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package eu.etaxonomy.cdm.io.taxonx2013;
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import java.net.URI;
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import java.util.Map;
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import org.apache.log4j.Logger;
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import org.w3c.dom.Document;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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public class TaxonXXMLFieldGetter {
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private static final Logger logger = Logger.getLogger(TaxonXXMLFieldGetter.class);
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private final Document doc;
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private final NomenclaturalCode nomenclaturalCode;
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private Classification classification;
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private final TaxonXImport importer;
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private final TaxonXImportState taxonXstate;
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private TaxonXModsExtractor modsextractor;
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private TaxonXTreatmentExtractor treatmentextractor ;
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public TaxonXXMLFieldGetter(TaxonXDataHolder dataholder, String prefix,Document document, TaxonXImport taxonXImport,
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TaxonXImportState taxonXstate, Classification classif, Map<String,Feature> featuresMap){
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this.doc = document;
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this.importer = taxonXImport;
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this.nomenclaturalCode = taxonXstate.getConfig().getNomenclaturalCode();
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this.classification = classif;
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logger.info("CLASSIFICATION "+classification);
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this.taxonXstate=taxonXstate;
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modsextractor = new TaxonXModsExtractor(importer);
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Reference originalSourceUrl =taxonXstate.getConfig().getOriginalSourceURL();
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treatmentextractor = new TaxonXTreatmentExtractor(nomenclaturalCode,classification,importer, taxonXstate,featuresMap,originalSourceUrl );
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}
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/**
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* parse the Mods from the TaxonX file
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*
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*@return the created Reference object
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**/
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public Reference parseMods(){
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// System.out.println("PARSEMODS");
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//taxonx
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Node root = doc.getFirstChild();
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//taxonHeader, taxonBody
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NodeList nodes = root.getChildNodes();
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Reference ref = null;
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for (int i=0; i< nodes.getLength();i++) {
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// System.out.println(nodes.item(i).getNodeName());
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if (nodes.item(i).getNodeName().equalsIgnoreCase("tax:taxonxheader")){
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NodeList nodes2 = nodes.item(i).getChildNodes();
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for (int j=0; j< nodes2.getLength();j++){
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if (nodes2.item(j).getNodeName().equalsIgnoreCase("mods:mods")){
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ref = modsextractor.extractMods(nodes2.item(j));
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importer.getReferenceService().saveOrUpdate(ref);
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}
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}
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}
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}
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if (ref!=null) {
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taxonXstate.getConfig().setClassificationName(ref.getCitation());
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} else {
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taxonXstate.getConfig().setClassificationName("no reference title");
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}
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ref=CdmBase.deproxy(ref, Reference.class);
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return ref;
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}
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/**
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* Foreach treatment section, launches the treatment "extractor"
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* @param ref : the current reference, extracted from the mods
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* @param sourcename: the URI of the TaxonX document
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*/
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public void parseTreatment(Reference ref, URI sourceName){
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System.out.println("PARSETREATMENT "+ref);
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//taxonx
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Node root = doc.getFirstChild();
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//taxonHeader, taxonBody
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NodeList nodes = root.getChildNodes();
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for ( int i=0; i< nodes.getLength();i++) {
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// System.out.println(nodes.item(i).getNodeName());
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if (nodes.item(i).getNodeName().equalsIgnoreCase("tax:taxonxBody")){
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NodeList nodes2 = nodes.item(i).getChildNodes();
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for (int j=0; j< nodes2.getLength();j++){
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if (nodes2.item(j).getNodeName().equalsIgnoreCase("tax:treatment")){
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try {
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treatmentextractor.extractTreatment(nodes2.item(j), ref,sourceName);
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} catch (Exception e) {
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logger.error("Unhandled exception occurred in treatment. Treatment not fully imported.");
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e.printStackTrace();
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}
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}
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}
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}
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}
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}
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/**
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* updates the classification in the treatment extractor
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* @param classification2
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*/
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public void updateClassification(Classification classification2) {
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//System.out.println("UPDATECLASSIFICATIONS "+classification2);
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classification=classification2;
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if (treatmentextractor != null) {
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treatmentextractor.updateClassification(classification);
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}
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}
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/**
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* @return
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*/
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public Map<String,Feature> getFeaturesUsed() {
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return treatmentextractor.getFeaturesUsed();
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}
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}
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