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

Example 1 with OrderLibraryAliquot

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

the class DefaultPoolOrderService method loadChildEntities.

@Override
protected void loadChildEntities(PoolOrder object) throws IOException {
    loadChildEntity(object.getParameters(), object::setParameters, sequencingParametersService);
    loadChildEntity(object.getPurpose(), object::setPurpose, runPurposeService);
    loadChildEntity(object.getContainerModel(), object::setContainerModel, containerModelService);
    for (OrderLibraryAliquot orderAliquot : object.getOrderLibraryAliquots()) {
        orderAliquot.setAliquot(libraryAliquotService.get(orderAliquot.getAliquot().getId()));
    }
    loadChildEntity(object.getPool(), object::setPool, poolService);
    loadChildEntity(object.getSequencingOrder(), object::setSequencingOrder, sequencingOrderService);
}

Example 2 with OrderLibraryAliquot

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

the class DefaultPoolService method getMismatchesWithOrders.

private List<ValidationError> getMismatchesWithOrders(Pool pool, List<PoolOrder> poolOrders) throws IOException {
    Set<Long> poolAliquotIds = new HashSet<>();
    List<ValidationError> errors = new LinkedList<>();
    for (PoolElement pe : pool.getPoolContents()) {
        poolAliquotIds.add(pe.getAliquot().getId());
        for (ParentAliquot parent = pe.getAliquot().getParentAliquot(); parent != null; parent = parent.getParentAliquot()) {
            poolAliquotIds.add(parent.getId());
        }
    }
    for (PoolOrder order : poolOrders) {
        for (OrderLibraryAliquot orderAliquot : order.getOrderLibraryAliquots()) {
            if (!poolAliquotIds.contains(orderAliquot.getAliquot().getId())) {
                String errorMessage = String.format("Pool must contain library aliquot '%s', as specified by pool order '%s'", orderAliquot.getAliquot().getAlias(), order.getAlias());
                errors.add(new ValidationError("poolElements", errorMessage));
            }
        }
    }
    return errors;
}

Example 3 with OrderLibraryAliquot

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

the class EditPoolOrderController method create.

@GetMapping("/new")
public ModelAndView create(@RequestParam(name = "aliquotIds", required = false) String aliquotIds, ModelMap model) throws IOException {
    model.put("title", "New Pool Order");
    model.put(PageMode.PROPERTY, PageMode.CREATE.getLabel());
    PoolOrder order = new PoolOrder();
    if (aliquotIds != null) {
        for (Long aliquotId : LimsUtils.parseIds(aliquotIds)) {
            LibraryAliquot ali = libraryAliquotService.get(aliquotId);
            if (ali == null) {
                throw new ClientErrorException("Library aliquot " + aliquotId + " not found");
            }
            OrderLibraryAliquot orderLib = new OrderLibraryAliquot();
            orderLib.setAliquot(ali);
            order.getOrderLibraryAliquots().add(orderLib);
        }
    }
    return orderPage(order, model);
}

Example 4 with OrderLibraryAliquot

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

the class DefaultPoolOrderService method applyChanges.

@Override
protected void applyChanges(PoolOrder to, PoolOrder from) throws IOException {
    to.setPartitions(from.getPartitions());
    to.setContainerModel(from.getContainerModel());
    to.setParameters(from.getParameters());
    to.setAlias(from.getAlias());
    to.setPurpose(from.getPurpose());
    to.setDescription(from.getDescription());
    to.setDraft(from.isDraft());
    // remove from TO if library isn't in FROM
    // add to TO if library isn't in TO
    // update proportion in TO if different in FROM
    Set<Long> fromIds = new HashSet<>();
    for (OrderLibraryAliquot fromOrderAli : from.getOrderLibraryAliquots()) {
        fromIds.add(fromOrderAli.getAliquot().getId());
    }
    Set<OrderLibraryAliquot> removed = new HashSet<>();
    List<String> aliquotChangeMessages = new ArrayList<>();
    for (OrderLibraryAliquot toOrderAli : to.getOrderLibraryAliquots()) {
        if (!fromIds.contains(toOrderAli.getAliquot().getId())) {
            aliquotChangeMessages.add("Removed library aliquot: " + toOrderAli.getAliquot().getAlias());
            removed.add(toOrderAli);
        }
    }
    to.getOrderLibraryAliquots().removeAll(removed);
    for (OrderLibraryAliquot fromOrderAli : from.getOrderLibraryAliquots()) {
        OrderLibraryAliquot toOrderAli = to.getOrderLibraryAliquots().stream().filter(lib -> lib.getAliquot().getId() == fromOrderAli.getAliquot().getId()).findFirst().orElse(null);
        if (toOrderAli == null) {
            aliquotChangeMessages.add("Added library aliquot: " + fromOrderAli.getAliquot().getAlias());
            to.getOrderLibraryAliquots().add(fromOrderAli);
        } else {
            if (toOrderAli.getProportion() != fromOrderAli.getProportion()) {
                aliquotChangeMessages.add(fromOrderAli.getAliquot().getAlias() + " proportion changed: " + toOrderAli.getProportion() + " to " + fromOrderAli.getProportion());
                toOrderAli.setProportion(fromOrderAli.getProportion());
            }
        }
    }
    if (!aliquotChangeMessages.isEmpty()) {
        changeLogService.create(to.createChangeLog(String.join("\n", aliquotChangeMessages), "library aliquots", authorizationManager.getCurrentUser()));
    }
    to.setPool(from.getPool());
    to.setSequencingOrder(from.getSequencingOrder());
}

Example 5 with OrderLibraryAliquot

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

the class DefaultPoolOrderService method collectValidationErrors.

@Override
protected void collectValidationErrors(PoolOrder object, PoolOrder beforeChange, List<ValidationError> errors) throws IOException {
    if (object.getPool() != null || object.getSequencingOrder() != null) {
        // order should be fulfilled
        if (object.isDraft()) {
            errors.add(new ValidationError("draft", "Fulfilled order cannot be a draft"));
        }
        if (object.getPool() == null) {
            errors.add(new ValidationError("poolId", "Pool must be provided if a sequencing order is linked"));
        } else {
            for (OrderLibraryAliquot orderAli : object.getOrderLibraryAliquots()) {
                if (object.getPool().getPoolContents().stream().map(PoolElement::getAliquot).noneMatch(poolElement -> {
                    if (poolElement.getId() == orderAli.getAliquot().getId()) {
                        return true;
                    }
                    for (ParentAliquot parent = poolElement.getParentAliquot(); parent != null; parent = parent.getParentAliquot()) {
                        if (parent.getId() == orderAli.getAliquot().getId()) {
                            return true;
                        }
                    }
                    return false;
                })) {
                    errors.add(new ValidationError("Pool does not contain all of the required aliquots"));
                    break;
                }
            }
            if (object.getSequencingOrder() != null) {
                SequencingOrder seqOrder = object.getSequencingOrder();
                if (seqOrder.getPurpose().getId() != object.getPurpose().getId() || seqOrder.getSequencingParameter().getId() != object.getParameters().getId() || !seqOrder.getPartitions().equals(object.getPartitions()) || seqOrder.getPool().getId() != object.getPool().getId() || (object.getContainerModel() != null && (seqOrder.getContainerModel() == null || seqOrder.getContainerModel().getId() != object.getContainerModel().getId()))) {
                    errors.add(new ValidationError("Sequencing order does not match the pool order"));
                }
            }
        }
        preventFulfilledChange("partitions", PoolOrder::getPartitions, object, beforeChange, errors);
        preventFulfilledChange("parametersId", PoolOrder::getParameters, object, beforeChange, errors);
        preventFulfilledChange("containerModelId", PoolOrder::getContainerModel, object, beforeChange, errors);
        preventFulfilledChange("description", PoolOrder::getDescription, object, beforeChange, errors);
        preventFulfilledChange("alias", PoolOrder::getAlias, object, beforeChange, errors);
        preventFulfilledChange("purposeId", PoolOrder::getPurpose, object, beforeChange, errors);
        if (!allMatch(object.getOrderLibraryAliquots(), beforeChange.getOrderLibraryAliquots())) {
            errors.add(new ValidationError("Aliquots cannot be changed after the order is fulfilled"));
        }
    }
    // if any sequencing requirements are specified, all are required
    if (object.getContainerModel() != null || object.getParameters() != null || object.getPartitions() != null) {
        // exception: container model not required for legacy orders (from before container model was added to orders)
        if ((beforeChange == null || beforeChange.getContainerModel() != null) && object.getContainerModel() == null) {
            errors.add(ValidationUtils.makeNoNullError("containerModelId"));
        }
        if (object.getParameters() == null) {
            errors.add(ValidationUtils.makeNoNullError("parametersId"));
        }
        if (object.getPartitions() == null) {
            errors.add(ValidationUtils.makeNoNullError("partitions"));
        }
    }
    // Container model and seq params must be linked to same instrument model
    if (object.getContainerModel() != null && object.getParameters().getInstrumentModel().getContainerModels().stream().noneMatch(model -> model.getId() == object.getContainerModel().getId())) {
        errors.add(new ValidationError("containerModelId", "Not compatible with the selected sequencing parameters"));
    }
    PlatformType orderPlatform = object.getParameters() == null ? null : object.getParameters().getInstrumentModel().getPlatformType();
    for (OrderLibraryAliquot orderAli : object.getOrderLibraryAliquots()) {
        PlatformType libPlatform = orderAli.getAliquot().getLibrary().getPlatformType();
        if (orderPlatform == null) {
            orderPlatform = libPlatform;
        } else if (!libPlatform.equals(orderPlatform)) {
            errors.add(new ValidationError("Platform for all aliquots and sequencing parameters (if specified) must match"));
            break;
        }
    }
    if (!object.isDraft() && object.getOrderLibraryAliquots().isEmpty()) {
        errors.add(new ValidationError("Non-draft order must include at least one library aliquot"));
    }
    if (strictPools) {
        validateNoNewDuplicateIndices(object, beforeChange, errors);
    }
}