*/
package eu.etaxonomy.cdm.io.redlist.bfnXml.out;
-import java.io.FileWriter;
-import java.io.IOException;
import java.util.Comparator;
import java.util.List;
import java.util.Set;
import org.jdom2.Attribute;
import org.jdom2.Document;
import org.jdom2.Element;
-import org.jdom2.output.Format;
-import org.jdom2.output.XMLOutputter;
import org.springframework.stereotype.Component;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.io.redlist.bfnXml.BfnXmlConstants;
import eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlTransformer;
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
+import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.common.OriginalSourceType;
import eu.etaxonomy.cdm.model.common.TermVocabulary;
+import eu.etaxonomy.cdm.model.description.CategoricalData;
import eu.etaxonomy.cdm.model.description.CommonTaxonName;
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
import eu.etaxonomy.cdm.model.description.Feature;
import eu.etaxonomy.cdm.model.description.State;
+import eu.etaxonomy.cdm.model.description.StateData;
import eu.etaxonomy.cdm.model.description.TaxonDescription;
+import eu.etaxonomy.cdm.model.description.TextData;
import eu.etaxonomy.cdm.model.name.NonViralName;
import eu.etaxonomy.cdm.model.name.Rank;
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import eu.etaxonomy.cdm.model.taxon.Classification;
+import eu.etaxonomy.cdm.model.taxon.Synonym;
import eu.etaxonomy.cdm.model.taxon.Taxon;
+import eu.etaxonomy.cdm.model.taxon.TaxonBase;
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
Document document = state.getConfig().getDocument();
-
//get all classifications
List<Classification> classifications = getClassificationService().list(Classification.class, null, null, null, null);
for (Classification classification : classifications) {
roteListeDaten.setAttribute(new Attribute(BfnXmlConstants.ATT_INHALT, classification.getTitleCache()));
document.getRootElement().addContent(roteListeDaten);
- //export features
- Element eigenschaften = new Element(BfnXmlConstants.EL_EIGENSCHAFTEN);
- roteListeDaten.addContent(eigenschaften);
- TermVocabulary<Feature> redListFeaturesVoc = getVocabularyService().load(BfnXmlConstants.vocRLFeatures);
- Set<Feature> terms = redListFeaturesVoc.getTerms();
- for (Feature feature : terms) {
- //export red list features
- Element eigenschaft = new Element(BfnXmlConstants.EL_EIGENSCHAFT);
- eigenschaft.setAttribute(new Attribute(BfnXmlConstants.ATT_STANDARDNAME, feature.getLabel()));
- eigenschaften.addContent(eigenschaft);
+ exportFeatures(roteListeDaten);
+
+ exportTaxonomy(classification, roteListeDaten);
+
+ }
+
+ }
+
+ private void exportTaxonomy(Classification classification, Element roteListeDaten) {
+ Element taxonyme = new Element(BfnXmlConstants.EL_TAXONYME);
+ roteListeDaten.addContent(taxonyme);
+ List<TaxonNode> childNodes = classification.getChildNodes();
+ java.util.Collections.sort(childNodes, new OriginalSourceComparator());
+ for (TaxonNode taxonNode : childNodes) {
+ exportTaxon(taxonNode.getTaxon(), taxonyme);
+ }
+ }
+
+ private void exportFactualData(Taxon taxon, Element parent) {
+ Element informationen = new Element(BfnXmlConstants.EL_INFORMATIONEN);
+ parent.addContent(informationen);
+ Element bezugsraum = new Element(BfnXmlConstants.EL_BEZUGSRAUM);
+ bezugsraum.setAttribute(new Attribute(BfnXmlConstants.ATT_NAME, BfnXmlConstants.BEZUGRAUM_BUND));
+ informationen.addContent(bezugsraum);
+
+ Set<TaxonDescription> descriptions = taxon.getDescriptions();
+ for (TaxonDescription taxonDescription : descriptions) {
+ //TODO: export only red list features ??
+ Set<DescriptionElementBase> descriptionElements = taxonDescription.getElements();
+ for (DescriptionElementBase descriptionElementBase : descriptionElements) {
+ if(descriptionElementBase.isInstanceOf(CategoricalData.class)){
+ CategoricalData categoricalData = HibernateProxyHelper.deproxy(descriptionElementBase, CategoricalData.class);
+ Feature feature = categoricalData.getFeature();
+ List<StateData> stateData = categoricalData.getStateData();
+ if(stateData.size()!=1){
+ logger.error("StateData does not have a size of 1 for feature "+feature.getLabel()+" in taxon "+taxon.getTitleCache());
+ continue;
+ }
+ exportIwert(bezugsraum, feature, stateData.iterator().next().getState().getLabel());
+ }
+ else if(descriptionElementBase.isInstanceOf(TextData.class)){
+ TextData textData = HibernateProxyHelper.deproxy(descriptionElementBase, TextData.class);
+ exportIwert(bezugsraum, textData.getFeature(), textData.getLanguageText(Language.GERMAN()).getText());
+ }
+ }
+ }
+ }
+
+ private void exportIwert(Element parent, Feature feature, String wertString) {
+ Element iwert = new Element(BfnXmlConstants.EL_IWERT);
+ iwert.setAttribute(new Attribute(BfnXmlConstants.ATT_STANDARDNAME, feature.getLabel()));
+ parent.addContent(iwert);
+
+ Element wert = new Element(BfnXmlConstants.EL_WERT);
+ wert.addContent(wertString);
+ iwert.addContent(wert);
+ }
+
+ private void exportFeatures(Element roteListeDaten) {
+ Element eigenschaften = new Element(BfnXmlConstants.EL_EIGENSCHAFTEN);
+ roteListeDaten.addContent(eigenschaften);
+ TermVocabulary<Feature> redListFeaturesVoc = getVocabularyService().load(BfnXmlConstants.vocRLFeatures);
+ Set<Feature> terms = redListFeaturesVoc.getTerms();
+ for (Feature feature : terms) {
+ //export red list features
+ Element eigenschaft = new Element(BfnXmlConstants.EL_EIGENSCHAFT);
+ eigenschaft.setAttribute(new Attribute(BfnXmlConstants.ATT_STANDARDNAME, feature.getLabel()));
+ eigenschaften.addContent(eigenschaft);
+ if(feature.isSupportsCategoricalData()){
//export feature states
Element listenwerte = new Element(BfnXmlConstants.EL_LISTENWERTE);
- eigenschaften.addContent(listenwerte);
+ eigenschaft.addContent(listenwerte);
Set<TermVocabulary<State>> supportedCategoricalEnumerations = feature.getSupportedCategoricalEnumerations();
for (TermVocabulary<State> termVocabulary : supportedCategoricalEnumerations) {
Set<State> featureStates = termVocabulary.getTerms();
-// int reihenfolge = 1;
+ // int reihenfolge = 1;
for (State featureState : featureStates) {
Element lwert = new Element(BfnXmlConstants.EL_LWERT);
-// lwert.setAttribute(new Attribute(BfnXmlConstants.ATT_REIHENFOLGE, String.valueOf(reihenfolge)));
+ // lwert.setAttribute(new Attribute(BfnXmlConstants.ATT_REIHENFOLGE, String.valueOf(reihenfolge)));
lwert.addContent(featureState.getLabel());
listenwerte.addContent(lwert);
-// reihenfolge++;
+ // reihenfolge++;
}
}
}
+ }
+ }
- //export taxonomy
- Element taxonyme = new Element(BfnXmlConstants.EL_TAXONYME);
- roteListeDaten.addContent(taxonyme);
- List<TaxonNode> childNodes = classification.getChildNodes();
- java.util.Collections.sort(childNodes, new Comparator<TaxonNode>() {
-
- @Override
- public int compare(TaxonNode o1, TaxonNode o2) {
- Taxon taxon1 = o1.getTaxon();
- Taxon taxon2 = o2.getTaxon();
- int id1 = 0;
- int id2 = 0;
-
- Set<IdentifiableSource> sources1 = taxon1.getSources();
- for (IdentifiableSource identifiableSource : sources1) {
- if(identifiableSource.getType().equals(OriginalSourceType.Import)
- && identifiableSource.getIdNamespace().equals(BfnXmlConstants.EL_TAXONYM+":"
- +BfnXmlConstants.EL_WISSNAME+":"+BfnXmlConstants.EL_NANTEIL+":"+BfnXmlConstants.BEREICH_EINDEUTIGER_CODE)){
- id1 = Integer.parseInt(identifiableSource.getIdInSource());
- }
- }
- Set<IdentifiableSource> sources2 = taxon2.getSources();
- for (IdentifiableSource identifiableSource : sources2) {
- if(identifiableSource.getType().equals(OriginalSourceType.Import)
- && identifiableSource.getIdNamespace().equals(BfnXmlConstants.EL_TAXONYM+":"
- +BfnXmlConstants.EL_WISSNAME+":"+BfnXmlConstants.EL_NANTEIL+":"+BfnXmlConstants.BEREICH_EINDEUTIGER_CODE)){
- id2 = Integer.parseInt(identifiableSource.getIdInSource());
- }
- }
- return id1-id2;
- }
- });
- for (TaxonNode taxonNode : childNodes) {
- exportTaxon(taxonNode.getTaxon(), taxonyme);
+ private void exportTaxon(Taxon taxon, Element parent) {
+ Element taxonym = new Element(BfnXmlConstants.EL_TAXONYM);
+ parent.addContent(taxonym);
+
+ exportWissName(taxon, taxonym);
+
+ //synonyms
+ Set<Synonym> synonyms = taxon.getSynonyms();
+ if(synonyms.size()>0){
+ Element synonymeElement = new Element(BfnXmlConstants.EL_SYNONYME);
+ taxonym.addContent(synonymeElement);
+ for (Synonym synonym : synonyms) {
+ Element synonymElement = new Element(BfnXmlConstants.EL_SYNONYM);
+ synonymeElement.addContent(synonymElement);
+ exportWissName(synonym, synonymElement);
}
}
- XMLOutputter outputter = new XMLOutputter();
- outputter.setFormat(Format.getPrettyFormat());
- try {
- outputter.output(document, new FileWriter(state.getConfig().getDestination()));
- } catch (IOException e) {
- logger.error("Error writing file", e);
- }
+ //common name
+ exportCommonName(taxon, taxonym);
- }
+ //factual data
+ exportFactualData(taxon, taxonym);
- private void exportTaxon(Taxon taxon, Element parent) {
- Element taxonym = new Element(BfnXmlConstants.EL_TAXONYM);
- parent.addContent(taxonym);
- NonViralName name = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
+ }
+
+ private void exportWissName(TaxonBase<?> taxon, Element parent) {
+ Element wissName = new Element(BfnXmlConstants.EL_WISSNAME);
+ parent.addContent(wissName);
+
+ NonViralName<?> name = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class);
Rank rank = name.getRank();
//wissName
- addNanteil(taxonym, BfnXmlConstants.BEREICH_WISSNAME, taxon.getTitleCache());
- //epitithon 1,2,3
- addNanteil(taxonym, BfnXmlConstants.BEREICH_EPITHETON1, name.getGenusOrUninomial());
+ addNanteil(wissName, BfnXmlConstants.BEREICH_WISSNAME, name.getTitleCache());
+ //epithet 1,2,3
+ exportEpithet(taxon, wissName, name, rank);
+
+ //rank
+ addNanteil(wissName, BfnXmlConstants.BEREICH_RANG, BfnXmlTransformer.getRankmap().get(rank));
+
+ //authors
+ addNanteil(wissName, BfnXmlConstants.BEREICH_AUTOREN, name.getAuthorshipCache());
+ }
+
+ private void exportEpithet(TaxonBase<?> taxon, Element wissName, NonViralName<?> name, Rank rank) {
+ addNanteil(wissName, BfnXmlConstants.BEREICH_EPITHETON1, name.getGenusOrUninomial());
if(rank.isLower(Rank.GENUS())){
String epitheton2 = name.getInfraGenericEpithet();
if(epitheton2==null){
epitheton2 = name.getSpecificEpithet();
}
- addNanteil(taxonym, BfnXmlConstants.BEREICH_EPITHETON2, epitheton2);
+ addNanteil(wissName, BfnXmlConstants.BEREICH_EPITHETON2, epitheton2);
}
if(rank.isLower(Rank.SPECIES())){
String epitheton3 = name.getInfraSpecificEpithet();
if(epitheton3==null){
epitheton3 = name.getSpecificEpithet();
}
- addNanteil(taxonym, BfnXmlConstants.BEREICH_EPITHETON3, epitheton3);
+ addNanteil(wissName, BfnXmlConstants.BEREICH_EPITHETON3, epitheton3);
}
Set<IdentifiableSource> sources = taxon.getSources();
for (IdentifiableSource identifiableSource : sources) {
if(identifiableSource.getType().equals(OriginalSourceType.Import)
&& identifiableSource.getIdNamespace().equals(BfnXmlConstants.EL_TAXONYM+":"
+BfnXmlConstants.EL_WISSNAME+":"+BfnXmlConstants.EL_NANTEIL+":"+BfnXmlConstants.BEREICH_EINDEUTIGER_CODE)){
- addNanteil(taxonym, BfnXmlConstants.BEREICH_EINDEUTIGER_CODE, identifiableSource.getIdInSource());
+ addNanteil(wissName, BfnXmlConstants.BEREICH_EINDEUTIGER_CODE, identifiableSource.getIdInSource());
}
}
- //rank
- addNanteil(taxonym, BfnXmlConstants.BEREICH_RANG, BfnXmlTransformer.getRankmap().get(rank));
+ }
- //common name
+ private void exportCommonName(Taxon taxon, Element taxonym) {
Element deutscheNamen = new Element(BfnXmlConstants.EL_DEUTSCHENAMEN);
taxonym.addContent(deutscheNamen);
Set<DescriptionElementBase> elements = taxonDescription.getElements();
for (DescriptionElementBase descriptionElementBase : elements) {
if(descriptionElementBase.isInstanceOf(CommonTaxonName.class)){
- Element dName = new Element(BfnXmlConstants.EL_DNAME);
- Element trivialName = new Element(BfnXmlConstants.EL_TRIVIALNAME);
- deutscheNamen.addContent(dName);
- dName.addContent(trivialName);
+ CommonTaxonName commonName = HibernateProxyHelper.deproxy(descriptionElementBase, CommonTaxonName.class);
+ if(commonName.getLanguage().equals(Language.GERMAN())){
+ Element dName = new Element(BfnXmlConstants.EL_DNAME);
+ Element trivialName = new Element(BfnXmlConstants.EL_TRIVIALNAME);
+ deutscheNamen.addContent(dName);
+ dName.addContent(trivialName);
- dName.setAttribute(new Attribute(BfnXmlConstants.ATT_SEQUENZ, String.valueOf(sequenz)));
- trivialName.addContent(((CommonTaxonName)descriptionElementBase).getName());
+ dName.setAttribute(new Attribute(BfnXmlConstants.ATT_SEQUENZ, String.valueOf(sequenz)));
+ trivialName.addContent(commonName.getName());
+ }
}
}
sequenz++;
}
-
}
private void addNanteil(Element element, String bereich, String textContent) {
return false;
}
+ private final class OriginalSourceComparator implements Comparator<TaxonNode> {
+ @Override
+ public int compare(TaxonNode o1, TaxonNode o2) {
+ Taxon taxon1 = o1.getTaxon();
+ Taxon taxon2 = o2.getTaxon();
+ int id1 = 0;
+ int id2 = 0;
+
+ Set<IdentifiableSource> sources1 = taxon1.getSources();
+ for (IdentifiableSource identifiableSource : sources1) {
+ if(identifiableSource.getType().equals(OriginalSourceType.Import)
+ && identifiableSource.getIdNamespace().equals(BfnXmlConstants.EL_TAXONYM+":"
+ +BfnXmlConstants.EL_WISSNAME+":"+BfnXmlConstants.EL_NANTEIL+":"+BfnXmlConstants.BEREICH_EINDEUTIGER_CODE)){
+ id1 = Integer.parseInt(identifiableSource.getIdInSource());
+ }
+ }
+ Set<IdentifiableSource> sources2 = taxon2.getSources();
+ for (IdentifiableSource identifiableSource : sources2) {
+ if(identifiableSource.getType().equals(OriginalSourceType.Import)
+ && identifiableSource.getIdNamespace().equals(BfnXmlConstants.EL_TAXONYM+":"
+ +BfnXmlConstants.EL_WISSNAME+":"+BfnXmlConstants.EL_NANTEIL+":"+BfnXmlConstants.BEREICH_EINDEUTIGER_CODE)){
+ id2 = Integer.parseInt(identifiableSource.getIdInSource());
+ }
+ }
+ return id1-id2;
+ }
+ }
+
}
BGBM BDI Projects / cdmlib-apps.git / blobdiff