Examples with Sample uk.ac.bbsrc.tgac.miso.core.data.Sample used on opensource projects

Example 21 with Sample

use of uk.ac.bbsrc.tgac.miso.core.data.Sample in project miso-lims by miso-lims.

the class Dtos method toArraySamples.

private static Map<String, Sample> toArraySamples(List<ArraySampleDto> dtos) {
    Map<String, Sample> samples = new HashMap<>();
    if (dtos != null) {
        for (ArraySampleDto dto : dtos) {
            Sample sample = new SampleImpl();
            sample.setId(dto.getId());
            sample.setAlias(dto.getAlias());
            sample.setName(dto.getName());
            sample.setIdentificationBarcode(dto.getIdentificationBarcode());
            samples.put(dto.getCoordinates(), sample);
        }
    }
    return samples;
}

Example 22 with Sample

use of uk.ac.bbsrc.tgac.miso.core.data.Sample in project miso-lims by miso-lims.

the class Dtos method to.

public static Transfer to(@Nonnull TransferDto from) {
    Transfer to = new Transfer();
    setLong(to::setId, from.getId(), false);
    setString(to::setTransferRequestName, from.getTransferRequestName());
    setDateTime(to::setTransferTime, from.getTransferTime());
    setObject(to::setSenderLab, LabImpl::new, from.getSenderLabId());
    setObject(to::setSenderGroup, Group::new, from.getSenderGroupId());
    setString(to::setRecipient, from.getRecipient());
    setObject(to::setRecipientGroup, Group::new, from.getRecipientGroupId());
    addTransferItems(to::getSampleTransfers, from.getItems(), EntityType.SAMPLE, TransferSample::new, SampleImpl::new, SampleBoxPosition::new, Sample::setBoxPosition);
    addTransferItems(to::getLibraryTransfers, from.getItems(), EntityType.LIBRARY, TransferLibrary::new, LibraryImpl::new, LibraryBoxPosition::new, Library::setBoxPosition);
    addTransferItems(to::getLibraryAliquotTransfers, from.getItems(), EntityType.LIBRARY_ALIQUOT, TransferLibraryAliquot::new, LibraryAliquot::new, LibraryAliquotBoxPosition::new, LibraryAliquot::setBoxPosition);
    addTransferItems(to::getPoolTransfers, from.getItems(), EntityType.POOL, TransferPool::new, PoolImpl::new, PoolBoxPosition::new, Pool::setBoxPosition);
    return to;
}

Example 23 with Sample

use of uk.ac.bbsrc.tgac.miso.core.data.Sample in project miso-lims by miso-lims.

the class Dtos method asDto.

public static LibraryAliquotDto asDto(@Nonnull LibraryAliquot from, boolean includeBoxPositions) {
    LibraryAliquotDto dto = null;
    Library library = from.getLibrary();
    Sample sample = library == null ? null : library.getSample();
    if (isDetailedLibraryAliquot(from)) {
        DetailedLibraryAliquotDto detailedDto = asDetailedDto((DetailedLibraryAliquot) from);
        DetailedSample detailed = (DetailedSample) sample;
        if (detailed.getSubproject() != null) {
            detailedDto.setSubprojectAlias(detailed.getSubproject().getAlias());
            detailedDto.setSubprojectPriority(detailed.getSubproject().getPriority());
        }
        if (detailed.getIdentityAttributes() != null) {
            ParentIdentityAttributes identity = detailed.getIdentityAttributes();
            setString(detailedDto::setIdentityConsentLevel, maybeGetProperty(identity.getConsentLevel(), ConsentLevel::getLabel));
            setString(detailedDto::setEffectiveExternalNames, identity.getExternalName());
        }
        if (detailed.getTissueAttributes() != null) {
            ParentTissueAttributes tissue = detailed.getTissueAttributes();
            setString(detailedDto::setEffectiveTissueOriginAlias, tissue.getTissueOrigin().getAlias());
            setString(detailedDto::setEffectiveTissueOriginDescription, tissue.getTissueOrigin().getDescription());
            setString(detailedDto::setEffectiveTissueTypeAlias, tissue.getTissueType().getAlias());
            setString(detailedDto::setEffectiveTissueTypeDescription, tissue.getTissueType().getDescription());
        }
        dto = detailedDto;
    } else {
        dto = new LibraryAliquotDto();
    }
    if (library != null) {
        setLong(dto::setLibraryId, library.getId(), true);
        setString(dto::setLibraryName, library.getName());
        setString(dto::setLibraryAlias, library.getAlias());
        setBoolean(dto::setLibraryLowQuality, library.isLowQuality(), false);
        setString(dto::setLibraryPlatformType, library.getPlatformType().getKey());
        if (library.getIndex1() != null) {
            List<Index> indices = Stream.of(library.getIndex1(), library.getIndex2()).filter(Objects::nonNull).collect(Collectors.toList());
            dto.setIndexIds(indices.stream().sorted(Comparator.comparingInt(Index::getPosition)).map(Index::getId).collect(Collectors.toList()));
            dto.setIndexLabels(indices.stream().sorted(Comparator.comparingInt(Index::getPosition)).map(Index::getLabel).collect(Collectors.toList()));
        }
        if (sample != null) {
            setLong(dto::setSampleId, sample.getId(), true);
            setString(dto::setSampleName, sample.getName());
            setString(dto::setSampleAlias, sample.getAlias());
        }
    }
    if (from.getParentAliquot() != null) {
        setLong(dto::setParentAliquotId, from.getParentAliquot().getId(), true);
        setString(dto::setParentAliquotAlias, from.getParentAliquot().getAlias());
    }
    setString(dto::setParentName, maybeGetProperty(from.getParent(), HierarchyEntity::getName));
    setString(dto::setParentVolume, maybeGetProperty(from.getParent(), HierarchyEntity::getVolume));
    dto.setId(from.getId());
    dto.setName(from.getName());
    setString(dto::setAlias, from.getAlias());
    setString(dto::setDescription, from.getDescription());
    dto.setCreatorName(from.getCreator().getFullName());
    setString(dto::setConcentration, from.getConcentration());
    dto.setConcentrationUnits(from.getConcentrationUnits());
    setString(dto::setVolume, from.getVolume());
    dto.setVolumeUnits(from.getVolumeUnits());
    setString(dto::setNgUsed, from.getNgUsed());
    setString(dto::setVolumeUsed, from.getVolumeUsed());
    setInteger(dto::setDnaSize, from.getDnaSize(), true);
    if (from.getCreationDate() != null) {
        dto.setCreationDate(formatDate(from.getCreationDate()));
    }
    dto.setIdentificationBarcode(from.getIdentificationBarcode());
    dto.setLocationLabel(BoxUtils.makeLocationLabel(from));
    if (from.getTargetedSequencing() != null) {
        dto.setTargetedSequencingId(from.getTargetedSequencing().getId());
    }
    if (from.getBox() != null) {
        dto.setBox(asDto(from.getBox(), includeBoxPositions));
        dto.setBoxPosition(from.getBoxPosition());
    }
    dto.setDiscarded(from.isDiscarded());
    setDateTimeString(dto::setLastModified, from.getLastModified());
    setId(dto::setDetailedQcStatusId, from.getDetailedQcStatus());
    setString(dto::setDetailedQcStatusNote, from.getDetailedQcStatusNote());
    setString(dto::setQcUserName, maybeGetProperty(from.getQcUser(), User::getFullName));
    setDateString(dto::setQcDate, from.getQcDate());
    setEffectiveQcFailure(from, dto);
    setId(dto::setKitDescriptorId, from.getKitDescriptor());
    setString(dto::setKitLot, from.getKitLot());
    Requisition requisition = from.getLibrary().getSample().getRequisition();
    if (requisition == null) {
        requisition = getParentRequisition(from.getLibrary().getSample());
    }
    setId(dto::setRequisitionId, requisition);
    setString(dto::setRequisitionAlias, maybeGetProperty(requisition, Requisition::getAlias));
    return dto;
}

Example 24 with Sample

use of uk.ac.bbsrc.tgac.miso.core.data.Sample in project miso-lims by miso-lims.

the class Dtos method to.

public static QC to(@Nonnull QcDto dto) {
    QC to;
    switch(dto.getQcTarget()) {
        case "Library":
            LibraryQC newLibraryQc = new LibraryQC();
            Library ownerLibrary = new LibraryImpl();
            ownerLibrary.setId(dto.getEntityId());
            newLibraryQc.setLibrary(ownerLibrary);
            to = newLibraryQc;
            break;
        case "Sample":
            SampleQC newSampleQc = new SampleQC();
            Sample ownerSample = new SampleImpl();
            ownerSample.setId(dto.getEntityId());
            newSampleQc.setSample(ownerSample);
            to = newSampleQc;
            break;
        case "Pool":
            PoolQC newPoolQc = new PoolQC();
            Pool ownerPool = new PoolImpl();
            ownerPool.setId(dto.getEntityId());
            newPoolQc.setPool(ownerPool);
            to = newPoolQc;
            break;
        case "Container":
            ContainerQC newContainerQc = new ContainerQC();
            SequencerPartitionContainer ownerContainer = new SequencerPartitionContainerImpl();
            ownerContainer.setId(dto.getEntityId());
            newContainerQc.setContainer(ownerContainer);
            to = newContainerQc;
            break;
        case "Requisition":
            RequisitionQC newRequisitionQc = new RequisitionQC();
            Requisition ownerRequisition = new Requisition();
            ownerRequisition.setId(dto.getEntityId());
            newRequisitionQc.setRequisition(ownerRequisition);
            to = newRequisitionQc;
            break;
        default:
            throw new IllegalArgumentException("No such QC target: " + dto.getQcTarget());
    }
    if (dto.getId() != null) {
        to.setId(dto.getId());
    }
    to.setDate(parseDate(dto.getDate()));
    setBigDecimal(to::setResults, dto.getResults());
    setObject(to::setType, QcType::new, dto.getQcTypeId());
    to.setDescription(dto.getDescription());
    setObject(to::setInstrument, InstrumentImpl::new, dto.getInstrumentId());
    setObject(to::setKit, KitDescriptor::new, dto.getKitDescriptorId());
    setString(to::setKitLot, dto.getKitLot());
    addQcControlRuns(dto.getControls(), to, QcTarget.valueOf(dto.getQcTarget()));
    return to;
}

Example 25 with Sample

use of uk.ac.bbsrc.tgac.miso.core.data.Sample in project miso-lims by miso-lims.

the class DefaultArrayService method applyChanges.

private void applyChanges(Array from, Array to) throws IOException {
    to.setAlias(from.getAlias());
    to.setSerialNumber(from.getSerialNumber());
    to.setDescription(from.getDescription());
    // have to add/remove samples individually to avoid unnecessary "sample removed; sample added" changelogs for non-changes
    Map<String, Sample> toSamples = to.getSamples();
    Set<String> removePositions = toSamples.keySet().stream().filter(key -> !from.getSamples().containsKey(key)).collect(Collectors.toSet());
    for (String key : removePositions) {
        recordRemoval(to, toSamples.get(key).getName(), key);
        toSamples.remove(key);
    }
    from.getSamples().forEach((key, val) -> {
        Sample current = toSamples.get(key);
        if (toSamples.get(key) == null || current.getId() != val.getId()) {
            toSamples.put(key, val);
        }
    });
}