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

Example 1 with Partition

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

the class HibernateRunPartitionAliquotDaoIT method testCreate.

@Test
public void testCreate() throws Exception {
    Run run = (Run) currentSession().get(Run.class, 1L);
    Partition partition = (Partition) currentSession().get(PartitionImpl.class, 2L);
    LibraryAliquot aliquot = (LibraryAliquot) currentSession().get(LibraryAliquot.class, 3L);
    RunPartitionAliquotId id = new RunPartitionAliquotId(run, partition, aliquot);
    assertNull(currentSession().get(RunPartitionAliquot.class, id));
    RunPartitionAliquot rpa = new RunPartitionAliquot(run, partition, aliquot);
    User user = (User) currentSession().get(UserImpl.class, 1L);
    rpa.setLastModifier(user);
    RunLibraryQcStatus qc = (RunLibraryQcStatus) currentSession().get(RunLibraryQcStatus.class, 1L);
    rpa.setQcStatus(qc);
    rpa.setQcUser(user);
    rpa.setQcDate(new Date());
    sut.create(rpa);
    clearSession();
    RunPartitionAliquot saved = (RunPartitionAliquot) currentSession().get(RunPartitionAliquot.class, id);
    assertNotNull(saved);
    assertEquals(1L, saved.getRun().getId());
    assertEquals(2L, saved.getPartition().getId());
    assertEquals(3L, saved.getAliquot().getId());
}

Example 2 with Partition

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

the class DefaultQcStatusService method findPartitionInRun.

private Partition findPartitionInRun(Run run, long partitionId) {
    Partition partition = run.getRunPositions().stream().map(RunPosition::getContainer).flatMap(x -> x.getPartitions().stream()).filter(x -> x.getId() == partitionId).findFirst().orElse(null);
    throwIfNull("Partition", partition);
    return partition;
}

Example 3 with Partition

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

the class DefaultContainerService method update.

@Override
public void update(Partition partition) throws IOException {
    Partition original = containerDao.getPartitionById(partition.getId());
    if (partition.getPool() != null) {
        partition.setPool(poolService.get(partition.getPool().getId()));
    }
    validateChange(partition, original);
    applyChanges(original, partition);
    original.getSequencerPartitionContainer().setChangeDetails(authorizationManager.getCurrentUser());
    containerDao.save(original.getSequencerPartitionContainer());
}

Example 4 with Partition

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

the class DefaultContainerService method applyChanges.

@Override
public void applyChanges(SequencerPartitionContainer source, SequencerPartitionContainer managed) throws IOException {
    managed.setIdentificationBarcode(source.getIdentificationBarcode());
    managed.setDescription(source.getDescription());
    managed.setClusteringKit(source.getClusteringKit());
    managed.setClusteringKitLot(source.getClusteringKitLot());
    managed.setMultiplexingKit(source.getMultiplexingKit());
    managed.setMultiplexingKitLot(source.getMultiplexingKitLot());
    managed.setModel(source.getModel());
    if (LimsUtils.isOxfordNanoporeContainer(managed)) {
        applyOxfordNanoporeChanges((OxfordNanoporeContainer) source, (OxfordNanoporeContainer) managed);
    }
    for (Partition sourcePartition : source.getPartitions()) {
        for (Partition managedPartition : managed.getPartitions()) {
            if (sourcePartition == null || managedPartition == null) {
                throw new IOException("Partition from " + (sourcePartition == null ? "client" : "database") + " is null.");
            }
            if (sourcePartition.getId() == managedPartition.getId()) {
                Pool sourcePool = sourcePartition.getPool();
                Pool managedPool = managedPartition.getPool();
                if (sourcePool == null) {
                    managedPartition.setPool(null);
                } else if (managedPool == null || sourcePool.getId() != managedPool.getId()) {
                    managedPartition.setPool(poolService.get(sourcePool.getId()));
                }
                break;
            }
        }
    }
}

Example 5 with Partition

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

the class RunRestController method getSpreadsheet.

@PostMapping(value = "/spreadsheet")
@ResponseBody
public HttpEntity<byte[]> getSpreadsheet(@RequestBody SpreadsheetRequest request, HttpServletResponse response, UriComponentsBuilder uriBuilder) throws IOException {
    // Note: not retrieving persisted run-libraries, so QC data will be missing
    List<Run> runs = runService.listByIdList(request.getIds());
    List<RunPartitionAliquot> runLibraries = new ArrayList<>();
    for (Run run : runs) {
        for (RunPosition runPosition : run.getRunPositions()) {
            for (Partition partition : runPosition.getContainer().getPartitions()) {
                if (partition.getPool() != null) {
                    for (PoolElement element : partition.getPool().getPoolContents()) {
                        LibraryAliquot aliquot = libraryAliquotService.get(element.getAliquot().getId());
                        runLibraries.add(new RunPartitionAliquot(run, partition, aliquot));
                    }
                }
            }
        }
    }
    return MisoWebUtils.generateSpreadsheet(request, runLibraries.stream(), detailedSample, RunLibrarySpreadsheets::valueOf, response);
}