Revision 81c01935
Added by Andreas Kohlbecker almost 6 years ago
| cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/hibernate/taxonGraph/AbstractHibernateTaxonGraphProcessor.java | ||
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*/ |
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package eu.etaxonomy.cdm.persistence.dao.hibernate.taxonGraph; |
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import java.util.ArrayList; |
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import java.util.EnumSet; |
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import java.util.List; |
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import java.util.UUID; |
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import org.apache.log4j.Logger; |
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import org.hibernate.Query; |
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import org.hibernate.Session; |
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import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction; |
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import eu.etaxonomy.cdm.model.metadata.CdmPreference; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.TaxonName; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.reference.ReferenceType; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship; |
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
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import eu.etaxonomy.cdm.persistence.dao.taxonGraph.TaxonGraphException; |
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/** |
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private static final Logger logger = Logger.getLogger(AbstractHibernateTaxonGraphProcessor.class); |
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EnumSet<ReferenceType> referenceSectionTypes = EnumSet.of(ReferenceType.Section, ReferenceType.BookSection); |
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private Reference secReference = null; |
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private TaxonRelationshipType relType = TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(); |
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protected TaxonRelationshipType relType() {
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if(relType == null){
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relType = TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(); |
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} |
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return relType; |
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} |
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/** |
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* MUST ONLY BE USED IN TESTS |
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*/ |
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return secReference; |
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} |
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/** |
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* Create all missing edges from the <code>taxon</code>. |
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* |
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* @param taxonName |
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*/ |
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protected void updateEdges(Taxon taxon) throws TaxonGraphException {
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List<TaxonName> relatedHigherNames = relatedHigherNames(taxon.getName()); |
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Reference conceptReference = conceptReference(taxon.getName().getNomenclaturalReference()); |
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if(conceptReference != null){
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List<TaxonRelationship> relations = taxonGraphRelationsFrom(taxon, conceptReference); |
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List<TaxonName> relatedHigherNamesWithoutRels = new ArrayList<>(relatedHigherNames); |
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for(TaxonRelationship rel : relations){
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boolean isRelToHigherName = relatedHigherNames.contains(rel.getToTaxon().getName()); |
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if(isRelToHigherName){
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relatedHigherNamesWithoutRels.remove(rel.getToTaxon().getName()); |
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} else {
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taxon.removeTaxonRelation(rel); |
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} |
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} |
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for(TaxonName name : relatedHigherNamesWithoutRels){
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Taxon toTaxon = assureSingleTaxon(name); |
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taxon.addTaxonRelation(toTaxon, relType(), conceptReference, null); |
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} |
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} |
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} |
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/** |
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* Remove all edges from the <code>taxon</code> having the <code>conceptReference</code> |
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* |
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* @param taxon |
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* @param oldConceptReference |
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*/ |
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protected void removeEdges(Taxon taxon, Reference conceptReference) {
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List<TaxonRelationship> relations = taxonGraphRelationsFrom(taxon, conceptReference); |
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List<TaxonName> relatedHigherNames = relatedHigherNames(taxon.getName()); |
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for(TaxonRelationship rel : relations){
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boolean isRelToHigherName = relatedHigherNames.contains(rel.getToTaxon().getName()); |
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if(isRelToHigherName){
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taxon.removeTaxonRelation(rel); |
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} |
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} |
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} |
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/** |
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* @param taxon |
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*/ |
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protected void updateConceptReferenceInEdges(Taxon taxon, Reference oldNomReference) throws TaxonGraphException {
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Reference conceptReference = conceptReference(taxon.getName().getNomenclaturalReference()); |
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Reference oldConceptReference = conceptReference(oldNomReference); |
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if(conceptReference != null && oldConceptReference != null){
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// update old with new ref |
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updateReferenceInEdges(taxon, conceptReference, oldConceptReference); |
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} else if(conceptReference != null && oldConceptReference == null) {
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// create new relations for the name as there are none so far |
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updateEdges(taxon); |
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} else if(conceptReference == null && oldConceptReference != null){
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// remove all relations |
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removeEdges(taxon, oldConceptReference); |
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} |
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} |
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/** |
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* @param taxon |
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* @param conceptReference |
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* @param oldConceptReference |
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*/ |
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protected void updateReferenceInEdges(Taxon taxon, Reference conceptReference, Reference oldConceptReference) {
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List<TaxonRelationship> relations = taxonGraphRelationsFrom(taxon, oldConceptReference); |
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List<TaxonName> relatedHigherNames = relatedHigherNames(taxon.getName()); |
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for(TaxonRelationship rel : relations){
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boolean isRelToHigherName = relatedHigherNames.contains(rel.getToTaxon().getName()); |
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if(isRelToHigherName){
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rel.setCitation(conceptReference); |
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getSession().saveOrUpdate(rel); |
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} |
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} |
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} |
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abstract Session getSession(); |
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public Taxon assureSingleTaxon(TaxonName taxonName) throws TaxonGraphException {
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return session.load(Taxon.class, taxon.getId()); |
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} |
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protected Reference conceptReference(Reference nomenclaturalReference) {
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Reference conceptRef = nomenclaturalReference; |
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if(conceptRef != null){
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while(referenceSectionTypes.contains(conceptRef.getType()) && conceptRef.getInReference() != null){
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conceptRef = conceptRef.getInReference(); |
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} |
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} |
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return conceptRef; |
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} |
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/** |
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* @param name |
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* @return |
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*/ |
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protected List<TaxonName> relatedHigherNames(TaxonName name) {
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List<TaxonName> relatedNames = new ArrayList<>(); |
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if(name.getRank().isSpecies() || name.getRank().isInfraSpecific()){
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if(name.getGenusOrUninomial() != null){
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List<TaxonName> names = listNames(Rank.GENUS(), name.getGenusOrUninomial(), null); |
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if(names.size() == 0){
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logger.warn("Genus entity with \"" + name.getGenusOrUninomial() + "\" missing");
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} else {
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if(names.size() > 1){
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logger.warn("Duplicate genus entities found for \"" + name.getGenusOrUninomial() + "\", will create taxon graph relation to all of them!");
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} |
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relatedNames.addAll(names); |
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} |
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} |
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} |
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if(name.getRank().isInfraSpecific()){
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if(name.getGenusOrUninomial() != null && name.getSpecificEpithet() != null){
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List<TaxonName> names = listNames(Rank.SPECIES(), name.getGenusOrUninomial(), name.getSpecificEpithet()); |
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if(names.size() == 0){
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logger.warn("Species entity with \"" + name.getGenusOrUninomial() + " " + name.getSpecificEpithet() + "\" missing");
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} else {
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if(names.size() > 1){
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logger.warn("Duplicate species entities found for \"" + name.getGenusOrUninomial() + " " + name.getSpecificEpithet() + "\", will create taxon graph relation to all of them!");
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} |
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relatedNames.addAll(names); |
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} |
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} |
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} |
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return relatedNames; |
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} |
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/** |
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* @param taxon |
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*/ |
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protected List<TaxonRelationship> taxonGraphRelationsFrom(Taxon taxon, Reference citation) {
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List<TaxonRelationship> relations = getTaxonRelationships(taxon, relType(), citation, TaxonRelationship.Direction.relatedFrom); |
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return relations; |
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} |
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/** |
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* @param taxon |
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*/ |
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protected List<TaxonRelationship> taxonGraphRelationsTo(Taxon taxon, Reference citation) {
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List<TaxonRelationship> relations = getTaxonRelationships(taxon, relType(), citation, TaxonRelationship.Direction.relatedTo); |
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return relations; |
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} |
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protected List<TaxonName> listNames(Rank rank, String genusOrUninomial, String specificEpithet){
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String hql = "SELECT n FROM TaxonName n WHERE n.rank = :rank AND n.genusOrUninomial = :genusOrUninomial"; |
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if(specificEpithet != null){
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hql += " AND n.specificEpithet = :specificEpithet"; |
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} |
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Query q = getSession().createQuery(hql); |
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q.setParameter("rank", rank);
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q.setParameter("genusOrUninomial", genusOrUninomial);
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if(specificEpithet != null){
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q.setParameter("specificEpithet", specificEpithet);
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} |
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List<TaxonName> result = q.list(); |
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return result; |
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} |
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protected List<TaxonRelationship> getTaxonRelationships(Taxon relatedTaxon, TaxonRelationshipType type, Reference citation, Direction direction){
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String hql = "SELECT rel FROM TaxonRelationship rel WHERE rel."+direction+" = :relatedTaxon AND rel.type = :type AND rel.citation = :citation"; |
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Query q = getSession().createQuery(hql); |
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q.setParameter("relatedTaxon", relatedTaxon);
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q.setParameter("type", type);
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q.setParameter("citation", citation);
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List<TaxonRelationship> rels = q.list(); |
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return rels; |
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} |
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} |
Also available in: Unified diff
ref #7648 more pulling up into AbstractHibernateTaxonGraphProcessor