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);
}
private HashMap populateHumanSampleOneMap(
Patient patient,
Person person,
Provider provider,
Person providerPerson,
Sample sample,
SampleHuman sampleHuman,
SampleOrganization sampleOrganization,
SampleItem sampleItem,
List analyses) {
HashMap humanSampleOneMap = new HashMap();
List sampleProjects = new ArrayList();
SampleProject sampleProject = null;
SampleProject sampleProject2 = null;
sampleProjects = sample.getSampleProjects();
if (sampleProjects != null && sampleProjects.size() > 0) {
sampleProject = (SampleProject) sampleProjects.get(0);
if (sampleProjects.size() > 1) {
sampleProject2 = (SampleProject) sampleProjects.get(1);
}
}
if (sample.getAccessionNumber() != null) {
humanSampleOneMap.put("accessionNumber", sample.getAccessionNumber());
} else {
humanSampleOneMap.put("accessionNumber", "");
}
if (patient.getBirthDateForDisplay() != null) {
humanSampleOneMap.put("birthDateForDisplay", patient.getBirthDateForDisplay());
} else {
humanSampleOneMap.put("birthDateForDisplay", "");
}
if (sample.getCollectionDateForDisplay() != null) {
humanSampleOneMap.put("collectionDateForDisplay", sample.getCollectionDateForDisplay());
} else {
humanSampleOneMap.put("collectionDateForDisplay", "");
}
if (sample.getCollectionTimeForDisplay() != null) {
humanSampleOneMap.put("collectionTimeForDisplay", sample.getCollectionTimeForDisplay());
} else {
// bugzilla 1894
humanSampleOneMap.put(
"collectionTimeForDisplay",
SystemConfiguration.getInstance().getHumanSampleOneDefaultCollectionTimeForDisplay());
}
// bugzilla 1904
if (patient.getChartNumber() != null) {
humanSampleOneMap.put("chartNumber", patient.getChartNumber());
} else {
humanSampleOneMap.put("chartNumber", "");
}
if (person.getCity() != null) {
// bugzilla 1766
humanSampleOneMap.put("city", person.getCity().toUpperCase().trim());
} else {
humanSampleOneMap.put("city", "");
}
if (sample.getClientReference() != null) {
humanSampleOneMap.put("clientReference", sample.getClientReference());
} else {
humanSampleOneMap.put("clientReference", "");
}
if (patient.getExternalId() != null) {
humanSampleOneMap.put("externalId", patient.getExternalId());
} else {
humanSampleOneMap.put("externalId", "");
}
if (person.getFirstName() != null) {
humanSampleOneMap.put("firstName", person.getFirstName());
} else {
humanSampleOneMap.put("firstName", "");
}
if (patient.getGender() != null) {
humanSampleOneMap.put("gender", patient.getGender());
} else {
humanSampleOneMap.put("gender", "");
}
if (person.getLastName() != null) {
humanSampleOneMap.put("lastName", person.getLastName());
} else {
humanSampleOneMap.put("lastName", "");
}
if (person.getMiddleName() != null) {
humanSampleOneMap.put("middleName", person.getMiddleName());
} else {
humanSampleOneMap.put("middleName", "");
}
if (person.getMultipleUnit() != null) {
humanSampleOneMap.put("multipleUnit", person.getMultipleUnit());
} else {
humanSampleOneMap.put("multipleUnit", "");
}
if (sampleOrganization != null && sampleOrganization.getOrganization() != null) {
// bugzilla 2069
humanSampleOneMap.put(
"organizationLocalAbbreviation",
sampleOrganization.getOrganization().getOrganizationLocalAbbreviation());
humanSampleOneMap.put(
"organizationNameForDisplay", sampleOrganization.getOrganization().getOrganizationName());
} else {
humanSampleOneMap.put("organizationLocalAbbreviation", "");
humanSampleOneMap.put("organizationNameForDisplay", "");
}
if (sampleProject != null && sampleProject.getProject() != null) {
// bugzilla 2438
humanSampleOneMap.put("projectId", sampleProject.getProject().getLocalAbbreviation());
// bugzilla 1766 since we capitolize project name do this here
// for comparison purposes
humanSampleOneMap.put(
"projectName", sampleProject.getProject().getProjectName().toUpperCase().trim());
} else {
humanSampleOneMap.put("projectId", "");
humanSampleOneMap.put("projectName", "");
}
if (sampleProject2 != null && sampleProject2.getProject() != null) {
// bugzilla 2438
humanSampleOneMap.put("projectId2", sampleProject2.getProject().getLocalAbbreviation());
// bugzilla 1766 since we capitolize project name do this here
// for comparison purposes
humanSampleOneMap.put(
"projectName2", sampleProject2.getProject().getProjectName().toUpperCase().trim());
} else {
humanSampleOneMap.put("projectId2", "");
humanSampleOneMap.put("projectName2", "");
}
if (providerPerson.getFirstName() != null) {
humanSampleOneMap.put("providerFirstName", providerPerson.getFirstName());
} else {
humanSampleOneMap.put("providerFirstName", "");
}
if (providerPerson.getLastName() != null) {
humanSampleOneMap.put("providerLastName", providerPerson.getLastName());
} else {
humanSampleOneMap.put("providerLastName", "");
}
if (providerPerson.getWorkPhone() != null) {
String storedResult = providerPerson.getWorkPhone();
humanSampleOneMap.put("providerWorkPhone", StringUtil.formatPhoneForDisplay(storedResult));
} else {
humanSampleOneMap.put("providerWorkPhone", "");
}
if (providerPerson.getWorkPhone() != null) {
String storedResult = providerPerson.getWorkPhone();
// bugzilla 2442
String extension = StringUtil.formatExtensionForDisplay(storedResult);
humanSampleOneMap.put("providerWorkPhoneExtension", StringUtil.trim(extension));
} else {
humanSampleOneMap.put("providerWorkPhoneExtension", "");
}
if (sample.getReceivedDateForDisplay() != null) {
humanSampleOneMap.put("receivedDateForDisplay", sample.getReceivedDateForDisplay());
} else {
humanSampleOneMap.put("receivedDateForDisplay", "");
}
if (sample.getReferredCultureFlag() != null) {
humanSampleOneMap.put("referredCultureFlag", sample.getReferredCultureFlag());
} else {
humanSampleOneMap.put("referredCultureFlag", "");
}
if (sampleItem.getSourceOfSample() != null) {
SourceOfSample sos = (SourceOfSample) sampleItem.getSourceOfSample();
// bugzilla 1766
humanSampleOneMap.put("sourceOfSampleDesc", sos.getDescription().toUpperCase().trim());
// bugzilla 1465
humanSampleOneMap.put("sourceOfSampleId", sos.getId());
} else {
humanSampleOneMap.put("sourceOfSampleDesc", "");
// bugzilla 1465
humanSampleOneMap.put("sourceOfSampleId", "");
}
if (sampleItem.getSourceOther() != null) {
humanSampleOneMap.put("sourceOther", sampleItem.getSourceOther().trim());
} else {
humanSampleOneMap.put("sourceOther", "");
}
if (person.getState() != null) {
humanSampleOneMap.put("state", person.getState());
} else {
humanSampleOneMap.put("state", "");
}
if (sample.getStickerReceivedFlag() != null) {
humanSampleOneMap.put("stickerReceivedFlag", sample.getStickerReceivedFlag());
} else {
humanSampleOneMap.put("stickerReceivedFlag", "");
}
if (person.getStreetAddress() != null) {
humanSampleOneMap.put("streetAddress", person.getStreetAddress().trim());
} else {
humanSampleOneMap.put("streetAddress", "");
}
if (sampleItem.getTypeOfSample() != null) {
TypeOfSample tos = (TypeOfSample) sampleItem.getTypeOfSample();
// bugzilla 1766
humanSampleOneMap.put("typeOfSampleDesc", tos.getDescription().toUpperCase().trim());
// bugzilla 1465
humanSampleOneMap.put("typeOfSampleId", tos.getId());
} else {
humanSampleOneMap.put("typeOfSampleDesc", "");
// bugzilla 1465
humanSampleOneMap.put("typeOfSampleId", "");
}
if (person.getZipCode() != null) {
humanSampleOneMap.put("zipCode", person.getZipCode().trim());
} else {
humanSampleOneMap.put("zipCode", "");
}
return humanSampleOneMap;
}