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

Example 1 with RunPurpose

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

the class Dtos method to.

public static Instrument to(@Nonnull InstrumentDto dto) {
    Instrument to = new InstrumentImpl();
    setLong(to::setId, dto.getId(), false);
    setDate(to::setDateCommissioned, dto.getDateCommissioned());
    setDate(to::setDateDecommissioned, dto.getDateDecommissioned());
    setString(to::setName, dto.getName());
    setObject(to::setInstrumentModel, InstrumentModel::new, dto.getInstrumentModelId());
    setString(to::setSerialNumber, dto.getSerialNumber());
    setObject(to::setUpgradedInstrument, InstrumentImpl::new, dto.getUpgradedInstrumentId());
    setObject(to::setDefaultRunPurpose, RunPurpose::new, dto.getDefaultRunPurposeId());
    setString(to::setIdentificationBarcode, dto.getIdentificationBarcode());
    setObject(to::setWorkstation, Workstation::new, dto.getWorkstationId());
    return to;
}

Example 2 with RunPurpose

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

the class Dtos method to.

public static RunPartitionAliquot to(@Nonnull RunPartitionAliquotDto from) {
    RunPartitionAliquot to = new RunPartitionAliquot();
    PlatformType platform = PlatformType.valueOf(from.getPlatformType());
    setObject(to::setRun, platform::createRun, from.getRunId());
    setObject(to::setPartition, PartitionImpl::new, from.getPartitionId());
    setObject(to::setAliquot, LibraryAliquot::new, from.getAliquotId());
    setObject(to::setPurpose, RunPurpose::new, from.getRunPurposeId());
    setObject(to::setQcStatus, RunLibraryQcStatus::new, from.getQcStatusId());
    setString(to::setQcNote, from.getQcNote());
    setBoolean(to::setDataReview, from.getDataReview(), true);
    return to;
}

Example 3 with RunPurpose

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

the class RunRestController method setPartitionPurposes.

@PutMapping("/{runId}/partition-purposes")
@ResponseStatus(HttpStatus.NO_CONTENT)
public void setPartitionPurposes(@PathVariable long runId, @RequestBody RunPartitionPurposeRequest request) throws IOException {
    Run run = RestUtils.retrieve("Run", runId, runService);
    RunPurpose purpose = RestUtils.retrieve("Run purpose", request.getRunPurposeId(), runPurposeService);
    List<Partition> partitions = run.getSequencerPartitionContainers().stream().flatMap(container -> container.getPartitions().stream()).filter(partition -> request.getPartitionIds().contains(partition.getId())).collect(Collectors.toList());
    for (Partition partition : partitions) {
        RunPartition runPartition = runPartitionService.get(run, partition);
        if (runPartition == null) {
            runPartition = new RunPartition();
            runPartition.setRunId(run.getId());
            runPartition.setPartitionId(partition.getId());
        }
        runPartition.setPurpose(purpose);
        runPartitionService.save(runPartition);
    }
}

Example 4 with RunPurpose

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

the class HibernateRunPurposeDaoIT method getCreateItem.

@Override
public RunPurpose getCreateItem() {
    RunPurpose purpose = new RunPurpose();
    purpose.setAlias("New Purpose");
    return purpose;
}

Example 5 with RunPurpose

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

the class HibernatePoolOrderDaoIT method testCreate.

@Test
public void testCreate() throws IOException {
    String alias = "New Category";
    PoolOrder order = new PoolOrder();
    order.setAlias(alias);
    Date now = new Date();
    order.setCreationTime(now);
    order.setLastModified(now);
    User user = (User) currentSession().get(UserImpl.class, 1L);
    order.setCreator(user);
    order.setLastModifier(user);
    RunPurpose purpose = (RunPurpose) currentSession().get(RunPurpose.class, 1L);
    order.setPurpose(purpose);
    long savedId = sut.create(order);
    clearSession();
    PoolOrder saved = (PoolOrder) getSessionFactory().getCurrentSession().get(PoolOrder.class, savedId);
    assertEquals(alias, saved.getAlias());
}