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db727ae6
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Andreas Müller
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package eu.etaxonomy.cdm.api.service;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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d49e88fa
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Patrick Plitzner
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import java.util.HashMap;
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import java.util.HashSet;
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db727ae6
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Andreas Müller
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Service;
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import org.springframework.transaction.annotation.Transactional;
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import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.common.monitor.IRemotingProgressMonitor;
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import eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread;
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import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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d49e88fa
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Patrick Plitzner
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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db727ae6
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Andreas Müller
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
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import eu.etaxonomy.cdm.model.description.DescriptiveSystemRole;
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import eu.etaxonomy.cdm.model.description.Feature;
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d49e88fa
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Patrick Plitzner
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import eu.etaxonomy.cdm.model.description.QuantitativeData;
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import eu.etaxonomy.cdm.model.description.SpecimenDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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db727ae6
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Andreas Müller
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.persistence.dao.description.IDescriptiveDataSetDao;
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import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
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@Service
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@Transactional(readOnly = false)
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public class DescriptiveDataSetService
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extends IdentifiableServiceBase<DescriptiveDataSet, IDescriptiveDataSetDao>
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implements IDescriptiveDataSetService {
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private static Logger logger = Logger.getLogger(DescriptiveDataSetService.class);
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@Autowired
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private IOccurrenceService occurrenceService;
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d49e88fa
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Patrick Plitzner
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@Autowired
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private IDescriptionService descriptionService;
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db727ae6
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Andreas Müller
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@Autowired
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private ITaxonNodeService taxonNodeService;
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@Autowired
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private IProgressMonitorService progressMonitorService;
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@Override
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@Autowired
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protected void setDao(IDescriptiveDataSetDao dao) {
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this.dao = dao;
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}
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@Override
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public Map<DescriptionBase, Set<DescriptionElementBase>> getDescriptionElements(DescriptiveDataSet descriptiveDataSet, Set<Feature> features, Integer pageSize, Integer pageNumber,
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List<String> propertyPaths) {
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return dao.getDescriptionElements(descriptiveDataSet, features, pageSize, pageNumber, propertyPaths);
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}
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@Override
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public <T extends DescriptionElementBase> Map<UuidAndTitleCache, Map<UUID, Set<T>>> getTaxonFeatureDescriptionElementMap(
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Class<T> clazz, UUID descriptiveDataSetUuid, DescriptiveSystemRole role) {
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return dao.getTaxonFeatureDescriptionElementMap(clazz, descriptiveDataSetUuid, role);
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}
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@Override
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public List<UuidAndTitleCache<DescriptiveDataSet>> getDescriptiveDataSetUuidAndTitleCache(Integer limitOfInitialElements, String pattern) {
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return dao.getDescriptiveDataSetUuidAndTitleCache( limitOfInitialElements, pattern);
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}
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@Override
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@Transactional
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public UUID monitGetRowWrapper(DescriptiveDataSet descriptiveDataSet) {
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RemotingProgressMonitorThread monitorThread = new RemotingProgressMonitorThread() {
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@Override
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public Serializable doRun(IRemotingProgressMonitor monitor) {
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return getRowWrapper(descriptiveDataSet, monitor);
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}
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};
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UUID uuid = progressMonitorService.registerNewRemotingMonitor(monitorThread);
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monitorThread.setPriority(3);
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monitorThread.start();
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return uuid;
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}
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@Override
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public ArrayList<RowWrapperDTO> getRowWrapper(DescriptiveDataSet descriptiveDataSet, IProgressMonitor monitor) {
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monitor.beginTask("Load row wrapper", descriptiveDataSet.getDescriptions().size());
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ArrayList<RowWrapperDTO> wrappers = new ArrayList<>();
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Set<DescriptionBase> descriptions = descriptiveDataSet.getDescriptions();
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for (DescriptionBase description : descriptions) {
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if(monitor.isCanceled()){
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return new ArrayList<>();
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}
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wrappers.add(createRowWrapper(null, description, null, descriptiveDataSet));
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monitor.worked(1);
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}
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return wrappers;
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}
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@Override
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public Collection<SpecimenNodeWrapper> loadSpecimens(DescriptiveDataSet descriptiveDataSet){
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//set filter parameters
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TaxonNodeFilter filter = TaxonNodeFilter.NewRankInstance(descriptiveDataSet.getMinRank(), descriptiveDataSet.getMaxRank());
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descriptiveDataSet.getGeoFilter().forEach(area -> filter.orArea(area.getUuid()));
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descriptiveDataSet.getTaxonSubtreeFilter().forEach(node -> filter.orSubtree(node));
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filter.setIncludeUnpublished(true);
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List<UUID> filteredNodes = taxonNodeService.uuidList(filter);
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return occurrenceService.listUuidAndTitleCacheByAssociatedTaxon(filteredNodes, null, null);
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}
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@Override
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public RowWrapperDTO createRowWrapper(DescriptionBase description, DescriptiveDataSet descriptiveDataSet){
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return createRowWrapper(null, description, null, descriptiveDataSet);
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}
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@Override
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public RowWrapperDTO createRowWrapper(SpecimenOrObservationBase specimen, DescriptiveDataSet descriptiveDataSet){
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return createRowWrapper(specimen, null, null, descriptiveDataSet);
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}
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private RowWrapperDTO createRowWrapper(SpecimenOrObservationBase specimen, DescriptionBase description, TaxonNode taxonNode, DescriptiveDataSet descriptiveDataSet){
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if(description!=null){
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specimen = description.getDescribedSpecimenOrObservation();
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}
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FieldUnit fieldUnit = null;
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String identifier = null;
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NamedArea country = null;
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//supplemental information
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if(specimen!=null){
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if(taxonNode==null){
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Collection<TaxonBase<?>> associatedTaxa = occurrenceService.listAssociatedTaxa(specimen, null, null, null,
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Arrays.asList(new String[]{
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"taxonNodes",
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"taxonNodes.classification",
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}));
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158 |
897ab6d1
|
Patrick Plitzner
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if(associatedTaxa!=null && !associatedTaxa.isEmpty()){
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159 |
db727ae6
|
Andreas Müller
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//FIXME: what about multiple associated taxa
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Set<TaxonNode> taxonSubtreeFilter = descriptiveDataSet.getTaxonSubtreeFilter();
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if(taxonSubtreeFilter!=null && !taxonSubtreeFilter.isEmpty()){
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Taxon taxon = HibernateProxyHelper.deproxy(associatedTaxa.iterator().next(), Taxon.class);
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taxonNode = taxon.getTaxonNode(taxonSubtreeFilter.iterator().next().getClassification());
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}
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}
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}
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167 |
592f88ca
|
Katja Luther
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Collection<FieldUnit> fieldUnits = occurrenceService.findFieldUnits(specimen.getUuid(),
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168 |
db727ae6
|
Andreas Müller
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Arrays.asList(new String[]{
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"gatheringEvent",
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"gatheringEvent.country"
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}));
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if(fieldUnits.size()!=1){
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logger.error("More than one or no field unit found for specimen"); //$NON-NLS-1$
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}
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else{
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fieldUnit = fieldUnits.iterator().next();
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}
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if(specimen instanceof DerivedUnit){
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identifier = occurrenceService.getMostSignificantIdentifier(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class));
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}
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if(fieldUnit!=null && fieldUnit.getGatheringEvent()!=null){
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country = fieldUnit.getGatheringEvent().getCountry();
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}
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}
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return new RowWrapperDTO(description, specimen, taxonNode, fieldUnit, identifier, country);
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}
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@Override
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@Transactional(readOnly = false)
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public void updateTitleCache(Class<? extends DescriptiveDataSet> clazz, Integer stepSize,
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IIdentifiableEntityCacheStrategy<DescriptiveDataSet> cacheStrategy, IProgressMonitor monitor) {
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if (clazz == null) {
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clazz = DescriptiveDataSet.class;
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}
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super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
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}
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198 |
d49e88fa
|
Patrick Plitzner
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@Override
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public SpecimenDescription findDescriptionForDescriptiveDataSet(UUID descriptiveDataSetUuid, UUID specimenUuid){
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DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);
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SpecimenOrObservationBase specimen = occurrenceService.load(specimenUuid);
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Set<Feature> datasetFeatures = dataSet.getDescriptiveSystem().getDistinctFeatures();
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List<DescriptionElementBase> matchingDescriptionElements = new ArrayList<>();
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for (SpecimenDescription specimenDescription : (Set<SpecimenDescription>) specimen.getDescriptions()) {
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specimenDescription = (SpecimenDescription) descriptionService.load(specimenDescription.getUuid());
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Set<Feature> specimenDescriptionFeatures = new HashSet<>();
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//gather specimen description features and check for match with dataset features
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for (DescriptionElementBase specimenDescriptionElement : specimenDescription.getElements()) {
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Feature feature = specimenDescriptionElement.getFeature();
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specimenDescriptionFeatures.add(feature);
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if(datasetFeatures.contains(feature)){
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matchingDescriptionElements.add(specimenDescriptionElement);
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}
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}
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//if description with the exact same features is found return the description
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if(specimenDescriptionFeatures.equals(datasetFeatures)){
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return specimenDescription;
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}
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}
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//Create new specimen description if no match was found
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SpecimenDescription newDesription = SpecimenDescription.NewInstance(specimen);
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newDesription.setTitleCache("Dataset"+dataSet.getLabel()+": "+newDesription.generateTitle(), true); //$NON-NLS-2$
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//check for equals description element (same feature and same values)
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Map<Feature, List<DescriptionElementBase>> featureToElementMap = new HashMap<>();
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for(DescriptionElementBase element:matchingDescriptionElements){
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List<DescriptionElementBase> list = featureToElementMap.get(element.getFeature());
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if(list==null){
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list = new ArrayList<>();
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}
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list.add(element);
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featureToElementMap.put(element.getFeature(), list);
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}
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Set<DescriptionElementBase> descriptionElementsToClone = new HashSet<>();
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for(Feature feature:featureToElementMap.keySet()){
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List<DescriptionElementBase> elements = featureToElementMap.get(feature);
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//no duplicate description elements found for this feature
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if(elements.size()==1){
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descriptionElementsToClone.add(elements.get(0));
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}
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243 |
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//duplicates found -> check if all are equal
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else{
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DescriptionElementBase match = null;
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for (DescriptionElementBase descriptionElementBase : elements) {
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247 |
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if(match==null){
|
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match = descriptionElementBase;
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249 |
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}
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else if(!new DescriptionElementCompareWrapper(match).equals(new DescriptionElementCompareWrapper(descriptionElementBase))){
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match = null;
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252 |
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//TODO: propagate message
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253 |
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// MessagingUtils.informationDialog(Messages.CharacterMatrix_MULTIPLE_DATA,
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// String.format(Messages.CharacterMatrix_MULTIPLE_DATA_MESSAGE, feature.getLabel()));
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255 |
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break;
|
256 |
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}
|
257 |
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}
|
258 |
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if(match!=null){
|
259 |
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descriptionElementsToClone.add(match);
|
260 |
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}
|
261 |
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}
|
262 |
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}
|
263 |
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//clone matching descriptionElements
|
264 |
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for (DescriptionElementBase descriptionElementBase : descriptionElementsToClone) {
|
265 |
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DescriptionElementBase clone;
|
266 |
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try {
|
267 |
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clone = descriptionElementBase.clone(newDesription);
|
268 |
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clone.getSources().forEach(source -> {
|
269 |
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if(descriptionElementBase instanceof CategoricalData){
|
270 |
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TextData label = new DefaultCategoricalDescriptionBuilder().build((CategoricalData) descriptionElementBase, null);
|
271 |
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source.setOriginalNameString(label.getText(Language.DEFAULT()));
|
272 |
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}
|
273 |
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else if(descriptionElementBase instanceof QuantitativeData){
|
274 |
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TextData label = new DefaultQuantitativeDescriptionBuilder().build((QuantitativeData) descriptionElementBase, null);
|
275 |
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source.setOriginalNameString(label.getText(Language.DEFAULT()));
|
276 |
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}
|
277 |
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});
|
278 |
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} catch (CloneNotSupportedException e) {
|
279 |
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// MessagingUtils.error(CharacterMatrix.class, e);
|
280 |
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}
|
281 |
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}
|
282 |
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|
283 |
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//add all remaining description elements to the new description
|
284 |
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for(Feature wsFeature:datasetFeatures){
|
285 |
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boolean featureFound = false;
|
286 |
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for(DescriptionElementBase element:newDesription.getElements()){
|
287 |
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if(element.getFeature().equals(wsFeature)){
|
288 |
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featureFound = true;
|
289 |
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break;
|
290 |
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}
|
291 |
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}
|
292 |
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if(!featureFound){
|
293 |
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if(wsFeature.isSupportsCategoricalData()){
|
294 |
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newDesription.addElement(CategoricalData.NewInstance(wsFeature));
|
295 |
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}
|
296 |
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else if(wsFeature.isSupportsQuantitativeData()){
|
297 |
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newDesription.addElement(QuantitativeData.NewInstance(wsFeature));
|
298 |
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}
|
299 |
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}
|
300 |
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}
|
301 |
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return newDesription;
|
302 |
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303 |
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}
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304 |
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305 |
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private class DescriptionElementCompareWrapper {
|
306 |
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|
307 |
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private DescriptionElementBase element;
|
308 |
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private Set<UUID> stateUuids = new HashSet<>();
|
309 |
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private Float min = null;
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310 |
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private Float max = null;
|
311 |
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|
312 |
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public DescriptionElementCompareWrapper(DescriptionElementBase element) {
|
313 |
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this.element = element;
|
314 |
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if(element.isInstanceOf(CategoricalData.class)){
|
315 |
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CategoricalData elementData = (CategoricalData)element;
|
316 |
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elementData.getStatesOnly().forEach(state->stateUuids.add(state.getUuid()));
|
317 |
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}
|
318 |
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else if(element.isInstanceOf(QuantitativeData.class)){
|
319 |
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QuantitativeData elementData = (QuantitativeData)element;
|
320 |
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min = elementData.getMin();
|
321 |
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max = elementData.getMax();
|
322 |
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}
|
323 |
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}
|
324 |
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|
325 |
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public DescriptionElementBase unwrap() {
|
326 |
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return element;
|
327 |
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|
}
|
328 |
|
|
|
329 |
|
|
@Override
|
330 |
|
|
public int hashCode() {
|
331 |
|
|
final int prime = 31;
|
332 |
|
|
int result = 1;
|
333 |
|
|
result = prime * result + ((max == null) ? 0 : max.hashCode());
|
334 |
|
|
result = prime * result + ((min == null) ? 0 : min.hashCode());
|
335 |
|
|
result = prime * result + ((stateUuids == null) ? 0 : stateUuids.hashCode());
|
336 |
|
|
return result;
|
337 |
|
|
}
|
338 |
|
|
|
339 |
|
|
@Override
|
340 |
|
|
public boolean equals(Object obj) {
|
341 |
|
|
if (this == obj) {
|
342 |
|
|
return true;
|
343 |
|
|
}
|
344 |
|
|
if (obj == null) {
|
345 |
|
|
return false;
|
346 |
|
|
}
|
347 |
|
|
if (getClass() != obj.getClass()) {
|
348 |
|
|
return false;
|
349 |
|
|
}
|
350 |
|
|
DescriptionElementCompareWrapper other = (DescriptionElementCompareWrapper) obj;
|
351 |
|
|
if (max == null) {
|
352 |
|
|
if (other.max != null) {
|
353 |
|
|
return false;
|
354 |
|
|
}
|
355 |
|
|
} else if (!max.equals(other.max)) {
|
356 |
|
|
return false;
|
357 |
|
|
}
|
358 |
|
|
if (min == null) {
|
359 |
|
|
if (other.min != null) {
|
360 |
|
|
return false;
|
361 |
|
|
}
|
362 |
|
|
} else if (!min.equals(other.min)) {
|
363 |
|
|
return false;
|
364 |
|
|
}
|
365 |
|
|
if (stateUuids == null) {
|
366 |
|
|
if (other.stateUuids != null) {
|
367 |
|
|
return false;
|
368 |
|
|
}
|
369 |
|
|
} else if (!stateUuids.equals(other.stateUuids)) {
|
370 |
|
|
return false;
|
371 |
|
|
}
|
372 |
|
|
return true;
|
373 |
|
|
}
|
374 |
|
|
}
|
375 |
|
|
|
376 |
db727ae6
|
Andreas Müller
|
}
|