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

Example 16 with Library

use of uk.ac.bbsrc.tgac.miso.core.data.Library 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 17 with Library

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

the class NotificationManager method makeLibraryAliquotTable.

private static ContainerTag makeLibraryAliquotTable(Collection<TransferLibraryAliquot> transferLibraryAliquots) {
    ContainerTag headerRow = tr(makeTh("Alias"), makeTh("Barcode"), makeTh("Location"), makeTh("Platform"), makeTh("Type"), makeTh("i7 Index Name"), makeTh("i7 Index"), makeTh("i5 Index Name"), makeTh("i5 Index"), makeTh("Targeted Sequencing"));
    List<ContainerTag> rows = new ArrayList<>();
    List<TransferLibraryAliquot> sorted = sortByAlias(transferLibraryAliquots);
    for (TransferLibraryAliquot transferLibraryAliquot : sorted) {
        LibraryAliquot libraryAliquot = transferLibraryAliquot.getItem();
        Library library = libraryAliquot.getLibrary();
        List<DomContent> cells = new ArrayList<>();
        cells.add(makeTd(libraryAliquot.getAlias()));
        cells.add(makeTd(libraryAliquot.getIdentificationBarcode()));
        cells.add(makeTd(makeLocationLabel(transferLibraryAliquot)));
        cells.add(makeTd(library.getPlatformType().getKey()));
        cells.add(makeTd(library.getLibraryType().getDescription()));
        cells.add(makeTd(library.getIndex1() == null ? null : library.getIndex1().getName()));
        cells.add(makeTd(library.getIndex1() == null ? null : library.getIndex1().getSequence()));
        cells.add(makeTd(library.getIndex2() == null ? null : library.getIndex2().getName()));
        cells.add(makeTd(library.getIndex2() == null ? null : library.getIndex2().getSequence()));
        rows.add(tr().with(cells));
    }
    return makeTable(headerRow, rows);
}

Example 18 with Library

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

the class HibernateLibraryDao method listBySampleId.

@Override
public List<Library> listBySampleId(long sampleId) throws IOException {
    Criteria criteria = currentSession().createCriteria(LibraryImpl.class);
    criteria.add(Restrictions.eq("sample.id", sampleId));
    @SuppressWarnings("unchecked") List<Library> records = criteria.list();
    return records;
}

Example 19 with Library

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

the class HibernateLibraryDao method listAll.

@Override
public List<Library> listAll() throws IOException {
    Criteria criteria = currentSession().createCriteria(LibraryImpl.class);
    @SuppressWarnings("unchecked") List<Library> records = criteria.list();
    return records;
}

Example 20 with Library

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

the class HibernateLibraryDao method listByProjectId.

@Override
public List<Library> listByProjectId(long projectId) throws IOException {
    Criteria criteria = currentSession().createCriteria(LibraryImpl.class);
    criteria.createAlias("sample.project", "project");
    criteria.add(Restrictions.eq("project.id", projectId));
    @SuppressWarnings("unchecked") List<Library> records = criteria.list();
    return records;
}