem = dib.getMetadata().isShowItem();
if (!showItem && dib.getScdData().getScdItemMetadataBean().getScdItemFormMetadataId() > 0) {
showItem = true;
}
boolean showDuplicateItem =
getItemMetadataService()
.hasPassedDDE(
dib.getMetadata(),
ecb,
valueToCompare); // .isShown(dib.getItem().getId(), ecb, dib.getDbData());// where
// is the set db data?
logger.debug(
"*** show original item has value "
+ dib.getData().getValue()
+ " and show item has value "
+ valueToCompare.getValue());
logger.debug(
"--- show original: "
+ showOriginalItem
+ " show duplicate: "
+ showDuplicateItem
+ " and just show item: "
+ showItem);
logger.debug("VALIDATION COUNT " + validationCount);
if (showOriginalItem && showDuplicateItem || showItem) {
if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.TEXT)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.TEXTAREA)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.FILE)) {
dib = validateDisplayItemBeanText(v, dib, inputName, request);
if (validationCount == null || validationCount.intValue() == 0) {
v.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, false);
v.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ valueToCompare.getValue()
+ " "
+ respage.getString("from_initial_data_entry"));
}
} else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.RADIO)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECT)) {
dib = validateDisplayItemBeanSingleCV(v, dib, inputName);
// ItemFormMetadataBean ifmdb = dib.getMetadata();
// ResponseSetBean rsBean = ifmdb.getResponseSet();
// logger.info("### found a response set count of "+inputName+"
// "+rsBean.getOptions().size());
// TODO sees it at this end tbh 1878
if (validationCount == null || validationCount.intValue() == 0) {
v.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, false);
String errorValue = valueToCompare.getValue();
java.util.ArrayList options = dib.getMetadata().getResponseSet().getOptions();
for (int u = 0; u < options.size(); u++) {
ResponseOptionBean rob = (ResponseOptionBean) options.get(u);
if (rob.getValue().equals(errorValue)) {
errorValue = rob.getText();
}
}
v.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ errorValue
+ " "
+ respage.getString("from_initial_data_entry"));
}
} else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.CHECKBOX)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECTMULTI)) {
dib = validateDisplayItemBeanMultipleCV(v, dib, inputName);
if (validationCount == null || validationCount.intValue() == 0) {
v.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, true);
// repeated from above, tbh 112007
String errorValue = valueToCompare.getValue();
String errorTexts = "";
java.util.ArrayList options = dib.getMetadata().getResponseSet().getOptions();
for (int u = 0; u < options.size(); u++) {
ResponseOptionBean rob = (ResponseOptionBean) options.get(u);
if (errorValue.contains(rob.getValue())) {
errorTexts = errorTexts + rob.getText();
if (u < options.size() - 1) {
// the values for multi-select are seperated by
// comma
errorTexts = errorTexts + ", ";
}
}
}
v.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ errorTexts
+ " "
+ respage.getString("from_initial_data_entry"));
}
}
}
// // only load form value when an item is not in a group,
// // if in group, the value is already loaded
// // see formGroups = loadFormValueForItemGroup(digb,digbs,formGroups);
// if (isSingleItem) {
// dib = loadFormValue(dib, request);
// }
return dib;
}
@Override
public void processRequest() throws Exception {
String studySubIdString = request.getParameter("id"); // studySubjectId
String subIdString = request.getParameter("subjectId");
String studyIdString = request.getParameter("studyId");
SubjectDAO sdao = new SubjectDAO(sm.getDataSource());
StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
if (StringUtil.isBlank(studySubIdString)
|| StringUtil.isBlank(subIdString)
|| StringUtil.isBlank(studyIdString)) {
addPageMessage(respage.getString("please_choose_a_study_subject_to_remove"));
forwardPage(Page.LIST_STUDY_SUBJECT_SERVLET);
} else {
int studyId = Integer.valueOf(studyIdString.trim()).intValue();
int studySubId = Integer.valueOf(studySubIdString.trim()).intValue();
int subjectId = Integer.valueOf(subIdString.trim()).intValue();
SubjectBean subject = (SubjectBean) sdao.findByPK(subjectId);
StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
StudyDAO studydao = new StudyDAO(sm.getDataSource());
StudyBean study = (StudyBean) studydao.findByPK(studyId);
// find study events
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
ArrayList events = sedao.findAllByStudyAndStudySubjectId(study, studySubId);
String action = request.getParameter("action");
if ("confirm".equalsIgnoreCase(action)) {
if (!studySub.getStatus().equals(Status.AVAILABLE)) {
addPageMessage(
respage.getString("this_subject_is_not_available_for_this_study")
+ " "
+ respage.getString("please_contact_sysadmin_for_more_information"));
forwardPage(Page.LIST_STUDY_SUBJECT_SERVLET);
return;
}
request.setAttribute("subject", subject);
request.setAttribute("study", study);
request.setAttribute("studySub", studySub);
request.setAttribute("events", events);
forwardPage(Page.REMOVE_STUDY_SUBJECT);
} else {
logger.info("submit to remove the subject from study");
// remove subject from study
studySub.setStatus(Status.DELETED);
studySub.setUpdater(ub);
studySub.setUpdatedDate(new Date());
subdao.update(studySub);
// remove all study events
// remove all event crfs
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
for (int j = 0; j < events.size(); j++) {
StudyEventBean event = (StudyEventBean) events.get(j);
if (!event.getStatus().equals(Status.DELETED)) {
event.setStatus(Status.AUTO_DELETED);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
sedao.update(event);
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
for (int k = 0; k < eventCRFs.size(); k++) {
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
if (!eventCRF.getStatus().equals(Status.DELETED)) {
eventCRF.setStatus(Status.AUTO_DELETED);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
ecdao.update(eventCRF);
// remove all the item data
ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
for (int a = 0; a < itemDatas.size(); a++) {
ItemDataBean item = (ItemDataBean) itemDatas.get(a);
if (!item.getStatus().equals(Status.DELETED)) {
item.setStatus(Status.AUTO_DELETED);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
}
}
}
String emailBody =
respage.getString("the_subject")
+ " "
+ subject.getName()
+ " "
+ respage.getString("has_been_removed_from_the_study")
+ study.getName()
+ ".";
addPageMessage(emailBody);
sendEmail(emailBody);
forwardPage(Page.LIST_STUDY_SUBJECT_SERVLET);
}
}
}
public MessageContainer runRules(
List<RuleSetBean> ruleSets,
ExecutionMode executionMode,
StudyBean currentStudy,
HashMap<String, String> variableAndValue,
UserAccountBean ub,
Phase phase) {
if (variableAndValue == null || variableAndValue.isEmpty()) {
logger.warn("You must be executing Rules in Batch");
variableAndValue = new HashMap<String, String>();
}
MessageContainer messageContainer = new MessageContainer();
HashMap<String, ArrayList<RuleActionContainer>> toBeExecuted =
new HashMap<String, ArrayList<RuleActionContainer>>();
for (RuleSetBean ruleSet : ruleSets) {
String key = getExpressionService().getItemOid(ruleSet.getOriginalTarget().getValue());
List<RuleActionContainer> allActionContainerListBasedOnRuleExecutionResult = null;
if (toBeExecuted.containsKey(key)) {
allActionContainerListBasedOnRuleExecutionResult = toBeExecuted.get(key);
} else {
toBeExecuted.put(key, new ArrayList<RuleActionContainer>());
allActionContainerListBasedOnRuleExecutionResult = toBeExecuted.get(key);
}
ItemDataBean itemData = null;
for (ExpressionBean expressionBean : ruleSet.getExpressions()) {
ruleSet.setTarget(expressionBean);
for (RuleSetRuleBean ruleSetRule : ruleSet.getRuleSetRules()) {
String result = null;
RuleBean rule = ruleSetRule.getRuleBean();
ExpressionObjectWrapper eow =
new ExpressionObjectWrapper(
ds, currentStudy, rule.getExpression(), ruleSet, variableAndValue, ecb);
try {
OpenClinicaExpressionParser oep = new OpenClinicaExpressionParser(eow);
result = oep.parseAndEvaluateExpression(rule.getExpression().getValue());
itemData = getExpressionService().getItemDataBeanFromDb(ruleSet.getTarget().getValue());
// Actions
List<RuleActionBean> actionListBasedOnRuleExecutionResult =
ruleSetRule.getActions(result, phase);
if (itemData != null) {
Iterator<RuleActionBean> itr = actionListBasedOnRuleExecutionResult.iterator();
while (itr.hasNext()) {
RuleActionBean ruleActionBean = itr.next();
RuleActionRunLogBean ruleActionRunLog =
new RuleActionRunLogBean(
ruleActionBean.getActionType(),
itemData,
itemData.getValue(),
ruleSetRule.getRuleBean().getOid());
if (getRuleActionRunLogDao().findCountByRuleActionRunLogBean(ruleActionRunLog)
> 0) {
itr.remove();
}
}
}
for (RuleActionBean ruleActionBean : actionListBasedOnRuleExecutionResult) {
RuleActionContainer ruleActionContainer =
new RuleActionContainer(ruleActionBean, expressionBean, itemData, ruleSet);
allActionContainerListBasedOnRuleExecutionResult.add(ruleActionContainer);
}
logger.info(
"RuleSet with target : {} , Ran Rule : {} The Result was : {} , Based on that {} action will be executed in {} mode. ",
new Object[] {
ruleSet.getTarget().getValue(),
rule.getName(),
result,
actionListBasedOnRuleExecutionResult.size(),
executionMode.name()
});
} catch (OpenClinicaSystemException osa) {
// TODO: report something useful
}
}
}
}
for (Map.Entry<String, ArrayList<RuleActionContainer>> entry : toBeExecuted.entrySet()) {
// Sort the list of actions
Collections.sort(entry.getValue(), new RuleActionContainerComparator());
for (RuleActionContainer ruleActionContainer : entry.getValue()) {
logger.info(
"START Expression is : {} , RuleAction : {} , ExecutionMode : {} ",
new Object[] {
ruleActionContainer.getExpressionBean().getValue(),
ruleActionContainer.getRuleAction().toString(),
executionMode
});
ruleActionContainer.getRuleSetBean().setTarget(ruleActionContainer.getExpressionBean());
ruleActionContainer
.getRuleAction()
.setCuratedMessage(
curateMessage(
ruleActionContainer.getRuleAction(),
(ruleActionContainer.getRuleAction().getRuleSetRule())));
ActionProcessor ap =
ActionProcessorFacade.getActionProcessor(
ruleActionContainer.getRuleAction().getActionType(),
ds,
getMailSender(),
dynamicsMetadataService,
ruleActionContainer.getRuleSetBean(),
getRuleActionRunLogDao(),
ruleActionContainer.getRuleAction().getRuleSetRule());
RuleActionBean rab =
ap.execute(
RuleRunnerMode.DATA_ENTRY,
executionMode,
ruleActionContainer.getRuleAction(),
ruleActionContainer.getItemDataBean(),
DiscrepancyNoteBean.ITEM_DATA,
currentStudy,
ub,
prepareEmailContents(
ruleActionContainer.getRuleSetBean(),
ruleActionContainer.getRuleAction().getRuleSetRule(),
currentStudy,
ruleActionContainer.getRuleAction()));
if (rab != null) {
messageContainer.add(
getExpressionService()
.getGroupOrdninalConcatWithItemOid(
ruleActionContainer.getRuleSetBean().getTarget().getValue()),
ruleActionContainer.getRuleAction());
}
logger.info(
"END Expression is : {} , RuleAction : {} , ExecutionMode : {} ",
new Object[] {
ruleActionContainer.getExpressionBean().getValue(),
ruleActionContainer.getRuleAction().toString(),
executionMode
});
}
}
return messageContainer;
}
/**
* Re-do calculations if funcs include changed item(s) and funcs are not included in the current
* section. If calculation can not sucessfully redo, old value will be erased and "<erased>" will
* be saved in database. <br>
* The parameter 'itemdata' might be overwritten.
*
* @param itemGroupSizes
* @param items
* @param itemdata
* @param oldItemdata
* @param updatedData
* @param sectionId
* @return ArrayList<String> which records left_item_text of items who failed to be updated into
* database.
*/
public ArrayList<String> redoCalculations(
HashMap<String, ItemBean> items,
HashMap<String, String> itemdata,
TreeSet<String> changedItems,
HashMap<Integer, TreeSet<Integer>> itemOrdinals,
int sectionId) {
ArrayList<String> updateFailedItems = new ArrayList<String>();
if (itemdata == null) {
logger.error("In ScoreCalculator redoCalculations(), itemdata is empty!");
errors.add("In ScoreCalculator redoCalculations(), 'itemdata' map is empty!");
return updateFailedItems;
}
if (changedItems == null) {
logger.error("In ScoreCalculator redoCalculations(), 'changeItems' set is empty!");
errors.add("In ScoreCalculator redoCalculations(), 'changeItems' set is empty!");
return updateFailedItems;
}
ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
ItemDAO idao = new ItemDAO(sm.getDataSource());
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
NumberFormat nf = NumberFormat.getInstance();
Parser parser = new Parser(items, itemdata);
try {
// for calculation type
List<ItemFormMetadataBean> derivedItemList =
ifmdao.findAllByCRFVersionIdAndResponseTypeId(
ecb.getCRFVersionId(), ResponseType.CALCULATION.getId());
if (derivedItemList.size() > 0) {
Collections.sort(derivedItemList);
for (ItemFormMetadataBean ifmb : derivedItemList) {
if (ifmb.getSectionId() != sectionId) {
ItemBean ib = (ItemBean) idao.findByPK(ifmb.getItemId());
ResponseOptionBean rob = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0);
int groupsize = 1;
if (itemOrdinals.containsKey(ib.getId())) {
groupsize = itemOrdinals.get(ib.getId()).size();
}
String value = "";
ArrayList<ScoreToken> parsedExp = new ArrayList<ScoreToken>();
for (int i = 0; i < groupsize; ++i) {
ItemDataBean idb =
iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb.getItemId(), ecb.getId(), i + 1);
// is there any changed item
Parser p = new Parser(items, itemdata);
parsedExp = parser.parseScoreTokens(rob.getValue());
if (p.isChanged(changedItems, parsedExp)) {
StringBuffer err = new StringBuffer();
parsedExp = parser.assignVariables(parsedExp, i + 1);
// if parser has error and has been calculated
// before, set "<erased>"
if (parser.getErrors().length() > 0) {
err.append(parser.getErrors());
if (idb.isActive()) {
idb.setValue("<erased>");
idb.setStatus(Status.UNAVAILABLE);
idb = (ItemDataBean) iddao.update(idb);
if (!idb.isActive()) {
String key =
i + 1 > 1
? ifmb.getLeftItemText() + "_" + (i + 1)
: ifmb.getLeftItemText();
updateFailedItems.add(key);
}
}
parser.setErrors(new StringBuffer());
}
// otherwise do calculation
else {
try {
value = ScoreUtil.eval(parsedExp);
} catch (ScoreException se) {
logger.error(se.getMessage());
}
String exp = rob.getValue();
exp = exp.replace("##", ",");
if (writeToDB(ib, ifmb, idb, exp, value, err)) {
changedItems.add(ib.getName());
itemdata.put(ib.getId() + "_" + (i + 1), idb.getValue());
} else {
String key =
i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
updateFailedItems.add(key);
}
}
if (err.length() > 0) {
String key =
i + 1 > 1 ? ifmb.getLeftItemText() + "_" + (i + 1) : ifmb.getLeftItemText();
errors.add("Item " + key + " contains calculation errors: " + err.toString());
}
}
}
}
}
}
List<ItemFormMetadataBean> itemList =
ifmdao.findAllByCRFVersionIdAndResponseTypeId(
ecb.getCRFVersionId(), ResponseType.GROUP_CALCULATION.getId());
if (itemList.size() > 0) {
Collections.sort(itemList);
for (ItemFormMetadataBean ifmb : itemList) {
if (ifmb.getSectionId() != sectionId) {
ItemBean ib = (ItemBean) idao.findByPK(ifmb.getItemId());
ResponseOptionBean rob = (ResponseOptionBean) ifmb.getResponseSet().getOptions().get(0);
String value = "";
Parser p = new Parser(items, itemdata);
ArrayList<ScoreToken> parsedExp = parser.parseScoreTokens(rob.getValue());
if (p.isChanged(changedItems, parsedExp)) {
StringBuffer err = new StringBuffer();
parser.setErrors(err);
parsedExp = parser.assignVariables(parsedExp, itemOrdinals);
ItemDataBean idb =
iddao.findByItemIdAndEventCRFIdAndOrdinal(ifmb.getItemId(), ecb.getId(), 1);
if (parser.getErrors().length() > 0) {
err.append(parser.getErrors());
if (idb.isActive()) {
idb.setValue("<erased>");
idb.setStatus(Status.UNAVAILABLE);
idb = (ItemDataBean) iddao.update(idb);
if (!idb.isActive()) {
updateFailedItems.add(ifmb.getLeftItemText());
}
}
} else {
try {
value = ScoreUtil.eval(parsedExp);
} catch (ScoreException se) {
logger.error(se.getMessage());
}
String exp = rob.getValue();
exp = exp.replace("##", ",");
if (writeToDB(ib, ifmb, idb, exp, value, err)) {
changedItems.add(ib.getName());
itemdata.put(ib.getId() + "_" + idb.getOrdinal(), idb.getValue());
} else {
updateFailedItems.add(ifmb.getLeftItemText());
}
}
if (err.length() > 0) {
errors.add(
"Item "
+ ifmb.getLeftItemText()
+ " contains calculation errors: "
+ err.toString());
}
}
}
}
}
} catch (OpenClinicaException e) {
logger.error(e.getMessage());
}
return updateFailedItems;
}
protected boolean writeToDB(
ItemBean ib,
ItemFormMetadataBean ifm,
ItemDataBean idb,
String exp,
String value,
StringBuffer err) {
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
NumberFormat nf = NumberFormat.getInstance();
if (idb == null) {
idb = new ItemDataBean();
}
ItemDataType idt = ib.getDataType();
if (value == null || value.length() == 0) {
if (idb.isActive() && !"".equals(idb.getValue())) {
idb.setValue("<erased>");
} else {
idb.setValue("");
}
err.append("Result is empty in" + " " + exp + "; ");
} else {
idb.setValue(this.getMathContextValue(value, ifm, idt, err));
}
idb.setStatus(Status.UNAVAILABLE);
// idb.setNeedsRecalc(false);
if (!idb.isActive()) {
// will this need to change for double data entry?
idb.setCreatedDate(new Date());
idb.setOwner(ub);
idb.setItemId(ib.getId());
idb.setEventCRFId(ecb.getId());
idb = (ItemDataBean) iddao.create(idb);
} else {
idb = (ItemDataBean) iddao.update(idb);
}
return idb.isActive();
}
@Override
protected DisplayItemBean validateDisplayItemBean(
DiscrepancyValidator v, DisplayItemBean dib, String inputName) {
org.akaza.openclinica.bean.core.ResponseType rt =
dib.getMetadata().getResponseSet().getResponseType();
boolean isSingleItem = false;
if (StringUtil.isBlank(inputName)) { // for single items
inputName = getInputName(dib);
isSingleItem = true;
}
// we only give warning to user if data entered in DDE is different from
// IDE when the first
// time user hits 'save'
int keyId = ecb.getId();
Integer validationCount = (Integer) session.getAttribute(COUNT_VALIDATE + keyId);
ItemDataBean valueToCompare = dib.getData();
if (!isSingleItem) {
valueToCompare = dib.getDbData();
}
boolean showOriginalItem =
getItemMetadataService()
.isShown(dib.getItem().getId(), ecb, valueToCompare); // was dib.getData()
boolean showItem = dib.getMetadata().isShowItem();
boolean showDuplicateItem =
getItemMetadataService()
.hasPassedDDE(
dib.getMetadata(),
ecb,
valueToCompare); // .isShown(dib.getItem().getId(), ecb, dib.getDbData());// where
// is the set db data?
logger.debug(
"*** show original item has value "
+ dib.getData().getValue()
+ " and show item has value "
+ valueToCompare.getValue());
logger.debug(
"--- show original: "
+ showOriginalItem
+ " show duplicate: "
+ showDuplicateItem
+ " and just show item: "
+ showItem);
logger.debug("VALIDATION COUNT " + validationCount);
if (showOriginalItem && showDuplicateItem || showItem) {
// it should either be shown already, OR shown in the database?
// logger.debug("=== we passed, adding validation here");
Integer indValidationCount =
(Integer) session.getAttribute(COUNT_VALIDATE + keyId + dib.getMetadata().getId());
if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.TEXT)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.TEXTAREA)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.FILE)) {
dib = validateDisplayItemBeanText(v, dib, inputName);
// necessary?
// if (indValidationCount == null || validationCount == null || validationCount.intValue()
// == 0) {
logger.debug("=== we passed, adding validation here TEXT " + valueToCompare.getId());
v.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, false);
v.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ valueToCompare.getValue()
+ " "
+ respage.getString("from_initial_data_entry"));
// session.setAttribute(COUNT_VALIDATE + keyId + dib.getMetadata().getId(), new Integer(1));
// }
} else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.RADIO)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECT)) {
dib = validateDisplayItemBeanSingleCV(v, dib, inputName);
// ItemFormMetadataBean ifmdb = dib.getMetadata();
// ResponseSetBean rsBean = ifmdb.getResponseSet();
// logger.info("### found a response set count of "+inputName+"
// "+rsBean.getOptions().size());
// TODO sees it at this end tbh 1878
// if (indValidationCount == null || validationCount == null || validationCount.intValue()
// == 0) {
logger.debug("=== we passed, adding validation here RADIO " + valueToCompare.getId());
v.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, false);
String errorValue = valueToCompare.getValue();
java.util.ArrayList options = dib.getMetadata().getResponseSet().getOptions();
for (int u = 0; u < options.size(); u++) {
ResponseOptionBean rob = (ResponseOptionBean) options.get(u);
if (rob.getValue().equals(errorValue)) {
errorValue = rob.getText();
}
}
v.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ errorValue
+ " "
+ respage.getString("from_initial_data_entry"));
// session.setAttribute(COUNT_VALIDATE + keyId + dib.getMetadata().getId(), new Integer(1));
// }
} else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.CHECKBOX)
|| rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECTMULTI)) {
dib = validateDisplayItemBeanMultipleCV(v, dib, inputName);
// if (indValidationCount == null || validationCount == null || validationCount.intValue()
// == 0) {
logger.debug("=== we passed, adding validation here CHECKBOX " + valueToCompare.getId());
v.addValidation(
inputName, Validator.MATCHES_INITIAL_DATA_ENTRY_VALUE, valueToCompare, true);
// repeated from above, tbh 112007
String errorValue = valueToCompare.getValue();
String errorTexts = "";
java.util.ArrayList options = dib.getMetadata().getResponseSet().getOptions();
for (int u = 0; u < options.size(); u++) {
ResponseOptionBean rob = (ResponseOptionBean) options.get(u);
if (errorValue.contains(rob.getValue())) {
errorTexts = errorTexts + rob.getText();
if (u < options.size() - 1) {
// the values for multi-select are seperated by
// comma
errorTexts = errorTexts + ", ";
}
}
}
v.setErrorMessage(
respage.getString("value_you_specified")
+ " "
+ errorTexts
+ " "
+ respage.getString("from_initial_data_entry"));
// session.setAttribute(COUNT_VALIDATE + keyId + dib.getMetadata().getId(), new Integer(1));
// }
}
}
// only load form value when an item is not in a group,
// if in group, the value is already loaded
// see formGroups = loadFormValueForItemGroup(digb,digbs,formGroups);
if (isSingleItem) {
dib = loadFormValue(dib);
}
return dib;
}
public void processRequest() throws Exception {
StudyDAO sdao = new StudyDAO(sm.getDataSource());
FormProcessor fp = new FormProcessor(request);
int studyId = fp.getInt("id");
StudyBean study = (StudyBean) sdao.findByPK(studyId);
// find all sites
ArrayList sites = (ArrayList) sdao.findAllByParent(studyId);
// find all user and roles in the study, include ones in sites
UserAccountDAO udao = new UserAccountDAO(sm.getDataSource());
ArrayList userRoles = udao.findAllByStudyId(studyId);
// find all subjects in the study, include ones in sites
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
ArrayList subjects = ssdao.findAllByStudy(study);
// find all events in the study, include ones in sites
StudyEventDefinitionDAO sefdao = new StudyEventDefinitionDAO(sm.getDataSource());
ArrayList definitions = sefdao.findAllByStudy(study);
String action = request.getParameter("action");
if (studyId == 0) {
addPageMessage("Please choose a study to restore.");
forwardPage(Page.STUDY_LIST_SERVLET);
} else {
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("studyToRestore", study);
request.setAttribute("sitesToRestore", sites);
request.setAttribute("userRolesToRestore", userRoles);
request.setAttribute("subjectsToRestore", subjects);
request.setAttribute("definitionsToRRestore", definitions);
forwardPage(Page.RESTORE_STUDY);
} else {
logger.info("submit to restore the study");
// change all statuses to unavailable
StudyDAO studao = new StudyDAO(sm.getDataSource());
study.setStatus(Status.AVAILABLE);
study.setUpdater(ub);
study.setUpdatedDate(new Date());
studao.update(study);
// remove all sites
for (int i = 0; i < sites.size(); i++) {
StudyBean site = (StudyBean) sites.get(i);
site.setStatus(Status.AVAILABLE);
site.setUpdater(ub);
site.setUpdatedDate(new Date());
sdao.update(site);
}
// remove all users and roles
for (int i = 0; i < userRoles.size(); i++) {
StudyUserRoleBean role = (StudyUserRoleBean) userRoles.get(i);
role.setStatus(Status.AVAILABLE);
role.setUpdater(ub);
role.setUpdatedDate(new Date());
udao.updateStudyUserRole(role, role.getUserName());
}
// remove all subjects
for (int i = 0; i < subjects.size(); i++) {
StudySubjectBean subject = (StudySubjectBean) subjects.get(i);
subject.setStatus(Status.AVAILABLE);
subject.setUpdater(ub);
subject.setUpdatedDate(new Date());
ssdao.update(subject);
}
// remove all study_group
StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
SubjectGroupMapDAO sgmdao = new SubjectGroupMapDAO(sm.getDataSource());
ArrayList groups = sgdao.findAllByStudy(study);
for (int i = 0; i < groups.size(); i++) {
StudyGroupBean group = (StudyGroupBean) groups.get(i);
group.setStatus(Status.AVAILABLE);
group.setUpdater(ub);
group.setUpdatedDate(new Date());
sgdao.update(group);
// all subject_group_map
ArrayList subjectGroupMaps = sgmdao.findAllByStudyGroupId(group.getId());
for (int j = 0; j < subjectGroupMaps.size(); j++) {
SubjectGroupMapBean sgMap = (SubjectGroupMapBean) subjectGroupMaps.get(j);
sgMap.setStatus(Status.AVAILABLE);
sgMap.setUpdater(ub);
sgMap.setUpdatedDate(new Date());
sgmdao.update(sgMap);
}
}
// remove all event definitions and event
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
for (int i = 0; i < definitions.size(); i++) {
StudyEventDefinitionBean definition = (StudyEventDefinitionBean) definitions.get(i);
definition.setStatus(Status.AVAILABLE);
definition.setUpdater(ub);
definition.setUpdatedDate(new Date());
sefdao.update(definition);
ArrayList edcs = (ArrayList) edcdao.findAllByDefinition(definition.getId());
for (int j = 0; j < edcs.size(); j++) {
EventDefinitionCRFBean edc = (EventDefinitionCRFBean) edcs.get(j);
edc.setStatus(Status.AVAILABLE);
edc.setUpdater(ub);
edc.setUpdatedDate(new Date());
edcdao.update(edc);
}
ArrayList events = (ArrayList) sedao.findAllByDefinition(definition.getId());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
for (int j = 0; j < events.size(); j++) {
StudyEventBean event = (StudyEventBean) events.get(j);
event.setStatus(Status.AVAILABLE);
event.setUpdater(ub);
event.setUpdatedDate(new Date());
sedao.update(event);
ArrayList eventCRFs = ecdao.findAllByStudyEvent(event);
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
for (int k = 0; k < eventCRFs.size(); k++) {
EventCRFBean eventCRF = (EventCRFBean) eventCRFs.get(k);
eventCRF.setStatus(Status.AVAILABLE);
eventCRF.setUpdater(ub);
eventCRF.setUpdatedDate(new Date());
ecdao.update(eventCRF);
ArrayList itemDatas = iddao.findAllByEventCRFId(eventCRF.getId());
for (int a = 0; a < itemDatas.size(); a++) {
ItemDataBean item = (ItemDataBean) itemDatas.get(a);
item.setStatus(Status.AVAILABLE);
item.setUpdater(ub);
item.setUpdatedDate(new Date());
iddao.update(item);
}
}
}
} // for definitions
DatasetDAO datadao = new DatasetDAO(sm.getDataSource());
ArrayList dataset = datadao.findAllByStudyId(study.getId());
for (int i = 0; i < dataset.size(); i++) {
DatasetBean data = (DatasetBean) dataset.get(i);
data.setStatus(Status.AVAILABLE);
data.setUpdater(ub);
data.setUpdatedDate(new Date());
datadao.update(data);
}
addPageMessage("This study has been restored successfully.");
forwardPage(Page.STUDY_LIST_SERVLET);
}
}
}
public boolean prepareRequestForResolution(
HttpServletRequest request,
DataSource ds,
StudyBean currentStudy,
DiscrepancyNoteBean note,
boolean isCompleted) {
String entityType = note.getEntityType().toLowerCase();
int id = note.getEntityId();
if ("subject".equalsIgnoreCase(entityType)) {
StudySubjectDAO ssdao = new StudySubjectDAO(ds);
StudySubjectBean ssb = ssdao.findBySubjectIdAndStudy(id, currentStudy);
request.setAttribute("action", "show");
request.setAttribute("id", String.valueOf(note.getEntityId()));
request.setAttribute("studySubId", String.valueOf(ssb.getId()));
} else if ("studysub".equalsIgnoreCase(entityType)) {
request.setAttribute("action", "show");
request.setAttribute("id", String.valueOf(note.getEntityId()));
} else if ("eventcrf".equalsIgnoreCase(entityType)) {
request.setAttribute("editInterview", "1");
EventCRFDAO ecdao = new EventCRFDAO(ds);
EventCRFBean ecb = (EventCRFBean) ecdao.findByPK(id);
request.setAttribute(TableOfContentsServlet.INPUT_EVENT_CRF_BEAN, ecb);
// If the request is passed along to ViewSectionDataEntryServlet,
// that code needs
// an event crf id; the (ecb.getId()+"") is necessary because
// FormProcessor throws
// a ClassCastException without the casting to a String
request.setAttribute(ViewSectionDataEntryServlet.EVENT_CRF_ID, ecb.getId() + "");
} else if ("studyevent".equalsIgnoreCase(entityType)) {
StudyEventDAO sedao = new StudyEventDAO(ds);
StudyEventBean seb = (StudyEventBean) sedao.findByPK(id);
request.setAttribute(EnterDataForStudyEventServlet.INPUT_EVENT_ID, String.valueOf(id));
request.setAttribute(UpdateStudyEventServlet.EVENT_ID, String.valueOf(id));
request.setAttribute(
UpdateStudyEventServlet.STUDY_SUBJECT_ID, String.valueOf(seb.getStudySubjectId()));
}
// this is for item data
else if ("itemdata".equalsIgnoreCase(entityType)) {
ItemDataDAO iddao = new ItemDataDAO(ds);
ItemDataBean idb = (ItemDataBean) iddao.findByPK(id);
EventCRFDAO ecdao = new EventCRFDAO(ds);
EventCRFBean ecb = (EventCRFBean) ecdao.findByPK(idb.getEventCRFId());
StudySubjectDAO ssdao = new StudySubjectDAO(sm.getDataSource());
StudySubjectBean ssb = (StudySubjectBean) ssdao.findByPK(ecb.getStudySubjectId());
ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(ds);
ItemFormMetadataBean ifmb =
ifmdao.findByItemIdAndCRFVersionId(idb.getItemId(), ecb.getCRFVersionId());
if (currentRole.getRole().equals(Role.MONITOR) || !isCompleted) {
StudyEventDAO sedao = new StudyEventDAO(ds);
StudyEventBean seb = (StudyEventBean) sedao.findByPK(id);
request.setAttribute(EVENT_CRF_ID, String.valueOf(idb.getEventCRFId()));
request.setAttribute(STUDY_SUB_ID, String.valueOf(seb.getStudySubjectId()));
} else {
request.setAttribute(
DataEntryServlet.INPUT_EVENT_CRF_ID, String.valueOf(idb.getEventCRFId()));
request.setAttribute(
DataEntryServlet.INPUT_SECTION_ID, String.valueOf(ifmb.getSectionId()));
}
DataEntryStage stage = ecb.getStage();
// if (!stage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE)) {
// return false;
// }
}
return true;
}