public void updateData(SampleHuman sampleHuman) throws LIMSRuntimeException {
SampleHuman oldData = readSampleHuman(sampleHuman.getId());
SampleHuman newData = sampleHuman;
// add to audit trail
try {
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
String sysUserId = sampleHuman.getSysUserId();
String event = IActionConstants.AUDIT_TRAIL_UPDATE;
String tableName = "SAMPLE_HUMAN";
auditDAO.saveHistory(newData, oldData, sysUserId, event, tableName);
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("SampleHumanDAOImpl", "updateData()", e.toString());
throw new LIMSRuntimeException("Error in SampleHuman AuditTrail updateData()", e);
}
try {
HibernateUtil.getSession().merge(sampleHuman);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
HibernateUtil.getSession().evict(sampleHuman);
HibernateUtil.getSession().refresh(sampleHuman);
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("SampleHumanDAOImpl", "updateData()", e.toString());
throw new LIMSRuntimeException("Error in SampleHuman updateData()", e);
}
}
public void deleteData(List sampleHumans) throws LIMSRuntimeException {
// add to audit trail
try {
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
for (int i = 0; i < sampleHumans.size(); i++) {
SampleHuman data = (SampleHuman) sampleHumans.get(i);
SampleHuman oldData = (SampleHuman) readSampleHuman(data.getId());
SampleHuman newData = new SampleHuman();
String sysUserId = data.getSysUserId();
String event = IActionConstants.AUDIT_TRAIL_DELETE;
String tableName = "SAMPLE_HUMAN";
auditDAO.saveHistory(newData, oldData, sysUserId, event, tableName);
}
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("SampleHumanDAOImpl", "AuditTrail deleteData()", e.toString());
throw new LIMSRuntimeException("Error in SampleHuman AuditTrail deleteData()", e);
}
try {
for (int i = 0; i < sampleHumans.size(); i++) {
SampleHuman data = (SampleHuman) sampleHumans.get(i);
// bugzilla 2206
data = (SampleHuman) readSampleHuman(data.getId());
HibernateUtil.getSession().delete(data);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
}
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("SampleHumanDAOImpl", "deleteData()", e.toString());
throw new LIMSRuntimeException("Error in SampleHuman deleteData()", e);
}
}
public void getData(SampleHuman sampleHuman) throws LIMSRuntimeException {
try {
SampleHuman sampHuman =
(SampleHuman) HibernateUtil.getSession().get(SampleHuman.class, sampleHuman.getId());
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
if (sampHuman != null) {
PropertyUtils.copyProperties(sampleHuman, sampHuman);
} else {
sampleHuman.setId(null);
}
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("SampleHumanDAOImpl", "getData()", e.toString());
throw new LIMSRuntimeException("Error in SampleHuman getData()", e);
}
}
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);
}