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

Example 6 with DAOException

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

the class AccountDAO method getAccountsCount.

/**
     * Retrieves maximum number of distinct accounts available and, if specified, whose firstName, lastName and email
     * fields match the filter token. This is intended to be used for paging.
     *
     * @param filter optional token used to match against the firstName, lastName and email fields of accounts
     * @return number of accounts that match the optional filter.
     * @throws DAOException on {@link HibernateException} retrieving the number
     */
public long getAccountsCount(String filter) {
    try {
        CriteriaQuery<Long> query = getBuilder().createQuery(Long.class);
        Root<Account> from = query.from(Account.class);
        if (filter != null && !filter.isEmpty()) {
            filter = filter.toLowerCase();
            query.where(getBuilder().or(getBuilder().like(getBuilder().lower(from.get("firstName")), "%" + filter + "%"), getBuilder().like(getBuilder().lower(from.get("lastName")), "%" + filter + "%"), getBuilder().like(getBuilder().lower(from.get("email")), "%" + filter + "%")));
        }
        query.select(getBuilder().countDistinct(from.get("id")));
        return currentSession().createQuery(query).uniqueResult();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 7 with DAOException

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

the class SequenceFeatureDAO method getEntrySequenceFeatures.

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

Example 8 with DAOException

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

the class TraceSequenceDAO method save.

/**
     * Save the given {@link TraceSequence} object in the database.
     *
     * @param traceSequence object to save
     * @return Saved TraceSequence object.
     * @throws DAOException on hibernate exception saving
     */
public TraceSequence save(TraceSequence traceSequence) {
    TraceSequenceAlignment traceSequenceAlignment = traceSequence.getTraceSequenceAlignment();
    Session session = currentSession();
    try {
        session.saveOrUpdate(traceSequenceAlignment);
        traceSequence.setTraceSequenceAlignment(traceSequenceAlignment);
        session.saveOrUpdate(traceSequence);
        return traceSequence;
    } catch (HibernateException e) {
        throw new DAOException("Error saving trace sequence", e);
    }
}

Example 9 with DAOException

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

the class TraceSequenceDAO method getByEntry.

/**
     * Retrieve all {@link TraceSequence} objects associated with the given {@link Entry} object
     * using the paging parameters, ordered by creation time in ascending order
     *
     * @param entry entry whose trace sequences are being retrieved
     * @param start start for traces retrieval
     * @param limit maximum number of trace records to retrieve
     * @return List of TraceSequence objects.
     * @throws DAOException
     */
public List<TraceSequence> getByEntry(Entry entry, int start, int limit) {
    try {
        CriteriaQuery<TraceSequence> query = getBuilder().createQuery(TraceSequence.class);
        Root<TraceSequence> from = query.from(TraceSequence.class);
        query.where(getBuilder().equal(from.get("entry"), entry));
        query.orderBy(getBuilder().asc(from.get("creationTime")));
        return currentSession().createQuery(query).setMaxResults(limit).setFirstResult(start).list();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 10 with DAOException

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

the class TraceSequenceDAO method getByFileId.

/**
     * Retrieve the {@link TraceSequence} object by its fileId.
     *
     * @param fileId unique file identifier
     * @return {@link Optional} container that contains the trace sequence if found.
     * @throws DAOException
     */
public Optional<TraceSequence> getByFileId(String fileId) {
    try {
        CriteriaQuery<TraceSequence> query = getBuilder().createQuery(TraceSequence.class);
        Root<TraceSequence> from = query.from(TraceSequence.class);
        query.where(getBuilder().equal(from.get("fileId"), fileId));
        return currentSession().createQuery(query).uniqueResultOptional();
    } catch (HibernateException e) {
        throw new DAOException("Failed to retrieve entry by fileId: " + fileId, e);
    }
}