Example 16 with OpenClinicaException
use of org.akaza.openclinica.exception.OpenClinicaException in project OpenClinica by OpenClinica.
the class CreateNewStudyEventServlet method processRequest.
@Override
protected void processRequest() throws Exception {
checkStudyLocked(Page.LIST_STUDY_SUBJECTS, respage.getString("current_study_locked"));
panel.setStudyInfoShown(false);
fp = new FormProcessor(request);
FormDiscrepancyNotes discNotes = null;
int studySubjectId = fp.getInt(INPUT_STUDY_SUBJECT_ID_FROM_VIEWSUBJECT);
// input from manage subject matrix, user has specified definition id
int studyEventDefinitionId = fp.getInt(INPUT_STUDY_EVENT_DEFINITION);
// TODO: make this sensitive to permissions
StudySubjectDAO sdao = new StudySubjectDAO(sm.getDataSource());
StudySubjectBean ssb;
if (studySubjectId <= 0) {
ssb = (StudySubjectBean) request.getAttribute(INPUT_STUDY_SUBJECT);
} else {
// YW 11-08-2007, << a new study event could not be added if its
// study subject has been removed
ssb = (StudySubjectBean) sdao.findByPK(studySubjectId);
Status s = ssb.getStatus();
if ("removed".equalsIgnoreCase(s.getName()) || "auto-removed".equalsIgnoreCase(s.getName())) {
addPageMessage(resword.getString("study_event") + resterm.getString("could_not_be") + resterm.getString("added") + "." + respage.getString("study_subject_has_been_deleted"));
request.setAttribute("id", new Integer(studySubjectId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
}
// YW >>
request.setAttribute(INPUT_REQUEST_STUDY_SUBJECT, "no");
}
// running this crashes the server, or so we think...instead, let's grab a count
// or remove it altogether tbh 10/2009
// ArrayList subjects = sdao.findAllActiveByStudyOrderByLabel(currentStudy);
// TODO: make this sensitive to permissions
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyBean studyWithEventDefinitions = currentStudy;
if (currentStudy.getParentStudyId() > 0) {
studyWithEventDefinitions = new StudyBean();
studyWithEventDefinitions.setId(currentStudy.getParentStudyId());
}
// find all active definitions with CRFs
ArrayList eventDefinitions = seddao.findAllActiveByStudy(studyWithEventDefinitions);
// EventDefinitionCRFDAO edcdao = new
// EventDefinitionCRFDAO(sm.getDataSource());
// ArrayList definitionsWithCRF = new ArrayList();
// for (int i=0; i<eventDefinitions.size(); i++) {
// StudyEventDefinitionBean sed =
// (StudyEventDefinitionBean)eventDefinitions.get(i);
// logger.info("StudyEventDefinition name[" + sed.getName() + "]");
// ArrayList edcs = edcdao.findAllByEventDefinitionId(sed.getId());
// if (!edcs.isEmpty()) {
// definitionsWithCRF.add(sed);
// }
// }
// Collections.sort(definitionsWithCRF);
Collections.sort(eventDefinitions);
/*
* ArrayList eventDefinitionsScheduled = new ArrayList(); for (int i =
* 0; i < eventDefinitions.size(); i++) { StudyEventDefinitionBean sed =
* (StudyEventDefinitionBean) eventDefinitions.get(i); if
* (sed.getType().equalsIgnoreCase("scheduled")) {
* eventDefinitionsScheduled.add(sed); } }
*/
// all definitions will appear in scheduled event creation box-11/26/05
ArrayList eventDefinitionsScheduled = eventDefinitions;
if (!fp.isSubmitted()) {
// StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
// sed.updateSampleOrdinals_v092();
HashMap presetValues = new HashMap();
// YW 08-16-2007 << set default as blank for time
presetValues.put(INPUT_STARTDATE_PREFIX + "Hour", new Integer(-1));
presetValues.put(INPUT_STARTDATE_PREFIX + "Minute", new Integer(-1));
presetValues.put(INPUT_STARTDATE_PREFIX + "Half", new String(""));
presetValues.put(INPUT_ENDDATE_PREFIX + "Hour", new Integer(-1));
presetValues.put(INPUT_ENDDATE_PREFIX + "Minute", new Integer(-1));
presetValues.put(INPUT_ENDDATE_PREFIX + "Half", new String(""));
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Hour", new Integer(-1));
presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Minute", new Integer(-1));
presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Half", new String(""));
presetValues.put(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Hour", new Integer(-1));
presetValues.put(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Minute", new Integer(-1));
presetValues.put(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Half", new String(""));
}
// SimpleDateFormat sdf = new SimpleDateFormat("MM/dd/yyyy");
// example of taking the above line and transferring to i18n on the
// below line, tbh
String dateValue = local_df.format(new Date(System.currentTimeMillis()));
presetValues.put(INPUT_STARTDATE_PREFIX + "Date", dateValue);
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
presetValues.put(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Date", dateValue);
// location
presetValues.put(INPUT_SCHEDULED_LOCATION[i], currentStudy.getFacilityCity());
presetValues.put(this.DISPLAY_SCHEDULED[i], "none");
}
// defualt
presetValues.put(INPUT_LOCATION, currentStudy.getFacilityCity());
if (ssb != null && ssb.isActive()) {
presetValues.put(INPUT_STUDY_SUBJECT, ssb);
String requestStudySubject = (String) request.getAttribute(INPUT_REQUEST_STUDY_SUBJECT);
if (requestStudySubject != null) {
presetValues.put(INPUT_REQUEST_STUDY_SUBJECT, requestStudySubject);
dateValue = local_df.format(new Date());
presetValues.put(INPUT_STARTDATE_PREFIX + "Date", dateValue);
}
}
if (studyEventDefinitionId > 0) {
StudyEventDefinitionBean sed = (StudyEventDefinitionBean) seddao.findByPK(studyEventDefinitionId);
presetValues.put(INPUT_STUDY_EVENT_DEFINITION, sed);
}
// tbh
logger.debug("set preset values: " + presetValues.toString());
logger.debug("found def.w.CRF list, size " + eventDefinitions.size());
// tbh
setPresetValues(presetValues);
ArrayList subjects = new ArrayList();
setupBeans(subjects, eventDefinitions);
discNotes = new FormDiscrepancyNotes();
session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
request.setAttribute("eventDefinitionsScheduled", eventDefinitionsScheduled);
setInputMessages(new HashMap());
forwardPage(Page.CREATE_NEW_STUDY_EVENT);
} else {
// tbh
// String dateCheck = (String)request.getAttribute("startDate");
// String endCheck = (String)request.getAttribute("endDate");
// logger.debug(dateCheck+"; "+endCheck);
String dateCheck2 = request.getParameter("startDate");
String endCheck2 = request.getParameter("endDate");
logger.debug(dateCheck2 + "; " + endCheck2);
// YW, 3-12-2008, 2220 fix <<
String strEnd = fp.getDateTimeInputString(INPUT_ENDDATE_PREFIX);
String[] strEndScheduled = new String[ADDITIONAL_SCHEDULED_NUM];
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
strEndScheduled[i] = fp.getDateTimeInputString(INPUT_ENDDATE_PREFIX_SCHEDULED[i]);
}
Date start = getInputStartDate();
Date end = null;
Date[] startScheduled = new Date[ADDITIONAL_SCHEDULED_NUM];
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
startScheduled[i] = getInputStartDateScheduled(i);
}
Date[] endScheduled = new Date[ADDITIONAL_SCHEDULED_NUM];
// YW >>
// for (java.util.Enumeration enu = request.getAttributeNames();
// enu.hasMoreElements() ;) {
// logger.debug(">>> found "+enu.nextElement().toString());
// }
// tbh
discNotes = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
if (discNotes == null) {
discNotes = new FormDiscrepancyNotes();
session.setAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME, discNotes);
}
DiscrepancyValidator v = new DiscrepancyValidator(request, discNotes);
v.addValidation(INPUT_STARTDATE_PREFIX, Validator.IS_DATE_TIME);
v.alwaysExecuteLastValidation(INPUT_STARTDATE_PREFIX);
if (!strEnd.equals("")) {
v.addValidation(INPUT_ENDDATE_PREFIX, Validator.IS_DATE_TIME);
v.alwaysExecuteLastValidation(INPUT_ENDDATE_PREFIX);
}
v.addValidation(INPUT_STUDY_EVENT_DEFINITION, Validator.ENTITY_EXISTS_IN_STUDY, seddao, studyWithEventDefinitions);
// v.addValidation(INPUT_STUDY_SUBJECT, Validator.ENTITY_EXISTS_IN_STUDY, sdao, currentStudy);
// removed tbh 11/2009
//Made optional field-issue-4904.
//v.addValidation(INPUT_LOCATION, Validator.NO_BLANKS);
v.addValidation(INPUT_STUDY_SUBJECT_LABEL, Validator.NO_BLANKS);
v.addValidation(INPUT_LOCATION, Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 2000);
if (currentStudy.getStudyParameterConfig().getEventLocationRequired().equalsIgnoreCase("required")) {
v.addValidation(INPUT_LOCATION, Validator.NO_BLANKS);
}
v.alwaysExecuteLastValidation(INPUT_LOCATION);
boolean hasScheduledEvent = false;
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
if (!StringUtil.isBlank(fp.getString(this.INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i]))) {
// logger.debug("has scheduled definition******");
v.addValidation(this.INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i], Validator.ENTITY_EXISTS_IN_STUDY, seddao, studyWithEventDefinitions);
if (currentStudy.getStudyParameterConfig().getEventLocationRequired().equalsIgnoreCase("required")) {
v.addValidation(INPUT_SCHEDULED_LOCATION[i], Validator.NO_BLANKS);
v.addValidation(INPUT_SCHEDULED_LOCATION[i], Validator.LENGTH_NUMERIC_COMPARISON, NumericComparisonOperator.LESS_THAN_OR_EQUAL_TO, 2000);
v.alwaysExecuteLastValidation(INPUT_SCHEDULED_LOCATION[i]);
}
v.addValidation(INPUT_STARTDATE_PREFIX_SCHEDULED[i], Validator.IS_DATE_TIME);
v.alwaysExecuteLastValidation(INPUT_STARTDATE_PREFIX_SCHEDULED[i]);
if (!strEndScheduled[i].equals("")) {
v.addValidation(INPUT_ENDDATE_PREFIX_SCHEDULED[i], Validator.IS_DATE_TIME);
v.alwaysExecuteLastValidation(INPUT_ENDDATE_PREFIX_SCHEDULED[i]);
}
hasScheduledEvent = true;
fp.addPresetValue(DISPLAY_SCHEDULED[i], "all");
} else {
fp.addPresetValue(DISPLAY_SCHEDULED[i], "none");
}
}
HashMap errors = v.validate();
// logger.debug("v is not null *****");
String location = resword.getString("location");
// is a required field
if (!StringUtil.isBlank(fp.getString(INPUT_LOCATION)) && fp.getString(INPUT_LOCATION).equalsIgnoreCase(location)) {
Validator.addError(errors, INPUT_LOCATION, restext.getString("not_a_valid_location"));
}
StudyEventDefinitionBean definition = (StudyEventDefinitionBean) seddao.findByPK(fp.getInt(INPUT_STUDY_EVENT_DEFINITION));
// StudySubjectBean studySubject = (StudySubjectBean) sdao.findByPK(fp.getInt(INPUT_STUDY_SUBJECT));
// sdao.findByLabelAndStudy(label, study)
StudySubjectBean studySubject = sdao.findByLabelAndStudy(fp.getString(INPUT_STUDY_SUBJECT_LABEL), currentStudy);
// what if we are sent here from AddNewSubjectServlet.java??? we need to get that study subject bean
if (request.getAttribute(INPUT_STUDY_SUBJECT) != null) {
studySubject = (StudySubjectBean) request.getAttribute(INPUT_STUDY_SUBJECT);
}
// << tbh
if (studySubject.getLabel() == "") {
// add an error here, tbh
Validator.addError(errors, INPUT_STUDY_SUBJECT, respage.getString("must_enter_subject_ID_for_identifying"));
}
if (!subjectMayReceiveStudyEvent(sm.getDataSource(), definition, studySubject)) {
Validator.addError(errors, INPUT_STUDY_EVENT_DEFINITION, restext.getString("not_added_since_event_not_repeating"));
}
ArrayList<StudyEventDefinitionBean> definitionScheduleds = new ArrayList<StudyEventDefinitionBean>();
int[] scheduledDefinitionIds = new int[ADDITIONAL_SCHEDULED_NUM];
if (hasScheduledEvent) {
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
int pk = fp.getInt(INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i]);
if (pk > 0) {
StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(pk);
logger.debug("scheduled def:" + pk + " " + INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i] + " " + sedb.getName());
definitionScheduleds.add(sedb);
scheduledDefinitionIds[i] = pk;
if (!subjectMayReceiveStudyEvent(sm.getDataSource(), sedb, studySubject)) {
Validator.addError(errors, INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i], restext.getString("not_added_since_event_not_repeating"));
}
} else {
definitionScheduleds.add(new StudyEventDefinitionBean());
}
}
}
// YW, 3-12-2008, 2220 fix >>
if (!"".equals(strEnd) && !errors.containsKey(INPUT_STARTDATE_PREFIX) && !errors.containsKey(INPUT_ENDDATE_PREFIX)) {
end = getInputEndDate();
if (!fp.getString(INPUT_STARTDATE_PREFIX + "Date").equals(fp.getString(INPUT_ENDDATE_PREFIX + "Date"))) {
if (end.before(start)) {
Validator.addError(errors, INPUT_ENDDATE_PREFIX, resexception.getString("input_provided_not_occure_after_previous_start_date_time"));
}
} else {
// if in same date, only check when both had time entered
if (fp.timeEntered(INPUT_STARTDATE_PREFIX) && fp.timeEntered(INPUT_ENDDATE_PREFIX)) {
if (end.before(start) || end.equals(start)) {
Validator.addError(errors, INPUT_ENDDATE_PREFIX, resexception.getString("input_provided_not_occure_after_previous_start_date_time"));
}
}
}
}
String prevStartPrefix = INPUT_STARTDATE_PREFIX;
Set<Integer> pickedSeds = new TreeSet<Integer>();
pickedSeds.add(studyEventDefinitionId);
HashMap<Integer, Integer> scheduledSeds = new HashMap<Integer, Integer>();
scheduledSeds.put(studyEventDefinitionId, -1);
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
if (scheduledDefinitionIds[i] > 0 && !errors.containsKey(INPUT_STARTDATE_PREFIX_SCHEDULED[i]) && !errors.containsKey(INPUT_ENDDATE_PREFIX_SCHEDULED[i])) {
if (scheduledSeds.containsKey(scheduledDefinitionIds[i])) {
int prevStart = scheduledSeds.get(scheduledDefinitionIds[i]);
prevStartPrefix = prevStart == -1 ? INPUT_STARTDATE_PREFIX : INPUT_STARTDATE_PREFIX_SCHEDULED[prevStart];
Date prevStartDate = prevStart == -1 ? this.getInputStartDate() : this.getInputStartDateScheduled(Integer.parseInt(prevStartPrefix.charAt(prevStartPrefix.length() - 1) + ""));
if (fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Date").equals(fp.getString(prevStartPrefix + "Date"))) {
// if in same day, only check when both have time
// inputs.
boolean schStartTime = fp.timeEntered(INPUT_STARTDATE_PREFIX_SCHEDULED[i]);
boolean startTime = fp.timeEntered(prevStartPrefix);
if (schStartTime && startTime) {
if (startScheduled[i].before(prevStartDate)) {
Validator.addError(errors, INPUT_STARTDATE_PREFIX_SCHEDULED[i], resexception.getString("input_provided_not_occure_after_previous_start_date_time"));
}
}
} else {
if (startScheduled[i].before(prevStartDate)) {
Validator.addError(errors, INPUT_STARTDATE_PREFIX_SCHEDULED[i], resexception.getString("input_provided_not_occure_after_previous_start_date_time"));
}
}
}
scheduledSeds.put(scheduledDefinitionIds[i], i);
if (!strEndScheduled[i].equals("")) {
endScheduled[i] = fp.getDateTime(INPUT_ENDDATE_PREFIX_SCHEDULED[i]);
String prevEndPrefix = i > 0 ? INPUT_ENDDATE_PREFIX_SCHEDULED[i - 1] : INPUT_ENDDATE_PREFIX;
if (!fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Date").equals(fp.getString(prevEndPrefix + "Date"))) {
if (endScheduled[i].before(startScheduled[i])) {
Validator.addError(errors, INPUT_ENDDATE_PREFIX_SCHEDULED[i], resexception.getString("input_provided_not_occure_after_previous_start_date_time"));
}
} else {
// entered
if (fp.timeEntered(INPUT_STARTDATE_PREFIX_SCHEDULED[i]) && fp.timeEntered(INPUT_ENDDATE_PREFIX_SCHEDULED[i])) {
if (endScheduled[i].before(startScheduled[i]) || endScheduled[i].equals(startScheduled[i])) {
Validator.addError(errors, INPUT_ENDDATE_PREFIX_SCHEDULED[i], resexception.getString("input_provided_not_occure_after_previous_start_date_time"));
}
}
}
}
}
}
// YW >>
logger.error("we have errors; number of this; " + errors.size());
if (!errors.isEmpty()) {
logger.debug("we have errors; number of this; " + errors.size());
logger.error("found request study subject: " + fp.getString(INPUT_REQUEST_STUDY_SUBJECT));
addPageMessage(respage.getString("errors_in_submission_see_below"));
setInputMessages(errors);
fp.addPresetValue(INPUT_STUDY_EVENT_DEFINITION, definition);
fp.addPresetValue(INPUT_STUDY_SUBJECT, studySubject);
fp.addPresetValue(INPUT_STUDY_SUBJECT_LABEL, fp.getString(INPUT_STUDY_SUBJECT_LABEL));
fp.addPresetValue(INPUT_REQUEST_STUDY_SUBJECT, fp.getString(INPUT_REQUEST_STUDY_SUBJECT));
fp.addPresetValue(INPUT_LOCATION, fp.getString(INPUT_LOCATION));
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
fp.addPresetValue(INPUT_SCHEDULED_LOCATION[i], fp.getString(INPUT_SCHEDULED_LOCATION[i]));
}
String[] prefixes = new String[2 + 2 * ADDITIONAL_SCHEDULED_NUM];
prefixes[0] = INPUT_STARTDATE_PREFIX;
prefixes[1] = INPUT_ENDDATE_PREFIX;
int b = ADDITIONAL_SCHEDULED_NUM + 2;
for (int i = 2; i < b; ++i) {
prefixes[i] = INPUT_STARTDATE_PREFIX_SCHEDULED[i - 2];
}
for (int i = b; i < ADDITIONAL_SCHEDULED_NUM + b; ++i) {
prefixes[i] = INPUT_ENDDATE_PREFIX_SCHEDULED[i - b];
}
fp.setCurrentDateTimeValuesAsPreset(prefixes);
if (hasScheduledEvent) {
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
fp.addPresetValue(INPUT_STUDY_EVENT_DEFINITION_SCHEDULED[i], definitionScheduleds.get(i));
}
}
setPresetValues(fp.getPresetValues());
ArrayList subjects = new ArrayList();
setupBeans(subjects, eventDefinitions);
request.setAttribute("eventDefinitionsScheduled", eventDefinitionsScheduled);
forwardPage(Page.CREATE_NEW_STUDY_EVENT);
} else {
logger.debug("error is empty");
StudyEventDAO sed = new StudyEventDAO(sm.getDataSource());
StudyEventBean studyEvent = new StudyEventBean();
studyEvent.setStudyEventDefinitionId(definition.getId());
studyEvent.setStudySubjectId(studySubject.getId());
// YW 08-17-2007 <<
if ("-1".equals(getInputStartHour()) && "-1".equals(getInputStartMinute()) && "".equals(getInputStartHalf())) {
studyEvent.setStartTimeFlag(false);
} else {
studyEvent.setStartTimeFlag(true);
}
// YW >>
studyEvent.setDateStarted(start);
// comment to find bug 1389, tbh
logger.debug("found start date: " + local_df.format(start));
Date[] startScheduled2 = new Date[ADDITIONAL_SCHEDULED_NUM];
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
startScheduled2[i] = getInputStartDateScheduled(i);
}
// YW, 3-12-2008, 2220 fix <<
if (!"".equals(strEnd)) {
// YW >>
if ("-1".equals(getInputEndHour()) && "-1".equals(getInputEndMinute()) && "".equals(getInputEndHalf())) {
studyEvent.setEndTimeFlag(false);
} else {
studyEvent.setEndTimeFlag(true);
}
studyEvent.setDateEnded(end);
}
studyEvent.setOwner(ub);
studyEvent.setStatus(Status.AVAILABLE);
studyEvent.setLocation(fp.getString(INPUT_LOCATION));
studyEvent.setSubjectEventStatus(SubjectEventStatus.SCHEDULED);
// ArrayList subjectsExistingEvents =
// sed.findAllByStudyAndStudySubjectId(currentStudy,
// studySubject.getId());
studyEvent.setSampleOrdinal(sed.getMaxSampleOrdinal(definition, studySubject) + 1);
studyEvent = (StudyEventBean) sed.create(studyEvent);
if (!studyEvent.isActive()) {
throw new OpenClinicaException(restext.getString("event_not_created_in_database"), "2");
}
addPageMessage(restext.getString("X_event_wiht_definition") + definition.getName() + restext.getString("X_and_subject") + studySubject.getName() + respage.getString("X_was_created_succesfully"));
// save discrepancy notes into DB
FormDiscrepancyNotes fdn = (FormDiscrepancyNotes) session.getAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
DiscrepancyNoteDAO dndao = new DiscrepancyNoteDAO(sm.getDataSource());
String[] eventFields = { INPUT_LOCATION, INPUT_STARTDATE_PREFIX, INPUT_ENDDATE_PREFIX };
for (String element : eventFields) {
AddNewSubjectServlet.saveFieldNotes(element, fdn, dndao, studyEvent.getId(), "studyEvent", currentStudy);
}
// logger.debug("here ok 3333333333333333");
if (hasScheduledEvent) {
for (int i = 0; i < ADDITIONAL_SCHEDULED_NUM; ++i) {
// which is scheduledDefinitionIds[i] > 0
if (scheduledDefinitionIds[i] > 0) {
if (subjectMayReceiveStudyEvent(sm.getDataSource(), definitionScheduleds.get(i), studySubject)) {
StudyEventBean studyEventScheduled = new StudyEventBean();
studyEventScheduled.setStudyEventDefinitionId(scheduledDefinitionIds[i]);
studyEventScheduled.setStudySubjectId(studySubject.getId());
// YW 11-14-2007
if ("-1".equals(fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Hour")) && "-1".equals(fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Minute")) && "".equals(fp.getString(INPUT_STARTDATE_PREFIX_SCHEDULED[i] + "Half"))) {
studyEventScheduled.setStartTimeFlag(false);
} else {
studyEventScheduled.setStartTimeFlag(true);
}
// YW >>
studyEventScheduled.setDateStarted(startScheduled[i]);
// YW, 3-12-2008, 2220 fix<<
if (!"".equals(strEndScheduled[i])) {
endScheduled[i] = fp.getDateTime(INPUT_ENDDATE_PREFIX_SCHEDULED[i]);
if ("-1".equals(fp.getString(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Hour")) && "-1".equals(fp.getString(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Minute")) && "".equals(fp.getString(INPUT_ENDDATE_PREFIX_SCHEDULED[i] + "Half"))) {
studyEventScheduled.setEndTimeFlag(false);
} else {
studyEventScheduled.setEndTimeFlag(true);
}
}
studyEventScheduled.setDateEnded(endScheduled[i]);
// YW >>
studyEventScheduled.setOwner(ub);
studyEventScheduled.setStatus(Status.AVAILABLE);
studyEventScheduled.setLocation(fp.getString(INPUT_SCHEDULED_LOCATION[i]));
studyEvent.setSubjectEventStatus(SubjectEventStatus.SCHEDULED);
// subjectsExistingEvents =
// sed.findAllByStudyAndStudySubjectId(
// currentStudy,
// studySubject.getId());
studyEventScheduled.setSampleOrdinal(sed.getMaxSampleOrdinal(definitionScheduleds.get(i), studySubject) + 1);
//System.out.println("create scheduled events");
studyEventScheduled = (StudyEventBean) sed.create(studyEventScheduled);
if (!studyEventScheduled.isActive()) {
throw new OpenClinicaException(restext.getString("scheduled_event_not_created_in_database"), "2");
}
AddNewSubjectServlet.saveFieldNotes(INPUT_SCHEDULED_LOCATION[i], fdn, dndao, studyEventScheduled.getId(), "studyEvent", currentStudy);
// YW 3-12-2008, 2220 fix <<
AddNewSubjectServlet.saveFieldNotes(INPUT_STARTDATE_PREFIX_SCHEDULED[i], fdn, dndao, studyEventScheduled.getId(), "studyEvent", currentStudy);
AddNewSubjectServlet.saveFieldNotes(INPUT_ENDDATE_PREFIX_SCHEDULED[i], fdn, dndao, studyEventScheduled.getId(), "studyEvent", currentStudy);
// YW >>
} else {
addPageMessage(restext.getString("scheduled_event_definition") + definitionScheduleds.get(i).getName() + restext.getString("X_and_subject") + studySubject.getName() + restext.getString("not_created_since_event_not_repeating") + restext.getString("event_type_already_exists"));
}
}
}
}
// if
session.removeAttribute(AddNewSubjectServlet.FORM_DISCREPANCY_NOTES_NAME);
request.setAttribute(EnterDataForStudyEventServlet.INPUT_EVENT_ID, String.valueOf(studyEvent.getId()));
ArrayList<String> pMessage = (ArrayList<String>) request.getAttribute(SecureController.PAGE_MESSAGE);
String url = response.encodeRedirectURL("EnterDataForStudyEvent?eventId=" + studyEvent.getId() + "&alertmessage=" + URLEncoder.encode(pMessage.get(0), "UTF-8"));
response.sendRedirect(url);
// + studyEvent.getId()));
return;
}
}
}
Also used :
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
StudyEventDefinitionBean(org.akaza.openclinica.bean.managestudy.StudyEventDefinitionBean)
StudyEventBean(org.akaza.openclinica.bean.managestudy.StudyEventBean)
OpenClinicaException(org.akaza.openclinica.exception.OpenClinicaException)
TreeSet(java.util.TreeSet)
StudyEventDAO(org.akaza.openclinica.dao.managestudy.StudyEventDAO)
Status(org.akaza.openclinica.bean.core.Status)
SubjectEventStatus(org.akaza.openclinica.bean.core.SubjectEventStatus)
DiscrepancyNoteDAO(org.akaza.openclinica.dao.managestudy.DiscrepancyNoteDAO)
FormDiscrepancyNotes(org.akaza.openclinica.control.form.FormDiscrepancyNotes)
FormProcessor(org.akaza.openclinica.control.form.FormProcessor)
StudyBean(org.akaza.openclinica.bean.managestudy.StudyBean)
StudySubjectDAO(org.akaza.openclinica.dao.managestudy.StudySubjectDAO)
Date(java.util.Date)
DiscrepancyValidator(org.akaza.openclinica.control.form.DiscrepancyValidator)
StudySubjectBean(org.akaza.openclinica.bean.managestudy.StudySubjectBean)
StudyEventDefinitionDAO(org.akaza.openclinica.dao.managestudy.StudyEventDefinitionDAO)
Example 17 with OpenClinicaException
use of org.akaza.openclinica.exception.OpenClinicaException in project OpenClinica by OpenClinica.
the class DataImportService method validateData.
/**
* Import Data, the logic which imports the data for our data service. Note that we will return three strings string
* 0: status, either 'success', 'fail', or 'warn'. string 1: the message string which will be returned in our soap
* response string 2: the audit message, currently not used but will be saved in the event of a success.
*
* import consist from 3 steps 1) parse xml and extract data 2) validation 3) data submission
*
* @author thickerson
* @param dataSource
* @param resources
* @param studyBean
* @param userBean
* @param xml
* @return
* @throws Exception
*
* /* VALIDATE data on all levels
*
* msg - contains status messages
* @return list of errors
*/
public List<String> validateData(ODMContainer odmContainer, DataSource dataSource, CoreResources resources, StudyBean studyBean, UserAccountBean userBean, List<DisplayItemBeanWrapper> displayItemBeanWrappers, HashMap<Integer, String> importedCRFStatuses) {
ResourceBundle respage = ResourceBundleProvider.getPageMessagesBundle();
setRespage(respage);
TriggerService triggerService = new TriggerService();
StringBuffer auditMsg = new StringBuffer();
List<String> errors = new ArrayList<String>();
// htaycher: return back later?
auditMsg.append(respage.getString("passed_study_check") + " ");
auditMsg.append(respage.getString("passed_oid_metadata_check") + " ");
// validation errors, the same as in the ImportCRFDataServlet. DRY?
Boolean eventCRFStatusesValid = getImportCRFDataService(dataSource).eventCRFStatusesValid(odmContainer, userBean);
List<EventCRFBean> eventCRFBeans = getImportCRFDataService(dataSource).fetchEventCRFBeans(odmContainer, userBean);
// The following line updates a map that is used for setting the EventCRF status post import
getImportCRFDataService(dataSource).fetchEventCRFStatuses(odmContainer, importedCRFStatuses);
ArrayList<Integer> permittedEventCRFIds = new ArrayList<Integer>();
// -- does the event already exist? if not, fail
if (eventCRFBeans == null) {
errors.add(respage.getString("the_event_crf_not_correct_status"));
return errors;
} else if (eventCRFBeans.isEmpty() && !eventCRFStatusesValid) {
errors.add(respage.getString("the_event_crf_not_correct_status"));
return errors;
} else if (eventCRFBeans.isEmpty()) {
errors.add(respage.getString("no_event_crfs_matching_the_xml_metadata"));
return errors;
}
logger.debug("found a list of eventCRFBeans: " + eventCRFBeans.toString());
for (EventCRFBean eventCRFBean : eventCRFBeans) {
DataEntryStage dataEntryStage = eventCRFBean.getStage();
Status eventCRFStatus = eventCRFBean.getStatus();
logger.debug("Event CRF Bean: id " + eventCRFBean.getId() + ", data entry stage " + dataEntryStage.getName() + ", status " + eventCRFStatus.getName());
if (eventCRFStatus.equals(Status.AVAILABLE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
permittedEventCRFIds.add(new Integer(eventCRFBean.getId()));
} else {
errors.add(respage.getString("your_listed_crf_in_the_file") + " " + eventCRFBean.getEventName());
continue;
}
}
if (eventCRFBeans.size() >= permittedEventCRFIds.size()) {
auditMsg.append(respage.getString("passed_event_crf_status_check") + " ");
} else {
auditMsg.append(respage.getString("the_event_crf_not_correct_status") + " ");
}
// List<DisplayItemBeanWrapper> displayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
HashMap<String, String> totalValidationErrors = new HashMap<String, String>();
HashMap<String, String> hardValidationErrors = new HashMap<String, String>();
try {
List<DisplayItemBeanWrapper> tempDisplayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
// htaycher: this should be rewritten with validator not to use request to store data
MockHttpServletRequest request = new MockHttpServletRequest();
request.addPreferredLocale(getLocale());
tempDisplayItemBeanWrappers = getImportCRFDataService(dataSource).lookupValidationErrors(request, odmContainer, userBean, totalValidationErrors, hardValidationErrors, permittedEventCRFIds);
displayItemBeanWrappers.addAll(tempDisplayItemBeanWrappers);
logger.debug("size of total validation errors: " + (totalValidationErrors.size() + hardValidationErrors.size()));
ArrayList<SubjectDataBean> subjectData = odmContainer.getCrfDataPostImportContainer().getSubjectData();
if (!hardValidationErrors.isEmpty()) {
// check here where to get group repeat key
errors.add(triggerService.generateHardValidationErrorMessage(subjectData, hardValidationErrors, "1"));
}
if (!totalValidationErrors.isEmpty()) {
errors.add(triggerService.generateHardValidationErrorMessage(subjectData, totalValidationErrors, "1"));
}
} catch (NullPointerException npe1) {
// what if you have 2 event crfs but the third is a fake?
npe1.printStackTrace();
errors.add(respage.getString("an_error_was_thrown_while_validation_errors"));
logger.debug("=== threw the null pointer, import === " + npe1.getMessage());
} catch (OpenClinicaException oce1) {
errors.add(oce1.getOpenClinicaMessage());
logger.debug("=== threw the openclinica message, import === " + oce1.getOpenClinicaMessage());
}
auditMsg.append(respage.getString("passing_crf_edit_checks") + " ");
return errors;
}
Also used :
Status(org.akaza.openclinica.bean.core.Status)
ResolutionStatus(org.akaza.openclinica.bean.core.ResolutionStatus)
HashMap(java.util.HashMap)
MockHttpServletRequest(org.springframework.mock.web.MockHttpServletRequest)
ArrayList(java.util.ArrayList)
OpenClinicaException(org.akaza.openclinica.exception.OpenClinicaException)
DataEntryStage(org.akaza.openclinica.bean.core.DataEntryStage)
TriggerService(org.akaza.openclinica.web.job.TriggerService)
EventCRFBean(org.akaza.openclinica.bean.submit.EventCRFBean)
SubjectDataBean(org.akaza.openclinica.bean.submit.crfdata.SubjectDataBean)
ResourceBundle(java.util.ResourceBundle)
DisplayItemBeanWrapper(org.akaza.openclinica.bean.submit.DisplayItemBeanWrapper)
Example 18 with OpenClinicaException
use of org.akaza.openclinica.exception.OpenClinicaException in project OpenClinica by OpenClinica.
the class ImportCRFDataService method attachValidator.
private void attachValidator(DisplayItemBean displayItemBean, ImportHelper importHelper, DiscrepancyValidator discValidator, HashMap<String, String> hardv, javax.servlet.http.HttpServletRequest request, String eventCRFRepeatKey, String studySubjectOID) throws OpenClinicaException {
org.akaza.openclinica.bean.core.ResponseType rt = displayItemBean.getMetadata().getResponseSet().getResponseType();
String itemOid = displayItemBean.getItem().getOid() + "_" + eventCRFRepeatKey + "_" + displayItemBean.getData().getOrdinal() + "_" + studySubjectOID;
if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.TEXT) || rt.equals(org.akaza.openclinica.bean.core.ResponseType.TEXTAREA)) {
ItemFormMetadataBean ifm = displayItemBean.getMetadata();
String widthDecimal = ifm.getWidthDecimal();
// mm/dd/yyyy
if (displayItemBean.getItem().getDataType().equals(ItemDataType.DATE)) {
// pass it if it is blank, tbh
if (!"".equals(displayItemBean.getData().getValue())) {
String dateValue = displayItemBean.getData().getValue();
SimpleDateFormat sdf_sqldate = new SimpleDateFormat("yyyy-MM-dd");
sdf_sqldate.setLenient(false);
try {
// htaycher: database exspects format YYYY-MM-DD
Date originalDate = sdf_sqldate.parse(dateValue);
// String replacementValue = new SimpleDateFormat("MM/dd/yyyy").format(originalDate);
String replacementValue = new SimpleDateFormat("yyyy-MM-dd").format(originalDate);
displayItemBean.getData().setValue(replacementValue);
} catch (ParseException pe1) {
// next version; fail if it does not pass iso 8601
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("you_have_a_date_value_which_is_not"));
Object[] arguments = { displayItemBean.getItem().getOid() };
hardv.put(itemOid, mf.format(arguments));
}
}
} else if (displayItemBean.getItem().getDataType().equals(ItemDataType.ST)) {
int width = Validator.parseWidth(widthDecimal);
if (width > 0 && displayItemBean.getData().getValue().length() > width) {
hardv.put(itemOid, "This value exceeds required width=" + width);
}
} else // what if it's a number? should be only numbers
if (displayItemBean.getItem().getDataType().equals(ItemDataType.INTEGER)) {
try {
Integer testInt = new Integer(displayItemBean.getData().getValue());
int width = Validator.parseWidth(widthDecimal);
if (width > 0 && displayItemBean.getData().getValue().length() > width) {
hardv.put(itemOid, "This value exceeds required width=" + width);
}
// now, didn't check decimal for testInt.
} catch (Exception e) {
// pass if blank, tbh 07/2010
if (!"".equals(displayItemBean.getData().getValue())) {
hardv.put(itemOid, "This value is not an integer.");
}
}
} else // what if it's a float? should be only numbers
if (displayItemBean.getItem().getDataType().equals(ItemDataType.REAL)) {
try {
Float testFloat = new Float(displayItemBean.getData().getValue());
int width = Validator.parseWidth(widthDecimal);
if (width > 0 && displayItemBean.getData().getValue().length() > width) {
hardv.put(itemOid, "This value exceeds required width=" + width);
}
int decimal = Validator.parseDecimal(widthDecimal);
if (decimal > 0 && BigDecimal.valueOf(new Double(displayItemBean.getData().getValue()).doubleValue()).scale() > decimal) {
hardv.put(itemOid, "This value exceeds required decimal=" + decimal);
}
} catch (Exception ee) {
// pass if blank, tbh
if (!"".equals(displayItemBean.getData().getValue())) {
hardv.put(itemOid, "This value is not a real number.");
}
}
}
// what if it's a phone number? how often does that happen?
request.setAttribute(itemOid, displayItemBean.getData().getValue());
displayItemBean = importHelper.validateDisplayItemBeanText(discValidator, displayItemBean, itemOid);
// errors = v.validate();
} else if (rt.equals(ResponseType.CALCULATION) || rt.equals(ResponseType.GROUP_CALCULATION)) {
if (displayItemBean.getItem().getDataType().equals(ItemDataType.REAL)) {
ItemFormMetadataBean ifm = displayItemBean.getMetadata();
String widthDecimal = ifm.getWidthDecimal();
int decimal = Validator.parseDecimal(widthDecimal);
if (decimal > 0) {
try {
Double d = new Double(displayItemBean.getData().getValue());
if (BigDecimal.valueOf(d).scale() > decimal) {
hardv.put(itemOid, "This value exceeds required decimal=" + decimal);
}
} catch (Exception e) {
if (!"".equals(displayItemBean.getData().getValue())) {
hardv.put(itemOid, "This value is not a real number.");
}
}
}
}
} else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.RADIO) || rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECT)) {
// logger.info(itemOid + "is a RADIO or
// a SELECT ");
// adding a new hard edit check here; response_option mismatch
String theValue = matchValueWithOptions(displayItemBean, displayItemBean.getData().getValue(), displayItemBean.getMetadata().getResponseSet().getOptions());
request.setAttribute(itemOid, theValue);
logger.debug(" found the value for radio/single: " + theValue);
if (theValue == null && displayItemBean.getData().getValue() != null && !displayItemBean.getData().getValue().isEmpty()) {
// fail it here
logger.debug("-- theValue was NULL, the real value was " + displayItemBean.getData().getValue());
hardv.put(itemOid, "This is not in the correct response set.");
// throw new OpenClinicaException("One of your items did not
// have the correct response set. Please review Item OID "
// + displayItemBean.getItem().getOid() + " repeat key " +
// displayItemBean.getData().getOrdinal(), "");
}
displayItemBean = importHelper.validateDisplayItemBeanSingleCV(discValidator, displayItemBean, itemOid);
// errors = v.validate();
} else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.CHECKBOX) || rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECTMULTI)) {
// logger.info(itemOid + "is a CHECKBOX
// or a SELECTMULTI ");
String theValue = matchValueWithManyOptions(displayItemBean, displayItemBean.getData().getValue(), displayItemBean.getMetadata().getResponseSet().getOptions());
request.setAttribute(itemOid, theValue);
// logger.debug(" found the value for checkbx/multi: " + theValue);
if (theValue == null && displayItemBean.getData().getValue() != null && !displayItemBean.getData().getValue().isEmpty()) {
// fail it here? found an 0,1 in the place of a NULL
// logger.debug("-- theValue was NULL, the real value was " + displayItemBean.getData().getValue());
hardv.put(itemOid, "This is not in the correct response set.");
}
displayItemBean = importHelper.validateDisplayItemBeanMultipleCV(discValidator, displayItemBean, itemOid);
// errors = v.validate();
}
}
Also used :
MessageFormat(java.text.MessageFormat)
Date(java.util.Date)
OpenClinicaException(org.akaza.openclinica.exception.OpenClinicaException)
ParseException(java.text.ParseException)
ResponseType(org.akaza.openclinica.bean.core.ResponseType)
ParseException(java.text.ParseException)
SimpleDateFormat(java.text.SimpleDateFormat)
ItemFormMetadataBean(org.akaza.openclinica.bean.submit.ItemFormMetadataBean)
Example 19 with OpenClinicaException
use of org.akaza.openclinica.exception.OpenClinicaException in project OpenClinica by OpenClinica.
the class ImportCRFDataService method lookupValidationErrors.
public List<DisplayItemBeanWrapper> lookupValidationErrors(HttpServletRequest request, ODMContainer odmContainer, UserAccountBean ub, HashMap<String, String> totalValidationErrors, HashMap<String, String> hardValidationErrors, ArrayList<Integer> permittedEventCRFIds) throws OpenClinicaException {
DisplayItemBeanWrapper displayItemBeanWrapper = null;
HashMap validationErrors = new HashMap();
List<DisplayItemBeanWrapper> wrappers = new ArrayList<DisplayItemBeanWrapper>();
ImportHelper importHelper = new ImportHelper();
FormDiscrepancyNotes discNotes = new FormDiscrepancyNotes();
DiscrepancyValidator discValidator = new DiscrepancyValidator(request, discNotes);
// create a second Validator, this one for hard edit checks
HashMap<String, String> hardValidator = new HashMap<String, String>();
StudyEventDAO studyEventDAO = new StudyEventDAO(ds);
StudyDAO studyDAO = new StudyDAO(ds);
StudyBean studyBean = studyDAO.findByOid(odmContainer.getCrfDataPostImportContainer().getStudyOID());
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(ds);
HashMap<String, ItemDataBean> blankCheck = new HashMap<String, ItemDataBean>();
String hardValidatorErrorMsgs = "";
ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
int totalEventCRFCount = 0;
int totalItemDataBeanCount = 0;
for (SubjectDataBean subjectDataBean : subjectDataBeans) {
ArrayList<DisplayItemBean> displayItemBeans = new ArrayList<DisplayItemBean>();
logger.debug("iterating through subject data beans: found " + subjectDataBean.getSubjectOID());
ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
totalEventCRFCount += studyEventDataBeans.size();
StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(subjectDataBean.getSubjectOID(), studyBean.getId());
for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
int parentStudyId = studyBean.getParentStudyId();
StudyEventDefinitionBean sedBean = sedDao.findByOidAndStudy(studyEventDataBean.getStudyEventOID(), studyBean.getId(), parentStudyId);
ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
logger.debug("iterating through study event data beans: found " + studyEventDataBean.getStudyEventOID());
int ordinal = 1;
try {
ordinal = new Integer(studyEventDataBean.getStudyEventRepeatKey()).intValue();
} catch (Exception e) {
// trying to catch NPEs, because tags can be without the
// repeat key
}
StudyEventBean studyEvent = (StudyEventBean) studyEventDAO.findByStudySubjectIdAndDefinitionIdAndOrdinal(studySubjectBean.getId(), sedBean.getId(), ordinal);
displayItemBeans = new ArrayList<DisplayItemBean>();
for (FormDataBean formDataBean : formDataBeans) {
Map<String, Integer> groupMaxOrdinals = new HashMap<String, Integer>();
displayItemBeanWrapper = null;
CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
EventCRFDAO eventCRFDAO = new EventCRFDAO(ds);
ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formDataBean.getFormOID());
ArrayList<ImportItemGroupDataBean> itemGroupDataBeans = formDataBean.getItemGroupData();
if ((crfVersionBeans == null) || (crfVersionBeans.size() == 0)) {
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_crf_version_oid_did_not_generate"));
Object[] arguments = { formDataBean.getFormOID() };
throw new OpenClinicaException(mf.format(arguments), "");
}
CRFVersionBean crfVersion = crfVersionBeans.get(0);
// if you have a mispelled form oid you get an error here
// need to error out gracefully and post an error
logger.debug("iterating through form beans: found " + crfVersion.getOid());
// may be the point where we cut off item groups etc and
// instead work on sections
EventCRFBean eventCRFBean = eventCRFDAO.findByEventCrfVersion(studyEvent, crfVersion);
EventDefinitionCRFDAO eventDefinitionCRFDAO = new EventDefinitionCRFDAO(ds);
EventDefinitionCRFBean eventDefinitionCRF = eventDefinitionCRFDAO.findByStudyEventIdAndCRFVersionId(studyBean, studyEvent.getId(), crfVersion.getId());
if (eventCRFBean != null) {
if (permittedEventCRFIds.contains(new Integer(eventCRFBean.getId()))) {
for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
groupMaxOrdinals.put(itemGroupDataBean.getItemGroupOID(), 1);
}
// correctness, tbh
for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
ArrayList<ItemBean> blankCheckItems = new ArrayList<ItemBean>();
ArrayList<ImportItemDataBean> itemDataBeans = itemGroupDataBean.getItemData();
logger.debug("iterating through group beans: " + itemGroupDataBean.getItemGroupOID());
// put a checker in here
ItemGroupDAO itemGroupDAO = new ItemGroupDAO(ds);
ItemGroupBean testBean = itemGroupDAO.findByOid(itemGroupDataBean.getItemGroupOID());
if (testBean == null) {
// TODO i18n of message
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_item_group_oid_for_form_oid"));
Object[] arguments = { itemGroupDataBean.getItemGroupOID(), formDataBean.getFormOID() };
throw new OpenClinicaException(mf.format(arguments), "");
}
totalItemDataBeanCount += itemDataBeans.size();
for (ImportItemDataBean importItemDataBean : itemDataBeans) {
logger.debug(" iterating through item data beans: " + importItemDataBean.getItemOID());
ItemDAO itemDAO = new ItemDAO(ds);
ItemFormMetadataDAO itemFormMetadataDAO = new ItemFormMetadataDAO(ds);
List<ItemBean> itemBeans = itemDAO.findByOid(importItemDataBean.getItemOID());
if (!itemBeans.isEmpty()) {
ItemBean itemBean = itemBeans.get(0);
logger.debug(" found " + itemBean.getName());
// throw a null pointer? hopefully not if its been checked...
DisplayItemBean displayItemBean = new DisplayItemBean();
displayItemBean.setItem(itemBean);
ArrayList<ItemFormMetadataBean> metadataBeans = itemFormMetadataDAO.findAllByItemId(itemBean.getId());
logger.debug(" found metadata item beans: " + metadataBeans.size());
int groupOrdinal = 1;
if (itemGroupDataBean.getItemGroupRepeatKey() != null) {
try {
groupOrdinal = new Integer(itemGroupDataBean.getItemGroupRepeatKey()).intValue();
if (groupOrdinal > groupMaxOrdinals.get(itemGroupDataBean.getItemGroupOID())) {
groupMaxOrdinals.put(itemGroupDataBean.getItemGroupOID(), groupOrdinal);
}
} catch (Exception e) {
// do nothing here currently, we are
// looking for a number format
// exception
// from the above.
logger.debug("found npe for group ordinals, line 344!");
}
}
ItemDataBean itemDataBean = createItemDataBean(itemBean, eventCRFBean, importItemDataBean.getValue(), ub, groupOrdinal);
blankCheckItems.add(itemBean);
String newKey = groupOrdinal + "_" + itemGroupDataBean.getItemGroupOID() + "_" + itemBean.getOid() + "_" + subjectDataBean.getSubjectOID();
blankCheck.put(newKey, itemDataBean);
logger.info("adding " + newKey + " to blank checks");
if (!metadataBeans.isEmpty()) {
ItemFormMetadataBean metadataBean = metadataBeans.get(0);
// also possible nullpointer
displayItemBean.setData(itemDataBean);
displayItemBean.setMetadata(metadataBean);
displayItemBean.setEventDefinitionCRF(eventDefinitionCRF);
String eventCRFRepeatKey = studyEventDataBean.getStudyEventRepeatKey();
// if you do indeed leave off this in the XML it will pass but return 'null'
// tbh
attachValidator(displayItemBean, importHelper, discValidator, hardValidator, request, eventCRFRepeatKey, studySubjectBean.getOid());
displayItemBeans.add(displayItemBean);
} else {
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("no_metadata_could_be_found"));
Object[] arguments = { importItemDataBean.getItemOID() };
throw new OpenClinicaException(mf.format(arguments), "");
}
} else {
// report the error there
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("no_item_could_be_found"));
Object[] arguments = { importItemDataBean.getItemOID() };
throw new OpenClinicaException(mf.format(arguments), "");
}
}
// end item data beans
logger.debug(".. found blank check: " + blankCheck.toString());
for (int i = 1; i <= groupMaxOrdinals.get(itemGroupDataBean.getItemGroupOID()); i++) {
for (ItemBean itemBean : blankCheckItems) {
String newKey = i + "_" + itemGroupDataBean.getItemGroupOID() + "_" + itemBean.getOid() + "_" + subjectDataBean.getSubjectOID();
if (blankCheck.get(newKey) == null) {
// if it already exists, Do Not Add It.
ItemDataBean itemDataCheck = getItemDataDao().findByItemIdAndEventCRFIdAndOrdinal(itemBean.getId(), eventCRFBean.getId(), i);
logger.debug("found item data bean id: " + itemDataCheck.getId() + " for ordinal " + i);
if (itemDataCheck.getId() == 0) {
ItemDataBean blank = createItemDataBean(itemBean, eventCRFBean, "", ub, i);
DisplayItemBean displayItemBean = new DisplayItemBean();
displayItemBean.setItem(itemBean);
displayItemBean.setData(blank);
// displayItemBean.setMetadata(metadataBean);
// set event def crf?
displayItemBean.setEventDefinitionCRF(eventDefinitionCRF);
String eventCRFRepeatKey = studyEventDataBean.getStudyEventRepeatKey();
// if you do indeed leave off this in the XML it will pass but return
// 'null'
// tbh
displayItemBeans.add(displayItemBean);
logger.debug("... adding display item bean");
}
}
logger.debug("found a blank at " + i + ", adding " + blankCheckItems.size() + " blank items");
}
}
// << tbh #5548
blankCheckItems = new ArrayList<ItemBean>();
}
// end item group data beans
}
// matches if on permittedCRFIDs
CRFDAO crfDAO = new CRFDAO(ds);
CRFBean crfBean = crfDAO.findByVersionId(crfVersion.getCrfId());
// seems like an extravagance, but is not contained in crf
// version or event crf bean
validationErrors = discValidator.validate();
// totalValidationErrors.addAll(validationErrors);
for (Object errorKey : validationErrors.keySet()) {
// JN: to avoid duplicate errors
if (!totalValidationErrors.containsKey(errorKey.toString()))
totalValidationErrors.put(errorKey.toString(), validationErrors.get(errorKey).toString());
// assuming that this will be put back in to the core
// method's hashmap, updating statically, tbh 06/2008
logger.debug("+++ adding " + errorKey.toString());
}
logger.debug("-- hard validation checks: --");
for (Object errorKey : hardValidator.keySet()) {
logger.debug(errorKey.toString() + " -- " + hardValidator.get(errorKey));
hardValidationErrors.put(errorKey.toString(), hardValidator.get(errorKey));
// updating here 'statically' tbh 06/2008
hardValidatorErrorMsgs += hardValidator.get(errorKey) + "<br/><br/>";
}
String studyEventId = studyEvent.getId() + "";
String crfVersionId = crfVersion.getId() + "";
logger.debug("creation of wrapper: original count of display item beans " + displayItemBeans.size() + ", count of item data beans " + totalItemDataBeanCount + " count of validation errors " + validationErrors.size() + " count of study subjects " + subjectDataBeans.size() + " count of event crfs " + totalEventCRFCount + " count of hard error checks " + hardValidator.size());
// check if we need to overwrite
DataEntryStage dataEntryStage = eventCRFBean.getStage();
Status eventCRFStatus = eventCRFBean.getStatus();
boolean overwrite = false;
// //JN: Commenting out the following 2 lines, coz the prompt should come in the cases on
if (// eventCRFStatus.equals(Status.UNAVAILABLE) ||
dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
overwrite = true;
}
// << tbh, adding extra statuses to prevent appending, 06/2009
// SummaryStatsBean ssBean = new SummaryStatsBean();
// ssBean.setDiscNoteCount(totalValidationErrors);
// ssBean.setEventCrfCount(totalEventCRFCount);
// ssBean.setStudySubjectCount(subjectDataBeans.size());
// // add other stats here, tbh
// not working here, need to do it in a different method,
// tbh
// summary stats added tbh 05/2008
// JN: Changed from validationErrors to totalValidationErrors to create discrepancy notes for
// all
// the
displayItemBeanWrapper = new DisplayItemBeanWrapper(displayItemBeans, true, overwrite, validationErrors, studyEventId, crfVersionId, studyEventDataBean.getStudyEventOID(), studySubjectBean.getLabel(), eventCRFBean.getCreatedDate(), crfBean.getName(), crfVersion.getName(), studySubjectBean.getOid(), studyEventDataBean.getStudyEventRepeatKey());
// JN: Commenting out the following code, since we shouldn't re-initialize at this point, as
// validationErrors would get overwritten and the
// older errors will be overriden. Moving it after the form.
// Removing the comments for now, since it seems to be creating duplicate Discrepancy Notes.
validationErrors = new HashMap();
discValidator = new DiscrepancyValidator(request, discNotes);
// reset to allow for new errors...
}
}
// discValidator = new DiscrepancyValidator(request, discNotes);
if (displayItemBeanWrapper != null && displayItemBeans.size() > 0)
wrappers.add(displayItemBeanWrapper);
}
// after study events
// remove repeats here? remove them below by only forwarding the
// first
// each wrapper represents an Event CRF and a Form, but we don't
// have all events for all forms
// need to not add a wrapper for every event + form combination,
// but instead for every event + form combination which is present
// look at the hack below and see what happens
}
// thrown, tbh 06/2008
if (!hardValidator.isEmpty()) {
// throw new OpenClinicaException(hardValidatorErrorMsgs, "");
}
return wrappers;
}
Also used :
ItemBean(org.akaza.openclinica.bean.submit.ItemBean)
DisplayItemBean(org.akaza.openclinica.bean.submit.DisplayItemBean)
HashMap(java.util.HashMap)
ItemDAO(org.akaza.openclinica.dao.submit.ItemDAO)
ArrayList(java.util.ArrayList)
ItemGroupDAO(org.akaza.openclinica.dao.submit.ItemGroupDAO)
StudyEventDefinitionBean(org.akaza.openclinica.bean.managestudy.StudyEventDefinitionBean)
StudyEventBean(org.akaza.openclinica.bean.managestudy.StudyEventBean)
OpenClinicaException(org.akaza.openclinica.exception.OpenClinicaException)
EventCRFBean(org.akaza.openclinica.bean.submit.EventCRFBean)
ItemDataBean(org.akaza.openclinica.bean.submit.ItemDataBean)
ImportItemDataBean(org.akaza.openclinica.bean.submit.crfdata.ImportItemDataBean)
StudyEventDAO(org.akaza.openclinica.dao.managestudy.StudyEventDAO)
StudyDAO(org.akaza.openclinica.dao.managestudy.StudyDAO)
DisplayItemBeanWrapper(org.akaza.openclinica.bean.submit.DisplayItemBeanWrapper)
Status(org.akaza.openclinica.bean.core.Status)
SubjectEventStatus(org.akaza.openclinica.bean.core.SubjectEventStatus)
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)
FormDiscrepancyNotes(org.akaza.openclinica.control.form.FormDiscrepancyNotes)
StudyBean(org.akaza.openclinica.bean.managestudy.StudyBean)
EventDefinitionCRFDAO(org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO)
EventDefinitionCRFBean(org.akaza.openclinica.bean.managestudy.EventDefinitionCRFBean)
EventCRFBean(org.akaza.openclinica.bean.submit.EventCRFBean)
CRFBean(org.akaza.openclinica.bean.admin.CRFBean)
DataEntryStage(org.akaza.openclinica.bean.core.DataEntryStage)
StudyEventDefinitionDAO(org.akaza.openclinica.dao.managestudy.StudyEventDefinitionDAO)
StudySubjectBean(org.akaza.openclinica.bean.managestudy.StudySubjectBean)
EventDefinitionCRFBean(org.akaza.openclinica.bean.managestudy.EventDefinitionCRFBean)
ItemGroupBean(org.akaza.openclinica.bean.submit.ItemGroupBean)
ImportItemGroupDataBean(org.akaza.openclinica.bean.submit.crfdata.ImportItemGroupDataBean)
ImportItemDataBean(org.akaza.openclinica.bean.submit.crfdata.ImportItemDataBean)
DisplayItemBean(org.akaza.openclinica.bean.submit.DisplayItemBean)
EventCRFDAO(org.akaza.openclinica.dao.submit.EventCRFDAO)
ItemFormMetadataDAO(org.akaza.openclinica.dao.submit.ItemFormMetadataDAO)
MessageFormat(java.text.MessageFormat)
StudyEventDataBean(org.akaza.openclinica.bean.submit.crfdata.StudyEventDataBean)
StudySubjectDAO(org.akaza.openclinica.dao.managestudy.StudySubjectDAO)
OpenClinicaException(org.akaza.openclinica.exception.OpenClinicaException)
ParseException(java.text.ParseException)
DiscrepancyValidator(org.akaza.openclinica.control.form.DiscrepancyValidator)
SubjectDataBean(org.akaza.openclinica.bean.submit.crfdata.SubjectDataBean)
FormDataBean(org.akaza.openclinica.bean.submit.crfdata.FormDataBean)
CRFVersionBean(org.akaza.openclinica.bean.submit.CRFVersionBean)
ItemFormMetadataBean(org.akaza.openclinica.bean.submit.ItemFormMetadataBean)
Example 20 with OpenClinicaException
use of org.akaza.openclinica.exception.OpenClinicaException in project OpenClinica by OpenClinica.
the class ImportSpringJob method processData.
/*
* processData, a method which should take in all XML files, check to see if they were imported previously, ? insert
* them into the database if not, and return a message which will go to audit and to the end user.
*/
private ArrayList<String> processData(File[] dest, DataSource dataSource, ResourceBundle respage, ResourceBundle resword, UserAccountBean ub, StudyBean studyBean, File destDirectory, TriggerBean triggerBean, RuleSetServiceInterface ruleSetService) throws Exception {
StringBuffer msg = new StringBuffer();
StringBuffer auditMsg = new StringBuffer();
Mapping myMap = new Mapping();
String propertiesPath = CoreResources.PROPERTIES_DIR;
new File(propertiesPath + File.separator + "ODM1-3-0.xsd");
File xsdFile2 = new File(propertiesPath + File.separator + "ODM1-2-1.xsd");
// @pgawade 18-April-2011 Fix for issue 8394
String ODM_MAPPING_DIR_path = CoreResources.ODM_MAPPING_DIR;
myMap.loadMapping(ODM_MAPPING_DIR_path + File.separator + "cd_odm_mapping.xml");
Unmarshaller um1 = new Unmarshaller(myMap);
ODMContainer odmContainer = new ODMContainer();
// File("log.txt")));
for (File f : dest) {
// >> tbh
boolean fail = false;
// all whitespace, one or more times
String regex = "\\s+";
// replace with underscores
String replacement = "_";
String pattern = "yyyy" + File.separator + "MM" + File.separator + "dd" + File.separator + "HHmmssSSS" + File.separator;
SimpleDateFormat sdfDir = new SimpleDateFormat(pattern);
String generalFileDir = sdfDir.format(new java.util.Date());
File logDestDirectory = new File(destDirectory + File.separator + generalFileDir + f.getName().replaceAll(regex, replacement) + ".log.txt");
if (!logDestDirectory.isDirectory()) {
logger.debug("creating new dir: " + logDestDirectory.getAbsolutePath());
logDestDirectory.mkdirs();
}
File newFile = new File(logDestDirectory, "log.txt");
// FileOutputStream out = new FileOutputStream(new
// File(logDestDirectory, "log.txt"));
// BufferedWriter out = null;
// wrap the below in a try-catch?
BufferedWriter out = new BufferedWriter(new FileWriter(newFile));
// << tbh 06/2010
if (f != null) {
String firstLine = "<P>" + f.getName() + ": ";
msg.append(firstLine);
out.write(firstLine);
auditMsg.append(firstLine);
} else {
msg.append("<P>" + respage.getString("unreadable_file") + ": ");
out.write("<P>" + respage.getString("unreadable_file") + ": ");
auditMsg.append("<P>" + respage.getString("unreadable_file") + ": ");
}
try {
// schemaValidator.validateAgainstSchema(f, xsdFile);
odmContainer = (ODMContainer) um1.unmarshal(new FileReader(f));
logger.debug("Found crf data container for study oid: " + odmContainer.getCrfDataPostImportContainer().getStudyOID());
logger.debug("found length of subject list: " + odmContainer.getCrfDataPostImportContainer().getSubjectData().size());
} catch (Exception me1) {
// fail against one, try another
try {
schemaValidator.validateAgainstSchema(f, xsdFile2);
// for backwards compatibility, we also try to validate vs
// 1.2.1 ODM 06/2008
odmContainer = (ODMContainer) um1.unmarshal(new FileReader(f));
} catch (Exception me2) {
// not sure if we want to report me2
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_xml_is_not_well_formed"));
Object[] arguments = { me1.getMessage() };
msg.append(mf.format(arguments) + "<br/>");
auditMsg.append(mf.format(arguments) + "<br/>");
// break here with an exception
logger.error("found an error with XML: " + msg.toString());
// continue looping
continue;
}
}
// next: check, then import
List<String> errors = getImportCRFDataService(dataSource).validateStudyMetadata(odmContainer, studyBean.getId());
// the user could be in any study ...
if (errors != null) {
if (errors.size() > 0) {
out.write("<P>Errors:<br/>");
for (String error : errors) {
out.write(error + "<br/>");
}
out.write("</P>");
// fail = true;
// forwardPage(Page.IMPORT_CRF_DATA);
// break here with an exception
// throw new Exception("Your XML in the file " + f.getName()
// + " was well formed, but generated metadata errors: " +
// errors.toString());
// msg.append("Your XML in the file " + f.getName() +
// " was well formed, but generated metadata errors: " +
// errors.toString());
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_xml_in_the_file"));
Object[] arguments = { f.getName(), errors.size() };
auditMsg.append(mf.format(arguments) + "<br/>");
msg.append(mf.format(arguments) + "<br/>");
auditMsg.append("You can see the log file <a href='" + SQLInitServlet.getField("sysURL.base") + "ViewLogMessage?n=" + generalFileDir + f.getName() + "&tn=" + triggerBean.getName() + "&gn=1'>here</a>.<br/>");
msg.append("You can see the log file <a href='" + SQLInitServlet.getField("sysURL.base") + "ViewLogMessage?n=" + generalFileDir + f.getName() + "&tn=" + triggerBean.getName() + "&gn=1'>here</a>.<br/>");
// auditMsg.append("Your XML in the file " + f.getName() +
// " was well formed, but generated " + errors.size() +
// " metadata errors." + "<br/>");
out.close();
continue;
} else {
msg.append(respage.getString("passed_study_check") + "<br/>");
msg.append(respage.getString("passed_oid_metadata_check") + "<br/>");
auditMsg.append(respage.getString("passed_study_check") + "<br/>");
auditMsg.append(respage.getString("passed_oid_metadata_check") + "<br/>");
}
}
ImportCRFInfoContainer importCrfInfo = new ImportCRFInfoContainer(odmContainer, dataSource);
// validation errors, the same as in the ImportCRFDataServlet. DRY?
List<EventCRFBean> eventCRFBeans = getImportCRFDataService(dataSource).fetchEventCRFBeans(odmContainer, ub);
ArrayList<Integer> permittedEventCRFIds = new ArrayList<Integer>();
Boolean eventCRFStatusesValid = getImportCRFDataService(dataSource).eventCRFStatusesValid(odmContainer, ub);
List<DisplayItemBeanWrapper> displayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
HashMap<String, String> totalValidationErrors = new HashMap<String, String>();
HashMap<String, String> hardValidationErrors = new HashMap<String, String>();
// The following map is used for setting the EventCRF status post import.
HashMap<Integer, String> importedCRFStatuses = getImportCRFDataService(dataSource).fetchEventCRFStatuses(odmContainer);
// -- does the event already exist? if not, fail
if (eventCRFBeans == null) {
fail = true;
msg.append(respage.getString("no_event_status_matching"));
out.write(respage.getString("no_event_status_matching"));
out.close();
continue;
} else if (!eventCRFBeans.isEmpty()) {
logger.debug("found a list of eventCRFBeans: " + eventCRFBeans.toString());
for (EventCRFBean eventCRFBean : eventCRFBeans) {
DataEntryStage dataEntryStage = eventCRFBean.getStage();
Status eventCRFStatus = eventCRFBean.getStatus();
logger.debug("Event CRF Bean: id " + eventCRFBean.getId() + ", data entry stage " + dataEntryStage.getName() + ", status " + eventCRFStatus.getName());
if (eventCRFStatus.equals(Status.AVAILABLE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
permittedEventCRFIds.add(new Integer(eventCRFBean.getId()));
} else {
// break out here with an exception
// throw new
// Exception("Your listed Event CRF in the file " +
// f.getName() +
// " does not exist, or has already been locked for import."
// );
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_listed_crf_in_the_file"));
Object[] arguments = { f.getName() };
msg.append(mf.format(arguments) + "<br/>");
auditMsg.append(mf.format(arguments) + "<br/>");
out.write(mf.format(arguments) + "<br/>");
out.close();
continue;
}
}
if (eventCRFBeans.size() >= permittedEventCRFIds.size()) {
msg.append(respage.getString("passed_event_crf_status_check") + "<br/>");
auditMsg.append(respage.getString("passed_event_crf_status_check") + "<br/>");
} else {
fail = true;
msg.append(respage.getString("the_event_crf_not_correct_status") + "<br/>");
auditMsg.append(respage.getString("the_event_crf_not_correct_status") + "<br/>");
}
// create a 'fake' request to generate the validation errors
// here, tbh 05/2009
MockHttpServletRequest request = new MockHttpServletRequest();
// Locale locale = new Locale("en-US");
request.addPreferredLocale(locale);
try {
List<DisplayItemBeanWrapper> tempDisplayItemBeanWrappers = new ArrayList<DisplayItemBeanWrapper>();
tempDisplayItemBeanWrappers = getImportCRFDataService(dataSource).lookupValidationErrors(request, odmContainer, ub, totalValidationErrors, hardValidationErrors, permittedEventCRFIds);
logger.debug("size of total validation errors: " + totalValidationErrors.size());
displayItemBeanWrappers.addAll(tempDisplayItemBeanWrappers);
} catch (NullPointerException npe1) {
// what if you have 2 event crfs but the third is a fake?
npe1.printStackTrace();
fail = true;
logger.debug("threw a NPE after calling lookup validation errors");
msg.append(respage.getString("an_error_was_thrown_while_validation_errors") + "<br/>");
auditMsg.append(respage.getString("an_error_was_thrown_while_validation_errors") + "<br/>");
out.write(respage.getString("an_error_was_thrown_while_validation_errors") + "<br/>");
logger.debug("=== threw the null pointer, import ===");
} catch (OpenClinicaException oce1) {
fail = true;
logger.error("threw an OCE after calling lookup validation errors " + oce1.getOpenClinicaMessage());
msg.append(oce1.getOpenClinicaMessage() + "<br/>");
// auditMsg.append(oce1.getOpenClinicaMessage() + "<br/>");
out.write(oce1.getOpenClinicaMessage() + "<br/>");
}
} else if (!eventCRFStatusesValid) {
fail = true;
msg.append(respage.getString("the_event_crf_not_correct_status"));
out.write(respage.getString("the_event_crf_not_correct_status"));
out.close();
continue;
} else {
// fail = true;
// break here with an exception
msg.append(respage.getString("no_event_crfs_matching_the_xml_metadata") + "<br/>");
// auditMsg.append(respage.getString("no_event_crfs_matching_the_xml_metadata")
// + "<br/>");
out.write(respage.getString("no_event_crfs_matching_the_xml_metadata") + "<br/>");
// throw new Exception(msg.toString());
out.close();
continue;
}
ArrayList<SubjectDataBean> subjectData = odmContainer.getCrfDataPostImportContainer().getSubjectData();
if (!hardValidationErrors.isEmpty()) {
String messageHardVals = triggerService.generateHardValidationErrorMessage(subjectData, hardValidationErrors, false);
// byte[] messageHardValsBytes = messageHardVals.getBytes();
out.write(messageHardVals);
msg.append(respage.getString("file_generated_hard_validation_error"));
// here we create a file and append the data, tbh 06/2010
fail = true;
} else {
if (!totalValidationErrors.isEmpty()) {
String totalValErrors = triggerService.generateHardValidationErrorMessage(subjectData, totalValidationErrors, false);
out.write(totalValErrors);
// here we also append data to the file, tbh 06/2010
}
String validMsgs = triggerService.generateValidMessage(subjectData, totalValidationErrors);
out.write(validMsgs);
// third place to append data to the file? tbh 06/2010
}
// << tbh 05/2010, bug #5110, leave off the detailed reports
out.close();
if (fail) {
// forwardPage(Page.IMPORT_CRF_DATA);
// break here with an exception
// throw new Exception("Problems encountered with file " +
// f.getName() + ": " + msg.toString());
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("problems_encountered_with_file"));
Object[] arguments = { f.getName(), msg.toString() };
msg = new StringBuffer(mf.format(arguments) + "<br/>");
out.close();
auditMsg.append("You can see the log file <a href='" + SQLInitServlet.getField("sysURL.base") + "ViewLogMessage?n=" + generalFileDir + f.getName() + "&tn=" + triggerBean.getName() + "&gn=1'>here</a>.<br/>");
msg.append("You can see the log file <a href='" + SQLInitServlet.getField("sysURL.base") + "ViewLogMessage?n=" + generalFileDir + f.getName() + "&tn=" + triggerBean.getName() + "&gn=1'>here</a>.<br/>");
// ": " + msg.toString() + "<br/>");
continue;
} else {
msg.append(respage.getString("passing_crf_edit_checks") + "<br/>");
auditMsg.append(respage.getString("passing_crf_edit_checks") + "<br/>");
// session.setAttribute("importedData",
// displayItemBeanWrappers);
// session.setAttribute("validationErrors",
// totalValidationErrors);
// session.setAttribute("hardValidationErrors",
// hardValidationErrors);
// above are to be sent to the user, but what kind of message
// can we make of them here?
// if hard validation errors are present, we only generate one
// table
// otherwise, we generate the other two: validation errors and
// valid data
logger.debug("found total validation errors: " + totalValidationErrors.size());
SummaryStatsBean ssBean = getImportCRFDataService(dataSource).generateSummaryStatsBean(odmContainer, displayItemBeanWrappers, importCrfInfo);
// msg.append("===+");
// the above is a special key that we will use to split the
// message into two parts
// a shorter version for the audit and
// a longer version for the email
msg.append(triggerService.generateSummaryStatsMessage(ssBean, respage) + "<br/>");
// session.setAttribute("summaryStats", ssBean);
// will have to set hard edit checks here as well
// session.setAttribute("subjectData",
// ArrayList<SubjectDataBean> subjectData =
// odmContainer.getCrfDataPostImportContainer().getSubjectData();
// forwardPage(Page.VERIFY_IMPORT_SERVLET);
// instead of forwarding, go ahead and save it all, sending a
// message at the end
msg.append(triggerService.generateSkippedCRFMessage(importCrfInfo, resword) + "<br/>");
// setup ruleSets to run if applicable
List<ImportDataRuleRunnerContainer> containers = this.ruleRunSetup(dataSource, studyBean, ub, ruleSetService, odmContainer);
CrfBusinessLogicHelper crfBusinessLogicHelper = new CrfBusinessLogicHelper(dataSource);
for (DisplayItemBeanWrapper wrapper : displayItemBeanWrappers) {
boolean resetSDV = false;
int eventCrfBeanId = -1;
EventCRFBean eventCrfBean = new EventCRFBean();
logger.debug("right before we check to make sure it is savable: " + wrapper.isSavable());
if (wrapper.isSavable()) {
ArrayList<Integer> eventCrfInts = new ArrayList<Integer>();
logger.debug("wrapper problems found : " + wrapper.getValidationErrors().toString());
itemDataDao.setFormatDates(false);
for (DisplayItemBean displayItemBean : wrapper.getDisplayItemBeans()) {
eventCrfBeanId = displayItemBean.getData().getEventCRFId();
eventCrfBean = (EventCRFBean) eventCrfDao.findByPK(eventCrfBeanId);
logger.debug("found value here: " + displayItemBean.getData().getValue());
logger.debug("found status here: " + eventCrfBean.getStatus().getName());
ItemDataBean itemDataBean = new ItemDataBean();
itemDataBean = itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(displayItemBean.getItem().getId(), eventCrfBean.getId(), displayItemBean.getData().getOrdinal());
if (wrapper.isOverwrite() && itemDataBean.getStatus() != null) {
logger.debug("just tried to find item data bean on item name " + displayItemBean.getItem().getName());
if (!itemDataBean.getValue().equals(displayItemBean.getData().getValue()))
resetSDV = true;
itemDataBean.setUpdatedDate(new Date());
itemDataBean.setUpdater(ub);
itemDataBean.setValue(displayItemBean.getData().getValue());
// set status?
itemDataDao.update(itemDataBean);
logger.debug("updated: " + itemDataBean.getItemId());
// need to set pk here in order to create dn
displayItemBean.getData().setId(itemDataBean.getId());
} else {
resetSDV = true;
itemDataDao.create(displayItemBean.getData());
logger.debug("created: " + displayItemBean.getData().getItemId());
ItemDataBean itemDataBean2 = itemDataDao.findByItemIdAndEventCRFIdAndOrdinal(displayItemBean.getItem().getId(), eventCrfBean.getId(), displayItemBean.getData().getOrdinal());
logger.debug("found: id " + itemDataBean2.getId() + " name " + itemDataBean2.getName());
displayItemBean.getData().setId(itemDataBean2.getId());
}
ItemDAO idao = new ItemDAO(dataSource);
ItemBean ibean = (ItemBean) idao.findByPK(displayItemBean.getData().getItemId());
logger.debug("*** checking for validation errors: " + ibean.getName());
String itemOid = displayItemBean.getItem().getOid() + "_" + wrapper.getStudyEventRepeatKey() + "_" + displayItemBean.getData().getOrdinal() + "_" + wrapper.getStudySubjectOid();
if (wrapper.getValidationErrors().containsKey(itemOid)) {
ArrayList messageList = (ArrayList) wrapper.getValidationErrors().get(itemOid);
for (int iter = 0; iter < messageList.size(); iter++) {
String message = (String) messageList.get(iter);
DiscrepancyNoteBean parentDn = createDiscrepancyNote(ibean, message, eventCrfBean, displayItemBean, null, ub, dataSource, studyBean);
createDiscrepancyNote(ibean, message, eventCrfBean, displayItemBean, parentDn.getId(), ub, dataSource, studyBean);
logger.debug("*** created disc note with message: " + message);
// displayItemBean);
}
}
// Update CRF status
if (!eventCrfInts.contains(new Integer(eventCrfBean.getId()))) {
String eventCRFStatus = importedCRFStatuses.get(new Integer(eventCrfBean.getId()));
if (eventCRFStatus != null && eventCRFStatus.equals(DataEntryStage.INITIAL_DATA_ENTRY.getName()) && eventCrfBean.getStatus().isAvailable()) {
crfBusinessLogicHelper.markCRFStarted(eventCrfBean, ub);
} else {
crfBusinessLogicHelper.markCRFComplete(eventCrfBean, ub);
}
logger.debug("*** just updated event crf bean: " + eventCrfBean.getId());
eventCrfInts.add(new Integer(eventCrfBean.getId()));
}
}
itemDataDao.setFormatDates(true);
// Reset the SDV status if item data has been changed or added
if (eventCrfBean != null && resetSDV)
eventCrfDao.setSDVStatus(false, ub.getId(), eventCrfBean.getId());
}
}
// msg.append("===+");
msg.append(respage.getString("data_has_been_successfully_import") + "<br/>");
auditMsg.append(respage.getString("data_has_been_successfully_import") + "<br/>");
// MessageFormat mf = new MessageFormat("");
String linkMessage = respage.getString("you_can_review_the_data") + SQLInitServlet.getField("sysURL.base") + respage.getString("you_can_review_the_data_2") + SQLInitServlet.getField("sysURL.base") + respage.getString("you_can_review_the_data_3") + generalFileDir + f.getName() + "&tn=" + triggerBean.getFullName() + "&gn=1" + respage.getString("you_can_review_the_data_4") + "<br/>";
// mf.applyPattern(respage.getString("you_can_review_the_data"));
// Object[] arguments = {
// SQLInitServlet.getField("sysURL.base"),
// SQLInitServlet.getField("sysURL.base"), f.getName() };
msg.append(linkMessage);
auditMsg.append(linkMessage);
// was here but is now moved up, tbh
// String finalLine =
// "<p>You can review the entered data <a href='" +
// SQLInitServlet.getField("sysURL.base") +
// "ListStudySubjects'>here</a>.";
// >> tbh additional message
// "you can review the validation messages here" <-- where
// 'here' is a link to view an external file
// i.e. /ViewExternal?n=file_name.txt
// << tbh 06/2010
// msg.append(finalLine);
// auditMsg.append(finalLine);
auditMsg.append(this.runRules(studyBean, ub, containers, ruleSetService, ExecutionMode.SAVE));
}
}
// end for loop
// is the writer still not closed? try to close it
ArrayList<String> retList = new ArrayList<String>();
retList.add(msg.toString());
retList.add(auditMsg.toString());
// msg.toString();
return retList;
}
Also used :
ItemBean(org.akaza.openclinica.bean.submit.ItemBean)
DisplayItemBean(org.akaza.openclinica.bean.submit.DisplayItemBean)
HashMap(java.util.HashMap)
ItemDAO(org.akaza.openclinica.dao.submit.ItemDAO)
Date(java.util.Date)
ArrayList(java.util.ArrayList)
Mapping(org.exolab.castor.mapping.Mapping)
SummaryStatsBean(org.akaza.openclinica.bean.submit.crfdata.SummaryStatsBean)
OpenClinicaException(org.akaza.openclinica.exception.OpenClinicaException)
EventCRFBean(org.akaza.openclinica.bean.submit.EventCRFBean)
ItemDataBean(org.akaza.openclinica.bean.submit.ItemDataBean)
List(java.util.List)
ArrayList(java.util.ArrayList)
Unmarshaller(org.exolab.castor.xml.Unmarshaller)
DisplayItemBeanWrapper(org.akaza.openclinica.bean.submit.DisplayItemBeanWrapper)
TransactionStatus(org.springframework.transaction.TransactionStatus)
Status(org.akaza.openclinica.bean.core.Status)
ResolutionStatus(org.akaza.openclinica.bean.core.ResolutionStatus)
DataEntryStage(org.akaza.openclinica.bean.core.DataEntryStage)
DiscrepancyNoteBean(org.akaza.openclinica.bean.managestudy.DiscrepancyNoteBean)
File(java.io.File)
FileWriter(java.io.FileWriter)
ImportDataRuleRunnerContainer(org.akaza.openclinica.logic.rulerunner.ImportDataRuleRunnerContainer)
BufferedWriter(java.io.BufferedWriter)
ODMContainer(org.akaza.openclinica.bean.submit.crfdata.ODMContainer)
ImportCRFInfoContainer(org.akaza.openclinica.control.submit.ImportCRFInfoContainer)
DisplayItemBean(org.akaza.openclinica.bean.submit.DisplayItemBean)
FileReader(java.io.FileReader)
MessageFormat(java.text.MessageFormat)
MockHttpServletRequest(org.springframework.mock.web.MockHttpServletRequest)
OpenClinicaException(org.akaza.openclinica.exception.OpenClinicaException)
JobExecutionException(org.quartz.JobExecutionException)
OpenClinicaSystemException(org.akaza.openclinica.exception.OpenClinicaSystemException)
SchedulerException(org.quartz.SchedulerException)
IOException(java.io.IOException)
Date(java.util.Date)
SubjectDataBean(org.akaza.openclinica.bean.submit.crfdata.SubjectDataBean)
SimpleDateFormat(java.text.SimpleDateFormat)
Aggregations
OpenClinicaException (org.akaza.openclinica.exception.OpenClinicaException)23
ArrayList (java.util.ArrayList)18
HashMap (java.util.HashMap)11
ItemBean (org.akaza.openclinica.bean.submit.ItemBean)8
DisplayItemBean (org.akaza.openclinica.bean.submit.DisplayItemBean)7
ItemFormMetadataBean (org.akaza.openclinica.bean.submit.ItemFormMetadataBean)7
ItemDAO (org.akaza.openclinica.dao.submit.ItemDAO)7
Connection (java.sql.Connection)6
PreparedStatement (java.sql.PreparedStatement)6
ResultSet (java.sql.ResultSet)6
SQLException (java.sql.SQLException)6
StudyBean (org.akaza.openclinica.bean.managestudy.StudyBean)6
ItemFormMetadataDAO (org.akaza.openclinica.dao.submit.ItemFormMetadataDAO)6
MessageFormat (java.text.MessageFormat)5
EventCRFBean (org.akaza.openclinica.bean.submit.EventCRFBean)5
ItemGroupBean (org.akaza.openclinica.bean.submit.ItemGroupBean)5
StudyDAO (org.akaza.openclinica.dao.managestudy.StudyDAO)5
Iterator (java.util.Iterator)4
List (java.util.List)4
Status (org.akaza.openclinica.bean.core.Status)4
