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

Example 66 with DAOException

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

the class FeatureDAO method getFeaturesGroupBy.

public Map<String, List<Feature>> getFeaturesGroupBy(int offset, int size) {
    Map<String, List<Feature>> results = new HashMap<>();
    try {
        CriteriaQuery<String> query = getBuilder().createQuery(String.class);
        Root<Feature> from = query.from(Feature.class);
        query.select(from.get("name")).distinct(true);
        query.where(getBuilder().isNotNull(from.get("name")), getBuilder().notEqual(from.get("name"), ""));
        query.orderBy(getBuilder().asc(from.get("name")));
        List<String> names = currentSession().createQuery(query).setFirstResult(offset).setMaxResults(size).list();
        for (String name : names) {
            CriteriaQuery<Feature> featureQuery = getBuilder().createQuery(Feature.class);
            Root<Feature> root = featureQuery.from(Feature.class);
            featureQuery.where(getBuilder().equal(getBuilder().lower(root.get("name")), name.toLowerCase()));
            List<Feature> result = currentSession().createQuery(featureQuery).list();
            results.put(name, result);
        }
        return results;
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 67 with DAOException

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

the class FolderDAO method getFoldersByType.

public List<Folder> getFoldersByType(FolderType type) {
    try {
        CriteriaQuery<Folder> query = getBuilder().createQuery(Folder.class);
        Root<Folder> from = query.from(Folder.class);
        query.where(getBuilder().equal(from.get("type"), type));
        return currentSession().createQuery(query).list();
    } catch (HibernateException e) {
        Logger.error(e);
        throw new DAOException(e);
    }
}

Example 68 with DAOException

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

the class FolderDAO method getCanEditFolders.

/**
     * Retrieves folders that the specified account owns, or has write privileges on based on the permissions
     *
     * @param account       account that is expected to have write privileges on the folders that are returned
     * @param accountGroups groups that account belongs to that is expected to have write privileges
     * @return list of folders that the account or groups that the account belongs to has write privileges on
     * @throws DAOException
     */
public List<Folder> getCanEditFolders(Account account, Set<Group> accountGroups) {
    try {
        CriteriaQuery<Folder> query = getBuilder().createQuery(Folder.class);
        Root<Permission> from = query.from(Permission.class);
        Join<Permission, Folder> folder = from.join("folder");
        // where ((account = account or group in groups) and canWrite)) or is owner
        Predicate predicate = getBuilder().and(getBuilder().or(getBuilder().equal(from.get("account"), account), from.get("group").in(accountGroups)), getBuilder().equal(from.get("canWrite"), true), getBuilder().isNotNull(from.get("folder")));
        query.select(folder).where(predicate);
        return currentSession().createQuery(query).list();
    } catch (HibernateException e) {
        Logger.error(e);
        throw new DAOException(e);
    }
}

Example 69 with DAOException

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

the class ExperimentDAO method getExperimentCount.

public int getExperimentCount(long entryId) throws DAOException {
    try {
        String sql = "SELECT count(*) FROM experiment_entry WHERE entry_id=:id";
        NativeQuery query = currentSession().createNativeQuery(sql);
        query.setParameter("id", entryId);
        Number result = (Number) query.uniqueResult();
        return result.intValue();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 70 with DAOException

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

the class FeatureDAO method getFeatureCount.

public long getFeatureCount(String filter) {
    try {
        CriteriaQuery<Long> query = getBuilder().createQuery(Long.class);
        Root<Feature> from = query.from(Feature.class);
        query.select(getBuilder().countDistinct(from.get("id")));
        if (filter != null && !filter.isEmpty())
            query.where(getBuilder().like(getBuilder().lower(from.get("name")), "%" + filter.toLowerCase() + "%"));
        else
            query.where(getBuilder().isNotNull(from.get("name")), getBuilder().notEqual(from.get("name"), ""));
        return currentSession().createQuery(query).uniqueResult();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}