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

Example 1 with PartitionImpl

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

the class DefaultRunService method updateContainerFromNotification.

private boolean updateContainerFromNotification(final Run target, User user, SequencingContainerModel containerModel, String containerSerialNumber, final GetLaneContents getLaneContents, String positionName) throws IOException {
    if (LimsUtils.isStringBlankOrNull(containerSerialNumber)) {
        return false;
    }
    final Collection<SequencerPartitionContainer> containers = containerService.listByBarcode(containerSerialNumber);
    int laneCount = containerModel.getPartitionCount();
    InstrumentPosition position = null;
    if (!isStringEmptyOrNull(positionName)) {
        position = target.getSequencer().getInstrumentModel().getPositions().stream().filter(pos -> positionName.equals(pos.getAlias())).findFirst().orElseThrow(() -> new IllegalArgumentException(String.format("Unknown position '%s' for platform '%s'", positionName, target.getSequencer().getInstrumentModel().getAlias())));
    }
    switch(containers.size()) {
        case 0:
            SequencerPartitionContainer newContainer = containerModel.getPlatformType().createContainer();
            newContainer.setModel(containerModel);
            newContainer.setCreator(user);
            newContainer.setIdentificationBarcode(containerSerialNumber);
            newContainer.setPartitionLimit(laneCount);
            newContainer.setPartitions(IntStream.range(0, laneCount).mapToObj(i -> new PartitionImpl(newContainer, i + 1)).collect(Collectors.toList()));
            updatePartitionContents(getLaneContents, newContainer);
            RunPosition newRunPos = new RunPosition();
            newRunPos.setRun(target);
            newRunPos.setContainer(newContainer);
            newRunPos.setPosition(position);
            target.getRunPositions().clear();
            target.getRunPositions().add(newRunPos);
            return true;
        case 1:
            SequencerPartitionContainer container = containers.iterator().next();
            boolean isMutated = false;
            if (container.getPartitions().size() != laneCount) {
                throw new IllegalArgumentException(String.format("The container %s has %d partitions, but %d were detected by the scanner.", containerSerialNumber, container.getPartitions().size(), laneCount));
            }
            // only update container model from fallback to non-fallback
            if (container.getModel().isFallback() && !containerModel.isFallback() && container.getModel().getId() != containerModel.getId()) {
                container.setModel(containerModel);
                isMutated = true;
            }
            if (target.getSequencerPartitionContainers().stream().noneMatch(c -> c.getId() == container.getId())) {
                target.addSequencerPartitionContainer(container, position);
                updatePartitionContents(getLaneContents, container);
                isMutated = true;
            }
            return isMutated;
        default:
            throw new IllegalArgumentException("Multiple containers with same identifier: " + containerSerialNumber);
    }
}

Example 2 with PartitionImpl

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

the class Dtos method to.

public static RunPartitionAliquot to(@Nonnull RunPartitionAliquotDto from) {
    RunPartitionAliquot to = new RunPartitionAliquot();
    PlatformType platform = PlatformType.valueOf(from.getPlatformType());
    setObject(to::setRun, platform::createRun, from.getRunId());
    setObject(to::setPartition, PartitionImpl::new, from.getPartitionId());
    setObject(to::setAliquot, LibraryAliquot::new, from.getAliquotId());
    setObject(to::setPurpose, RunPurpose::new, from.getRunPurposeId());
    setObject(to::setQcStatus, RunLibraryQcStatus::new, from.getQcStatusId());
    setString(to::setQcNote, from.getQcNote());
    setBoolean(to::setDataReview, from.getDataReview(), true);
    return to;
}

Example 3 with PartitionImpl

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

the class Dtos method to.

public static Partition to(@Nonnull PartitionDto dto) {
    Partition to = new PartitionImpl();
    to.setId(dto.getId());
    return to;
}

Example 4 with PartitionImpl

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

the class EditSequencerPartitionContainerController method setupNewForm.

@GetMapping(value = "/new/{modelId}")
public ModelAndView setupNewForm(@PathVariable("modelId") Long modelId, ModelMap model) throws IOException {
    SequencingContainerModel containerModel = containerModelService.get(modelId);
    if (containerModel == null)
        throw new NotFoundException("No container model found for ID " + modelId.toString());
    SequencerPartitionContainer container = containerModel.getPlatformType().createContainer();
    container.setModel(containerModel);
    model.put("title", "New " + containerModel.getPlatformType().getContainerName());
    container.setPartitions(IntStream.range(0, containerModel.getPartitionCount()).mapToObj(number -> new PartitionImpl(container, number + 1)).collect(Collectors.toList()));
    return setupForm(container, model);
}