Examples with QcStatusUpdate uk.ac.bbsrc.tgac.miso.core.data.impl.view.qc.QcStatusUpdate used on opensource projects

Example 1 with QcStatusUpdate

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

the class Dtos method to.

public static QcStatusUpdate to(@Nonnull QcNodeDto from) {
    QcStatusUpdate to = new QcStatusUpdate();
    setLong(to::setId, from.getId(), true);
    to.setIds(from.getIds());
    setObject(to::setEntityType, from.getEntityType(), QcNodeType::lookup);
    setBoolean(to::setQcPassed, from.getQcPassed(), true);
    setLong(to::setQcStatusId, from.getQcStatusId(), true);
    setString(to::setQcNote, from.getQcNote());
    setBoolean(to::setDataReview, from.getDataReview(), true);
    return to;
}

Example 2 with QcStatusUpdate

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

the class QcStatusRestController method update.

@PutMapping
@ResponseStatus(HttpStatus.NO_CONTENT)
@ResponseBody
public void update(@RequestBody QcNodeDto dto) throws IOException {
    QcStatusUpdate update = Dtos.to(dto);
    qcStatusService.update(update);
}

Example 3 with QcStatusUpdate

use of uk.ac.bbsrc.tgac.miso.core.data.impl.view.qc.QcStatusUpdate 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");
    }
}