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

Example 1 with InstrumentPosition

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

the class DefaultRunService method updateContainerFromNotification.

private boolean updateContainerFromNotification(final Run target, User user, SequencingContainerModel containerModel, String containerSerialNumber, final GetLaneContents getLaneContents, String positionName) throws IOException {
    if (LimsUtils.isStringBlankOrNull(containerSerialNumber)) {
        return false;
    }
    final Collection<SequencerPartitionContainer> containers = containerService.listByBarcode(containerSerialNumber);
    int laneCount = containerModel.getPartitionCount();
    InstrumentPosition position = null;
    if (!isStringEmptyOrNull(positionName)) {
        position = target.getSequencer().getInstrumentModel().getPositions().stream().filter(pos -> positionName.equals(pos.getAlias())).findFirst().orElseThrow(() -> new IllegalArgumentException(String.format("Unknown position '%s' for platform '%s'", positionName, target.getSequencer().getInstrumentModel().getAlias())));
    }
    switch(containers.size()) {
        case 0:
            SequencerPartitionContainer newContainer = containerModel.getPlatformType().createContainer();
            newContainer.setModel(containerModel);
            newContainer.setCreator(user);
            newContainer.setIdentificationBarcode(containerSerialNumber);
            newContainer.setPartitionLimit(laneCount);
            newContainer.setPartitions(IntStream.range(0, laneCount).mapToObj(i -> new PartitionImpl(newContainer, i + 1)).collect(Collectors.toList()));
            updatePartitionContents(getLaneContents, newContainer);
            RunPosition newRunPos = new RunPosition();
            newRunPos.setRun(target);
            newRunPos.setContainer(newContainer);
            newRunPos.setPosition(position);
            target.getRunPositions().clear();
            target.getRunPositions().add(newRunPos);
            return true;
        case 1:
            SequencerPartitionContainer container = containers.iterator().next();
            boolean isMutated = false;
            if (container.getPartitions().size() != laneCount) {
                throw new IllegalArgumentException(String.format("The container %s has %d partitions, but %d were detected by the scanner.", containerSerialNumber, container.getPartitions().size(), laneCount));
            }
            // only update container model from fallback to non-fallback
            if (container.getModel().isFallback() && !containerModel.isFallback() && container.getModel().getId() != containerModel.getId()) {
                container.setModel(containerModel);
                isMutated = true;
            }
            if (target.getSequencerPartitionContainers().stream().noneMatch(c -> c.getId() == container.getId())) {
                target.addSequencerPartitionContainer(container, position);
                updatePartitionContents(getLaneContents, container);
                isMutated = true;
            }
            return isMutated;
        default:
            throw new IllegalArgumentException("Multiple containers with same identifier: " + containerSerialNumber);
    }
}

Example 2 with InstrumentPosition

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

the class Dtos method to.

public static InstrumentPosition to(@Nonnull InstrumentPositionDto from) {
    InstrumentPosition to = new InstrumentPosition();
    setLong(to::setId, from.getId(), false);
    setString(to::setAlias, from.getAlias());
    return to;
}

Example 3 with InstrumentPosition

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

the class DefaultInstrumentModelService method loadChildEntities.

@Override
protected void loadChildEntities(InstrumentModel object) throws IOException {
    Set<InstrumentPosition> positions = new HashSet<>();
    for (InstrumentPosition pos : object.getPositions()) {
        if (pos.isSaved()) {
            positions.add(instrumentModelStore.getPosition(pos.getId()));
        } else {
            positions.add(pos);
        }
    }
    object.getPositions().clear();
    object.getPositions().addAll(positions);
    Set<SequencingContainerModel> models = new HashSet<>();
    for (SequencingContainerModel model : object.getContainerModels()) {
        models.add(containerModelService.get(model.getId()));
    }
    object.getContainerModels().clear();
    object.getContainerModels().addAll(models);
}

Example 4 with InstrumentPosition

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

the class EditServiceRecordController method showPage.

public ModelAndView showPage(ServiceRecord record, ModelMap model) throws JsonProcessingException {
    if (!record.isSaved()) {
        model.put("title", "New Service Record");
    } else {
        model.put("title", "Service Record " + record.getId());
    }
    ObjectMapper mapper = new ObjectMapper();
    model.put("serviceRecord", record);
    model.put("serviceRecordDto", mapper.writeValueAsString(Dtos.asDto(record)));
    ArrayNode positions = mapper.createArrayNode();
    for (InstrumentPosition pos : record.getInstrument().getInstrumentModel().getPositions()) {
        ObjectNode dto = positions.addObject();
        dto.put("id", pos.getId());
        dto.put("alias", pos.getAlias());
    }
    model.put("instrumentPositions", mapper.writeValueAsString(positions));
    return new ModelAndView("/WEB-INF/pages/editServiceRecord.jsp", model);
}

Example 5 with InstrumentPosition

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

the class HibernateInstrumentModelDaoIT method testDeletePosition.

@Test
public void testDeletePosition() throws Exception {
    long id = 3L;
    InstrumentPosition before = (InstrumentPosition) currentSession().get(InstrumentPosition.class, id);
    assertNotNull(before);
    dao.deletePosition(before);
    clearSession();
    InstrumentPosition after = (InstrumentPosition) currentSession().get(InstrumentPosition.class, id);
    assertNull(after);
}