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

Example 31 with DAOException

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

the class SampleDAO method getSampleCount.

public int getSampleCount(Entry entry) {
    try {
        CriteriaQuery<Long> query = getBuilder().createQuery(Long.class);
        Root<Sample> from = query.from(Sample.class);
        query.select(getBuilder().countDistinct(from.get("id")));
        query.where(getBuilder().equal(from.get("entry"), entry));
        return currentSession().createQuery(query).uniqueResult().intValue();
    } catch (HibernateException e) {
        Logger.error(e);
        throw new DAOException(e);
    }
}

Example 32 with DAOException

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

the class SequenceDAO method getByEntry.

/**
     * Retrieve the {@link Sequence} object associated with the given {@link Entry} object.
     *
     * @param entry entry associated with sequence
     * @return Sequence object.
     */
public Sequence getByEntry(Entry entry) {
    try {
        CriteriaQuery<Sequence> query = getBuilder().createQuery(Sequence.class);
        Root<Sequence> from = query.from(Sequence.class);
        query.where(getBuilder().equal(from.get("entry"), entry));
        Optional<Sequence> sequence = currentSession().createQuery(query).uniqueResultOptional();
        if (!sequence.isPresent())
            return null;
        return normalizeAnnotationLocations(sequence.get());
    } catch (HibernateException e) {
        Logger.error(e);
        throw new DAOException("Failed to retrieve sequence by entry: " + entry.getId(), e);
    }
}

Example 33 with DAOException

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

the class SequenceDAO method getSequenceFilename.

public String getSequenceFilename(Entry entry) {
    try {
        CriteriaQuery<String> query = getBuilder().createQuery(String.class);
        Root<Sequence> from = query.from(Sequence.class);
        query.select(from.get("fileName")).where(getBuilder().equal(from.get("entry"), entry));
        return currentSession().createQuery(query).getSingleResult();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 34 with DAOException

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

the class SequenceDAO method getFeatureBySequence.

/**
     * Retrieve the {@link Feature} object with the given DNA sequence string.
     *
     * @param featureDnaSequence dna sequence of feature
     * @return Feature object.
     * @throws DAOException
     */
private Feature getFeatureBySequence(String featureDnaSequence) {
    featureDnaSequence = featureDnaSequence.toLowerCase();
    try {
        String hash = SequenceUtils.calculateSequenceHash(featureDnaSequence);
        CriteriaQuery<Feature> query = getBuilder().createQuery(Feature.class);
        Root<Feature> from = query.from(Feature.class);
        query.where(getBuilder().equal(from.get("hash"), hash));
        Optional<Feature> result = currentSession().createQuery(query).uniqueResultOptional();
        if (result.isPresent())
            return result.get();
        String reverseComplement = SequenceUtils.reverseComplement(featureDnaSequence);
        String sequenceHash = SequenceUtils.calculateSequenceHash(reverseComplement);
        query.getRestriction().getExpressions().clear();
        query.where(getBuilder().equal(from.get("hash"), sequenceHash));
        return currentSession().createQuery(query).uniqueResult();
    } catch (HibernateException | UtilityException e) {
        Logger.error(e);
        throw new DAOException("Failed to get Feature by sequence!", e);
    }
}

Example 35 with DAOException

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

the class RequestDAO method getSampleRequestInCart.

public Request getSampleRequestInCart(Account account, Entry entry) {
    try {
        CriteriaQuery<Request> query = getBuilder().createQuery(Request.class);
        Root<Request> from = query.from(Request.class);
        query.where(getBuilder().and(getBuilder().equal(from.get("status"), SampleRequestStatus.IN_CART), getBuilder().equal(from.get("entry"), entry), getBuilder().equal(from.get("account"), account)));
        List<Request> list = currentSession().createQuery(query).list();
        if (list.isEmpty())
            return null;
        HashSet<Request> inCart = new HashSet<>(list);
        if (inCart.size() > 1) {
            Logger.error("Multiple sample requests found for entry " + entry.getId());
        }
        return (Request) inCart.toArray()[0];
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}