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/**
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* Copyright (C) 2013 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.api.service.description;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.LinkedList;
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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.hibernate.HibernateException;
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import org.hibernate.search.Search;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.DescriptionType;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.term.OrderedTermBase;
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import eu.etaxonomy.cdm.model.term.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.term.TermCollection;
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import eu.etaxonomy.cdm.model.term.TermNode;
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import eu.etaxonomy.cdm.model.term.TermTree;
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import eu.etaxonomy.cdm.model.term.VocabularyEnum;
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/**
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*
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* <h2>GENERAL NOTES </h2>
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* <em>TODO: These notes are directly taken from original Transmission Engine Occurrence
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* version 14 written in Visual Basic and still need to be
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* adapted to the java version of the transmission engine!</em>
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*
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* <h3>summaryStatus</h3>
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*
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* Each distribution information has a summaryStatus, this is an summary of the status codes
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* as stored in the fields of emOccurrence native, introduced, cultivated, ...
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* The summaryStatus seems to be equivalent to the CDM DistributionStatus
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*
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* <h3>map generation</h3>
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*
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* When generating maps from the accumulated distribution information some special cases have to be handled:
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* <ol>
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* <li>if an entered or imported status information exists for the same area for which calculated (accumulated)
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* data is available, the calculated data has to be given preference over other data.
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* </li>
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* <li>If there is an area with a sub area and both areas have the same calculated status only the subarea
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* status should be shown in the map, whereas the super area should be ignored.
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* </li>
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* </ol>
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*
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* @author Anton Güntsch (author of original Transmission Engine Occurrence version 14 written in Visual Basic)
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* @author Andreas Kohlbecker (2013, porting Transmission Engine Occurrence to Java)
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* @author a.mueller (refactoring and merge with Structured Description Aggregation)
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* @since Feb 22, 2013
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*/
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public class DistributionAggregation
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extends DescriptionAggregationBase<DistributionAggregation,DistributionAggregationConfiguration>{
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public static final Logger logger = Logger.getLogger(DistributionAggregation.class);
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protected static final List<String> TAXONDESCRIPTION_INIT_STRATEGY = Arrays.asList(new String [] {
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"description.elements.area",
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"description.elements.status",
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"description.elements.sources.citation.authorship",
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// "description.elements.sources.nameUsedInSource",
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// "description.elements.multilanguageText",
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// "name.status.type",
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});
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/**
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* A map which contains the status terms as key and the priority as value
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* The map will contain both, the PresenceTerms and the AbsenceTerms
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*/
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private List<PresenceAbsenceTerm> statusOrder = null;
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private final Map<NamedArea, Set<NamedArea>> subAreaMap = new HashMap<>();
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// ******************* CONSTRUCTOR *********************************/
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public DistributionAggregation() {}
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@Override
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protected String pluralDataType(){
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return "distributions";
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}
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// ********************* METHODS *********************************/
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@Override
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protected void preAggregate(IProgressMonitor monitor) {
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monitor.subTask("make status order");
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// take start time for performance testing
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double start = System.currentTimeMillis();
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makeStatusOrder();
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double end1 = System.currentTimeMillis();
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logger.info("Time elapsed for making status order : " + (end1 - start) / (1000) + "s");
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makeSuperAreas();
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double end2 = System.currentTimeMillis();
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logger.info("Time elapsed for making super areas : " + (end2 - end1) / (1000) + "s");
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}
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@Override
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protected void initTransaction() {
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}
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List<NamedArea> superAreaList;
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private void makeSuperAreas() {
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TransactionStatus tx = startTransaction(true);
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if (getConfig().getSuperAreas()!= null){
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Set<UUID> superAreaUuids = new HashSet<>(getConfig().getSuperAreas());
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superAreaList = getTermService().find(NamedArea.class, superAreaUuids);
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for (NamedArea superArea : superAreaList){
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Set<NamedArea> subAreas = getSubAreasFor(superArea);
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for(NamedArea subArea : subAreas){
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if (logger.isTraceEnabled()) {
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logger.trace("Initialize " + subArea.getTitleCache());
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}
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}
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}
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}
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commitTransaction(tx);
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}
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@Override
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protected List<String> descriptionInitStrategy() {
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return TAXONDESCRIPTION_INIT_STRATEGY;
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}
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// ********************* METHODS *****************************************/
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private List<PresenceAbsenceTerm> getByAreaIgnoreStatusList() {
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return getConfig().getByAreaIgnoreStatusList();
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}
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private List<PresenceAbsenceTerm> getByRankIgnoreStatusList() {
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return getConfig().getByRankIgnoreStatusList();
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}
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/**
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* Compares the PresenceAbsenceTermBase terms contained in <code>a.status</code> and <code>b.status</code> after
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* the priority as stored in the statusPriorityMap. The StatusAndSources object with
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* the higher priority is returned. In the case of <code>a == b</code> the sources of b will be added to the sources
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* of a.
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*
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* If either a or b or the status are null b or a is returned.
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*
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* @see initializeStatusPriorityMap()
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*
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* @param accumulatedStatus
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* @param newStatus
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* @param additionalSourcesForWinningNewStatus Not in Use!
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* In the case when <code>newStatus</code> is preferred over <code>accumulatedStatus</code> these Set of sources will be added to the sources of <code>b</code>
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* @param aggregationSourceMode
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* @return
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*/
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private StatusAndSources choosePreferredOrMerge(StatusAndSources accumulatedStatus, StatusAndSources newStatus,
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Set<DescriptionElementSource> additionalSourcesForWinningNewStatus, AggregationSourceMode aggregationSourceMode){
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if (newStatus == null || newStatus.status == null) {
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return accumulatedStatus;
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}
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if (accumulatedStatus == null || accumulatedStatus.status == null) {
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return newStatus;
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}
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Integer indexAcc = statusOrder.indexOf(accumulatedStatus.status);
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Integer indexNew = statusOrder.indexOf(newStatus.status);
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if (indexNew == -1) {
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logger.warn("No priority found in map for " + newStatus.status.getLabel());
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return accumulatedStatus;
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}
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if (indexAcc == -1) {
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logger.warn("No priority found in map for " + accumulatedStatus.status.getLabel());
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return newStatus;
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}
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if(indexAcc < indexNew){
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if(additionalSourcesForWinningNewStatus != null) {
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newStatus.addSources(additionalSourcesForWinningNewStatus);
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}
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if (aggregationSourceMode == AggregationSourceMode.ALL){
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newStatus.addSources(accumulatedStatus.sources);
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}
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return newStatus;
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} else {
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if (indexAcc == indexNew || aggregationSourceMode == AggregationSourceMode.ALL){
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accumulatedStatus.addSources(newStatus.sources);
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}
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return accumulatedStatus;
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}
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}
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@Override
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protected void addAggregationResultToDescription(TaxonDescription targetDescription,
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ResultHolder resultHolder) {
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Map<NamedArea, StatusAndSources> accumulatedStatusMap = ((DistributionResultHolder)resultHolder).accumulatedStatusMap;
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Set<Distribution> toDelete = new HashSet<>();
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if (getConfig().isDoClearExistingDescription()){
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clearDescription(targetDescription);
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}else{
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toDelete = new HashSet<>();
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}
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for (NamedArea area : accumulatedStatusMap.keySet()) {
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PresenceAbsenceTerm status = accumulatedStatusMap.get(area).status;
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Distribution distribution = findDistributionForArea(targetDescription, area);
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//old: if we want to reuse distribution only with exact same status
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// Distribution distribution = findDistributionForAreaAndStatus(aggregationDescription, area, status);
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if(distribution == null) {
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// create a new distribution element
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distribution = Distribution.NewInstance(area, status);
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targetDescription.addElement(distribution);
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}else{
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distribution.setStatus(status);
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toDelete.remove(distribution); //we keep the distribution for reuse
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}
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replaceSources(distribution.getSources(), accumulatedStatusMap.get(area).sources);
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// addSourcesDeduplicated(distribution.getSources(), accumulatedStatusMap.get(area).sources);
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}
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for(Distribution toDeleteDist: toDelete){
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targetDescription.removeElement(toDeleteDist);
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}
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}
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/**
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* Removes all description elements of type {@link Distribution} from the
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* (aggregation) description.
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*/
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private void clearDescription(TaxonDescription aggregationDescription) {
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int deleteCount = 0;
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Set<DescriptionElementBase> deleteCandidates = new HashSet<>();
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for (DescriptionElementBase descriptionElement : aggregationDescription.getElements()) {
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if(descriptionElement.isInstanceOf(Distribution.class)) {
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deleteCandidates.add(descriptionElement);
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}
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}
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aggregationDescription.addType(DescriptionType.AGGREGATED_DISTRIBUTION);
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if(deleteCandidates.size() > 0){
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for(DescriptionElementBase descriptionElement : deleteCandidates) {
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aggregationDescription.removeElement(descriptionElement);
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getDescriptionService().deleteDescriptionElement(descriptionElement);
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descriptionElement = null;
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deleteCount++;
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}
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getDescriptionService().saveOrUpdate(aggregationDescription);
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logger.debug("\t" + deleteCount +" distributions cleared");
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}
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}
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@Override
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protected void aggregateWithinSingleTaxon(Taxon taxon,
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ResultHolder resultHolder,
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Set<TaxonDescription> excludedDescriptions) {
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Map<NamedArea, StatusAndSources> accumulatedStatusMap =
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((DistributionResultHolder)resultHolder).accumulatedStatusMap;
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if(logger.isDebugEnabled()){
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logger.debug("accumulateByArea() - taxon :" + taxonToString(taxon));
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}
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Set<TaxonDescription> descriptions = descriptionsFor(taxon, excludedDescriptions);
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Set<Distribution> distributions = distributionsFor(descriptions);
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// Step through superAreas for accumulation of subAreas
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for (NamedArea superArea : superAreaList){
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// accumulate all sub area status
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StatusAndSources accumulatedStatusAndSources = null;
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AggregationSourceMode aggregationSourceMode = getConfig().getWithinTaxonSourceMode();
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// TODO consider using the TermHierarchyLookup (only in local branch a.kohlbecker)
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Set<NamedArea> subAreas = getSubAreasFor(superArea);
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for(NamedArea subArea : subAreas){
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if(logger.isTraceEnabled()){
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logger.trace("accumulateByArea() - \t\t" + termToString(subArea));
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}
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// step through all distributions for the given subArea
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for(Distribution distribution : distributions){
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//TODO AM is the status handling here correct? The mapping to CDM handled
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if(subArea.equals(distribution.getArea()) && distribution.getStatus() != null) {
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PresenceAbsenceTerm status = distribution.getStatus();
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if(logger.isTraceEnabled()){
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logger.trace("accumulateByArea() - \t\t" + termToString(subArea) + ": " + termToString(status));
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}
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// skip all having a status value in the ignore list
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if (status == null || getByAreaIgnoreStatusList().contains(status)
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|| (getConfig().isIgnoreAbsentStatusByArea() && status.isAbsenceTerm())){
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continue;
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}
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StatusAndSources subAreaStatusAndSources = new StatusAndSources(status, distribution, aggregationSourceMode);
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accumulatedStatusAndSources = choosePreferredOrMerge(accumulatedStatusAndSources, subAreaStatusAndSources, null, aggregationSourceMode);
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}
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}
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} // next sub area
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if (accumulatedStatusAndSources != null) {
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StatusAndSources preferedStatus = choosePreferredOrMerge(accumulatedStatusMap.get(superArea), accumulatedStatusAndSources, null, aggregationSourceMode);
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accumulatedStatusMap.put(superArea, preferedStatus);
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}
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} // next super area ....
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}
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private class DistributionResultHolder implements ResultHolder{
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Map<NamedArea, StatusAndSources> accumulatedStatusMap = new HashMap<>();
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}
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@Override
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protected ResultHolder createResultHolder() {
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return new DistributionResultHolder();
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}
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protected class StatusAndSources {
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private final PresenceAbsenceTerm status;
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private final Set<DescriptionElementSource> sources = new HashSet<>();
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public StatusAndSources(PresenceAbsenceTerm status, DescriptionElementBase deb, AggregationSourceMode aggregationSourceMode) {
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this.status = status;
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if (aggregationSourceMode == AggregationSourceMode.NONE){
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return;
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}else if (aggregationSourceMode == AggregationSourceMode.DESCRIPTION){
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sources.add(DescriptionElementSource.NewAggregationInstance(deb.getInDescription()));
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}else if (aggregationSourceMode == AggregationSourceMode.TAXON){
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if (deb.getInDescription().isInstanceOf(TaxonDescription.class)){
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TaxonDescription td = CdmBase.deproxy(deb.getInDescription(), TaxonDescription.class);
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sources.add(DescriptionElementSource.NewAggregationInstance(td.getTaxon()));
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}else{
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logger.warn("Description is not of type TaxonDescription. Adding source not possible");
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}
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}else if (aggregationSourceMode == AggregationSourceMode.ALL || aggregationSourceMode == AggregationSourceMode.ALL_SAMEVALUE){
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addSourcesDeduplicated(this.sources, deb.getSources());
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}else{
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|
360
|
throw new RuntimeException("Unhandled source aggregation mode: " + aggregationSourceMode);
|
|
361
|
}
|
|
362
|
}
|
|
363
|
|
|
364
|
public void addSources(Set<DescriptionElementSource> sources) {
|
|
365
|
addSourcesDeduplicated(this.sources, sources);
|
|
366
|
}
|
|
367
|
}
|
|
368
|
|
|
369
|
@Override
|
|
370
|
protected void aggregateToParentTaxon(TaxonNode taxonNode,
|
|
371
|
ResultHolder resultHolder,
|
|
372
|
Set<TaxonDescription> excludedDescriptions) {
|
|
373
|
|
|
374
|
Map<NamedArea, StatusAndSources> accumulatedStatusMap =
|
|
375
|
((DistributionResultHolder)resultHolder).accumulatedStatusMap;
|
|
376
|
|
|
377
|
Taxon taxon = CdmBase.deproxy(taxonNode.getTaxon());
|
|
378
|
if(logger.isDebugEnabled()){
|
|
379
|
logger.debug("accumulateByRank() [" + /*rank.getLabel() +*/ "] - taxon :" + taxonToString(taxon));
|
|
380
|
}
|
|
381
|
|
|
382
|
if(!taxonNode.getChildNodes().isEmpty()) {
|
|
383
|
|
|
384
|
LinkedList<Taxon> childStack = new LinkedList<>();
|
|
385
|
for (TaxonNode node : taxonNode.getChildNodes()){
|
|
386
|
if (node == null){
|
|
387
|
continue; //just in case if sortindex is broken
|
|
388
|
}
|
|
389
|
Taxon child = CdmBase.deproxy(node.getTaxon());
|
|
390
|
//TODO maybe we should also use child catching from taxon node filter
|
|
391
|
// we could e.g. clone the filter and set the parent as subtree filter
|
|
392
|
// and this way get all children via service layer, this may improve also
|
|
393
|
// memory usage
|
|
394
|
if (getConfig().getTaxonNodeFilter().isIncludeUnpublished()||
|
|
395
|
taxon.isPublish()){
|
|
396
|
childStack.add(child);
|
|
397
|
}
|
|
398
|
}
|
|
399
|
|
|
400
|
while(childStack.size() > 0){
|
|
401
|
|
|
402
|
Taxon childTaxon = childStack.pop();
|
|
403
|
getSession().setReadOnly(childTaxon, true);
|
|
404
|
if(logger.isTraceEnabled()){
|
|
405
|
logger.trace(" subtaxon :" + taxonToString(childTaxon));
|
|
406
|
}
|
|
407
|
|
|
408
|
Set<Distribution> distributions = distributionsFor(descriptionsFor(childTaxon, excludedDescriptions));
|
|
409
|
for(Distribution distribution : distributions) {
|
|
410
|
|
|
411
|
PresenceAbsenceTerm status = distribution.getStatus();
|
|
412
|
if (status == null || getByRankIgnoreStatusList().contains(status)
|
|
413
|
|| (getConfig().isIgnoreAbsentStatusByRank() && status.isAbsenceTerm())){
|
|
414
|
continue;
|
|
415
|
}
|
|
416
|
|
|
417
|
NamedArea area = distribution.getArea();
|
|
418
|
AggregationSourceMode aggregationSourceMode = getConfig().getToParentSourceMode();
|
|
419
|
|
|
420
|
StatusAndSources childStatusAndSources = new StatusAndSources(status, distribution, aggregationSourceMode);
|
|
421
|
StatusAndSources preferedStatus = choosePreferredOrMerge(accumulatedStatusMap.get(area),
|
|
422
|
childStatusAndSources, null, aggregationSourceMode );
|
|
423
|
accumulatedStatusMap.put(area, preferedStatus);
|
|
424
|
}
|
|
425
|
|
|
426
|
// evict all initialized entities of the childTaxon
|
|
427
|
// TODO consider using cascade="evict" in the model classes
|
|
428
|
// for( TaxonDescription description : ((Taxon)childTaxonBase).getDescriptions()) {
|
|
429
|
// for (DescriptionElementBase deb : description.getElements()) {
|
|
430
|
// getSession().evict(deb);
|
|
431
|
// }
|
|
432
|
// getSession().evict(description); // this causes in some cases the taxon object to be detached from the session
|
|
433
|
// }
|
|
434
|
// getSession().evict(childTaxon); // no longer needed, save heap
|
|
435
|
}
|
|
436
|
}
|
|
437
|
}
|
|
438
|
|
|
439
|
private Distribution findDistributionForArea(TaxonDescription description, NamedArea area) {
|
|
440
|
for(DescriptionElementBase item : description.getElements()) {
|
|
441
|
if(!(item.isInstanceOf(Distribution.class))) {
|
|
442
|
continue;
|
|
443
|
}
|
|
444
|
Distribution distribution = CdmBase.deproxy(item, Distribution.class);
|
|
445
|
if(distribution.getArea().equals(area)) {
|
|
446
|
return distribution;
|
|
447
|
}
|
|
448
|
}
|
|
449
|
return null;
|
|
450
|
}
|
|
451
|
|
|
452
|
/**
|
|
453
|
* Old: For if we want to reuse distributions only for the exact same status or
|
|
454
|
* if we aggregate for each status separately. Otherwise use {@link #findDistributionForArea(TaxonDescription, NamedArea)}
|
|
455
|
*/
|
|
456
|
private Distribution findDistributionForAreaAndStatus(TaxonDescription description, NamedArea area, PresenceAbsenceTerm status) {
|
|
457
|
for(DescriptionElementBase item : description.getElements()) {
|
|
458
|
if(!(item.isInstanceOf(Distribution.class))) {
|
|
459
|
continue;
|
|
460
|
}
|
|
461
|
Distribution distribution = CdmBase.deproxy(item, Distribution.class);
|
|
462
|
if(distribution.getArea().equals(area) && distribution.getStatus().equals(status)) {
|
|
463
|
return distribution;
|
|
464
|
}
|
|
465
|
}
|
|
466
|
return null;
|
|
467
|
}
|
|
468
|
|
|
469
|
private void flush() {
|
|
470
|
logger.debug("flushing session ...");
|
|
471
|
getSession().flush();
|
|
472
|
try {
|
|
473
|
logger.debug("flushing to indexes ...");
|
|
474
|
Search.getFullTextSession(getSession()).flushToIndexes();
|
|
475
|
} catch (HibernateException e) {
|
|
476
|
/* IGNORE - Hibernate Search Event listeners not configured ... */
|
|
477
|
if(!e.getMessage().startsWith("Hibernate Search Event listeners not configured")){
|
|
478
|
throw e;
|
|
479
|
}
|
|
480
|
}
|
|
481
|
}
|
|
482
|
|
|
483
|
private void flushAndClear() {
|
|
484
|
flush();
|
|
485
|
logger.debug("clearing session ...");
|
|
486
|
getSession().clear();
|
|
487
|
}
|
|
488
|
|
|
489
|
@Override
|
|
490
|
protected TaxonDescription createNewDescription(Taxon taxon) {
|
|
491
|
String title = taxon.getTitleCache();
|
|
492
|
logger.debug("creating new description for " + title);
|
|
493
|
TaxonDescription description = TaxonDescription.NewInstance(taxon);
|
|
494
|
description.addType(DescriptionType.AGGREGATED_DISTRIBUTION);
|
|
495
|
setDescriptionTitle(description, taxon);
|
|
496
|
return description;
|
|
497
|
}
|
|
498
|
|
|
499
|
@Override
|
|
500
|
protected boolean hasDescriptionType(TaxonDescription description) {
|
|
501
|
return description.isAggregatedDistribution();
|
|
502
|
}
|
|
503
|
|
|
504
|
@Override
|
|
505
|
protected void setDescriptionTitle(TaxonDescription description, Taxon taxon) {
|
|
506
|
String title = taxon.getName() != null? taxon.getName().getTitleCache() : taxon.getTitleCache();
|
|
507
|
description.setTitleCache("Aggregated distribution for " + title, true);
|
|
508
|
return;
|
|
509
|
}
|
|
510
|
|
|
511
|
private Set<NamedArea> getSubAreasFor(NamedArea superArea) {
|
|
512
|
|
|
513
|
if(!subAreaMap.containsKey(superArea)) {
|
|
514
|
if(logger.isDebugEnabled()){
|
|
515
|
logger.debug("loading included areas for " + superArea.getLabel());
|
|
516
|
}
|
|
517
|
subAreaMap.put(superArea, superArea.getIncludes());
|
|
518
|
}
|
|
519
|
return subAreaMap.get(superArea);
|
|
520
|
}
|
|
521
|
|
|
522
|
private Set<TaxonDescription> descriptionsFor(Taxon taxon, Set<TaxonDescription> excludedDescriptions) {
|
|
523
|
Set<TaxonDescription> result = new HashSet<>();
|
|
524
|
for(TaxonDescription description: taxon.getDescriptions()) {
|
|
525
|
// readOnlyIfInSession(description); //not needed for tests anymore
|
|
526
|
if (!excludedDescriptions.contains(description)){
|
|
527
|
result.add(description);
|
|
528
|
}
|
|
529
|
}
|
|
530
|
return result;
|
|
531
|
}
|
|
532
|
|
|
533
|
private Set<Distribution> distributionsFor(Set<TaxonDescription> descriptions) {
|
|
534
|
Set<Distribution> result = new HashSet<>();
|
|
535
|
for(TaxonDescription description: descriptions) {
|
|
536
|
for(DescriptionElementBase deb : description.getElements()) {
|
|
537
|
if(deb.isInstanceOf(Distribution.class)) {
|
|
538
|
// readOnlyIfInSession(deb); //not needed for tests anymore
|
|
539
|
result.add(CdmBase.deproxy(deb, Distribution.class));
|
|
540
|
}
|
|
541
|
}
|
|
542
|
}
|
|
543
|
return result;
|
|
544
|
}
|
|
545
|
|
|
546
|
/**
|
|
547
|
* This method avoids problems when running the {@link DistributionAggregationTest}.
|
|
548
|
* For some unknown reason entities are not in the PersitenceContext even if they are
|
|
549
|
* loaded by a service method. Setting these entities to read-only would raise a
|
|
550
|
* TransientObjectException("Instance was not associated with this persistence context")
|
|
551
|
*
|
|
552
|
* @param entity
|
|
553
|
*/
|
|
554
|
private void readOnlyIfInSession(CdmBase entity) {
|
|
555
|
if(getSession().contains(entity)) {
|
|
556
|
getSession().setReadOnly(entity, true);
|
|
557
|
}
|
|
558
|
}
|
|
559
|
|
|
560
|
|
|
561
|
private String termToString(OrderedTermBase<?> term) {
|
|
562
|
if(logger.isTraceEnabled()) {
|
|
563
|
return term.getLabel() + " [" + term.getIdInVocabulary() + "]";
|
|
564
|
} else {
|
|
565
|
return term.getIdInVocabulary();
|
|
566
|
}
|
|
567
|
}
|
|
568
|
|
|
569
|
/**
|
|
570
|
* Sets the priorities for presence and absence terms, the priorities are stored in extensions.
|
|
571
|
* This method will start a new transaction and commits it after the work is done.
|
|
572
|
*/
|
|
573
|
private void makeStatusOrder() {
|
|
574
|
|
|
575
|
TransactionStatus txStatus = startTransaction(false);
|
|
576
|
|
|
577
|
@SuppressWarnings("rawtypes")
|
|
578
|
TermCollection<PresenceAbsenceTerm, TermNode> stOrder = getConfig().getStatusOrder();
|
|
579
|
if (stOrder == null){
|
|
580
|
stOrder = defaultStatusOrder();
|
|
581
|
}
|
|
582
|
if (stOrder.isInstanceOf(TermTree.class)){
|
|
583
|
statusOrder = CdmBase.deproxy(stOrder, TermTree.class).asTermList();
|
|
584
|
}else if (stOrder.isInstanceOf(OrderedTermVocabulary.class)){
|
|
585
|
statusOrder = new ArrayList<>(CdmBase.deproxy(stOrder, OrderedTermVocabulary.class).getOrderedTerms());
|
|
586
|
}else{
|
|
587
|
throw new RuntimeException("TermCollection type for status order not supported: " + statusOrder.getClass().getSimpleName());
|
|
588
|
}
|
|
589
|
|
|
590
|
commitTransaction(txStatus);
|
|
591
|
}
|
|
592
|
|
|
593
|
private OrderedTermVocabulary<PresenceAbsenceTerm> defaultStatusOrder() {
|
|
594
|
@SuppressWarnings("unchecked")
|
|
595
|
OrderedTermVocabulary<PresenceAbsenceTerm> voc = (OrderedTermVocabulary<PresenceAbsenceTerm>)getRepository().getVocabularyService().find(VocabularyEnum.PresenceAbsenceTerm.getUuid());
|
|
596
|
return voc;
|
|
597
|
}
|
|
598
|
|
|
599
|
private void replaceSources(Set<DescriptionElementSource> oldSources, Set<DescriptionElementSource> newSources) {
|
|
600
|
Set<DescriptionElementSource> toDeleteSources = new HashSet<>(oldSources);
|
|
601
|
for(DescriptionElementSource newSource : newSources) {
|
|
602
|
boolean contained = false;
|
|
603
|
for(DescriptionElementSource existingSource: oldSources) {
|
|
604
|
if(existingSource.equalsByShallowCompare(newSource)) {
|
|
605
|
contained = true;
|
|
606
|
toDeleteSources.remove(existingSource);
|
|
607
|
break;
|
|
608
|
}
|
|
609
|
}
|
|
610
|
if(!contained) {
|
|
611
|
try {
|
|
612
|
oldSources.add(newSource.clone());
|
|
613
|
} catch (CloneNotSupportedException e) {
|
|
614
|
// should never happen
|
|
615
|
throw new RuntimeException(e);
|
|
616
|
}
|
|
617
|
}
|
|
618
|
}
|
|
619
|
for (DescriptionElementSource toDeleteSource : toDeleteSources){
|
|
620
|
oldSources.remove(toDeleteSource);
|
|
621
|
}
|
|
622
|
}
|
|
623
|
|
|
624
|
|
|
625
|
}
|