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

Example 96 with DAOException

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

the class SequenceDAO method getSequence.

/**
     * Enables retrieving sequences in the database without loading everything in memory
     * <p/>
     * Expected usage is
     * <code>
     * long count = getSequenceCount();
     * int offset = 0;
     * while( offset < count ) {
     * Sequence sequence = dao.getSequence(offset);
     * // do something with sequence
     * }
     * </code>
     *
     * @return Sequence at the specified offset
     * @throws DAOException
     */
public Sequence getSequence(int offset) {
    try {
        CriteriaQuery<Sequence> query = getBuilder().createQuery(Sequence.class);
        Root<Sequence> from = query.from(Sequence.class);
        Join<Sequence, Entry> entry = from.join("entry");
        query.where(getBuilder().equal(entry.get("visibility"), Visibility.OK.getValue()));
        return currentSession().createQuery(query).setFirstResult(offset).setMaxResults(1).uniqueResult();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 97 with DAOException

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

the class SequenceDAO method hasOriginalSequence.

/**
     * Determines if the user uploaded a sequence file and associated it with an entry
     *
     * @param entryId unique identifier for entry
     * @return true if there is a sequence file that was originally uploaded by user, false otherwise
     * @throws DAOException
     */
public boolean hasOriginalSequence(long entryId) {
    try {
        CriteriaQuery<Long> query = getBuilder().createQuery(Long.class);
        Root<Sequence> from = query.from(Sequence.class);
        Join<Sequence, Entry> entry = from.join("entry");
        query.select(getBuilder().countDistinct(from.get("id"))).where(getBuilder().equal(entry.get("id"), entryId), getBuilder().notEqual(from.get("sequenceUser"), ""), getBuilder().isNotNull(from.get("sequenceUser")));
        return currentSession().createQuery(query).uniqueResult() > 0;
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 98 with DAOException

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

the class RequestRetriever method placeSampleInCart.

/**
     * Creates a new sample request for the specified user and specified entry.
     * The default status is "IN CART"
     */
public boolean placeSampleInCart(String userId, SampleRequest sampleRequest) {
    long partId = sampleRequest.getPartData().getId();
    Entry entry = entryDAO.get(sampleRequest.getPartData().getId());
    if (entry == null)
        throw new IllegalArgumentException("Cannot find entry with id: " + partId);
    Account account = DAOFactory.getAccountDAO().getByEmail(userId);
    // check if sample is already in cart with status of "IN CART"
    try {
        List<Request> requests = dao.getSampleRequestByStatus(account, entry, SampleRequestStatus.IN_CART);
        if (requests != null && !requests.isEmpty())
            return true;
        Request request = new Request();
        request.setAccount(account);
        request.setGrowthTemperature(sampleRequest.getGrowthTemperature());
        request.setEntry(entry);
        if (sampleRequest.getRequestType() == null)
            sampleRequest.setRequestType(SampleRequestType.LIQUID_CULTURE);
        request.setType(sampleRequest.getRequestType());
        request.setRequested(new Date(System.currentTimeMillis()));
        request.setUpdated(request.getRequested());
        request.setPlateDescription(sampleRequest.getPlateDescription());
        return dao.create(request) != null;
    } catch (DAOException e) {
        Logger.error(e);
        return false;
    }
}

Example 99 with DAOException

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

the class AuditDAO method getAuditsForEntry.

public List<Audit> getAuditsForEntry(Entry entry, int limit, int offset, boolean asc, String sort) {
    try {
        if (sort == null)
            sort = "id";
        CriteriaQuery<Audit> query = getBuilder().createQuery(Audit.class);
        Root<Audit> from = query.from(Audit.class);
        query.where(getBuilder().equal(from.get("entry"), entry));
        query.orderBy(asc ? getBuilder().asc(from.get(sort)) : getBuilder().desc(from.get(sort)));
        return currentSession().createQuery(query).setFirstResult(offset).setMaxResults(limit).list();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 100 with DAOException

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

the class AuditDAO method deleteAll.

public int deleteAll(Entry entry) {
    try {
        CriteriaDelete<Audit> query = getBuilder().createCriteriaDelete(Audit.class);
        Root<Audit> from = query.from(Audit.class);
        query.where(getBuilder().equal(from.get("entry"), entry));
        return currentSession().createQuery(query).executeUpdate();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}