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);
}