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package eu.etaxonomy.cdm.persistence.dao.hibernate.statistics;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.hibernate.Criteria;
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import org.hibernate.Query;
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import org.hibernate.criterion.Projections;
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import org.hibernate.criterion.Restrictions;
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import org.springframework.stereotype.Repository;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.persistence.dao.hibernate.common.DaoBase;
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import eu.etaxonomy.cdm.persistence.dao.statistics.IStatisticsDao;
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/**
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* this dao provides counting methods for elements in a database in general or
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* in a specific class (or tree - TODO) in the database.
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*
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* only functionality, that is not covered by other daos is implemented
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*
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* MAYDO: restructure and using {@link Criteria} and methods like prepareQuery
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*
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* @author s.buers
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*
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*/
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@Repository
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public class StatisticsDaoHibernateImpl extends DaoBase implements
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IStatisticsDao {
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// TODO remove every commented query related to
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// DescriptionBase.descriptionSources
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/*
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* (non-Javadoc)
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*
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* @see eu.etaxonomy.cdm.persistence.dao.statistics.IStatisticsDao#
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* countDescriptiveSourceReferences()
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*/
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private static final int REFERENCE_LINK_RECURSION_DEPTH = 1;
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private static final Logger logger = Logger
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.getLogger(StatisticsDaoHibernateImpl.class);
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@Override
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public Long countDescriptiveSourceReferences() {
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List<String> queryStrings = new ArrayList<String>();
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// this query does not work...
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// query = getSession().createQuery(
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// "select count(distinct(r.id, desc.id)) from DescriptionBase as d "
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// + "join d.descriptionElements as de "
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// + "join de.sources as des "
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// + "join des.citation as desc "
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// + "join d.descriptionSources as r "
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// + "where "
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// + "desc is not null"
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// + " and "
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// + "r is not null ");
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// ... here is the manual version:
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// count sources from Descriptions:
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// as the descriptionSources of DescriptionBase are depricated:
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// queryStrings.add("select distinct r.id from DescriptionBase as d "
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// + "join d.descriptionSources as r ");
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// count sources from DescriptionElements:
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queryStrings
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.add("select distinct s.citation.uuid from DescriptionElementBase as d "
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+ "join d.sources as s where s.citation is not null ");
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return Long.valueOf(processQueriesWithIdDistinctListResult(
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queryStrings, null).size());
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}
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/*
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* (non-Javadoc)
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*
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* @see eu.etaxonomy.cdm.persistence.dao.statistics.IStatisticsDao#
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* countDescriptiveSourceReferences
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* (eu.etaxonomy.cdm.model.taxon.Classification)
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*/
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@Override
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public Long countDescriptive(Boolean sourceRef,
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Classification classification) {
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return Long.valueOf(listDescriptiveIds(sourceRef, classification)
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.size());
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}
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// private Set<Integer> listDescriptiveSourceReferenceIds(
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// Classification classification) {
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//
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// if (classification == null)
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// return null; // or MAYDO: throw some Exception???
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//
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// Map<String, Object> parameters = new HashMap<String, Object>();
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//
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// List<String> queryStrings = new ArrayList<String>();
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//
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// // // Taxon description elements:
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// queryStrings
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// .add("select distinct des.citation.id from TaxonNode as tn "
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// + "join tn.taxon.descriptions as d "
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// + "join d.descriptionElements as de "
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// + "join de.sources as des "
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// + "where tn.classification=:classification "
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// + "and des.citation is not null ");
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//
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// parameters.put("classification", classification);
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//
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// // TaxonNameBase description elements for taxa:
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// queryStrings.add("select distinct des.citation.id from TaxonNode tn "
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// + "join tn.taxon.name.descriptions as d "
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// + "join d.descriptionElements as de "
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// + "join de.sources as des "
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// + "where tn.classification=:classification "
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// + "and tn.taxon is not null "
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// + "and tn.taxon.name is not null "
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// + "and des.citation is not null ");
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//
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// // TaxonNameBase description elements for synonyms:
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// queryStrings.add("select distinct des.citation.id from TaxonNode tn "
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// + "join tn.taxon.synonymRelations as syr "
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// + "join syr.relatedFrom as sy "
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// + "join sy.name.descriptions as d "
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// + "join d.descriptionElements as de "
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// + "join de.sources as des "
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// + "where tn.classification=:classification "
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// + "and des.citation is not null " + "and sy is not null " // TODO:
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// // is
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// // this
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// // case
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// // actually
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// // possible???
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// + "and sy.name is not null ");
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//
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// // SpecimenOrObservationBase description elements:
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// // 1. via determinations
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// queryStrings
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// .add("select distinct des.citation.id from DescriptionBase db, TaxonNode tn "
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// + "join db.describedSpecimenOrObservation as so "
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// + "join so.determinations as det "
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// + "join db.descriptionElements as de "
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// + "join de.sources as des "
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// + "where tn.classification=:classification "
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// + "and tn.taxon=det.taxon ");
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//
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// // 2. via derived units in taxon description
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// // already done with the taxon/synonym descriptions
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//
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// // 3. via SpecimenTypeDesignation in TaxonName:
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// // a. taxon names:
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// queryStrings.add("select distinct des.citation.id from TaxonNode tn "
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// + " join tn.taxon.name.typeDesignations as tdes "
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// + "join tdes.typeSpecimen.descriptions as d "
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// + "join d.descriptionElements as de "
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// + "join de.sources as des "
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// + "where tn.classification=:classification "
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// + "and tdes.class=:type " + "and tn.taxon is not null "
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// + "and tn.taxon.name is not null "
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// + "and des.citation is not null ");
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//
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// parameters.put("type", "SpecimenTypeDesignation");
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//
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// // b. synonym names:
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// queryStrings.add("select distinct des.citation.id from TaxonNode tn "
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//
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// + "join tn.taxon.synonymRelations as syr "
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// + "join syr.relatedFrom as sy "
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// + " join sy.name.typeDesignations as tdes "
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// + "join tdes.typeSpecimen.descriptions as d "
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// + "join d.descriptionElements as de "
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// + "join de.sources as des "
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// + "where tn.classification=:classification "
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// + "and tdes.class=:type " + "and tn.taxon is not null "
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// + "and sy.name is not null " + "and des.citation is not null ");
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//
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// // 4. via HomotypicalGroup in TaxonBase
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// // we get this automatically with the names
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//
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// return processQueriesWithIdDistinctListResult(queryStrings, parameters);
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//
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// }
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private Set<UUID> listDescriptiveIds(Boolean sourceReferences,
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Classification classification) {
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// Boolean sourceReferences = true;
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String sourceRefJoins = "";
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String sourceRefWhere = "";
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// String selection = "d.id ";
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String selection = "d.uuid ";
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if (sourceReferences) {
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sourceRefJoins = "join d.descriptionElements as de "
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+ "join de.sources as des ";
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sourceRefWhere = "and des.citation is not null ";
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// selection = "des.citation.id ";
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selection = "des.citation.uuid ";
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}
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if (classification == null)
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return null; // or MAYDO: throw some Exception???
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Map<String, Object> parameters = new HashMap<String, Object>();
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List<String> queryStrings = new ArrayList<String>();
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// // Taxon description elements:
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queryStrings.add("select distinct " + selection
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+ "from TaxonNode as tn " + "join tn.taxon.descriptions as d "
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+ sourceRefJoins + "where tn.classification=:classification "
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+ sourceRefWhere);
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parameters.put("classification", classification);
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// TaxonNameBase description elements for taxa:
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queryStrings.add("select distinct " + selection + "from TaxonNode tn "
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+ "join tn.taxon.name.descriptions as d " + sourceRefJoins
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+ "where tn.classification=:classification "
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+ "and tn.taxon is not null "
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+ "and tn.taxon.name is not null " + sourceRefWhere);
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// TaxonNameBase description elements for synonyms:
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queryStrings.add("select distinct " + selection + "from TaxonNode tn "
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+ "join tn.taxon.synonymRelations as syr "
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+ "join syr.relatedFrom as sy "
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+ "join sy.name.descriptions as d " + sourceRefJoins
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+ "where tn.classification=:classification " + sourceRefWhere
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+ "and sy is not null " // TODO:
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// is
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// this
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// case
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// actually
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// possible???
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+ "and sy.name is not null ");
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// SpecimenOrObservationBase description elements:
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// 1. via determinations
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queryStrings.add("select distinct " + selection
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+ "from DescriptionBase d, TaxonNode tn "
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+ "join d.describedSpecimenOrObservation as so "
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+ "join so.determinations as det " + sourceRefJoins
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+ "where tn.classification=:classification "
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+ "and tn.taxon=det.taxon " + sourceRefWhere);
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// 2. via derived units in taxon description
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// already done with the taxon/synonym descriptions
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// 3. via SpecimenTypeDesignation in TaxonName:
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// a. taxon names:
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queryStrings.add("select distinct " + selection + "from TaxonNode tn "
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+ " join tn.taxon.name.typeDesignations as tdes "
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+ "join tdes.typeSpecimen.descriptions as d " + sourceRefJoins
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+ "where tn.classification=:classification "
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+ "and tdes.class=:type " + "and tn.taxon is not null "
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+ "and tn.taxon.name is not null " + sourceRefWhere);
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parameters.put("type", "SpecimenTypeDesignation");
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// b. synonym names:
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queryStrings.add("select distinct " + selection + "from TaxonNode tn "
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+ "join tn.taxon.synonymRelations as syr "
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+ "join syr.relatedFrom as sy "
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+ " join sy.name.typeDesignations as tdes "
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+ "join tdes.typeSpecimen.descriptions as d " + sourceRefJoins
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+ "where tn.classification=:classification "
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+ "and tdes.class=:type " + "and tn.taxon is not null "
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+ "and sy.name is not null " + sourceRefWhere);
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// 4. via HomotypicalGroup in TaxonBase
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// we get this automatically with the names
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//###TODO
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return processQueriesWithIdDistinctListResult(queryStrings, parameters);
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// return null;
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}
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/*
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* (non-Javadoc)
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*
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* @see eu.etaxonomy.cdm.persistence.dao.statistics.IStatisticsDao#
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* countTaxaInClassification(java.lang.Class,
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* eu.etaxonomy.cdm.model.taxon.Classification)
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*/
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@Override
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public Long countTaxaInClassification(Class<? extends TaxonBase> clazz,
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Classification classification) {
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if (classification == null)
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return null; // or MAYDO: throw some Exception???
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if (clazz.equals(TaxonBase.class)) {
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return countTaxaInClassification(Taxon.class, classification)
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+ countTaxaInClassification(Synonym.class, classification);
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}
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if (clazz.equals(Taxon.class)) {
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Criteria criteria = getSession().createCriteria(TaxonNode.class);
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criteria.add(Restrictions.eq("classification", classification));
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criteria.setProjection(Projections.rowCount());
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return Long.valueOf((Long) criteria.uniqueResult());
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}
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else if (clazz.equals(Synonym.class)) {
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// criteria= getSession().createCriteria(TaxonNode.class);
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Query query = getSession().createQuery(
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"select count(distinct sr.relatedFrom.uuid) from TaxonNode tn "
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+ "join tn.taxon.synonymRelations as sr "
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+ "where tn.classification=:classification ");
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query.setParameter("classification", classification);
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return (Long) query.uniqueResult();
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}
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// this should never happen:
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return null;
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}
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/*
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* (non-Javadoc)
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*
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* @see
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* eu.etaxonomy.cdm.persistence.dao.statistics.IStatisticsDao#countTaxonNames
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* (eu.etaxonomy.cdm.model.taxon.Classification)
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*/
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@Override
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public Long countTaxonNames(Classification classification) {
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if (classification == null)
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return null; // or MAYDO: throw some Exception???
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Map<String, Object> parameters = new HashMap<String, Object>();
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parameters.put("classification", classification);
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// the query would be:
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// "select count (distinct n) from (
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// + "select distinct tn.taxon.name as c from TaxonNode tn "
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// + "where tn.classification=:classification "
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// + "UNION "
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// + "select distinct sr.relatedFrom.name as c from TaxonNode tn "
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// + "join tn.taxon.synonymRelations sr "
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// + "where tn.classification=:classification "
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// ") as n "
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// as hibernate does not accept brackets in from and no unions
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// we have to do it otherwise:
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// so instead of "UNION" we use 2 queries
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// and count the names manually
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List<String> queryStrings = new ArrayList<String>();
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queryStrings
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.add("select distinct tn.taxon.name.uuid as c from TaxonNode tn "
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+ "where tn.classification=:classification "
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+ "and tn.taxon.name is not null ");
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queryStrings
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.add("select distinct sr.relatedFrom.name.uuid as c from TaxonNode tn "
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+ "join tn.taxon.synonymRelations sr "
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+ "where tn.classification=:classification "
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+ "and sr.relatedFrom.name is not null ");
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return Long.valueOf(processQueriesWithIdDistinctListResult(
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queryStrings, parameters).size());
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}
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386
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/*
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* (non-Javadoc)
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*
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* @see eu.etaxonomy.cdm.persistence.dao.statistics.IStatisticsDao#
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* countNomenclaturalReferences()
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*/
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// @Override
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public Long countNomenclaturalReferences() {
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Query query = getSession()
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.createQuery(
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"select count(distinct nomenclaturalReference) from TaxonNameBase ");
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return (Long) query.uniqueResult();
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}
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@Override
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public Long countNomenclaturalReferences(
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Classification classification) {
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if (classification == null)
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return null; // or MAYDO: throw some Exception???
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407
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Map<String, Object> parameters = new HashMap<String, Object>();
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parameters.put("classification", classification);
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// so instead of "UNION" we use 2 queries
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// and count the names manually
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List<String> queryStrings = new ArrayList<String>();
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queryStrings
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.add("select distinct tn.taxon.name.nomenclaturalReference.uuid from TaxonNode tn "
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+ "where tn.classification=:classification "
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+ "and tn.taxon.name.nomenclaturalReference is not null ");
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queryStrings
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419
|
.add("select distinct sr.relatedFrom.name.nomenclaturalReference.uuid as c from TaxonNode tn "
|
420
|
+ "join tn.taxon.synonymRelations as sr "
|
421
|
+ "where tn.classification=:classification "
|
422
|
+ "and sr.relatedFrom.name.nomenclaturalReference is not null ");
|
423
|
|
424
|
return Long.valueOf(processQueriesWithIdDistinctListResult(
|
425
|
queryStrings, parameters).size());
|
426
|
}
|
427
|
|
428
|
|
429
|
@Override
|
430
|
public Long countReferencesInClassificationWithUuids(Classification classification) {
|
431
|
if (classification == null)
|
432
|
return null; // or MAYDO: throw some Exception???
|
433
|
|
434
|
// get all the descriptive source reference ids
|
435
|
// ---------------------------------------------
|
436
|
|
437
|
// preparation
|
438
|
List<String> queryStrings = new ArrayList<String>();
|
439
|
Map<String, Object> parameters = new HashMap<String, Object>();
|
440
|
|
441
|
parameters.put("classification", classification);
|
442
|
|
443
|
// get the ids from the Descriptive source references to add them to the
|
444
|
// count
|
445
|
|
446
|
//TODO
|
447
|
//Set<Integer> ids = listDescriptiveIds(true, classification);
|
448
|
Set<UUID> ids = new HashSet<UUID>();
|
449
|
|
450
|
// get classification reference
|
451
|
queryStrings.add("select c.reference.uuid from Classification as c "
|
452
|
+ "where c.uuid=:classificationId ");
|
453
|
// TODO ???
|
454
|
// +"join c.souces as s "
|
455
|
// +"join s.citation "
|
456
|
|
457
|
parameters.put("classificationId", classification.getUuid());
|
458
|
|
459
|
// get node relations references:
|
460
|
queryStrings
|
461
|
.add("select distinct tn.referenceForParentChildRelation.uuid as c from TaxonNode tn "
|
462
|
+ "where tn.classification=:classification "
|
463
|
+ "and tn.referenceForParentChildRelation is not null ");
|
464
|
|
465
|
// get sec references
|
466
|
// -------------------------------------------------------------------
|
467
|
// taxa
|
468
|
queryStrings
|
469
|
.add("select distinct tn.taxon.sec.uuid as c from TaxonNode tn "
|
470
|
+ "where tn.classification=:classification "
|
471
|
+ "and tn.taxon.sec is not null ");
|
472
|
|
473
|
// synonyms
|
474
|
queryStrings
|
475
|
.add("select distinct sr.relatedFrom.sec.uuid as c from TaxonNode tn "
|
476
|
+ "join tn.taxon.synonymRelations sr "
|
477
|
+ "where tn.classification=:classification "
|
478
|
+ "and sr.relatedFrom.sec is not null ");
|
479
|
|
480
|
// get relationship citations
|
481
|
// ---------------------------------------------------------------
|
482
|
|
483
|
// taxon relations
|
484
|
queryStrings.add("select distinct tr.citation.uuid from TaxonNode tn "
|
485
|
+ "join tn.taxon.relationsFromThisTaxon as tr "
|
486
|
+ "where tn.classification=:classification "
|
487
|
+ "and tn.taxon is not null " + "and tr.citation is not null ");
|
488
|
|
489
|
// synonym relations
|
490
|
|
491
|
queryStrings.add("select distinct sr.citation.uuid from TaxonNode tn "
|
492
|
+ "join tn.taxon.synonymRelations as sr "
|
493
|
+ "where tn.classification=:classification "
|
494
|
+ "and tn.taxon is not null " + "and sr.citation is not null ");
|
495
|
|
496
|
// get hybrid relation citations
|
497
|
// Taxa:
|
498
|
queryStrings.add("select distinct hr.citation.uuid from TaxonNode tn "
|
499
|
+ "join tn.taxon.name.hybridParentRelations as hr "
|
500
|
+ "where tn.classification=:classification "
|
501
|
+ "and tn.taxon.name.class=:nonViralName "
|
502
|
+ "and tn.taxon is not null "
|
503
|
+ "and tn.taxon.name is not null ");
|
504
|
|
505
|
parameters.put("nonViralName", "NonViralName");
|
506
|
|
507
|
// synonyms:
|
508
|
queryStrings.add("select distinct hr.citation.uuid from TaxonNode tn "
|
509
|
+ "join tn.taxon.synonymRelations as syr "
|
510
|
+ "join syr.relatedFrom as sy "
|
511
|
+ "join sy.name.hybridParentRelations as hr "
|
512
|
+ "where tn.classification=:classification "
|
513
|
+ "and sy.name.class=:nonViralName " + "and sy is not null " // TODO:
|
514
|
// is
|
515
|
// this
|
516
|
// case
|
517
|
// actually
|
518
|
// possible???
|
519
|
+ "and sy.name is not null ");
|
520
|
|
521
|
// get name relations references:
|
522
|
// -------------------------------------------------------
|
523
|
// Taxa:
|
524
|
queryStrings.add("select distinct nr.citation.uuid from TaxonNode tn "
|
525
|
+ "join tn.taxon.name.relationsFromThisName as nr "
|
526
|
+ "where tn.classification=:classification "
|
527
|
+ "and tn.taxon is not null "
|
528
|
+ "and tn.taxon.name is not null ");
|
529
|
|
530
|
// synonyms:
|
531
|
queryStrings.add("select distinct nr.citation.uuid from TaxonNode tn "
|
532
|
+ "join tn.taxon.synonymRelations as syr "
|
533
|
+ "join syr.relatedFrom as sy "
|
534
|
+ "join sy.name.relationsFromThisName as nr "
|
535
|
+ "where tn.classification=:classification "
|
536
|
+ "and sy is not null " // TODO: is this case actually
|
537
|
// possible???
|
538
|
+ "and sy.name is not null ");
|
539
|
|
540
|
// get Nomenclatural status citation
|
541
|
|
542
|
// Taxa:
|
543
|
queryStrings.add("select distinct s.citation.uuid from TaxonNode tn "
|
544
|
+ "join tn.taxon.name.status as s "
|
545
|
+ "where tn.classification=:classification "
|
546
|
+ "and tn.taxon is not null "
|
547
|
+ "and tn.taxon.name is not null ");
|
548
|
|
549
|
// synonyms:
|
550
|
queryStrings.add("select distinct s.citation.uuid from TaxonNode tn "
|
551
|
+ "join tn.taxon.synonymRelations as syr "
|
552
|
+ "join syr.relatedFrom as sy " + "join sy.name.status as s "
|
553
|
+ "where tn.classification=:classification "
|
554
|
+ "and sy is not null " // TODO: is this case actually
|
555
|
// possible???
|
556
|
+ "and sy.name is not null ");
|
557
|
|
558
|
// get sequences which contain citations and publishedIn ------
|
559
|
// and contain "Media" which could be of the subtype
|
560
|
// "ReferencedMediaBase"
|
561
|
// which has a citation
|
562
|
|
563
|
queryStrings.add("select distinct cit.uuid " + " from TaxonNode tn "
|
564
|
+ "join tn.taxon.descriptions as db "
|
565
|
|
566
|
+ "join db.describedSpecimenOrObservation as so "
|
567
|
+ "join so.sequences as seq " + "join seq.citations as cit "
|
568
|
|
569
|
+ "where so.class=:dnaSample "
|
570
|
+ "and tn.classification=:classification "
|
571
|
+ "and cit is not null ");
|
572
|
|
573
|
// traverse to specimenOrObservation via individualsAssociation
|
574
|
|
575
|
queryStrings.add("select distinct cit.uuid from TaxonNode tn "
|
576
|
+ "join tn.taxon.descriptions as db "
|
577
|
+ "join db.descriptionElements as ia "
|
578
|
+ "join ia.associatedSpecimenOrObservation as so "
|
579
|
+ "join so.sequences as seq " + "join seq.citations as cit "
|
580
|
|
581
|
+ "where so.class=:dnaSample "
|
582
|
+ "and ia.class=:individualsAssociation "
|
583
|
+ "and tn.classification=:classification "
|
584
|
+ "and cit is not null ");
|
585
|
|
586
|
// we do assume, that a name description would not have a
|
587
|
// SpecimenOrObservation element
|
588
|
|
589
|
//
|
590
|
parameters.put("dnaSample", "DnaSample");
|
591
|
parameters.put("individualsAssociation", "IndividualsAssociation");
|
592
|
|
593
|
//
|
594
|
//
|
595
|
// //### TODO v3.3, preliminary removed for adaptation to model v3.3
|
596
|
// this was all about ReferencedMedia
|
597
|
{
|
598
|
// // media
|
599
|
// queryStrings.add("select distinct me.citation.id from TaxonNode tn "
|
600
|
// + "join tn.taxon.descriptions as db "
|
601
|
// + "join db.describedSpecimenOrObservation as so "
|
602
|
// + "join so.sequences as seq "
|
603
|
// + "join seq.chromatograms as me "
|
604
|
//
|
605
|
// + "where so.class=:dnaSample "
|
606
|
// + "and me.class=:referencedMediaBase "
|
607
|
// + "and tn.classification=:classification "
|
608
|
//
|
609
|
// + "and me.citation is not null ");
|
610
|
//
|
611
|
// // traverse to specimenOrObservation via individualsAssociation
|
612
|
//
|
613
|
// queryStrings.add("select distinct me.citation.id from TaxonNode tn "
|
614
|
// + "join tn.taxon.descriptions as db "
|
615
|
// + "join db.descriptionElements as ia "
|
616
|
// + "join ia.associatedSpecimenOrObservation as so "
|
617
|
// + "join so.sequences as seq "
|
618
|
// + "join seq.chromatograms as me "
|
619
|
// + "where so.class=:dnaSample "
|
620
|
// + "and ia.class=:individualsAssociation "
|
621
|
// + "and me.class=:referencedMediaBase "
|
622
|
// + "and tn.classification=:classification "
|
623
|
//
|
624
|
// + "and me.citation is not null ");
|
625
|
//
|
626
|
// // TODO v3.3, preliminary removed for adaptation to model v3.3,
|
627
|
// Media.citation does not exist anymore, use OriginalSource instead
|
628
|
// // via media via name description
|
629
|
// // Taxa:
|
630
|
// queryStrings.add("select distinct me.citation.id from TaxonNode tn "
|
631
|
// + "join tn.taxon.name.descriptions as d "
|
632
|
// + "join d.descriptionElements as de "
|
633
|
// + "join de.media as me "
|
634
|
// + "where tn.classification=:classification "
|
635
|
// + "and tn.taxon.name is not null "
|
636
|
// + "and me.class=:referencedMediaBase "
|
637
|
// + "and me.citation is not null " + "and tn.taxon is not null "
|
638
|
// + "and tn.taxon.name is not null ");
|
639
|
//
|
640
|
// // synonyms:
|
641
|
// queryStrings.add("select distinct me.citation.id from TaxonNode tn "
|
642
|
// + "join tn.taxon.synonymRelations as syr "
|
643
|
// + "join syr.relatedFrom as sy "
|
644
|
// + "join sy.name.descriptions as d "
|
645
|
// + "join d.descriptionElements as de "
|
646
|
// + "join de.media as me "
|
647
|
// + "where tn.classification=:classification "
|
648
|
// + "and sy.name is not null "
|
649
|
// + "and me.class=:referencedMediaBase "
|
650
|
// + "and me.citation is not null " + "and tn.taxon is not null "
|
651
|
// + "and tn.taxon.name is not null ");
|
652
|
//
|
653
|
// // get all "Media" from everywhere because it could be
|
654
|
// // of the subtype "ReferencedMediaBase"
|
655
|
// // which has a citation
|
656
|
//
|
657
|
// // TODO do we need the media from DefinedTermBase???
|
658
|
// // what can be a Feature!
|
659
|
//
|
660
|
// // from description element
|
661
|
// queryStrings.add("select distinct me.citation.id from TaxonNode as tn "
|
662
|
// + "join tn.taxon.descriptions as d "
|
663
|
// + "join d.descriptionElements as de "
|
664
|
// + "join de.media as me "
|
665
|
// + "where tn.classification=:classification "
|
666
|
// + "and me.class=:referencedMediaBase "
|
667
|
// + "and me.citation is not null ");
|
668
|
//
|
669
|
// // via NamedArea that has 2 media parameter
|
670
|
// // and a waterbodyOrContinet that has media parameter and has
|
671
|
// continent
|
672
|
// // parameter
|
673
|
// // which also has media parameter:
|
674
|
//
|
675
|
//
|
676
|
//
|
677
|
// // from CommonTaxonName or Distribution
|
678
|
// queryStrings
|
679
|
// .add("select distinct de.area.shape.citation.id, me1.citation.id, "
|
680
|
// + "me2.citation.id, me3.citation.id from TaxonNode as tn "
|
681
|
// + "join tn.taxon.descriptions as d "
|
682
|
// + "join d.descriptionElements as de "
|
683
|
// + "join de.area.media as me1 "
|
684
|
// + "join de.area.waterbodiesOrCountries as wboc "
|
685
|
// + "join wboc.media as me2 "
|
686
|
// + "join wboc.continents as co "
|
687
|
// + "join co.media as me3 "
|
688
|
// + "where tn.classification=:classification "
|
689
|
// + "and (de.class=:commonTaxonName or de.class=:distribution) "
|
690
|
// + "and me1.class=:referencedMediaBase "
|
691
|
// + "and me1.citation is not null "
|
692
|
// + "and me2.class=:referencedMediaBase "
|
693
|
// + "and me2.citation is not null "
|
694
|
// + "and me3.class=:referencedMediaBase "
|
695
|
// + "and me3.citation is not null "
|
696
|
// + "and de.area.shape.class=:referencedMediaBase "
|
697
|
// + "and de.area is not null "
|
698
|
// + "and de.area.shape is not null ");
|
699
|
//
|
700
|
// parameters.put("commonTaxonName", "CommonTaxonName");
|
701
|
// parameters.put("distribution", "Distribution");
|
702
|
// //***
|
703
|
// // from TaxonDescription:
|
704
|
// queryStrings
|
705
|
// .add("select distinct na.shape.citation.id, me1.citation.id, "
|
706
|
// + "me2.citation.id, me3.citation.id from TaxonNode as tn "
|
707
|
// + "join tn.taxon.descriptions as d "
|
708
|
// + "join d.geoScopes as na " + "join na.media as me1 "
|
709
|
// + "join na.waterbodiesOrCountries as wboc "
|
710
|
// + "join wboc.media as me2 "
|
711
|
// + "join wboc.continents as co "
|
712
|
// + "join co.media as me3 "
|
713
|
// + "where tn.classification=:classification "
|
714
|
// + "and me1.class=:referencedMediaBase "
|
715
|
// + "and me1.citation is not null "
|
716
|
// + "and me2.class=:referencedMediaBase "
|
717
|
// + "and me2.citation is not null "
|
718
|
// + "and me3.class=:referencedMediaBase "
|
719
|
// + "and me3.citation is not null "
|
720
|
// + "and na.shape.class=:referencedMediaBase "
|
721
|
// + "and na.shape is not null ");
|
722
|
//
|
723
|
// // from gathering event
|
724
|
// queryStrings
|
725
|
// .add("select fo.gatheringEvent.country.shape.citation.id, ca.shape.citation.id "
|
726
|
// +
|
727
|
// " from TaxonNode tn "
|
728
|
// + "join tn.taxon.descriptions as db "
|
729
|
// + "join db.describedSpecimenOrObservation as fo "
|
730
|
// + "join fo.gatheringEvent.collectingAreas as ca "
|
731
|
// + "where fo.class=:fieldObservation "
|
732
|
// + "and fo.gatheringEvent is not null "
|
733
|
// + "and fo.gatheringEvent.country is not null "
|
734
|
// + "and fo.gatheringEvent.country.shape is not null "
|
735
|
// + "and ca.shape is not null "
|
736
|
// + "and ca.shape.class=:referencedMediaBase "
|
737
|
// + "and ca.shape.citation is not null "
|
738
|
// +
|
739
|
// "and fo.gatheringEvent.country.shape.class=:referencedMediaBase "
|
740
|
// + " and fo.gatheringEvent.country.shape.citation is not null "
|
741
|
// + "and tn.classification=:classification ");
|
742
|
//
|
743
|
// // traverse to specimenOrObservation via individualsAssociation
|
744
|
//
|
745
|
// queryStrings
|
746
|
// .add("select fo.gatheringEvent.country.shape.citation.id, ca.shape.citation.id "
|
747
|
// + "from TaxonNode tn "
|
748
|
// + "join tn.taxon.descriptions as db "
|
749
|
// + "join db.descriptionElements as ia "
|
750
|
// + "join ia.associatedSpecimenOrObservation as fo "
|
751
|
// + "join fo.gatheringEvent.collectingAreas as ca "
|
752
|
// + "where fo.class=:fieldObservation "
|
753
|
// + "and fo.gatheringEvent is not null "
|
754
|
// + "and fo.gatheringEvent.country is not null "
|
755
|
// + "and fo.gatheringEvent.country.shape is not null "
|
756
|
// + "and ca.shape is not null "
|
757
|
// + "and ca.shape.class=:referencedMediaBase "
|
758
|
// + "and ca.shape.citation is not null "
|
759
|
// +
|
760
|
// "and fo.gatheringEvent.country.shape.class=:referencedMediaBase "
|
761
|
// + " and fo.gatheringEvent.country.shape.citation is not null "
|
762
|
// + "and ia.class=:individualsAssociation "
|
763
|
// + "and tn.classification=:classification ");
|
764
|
//
|
765
|
//
|
766
|
//
|
767
|
// parameters.put("fieldObservation", "FieldObservation");
|
768
|
// parameters.put("referencedMediaBase", "ReferencedMediaBase");
|
769
|
//
|
770
|
// parameters.put("classification", classification);
|
771
|
//
|
772
|
// // via events
|
773
|
// // ----------------------------------------
|
774
|
// // determination event:
|
775
|
// // taxa
|
776
|
// queryStrings
|
777
|
// .add("select distinct sor.id from DeterminationEvent dtev, TaxonNode tn "
|
778
|
// + "join dtev.setOfReferences as sor "
|
779
|
//
|
780
|
// + "where tn.classification=:classification "
|
781
|
// + "and tn.taxon=dtev.taxon ");
|
782
|
//
|
783
|
// // synonyms
|
784
|
//
|
785
|
// queryStrings
|
786
|
// .add("select distinct sor.id from DeterminationEvent dtev, TaxonNode tn "
|
787
|
// + "join dtev.setOfReferences as sor "
|
788
|
// + "join tn.taxon.synonymRelations as syr "
|
789
|
// + "join syr.relatedTo as sy "
|
790
|
// + "where tn.classification=:classification "
|
791
|
// + "and sy=dtev.taxon ");
|
792
|
//
|
793
|
}
|
794
|
|
795
|
// ------------------------------------------------------------------
|
796
|
// TODO get all objects that inherit IdentifiableEntity because it has
|
797
|
// an
|
798
|
// IdentifiableSource which inherits from OriginalSourceBase
|
799
|
// which inherits from ReferencedEntityBase
|
800
|
// which has a citation
|
801
|
// furthermore recources can recursivly link to recources:
|
802
|
// get sources of all references from ids and add the references of
|
803
|
// the sources...
|
804
|
// iterate in a certain depth REFERENCE_LINK_RECURSION_DEPTH
|
805
|
|
806
|
// ----------------------------------------------------------
|
807
|
|
808
|
ids.addAll(processQueriesWithIdDistinctListResult(queryStrings,
|
809
|
parameters));
|
810
|
|
811
|
return Long.valueOf(ids.size());
|
812
|
}
|
813
|
|
814
|
|
815
|
// TODO!!!
|
816
|
// TODO this is the old reference counter where i counted the referenced
|
817
|
// media as well and fetched ids from the database to erase dublettes
|
818
|
@Override
|
819
|
public Long countReferencesInClassification(Classification classification) {
|
820
|
if (classification == null)
|
821
|
return null; // or MAYDO: throw some Exception???
|
822
|
|
823
|
// get all the descriptive source reference ids
|
824
|
// ---------------------------------------------
|
825
|
|
826
|
// preparation
|
827
|
List<String> queryStrings = new ArrayList<String>();
|
828
|
Map<String, Object> parameters = new HashMap<String, Object>();
|
829
|
|
830
|
parameters.put("classification", classification);
|
831
|
|
832
|
// get the ids from the Descriptive source references to add them to the
|
833
|
// count
|
834
|
//###TODO
|
835
|
// Set<Integer> ids = listDescriptiveIds(true, classification);
|
836
|
|
837
|
// get classification reference
|
838
|
queryStrings.add("select count(c.reference.id) from Classification as c "
|
839
|
+ "where c.id=:classificationId ");
|
840
|
// TODO ???
|
841
|
// +"join c.souces as s "
|
842
|
// +"join s.citation "
|
843
|
|
844
|
parameters.put("classificationId", classification.getId());
|
845
|
|
846
|
// get node relations references:
|
847
|
queryStrings
|
848
|
.add("select count(distinct tn.referenceForParentChildRelation.id) as c from TaxonNode tn "
|
849
|
+ "where tn.classification=:classification "
|
850
|
+ "and tn.referenceForParentChildRelation is not null ");
|
851
|
|
852
|
// get sec references
|
853
|
// -------------------------------------------------------------------
|
854
|
// taxa
|
855
|
queryStrings
|
856
|
.add("select count(distinct tn.taxon.sec.id) as c from TaxonNode tn "
|
857
|
+ "where tn.classification=:classification "
|
858
|
+ "and tn.taxon.sec is not null ");
|
859
|
|
860
|
// synonyms
|
861
|
queryStrings
|
862
|
.add("select count(distinct sr.relatedFrom.sec.id) as c from TaxonNode tn "
|
863
|
+ "join tn.taxon.synonymRelations sr "
|
864
|
+ "where tn.classification=:classification "
|
865
|
+ "and sr.relatedFrom.sec is not null ");
|
866
|
|
867
|
// get relationship citations
|
868
|
// ---------------------------------------------------------------
|
869
|
|
870
|
// taxon relations
|
871
|
queryStrings.add("select count(distinct tr.citation.id) from TaxonNode tn "
|
872
|
+ "join tn.taxon.relationsFromThisTaxon as tr "
|
873
|
+ "where tn.classification=:classification "
|
874
|
+ "and tn.taxon is not null " + "and tr.citation is not null ");
|
875
|
|
876
|
// synonym relations
|
877
|
//TODO
|
878
|
queryStrings.add("select count(distinct sr.citation.id) from TaxonNode tn "
|
879
|
+ "join tn.taxon.synonymRelations as sr "
|
880
|
+ "where tn.classification=:classification "
|
881
|
+ "and tn.taxon is not null " + "and sr.citation is not null ");
|
882
|
|
883
|
// get hybrid relation citations
|
884
|
// Taxa:
|
885
|
queryStrings.add("select count(distinct hr.citation.id) from TaxonNode tn "
|
886
|
+ "join tn.taxon.name.hybridParentRelations as hr "
|
887
|
+ "where tn.classification=:classification "
|
888
|
+ "and tn.taxon.name.class=:nonViralName "
|
889
|
+ "and tn.taxon is not null "
|
890
|
+ "and tn.taxon.name is not null ");
|
891
|
|
892
|
parameters.put("nonViralName", "NonViralName");
|
893
|
|
894
|
// synonyms:
|
895
|
queryStrings.add("select count(distinct hr.citation.id) from TaxonNode tn "
|
896
|
+ "join tn.taxon.synonymRelations as syr "
|
897
|
+ "join syr.relatedFrom as sy "
|
898
|
+ "join sy.name.hybridParentRelations as hr "
|
899
|
+ "where tn.classification=:classification "
|
900
|
+ "and sy.name.class=:nonViralName " + "and sy is not null " // TODO:
|
901
|
// is
|
902
|
// this
|
903
|
// case
|
904
|
// actually
|
905
|
// possible???
|
906
|
+ "and sy.name is not null ");
|
907
|
|
908
|
// get name relations references:
|
909
|
// -------------------------------------------------------
|
910
|
// Taxa:
|
911
|
queryStrings.add("select count(distinct nr.citation.id) from TaxonNode tn "
|
912
|
+ "join tn.taxon.name.relationsFromThisName as nr "
|
913
|
+ "where tn.classification=:classification "
|
914
|
+ "and tn.taxon is not null "
|
915
|
+ "and tn.taxon.name is not null ");
|
916
|
|
917
|
// synonyms:
|
918
|
queryStrings.add("select count(distinct nr.citation.id) from TaxonNode tn "
|
919
|
+ "join tn.taxon.synonymRelations as syr "
|
920
|
+ "join syr.relatedFrom as sy "
|
921
|
+ "join sy.name.relationsFromThisName as nr "
|
922
|
+ "where tn.classification=:classification "
|
923
|
+ "and sy is not null " // TODO: is this case actually
|
924
|
// possible???
|
925
|
+ "and sy.name is not null ");
|
926
|
|
927
|
// get Nomenclatural status citation
|
928
|
|
929
|
// Taxa:
|
930
|
queryStrings.add("select count(distinct s.citation.id) from TaxonNode tn "
|
931
|
+ "join tn.taxon.name.status as s "
|
932
|
+ "where tn.classification=:classification "
|
933
|
+ "and tn.taxon is not null "
|
934
|
+ "and tn.taxon.name is not null ");
|
935
|
|
936
|
// synonyms:
|
937
|
queryStrings.add("select count(distinct s.citation.id) from TaxonNode tn "
|
938
|
+ "join tn.taxon.synonymRelations as syr "
|
939
|
+ "join syr.relatedFrom as sy " + "join sy.name.status as s "
|
940
|
+ "where tn.classification=:classification "
|
941
|
+ "and sy is not null " // TODO: is this case actually
|
942
|
// possible???
|
943
|
+ "and sy.name is not null ");
|
944
|
|
945
|
// get sequences which contain citations and publishedIn ------
|
946
|
// and contain "Media" which could be of the subtype
|
947
|
// "ReferencedMediaBase"
|
948
|
// which has a citation
|
949
|
|
950
|
queryStrings.add("select count(distinct cit.id) from TaxonNode tn "
|
951
|
+ "join tn.taxon.descriptions as db "
|
952
|
|
953
|
+ "join db.describedSpecimenOrObservation as so "
|
954
|
+ "join so.sequences as seq " + "join seq.citations as cit "
|
955
|
|
956
|
+ "where so.class=:dnaSample "
|
957
|
+ "and tn.classification=:classification "
|
958
|
+ "and cit is not null ");
|
959
|
|
960
|
// traverse to specimenOrObservation via individualsAssociation
|
961
|
|
962
|
queryStrings.add("select count(distinct cit.id) from TaxonNode tn "
|
963
|
+ "join tn.taxon.descriptions as db "
|
964
|
+ "join db.descriptionElements as ia "
|
965
|
+ "join ia.associatedSpecimenOrObservation as so "
|
966
|
+ "join so.sequences as seq " + "join seq.citations as cit "
|
967
|
|
968
|
+ "where so.class=:dnaSample "
|
969
|
+ "and ia.class=:individualsAssociation "
|
970
|
+ "and tn.classification=:classification "
|
971
|
+ "and cit is not null ");
|
972
|
|
973
|
// we do assume, that a name description would not have a
|
974
|
// SpecimenOrObservation element
|
975
|
|
976
|
parameters.put("dnaSample", "DnaSample");
|
977
|
parameters.put("individualsAssociation", "IndividualsAssociation");
|
978
|
|
979
|
//###TODO???
|
980
|
// ids.addAll(processQueriesWithIdDistinctListResult(queryStrings,
|
981
|
// parameters));
|
982
|
|
983
|
return processQueries(queryStrings, parameters);
|
984
|
}
|
985
|
|
986
|
// TODO: this is used by countReferencesInClassificationWithIds()
|
987
|
|
988
|
private Set<UUID> processQueriesWithIdDistinctListResult(
|
989
|
List<String> queryStrings, Map<String, Object> parameters) {
|
990
|
|
991
|
// MAYDO catch error if queries deliver wrong type
|
992
|
Query query;
|
993
|
Set<UUID> ids = new HashSet<UUID>();
|
994
|
List queryList;
|
995
|
for (String queryString : queryStrings) {
|
996
|
|
997
|
query = getSession().createQuery(queryString);
|
998
|
|
999
|
List<String> queryParameters = new ArrayList<String>(
|
1000
|
Arrays.asList(query.getNamedParameters()));
|
1001
|
|
1002
|
if (parameters != null) {
|
1003
|
for (Map.Entry<String, Object> entry : parameters.entrySet()) {
|
1004
|
|
1005
|
if (queryParameters.contains(entry.getKey())) {
|
1006
|
query.setParameter(entry.getKey(), entry.getValue());
|
1007
|
}
|
1008
|
}
|
1009
|
}
|
1010
|
|
1011
|
queryList = query.list();
|
1012
|
|
1013
|
ids.addAll((ArrayList<UUID>) queryList);
|
1014
|
System.out.println();
|
1015
|
}
|
1016
|
return ids;
|
1017
|
}
|
1018
|
|
1019
|
|
1020
|
|
1021
|
/**
|
1022
|
* @param queryStrings
|
1023
|
* - should be a list of strings that each represent a count hibernate query
|
1024
|
* @param parameters parameters for all the queries
|
1025
|
*
|
1026
|
* @return sum of the values all queries result in
|
1027
|
*/
|
1028
|
private Long processQueries(
|
1029
|
List<String> queryStrings, Map<String, Object> parameters) {
|
1030
|
|
1031
|
// MAYDO catch error if queries deliver wrong type
|
1032
|
Query query;
|
1033
|
Long all = new Long(0);
|
1034
|
Long result;
|
1035
|
|
1036
|
|
1037
|
for (String queryString : queryStrings) {
|
1038
|
|
1039
|
query = getSession().createQuery(queryString);
|
1040
|
|
1041
|
//add matching parameters to query
|
1042
|
List<String> queryParameters = new ArrayList<String>(
|
1043
|
Arrays.asList(query.getNamedParameters()));
|
1044
|
|
1045
|
if (parameters != null) {
|
1046
|
for (Map.Entry<String, Object> entry : parameters.entrySet()) {
|
1047
|
|
1048
|
if (queryParameters.contains(entry.getKey())) {
|
1049
|
query.setParameter(entry.getKey(), entry.getValue());
|
1050
|
}
|
1051
|
}
|
1052
|
}
|
1053
|
result=(Long)query.uniqueResult();
|
1054
|
all += result;
|
1055
|
}
|
1056
|
return all;
|
1057
|
|
1058
|
}
|
1059
|
|
1060
|
|
1061
|
@Override
|
1062
|
public List<UUID> getTaxonTree(IdentifiableEntity filter) {
|
1063
|
// TODO Auto-generated method stub
|
1064
|
return null;
|
1065
|
}
|
1066
|
|
1067
|
@Override
|
1068
|
public List<UUID> getAllChildNodeIds(UUID rootUuid) {
|
1069
|
|
1070
|
Set<UUID> uuids = new HashSet<UUID>();
|
1071
|
List<UUID> children = new ArrayList<UUID>();
|
1072
|
List<UUID> parents = new ArrayList<UUID>();
|
1073
|
String queryString;
|
1074
|
String parameter;
|
1075
|
|
1076
|
// it should be this one!
|
1077
|
// queryString="select distinct chn.uuid from TaxonNode tn " +
|
1078
|
// "join tn.childNodes as chn " +
|
1079
|
// "where tn.uuid in (:parents) ";
|
1080
|
|
1081
|
// just for testing, but does not work anyway
|
1082
|
queryString = "select distinct chn.uuid from TaxonNode tn "
|
1083
|
+ "join tn.childNodes as chn " + "where tn.uuid = :parent ";
|
1084
|
|
1085
|
Query query = getSession().createQuery(queryString);
|
1086
|
|
1087
|
parents.add(rootUuid);
|
1088
|
uuids.add(rootUuid);
|
1089
|
|
1090
|
// while(!(parents.isEmpty())){
|
1091
|
// query.setParameterList("parents",parents);
|
1092
|
query.setParameter("parent", parents.get(0));
|
1093
|
children = query.list();
|
1094
|
uuids.addAll(children);
|
1095
|
parents = children;
|
1096
|
// }
|
1097
|
List<UUID> uuidList = new ArrayList<UUID>();
|
1098
|
uuidList.addAll(uuids);
|
1099
|
return uuidList;
|
1100
|
|
1101
|
}
|
1102
|
|
1103
|
// @Override
|
1104
|
// public List<UUID> getAllTaxonIds(UUID rootUuid){
|
1105
|
//
|
1106
|
// Set<UUID> uuids= new HashSet<UUID>();
|
1107
|
// List<UUID> children= new ArrayList<UUID>();
|
1108
|
// List<UUID> parents= new ArrayList<UUID>();
|
1109
|
// String queryString;
|
1110
|
// String parameter;
|
1111
|
//
|
1112
|
// queryString="select distinct chn.taxon.uuid from TaxonNode tn " +
|
1113
|
// "join tn.childNodes as chn " +
|
1114
|
// "where tn.taxon.uuid in :parents ";
|
1115
|
//
|
1116
|
// Query query= getSession().createQuery(queryString);
|
1117
|
//
|
1118
|
// parents.add(rootUuid);
|
1119
|
//
|
1120
|
// //while(!(parents.isEmpty())){
|
1121
|
// parents.add(UUID.fromString("54e767ee-894e-4540-a758-f906ecb4e2d9"));
|
1122
|
// parameter=parents.toString();
|
1123
|
// System.out.println("parameter: "+parameter);
|
1124
|
//
|
1125
|
// //children = query.list();
|
1126
|
// // parents=children
|
1127
|
// //}
|
1128
|
//
|
1129
|
// return parents;
|
1130
|
//
|
1131
|
// }
|
1132
|
|
1133
|
@Override
|
1134
|
public void getAllTaxonIds() {
|
1135
|
|
1136
|
Set<UUID> uuids = new HashSet<UUID>();
|
1137
|
|
1138
|
// return (List<UUID>) uuids;
|
1139
|
|
1140
|
}
|
1141
|
|
1142
|
}
|