/**
* To associate existing participant to the report and to create new SCG.
*
* @param request : request
* @param reportQueueId : reportQueueId
* @param participantIdToAssociate : participantIdToAssociate
* @throws NumberFormatException : NumberFormatException
* @throws BizLogicException : BizLogicException
*/
private void createNewSCG(
HttpServletRequest request, String reportQueueId, String participantIdToAssociate)
throws NumberFormatException, BizLogicException {
ReportLoaderQueue reportLoaderQueue = null;
reportLoaderQueue = Utility.getReportQueueObject(reportQueueId);
// Changing the status of the report in the queue to NEW
reportLoaderQueue.setStatus(CaTIESConstants.NEW);
// Create new SCG
reportLoaderQueue.setSpecimenCollectionGroup(null);
// removing all participants from CATISSUE_REPORT_PARTICIP_REL other
// than the selected participant
final Collection participantColl = reportLoaderQueue.getParticipantCollection();
final Iterator iter = participantColl.iterator();
final Set tempColl = new HashSet();
while (iter.hasNext()) {
final Participant participant = (Participant) iter.next();
if (participant.getId().toString().equals(participantIdToAssociate.trim())) {
tempColl.add(participant);
}
}
reportLoaderQueue.setParticipantCollection(tempColl);
// Updating the report queue obj
this.updateReportLoaderQueue(reportLoaderQueue, request);
}
/**
* Associate the existing SCG to the report.
*
* @param request : request
* @param reportQueueId : reportQueueId
* @param participantIdToAssociate : participantIdToAssociate
* @param specimenCollGrpId : specimenCollGrpId
* @throws DAOException : DAOException
* @throws BizLogicException : BizLogicException
* @throws UserNotAuthorizedException : UserNotAuthorizedException
*/
private void associateSCGWithReport(
HttpServletRequest request,
String reportQueueId,
String participantIdToAssociate,
String specimenCollGrpId)
throws DAOException, BizLogicException, UserNotAuthorizedException {
Long cprId = null;
ReportLoaderQueue reportLoaderQueue = null;
reportLoaderQueue = Utility.getReportQueueObject(reportQueueId);
// Changing the status of the report in the queue to NEW
reportLoaderQueue.setStatus(CaTIESConstants.NEW);
// Associating the SCG
if (specimenCollGrpId != null && !specimenCollGrpId.equals("")) {
SpecimenCollectionGroup scg = null;
final IFactory factory = AbstractFactoryConfig.getInstance().getBizLogicFactory();
final ReportLoaderQueueBizLogic reportLoaderQueueBizLogic =
(ReportLoaderQueueBizLogic) factory.getBizLogic(ReportLoaderQueue.class.getName());
final Object object =
reportLoaderQueueBizLogic.retrieve(
SpecimenCollectionGroup.class.getName(), new Long(specimenCollGrpId));
if (object != null) {
scg = (SpecimenCollectionGroup) object;
}
cprId = scg.getCollectionProtocolRegistration().getId();
reportLoaderQueue.setSpecimenCollectionGroup(scg);
}
// Retrieving participantID if it is null
if (participantIdToAssociate == null || participantIdToAssociate.equals("")) {
final DefaultBizLogic defaultBizLogic = new DefaultBizLogic();
final Long partID =
(Long)
defaultBizLogic.retrieveAttribute(
CollectionProtocolRegistration.class.getName(),
cprId,
Constants.COLUMN_NAME_PARTICIPANT_ID);
participantIdToAssociate = partID.toString();
}
// removing all participants from CATISSUE_REPORT_PARTICIP_REL other
// than the selected participant
final Collection participantColl = reportLoaderQueue.getParticipantCollection();
final Iterator iter = participantColl.iterator();
final Set tempColl = new HashSet();
Participant participant = null;
while (iter.hasNext()) {
participant = (Participant) iter.next();
if (participant.getId().toString().equals(participantIdToAssociate.trim())) {
tempColl.add(participant);
}
}
reportLoaderQueue.setParticipantCollection(tempColl);
// Updating the report queue obj
this.updateReportLoaderQueue(reportLoaderQueue, request);
}
/**
* Soft deletes Participant in CaTissue. That is to mark it as disabled with SSN set as NULL.
*
* @param participant - Participant to be deleted
* @return instance of Participant
* @throws ApplicationException - ApplicationException
*/
public Participant deleteParticipant(Participant participant) throws ApplicationException {
final Participant persistedParticipant =
getParticipantForPatientId(
participant.getLastName(), getShortTitleForParticipant(participant));
if (persistedParticipant == null) {
return null;
}
persistedParticipant.setActivityStatus(DISABLED);
persistedParticipant.setSocialSecurityNumber(null);
persistedParticipant.setLastName(null);
final Iterator<CollectionProtocolRegistration> iter =
persistedParticipant.getCollectionProtocolRegistrationCollection().iterator();
while (iter.hasNext()) {
final CollectionProtocolRegistration collectionProtocolRegistration =
(CollectionProtocolRegistration) iter.next();
collectionProtocolRegistration.setProtocolParticipantIdentifier("");
collectionProtocolRegistration.setActivityStatus(DISABLED);
caTissueAPIClient.update(collectionProtocolRegistration);
}
/*
* Iterator<ParticipantMedicalIdentifier> iter = persistedParticipant.getParticipantMedicalIdentifierCollection
* ().iterator(); while (iter.hasNext()) { ParticipantMedicalIdentifier participantMedicalIdentifier =
* (ParticipantMedicalIdentifier) iter .next();//caTissueAPIClient.delete(
* "Delete from ParticipantMedicalIdentifier pmi where pmi.id=" + participantMedicalIdentifier.getId());
* caTissueAPIClient.delete(participantMedicalIdentifier); }
*/
persistedParticipant.getParticipantMedicalIdentifierCollection().clear();
return caTissueAPIClient.update(persistedParticipant);
}
/**
* This method is used to check if the CollectionProtocol of incoming participant is different
* from existingParticipant
*
* @return true if the CP is different
*/
private boolean isCollectionProtocolChanged(
Participant participant, Participant existingParticipant) {
boolean isCPChanged = false;
final List<CollectionProtocolRegistration> existCPRList =
new ArrayList<CollectionProtocolRegistration>(
existingParticipant.getCollectionProtocolRegistrationCollection());
final CollectionProtocolRegistration existCPR =
(CollectionProtocolRegistration) existCPRList.get(0);
final String existShortTitle = existCPR.getCollectionProtocol().getShortTitle();
final ArrayList<CollectionProtocolRegistration> cprColl =
new ArrayList<CollectionProtocolRegistration>(
participant.getCollectionProtocolRegistrationCollection());
final String shortTitle = cprColl.get(0).getCollectionProtocol().getShortTitle();
if (!shortTitle.equals(existShortTitle)) {
isCPChanged = true;
}
return isCPChanged;
}
/**
* Registers Participant in CaTissue
*
* @param participant - Participant to be registered
* @return instance of Participant
* @throws ApplicationException - ApplicationException
*/
public Participant registerParticipant(Participant participant) throws ApplicationException {
if (participant == null || StringUtils.isEmpty(participant.getLastName())) {
throw new ApplicationException("Participant does not contain the unique medical identifier");
}
// populate the CP-Title inside Participant-CPR-CP-Title. Also call
// populateConsentTierResponse()
populateCP(participant);
Participant returnParticipant = null;
try {
returnParticipant = caTissueAPIClient.insert(participant);
} catch (ApplicationException ae) {
LOG.error(
"Create Registration Failed for Participant with Subject ID as "
+ participant.getLastName(),
ae);
throw new ApplicationException(ae);
}
return returnParticipant;
}
private String getShortTitleForParticipant(Participant participant) {
String shortTitle = "";
final ArrayList<CollectionProtocolRegistration> cprColl =
new ArrayList<CollectionProtocolRegistration>(
participant.getCollectionProtocolRegistrationCollection());
if (!cprColl.isEmpty()) {
// We are expecting only ONE CPR here
final CollectionProtocolRegistration cpr = cprColl.get(0);
final CollectionProtocol collectionProtocol = cpr.getCollectionProtocol();
shortTitle = collectionProtocol.getShortTitle();
}
return shortTitle;
}
/**
* This method is used to update the Race collection. It will replace the existing Race with the
* current Race and then if the current race is MORE, then it will add remaining new race inside
* the collection. If the new Race is LESSER than existing then it will set the remaining
* existing(after replacing with current race) to null. This logic is implemented to avoid
* unnecessary null records in the database.
*
* @return
*/
private Participant updateParticipantRaceCollection(
Participant existingParticipant, Participant participant) {
final Race[] existRaceArray =
(Race[])
existingParticipant
.getRaceCollection()
.toArray(new Race[existingParticipant.getRaceCollection().size()]);
final Race[] newRaceArray =
(Race[])
participant
.getRaceCollection()
.toArray(new Race[participant.getRaceCollection().size()]);
final int existRaceCount = existRaceArray.length;
final int newRaceCount = newRaceArray.length;
// if the existing Race are more than the new/incoming Race
if (existRaceCount >= newRaceCount) {
int i = 0;
for (; i < newRaceCount; i++) {
// Iterate(till newRaceCount) & Replace the existing Race with the new/incoming Race
existRaceArray[i].setRaceName(newRaceArray[i].getRaceName());
existRaceArray[i].setParticipant(newRaceArray[i].getParticipant());
}
for (; i < existRaceCount; i++) {
// set the remaining(more) existing Race to NULL
existRaceArray[i].setRaceName(null);
existRaceArray[i].setParticipant(null);
}
final Set<Race> mySet = new HashSet<Race>();
Collections.addAll(mySet, existRaceArray);
participant.setRaceCollection(mySet);
} else {
// if the existing Race are LESS than the new/incoming Race
int i = 0;
for (; i < existRaceCount; i++) {
// Iterate(till existRaceCount) & Replace the existing Race with the new/incoming Race
existRaceArray[i].setRaceName(newRaceArray[i].getRaceName());
existRaceArray[i].setParticipant(newRaceArray[i].getParticipant());
}
final Set<Race> mySet = new HashSet<Race>();
Collections.addAll(mySet, existRaceArray);
participant.setRaceCollection(mySet);
for (; i < newRaceCount; i++) {
// add the remaining left new/incoming Race in the collection
participant.getRaceCollection().add(newRaceArray[i]);
}
}
return participant;
}
/**
* This method is used to populate the CP-title inside Participant object for given CP-shortTitle.
* Also it will call method to populate the default ConsentTierResponse
*
* @param participant
* @return Participant with Title populated
* @throws ApplicationException - ApplicationException
*/
private Participant populateCP(Participant participant) throws ApplicationException {
final ArrayList<CollectionProtocolRegistration> cprColl =
new ArrayList<CollectionProtocolRegistration>(
participant.getCollectionProtocolRegistrationCollection());
if (!cprColl.isEmpty()) {
// We are expecting only ONE CPR here
final CollectionProtocolRegistration incomingCPR = cprColl.get(0);
final CollectionProtocol incomingCP = incomingCPR.getCollectionProtocol();
// get the existing CollectionProtocol for given shortTitle
final CollectionProtocol fetchedCP =
getExistingCollectionProtocol(incomingCP.getShortTitle());
if (fetchedCP != null) {
// set the fetched CP_Title into the Participant-CPR-CP-title
incomingCP.setTitle(fetchedCP.getTitle());
populateConsentTierResponse(incomingCPR, fetchedCP);
}
}
return participant;
}
private Participant copyFrom(Participant participant) {
final Participant p = ParticipantFactory.getInstance().createObject();
p.setId(participant.getId());
p.setActivityStatus(participant.getActivityStatus());
p.setBirthDate(participant.getBirthDate());
p.setEthnicity(participant.getEthnicity());
p.setFirstName(participant.getFirstName());
p.setLastName(participant.getLastName());
p.setGender(participant.getGender());
p.setMetaPhoneCode(participant.getMetaPhoneCode());
p.setSocialSecurityNumber(participant.getSocialSecurityNumber());
p.setVitalStatus(participant.getVitalStatus());
final Iterator<Race> iter = participant.getRaceCollection().iterator();
while (iter.hasNext()) {
final Race race = (Race) iter.next();
final Race r = RaceFactory.getInstance().createObject();
r.setParticipant(p);
r.setRaceName(race.getRaceName());
p.getRaceCollection().add(r);
}
final Iterator<CollectionProtocolRegistration> cprIter =
participant.getCollectionProtocolRegistrationCollection().iterator();
while (cprIter.hasNext()) {
final CollectionProtocolRegistration collectionProtocolRegistration =
(CollectionProtocolRegistration) cprIter.next();
final CollectionProtocol collectionProtocol =
collectionProtocolRegistration.getCollectionProtocol();
final CollectionProtocol cp = CollectionProtocolFactory.getInstance().createObject();
cp.setActivityStatus(collectionProtocol.getActivityStatus());
cp.setTitle(collectionProtocol.getTitle());
cp.setShortTitle(collectionProtocol.getShortTitle());
final CollectionProtocolRegistration cpr =
CollectionProtocolRegistrationFactory.getInstance().createObject();
cpr.setParticipant(p);
cpr.setConsentSignatureDate(collectionProtocolRegistration.getConsentSignatureDate());
cpr.setRegistrationDate(collectionProtocolRegistration.getRegistrationDate());
cpr.setProtocolParticipantIdentifier(
collectionProtocolRegistration.getProtocolParticipantIdentifier());
// setting empty consenttier status collection, as update flow will not update consent tier
cpr.setConsentTierResponseCollection(
(Collection<ConsentTierResponse>) new LinkedHashSet<ConsentTierResponse>());
cpr.setCollectionProtocol(cp);
p.getCollectionProtocolRegistrationCollection().add(cpr);
}
return p;
}
/**
* updates Participant registration in CaTissue
*
* @param participant - Participant to be registered
* @return instance of Participant
* @throws ApplicationException - ApplicationException
*/
public Participant updateParticipantRegistration(Participant participant)
throws ApplicationException {
if (participant == null || StringUtils.isEmpty(participant.getLastName())) {
LOG.error(
"Participant does not contain the unique medical identifier "
+ participant.getLastName());
throw new ApplicationException("Participant does not contain the unique medical identifier");
}
final Participant existingParticipant =
getParticipantForPatientId(
participant.getLastName(), getShortTitleForParticipant(participant));
if (existingParticipant == null) {
LOG.error(
"CaTissue does not contain a participant with the unique identifier, "
+ participant.getLastName());
throw new ApplicationException(
"CaTissue does not contain a participant with the unique identifier, "
+ participant.getLastName());
}
// check if the collection protocol is different, if different then throw exception
if (isCollectionProtocolChanged(participant, existingParticipant)) {
LOG.error(
"Update Participant Registration failed for "
+ participant.getLastName()
+ "and exception is Study can't be changed while updating the Participant.");
throw new ApplicationException(
"Update Participant Registration failed for "
+ participant.getLastName()
+ "and exception is Study can't be changed while updating the Participant.");
}
participant.setId(existingParticipant.getId());
// Set the values in CPR only for Create Participant Flow and don't set it for UpdateParticipant
participant.setCollectionProtocolRegistrationCollection(
new HashSet<CollectionProtocolRegistration>());
// code to handle the existing/new race collection
updateParticipantRaceCollection(existingParticipant, participant);
try {
caTissueAPIClient.update(participant);
} catch (ApplicationException ae) {
LOG.error(
"Update Registration Failed for Participant with Subject ID " + participant.getLastName(),
ae);
throw new ApplicationException(ae);
}
return copyFrom(existingParticipant);
}
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);
}
}