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

Example 1 with LibrarySpikeIn

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

the class Dtos method to.

public static LibrarySpikeIn to(@Nonnull LibrarySpikeInDto from) {
    LibrarySpikeIn to = new LibrarySpikeIn();
    setLong(to::setId, from.getId(), false);
    setString(to::setAlias, from.getAlias());
    return to;
}

Example 2 with LibrarySpikeIn

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

the class HibernateLibrarySpikeInDaoIT method testGet.

@Test
public void testGet() throws IOException {
    long id = 1L;
    LibrarySpikeIn spikeIn = sut.get(id);
    assertNotNull(spikeIn);
    assertEquals(id, spikeIn.getId());
}

Example 3 with LibrarySpikeIn

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

the class Dtos method to.

public static Library to(@Nonnull LibraryDto from) {
    Library to = null;
    if (from instanceof DetailedLibraryDto) {
        to = toDetailedLibrary((DetailedLibraryDto) from);
    } else {
        to = new LibraryImpl();
    }
    if (from.getId() != null)
        to.setId(from.getId());
    to.setAlias(from.getAlias());
    to.setName(from.getName());
    to.setDescription(from.getDescription());
    to.setIdentificationBarcode(from.getIdentificationBarcode());
    setBigDecimal(to::setConcentration, from.getConcentration());
    to.setConcentrationUnits(from.getConcentrationUnits());
    to.setLowQuality(from.getLowQuality());
    if (from.getPaired() != null) {
        to.setPaired(from.getPaired());
    }
    to.setPlatformType(PlatformType.get(from.getPlatformType()));
    if (from.getParentSampleId() != null) {
        to.setSample(new SampleImpl());
        to.getSample().setId(from.getParentSampleId());
    }
    setObject(to::setLibrarySelectionType, LibrarySelectionType::new, from.getLibrarySelectionTypeId());
    if (from.getLibraryStrategyTypeId() != null) {
        LibraryStrategyType strat = new LibraryStrategyType();
        strat.setId(from.getLibraryStrategyTypeId());
        to.setLibraryStrategyType(strat);
    }
    if (from.getLibraryTypeId() != null) {
        LibraryType type = new LibraryType();
        type.setId(from.getLibraryTypeId());
        if (from.getLibraryTypeAlias() != null)
            type.setDescription(from.getLibraryTypeAlias());
        to.setLibraryType(type);
    }
    setObject(to::setDetailedQcStatus, DetailedQcStatusImpl::new, from.getDetailedQcStatusId());
    setString(to::setDetailedQcStatusNote, from.getDetailedQcStatusNote());
    if (from.getIndex1Id() != null) {
        Index tb1 = new Index();
        tb1.setId(from.getIndex1Id());
        to.setIndex1(tb1);
        if (from.getIndex2Id() != null) {
            Index tb2 = new Index();
            tb2.setId(from.getIndex2Id());
            to.setIndex2(tb2);
        }
    }
    setBigDecimal(to::setInitialVolume, from.getInitialVolume());
    setBigDecimal(to::setVolume, from.getVolume());
    to.setVolumeUnits(from.getVolumeUnits());
    setBigDecimal(to::setVolumeUsed, from.getVolumeUsed());
    setBigDecimal(to::setNgUsed, from.getNgUsed());
    to.setDnaSize(from.getDnaSize());
    if (from.getKitDescriptorId() != null) {
        KitDescriptor kitDescriptor = new KitDescriptor();
        kitDescriptor.setId(from.getKitDescriptorId());
        to.setKitDescriptor(kitDescriptor);
    }
    setString(to::setKitLot, from.getKitLot());
    to.setLocationBarcode(from.getLocationBarcode());
    to.setCreationDate(parseDate(from.getCreationDate()));
    to.setBoxPosition((LibraryBoxPosition) makeBoxablePosition(from, (LibraryImpl) to));
    to.setDiscarded(from.isDiscarded());
    setObject(to::setSpikeIn, LibrarySpikeIn::new, from.getSpikeInId());
    setBigDecimal(to::setSpikeInVolume, from.getSpikeInVolume());
    setObject(to::setSpikeInDilutionFactor, from.getSpikeInDilutionFactor(), DilutionFactor::get);
    setBoolean(to::setUmis, from.getUmis(), false);
    setObject(to::setWorkstation, Workstation::new, from.getWorkstationId());
    setObject(to::setThermalCycler, InstrumentImpl::new, from.getThermalCyclerId());
    setObject(to::setSop, Sop::new, from.getSopId());
    to.setCreationReceiptInfo(toReceiptTransfer(from, to));
    return to;
}

Example 4 with LibrarySpikeIn

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

the class HibernateLibrarySpikeInDaoIT method testGetUsage.

@Test
public void testGetUsage() throws IOException {
    LibrarySpikeIn spikeIn = (LibrarySpikeIn) getSessionFactory().getCurrentSession().get(LibrarySpikeIn.class, 1L);
    assertEquals("ERCC Mix 1", spikeIn.getAlias());
    assertEquals(0L, sut.getUsage(spikeIn));
}

Example 5 with LibrarySpikeIn

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

the class HibernateLibrarySpikeInDaoIT method testCreate.

@Test
public void testCreate() throws IOException {
    String alias = "New LibrarySpikeIn";
    LibrarySpikeIn spikeIn = new LibrarySpikeIn();
    spikeIn.setAlias(alias);
    long savedId = sut.create(spikeIn);
    clearSession();
    LibrarySpikeIn saved = (LibrarySpikeIn) getSessionFactory().getCurrentSession().get(LibrarySpikeIn.class, savedId);
    assertEquals(alias, saved.getAlias());
}