private String getSendDateOrDefault(Referral referral) {
if (referral.getSentDate() == null) {
return DateUtil.getCurrentDateAsText();
} else {
return DateUtil.convertTimestampToStringDate(referral.getSentDate());
}
}
private void addAnalyzerResultFromLine(List<AnalyzerResults> results, String line) {
String[] fields = StringUtil.separateCSVWithMixedEmbededQuotes(line);
// This insures that the row has not been truncated
if (fields.length < maxViewedIndex) {
return;
}
AnalyzerReaderUtil readerUtil = new AnalyzerReaderUtil();
String analyzerAccessionNumber = fields[Sample_ID].replace("\"", "");
analyzerAccessionNumber = StringUtil.strip(analyzerAccessionNumber, " ");
String date = fields[Date_Analyzed].replace("\"", "");
// this is sort of dumb, we have the indexes we are interested in
for (int i = 0; i < testNameIndex.length; i++) {
if (!GenericValidator.isBlankOrNull(testNameIndex[i])) {
MappedTestName mappedName =
AnalyzerTestNameCache.instance()
.getMappedTest(AnalyzerType.FACSCANTO, testNameIndex[i].replace("\"", ""));
if (mappedName == null) {
mappedName =
AnalyzerTestNameCache.instance()
.getEmptyMappedTestName(
AnalyzerType.FACSCANTO, testNameIndex[i].replace("\"", ""));
}
AnalyzerResults analyzerResults = new AnalyzerResults();
analyzerResults.setAnalyzerId(mappedName.getAnalyzerId());
String result = fields[i].replace("\"", "");
result = roundTwoDigits(result);
analyzerResults.setResult(result);
analyzerResults.setUnits(unitsIndex[i]);
analyzerResults.setCompleteDate(
DateUtil.convertStringDateToTimestampWithPatternNoLocale(date, DATE_PATTERN));
// analyzerResults.setCompleteTime(DateUtil.convertStringDateToTimestamp(date));
analyzerResults.setTestId(mappedName.getTestId());
analyzerResults.setAccessionNumber(analyzerAccessionNumber);
analyzerResults.setTestName(mappedName.getOpenElisTestName());
if (analyzerAccessionNumber != null) {
analyzerResults.setIsControl(
analyzerAccessionNumber.startsWith(CONTROL_ACCESSION_PREFIX));
} else {
analyzerResults.setIsControl(false);
}
results.add(analyzerResults);
AnalyzerResults resultFromDB = readerUtil.createAnalyzerResultFromDB(analyzerResults);
if (resultFromDB != null) {
results.add(resultFromDB);
}
}
}
}
private double getCurrPatientAge(Patient patient) {
if (currPatientAge == INVALID_PATIENT_AGE && patient.getBirthDate() != null) {
Calendar dob = Calendar.getInstance();
dob.setTime(patient.getBirthDate());
currPatientAge = DateUtil.getAgeInMonths(patient.getBirthDate(), new Date());
}
return currPatientAge;
}
private ReportExternalImport createReportExternalImport(
String sendingSiteId, String eventDate, String data) {
ReportExternalImport importReport = new ReportExternalImport();
importReport.setEventDate(
DateUtil.convertStringDateToTimestampWithPatternNoLocale(eventDate, DATE_PATTERN));
importReport.setSendingSite(sendingSiteId);
importReport.setReportType("testIndicators");
ReportExternalImport rei = reportImportDAO.getReportByEventDateSiteType(importReport);
if (rei != null) {
importReport = rei;
}
importReport.setData(data);
importReport.setSysUserId("1");
importReport.setRecievedDate(DateUtil.getTimestampAtMidnightForDaysAgo(0));
return importReport;
}
@Override
public void initializeReport(BaseActionForm dynaForm) {
super.initializeReport();
errorFound = false;
lowerDateRange = dynaForm.getString("lowerDateRange");
upperDateRange = dynaForm.getString("upperDateRange");
if (GenericValidator.isBlankOrNull(lowerDateRange)) {
errorFound = true;
ErrorMessages msgs = new ErrorMessages();
msgs.setMsgLine1(StringUtil.getMessageForKey("report.error.message.noPrintableItems"));
errorMsgs.add(msgs);
}
if (GenericValidator.isBlankOrNull(upperDateRange)) {
upperDateRange = lowerDateRange;
}
try {
lowDate = DateUtil.convertStringDateToSqlDate(lowerDateRange);
highDate = DateUtil.convertStringDateToSqlDate(upperDateRange);
} catch (LIMSRuntimeException re) {
errorFound = true;
ErrorMessages msgs = new ErrorMessages();
msgs.setMsgLine1(StringUtil.getMessageForKey("report.error.message.date.format"));
errorMsgs.add(msgs);
}
createReportParameters();
initializeReportItems();
setTestMapForAllTests();
setAnalysisForDateRange();
setTestAggregates();
}
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 RejectionReportBean createRejectionReportBean(
String noteText, Analysis analysis, boolean useTestName) {
RejectionReportBean item = new RejectionReportBean();
AnalysisService analysisService = new AnalysisService(analysis);
SampleService sampleService =
new SampleService(analysisService.getAnalysis().getSampleItem().getSample());
PatientService patientService = new PatientService(sampleService.getSample());
List<Result> results = analysisService.getResults();
for (Result result : results) {
String signature = new ResultService(result).getSignature();
if (!GenericValidator.isBlankOrNull(signature)) {
item.setTechnician(signature);
break;
}
}
item.setAccessionNumber(sampleService.getAccessionNumber().substring(PREFIX_LENGTH));
item.setReceivedDate(sampleService.getTwoYearReceivedDateForDisplay());
item.setCollectionDate(
DateUtil.convertTimestampToTwoYearStringDate(
analysisService.getAnalysis().getSampleItem().getCollectionDate()));
item.setRejectionReason(noteText);
StringBuilder nameBuilder = new StringBuilder(patientService.getLastName().toUpperCase());
if (!GenericValidator.isBlankOrNull(patientService.getNationalId())) {
if (nameBuilder.length() > 0) {
nameBuilder.append(" / ");
}
nameBuilder.append(patientService.getNationalId());
}
if (useTestName) {
item.setPatientOrTestName(analysisService.getTest().getLocalizedName());
item.setNonPrintingPatient(nameBuilder.toString());
} else {
item.setPatientOrTestName(nameBuilder.toString());
}
return item;
}
private List<ReferredTest> getAdditionalReferralTests(List<ReferralResult> referralResults) {
List<ReferredTest> additionalTestList = new ArrayList<ReferredTest>();
while (!referralResults.isEmpty()) {
ReferralResult referralResult =
referralResults.get(0); // use the top one to load various bits of information.
ReferredTest referralTest = new ReferredTest();
referralTest.setReferralId(referralResult.getReferralId());
referralResults =
setReferralItemForNextTest(
referralTest,
referralResults); // remove one or more referralResults from the list as needed (for
// multiResults).
referralTest.setReferredReportDate(
DateUtil.convertTimestampToStringDate(referralResult.getReferralReportDate()));
referralTest.setReferralResultId(referralResult.getId());
additionalTestList.add(referralTest);
}
return additionalTestList;
}
/**
* 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;
}
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);
}
protected List populateHistoryList(
HttpServletRequest request,
List historyRecords,
String rootNodeName,
String xslMappingFileName)
throws LIMSRuntimeException {
List list = new ArrayList();
try {
SystemUserDAO systemUserDAO = new SystemUserDAOImpl();
AuditTrailDAO auditTrailDAO = new AuditTrailDAOImpl();
for (int i = 0; i < historyRecords.size(); i++) {
History historyRecord = (History) historyRecords.get(i);
Timestamp date = historyRecord.getTimestamp();
String stringLocale = SystemConfiguration.getInstance().getDefaultLocale().toString();
String dateForDisplay = DateUtil.convertTimestampToStringDateAndTime(date, stringLocale);
SystemUser systemUser = new SystemUser();
systemUser.setId(historyRecord.getSysUserId());
systemUserDAO.getData(systemUser);
String blob = null;
if (!historyRecord.getActivity().equals(AUDIT_TRAIL_INSERT)) {
blob = auditTrailDAO.retrieveBlobData(historyRecord.getId());
}
// this is temporary until 2593 has been completed
if (historyRecord.getActivity().equals(IActionConstants.AUDIT_TRAIL_UPDATE)) {
blob = "<" + rootNodeName + ">" + blob + "</" + rootNodeName + ">";
}
if (!StringUtil.isNullorNill(blob)) {
HistoryXmlHelper historyXmlHelper = new HistoryXmlHelper();
historyXmlHelper.setActivity(historyRecord.getActivity());
historyXmlHelper.setUserName(systemUser.getNameForDisplay());
String media = null, title = null, charset = null, xsldata = "";
ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
try {
// NOTE!!!!
// in order to run this in oc4j I needed to do the following:
// add this to OC4J startup:
// -Djavax.xml.transform.TransformerFactory=org.apache.xalan.processor.TransformerFactoryImpl
// to make sure that oc4j uses correct XSL processor (else it could not handle "function
// extensions" used to bring in MessageResources labels
// place xalan.jar, xml-apis.jar, XercesImpl.jar into the applib folder of the oc4j
// installation
TransformerFactory tFactory = TransformerFactory.newInstance();
HttpSession session = request.getSession();
ServletContext context = session.getServletContext();
File xslFile =
new File(context.getRealPath("/WEB-INF/transformation/" + xslMappingFileName));
Source stylesheet = new StreamSource(xslFile);
Transformer transformer = tFactory.newTransformer(stylesheet);
System.out.println("This is blob " + blob);
transformer.transform(
new StreamSource(new StringReader(blob)), new StreamResult(outputStream));
} catch (TransformerConfigurationException tce) {
tce.printStackTrace();
} catch (TransformerException te) {
te.printStackTrace();
} catch (Exception e) {
e.printStackTrace();
}
System.out.println("This is xml " + outputStream.toString());
historyXmlHelper.setChange(outputStream.toString());
historyXmlHelper.setDate(dateForDisplay);
if (!StringUtil.isNullorNill(historyXmlHelper.getChange())) {
historyXmlHelper.setChange(historyXmlHelper.getChange().trim());
}
if (!StringUtil.isNullorNill(historyXmlHelper.getChange())) {
list.add(historyXmlHelper);
}
}
}
} catch (Exception e) {
throw new LIMSRuntimeException(e);
}
return list;
}
protected ActionForward performAction(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
// The first job is to determine if we are coming to this action with an
// ID parameter in the request. If there is no parameter, we are
// creating a new Sample.
// If there is a parameter present, we should bring up an existing
// Sample to edit.
String forward = FWD_SUCCESS;
request.setAttribute(ALLOW_EDITS_KEY, "true");
String id = request.getParameter(ID);
if (StringUtil.isNullorNill(id) || "0".equals(id)) {
isNew = true;
} else {
isNew = false;
}
BaseActionForm dynaForm = (BaseActionForm) form;
// first get the accessionNumber and whether we are on blank page or not
String accessionNumber = (String) dynaForm.get("accessionNumber");
// bugzilla 2154
LogEvent.logDebug(
"HumanSampleTwoPopulateHashMapFromDE1Action",
"performAction()",
"accessionNumber coming in: " + accessionNumber);
String start = (String) request.getParameter("startingRecNo");
String typeOfSample = (String) dynaForm.get("typeOfSampleDesc");
String sourceOfSample = (String) dynaForm.get("sourceOfSampleDesc");
List typeOfSamples = new ArrayList();
List sourceOfSamples = new ArrayList();
if (dynaForm.get("typeOfSamples") != null) {
typeOfSamples = (List) dynaForm.get("typeOfSamples");
} else {
TypeOfSampleDAO typeOfSampleDAO = new TypeOfSampleDAOImpl();
typeOfSamples = typeOfSampleDAO.getAllTypeOfSamples();
}
if (dynaForm.get("sourceOfSamples") != null) {
sourceOfSamples = (List) dynaForm.get("sourceOfSamples");
} else {
SourceOfSampleDAO sourceOfSampleDAO = new SourceOfSampleDAOImpl();
sourceOfSamples = sourceOfSampleDAO.getAllSourceOfSamples();
}
HashMap humanSampleOneMap = new HashMap();
if (dynaForm.get("humanSampleOneMap") != null) {
humanSampleOneMap = (HashMap) dynaForm.get("humanSampleOneMap");
}
String projectIdOrName = (String) dynaForm.get("projectIdOrName");
String project2IdOrName = (String) dynaForm.get("project2IdOrName");
String projectNameOrId = (String) dynaForm.get("projectNameOrId");
String project2NameOrId = (String) dynaForm.get("project2NameOrId");
String projectId = null;
String project2Id = null;
if (projectIdOrName != null && projectNameOrId != null) {
try {
Integer i = Integer.valueOf(projectIdOrName);
projectId = projectIdOrName;
} catch (NumberFormatException nfe) {
// bugzilla 2154
LogEvent.logError(
"HumanSampleTwoPopulateHashMapFromDE1Action", "performAction()", nfe.toString());
projectId = projectNameOrId;
}
}
if (project2IdOrName != null && project2NameOrId != null) {
try {
Integer i = Integer.valueOf(project2IdOrName);
project2Id = project2IdOrName;
} catch (NumberFormatException nfe) {
// bugzilla 2154
LogEvent.logError(
"HumanSampleTwoPopulateHashMapFromDE1Action", "performAction()", nfe.toString());
project2Id = project2NameOrId;
}
}
// bugzilla 2154
LogEvent.logDebug(
"HumanSampleTwoPopulateHashMapFromDE1Action",
"performAction()",
"ProjectId is: " + projectId + " Project2Id is: " + project2Id);
// set current date for validation of dates
Date today = Calendar.getInstance().getTime();
Locale locale = (Locale) request.getSession().getAttribute("org.apache.struts.action.LOCALE");
String dateAsText = DateUtil.formatDateAsText(today, locale);
Patient patient = new Patient();
Person person = new Person();
Provider provider = new Provider();
Person providerPerson = new Person();
Sample sample = new Sample();
SampleHuman sampleHuman = new SampleHuman();
SampleOrganization sampleOrganization = new SampleOrganization();
List sampleProjects = new ArrayList();
List updatedSampleProjects = new ArrayList();
SampleItem sampleItem = new SampleItem();
// TODO need to populate this with tests entered in HSE I
List analyses = new ArrayList();
// tests are not handled in HSE II
/*
* String stringOfTestIds = (String) dynaForm.get("selectedTestIds");
*
* String[] listOfTestIds = stringOfTestIds.split(SystemConfiguration
* .getInstance().getDefaultIdSeparator(), -1);
*
* List analyses = new ArrayList(); for (int i = 0; i <
* listOfTestIds.length; i++) { if
* (!StringUtil.isNullorNill(listOfTestIds[i])) { Analysis analysis =
* new Analysis(); analysis.setTestId(listOfTestIds[i]); // TODO: need
* to populate this with actual data!!!
* analysis.setAnalysisType("TEST"); analyses.add(analysis); } }
*/
ActionMessages errors = null;
// validate on server-side sample accession number
try {
errors = new ActionMessages();
errors = validateAccessionNumber(request, errors, dynaForm);
// System.out.println("Just validated accessionNumber");
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError(
"HumanSampleTwoPopulateHashMapFromDE1Action", "performAction()", e.toString());
ActionError error = new ActionError("errors.ValidationException", null, null);
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
}
// System.out.println("This is errors after validation of accn Number "
// + errors);
if (errors != null && errors.size() > 0) {
saveErrors(request, errors);
// initialize the form but retain the invalid accessionNumber
dynaForm.initialize(mapping);
dynaForm.set("accessionNumber", accessionNumber);
// repopulate lists
PropertyUtils.setProperty(dynaForm, "typeOfSamples", typeOfSamples);
PropertyUtils.setProperty(dynaForm, "sourceOfSamples", sourceOfSamples);
request.setAttribute(ALLOW_EDITS_KEY, "false");
return mapping.findForward(FWD_FAIL);
}
// System.out.println("Now try to get data for accession number ");
try {
PatientDAO patientDAO = new PatientDAOImpl();
PersonDAO personDAO = new PersonDAOImpl();
ProviderDAO providerDAO = new ProviderDAOImpl();
SampleDAO sampleDAO = new SampleDAOImpl();
SampleItemDAO sampleItemDAO = new SampleItemDAOImpl();
SampleHumanDAO sampleHumanDAO = new SampleHumanDAOImpl();
SampleOrganizationDAO sampleOrganizationDAO = new SampleOrganizationDAOImpl();
AnalysisDAO analysisDAO = new AnalysisDAOImpl();
sample.setAccessionNumber(accessionNumber);
sampleDAO.getSampleByAccessionNumber(sample);
if (!StringUtil.isNullorNill(sample.getId())) {
sampleHuman.setSampleId(sample.getId());
sampleHumanDAO.getDataBySample(sampleHuman);
sampleOrganization.setSampleId(sample.getId());
sampleOrganizationDAO.getDataBySample(sampleOrganization);
// bugzilla 1773 need to store sample not sampleId for use in
// sorting
sampleItem.setSample(sample);
sampleItemDAO.getDataBySample(sampleItem);
patient.setId(sampleHuman.getPatientId());
patientDAO.getData(patient);
person = patient.getPerson();
personDAO.getData(person);
provider.setId(sampleHuman.getProviderId());
providerDAO.getData(provider);
providerPerson = provider.getPerson();
personDAO.getData(providerPerson);
// bugzilla 2227
analyses = analysisDAO.getMaxRevisionAnalysesBySample(sampleItem);
humanSampleOneMap =
populateHumanSampleOneMap(
patient,
person,
provider,
providerPerson,
sample,
sampleHuman,
sampleOrganization,
sampleItem,
analyses);
}
} catch (LIMSRuntimeException lre) {
// if error then forward to fail and don't update to blank page
// = false
// bugzilla 2154
LogEvent.logError(
"HumanSampleTwoPopulateHashMapFromDE1Action", "performAction()", lre.toString());
errors = new ActionMessages();
ActionError error = null;
if (lre.getException() instanceof org.hibernate.StaleObjectStateException) {
// how can I get popup instead of struts error at the top of
// page?
// ActionMessages errors = dynaForm.validate(mapping,
// request);
error = new ActionError("errors.OptimisticLockException", null, null);
// bugzilla 2154
LogEvent.logError(
"HumanSampleTwoPopulateHashMapFromDE1Action",
"performAction()",
"errors.OptimisticLockException");
} else {
error = new ActionError("errors.GetException", null, null);
// bugzilla 2154
LogEvent.logError(
"HumanSampleTwoPopulateHashMapFromDE1Action", "performAction()", "errors.GetException");
}
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
saveErrors(request, errors);
request.setAttribute(Globals.ERROR_KEY, errors);
request.setAttribute(ALLOW_EDITS_KEY, "false");
return mapping.findForward(FWD_FAIL);
}
// initialize the form
dynaForm.initialize(mapping);
// set lastupdated fields
dynaForm.set("lastupdated", sample.getLastupdated());
dynaForm.set("personLastupdated", person.getLastupdated());
dynaForm.set("patientLastupdated", patient.getLastupdated());
dynaForm.set("providerPersonLastupdated", providerPerson.getLastupdated());
dynaForm.set("providerLastupdated", provider.getLastupdated());
dynaForm.set("sampleItemLastupdated", sampleItem.getLastupdated());
dynaForm.set("sampleHumanLastupdated", sampleHuman.getLastupdated());
dynaForm.set("sampleOrganizationLastupdated", sampleOrganization.getLastupdated());
if (updatedSampleProjects != null && updatedSampleProjects.size() > 0) {
if (updatedSampleProjects.size() == 1) {
SampleProject sp = (SampleProject) updatedSampleProjects.get(0);
dynaForm.set("sampleProject1Lastupdated", sp.getLastupdated());
// bugzilla 1857 deprecated stuff
// System.out.println("This is sp ts "
// + StringUtil.formatDateAsText(sp.getLastupdated(),
// SystemConfiguration.getInstance()
// .getDefaultLocale()));
}
if (updatedSampleProjects.size() == 2) {
SampleProject sp2 = (SampleProject) updatedSampleProjects.get(1);
dynaForm.set("sampleProject2Lastupdated", sp2.getLastupdated());
// bugzilla 1857 deprecated stuff
// System.out.println("This is sp2 ts "
// + StringUtil.formatDateAsText(sp2.getLastupdated(),
// SystemConfiguration.getInstance()
// .getDefaultLocale()));
}
}
if (dynaForm.get("sampleProject1Lastupdated") == null) {
PropertyUtils.setProperty(
form, "sampleProject1Lastupdated", new Timestamp(System.currentTimeMillis()));
}
if (dynaForm.get("sampleProject2Lastupdated") == null) {
PropertyUtils.setProperty(
form, "sampleProject2Lastupdated", new Timestamp(System.currentTimeMillis()));
}
PropertyUtils.setProperty(dynaForm, "currentDate", dateAsText);
PropertyUtils.setProperty(dynaForm, "accessionNumber", sample.getAccessionNumber());
// set receivedDate
PropertyUtils.setProperty(
dynaForm, "receivedDateForDisplay", (String) sample.getReceivedDateForDisplay());
PropertyUtils.setProperty(dynaForm, "typeOfSamples", typeOfSamples);
PropertyUtils.setProperty(dynaForm, "sourceOfSamples", sourceOfSamples);
PropertyUtils.setProperty(dynaForm, "humanSampleOneMap", humanSampleOneMap);
if ("true".equalsIgnoreCase(request.getParameter("close"))) {
forward = FWD_CLOSE;
}
if (sample.getId() != null && !sample.getId().equals("0")) {
request.setAttribute(ID, sample.getId());
}
if (forward.equals(FWD_SUCCESS)) {
request.setAttribute("menuDefinition", "default");
}
// bugzilla 2154
LogEvent.logDebug(
"HumanSampleTwoPopulateHashMapFromDE1Action",
"performAction()",
"forwarding to: " + forward);
// pdf - get accession number List
if (SystemConfiguration.getInstance().getEnabledSamplePdf().equals(YES)) {
String status =
SystemConfiguration.getInstance().getSampleStatusEntry1Complete(); // status = 2
String humanDomain = SystemConfiguration.getInstance().getHumanDomain();
UserTestSectionDAO userTestSectionDAO = new UserTestSectionDAOImpl();
List accessionNumberListTwo =
userTestSectionDAO.getSamplePdfList(request, locale, status, humanDomain);
PropertyUtils.setProperty(form, "accessionNumberListTwo", accessionNumberListTwo);
}
// return getForward(mapping.findForward(forward), id, start);
return mapping.findForward(forward);
}
private String getTwoDigitCurrentYear() {
return DateUtil.getTwoDigitYear();
}
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;
}