private void setCode(String code, SpecimenRequirement sr, OpenSpecimenException ose) {
if (StringUtils.isNotBlank(code)) {
sr.setCode(code.trim());
} else {
sr.setCode(null);
}
}
@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;
}
private SpecimenRequirement createSpecimenPoolReq(
SpecimenRequirement pooledSpmnReq, SpecimenRequirementDetail req, OpenSpecimenException ose) {
SpecimenRequirement specimenPoolReq = pooledSpmnReq.copy();
setInitialQty(req, specimenPoolReq, ose);
setCode(req, specimenPoolReq, ose);
specimenPoolReq.setPooledSpecimenRequirement(pooledSpmnReq);
return specimenPoolReq;
}
private void setPathologyStatus(
String pathology, SpecimenRequirement sr, OpenSpecimenException ose) {
if (StringUtils.isBlank(pathology) && sr.isDerivative()) {
//
// If pathology status is not specified for derivative requirement
// then its value is picked from parent requirement
//
return;
}
ensureNotEmptyAndValid(
PATH_STATUS, pathology, PATHOLOGY_STATUS_REQUIRED, INVALID_PATHOLOGY_STATUS, ose);
sr.setPathologyStatus(pathology);
}
private void setSpecimenPoolReqs(
SpecimenRequirementDetail detail, SpecimenRequirement sr, OpenSpecimenException ose) {
if (sr.getParentSpecimenRequirement() != null || sr.getPooledSpecimenRequirement() != null) {
return;
}
if (CollectionUtils.isEmpty(detail.getSpecimensPool())) {
return;
}
for (SpecimenRequirementDetail specimenPoolReqDetail : detail.getSpecimensPool()) {
sr.getSpecimenPoolReqs().add(createSpecimenPoolReq(sr, specimenPoolReqDetail, ose));
ose.checkAndThrow();
}
}
private void setLaterality(
SpecimenRequirementDetail detail, SpecimenRequirement sr, OpenSpecimenException ose) {
String laterality = detail.getLaterality();
ensureNotEmptyAndValid(
SPECIMEN_LATERALITY, laterality, LATERALITY_REQUIRED, INVALID_LATERALITY, ose);
sr.setLaterality(laterality);
}
@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;
}
private void setConcentration(
BigDecimal concentration, SpecimenRequirement sr, OpenSpecimenException ose) {
if (concentration != null && NumUtil.lessThanZero(concentration)) {
ose.addError(CONCENTRATION_MUST_BE_POSITIVE);
return;
}
sr.setConcentration(concentration);
}
private void setInitialQty(
BigDecimal initialQty, SpecimenRequirement sr, OpenSpecimenException ose) {
if (initialQty == null || NumUtil.lessThanZero(initialQty)) {
ose.addError(INVALID_QTY);
return;
}
sr.setInitialQuantity(initialQty);
}
private void setLabelFormat(String labelFmt, SpecimenRequirement sr, OpenSpecimenException ose) {
if (StringUtils.isBlank(labelFmt)) {
return;
}
if (!specimenLabelGenerator.isValidLabelTmpl(labelFmt)) {
ose.addError(INVALID_LABEL_FMT);
}
sr.setLabelFormat(labelFmt);
}
@Override
public SpecimenRequirement createSpecimenRequirement(SpecimenRequirementDetail detail) {
SpecimenRequirement requirement = new SpecimenRequirement();
OpenSpecimenException ose = new OpenSpecimenException(ErrorType.USER_ERROR);
requirement.setId(detail.getId());
requirement.setName(detail.getName());
requirement.setLineage(Specimen.NEW);
setCode(detail, requirement, ose);
setLabelFormat(detail, requirement, ose);
setLabelAutoPrintMode(detail, requirement, ose);
setSpecimenClass(detail, requirement, ose);
setSpecimenType(detail, requirement, ose);
setAnatomicSite(detail, requirement, ose);
setLaterality(detail, requirement, ose);
setPathologyStatus(detail, requirement, ose);
setStorageType(detail, requirement, ose);
setInitialQty(detail, requirement, ose);
setConcentration(detail, requirement, ose);
setCollector(detail, requirement, ose);
setCollectionProcedure(detail, requirement, ose);
setCollectionContainer(detail, requirement, ose);
setReceiver(detail, requirement, ose);
setCpe(detail, requirement, ose);
requirement.setSortOrder(detail.getSortOrder());
requirement.setActivityStatus(Status.ACTIVITY_STATUS_ACTIVE.getStatus());
ose.checkAndThrow();
setSpecimenPoolReqs(detail, requirement, ose);
return requirement;
}
@Override
public SpecimenRequirement createForUpdate(String lineage, SpecimenRequirementDetail req) {
SpecimenRequirement sr = new SpecimenRequirement();
OpenSpecimenException ose = new OpenSpecimenException(ErrorType.USER_ERROR);
sr.setName(req.getName());
sr.setSortOrder(req.getSortOrder());
//
// Specimen class and type are set here so that properties dependent on these can
// be calculated and set appropriately.
//
setSpecimenClass(req, sr, ose);
setSpecimenType(req, sr, ose);
setInitialQty(req, sr, ose);
setStorageType(req, sr, ose);
setLabelFormat(req, sr, ose);
setLabelAutoPrintMode(req, sr, ose);
setCode(req, sr, ose);
setConcentration(req, sr, ose);
if (!lineage.equals(Specimen.ALIQUOT)) {
setPathologyStatus(req, sr, ose);
}
if (!lineage.equals(Specimen.NEW)) {
return sr;
}
setAnatomicSite(req, sr, ose);
setLaterality(req, sr, ose);
setCollector(req, sr, ose);
setCollectionProcedure(req, sr, ose);
setCollectionContainer(req, sr, ose);
setReceiver(req, sr, ose);
ose.checkAndThrow();
return sr;
}
private void setSpecimenType(
String specimenClass, String type, SpecimenRequirement sr, OpenSpecimenException ose) {
if (StringUtils.isBlank(type)) {
ose.addError(SPECIMEN_TYPE_REQUIRED);
return;
}
if (!isValid(SPECIMEN_CLASS, specimenClass, type)) {
ose.addError(INVALID_SPECIMEN_TYPE);
return;
}
sr.setSpecimenType(type);
}
@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;
}
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);
}
private void setAnatomicSite(
SpecimenRequirementDetail detail, SpecimenRequirement sr, OpenSpecimenException ose) {
String anatomicSite = detail.getAnatomicSite();
if (StringUtils.isBlank(anatomicSite)) {
ose.addError(ANATOMIC_SITE_REQUIRED);
return;
}
if (!isValid(SPECIMEN_ANATOMIC_SITE, anatomicSite, true)) {
ose.addError(INVALID_ANATOMIC_SITE, anatomicSite);
return;
}
sr.setAnatomicSite(anatomicSite);
}
private void setLabelAutoPrintMode(
String input, SpecimenRequirement sr, OpenSpecimenException ose) {
if (StringUtils.isBlank(input)) {
return;
}
LabelAutoPrintMode labelAutoPrintMode = null;
try {
labelAutoPrintMode = LabelAutoPrintMode.valueOf(input);
} catch (IllegalArgumentException iae) {
ose.addError(INVALID_LABEL_AUTO_PRINT_MODE, input);
return;
}
sr.setLabelAutoPrintMode(labelAutoPrintMode);
}
private void setStorageType(
String storageType, SpecimenRequirement sr, OpenSpecimenException ose) {
storageType = ensureNotEmpty(storageType, SrErrorCode.STORAGE_TYPE_REQUIRED, ose);
sr.setStorageType(storageType);
// TODO: check for valid storage type
}
private void setSpecimenClass(
String specimenClass, SpecimenRequirement sr, OpenSpecimenException ose) {
ensureNotEmptyAndValid(
SPECIMEN_CLASS, specimenClass, SPECIMEN_CLASS_REQUIRED, INVALID_SPECIMEN_CLASS, ose);
sr.setSpecimenClass(specimenClass);
}
private void setReceiver(
SpecimenRequirementDetail detail, SpecimenRequirement sr, OpenSpecimenException ose) {
sr.setReceiver(ensureValidUser(detail.getReceiver(), RECEIVER_NOT_FOUND, ose));
}
private void setCollectionContainer(
SpecimenRequirementDetail detail, SpecimenRequirement sr, OpenSpecimenException ose) {
String collCont = detail.getCollectionContainer();
ensureNotEmptyAndValid(CONTAINER, collCont, COLL_CONT_REQUIRED, INVALID_COLL_CONT, ose);
sr.setCollectionContainer(collCont);
}
private void setCollectionProcedure(
SpecimenRequirementDetail detail, SpecimenRequirement sr, OpenSpecimenException ose) {
String collProc = detail.getCollectionProcedure();
ensureNotEmptyAndValid(COLL_PROC, collProc, COLL_PROC_REQUIRED, INVALID_COLL_PROC, ose);
sr.setCollectionProcedure(collProc);
}
private void setCollector(
SpecimenRequirementDetail detail, SpecimenRequirement sr, OpenSpecimenException ose) {
sr.setCollector(ensureValidUser(detail.getCollector(), COLLECTOR_NOT_FOUND, ose));
}