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/**
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*
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*/
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package eu.etaxonomy.cdm.persistence.dao.hibernate.taxon;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.UUID;
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import org.hibernate.query.Query;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Repository;
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import org.springframework.util.StringUtils;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.filter.LogicFilter;
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import eu.etaxonomy.cdm.filter.LogicFilter.Op;
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import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.persistence.dao.hibernate.common.CdmEntityDaoBase;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeFilterDao;
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import eu.etaxonomy.cdm.persistence.dao.term.IDefinedTermDao;
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/**
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* DAO to retrieve taxon node uuids according to a {@link TaxonNodeFilter}.
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*
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* @author a.mueller
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*/
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@Repository
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public class TaxonNodeFilterDaoHibernateImpl extends CdmEntityDaoBase<TaxonNode> implements ITaxonNodeFilterDao {
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private static final String DESCRIPTION_ELEMENTS = "descriptionElements";
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private static final String FEATURE_UUID = "9fc9d10c-ba50-49ee-b174-ce83fc3f80c6";
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private static final String HQL_TRUE = " 1 "; //maybe we can/should use 'true' instead, needs to be checked for all DB types
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private static final String HQL_FALSE = " 0 "; //maybe we can/should use 'false' instead, needs to be checked for all DB types
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@Autowired
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private ITaxonNodeDao taxonNodeDao;
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@Autowired
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private IDefinedTermDao termDao;
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public TaxonNodeFilterDaoHibernateImpl() {
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super(TaxonNode.class);
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}
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@Override
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public long count(TaxonNodeFilter filter){
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String queryStr = query(filter, "count(*) as n ");
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Query<Long> query = getSession().createQuery(queryStr, Long.class);
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long result = query.uniqueResult();
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return result;
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}
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@Override
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public List<UUID> listUuids(TaxonNodeFilter filter){
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String queryStr = query(filter, "tn.uuid");
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Query<UUID> query = getSession().createQuery(queryStr, UUID.class);
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List<UUID> list = query.list();
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list = deduplicate(list);
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return list;
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}
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@Override
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public List<Integer> idList(TaxonNodeFilter filter){
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String queryStr = query(filter, "tn.id");
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Query<Integer> query = getSession().createQuery(queryStr, Integer.class);
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List<Integer> list = query.list();
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list = deduplicate(list);
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return list;
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}
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//maybe we will later want to have ordering included
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private String query(TaxonNodeFilter filter, String selectPart){
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String select = " SELECT " + selectPart;
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String from = getFrom(filter);
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String subtreeFilter = getSubtreeFilter(filter);
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String taxonNodeFilter = getTaxonNodeFilter(filter);
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String classificationFilter = getClassificationFilter(filter);
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String taxonFilter = getTaxonFilter(filter);
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String rootNodeFilter = getRootNodeFilter(filter);
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String rankMaxFilter = getRankMaxFilter(filter);
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String rankMinFilter = getRankMinFilter(filter);
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String areaFilter = getAreaFilter(filter);
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String unpublishFilter = getUnpublishFilter(filter);
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String fullFilter = getFullFilter(subtreeFilter, taxonNodeFilter,
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classificationFilter, taxonFilter,
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rankMaxFilter, rankMinFilter, areaFilter, rootNodeFilter,
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unpublishFilter);
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// String groupBy = " GROUP BY tn.uuid ";
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String groupBy = "";
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String orderBy = getOrderBy(filter, selectPart);
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String fullQuery = select + from + " WHERE " + fullFilter + groupBy + orderBy;
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return fullQuery;
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}
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private String getOrderBy(TaxonNodeFilter filter, String selectPart) {
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String orderBy = "";
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if (filter.getOrderBy()!= null && !selectPart.contains("count")){
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orderBy = "ORDER BY " + filter.getOrderBy().getHql();
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}
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return orderBy;
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}
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private String getFrom(TaxonNodeFilter filter){
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String from = " FROM TaxonNode tn ";
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if (hasTaxonFilter(filter)){
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from += " LEFT JOIN tn.taxon taxon "; //LEFT to allow includeRootNode
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}
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if(!filter.getAreaFilter().isEmpty()){
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from += " INNER JOIN taxon.descriptions descriptions "
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+ " INNER JOIN descriptions.descriptionElements " + DESCRIPTION_ELEMENTS + " ";
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}
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return from;
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}
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private boolean hasTaxonFilter(TaxonNodeFilter filter) {
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boolean result = !filter.getAreaFilter().isEmpty()
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|| !filter.isIncludeUnpublished();
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return result;
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}
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private String getAreaFilter(TaxonNodeFilter filter) {
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String result = "";
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List<LogicFilter<NamedArea>> areaFilter = filter.getAreaFilter();
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boolean isFirst = true;
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List<Integer> areaIds = new ArrayList<>();
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for (LogicFilter<NamedArea> singleFilter : areaFilter){
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areaIds = getChildAreasRecursively(singleFilter.getUuid());
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String op = isFirst ? "" : op2Hql(singleFilter.getOperator());
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result = String.format("(%s%s(" + DESCRIPTION_ELEMENTS + ".feature.uuid='" + FEATURE_UUID + "' "
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+ " AND " + DESCRIPTION_ELEMENTS + ".area.id in (%s)))"
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+ " AND " + DESCRIPTION_ELEMENTS + ".status.absenceTerm = %s " ,
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result, op, StringUtils.collectionToCommaDelimitedString(areaIds),
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HQL_FALSE);
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isFirst = false;
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}
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return result;
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}
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private List<Integer> getChildAreasRecursively(UUID uuid){
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List<Integer> areaIds = new ArrayList<>();
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NamedArea area = HibernateProxyHelper.deproxy(termDao.load(uuid), NamedArea.class);
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areaIds.add(area.getId());
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String queryStr = String.format("SELECT includes.uuid FROM DefinedTermBase t inner join t.includes includes WHERE t.uuid = '%s'",
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area.getUuid().toString());
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Query<UUID> query = getSession().createQuery(queryStr, UUID.class);
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List<UUID> childAreas = query.list();
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for (UUID childArea : childAreas) {
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areaIds.addAll(getChildAreasRecursively(childArea));
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}
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return areaIds;
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}
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/**
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* @param filter
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* @return
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*/
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private String getRootNodeFilter(TaxonNodeFilter filter) {
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String result = "";
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if (!filter.isIncludeRootNodes()){
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result = " ( tn.parent IS NOT NULL ) ";
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}
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return result;
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}
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private String getUnpublishFilter(TaxonNodeFilter filter) {
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String result = "";
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if (!filter.isIncludeUnpublished()){
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result = " ( taxon.publish = "+HQL_TRUE+" OR tn.parent IS NULL ) ";
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}
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return result;
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}
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/**
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* @param subtreeFilter
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* @param taxonNodeFilter
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* @param classificationFilter
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* @param taxonFilter
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* @param rankMinFilter
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* @param rankMaxFilter
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* @param rootNodeFilter
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* @return
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*/
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private String getFullFilter(String subtreeFilter, String taxonNodeFilter, String classificationFilter,
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String taxonFilter, String rankMaxFilter, String rankMinFilter, String areaFilter, String rootNodeFilter,
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String unpublishFilter) {
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String result = " (1=1 ";
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result = CdmUtils.concat(") AND (", result, subtreeFilter, taxonNodeFilter,
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classificationFilter, taxonFilter, rankMaxFilter, rankMinFilter, areaFilter, rootNodeFilter,
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unpublishFilter) + ") ";
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return result;
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}
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/**
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* @param list
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* @return
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*/
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private <T> List<T> deduplicate(List<T> list) {
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List<T> result = new ArrayList<>();
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for (T uuid : list){
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if (!result.contains(uuid)){
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result.add(uuid);
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}
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}
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return result;
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}
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private String getSubtreeFilter(TaxonNodeFilter filter) {
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String result = "";
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List<LogicFilter<TaxonNode>> subtreeFilter = filter.getSubtreeFilter();
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initializeSubtreeIndex(subtreeFilter);
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boolean isFirst = true;
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for (LogicFilter<TaxonNode> singleFilter : subtreeFilter){
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String treeIndex = singleFilter.getTreeIndex();
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String op = isFirst ? "" : op2Hql(singleFilter.getOperator());
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if (treeIndex != null){
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result = String.format("(%s%s(tn.treeIndex like '%s%%'))", result, op, treeIndex);
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}else{
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result = String.format("(%s%s(%s))", result, op, "(1=0)");
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}
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isFirst = false;
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}
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return result;
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}
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private String getTaxonNodeFilter(TaxonNodeFilter filter) {
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String result = "";
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List<LogicFilter<TaxonNode>> taxonNodeFilter = filter.getTaxonNodesFilter();
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boolean isFirst = true;
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for (LogicFilter<TaxonNode> singleFilter : taxonNodeFilter){
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String uuid = singleFilter.getUuid().toString();
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String op = isFirst ? "" : op2Hql(singleFilter.getOperator());
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result = String.format("(%s%s(tn.uuid = '%s'))", result, op, uuid);
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isFirst = false;
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}
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return result;
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}
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private String getRankMaxFilter(TaxonNodeFilter filter) {
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String result = "";
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LogicFilter<Rank> rankFilter = filter.getRankMax();
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if(rankFilter!=null){
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UUID rankUuid = rankFilter.getUuid();
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Rank rank = (Rank) termDao.load(rankUuid);
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result = String.format("(tn.taxon.name.rank.orderIndex >= %s)", rank.getOrderIndex());
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}
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return result;
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}
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private String getRankMinFilter(TaxonNodeFilter filter) {
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String result = "";
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LogicFilter<Rank> rankFilter = filter.getRankMin();
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if(rankFilter!=null){
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UUID rankUuid = rankFilter.getUuid();
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Rank rank = (Rank) termDao.load(rankUuid);
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result = String.format("(tn.taxon.name.rank.orderIndex <= %s)", rank.getOrderIndex());
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}
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return result;
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}
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private String getClassificationFilter(TaxonNodeFilter filter) {
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String result = "";
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List<LogicFilter<Classification>> classificationFilter = filter.getClassificationFilter();
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boolean isFirst = true;
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for (LogicFilter<Classification> singleFilter : classificationFilter){
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String uuid = singleFilter.getUuid().toString();
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String op = isFirst ? "" : op2Hql(singleFilter.getOperator());
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result = String.format("(%s%s(tn.classification.uuid = '%s'))", result, op, uuid);
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isFirst = false;
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}
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return result;
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}
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private String getTaxonFilter(TaxonNodeFilter filter) {
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String result = "";
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List<LogicFilter<Taxon>> taxonFilter = filter.getTaxonFilter();
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boolean isFirst = true;
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for (LogicFilter<Taxon> singleFilter : taxonFilter){
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String uuid = singleFilter.getUuid().toString();
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String op = isFirst ? "" : op2Hql(singleFilter.getOperator());
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result = String.format("(%s%s(tn.taxon.uuid = '%s'))", result, op, uuid);
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// System.out.println(result);
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isFirst = false;
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}
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return result;
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}
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private void initializeSubtreeIndex(List<LogicFilter<TaxonNode>> subtreeFilter) {
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for (LogicFilter<TaxonNode> filter : subtreeFilter){
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if (filter.getTreeIndex() == null){
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//TODO finde without loading, best be sending full list and returning tree indexes
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TaxonNode node = taxonNodeDao.findByUuid(filter.getUuid());
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if (node != null){
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filter.setTreeIndex(node.treeIndex());
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}
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}
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}
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}
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/**
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* Returns the HQL string for this operation
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*/
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private String op2Hql(Op op){
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return op == Op.NOT ? " AND NOT " : op.toString();
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}
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}
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