@SuppressWarnings("unchecked")
private void setUpForNotes(Sample sample) {
noteIdToIndicatorMap = new HashMap<String, String>();
List<Result> results = resultDAO.getResultsForSample(sample);
History searchHistory = new History();
searchHistory.setReferenceTable(NOTE_TABLE_ID);
historyList = new ArrayList<History>();
Note searchNote = new Note();
searchNote.setReferenceTableId(RESULT_TABLE_ID);
for (Result result : results) {
searchNote.setReferenceId(result.getId());
List<Note> notes = noteDAO.getAllNotesByRefIdRefTable(searchNote);
for (Note note : notes) {
searchHistory.setReferenceId(note.getId());
noteIdToIndicatorMap.put(
note.getId(), TestService.getLocalizedTestName(result.getAnalysis().getTest()));
historyList.addAll(auditTrailDAO.getHistoryByRefIdAndRefTableId(searchHistory));
}
}
newValueMap = new HashMap<String, String>();
}
private void addResultSets(Analysis analysis, Result result) {
Sample sample = analysis.getSampleItem().getSample();
Patient patient = sampleHumanDAO.getPatientForSample(sample);
List<DocumentTrack> documents =
documentTrackDAO.getByTypeRecordAndTable(RESULT_REPORT_ID, RESULT_TABLE_ID, result.getId());
if (documents.isEmpty()) {
newResultSet.add(new ResultSet(result, null, null, patient, sample, null, false));
} else {
modifiedResultSet.add(new ResultSet(result, null, null, patient, sample, null, false));
}
}
/**
* Move everything appropriate to the referralItem including one or more of the referralResults
* from the given list. Note: This method removes an item from the referralResults list.
*
* @param referralItem The source item
* @param referralResults The created list
*/
private List<ReferralResult> setReferralItemForNextTest(
IReferralResultTest referralItem, List<ReferralResult> referralResults) {
ReferralResult nextTestFirstResult = referralResults.remove(0);
List<ReferralResult> resultsForOtherTests = new ArrayList<ReferralResult>(referralResults);
referralItem.setReferredTestId(nextTestFirstResult.getTestId());
referralItem.setReferredTestIdShadow(referralItem.getReferredTestId());
referralItem.setReferredReportDate(
DateUtil.convertTimestampToStringDate(nextTestFirstResult.getReferralReportDate()));
// We can not use ResultService because that assumes the result is for an analysis, not a
// referral
Result result = nextTestFirstResult.getResult();
String resultType = (result != null) ? result.getResultType() : "N";
referralItem.setReferredResultType(resultType);
if (!ResultType.isMultiSelectVariant(resultType)) {
if (result != null) {
String resultValue =
GenericValidator.isBlankOrNull(result.getValue()) ? "" : result.getValue();
referralItem.setReferredResult(resultValue);
referralItem.setReferredDictionaryResult(resultValue);
}
} else {
ArrayList<Result> resultList = new ArrayList<Result>();
resultList.add(nextTestFirstResult.getResult());
for (ReferralResult referralResult : referralResults) {
if (nextTestFirstResult.getTestId().equals(referralResult.getTestId())
&& !GenericValidator.isBlankOrNull(referralResult.getResult().getValue())) {
resultList.add(referralResult.getResult());
resultsForOtherTests.remove(referralResult);
}
}
referralItem.setMultiSelectResultValues(
ResultService.getJSONStringForMultiSelect(resultList));
}
return resultsForOtherTests;
}
private String getAppropriateResultValue(List<Result> results) {
Result result = results.get(0);
if (ResultType.DICTIONARY.matches(result.getResultType())) {
Dictionary dictionary = dictionaryDAO.getDictionaryById(result.getValue());
if (dictionary != null) {
return dictionary.getLocalizedName();
}
} else if (ResultType.isMultiSelectVariant(result.getResultType())) {
Dictionary dictionary = new Dictionary();
StringBuilder multiResult = new StringBuilder();
for (Result subResult : results) {
dictionary.setId(subResult.getValue());
dictionaryDAO.getData(dictionary);
if (dictionary.getId() != null) {
multiResult.append(dictionary.getLocalizedName());
multiResult.append(", ");
}
}
if (multiResult.length() > 0) {
multiResult.setLength(multiResult.length() - 2); // remove last ", "
}
return multiResult.toString();
} else {
String resultValue =
GenericValidator.isBlankOrNull(result.getValue()) ? "" : result.getValue();
if (!GenericValidator.isBlankOrNull(resultValue)
&& result.getAnalysis().getTest().getUnitOfMeasure() != null) {
resultValue += " " + result.getAnalysis().getTest().getUnitOfMeasure().getName();
}
return resultValue;
}
return "";
}
protected ActivityReportBean createActivityReportBean(Result result, boolean useTestName) {
ActivityReportBean item = new ActivityReportBean();
ResultService resultService = new ResultService(result);
SampleService sampleService =
new SampleService(result.getAnalysis().getSampleItem().getSample());
PatientService patientService = new PatientService(sampleService.getSample());
item.setResultValue(resultService.getResultValue("\n", true, true));
item.setTechnician(resultService.getSignature());
item.setAccessionNumber(sampleService.getAccessionNumber().substring(PREFIX_LENGTH));
item.setReceivedDate(sampleService.getReceivedDateWithTwoYearDisplay());
item.setResultDate(DateUtil.convertTimestampToTwoYearStringDate(result.getLastupdated()));
item.setCollectionDate(
DateUtil.convertTimestampToTwoYearStringDate(
result.getAnalysis().getSampleItem().getCollectionDate()));
List<String> values = new ArrayList<String>();
values.add(
patientService.getLastName() == null ? "" : patientService.getLastName().toUpperCase());
values.add(patientService.getNationalId());
String referringPatientId =
ObservationHistoryService.getValueForSample(
ObservationType.REFERRERS_PATIENT_ID, sampleService.getSample().getId());
values.add(referringPatientId == null ? "" : referringPatientId);
String name = StringUtil.buildDelimitedStringFromList(values, " / ", true);
if (useTestName) {
item.setPatientOrTestName(resultService.getTestName());
item.setNonPrintingPatient(name);
} else {
item.setPatientOrTestName(name);
}
return item;
}
protected ActionForward performAction(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
String forward = FWD_SUCCESS;
request.setAttribute(ALLOW_EDITS_KEY, "true");
BaseActionForm dynaForm = (BaseActionForm) form;
// server-side validation (validation.xml)
ActionMessages errors = dynaForm.validate(mapping, request);
// bugzilla 2614 allow for NB domain samples
String selectedTestId = "";
String referenceTableId = SystemConfiguration.getInstance().getResultReferenceTableId();
String refId = (String) dynaForm.get("noteRefId");
String noteIds = (String) dynaForm.get("noteIds");
String noteSubjects = (String) dynaForm.get("noteSubjects");
String noteTexts = (String) dynaForm.get("noteTexts");
String noteTypes = (String) dynaForm.get("noteTypes");
String noteLastupdateds = (String) dynaForm.get("noteLastupdateds");
List noteIdList = new ArrayList();
List noteSubjectList = new ArrayList();
List noteTextList = new ArrayList();
List noteTypeList = new ArrayList();
List noteLastupdatedList = new ArrayList();
String textSeparator = SystemConfiguration.getInstance().getDefaultTextSeparator();
NoteDAO noteDAO = new NoteDAOImpl();
SystemUserDAO systemUserDAO = new SystemUserDAOImpl();
// bugzilla 2571 go through ReferenceTablesDAO to get reference tables info
ReferenceTablesDAO referenceTablesDAO = new ReferenceTablesDAOImpl();
// get sysUserId from login module
UserSessionData usd = (UserSessionData) request.getSession().getAttribute(USER_SESSION_DATA);
String sysUserId = String.valueOf(usd.getSystemUserId());
org.hibernate.Transaction tx = HibernateUtil.getSession().beginTransaction();
try {
textSeparator = StringUtil.convertStringToRegEx(textSeparator);
SystemUser systemUser = new SystemUser();
systemUser.setId(sysUserId);
systemUserDAO.getData(systemUser);
// get all the data required to forward to correct page
// get analysis id from result
ResultDAO resultDAO = new ResultDAOImpl();
Result result = new Result();
result.setId(refId);
resultDAO.getData(result);
String analysisId = result.getAnalysis().getId();
AnalysisDAO analysisDAO = new AnalysisDAOImpl();
Analysis analysis = new Analysis();
analysis.setId(analysisId);
analysisDAO.getData(analysis);
// get test id from analysis
selectedTestId = analysis.getTest().getId();
// get domain from sample
SampleItemDAO sampleItemDAO = new SampleItemDAOImpl();
SampleItem sampleItem = new SampleItem();
sampleItem.setId(analysis.getSampleItem().getId());
sampleItemDAO.getData(sampleItem);
SampleDAO sampleDAO = new SampleDAOImpl();
Sample sample = new Sample();
// bugzilla 1773 need to store sample not sampleId for use in sorting
sample.setId(sampleItem.getSample().getId());
sampleDAO.getData(sample);
// bugzilla 2614 allow for NB domain samples
// now that we have the domain (for forwarding to correct fail page)
// validate note popup form data!
try {
// bugzilla 2254 moved loadListFromStringOfElements to StringUtil
noteIdList = StringUtil.loadListFromStringOfElements(noteIds, textSeparator, false);
noteLastupdatedList =
StringUtil.loadListFromStringOfElements(noteLastupdateds, textSeparator, false);
// these three need to be validated for empty strings
noteSubjectList =
StringUtil.loadListFromStringOfElements(noteSubjects, textSeparator, true);
noteTextList = StringUtil.loadListFromStringOfElements(noteTexts, textSeparator, true);
noteTypeList = StringUtil.loadListFromStringOfElements(noteTypes, textSeparator, true);
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ResultsEntryNotesUpdateAction", "performAction()", e.toString());
String messageKey = "note.note";
ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null);
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
saveErrors(request, errors);
forward = FWD_FAIL;
return mapping.findForward(forward);
}
for (int i = 0; i < noteIdList.size(); i++) {
Note note = new Note();
String noteId = (String) noteIdList.get(i);
note.setReferenceId(refId);
// bugzilla 1922
// bugzilla 2571 go through ReferenceTablesDAO to get reference tables info
ReferenceTables referenceTables = new ReferenceTables();
referenceTables.setId(referenceTableId);
// bugzilla 2571
referenceTablesDAO.getData(referenceTables);
note.setReferenceTables(referenceTables);
note.setSystemUser(systemUser);
note.setSystemUserId(sysUserId);
// 1926 for audit trail
note.setSysUserId(sysUserId);
if (noteId != null && !noteId.equals("0")) {
note.setId((String) noteIdList.get(i));
note.setSubject((String) noteSubjectList.get(i));
note.setText((String) noteTextList.get(i));
note.setNoteType((String) noteTypeList.get(i));
Timestamp noteTimestamp = null;
if (!StringUtil.isNullorNill((String) noteLastupdatedList.get(i))) {
noteTimestamp = DateUtil.formatStringToTimestamp((String) noteLastupdatedList.get(i));
}
note.setLastupdated(noteTimestamp);
// UPDATE
noteDAO.updateData(note);
// }
} else {
// this is a new note
note.setSubject((String) noteSubjectList.get(i));
note.setText((String) noteTextList.get(i));
note.setNoteType((String) noteTypeList.get(i));
// INSERT
noteDAO.insertData(note);
}
}
tx.commit();
return getForward(mapping.findForward(forward), selectedTestId, analysisId);
} catch (LIMSRuntimeException lre) {
// bugzilla 2154
LogEvent.logError("ResultsEntryNotesUpdateAction", "performAction()", lre.toString());
tx.rollback();
errors = new ActionMessages();
ActionError error = null;
if (lre.getException() instanceof org.hibernate.StaleObjectStateException) {
error = new ActionError("errors.OptimisticLockException", null, null);
} else {
if (lre.getException() instanceof LIMSDuplicateRecordException) {
java.util.Locale locale =
(java.util.Locale)
request.getSession().getAttribute("org.apache.struts.action.LOCALE");
String messageKey = "note.note";
String msg =
ResourceLocator.getInstance().getMessageResources().getMessage(locale, messageKey);
error = new ActionError("errors.DuplicateRecord", msg, null);
} else {
error = new ActionError("errors.UpdateException", null, null);
}
}
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
saveErrors(request, errors);
request.setAttribute(Globals.ERROR_KEY, errors);
// disable previous and next
request.setAttribute(PREVIOUS_DISABLED, "true");
request.setAttribute(NEXT_DISABLED, "true");
// default forward fail
forward = FWD_FAIL;
} finally {
HibernateUtil.closeSession();
}
if (forward.equals(FWD_FAIL)
|| forward.equals(FWD_FAIL_HUMAN)
|| forward.equals(FWD_FAIL_ANIMAL)) return mapping.findForward(forward);
// initialize the form
dynaForm.initialize(mapping);
// we need this for subsequent actions to
// get data related to note parent for forwarding to next page
request.setAttribute("refId", refId);
request.setAttribute(SELECTED_TEST_ID, selectedTestId);
return mapping.findForward(forward);
}
@Override
protected ActionForward performAction(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
String forward = FWD_SUCCESS;
List<IResultUpdate> updaters = ValidationUpdateRegister.getRegisteredUpdaters();
boolean areListeners = updaters != null && !updaters.isEmpty();
request.getSession().setAttribute(SAVE_DISABLED, "true");
BaseActionForm dynaForm = (BaseActionForm) form;
ResultValidationPaging paging = new ResultValidationPaging();
paging.updatePagedResults(request, dynaForm);
List<AnalysisItem> resultItemList = paging.getResults(request);
String testSectionName = (String) dynaForm.get("testSection");
String testName = (String) dynaForm.get("testName");
setRequestType(testSectionName);
ActionMessages errors = validateModifiedItems(resultItemList);
if (errors.size() > 0) {
saveErrors(request, errors);
request.setAttribute(Globals.ERROR_KEY, errors);
return mapping.findForward(FWD_VALIDATION_ERROR);
}
createSystemUser();
setSampleFinishedStatuses();
noteUpdateList = new ArrayList<Note>();
resultUpdateList = new ArrayList<Result>();
analysisUpdateList = new ArrayList<Analysis>();
modifiedResultSet = new ArrayList<ResultSet>();
newResultSet = new ArrayList<ResultSet>();
deletableList = new ArrayList<Result>();
if (testSectionName.equals("serology")) {
createUpdateElisaList(resultItemList);
} else {
createUpdateList(resultItemList, areListeners);
}
Transaction tx = HibernateUtil.getSession().beginTransaction();
try {
ResultSaveService.removeDeletedResultsInTransaction(deletableList, currentUserId);
// update analysis
for (Analysis analysis : analysisUpdateList) {
analysisDAO.updateData(analysis);
}
for (Result result : resultUpdateList) {
if (result.getId() != null) {
resultDAO.updateData(result);
} else {
resultDAO.insertData(result);
}
}
checkIfSamplesFinished(resultItemList);
// update finished samples
for (Sample sample : sampleUpdateList) {
sampleDAO.updateData(sample);
}
// create or update notes
for (Note note : noteUpdateList) {
if (note != null) {
if (note.getId() == null) {
noteDAO.insertData(note);
} else {
noteDAO.updateData(note);
}
}
}
for (IResultUpdate updater : updaters) {
updater.transactionalUpdate(this);
}
tx.commit();
} catch (LIMSRuntimeException lre) {
tx.rollback();
}
for (IResultUpdate updater : updaters) {
updater.postTransactionalCommitUpdate(this);
}
if (isBlankOrNull(testSectionName)) {
return mapping.findForward(forward);
} else {
Map<String, String> params = new HashMap<String, String>();
params.put("type", testSectionName);
params.put("test", testName);
params.put("forward", forward);
return getForwardWithParameters(mapping.findForward(forward), params);
}
}
private ReferralItem getReferralItem(Referral referral) {
boolean allReferralResultsHaveResults = true;
List<ReferralResult> referralResults =
referralResultDAO.getReferralResultsForReferral(referral.getId());
for (ReferralResult referralResult : referralResults) {
if (referralResult.getResult() == null
|| GenericValidator.isBlankOrNull(referralResult.getResult().getValue())) {
allReferralResultsHaveResults = false;
break;
}
}
if (allReferralResultsHaveResults) {
return null;
}
ReferralItem referralItem = new ReferralItem();
AnalysisService analysisService = new AnalysisService(referral.getAnalysis());
referralItem.setCanceled(false);
referralItem.setReferredResultType("N");
referralItem.setAccessionNumber(analysisService.getOrderAccessionNumber());
TypeOfSample typeOfSample = analysisService.getTypeOfSample();
referralItem.setSampleType(typeOfSample.getLocalizedName());
referralItem.setReferringTestName(
TestService.getUserLocalizedTestName(analysisService.getAnalysis().getTest()));
List<Result> resultList = analysisService.getResults();
String resultString = "";
if (!resultList.isEmpty()) {
Result result = resultList.get(0);
resultString = getAppropriateResultValue(resultList);
referralItem.setInLabResultId(result.getId());
}
referralItem.setReferralId(referral.getId());
if (!referralResults.isEmpty()) {
referralResults = setReferralItemForNextTest(referralItem, referralResults);
if (!referralResults.isEmpty()) {
referralItem.setAdditionalTests(getAdditionalReferralTests(referralResults));
}
}
referralItem.setReferralResults(resultString);
referralItem.setReferralDate(DateUtil.convertTimestampToStringDate(referral.getRequestDate()));
referralItem.setReferredSendDate(getSendDateOrDefault(referral));
referralItem.setReferrer(referral.getRequesterName());
referralItem.setReferralReasonId(referral.getReferralReasonId());
referralItem.setTestSelectionList(getTestsForTypeOfSample(typeOfSample));
referralItem.setReferralId(referral.getId());
if (referral.getOrganization() != null) {
referralItem.setReferredInstituteId(referral.getOrganization().getId());
}
String notes = analysisService.getNotesAsString(true, true, "<br/>", false);
if (notes != null) {
referralItem.setPastNotes(notes);
}
return referralItem;
}