Revision d2ca0a1c
Added by Patrick Plitzner almost 8 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/bfnXml/out/BfnXmlTaxonNameExport.java | ||
|---|---|---|
| 8 | 8 |
*/ |
| 9 | 9 |
package eu.etaxonomy.cdm.io.redlist.bfnXml.out; |
| 10 | 10 |
|
| 11 |
import java.io.FileWriter; |
|
| 12 |
import java.io.IOException; |
|
| 13 | 11 |
import java.util.Comparator; |
| 14 | 12 |
import java.util.List; |
| 15 | 13 |
import java.util.Set; |
| ... | ... | |
| 18 | 16 |
import org.jdom2.Attribute; |
| 19 | 17 |
import org.jdom2.Document; |
| 20 | 18 |
import org.jdom2.Element; |
| 21 |
import org.jdom2.output.Format; |
|
| 22 |
import org.jdom2.output.XMLOutputter; |
|
| 23 | 19 |
import org.springframework.stereotype.Component; |
| 24 | 20 |
|
| 25 | 21 |
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper; |
| 26 | 22 |
import eu.etaxonomy.cdm.io.redlist.bfnXml.BfnXmlConstants; |
| 27 | 23 |
import eu.etaxonomy.cdm.io.redlist.bfnXml.in.BfnXmlTransformer; |
| 28 | 24 |
import eu.etaxonomy.cdm.model.common.IdentifiableSource; |
| 25 |
import eu.etaxonomy.cdm.model.common.Language; |
|
| 29 | 26 |
import eu.etaxonomy.cdm.model.common.OriginalSourceType; |
| 30 | 27 |
import eu.etaxonomy.cdm.model.common.TermVocabulary; |
| 28 |
import eu.etaxonomy.cdm.model.description.CategoricalData; |
|
| 31 | 29 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
| 32 | 30 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
| 33 | 31 |
import eu.etaxonomy.cdm.model.description.Feature; |
| 34 | 32 |
import eu.etaxonomy.cdm.model.description.State; |
| 33 |
import eu.etaxonomy.cdm.model.description.StateData; |
|
| 35 | 34 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 35 |
import eu.etaxonomy.cdm.model.description.TextData; |
|
| 36 | 36 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| 37 | 37 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 38 | 38 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| 40 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
| 40 | 41 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
| 42 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
| 41 | 43 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
| 42 | 44 |
|
| 43 | 45 |
|
| ... | ... | |
| 65 | 67 |
|
| 66 | 68 |
Document document = state.getConfig().getDocument(); |
| 67 | 69 |
|
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|
|
| 69 | 70 |
//get all classifications |
| 70 | 71 |
List<Classification> classifications = getClassificationService().list(Classification.class, null, null, null, null); |
| 71 | 72 |
for (Classification classification : classifications) {
|
| ... | ... | |
| 73 | 74 |
roteListeDaten.setAttribute(new Attribute(BfnXmlConstants.ATT_INHALT, classification.getTitleCache())); |
| 74 | 75 |
document.getRootElement().addContent(roteListeDaten); |
| 75 | 76 |
|
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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); |
|
| 98 | 78 |
|
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// reihenfolge++; |
|
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exportTaxonomy(classification, roteListeDaten); |
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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 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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|
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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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|
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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()); |
|
| 100 | 104 |
} |
| 101 | 105 |
} |
| 106 |
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; |
|
| 102 | 115 |
} |
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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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} |
|
| 103 | 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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|
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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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|
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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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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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|
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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 "+((NonViralName<?>) taxon.getName()).getNameCache());
|
|
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continue; |
|
| 132 | 141 |
} |
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return id1-id2; |
|
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exportIwert(bezugsraum, feature, 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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exportIwert(bezugsraum, textData.getFeature(), textData.getText(Language.getDefaultLanguage())); |
|
| 134 | 147 |
} |
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}); |
|
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for (TaxonNode taxonNode : childNodes) {
|
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exportTaxon(taxonNode.getTaxon(), taxonyme); |
|
| 138 | 148 |
} |
| 139 | 149 |
} |
| 150 |
} |
|
| 140 | 151 |
|
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XMLOutputter outputter = new XMLOutputter(); |
|
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outputter.setFormat(Format.getPrettyFormat()); |
|
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try {
|
|
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outputter.output(document, new FileWriter(state.getConfig().getDestination())); |
|
| 145 |
} catch (IOException e) {
|
|
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logger.error("Error writing file", e);
|
|
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} |
|
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private void exportIwert(Element parent, Feature feature, String wertString) {
|
|
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Element iwert = new Element(BfnXmlConstants.EL_IWERT); |
|
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iwert.setAttribute(new Attribute(BfnXmlConstants.ATT_STANDARDNAME, feature.getLabel())); |
|
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parent.addContent(iwert); |
|
| 148 | 156 |
|
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} |
|
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Element wert = new Element(BfnXmlConstants.EL_WERT); |
|
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wert.addContent(wertString); |
|
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iwert.addContent(wert); |
|
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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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//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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|
|
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// reihenfolge++; |
|
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} |
|
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} |
|
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} |
|
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} |
|
| 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 |
|
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NonViralName name = HibernateProxyHelper.deproxy(taxon.getName(), NonViralName.class); |
|
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exportWissName(taxon, taxonym); |
|
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|
|
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//synonyms |
|
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Set<Synonym> synonyms = taxon.getSynonyms(); |
|
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if(synonyms.size()>0){
|
|
| 200 |
Element synonymeElement = new Element(BfnXmlConstants.EL_SYNONYME); |
|
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taxonym.addContent(synonymeElement); |
|
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for (Synonym synonym : synonyms) {
|
|
| 203 |
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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} |
|
| 208 |
|
|
| 209 |
//common name |
|
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exportCommonName(taxon, taxonym); |
|
| 211 |
|
|
| 212 |
//factual data |
|
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exportFactualData(taxon, taxonym); |
|
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|
|
| 215 |
|
|
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} |
|
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|
|
| 218 |
private void exportWissName(TaxonBase<?> taxon, Element parent) {
|
|
| 219 |
Element wissName = new Element(BfnXmlConstants.EL_WISSNAME); |
|
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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 |
|
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addNanteil(taxonym, BfnXmlConstants.BEREICH_EPITHETON1, name.getGenusOrUninomial()); |
|
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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) {
|
Also available in: Unified diff
Export synonymy and TextData