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

Example 56 with DAOException

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

the class EntryDAO method getAllEntryCount.

/**
     * @return number of entries that have visibility of "OK"
     */
public long getAllEntryCount(String filter) {
    try {
        CriteriaQuery<Long> query = getBuilder().createQuery(Long.class);
        Root<Entry> from = query.from(Entry.class);
        query.select(getBuilder().countDistinct(from.get("id")));
        ArrayList<Predicate> predicates = new ArrayList<>();
        checkAddFilter(predicates, from, filter);
        predicates.add(getBuilder().or(getBuilder().equal(from.get("visibility"), Visibility.OK.getValue()), getBuilder().equal(from.get("visibility"), Visibility.PENDING.getValue())));
        query.where(predicates.toArray(new Predicate[predicates.size()]));
        return currentSession().createQuery(query).uniqueResult();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 57 with DAOException

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

the class ExperimentDAO method getByUrl.

public Experiment getByUrl(String url) throws DAOException {
    try {
        CriteriaQuery<Experiment> query = getBuilder().createQuery(Experiment.class);
        Root<Experiment> from = query.from(Experiment.class);
        query.where(getBuilder().equal(from.get("url"), url));
        return currentSession().createQuery(query).uniqueResult();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 58 with DAOException

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

the class EntryDAO method getRecordTypes.

public List<String> getRecordTypes(List<Long> list) {
    try {
        CriteriaQuery<String> query = getBuilder().createQuery(String.class);
        Root<Entry> from = query.from(Entry.class);
        query.select(from.get("recordType")).where(from.get("id").in(list));
        return currentSession().createQuery(query).list();
    } catch (HibernateException e) {
        Logger.error(e);
        throw new DAOException(e);
    }
}

Example 59 with DAOException

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

the class EntryDAO method getVisibleEntryIds.

public List<Long> getVisibleEntryIds(boolean admin, Group publicGroup) {
    try {
        if (admin) {
            CriteriaQuery<Long> query = getBuilder().createQuery(Long.class);
            Root<Entry> from = query.from(Entry.class);
            query.select(getBuilder().countDistinct(from.get("id"))).where(getBuilder().or(getBuilder().equal(from.get("visibility"), Visibility.OK.getValue()), getBuilder().equal(from.get("visibility"), Visibility.PENDING.getValue())));
            return currentSession().createQuery(query).list();
        }
        // non admins, check permissions
        CriteriaQuery<Long> query = getBuilder().createQuery(Long.class);
        Root<Permission> from = query.from(Permission.class);
        Join<Permission, Entry> permissionEntry = from.join("entry");
        query.select(permissionEntry.get("id")).where(//                    getBuilder().equal(from.get("entry"), permissionEntry)
        getBuilder().equal(from.get("group"), publicGroup), getBuilder().equal(permissionEntry.get("visibility"), Visibility.OK.getValue()));
        return currentSession().createQuery(query).list();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 60 with DAOException

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

the class EntryDAO method retrieveVisibleEntries.

/**
     * Retrieve {@link Entry Entries} visible to everyone.
     *
     * @return Number of visible entries.
     * @throws DAOException on hibernate exception
     */
public List<Entry> retrieveVisibleEntries(Account account, Set<Group> groups, ColumnField sortField, boolean asc, int start, int count, String filter) {
    try {
        CriteriaQuery<Entry> query = getBuilder().createQuery(Entry.class).distinct(true);
        Root<Entry> from = query.from(Entry.class);
        Join<Entry, Permission> entryPermission = from.join("permissions");
        ArrayList<Predicate> predicates = new ArrayList<>();
        predicates.add(getBuilder().equal(from.get("visibility"), Visibility.OK.getValue()));
        String fieldName = columnFieldToString(sortField);
        if (account != null) {
            predicates.add(getBuilder().or(getBuilder().equal(entryPermission.get("account"), account), entryPermission.get("group").in(groups)));
        } else if (!groups.isEmpty()) {
            predicates.add(entryPermission.get("group").in(groups));
        }
        // check filter
        if (filter != null && !filter.trim().isEmpty()) {
            filter = filter.toLowerCase();
            predicates.add(getBuilder().or(getBuilder().like(getBuilder().lower(from.get("name")), "%" + filter + "%"), getBuilder().like(getBuilder().lower(from.get("alias")), "%" + filter + "%"), getBuilder().like(getBuilder().lower(from.get("partNumber")), "%" + filter + "%")));
        }
        query.where(predicates.toArray(new Predicate[predicates.size()]));
        query.orderBy(asc ? getBuilder().asc(from.get(fieldName)) : getBuilder().desc(from.get(fieldName)));
        return currentSession().createQuery(query).setMaxResults(count).setFirstResult(start).list();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}