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

Example 6 with PartitionQCType

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

the class DefaultQcStatusService method update.

@Override
public void update(QcStatusUpdate update) throws IOException {
    // to detect changes and set QC users
    switch(update.getEntityType()) {
        case SAMPLE:
            {
                Sample sample = sampleService.get(update.getId());
                updateDetailedStatus(EntityType.SAMPLE.getLabel(), sample, update);
                sampleService.update(sample);
                break;
            }
        case LIBRARY:
            {
                Library library = libraryService.get(update.getId());
                updateDetailedStatus(EntityType.LIBRARY.getLabel(), library, update);
                libraryService.update(library);
                break;
            }
        case LIBRARY_ALIQUOT:
            {
                LibraryAliquot aliquot = libraryAliquotService.get(update.getId());
                updateDetailedStatus(EntityType.LIBRARY_ALIQUOT.getLabel(), aliquot, update);
                libraryAliquotService.update(aliquot);
                break;
            }
        case POOL:
            {
                Pool pool = poolService.get(update.getId());
                throwIfNull(EntityType.POOL.getLabel(), pool);
                pool.setQcPassed(update.getQcPassed());
                poolService.update(pool);
                break;
            }
        case RUN:
            {
                Run run = runService.get(update.getId());
                throwIfNull("Run", run);
                if (update.getQcPassed() == null) {
                    // QC Passed not set
                    run.setQcPassed(null);
                    run.setQcUser(null);
                    run.setQcDate(null);
                    clearDataReview(run);
                } else if (!update.getQcPassed().equals(run.getQcPassed())) {
                    // QC Passed set and changed
                    run.setQcPassed(update.getQcPassed());
                    run.setQcUser(authorizationManager.getCurrentUser());
                    run.setQcDate(new Date());
                    clearDataReview(run);
                } else if (update.getDataReview() == null) {
                    // QC Passed set and not changed, data review not set
                    clearDataReview(run);
                } else {
                    // QC Passed set and not changed, data review set and changed
                    run.setDataReview(update.getDataReview());
                    run.setDataReviewer(authorizationManager.getCurrentUser());
                    run.setDataReviewDate(new Date());
                }
                runService.update(run);
                break;
            }
        case RUN_PARTITION:
            {
                if (update.getIds() == null || update.getIds().length != 2) {
                    throw new ValidationException("Invalid ID for run-partition");
                }
                Run run = runService.get(update.getIds()[0]);
                throwIfNull("Run", run);
                Partition partition = findPartitionInRun(run, update.getIds()[1]);
                RunPartition runPartition = runPartitionService.get(run, partition);
                if (update.getQcStatusId() == null) {
                    runPartition.setQcType(null);
                } else {
                    PartitionQCType status = partitionQcTypeService.get(update.getQcStatusId());
                    throwIfNull("Partition QC type", status);
                    runPartition.setQcType(status);
                }
                runPartition.setNotes(update.getQcNote());
                runPartition.setLastModifier(authorizationManager.getCurrentUser());
                runPartitionService.save(runPartition);
                break;
            }
        case RUN_LIBRARY:
            {
                if (update.getIds() == null || update.getIds().length != 3) {
                    throw new ValidationException("Invalid ID for run-partition");
                }
                Run run = runService.get(update.getIds()[0]);
                throwIfNull("Run", run);
                Partition partition = findPartitionInRun(run, update.getIds()[1]);
                ListLibraryAliquotView aliquotView = partition.getPool().getPoolContents().stream().map(PoolElement::getAliquot).filter(x -> x.getId() == update.getIds()[2]).findFirst().orElse(null);
                throwIfNull("Run-library", aliquotView);
                LibraryAliquot aliquot = libraryAliquotService.get(update.getIds()[2]);
                RunPartitionAliquot runLib = runPartitionAliquotService.get(run, partition, aliquot);
                if (update.getQcStatusId() == null) {
                    // QC status not set
                    runLib.setQcStatus(null);
                    runLib.setQcUser(null);
                    runLib.setQcDate(null);
                    clearDataReview(runLib);
                } else if (runLib.getQcStatus() == null || runLib.getQcStatus().getId() != update.getQcStatusId().longValue()) {
                    // QC status set and changed
                    RunLibraryQcStatus status = runLibraryQcStatusService.get(update.getQcStatusId());
                    throwIfNull("Run-library QC status", status);
                    runLib.setQcStatus(status);
                    runLib.setQcUser(authorizationManager.getCurrentUser());
                    runLib.setQcDate(new Date());
                    clearDataReview(runLib);
                } else if (update.getDataReview() == null) {
                    // QC status set and not changed, data review not set
                    clearDataReview(runLib);
                } else if (update.getDataReview() != runLib.getDataReview()) {
                    // QC status set and not changed, data review set and changed
                    runLib.setDataReview(update.getDataReview());
                    runLib.setDataReviewer(authorizationManager.getCurrentUser());
                    runLib.setDataReviewDate(new Date());
                }
                runLib.setQcNote(update.getQcNote());
                runPartitionAliquotService.save(runLib);
                break;
            }
        default:
            throw new ValidationException("Unsupported entity type");
    }
}

Example 7 with PartitionQCType

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

the class RunRestController method setQc.

@PostMapping(value = "/{runId}/qc", produces = "application/json")
@ResponseStatus(code = HttpStatus.NO_CONTENT)
public void setQc(@PathVariable Long runId, @RequestBody RunPartitionQCRequest request) throws IOException {
    Run run = RestUtils.retrieve("Run", runId, runService);
    PartitionQCType qcType = partitionQcTypeService.list().stream().filter(qt -> qt.getId() == request.getQcTypeId().longValue()).findAny().orElseThrow(() -> new RestException(String.format("No partition QC type found with ID: %d", request.getQcTypeId()), Status.BAD_REQUEST));
    // 
    run.getSequencerPartitionContainers().stream().flatMap(// 
    container -> container.getPartitions().stream()).filter(// 
    partition -> request.partitionIds.contains(partition.getId())).map(WhineyFunction.rethrow(partition -> {
        RunPartition runPartition = runPartitionService.get(run, partition);
        if (runPartition == null) {
            runPartition = new RunPartition();
            runPartition.setRunId(run.getId());
            runPartition.setPartitionId(partition.getId());
        }
        runPartition.setQcType(qcType);
        runPartition.setNotes(request.notes);
        return runPartition;
    })).forEach(WhineyConsumer.rethrow(runPartitionService::save));
}

Example 8 with PartitionQCType

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

the class HibernateRunPartitionDaoIT method testCreate.

@Test
public void testCreate() throws Exception {
    long runId = 2L;
    long partitionId = 2L;
    PartitionQCType type = (PartitionQCType) currentSession().get(PartitionQCType.class, 1L);
    RunPurpose purpose = (RunPurpose) currentSession().get(RunPurpose.class, 1L);
    RunPartition qc = new RunPartition();
    User user = (User) currentSession().get(UserImpl.class, 1L);
    qc.setRunId(runId);
    qc.setPartitionId(partitionId);
    qc.setQcType(type);
    qc.setPurpose(purpose);
    qc.setLastModifier(user);
    dao.create(qc);
    RunPartition fetchedQc = dao.get(runId, partitionId);
    assertNotNull(fetchedQc);
    assertEquals(qc.getQcType().getId(), fetchedQc.getQcType().getId());
    assertEquals(qc.getNotes(), fetchedQc.getNotes());
}

Example 9 with PartitionQCType

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

the class HibernatePartitionQcTypeDaoIT method testGetByName.

@Test
public void testGetByName() throws IOException {
    String desc = "Failed: Instrument problem";
    PartitionQCType st = sut.getByDescription(desc);
    assertNotNull(st);
    assertEquals(desc, st.getDescription());
}

Example 10 with PartitionQCType

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

the class HibernatePartitionQcTypeDaoIT method testCreate.

@Test
public void testCreate() throws IOException {
    String desc = "New Type";
    PartitionQCType st = new PartitionQCType();
    st.setDescription(desc);
    long savedId = sut.create(st);
    clearSession();
    PartitionQCType saved = (PartitionQCType) getSessionFactory().getCurrentSession().get(PartitionQCType.class, savedId);
    assertEquals(desc, saved.getDescription());
}