/**
* gets the site list.
*
* @param permittedSitesForUser collection of sites.
* @return list containing objects of NaneValueBean class.
*/
public static List<NameValueBean> getSitesAsNVBList(Collection<Site> permittedSitesForUser) {
final List<NameValueBean> siteNVBList = new ArrayList<NameValueBean>();
if (permittedSitesForUser != null && permittedSitesForUser.size() > 0) {
final Iterator<Site> siteIterator = permittedSitesForUser.iterator();
while (siteIterator.hasNext()) {
final Site site = siteIterator.next();
final NameValueBean valueBean = new NameValueBean(site.getName(), site.getId());
siteNVBList.add(valueBean);
}
}
return siteNVBList;
}
/**
* 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();
}
// Overload the method createInTransitContainer(BaseShipmentForm shipmentForm)
public static StorageContainer createInTransitContainer(String containerName) {
final StorageContainer container = new StorageContainer();
// Set storage type for the container type being created
final StorageType storageType = new StorageType();
storageType.setName(Constants.SHIPMENT_CONTAINER_TYPE_NAME);
container.setStorageType(storageType);
// Set site for the container being created
final Site site = new Site();
site.setName(Constants.IN_TRANSIT_SITE_NAME);
container.setSite(site);
// Set capacity, create a container of dimensions (number of specimens to be stored) X 1
final Capacity capacity = new Capacity();
// Keep the capacity 1 initially and increment on adding a new specimen
capacity.setOneDimensionCapacity(1);
capacity.setTwoDimensionCapacity(1);
container.setCapacity(capacity);
container.setName(containerName);
container.setSpecimenPositionCollection(new LinkedHashSet<SpecimenPosition>());
return container;
}
/**
* creates the transit container.
*
* @param shipmentForm form containing all values.
* @return object of StorageContainer class.
*/
public static StorageContainer createInTransitContainer(BaseShipmentForm shipmentForm) {
final StorageContainer container = new StorageContainer();
// Set storage type for the container type being created
final StorageType storageType = new StorageType();
storageType.setName(Constants.SHIPMENT_CONTAINER_TYPE_NAME);
container.setStorageType(storageType);
// Set site for the container being created
final Site site = new Site();
site.setName(Constants.IN_TRANSIT_SITE_NAME);
container.setSite(site);
// Set capacity, create a container of dimensions (number of specimens to be stored) X 1
final Capacity capacity = new Capacity();
capacity.setOneDimensionCapacity(shipmentForm.getSpecimenCounter());
capacity.setTwoDimensionCapacity(1);
container.setCapacity(capacity);
container.getHoldsSpecimenArrayTypeCollection();
container.setName(Constants.IN_TRANSIT_CONTAINER_NAME_PREFIX + shipmentForm.getLabel());
container.setSpecimenPositionCollection(new LinkedHashSet<SpecimenPosition>());
return container;
}
private void createSCGUnderCPHavingScientistAsPI() {
try {
CollectionProtocol cp = new CollectionProtocol();
cp.setId(new Long(BizTestCaseUtility.CP_WITH_SCIENTIST_AS_PI));
Participant participant = BaseTestCaseUtility.initParticipant();
participant.setSocialSecurityNumber("111-22-3233");
try {
participant.setBirthDate(
Utility.parseDate("05-02-1984", CommonServiceLocator.getInstance().getDatePattern()));
} catch (ParseException e) {
Logger.out.debug("" + e);
}
System.out.println("Participant" + participant);
SessionDataBean bean = (SessionDataBean) getSession().getAttribute("sessionData");
try {
participant = (Participant) appService.createObject(participant);
} catch (Exception e) {
e.printStackTrace();
assertFalse(e.getMessage(), true);
}
BizTestCaseUtility.setNameObjectMap("ParticipantWithScientistAsPI", participant);
CollectionProtocolRegistration collectionProtocolRegistration =
new CollectionProtocolRegistration();
collectionProtocolRegistration.setCollectionProtocol(cp);
collectionProtocolRegistration.setParticipant(participant);
collectionProtocolRegistration.setProtocolParticipantIdentifier("");
collectionProtocolRegistration.setActivityStatus("Active");
try {
collectionProtocolRegistration.setRegistrationDate(
Utility.parseDate("08/15/2006", Utility.datePattern("08/15/2006")));
collectionProtocolRegistration.setConsentSignatureDate(
Utility.parseDate("11/23/2006", Utility.datePattern("11/23/2006")));
System.out.println("Creating CPR");
} catch (ParseException e) {
e.printStackTrace();
}
collectionProtocolRegistration.setSignedConsentDocumentURL("F:/doc/consentDoc.doc");
User user = new User();
user.setId(new Long(1));
collectionProtocolRegistration.setConsentWitness(user);
// Collection consentTierResponseCollection = new LinkedHashSet();
// Collection consentTierCollection = new LinkedHashSet();
//
// consentTierCollection = cp.getConsentTierCollection();
// System.out.println("Creating CPR");
// Iterator consentTierItr = consentTierCollection.iterator();
// System.out.println("Creating CPR");
// while(consentTierItr.hasNext())
// {
// ConsentTier consent= (ConsentTier) consentTierItr.next();
// ConsentTierResponse response= new ConsentTierResponse();
// response.setResponse("Yes");
// response.setConsentTier(consent);
// consentTierResponseCollection.add(response);
// }
//
//
// collectionProtocolRegistration.setConsentTierResponseCollection(consentTierResponseCollection);
try {
collectionProtocolRegistration =
(CollectionProtocolRegistration)
appService.createObject(collectionProtocolRegistration);
} catch (Exception e) {
Logger.out.error(e.getMessage(), e);
e.printStackTrace();
assertFalse(e.getMessage(), true);
}
BizTestCaseUtility.setNameObjectMap("CPRWithScientistAsPI", collectionProtocolRegistration);
SpecimenCollectionGroup scg = new SpecimenCollectionGroup();
scg = (SpecimenCollectionGroup) BaseTestCaseUtility.createSCG(collectionProtocolRegistration);
Site site = new Site();
site.setId(new Long(BizTestCaseUtility.CP_WITH_ALLOW_READ_PRIV));
scg.setSpecimenCollectionSite(site);
scg.setName("New SCG" + UniqueKeyGeneratorUtil.getUniqueKey());
scg = (SpecimenCollectionGroup) BaseTestCaseUtility.setEventParameters(scg);
scg.setSurgicalPathologyNumber("SPN" + UniqueKeyGeneratorUtil.getUniqueKey());
System.out.println("Creating SCG");
try {
scg = (SpecimenCollectionGroup) appService.createObject(scg);
System.out.println("SCG::" + scg.getName());
} catch (Exception e) {
Logger.out.error(e.getMessage(), e);
e.printStackTrace();
assertFalse(e.getMessage(), true);
}
IdentifiedSurgicalPathologyReport identifiedSurgicalPathologyReport =
new IdentifiedSurgicalPathologyReport();
identifiedSurgicalPathologyReport.setActivityStatus(Status.ACTIVITY_STATUS_ACTIVE.toString());
identifiedSurgicalPathologyReport.setCollectionDateTime(new Date());
identifiedSurgicalPathologyReport.setIsFlagForReview(new Boolean(false));
identifiedSurgicalPathologyReport.setReportStatus(CaTIESConstants.PENDING_FOR_DEID);
identifiedSurgicalPathologyReport.setReportSource(site);
TextContent textContent = new TextContent();
String data =
"[FINAL DIAGNOSIS]\n"
+ "This is the Final Diagnosis Text"
+ "\n\n[GROSS DESCRIPTION]"
+ "The specimen is received unfixed labeled hernia sac and consists of a soft, pink to yellow segment of fibrous and fatty tissue measuring 7.5cm in length x 3.2 x 0.9cm with a partly defined lumen. Representative tissue submitted labeled 1A.";
textContent.setData(data);
textContent.setSurgicalPathologyReport(identifiedSurgicalPathologyReport);
Set reportSectionCollection = new HashSet();
ReportSection reportSection1 = new ReportSection();
reportSection1.setName("GDT");
reportSection1.setDocumentFragment(
"The specimen is received unfixed labeled hernia sac and consists of a soft, pink to yellow segment of fibrous and fatty tissue measuring 7.5cm in length x 3.2 x 0.9cm with a partly defined lumen. Representative tissue submitted labeled 1A.");
reportSection1.setTextContent(textContent);
ReportSection reportSection2 = new ReportSection();
reportSection2.setName("FIN");
reportSection2.setDocumentFragment("This is the Final Diagnosis Text");
reportSection2.setTextContent(textContent);
reportSectionCollection.add(reportSection1);
reportSectionCollection.add(reportSection2);
textContent.setReportSectionCollection(reportSectionCollection);
identifiedSurgicalPathologyReport.setTextContent(textContent);
identifiedSurgicalPathologyReport.setSpecimenCollectionGroup(scg);
scg.setSurgicalPathologyNumber("SPN" + UniqueKeyGeneratorUtil.getUniqueKey());
try {
identifiedSurgicalPathologyReport =
(IdentifiedSurgicalPathologyReport)
appService.createObject(identifiedSurgicalPathologyReport);
} catch (Exception e) {
Logger.out.error(e.getMessage(), e);
e.printStackTrace();
assertFalse(e.getMessage(), true);
}
BizTestCaseUtility.setObjectMap(
identifiedSurgicalPathologyReport, IdentifiedSurgicalPathologyReport.class);
BizTestCaseUtility.setNameObjectMap("SCGWithScientistAsPI", scg);
// TissueSpecimen specimenObj = (TissueSpecimen) BaseTestCaseUtility.initTissueSpecimen();
// specimenObj.setSpecimenCollectionGroup(scg);
// StorageContainer sc = new StorageContainer();
// sc.setId(new Long(1));
// specimenObj.setStorageContainer(sc);
// specimenObj.setPositionDimensionOne(new Integer(3));
// specimenObj.setPositionDimensionTwo(new Integer(1));
// try{
// specimenObj = (TissueSpecimen) appService.createObject(specimenObj);
// System.out.println("Mol Specimen:"+ specimenObj.getLabel());
// }
// catch(Exception e){
// Logger.out.error(e.getMessage(),e);
// e.printStackTrace();
// assertFalse("Failed to register participant", true);
// }
} catch (Exception e) {
Logger.out.error(e.getMessage(), e);
e.printStackTrace();
assertFalse(e.getMessage(), true);
}
}
/**
* 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", "");
}
}