private AnalyzerTestMapping validateAnalyzerAndTestName(
String analyzerId,
String analyzerTestName,
String testId,
ActionMessages errors,
boolean newMapping) {
// This is not very efficient but this is a very low usage action
if (GenericValidator.isBlankOrNull(analyzerId)
|| GenericValidator.isBlankOrNull(analyzerTestName)
|| GenericValidator.isBlankOrNull(testId)) {
errors.add(ActionErrors.GLOBAL_MESSAGE, new ActionError("error.all.required"));
return null;
}
AnalyzerTestMapping existingMapping = null;
AnalyzerTestMappingDAO mappingDAO = new AnalyzerTestMappingDAOImpl();
List<AnalyzerTestMapping> testMappingList = mappingDAO.getAllAnalyzerTestMappings();
for (AnalyzerTestMapping testMapping : testMappingList) {
if (analyzerId.equals(testMapping.getAnalyzerId())
&& analyzerTestName.equals(testMapping.getAnalyzerTestName())) {
if (newMapping) {
errors.add(
ActionErrors.GLOBAL_MESSAGE, new ActionError("error.analyzer.test.name.duplicate"));
return null;
} else {
existingMapping = testMapping;
testMapping.setTestId(testId);
break;
}
}
}
return existingMapping;
}
private static void addChildMenuItems(
StringBuffer html, List<MenuItem> menuTree, String contextPath, boolean topLevel) {
int topLevelCount = 0;
for (MenuItem menuItem : menuTree) {
Menu menu = menuItem.getMenu();
if (topLevel) {
if (topLevelCount == 0) {
html.append("\t<li id=\"nav-first\" >\n");
} else if (topLevelCount == menuTree.size() - 1) {
html.append("\t<li id=\"nav-last\" >\n");
} else {
html.append("\t<li>\n");
}
topLevelCount++;
} else {
html.append("\t<li>\n");
}
html.append("\t\t<a ");
html.append("id=\"");
html.append(menu.getElementId());
html.append("\" ");
if (!GenericValidator.isBlankOrNull(menu.getLocalizedTooltip())) {
html.append(" title=\"");
html.append(menu.getLocalizedTooltip());
html.append("\" ");
}
if (menu.isOpenInNewWindow()) {
html.append(" target=\"_blank\" ");
}
if (GenericValidator.isBlankOrNull(menu.getActionURL())
&& GenericValidator.isBlankOrNull(menu.getClickAction())) {
html.append(" class=\"no-link\" >");
} else {
html.append(" href=\"");
html.append(contextPath);
html.append(menu.getActionURL());
html.append("\" >");
}
html.append(menu.getLocalizedTitle());
html.append("</a>\n");
if (!menuItem.getChildMenus().isEmpty()) {
html.append("<ul>\n");
addChildMenuItems(html, menuItem.getChildMenus(), contextPath, false);
html.append("</ul>\n");
}
html.append("\t</li>\n");
}
}
public boolean matchRegExp(String regExp, String inputValue) {
boolean validation = true;
MiscUtils.getLogger().debug("matchRegExp function is called.");
if (!GenericValidator.isBlankOrNull(regExp) && !GenericValidator.isBlankOrNull(inputValue)) {
MiscUtils.getLogger().debug("both the regExp and inputValue is not blank nor null.");
if (!inputValue.matches(regExp)) {
MiscUtils.getLogger().debug("Regexp not matched");
validation = false;
}
}
return validation;
}
public String validateNewFullName(JiraClient client, String fullName) {
if (GenericValidator.isBlankOrNull(fullName)) {
return "Please enter a full name.";
}
return null;
}
/** @see javax.servlet.jsp.tagext.BodyTagSupport#doStartTag() */
public int doStartTag() throws JspException {
final String pageAccess = (String) pageContext.getAttribute("access");
if ((pageAccess != null) && pageAccess.equals(Access.READONLY) && !forceReadWrite) {
return SKIP_BODY;
}
// Recherche si un parent est du bon type
Tag curParent = null;
for (curParent = getParent(); (curParent != null) && !(curParent instanceof ColsTag); ) {
curParent = curParent.getParent();
}
if (curParent == null) {
throw new JspException("ColTag must be used between Cols Tag.");
}
colsTag = (ColsTag) curParent;
if (!GenericValidator.isBlankOrNull(colsTag.getEmptyKey())
&& (pageContext.getAttribute(colsTag.getId()) == null)) {
return SKIP_BODY;
} else {
return EVAL_PAGE;
}
}
public void validate(Errors errors) {
if (StringUtils.isBlank(getUser().getCsmUser().getLoginName())) {
errors.rejectValue("user.csmUser.loginName", "error.user.name.not.specified");
} else {
User existing = authorizationManager.getUser(getUser().getCsmUser().getLoginName());
boolean existingMismatch =
existing != null && !existing.getUserId().equals(getUser().getCsmUser().getUserId());
if (!lookUpBoundUser && ((isNewUser() && existing != null) || existingMismatch)) {
errors.rejectValue("user.csmUser.loginName", "error.user.name.already.exists");
}
}
if (StringUtils.isBlank(getUser().getCsmUser().getFirstName())) {
errors.rejectValue("user.csmUser.firstName", "error.user.firstName.not.specified");
}
if (StringUtils.isBlank(getUser().getCsmUser().getLastName())) {
errors.rejectValue("user.csmUser.lastName", "error.user.lastName.not.specified");
}
if (!GenericValidator.isEmail(getUser().getCsmUser().getEmailId())) {
errors.rejectValue("user.csmUser.emailId", "error.user.email.invalid");
}
if (isNewUser() && getUsesLocalPasswords() && (StringUtils.isBlank(getPassword()))) {
errors.rejectValue("password", "error.user.password.not.specified");
}
if (getPassword() != null || getRePassword() != null) {
if (!ComparisonUtils.nullSafeEquals(getPassword(), getRePassword())) {
errors.rejectValue("rePassword", "error.user.repassword.does.not.match.password");
}
}
}
/**
* Validates that two fields match.
*
* @param bean
* @param va
* @param field
* @param errors
* @param request
* @return boolean
*/
public static boolean validateTwoFields(
Object bean,
ValidatorAction va,
Field field,
ActionMessages errors,
HttpServletRequest request) {
String value = ValidatorUtils.getValueAsString(bean, field.getProperty());
String sProperty2 = field.getVarValue("secondProperty");
String value2 = ValidatorUtils.getValueAsString(bean, sProperty2);
if (!GenericValidator.isBlankOrNull(value)) {
try {
if (!value.equals(value2)) {
errors.add(field.getKey(), Resources.getActionMessage(request, va, field));
return false;
}
} catch (Exception e) {
errors.add(field.getKey(), Resources.getActionMessage(request, va, field));
return false;
}
}
return true;
}
public void validate(Customer customer, String password, String passwordConfirm, Errors errors) {
ValidationUtils.rejectIfEmptyOrWhitespace(errors, "password", "password.required");
ValidationUtils.rejectIfEmptyOrWhitespace(
errors, "passwordConfirm", "passwordConfirm.required");
errors.pushNestedPath("customer");
ValidationUtils.rejectIfEmptyOrWhitespace(errors, "firstName", "firstName.required");
ValidationUtils.rejectIfEmptyOrWhitespace(errors, "lastName", "lastName.required");
ValidationUtils.rejectIfEmptyOrWhitespace(errors, "emailAddress", "emailAddress.required");
errors.popNestedPath();
if (errors.hasErrors()) {
if (!passwordConfirm.equals(password)) {
errors.rejectValue("passwordConfirm", "invalid");
}
if (!customer.getFirstName().matches(validNameRegex)) {
errors.rejectValue("firstName", "firstName.invalid", null, null);
}
if (!customer.getLastName().matches(validNameRegex)) {
errors.rejectValue("lastName", "lastName.invalid", null, null);
}
if (!customer.getPassword().matches(validPasswordRegex)) {
errors.rejectValue("password", "password.invalid", null, null);
}
if (!password.equals(passwordConfirm)) {
errors.rejectValue("password", "passwordConfirm.invalid", null, null);
}
if (!GenericValidator.isEmail(customer.getEmailAddress())) {
errors.rejectValue("emailAddress", "emailAddress.invalid", null, null);
}
}
}
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 ResultLimit ageBasedResultLimit(List<ResultLimit> resultLimits, Patient patient) {
ResultLimit resultLimit = null;
// First we look for a limit with no gender
for (ResultLimit limit : resultLimits) {
if (GenericValidator.isBlankOrNull(limit.getGender())
&& !limit.ageLimitsAreDefault()
&& getCurrPatientAge(patient) >= limit.getMinAge()
&& getCurrPatientAge(patient) <= limit.getMaxAge()) {
resultLimit = limit;
break;
}
}
// if none is found then drop the no gender requirement
if (resultLimit == null) {
for (ResultLimit limit : resultLimits) {
if (!limit.ageLimitsAreDefault()
&& getCurrPatientAge(patient) >= limit.getMinAge()
&& getCurrPatientAge(patient) <= limit.getMaxAge()) {
resultLimit = limit;
break;
}
}
}
return resultLimit == null ? defaultResultLimit(resultLimits) : resultLimit;
}
private void merge(String[] base, String[] line) {
for (int i = 0; i < base.length; ++i) {
if (GenericValidator.isBlankOrNull(base[i])) {
base[i] = line[i];
}
}
}
public boolean isInRange(Double dMax, Double dMin, String inputValue) {
boolean validation = true;
if ((dMax != null && dMax != 0) || (dMin != null && dMin != 0)) {
if (GenericValidator.isDouble(inputValue)) {
double dValue = Double.parseDouble(inputValue);
if (!GenericValidator.isInRange(dValue, dMin, dMax)) {
validation = false;
}
} else if (!GenericValidator.isBlankOrNull(inputValue)) {
validation = false;
}
}
return validation;
}
@JavaScriptMethod
public String isValidGroupName(String value) {
if (GenericValidator.isBlankOrNull(value) || value.length() < 3) {
return "Please use at least three character long group names.";
}
return null;
}
private ResultLimit defaultResultLimit(List<ResultLimit> resultLimits) {
for (ResultLimit limit : resultLimits) {
if (GenericValidator.isBlankOrNull(limit.getGender()) && limit.ageLimitsAreDefault()) {
return limit;
}
}
return new ResultLimit();
}
public static String getDisplayReferenceRange(
ResultLimit resultLimit, String significantDigits, String separator) {
String range = "";
if (resultLimit != null && !GenericValidator.isBlankOrNull(resultLimit.getResultTypeId())) {
if (NUMERIC_RESULT_TYPE_ID.equals(resultLimit.getResultTypeId())) {
range =
getDisplayNormalRange(
resultLimit.getLowNormal(),
resultLimit.getHighNormal(),
significantDigits,
separator);
} else if (SELECT_LIST_RESULT_TYPE_IDS.contains(resultLimit.getResultTypeId())
&& !GenericValidator.isBlankOrNull(resultLimit.getDictionaryNormalId())) {
return dictionaryDAO.getDataForId(resultLimit.getDictionaryNormalId()).getLocalizedName();
}
}
return range;
}
public String validateNewUsername(JiraClient client, String username) {
if (GenericValidator.isBlankOrNull(username)) {
return "Please enter a username.";
} else if (isUsernameRegistered(client, username)) {
return "This username is already used.";
}
return null;
}
public String validateNewPassword(JiraClient client, String password) {
if (GenericValidator.isBlankOrNull(password)) {
return "Please enter a password.";
} else if (password.length() < 5) {
return "Minimum password length is 5 characters.";
}
return null;
}
public ResultLimit getResultLimitForTestAndPatient(Test test, Patient patient) {
currPatientAge = INVALID_PATIENT_AGE;
@SuppressWarnings("unchecked")
List<ResultLimit> resultLimits = resultLimitDAO.getAllResultLimitsForTest(test);
if (resultLimits.isEmpty()) {
return null;
} else if (patient == null
|| patient.getBirthDate() == null && GenericValidator.isBlankOrNull(patient.getGender())) {
return defaultResultLimit(resultLimits);
} else if (GenericValidator.isBlankOrNull(patient.getGender())) {
return ageBasedResultLimit(resultLimits, patient);
} else if (patient.getBirthDate() == null) {
return genderBasedResultLimit(resultLimits, patient);
} else {
return ageAndGenderBasedResultLimit(resultLimits, patient);
}
}
public boolean isInteger(String inputValue) {
boolean validation = true;
if (!GenericValidator.isInt(inputValue)) {
validation = false;
}
return validation;
}
private List<IdValuePair> getDictionaryValuesForTest(String testId) {
if (!GenericValidator.isBlankOrNull(testId)) {
for (NonNumericTests test : nonNumericTests) {
if (testId.equals(test.testId)) {
return test.dictionaryValues;
}
}
}
return new ArrayList<IdValuePair>();
}
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 boolean validateSelection(ReportSpecificationList selectList) {
boolean complete =
!GenericValidator.isBlankOrNull(selectList.getSelection())
&& !"0".equals(selectList.getSelection());
if (!complete) {
add1LineErrorMessage("report.error.message.activity.missing");
}
return complete;
}
public boolean minLength(Integer iMin, String inputValue) {
boolean validation = true;
if (iMin != null && iMin != 0) {
if (!GenericValidator.minLength(inputValue, iMin)) {
validation = false;
}
}
return validation;
}
public String validateNewEmail(JiraClient client, String email) {
if (GenericValidator.isBlankOrNull(email)) {
return "Please enter an email address.";
} else if (!EmailValidator.getInstance().isValid(email)) {
return "Please enter a valid email address.";
} else if (isEmailAddressRegistered(client, email)) {
return "Email address already registered.";
}
return null;
}
/**
* 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;
}
public boolean validate(
CheckResultSourceInterface source,
String propertyName,
List<CheckResultInterface> remarks,
ValidatorContext context) {
String value = null;
value = getValueAsString(source, propertyName);
if (!GenericValidator.isBlankOrNull(value) && !GenericValidator.isEmail(value)) {
JobEntryValidatorUtils.addFailureRemark(
source,
propertyName,
VALIDATOR_NAME,
remarks,
JobEntryValidatorUtils.getLevelOnFail(context, VALIDATOR_NAME));
return false;
} else {
return true;
}
}
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 "";
}
@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();
}
public int compare(PatientSearchResults o1, PatientSearchResults o2) {
if (o1.getLastName() == null) {
return o2.getLastName() == null ? 0 : 1;
} else if (o2.getLastName() == null) {
return -1;
}
int lastNameResults = o1.getLastName().compareToIgnoreCase(o2.getLastName());
if (lastNameResults == 0) {
if (GenericValidator.isBlankOrNull(o1.getFirstName())
&& GenericValidator.isBlankOrNull(o2.getFirstName())) {
return 0;
}
String oneName = (o1.getFirstName() == null) ? " " : o1.getFirstName();
String twoName = (o2.getFirstName() == null) ? " " : o2.getFirstName();
return oneName.compareToIgnoreCase(twoName);
} else {
return lastNameResults;
}
}
public static boolean validate(
Object bean,
ValidatorAction va,
Field field,
ActionMessages errors,
HttpServletRequest request,
ServletContext application) {
String valueString = ValidatorUtils.getValueAsString(bean, field.getProperty());
String sProperty2 = ValidatorUtils.getValueAsString(bean, field.getVarValue("month"));
String sProperty3 = ValidatorUtils.getValueAsString(bean, field.getVarValue("day"));
if (((valueString == null) && (sProperty2 == null) && (sProperty3 == null))
|| ((valueString.length() == 0)
&& (sProperty2.length() == 0)
&& (sProperty3.length() == 0))) {
// errors.add(field.getKey(),Resources.getActionError(request, va,
// field));
return true;
}
Integer year = null;
Integer month = null;
Integer day = null;
try {
year = new Integer(valueString);
month = new Integer(sProperty2);
day = new Integer(sProperty3);
} catch (NumberFormatException e) {
errors.add(field.getKey(), Resources.getActionMessage(request, va, field));
return false;
}
if (!GenericValidator.isBlankOrNull(valueString)) {
if (!Data.validDate(day, month, year)
|| year == null
|| month == null
|| day == null
|| year.intValue() < 1
|| month.intValue() < 0
|| day.intValue() < 1) {
errors.add(field.getKey(), Resources.getActionMessage(request, va, field));
}
return false;
}
return true;
}