import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
+import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.UUID;
import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
import eu.etaxonomy.cdm.api.service.config.TaxonNodeDeletionConfigurator;
import eu.etaxonomy.cdm.api.service.dto.CdmEntityIdentifier;
+import eu.etaxonomy.cdm.api.service.dto.CreateTaxonDTO;
import eu.etaxonomy.cdm.api.service.dto.TaxonDistributionDTO;
+import eu.etaxonomy.cdm.api.service.dto.TaxonDistributionDTOComparator;
import eu.etaxonomy.cdm.api.service.pager.Pager;
import eu.etaxonomy.cdm.api.service.pager.PagerUtils;
import eu.etaxonomy.cdm.api.service.pager.impl.AbstractPagerImpl;
import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeFilterDao;
+import eu.etaxonomy.cdm.persistence.dto.MergeResult;
import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
-import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
import eu.etaxonomy.cdm.persistence.hibernate.permission.ICdmPermissionEvaluator;
import eu.etaxonomy.cdm.persistence.query.OrderHint;
+import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
/**
* @author n.hoffmann
return dao.listChildrenOf(node, pageSize, pageIndex, recursive, includeUnpublished, propertyPaths);
}
- /**
- * {@inheritDoc}
- */
@Override
public TaxonNodeDto getParentUuidAndTitleCache(ITaxonTreeNode child) {
UUID uuid = child.getUuid();
return getParentUuidAndTitleCache(uuidAndTitleCache);
}
- /**
- * {@inheritDoc}
- */
@Override
public TaxonNodeDto getParentUuidAndTitleCache(TaxonNodeDto child) {
return dao.getParentUuidAndTitleCache(child);
return dao.listChildNodesAsTaxonNodeDto(parent);
}
-
-
@Override
- public List<UuidAndTitleCache<TaxonNode>> getUuidAndTitleCache(Integer limit, String pattern, UUID classificationUuid) {
+ public List<TaxonNodeDto> getUuidAndTitleCache(Integer limit, String pattern, UUID classificationUuid) {
return dao.getUuidAndTitleCache(limit, pattern, classificationUuid);
}
@Override
public List<TaxonNodeDto> listChildNodesAsTaxonNodeDto(ITaxonTreeNode parent) {
+ List<String> propertyPaths = new ArrayList<>();
+ propertyPaths.add("parent");
+ parent = dao.load(parent.getId(), propertyPaths);
TaxonNodeDto uuidAndTitleCache = new TaxonNodeDto(parent);
return listChildNodesAsTaxonNodeDto(uuidAndTitleCache);
}
-
@Override
- public TaxonNodeDto taxonNodeDtoParentRank(Classification classification, Rank rank, TaxonName name) {
+ public List<TaxonNodeDto> taxonNodeDtoParentRank(Classification classification, Rank rank, TaxonName name) {
return dao.getParentTaxonNodeDtoForRank(classification, rank, name);
}
+ @Override
+ public List<TaxonNodeDto> taxonNodeDtoParentRank(Classification classification, Rank rank, TaxonBase<?> taxonBase) {
+ return dao.getParentTaxonNodeDtoForRank(classification, rank, taxonBase);
+ }
+
@Override
public Pager<TaxonNodeDto> pageChildNodesDTOs(UUID taxonNodeUuid, boolean recursive, boolean includeUnpublished,
boolean doSynonyms, NodeSortMode sortMode,
@Override
public TaxonNodeDto parentDto(UUID taxonNodeUuid) {
+ if (taxonNodeUuid == null){
+ return null;
+ }
TaxonNode taxonNode = dao.load(taxonNodeUuid);
if(taxonNode.getParent() != null) {
return new TaxonNodeDto(taxonNode.getParent());
@Override
public TaxonNodeDto dto(UUID taxonNodeUuid) {
+ if (taxonNodeUuid == null){
+ return null;
+ }
TaxonNode taxonNode = dao.load(taxonNodeUuid);
- if(taxonNode.getParent() != null) {
+ if (taxonNode != null){
return new TaxonNodeDto(taxonNode);
}
return null;
if (treeNode != null){
TaxonNode taxonNode;
- taxonNode = HibernateProxyHelper.deproxy(treeNode, TaxonNode.class);
+ taxonNode = CdmBase.deproxy(treeNode);
TaxonNode parent = taxonNode.getParent();
//check whether the node has children or the children are already deleted
if(taxonNode.hasChildNodes()) {
- List<TaxonNode> children = new ArrayList<TaxonNode> ();
+ List<TaxonNode> children = new ArrayList<> ();
List<TaxonNode> childNodesList = taxonNode.getChildNodes();
children.addAll(childNodesList);
//To avoid NPE when child is also in list of taxonNodes, remove it from the list
} else {
//classification = null;
Taxon taxon = taxonNode.getTaxon();
- taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);
+ taxon = CdmBase.deproxy(taxon);
if (taxon != null){
taxon.removeTaxonNode(taxonNode);
if (config.getTaxonNodeConfig().isDeleteTaxon()){
@Transactional(readOnly = false)
public DeleteResult deleteTaxonNode(UUID nodeUUID, TaxonDeletionConfigurator config) {
- TaxonNode node = HibernateProxyHelper.deproxy(dao.load(nodeUUID), TaxonNode.class);
+ TaxonNode node = CdmBase.deproxy(dao.load(nodeUUID));
return deleteTaxonNode(node, config);
}
@Override
@Transactional
- public UpdateResult createNewTaxonNode(UUID parentNodeUuid, Taxon newTaxon, Reference ref, String microref){
+ public UpdateResult createNewTaxonNode(UUID parentNodeUuid, CreateTaxonDTO taxonDto, UUID refUuid, String microref, boolean unplaced, boolean doubtful, boolean excluded, Map<Language,LanguageString> excludedNote){
UpdateResult result = new UpdateResult();
- if (newTaxon.getName().getId() != 0){
- TaxonName name = nameService.load(newTaxon.getName().getUuid());
- newTaxon.setName(name);
+ TaxonName name = null;
+ if (taxonDto.getNameUuid() != null){
+ name = nameService.load(taxonDto.getNameUuid());
+
}else{
- for (HybridRelationship rel : newTaxon.getName().getHybridChildRelations()){
+ NonViralNameParserImpl nonViralNameParser = NonViralNameParserImpl.NewInstance();
+ name = (TaxonName) nonViralNameParser.parseFullName(taxonDto.getTaxonNameString());
+ }
+ Reference sec = null;
+ if (taxonDto.getSecUuid() != null ){
+ sec = referenceService.load(taxonDto.getSecUuid());
+
+ }
+ if (!name.isPersited()){
+ for (HybridRelationship rel : name.getHybridChildRelations()){
if (!rel.getHybridName().isPersited()) {
nameService.save(rel.getHybridName());
}
}
}
}
- UUID taxonUUID = taxonService.saveOrUpdate(newTaxon);
- newTaxon = (Taxon) taxonService.load(taxonUUID);
- TaxonNode parent = dao.load(parentNodeUuid);
- TaxonNode child = null;
- try{
- child = parent.addChildTaxon(newTaxon,ref, microref);
+ Taxon newTaxon = Taxon.NewInstance(name, sec);
+// UUID taxonUuid = taxonService.saveOrUpdate(newTaxon);
+// newTaxon = (Taxon) taxonService.load(taxonUuid);
+
+ TaxonNode parent = dao.load(parentNodeUuid);
+ TaxonNode child = null;
+ Reference ref = null;
+ if (refUuid != null){
+ ref = referenceService.load(refUuid);
+ }
+
+ try{
+ child = parent.addChildTaxon(newTaxon, ref, microref);
+ child.setDoubtful(doubtful);
+ child.setExcluded(excluded);
+ child.setUnplaced(unplaced);
+ child.getExcludedNote().putAll(excludedNote);
+
}catch(Exception e){
result.addException(e);
result.setError();
result.setCdmEntity(child);
}
return result;
-
}
-
@Override
@Transactional
public UpdateResult saveNewTaxonNode(TaxonNode newTaxonNode){
UUID parentUuid = newTaxonNode.getParent().getUuid();
Taxon taxon = null;
- if (newTaxonNode.getTaxon().getId() != 0){
+ if (newTaxonNode.getTaxon().isPersited()){
taxon = (Taxon)taxonService.load(newTaxonNode.getTaxon().getUuid());
- //newTaxonNode.setTaxon(taxon);
- }else if (newTaxonNode.getTaxon().getName().getId() != 0){
+ }else if (newTaxonNode.getTaxon().getName().isPersited()){
TaxonName name = nameService.load(newTaxonNode.getTaxon().getName().getUuid());
taxon = newTaxonNode.getTaxon();
taxon.setName(name);
}else{
+ //taxon and name is not persisted, persist possible related names
for (HybridRelationship rel : newTaxonNode.getTaxon().getName().getHybridChildRelations()){
if (!rel.getHybridName().isPersited()) {
nameService.save(rel.getHybridName());
Reference sec = referenceService.load(taxon.getSec().getUuid());
taxon.setSec(sec);
}
- if (taxon.getId() == 0){
- UUID taxonUUID = taxonService.saveOrUpdate(taxon);
- taxon = (Taxon) taxonService.load(taxonUUID);
+ if (!taxon.isPersited()){
+ MergeResult<TaxonBase> mergeResult = taxonService.merge(taxon, true);
+ taxon = (Taxon) mergeResult.getMergedEntity();
}
-
TaxonNode parent = dao.load(parentUuid);
TaxonNode child = null;
try{
child = parent.addChildTaxon(taxon, newTaxonNode.getReference(), newTaxonNode.getMicroReference());
-
}catch(Exception e){
result.addException(e);
result.setError();
return result;
}
+ //TODO can't we work with clone method here?
child.setUnplaced(newTaxonNode.isUnplaced());
child.setExcluded(newTaxonNode.isExcluded());
child.setDoubtful(newTaxonNode.isDoubtful());
}
newTaxonNode = null;
- dao.saveOrUpdate(child);
-
+ MergeResult<TaxonNode> mergeNode = dao.merge(child,true);
+ child = mergeNode.getMergedEntity();
result.addUpdatedObject(child.getParent());
- if (child != null){
- result.setCdmEntity(child);
- }
+ result.setCdmEntity(child);
return result;
-
-
}
-
-
@Override
@Transactional
- public UpdateResult createNewTaxonNode(UUID parentNodeUuid, UUID taxonUuid, Reference ref, String microref){
+ public UpdateResult createNewTaxonNode(UUID parentNodeUuid, UUID taxonUuid, UUID refUuid, String microref){
UpdateResult result = new UpdateResult();
TaxonNode parent = dao.load(parentNodeUuid);
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
result.setCdmEntity(child);
}
return result;
-
}
@Override
return result;
}
-
@Override
@Transactional(readOnly=false)
public UpdateResult setPublishForSubtree(PublishForSubtreeConfigurator config){
if (includeAcceptedTaxa){
monitor.subTask("Update Accepted Taxa");
+ @SuppressWarnings("rawtypes")
Set<TaxonBase> updatedTaxa = dao.setPublishForSubtreeAcceptedTaxa(subTreeIndex, publish, includeSharedTaxa, includeHybrids, monitor);
result.addUpdatedObjects(updatedTaxa);
}
if (includeSynonyms){
monitor.subTask("Update Synonyms");
+ @SuppressWarnings("rawtypes")
Set<TaxonBase> updatedSynonyms = dao.setPublishForSubtreeSynonyms(subTreeIndex, publish, includeSharedTaxa, includeHybrids, monitor);
result.addUpdatedObjects(updatedSynonyms);
}
if (config.isIncludeProParteSynonyms()){
relationTypes.addAll(TaxonRelationshipType.proParteOrPartialSynonymUuids());
}
+ @SuppressWarnings("rawtypes")
Set<TaxonBase> updatedTaxa = dao.setPublishForSubtreeRelatedTaxa(subTreeIndex, publish,
relationTypes, includeSharedTaxa, includeHybrids, monitor);
result.addUpdatedObjects(updatedTaxa);
return result;
}
-
-
@Override
public long count(TaxonNodeFilter filter){
return nodeFilterDao.count(filter);
return commonParent;
}
-
-
@Override
- public List<TaxonDistributionDTO> getTaxonDistributionDTOForSubtree(UUID parentNodeUuid, List<String> propertyPaths, Authentication authentication){
- List<TaxonNode> nodes = listChildrenOf(load(parentNodeUuid), null, null,
- true, true, propertyPaths);
+ public List<TaxonDistributionDTO> getTaxonDistributionDTO(List<UUID> nodeUuids, List<String> propertyPaths, Authentication authentication, boolean openChildren){
+ Set<TaxonNode> nodes = new HashSet<>();
+ if (openChildren){
+ List<TaxonNode> parentNodes = load(nodeUuids, propertyPaths);
+ for (TaxonNode node: parentNodes){
+ nodes.addAll(listChildrenOf(node, null, null, true, true, propertyPaths));
+ }
+ nodes.addAll(parentNodes);
+
+ }
List<TaxonDistributionDTO> result = new ArrayList<>();
boolean hasPermission = false;
//TaxonDescription instance = TaxonDescription.NewInstance();
for(TaxonNode node:nodes){
if (authentication != null ) {
hasPermission = permissionEvaluator.hasPermission(authentication, node, Operation.UPDATE);
- }else if (authentication == null){
+ }else {
hasPermission = true;
}
if (node.getTaxon() != null && hasPermission){
TaxonDistributionDTO dto = new TaxonDistributionDTO(node.getTaxon());
result.add(dto);
}catch(Exception e){
- System.err.println(node.getTaxon().getTitleCache());
+ logger.error(e.getMessage(), e);
}
-
}
-
}
-
+ result.sort(new TaxonDistributionDTOComparator());
return result;
}
return pager;
}
- @Override
- public List<TaxonDistributionDTO> getTaxonDistributionDTOForSubtree(UUID parentNodeUuid,
- List<String> propertyPaths) {
- return getTaxonDistributionDTOForSubtree(parentNodeUuid, propertyPaths, null);
- }
+// @Override
+// public List<TaxonDistributionDTO> getTaxonDistributionDTOForSubtree(UUID parentNodeUuid,
+// List<String> propertyPaths, boolean openChildren) {
+// return getTaxonDistributionDTOForSubtree(parentNodeUuid, propertyPaths, null, openChildren);
+// }
@Override
- public List<TaxonNodeDto> getTaxonNodeDto(Integer limit, String pattern, UUID classificationUuid) {
- return dao.getTaxonNodeDto(limit, pattern, classificationUuid);
+ public List<TaxonDistributionDTO> getTaxonDistributionDTO(List<UUID> nodeUuids,
+ List<String> propertyPaths, boolean openChildren) {
+ return getTaxonDistributionDTO(nodeUuids, propertyPaths, null, openChildren);
}
-
- @Override
- public List<UuidAndTitleCache<TaxonNode>> listChildNodesAsUuidAndTitleCache(ITaxonTreeNode parent) {
- UUID uuid = parent.getUuid();
- int id = parent.getId();
- UuidAndTitleCache<TaxonNode> uuidAndTitleCache = new UuidAndTitleCache<>(uuid, id, null);
- return listChildNodesAsUuidAndTitleCache(uuidAndTitleCache);
- }
-
- @Override
- public List<UuidAndTitleCache<TaxonNode>> listChildNodesAsUuidAndTitleCache(UuidAndTitleCache<TaxonNode> parent) {
- return dao.listChildNodesAsUuidAndTitleCache(parent);
- }
-
-
}
BGBM BDI Projects / cdmlib.git / blobdiff