// $Id$
/**
* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
+* European Distributed Institute of Taxonomy
* http://www.e-taxonomy.eu
-*
+*
* 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.
*/
import java.util.ArrayList;
import java.util.Collection;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.UUID;
-import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import eu.etaxonomy.cdm.api.service.pager.Pager;
+import eu.etaxonomy.cdm.api.service.pager.impl.AbstractPagerImpl;
import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
+import eu.etaxonomy.cdm.api.utility.DescriptionUtility;
+import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
import eu.etaxonomy.cdm.model.common.Annotation;
+import eu.etaxonomy.cdm.model.common.DefinedTerm;
import eu.etaxonomy.cdm.model.common.Language;
+import eu.etaxonomy.cdm.model.common.Marker;
import eu.etaxonomy.cdm.model.common.MarkerType;
import eu.etaxonomy.cdm.model.common.TermVocabulary;
import eu.etaxonomy.cdm.model.description.DescriptionBase;
import eu.etaxonomy.cdm.model.description.Feature;
import eu.etaxonomy.cdm.model.description.FeatureTree;
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
-import eu.etaxonomy.cdm.model.description.Scope;
import eu.etaxonomy.cdm.model.description.TaxonDescription;
import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
import eu.etaxonomy.cdm.model.description.TextData;
import eu.etaxonomy.cdm.model.media.Media;
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import eu.etaxonomy.cdm.model.taxon.Taxon;
+import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
import eu.etaxonomy.cdm.persistence.dao.common.ITermVocabularyDao;
import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;
import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionElementDao;
import eu.etaxonomy.cdm.persistence.dao.description.IFeatureTreeDao;
import eu.etaxonomy.cdm.persistence.dao.description.IStatisticalMeasurementValueDao;
import eu.etaxonomy.cdm.persistence.query.OrderHint;
+import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
/**
* @author a.mueller
* @created 24.06.2008
* @version 1.0
*/
+/**
+ * @author a.kohlbecker
+ * @date Dec 5, 2013
+ *
+ */
@Service
-@Transactional(readOnly = true, propagation = Propagation.SUPPORTS)
+@Transactional(readOnly = true)
public class DescriptionServiceImpl extends IdentifiableServiceBase<DescriptionBase,IDescriptionDao> implements IDescriptionService {
-
- private static final Logger logger = Logger.getLogger(DescriptionServiceImpl.class);
-
- protected IDescriptionElementDao descriptionElementDao;
- protected IFeatureTreeDao featureTreeDao;
- protected IFeatureNodeDao featureNodeDao;
- protected IFeatureDao featureDao;
- protected ITermVocabularyDao vocabularyDao;
- protected IStatisticalMeasurementValueDao statisticalMeasurementValueDao;
- private INaturalLanguageGenerator naturalLanguageGenerator;
-
- @Autowired
- protected void setFeatureTreeDao(IFeatureTreeDao featureTreeDao) {
- this.featureTreeDao = featureTreeDao;
- }
-
- @Autowired
- protected void setFeatureNodeDao(IFeatureNodeDao featureNodeDao) {
- this.featureNodeDao = featureNodeDao;
- }
-
- @Autowired
- protected void setFeatureDao(IFeatureDao featureDao) {
- this.featureDao = featureDao;
- }
-
- @Autowired
- protected void setVocabularyDao(ITermVocabularyDao vocabularyDao) {
- this.vocabularyDao = vocabularyDao;
- }
-
- @Autowired
- protected void statisticalMeasurementValueDao(IStatisticalMeasurementValueDao statisticalMeasurementValueDao) {
- this.statisticalMeasurementValueDao = statisticalMeasurementValueDao;
- }
-
- @Autowired
- protected void setDescriptionElementDao(IDescriptionElementDao descriptionElementDao) {
- this.descriptionElementDao = descriptionElementDao;
- }
-
- @Autowired
- protected void setNaturalLanguageGenerator(INaturalLanguageGenerator naturalLanguageGenerator) {
- this.naturalLanguageGenerator = naturalLanguageGenerator;
- }
-
- /**
- *
- */
- public DescriptionServiceImpl() {
- logger.debug("Load DescriptionService Bean");
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache()
- */
- @Override
- public void updateTitleCache() {
- Class<DescriptionBase> clazz = DescriptionBase.class;
- super.updateTitleCache(clazz, null, null);
- }
-
- public TermVocabulary<Feature> getDefaultFeatureVocabulary(){
- String uuidFeature = "b187d555-f06f-4d65-9e53-da7c93f8eaa8";
- UUID featureUuid = UUID.fromString(uuidFeature);
- return (TermVocabulary)vocabularyDao.findByUuid(featureUuid);
- }
-
- @Autowired
- protected void setDao(IDescriptionDao dao) {
- this.dao = dao;
- }
-
- public int count(Class<? extends DescriptionBase> type, Boolean hasImages, Boolean hasText,Set<Feature> feature) {
- return dao.countDescriptions(type, hasImages, hasText, feature);
- }
-
- /**
- * FIXME Candidate for harmonization
- * rename -> getElements
- */
- public Pager<DescriptionElementBase> getDescriptionElements(DescriptionBase description,
- Set<Feature> features, Class<? extends DescriptionElementBase> type, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
-
- List<DescriptionElementBase> results = listDescriptionElements(description, features, type, pageSize, pageNumber, propertyPaths);
- return new DefaultPagerImpl<DescriptionElementBase>(pageNumber, results.size(), pageSize, results);
- }
-
- public List<DescriptionElementBase> listDescriptionElements(DescriptionBase description,
- Set<Feature> features, Class<? extends DescriptionElementBase> type, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
- Integer numberOfResults = dao.countDescriptionElements(description, features, type);
-
- List<DescriptionElementBase> results = new ArrayList<DescriptionElementBase>();
- if(numberOfResults > 0) { // no point checking again
- results = dao.getDescriptionElements(description, features, type, pageSize, pageNumber, propertyPaths);
- }
- return results;
- }
- public Pager<Annotation> getDescriptionElementAnnotations(DescriptionElementBase annotatedObj, MarkerType status, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
- Integer numberOfResults = descriptionElementDao.countAnnotations(annotatedObj, status);
-
- List<Annotation> results = new ArrayList<Annotation>();
- if(numberOfResults > 0) { // no point checking again
- results = descriptionElementDao.getAnnotations(annotatedObj, status, pageSize, pageNumber, orderHints, propertyPaths);
- }
-
- return new DefaultPagerImpl<Annotation>(pageNumber, numberOfResults, pageSize, results);
- }
-
-
-
- public Pager<Media> getMedia(DescriptionElementBase descriptionElement, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
+
+ private static final Logger logger = Logger.getLogger(DescriptionServiceImpl.class);
+
+ protected IDescriptionElementDao descriptionElementDao;
+ protected IFeatureTreeDao featureTreeDao;
+ protected IFeatureNodeDao featureNodeDao;
+ protected IFeatureDao featureDao;
+ protected ITermVocabularyDao vocabularyDao;
+ protected IDefinedTermDao definedTermDao;
+ protected IStatisticalMeasurementValueDao statisticalMeasurementValueDao;
+ //TODO change to Interface
+ private NaturalLanguageGenerator naturalLanguageGenerator;
+
+ @Autowired
+ protected void setFeatureTreeDao(IFeatureTreeDao featureTreeDao) {
+ this.featureTreeDao = featureTreeDao;
+ }
+
+ @Autowired
+ protected void setFeatureNodeDao(IFeatureNodeDao featureNodeDao) {
+ this.featureNodeDao = featureNodeDao;
+ }
+
+ @Autowired
+ protected void setFeatureDao(IFeatureDao featureDao) {
+ this.featureDao = featureDao;
+ }
+
+ @Autowired
+ protected void setVocabularyDao(ITermVocabularyDao vocabularyDao) {
+ this.vocabularyDao = vocabularyDao;
+ }
+
+ @Autowired
+ protected void setDefinedTermDao(IDefinedTermDao definedTermDao) {
+ this.definedTermDao = definedTermDao;
+ }
+
+ @Autowired
+ protected void statisticalMeasurementValueDao(IStatisticalMeasurementValueDao statisticalMeasurementValueDao) {
+ this.statisticalMeasurementValueDao = statisticalMeasurementValueDao;
+ }
+
+ @Autowired
+ protected void setDescriptionElementDao(IDescriptionElementDao descriptionElementDao) {
+ this.descriptionElementDao = descriptionElementDao;
+ }
+
+ @Autowired
+ protected void setNaturalLanguageGenerator(NaturalLanguageGenerator naturalLanguageGenerator) {
+ this.naturalLanguageGenerator = naturalLanguageGenerator;
+ }
+
+ /**
+ *
+ */
+ public DescriptionServiceImpl() {
+ logger.debug("Load DescriptionService Bean");
+ }
+
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
+ */
+ @Override
+ @Transactional(readOnly = false)
+ public void updateTitleCache(Class<? extends DescriptionBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<DescriptionBase> cacheStrategy, IProgressMonitor monitor) {
+ if (clazz == null){
+ clazz = DescriptionBase.class;
+ }
+ super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
+ }
+
+
+ @Override
+ public TermVocabulary<Feature> getDefaultFeatureVocabulary(){
+ String uuidFeature = "b187d555-f06f-4d65-9e53-da7c93f8eaa8";
+ UUID featureUuid = UUID.fromString(uuidFeature);
+ return vocabularyDao.findByUuid(featureUuid);
+ }
+
+ @Override
+ @Autowired
+ protected void setDao(IDescriptionDao dao) {
+ this.dao = dao;
+ }
+
+ @Override
+ public int count(Class<? extends DescriptionBase> type, Boolean hasImages, Boolean hasText,Set<Feature> feature) {
+ return dao.countDescriptions(type, hasImages, hasText, feature);
+ }
+
+ @Override
+ public Pager<DescriptionElementBase> pageDescriptionElements(DescriptionBase description, Class<? extends DescriptionBase> descriptionType,
+ Set<Feature> features, Class<? extends DescriptionElementBase> type, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
+
+ List<DescriptionElementBase> results = listDescriptionElements(description, descriptionType, features, type, pageSize, pageNumber, propertyPaths);
+ return new DefaultPagerImpl<DescriptionElementBase>(pageNumber, results.size(), pageSize, results);
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.api.service.IDescriptionService#getDescriptionElements(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.Set, java.lang.Class, java.lang.Integer, java.lang.Integer, java.util.List)
+ */
+ @Override
+ @Deprecated
+ public Pager<DescriptionElementBase> getDescriptionElements(DescriptionBase description,
+ Set<Feature> features, Class<? extends DescriptionElementBase> type, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
+ return pageDescriptionElements(description, null, features, type, pageSize, pageNumber, propertyPaths);
+ }
+
+ @Override
+ public List<DescriptionElementBase> listDescriptionElements(DescriptionBase description, Class<? extends DescriptionBase> descriptionType,
+ Set<Feature> features, Class<? extends DescriptionElementBase> type, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
+
+ Integer numberOfResults = dao.countDescriptionElements(description, descriptionType, features, type);
+ List<DescriptionElementBase> results = new ArrayList<DescriptionElementBase>();
+ if(AbstractPagerImpl.hasResultsInRange(numberOfResults.longValue(), pageNumber, pageSize)) {
+ results = dao.getDescriptionElements(description, descriptionType, features, type, pageSize, pageNumber, propertyPaths);
+ }
+ return results;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.api.service.IDescriptionService#listDescriptionElements(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.Set, java.lang.Class, java.lang.Integer, java.lang.Integer, java.util.List)
+ */
+ @Override
+ @Deprecated
+ public List<DescriptionElementBase> listDescriptionElements(DescriptionBase description,
+ Set<Feature> features, Class<? extends DescriptionElementBase> type, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
+
+ return listDescriptionElements(description, null, features, type, pageSize, pageNumber, propertyPaths);
+ }
+
+ @Override
+ public Pager<Annotation> getDescriptionElementAnnotations(DescriptionElementBase annotatedObj, MarkerType status, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
+ Integer numberOfResults = descriptionElementDao.countAnnotations(annotatedObj, status);
+
+ List<Annotation> results = new ArrayList<Annotation>();
+ if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
+ results = descriptionElementDao.getAnnotations(annotatedObj, status, pageSize, pageNumber, orderHints, propertyPaths);
+ }
+
+ return new DefaultPagerImpl<Annotation>(pageNumber, numberOfResults, pageSize, results);
+ }
+
+
+
+ @Override
+ public Pager<Media> getMedia(DescriptionElementBase descriptionElement, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
Integer numberOfResults = descriptionElementDao.countMedia(descriptionElement);
-
- List<Media> results = new ArrayList<Media>();
- if(numberOfResults > 0) { // no point checking again
- results = descriptionElementDao.getMedia(descriptionElement, pageSize, pageNumber, propertyPaths);
- }
-
- return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
- }
-
- public Pager<TaxonDescription> getTaxonDescriptions(Taxon taxon, Set<Scope> scopes, Set<NamedArea> geographicalScope, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
- Integer numberOfResults = dao.countTaxonDescriptions(taxon, scopes, geographicalScope);
-
- List<TaxonDescription> results = new ArrayList<TaxonDescription>();
- if(numberOfResults > 0) { // no point checking again
- results = dao.getTaxonDescriptions(taxon, scopes, geographicalScope, pageSize, pageNumber, propertyPaths);
- }
-
- return new DefaultPagerImpl<TaxonDescription>(pageNumber, numberOfResults, pageSize, results);
- }
-
- public NamedAreaTree getOrderedDistributions(Set<TaxonDescription> taxonDescriptions, Set<NamedAreaLevel> omitLevels){
- List<NamedArea> areaList = new ArrayList<NamedArea>();
- NamedAreaTree tree = new NamedAreaTree();
- //getting all the areas
- for (TaxonDescription taxonDescription : taxonDescriptions) {
- taxonDescription = (TaxonDescription) dao.load(taxonDescription.getUuid());
- Set<DescriptionElementBase> elements = taxonDescription.getElements();
- for (DescriptionElementBase element : elements) {
- if(element.isInstanceOf(Distribution.class)){
- Distribution distribution = (Distribution) element;
- areaList.add(distribution.getArea());
- }
- }
- }
- //ordering the areas
- tree.merge(areaList, omitLevels);
- tree.sortChildren();
- return tree;
- }
-
- public DistributionTree getOrderedDistributionsB(
- Set<TaxonDescription> taxonDescriptions,
- Set<NamedAreaLevel> omitLevels){
-
- DistributionTree tree = new DistributionTree();
- List<Distribution> distList = new ArrayList<Distribution>();
-
- for (TaxonDescription taxonDescription : taxonDescriptions) {
- taxonDescription = (TaxonDescription) dao.load(taxonDescription.getUuid());
- Set<DescriptionElementBase> elements = taxonDescription.getElements();
- for (DescriptionElementBase element : elements) {
- if(element.isInstanceOf(Distribution.class)){
- Distribution distribution = (Distribution) element;
- distList.add(distribution);
- }
- }
- }
-
- //ordering the areas
- tree.merge(distList, omitLevels);
- tree.sortChildren();
- return tree;
- }
-
- public Pager<TaxonNameDescription> getTaxonNameDescriptions(TaxonNameBase name, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
+
+ List<Media> results = new ArrayList<Media>();
+ if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
+ results = descriptionElementDao.getMedia(descriptionElement, pageSize, pageNumber, propertyPaths);
+ }
+
+ return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
+ }
+
+ @Override
+ public Pager<TaxonDescription> pageTaxonDescriptions(Taxon taxon, Set<DefinedTerm> scopes, Set<NamedArea> geographicalScope, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
+ Set<MarkerType> markerTypes = null;
+ return pageTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, pageSize, pageNumber, propertyPaths);
+ }
+
+ @Override
+ public List<TaxonDescription> listTaxonDescriptions(Taxon taxon, Set<DefinedTerm> scopes, Set<NamedArea> geographicalScope, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
+ Set<MarkerType> markerTypes = null;
+ return listTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, pageSize, pageNumber, propertyPaths);
+ }
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.api.service.IDescriptionService#pageMarkedTaxonDescriptions(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.Set, java.util.Set, java.util.Set, java.lang.Integer, java.lang.Integer, java.util.List)
+ */
+ @Override
+ public Pager<TaxonDescription> pageTaxonDescriptions(Taxon taxon, Set<DefinedTerm> scopes, Set<NamedArea> geographicalScope, Set<MarkerType> markerTypes, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
+ Integer numberOfResults = dao.countTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes);
+
+ List<TaxonDescription> results = new ArrayList<TaxonDescription>();
+ if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
+ results = dao.listTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, pageSize, pageNumber, propertyPaths);
+ }
+
+ return new DefaultPagerImpl<TaxonDescription>(pageNumber, numberOfResults, pageSize, results);
+ }
+
+ @Override
+ public List<TaxonDescription> listTaxonDescriptions(Taxon taxon, Set<DefinedTerm> scopes, Set<NamedArea> geographicalScope, Set<MarkerType> markerTypes, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
+ List<TaxonDescription> results = dao.listTaxonDescriptions(taxon, scopes, geographicalScope, markerTypes, pageSize, pageNumber, propertyPaths);
+ return results;
+ }
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.api.service.IDescriptionService#listTaxonDescriptionMedia(UUID, boolean, Set, Integer, Integer, List)
+ */
+ @Override
+ public List<Media> listTaxonDescriptionMedia(UUID taxonUuid, boolean limitToGalleries, Set<MarkerType> markerTypes, Integer pageSize, Integer pageNumber, List<String> propertyPaths){
+ return this.dao.listTaxonDescriptionMedia(taxonUuid, limitToGalleries, markerTypes, pageSize, pageNumber, propertyPaths);
+ }
+
+ /*
+ * @see IDescriptionService#countTaxonDescriptionMedia(UUID, boolean, Set)
+ */
+ @Override
+ public int countTaxonDescriptionMedia(UUID taxonUuid, boolean limitToGalleries, Set<MarkerType> markerTypes){
+ return this.dao.countTaxonDescriptionMedia(taxonUuid, limitToGalleries, markerTypes);
+ }
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.api.service.IDescriptionService#getOrderedDistributions(java.util.Set, boolean, boolean, java.util.Set, java.util.List)
+ */
+ @Override
+ @Deprecated
+ public DistributionTree getOrderedDistributions(
+ Set<TaxonDescription> taxonDescriptions,
+ boolean subAreaPreference,
+ boolean statusOrderPreference,
+ Set<MarkerType> hideMarkedAreas,
+ Set<NamedAreaLevel> omitLevels, List<String> propertyPaths){
+
+ List<Distribution> distList = new ArrayList<Distribution>();
+
+ List<UUID> uuids = new ArrayList<UUID>();
+ for (TaxonDescription taxonDescription : taxonDescriptions) {
+ if (! taxonDescription.isImageGallery()){ //image galleries should not have descriptions, but better filter fully on DTYPE of description element
+ uuids.add(taxonDescription.getUuid());
+ }
+ }
+
+ List<DescriptionBase> desclist = dao.list(uuids, null, null, null, propertyPaths);
+ for (DescriptionBase desc : desclist) {
+ if (desc.isInstanceOf(TaxonDescription.class)){
+ Set<DescriptionElementBase> elements = desc.getElements();
+ for (DescriptionElementBase element : elements) {
+ if (element.isInstanceOf(Distribution.class)) {
+ Distribution distribution = (Distribution) element;
+ if(distribution.getArea() != null){
+ distList.add(distribution);
+ }
+ }
+ }
+ }
+ }
+
+ //old
+// for (TaxonDescription taxonDescription : taxonDescriptions) {
+// if (logger.isDebugEnabled()){ logger.debug("load taxon description " + taxonDescription.getUuid());}
+// //TODO why not loading all description via .list ? This may improve performance
+// taxonDescription = (TaxonDescription) dao.load(taxonDescription.getUuid(), propertyPaths);
+// Set<DescriptionElementBase> elements = taxonDescription.getElements();
+// for (DescriptionElementBase element : elements) {
+// if (element.isInstanceOf(Distribution.class)) {
+// Distribution distribution = (Distribution) element;
+// if(distribution.getArea() != null){
+// distList.add(distribution);
+// }
+// }
+// }
+// }
+
+ if (logger.isDebugEnabled()){logger.debug("filter tree for " + distList.size() + " distributions ...");}
+
+ // filter distributions
+ Collection<Distribution> filteredDistributions = DescriptionUtility.filterDistributions(distList, subAreaPreference, statusOrderPreference, hideMarkedAreas);
+ distList.clear();
+ distList.addAll(filteredDistributions);
+
+ return DescriptionUtility.orderDistributions(omitLevels, distList);
+ }
+
+
+ @Override
+ public Pager<TaxonNameDescription> getTaxonNameDescriptions(TaxonNameBase name, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
Integer numberOfResults = dao.countTaxonNameDescriptions(name);
-
- List<TaxonNameDescription> results = new ArrayList<TaxonNameDescription>();
- if(numberOfResults > 0) { // no point checking again
- results = dao.getTaxonNameDescriptions(name, pageSize, pageNumber,propertyPaths);
- }
-
- return new DefaultPagerImpl<TaxonNameDescription>(pageNumber, numberOfResults, pageSize, results);
- }
-
-
- public Pager<DescriptionBase> page(Class<? extends DescriptionBase> type, Boolean hasImages, Boolean hasText, Set<Feature> feature, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
+
+ List<TaxonNameDescription> results = new ArrayList<TaxonNameDescription>();
+ if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
+ results = dao.getTaxonNameDescriptions(name, pageSize, pageNumber,propertyPaths);
+ }
+
+ return new DefaultPagerImpl<TaxonNameDescription>(pageNumber, numberOfResults, pageSize, results);
+ }
+
+
+ @Override
+ public Pager<DescriptionBase> page(Class<? extends DescriptionBase> type, Boolean hasImages, Boolean hasText, Set<Feature> feature, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
Integer numberOfResults = dao.countDescriptions(type, hasImages, hasText, feature);
-
- List<DescriptionBase> results = new ArrayList<DescriptionBase>();
- if(numberOfResults > 0) { // no point checking again
- results = dao.listDescriptions(type, hasImages, hasText, feature, pageSize, pageNumber,orderHints,propertyPaths);
- }
-
- return new DefaultPagerImpl<DescriptionBase>(pageNumber, numberOfResults, pageSize, results);
- }
-
- /**
- * FIXME Candidate for harmonization
- * Rename: searchByDistribution
- */
- public Pager<TaxonDescription> searchDescriptionByDistribution(Set<NamedArea> namedAreas, PresenceAbsenceTermBase presence, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
+
+ List<DescriptionBase> results = new ArrayList<DescriptionBase>();
+ if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
+ results = dao.listDescriptions(type, hasImages, hasText, feature, pageSize, pageNumber,orderHints,propertyPaths);
+ }
+
+ return new DefaultPagerImpl<DescriptionBase>(pageNumber, numberOfResults, pageSize, results);
+ }
+
+ /**
+ * FIXME Candidate for harmonization
+ * Rename: searchByDistribution
+ */
+ @Override
+ public Pager<TaxonDescription> searchDescriptionByDistribution(Set<NamedArea> namedAreas, PresenceAbsenceTermBase presence, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
Integer numberOfResults = dao.countDescriptionByDistribution(namedAreas, presence);
-
- List<TaxonDescription> results = new ArrayList<TaxonDescription>();
- if(numberOfResults > 0) { // no point checking again
- results = dao.searchDescriptionByDistribution(namedAreas, presence, pageSize, pageNumber,orderHints,propertyPaths);
- }
-
- return new DefaultPagerImpl<TaxonDescription>(pageNumber, numberOfResults, pageSize, results);
- }
-
- /**
- * FIXME Candidate for harmonization
- * move: descriptionElementService.search
- */
- public Pager<DescriptionElementBase> searchElements(Class<? extends DescriptionElementBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
- Integer numberOfResults = descriptionElementDao.count(clazz,queryString);
-
- List<DescriptionElementBase> results = new ArrayList<DescriptionElementBase>();
- if(numberOfResults > 0) { // no point checking again
- results = descriptionElementDao.search(clazz, queryString, pageSize, pageNumber, orderHints, propertyPaths);
- }
-
- return new DefaultPagerImpl<DescriptionElementBase>(pageNumber, numberOfResults, pageSize, results);
- }
-
- /**
- * FIXME Candidate for harmonization
- * descriptionElementService.find
- */
- public DescriptionElementBase getDescriptionElementByUuid(UUID uuid) {
- return descriptionElementDao.findByUuid(uuid);
- }
-
- /**
- * FIXME Candidate for harmonization
- * descriptionElementService.load
- */
- public DescriptionElementBase loadDescriptionElement(UUID uuid, List<String> propertyPaths) {
- return descriptionElementDao.load(uuid, propertyPaths);
- }
+
+ List<TaxonDescription> results = new ArrayList<TaxonDescription>();
+ if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
+ results = dao.searchDescriptionByDistribution(namedAreas, presence, pageSize, pageNumber,orderHints,propertyPaths);
+ }
+
+ return new DefaultPagerImpl<TaxonDescription>(pageNumber, numberOfResults, pageSize, results);
+ }
+
+ /**
+ * FIXME Candidate for harmonization
+ * move: descriptionElementService.search
+ */
+ @Override
+ public Pager<DescriptionElementBase> searchElements(Class<? extends DescriptionElementBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
+ Integer numberOfResults = descriptionElementDao.count(clazz, queryString);
+
+ List<DescriptionElementBase> results = new ArrayList<DescriptionElementBase>();
+ if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
+ results = descriptionElementDao.search(clazz, queryString, pageSize, pageNumber, orderHints, propertyPaths);
+ }
+
+ return new DefaultPagerImpl<DescriptionElementBase>(pageNumber, numberOfResults, pageSize, results);
+ }
+
+ /**
+ * FIXME Candidate for harmonization
+ * descriptionElementService.find
+ */
+ @Override
+ public DescriptionElementBase getDescriptionElementByUuid(UUID uuid) {
+ return descriptionElementDao.findByUuid(uuid);
+ }
+
+ /**
+ * FIXME Candidate for harmonization
+ * descriptionElementService.load
+ */
+ @Override
+ public DescriptionElementBase loadDescriptionElement(UUID uuid, List<String> propertyPaths) {
+ return descriptionElementDao.load(uuid, propertyPaths);
+ }
/**
* FIXME Candidate for harmonization
* descriptionElementService.save
*/
- @Transactional(readOnly = false)
- public UUID saveDescriptionElement(DescriptionElementBase descriptionElement) {
- return descriptionElementDao.save(descriptionElement);
- }
-
+ @Override
+ @Transactional(readOnly = false)
+ public UUID saveDescriptionElement(DescriptionElementBase descriptionElement) {
+ return descriptionElementDao.save(descriptionElement);
+ }
+
/**
* FIXME Candidate for harmonization
* descriptionElementService.save
*/
- @Transactional(readOnly = false)
- public Map<UUID, DescriptionElementBase> saveDescriptionElement(Collection<DescriptionElementBase> descriptionElements) {
- return descriptionElementDao.saveAll(descriptionElements);
- }
+ @Override
+ @Transactional(readOnly = false)
+ public Map<UUID, DescriptionElementBase> saveDescriptionElement(Collection<DescriptionElementBase> descriptionElements) {
+ return descriptionElementDao.saveAll(descriptionElements);
+ }
/**
* FIXME Candidate for harmonization
* descriptionElementService.delete
*/
- public UUID deleteDescriptionElement(DescriptionElementBase descriptionElement) {
- return descriptionElementDao.delete(descriptionElement);
- }
-
- public TermVocabulary<Feature> getFeatureVocabulary(UUID uuid) {
- return (TermVocabulary)vocabularyDao.findByUuid(uuid);
- }
-
- public List<DescriptionElementBase> getDescriptionElementsForTaxon(
- Taxon taxon, Set<Feature> features,
- Class<? extends DescriptionElementBase> type, Integer pageSize,
- Integer pageNumber, List<String> propertyPaths) {
- return dao.getDescriptionElementForTaxon(taxon, features, type, pageSize, pageNumber, propertyPaths);
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.api.service.IDescriptionService#generateNaturalLanguageDescription(eu.etaxonomy.cdm.model.description.FeatureTree, eu.etaxonomy.cdm.model.description.TaxonDescription, eu.etaxonomy.cdm.model.common.Language, java.util.List)
- */
- @Override
- public String generateNaturalLanguageDescription(FeatureTree featureTree,
- TaxonDescription description, List<Language> preferredLanguages, String separator) {
-
- Language lang = preferredLanguages.size() > 0 ? preferredLanguages.get(0) : Language.DEFAULT();
-
- description = (TaxonDescription)load(description.getUuid());
- featureTree = featureTreeDao.load(featureTree.getUuid());
-
- StringBuilder naturalLanguageDescription = new StringBuilder();
-
- if(description.hasStructuredData()){
-
- List<TextData> textDataList = naturalLanguageGenerator.generateNaturalLanguageDescription(
- featureTree,
- ((TaxonDescription)description),
- lang);
-
- String lastCategory = null;
- String categorySeparator = ". ";
-
- String sep = separator;
-
- boolean doItBetter = true;
-
- for (TextData textData : textDataList.toArray(new TextData[textDataList.size()])){
- if(textData.getMultilanguageText().size() > 0){
-
- if (!textData.getFeature().equals(Feature.UNKNOWN())) {
- String featureLabel = textData.getFeature().getLabel(lang);
-
- if(doItBetter){
- /*
- * WARNING
- * The code lines below are desinged to handle
- * a special case where as the fealure label contains
- * hirarchical information on the features. This code
- * exist only as a base for discussion, and is not
- * intendet to be used in production.
- */
- featureLabel = StringUtils.remove(featureLabel, '>');
-
- String[] labelTokens = StringUtils.split(featureLabel, '<');
- if(labelTokens[0].equals(lastCategory) && labelTokens.length > 1){
- if(naturalLanguageDescription.length() > 0){
- naturalLanguageDescription.append(separator);
-}
- naturalLanguageDescription.append(labelTokens[1]);
- } else {
- if(naturalLanguageDescription.length() > 0){
- naturalLanguageDescription.append(categorySeparator);
- }
- naturalLanguageDescription.append(StringUtils.join(labelTokens));
- }
- lastCategory = labelTokens[0];
- // end of demo code
- } else {
- if(naturalLanguageDescription.length() > 0){
- naturalLanguageDescription.append(categorySeparator);
- }
- naturalLanguageDescription.append(textData.getFeature().getLabel(lang));
- }
- }
- String text = textData.getMultilanguageText().values().iterator().next().getText();
- naturalLanguageDescription.append(text);
-
- }
- }
-
- }
- return naturalLanguageDescription.toString();
- }
-
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.api.service.IDescriptionService#hasStructuredData(eu.etaxonomy.cdm.model.description.DescriptionBase)
- */
- @Override
- public boolean hasStructuredData(DescriptionBase<?> description) {
- return load(description.getUuid()).hasStructuredData();
- }
+ @Override
+ public UUID deleteDescriptionElement(DescriptionElementBase descriptionElement) {
+ return descriptionElementDao.delete(descriptionElement);
+ }
+
+ @Override
+ public TermVocabulary<Feature> getFeatureVocabulary(UUID uuid) {
+ return vocabularyDao.findByUuid(uuid);
+ }
+
+ @Override
+ @Deprecated
+ public <T extends DescriptionElementBase> List<T> getDescriptionElementsForTaxon(
+ Taxon taxon, Set<Feature> features,
+ Class<T> type, Integer pageSize,
+ Integer pageNumber, List<String> propertyPaths) {
+ return listDescriptionElementsForTaxon(taxon, features, type, pageSize, pageNumber, propertyPaths);
+ }
+
+ @Override
+ public <T extends DescriptionElementBase> List<T> listDescriptionElementsForTaxon(
+ Taxon taxon, Set<Feature> features,
+ Class<T> type, Integer pageSize,
+ Integer pageNumber, List<String> propertyPaths) {
+ return dao.getDescriptionElementForTaxon(taxon.getUuid(), features, type, pageSize, pageNumber, propertyPaths);
+ }
+
+ @Override
+ public <T extends DescriptionElementBase> Pager<T> pageDescriptionElementsForTaxon(
+ Taxon taxon, Set<Feature> features,
+ Class<T> type, Integer pageSize,
+ Integer pageNumber, List<String> propertyPaths) {
+ if (logger.isDebugEnabled()){logger.debug(" get count ...");}
+ Long count = dao.countDescriptionElementForTaxon(taxon.getUuid(), features, type);
+ List<T> descriptionElements;
+ if(AbstractPagerImpl.hasResultsInRange(count, pageNumber, pageSize)){ // no point checking again
+ if (logger.isDebugEnabled()){logger.debug(" get list ...");}
+ descriptionElements = listDescriptionElementsForTaxon(taxon, features, type, pageSize, pageNumber, propertyPaths);
+ } else {
+ descriptionElements = new ArrayList<T>(0);
+ }
+ if (logger.isDebugEnabled()){logger.debug(" service - DONE ...");}
+ return new DefaultPagerImpl<T>(pageNumber, count.intValue(), pageSize, descriptionElements);
+ }
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.api.service.IDescriptionService#generateNaturalLanguageDescription(eu.etaxonomy.cdm.model.description.FeatureTree, eu.etaxonomy.cdm.model.description.TaxonDescription, eu.etaxonomy.cdm.model.common.Language, java.util.List)
+ */
+ @Override
+ public String generateNaturalLanguageDescription(FeatureTree featureTree,
+ TaxonDescription description, List<Language> preferredLanguages, String separator) {
+
+ Language lang = preferredLanguages.size() > 0 ? preferredLanguages.get(0) : Language.DEFAULT();
+
+ description = (TaxonDescription)load(description.getUuid());
+ featureTree = featureTreeDao.load(featureTree.getUuid());
+
+ StringBuilder naturalLanguageDescription = new StringBuilder();
+
+ MarkerType useMarkerType = (MarkerType) definedTermDao.load(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
+ boolean isUseDescription = false;
+ if(!description.getMarkers().isEmpty()) {
+ for (Marker marker: description.getMarkers()) {
+ MarkerType markerType = marker.getMarkerType();
+ if (markerType.equals(useMarkerType)) {
+ isUseDescription = true;
+ }
+
+ }
+ }
+
+ if(description.hasStructuredData() && !isUseDescription){
+
+
+ String lastCategory = null;
+ String categorySeparator = ". ";
+
+ List<TextData> textDataList;
+ TextData naturalLanguageDescriptionText = null;
+
+ boolean useMicroFormatQuantitativeDescriptionBuilder = false;
+
+ if(useMicroFormatQuantitativeDescriptionBuilder){
+
+ MicroFormatQuantitativeDescriptionBuilder micro = new MicroFormatQuantitativeDescriptionBuilder();
+ naturalLanguageGenerator.setQuantitativeDescriptionBuilder(micro);
+ naturalLanguageDescriptionText = naturalLanguageGenerator.generateSingleTextData(featureTree, (description), lang);
+
+ } else {
+
+ naturalLanguageDescriptionText = naturalLanguageGenerator.generateSingleTextData(
+ featureTree,
+ (description),
+ lang);
+ }
+
+ return naturalLanguageDescriptionText.getText(lang);
+
+//
+// boolean doItBetter = false;
+//
+// for (TextData textData : textDataList.toArray(new TextData[textDataList.size()])){
+// if(textData.getMultilanguageText().size() > 0){
+//
+// if (!textData.getFeature().equals(Feature.UNKNOWN())) {
+// String featureLabel = textData.getFeature().getLabel(lang);
+//
+// if(doItBetter){
+// /*
+// * WARNING
+// * The code lines below are desinged to handle
+// * a special case where as the feature label contains
+// * hierarchical information on the features. This code
+// * exist only as a base for discussion, and is not
+// * intendet to be used in production.
+// */
+// featureLabel = StringUtils.remove(featureLabel, '>');
+//
+// String[] labelTokens = StringUtils.split(featureLabel, '<');
+// if(labelTokens[0].equals(lastCategory) && labelTokens.length > 1){
+// if(naturalLanguageDescription.length() > 0){
+// naturalLanguageDescription.append(separator);
+// }
+// naturalLanguageDescription.append(labelTokens[1]);
+// } else {
+// if(naturalLanguageDescription.length() > 0){
+// naturalLanguageDescription.append(categorySeparator);
+// }
+// naturalLanguageDescription.append(StringUtils.join(labelTokens));
+// }
+// lastCategory = labelTokens[0];
+// // end of demo code
+// } else {
+// if(naturalLanguageDescription.length() > 0){
+// naturalLanguageDescription.append(separator);
+// }
+// naturalLanguageDescription.append(textData.getFeature().getLabel(lang));
+// }
+// } else {
+// if(naturalLanguageDescription.length() > 0){
+// naturalLanguageDescription.append(separator);
+// }
+// }
+// String text = textData.getMultilanguageText().values().iterator().next().getText();
+// naturalLanguageDescription.append(text);
+//
+// }
+// }
+
+ }
+ else if (isUseDescription) {
+ //AT: Left Blank in case we need to generate a Natural language text string.
+ }
+ return naturalLanguageDescription.toString();
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.api.service.IDescriptionService#hasStructuredData(eu.etaxonomy.cdm.model.description.DescriptionBase)
+ */
+ @Override
+ public boolean hasStructuredData(DescriptionBase<?> description) {
+ return load(description.getUuid()).hasStructuredData();
+ }
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.api.service.IDescriptionService#moveDescriptionElementsToDescription(java.util.Collection, eu.etaxonomy.cdm.model.description.DescriptionBase, boolean)
+ */
+ @Override
+ public void moveDescriptionElementsToDescription(Collection<DescriptionElementBase> descriptionElements,
+ DescriptionBase targetDescription, boolean isCopy) {
+
+ if (descriptionElements.isEmpty() ){
+ return ;
+ }
+
+ if (! isCopy && descriptionElements == descriptionElements.iterator().next().getInDescription().getElements()){
+ //if the descriptionElements collection is the elements set of a description, put it in a separate set before to avoid concurrent modification exceptions
+ descriptionElements = new HashSet<DescriptionElementBase>(descriptionElements);
+// descriptionElementsTmp.addAll(descriptionElements);
+// descriptionElements = descriptionElementsTmp;
+ }
+ for (DescriptionElementBase element : descriptionElements){
+ DescriptionBase description = element.getInDescription();
+ try {
+ DescriptionElementBase newElement = (DescriptionElementBase)element.clone();
+ targetDescription.addElement(newElement);
+ } catch (CloneNotSupportedException e) {
+ new RuntimeException ("Clone not yet implemented for class " + element.getClass().getName(), e);
+ }
+ if (! isCopy){
+ description.removeElement(element);
+ }
+
+ }
+ }
+
+ @Override
+ public Pager<NamedArea> pageNamedAreasInUse(Integer pageSize,
+ Integer pageNumber, List<String> propertyPaths){
+
+ List<NamedArea> results = dao.listNamedAreasInUse(pageSize, pageNumber, propertyPaths);
+ return new DefaultPagerImpl<NamedArea>(pageNumber, results.size(), pageSize, results);
+ }
+
}
BGBM BDI Projects / cdmlib.git / blobdiff