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);
}
}
}
}
public String validateAndUpdateAnalyzerTestName(
ActionMapping mapping, HttpServletRequest request, BaseActionForm dynaForm) {
String forward = FWD_SUCCESS_INSERT;
String analyzerId = dynaForm.getString("analyzerId");
String testId = dynaForm.getString("testId");
String analyzerTestName = dynaForm.getString("analyzerTestName");
boolean newMapping = "0".equals(request.getParameter("ID"));
ActionMessages errors = new ActionMessages();
AnalyzerTestMapping analyzerTestNameMapping =
validateAnalyzerAndTestName(analyzerId, analyzerTestName, testId, errors, newMapping);
if (errors.size() > 0) {
saveErrors(request, errors);
return FWD_FAIL;
}
if (newMapping) {
analyzerTestNameMapping = new AnalyzerTestMapping();
analyzerTestNameMapping.setAnalyzerId(analyzerId);
analyzerTestNameMapping.setAnalyzerTestName(analyzerTestName);
analyzerTestNameMapping.setTestId(testId);
}
AnalyzerTestMappingDAO mappingDAO = new AnalyzerTestMappingDAOImpl();
Transaction tx = HibernateUtil.getSession().beginTransaction();
try {
if (newMapping) {
mappingDAO.insertData(analyzerTestNameMapping, currentUserId);
} else {
mappingDAO.updateMapping(analyzerTestNameMapping, currentUserId);
}
} catch (LIMSRuntimeException lre) {
tx.rollback();
ActionError error = null;
if (lre.getException() instanceof org.hibernate.StaleObjectStateException) {
error = new ActionError("errors.OptimisticLockException", null, null);
} else {
error = new ActionError("errors.UpdateException", null, null);
}
persisteError(request, error);
disableNavigationButtons(request);
forward = FWD_FAIL;
} finally {
if (!tx.wasRolledBack()) {
tx.commit();
}
HibernateUtil.closeSession();
}
AnalyzerTestNameCache.instance().reloadCache();
return forward;
}