import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
+import java.util.Map.Entry;
import java.util.Set;
import java.util.UUID;
import eu.etaxonomy.cdm.api.service.UpdateResult.Status;
import eu.etaxonomy.cdm.api.service.config.NodeDeletionConfigurator.ChildHandling;
+import eu.etaxonomy.cdm.api.service.config.PublishForSubtreeConfigurator;
import eu.etaxonomy.cdm.api.service.config.SecundumForSubtreeConfigurator;
import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
import eu.etaxonomy.cdm.api.service.config.TaxonNodeDeletionConfigurator;
import eu.etaxonomy.cdm.api.service.dto.TaxonDistributionDTO;
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.api.service.pager.impl.DefaultPagerImpl;
import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
import eu.etaxonomy.cdm.model.common.CdmBase;
-import eu.etaxonomy.cdm.model.common.DefinedTerm;
+import eu.etaxonomy.cdm.model.common.Language;
+import eu.etaxonomy.cdm.model.common.LanguageString;
import eu.etaxonomy.cdm.model.common.TreeIndex;
+import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
+import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
import eu.etaxonomy.cdm.model.description.TaxonDescription;
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
import eu.etaxonomy.cdm.model.taxon.TaxonNodeAgentRelation;
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
+import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
+import eu.etaxonomy.cdm.model.term.DefinedTerm;
+import eu.etaxonomy.cdm.persistence.dao.common.Restriction;
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.TaxonNodeDto;
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
+import eu.etaxonomy.cdm.persistence.query.OrderHint;
/**
* @author n.hoffmann
@Autowired
private ITaxonService taxonService;
+ @Autowired
+ private IReferenceService referenceService;
+
@Autowired
private IDescriptiveDataSetService dataSetService;
@Override
@Transactional(readOnly = false)
public DeleteResult makeTaxonNodeASynonymOfAnotherTaxonNode(TaxonNode oldTaxonNode, TaxonNode newAcceptedTaxonNode,
- SynonymType synonymType, Reference citation, String citationMicroReference) {
+ SynonymType synonymType, Reference citation, String citationMicroReference, boolean setNameInSource) {
// TODO at the moment this method only moves synonym-, concept relations and descriptions to the new accepted taxon
// in a future version we also want to move cdm data like annotations, marker, so., but we will need a policy for that
taxonRelationship.setFromTaxon(null);
}
-
//Move descriptions to new taxon
List<TaxonDescription> descriptions = new ArrayList<TaxonDescription>( oldTaxon.getDescriptions()); //to avoid concurrent modification errors (newAcceptedTaxon.addDescription() modifies also oldtaxon.descritpions())
for(TaxonDescription description : descriptions){
String message = "Description copied from former accepted taxon: %s (Old title: %s)";
message = String.format(message, oldTaxon.getTitleCache(), description.getTitleCache());
description.setTitleCache(message, true);
+ if (setNameInSource) {
+ for (DescriptionElementBase element: description.getElements()){
+ for (DescriptionElementSource source: element.getSources()){
+ if (source.getNameUsedInSource() == null){
+ source.setNameUsedInSource(newSynonymName);
+ }
+ }
+ }
+ }
//oldTaxon.removeDescription(description, false);
newAcceptedTaxon.addDescription(description);
}
UUID newAcceptedTaxonNodeUUIDs,
SynonymType synonymType,
Reference citation,
- String citationMicroReference) {
+ String citationMicroReference,
+ boolean setNameInSource) {
UpdateResult result = new UpdateResult();
for (UUID nodeUuid: oldTaxonNodeUuids) {
- result.includeResult(makeTaxonNodeASynonymOfAnotherTaxonNode(nodeUuid, newAcceptedTaxonNodeUUIDs, synonymType, citation, citationMicroReference));
+ result.includeResult(makeTaxonNodeASynonymOfAnotherTaxonNode(nodeUuid, newAcceptedTaxonNodeUUIDs, synonymType, citation, citationMicroReference, setNameInSource));
}
return result;
}
UUID newAcceptedTaxonNodeUUID,
SynonymType synonymType,
Reference citation,
- String citationMicroReference) {
+ String citationMicroReference,
+ boolean setNameInSource) {
TaxonNode oldTaxonNode = dao.load(oldTaxonNodeUuid);
TaxonNode oldTaxonParentNode = oldTaxonNode.getParent();
newTaxonNode,
synonymType,
citation,
- citationMicroReference);
+ citationMicroReference, setNameInSource);
result.addUpdatedCdmId(new CdmEntityIdentifier(oldTaxonParentNode.getId(), TaxonNode.class));
result.addUpdatedCdmId(new CdmEntityIdentifier(newTaxonNode.getId(), TaxonNode.class));
result.setCdmEntity(oldTaxonParentNode);
TaxonNode parent = dao.load(parentNodeUuid);
TaxonNode child = null;
try{
- child = parent.addChildTaxon(newTaxon, parent.getReference(), parent.getMicroReference());
+ child = parent.addChildTaxon(newTaxon,ref, microref);
}catch(Exception e){
result.addException(e);
result.setError();
public UpdateResult saveNewTaxonNode(TaxonNode newTaxonNode){
UpdateResult result = new UpdateResult();
UUID parentUuid = newTaxonNode.getParent().getUuid();
- TaxonNode parent = dao.load(parentUuid);
- if (newTaxonNode.getTaxon().getId() != 0){
- Taxon taxon = (Taxon)taxonService.load(newTaxonNode.getTaxon().getUuid());
- newTaxonNode.setTaxon(taxon);
- }else{
- Taxon taxon = newTaxonNode.getTaxon();
- taxon.removeTaxonNode(newTaxonNode);
- UUID taxonUUID = taxonService.saveOrUpdate(taxon);
- taxon = (Taxon) taxonService.load(taxonUUID);
- newTaxonNode.setTaxon(taxon);
- }
+ Taxon taxon = null;
- if (newTaxonNode.getTaxon().getName().getId() != 0){
+ if (newTaxonNode.getTaxon().getId() != 0){
+ taxon = (Taxon)taxonService.load(newTaxonNode.getTaxon().getUuid());
+ //newTaxonNode.setTaxon(taxon);
+ }else if (newTaxonNode.getTaxon().getName().getId() != 0){
TaxonName name = nameService.load(newTaxonNode.getTaxon().getName().getUuid());
- newTaxonNode.getTaxon().setName(name);
+ taxon = newTaxonNode.getTaxon();
+ taxon.setName(name);
}else{
for (HybridRelationship rel : newTaxonNode.getTaxon().getName().getHybridChildRelations()){
if (!rel.getHybridName().isPersited()) {
}
}
}
+ if (taxon == null){
+ taxon = newTaxonNode.getTaxon();
+ }
+ taxon.removeTaxonNode(newTaxonNode);
+
+ if (taxon.getSec() != null && taxon.getSec().isPersited()){
+ Reference sec = referenceService.load(taxon.getSec().getUuid());
+ taxon.setSec(sec);
+ }
+ if (taxon.getId() == 0){
+ UUID taxonUUID = taxonService.saveOrUpdate(taxon);
+ taxon = (Taxon) taxonService.load(taxonUUID);
+
+ }
+
+ TaxonNode parent = dao.load(parentUuid);
TaxonNode child = null;
try{
- child = parent.addChildNode(newTaxonNode, newTaxonNode.getReference(), newTaxonNode.getMicroReference());
+ child = parent.addChildTaxon(taxon, newTaxonNode.getReference(), newTaxonNode.getMicroReference());
}catch(Exception e){
result.addException(e);
result.setError();
return result;
}
+
+ child.setUnplaced(newTaxonNode.isUnplaced());
+ child.setExcluded(newTaxonNode.isExcluded());
+ child.setDoubtful(newTaxonNode.isDoubtful());
+ for (TaxonNodeAgentRelation agentRel :newTaxonNode.getAgentRelations()){
+ child.addAgentRelation(agentRel.getType(), agentRel.getAgent());
+ }
+ for (Entry<Language, LanguageString> entry: newTaxonNode.getExcludedNote().entrySet()){
+ child.putExcludedNote(entry.getKey(), entry.getValue().getText());
+ }
+
+ newTaxonNode = null;
dao.saveOrUpdate(child);
result.addUpdatedObject(child.getParent());
}
- /**
- * {@inheritDoc}
- */
@Override
@Transactional(readOnly=false)
- public UpdateResult setPublishForSubtree(UUID subtreeUuid, boolean publish, boolean includeAcceptedTaxa,
- boolean includeSynonyms, boolean includeSharedTaxa, IProgressMonitor monitor) {
+ public UpdateResult setPublishForSubtree(PublishForSubtreeConfigurator config){
UpdateResult result = new UpdateResult();
+ IProgressMonitor monitor = config.getMonitor();
if (monitor == null){
monitor = DefaultProgressMonitor.NewInstance();
}
TreeIndex subTreeIndex = null;
- if (subtreeUuid == null){
+ if (config.getSubtreeUuid() == null){
result.setError();
result.addException(new NullPointerException("No subtree given"));
monitor.done();
return result;
}
- TaxonNode subTree = find(subtreeUuid);
+ TaxonNode subTree = find(config.getSubtreeUuid());
+ boolean includeAcceptedTaxa = config.isIncludeAcceptedTaxa();
+ boolean publish = config.isPublish();
+ boolean includeSynonyms = config.isIncludeSynonyms();
+ boolean includeSharedTaxa = config.isIncludeSharedTaxa();
+ boolean includeHybrids = config.isIncludeHybrids();
+ boolean includeRelatedTaxa = config.isIncludeProParteSynonyms() || config.isIncludeMisapplications();
if (subTree == null){
result.setError();
result.addException(new NullPointerException("Subtree does not exist"));
return result;
}else{
subTreeIndex = TreeIndex.NewInstance(subTree.treeIndex());
- int count = includeAcceptedTaxa ? dao.countPublishForSubtreeAcceptedTaxa(subTreeIndex, publish, includeSharedTaxa):0;
- count += includeSynonyms ? dao.countPublishForSubtreeSynonyms(subTreeIndex, publish, includeSharedTaxa):0;
+ int count = includeAcceptedTaxa ? dao.countPublishForSubtreeAcceptedTaxa(subTreeIndex, publish, includeSharedTaxa, includeHybrids):0;
+ count += includeSynonyms ? dao.countPublishForSubtreeSynonyms(subTreeIndex, publish, includeSharedTaxa, includeHybrids):0;
+ count += includeRelatedTaxa ? dao.countPublishForSubtreeRelatedTaxa(subTreeIndex, publish, includeSharedTaxa, includeHybrids):0;
monitor.beginTask("Update publish flag", count);
}
if (includeAcceptedTaxa){
monitor.subTask("Update Accepted Taxa");
- Set<TaxonBase> updatedTaxa = dao.setPublishForSubtreeAcceptedTaxa(subTreeIndex, publish, includeSharedTaxa, monitor);
+ Set<TaxonBase> updatedTaxa = dao.setPublishForSubtreeAcceptedTaxa(subTreeIndex, publish, includeSharedTaxa, includeHybrids, monitor);
result.addUpdatedObjects(updatedTaxa);
}
if (includeSynonyms){
monitor.subTask("Update Synonyms");
- Set<TaxonBase> updatedSynonyms = dao.setPublishForSubtreeSynonyms(subTreeIndex, publish, includeSharedTaxa, monitor);
+ Set<TaxonBase> updatedSynonyms = dao.setPublishForSubtreeSynonyms(subTreeIndex, publish, includeSharedTaxa, includeHybrids, monitor);
result.addUpdatedObjects(updatedSynonyms);
}
+ if (includeRelatedTaxa){
+ monitor.subTask("Update Related Taxa");
+ Set<UUID> relationTypes = new HashSet<>();
+ if (config.isIncludeMisapplications()){
+ relationTypes.addAll(TaxonRelationshipType.misappliedNameUuids());
+ }
+ if (config.isIncludeProParteSynonyms()){
+ relationTypes.addAll(TaxonRelationshipType.proParteOrPartialSynonymUuids());
+ }
+ Set<TaxonBase> updatedTaxa = dao.setPublishForSubtreeRelatedTaxa(subTreeIndex, publish,
+ relationTypes, includeSharedTaxa, includeHybrids, monitor);
+ result.addUpdatedObjects(updatedTaxa);
+ }
monitor.done();
return result;
}
-
@Override
public long count(TaxonNodeFilter filter){
return nodeFilterDao.count(filter);
return result;
}
+ @Override
+ public <S extends TaxonNode> Pager<S> page(Class<S> clazz, List<Restriction<?>> restrictions, Integer pageSize,
+ Integer pageIndex, List<OrderHint> orderHints, List<String> propertyPaths) {
+ return page(clazz, restrictions, pageSize, pageIndex, orderHints, propertyPaths, INCLUDE_UNPUBLISHED);
+ }
+
+ @Override
+ public <S extends TaxonNode> Pager<S> page(Class<S> clazz, List<Restriction<?>> restrictions, Integer pageSize,
+ Integer pageIndex, List<OrderHint> orderHints, List<String> propertyPaths, boolean includeUnpublished) {
+
+ List<S> records;
+ long resultSize = dao.count(clazz, restrictions);
+ if(AbstractPagerImpl.hasResultsInRange(resultSize, pageIndex, pageSize)){
+ records = dao.list(clazz, restrictions, pageSize, pageIndex, orderHints, propertyPaths, includeUnpublished);
+ } else {
+ records = new ArrayList<>();
+ }
+ Pager<S> pager = new DefaultPagerImpl<>(pageIndex, resultSize, pageSize, records);
+ return pager;
+ }
}
BGBM BDI Projects / cdmlib.git / blobdiff