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

Example 1 with Assay

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

the class RequisitionRestController method moveSamples.

@PostMapping("/{requisitionId}/samples/move")
@ResponseBody
public RequisitionDto moveSamples(@PathVariable long requisitionId, @RequestBody MoveSamplesRequest request) throws IOException {
    List<Sample> samples = new ArrayList<>();
    for (Long id : request.sampleIds) {
        Sample sample = RestUtils.retrieve("Sample", id, sampleService, Status.BAD_REQUEST);
        samples.add(sample);
    }
    Requisition requisition = null;
    if (request.requisitionId != null) {
        requisition = RestUtils.retrieve("Requisition", request.requisitionId, requisitionService, Status.BAD_REQUEST);
    } else {
        requisition = new Requisition();
        requisition.setAlias(request.requisitionAlias);
        Assay assay = new Assay();
        assay.setId(request.assayId);
        requisition.setAssay(assay);
        requisition.setStopped(request.stopped);
    }
    Requisition saved = requisitionService.moveToRequisition(requisition, samples);
    return RequisitionDto.from(saved);
}

Example 2 with Assay

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

the class HibernateAssayDaoIT method testGetUsage.

@Test
public void testGetUsage() throws Exception {
    Assay assay = (Assay) currentSession().get(Assay.class, 1L);
    assertEquals(1L, getTestSubject().getUsage(assay));
}

Example 3 with Assay

use of uk.ac.bbsrc.tgac.miso.core.data.impl.Assay 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 4 with Assay

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

the class AssayDto method to.

public Assay to() {
    Assay to = new Assay();
    setLong(to::setId, getId(), false);
    setString(to::setAlias, getAlias());
    setString(to::setVersion, getVersion());
    setString(to::setDescription, getDescription());
    setBoolean(to::setArchived, isArchived(), false);
    if (getTests() != null) {
        getTests().stream().map(AssayTestDto::to).forEach(x -> to.getAssayTests().add(x));
    }
    if (getMetrics() != null) {
        getMetrics().stream().map(AssayMetricDto::to).forEach(x -> to.getAssayMetrics().add(x));
    }
    return to;
}

Example 5 with Assay

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

the class RequisitionDto method to.

public Requisition to() {
    Requisition to = new Requisition();
    setLong(to::setId, getId(), false);
    setString(to::setAlias, getAlias());
    setObject(to::setAssay, Assay::new, getAssayId());
    setBoolean(to::setStopped, isStopped(), false);
    return to;
}