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

Example 16 with DAOException

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

the class EntryDAO method generateNextStrainNameForEntry.

// todo : look at this again (can restrict to strain type and also order by id)
public synchronized void generateNextStrainNameForEntry(Entry entry, String prefix) {
    try {
        CriteriaQuery<Entry> query = getBuilder().createQuery(Entry.class);
        Root<Entry> from = query.from(Entry.class);
        query.where(getBuilder().like(getBuilder().lower(from.get("name")), prefix.toLowerCase() + "1%")).orderBy(getBuilder().desc(from.get("name")));
        Entry result = currentSession().createQuery(query).setMaxResults(1).uniqueResult();
        int next = 0;
        if (result != null) {
            String name = result.getName();
            next = Integer.decode(name.split(prefix)[1]);
        }
        next += 1;
        String nextName = prefix + next;
        entry.setName(nextName);
        currentSession().update(entry);
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 17 with DAOException

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

the class EntryDAO method getMatchingPlasmidField.

public List<String> getMatchingPlasmidField(AutoCompleteField field, String token, int limit) {
    String fieldString;
    switch(field) {
        case ORIGIN_OF_REPLICATION:
        default:
            fieldString = "originOfReplication";
            break;
        case PROMOTERS:
            fieldString = "promoters";
            break;
        case REPLICATES_IN:
            fieldString = "replicatesIn";
            break;
    }
    try {
        CriteriaQuery<String> query = getBuilder().createQuery(String.class);
        Root<Plasmid> from = query.from(Plasmid.class);
        query.select(from.get(fieldString)).where(getBuilder().like(getBuilder().lower(from.get(fieldString)), token.toLowerCase() + "%"));
        return currentSession().createQuery(query).setMaxResults(limit).list();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 18 with DAOException

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

the class EntryDAO method retrieveUserEntries.

/**
     * Retrieves the entries for the specified owner, that the requester has read access to
     *
     * @param requester       account for user making request
     * @param owner           user id of entries' owner
     * @param requesterGroups groups that the requester is a member of. Used to check access permissions
     * @param sortField       field for sort
     * @param asc             sort order
     * @param start           index to start retrieving records from
     * @param limit           maximum number of entries to retrieve
     * @return list of entries matching specified criteria
     * @throws DAOException on HibernateException
     */
public List<Entry> retrieveUserEntries(Account requester, String owner, Set<Group> requesterGroups, ColumnField sortField, boolean asc, int start, int limit, String filter) {
    try {
        CriteriaQuery<Entry> query = getBuilder().createQuery(Entry.class);
        Root<Permission> from = query.from(Permission.class);
        Join<Permission, Entry> join = from.join("entry");
        query.select(join).distinct(true);
        ArrayList<Predicate> predicates = new ArrayList<>();
        predicates.add(getBuilder().or(from.get("group").in(requesterGroups), getBuilder().equal(from.get("account"), requester)));
        predicates.add(getBuilder().equal(join.get("visibility"), Visibility.OK.getValue()));
        predicates.add(getBuilder().equal(join.get("ownerEmail"), owner));
        if (filter != null && !filter.trim().isEmpty()) {
            filter = filter.toLowerCase();
            predicates.add(getBuilder().or(getBuilder().like(getBuilder().lower(join.get("name")), "%" + filter + "%"), getBuilder().like(getBuilder().lower(join.get("alias")), "%" + filter + "%"), getBuilder().like(getBuilder().lower(join.get("partNumber")), "%" + filter + "%")));
        }
        query.where(predicates.toArray(new Predicate[predicates.size()]));
        String fieldName = sortField == ColumnField.CREATED ? "id" : columnFieldToString(sortField);
        query.orderBy(asc ? getBuilder().asc(join.get(fieldName)) : getBuilder().desc(join.get(fieldName)));
        return currentSession().createQuery(query).setMaxResults(limit).setFirstResult(start).list();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}

Example 19 with DAOException

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

the class BulkUploadDAO method setEntryStatus.

public int setEntryStatus(BulkUpload upload, Visibility status) {
    try {
        List<Long> entryIds = getEntryIds(upload);
        if (entryIds.isEmpty())
            return 0;
        // include linked entries
        CriteriaQuery<Long> query = getBuilder().createQuery(Long.class);
        Root<Entry> from = query.from(Entry.class);
        Join<Entry, Entry> linked = from.join("linkedEntries");
        query.select(linked.get("id")).where(from.get("id").in(entryIds));
        List<Long> linkedIds = currentSession().createQuery(query).list();
        entryIds.addAll(linkedIds);
        CriteriaUpdate<Entry> update = getBuilder().createCriteriaUpdate(Entry.class);
        Root<Entry> root = update.from(Entry.class);
        update.set(root.get("visibility"), status.getValue());
        update.where(root.get("id").in(entryIds));
        return currentSession().createQuery(update).executeUpdate();
    } catch (HibernateException e) {
        Logger.error(e);
        throw new DAOException(e);
    }
}

Example 20 with DAOException

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

the class EntryDAO method retrieveOwnerEntries.

/**
     * Retrieves entries owned by account with specified email and with visibility of "pending" or "ok"
     *
     * @param ownerEmail email for account whose entries are to be retrieved
     * @param sort       field to sort results on
     * @param asc        sort order
     * @param start      start of retrieve
     * @param limit      maximum number of records to retrieve from
     * @param filter     filter for entries
     * @return list of matching entries
     * @throws DAOException on Hibernate Exception
     */
public List<Entry> retrieveOwnerEntries(String ownerEmail, ColumnField sort, boolean asc, int start, int limit, String filter) {
    try {
        CriteriaQuery<Entry> query = getBuilder().createQuery(Entry.class);
        Root<Entry> from = query.from(Entry.class);
        ArrayList<Predicate> predicates = new ArrayList<>();
        predicates.add(getBuilder().equal(from.get("ownerEmail"), ownerEmail));
        predicates.add(getBuilder().or(getBuilder().equal(from.get("visibility"), Visibility.OK.getValue()), getBuilder().equal(from.get("visibility"), Visibility.PENDING.getValue())));
        checkAddFilter(predicates, from, filter);
        query.where(predicates.toArray(new Predicate[predicates.size()]));
        String fieldName = columnFieldToString(sort);
        query.orderBy(asc ? getBuilder().asc(from.get(fieldName)) : getBuilder().desc(from.get(fieldName)));
        return currentSession().createQuery(query).setMaxResults(limit).setFirstResult(start).list();
    } catch (HibernateException he) {
        Logger.error(he);
        throw new DAOException(he);
    }
}