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

Example 1 with SequencerPartitionContainerImpl

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

the class LoadSequencerWorkflow method execute.

@Override
public void execute(WorkflowExecutor workflowExecutor) throws IOException {
    if (!isComplete())
        throw new IllegalStateException("Workflow is not complete");
    SequencerPartitionContainer spc;
    if (containerStep.isExistingContainer()) {
        spc = containerStep.getContainer();
    } else {
        spc = new SequencerPartitionContainerImpl();
        SequencingContainerModel model = containerModelStep.getModel();
        spc.setModel(model);
        spc.setIdentificationBarcode(containerStep.getBarcode());
        spc.setPartitionLimit(model.getPartitionCount());
    }
    for (int i = 0; i < partitionSteps.size(); ++i) {
        spc.getPartitionAt(i + 1).setPool(partitionSteps.get(i).getPool());
    }
    workflowExecutor.save(spc);
}

Example 2 with SequencerPartitionContainerImpl

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

the class LoadSequencerWorkflowTest method makeContainerStep.

private SequencerPartitionContainerProgressStep makeContainerStep(String serialNumber, String modelAlias, int partitionCount, PlatformType platformType) {
    SequencerPartitionContainer container = new SequencerPartitionContainerImpl();
    container.setIdentificationBarcode(serialNumber);
    container.setModel(makeModel(modelAlias, partitionCount, platformType));
    container.setPartitionLimit(partitionCount);
    SequencerPartitionContainerProgressStep step = new SequencerPartitionContainerProgressStep();
    step.setInput(container);
    return step;
}

Example 3 with SequencerPartitionContainerImpl

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

the class DefaultRunServiceTest method makeContainer.

private static SequencerPartitionContainer makeContainer() {
    SequencerPartitionContainer container = new SequencerPartitionContainerImpl();
    container.setPartitionLimit(1);
    container.setIdentificationBarcode(CONTAINER_SERIAL_NO);
    container.setModel(makeContainerModel());
    return container;
}

Example 4 with SequencerPartitionContainerImpl

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

the class Dtos method to.

public static SequencerPartitionContainer to(@Nonnull ContainerDto from) {
    SequencerPartitionContainer to = null;
    if (from instanceof OxfordNanoporeContainerDto) {
        OxfordNanoporeContainerDto ontFrom = (OxfordNanoporeContainerDto) from;
        OxfordNanoporeContainer ontTo = new OxfordNanoporeContainer();
        setObject(ontTo::setPoreVersion, PoreVersion::new, ontFrom.getPoreVersionId());
        setDate(ontTo::setReceivedDate, ontFrom.getReceivedDate());
        setDate(ontTo::setReturnedDate, ontFrom.getReturnedDate());
        to = ontTo;
    } else {
        to = new SequencerPartitionContainerImpl();
    }
    setLong(to::setId, from.getId(), false);
    setString(to::setIdentificationBarcode, from.getIdentificationBarcode());
    setObject(to::setModel, SequencingContainerModel::new, maybeGetProperty(from.getModel(), SequencingContainerModelDto::getId));
    setString(to::setDescription, from.getDescription());
    setObject(to::setClusteringKit, KitDescriptor::new, from.getClusteringKitId());
    setString(to::setClusteringKitLot, from.getClusteringKitLot());
    setObject(to::setMultiplexingKit, KitDescriptor::new, from.getMultiplexingKitId());
    setString(to::setMultiplexingKitLot, from.getMultiplexingKitLot());
    return to;
}

Example 5 with SequencerPartitionContainerImpl

use of uk.ac.bbsrc.tgac.miso.core.data.impl.SequencerPartitionContainerImpl 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;
}