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 {
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);
}
static {
ReferenceTablesDAO tableDAO = new ReferenceTablesDAOImpl();
NOTE_TABLE_ID = tableDAO.getReferenceTableByName("NOTE").getId();
RESULT_TABLE_ID = tableDAO.getReferenceTableByName("RESULT").getId();
}