protected ActionForward getForward(ActionForward forward, String accessionNumber) {
ActionRedirect redirect = new ActionRedirect(forward);
if (!StringUtil.isNullorNill(accessionNumber))
redirect.addParameter(ACCESSION_NUMBER, accessionNumber);
return redirect;
}
protected String convertToDisplayableXML(String xml) {
if (!StringUtil.isNullorNill(xml)) {
xml = xml.replaceAll("<", "<");
xml = xml.replaceAll(">", ">");
// the following 2 lines are for display on page (not for system
// out)
xml = xml.replaceAll("\n", "<br>");
xml = xml.replaceAll(" ", " ");
}
return xml;
}
// bugzilla 1482
private boolean duplicateReferenceTablesExists(ReferenceTables referenceTables, boolean isNew)
throws LIMSRuntimeException {
try {
List list = new ArrayList();
String sql;
// not case sensitive hemolysis and Hemolysis are considered
// duplicates
if (isNew) {
sql = "from ReferenceTables t where trim(lower(t.tableName)) = :param";
} else {
sql = "from ReferenceTables t where trim(lower(t.tableName)) = :param and id != :param2";
}
// System.out.println("Yi in duplicateReferencetables sql is " + sql);
org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql);
// System.out.println("duplicateReferencetables sql is " + sql);
query.setParameter("param", referenceTables.getTableName().toLowerCase().trim());
// initialize with 0 (for new records where no id has been generated
// yet
String referenceTablesId = "0";
if (!StringUtil.isNullorNill(referenceTables.getId())) {
referenceTablesId = referenceTables.getId();
}
if (!isNew) {
query.setParameter("param2", referenceTablesId);
}
list = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
if (list.size() > 0) {
return true;
} else {
return false;
}
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "duplicateReferenceTablesExists()", e.toString());
throw new LIMSRuntimeException("Error in duplicateReferenceTablesExists()", e);
}
}
protected ActionForward performAction(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
DynaActionForm dynaForm = (DynaActionForm) form;
HttpSession session = request.getSession();
String forward = FWD_SUCCESS;
ResultsEntryRoutingSwitchSessionHandler.switchOff(
RESULTS_ENTRY_ROUTING_FROM_QAEVENTS_ENTRY_LINELISTING, session);
String accessionNumber = (String) request.getParameter(ACCESSION_NUMBER);
if (StringUtil.isNullorNill(accessionNumber)) {
accessionNumber = (String) dynaForm.get("accessionNumber");
}
return getForward(mapping.findForward(forward), accessionNumber);
}
protected ActionForward performAction(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
String forward = FWD_SUCCESS;
request.setAttribute(ALLOW_EDITS_KEY, "true");
request.setAttribute(PREVIOUS_DISABLED, "true");
request.setAttribute(NEXT_DISABLED, "true");
BaseActionForm dynaForm = (BaseActionForm) form;
HttpSession session = request.getSession();
String accessionNumber = (String) request.getParameter(ACCESSION_NUMBER);
String viewMode = (String) dynaForm.get("viewMode");
String fullScreenSection = (String) dynaForm.get("fullScreenSection");
String multipleSampleMode = (String) dynaForm.get("multipleSampleMode");
// bugzila 2555 initialize the form
dynaForm.initialize(mapping);
// initialize test management routing switch to on/initializes other switches to off
QaEventRoutingSwitchSessionHandler.switchOn(
QA_EVENTS_ENTRY_ROUTING_FROM_QAEVENTS_ENTRY_LINELISTING, session);
// PropertyUtils.setProperty(dynaForm, "viewMode", viewMode);
// PropertyUtils.setProperty(dynaForm, "fullScreenSection", fullScreenSection);
session.setAttribute(QAEVENTS_ENTRY_PARAM_VIEW_MODE, viewMode);
session.setAttribute(QAEVENTS_ENTRY_FULL_SCREEN_VIEW_SECTION, fullScreenSection);
request.setAttribute(ACCESSION_NUMBER, accessionNumber);
if (!StringUtil.isNullorNill(multipleSampleMode)) {
forward = FWD_SUCCESS_MULTIPLE_SAMPLE_MODE;
}
return mapping.findForward(forward);
}
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);
}
// modified for efficiency bugzilla 1367
public String validate(String targetId) throws LIMSRuntimeException {
StringBuffer s = new StringBuffer();
// bgm added StringUtil to check against a space being entered.
if (!StringUtil.isNullorNill(targetId)) {
ProjectDAO projectDAO = new ProjectDAOImpl();
Project project = new Project();
try {
int i = Integer.parseInt(targetId);
// bugzilla 2438
project.setLocalAbbreviation(targetId.trim());
} catch (NumberFormatException nfe) {
// bugzilla 2154
LogEvent.logError("ProjectIdOrNameValidationProvider", "validate()", nfe.toString());
// if the id was not a number
project = null;
}
if (project != null) {
// bugzilla 2438
project = projectDAO.getProjectByLocalAbbreviation(project, true);
}
// bugzilla 2112
try {
if (null != project) {
// bugzilla 1978
if (project.getIsActive().equals(YES)) {
// This is particular to projId validation for HSE1 and HSE2:
// the message appended to VALID is the projectName that
// can then be displayed when User enters valid Project Id
// (see humanSampleOne.jsp, humanSampleTwo.jsp)
// bgm - bugzilla 1535 commented out s.append(project.getProjectName()); to check first
if (null != project.getProjectName()) {
s.append(VALID);
s.append(project.getProjectName());
} else s.append(INVALID);
} else {
s.append(INVALID);
}
} else {
project = new Project();
project.setId("");
project.setProjectName(targetId.trim());
project = projectDAO.getProjectByName(project, true, true);
if (project != null) {
s.append(VALID);
// bugzilla 2438
s.append(project.getLocalAbbreviation());
} else {
s.append(INVALID);
}
}
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ProjectIdOrNameValidationProvider", "validate()", e.toString());
s.append(INVALID);
}
} else {
// bugzilla 1697
s.append(VALID);
}
/*
* System.out.println("I am in projIdValidator returning " +
* s.toString() + " targetId " + targetId);
*/
return s.toString();
}
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 TestAnalyte.
// If there is a parameter present, we should bring up an existing
// TestAnalyte to edit.
TestAnalyteTestResultActionForm dynaForm = (TestAnalyteTestResultActionForm) form;
String forward = FWD_SUCCESS;
request.setAttribute(ALLOW_EDITS_KEY, "false");
request.setAttribute(PREVIOUS_DISABLED, "true");
request.setAttribute(NEXT_DISABLED, "true");
// CHANGED
// String selectedTestId = (String) request.getParameter("Test");
List methods = new ArrayList();
MethodDAO methodDAO = new MethodDAOImpl();
methods = methodDAO.getAllMethods();
// Get tests/testsections by user system id
// bugzilla 2160
UserTestSectionDAO userTestSectionDAO = new UserTestSectionDAOImpl();
List testSections = userTestSectionDAO.getAllUserTestSections(request);
// bugzilla 2291
List tests = userTestSectionDAO.getAllUserTests(request, false);
List selectedAnalyteTypes = new ArrayList();
// bugzilla 1870
List selectedAnalyteIsReportables = new ArrayList();
List selectedAnalyteResultGroups = new ArrayList();
List selectedAnalyteIds = new ArrayList();
List selectedAnalyteNames = new ArrayList();
List selectedTestAnalyteIds = new ArrayList();
List testAnalyteLastupdatedList = new ArrayList();
List testResultResultGroups = new ArrayList();
List testResultResultGroupTypes = new ArrayList();
List testResultValueList = new ArrayList();
List dictionaryEntryIdList = new ArrayList();
List flagsList = new ArrayList();
// bugzilla 1845 add testResult sortOrder
List sortList = new ArrayList();
List significantDigitsList = new ArrayList();
List quantLimitList = new ArrayList();
List testResultIdList = new ArrayList();
List testResultLastupdatedList = new ArrayList();
Test test = new Test();
// FIXED BUG - NEED TO REFRESH SELECTIONS ON GOING INTO FORM
// get 3 drop down selections so we can repopulate
// String selectedTestSectionId = (String) dynaForm
// .get("selectedTestSectionId");
// String selectedMethodId = (String) dynaForm.get("selectedMethodId");
// String selectedTestId = (String) dynaForm.get("selectedTestId");
String selectedTestId = null;
String selectedTestSectionId = null;
String selectedMethodId = null;
// END BUG FIX
// initialize the form
dynaForm.initialize(mapping);
dynaForm.resetLists();
// bugzilla 1350 need to check if test has been selected so stray
// components don't display
if (!StringUtil.isNullorNill(selectedTestId)) {
// if test is selected enable the save button
request.setAttribute(ALLOW_EDITS_KEY, "true");
test.setId(selectedTestId);
TestDAO testDAO = new TestDAOImpl();
testDAO.getData(test);
TestAnalyteDAO testAnalyteDAO = new TestAnalyteDAOImpl();
List testAnalytes = testAnalyteDAO.getAllTestAnalytesPerTest(test);
TestResultDAO testResultDAO = new TestResultDAOImpl();
List testResults = testResultDAO.getAllActiveTestResultsPerTest(test);
DictionaryDAO dictDAO = new DictionaryDAOImpl();
if (testAnalytes != null && testAnalytes.size() > 0) {
for (int i = 0; i < testAnalytes.size(); i++) {
TestAnalyte ta = (TestAnalyte) testAnalytes.get(i);
selectedAnalyteTypes.add(ta.getTestAnalyteType());
// bugzilla 1870
selectedAnalyteIsReportables.add(ta.getIsReportable());
if (ta.getResultGroup() != null) {
selectedAnalyteResultGroups.add(ta.getResultGroup());
} else {
selectedAnalyteResultGroups.add("");
}
selectedAnalyteIds.add(ta.getAnalyte().getId());
selectedAnalyteNames.add(ta.getAnalyte().getAnalyteName());
selectedTestAnalyteIds.add(ta.getId());
}
if (testResults != null && testResults.size() > 0) {
for (int i = 0; i < testResults.size(); i++) {
TestResult tr = (TestResult) testResults.get(i);
testResultIdList.add(tr.getId());
testResultLastupdatedList.add(tr.getLastupdated());
testResultResultGroups.add(tr.getResultGroup());
testResultResultGroupTypes.add(tr.getTestResultType());
if (tr.getTestResultType()
.equals(SystemConfiguration.getInstance().getDictionaryType())) {
dictionaryEntryIdList.add(tr.getValue());
Dictionary dict = new Dictionary();
dict.setId(tr.getValue());
dictDAO.getData(dict);
// bugzilla 1847: use dictEntryDisplayValue
testResultValueList.add(dict.getDictEntryDisplayValue());
} else {
dictionaryEntryIdList.add("");
testResultValueList.add(tr.getValue());
}
if (tr.getFlags() == null) {
flagsList.add("");
} else {
flagsList.add(tr.getFlags());
}
// bugzilla 1845 add testResult sortOrder
if (tr.getSortOrder() == null) {
sortList.add("");
} else {
sortList.add(tr.getSortOrder());
}
if (tr.getSignificantDigits() == null) {
significantDigitsList.add("");
} else {
significantDigitsList.add(tr.getSignificantDigits());
}
if (tr.getQuantLimit() == null) {
quantLimitList.add("");
} else {
quantLimitList.add(tr.getQuantLimit());
}
}
}
isNew = false;
} else {
isNew = true;
}
} else {
isNew = true;
}
PropertyUtils.setProperty(dynaForm, "selectedAnalyteTypes", selectedAnalyteTypes);
// bugzilla 1870
PropertyUtils.setProperty(
dynaForm, "selectedAnalyteIsReportables", selectedAnalyteIsReportables);
PropertyUtils.setProperty(dynaForm, "selectedAnalyteResultGroups", selectedAnalyteResultGroups);
PropertyUtils.setProperty(dynaForm, "selectedAnalyteIds", selectedAnalyteIds);
PropertyUtils.setProperty(dynaForm, "selectedTestAnalyteIds", selectedTestAnalyteIds);
PropertyUtils.setProperty(dynaForm, "testAnalyteLastupdatedList", testAnalyteLastupdatedList);
PropertyUtils.setProperty(dynaForm, "selectedAnalyteNames", selectedAnalyteNames);
PropertyUtils.setProperty(dynaForm, "testResultResultGroups", testResultResultGroups);
PropertyUtils.setProperty(dynaForm, "testResultResultGroupTypes", testResultResultGroupTypes);
PropertyUtils.setProperty(dynaForm, "testResultValueList", testResultValueList);
PropertyUtils.setProperty(dynaForm, "testResultIdList", testResultIdList);
PropertyUtils.setProperty(dynaForm, "testResultLastupdatedList", testResultLastupdatedList);
PropertyUtils.setProperty(dynaForm, "dictionaryEntryIdList", dictionaryEntryIdList);
PropertyUtils.setProperty(dynaForm, "flagsList", flagsList);
// bugzilla 1845 add testResult sortOrder
PropertyUtils.setProperty(dynaForm, "sortList", sortList);
PropertyUtils.setProperty(dynaForm, "significantDigitsList", significantDigitsList);
PropertyUtils.setProperty(dynaForm, "quantLimitList", quantLimitList);
PropertyUtils.setProperty(dynaForm, "test", (test == null ? new Test() : test));
// sort three drop down lists
Collections.sort(testSections, TestSectionComparator.NAME_COMPARATOR);
// bugzilla 1844 - no longer sort by name but by description
Collections.sort(tests, TestComparator.DESCRIPTION_COMPARATOR);
Collections.sort(methods, MethodComparator.NAME_COMPARATOR);
PropertyUtils.setProperty(dynaForm, "testSections", testSections);
PropertyUtils.setProperty(dynaForm, "methods", methods);
PropertyUtils.setProperty(dynaForm, "tests", tests);
PropertyUtils.setProperty(dynaForm, "selectedTestSectionId", selectedTestSectionId);
PropertyUtils.setProperty(dynaForm, "selectedMethodId", selectedMethodId);
PropertyUtils.setProperty(dynaForm, "selectedTestId", selectedTestId);
return mapping.findForward(forward);
}
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;
ActionMessages errors = dynaForm.validate(mapping, request);
UserSessionData usd = (UserSessionData) request.getSession().getAttribute(USER_SESSION_DATA);
String sysUserId = String.valueOf(usd.getSystemUserId());
String birthDateForDisplay = dynaForm.getString("birthDateForDisplay");
String birthTimeForDisplay = dynaForm.getString("birthTimeForDisplay");
String format = "MM/dd/yyyy";
java.sql.Timestamp dob = null;
if ((birthDateForDisplay != null) && (birthDateForDisplay.length() > 0)) {
java.text.SimpleDateFormat f = new java.text.SimpleDateFormat(format);
dob = new java.sql.Timestamp(f.parse(birthDateForDisplay).getTime());
if ((birthTimeForDisplay != null) && (birthTimeForDisplay.length() > 0)) {
Calendar cal = Calendar.getInstance();
cal.setTime(dob);
cal.set(
Calendar.HOUR_OF_DAY, Integer.valueOf(birthTimeForDisplay.substring(0, 2)).intValue());
cal.set(Calendar.MINUTE, Integer.valueOf(birthTimeForDisplay.substring(3, 5)).intValue());
dob = new java.sql.Timestamp(cal.getTimeInMillis());
}
}
String dateFirstFeedingForDisplay = dynaForm.getString("dateFirstFeedingForDisplay");
String timeFirstFeedingForDisplay = dynaForm.getString("timeFirstFeedingForDisplay");
java.sql.Timestamp dateFirstFeeding = null;
if ((dateFirstFeedingForDisplay != null) && (dateFirstFeedingForDisplay.length() > 0)) {
java.text.SimpleDateFormat f = new java.text.SimpleDateFormat(format);
dateFirstFeeding = new java.sql.Timestamp(f.parse(dateFirstFeedingForDisplay).getTime());
if ((timeFirstFeedingForDisplay != null) && (timeFirstFeedingForDisplay.length() > 0)) {
Calendar cal = Calendar.getInstance();
cal.setTime(dob);
cal.set(
Calendar.HOUR_OF_DAY,
Integer.valueOf(timeFirstFeedingForDisplay.substring(0, 2)).intValue());
cal.set(
Calendar.MINUTE,
Integer.valueOf(timeFirstFeedingForDisplay.substring(3, 5)).intValue());
dateFirstFeeding = new java.sql.Timestamp(cal.getTimeInMillis());
}
}
String collectionDateForDisplay = dynaForm.getString("collectionDateForDisplay");
String collectionTimeForDisplay = dynaForm.getString("collectionTimeForDisplay");
java.sql.Timestamp collDate = null;
if ((collectionDateForDisplay != null) && (collectionDateForDisplay.length() > 0)) {
java.text.SimpleDateFormat f = new java.text.SimpleDateFormat(format);
collDate = new java.sql.Timestamp(f.parse(collectionDateForDisplay).getTime());
if ((collectionTimeForDisplay != null) && (collectionTimeForDisplay.length() > 0)) {
Calendar cal = Calendar.getInstance();
cal.setTime(collDate);
cal.set(
Calendar.HOUR_OF_DAY,
Integer.valueOf(collectionTimeForDisplay.substring(0, 2)).intValue());
cal.set(
Calendar.MINUTE, Integer.valueOf(collectionTimeForDisplay.substring(3, 5)).intValue());
collDate = new java.sql.Timestamp(cal.getTimeInMillis());
}
}
String dateTransfutionForDisplay = (String) dynaForm.getString("dateTransfutionForDisplay");
java.sql.Timestamp dateTransfution = null;
if ((dateTransfutionForDisplay != null) && (dateTransfutionForDisplay.length() > 0)) {
java.text.SimpleDateFormat f = new java.text.SimpleDateFormat(format);
dateTransfution = new java.sql.Timestamp(f.parse(dateTransfutionForDisplay).getTime());
}
String motherBirthDateForDisplay = (String) dynaForm.get("motherBirthDateForDisplay");
java.sql.Timestamp motherBirthDate = null;
if ((motherBirthDateForDisplay != null) && (motherBirthDateForDisplay.length() > 0)) {
java.text.SimpleDateFormat f = new java.text.SimpleDateFormat(format);
motherBirthDate = new java.sql.Timestamp(f.parse(motherBirthDateForDisplay).getTime());
}
org.hibernate.Transaction tx = HibernateUtil.getSession().beginTransaction();
String accessionNumber = (String) dynaForm.get("accessionNumber");
try {
// Sample
Sample sample = new Sample();
SampleDAO sampleDAO = new SampleDAOImpl();
sample.setSysUserId(sysUserId);
sample.setAccessionNumber(accessionNumber);
sampleDAO.getSampleByAccessionNumber(sample);
sample.setBarCode((String) dynaForm.get("barcode"));
sample.setStatus(SystemConfiguration.getInstance().getSampleStatusEntry2Complete());
sample.setCollectionDate(collDate);
sampleDAO.updateData(sample);
// SampleHuman
SampleHumanDAO sampleHumanDAO = new SampleHumanDAOImpl();
SampleHuman sampleHuman = new SampleHuman();
sampleHuman.setSampleId(sample.getId());
sampleHumanDAO.getDataBySample(sampleHuman);
// Patient - child
Patient childPatient = new Patient();
PatientDAO patientDAO = new PatientDAOImpl();
Person childPerson = new Person();
childPatient.setId(sampleHuman.getPatientId());
patientDAO.getData(childPatient);
// Person - child
PersonDAO personDAO = new PersonDAOImpl();
childPerson = childPatient.getPerson();
personDAO.getData(childPerson);
childPerson.setSysUserId(sysUserId);
childPerson.setLastName((String) dynaForm.get("lastName"));
childPerson.setFirstName((String) dynaForm.get("firstName"));
personDAO.updateData(childPerson);
childPatient.setSysUserId(sysUserId);
childPatient.setBirthDate(dob);
childPatient.setGender((String) dynaForm.get("gender"));
patientDAO.updateData(childPatient);
// PatientRelation
PatientRelation patientRelation = new PatientRelation();
PatientRelationDAO patientRelationDAO = new PatientRelationDAOImpl();
patientRelation.setPatientIdSource(childPatient.getId());
patientRelation = patientRelationDAO.getPatientRelationByChildId(patientRelation);
Person motherPerson = new Person();
Patient motherPatient = new Patient();
if (!StringUtil.isNullorNill(patientRelation.getId())) {
motherPatient.setId(patientRelation.getPatientId());
patientDAO.getData(motherPatient);
motherPerson = motherPatient.getPerson();
personDAO.getData(motherPerson);
}
motherPerson.setLastName((String) dynaForm.get("motherLastName"));
motherPerson.setFirstName((String) dynaForm.get("motherFirstName"));
String motherHomePhone = (String) dynaForm.get("motherPhoneNumber");
if ((motherHomePhone != null) && (motherHomePhone.length() > 0))
motherHomePhone = StringUtil.formatPhone(motherHomePhone, null);
motherPerson.setHomePhone(motherHomePhone);
motherPerson.setStreetAddress((String) dynaForm.get("motherStreetAddress"));
motherPerson.setCity((String) dynaForm.get("city"));
motherPerson.setState((String) dynaForm.get("state"));
motherPerson.setZipCode((String) dynaForm.get("zipCode"));
motherPerson.setSysUserId(sysUserId);
if (!StringUtil.isNullorNill(motherPerson.getId())) personDAO.updateData(motherPerson);
else personDAO.insertData(motherPerson);
motherPatient.setBirthDate(motherBirthDate);
motherPatient.setPerson(motherPerson);
motherPatient.setSysUserId(sysUserId);
if (!StringUtil.isNullorNill(motherPatient.getId())) patientDAO.updateData(motherPatient);
else patientDAO.insertData(motherPatient);
patientRelation.setSysUserId(sysUserId);
patientRelation.setPatientId(motherPatient.getId());
String motherRelation = SystemConfiguration.getInstance().getNewbornPatientRelation();
patientRelation.setRelation(motherRelation);
if (!StringUtil.isNullorNill(patientRelation.getId()))
patientRelationDAO.updateData(patientRelation);
else patientRelationDAO.insertData(patientRelation);
// SampleNewborn
SampleNewborn sampleNewborn = new SampleNewborn();
SampleNewbornDAO sampleNewbornDAO = new SampleNewbornDAOImpl();
sampleNewborn.setId(sampleHuman.getId());
sampleNewbornDAO.getData(sampleNewborn);
sampleNewborn.setSysUserId(sysUserId);
sampleNewborn.setMedicalRecordNumber((String) dynaForm.get("medicalRecordNumber"));
sampleNewborn.setYnumber((String) dynaForm.get("ynumber"));
sampleNewborn.setYellowCard((String) dynaForm.get("yellowCard"));
sampleNewborn.setWeight((String) dynaForm.get("birthWeight"));
sampleNewborn.setMultiBirth((String) dynaForm.get("multipleBirth"));
sampleNewborn.setBirthOrder((String) dynaForm.get("birthOrder"));
sampleNewborn.setGestationalWeek((Double) dynaForm.get("gestationalWeek"));
sampleNewborn.setDateFirstFeeding(dateFirstFeeding);
sampleNewborn.setBreast((String) dynaForm.get("breast"));
sampleNewborn.setTpn((String) dynaForm.get("tpn"));
sampleNewborn.setFormula((String) dynaForm.get("formula"));
sampleNewborn.setMilk((String) dynaForm.get("milk"));
sampleNewborn.setSoy((String) dynaForm.get("soy"));
sampleNewborn.setJaundice((String) dynaForm.get("jaundice"));
sampleNewborn.setAntibiotic((String) dynaForm.get("antibiotic"));
sampleNewborn.setTransfused((String) dynaForm.get("transfused"));
sampleNewborn.setNicu((String) dynaForm.get("nicuPatient"));
sampleNewborn.setBirthDefect((String) dynaForm.get("birthDefect"));
sampleNewborn.setPregnancyComplication((String) dynaForm.get("pregnancyComplication"));
sampleNewborn.setDeceasedSibling((String) dynaForm.get("deceasedSibling"));
sampleNewborn.setCauseOfDeath((String) dynaForm.get("causeOfDeath"));
sampleNewborn.setFamilyHistory((String) dynaForm.get("familyHistory"));
sampleNewborn.setOther((String) dynaForm.get("other"));
sampleNewborn.setDateTransfution(dateTransfution);
if (!StringUtil.isNullorNill(sampleNewborn.getId()))
sampleNewbornDAO.updateData(sampleNewborn);
else {
sampleNewborn.setId(sampleHuman.getId());
sampleNewbornDAO.insertData(sampleNewborn);
}
// Provider
Provider provider = new Provider();
Person providerPerson = new Person();
ProviderDAO providerDAO = new ProviderDAOImpl();
if (!StringUtil.isNullorNill(sampleHuman.getProviderId())) {
provider.setId(sampleHuman.getProviderId());
providerDAO.getData(provider);
}
if (!StringUtil.isNullorNill(sampleHuman.getProviderId())) {
provider.setId(sampleHuman.getProviderId());
providerDAO.getData(provider);
providerPerson = (Person) provider.getPerson();
}
// SampleOrganization
Organization o = new Organization();
OrganizationDAO organizationDAO = new OrganizationDAOImpl();
o.setOrganizationLocalAbbreviation((String) dynaForm.get("submitterNumber"));
o = organizationDAO.getOrganizationByLocalAbbreviation(o, true);
SampleOrganization sampleOrganization = new SampleOrganization();
SampleOrganizationDAO sampleOrganizationDAO = new SampleOrganizationDAOImpl();
sampleOrganizationDAO.getDataBySample(sampleOrganization);
sampleOrganization.setSample(sample);
sampleOrganization.setOrganization(o);
sampleOrganization.setSysUserId(sysUserId);
if (!StringUtil.isNullorNill(sampleOrganization.getId()))
sampleOrganizationDAO.updateData(sampleOrganization);
else sampleOrganizationDAO.insertData(sampleOrganization);
// Person - provider
providerPerson.setSysUserId(sysUserId);
providerPerson.setFirstName((String) dynaForm.get("physicianFirstName"));
providerPerson.setLastName((String) dynaForm.get("physicianLastName"));
String providerHomePhone = (String) dynaForm.get("physicianPhoneNumber");
if ((providerHomePhone != null) && (providerHomePhone.length() > 0))
providerHomePhone = StringUtil.formatPhone(providerHomePhone, null);
providerPerson.setHomePhone(providerHomePhone);
if (!StringUtil.isNullorNill(providerPerson.getId())) personDAO.updateData(providerPerson);
else personDAO.insertData(providerPerson);
provider.setPerson(providerPerson);
provider.setExternalId(BLANK);
provider.setSysUserId(sysUserId);
if (!StringUtil.isNullorNill(provider.getId())) providerDAO.updateData(provider);
else providerDAO.insertData(provider);
sampleHuman.setProviderId(provider.getId());
sampleHuman.setSysUserId(sysUserId);
sampleHumanDAO.updateData(sampleHuman);
tx.commit();
} catch (LIMSRuntimeException lre) {
LogEvent.logError("NewbornSampleFullUpdateAction", "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 {
error = new ActionError("errors.UpdateException", null, null);
}
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
saveErrors(request, errors);
request.setAttribute(Globals.ERROR_KEY, errors);
request.setAttribute(ALLOW_EDITS_KEY, "false");
forward = FWD_FAIL;
} finally {
HibernateUtil.closeSession();
}
if (forward.equals(FWD_FAIL)) return mapping.findForward(forward);
// Trigger QA if birthWeight < 200 grams
int birthWeight = Integer.parseInt((String) dynaForm.get("birthWeight"));
if ((birthWeight > 0) && (birthWeight < 200)) {
forward = FWD_SUCCESS_QA_EVENTS_ENTRY;
return getForward(mapping.findForward(forward), accessionNumber);
}
return mapping.findForward(FWD_SUCCESS);
}
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 Scriptlet.
// If there is a parameter present, we should bring up an existing
// Scriptlet to edit.
String forward = FWD_SUCCESS;
request.setAttribute(ALLOW_EDITS_KEY, "true");
request.setAttribute(PREVIOUS_DISABLED, "false");
request.setAttribute(NEXT_DISABLED, "false");
String id = request.getParameter(ID);
if (StringUtil.isNullorNill(id) || "0".equals(id)) {
isNew = true;
} else {
isNew = false;
}
BaseActionForm dynaForm = (BaseActionForm) form;
// server-side validation (validation.xml)
ActionMessages errors = dynaForm.validate(mapping, request);
if (errors != null && errors.size() > 0) {
saveErrors(request, errors);
// since we forward to jsp - not Action we don't need to repopulate
// the lists here
return mapping.findForward(FWD_FAIL);
}
String start = (String) request.getParameter("startingRecNo");
String direction = (String) request.getParameter("direction");
Scriptlet scriptlet = new Scriptlet();
// get sysUserId from login module
UserSessionData usd = (UserSessionData) request.getSession().getAttribute(USER_SESSION_DATA);
String sysUserId = String.valueOf(usd.getSystemUserId());
scriptlet.setSysUserId(sysUserId);
// populate valueholder from form
PropertyUtils.copyProperties(scriptlet, dynaForm);
try {
ScriptletDAO scriptletDAO = new ScriptletDAOImpl();
if (!isNew) {
// UPDATE
scriptletDAO.updateData(scriptlet);
} else {
// INSERT
scriptletDAO.insertData(scriptlet);
}
} catch (LIMSRuntimeException lre) {
// bugzilla 2154
LogEvent.logError("ScriptletUpdateAction", "performAction()", lre.toString());
request.setAttribute(IActionConstants.REQUEST_FAILED, true);
errors = new ActionMessages();
java.util.Locale locale =
(java.util.Locale) request.getSession().getAttribute("org.apache.struts.action.LOCALE");
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);
} else {
// bugzilla 1482
if (lre.getException() instanceof LIMSDuplicateRecordException) {
String messageKey = "scriptlet.scriptletName";
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);
// bugzilla 1485: allow change and try updating again (enable save button)
// request.setAttribute(IActionConstants.ALLOW_EDITS_KEY, "false");
// disable previous and next
request.setAttribute(PREVIOUS_DISABLED, "true");
request.setAttribute(NEXT_DISABLED, "true");
forward = FWD_FAIL;
}
if (forward.equals(FWD_FAIL)) return mapping.findForward(forward);
// initialize the form
dynaForm.initialize(mapping);
// repopulate the form from valueholder
PropertyUtils.copyProperties(dynaForm, scriptlet);
if ("true".equalsIgnoreCase(request.getParameter("close"))) {
forward = FWD_CLOSE;
}
if (scriptlet.getId() != null && !scriptlet.getId().equals("0")) {
request.setAttribute(ID, scriptlet.getId());
}
// bugzilla 1400
if (isNew) forward = FWD_SUCCESS_INSERT;
// bugzilla 1467 added direction for redirect to NextPreviousAction
return getForward(mapping.findForward(forward), scriptlet.getId(), start, direction);
}
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 {
String forward = FWD_SUCCESS;
BaseActionForm dynaForm = (BaseActionForm) form;
ActionMessages errors = null;
request.setAttribute(ALLOW_EDITS_KEY, "false");
request.setAttribute(PREVIOUS_DISABLED, "true");
request.setAttribute(NEXT_DISABLED, "true");
String accessionNumber = (String) dynaForm.getString("accessionNumber");
SampleXmlHelper sampleXmlHelper = new SampleXmlHelper();
if (!StringUtil.isNullorNill(accessionNumber)) {
Sample sample = new Sample();
SampleDAO sampleDAO = new SampleDAOImpl();
sample.setAccessionNumber(accessionNumber);
List testTestAnalytes = new ArrayList();
try {
sampleDAO.getSampleByAccessionNumber(sample);
if (!StringUtil.isNullorNill(sample.getStatus())
&& sample
.getStatus()
.equals(SystemConfiguration.getInstance().getSampleStatusLabelPrinted())) {
dynaForm.set("accessionNumber", accessionNumber);
request.setAttribute(ALLOW_EDITS_KEY, "false");
return mapping.findForward(FWD_FAIL);
}
} catch (LIMSRuntimeException lre) {
LogEvent.logError(
"AuditTrailReportBySampleProcessAction", "performAction()", lre.toString());
errors = new ActionMessages();
ActionError error = null;
error = new ActionError("errors.GetException", null, null);
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);
}
String domain = sample.getDomain();
String humanDomain = SystemConfiguration.getInstance().getHumanDomain();
String animalDomain = SystemConfiguration.getInstance().getAnimalDomain();
if (domain != null && domain.equals(humanDomain)) {
// go to human view
Patient patient = new Patient();
Person patientPerson = new Person();
Provider provider = new Provider();
Person providerPerson = new Person();
SampleHuman sampleHuman = new SampleHuman();
SampleOrganization sampleOrganization = new SampleOrganization();
Organization organization = new Organization();
List sampleProjects = new ArrayList();
Project project = new Project();
Project project2 = new Project();
SampleItem sampleItem = new SampleItem();
try {
PatientDAO patientDAO = new PatientDAOImpl();
ProviderDAO providerDAO = new ProviderDAOImpl();
SampleItemDAO sampleItemDAO = new SampleItemDAOImpl();
SampleHumanDAO sampleHumanDAO = new SampleHumanDAOImpl();
SampleOrganizationDAO sampleOrganizationDAO = new SampleOrganizationDAOImpl();
AuditTrailDAO auditTrailDAO = new AuditTrailDAOImpl();
SystemUserDAO systemUserDAO = new SystemUserDAOImpl();
if (!StringUtil.isNullorNill(sample.getId())) {
sampleHuman.setSampleId(sample.getId());
sampleHumanDAO.getDataBySample(sampleHuman);
sampleOrganization.setSampleId(sample.getId());
sampleOrganizationDAO.getDataBySample(sampleOrganization);
sampleItem.setSample(sample);
sampleItemDAO.getDataBySample(sampleItem);
if (sampleHuman != null) {
if (sampleHuman.getPatientId() != null) {
patient.setId(sampleHuman.getPatientId());
patientDAO.getData(patient);
patientPerson = patient.getPerson();
provider.setId(sampleHuman.getProviderId());
providerDAO.getData(provider);
providerPerson = provider.getPerson();
}
}
}
organization = (Organization) sampleOrganization.getOrganization();
sampleProjects = sample.getSampleProjects();
if (sampleProjects != null && sampleProjects.size() > 0) {
SampleProject sampleProject = (SampleProject) sampleProjects.get(0);
project = sampleProject.getProject();
if (sampleProjects.size() > 1) {
SampleProject sampleProject2 = (SampleProject) sampleProjects.get(1);
project2 = sampleProject2.getProject();
}
}
String tableName = "SAMPLE";
ReferenceTablesDAO referenceTablesDAO = new ReferenceTablesDAOImpl();
ReferenceTables referenceTables = new ReferenceTables();
referenceTables.setTableName(tableName);
ReferenceTables rt = referenceTablesDAO.getReferenceTableByName(referenceTables);
PropertyUtils.copyProperties(sampleXmlHelper, sample);
// String data = auditTrailDAO.retrieveBlobData(sample.getId());
// String data = auditTrailDAO.retrieveBlobData("9446");
History history = new History();
history.setReferenceId(sample.getId());
history.setReferenceTable(rt.getId());
List historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history);
List sampleHistoryRecords =
populateHistoryList(request, historyRecords, "sample", "sampleHistoryMapping.xsl");
sampleXmlHelper.setHistoryRecords((ArrayList) sampleHistoryRecords);
tableName = "SAMPLE_ITEM";
referenceTables = new ReferenceTables();
referenceTables.setTableName(tableName);
rt = referenceTablesDAO.getReferenceTableByName(referenceTables);
history = new History();
history.setReferenceId(sampleItem.getId());
history.setReferenceTable(rt.getId());
historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history);
List sampleItemHistoryRecords =
populateHistoryList(
request, historyRecords, "sampleItem", "sampleItemHistoryMapping.xsl");
sampleXmlHelper.addHistoryRecords((ArrayList) sampleItemHistoryRecords);
tableName = "PATIENT";
referenceTables = new ReferenceTables();
referenceTables.setTableName(tableName);
rt = referenceTablesDAO.getReferenceTableByName(referenceTables);
history = new History();
history.setReferenceId(patient.getId());
history.setReferenceTable(rt.getId());
historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history);
List patientHistoryRecords =
populateHistoryList(request, historyRecords, "patient", "patientHistoryMapping.xsl");
sampleXmlHelper.addHistoryRecords((ArrayList) patientHistoryRecords);
tableName = "PERSON";
referenceTables = new ReferenceTables();
referenceTables.setTableName(tableName);
rt = referenceTablesDAO.getReferenceTableByName(referenceTables);
history = new History();
history.setReferenceId(patientPerson.getId());
history.setReferenceTable(rt.getId());
historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history);
// List patientPersonHistoryRecords = populateHistoryList(request, historyRecords,
// "person", "personHistoryMapping.xsl");
// sampleXmlHelper.addHistoryRecords((ArrayList)patientPersonHistoryRecords);
tableName = "PERSON";
referenceTables = new ReferenceTables();
referenceTables.setTableName(tableName);
rt = referenceTablesDAO.getReferenceTableByName(referenceTables);
history = new History();
history.setReferenceId(providerPerson.getId());
history.setReferenceTable(rt.getId());
historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history);
// List providerPersonHistoryRecords = populateHistoryList(request, historyRecords,
// "person", "personHistoryMapping.xsl");
// sampleXmlHelper.addHistoryRecords((ArrayList)providerPersonHistoryRecords);
tableName = "SAMPLE_PROJECTS";
referenceTables = new ReferenceTables();
referenceTables.setTableName(tableName);
rt = referenceTablesDAO.getReferenceTableByName(referenceTables);
history = new History();
history.setReferenceId(providerPerson.getId());
history.setReferenceTable(rt.getId());
historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history);
List sampleProjectHistoryRecords =
populateHistoryList(
request, historyRecords, "sampleProject", "sampleProjectHistoryMapping.xsl");
sampleXmlHelper.addHistoryRecords((ArrayList) sampleProjectHistoryRecords);
// initialize the form
dynaForm.initialize(mapping);
tableName = "SAMPLE_ORGANIZATION";
referenceTables = new ReferenceTables();
referenceTables.setTableName(tableName);
rt = referenceTablesDAO.getReferenceTableByName(referenceTables);
history = new History();
history.setReferenceId(sampleOrganization.getId());
history.setReferenceTable(rt.getId());
historyRecords = auditTrailDAO.getHistoryByRefIdAndRefTableId(history);
List sampleOrganizationHistoryRecords =
populateHistoryList(
request,
historyRecords,
"sampleOrganization",
"sampleOrganizationHistoryMapping.xsl");
sampleXmlHelper.addHistoryRecords((ArrayList) sampleOrganizationHistoryRecords);
List historyRecordsForSorting = sampleXmlHelper.getHistoryRecords();
Collections.sort(historyRecordsForSorting, HistoryComparator.NAME_COMPARATOR);
String savedUserName = "";
List dateSortList = new ArrayList();
List finalList = new ArrayList();
// now within name sort by date desc
for (int i = 0; i < historyRecordsForSorting.size(); i++) {
// break down into chunks by name
HistoryXmlHelper hist = (HistoryXmlHelper) historyRecordsForSorting.get(i);
if (i > 0 && !hist.getUserName().equals(savedUserName)) {
// now sort chunk so far
Collections.sort(dateSortList, HistoryComparator.DATE_COMPARATOR);
finalList.addAll(dateSortList);
dateSortList.clear();
}
dateSortList.add(hist);
savedUserName = hist.getUserName();
}
if (dateSortList != null && dateSortList.size() > 0) {
Collections.sort(dateSortList, HistoryComparator.DATE_COMPARATOR);
finalList.addAll(dateSortList);
dateSortList.clear();
}
sampleXmlHelper.setHistoryRecords((ArrayList) finalList);
// initialize the form
dynaForm.initialize(mapping);
} catch (LIMSRuntimeException lre) {
// if error then forward to fail and don't update to blank
// page
// = false
// bugzilla 2154
LogEvent.logError("ResultsEntryViewAction", "performAction()", lre.toString());
errors = new ActionMessages();
ActionError error = null;
error = new ActionError("errors.GetException", null, null);
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);
}
// populate form from valueholder
// PropertyUtils.setProperty(dynaForm, "sampleLastupdated", sample
// .getLastupdated());
PropertyUtils.setProperty(dynaForm, "patientFirstName", patientPerson.getFirstName());
PropertyUtils.setProperty(dynaForm, "patientLastName", patientPerson.getLastName());
PropertyUtils.setProperty(dynaForm, "patientId", patient.getExternalId());
PropertyUtils.setProperty(dynaForm, "gender", patient.getGender());
PropertyUtils.setProperty(dynaForm, "chartNumber", patient.getChartNumber());
PropertyUtils.setProperty(
dynaForm, "birthDateForDisplay", (String) patient.getBirthDateForDisplay());
TypeOfSample typeOfSample = sampleItem.getTypeOfSample();
SourceOfSample sourceOfSample = sampleItem.getSourceOfSample();
if (typeOfSample == null) {
PropertyUtils.setProperty(dynaForm, "typeOfSample", new TypeOfSample());
} else {
PropertyUtils.setProperty(dynaForm, "typeOfSample", typeOfSample);
}
if (sourceOfSample == null) {
PropertyUtils.setProperty(dynaForm, "sourceOfSample", new SourceOfSample());
} else {
PropertyUtils.setProperty(dynaForm, "sourceOfSample", sourceOfSample);
}
PropertyUtils.setProperty(dynaForm, "sourceOther", sampleItem.getSourceOther());
PropertyUtils.setProperty(
dynaForm, "receivedDateForDisplay", (String) sample.getReceivedDateForDisplay());
PropertyUtils.setProperty(
dynaForm, "collectionDateForDisplay", (String) sample.getCollectionDateForDisplay());
PropertyUtils.setProperty(
dynaForm, "collectionTimeForDisplay", (String) sample.getCollectionTimeForDisplay());
PropertyUtils.setProperty(
dynaForm, "referredCultureFlag", (String) sample.getReferredCultureFlag());
PropertyUtils.setProperty(
dynaForm, "stickerReceivedFlag", (String) sample.getStickerReceivedFlag());
if (organization == null) {
PropertyUtils.setProperty(dynaForm, "organization", new Organization());
} else {
PropertyUtils.setProperty(dynaForm, "organization", organization);
}
if (project == null) {
PropertyUtils.setProperty(dynaForm, "project", new Project());
} else {
PropertyUtils.setProperty(dynaForm, "project", project);
}
if (project2 == null) {
PropertyUtils.setProperty(dynaForm, "project2", new Project());
} else {
PropertyUtils.setProperty(dynaForm, "project2", project2);
}
// reload accession number
PropertyUtils.setProperty(dynaForm, "accessionNumber", accessionNumber);
PropertyUtils.setProperty(dynaForm, "domain", domain);
PropertyUtils.setProperty(dynaForm, "sampleXmlHelper", sampleXmlHelper);
forward = FWD_SUCCESS_HUMAN;
} else if (domain != null && domain.equals(animalDomain)) {
// go to animal view
// System.out.println("Going to animal view");
forward = FWD_SUCCESS_ANIMAL;
} else {
forward = FWD_SUCCESS;
}
}
return mapping.findForward(forward);
}
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 Analyte.
// If there is a parameter present, we should bring up an existing
// Analyte to edit.
String forward = FWD_SUCCESS;
request.setAttribute(ALLOW_EDITS_KEY, "true");
request.setAttribute(PREVIOUS_DISABLED, "false");
request.setAttribute(NEXT_DISABLED, "false");
String id = request.getParameter(ID);
if (StringUtil.isNullorNill(id) || "0".equals(id)) {
isNew = true;
} else {
isNew = false;
}
BaseActionForm dynaForm = (BaseActionForm) form;
String start = (String) request.getParameter("startingRecNo");
String direction = (String) request.getParameter("direction");
// System.out.println("This is ID from request " + id);
Panel panel = new Panel();
panel.setId(id);
try {
PanelDAO panelDAO = new PanelDAOImpl();
// retrieve analyte by id since the name may have changed
panelDAO.getData(panel);
if (FWD_NEXT.equals(direction)) {
// bugzilla 1427 pass in name not id
List panels = panelDAO.getNextPanelRecord(panel.getPanelName());
if (panels != null && panels.size() > 0) {
panel = (Panel) panels.get(0);
panelDAO.getData(panel);
if (panels.size() < 2) {
// disable next button
request.setAttribute(NEXT_DISABLED, "true");
}
id = panel.getId();
} else {
// just disable next button
request.setAttribute(NEXT_DISABLED, "true");
}
}
if (FWD_PREVIOUS.equals(direction)) {
// bugzilla 1427 pass in name not id
List panels = panelDAO.getPreviousPanelRecord(panel.getPanelName());
if (panels != null && panels.size() > 0) {
panel = (Panel) panels.get(0);
panelDAO.getData(panel);
if (panels.size() < 2) {
// disable previous button
request.setAttribute(PREVIOUS_DISABLED, "true");
}
id = panel.getId();
} else {
// just disable next button
request.setAttribute(PREVIOUS_DISABLED, "true");
}
}
} catch (LIMSRuntimeException lre) {
// bugzilla 2154
LogEvent.logError("PanelNextPreviousAction", "performAction()", lre.toString());
request.setAttribute(ALLOW_EDITS_KEY, "false");
// disable previous and next
request.setAttribute(PREVIOUS_DISABLED, "true");
request.setAttribute(NEXT_DISABLED, "true");
forward = FWD_FAIL;
}
if (forward.equals(FWD_FAIL)) return mapping.findForward(forward);
if (panel.getId() != null && !panel.getId().equals("0")) {
request.setAttribute(ID, panel.getId());
}
return getForward(mapping.findForward(forward), id, start);
}
protected List createMenuList(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
// System.out.println("I am in OrganizationMenuAction createMenuList()");
List organizations = new ArrayList();
String stringStartingRecNo = (String) request.getAttribute("startingRecNo");
int startingRecNo = Integer.parseInt(stringStartingRecNo);
// bugzilla 2372
String searchString = (String) request.getParameter("searchString");
String doingSearch = (String) request.getParameter("search");
OrganizationDAO organizationDAO = new OrganizationDAOImpl();
if (!StringUtil.isNullorNill(doingSearch) && doingSearch.equals(YES))
organizations = organizationDAO.getPagesOfSearchedOrganizations(startingRecNo, searchString);
else organizations = organizationDAO.getPageOfOrganizations(startingRecNo);
request.setAttribute("menuDefinition", "OrganizationMenuDefinition");
// bugzilla 1411 set pagination variables
// bugzilla 2372 set pagination variables for searched results
if (!StringUtil.isNullorNill(doingSearch) && doingSearch.equals(YES))
request.setAttribute(
MENU_TOTAL_RECORDS,
String.valueOf(organizationDAO.getTotalSearchedOrganizationCount(searchString)));
else
request.setAttribute(
MENU_TOTAL_RECORDS, String.valueOf(organizationDAO.getTotalOrganizationCount()));
request.setAttribute(MENU_FROM_RECORD, String.valueOf(startingRecNo));
int numOfRecs = 0;
if (organizations != null) {
if (organizations.size() > SystemConfiguration.getInstance().getDefaultPageSize()) {
numOfRecs = SystemConfiguration.getInstance().getDefaultPageSize();
} else {
numOfRecs = organizations.size();
}
numOfRecs--;
}
int endingRecNo = startingRecNo + numOfRecs;
request.setAttribute(MENU_TO_RECORD, String.valueOf(endingRecNo));
// end bugzilla 1411
// bugzilla 2372
request.setAttribute(MENU_SEARCH_BY_TABLE_COLUMN, "organization.organizationName");
// bugzilla 2372 set up a seraching mode so the next and previous action will know
// what to do
if (!StringUtil.isNullorNill(doingSearch) && doingSearch.equals(YES)) {
request.setAttribute(IN_MENU_SELECT_LIST_HEADER_SEARCH, "true");
request.setAttribute(MENU_SELECT_LIST_HEADER_SEARCH_STRING, searchString);
}
return organizations;
}
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);
}
// compares values against HashMap of HSE1 values before going to dbase to
// revalidate submitted values
// bugzilla 1765 changes to city state zip validation
protected ActionMessages validateAll(
HttpServletRequest request,
ActionMessages errors,
BaseActionForm dynaForm,
HashMap humanSampleOneMap)
throws Exception {
String result;
String messageKey;
ProjectIdValidationProvider projIdValidator = new ProjectIdValidationProvider();
String projNum = (String) dynaForm.get("projectIdOrName");
if (!StringUtil.isNullorNill(projNum)) {
// project ID validation against database (reusing ajax
// validation logic)
result = compareAgainstHSE1HashMap(humanSampleOneMap, projNum, "projectId");
if (result.equals(INVALID)) {
result = projIdValidator.validate(projNum);
messageKey = "humansampleone.projectNumber";
if (result.equals(INVALID)) {
String projName = (String) dynaForm.get("projectNameOrId");
result = compareAgainstHSE1HashMap(humanSampleOneMap, projName, "projectName");
if (result.equals(INVALID)) {
result = projIdValidator.validate(projName);
if (result.equals(INVALID)) {
ActionError error =
new ActionError("errors.invalid", getMessageForKey(messageKey), null);
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
}
}
}
}
}
String proj2Num = (String) dynaForm.get("project2IdOrName");
if (!StringUtil.isNullorNill(proj2Num)) {
result = compareAgainstHSE1HashMap(humanSampleOneMap, proj2Num, "projectId2");
if (result.equals(INVALID)) {
result = projIdValidator.validate(proj2Num);
messageKey = "humansampleone.project2Number";
if (result.equals(INVALID)) {
String proj2Name = (String) dynaForm.get("project2NameOrId");
result = compareAgainstHSE1HashMap(humanSampleOneMap, proj2Name, "projectName2");
if (result.equals(INVALID)) {
result = projIdValidator.validate(proj2Name);
if (result.equals(INVALID)) {
ActionError error =
new ActionError("errors.invalid", getMessageForKey(messageKey), null);
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
}
}
}
}
}
// accession number validation against database (reusing ajax
// validation logic)
String accnNum = (String) dynaForm.get("accessionNumber");
if (!StringUtil.isNullorNill(accnNum)) {
result = compareAgainstHSE1HashMap(humanSampleOneMap, accnNum, "accessionNumber");
if (result.equals(INVALID)) {
errors = validateAccessionNumber(request, errors, dynaForm);
}
}
// organization ID (submitter) validation against database (reusing ajax
// validation logic)
// bugzilla 2069
String organizationLocalAbbreviation = (String) dynaForm.get("organizationLocalAbbreviation");
if (!StringUtil.isNullorNill(organizationLocalAbbreviation)) {
result =
compareAgainstHSE1HashMap(
humanSampleOneMap, organizationLocalAbbreviation, "organizationLocalAbbreviation");
if (result.equals(INVALID)) {
// bugzilla 2531
OrganizationLocalAbbreviationValidationProvider organizationLocalAbbreviationValidator =
new OrganizationLocalAbbreviationValidationProvider();
result =
organizationLocalAbbreviationValidator.validate(
(String) dynaForm.get("organizationLocalAbbreviation"), null);
messageKey = "humansampleone.provider.organization.localAbbreviation";
if (result.equals(INVALID)) {
ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null);
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
}
}
}
boolean stateValid = true;
String state = (String) dynaForm.get("state");
if (!StringUtil.isNullorNill(state)) {
result = compareAgainstHSE1HashMap(humanSampleOneMap, state, "state");
if (result.equals(INVALID)) {
// state validation against database (reusing ajax validation
// logic
StateValidationProvider stateValidator = new StateValidationProvider();
result = stateValidator.validate(state);
messageKey = "person.state";
if (result.equals(INVALID)) {
stateValid = false;
ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null);
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
}
}
}
boolean cityValid = true;
String city = (String) dynaForm.get("city");
if (!StringUtil.isNullorNill(city)) {
result = compareAgainstHSE1HashMap(humanSampleOneMap, city, "city");
if (result.equals(INVALID)) {
// city validation against database (reusing ajax validation
// logic
CityValidationProvider cityValidator = new CityValidationProvider();
result = cityValidator.validate(city);
messageKey = "person.city";
if (result.equals(INVALID)) {
cityValid = false;
ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null);
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
}
}
}
boolean zipValid = true;
String zip = (String) dynaForm.get("zipCode");
if (!StringUtil.isNullorNill(zip)) {
result = compareAgainstHSE1HashMap(humanSampleOneMap, zip, "zipCode");
if (result.equals(INVALID)) {
// zip validation against database (reusing ajax validation
// logic
ZipValidationProvider zipValidator = new ZipValidationProvider();
result = zipValidator.validate((String) dynaForm.get("zipCode"));
messageKey = "person.zipCode";
if (result.equals(INVALID)) {
zipValid = false;
ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null);
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
}
}
}
if (stateValid && cityValid && zipValid) {
String messageKey1 = "person.city";
String messageKey2 = "person.zipCode";
String messageKey3 = "person.state";
CityStateZipComboValidationProvider cityStateZipComboValidator =
new CityStateZipComboValidationProvider();
result =
cityStateZipComboValidator.validate(
(String) dynaForm.get("city"),
(String) dynaForm.get("state"),
(String) dynaForm.get("zipCode"));
// combination is invalid if result is invalid
if ("invalid".equals(result)) {
ActionError error =
new ActionError(
"errors.combo.3.invalid",
getMessageForKey(messageKey1),
getMessageForKey(messageKey2),
getMessageForKey(messageKey3),
null);
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
}
}
// sample type validation against database (reusing ajax validation
// logic
String sampleType = (String) dynaForm.get("typeOfSampleDesc");
if (!StringUtil.isNullorNill(sampleType)) {
result = compareAgainstHSE1HashMap(humanSampleOneMap, sampleType, "typeOfSampleDesc");
if (result.equals(INVALID)) {
HumanSampleTypeValidationProvider typeValidator = new HumanSampleTypeValidationProvider();
result = typeValidator.validate(sampleType);
messageKey = "sampleitem.typeOfSample";
if (result.equals(INVALID)) {
ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null);
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
}
}
}
String sampleSource = (String) dynaForm.get("sourceOfSampleDesc");
if (!StringUtil.isNullorNill(sampleSource)) {
result = compareAgainstHSE1HashMap(humanSampleOneMap, sampleSource, "sourceOfSampleDesc");
// sample source validation against database (reusing ajax
// validation
// logic
if (result.equals(INVALID)) {
HumanSampleSourceValidationProvider sourceValidator =
new HumanSampleSourceValidationProvider();
result = sourceValidator.validate(sampleSource);
messageKey = "sampleitem.sourceOfSample";
if (result.equals(INVALID)) {
ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null);
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
}
}
}
return errors;
}