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

Example 6 with Partition

use of uk.ac.bbsrc.tgac.miso.core.data.Partition 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 7 with Partition

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

the class HibernateSequencerPartitionContainerDao method listAllPartitionsByPoolId.

@Override
public List<Partition> listAllPartitionsByPoolId(long poolId) throws IOException {
    Criteria criteria = currentSession().createCriteria(PartitionImpl.class);
    criteria.createAlias("pool", "pool");
    criteria.add(Restrictions.eq("pool.id", poolId));
    @SuppressWarnings("unchecked") List<Partition> records = criteria.list();
    return records;
}

Example 8 with Partition

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

the class HibernateRunPartitionAliquotDaoIT method testSaveCreate.

@Test
public void testSaveCreate() 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.save(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 9 with Partition

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

the class ExperimentRestController method addPartition.

@PostMapping(value = "/{experimentId}/add", produces = "application/json")
@ResponseBody
public ExperimentDto addPartition(@PathVariable Long experimentId, @RequestParam("runId") Long runId, @RequestParam("partitionId") Long partitionId) throws IOException {
    Experiment experiment = experimentService.get(experimentId);
    if (experiment == null) {
        throw new RestException("No such experiment.", Status.NOT_FOUND);
    }
    Run run = runService.get(runId);
    if (run == null) {
        throw new RestException("No such run.", Status.NOT_FOUND);
    }
    Partition partition = containerService.getPartition(partitionId);
    if (partition == null) {
        throw new RestException("No such partition.", Status.NOT_FOUND);
    }
    if (run.getSequencerPartitionContainers().stream().flatMap(container -> container.getPartitions().stream()).noneMatch(p -> p.getId() == partitionId)) {
        throw new RestException("Partition not in run.", Status.BAD_REQUEST);
    }
    if (experiment.getRunPartitions().stream().noneMatch(rp -> rp.getPartition().getId() == partition.getId() && rp.getRun().getId() == run.getId())) {
        RunPartition rp = new RunPartition();
        rp.setExperiment(experiment);
        rp.setPartition(partition);
        rp.setRun(run);
        experiment.getRunPartitions().add(rp);
        experimentService.update(experiment);
    }
    return get(experimentId);
}

Example 10 with Partition

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

the class SequencerPartitionContainerImpl method setPartitions.

@Override
public void setPartitions(List<Partition> partitions) {
    this.partitions = partitions;
    for (Partition p : partitions) {
        p.setSequencerPartitionContainer(this);
    }
    Collections.sort(partitions, partitionNumberComparator);
}