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package eu.etaxonomy.cdm.io.specimen.abcd206.in;
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import java.util.ArrayList;
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import java.util.HashMap;
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import org.apache.log4j.Logger;
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import org.w3c.dom.Element;
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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.name.SpecimenTypeDesignationStatus;
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public class Abcd206XMLFieldGetter {
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private static final Logger logger = Logger.getLogger(Abcd206Import.class);
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private final Abcd206DataHolder dataHolder;
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private final String prefix;
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private String path = "";
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boolean DEBUG =false;
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public Abcd206XMLFieldGetter(Abcd206DataHolder dataholder, String prefix){
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this.dataHolder = dataholder;
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this.prefix = prefix;
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}
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/**
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* getType :
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* @param result
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*/
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protected void getType(Node result) {
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if (DEBUG) {
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logger.info("GetType");
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}
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NodeList results, types, ntds, ntd;
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String type;
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results = result.getChildNodes();
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boolean typeFound = false;
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try {
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for (int k = 0; k < results.getLength(); k++) {
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typeFound=false;
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if (results.item(k).getNodeName()
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.equals(prefix + "SpecimenUnit")) {
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types = results.item(k).getChildNodes();
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for (int l = 0; l < types.getLength(); l++) {
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if (types.item(l).getNodeName().equals(prefix+ "NomenclaturalTypeDesignations")) {
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ntds = types.item(l).getChildNodes();
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for (int m = 0; m < ntds.getLength(); m++) {
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if (ntds.item(m).getNodeName().equals(prefix+ "NomenclaturalTypeDesignation")) {
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ntd = ntds.item(m).getChildNodes();
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for (int n = 0; n < ntd.getLength(); n++) {
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if (ntd.item(n).getNodeName().equals(prefix + "TypeStatus"))
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{
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type = ntd.item(n).getTextContent();
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if(DEBUG) {
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logger.info("ADD "+type);
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}
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dataHolder.statusList.add(getSpecimenTypeDesignationStatusByKey(type));
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typeFound=true;
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path = ntd.item(l).getNodeName();
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getHierarchie(ntd.item(l));
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dataHolder.knownABCDelements.add(path);
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path = "";
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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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if (!typeFound) {
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dataHolder.statusList.add(null);
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}
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}
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} catch (NullPointerException e) {
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dataHolder.statusList = new ArrayList<SpecimenTypeDesignationStatus>();
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}
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}
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/**
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* getScientificNames : get the list of scientific names (preferred and non preferred)
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* @param group
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*/
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protected void getScientificNames(NodeList group) {
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NodeList identifications, results;
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String tmpName = null;
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for (int j = 0; j < group.getLength(); j++) {
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if (group.item(j).getNodeName().equals(prefix + "Identification")) {
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identifications = group.item(j).getChildNodes();
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for (int m = 0; m < identifications.getLength(); m++) {
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if (identifications.item(m).getNodeName()
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.equals(prefix + "Result")) {
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results = identifications.item(m).getChildNodes();
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for (int k = 0; k < results.getLength(); k++) {
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if (results.item(k).getNodeName().equals(prefix + "TaxonIdentified")) {
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tmpName = this.getScientificName(results.item(k));
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// logger.info("TMP NAME " + tmpName);dataHolder.identificationList.add(tmpName);nameFound = true;
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}
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}
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} else if (identifications.item(m).getNodeName().equals(prefix + "PreferredFlag")) {
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if (dataHolder.nomenclatureCode != null&& dataHolder.nomenclatureCode != "") {
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// logger.info("TMP NAME P" + tmpName);
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dataHolder.identificationList.add(new Identification(tmpName, identifications.item(m).getTextContent(), dataHolder.nomenclatureCode));
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} else {
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dataHolder.identificationList.add(new Identification(tmpName, identifications.item(m).getTextContent()));
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}
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path = identifications.item(m).getNodeName();
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// getHierarchie(identifications.item(m));
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dataHolder.knownABCDelements.add(path);
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path = "";
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} else if (identifications.item(m).getNodeName().equals(prefix + "References")) {
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this.getReferences(identifications.item(m));
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}
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}
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}
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}
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boolean hasPref = false;
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for (int j = 0; j < group.getLength(); j++) {
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if (group.item(j).getNodeName().equals(prefix + "Identification")) {
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dataHolder.nomenclatureCode = "";
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identifications = group.item(j).getChildNodes();
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for (int m = 0; m < identifications.getLength(); m++) {
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if (identifications.item(m).getNodeName().equals(prefix + "Result")) {
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results = identifications.item(m).getChildNodes();
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for (int k = 0; k < results.getLength(); k++) {
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if (results.item(k).getNodeName().equals(prefix + "TaxonIdentified")) {
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tmpName = this.getScientificName(results.item(k));
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}
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}
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}
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if (identifications.item(m).getNodeName()
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.equals(prefix + "PreferredFlag")) {
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hasPref = true;
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}
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}
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if (!hasPref && tmpName != null) {
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if (dataHolder.nomenclatureCode != null
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&& dataHolder.nomenclatureCode != "") {
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dataHolder.identificationList.add(new Identification(tmpName, "0", dataHolder.nomenclatureCode));
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} else {
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dataHolder.identificationList.add(new Identification(tmpName, "0"));
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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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* getScientificName : get the list of scientific names
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* @param result
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* @return
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*/
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private String getScientificName(Node result) {
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// logger.info("IN getScientificName " + dataHolder.nomenclatureCode);
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NodeList taxonsIdentified, scnames, atomised;
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String tmpName = "";
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taxonsIdentified = result.getChildNodes();
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for (int l = 0; l < taxonsIdentified.getLength(); l++) {
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if (taxonsIdentified.item(l).getNodeName().equals(prefix + "ScientificName")) {
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scnames = taxonsIdentified.item(l).getChildNodes();
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for (int n = 0; n < scnames.getLength(); n++) {
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if (scnames.item(n).getNodeName().equals(prefix + "FullScientificNameString")) {
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path = scnames.item(n).getNodeName();
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tmpName = scnames.item(n).getTextContent();
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getHierarchie(scnames.item(n));
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dataHolder.knownABCDelements.add(path);
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path = "";
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}
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else if (scnames.item(n).getNodeName().equals(prefix + "NameAtomised")) {
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try {
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if (scnames.item(n).hasChildNodes()) {
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String tmp = scnames.item(n).getChildNodes().item(1).getNodeName();
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if (tmp.indexOf(prefix) != -1&& prefix.length() > 0) {
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dataHolder.nomenclatureCode = tmp.split(prefix)[1];
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}
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else {
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dataHolder.nomenclatureCode = scnames.item(n).getChildNodes().item(1).getNodeName();
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}
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}
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} catch (Exception e) {
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if(DEBUG) {
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logger.warn("PB nomenclaturecode");
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}
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dataHolder.nomenclatureCode = "";
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}
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atomised = scnames.item(n).getChildNodes().item(1).getChildNodes();
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dataHolder.atomisedIdentificationList.add(this.getAtomisedNames(dataHolder.nomenclatureCode,atomised));
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}
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}
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}
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}
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return tmpName;
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}
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/**
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* getRerences : get the reference and citations
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* @param result
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* @return
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*/
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protected boolean getReferences(Node result) {
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// logger.info("GET REFERENCE");
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NodeList results, reference;
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results = result.getChildNodes();
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boolean referencefound = false;
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String[] refDetails =new String[3];;
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for (int k = 0; k < results.getLength(); k++) {
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if (results.item(k).getNodeName().equals(prefix + "SourceReference")) {
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reference = results.item(k).getChildNodes();
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for (int l = 0; l < reference.getLength(); l++) {
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if (reference.item(l).getNodeName().equals(prefix + "TitleCitation")) {
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path = reference.item(l).getNodeName();
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refDetails[0]=reference.item(l).getTextContent();
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getHierarchie(reference.item(l));
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dataHolder.knownABCDelements.add(path);
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path = "";
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referencefound = true;
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}
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if (reference.item(l).getNodeName().equals(prefix + "CitationDetail")) {
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path = reference.item(l).getNodeName();
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refDetails[1]=reference.item(l).getTextContent();
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getHierarchie(reference.item(l));
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dataHolder.knownABCDelements.add(path);
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path = "";
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referencefound = true;
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}
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if (reference.item(l).getNodeName().equals(prefix + "URI")) {
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path = reference.item(l).getNodeName();
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refDetails[2]=reference.item(l).getTextContent();
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getHierarchie(reference.item(l));
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dataHolder.knownABCDelements.add(path);
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path = "";
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referencefound = true;
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}
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}
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if (refDetails!=null){
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for (int i=0;i<3;i++) {
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if (refDetails[i]==null) {
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refDetails[i]="";
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}
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}
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dataHolder.referenceList.add(refDetails);
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refDetails =new String[3];
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}
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}
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}
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return referencefound;
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}
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252
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253
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/**
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* Traverses the tree for compareABCDtoCDM
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*
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* @param node
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* @param dataHolder
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*/
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protected void traverse(Node node) {
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// Extract node info:
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String test = node.getTextContent();
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262
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// Print and continue traversing.
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if (test != null && test != "#text" && node.getNodeName() != "#text"&& test.split("\n").length == 1 && test.length() > 0) {
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path = node.getNodeName();
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266
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getHierarchie(node);
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dataHolder.allABCDelements.put(path, test);
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268
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path = "";
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}
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// Now traverse the rest of the tree in depth-first order.
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if (node.hasChildNodes()) {
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// Get the children in a list.
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NodeList nl = node.getChildNodes();
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// How many of them?
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int size = nl.getLength();
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276
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for (int i = 0; i < size; i++) {
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277
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// Recursively traverse each of the children.
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traverse(nl.item(i));
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}
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280
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}
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281
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}
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282
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283
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284
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285
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/*
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286
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* (non-Javadoc)
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287
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*
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288
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* @see eu.etaxonomy.cdm.io.common.mapping.IInputTransformer#
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* getSpecimenTypeDesignationStatusByKey(java.lang.String)
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290
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*/
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291
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private SpecimenTypeDesignationStatus getSpecimenTypeDesignationStatusByKey(
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String key) {
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293
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if (key == null) {
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return null;
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295
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} else if (key.matches("(?i)(T|Type)")) {
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return SpecimenTypeDesignationStatus.TYPE();
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} else if (key.matches("(?i)(HT|Holotype)")) {
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298
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return SpecimenTypeDesignationStatus.HOLOTYPE();
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} else if (key.matches("(?i)(LT|Lectotype)")) {
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300
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return SpecimenTypeDesignationStatus.LECTOTYPE();
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301
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} else if (key.matches("(?i)(NT|Neotype)")) {
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return SpecimenTypeDesignationStatus.NEOTYPE();
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303
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} else if (key.matches("(?i)(ST|Syntype)")) {
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304
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return SpecimenTypeDesignationStatus.SYNTYPE();
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305
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} else if (key.matches("(?i)(ET|Epitype)")) {
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return SpecimenTypeDesignationStatus.EPITYPE();
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307
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} else if (key.matches("(?i)(IT|Isotype)")) {
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308
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return SpecimenTypeDesignationStatus.ISOTYPE();
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309
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} else if (key.matches("(?i)(ILT|Isolectotype)")) {
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310
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return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
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311
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} else if (key.matches("(?i)(INT|Isoneotype)")) {
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312
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return SpecimenTypeDesignationStatus.ISONEOTYPE();
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313
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} else if (key.matches("(?i)(IET|Isoepitype)")) {
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314
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return SpecimenTypeDesignationStatus.ISOEPITYPE();
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315
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} else if (key.matches("(?i)(PT|Paratype)")) {
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316
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return SpecimenTypeDesignationStatus.PARATYPE();
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317
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} else if (key.matches("(?i)(PLT|Paralectotype)")) {
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318
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return SpecimenTypeDesignationStatus.PARALECTOTYPE();
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319
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} else if (key.matches("(?i)(PNT|Paraneotype)")) {
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return SpecimenTypeDesignationStatus.PARANEOTYPE();
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321
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} else if (key.matches("(?i)(unsp.|Unspecified)")) {
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return SpecimenTypeDesignationStatus.UNSPECIFIC();
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} else if (key.matches("(?i)(2LT|Second Step Lectotype)")) {
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return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
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} else if (key.matches("(?i)(2NT|Second Step Neotype)")) {
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return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
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} else if (key.matches("(?i)(OM|Original Material)")) {
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return SpecimenTypeDesignationStatus.ORIGINAL_MATERIAL();
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329
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} else if (key.matches("(?i)(IcT|Iconotype)")) {
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return SpecimenTypeDesignationStatus.ICONOTYPE();
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331
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} else if (key.matches("(?i)(PT|Phototype)")) {
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return SpecimenTypeDesignationStatus.PHOTOTYPE();
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} else if (key.matches("(?i)(IST|Isosyntype)")) {
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return SpecimenTypeDesignationStatus.ISOSYNTYPE();
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335
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} else {
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336
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return null;
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337
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}
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338
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}
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339
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340
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/**
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341
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* getHierarchie : get the whole path
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342
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* @param node
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343
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*/
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344
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private void getHierarchie(Node node) {
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345
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// logger.info("getHierarchie");
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346
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while (node != null && node.getNodeName() != prefix + "DataSets" && node.getParentNode() != null) {
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347
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// logger.info("nodeparent "+node.getParentNode().getNodeName());
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348
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path = node.getParentNode().getNodeName() + "/" + path;
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349
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node = node.getParentNode();
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350
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}
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351
|
// logger.info("path gethierarchie: "+path);
|
|
352
|
}
|
|
353
|
|
|
354
|
|
|
355
|
/**
|
|
356
|
* getIDs : get the source institution id, source id...
|
|
357
|
* @param root
|
|
358
|
*/
|
|
359
|
protected void getIDs(Element root) {
|
|
360
|
NodeList group;
|
|
361
|
try {
|
|
362
|
group = root.getElementsByTagName(prefix + "SourceInstitutionID");
|
|
363
|
path = group.item(0).getNodeName();
|
|
364
|
getHierarchie(group.item(0));
|
|
365
|
dataHolder.knownABCDelements.add(path);
|
|
366
|
path = "";
|
|
367
|
dataHolder.institutionCode = group.item(0).getTextContent();
|
|
368
|
} catch (NullPointerException e) {
|
|
369
|
dataHolder.institutionCode = "";
|
|
370
|
}
|
|
371
|
try {
|
|
372
|
group = root.getElementsByTagName(prefix + "SourceID");
|
|
373
|
path = group.item(0).getNodeName();
|
|
374
|
getHierarchie(group.item(0));
|
|
375
|
dataHolder.knownABCDelements.add(path);
|
|
376
|
path = "";
|
|
377
|
dataHolder.collectionCode = group.item(0).getTextContent();
|
|
378
|
} catch (NullPointerException e) {
|
|
379
|
dataHolder.collectionCode = "";
|
|
380
|
}
|
|
381
|
try {
|
|
382
|
group = root.getElementsByTagName(prefix + "UnitID");
|
|
383
|
path = group.item(0).getNodeName();
|
|
384
|
getHierarchie(group.item(0));
|
|
385
|
dataHolder.knownABCDelements.add(path);
|
|
386
|
path = "";
|
|
387
|
dataHolder.unitID = group.item(0).getTextContent();
|
|
388
|
} catch (NullPointerException e) {
|
|
389
|
dataHolder.unitID = "";
|
|
390
|
}
|
|
391
|
}
|
|
392
|
|
|
393
|
/**
|
|
394
|
* getRecordBasis : extract the recordBasis out of the ABCD document
|
|
395
|
* @param root
|
|
396
|
*/
|
|
397
|
protected void getRecordBasis(Element root) {
|
|
398
|
NodeList group;
|
|
399
|
try {
|
|
400
|
group = root.getElementsByTagName(prefix + "RecordBasis");
|
|
401
|
path = group.item(0).getNodeName();
|
|
402
|
getHierarchie(group.item(0));
|
|
403
|
dataHolder.knownABCDelements.add(path);
|
|
404
|
path = "";
|
|
405
|
dataHolder.recordBasis = group.item(0).getTextContent();
|
|
406
|
} catch (NullPointerException e) {
|
|
407
|
dataHolder.recordBasis = "";
|
|
408
|
}
|
|
409
|
}
|
|
410
|
|
|
411
|
protected void getKindOfUnit(Element root) {
|
|
412
|
NodeList group;
|
|
413
|
try {
|
|
414
|
group = root.getElementsByTagName(prefix + "KindOfUnit");
|
|
415
|
path = group.item(0).getNodeName();
|
|
416
|
getHierarchie(group.item(0));
|
|
417
|
dataHolder.knownABCDelements.add(path);
|
|
418
|
path = "";
|
|
419
|
dataHolder.kindOfUnit = group.item(0).getTextContent();
|
|
420
|
} catch (NullPointerException e) {
|
|
421
|
dataHolder.kindOfUnit = "";
|
|
422
|
}
|
|
423
|
}
|
|
424
|
|
|
425
|
/**
|
|
426
|
* getNumbers : getAccessionNumber, collector number ...
|
|
427
|
* @param root
|
|
428
|
*/
|
|
429
|
protected void getNumbers(Element root) {
|
|
430
|
NodeList group;
|
|
431
|
try {
|
|
432
|
group = root.getElementsByTagName(prefix + "AccessionNumber");
|
|
433
|
path = group.item(0).getNodeName();
|
|
434
|
getHierarchie(group.item(0));
|
|
435
|
dataHolder.knownABCDelements.add(path);
|
|
436
|
path = "";
|
|
437
|
dataHolder.accessionNumber = group.item(0).getTextContent();
|
|
438
|
} catch (NullPointerException e) {
|
|
439
|
dataHolder.accessionNumber = "";
|
|
440
|
}
|
|
441
|
try {
|
|
442
|
group = root.getElementsByTagName(prefix + "CollectorsFieldNumber");
|
|
443
|
path = group.item(0).getNodeName();
|
|
444
|
getHierarchie(group.item(0));
|
|
445
|
dataHolder.knownABCDelements.add(path);
|
|
446
|
path = "";
|
|
447
|
dataHolder.fieldNumber = group.item(0).getTextContent();
|
|
448
|
} catch (NullPointerException e) {
|
|
449
|
dataHolder.fieldNumber = "";
|
|
450
|
}
|
|
451
|
|
|
452
|
//try {
|
|
453
|
//group = root.getElementsByTagName(prefix + "AccessionNumber");
|
|
454
|
//path = group.item(0).getNodeName();
|
|
455
|
//getHierarchie(group.item(0));
|
|
456
|
//dataHolder.knownABCDelements.add(path);
|
|
457
|
//path = "";
|
|
458
|
//dataHolder.accessionNumber = group.item(0).getTextContent();
|
|
459
|
//} catch (NullPointerException e) {
|
|
460
|
//dataHolder.accessionNumber = "";
|
|
461
|
//}
|
|
462
|
}
|
|
463
|
|
|
464
|
/**
|
|
465
|
* getGeolocation : get locality
|
|
466
|
* @param root
|
|
467
|
* @param state
|
|
468
|
*/
|
|
469
|
protected void getGeolocation(Element root, Abcd206ImportState state) {
|
|
470
|
NodeList group, childs;
|
|
471
|
try {
|
|
472
|
group = root.getElementsByTagName(prefix + "LocalityText");
|
|
473
|
path = group.item(0).getNodeName();
|
|
474
|
getHierarchie(group.item(0));
|
|
475
|
dataHolder.knownABCDelements.add(path);
|
|
476
|
path = "";
|
|
477
|
dataHolder.locality = group.item(0).getTextContent();
|
|
478
|
if (group.item(0).hasAttributes()) {
|
|
479
|
if (group.item(0).getAttributes().getNamedItem("lang") != null) {
|
|
480
|
dataHolder.languageIso = group.item(0).getAttributes().getNamedItem("lang").getTextContent();
|
|
481
|
}
|
|
482
|
}
|
|
483
|
} catch (NullPointerException e) {
|
|
484
|
dataHolder.locality = "";
|
|
485
|
}
|
|
486
|
try {
|
|
487
|
group = root.getElementsByTagName(prefix + "LongitudeDecimal");
|
|
488
|
path = group.item(0).getNodeName();
|
|
489
|
getHierarchie(group.item(0));
|
|
490
|
dataHolder.knownABCDelements.add(path);
|
|
491
|
path = "";
|
|
492
|
dataHolder.longitude = Double.valueOf(group.item(0).getTextContent());
|
|
493
|
} catch (NullPointerException e) {
|
|
494
|
dataHolder.longitude = null;
|
|
495
|
}
|
|
496
|
try {
|
|
497
|
group = root.getElementsByTagName(prefix + "LatitudeDecimal");
|
|
498
|
path = group.item(0).getNodeName();
|
|
499
|
getHierarchie(group.item(0));
|
|
500
|
dataHolder.knownABCDelements.add(path);
|
|
501
|
path = "";
|
|
502
|
dataHolder.latitude = Double.valueOf(group.item(0).getTextContent());
|
|
503
|
} catch (NullPointerException e) {
|
|
504
|
dataHolder.latitude = null;
|
|
505
|
}
|
|
506
|
try {
|
|
507
|
group = root.getElementsByTagName(prefix + "Country");
|
|
508
|
childs = group.item(0).getChildNodes();
|
|
509
|
for (int i = 0; i < childs.getLength(); i++) {
|
|
510
|
if (childs.item(i).getNodeName().contains("Name")) {
|
|
511
|
path = childs.item(i).getNodeName();
|
|
512
|
getHierarchie(childs.item(i));
|
|
513
|
dataHolder.knownABCDelements.add(path);
|
|
514
|
path = "";
|
|
515
|
dataHolder.country = childs.item(i).getTextContent();
|
|
516
|
}
|
|
517
|
}
|
|
518
|
} catch (NullPointerException e) {
|
|
519
|
dataHolder.country = "";
|
|
520
|
}
|
|
521
|
try {
|
|
522
|
group = root.getElementsByTagName(prefix + "Country");
|
|
523
|
childs = group.item(0).getChildNodes();
|
|
524
|
for (int i = 0; i < childs.getLength(); i++) {
|
|
525
|
if (childs.item(i).getNodeName().contains("ISO3166Code")) {
|
|
526
|
path = childs.item(i).getNodeName();
|
|
527
|
getHierarchie(childs.item(i));
|
|
528
|
dataHolder.knownABCDelements.add(path);
|
|
529
|
path = "";
|
|
530
|
dataHolder.isocountry = childs.item(i).getTextContent();
|
|
531
|
}
|
|
532
|
}
|
|
533
|
} catch (NullPointerException e) {
|
|
534
|
dataHolder.isocountry = "";
|
|
535
|
}
|
|
536
|
try {
|
|
537
|
group = root.getElementsByTagName(prefix + "Altitude");
|
|
538
|
for (int i = 0; i < group.getLength(); i++) {
|
|
539
|
childs = group.item(i).getChildNodes();
|
|
540
|
for (int j = 0; j < childs.getLength(); j++) {
|
|
541
|
if (childs.item(j).getNodeName().equals(prefix + "MeasurementOrFactText")) {
|
|
542
|
path = childs.item(j).getNodeName();
|
|
543
|
getHierarchie(childs.item(j));
|
|
544
|
dataHolder.knownABCDelements.add(path);
|
|
545
|
path = "";
|
|
546
|
dataHolder.altitude = Integer.valueOf(childs.item(j).getTextContent());
|
|
547
|
}
|
|
548
|
}
|
|
549
|
}
|
|
550
|
} catch (NullPointerException e) {
|
|
551
|
dataHolder.altitude = -9999;
|
|
552
|
}
|
|
553
|
|
|
554
|
try {
|
|
555
|
group = root.getElementsByTagName(prefix + "Depth");
|
|
556
|
path = group.item(0).getNodeName();
|
|
557
|
getHierarchie(group.item(0));
|
|
558
|
dataHolder.knownABCDelements.add(path);
|
|
559
|
path = "";
|
|
560
|
dataHolder.depth = Integer.valueOf(group.item(0).getTextContent());
|
|
561
|
} catch (NullPointerException e) {
|
|
562
|
dataHolder.depth = -9999;
|
|
563
|
}
|
|
564
|
|
|
565
|
try {
|
|
566
|
group = root.getElementsByTagName(prefix + "NamedArea");
|
|
567
|
dataHolder.namedAreaList = new HashMap<String, String>();
|
|
568
|
for (int i = 0; i < group.getLength(); i++) {
|
|
569
|
childs = group.item(i).getChildNodes();
|
|
570
|
String currentArea = null;
|
|
571
|
for (int j = 0; j < childs.getLength(); j++) {
|
|
572
|
if (childs.item(j).getNodeName() .equals(prefix + "AreaName")) {
|
|
573
|
path = childs.item(j).getNodeName();
|
|
574
|
getHierarchie(childs.item(j));
|
|
575
|
dataHolder.knownABCDelements.add(path);
|
|
576
|
path = "";
|
|
577
|
currentArea = childs.item(j).getTextContent();
|
|
578
|
dataHolder.namedAreaList.put(currentArea, null);
|
|
579
|
}
|
|
580
|
}
|
|
581
|
if(currentArea!=null){
|
|
582
|
for (int j = 0; j < childs.getLength(); j++) {
|
|
583
|
if (childs.item(j).getNodeName() .equals(prefix + "AreaClass")) {
|
|
584
|
path = childs.item(j).getNodeName();
|
|
585
|
getHierarchie(childs.item(j));
|
|
586
|
dataHolder.knownABCDelements.add(path);
|
|
587
|
path = "";
|
|
588
|
dataHolder.namedAreaList.put(currentArea, childs.item(j).getTextContent());
|
|
589
|
}
|
|
590
|
}
|
|
591
|
}
|
|
592
|
}
|
|
593
|
} catch (NullPointerException e) {
|
|
594
|
dataHolder.namedAreaList = new HashMap<String, String>();
|
|
595
|
}
|
|
596
|
|
|
597
|
if(state.getConfig().isRemoveCountryFromLocalityText()){
|
|
598
|
if(dataHolder.locality.startsWith(dataHolder.country)){
|
|
599
|
dataHolder.locality = dataHolder.locality.replaceFirst(dataHolder.country+"[\\W]", "");
|
|
600
|
}
|
|
601
|
for (String namedArea : ((HashMap<String, String>) dataHolder.namedAreaList).keySet()) {
|
|
602
|
if(dataHolder.locality.startsWith(namedArea)){
|
|
603
|
dataHolder.locality = dataHolder.locality.replaceFirst(namedArea+"[\\W]", "");
|
|
604
|
}
|
|
605
|
}
|
|
606
|
}
|
|
607
|
}
|
|
608
|
|
|
609
|
/**
|
|
610
|
* getMultimedia: get the FileURI objects
|
|
611
|
* @param root
|
|
612
|
*/
|
|
613
|
protected void getMultimedia(Element root) {
|
|
614
|
NodeList group, multimedias, multimedia;
|
|
615
|
try {
|
|
616
|
group = root.getElementsByTagName(prefix + "MultiMediaObjects");
|
|
617
|
for (int i = 0; i < group.getLength(); i++) {
|
|
618
|
multimedias = group.item(i).getChildNodes();
|
|
619
|
for (int j = 0; j < multimedias.getLength(); j++) {
|
|
620
|
if (multimedias.item(j).getNodeName().equals(prefix + "MultiMediaObject")) {
|
|
621
|
multimedia = multimedias.item(j).getChildNodes();
|
|
622
|
for (int k = 0; k < multimedia.getLength(); k++) {
|
|
623
|
if (multimedia.item(k).getNodeName().equals(prefix + "FileURI")) {
|
|
624
|
dataHolder.multimediaObjects.add(multimedia.item(k).getTextContent());
|
|
625
|
path = multimedia.item(k).getNodeName();
|
|
626
|
getHierarchie(multimedia.item(k));
|
|
627
|
dataHolder.knownABCDelements.add(path);
|
|
628
|
path = "";
|
|
629
|
}
|
|
630
|
}
|
|
631
|
}
|
|
632
|
}
|
|
633
|
}
|
|
634
|
} catch (NullPointerException e) {
|
|
635
|
logger.info(e);
|
|
636
|
}
|
|
637
|
}
|
|
638
|
|
|
639
|
protected void getAssociatedUnitIds(Element root) {
|
|
640
|
NodeList associations, childrenAssociations, childrenUnitAssociations;
|
|
641
|
try {
|
|
642
|
associations = root.getElementsByTagName(prefix + "Associations");
|
|
643
|
for (int i = 0; i < associations.getLength(); i++) {
|
|
644
|
childrenAssociations = associations.item(i).getChildNodes();
|
|
645
|
for (int j = 0; j < childrenAssociations.getLength(); j++) {
|
|
646
|
if (childrenAssociations.item(j).getNodeName().equals(prefix + "UnitAssociation")) {
|
|
647
|
childrenUnitAssociations = childrenAssociations.item(j).getChildNodes();
|
|
648
|
for (int k = 0; k < childrenUnitAssociations.getLength(); k++) {
|
|
649
|
if (childrenUnitAssociations.item(k).getNodeName().equals(prefix + "UnitID")) {
|
|
650
|
dataHolder.associatedUnitIds.add(childrenUnitAssociations.item(k).getTextContent());
|
|
651
|
path = childrenUnitAssociations.item(k).getNodeName();
|
|
652
|
getHierarchie(childrenUnitAssociations.item(k));
|
|
653
|
dataHolder.knownABCDelements.add(path);
|
|
654
|
path = "";
|
|
655
|
}
|
|
656
|
}
|
|
657
|
}
|
|
658
|
}
|
|
659
|
}
|
|
660
|
} catch (NullPointerException e) {
|
|
661
|
logger.info(e);
|
|
662
|
}
|
|
663
|
}
|
|
664
|
|
|
665
|
protected void getGatheringElevation(Element root) {
|
|
666
|
try {
|
|
667
|
//check for freetext elevation
|
|
668
|
NodeList group = root.getElementsByTagName(prefix + "Gathering");
|
|
669
|
for (int i = 0; i < group.getLength(); i++) {
|
|
670
|
NodeList children = group.item(i).getChildNodes();
|
|
671
|
for (int j = 0; j < children.getLength(); j++) {
|
|
672
|
if (children.item(j).getNodeName().equals(prefix + "Altitude")) {
|
|
673
|
NodeList altitudes = children.item(j).getChildNodes();
|
|
674
|
for (int k = 0; k < altitudes.getLength(); k++) {
|
|
675
|
if (altitudes.item(k).getNodeName().equals(prefix + "MeasurementOrFactText")) {
|
|
676
|
path = altitudes.item(k).getNodeName();
|
|
677
|
getHierarchie(altitudes.item(k));
|
|
678
|
dataHolder.knownABCDelements.add(path);
|
|
679
|
path = "";
|
|
680
|
dataHolder.gatheringElevationText = altitudes.item(k).getTextContent();
|
|
681
|
}
|
|
682
|
}
|
|
683
|
}
|
|
684
|
|
|
685
|
}
|
|
686
|
}
|
|
687
|
|
|
688
|
} catch (NullPointerException e) {
|
|
689
|
dataHolder.gatheringElevationText = null;
|
|
690
|
}
|
|
691
|
|
|
692
|
try{
|
|
693
|
//check for atomised elevation
|
|
694
|
if(dataHolder.gatheringElevationText==null){
|
|
695
|
NodeList group = root.getElementsByTagName(prefix + "Gathering");
|
|
696
|
for (int i = 0; i < group.getLength(); i++) {
|
|
697
|
NodeList children = group.item(i).getChildNodes();
|
|
698
|
for (int j = 0; j < children.getLength(); j++) {
|
|
699
|
if (children.item(j).getNodeName().equals(prefix + "Altitude")) {
|
|
700
|
NodeList altitudes = children.item(j).getChildNodes();
|
|
701
|
for (int k = 0; k < altitudes.getLength(); k++) {
|
|
702
|
if (altitudes.item(k).getNodeName().equals(prefix + "MeasurementOrFactAtomised")) {
|
|
703
|
NodeList facts = altitudes.item(k).getChildNodes();
|
|
704
|
for (int l = 0; l < facts.getLength(); l++) {
|
|
705
|
if (facts.item(l).getNodeName().equals(prefix + "LowerValue")) {
|
|
706
|
path = facts.item(l).getNodeName();
|
|
707
|
getHierarchie(facts.item(l));
|
|
708
|
dataHolder.knownABCDelements.add(path);
|
|
709
|
path = "";
|
|
710
|
dataHolder.gatheringElevationMin = facts.item(l).getTextContent();
|
|
711
|
}
|
|
712
|
else if (facts.item(l).getNodeName().equals(prefix + "UpperValue")) {
|
|
713
|
path = facts.item(l).getNodeName();
|
|
714
|
getHierarchie(facts.item(l));
|
|
715
|
dataHolder.knownABCDelements.add(path);
|
|
716
|
path = "";
|
|
717
|
dataHolder.gatheringElevationMax = facts.item(l).getTextContent();
|
|
718
|
}
|
|
719
|
else if (facts.item(l).getNodeName().equals(prefix + "UnitOfMeasurement")) {
|
|
720
|
path = facts.item(l).getNodeName();
|
|
721
|
getHierarchie(facts.item(l));
|
|
722
|
dataHolder.knownABCDelements.add(path);
|
|
723
|
path = "";
|
|
724
|
dataHolder.gatheringElevationUnit = facts.item(l).getTextContent();
|
|
725
|
}
|
|
726
|
}
|
|
727
|
}
|
|
728
|
}
|
|
729
|
}
|
|
730
|
}
|
|
731
|
}
|
|
732
|
}
|
|
733
|
} catch (NullPointerException e) {
|
|
734
|
dataHolder.gatheringElevationText = null;
|
|
735
|
}
|
|
736
|
}
|
|
737
|
|
|
738
|
protected void getGatheringDate(Element root) {
|
|
739
|
try {
|
|
740
|
NodeList group = root.getElementsByTagName(prefix + "Gathering");
|
|
741
|
for (int i = 0; i < group.getLength(); i++) {
|
|
742
|
NodeList children = group.item(i).getChildNodes();
|
|
743
|
for (int j = 0; j < children.getLength(); j++) {
|
|
744
|
if (children.item(j).getNodeName().equals(prefix + "DateTime")) {
|
|
745
|
NodeList dateTimes = children.item(j).getChildNodes();
|
|
746
|
for (int k = 0; k < dateTimes.getLength(); k++) {
|
|
747
|
if (dateTimes.item(k).getNodeName().equals(prefix + "DateText")) {
|
|
748
|
path = dateTimes.item(k).getNodeName();
|
|
749
|
getHierarchie(dateTimes.item(k));
|
|
750
|
dataHolder.knownABCDelements.add(path);
|
|
751
|
path = "";
|
|
752
|
dataHolder.gatheringDateText = dateTimes.item(k).getTextContent();
|
|
753
|
}
|
|
754
|
}
|
|
755
|
}
|
|
756
|
|
|
757
|
}
|
|
758
|
}
|
|
759
|
|
|
760
|
} catch (NullPointerException e) {
|
|
761
|
dataHolder.gatheringDateText = null;
|
|
762
|
}
|
|
763
|
}
|
|
764
|
|
|
765
|
/**
|
|
766
|
* getGatheringPeople : get GatheringAgent with fullname
|
|
767
|
* @param root
|
|
768
|
*/
|
|
769
|
protected void getGatheringPeople(Element root) {
|
|
770
|
try {
|
|
771
|
dataHolder.gatheringAgentList = new ArrayList<String>();
|
|
772
|
|
|
773
|
NodeList group = root.getElementsByTagName(prefix + "GatheringAgent");
|
|
774
|
for (int i = 0; i < group.getLength(); i++) {
|
|
775
|
NodeList children = group.item(i).getChildNodes();
|
|
776
|
for (int j = 0; j < children.getLength(); j++) {
|
|
777
|
if (children.item(j).getNodeName().equals(prefix + "Person")) {
|
|
778
|
NodeList persons = children.item(j).getChildNodes();
|
|
779
|
for (int k = 0; k < persons.getLength(); k++) {
|
|
780
|
if (persons.item(k).getNodeName().equals(prefix + "FullName")) {
|
|
781
|
path = persons.item(k).getNodeName();
|
|
782
|
getHierarchie(persons.item(k));
|
|
783
|
dataHolder.knownABCDelements.add(path);
|
|
784
|
path = "";
|
|
785
|
if (!persons.item(k).getTextContent().trim().equalsIgnoreCase("none")) {
|
|
786
|
dataHolder.gatheringAgentList.add(persons.item(k).getTextContent());
|
|
787
|
}
|
|
788
|
}
|
|
789
|
}
|
|
790
|
}
|
|
791
|
|
|
792
|
}
|
|
793
|
}
|
|
794
|
|
|
795
|
group = root.getElementsByTagName(prefix + "Gathering");
|
|
796
|
for (int i = 0; i < group.getLength(); i++) {
|
|
797
|
NodeList children = group.item(i).getChildNodes();
|
|
798
|
for (int j = 0; j < children.getLength(); j++) {
|
|
799
|
if (children.item(j).getNodeName().equals(prefix + "Agents")) {
|
|
800
|
NodeList persons = children.item(j).getChildNodes();
|
|
801
|
for (int k = 0; k < persons.getLength(); k++) {
|
|
802
|
if (persons.item(k).getNodeName().equals(prefix + "GatheringAgentsText")) {
|
|
803
|
path = persons.item(k).getNodeName();
|
|
804
|
getHierarchie(persons.item(k));
|
|
805
|
dataHolder.knownABCDelements.add(path);
|
|
806
|
path = "";
|
|
807
|
if (!persons.item(k).getTextContent().trim().equalsIgnoreCase("none")) {
|
|
808
|
dataHolder.gatheringAgentList.add(persons.item(k).getTextContent());
|
|
809
|
}
|
|
810
|
}
|
|
811
|
}
|
|
812
|
}
|
|
813
|
|
|
814
|
}
|
|
815
|
}
|
|
816
|
|
|
817
|
} catch (NullPointerException e) {
|
|
818
|
dataHolder.gatheringAgentList = new ArrayList<String>();
|
|
819
|
}
|
|
820
|
if (dataHolder.gatheringAgentList.size() > 1){
|
|
821
|
dataHolder.gatheringTeamList.addAll(dataHolder.gatheringAgentList);
|
|
822
|
dataHolder.gatheringAgentList = new ArrayList<String>();
|
|
823
|
}
|
|
824
|
}
|
|
825
|
|
|
826
|
/*PARSING METHODS*/
|
|
827
|
|
|
828
|
private HashMap<String, String> getAtomisedNames(String code,NodeList atomised) {
|
|
829
|
if (DEBUG) {
|
|
830
|
logger.info("code getatomised " + code);
|
|
831
|
}
|
|
832
|
if (code.indexOf("Botanical") != -1) {
|
|
833
|
return this.getAtomisedBotanical(atomised);
|
|
834
|
}
|
|
835
|
if (code.indexOf("Bacterial") != -1) {
|
|
836
|
return this.getAtomisedBacterial(atomised);
|
|
837
|
}
|
|
838
|
if (code.indexOf("Viral") != -1) {
|
|
839
|
return this.getAtomisedViral(atomised);
|
|
840
|
}
|
|
841
|
if (code.indexOf("Zoological") != -1) {
|
|
842
|
return this.getAtomisedZoological(atomised);
|
|
843
|
}
|
|
844
|
return new HashMap<String, String>();
|
|
845
|
}
|
|
846
|
|
|
847
|
private HashMap<String, String> getAtomisedZoological(NodeList atomised) {
|
|
848
|
if(DEBUG) {
|
|
849
|
logger.info("getAtomisedZoo");
|
|
850
|
}
|
|
851
|
HashMap<String, String> atomisedMap = new HashMap<String, String>();
|
|
852
|
|
|
853
|
for (int i = 0; i < atomised.getLength(); i++) {
|
|
854
|
if (atomised.item(i).getNodeName().equals(prefix + "GenusOrMonomial")) {
|
|
855
|
atomisedMap.put("Genus", atomised.item(i).getTextContent());
|
|
856
|
path = atomised.item(i).getNodeName();
|
|
857
|
getHierarchie(atomised.item(i));
|
|
858
|
dataHolder.knownABCDelements.add(path);
|
|
859
|
path = "";
|
|
860
|
}
|
|
861
|
else if (atomised.item(i).getNodeName().equals(prefix + "Subgenus")) {
|
|
862
|
atomisedMap.put("Subgenus", atomised.item(i).getTextContent());
|
|
863
|
path = atomised.item(i).getNodeName();
|
|
864
|
getHierarchie(atomised.item(i));
|
|
865
|
dataHolder.knownABCDelements.add(path);
|
|
866
|
path = "";
|
|
867
|
}
|
|
868
|
else if (atomised.item(i).getNodeName().equals(prefix + "SpeciesEpithet")) {
|
|
869
|
atomisedMap.put("SpeciesEpithet", atomised.item(i).getTextContent());
|
|
870
|
path = atomised.item(i).getNodeName();
|
|
871
|
getHierarchie(atomised.item(i));
|
|
872
|
dataHolder.knownABCDelements.add(path);
|
|
873
|
path = "";
|
|
874
|
}
|
|
875
|
else if (atomised.item(i).getNodeName().equals(prefix + "SubspeciesEpithet")) {
|
|
876
|
atomisedMap.put("SubspeciesEpithet", atomised.item(i).getTextContent());
|
|
877
|
path = atomised.item(i).getNodeName();
|
|
878
|
getHierarchie(atomised.item(i));
|
|
879
|
dataHolder.knownABCDelements.add(path);
|
|
880
|
path = "";
|
|
881
|
}
|
|
882
|
else if (atomised.item(i).getNodeName().equals(prefix + "AuthorTeamOriginalAndYear")) {
|
|
883
|
atomisedMap.put("AuthorTeamOriginalAndYear", atomised.item(i).getTextContent());
|
|
884
|
path = atomised.item(i).getNodeName();
|
|
885
|
getHierarchie(atomised.item(i));
|
|
886
|
dataHolder.knownABCDelements.add(path);
|
|
887
|
path = "";
|
|
888
|
}
|
|
889
|
else if (atomised.item(i).getNodeName().equals(prefix + "AuthorTeamParenthesisAndYear")) {
|
|
890
|
atomisedMap.put("AuthorTeamParenthesisAndYear", atomised.item(i).getTextContent());
|
|
891
|
path = atomised.item(i).getNodeName();
|
|
892
|
getHierarchie(atomised.item(i));
|
|
893
|
dataHolder.knownABCDelements.add(path);
|
|
894
|
path = "";
|
|
895
|
}
|
|
896
|
else if (atomised.item(i).getNodeName().equals(prefix + "CombinationAuthorTeamAndYear")) {
|
|
897
|
atomisedMap.put("CombinationAuthorTeamAndYear", atomised.item(i).getTextContent());
|
|
898
|
path = atomised.item(i).getNodeName();
|
|
899
|
getHierarchie(atomised.item(i));
|
|
900
|
dataHolder.knownABCDelements.add(path);
|
|
901
|
path = "";
|
|
902
|
}
|
|
903
|
else if (atomised.item(i).getNodeName().equals(prefix + "Breed")) {
|
|
904
|
atomisedMap.put("Breed", atomised.item(i).getTextContent());
|
|
905
|
path = atomised.item(i).getNodeName();
|
|
906
|
getHierarchie(atomised.item(i));
|
|
907
|
dataHolder.knownABCDelements.add(path);
|
|
908
|
path = "";
|
|
909
|
}
|
|
910
|
else if (atomised.item(i).getNodeName().equals(prefix + "NamedIndividual")) {
|
|
911
|
atomisedMap.put("NamedIndividual", atomised.item(i).getTextContent());
|
|
912
|
path = atomised.item(i).getNodeName();
|
|
913
|
getHierarchie(atomised.item(i));
|
|
914
|
dataHolder.knownABCDelements.add(path);
|
|
915
|
path = "";
|
|
916
|
}
|
|
917
|
}
|
|
918
|
return atomisedMap;
|
|
919
|
}
|
|
920
|
|
|
921
|
private HashMap<String, String> getAtomisedViral(NodeList atomised) {
|
|
922
|
HashMap<String, String> atomisedMap = new HashMap<String, String>();
|
|
923
|
for (int i = 0; i < atomised.getLength(); i++) {
|
|
924
|
if (atomised.item(i).getNodeName().equals(prefix + "GenusOrMonomial")) {
|
|
925
|
atomisedMap.put("Genus", atomised.item(i).getTextContent());
|
|
926
|
path = atomised.item(i).getNodeName();
|
|
927
|
getHierarchie(atomised.item(i));
|
|
928
|
dataHolder.knownABCDelements.add(path);
|
|
929
|
path = "";
|
|
930
|
}
|
|
931
|
if (atomised.item(i).getNodeName().equals(prefix + "ViralSpeciesDesignation")) {
|
|
932
|
atomisedMap.put("ViralSpeciesDesignation", atomised.item(i).getTextContent());
|
|
933
|
path = atomised.item(i).getNodeName();
|
|
934
|
getHierarchie(atomised.item(i));
|
|
935
|
dataHolder.knownABCDelements.add(path);
|
|
936
|
path = "";
|
|
937
|
}
|
|
938
|
if (atomised.item(i).getNodeName().equals(prefix + "Acronym")) {
|
|
939
|
atomisedMap.put("Acronym", atomised.item(i).getTextContent());
|
|
940
|
path = atomised.item(i).getNodeName();
|
|
941
|
getHierarchie(atomised.item(i));
|
|
942
|
dataHolder.knownABCDelements.add(path);
|
|
943
|
path = "";
|
|
944
|
}
|
|
945
|
}
|
|
946
|
return atomisedMap;
|
|
947
|
}
|
|
948
|
|
|
949
|
private HashMap<String, String> getAtomisedBotanical(NodeList atomised) {
|
|
950
|
HashMap<String, String> atomisedMap = new HashMap<String, String>();
|
|
951
|
for (int i = 0; i < atomised.getLength(); i++) {
|
|
952
|
if (atomised.item(i).getNodeName().equals(prefix + "GenusOrMonomial")) {
|
|
953
|
atomisedMap.put("Genus", atomised.item(i).getTextContent());
|
|
954
|
path = atomised.item(i).getNodeName();
|
|
955
|
getHierarchie(atomised.item(i));
|
|
956
|
dataHolder.knownABCDelements.add(path);
|
|
957
|
path = "";
|
|
958
|
}
|
|
959
|
if (atomised.item(i).getNodeName().equals(prefix + "FirstEpithet")) {
|
|
960
|
atomisedMap.put("FirstEpithet", atomised.item(i).getTextContent());
|
|
961
|
path = atomised.item(i).getNodeName();
|
|
962
|
getHierarchie(atomised.item(i));
|
|
963
|
dataHolder.knownABCDelements.add(path);
|
|
964
|
path = "";
|
|
965
|
}
|
|
966
|
if (atomised.item(i).getNodeName()
|
|
967
|
.equals(prefix + "InfraspecificEpithet")) {
|
|
968
|
atomisedMap.put("InfraSpeEpithet", atomised.item(i).getTextContent());
|
|
969
|
path = atomised.item(i).getNodeName();
|
|
970
|
getHierarchie(atomised.item(i));
|
|
971
|
dataHolder.knownABCDelements.add(path);
|
|
972
|
path = "";
|
|
973
|
}
|
|
974
|
if (atomised.item(i).getNodeName().equals(prefix + "Rank")) {
|
|
975
|
atomisedMap.put("Rank", atomised.item(i).getTextContent());
|
|
976
|
path = atomised.item(i).getNodeName();
|
|
977
|
getHierarchie(atomised.item(i));
|
|
978
|
dataHolder.knownABCDelements.add(path);
|
|
979
|
path = "";
|
|
980
|
}
|
|
981
|
if (atomised.item(i).getNodeName().equals(prefix + "HybridFlag")) {
|
|
982
|
atomisedMap.put("HybridFlag", atomised.item(i).getTextContent());
|
|
983
|
path = atomised.item(i).getNodeName();
|
|
984
|
getHierarchie(atomised.item(i));
|
|
985
|
dataHolder.knownABCDelements.add(path);
|
|
986
|
path = "";
|
|
987
|
}
|
|
988
|
if (atomised.item(i).getNodeName()
|
|
989
|
.equals(prefix + "AuthorTeamParenthesis")) {
|
|
990
|
atomisedMap.put("AuthorTeamParenthesis", atomised.item(i).getTextContent());
|
|
991
|
path = atomised.item(i).getNodeName();
|
|
992
|
getHierarchie(atomised.item(i));
|
|
993
|
dataHolder.knownABCDelements.add(path);
|
|
994
|
path = "";
|
|
995
|
}
|
|
996
|
if (atomised.item(i).getNodeName().equals(prefix + "AuthorTeam")) {
|
|
997
|
atomisedMap.put("AuthorTeam", atomised.item(i).getTextContent());
|
|
998
|
path = atomised.item(i).getNodeName();
|
|
999
|
getHierarchie(atomised.item(i));
|
|
1000
|
dataHolder.knownABCDelements.add(path);
|
|
1001
|
path = "";
|
|
1002
|
}
|
|
1003
|
if (atomised.item(i).getNodeName().equals(prefix + "CultivarGroupName")) {
|
|
1004
|
atomisedMap.put("CultivarGroupName", atomised.item(i).getTextContent());
|
|
1005
|
path = atomised.item(i).getNodeName();
|
|
1006
|
getHierarchie(atomised.item(i));
|
|
1007
|
dataHolder.knownABCDelements.add(path);
|
|
1008
|
path = "";
|
|
1009
|
}
|
|
1010
|
if (atomised.item(i).getNodeName().equals(prefix + "CultivarName")) {
|
|
1011
|
atomisedMap.put("CultivarName", atomised.item(i).getTextContent());
|
|
1012
|
path = atomised.item(i).getNodeName();
|
|
1013
|
getHierarchie(atomised.item(i));
|
|
1014
|
dataHolder.knownABCDelements.add(path);
|
|
1015
|
path = "";
|
|
1016
|
}
|
|
1017
|
if (atomised.item(i).getNodeName().equals(prefix + "TradeDesignationNames")) {
|
|
1018
|
atomisedMap.put("Trade", atomised.item(i).getTextContent());
|
|
1019
|
path = atomised.item(i).getNodeName();
|
|
1020
|
getHierarchie(atomised.item(i));
|
|
1021
|
dataHolder.knownABCDelements.add(path);
|
|
1022
|
path = "";
|
|
1023
|
}
|
|
1024
|
}
|
|
1025
|
return atomisedMap;
|
|
1026
|
}
|
|
1027
|
|
|
1028
|
private HashMap<String, String> getAtomisedBacterial(NodeList atomised) {
|
|
1029
|
HashMap<String, String> atomisedMap = new HashMap<String, String>();
|
|
1030
|
for (int i = 0; i < atomised.getLength(); i++) {
|
|
1031
|
if (atomised.item(i).getNodeName().equals(prefix + "GenusOrMonomial")) {
|
|
1032
|
atomisedMap.put("Genus", atomised.item(i).getTextContent());
|
|
1033
|
path = atomised.item(i).getNodeName();
|
|
1034
|
getHierarchie(atomised.item(i));
|
|
1035
|
dataHolder.knownABCDelements.add(path);
|
|
1036
|
path = "";
|
|
1037
|
}
|
|
1038
|
if (atomised.item(i).getNodeName().equals(prefix + "Subgenus")) {
|
|
1039
|
atomisedMap.put("SubGenus", atomised.item(i).getTextContent());
|
|
1040
|
path = atomised.item(i).getNodeName();
|
|
1041
|
getHierarchie(atomised.item(i));
|
|
1042
|
dataHolder.knownABCDelements.add(path);
|
|
1043
|
path = "";
|
|
1044
|
}
|
|
1045
|
if (atomised.item(i).getNodeName().equals(prefix + "SubgenusAuthorAndYear")) {
|
|
1046
|
atomisedMap.put("SubgenusAuthorAndYear", atomised.item(i).getTextContent());
|
|
1047
|
path = atomised.item(i).getNodeName();
|
|
1048
|
getHierarchie(atomised.item(i));
|
|
1049
|
dataHolder.knownABCDelements.add(path);
|
|
1050
|
path = "";
|
|
1051
|
}
|
|
1052
|
if (atomised.item(i).getNodeName().equals(prefix + "SpeciesEpithet")) {
|
|
1053
|
atomisedMap.put("SpeciesEpithet", atomised.item(i).getTextContent());
|
|
1054
|
path = atomised.item(i).getNodeName();
|
|
1055
|
getHierarchie(atomised.item(i));
|
|
1056
|
dataHolder.knownABCDelements.add(path);
|
|
1057
|
path = "";
|
|
1058
|
}
|
|
1059
|
if (atomised.item(i).getNodeName().equals(prefix + "SubspeciesEpithet")) {
|
|
1060
|
atomisedMap.put("SubspeciesEpithet", atomised.item(i).getTextContent());
|
|
1061
|
path = atomised.item(i).getNodeName();
|
|
1062
|
getHierarchie(atomised.item(i));
|
|
1063
|
dataHolder.knownABCDelements.add(path);
|
|
1064
|
path = "";
|
|
1065
|
}
|
|
1066
|
if (atomised.item(i).getNodeName().equals(prefix + "ParentheticalAuthorTeamAndYear")) {
|
|
1067
|
atomisedMap.put("ParentheticalAuthorTeamAndYear", atomised.item(i).getTextContent());
|
|
1068
|
path = atomised.item(i).getNodeName();
|
|
1069
|
getHierarchie(atomised.item(i));
|
|
1070
|
dataHolder.knownABCDelements.add(path);
|
|
1071
|
path = "";
|
|
1072
|
}
|
|
1073
|
if (atomised.item(i).getNodeName().equals(prefix + "AuthorTeamAndYear")) {
|
|
1074
|
atomisedMap.put("AuthorTeamAndYear", atomised.item(i).getTextContent());
|
|
1075
|
path = atomised.item(i).getNodeName();
|
|
1076
|
getHierarchie(atomised.item(i));
|
|
1077
|
dataHolder.knownABCDelements.add(path);
|
|
1078
|
path = "";
|
|
1079
|
}
|
|
1080
|
if (atomised.item(i).getNodeName().equals(prefix + "NameApprobation")) {
|
|
1081
|
atomisedMap.put("NameApprobation", atomised.item(i).getTextContent());
|
|
1082
|
path = atomised.item(i).getNodeName();
|
|
1083
|
getHierarchie(atomised.item(i));
|
|
1084
|
dataHolder.knownABCDelements.add(path);
|
|
1085
|
path = "";
|
|
1086
|
}
|
|
1087
|
}
|
|
1088
|
return atomisedMap;
|
|
1089
|
}
|
|
1090
|
|
|
1091
|
}
|