private CollectionProtocol getExistingCollectionProtocol(String shortTitle)
throws ApplicationException {
CollectionProtocol cp = new CollectionProtocol();
cp.setShortTitle(shortTitle);
cp = caTissueAPIClient.searchById(CollectionProtocol.class, cp);
return cp;
}
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;
}
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;
}
/**
* 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 void populateConsentTierResponse(
final CollectionProtocolRegistration incomingCPR, final CollectionProtocol fetchedCP)
throws ApplicationException {
final Collection<ConsentTier> consentTierCollection = fetchedCP.getConsentTierCollection();
if (consentTierCollection == null || consentTierCollection.isEmpty()) {
LOG.error("Collection Protocol's consent tier statements list is empty.");
throw new ApplicationException(
"Collection Protocol's consent tier statements list is empty.");
}
final Iterator<ConsentTier> it = consentTierCollection.iterator();
while (it.hasNext()) {
final ConsentTier consentTier = (ConsentTier) it.next();
final ConsentTierResponse ctResp = ConsentTierResponseFactory.getInstance().createObject();
ctResp.setConsentTier(consentTier);
ctResp.setResponse(NOT_SPECIFIED);
incomingCPR.getConsentTierResponseCollection().add(ctResp);
}
}
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);
}
}