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.exception.FilterException;
+import eu.etaxonomy.cdm.exception.UnpublishedException;
import eu.etaxonomy.cdm.hibernate.HHH_9751_Util;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.model.common.CdmBase;
/**
* @author n.hoffmann
- * @created Sep 21, 2009
+ * @since Sep 21, 2009
*/
@Service
@Transactional(readOnly = true)
-public class ClassificationServiceImpl extends IdentifiableServiceBase<Classification, IClassificationDao>
- implements IClassificationService {
+public class ClassificationServiceImpl
+ extends IdentifiableServiceBase<Classification, IClassificationDao>
+ implements IClassificationService {
private static final Logger logger = Logger.getLogger(ClassificationServiceImpl.class);
@Autowired
return loadTaxonNode(node.getUuid(), propertyPaths);
}
- @Override
- @Deprecated // use loadTaxonNode(UUID, List<String>) instead
- public TaxonNode loadTaxonNode(TaxonNode taxonNode, List<String> propertyPaths){
- return taxonNodeDao.load(taxonNode.getUuid(), propertyPaths);
- }
-
public TaxonNode loadTaxonNode(UUID taxonNodeUuid, List<String> propertyPaths){
return taxonNodeDao.load(taxonNodeUuid, propertyPaths);
}
}
@Override
- public List<TaxonNode> listRankSpecificRootNodes(Classification classification, Rank rank, Integer pageSize,
- Integer pageIndex, List<String> propertyPaths) {
- return pageRankSpecificRootNodes(classification, rank, pageSize, pageIndex, propertyPaths).getRecords();
+ public List<TaxonNode> listRankSpecificRootNodes(Classification classification, Rank rank,
+ boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
+ return listRankSpecificRootNodes(classification, null, rank, includeUnpublished, pageSize, pageIndex, propertyPaths);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public List<TaxonNode> listRankSpecificRootNodes(Classification classification,
+ TaxonNode subtree, Rank rank,
+ boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
+ return pageRankSpecificRootNodes(classification, subtree, rank, includeUnpublished, pageSize, pageIndex, propertyPaths).getRecords();
}
@Override
- public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, Rank rank, Integer pageSize,
- Integer pageIndex, List<String> propertyPaths) {
- long[] numberOfResults = dao.countRankSpecificRootNodes(classification, rank);
+ public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, Rank rank,
+ boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
+ return pageRankSpecificRootNodes(classification, null, rank, includeUnpublished, pageSize, pageIndex, propertyPaths);
+ }
+
+ @Override
+ public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, TaxonNode subtree, Rank rank,
+ boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
+ long[] numberOfResults = dao.countRankSpecificRootNodes(classification, subtree, includeUnpublished, rank);
long totalNumberOfResults = numberOfResults[0] + (numberOfResults.length > 1 ? numberOfResults[1] : 0);
- List<TaxonNode> results = new ArrayList<TaxonNode>();
+ List<TaxonNode> results = new ArrayList<>();
if (AbstractPagerImpl.hasResultsInRange(totalNumberOfResults, pageIndex, pageSize)) { // no point checking again
Integer limit = PagerUtils.limitFor(pageSize);
continue;
}
- List<TaxonNode> perQueryResults = dao.listRankSpecificRootNodes(classification, rank, remainingLimit, start, propertyPaths, queryIndex);
+ List<TaxonNode> perQueryResults = dao.listRankSpecificRootNodes(classification,
+ subtree, rank, includeUnpublished, remainingLimit,
+ start, propertyPaths, queryIndex);
results.addAll(perQueryResults);
if(remainingLimit != null ){
remainingLimit = remainingLimit - results.size();
// long start_t = System.currentTimeMillis();
Collections.sort(results, taxonNodeComparator); // TODO is ordering during the hibernate query in the dao possible?
// System.err.println("service.pageRankSpecificRootNodes() - Collections.sort(results, taxonNodeComparator) " + (System.currentTimeMillis() - start_t));
- return new DefaultPagerImpl<TaxonNode>(pageIndex, (int) totalNumberOfResults, pageSize, results);
+ return new DefaultPagerImpl<>(pageIndex, totalNumberOfResults, pageSize, results);
+
+ }
+ @Override
+ public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank,
+ boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
+ return loadTreeBranch(taxonNode, null, baseRank, includeUnpublished, propertyPaths);
}
/**
- * @implements {@link IClassificationService#loadTreeBranch(TaxonNode, Rank, List)
- * @see eu.etaxonomy.cdm.api.service.ITaxonService#loadTreeBranchTo(eu.etaxonomy.cdm.model.taxon.TaxonNode, eu.etaxonomy.cdm.model.name.Rank, java.util.List)
- * FIXME Candidate for harmonization
- * move to classification service
+ * {@inheritDoc}
*/
@Override
- public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank, List<String> propertyPaths){
+ public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, TaxonNode subtree, Rank baseRank,
+ boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
TaxonNode thisNode = taxonNodeDao.load(taxonNode.getUuid(), propertyPaths);
if(baseRank != null){
baseRank = (Rank) termDao.load(baseRank.getUuid());
}
- List<TaxonNode> pathToRoot = new ArrayList<TaxonNode>();
+ if (!includeUnpublished && thisNode.getTaxon() != null && !thisNode.getTaxon().isPublish()){
+ throw new UnpublishedException("Final taxon in tree branch is unpublished.");
+ }
+
+ List<TaxonNode> pathToRoot = new ArrayList<>();
pathToRoot.add(thisNode);
while(!thisNode.isTopmostNode()){
//TODO why do we need to deproxy here?
// without this thisNode.getParent() will return NULL in
// some cases (environment dependend?) even if the parent exits
- TaxonNode parentNode = CdmBase.deproxy(thisNode, TaxonNode.class).getParent();
+ TaxonNode parentNode = CdmBase.deproxy(thisNode).getParent();
if(parentNode == null){
- throw new NullPointerException("taxonNode " + thisNode + " must have a parent since it is not top most");
+ throw new NullPointerException("Taxon node " + thisNode + " must have a parent since it is not top most");
}
if(parentNode.getTaxon() == null){
- throw new NullPointerException("The taxon associated with taxonNode " + parentNode + " is NULL");
+ throw new NullPointerException("The taxon associated with taxon node " + parentNode + " is NULL");
+ }
+ if(!includeUnpublished && !parentNode.getTaxon().isPublish()){
+ throw new UnpublishedException("Some taxon in tree branch is unpublished.");
}
if(parentNode.getTaxon().getName() == null){
throw new NullPointerException("The name of the taxon associated with taxonNode " + parentNode + " is NULL");
}
- Rank parentNodeRank = parentNode.getTaxon().getName() == null ? null : parentNode.getTaxon().getName().getRank();
+ Rank parentNodeRank = (parentNode.getTaxon().getName() == null) ? null : parentNode.getTaxon().getName().getRank();
// stop if the next parent is higher than the baseRank
if(baseRank != null && parentNodeRank != null && baseRank.isLower(parentNodeRank)){
break;
}
+ if((subtree!= null && !subtree.isAncestor(parentNode) )){
+ break;
+ }
pathToRoot.add(parentNode);
thisNode = parentNode;
}
@Override
- public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification, Rank baseRank, List<String> propertyPaths){
- Classification tree = dao.load(classification.getUuid());
- taxon = (Taxon) taxonDao.load(taxon.getUuid());
- TaxonNode node = tree.getNode(taxon);
+ public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification, Rank baseRank,
+ boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
+ return loadTreeBranchToTaxon(taxon, classification, null, baseRank, includeUnpublished, propertyPaths);
+ }
+
+ @Override
+ public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
+ TaxonNode subtree, Rank baseRank,
+ boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
+
+ UUID nodeUuid = getTaxonNodeUuidByTaxonUuid(classification.getUuid(), taxon.getUuid());
+ TaxonNode node = taxonNodeService.find(nodeUuid);
if(node == null){
logger.warn("The specified taxon is not found in the given tree.");
return null;
+ }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 loadTreeBranch(node, baseRank, propertyPaths);
+
+ return loadTreeBranch(node, subtree, baseRank, includeUnpublished, propertyPaths);
}
}
@Override
- public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize,
- Integer pageIndex, List<String> propertyPaths){
+ public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid,
+ boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths){
+ try {
+ return listChildNodesOfTaxon(taxonUuid, classificationUuid, null, includeUnpublished, pageSize, pageIndex, propertyPaths);
+ } catch (FilterException e) {
+ throw new RuntimeException(e); //this should not happen as filter is null
+ }
+ }
+
+ @Override
+ public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid,
+ boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) throws FilterException{
Classification classification = dao.load(classificationUuid);
Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
+ TaxonNode subtree = taxonNodeDao.load(subtreeUuid);
+ if (subtreeUuid != null && subtree == null){
+ throw new FilterException("Taxon node for subtree filter can not be found in database", true);
+ }
- List<TaxonNode> results = dao.listChildrenOf(taxon, classification, pageSize, pageIndex, propertyPaths);
+ List<TaxonNode> results = dao.listChildrenOf(
+ taxon, classification, subtree, includeUnpublished, pageSize, pageIndex, propertyPaths);
Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
return results;
}
@Override
- public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize,
- Integer pageIndex, List<String> propertyPaths){
+ public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
+ Integer pageSize, Integer pageIndex, List<String> propertyPaths){
Classification classification = dao.load(classificationUuid);
Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
- long numberOfResults = dao.countSiblingsOf(taxon, classification);
+ long numberOfResults = dao.countSiblingsOf(taxon, classification, includeUnpublished);
List<TaxonNode> results;
if(PagerUtils.hasResultsInRange(numberOfResults, pageIndex, pageSize)) {
- results = dao.listSiblingsOf(taxon, classification, pageSize, pageIndex, propertyPaths);
+ results = dao.listSiblingsOf(taxon, classification, includeUnpublished, pageSize, pageIndex, propertyPaths);
Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
} else {
results = new ArrayList<>();
}
- return new DefaultPagerImpl<TaxonNode>(pageIndex, numberOfResults, pageSize, results);
+ return new DefaultPagerImpl<>(pageIndex, numberOfResults, pageSize, results);
}
@Override
- public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize,
- Integer pageIndex, List<String> propertyPaths){
+ public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
+ Integer pageSize, Integer pageIndex, List<String> propertyPaths){
- Pager<TaxonNode> pager = pageSiblingsOfTaxon(taxonUuid, classificationUuid, pageSize, pageIndex, propertyPaths);
+ Pager<TaxonNode> pager = pageSiblingsOfTaxon(taxonUuid, classificationUuid, includeUnpublished, pageSize, pageIndex, propertyPaths);
return pager.getRecords();
}
- @Override
- public TaxonNode getTaxonNodeByUuid(UUID uuid) {
- return taxonNodeDao.findByUuid(uuid);
- }
-
@Override
public ITaxonTreeNode getTreeNodeByUuid(UUID uuid){
ITaxonTreeNode treeNode = taxonNodeDao.findByUuid(uuid);
}
@Override
- public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, Integer limit, String pattern) {
- return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), limit, pattern);
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications) {
+ return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), limit, pattern, searchForClassifications);
}
@Override
- public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, Integer limit, String pattern) {
- return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, limit, pattern);
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, Integer limit, String pattern, boolean searchForClassifications) {
+ return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, limit, pattern, searchForClassifications);
}
@Override
- public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid ) {
- return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), null, null);
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, boolean searchForClassifications ) {
+ return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), null, null, searchForClassifications);
}
@Override
- public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification ) {
- return taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, null, null);
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, boolean searchForClassifications ) {
+ return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, null, null, searchForClassifications);
}
@Override
TaxonNode taxonNode, List<String> propertyPaths, int size,
int height, int widthOrDuration, String[] mimeTypes) {
- TreeMap<UUID, List<MediaRepresentation>> result = new TreeMap<UUID, List<MediaRepresentation>>();
- List<Media> taxonMedia = new ArrayList<Media>();
- List<MediaRepresentation> mediaRepresentations = new ArrayList<MediaRepresentation>();
+ TreeMap<UUID, List<MediaRepresentation>> result = new TreeMap<>();
+ List<MediaRepresentation> mediaRepresentations = new ArrayList<>();
//add all media of the children to the result map
if (taxonNode != null){
- List<TaxonNode> nodes = new ArrayList<TaxonNode>();
+ List<TaxonNode> nodes = new ArrayList<>();
- nodes.add(loadTaxonNode(taxonNode, propertyPaths));
+ nodes.add(loadTaxonNode(taxonNode.getUuid(), propertyPaths));
nodes.addAll(loadChildNodesOfTaxonNode(taxonNode, propertyPaths));
- if (nodes != null){
- for(TaxonNode node : nodes){
- Taxon taxon = node.getTaxon();
- for (TaxonDescription taxonDescription: taxon.getDescriptions()){
- for (DescriptionElementBase descriptionElement: taxonDescription.getElements()){
- for(Media media : descriptionElement.getMedia()){
- taxonMedia.add(media);
-
- //find the best matching representation
- mediaRepresentations.add(MediaUtils.findBestMatchingRepresentation(media,null, size, height, widthOrDuration, mimeTypes));
-
- }
+ for(TaxonNode node : nodes){
+ Taxon taxon = node.getTaxon();
+ for (TaxonDescription taxonDescription: taxon.getDescriptions()){
+ for (DescriptionElementBase descriptionElement: taxonDescription.getElements()){
+ for(Media media : descriptionElement.getMedia()){
+ //find the best matching representation
+ mediaRepresentations.add(MediaUtils.findBestMatchingRepresentation(media,null, size, height, widthOrDuration, mimeTypes));
}
}
- result.put(taxon.getUuid(), mediaRepresentations);
-
}
+ result.put(taxon.getUuid(), mediaRepresentations);
}
-
}
return result;
-
}
-
@Override
@Transactional(readOnly = false)
public void updateTitleCache(Class<? extends Classification> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<Classification> cacheStrategy, IProgressMonitor monitor) {
}
Map<String, List<TaxonNode>> sortedGenusMap = new HashMap<>();
for(TaxonNode node:allNodesOfClassification){
- final TaxonNode tn = node;
Taxon taxon = node.getTaxon();
INonViralName name = taxon.getName();
String genusOrUninomial = name.getGenusOrUninomial();
sortedGenusMap.put(genusOrUninomial, list);
}else{
//create List for genus
- List<TaxonNode> list = new ArrayList<TaxonNode>();
+ List<TaxonNode> list = new ArrayList<>();
list.add(node);
sortedGenusMap.put(genusOrUninomial, list);
}
*/
@Override
public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonBaseUuid,
- Boolean doChildren, Boolean doSynonyms, List<UUID> ancestorMarkers,
+ Boolean doChildren, Boolean doSynonyms, boolean includeUnpublished, List<UUID> ancestorMarkers,
NodeSortMode sortMode) {
TaxonInContextDTO result = new TaxonInContextDTO();
}
}
-
result.setTaxonUuid(taxonBaseUuid);
result.setClassificationUuid(classificationUuid);
if (taxonBase.getSec() != null){
boolean recursive = false;
Integer pageSize = null;
Integer pageIndex = null;
- Pager<TaxonNodeDto> children = taxonNodeService.pageChildNodesDTOs(taxonNodeUuid, recursive, doSynonyms, sortMode, pageSize, pageIndex);
+ Pager<TaxonNodeDto> children = taxonNodeService.pageChildNodesDTOs(taxonNodeUuid, recursive, includeUnpublished, doSynonyms,
+ sortMode, pageSize, pageIndex);
//children
if(! isSynonym) {
EntityDTO<Taxon> child = new EntityDTO<Taxon>(childDto.getTaxonUuid(), childDto.getTitleCache());
result.addChild(child);
}else if (doSynonyms && childDto.getStatus().isSynonym()){
- EntityDTO<Synonym> child = new EntityDTO<Synonym>(childDto.getTaxonUuid(), childDto.getTitleCache());
+ EntityDTO<Synonym> child = new EntityDTO<>(childDto.getTaxonUuid(), childDto.getTitleCache());
result.addSynonym(child);
}
}
//marked ancestors
if (ancestorMarkers != null && !ancestorMarkers.isEmpty()){
+ @SuppressWarnings("rawtypes")
List<DefinedTermBase> markerTypesTerms = termDao.list(ancestorMarkers, pageSize, null, null, null);
List<MarkerType> markerTypes = new ArrayList<>();
for (DefinedTermBase<?> term : markerTypesTerms){
}
}
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
+ Classification classification) {
+ return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, false);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
+ UUID classificationUuid) {
+ return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classificationUuid, false);
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
+ UUID classificationUuid, Integer limit, String pattern) {
+ return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classificationUuid, limit, pattern, false);
+ }
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
+ Classification classification, Integer limit, String pattern) {
+ return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, limit, pattern, false);
+ }
}