* The contents of this file are subject to the Mozilla Public License Version 1.1
* See LICENSE.TXT at the top of this package for the full license terms.
*/
-
package eu.etaxonomy.cdm.api.service;
import java.util.ArrayList;
import javax.persistence.EntityNotFoundException;
import org.apache.commons.collections.CollectionUtils;
-import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import eu.etaxonomy.cdm.api.service.config.CreateHierarchyForClassificationConfigurator;
import eu.etaxonomy.cdm.api.service.config.NodeDeletionConfigurator.ChildHandling;
-import eu.etaxonomy.cdm.api.service.config.SubtreeCloneConfigurator;
import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
-import eu.etaxonomy.cdm.api.service.dto.EntityDTO;
import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;
import eu.etaxonomy.cdm.api.service.dto.MarkedEntityDTO;
import eu.etaxonomy.cdm.api.service.dto.TaxonInContextDTO;
import eu.etaxonomy.cdm.api.service.pager.impl.AbstractPagerImpl;
import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
+import eu.etaxonomy.cdm.compare.taxon.ITaxonNodeComparator;
+import eu.etaxonomy.cdm.compare.taxon.TaxonNodeSortMode;
import eu.etaxonomy.cdm.exception.FilterException;
import eu.etaxonomy.cdm.exception.UnpublishedException;
-import eu.etaxonomy.cdm.hibernate.HHH_9751_Util;
import eu.etaxonomy.cdm.model.common.CdmBase;
import eu.etaxonomy.cdm.model.common.ITreeNode;
import eu.etaxonomy.cdm.model.common.MarkerType;
import eu.etaxonomy.cdm.model.name.INonViralName;
import eu.etaxonomy.cdm.model.name.Rank;
import eu.etaxonomy.cdm.model.name.TaxonName;
-import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.taxon.Classification;
-import eu.etaxonomy.cdm.model.taxon.ITaxonNodeComparator;
import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
import eu.etaxonomy.cdm.model.taxon.Synonym;
import eu.etaxonomy.cdm.model.taxon.Taxon;
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
-import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
import eu.etaxonomy.cdm.model.term.DefinedTermBase;
import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
-import eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao;
import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
import eu.etaxonomy.cdm.persistence.dao.term.IDefinedTermDao;
import eu.etaxonomy.cdm.persistence.dto.ClassificationLookupDTO;
+import eu.etaxonomy.cdm.persistence.dto.EntityDTO;
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
import eu.etaxonomy.cdm.persistence.dto.TaxonStatus;
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
extends IdentifiableServiceBase<Classification, IClassificationDao>
implements IClassificationService {
- private static final Logger logger = Logger.getLogger(ClassificationServiceImpl.class);
+ private static final Logger logger = LogManager.getLogger();
@Autowired
private ITaxonNodeDao taxonNodeDao;
@Autowired
private ITaxonNodeService taxonNodeService;
- @Autowired
- private IReferenceDao referenceDao;
-
@Autowired
private IDefinedTermDao termDao;
this.dao = dao;
}
- private Comparator<? super TaxonNode> taxonNodeComparator;
+ private Comparator<TaxonNode> taxonNodeComparator;
@Autowired
- public void setTaxonNodeComparator(ITaxonNodeComparator<? super TaxonNode> taxonNodeComparator){
- this.taxonNodeComparator = (Comparator<? super TaxonNode>) taxonNodeComparator;
+ public void setTaxonNodeComparator(ITaxonNodeComparator<TaxonNode> taxonNodeComparator){
+ this.taxonNodeComparator = (Comparator<TaxonNode>) taxonNodeComparator;
}
@Override
return taxonNodeDao.load(taxonNodeUuid, propertyPaths);
}
- @Override
- @Transactional(readOnly = false)
- public UpdateResult cloneClassification(SubtreeCloneConfigurator config) {
- UpdateResult result = new UpdateResult();
-
- if (config.getSubTreeUuids().isEmpty()){
- return result;
- }
-
- //TODO error handling
- Reference taxonSecundum = config.isReuseTaxa() || config.isReuseTaxonSecundum() || config.getTaxonSecundumUuid() == null ?
- null : referenceDao.findByUuid(config.getTaxonSecundumUuid());
- config.setTaxonSecundum(taxonSecundum);
-
- Reference parentChildReference = config.isReuseParentChildReference() || config.getParentChildReferenceUuid() == null ?
- null : referenceDao.findByUuid(config.getParentChildReferenceUuid());
- config.setParentChildReference(parentChildReference);
-
- Reference taxonRelationshipReference = config.getRelationTypeToOldTaxon() == null ?
- null : referenceDao.findByUuid(config.getRelationshipReferenceUuid());
- config.setRelationshipReference(taxonRelationshipReference);
-
- Classification classificationClone = Classification.NewInstance(config.getClassificationName());
-
- if (config.isReuseClassificationReference()){
- TaxonNode anyNode = taxonNodeDao.findByUuid(config.getSubTreeUuids().iterator().next());
- if (anyNode != null){
- Reference oldClassificationRef = anyNode.getClassification().getReference();
- classificationClone.setReference(oldClassificationRef);
- }
- }else if (config.getClassificationReferenceUuid() != null) {
- Reference classificationReference = referenceDao.findByUuid(config.getClassificationReferenceUuid());
- classificationClone.setReference(classificationReference);
- }
-
- //clone taxa and taxon nodes
-// List<Integer> childNodeIds = taxonNodeService.idList(taxonNodeFilter);
-// List<TaxonNode> childNodes = taxonNodeService.loadByIds(childNodeIds, null);
- List<TaxonNode> rootNodes = taxonNodeService.find(config.getSubTreeUuids());
- for (TaxonNode taxonNode : rootNodes) {
- addChildTaxaToClone(taxonNode, classificationClone.getRootNode(), config);
- }
- dao.saveOrUpdate(classificationClone);
- result.setCdmEntity(classificationClone);
- return result;
- }
-
- private void addChildTaxaToClone(TaxonNode originalParentNode, TaxonNode parentNodeClone,
- SubtreeCloneConfigurator config){
-
- Taxon originalTaxon = CdmBase.deproxy(originalParentNode.getTaxon());
- if (originalTaxon == null){
- for (TaxonNode originalChildChildNode : originalParentNode.getChildNodes()) {
- addChildTaxaToClone(originalChildChildNode, parentNodeClone, config);
- }
- }else{
- TaxonNode childNodeClone;
- String microReference = null;
- if (config.isReuseTaxa()){
- childNodeClone = parentNodeClone.addChildTaxon(originalTaxon, config.getParentChildReference(), microReference);
- }else{
- Taxon cloneTaxon = originalTaxon.clone(config.isIncludeSynonymsIncludingManAndProParte(),
- config.isIncludeTaxonRelationshipsExcludingManAndProParte(),
- config.isIncludeDescriptiveData(), config.isIncludeMedia());
-
- //name
- if (!config.isReuseNames()){
- cloneTaxon.setName(cloneTaxon.getName().clone());
- }
-
- if (!config.isReuseTaxonSecundum()){
- cloneTaxon.setSec(config.getTaxonSecundum());
- }
-
- //add relation between taxa
- if (config.getRelationTypeToOldTaxon() != null){
- TaxonRelationship rel = cloneTaxon.addTaxonRelation(originalParentNode.getTaxon(), config.getRelationTypeToOldTaxon(),
- config.getRelationshipReference(), microReference);
- rel.setDoubtful(config.isRelationDoubtful());
- }
- childNodeClone = parentNodeClone.addChildTaxon(cloneTaxon, config.getParentChildReference(), microReference);
- }
-
- //probably necessary as taxon nodes do not cascade
- taxonNodeDao.saveOrUpdate(childNodeClone);
- //add children
- List<TaxonNode> originalChildNodes = originalParentNode.getChildNodes();
- HHH_9751_Util.removeAllNull(originalChildNodes);
-
- for (TaxonNode originalChildNode : originalChildNodes) {
- addChildTaxaToClone(originalChildNode, childNodeClone, config);
- }
- }
- }
-
@Override
public List<TaxonNode> listRankSpecificRootNodes(Classification classification,
TaxonNode subtree, Rank rank,
Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode sortMode,
List<String> propertyPaths) {
List<TaxonNode> list = listRankSpecificRootNodes(classification, subtree, rank, includeUnpublished, pageSize, pageIndex, propertyPaths);
- return list.stream().filter(e -> e != null).map(e -> new TaxonNodeDto(e)).sorted(sortMode.newComparator()).collect(Collectors.toList());
+ return list.stream().filter(e -> e != null).map(e -> new TaxonNodeDto(e)).sorted(sortMode.comparator()).collect(Collectors.toList());
}
@Override
TaxonNode node = taxonNodeService.find(nodeUuid);
if(node == null){
logger.warn("The specified taxon is not found in the given tree.");
- return null;
+ return new ArrayList<>(0);
}else if (subtree != null && !node.isDescendant(subtree)){
//TODO handle as exception? E.g. FilterException, AccessDeniedException?
logger.warn("The specified taxon is not found for the given subtree.");
- return null;
+ return new ArrayList<>(0);
}
return loadTreeBranch(node, subtree, baseRank, includeUnpublished, propertyPaths);
}
@Override
- public List<TaxonNodeDto> listChildNodeDtosOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
- Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode sortMode, List<String> propertyPaths) throws FilterException{
+ public List<TaxonNodeDto> listChildNodeDtosOfTaxon(UUID taxonUuid, UUID classificationUuid,
+ UUID subtreeUuid, boolean includeUnpublished,
+ Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode sortMode) throws FilterException{
+
Classification classification = dao.load(classificationUuid);
Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
TaxonNode subtree = taxonNodeDao.load(subtreeUuid);
List<TaxonNode> results = dao.listChildrenOf(
taxon, classification, subtree, includeUnpublished, pageSize, pageIndex, propertyPaths);
- Comparator<TaxonNodeDto> comparator = sortMode.newComparator();
+ Comparator<TaxonNodeDto> comparator = sortMode.comparator();
// TODO order during the hibernate query in the dao?
- List<TaxonNodeDto> dtos = results.stream().map(e -> new TaxonNodeDto(e)).sorted(comparator).collect(Collectors.toList());
+ List<TaxonNodeDto> dtos = results.stream()
+ .map(tn -> new TaxonNodeDto(tn))
+ .sorted(comparator)
+ .collect(Collectors.toList());
return dtos;
}
@Transactional(readOnly = false)
@Override
public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator){
+
UpdateResult result = new UpdateResult();
+ Set<TaxonNode> taxonNodesToSave = new HashSet<>();
+
classification = dao.findByUuid(classification.getUuid());
Map<String, List<TaxonNode>> map = getSortedGenusList(classification.getAllNodes());
//get all childNodes
//save prior Hierarchy and remove them from the list
List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tNode, clone, result);
-// parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
- //FIXME remove classification
+// //FIXME remove classification
parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
//remove taxonNode from list because just added to classification
result.addUpdatedObject(tNode);
parentNode = newClassification.addChildTaxon(taxon, 0, null, null);
result.addUpdatedObject(parentNode);
}
- //iterate over the rest of the list
+ taxonNodesToSave.add(parentNode);
+
+ //iterate over the remaining list
for(TaxonNode tn : listOfTaxonNodes){
//if TaxonNode has a parent and this is not the classification then skip it
//and add to new classification via the parentNode as children of it
TaxonNode clone = tn.clone();
//FIXME: citation from node
- //TODO: addchildNode without citation and references
-// TaxonNode taxonNode = parentNode.addChildNode(clone, classification.getCitation(), classification.getMicroReference());
+ //TODO: addChildNode without citation and references
TaxonNode taxonNode = parentNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
+ taxonNodesToSave.add(taxonNode);
+
result.addUnChangedObject(clone);
if(tn.hasChildNodes()){
//save hierarchy in new classification
}
}
dao.saveOrUpdate(newClassification);
+ taxonNodeDao.saveOrUpdateAll(taxonNodesToSave);
result.setCdmEntity(newClassification);
return result;
}
BGBM BDI Projects / cdmlib.git / blobdiff