public void deleteData(String siteInformationId, String currentUserId)
throws LIMSRuntimeException {
try {
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
SiteInformation oldData = readSiteInformation(siteInformationId);
SiteInformation newData = new SiteInformation();
auditDAO.saveHistory(
newData, oldData, currentUserId, IActionConstants.AUDIT_TRAIL_DELETE, "SITE_INFORMATION");
} catch (Exception e) {
LogEvent.logError("SiteInformationDAOImpl", "AuditTrail deleteData()", e.toString());
throw new LIMSRuntimeException("Error in SiteInformation AuditTrail deleteData()", e);
}
try {
SiteInformation siteInformation = readSiteInformation(siteInformationId);
HibernateUtil.getSession().delete(siteInformation);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
LogEvent.logError("SiteInformationsDAOImpl", "deleteData()", e.toString());
throw new LIMSRuntimeException("Error in SiteInformation deleteData()", e);
}
}
public void updateData(SiteInformation siteInformation) throws LIMSRuntimeException {
SiteInformation oldData = readSiteInformation(siteInformation.getId());
SiteInformation newData = siteInformation;
try {
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
auditDAO.saveHistory(
newData,
oldData,
siteInformation.getSysUserId(),
IActionConstants.AUDIT_TRAIL_UPDATE,
"SITE_INFORMATION");
} catch (Exception e) {
LogEvent.logError("SiteInformationDAOImpl", "AuditTrail updateData()", e.toString());
throw new LIMSRuntimeException("Error in SiteInformation AuditTrail updateData()", e);
}
try {
HibernateUtil.getSession().merge(siteInformation);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
HibernateUtil.getSession().evict(siteInformation);
HibernateUtil.getSession().refresh(siteInformation);
} catch (Exception e) {
LogEvent.logError("SiteInformationsDAOImpl", "updateData()", e.toString());
throw new LIMSRuntimeException("Error in SiteInformation updateData()", e);
}
}
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 updateData(ReferenceTables referenceTables) throws LIMSRuntimeException {
// bugzilla 1482 throw Exception if record already exists
// String isHl7Encoded;
// String keepHistory;
boolean isNew = false;
/*isHl7Encoded = referencetables.getIsHl7Encoded();
System.out.println ("Yi isH17Encodded is " + isHl7Encoded);
if (StringUtil.isNullorNill(isHl7Encoded) || "0".equals(isHl7Encoded)) {
referencetables.setIsHl7Encoded ("N");
}
keepHistory = referencetables.getKeepHistory();
System.out.println ("Yi isH17Encodded is " + keepHistory);
if (StringUtil.isNullorNill(keepHistory) || "0".equals(keepHistory)) {
referencetables.setKeepHistory ("N");
}*/
try {
if (duplicateReferenceTablesExists(referenceTables, isNew)) {
throw new LIMSDuplicateRecordException(
"Duplicate record exists for " + referenceTables.getTableName());
}
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "updateData()", e.toString());
throw new LIMSRuntimeException("Error in Referencetables updateData()", e);
}
// System.out.println("This is name from updateData " + referencetables.getTableName());
ReferenceTables oldData = (ReferenceTables) readReferenceTables(referenceTables.getId());
ReferenceTables newData = referenceTables;
// System.out.println("updateDate " + newData.getTableName() + " " + oldData.getTableName());
// add to audit trail
try {
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
String sysUserId = referenceTables.getSysUserId();
String event = IActionConstants.AUDIT_TRAIL_UPDATE;
String tableName = "REFERENCE_TABLES";
auditDAO.saveHistory(newData, oldData, sysUserId, event, tableName);
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "AuditTrail updateData()", e.toString());
throw new LIMSRuntimeException("Error in Referencetables AuditTrail updateData()", e);
}
try {
HibernateUtil.getSession().merge(referenceTables);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
HibernateUtil.getSession().evict(referenceTables);
HibernateUtil.getSession().refresh(referenceTables);
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "updateData()", e.toString());
throw new LIMSRuntimeException("Error in Referencetables updateData()", e);
}
}
protected ActionForward performAction(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
String forward = FWD_SUCCESS;
DynaActionForm dynaForm = (DynaActionForm) form;
// get selected qaEvents
String[] selectedIDs = (String[]) dynaForm.get("selectedIDs");
// get sysUserId from login module
UserSessionData usd = (UserSessionData) request.getSession().getAttribute(USER_SESSION_DATA);
String sysUserId = String.valueOf(usd.getSystemUserId());
List qaEvents = new ArrayList();
for (int i = 0; i < selectedIDs.length; i++) {
QaEvent qaEvent = new QaEvent();
qaEvent.setId(selectedIDs[i]);
qaEvent.setSysUserId(sysUserId);
qaEvents.add(qaEvent);
}
ActionMessages errors = null;
try {
QaEventDAO qaEventDAO = new QaEventDAOImpl();
qaEventDAO.deleteData(qaEvents);
// System.out.println("Just deleted QaEvent");
// initialize the form
dynaForm.initialize(mapping);
} catch (LIMSRuntimeException lre) {
// bugzilla 2154
LogEvent.logError("QaEventDeleteAction", "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.DeleteException", null, null);
}
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
saveErrors(request, errors);
request.setAttribute(Globals.ERROR_KEY, errors);
forward = FWD_FAIL;
}
if (forward.equals(FWD_FAIL)) return mapping.findForward(forward);
if ("true".equalsIgnoreCase(request.getParameter("close"))) {
forward = FWD_CLOSE;
}
request.setAttribute("menuDefinition", "QaEventMenuDefinition");
return mapping.findForward(forward);
}
// bugzilla 1427
public List getPreviousRecord(String id, String table, Class clazz) throws LIMSRuntimeException {
int currentId = (Integer.valueOf(id)).intValue();
String tablePrefix = getTablePrefix(table);
List list = new Vector();
// bugzilla 1908
int rrn = 0;
try {
// bugzilla 1908 cannot use named query for postgres because of oracle ROWNUM
// instead get the list in this sortorder and determine the index of record with id =
// currentId
String sql = "select r.id from ReferenceTables r order by r.tableName";
org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql);
list = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
rrn = list.indexOf(String.valueOf(currentId));
list =
HibernateUtil.getSession()
.getNamedQuery(tablePrefix + "getPrevious")
.setFirstResult(rrn - 1)
.setMaxResults(2)
.list();
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "getPreviousRecord()", e.toString());
throw new LIMSRuntimeException("Error in getPreviousRecord() for " + table, e);
}
return list;
}
public void deleteData(List referenceTableses) throws LIMSRuntimeException {
// add to audit trail
try {
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
for (int i = 0; i < referenceTableses.size(); i++) {
ReferenceTables data = (ReferenceTables) referenceTableses.get(i);
ReferenceTables oldData = (ReferenceTables) readReferenceTables(data.getId());
ReferenceTables newData = new ReferenceTables();
String sysUserId = data.getSysUserId();
String event = IActionConstants.AUDIT_TRAIL_DELETE;
String tableName = "REFERENCE_TABLES";
auditDAO.saveHistory(newData, oldData, sysUserId, event, tableName);
}
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "AuditTrail deleteData()", e.toString());
throw new LIMSRuntimeException("Error in ReferenceTables AuditTrail deleteData()", e);
}
try {
for (int i = 0; i < referenceTableses.size(); i++) {
ReferenceTables data = (ReferenceTables) referenceTableses.get(i);
// bugzilla 2206
data = (ReferenceTables) readReferenceTables(data.getId());
HibernateUtil.getSession().delete(data);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
}
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "deleteData()", e.toString());
throw new LIMSRuntimeException("Error in ReferenceTables deleteData()", e);
}
}
public SampleHuman readSampleHuman(String idString) {
SampleHuman sh = null;
try {
sh = (SampleHuman) HibernateUtil.getSession().get(SampleHuman.class, idString);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("SampleHumanDAOImpl", "readSampleHuman()", e.toString());
throw new LIMSRuntimeException("Error in SampleHuman readSampleHuman()", e);
}
return sh;
}
public SiteInformation readSiteInformation(String idString) {
SiteInformation recoveredSiteInformation = null;
try {
recoveredSiteInformation =
(SiteInformation) HibernateUtil.getSession().get(SiteInformation.class, idString);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
LogEvent.logError("SiteInformationDAOImpl", "readSiteInformation()", e.toString());
throw new LIMSRuntimeException("Error in SiteInformation readSiteInformation()", e);
}
return recoveredSiteInformation;
}
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 ReferenceTables readReferenceTables(String idString) {
ReferenceTables referenceTables = null;
try {
referenceTables =
(ReferenceTables) HibernateUtil.getSession().get(ReferenceTables.class, idString);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "readReferenceTables()", e.toString());
throw new LIMSRuntimeException("Error in Referencetables readReferenceTables(idString)", e);
}
return referenceTables;
}
// bugzilla 1482
private boolean duplicateReferenceTablesExists(ReferenceTables referenceTables, boolean isNew)
throws LIMSRuntimeException {
try {
List list = new ArrayList();
String sql;
// not case sensitive hemolysis and Hemolysis are considered
// duplicates
if (isNew) {
sql = "from ReferenceTables t where trim(lower(t.tableName)) = :param";
} else {
sql = "from ReferenceTables t where trim(lower(t.tableName)) = :param and id != :param2";
}
// System.out.println("Yi in duplicateReferencetables sql is " + sql);
org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql);
// System.out.println("duplicateReferencetables sql is " + sql);
query.setParameter("param", referenceTables.getTableName().toLowerCase().trim());
// initialize with 0 (for new records where no id has been generated
// yet
String referenceTablesId = "0";
if (!StringUtil.isNullorNill(referenceTables.getId())) {
referenceTablesId = referenceTables.getId();
}
if (!isNew) {
query.setParameter("param2", referenceTablesId);
}
list = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
if (list.size() > 0) {
return true;
} else {
return false;
}
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "duplicateReferenceTablesExists()", e.toString());
throw new LIMSRuntimeException("Error in duplicateReferenceTablesExists()", 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);
}
}
public void getData(SiteInformation siteInformation) throws LIMSRuntimeException {
try {
SiteInformation tmpSiteInformation =
(SiteInformation)
HibernateUtil.getSession().get(SiteInformation.class, siteInformation.getId());
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
if (tmpSiteInformation != null) {
PropertyUtils.copyProperties(siteInformation, tmpSiteInformation);
} else {
siteInformation.setId(null);
}
} catch (Exception e) {
LogEvent.logError("SiteInformationsDAOImpl", "getData()", e.toString());
throw new LIMSRuntimeException("Error in SiteInformation getData()", e);
}
}
public void getData(ReferenceTables referenceTables) throws LIMSRuntimeException {
try {
ReferenceTables reftbl =
(ReferenceTables)
HibernateUtil.getSession().get(ReferenceTables.class, referenceTables.getId());
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
if (reftbl != null) {
PropertyUtils.copyProperties(referenceTables, reftbl);
} else {
referenceTables.setId(null);
}
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "getData()", e.toString());
throw new LIMSRuntimeException("Error in Referencetables getData()", e);
}
}
public List getAllReferenceTables() throws LIMSRuntimeException {
List list = new Vector();
try {
String sql = "from ReferenceTables";
org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql);
// query.setMaxResults(10);
// query.setFirstResult(3);
list = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "getAllReferenceTables()", e.toString());
throw new LIMSRuntimeException("Error in Referencetables getAllReferenceTables()", e);
}
return list;
}
public Patient getPatientForSample(Sample sample) throws LIMSRuntimeException {
Patient patient = null;
try {
String sql =
"select patient from Patient as patient, SampleHuman as sampleHuman where sampleHuman.patientId = patient.id and sampleHuman.sampleId = :sId";
Query query = HibernateUtil.getSession().createQuery(sql);
query.setInteger("sId", Integer.parseInt(sample.getId()));
patient = (Patient) query.uniqueResult();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (HibernateException he) {
LogEvent.logError("SampleHumanDAOImpl", "getPatientForSample()", he.toString());
throw new LIMSRuntimeException("Error in SampleHuman getPatientForSample()", he);
}
return patient;
}
public void getDataBySample(SampleHuman sampleHuman) throws LIMSRuntimeException {
try {
String sql = "from SampleHuman sh where samp_id = :param";
Query query = HibernateUtil.getSession().createQuery(sql);
query.setInteger("param", Integer.parseInt(sampleHuman.getSampleId()));
List list = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
SampleHuman sh = null;
if (list.size() > 0) {
sh = (SampleHuman) list.get(0);
PropertyUtils.copyProperties(sampleHuman, sh);
}
} catch (Exception e) {
LogEvent.logError("SampleHumanDAOImpl", "getDataBySample()", e.toString());
throw new LIMSRuntimeException("Error in SampleHuman getDataBySample()", e);
}
}
public boolean insertData(SiteInformation siteInformation) throws LIMSRuntimeException {
try {
String id = (String) HibernateUtil.getSession().save(siteInformation);
siteInformation.setId(id);
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
auditDAO.saveNewHistory(siteInformation, siteInformation.getSysUserId(), "SITE_INFORMATION");
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
LogEvent.logError("SiteInformationDAOImpl", "insertData()", e.toString());
throw new LIMSRuntimeException("Error in SiteInformation insertData()", e);
}
return true;
}
public boolean insertData(ReferenceTables referenceTables) throws LIMSRuntimeException {
// String isHl7Encoded;
// String keepHistory;
boolean isNew = true;
/*isHl7Encoded = referencetables.getIsHl7Encoded();
if (StringUtil.isNullorNill(isHl7Encoded) || "0".equals(isHl7Encoded)) {
referencetables.setIsHl7Encoded ("N");
}
keepHistory = referencetables.getKeepHistory();
if (StringUtil.isNullorNill(keepHistory) || "0".equals(keepHistory)) {
referencetables.setKeepHistory ("N");
}*/
try {
// bugzilla 1482 throw Exception if record already exists
if (duplicateReferenceTablesExists(referenceTables, isNew)) {
throw new LIMSDuplicateRecordException(
"Duplicate record exists for " + referenceTables.getTableName());
}
// System.out.println("This is ID from insert referencetables " + referencetables.getId());
String id = (String) HibernateUtil.getSession().save(referenceTables);
referenceTables.setId(id);
// bugzilla 1824 inserts will be logged in history table
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
String sysUserId = referenceTables.getSysUserId();
String tableName = "REFERENCE_TABLES";
auditDAO.saveNewHistory(referenceTables, sysUserId, tableName);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "insertData()", e.toString());
throw new LIMSRuntimeException("Error in Referencetables insertData()", e);
}
return true;
}
@SuppressWarnings("unchecked")
public List<Sample> getCollectedSamplesForPatient(String patientID) throws LIMSRuntimeException {
List<Sample> samples;
try {
String sql =
"select sample from Sample as sample, SampleHuman as sampleHuman where sampleHuman.sampleId = sample.id and sampleHuman.patientId = :patientId and sample.accessionNumber is not null order by sample.id";
Query query = HibernateUtil.getSession().createQuery(sql);
query.setInteger("patientId", Integer.parseInt(patientID));
samples = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (HibernateException he) {
LogEvent.logError("SampleHumanDAOImpl", "getSamplesForPatient()", he.toString());
throw new LIMSRuntimeException("Error in SampleHuman getSamplesForPatient()", he);
}
return samples;
}
public boolean insertData(SampleHuman sampleHuman) throws LIMSRuntimeException {
try {
String id = (String) HibernateUtil.getSession().save(sampleHuman);
sampleHuman.setId(id);
// bugzilla 1824 inserts will be logged in history table
AuditTrailDAO auditDAO = new AuditTrailDAOImpl();
String sysUserId = sampleHuman.getSysUserId();
String tableName = "SAMPLE_HUMAN";
auditDAO.saveNewHistory(sampleHuman, sysUserId, tableName);
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("SampleHumanDAOImpl", "insertData()", e.toString());
throw new LIMSRuntimeException("Error in SampleHuman insertData()", e);
}
return true;
}
public List getPageOfReferenceTables(int startingRecNo) throws LIMSRuntimeException {
List list = new Vector();
try {
// calculate maxRow to be one more than the page size
int endingRecNo =
startingRecNo + (SystemConfiguration.getInstance().getDefaultPageSize() + 1);
String sql = "from ReferenceTables r order by r.tableName";
org.hibernate.Query query = HibernateUtil.getSession().createQuery(sql);
query.setFirstResult(startingRecNo - 1);
query.setMaxResults(endingRecNo - 1);
// query.setCacheMode(org.hibernate.CacheMode.REFRESH);
list = query.list();
HibernateUtil.getSession().flush();
HibernateUtil.getSession().clear();
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ReferenceTablesDAOImpl", "getPageOfReferenceTables()", e.toString());
throw new LIMSRuntimeException("Error in Referencetables getPageOfReferenceTables()", e);
}
return list;
}
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 Analyte.
// If there is a parameter present, we should bring up an existing
// Analyte to edit.
String forward = FWD_SUCCESS;
request.setAttribute(ALLOW_EDITS_KEY, "true");
request.setAttribute(PREVIOUS_DISABLED, "false");
request.setAttribute(NEXT_DISABLED, "false");
String id = request.getParameter(ID);
if (StringUtil.isNullorNill(id) || "0".equals(id)) {
isNew = true;
} else {
isNew = false;
}
BaseActionForm dynaForm = (BaseActionForm) form;
String start = (String) request.getParameter("startingRecNo");
String direction = (String) request.getParameter("direction");
// System.out.println("This is ID from request " + id);
Panel panel = new Panel();
panel.setId(id);
try {
PanelDAO panelDAO = new PanelDAOImpl();
// retrieve analyte by id since the name may have changed
panelDAO.getData(panel);
if (FWD_NEXT.equals(direction)) {
// bugzilla 1427 pass in name not id
List panels = panelDAO.getNextPanelRecord(panel.getPanelName());
if (panels != null && panels.size() > 0) {
panel = (Panel) panels.get(0);
panelDAO.getData(panel);
if (panels.size() < 2) {
// disable next button
request.setAttribute(NEXT_DISABLED, "true");
}
id = panel.getId();
} else {
// just disable next button
request.setAttribute(NEXT_DISABLED, "true");
}
}
if (FWD_PREVIOUS.equals(direction)) {
// bugzilla 1427 pass in name not id
List panels = panelDAO.getPreviousPanelRecord(panel.getPanelName());
if (panels != null && panels.size() > 0) {
panel = (Panel) panels.get(0);
panelDAO.getData(panel);
if (panels.size() < 2) {
// disable previous button
request.setAttribute(PREVIOUS_DISABLED, "true");
}
id = panel.getId();
} else {
// just disable next button
request.setAttribute(PREVIOUS_DISABLED, "true");
}
}
} catch (LIMSRuntimeException lre) {
// bugzilla 2154
LogEvent.logError("PanelNextPreviousAction", "performAction()", lre.toString());
request.setAttribute(ALLOW_EDITS_KEY, "false");
// disable previous and next
request.setAttribute(PREVIOUS_DISABLED, "true");
request.setAttribute(NEXT_DISABLED, "true");
forward = FWD_FAIL;
}
if (forward.equals(FWD_FAIL)) return mapping.findForward(forward);
if (panel.getId() != null && !panel.getId().equals("0")) {
request.setAttribute(ID, panel.getId());
}
return getForward(mapping.findForward(forward), id, start);
}
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);
}
// modified for efficiency bugzilla 1367
public String validate(String targetId) throws LIMSRuntimeException {
StringBuffer s = new StringBuffer();
// bgm added StringUtil to check against a space being entered.
if (!StringUtil.isNullorNill(targetId)) {
ProjectDAO projectDAO = new ProjectDAOImpl();
Project project = new Project();
try {
int i = Integer.parseInt(targetId);
// bugzilla 2438
project.setLocalAbbreviation(targetId.trim());
} catch (NumberFormatException nfe) {
// bugzilla 2154
LogEvent.logError("ProjectIdOrNameValidationProvider", "validate()", nfe.toString());
// if the id was not a number
project = null;
}
if (project != null) {
// bugzilla 2438
project = projectDAO.getProjectByLocalAbbreviation(project, true);
}
// bugzilla 2112
try {
if (null != project) {
// bugzilla 1978
if (project.getIsActive().equals(YES)) {
// This is particular to projId validation for HSE1 and HSE2:
// the message appended to VALID is the projectName that
// can then be displayed when User enters valid Project Id
// (see humanSampleOne.jsp, humanSampleTwo.jsp)
// bgm - bugzilla 1535 commented out s.append(project.getProjectName()); to check first
if (null != project.getProjectName()) {
s.append(VALID);
s.append(project.getProjectName());
} else s.append(INVALID);
} else {
s.append(INVALID);
}
} else {
project = new Project();
project.setId("");
project.setProjectName(targetId.trim());
project = projectDAO.getProjectByName(project, true, true);
if (project != null) {
s.append(VALID);
// bugzilla 2438
s.append(project.getLocalAbbreviation());
} else {
s.append(INVALID);
}
}
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ProjectIdOrNameValidationProvider", "validate()", e.toString());
s.append(INVALID);
}
} else {
// bugzilla 1697
s.append(VALID);
}
/*
* System.out.println("I am in projIdValidator returning " +
* s.toString() + " targetId " + targetId);
*/
return s.toString();
}
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 Scriptlet.
// If there is a parameter present, we should bring up an existing
// Scriptlet to edit.
String forward = FWD_SUCCESS;
request.setAttribute(ALLOW_EDITS_KEY, "true");
request.setAttribute(PREVIOUS_DISABLED, "false");
request.setAttribute(NEXT_DISABLED, "false");
String id = request.getParameter(ID);
if (StringUtil.isNullorNill(id) || "0".equals(id)) {
isNew = true;
} else {
isNew = false;
}
BaseActionForm dynaForm = (BaseActionForm) form;
// server-side validation (validation.xml)
ActionMessages errors = dynaForm.validate(mapping, request);
if (errors != null && errors.size() > 0) {
saveErrors(request, errors);
// since we forward to jsp - not Action we don't need to repopulate
// the lists here
return mapping.findForward(FWD_FAIL);
}
String start = (String) request.getParameter("startingRecNo");
String direction = (String) request.getParameter("direction");
Scriptlet scriptlet = new Scriptlet();
// get sysUserId from login module
UserSessionData usd = (UserSessionData) request.getSession().getAttribute(USER_SESSION_DATA);
String sysUserId = String.valueOf(usd.getSystemUserId());
scriptlet.setSysUserId(sysUserId);
// populate valueholder from form
PropertyUtils.copyProperties(scriptlet, dynaForm);
try {
ScriptletDAO scriptletDAO = new ScriptletDAOImpl();
if (!isNew) {
// UPDATE
scriptletDAO.updateData(scriptlet);
} else {
// INSERT
scriptletDAO.insertData(scriptlet);
}
} catch (LIMSRuntimeException lre) {
// bugzilla 2154
LogEvent.logError("ScriptletUpdateAction", "performAction()", lre.toString());
request.setAttribute(IActionConstants.REQUEST_FAILED, true);
errors = new ActionMessages();
java.util.Locale locale =
(java.util.Locale) request.getSession().getAttribute("org.apache.struts.action.LOCALE");
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);
} else {
// bugzilla 1482
if (lre.getException() instanceof LIMSDuplicateRecordException) {
String messageKey = "scriptlet.scriptletName";
String msg =
ResourceLocator.getInstance().getMessageResources().getMessage(locale, messageKey);
error = new ActionError("errors.DuplicateRecord", msg, null);
} else {
error = new ActionError("errors.UpdateException", null, null);
}
}
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
saveErrors(request, errors);
request.setAttribute(Globals.ERROR_KEY, errors);
// bugzilla 1485: allow change and try updating again (enable save button)
// request.setAttribute(IActionConstants.ALLOW_EDITS_KEY, "false");
// disable previous and next
request.setAttribute(PREVIOUS_DISABLED, "true");
request.setAttribute(NEXT_DISABLED, "true");
forward = FWD_FAIL;
}
if (forward.equals(FWD_FAIL)) return mapping.findForward(forward);
// initialize the form
dynaForm.initialize(mapping);
// repopulate the form from valueholder
PropertyUtils.copyProperties(dynaForm, scriptlet);
if ("true".equalsIgnoreCase(request.getParameter("close"))) {
forward = FWD_CLOSE;
}
if (scriptlet.getId() != null && !scriptlet.getId().equals("0")) {
request.setAttribute(ID, scriptlet.getId());
}
// bugzilla 1400
if (isNew) forward = FWD_SUCCESS_INSERT;
// bugzilla 1467 added direction for redirect to NextPreviousAction
return getForward(mapping.findForward(forward), scriptlet.getId(), start, direction);
}
protected ActionForward performAction(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
String forward = FWD_SUCCESS;
request.setAttribute(ALLOW_EDITS_KEY, "true");
BaseActionForm dynaForm = (BaseActionForm) form;
// server-side validation (validation.xml)
ActionMessages errors = dynaForm.validate(mapping, request);
// bugzilla 2614 allow for NB domain samples
String selectedTestId = "";
String referenceTableId = SystemConfiguration.getInstance().getResultReferenceTableId();
String refId = (String) dynaForm.get("noteRefId");
String noteIds = (String) dynaForm.get("noteIds");
String noteSubjects = (String) dynaForm.get("noteSubjects");
String noteTexts = (String) dynaForm.get("noteTexts");
String noteTypes = (String) dynaForm.get("noteTypes");
String noteLastupdateds = (String) dynaForm.get("noteLastupdateds");
List noteIdList = new ArrayList();
List noteSubjectList = new ArrayList();
List noteTextList = new ArrayList();
List noteTypeList = new ArrayList();
List noteLastupdatedList = new ArrayList();
String textSeparator = SystemConfiguration.getInstance().getDefaultTextSeparator();
NoteDAO noteDAO = new NoteDAOImpl();
SystemUserDAO systemUserDAO = new SystemUserDAOImpl();
// bugzilla 2571 go through ReferenceTablesDAO to get reference tables info
ReferenceTablesDAO referenceTablesDAO = new ReferenceTablesDAOImpl();
// get sysUserId from login module
UserSessionData usd = (UserSessionData) request.getSession().getAttribute(USER_SESSION_DATA);
String sysUserId = String.valueOf(usd.getSystemUserId());
org.hibernate.Transaction tx = HibernateUtil.getSession().beginTransaction();
try {
textSeparator = StringUtil.convertStringToRegEx(textSeparator);
SystemUser systemUser = new SystemUser();
systemUser.setId(sysUserId);
systemUserDAO.getData(systemUser);
// get all the data required to forward to correct page
// get analysis id from result
ResultDAO resultDAO = new ResultDAOImpl();
Result result = new Result();
result.setId(refId);
resultDAO.getData(result);
String analysisId = result.getAnalysis().getId();
AnalysisDAO analysisDAO = new AnalysisDAOImpl();
Analysis analysis = new Analysis();
analysis.setId(analysisId);
analysisDAO.getData(analysis);
// get test id from analysis
selectedTestId = analysis.getTest().getId();
// get domain from sample
SampleItemDAO sampleItemDAO = new SampleItemDAOImpl();
SampleItem sampleItem = new SampleItem();
sampleItem.setId(analysis.getSampleItem().getId());
sampleItemDAO.getData(sampleItem);
SampleDAO sampleDAO = new SampleDAOImpl();
Sample sample = new Sample();
// bugzilla 1773 need to store sample not sampleId for use in sorting
sample.setId(sampleItem.getSample().getId());
sampleDAO.getData(sample);
// bugzilla 2614 allow for NB domain samples
// now that we have the domain (for forwarding to correct fail page)
// validate note popup form data!
try {
// bugzilla 2254 moved loadListFromStringOfElements to StringUtil
noteIdList = StringUtil.loadListFromStringOfElements(noteIds, textSeparator, false);
noteLastupdatedList =
StringUtil.loadListFromStringOfElements(noteLastupdateds, textSeparator, false);
// these three need to be validated for empty strings
noteSubjectList =
StringUtil.loadListFromStringOfElements(noteSubjects, textSeparator, true);
noteTextList = StringUtil.loadListFromStringOfElements(noteTexts, textSeparator, true);
noteTypeList = StringUtil.loadListFromStringOfElements(noteTypes, textSeparator, true);
} catch (Exception e) {
// bugzilla 2154
LogEvent.logError("ResultsEntryNotesUpdateAction", "performAction()", e.toString());
String messageKey = "note.note";
ActionError error = new ActionError("errors.invalid", getMessageForKey(messageKey), null);
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
saveErrors(request, errors);
forward = FWD_FAIL;
return mapping.findForward(forward);
}
for (int i = 0; i < noteIdList.size(); i++) {
Note note = new Note();
String noteId = (String) noteIdList.get(i);
note.setReferenceId(refId);
// bugzilla 1922
// bugzilla 2571 go through ReferenceTablesDAO to get reference tables info
ReferenceTables referenceTables = new ReferenceTables();
referenceTables.setId(referenceTableId);
// bugzilla 2571
referenceTablesDAO.getData(referenceTables);
note.setReferenceTables(referenceTables);
note.setSystemUser(systemUser);
note.setSystemUserId(sysUserId);
// 1926 for audit trail
note.setSysUserId(sysUserId);
if (noteId != null && !noteId.equals("0")) {
note.setId((String) noteIdList.get(i));
note.setSubject((String) noteSubjectList.get(i));
note.setText((String) noteTextList.get(i));
note.setNoteType((String) noteTypeList.get(i));
Timestamp noteTimestamp = null;
if (!StringUtil.isNullorNill((String) noteLastupdatedList.get(i))) {
noteTimestamp = DateUtil.formatStringToTimestamp((String) noteLastupdatedList.get(i));
}
note.setLastupdated(noteTimestamp);
// UPDATE
noteDAO.updateData(note);
// }
} else {
// this is a new note
note.setSubject((String) noteSubjectList.get(i));
note.setText((String) noteTextList.get(i));
note.setNoteType((String) noteTypeList.get(i));
// INSERT
noteDAO.insertData(note);
}
}
tx.commit();
return getForward(mapping.findForward(forward), selectedTestId, analysisId);
} catch (LIMSRuntimeException lre) {
// bugzilla 2154
LogEvent.logError("ResultsEntryNotesUpdateAction", "performAction()", lre.toString());
tx.rollback();
errors = new ActionMessages();
ActionError error = null;
if (lre.getException() instanceof org.hibernate.StaleObjectStateException) {
error = new ActionError("errors.OptimisticLockException", null, null);
} else {
if (lre.getException() instanceof LIMSDuplicateRecordException) {
java.util.Locale locale =
(java.util.Locale)
request.getSession().getAttribute("org.apache.struts.action.LOCALE");
String messageKey = "note.note";
String msg =
ResourceLocator.getInstance().getMessageResources().getMessage(locale, messageKey);
error = new ActionError("errors.DuplicateRecord", msg, null);
} else {
error = new ActionError("errors.UpdateException", null, null);
}
}
errors.add(ActionMessages.GLOBAL_MESSAGE, error);
saveErrors(request, errors);
request.setAttribute(Globals.ERROR_KEY, errors);
// disable previous and next
request.setAttribute(PREVIOUS_DISABLED, "true");
request.setAttribute(NEXT_DISABLED, "true");
// default forward fail
forward = FWD_FAIL;
} finally {
HibernateUtil.closeSession();
}
if (forward.equals(FWD_FAIL)
|| forward.equals(FWD_FAIL_HUMAN)
|| forward.equals(FWD_FAIL_ANIMAL)) return mapping.findForward(forward);
// initialize the form
dynaForm.initialize(mapping);
// we need this for subsequent actions to
// get data related to note parent for forwarding to next page
request.setAttribute("refId", refId);
request.setAttribute(SELECTED_TEST_ID, selectedTestId);
return mapping.findForward(forward);
}
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);
}
