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

Example 36 with DAOException

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

the class SequenceDAO method deleteSequence.

/**
     * Delete the given {@link Sequence} object in the database.
     *
     * @param sequence          sequence to delete
     * @param pigeonImageFolder path of the image folder where the pigeon images are cached
     */
public void deleteSequence(Sequence sequence, String pigeonImageFolder) {
    String sequenceHash = sequence.getFwdHash();
    try {
        sequence.setEntry(null);
        sequence.getSequenceFeatures();
        super.delete(sequence);
        currentSession().flush();
        Files.deleteIfExists(Paths.get(pigeonImageFolder, sequenceHash + ".png"));
    } catch (IOException e) {
        Logger.warn(e.getMessage());
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 37 with DAOException

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

the class SequenceDAO method hasSequence.

public boolean hasSequence(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)).distinct(true);
        return currentSession().createQuery(query).setMaxResults(1).uniqueResult() > 0;
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 38 with DAOException

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

the class RemoteClientModelDAO method getClientCount.

/**
     * Retrieves number of clients for the specified group
     *
     * @param group group whose clients are of interest
     * @return number of clients for group
     * @throws DAOException
     */
public int getClientCount(Group group) {
    try {
        CriteriaQuery<Long> query = getBuilder().createQuery(Long.class);
        Root<RemoteClientModel> from = query.from(RemoteClientModel.class);
        Join<RemoteClientModel, Group> groups = from.join("groups");
        query.select(getBuilder().countDistinct(from.get("id")));
        query.where(getBuilder().equal(groups.get("id"), group.getId()), getBuilder().isNotNull(from.get("email")));
        return currentSession().createQuery(query).uniqueResult().intValue();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 39 with DAOException

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

the class SelectionMarkerDAO method getMatchingSelectionMarkers.

public List<String> getMatchingSelectionMarkers(String token, int limit) {
    try {
        CriteriaQuery<String> query = getBuilder().createQuery(String.class);
        Root<SelectionMarker> from = query.from(SelectionMarker.class);
        query.where(getBuilder().like(getBuilder().lower(from.get("name")), "%" + token.toLowerCase() + "%"));
        query.select(from.get("name")).distinct(true);
        return currentSession().createQuery(query).setMaxResults(limit).list();
    //            return currentSession().createCriteria(SelectionMarker.class)
    //                    .add(Restrictions.ilike("name", token, MatchMode.ANYWHERE))
    //                    .setMaxResults(limit)
    //                    .setProjection(Projections.distinct(Projections.property("name")))
    //                    .list();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 40 with DAOException

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

the class SampleDAO method getSamplesByStorage.

/**
     * Retrieve {@link Sample} objects associated with the given {@link Storage} object.
     *
     * @param storage
     * @return ArrayList of Sample objects.
     * @throws DAOException
     */
public List<Sample> getSamplesByStorage(Storage storage) {
    try {
        CriteriaQuery<Sample> query = getBuilder().createQuery(Sample.class);
        Root<Sample> from = query.from(Sample.class);
        query.where(getBuilder().equal(from.get("storage"), storage));
        return currentSession().createQuery(query).list();
    } catch (HibernateException e) {
        Logger.error(e);
        throw new DAOException("Failed to retrieve sample by storage id: " + storage.getId(), e);
    }
}