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

Example 1 with RunPartition

use of uk.ac.bbsrc.tgac.miso.core.data.RunPartition 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 2 with RunPartition

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

the class HibernateRunPartitionDao method deleteForRunContainer.

@Override
public void deleteForRunContainer(Run run, SequencerPartitionContainer container) throws IOException {
    Set<Long> partitionIds = container.getPartitions().stream().map(Partition::getId).collect(Collectors.toSet());
    @SuppressWarnings("unchecked") List<RunPartition> items = currentSession().createCriteria(RunPartition.class).add(Restrictions.eq("runId", run.getId())).add(Restrictions.in("partitionId", partitionIds)).list();
    for (RunPartition item : items) {
        currentSession().delete(item);
    }
}

Example 3 with RunPartition

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

the class HibernateRunPartitionDaoIT method testDeleteForRun.

@Test
public void testDeleteForRun() throws Exception {
    Run run = (Run) currentSession().get(Run.class, 1L);
    List<RunPartition> before = getByRunId(run.getId());
    assertEquals(8, before.size());
    dao.deleteForRun(run);
    clearSession();
    List<RunPartition> after = getByRunId(run.getId());
    assertEquals(0, after.size());
}

Example 4 with RunPartition

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

the class HibernateRunPartitionDaoIT method testDeleteForRunContainer.

@Test
public void testDeleteForRunContainer() throws Exception {
    Run run = (Run) currentSession().get(Run.class, 2L);
    SequencerPartitionContainer container = (SequencerPartitionContainer) currentSession().get(SequencerPartitionContainerImpl.class, 2L);
    List<RunPartition> before = getByRunAndContainer(run, container);
    assertEquals(8, before.size());
    dao.deleteForRunContainer(run, container);
    clearSession();
    List<RunPartition> after = getByRunAndContainer(run, container);
    assertEquals(0, after.size());
}

Example 5 with RunPartition

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

the class DefaultRunPartitionService method save.

@Override
public void save(RunPartition runPartition) throws IOException {
    RunPartition managed = get(runPartition.getRunId(), runPartition.getPartitionId());
    User user = authorizationManager.getCurrentUser();
    ValidationUtils.loadChildEntity(runPartition::setPurpose, runPartition.getPurpose(), runPurposeService, "runPurposeId");
    ValidationUtils.loadChildEntity(runPartition::setQcType, runPartition.getQcType(), partitionQcTypeService, "qcType");
    if (runPartition.getQcType() != null && runPartition.getQcType().isNoteRequired() && runPartition.getNotes() == null) {
        throw new ValidationException("A note is required for the selected partition QC status");
    }
    if (managed == null) {
        runPartition.setLastModifier(user);
        runPartitionDao.create(runPartition);
    } else {
        managed.setQcType(runPartition.getQcType());
        managed.setNotes(runPartition.getNotes());
        managed.setPurpose(runPartition.getPurpose());
        managed.setLastModifier(user);
        runPartitionDao.update(managed);
    }
}