private void checkIfSamplesFinished(List<AnalysisItem> resultItemList) {
sampleUpdateList = new ArrayList<Sample>();
String currentSampleId = "";
boolean sampleFinished = true;
for (AnalysisItem analysisItem : resultItemList) {
String analysisSampleId =
sampleDAO.getSampleByAccessionNumber(analysisItem.getAccessionNumber()).getId();
if (!analysisSampleId.equals(currentSampleId)) {
currentSampleId = analysisSampleId;
List<Analysis> analysisList = analysisDAO.getAnalysesBySampleId(currentSampleId);
for (Analysis analysis : analysisList) {
if (!sampleFinishedStatus.contains(Integer.parseInt(analysis.getStatusId()))) {
sampleFinished = false;
break;
}
}
if (sampleFinished) {
Sample sample = new Sample();
sample.setId(currentSampleId);
sampleDAO.getData(sample);
sample.setStatusId(StatusService.getInstance().getStatusID(OrderStatus.Finished));
sampleUpdateList.add(sample);
}
sampleFinished = true;
}
}
}
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);
String accessionNumber = (String) dynaForm.get("accessionNumber");
String birthWeight = (String) dynaForm.get("birthWeight");
Patient patient = new Patient();
Person person = new Person();
Sample sample = new Sample();
SampleHuman sampleHuman = new SampleHuman();
SampleNewborn sampleNewborn = new SampleNewborn();
UserSessionData usd = (UserSessionData) request.getSession().getAttribute(USER_SESSION_DATA);
String sysUserId = String.valueOf(usd.getSystemUserId());
// populate valueholder from form
PropertyUtils.copyProperties(sample, dynaForm);
PropertyUtils.copyProperties(person, dynaForm);
PropertyUtils.copyProperties(sampleHuman, dynaForm);
PropertyUtils.copyProperties(sampleNewborn, dynaForm);
String birthDate = dynaForm.getString("birthDateForDisplay");
String birthTime = dynaForm.getString("birthTimeForDisplay");
String format = "MM/dd/yyyy";
if ((birthDate != null) && (birthDate.length() > 0)) {
java.text.SimpleDateFormat f = new java.text.SimpleDateFormat(format);
java.sql.Timestamp dob = new java.sql.Timestamp(f.parse(birthDate).getTime());
if ((birthTime != null) && (birthTime.length() > 0)) {
Calendar cal = Calendar.getInstance();
cal.setTime(dob);
cal.set(Calendar.HOUR_OF_DAY, Integer.valueOf(birthTime.substring(0, 2)).intValue());
cal.set(Calendar.MINUTE, Integer.valueOf(birthTime.substring(3, 5)).intValue());
dob = new java.sql.Timestamp(cal.getTimeInMillis());
}
patient.setBirthDate(dob);
}
String collectionDate = dynaForm.getString("collectionDateForDisplay");
String collectionTime = dynaForm.getString("collectionTimeForDisplay");
java.sql.Timestamp collDate = null;
if ((collectionDate != null) && (collectionDate.length() > 0)) {
java.text.SimpleDateFormat f = new java.text.SimpleDateFormat(format);
collDate = new java.sql.Timestamp(f.parse(collectionDate).getTime());
if ((collectionTime != null) && (collectionTime.length() > 0)) {
Calendar cal = Calendar.getInstance();
cal.setTime(collDate);
cal.set(Calendar.HOUR_OF_DAY, Integer.valueOf(collectionTime.substring(0, 2)).intValue());
cal.set(Calendar.MINUTE, Integer.valueOf(collectionTime.substring(3, 5)).intValue());
collDate = new java.sql.Timestamp(cal.getTimeInMillis());
}
}
SampleDAO sampleDAO = new SampleDAOImpl();
PersonDAO personDAO = new PersonDAOImpl();
PatientDAO patientDAO = new PatientDAOImpl();
SampleHumanDAO sampleHumanDAO = new SampleHumanDAOImpl();
SampleNewbornDAO sampleNewbornDAO = new SampleNewbornDAOImpl();
try {
sample.setSysUserId(sysUserId);
sample.setAccessionNumber(accessionNumber);
sampleDAO.getSampleByAccessionNumber(sample);
sample.setStatus(SystemConfiguration.getInstance().getSampleStatusEntry1Complete());
sample.setCollectionDate(collDate);
sampleDAO.updateData(sample);
person.setSysUserId(sysUserId);
patient.setSysUserId(sysUserId);
personDAO.insertData(person);
patient.setPerson(person);
patientDAO.insertData(patient);
sampleHuman.setSysUserId(sysUserId);
sampleHuman.setSampleId(sample.getId());
sampleHuman.setPatientId(patient.getId());
sampleHumanDAO.insertData(sampleHuman);
sampleNewborn.setSysUserId(sysUserId);
sampleNewborn.setId(sampleHuman.getId());
sampleNewborn.setWeight(birthWeight);
sampleNewbornDAO.insertData(sampleNewborn);
} catch (LIMSRuntimeException lre) {
LogEvent.logError("NewbornSampleOneUpdateAction", "performAction()", lre.toString());
request.setAttribute(IActionConstants.REQUEST_FAILED, true);
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;
}
if (forward.equals(FWD_FAIL)) return mapping.findForward(forward);
return mapping.findForward(FWD_SUCCESS);
}
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 {
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 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);
}