public static void update() {
try {
final String msg = "DatabaseSchemaUpdater: Begin";
log(msg);
final String applicationName = CommonServiceLocator.getInstance().getAppName();
DAO dao = DAOConfigFactory.getInstance().getDAOFactory(applicationName).getDAO();
Method getConnectionManagerMethod =
ReflectionUtils.findMethod(dao.getClass(), "getConnectionManager");
ReflectionUtils.makeAccessible(getConnectionManagerMethod);
IConnectionManager connectionManager =
(IConnectionManager) ReflectionUtils.invokeMethod(getConnectionManagerMethod, dao);
Connection c = null;
try {
c = connectionManager.getConnection();
update(c);
} finally {
try {
connectionManager.commit();
} catch (Exception e) {
}
connectionManager.closeConnection();
}
} catch (Exception e) {
final String msg = "DatabaseSchemaUpdater: Failed with " + e.getMessage();
log(msg);
}
}
/**
* This method would return the Clinical Diagnosis List
*
* @return List which contains the Clinical Diagnosis Data
* @throws BizLogicException
* @throws BizLogicException
*/
public List getClinicalDiagnosisList(String query, boolean showSubset) throws BizLogicException {
// populating clinical Diagnosis field
final List<NameValueBean> clinicalDiagnosisList = new ArrayList();
final String sourceObjectName = PermissibleValueImpl.class.getName();
final String[] selectColumnName = {"value"};
DAO dao = null;
try {
new DefaultBizLogic();
dao = this.openDAOSession(null);
String hql =
"Select PermissibleValueImpl.value from edu.wustl.common.cde.PermissibleValueImpl "
+ "PermissibleValueImpl WHERE LOWER(PermissibleValueImpl.value) like LOWER('%"
+ query
+ "%') AND PermissibleValueImpl.cde.publicId = 'Clinical_Diagnosis_PID' "
+ "order by PermissibleValueImpl.value desc";
List dataList = dao.executeQuery(hql);
clinicalDiagnosisList.add(
new NameValueBean(Constants.SELECT_OPTION, "" + Constants.SELECT_OPTION_VALUE));
if (showSubset) {
clinicalDiagnosisList.add(
new NameValueBean(Constants.SHOW_SUBSET + "start", Constants.SHOW_SUBSET));
}
int cnt = 1;
final Iterator<String> iterator = dataList.iterator();
while (iterator.hasNext()) {
final String clinicaDiagnosisvalue = iterator.next();
if (clinicaDiagnosisvalue.toString().toLowerCase().startsWith(query.toLowerCase())) {
clinicalDiagnosisList.add(
1, new NameValueBean(clinicaDiagnosisvalue, clinicaDiagnosisvalue));
cnt++;
} else {
clinicalDiagnosisList.add(
cnt, new NameValueBean(clinicaDiagnosisvalue, clinicaDiagnosisvalue));
}
}
if (showSubset) {
clinicalDiagnosisList.add(
new NameValueBean(Constants.SHOW_SUBSET + "end", Constants.SHOW_SUBSET));
}
this.closeDAOSession(dao);
} catch (final DAOException exp) {
this.logger.error(exp.getMessage(), exp);
exp.printStackTrace();
throw this.getBizLogicException(exp, exp.getErrorKeyName(), exp.getMsgValues());
} finally {
this.closeDAOSession(dao);
}
return clinicalDiagnosisList;
}
/**
* Called from DefaultBizLogic to get ObjectId for authorization check (non-Javadoc)
*
* @param dao : dao
* @param domainObject : domainObject
* @return String
* @see edu.wustl.common.bizlogic.DefaultBizLogic#getObjectId(edu.wustl.common.dao.DAO,
* java.lang.Object)
*/
@Override
public String getObjectId(DAO dao, Object domainObject) {
final StringBuffer stringBuffer = new StringBuffer();
stringBuffer.append(Site.class.getName());
try {
if (domainObject instanceof StorageContainer) {
final StorageContainer storageContainer = (StorageContainer) domainObject;
final Map similarContainerMap = storageContainer.getSimilarContainerMap();
final Object keys[] = similarContainerMap.keySet().toArray();
final Set<Long> scIds = new HashSet<Long>();
final Set<Long> siteIds = new HashSet<Long>();
for (final Object key : keys) {
if (key.toString().contains("parentContainerId")) {
scIds.add(Long.valueOf(similarContainerMap.get(key).toString()));
}
if (key.toString().contains("siteId")) {
siteIds.add(Long.valueOf(similarContainerMap.get(key).toString()));
}
}
for (final Long scId : scIds) {
Site site = null;
Object object = null;
object = dao.retrieveById(StorageContainer.class.getName(), scId);
if (object != null) {
final StorageContainer parentContainer = (StorageContainer) object;
site = parentContainer.getSite();
}
if (site != null) {
if (!siteIds.contains(site.getId())) {
stringBuffer.append("_" + site.getId().toString());
}
siteIds.add(site.getId());
}
}
for (final Long siteId : siteIds) {
stringBuffer.append("_" + siteId.toString());
}
}
} catch (final DAOException daoExp) {
this.logger.error(daoExp.getMessage(), daoExp);
daoExp.printStackTrace();
}
return stringBuffer.toString();
}
/**
* Overrides the executeSecureAction method of SecureAction class.
*
* @param mapping object of ActionMapping
* @param form : actionForm
* @param request object of HttpServletRequest
* @param response object of HttpServletResponse
* @throws Exception generic exception
* @return ActionForward : ActionForward
*/
@Override
public ActionForward executeSecureAction(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
DAO dao = null;
String pageOf = null;
try {
final SessionDataBean sessionDataBean =
(SessionDataBean) request.getSession().getAttribute(Constants.SESSION_DATA);
dao = AppUtility.openDAOSession(sessionDataBean);
final SpecimenArrayAliquotForm specimenArrayAliquotForm = (SpecimenArrayAliquotForm) form;
pageOf = request.getParameter(Constants.PAGE_OF);
final StorageContainerForSpArrayBizLogic bizLogic = new StorageContainerForSpArrayBizLogic();
final SessionDataBean sessionData =
(SessionDataBean) request.getSession().getAttribute(Constants.SESSION_DATA);
final List<NameValueBean> storagePositionListForSpecimenArrayAliquot =
AppUtility.getStoragePositionTypeListForTransferEvent();
request.setAttribute(
"storagePositionListForSpecimenArrayAliquot", storagePositionListForSpecimenArrayAliquot);
final String exceedingMaxLimit = "false";
if (specimenArrayAliquotForm.getButtonClicked().equalsIgnoreCase("submit")) {
final Map tempAliquotMap = new HashMap();
if (specimenArrayAliquotForm.getCheckedButton().equals("1")) {
tempAliquotMap.put("label", specimenArrayAliquotForm.getParentSpecimenArrayLabel());
} else {
tempAliquotMap.put("barcode", specimenArrayAliquotForm.getBarcode());
}
tempAliquotMap.put("aliquotcount", specimenArrayAliquotForm.getAliquotCount());
request.getSession().setAttribute("tempAliquotMap", tempAliquotMap);
} else if (specimenArrayAliquotForm.getButtonClicked().equalsIgnoreCase("create")) {
boolean arePropertiesChanged = false;
final Map tempAliquotMap = (HashMap) request.getSession().getAttribute("tempAliquotMap");
final String label = (String) tempAliquotMap.get("label");
final String barcode = (String) tempAliquotMap.get("barcode");
if (specimenArrayAliquotForm.getCheckedButton().equals("1")) {
if (label == null
|| !label
.trim()
.equalsIgnoreCase(
specimenArrayAliquotForm.getParentSpecimenArrayLabel().trim())) {
arePropertiesChanged = true;
}
} else {
if (barcode == null
|| !barcode.trim().equalsIgnoreCase(specimenArrayAliquotForm.getBarcode().trim())) {
arePropertiesChanged = true;
}
}
final String aliquotcount = (String) tempAliquotMap.get("aliquotcount");
if (!aliquotcount
.trim()
.equalsIgnoreCase(specimenArrayAliquotForm.getAliquotCount().trim())) {
arePropertiesChanged = true;
}
/**
* Repopulate the form with storage container locations in case user has changed any of
* label/barcode, aliquot count, quantity per aliquot.
*/
if (arePropertiesChanged == true) {
specimenArrayAliquotForm.setParentSpecimenArrayLabel(label);
specimenArrayAliquotForm.setAliquotCount(aliquotcount);
specimenArrayAliquotForm.setBarcode(barcode);
ActionErrors errors = this.getActionErrors(request);
if (errors == null) {
errors = new ActionErrors();
}
if (arePropertiesChanged == true) {
errors.add(
ActionErrors.GLOBAL_ERROR,
new ActionError("errors.specimenArrayAliquots.reSubmit"));
}
TreeMap containerMap = new TreeMap();
this.checkForSpecimenArray(request, specimenArrayAliquotForm, dao);
// int aliquotCount =
// Integer.parseInt(specimenArrayAliquotForm.getAliquotCount());
final Long id = (Long) request.getAttribute(Constants.STORAGE_TYPE_ID);
containerMap =
bizLogic.getAllocatedContainerMapForSpecimenArray(id.longValue(), sessionData, dao);
this.populateAliquotsStorageLocations(specimenArrayAliquotForm, containerMap);
request.setAttribute(Constants.AVAILABLE_CONTAINER_MAP, containerMap);
request.setAttribute(Constants.PAGE_OF, Constants.PAGE_OF_SPECIMEN_ARRAY_CREATE_ALIQUOT);
this.saveErrors(request, errors);
return mapping.findForward(Constants.PAGE_OF_SPECIMEN_ARRAY_CREATE_ALIQUOT);
} else {
// TODO
specimenArrayAliquotForm.setButtonClicked("none");
return mapping.findForward(Constants.COMMON_ADD_EDIT);
}
}
if (Constants.PAGE_OF_SPECIMEN_ARRAY_ALIQUOT_SUMMARY.equals(pageOf)) {
final Map map = (Map) request.getAttribute("forwardToHashMap");
if (map != null) {
// TODO
specimenArrayAliquotForm.setSpecimenClass(
CommonUtilities.toString(map.get(Constants.ALIQUOT_SPECIMEN_CLASS)));
specimenArrayAliquotForm.setSpecimenArrayType(
CommonUtilities.toString(map.get(Constants.ALIQUOT_SPECIMEN_ARRAY_TYPE)));
specimenArrayAliquotForm.setAliquotCount(
CommonUtilities.toString(map.get(Constants.ALIQUOT_ALIQUOT_COUNTS)));
final Collection specimenTypesCollection =
(Collection) map.get(Constants.ALIQUOT_SPECIMEN_TYPES);
final List specimenTypeList =
this.setSpecimenTypes(specimenTypesCollection, specimenArrayAliquotForm);
request.setAttribute(Constants.SPECIMEN_TYPE_LIST, specimenTypeList);
String containerNameKey = "";
String posDim1Key = "";
String posDim2Key = "";
/** This code is added to set storage positions in case of manual mode. bug 15085 */
for (int iCount = 1;
iCount <= Integer.parseInt(specimenArrayAliquotForm.getAliquotCount());
iCount++) {
if (map.get("radio_" + iCount) != null && map.get("radio_" + iCount).equals("2")) {
containerNameKey = "SpecimenArray:" + iCount + "_StorageContainer_name";
posDim1Key = "SpecimenArray:" + iCount + "_positionDimensionOne";
posDim2Key = "SpecimenArray:" + iCount + "_positionDimensionTwo";
map.put(containerNameKey, map.get(containerNameKey + "_fromMap"));
if (!map.get(posDim1Key + "_fromMap").equals("")) {
map.put(posDim1Key, map.get(posDim1Key + "_fromMap"));
}
if (!map.get(posDim2Key + "_fromMap").equals("")) {
map.put(posDim2Key, map.get(posDim2Key + "_fromMap"));
}
}
}
specimenArrayAliquotForm.setSpecimenArrayAliquotMap(map);
}
final ActionErrors errors = this.getActionErrors(request);
if (errors == null || errors.size() == 0) {
final ActionMessages messages = new ActionMessages();
messages.add(ActionMessages.GLOBAL_MESSAGE, new ActionMessage("aliquots.success"));
this.saveMessages(request, messages);
}
return mapping.findForward(pageOf);
}
Map containerMap = new HashMap();
if (Constants.PAGE_OF_SPECIMEN_ARRAY_CREATE_ALIQUOT.equals(
request.getParameter(Constants.PAGE_OF))) {
pageOf = this.validate(request, specimenArrayAliquotForm);
if (Constants.PAGE_OF_SPECIMEN_ARRAY_CREATE_ALIQUOT.equals(pageOf)) {
pageOf = this.checkForSpecimenArray(request, specimenArrayAliquotForm, dao);
if (Constants.PAGE_OF_SPECIMEN_ARRAY_CREATE_ALIQUOT.equals(pageOf)) {
final int aliquotCount = Integer.parseInt(specimenArrayAliquotForm.getAliquotCount());
final Long id = (Long) request.getAttribute(Constants.STORAGE_TYPE_ID);
containerMap =
bizLogic.getAllocatedContainerMapForSpecimenArray(id.longValue(), sessionData, dao);
pageOf = this.checkForSufficientAvailablePositions(request, containerMap, aliquotCount);
if (Constants.PAGE_OF_SPECIMEN_ARRAY_CREATE_ALIQUOT.equals(pageOf)) {
final ActionErrors errors = (ActionErrors) request.getAttribute(Globals.ERROR_KEY);
if (errors == null || errors.size() == 0) {
this.populateAliquotsStorageLocations(specimenArrayAliquotForm, containerMap);
}
}
}
}
}
request.setAttribute(Constants.EXCEEDS_MAX_LIMIT, exceedingMaxLimit);
request.setAttribute(Constants.AVAILABLE_CONTAINER_MAP, containerMap);
request.setAttribute(Constants.PAGE_OF, pageOf);
} finally {
dao.closeSession();
}
return mapping.findForward(pageOf);
}
/**
* @param request HttpServletRequest
* @param form SpecimenArrayAliquotForm
* @return String : String
* @throws BizLogicException : BizLogicException
* @throws Exception : Exception
*/
private String checkForSpecimenArray(
HttpServletRequest request, SpecimenArrayAliquotForm form, DAO dao)
throws BizLogicException, Exception {
List specimenArrayList = new ArrayList();
String errorString = "";
final String specimenArrayLabel = form.getParentSpecimenArrayLabel();
final int aliquotCount = Integer.parseInt(form.getAliquotCount());
if (form.getCheckedButton().equals("1")) {
specimenArrayList =
dao.retrieve(SpecimenArray.class.getName(), Constants.SYSTEM_NAME, specimenArrayLabel);
errorString = Constants.SYSTEM_LABEL;
} else {
final String barcode = form.getBarcode().trim();
specimenArrayList =
dao.retrieve(SpecimenArray.class.getName(), Constants.SYSTEM_BARCODE, barcode);
errorString = Constants.SYSTEM_BARCODE;
}
if (specimenArrayList.isEmpty()) {
final ActionErrors errors = this.getActionErrors(request);
errors.add(
ActionErrors.GLOBAL_ERROR,
new ActionError("errors.specimenArrayAliquots.notExists", errorString));
this.saveErrors(request, errors);
return Constants.PAGE_OF_SPECIMEN_ARRAY_ALIQUOT;
} else {
final SpecimenArray specimenArray = (SpecimenArray) specimenArrayList.get(0);
/**
* Name : Virender Reviewer: Prafull Retriving specimenArrayTypeObject replaced
* SpecimenArrayType arrayType = specimenArray.getSpecimenArrayType();
*/
if (Status.ACTIVITY_STATUS_DISABLED.toString().equals(specimenArray.getActivityStatus())) {
final ActionErrors errors = this.getActionErrors(request);
errors.add(
ActionErrors.GLOBAL_ERROR,
new ActionError("errors.specimenArrayAliquots.disabled", "Parent Specimen Array"));
this.saveErrors(request, errors);
return Constants.PAGE_OF_SPECIMEN_ARRAY_ALIQUOT;
// throw BizLogicException(
// "Fail to create Aliquots, Parent SpecimenArray" + " " +
// ApplicationProperties.getValue("error.object.disabled"));
}
final List arrayTypeList =
dao.retrieveAttribute(
SpecimenArray.class, "id", specimenArray.getId(), "specimenArrayType");
if ((arrayTypeList != null) && (arrayTypeList.size() > 0)) {
final SpecimenArrayType arrayType = (SpecimenArrayType) arrayTypeList.get(0);
form.setSpecimenArrayType(arrayType.getName());
form.setSpecimenClass(arrayType.getSpecimenClass());
/**
* Name: Virender Mehta Reviewer: Prafull Retrive Child Specimen Collection from parent
* Specimen String[] specimenTypeArr = new
* String[arrayType.getSpecimenTypeCollection().size()];
*/
final Collection specimenTypeCollection =
dao.retrieveAttribute(
SpecimenArrayType.class,
"id",
arrayType.getId(),
"elements(specimenTypeCollection)");
// String[] specimenTypeArr = new
// String[specimenTypeCollection.size()];
final List specimenTypeList = this.setSpecimenTypes(specimenTypeCollection, form);
request.setAttribute(Constants.SPECIMEN_TYPE_LIST, specimenTypeList);
request.setAttribute(Constants.STORAGE_TYPE_ID, arrayType.getId());
final Map aliquotMap = form.getSpecimenArrayAliquotMap();
final SpecimenArrayAliquotsBizLogic aliquotBizLogic =
(SpecimenArrayAliquotsBizLogic)
AbstractFactoryConfig.getInstance()
.getBizLogicFactory()
.getBizLogic(Constants.SPECIMEN_ARRAY_ALIQUOT_FORM_ID);
final long nextAvailablenumber =
aliquotBizLogic.getNextAvailableNumber("CATISSUE_SPECIMEN_ARRAY");
/** Putting the default label values in the AliquotMap */
for (int i = 1; i <= aliquotCount; i++) {
final String labelKey = "SpecimenArray:" + i + "_label";
final String aliquotLabel = specimenArrayLabel + "_" + (nextAvailablenumber + i - 1);
aliquotMap.put(labelKey, aliquotLabel);
}
form.setSpecimenArrayAliquotMap(aliquotMap);
form.setSpecimenArrayId("" + specimenArray.getId());
}
}
return Constants.PAGE_OF_SPECIMEN_ARRAY_CREATE_ALIQUOT;
}
/**
* Saves the storageContainer object in the database.
*
* @param dao : dao
* @param obj The storageType object to be saved.
* @param sessionDataBean The session in which the object is saved.
* @throws BizLogicException : BizLogicException
*/
@Override
protected void insert(Object obj, DAO dao, SessionDataBean sessionDataBean)
throws BizLogicException {
final StorageContainer container = (StorageContainer) obj;
container.setActivityStatus(Status.ACTIVITY_STATUS_ACTIVE.toString());
final List contList = new ArrayList();
final int noOfContainers = container.getNoOfContainers().intValue();
final Map simMap = container.getSimilarContainerMap();
// --- common values for all similar containers ---
new StorageTypeBizLogic().loadStorageType(dao, container);
this.logger.debug(simMap);
final int checkButton = Integer.parseInt((String) simMap.get("checkedButton"));
// int checkButton = 1;
try {
for (int i = 1; i <= noOfContainers; i++) {
final String simContPrefix = "simCont:" + i + "_";
final String IdKey = simContPrefix + "Id";
final String parentContNameKey = simContPrefix + "parentContName";
final String contName = (String) simMap.get(simContPrefix + "name");
String barcode = (String) simMap.get(simContPrefix + "barcode");
if (barcode != null && barcode.equals("")) // this is done
// because barcode
// is empty string
// set by struts
{ // but barcode in DB is unique but can be null.
barcode = null;
}
final StorageContainer cont = new StorageContainer(container);
if (checkButton == 1) // site
{
final String siteId = (String) simMap.get(simContPrefix + "siteId");
final String siteName = (String) simMap.get(simContPrefix + "siteName");
final Site site = new Site();
/**
* Start: Change for API Search --- Jitendra 06/10/2006 In Case of Api Search, previoulsy
* it was failing since there was default class level initialization on domain object. For
* example in User object, it was initialized as protected String lastName=""; So we
* removed default class level initialization on domain object and are initializing in
* method setAllValues() of domain object. But in case of Api Search, default values will
* not get set since setAllValues() method of domainObject will not get called. To avoid
* null pointer exception, we are setting the default values same as we were setting in
* setAllValues() method of domainObject.
*/
ApiSearchUtil.setSiteDefault(site);
site.setId(new Long(siteId));
site.setName(siteName);
cont.setSite(site);
new SiteBizLogic().loadSite(dao, cont);
} else
// parentContainer
{
StorageContainer parentContainer = null;
final String parentId = (String) simMap.get(simContPrefix + "parentContainerId");
final String posOne = (String) simMap.get(simContPrefix + "positionDimensionOne");
final String posTwo = (String) simMap.get(simContPrefix + "positionDimensionTwo");
final Object object =
dao.retrieveById(StorageContainer.class.getName(), new Long(parentId));
if (object != null) {
parentContainer = (StorageContainer) object;
cont.setSite(parentContainer.getSite());
}
final IFactory factory = AbstractFactoryConfig.getInstance().getBizLogicFactory();
final StorageContainerBizLogic storageContainerBizLogic =
(StorageContainerBizLogic) factory.getBizLogic(Constants.STORAGE_CONTAINER_FORM_ID);
storageContainerBizLogic.checkContainer(
dao,
StorageContainerUtil.setparameterList(
parentContainer.getId().toString(), posOne, posTwo, false),
sessionDataBean,
null);
ContainerPosition cntPos = cont.getLocatedAtPosition();
if (cntPos == null) {
cntPos = new ContainerPosition();
}
cntPos.setPositionDimensionOne(new Integer(posOne));
cntPos.setPositionDimensionTwo(new Integer(posTwo));
cntPos.setOccupiedContainer(cont);
cntPos.setParentContainer(parentContainer);
cont.setLocatedAtPosition(cntPos);
// Have to set Site object for parentContainer
SiteBizLogic siteBiz = new SiteBizLogic();
siteBiz.loadSite(dao, parentContainer);
siteBiz.loadSiteFromContainerId(dao, parentContainer);
cntPos.setPositionDimensionOne(new Integer(posOne));
cntPos.setPositionDimensionTwo(new Integer(posTwo));
cntPos.setOccupiedContainer(cont);
cont.setLocatedAtPosition(cntPos);
cont.setSite(parentContainer.getSite());
this.logger.debug("^^>> " + parentContainer.getSite());
simMap.put(parentContNameKey, parentContainer.getName());
}
// StorageContainer cont = new StorageContainer();
cont.setName(contName); // <<----
cont.setBarcode(barcode); // <<----
// by falguni
// Storage container label generator
// Call Storage container label generator if its specified to
// use automatic label generator
if (edu.wustl.catissuecore.util.global.Variables.isStorageContainerLabelGeneratorAvl) {
LabelGenerator storagecontLblGenerator;
storagecontLblGenerator =
LabelGeneratorFactory.getInstance(
Constants.STORAGECONTAINER_LABEL_GENERATOR_PROPERTY_NAME);
try {
storagecontLblGenerator.setLabel(cont);
} catch (LabelGenException e) {
this.logger.error(e.getMessage(), e);
}
}
simMap.put(simContPrefix + "name", cont.getName());
this.logger.debug(
"cont.getCollectionProtocol().size() " + cont.getCollectionProtocolCollection().size());
cont.setActivityStatus("Active");
dao.insert(cont.getCapacity());
dao.insert(cont);
contList.add(cont);
container.setId(cont.getId());
simMap.put(IdKey, cont.getId().toString());
}
} catch (final DAOException daoExp) {
this.logger.error(daoExp.getMessage(), daoExp);
daoExp.printStackTrace();
throw this.getBizLogicException(daoExp, daoExp.getErrorKeyName(), daoExp.getMsgValues());
} catch (final NameGeneratorException e) {
this.logger.error(e.getMessage(), e);
e.printStackTrace();
throw this.getBizLogicException(e, "utility.error", "");
}
}