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

Example 1 with RunPartition

use of uk.ac.bbsrc.tgac.miso.core.data.Experiment.RunPartition 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);
    }
}

Example 2 with RunPartition

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

the class EditExperimentController method setupForm.

@GetMapping(value = "/{experimentId}")
public ModelAndView setupForm(@PathVariable Long experimentId, ModelMap model) throws IOException {
    Experiment experiment = experimentService.get(experimentId);
    if (experiment == null)
        throw new NotFoundException("No experiment found for ID " + experimentId.toString());
    ObjectMapper mapper = new ObjectMapper();
    ObjectNode consumableConfig = mapper.createObjectNode();
    consumableConfig.put("experimentId", experiment.getId());
    Stream.<// 
    KitDescriptor>concat(// 
    Stream.of(experiment.getLibrary().getKitDescriptor()), // 
    experiment.getRunPartitions().stream().map(// 
    RunPartition::getPartition).flatMap(partition -> Stream.of(partition.getSequencerPartitionContainer().getClusteringKit(), // 
    partition.getSequencerPartitionContainer().getMultiplexingKit()))).filter(// 
    Objects::nonNull).distinct().map(// 
    Dtos::asDto).forEach(consumableConfig.putArray("allowedDescriptors")::addPOJO);
    model.put("experiment", experiment);
    model.put("experimentDto", mapper.writeValueAsString(Dtos.asDto(experiment)));
    model.put("consumables", experiment.getKits().stream().map(Dtos::asDto).collect(Collectors.toList()));
    model.put("consumableConfig", mapper.writeValueAsString(consumableConfig));
    model.put("runPartitions", experiment.getRunPartitions().stream().map(entry -> new ExperimentDto.RunPartitionDto(Dtos.asDto(entry.getRun()), Dtos.asDto(entry.getPartition(), indexChecker))).collect(Collectors.toList()));
    model.put("title", "Edit Experiment");
    return new ModelAndView("/WEB-INF/pages/editExperiment.jsp", model);
}

Example 3 with RunPartition

use of uk.ac.bbsrc.tgac.miso.core.data.Experiment.RunPartition 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 4 with RunPartition

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

the class Dtos method to.

public static Experiment to(@Nonnull ExperimentDto dto) {
    Experiment to = new Experiment();
    setLong(to::setId, dto.getId(), false);
    setString(to::setAccession, dto.getAccession());
    to.setAlias(dto.getAlias());
    to.setDescription(dto.getDescription());
    setString(to::setName, dto.getName());
    to.setLibrary(to(dto.getLibrary()));
    to.setInstrumentModel(to(dto.getInstrumentModel()));
    to.setRunPartitions(dto.getPartitions().stream().map(rpDto -> {
        RunPartition rpTo = new RunPartition();
        rpTo.setExperiment(to);
        rpTo.setPartition(to(rpDto.getPartition()));
        rpTo.setRun(PlatformType.get(rpDto.getRun().getPlatformType()).createRun());
        rpTo.getRun().setId(rpDto.getRun().getId());
        return rpTo;
    }).collect(Collectors.toList()));
    to.setStudy(to(dto.getStudy()));
    to.setTitle(dto.getTitle());
    return to;
}