Examples with DAOException org.jbei.ice.storage.DAOException used on opensource projects

Example 11 with DAOException

use of org.jbei.ice.storage.DAOException in project ice by JBEI.

the class TraceSequenceDAO method getCountByEntry.

/**
     * Get number of trace sequences available for specified entry
     *
     * @param entry entry whose entry count is being retrieved
     * @return number of traces available for the specified entry
     */
public int getCountByEntry(Entry entry) {
    try {
        CriteriaQuery<Long> query = getBuilder().createQuery(Long.class);
        Root<TraceSequence> from = query.from(TraceSequence.class);
        query.select(getBuilder().countDistinct(from.get("id"))).where(getBuilder().equal(from.get("entry"), entry));
        return currentSession().createQuery(query).uniqueResult().intValue();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 12 with DAOException

use of org.jbei.ice.storage.DAOException in project ice by JBEI.

the class StorageDAO method retrieveStorageByIndex.

/**
     * Retrieve a {@link Storage} object by its index and {@link SampleType} fields.
     *
     * @param index index value
     * @param type  storage type
     * @return List of Storage objects
     */
public List<Storage> retrieveStorageByIndex(String index, SampleType type) {
    try {
        CriteriaQuery<Storage> query = getBuilder().createQuery(Storage.class);
        Root<Storage> from = query.from(Storage.class);
        query.where(getBuilder().equal(from.get("index"), index), getBuilder().equal(from.get("storageType"), type));
        return currentSession().createQuery(query).list();
    } catch (Exception e) {
        String msg = "Could not get Storage by index: " + index + " " + e.toString();
        Logger.error(msg, e);
        throw new DAOException(msg);
    }
}

Example 13 with DAOException

use of org.jbei.ice.storage.DAOException in project ice by JBEI.

the class SequenceFeatureDAO method getEntryIdsByFeature.

public List<Long> getEntryIdsByFeature(Feature feature) {
    try {
        CriteriaQuery<Long> query = getBuilder().createQuery(Long.class);
        Root<SequenceFeature> from = query.from(SequenceFeature.class);
        Join<SequenceFeature, Sequence> sequence = from.join("sequence");
        Join<Sequence, Entry> entry = sequence.join("entry");
        query.select(entry.get("id")).where(getBuilder().equal(from.get("feature"), feature));
        return currentSession().createQuery(query).list();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 14 with DAOException

use of org.jbei.ice.storage.DAOException in project ice by JBEI.

the class ShotgunSequenceDAO method delete.

public void delete(Path dir, ShotgunSequence shotgunSequence) {
    try {
        super.delete(shotgunSequence);
        Files.deleteIfExists(Paths.get(dir.toString(), shotgunSequence.getFileId()));
    } catch (IOException e) {
        throw new DAOException("Failed to delete Shotgun Sequence file!", e);
    }
}

Example 15 with DAOException

use of org.jbei.ice.storage.DAOException in project ice by JBEI.

the class RequestRetriever method removeSampleFromCart.

public SampleRequest removeSampleFromCart(String userId, long requestId) {
    try {
        Request request = dao.get(requestId);
        if (request == null)
            return null;
        if (!request.getAccount().getEmail().equalsIgnoreCase(userId))
            return null;
        Logger.info(userId + ": Removing sample from cart for entry " + request.getEntry().getId());
        dao.delete(request);
        return request.toDataTransferObject();
    } catch (DAOException de) {
        Logger.error(de);
        return null;
    }
}