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

Example 1 with Sop

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

the class Dtos method to.

public static Run to(@Nonnull RunDto dto) {
    Run to = getPlatformRun(dto);
    setLong(to::setId, dto.getId(), false);
    setString(to::setName, dto.getName());
    setString(to::setAlias, dto.getAlias());
    setString(to::setDescription, dto.getDescription());
    setObject(to::setHealth, dto.getStatus(), status -> HealthType.get(status));
    setString(to::setAccession, dto.getAccession());
    setObject(to::setSequencer, InstrumentImpl::new, dto.getInstrumentId());
    setDate(to::setStartDate, dto.getStartDate());
    setDate(to::setCompletionDate, dto.getEndDate());
    setObject(to::setSequencingParameters, SequencingParameters::new, dto.getSequencingParametersId());
    setObject(to::setSequencingKit, KitDescriptor::new, dto.getSequencingKitId());
    setString(to::setSequencingKitLot, dto.getSequencingKitLot());
    setString(to::setFilePath, dto.getRunPath());
    setBoolean(to::setQcPassed, dto.getQcPassed(), true);
    setBoolean(to::setDataReview, dto.getDataReview(), true);
    setObject(to::setSop, Sop::new, dto.getSopId());
    setObject(to::setDataManglingPolicy, dto.getDataManglingPolicy(), InstrumentDataManglingPolicy::valueOf);
    return to;
}

Example 2 with Sop

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

the class HibernateSopDaoIT method testListByCategory.

@Test
public void testListByCategory() throws Exception {
    List<Sop> sops = getTestSubject().listByCategory(SopCategory.LIBRARY);
    assertNotNull(sops);
    assertEquals(2, sops.size());
    for (Sop sop : sops) {
        assertEquals(SopCategory.LIBRARY, sop.getCategory());
    }
}

Example 3 with Sop

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

the class Dtos method to.

public static Sop to(@Nonnull SopDto from) {
    Sop to = new Sop();
    setLong(to::setId, from.getId(), false);
    setString(to::setAlias, from.getAlias());
    setString(to::setVersion, from.getVersion());
    setObject(to::setCategory, from.getCategory(), SopCategory::valueOf);
    setString(to::setUrl, from.getUrl());
    setBoolean(to::setArchived, from.isArchived(), false);
    return to;
}

Example 4 with Sop

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

the class Dtos method to.

public static Sample to(@Nonnull SampleDto from) {
    Sample to = null;
    if (from instanceof DetailedSampleDto) {
        to = toDetailedSample((DetailedSampleDto) from);
    } else {
        to = new SampleImpl();
    }
    if (from.getId() != null)
        to.setId(from.getId());
    to.setAccession(nullifyStringIfBlank(from.getAccession()));
    to.setName(from.getName());
    to.setDescription(nullifyStringIfBlank(from.getDescription()));
    to.setIdentificationBarcode(nullifyStringIfBlank(from.getIdentificationBarcode()));
    to.setLocationBarcode(nullifyStringIfBlank(from.getLocationBarcode()));
    to.setSampleType(from.getSampleType());
    setObject(to::setDetailedQcStatus, DetailedQcStatusImpl::new, from.getDetailedQcStatusId());
    setString(to::setDetailedQcStatusNote, from.getDetailedQcStatusNote());
    setObject(to::setScientificName, ScientificName::new, from.getScientificNameId());
    to.setTaxonIdentifier(from.getTaxonIdentifier());
    to.setAlias(from.getAlias());
    to.setDescription(from.getDescription());
    setBigDecimal(to::setInitialVolume, from.getInitialVolume());
    setBigDecimal(to::setVolume, from.getVolume());
    to.setVolumeUnits(from.getVolumeUnits());
    setBigDecimal(to::setConcentration, from.getConcentration());
    to.setConcentrationUnits(from.getConcentrationUnits());
    to.setDiscarded(from.isDiscarded());
    if (from.getProjectId() != null) {
        to.setProject(new ProjectImpl());
        to.getProject().setId(from.getProjectId());
    }
    to.setBoxPosition((SampleBoxPosition) makeBoxablePosition(from, (SampleImpl) to));
    setObject(to::setRequisition, Requisition::new, from.getRequisitionId());
    if (to.getRequisition() != null) {
        Requisition toRequisition = to.getRequisition();
        setString(toRequisition::setAlias, from.getRequisitionAlias());
        if (from.getRequisitionAssayId() != null) {
            setObject(toRequisition::setAssay, Assay::new, from.getRequisitionAssayId());
        }
    }
    setObject(to::setSequencingControlType, SequencingControlType::new, from.getSequencingControlTypeId());
    setObject(to::setSop, Sop::new, from.getSopId());
    to.setCreationReceiptInfo(toReceiptTransfer(from, to));
    return to;
}

Example 5 with Sop

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