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

Example 6 with LibraryImpl

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

the class DefaultExperimentServiceTest method setUp.

@Before
public void setUp() {
    MockitoAnnotations.initMocks(this);
    Mockito.when(namingSchemeHolder.getPrimary()).thenReturn(namingScheme);
    Mockito.when(namingScheme.validateName(Matchers.anyString())).thenReturn(ValidationResult.success());
    experiment.setInstrumentModel(new InstrumentModel());
    experiment.getInstrumentModel().setId(2L);
    experiment.setLibrary(new LibraryImpl());
    experiment.getLibrary().setId(3L);
    experiment.setStudy(new StudyImpl());
    experiment.getStudy().setId(5L);
}

Example 7 with LibraryImpl

use of uk.ac.bbsrc.tgac.miso.core.data.impl.LibraryImpl 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 8 with LibraryImpl

use of uk.ac.bbsrc.tgac.miso.core.data.impl.LibraryImpl 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 9 with LibraryImpl

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

the class Dtos method to.

public static Workset to(@Nonnull WorksetDto from) {
    Workset workset = new Workset();
    setLong(workset::setId, from.getId(), false);
    setString(workset::setAlias, from.getAlias());
    setString(workset::setDescription, from.getDescription());
    setObject(workset::setCategory, WorksetCategory::new, from.getCategoryId());
    setObject(workset::setStage, WorksetStage::new, from.getStageId());
    setWorksetItems(workset::setWorksetSamples, from.getSampleIds(), WorksetSample::new, SampleImpl::new);
    setWorksetItems(workset::setWorksetLibraries, from.getLibraryIds(), WorksetLibrary::new, LibraryImpl::new);
    setWorksetItems(workset::setWorksetLibraryAliquots, from.getLibraryAliquotIds(), WorksetLibraryAliquot::new, LibraryAliquot::new);
    return workset;
}

Example 10 with LibraryImpl

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

the class HibernateLibraryAliquotDaoIT method testSaveNew.

@Test
public void testSaveNew() throws IOException {
    final LibraryAliquot ld = new LibraryAliquot();
    final Library lib = new LibraryImpl();
    UserImpl user = new UserImpl();
    user.setId(1L);
    user.setFullName("moi");
    lib.setId(1L);
    ld.setCreator(user);
    ld.setLastModifier(user);
    ld.setLibrary(lib);
    ld.setConcentration(new BigDecimal("12.5"));
    ld.setCreationDate(new Date());
    ld.setCreationTime(new Date());
    ld.setName("nom de plume");
    ld.setAlias("TEST");
    Long newId = dao.save(ld);
    final LibraryAliquot saved = dao.get(newId);
    assertNotNull(saved);
    assertEquals(new BigDecimal("12.5"), saved.getConcentration());
}