@Override
@PlusTransactional
public ResponseEvent<DistributionProtocolDetail> updateDistributionProtocol(
RequestEvent<DistributionProtocolDetail> req) {
try {
AccessCtrlMgr.getInstance().ensureUserIsAdmin();
Long protocolId = req.getPayload().getId();
String title = req.getPayload().getTitle();
DistributionProtocol existing = null;
if (protocolId != null) {
existing = daoFactory.getDistributionProtocolDao().getById(protocolId);
} else {
existing = daoFactory.getDistributionProtocolDao().getDistributionProtocol(title);
}
if (existing == null) {
return ResponseEvent.userError(DistributionProtocolErrorCode.NOT_FOUND);
}
DistributionProtocol distributionProtocol =
distributionProtocolFactory.createDistributionProtocol(req.getPayload());
ensureUniqueConstraints(distributionProtocol, existing);
existing.update(distributionProtocol);
daoFactory.getDistributionProtocolDao().saveOrUpdate(existing);
return ResponseEvent.response(DistributionProtocolDetail.from(existing));
} catch (OpenSpecimenException ose) {
return ResponseEvent.error(ose);
} catch (Exception ex) {
return ResponseEvent.serverError(ex);
}
}
@Override
public SpecimenRequirement createDerived(DerivedSpecimenRequirement req) {
OpenSpecimenException ose = new OpenSpecimenException(ErrorType.USER_ERROR);
Long parentId = req.getParentSrId();
if (parentId == null) {
ose.addError(PARENT_REQ_REQUIRED);
throw ose;
}
SpecimenRequirement parent = daoFactory.getSpecimenRequirementDao().getById(parentId);
if (parent == null) {
ose.addError(SrErrorCode.PARENT_NOT_FOUND);
throw ose;
}
SpecimenRequirement derived = parent.copy();
derived.setLabelFormat(null);
derived.setLineage(Specimen.DERIVED);
setSpecimenClass(req.getSpecimenClass(), derived, ose);
setSpecimenType(req.getSpecimenClass(), req.getType(), derived, ose);
setInitialQty(req.getQuantity(), derived, ose);
setStorageType(req.getStorageType(), derived, ose);
setConcentration(req.getConcentration(), derived, ose);
setPathologyStatus(req.getPathology(), derived, ose);
setLabelFormat(req.getLabelFmt(), derived, ose);
setLabelAutoPrintMode(req.getLabelAutoPrintMode(), derived, ose);
setCode(req.getCode(), derived, ose);
derived.setName(req.getName());
ose.checkAndThrow();
derived.setParentSpecimenRequirement(parent);
return derived;
}
@Override
@PlusTransactional
public ResponseEvent<List<DpRequirementDetail>> getRequirements(RequestEvent<Long> req) {
try {
AccessCtrlMgr.getInstance().ensureUserIsAdmin();
Long dpId = req.getPayload();
DistributionProtocol dp = daoFactory.getDistributionProtocolDao().getById(dpId);
if (dp == null) {
return ResponseEvent.userError(DistributionProtocolErrorCode.NOT_FOUND);
}
List<DpRequirementDetail> reqDetails = DpRequirementDetail.from(dp.getRequirements());
Map<Long, BigDecimal> distributedQty = getDprDao().getDistributedQtyByDp(dpId);
for (DpRequirementDetail reqDetail : reqDetails) {
BigDecimal qty = distributedQty.get(reqDetail.getId());
reqDetail.setDistributedQty(qty == null ? BigDecimal.ZERO : qty);
}
return ResponseEvent.response(reqDetails);
} catch (OpenSpecimenException ose) {
return ResponseEvent.error(ose);
} catch (Exception e) {
return ResponseEvent.serverError(e);
}
}
@Override
public List<SpecimenRequirement> createSpecimenPoolReqs(SpecimenPoolRequirements req) {
OpenSpecimenException ose = new OpenSpecimenException(ErrorType.USER_ERROR);
Long pooledSpmnReqId = req.getPooledSpecimenReqId();
if (pooledSpmnReqId == null) {
ose.addError(POOLED_SPMN_REQ);
throw ose;
}
SpecimenRequirement pooledSpecimenReq =
daoFactory.getSpecimenRequirementDao().getById(pooledSpmnReqId);
if (pooledSpecimenReq == null) {
ose.addError(POOLED_SPMN_REQ_NOT_FOUND, pooledSpmnReqId);
throw ose;
}
if (pooledSpecimenReq.getParentSpecimenRequirement() != null
|| pooledSpecimenReq.getPooledSpecimenRequirement() != null) {
ose.addError(INVALID_POOLED_SPMN, pooledSpmnReqId);
throw ose;
}
List<SpecimenRequirement> specimenPoolReqs = new ArrayList<SpecimenRequirement>();
for (SpecimenRequirementDetail detail : req.getSpecimenPoolReqs()) {
specimenPoolReqs.add(createSpecimenPoolReq(pooledSpecimenReq, detail, ose));
ose.checkAndThrow();
}
return specimenPoolReqs;
}
@Override
@PlusTransactional
public ResponseEvent<List<DistributionProtocolDetail>> getDistributionProtocols(
RequestEvent<DpListCriteria> req) {
try {
DpListCriteria crit = req.getPayload();
Set<Long> siteIds = AccessCtrlMgr.getInstance().getReadAccessDistributionOrderSites();
if (siteIds != null && CollectionUtils.isEmpty(siteIds)) {
return ResponseEvent.userError(RbacErrorCode.ACCESS_DENIED);
}
if (siteIds != null) {
crit.siteIds(siteIds);
}
List<DistributionProtocol> dps =
daoFactory.getDistributionProtocolDao().getDistributionProtocols(crit);
List<DistributionProtocolDetail> result = DistributionProtocolDetail.from(dps);
if (crit.includeStat()) {
addDpStats(result);
}
return ResponseEvent.response(result);
} catch (OpenSpecimenException ose) {
return ResponseEvent.error(ose);
} catch (Exception e) {
return ResponseEvent.serverError(e);
}
}
@Override
@PlusTransactional
public ResponseEvent<List<AuthDomainSummary>> getDomains(
RequestEvent<ListAuthDomainCriteria> req) {
List<AuthDomain> authDomains =
daoFactory.getAuthDao().getAuthDomains(req.getPayload().maxResults());
return ResponseEvent.response(AuthDomainSummary.from(authDomains));
}
private User ensureValidUser(
UserSummary userSummary, ErrorCode notFound, OpenSpecimenException ose) {
if (userSummary == null) {
return null;
}
User user = null;
if (userSummary.getId() != null) {
user = daoFactory.getUserDao().getById(userSummary.getId());
} else if (userSummary.getLoginName() != null && userSummary.getDomain() != null) {
user = daoFactory.getUserDao().getUser(userSummary.getLoginName(), userSummary.getDomain());
}
if (user == null) {
ose.addError(notFound);
}
return user;
}
private List<DistributionOrderStat> getOrderStats(DistributionOrderStatListCriteria crit) {
if (crit.dpId() != null) {
DistributionProtocol dp = daoFactory.getDistributionProtocolDao().getById(crit.dpId());
if (dp == null) {
throw OpenSpecimenException.userError(DistributionProtocolErrorCode.NOT_FOUND);
}
AccessCtrlMgr.getInstance().ensureReadDPRights(dp);
} else {
Set<Long> siteIds = AccessCtrlMgr.getInstance().getCreateUpdateAccessDistributionOrderSites();
if (siteIds != null && CollectionUtils.isEmpty(siteIds)) {
throw OpenSpecimenException.userError(RbacErrorCode.ACCESS_DENIED);
}
if (siteIds != null) {
crit.siteIds(siteIds);
}
}
return daoFactory.getDistributionProtocolDao().getOrderStats(crit);
}
@Override
@PlusTransactional
public ResponseEvent<DistributionProtocolDetail> deleteDistributionProtocol(
RequestEvent<Long> req) {
try {
AccessCtrlMgr.getInstance().ensureUserIsAdmin();
DistributionProtocol existing =
daoFactory.getDistributionProtocolDao().getById(req.getPayload());
if (existing == null) {
return ResponseEvent.userError(DistributionProtocolErrorCode.NOT_FOUND);
}
existing.delete();
daoFactory.getDistributionProtocolDao().saveOrUpdate(existing);
return ResponseEvent.response(DistributionProtocolDetail.from(existing));
} catch (OpenSpecimenException ose) {
return ResponseEvent.error(ose);
} catch (Exception e) {
return ResponseEvent.serverError(e);
}
}
private boolean isUniqueShortTitle(DistributionProtocol newDp, DistributionProtocol existingDp) {
if (existingDp != null && newDp.getShortTitle().equals(existingDp.getShortTitle())) {
return true;
}
DistributionProtocol existing =
daoFactory.getDistributionProtocolDao().getByShortTitle(newDp.getShortTitle());
if (existing != null) {
return false;
}
return true;
}
private void setCpe(
SpecimenRequirementDetail detail, SpecimenRequirement sr, OpenSpecimenException ose) {
Long eventId = detail.getEventId();
if (eventId == null) {
ose.addError(CPE_REQUIRED);
return;
}
CollectionProtocolEvent cpe = daoFactory.getCollectionProtocolDao().getCpe(eventId);
if (cpe == null) {
ose.addError(CpeErrorCode.NOT_FOUND);
}
sr.setCollectionProtocolEvent(cpe);
}
@Override
@PlusTransactional
public ResponseEvent<DistributionProtocolDetail> updateActivityStatus(
RequestEvent<DistributionProtocolDetail> req) {
try {
AccessCtrlMgr.getInstance().ensureUserIsAdmin();
Long dpId = req.getPayload().getId();
String status = req.getPayload().getActivityStatus();
if (StringUtils.isBlank(status) || !Status.isValidActivityStatus(status)) {
return ResponseEvent.userError(ActivityStatusErrorCode.INVALID);
}
DistributionProtocol existing = daoFactory.getDistributionProtocolDao().getById(dpId);
if (existing == null) {
return ResponseEvent.userError(DistributionProtocolErrorCode.NOT_FOUND);
}
if (existing.getActivityStatus().equals(status)) {
return ResponseEvent.response(DistributionProtocolDetail.from(existing));
}
if (status.equals(Status.ACTIVITY_STATUS_DISABLED.getStatus())) {
existing.delete();
} else {
existing.setActivityStatus(status);
}
daoFactory.getDistributionProtocolDao().saveOrUpdate(existing);
return ResponseEvent.response(DistributionProtocolDetail.from(existing));
} catch (OpenSpecimenException ose) {
return ResponseEvent.error(ose);
} catch (Exception e) {
return ResponseEvent.serverError(e);
}
}
@Override
@PlusTransactional
public ResponseEvent<List<DependentEntityDetail>> getDependentEntities(RequestEvent<Long> req) {
try {
DistributionProtocol existing =
daoFactory.getDistributionProtocolDao().getById(req.getPayload());
if (existing == null) {
return ResponseEvent.userError(DistributionProtocolErrorCode.NOT_FOUND);
}
return ResponseEvent.response(existing.getDependentEntities());
} catch (Exception e) {
return ResponseEvent.serverError(e);
}
}
private void addDpStats(List<DistributionProtocolDetail> dps) {
if (CollectionUtils.isEmpty(dps)) {
return;
}
Map<Long, DistributionProtocolDetail> dpMap = new HashMap<Long, DistributionProtocolDetail>();
for (DistributionProtocolDetail dp : dps) {
dpMap.put(dp.getId(), dp);
}
Map<Long, Integer> countMap =
daoFactory.getDistributionProtocolDao().getSpecimensCountByDpIds(dpMap.keySet());
for (Map.Entry<Long, Integer> count : countMap.entrySet()) {
dpMap.get(count.getKey()).setDistributedSpecimensCount(count.getValue());
}
}
@Override
@PlusTransactional
public ResponseEvent<AuthDomainDetail> registerDomain(RequestEvent<AuthDomainDetail> req) {
try {
AuthDomainDetail detail = req.getPayload();
AuthDomain authDomain = domainRegFactory.createDomain(detail);
ensureUniqueDomainName(authDomain.getName());
daoFactory.getAuthDao().saveOrUpdate(authDomain);
return ResponseEvent.response(AuthDomainDetail.from(authDomain));
} catch (OpenSpecimenException ose) {
return ResponseEvent.error(ose);
} catch (Exception e) {
return ResponseEvent.serverError(e);
}
}
@Override
public List<SpecimenRequirement> createAliquots(AliquotSpecimensRequirement req) {
OpenSpecimenException ose = new OpenSpecimenException(ErrorType.USER_ERROR);
Long parentSrId = req.getParentSrId();
if (parentSrId == null) {
ose.addError(PARENT_REQ_REQUIRED);
throw ose;
}
SpecimenRequirement parent = daoFactory.getSpecimenRequirementDao().getById(parentSrId);
if (parent == null) {
ose.addError(SrErrorCode.PARENT_NOT_FOUND);
throw ose;
}
if (req.getNoOfAliquots() == null || req.getNoOfAliquots() < 1L) {
ose.addError(SrErrorCode.INVALID_ALIQUOT_CNT);
throw ose;
}
if (req.getQtyPerAliquot() == null || NumUtil.lessThanEqualsZero(req.getQtyPerAliquot())) {
ose.addError(SrErrorCode.INVALID_QTY);
}
BigDecimal total = NumUtil.multiply(req.getQtyPerAliquot(), req.getNoOfAliquots());
if (NumUtil.greaterThan(total, parent.getQtyAfterAliquotsUse())) {
ose.addError(SrErrorCode.INSUFFICIENT_QTY);
}
List<SpecimenRequirement> aliquots = new ArrayList<SpecimenRequirement>();
for (int i = 0; i < req.getNoOfAliquots(); ++i) {
SpecimenRequirement aliquot = parent.copy();
aliquot.setLabelFormat(null);
aliquot.setLineage(Specimen.ALIQUOT);
setStorageType(req.getStorageType(), aliquot, ose);
setLabelFormat(req.getLabelFmt(), aliquot, ose);
setLabelAutoPrintMode(req.getLabelAutoPrintMode(), aliquot, ose);
aliquot.setInitialQuantity(req.getQtyPerAliquot());
aliquot.setParentSpecimenRequirement(parent);
aliquots.add(aliquot);
ose.checkAndThrow();
}
return aliquots;
}
@Override
@PlusTransactional
public ResponseEvent<DistributionProtocolDetail> getDistributionProtocol(RequestEvent<Long> req) {
try {
Long protocolId = req.getPayload();
DistributionProtocol existing = daoFactory.getDistributionProtocolDao().getById(protocolId);
if (existing == null) {
return ResponseEvent.userError(DistributionProtocolErrorCode.NOT_FOUND);
}
AccessCtrlMgr.getInstance().ensureReadDPRights(existing);
return ResponseEvent.response(DistributionProtocolDetail.from(existing));
} catch (OpenSpecimenException ose) {
return ResponseEvent.error(ose);
} catch (Exception e) {
return ResponseEvent.serverError(e);
}
}
@Override
@PlusTransactional
public ResponseEvent<DistributionProtocolDetail> createDistributionProtocol(
RequestEvent<DistributionProtocolDetail> req) {
try {
AccessCtrlMgr.getInstance().ensureUserIsAdmin();
DistributionProtocol dp =
distributionProtocolFactory.createDistributionProtocol(req.getPayload());
ensureUniqueConstraints(dp, null);
daoFactory.getDistributionProtocolDao().saveOrUpdate(dp);
return ResponseEvent.response(DistributionProtocolDetail.from(dp));
} catch (OpenSpecimenException ose) {
return ResponseEvent.error(ose);
} catch (Exception e) {
return ResponseEvent.serverError(e);
}
}
@PlusTransactional
public ResponseEvent<AuthDomainDetail> updateDomain(RequestEvent<AuthDomainDetail> req) {
try {
AuthDomainDetail detail = req.getPayload();
AuthDomain existingDomain = daoFactory.getAuthDao().getAuthDomainByName(detail.getName());
if (existingDomain == null) {
throw OpenSpecimenException.userError(AuthProviderErrorCode.DOMAIN_NOT_FOUND);
}
AuthDomain authDomain = domainRegFactory.createDomain(detail);
existingDomain.update(authDomain);
return ResponseEvent.response(AuthDomainDetail.from(existingDomain));
} catch (OpenSpecimenException ose) {
return ResponseEvent.error(ose);
} catch (Exception e) {
return ResponseEvent.serverError(e);
}
}
@Override
public String getLabel(Specimen specimen) {
String ppid = specimen.getVisit().getRegistration().getPpid();
while (specimen.isAliquot() || specimen.isDerivative()) {
specimen = specimen.getParentSpecimen();
}
Calendar cal = Calendar.getInstance();
SpecimenCollectionEvent collEvent = specimen.getCollectionEvent();
if (collEvent != null) {
cal.setTime(collEvent.getTime());
} else if (specimen.getCreatedOn() != null) {
cal.setTime(specimen.getCreatedOn());
}
int yoc = cal.get(Calendar.YEAR);
String key = ppid + "_" + yoc;
Long uniqueId = daoFactory.getUniqueIdGenerator().getUniqueId(name, key);
return uniqueId.toString();
}
private String deIdentifyParticipantName(String report, Map<String, Object> contextMap) {
Long visitId = (Long) contextMap.get("visitId");
Visit visit = daoFactory.getVisitsDao().getById(visitId);
Participant participant = visit.getRegistration().getParticipant();
StringBuilder regex = new StringBuilder();
String lastName = participant.getLastName();
if (StringUtils.isNotBlank(lastName)) {
regex.append(" ").append(lastName).append(" ");
}
String firstName = participant.getFirstName();
if (StringUtils.isNotBlank(firstName)) {
addOr(regex);
regex.append(" ").append(firstName).append(" ");
}
if (regex.length() > 0) {
regex.insert(0, "(?i)\\b(");
regex.append(")\\b");
report = report.replaceAll(regex.toString(), REPLACEMENT_STRING);
}
return report;
}
@Override
public String getNextTrid() {
return TRID_PREFIX + daoFactory.getUniqueIdGenerator().getUniqueId("TRID", "SGH");
}
@SuppressWarnings("unchecked")
@Override
public ResponseEvent<Map<String, Object>> importObject(
RequestEvent<ImportObjectDetail<Map<String, Object>>> req) {
try {
ImportObjectDetail<Map<String, Object>> importDetail = req.getPayload();
Map<String, Object> params = importDetail.getParams();
Map<String, Object> extnObj = importDetail.getObject();
String recordId = (String) extnObj.get("recordId");
if (importDetail.isCreate() && StringUtils.isNotBlank(recordId)) {
return ResponseEvent.userError(FormErrorCode.REC_ID_SPECIFIED_FOR_CREATE);
} else if (!importDetail.isCreate() && StringUtils.isBlank(recordId)) {
return ResponseEvent.userError(FormErrorCode.REC_ID_REQUIRED);
}
String entityType = (String) params.get("entityType");
Long objectId = null;
CollectionProtocol cp = null;
if (entityType.equals("Participant")) {
String ppid = (String) extnObj.get("ppid");
String cpShortTitle = (String) extnObj.get("cpShortTitle");
CollectionProtocolRegistration cpr =
daoFactory.getCprDao().getCprByCpShortTitleAndPpid(cpShortTitle, ppid);
if (cpr == null) {
return ResponseEvent.userError(CprErrorCode.NOT_FOUND);
}
objectId = cpr.getId();
cp = cpr.getCollectionProtocol();
} else if (entityType.equals("SpecimenCollectionGroup")) {
String visitName = (String) extnObj.get("visitName");
Visit visit = daoFactory.getVisitsDao().getByName(visitName);
if (visit == null) {
return ResponseEvent.userError(VisitErrorCode.NOT_FOUND);
}
objectId = visit.getId();
cp = visit.getCollectionProtocol();
} else if (entityType.equals("Specimen") || entityType.equals("SpecimenEvent")) {
String label = (String) extnObj.get("specimenLabel");
Specimen specimen = daoFactory.getSpecimenDao().getByLabel(label);
if (specimen == null) {
return ResponseEvent.userError(SpecimenErrorCode.NOT_FOUND, label);
}
objectId = specimen.getId();
cp = specimen.getCollectionProtocol();
}
String formName = (String) params.get("formName");
Container form = Container.getContainer(formName);
if (form == null) {
return ResponseEvent.userError(FormErrorCode.NOT_FOUND);
}
Long formCtxId = formDao.getFormCtxtId(form.getId(), entityType, cp.getId());
if (formCtxId == null) {
return ResponseEvent.userError(
FormErrorCode.NO_ASSOCIATION, cp.getShortTitle(), form.getCaption());
}
Map<String, Object> appData = new HashMap<String, Object>();
appData.put("formCtxtId", formCtxId);
appData.put("objectId", objectId);
Map<String, Object> formValueMap = (Map<String, Object>) extnObj.get("formValueMap");
formValueMap.put("appData", appData);
if (StringUtils.isNotBlank(recordId)) {
formValueMap.put("id", Long.parseLong(recordId));
}
FormData formData = FormData.getFormData(form, formValueMap, true, null);
FormDataDetail formDataDetail = new FormDataDetail();
formDataDetail.setFormId(form.getId());
formDataDetail.setRecordId(formData.getRecordId());
formDataDetail.setFormData(formData);
ResponseEvent<FormDataDetail> resp =
formSvc.saveFormData(new RequestEvent<FormDataDetail>(formDataDetail));
resp.throwErrorIfUnsuccessful();
return ResponseEvent.response(resp.getPayload().getFormData().getFieldNameValueMap(true));
} catch (OpenSpecimenException ose) {
return ResponseEvent.error(ose);
} catch (Exception e) {
return ResponseEvent.serverError(e);
}
}
private void ensureUniqueDomainName(String domainName) {
if (!daoFactory.getAuthDao().isUniqueAuthDomainName(domainName)) {
throw OpenSpecimenException.userError(AuthProviderErrorCode.DUP_DOMAIN_NAME);
}
}
private DpRequirementDao getDprDao() {
return daoFactory.getDistributionProtocolRequirementDao();
}