EDIT

import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;

    @Override

    public List<Taxon> getRootTaxa(Reference sec) {

        return getRootTaxa(sec, CdmFetch.FETCH_CHILDTAXA(), true, false);

    }

    @Override

    public List<Taxon> getRootTaxa(Rank rank, Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications, List<String> propertyPaths) {

        checkNotInPriorView("TaxonDaoHibernateImpl.getRootTaxa(Rank rank, Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications)");

        if (onlyWithChildren == null){

            onlyWithChildren = true;

        }

        if (withMisapplications == null){

            withMisapplications = true;

        }

        if (cdmFetch == null){

            cdmFetch = CdmFetch.NO_FETCH();

        }

        Criteria crit = getSession().createCriteria(Taxon.class);

        crit.setFetchMode("name", FetchMode.JOIN);

        crit.createAlias("name", "name");

        if (rank != null) {

            crit.add(Restrictions.eq("name.rank", rank));

        }else{

            crit.add(Restrictions.isNull("taxonomicParentCache"));

        }

        if (sec != null){

            crit.add(Restrictions.eq("sec", sec) );

        }

        if (! cdmFetch.includes(CdmFetch.FETCH_CHILDTAXA())){

            logger.info("Not fetching child taxa");

            //TODO overwrite LAZY (SELECT) does not work (bug in hibernate?)

            crit.setFetchMode("relationsToThisTaxon.fromTaxon", FetchMode.LAZY);

        }

        List<Taxon> results = new ArrayList<Taxon>();

        @SuppressWarnings("unchecked")

        List<Taxon> taxa = crit.list();

        for(Taxon taxon : taxa){

            //childTaxa

            //TODO create restriction instead

            // (a) not using cache fields

            /*Hibernate.initialize(taxon.getRelationsFromThisTaxon());

            if (onlyWithChildren == false || taxon.getRelationsFromThisTaxon().size() > 0){

                if (withMisapplications == true || ! taxon.isMisappliedName()){

                    defaultBeanInitializer.initialize(taxon, propertyPaths);

                    results.add(taxon);

                }

            }*/

            // (b) using cache fields

            if (onlyWithChildren == false || taxon.hasTaxonomicChildren()){

                if (withMisapplications == true || ! taxon.isMisapplication()){

                    defaultBeanInitializer.initialize(taxon, propertyPaths);

                    results.add(taxon);

                }

            }

        }

        return results;

    }

    @Override

    public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications) {

        return getRootTaxa(null, sec, cdmFetch, onlyWithChildren, withMisapplications, null);

    }

                // decrease children count of taxonomic parent by one

                if (relationFromThisTaxon.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())) {

                    Taxon toTaxon = relationFromThisTaxon.getToTaxon(); // parent

                    if (toTaxon != null) {

                        toTaxon.setTaxonomicChildrenCount(toTaxon.getTaxonomicChildrenCount() - 1);

                    }

                }