Examples with ContainerService uk.ac.bbsrc.tgac.miso.core.service.ContainerService used on opensource projects

Example 1 with ContainerService

use of uk.ac.bbsrc.tgac.miso.core.service.ContainerService in project miso-lims by miso-lims.

the class PoolRestController method assignPool.

@PostMapping(value = "/{poolId}/assign", produces = "application/json")
@ResponseStatus(code = HttpStatus.NO_CONTENT)
public void assignPool(@PathVariable Long poolId, @RequestBody AssignPoolDto request) throws IOException {
    Pool pool = poolId == 0 ? null : poolService.get(poolId);
    // Determine if this pool transition is allowed for this experiment. If removing a pool, it strictly isn't. If the new pool contains the
    // same library as the experiment, it's fine.
    Predicate<Experiment> isTransitionValid = pool == null ? experiment -> false : experiment -> pool.getPoolContents().stream().map(pd -> pd.getAliquot().getLibraryId()).anyMatch(id -> id == experiment.getLibrary().getId());
    // 
    request.getPartitionIds().stream().map(// 
    WhineyFunction.rethrow(containerService::getPartition)).peek(WhineyConsumer.rethrow(partition -> {
        for (RunPosition runPos : partition.getSequencerPartitionContainer().getRunPositions()) {
            Run run = runPos.getRun();
            // Check that we aren't going to hose any existing experiments through this reassignment
            boolean relatedExperimentsOkay = // 
            experimentService.listAllByRunId(run.getId()).stream().flatMap(// 
            experiment -> experiment.getRunPartitions().stream()).filter(// 
            rp -> rp.getRun().getId() == run.getId() && rp.getPartition().getId() == partition.getId()).map(// 
            RunPartition::getExperiment).allMatch(isTransitionValid);
            if (!relatedExperimentsOkay) {
                throw new RestException(String.format("%s %d is used in an experiment.", partition.getSequencerPartitionContainer().getModel().getPlatformType().getPartitionName(), partition.getPartitionNumber()), Status.BAD_REQUEST);
            }
        }
        if (pool != null && partition.getSequencerPartitionContainer().getModel().getPlatformType() != pool.getPlatformType()) {
            throw new RestException(String.format("%s %d in %s is not compatible with pool %s.", partition.getSequencerPartitionContainer().getModel().getPlatformType().getPartitionName(), partition.getPartitionNumber(), partition.getSequencerPartitionContainer().getIdentificationBarcode(), pool.getName()), Status.BAD_REQUEST);
        }
        partition.setPool(pool);
        if (request.getConcentration() != null) {
            partition.setLoadingConcentration(new BigDecimal(request.getConcentration()));
            partition.setLoadingConcentrationUnits(request.getUnits());
        } else {
            partition.setLoadingConcentration(null);
            partition.setLoadingConcentrationUnits(null);
        }
    })).forEach(WhineyConsumer.rethrow(containerService::update));
    if (pool != null) {
        poolService.update(pool);
    }
}