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/**
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* Copyright (C) 2007 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.io.redlist.bfnXml.out;
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import java.util.Comparator;
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import java.util.List;
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import java.util.Set;
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import org.jdom2.Attribute;
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import org.jdom2.Document;
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import org.jdom2.Element;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.redlist.bfnXml.BfnXmlConstants;
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import eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlTransformer;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.StateData;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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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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/**
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*
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* @author pplitzner
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* @date May 3, 2016
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*
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*/
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@Component
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public class BfnXmlTaxonNameExport extends BfnXmlExportBase {
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private static final long serialVersionUID = -931703660108981011L;
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public BfnXmlTaxonNameExport(){
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super();
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}
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@Override
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protected void doInvoke(BfnXmlExportState state){
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startTransaction(true);
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Document document = state.getConfig().getDocument();
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//get all classifications
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List<Classification> classifications = getClassificationService().list(Classification.class, null, null, null, null);
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for (Classification classification : classifications) {
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Element roteListeDaten = new Element(BfnXmlConstants.EL_ROTELISTEDATEN);
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roteListeDaten.setAttribute(new Attribute(BfnXmlConstants.ATT_INHALT, classification.getTitleCache()));
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document.getRootElement().addContent(roteListeDaten);
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exportFeatures(roteListeDaten);
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exportTaxonomy(classification, roteListeDaten, state);
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}
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}
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private void exportTaxonomy(Classification classification, Element roteListeDaten, BfnXmlExportState state) {
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Element taxonyme = new Element(BfnXmlConstants.EL_TAXONYME);
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roteListeDaten.addContent(taxonyme);
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List<TaxonNode> childNodes = classification.getChildNodes();
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java.util.Collections.sort(childNodes, new OriginalSourceComparator());
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for (TaxonNode taxonNode : childNodes) {
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exportTaxon(taxonNode.getTaxon(), taxonyme, state);
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}
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}
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private void exportFactualData(Taxon taxon, Element parent) {
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Element informationen = new Element(BfnXmlConstants.EL_INFORMATIONEN);
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parent.addContent(informationen);
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Element bezugsraum = new Element(BfnXmlConstants.EL_BEZUGSRAUM);
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bezugsraum.setAttribute(new Attribute(BfnXmlConstants.ATT_NAME, BfnXmlConstants.BEZUGRAUM_BUND));
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informationen.addContent(bezugsraum);
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Set<TaxonDescription> descriptions = taxon.getDescriptions();
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for (TaxonDescription taxonDescription : descriptions) {
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//TODO: export only red list features ??
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Set<DescriptionElementBase> descriptionElements = taxonDescription.getElements();
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for (DescriptionElementBase descriptionElementBase : descriptionElements) {
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if(descriptionElementBase.isInstanceOf(CategoricalData.class)){
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CategoricalData categoricalData = HibernateProxyHelper.deproxy(descriptionElementBase, CategoricalData.class);
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Feature feature = categoricalData.getFeature();
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List<StateData> stateData = categoricalData.getStateData();
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if(stateData.size()!=1){
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logger.error("StateData does not have a size of 1 for feature "+feature.getLabel()+" in taxon "+taxon.getTitleCache());
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continue;
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}
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addIwert(bezugsraum, feature.getLabel(), stateData.iterator().next().getState().getLabel());
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}
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else if(descriptionElementBase.isInstanceOf(TextData.class)){
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TextData textData = HibernateProxyHelper.deproxy(descriptionElementBase, TextData.class);
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addIwert(bezugsraum, textData.getFeature().getLabel(), textData.getLanguageText(Language.GERMAN()).getText());
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}
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}
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}
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}
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private void exportFeatures(Element roteListeDaten) {
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Element eigenschaften = new Element(BfnXmlConstants.EL_EIGENSCHAFTEN);
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roteListeDaten.addContent(eigenschaften);
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TermVocabulary<Feature> redListFeaturesVoc = getVocabularyService().load(BfnXmlConstants.vocRLFeatures);
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Set<Feature> terms = redListFeaturesVoc.getTerms();
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for (Feature feature : terms) {
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//export red list features
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Element eigenschaft = new Element(BfnXmlConstants.EL_EIGENSCHAFT);
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eigenschaft.setAttribute(new Attribute(BfnXmlConstants.ATT_STANDARDNAME, feature.getLabel()));
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eigenschaften.addContent(eigenschaft);
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if(feature.isSupportsCategoricalData()){
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//export feature states
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Element listenwerte = new Element(BfnXmlConstants.EL_LISTENWERTE);
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eigenschaft.addContent(listenwerte);
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Set<TermVocabulary<State>> supportedCategoricalEnumerations = feature.getSupportedCategoricalEnumerations();
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for (TermVocabulary<State> termVocabulary : supportedCategoricalEnumerations) {
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Set<State> featureStates = termVocabulary.getTerms();
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// int reihenfolge = 1;
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for (State featureState : featureStates) {
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Element lwert = new Element(BfnXmlConstants.EL_LWERT);
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// lwert.setAttribute(new Attribute(BfnXmlConstants.ATT_REIHENFOLGE, String.valueOf(reihenfolge)));
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lwert.addContent(featureState.getLabel());
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listenwerte.addContent(lwert);
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// reihenfolge++;
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}
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}
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}
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}
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}
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private void exportTaxon(Taxon taxon, Element parent, BfnXmlExportState state) {
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Element taxonym = new Element(BfnXmlConstants.EL_TAXONYM);
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parent.addContent(taxonym);
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DefinedTerm taxNrIdentifierType = HibernateProxyHelper.deproxy(getTermService().load(BfnXmlConstants.UUID_TAX_NR_IDENTIFIER_TYPE), DefinedTerm.class);
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Set<String> identifiers = taxon.getIdentifiers(taxNrIdentifierType);
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if(identifiers.size()==1){
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String taxNr = identifiers.iterator().next();
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taxonym.setAttribute(BfnXmlConstants.ATT_TAXNR, taxNr);
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}
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else{
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logger.error("Taxon "+taxon.getTitleCache()+" has none or multiple identifiers of type 'taxNr'");
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}
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exportWissName(taxon, taxonym);
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//synonyms
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Set<Synonym> synonyms = taxon.getSynonyms();
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if(synonyms.size()>0){
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Element synonymeElement = new Element(BfnXmlConstants.EL_SYNONYME);
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taxonym.addContent(synonymeElement);
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for (Synonym synonym : synonyms) {
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Element synonymElement = new Element(BfnXmlConstants.EL_SYNONYM);
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synonymeElement.addContent(synonymElement);
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exportWissName(synonym, synonymElement);
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}
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}
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//common name
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exportCommonName(taxon, taxonym);
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//factual data
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exportFactualData(taxon, taxonym);
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}
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private void exportWissName(TaxonBase<?> taxon, Element parent) {
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Element wissName = new Element(BfnXmlConstants.EL_WISSNAME);
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parent.addContent(wissName);
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NonViralName<?> name = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
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Rank rank = name.getRank();
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//wissName
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addNanteil(wissName, BfnXmlConstants.BEREICH_WISSNAME, name.getTitleCache());
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//epithet 1,2,3
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exportEpithet(taxon, wissName, name, rank);
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//rank
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addNanteil(wissName, BfnXmlConstants.BEREICH_RANG, BfnXmlTransformer.getRankCodeForRank(rank));
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//authors
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addNanteil(wissName, BfnXmlConstants.BEREICH_AUTOREN, name.getAuthorshipCache());
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}
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private void exportEpithet(TaxonBase<?> taxon, Element wissName, NonViralName<?> name, Rank rank) {
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addNanteil(wissName, BfnXmlConstants.BEREICH_EPITHETON1, name.getGenusOrUninomial());
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if(rank.isLower(Rank.GENUS())){
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String epitheton2 = name.getInfraGenericEpithet();
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if(epitheton2==null){
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epitheton2 = name.getSpecificEpithet();
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}
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addNanteil(wissName, BfnXmlConstants.BEREICH_EPITHETON2, epitheton2);
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}
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if(rank.isLower(Rank.SPECIES())){
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String epitheton3 = name.getInfraSpecificEpithet();
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if(epitheton3==null){
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epitheton3 = name.getSpecificEpithet();
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}
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addNanteil(wissName, BfnXmlConstants.BEREICH_EPITHETON3, epitheton3);
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}
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Set<IdentifiableSource> sources = taxon.getSources();
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for (IdentifiableSource identifiableSource : sources) {
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if(identifiableSource.getType().equals(OriginalSourceType.Import)
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&& identifiableSource.getIdNamespace().equals(BfnXmlConstants.EL_TAXONYM+":"
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+BfnXmlConstants.EL_WISSNAME+":"+BfnXmlConstants.EL_NANTEIL+":"+BfnXmlConstants.BEREICH_EINDEUTIGER_CODE)){
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addNanteil(wissName, BfnXmlConstants.BEREICH_EINDEUTIGER_CODE, identifiableSource.getIdInSource());
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}
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}
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}
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private void exportCommonName(Taxon taxon, Element taxonym) {
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Element deutscheNamen = new Element(BfnXmlConstants.EL_DEUTSCHENAMEN);
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taxonym.addContent(deutscheNamen);
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int sequenz = 1;
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Set<TaxonDescription> descriptions = taxon.getDescriptions();
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for (TaxonDescription taxonDescription : descriptions) {
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Set<DescriptionElementBase> elements = taxonDescription.getElements();
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for (DescriptionElementBase descriptionElementBase : elements) {
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if(descriptionElementBase.isInstanceOf(CommonTaxonName.class)){
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CommonTaxonName commonName = HibernateProxyHelper.deproxy(descriptionElementBase, CommonTaxonName.class);
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if(commonName.getLanguage().equals(Language.GERMAN())){
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Element dName = new Element(BfnXmlConstants.EL_DNAME);
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Element trivialName = new Element(BfnXmlConstants.EL_TRIVIALNAME);
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deutscheNamen.addContent(dName);
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dName.addContent(trivialName);
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dName.setAttribute(new Attribute(BfnXmlConstants.ATT_SEQUENZ, String.valueOf(sequenz)));
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trivialName.addContent(commonName.getName());
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}
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}
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}
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sequenz++;
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}
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}
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private void addNanteil(Element element, String bereich, String textContent) {
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Element nanteil = new Element(BfnXmlConstants.EL_NANTEIL);
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nanteil.setAttribute(new Attribute(BfnXmlConstants.ATT_BEREICH, bereich));
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nanteil.addContent(textContent);
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element.addContent(nanteil);
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}
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@Override
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protected boolean doCheck(BfnXmlExportState state) {
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return false;
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}
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@Override
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protected boolean isIgnore(BfnXmlExportState state) {
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return false;
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}
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private final class OriginalSourceComparator implements Comparator<TaxonNode> {
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@Override
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public int compare(TaxonNode o1, TaxonNode o2) {
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Taxon taxon1 = o1.getTaxon();
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Taxon taxon2 = o2.getTaxon();
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int id1 = 0;
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int id2 = 0;
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Set<IdentifiableSource> sources1 = taxon1.getSources();
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for (IdentifiableSource identifiableSource : sources1) {
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if(identifiableSource.getType().equals(OriginalSourceType.Import)
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&& identifiableSource.getIdNamespace().equals(BfnXmlConstants.EL_TAXONYM+":"
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+BfnXmlConstants.EL_WISSNAME+":"+BfnXmlConstants.EL_NANTEIL+":"+BfnXmlConstants.BEREICH_EINDEUTIGER_CODE)){
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id1 = Integer.parseInt(identifiableSource.getIdInSource());
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}
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}
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Set<IdentifiableSource> sources2 = taxon2.getSources();
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for (IdentifiableSource identifiableSource : sources2) {
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if(identifiableSource.getType().equals(OriginalSourceType.Import)
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&& identifiableSource.getIdNamespace().equals(BfnXmlConstants.EL_TAXONYM+":"
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+BfnXmlConstants.EL_WISSNAME+":"+BfnXmlConstants.EL_NANTEIL+":"+BfnXmlConstants.BEREICH_EINDEUTIGER_CODE)){
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id2 = Integer.parseInt(identifiableSource.getIdInSource());
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}
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}
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return id1-id2;
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}
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}
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}
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