private void applyTissueChanges(SampleTissue target, SampleTissue source) { target.setPassageNumber(source.getPassageNumber()); target.setTimesReceived(source.getTimesReceived()); target.setTubeNumber(source.getTubeNumber()); target.setSecondaryIdentifier(source.getSecondaryIdentifier()); target.setRegion(source.getRegion()); target.setTissueMaterial(source.getTissueMaterial()); target.setTissueOrigin(source.getTissueOrigin()); target.setTissueType(source.getTissueType()); target.setLab(source.getLab()); }
private SampleTissue buildTissue() { SampleTissue tissue = new SampleTissueImpl(); tissue.setTimesReceived(timesReceived); tissue.setTubeNumber(tubeNumber); tissue.setPassageNumber(passageNumber); tissue.setTissueType(tissueType); tissue.setTissueOrigin(tissueOrigin); tissue.setSecondaryIdentifier(secondaryIdentifier); tissue.setLab(lab); tissue.setTissueMaterial(tissueMaterial); tissue.setRegion(region); return tissue; }
private void validateGhostTissueLookup(SampleTissue tissue) { if (tissue.getParent() == null || tissue.getParent().getId() == SampleImpl.UNSAVED_ID || tissue.getTissueOrigin() == null || tissue.getTissueOrigin().getId() == TissueOrigin.UNSAVED_ID || tissue.getTissueType() == null || tissue.getTissueType().getId() == TissueTypeImpl.UNSAVED_ID || tissue.getTimesReceived() == null || tissue.getTubeNumber() == null) { throw new IllegalArgumentException("Missing tissue attributes required for lookup"); } }
private static SampleTissueDto asTissueSampleDto(@Nonnull SampleTissue from) { SampleTissueDto dto = new SampleTissueDto(); dto.setPassageNumber(from.getPassageNumber()); dto.setTimesReceived(from.getTimesReceived()); dto.setSecondaryIdentifier(from.getSecondaryIdentifier()); dto.setRegion(from.getRegion()); dto.setTubeNumber(from.getTubeNumber()); if (from.getLab() != null) { dto.setLabId(from.getLab().getId()); } if (from.getTissueOrigin() != null) { dto.setTissueOriginId(from.getTissueOrigin().getId()); } if (from.getTissueType() != null) { dto.setTissueTypeId(from.getTissueType().getId()); } if (from.getTissueMaterial() != null) { dto.setTissueMaterialId(from.getTissueMaterial().getId()); } return dto; }
if (st.getTissueMaterial() != null && st.getTissueMaterial().getId() != TissueMaterialImpl.UNSAVED_ID) { st.setTissueMaterial(tissueMaterialDao.getTissueMaterial(st.getTissueMaterial().getId())); if (st.getTissueOrigin() != null && st.getTissueOrigin().getId() != TissueOrigin.UNSAVED_ID) { st.setTissueOrigin(tissueOriginDao.getTissueOrigin(st.getTissueOrigin().getId())); if (st.getTissueType() != null && st.getTissueType().getId() != TissueTypeImpl.UNSAVED_ID) { st.setTissueType(tissueTypeDao.getTissueType(st.getTissueType().getId())); if (st.getLab() != null && st.getLab().getId() != LabImpl.UNSAVED_ID) { st.setLab(labService.get(st.getLab().getId()));
private static SampleTissue toTissueSample(@Nonnull SampleTissueDto from) { SampleTissue to = new SampleTissueImpl(); to.setPassageNumber(from.getPassageNumber()); to.setTimesReceived(from.getTimesReceived()); to.setTubeNumber(from.getTubeNumber()); to.setRegion(nullifyStringIfBlank(from.getRegion())); to.setSecondaryIdentifier(from.getSecondaryIdentifier()); if (from.getTissueOriginId() != null) { TissueOrigin tissueOrigin = new TissueOriginImpl(); tissueOrigin.setId(from.getTissueOriginId()); to.setTissueOrigin(tissueOrigin); } if (from.getTissueTypeId() != null) { TissueType tissueType = new TissueTypeImpl(); tissueType.setId(from.getTissueTypeId()); to.setTissueType(tissueType); } if (from.getTissueMaterialId() != null) { TissueMaterial tissueMaterial = new TissueMaterialImpl(); tissueMaterial.setId(from.getTissueMaterialId()); to.setTissueMaterial(tissueMaterial); } if (from.getLabId() != null) { Lab lab = new LabImpl(); lab.setId(from.getLabId()); to.setLab(lab); } return to; }
private String generateTissueAlias(SampleTissue tissue, SampleIdentity identity) { StringBuilder sb = new StringBuilder(); sb.append(identity.getAlias()) .append(SEPARATOR) .append(tissue.getTissueOrigin() == null ? TISSUE_ORIGIN_UNKNOWN : tissue.getTissueOrigin().getAlias()) .append(SEPARATOR) .append(tissue.getTissueType() == null ? TISSUE_TYPE_UNKNOWN : tissue.getTissueType().getAlias()) .append(SEPARATOR) .append(passageNumber(tissue.getPassageNumber())) .append(SEPARATOR) .append(tissue.getTimesReceived()); if (tissue.getTubeNumber() != null) { sb.append(DASH) .append(tissue.getTubeNumber()); } return sb.toString(); }
@Override public SampleTissue getMatchingGhostTissue(SampleTissue tissue) { validateGhostTissueLookup(tissue); Criteria criteria = currentSession().createCriteria(SampleTissueImpl.class); criteria.add(Restrictions.eq("isSynthetic", true)); criteria.add(Restrictions.eq("parent.id", tissue.getParent().getId())); criteria.add(Restrictions.eq("tissueOrigin.id", tissue.getTissueOrigin().getId())); criteria.add(Restrictions.eq("tissueType.id", tissue.getTissueType().getId())); criteria.add(Restrictions.eq("timesReceived", tissue.getTimesReceived())); criteria.add(Restrictions.eq("tubeNumber", tissue.getTubeNumber())); if (tissue.getPassageNumber() == null) { criteria.add(Restrictions.isNull("passageNumber")); } else { criteria.add(Restrictions.eq("passageNumber", tissue.getPassageNumber())); } return (SampleTissue) criteria.uniqueResult(); }