| 8 |
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*/
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package eu.etaxonomy.cdm.io.redlist.bfnXml.out;
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import java.io.FileWriter;
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import java.io.IOException;
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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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| ... | ... | |
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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.jdom2.output.Format;
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import org.jdom2.output.XMLOutputter;
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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.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.name.TaxonNameBase;
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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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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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| ... | ... | |
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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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//export features
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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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//export feature states
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Element listenwerte = new Element(BfnXmlConstants.EL_LISTENWERTE);
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eigenschaften.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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exportFeatures(roteListeDaten);
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// reihenfolge++;
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79 |
exportTaxonomy(classification, roteListeDaten);
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}
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}
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private void exportTaxonomy(Classification classification, Element roteListeDaten) {
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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 Comparator<TaxonNode>() {
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91 |
@Override
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92 |
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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97 |
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Set<IdentifiableSource> sources1 = taxon1.getSources();
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|
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for (IdentifiableSource identifiableSource : sources1) {
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if(identifiableSource.getType().equals(OriginalSourceType.Import)
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101 |
&& 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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| 100 |
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}
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105 |
}
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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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for (TaxonNode taxonNode : childNodes) {
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exportTaxon(taxonNode.getTaxon(), taxonyme);
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}
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}
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121 |
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//export taxonomy
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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 Comparator<TaxonNode>() {
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@Override
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public int compare(TaxonNode o1, TaxonNode o2) {
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| 112 |
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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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| 116 |
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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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| 125 |
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Set<IdentifiableSource> sources2 = taxon2.getSources();
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| 126 |
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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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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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128 |
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129 |
Set<TaxonDescription> descriptions = taxon.getDescriptions();
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130 |
for (TaxonDescription taxonDescription : descriptions) {
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//TODO: export only red list features ??
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132 |
Set<DescriptionElementBase> descriptionElements = taxonDescription.getElements();
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133 |
for (DescriptionElementBase descriptionElementBase : descriptionElements) {
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134 |
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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137 |
List<StateData> stateData = categoricalData.getStateData();
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138 |
if(stateData.size()!=1){
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139 |
logger.error("StateData does not have a size of 1 for feature "+feature.getLabel()+" in taxon "+((NonViralName<?>) taxon.getName()).getNameCache());
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140 |
continue;
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| 132 |
141 |
}
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| 133 |
|
return id1-id2;
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142 |
exportIwert(bezugsraum, feature, stateData.iterator().next().getState().getLabel());
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143 |
}
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144 |
else if(descriptionElementBase.isInstanceOf(TextData.class)){
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145 |
TextData textData = HibernateProxyHelper.deproxy(descriptionElementBase, TextData.class);
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146 |
exportIwert(bezugsraum, textData.getFeature(), textData.getText(Language.getDefaultLanguage()));
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147 |
}
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| 135 |
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});
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| 136 |
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for (TaxonNode taxonNode : childNodes) {
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| 137 |
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exportTaxon(taxonNode.getTaxon(), taxonyme);
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| 138 |
148 |
}
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| 139 |
149 |
}
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150 |
}
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| 140 |
151 |
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| 141 |
|
XMLOutputter outputter = new XMLOutputter();
|
| 142 |
|
outputter.setFormat(Format.getPrettyFormat());
|
| 143 |
|
try {
|
| 144 |
|
outputter.output(document, new FileWriter(state.getConfig().getDestination()));
|
| 145 |
|
} catch (IOException e) {
|
| 146 |
|
logger.error("Error writing file", e);
|
| 147 |
|
}
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|
152 |
private void exportIwert(Element parent, Feature feature, String wertString) {
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153 |
Element iwert = new Element(BfnXmlConstants.EL_IWERT);
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154 |
iwert.setAttribute(new Attribute(BfnXmlConstants.ATT_STANDARDNAME, feature.getLabel()));
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155 |
parent.addContent(iwert);
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| 148 |
156 |
|
| 149 |
|
}
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157 |
Element wert = new Element(BfnXmlConstants.EL_WERT);
|
|
158 |
wert.addContent(wertString);
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|
159 |
iwert.addContent(wert);
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|
160 |
}
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|
161 |
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162 |
private void exportFeatures(Element roteListeDaten) {
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163 |
Element eigenschaften = new Element(BfnXmlConstants.EL_EIGENSCHAFTEN);
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164 |
roteListeDaten.addContent(eigenschaften);
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165 |
TermVocabulary<Feature> redListFeaturesVoc = getVocabularyService().load(BfnXmlConstants.vocRLFeatures);
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|
166 |
Set<Feature> terms = redListFeaturesVoc.getTerms();
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|
167 |
for (Feature feature : terms) {
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|
168 |
//export red list features
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|
169 |
Element eigenschaft = new Element(BfnXmlConstants.EL_EIGENSCHAFT);
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|
170 |
eigenschaft.setAttribute(new Attribute(BfnXmlConstants.ATT_STANDARDNAME, feature.getLabel()));
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171 |
eigenschaften.addContent(eigenschaft);
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172 |
//export feature states
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|
173 |
Element listenwerte = new Element(BfnXmlConstants.EL_LISTENWERTE);
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|
174 |
eigenschaften.addContent(listenwerte);
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|
175 |
Set<TermVocabulary<State>> supportedCategoricalEnumerations = feature.getSupportedCategoricalEnumerations();
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|
176 |
for (TermVocabulary<State> termVocabulary : supportedCategoricalEnumerations) {
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|
177 |
Set<State> featureStates = termVocabulary.getTerms();
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|
178 |
// int reihenfolge = 1;
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|
179 |
for (State featureState : featureStates) {
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|
180 |
Element lwert = new Element(BfnXmlConstants.EL_LWERT);
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|
181 |
// lwert.setAttribute(new Attribute(BfnXmlConstants.ATT_REIHENFOLGE, String.valueOf(reihenfolge)));
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|
182 |
lwert.addContent(featureState.getLabel());
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|
183 |
listenwerte.addContent(lwert);
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|
184 |
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|
185 |
// reihenfolge++;
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|
186 |
}
|
|
187 |
}
|
|
188 |
}
|
|
189 |
}
|
| 150 |
190 |
|
| 151 |
191 |
private void exportTaxon(Taxon taxon, Element parent) {
|
| 152 |
192 |
Element taxonym = new Element(BfnXmlConstants.EL_TAXONYM);
|
| 153 |
193 |
parent.addContent(taxonym);
|
| 154 |
194 |
|
| 155 |
|
NonViralName name = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
|
|
195 |
exportWissName(taxon, taxonym);
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|
196 |
|
|
197 |
//synonyms
|
|
198 |
Set<Synonym> synonyms = taxon.getSynonyms();
|
|
199 |
if(synonyms.size()>0){
|
|
200 |
Element synonymeElement = new Element(BfnXmlConstants.EL_SYNONYME);
|
|
201 |
taxonym.addContent(synonymeElement);
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|
202 |
for (Synonym synonym : synonyms) {
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|
203 |
Element synonymElement = new Element(BfnXmlConstants.EL_SYNONYM);
|
|
204 |
synonymeElement.addContent(synonymElement);
|
|
205 |
exportWissName(synonym, synonymElement);
|
|
206 |
}
|
|
207 |
}
|
|
208 |
|
|
209 |
//common name
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|
210 |
exportCommonName(taxon, taxonym);
|
|
211 |
|
|
212 |
//factual data
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|
213 |
exportFactualData(taxon, taxonym);
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|
214 |
|
|
215 |
|
|
216 |
}
|
|
217 |
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|
218 |
private void exportWissName(TaxonBase<?> taxon, Element parent) {
|
|
219 |
Element wissName = new Element(BfnXmlConstants.EL_WISSNAME);
|
|
220 |
parent.addContent(wissName);
|
|
221 |
|
|
222 |
NonViralName<?> name = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
|
| 156 |
223 |
Rank rank = name.getRank();
|
| 157 |
224 |
//wissName
|
| 158 |
|
addNanteil(taxonym, BfnXmlConstants.BEREICH_WISSNAME, taxon.getTitleCache());
|
| 159 |
|
//epitithon 1,2,3
|
| 160 |
|
addNanteil(taxonym, BfnXmlConstants.BEREICH_EPITHETON1, name.getGenusOrUninomial());
|
|
225 |
addNanteil(wissName, BfnXmlConstants.BEREICH_WISSNAME, name.getTitleCache());
|
|
226 |
//epithet 1,2,3
|
|
227 |
exportEpithet(taxon, wissName, name, rank);
|
|
228 |
|
|
229 |
//rank
|
|
230 |
addNanteil(wissName, BfnXmlConstants.BEREICH_RANG, BfnXmlTransformer.getRankmap().get(rank));
|
|
231 |
|
|
232 |
//authors
|
|
233 |
addNanteil(wissName, BfnXmlConstants.BEREICH_AUTOREN, name.getAuthorshipCache());
|
|
234 |
}
|
|
235 |
|
|
236 |
private void exportEpithet(TaxonBase<?> taxon, Element wissName, NonViralName<?> name, Rank rank) {
|
|
237 |
addNanteil(wissName, BfnXmlConstants.BEREICH_EPITHETON1, name.getGenusOrUninomial());
|
| 161 |
238 |
if(rank.isLower(Rank.GENUS())){
|
| 162 |
239 |
String epitheton2 = name.getInfraGenericEpithet();
|
| 163 |
240 |
if(epitheton2==null){
|
| 164 |
241 |
epitheton2 = name.getSpecificEpithet();
|
| 165 |
242 |
}
|
| 166 |
|
addNanteil(taxonym, BfnXmlConstants.BEREICH_EPITHETON2, epitheton2);
|
|
243 |
addNanteil(wissName, BfnXmlConstants.BEREICH_EPITHETON2, epitheton2);
|
| 167 |
244 |
}
|
| 168 |
245 |
if(rank.isLower(Rank.SPECIES())){
|
| 169 |
246 |
String epitheton3 = name.getInfraSpecificEpithet();
|
| 170 |
247 |
if(epitheton3==null){
|
| 171 |
248 |
epitheton3 = name.getSpecificEpithet();
|
| 172 |
249 |
}
|
| 173 |
|
addNanteil(taxonym, BfnXmlConstants.BEREICH_EPITHETON3, epitheton3);
|
|
250 |
addNanteil(wissName, BfnXmlConstants.BEREICH_EPITHETON3, epitheton3);
|
| 174 |
251 |
}
|
| 175 |
252 |
Set<IdentifiableSource> sources = taxon.getSources();
|
| 176 |
253 |
for (IdentifiableSource identifiableSource : sources) {
|
| 177 |
254 |
if(identifiableSource.getType().equals(OriginalSourceType.Import)
|
| 178 |
255 |
&& identifiableSource.getIdNamespace().equals(BfnXmlConstants.EL_TAXONYM+":"
|
| 179 |
256 |
+BfnXmlConstants.EL_WISSNAME+":"+BfnXmlConstants.EL_NANTEIL+":"+BfnXmlConstants.BEREICH_EINDEUTIGER_CODE)){
|
| 180 |
|
addNanteil(taxonym, BfnXmlConstants.BEREICH_EINDEUTIGER_CODE, identifiableSource.getIdInSource());
|
|
257 |
addNanteil(wissName, BfnXmlConstants.BEREICH_EINDEUTIGER_CODE, identifiableSource.getIdInSource());
|
| 181 |
258 |
}
|
| 182 |
259 |
}
|
| 183 |
|
//rank
|
| 184 |
|
addNanteil(taxonym, BfnXmlConstants.BEREICH_RANG, BfnXmlTransformer.getRankmap().get(rank));
|
|
260 |
}
|
| 185 |
261 |
|
| 186 |
|
//common name
|
|
262 |
private void exportCommonName(Taxon taxon, Element taxonym) {
|
| 187 |
263 |
Element deutscheNamen = new Element(BfnXmlConstants.EL_DEUTSCHENAMEN);
|
| 188 |
264 |
taxonym.addContent(deutscheNamen);
|
| 189 |
265 |
|
| ... | ... | |
| 193 |
269 |
Set<DescriptionElementBase> elements = taxonDescription.getElements();
|
| 194 |
270 |
for (DescriptionElementBase descriptionElementBase : elements) {
|
| 195 |
271 |
if(descriptionElementBase.isInstanceOf(CommonTaxonName.class)){
|
| 196 |
|
Element dName = new Element(BfnXmlConstants.EL_DNAME);
|
| 197 |
|
Element trivialName = new Element(BfnXmlConstants.EL_TRIVIALNAME);
|
| 198 |
|
deutscheNamen.addContent(dName);
|
| 199 |
|
dName.addContent(trivialName);
|
|
272 |
CommonTaxonName commonName = HibernateProxyHelper.deproxy(descriptionElementBase, CommonTaxonName.class);
|
|
273 |
if(commonName.getLanguage().equals(Language.GERMAN())){
|
|
274 |
Element dName = new Element(BfnXmlConstants.EL_DNAME);
|
|
275 |
Element trivialName = new Element(BfnXmlConstants.EL_TRIVIALNAME);
|
|
276 |
deutscheNamen.addContent(dName);
|
|
277 |
dName.addContent(trivialName);
|
| 200 |
278 |
|
| 201 |
|
dName.setAttribute(new Attribute(BfnXmlConstants.ATT_SEQUENZ, String.valueOf(sequenz)));
|
| 202 |
|
trivialName.addContent(((CommonTaxonName)descriptionElementBase).getName());
|
|
279 |
dName.setAttribute(new Attribute(BfnXmlConstants.ATT_SEQUENZ, String.valueOf(sequenz)));
|
|
280 |
trivialName.addContent(commonName.getName());
|
|
281 |
}
|
| 203 |
282 |
}
|
| 204 |
283 |
}
|
| 205 |
284 |
sequenz++;
|
| 206 |
285 |
}
|
| 207 |
|
|
| 208 |
286 |
}
|
| 209 |
287 |
|
| 210 |
288 |
private void addNanteil(Element element, String bereich, String textContent) {
|
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