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package eu.etaxonomy.cdm.io.specimen.abcd206.in;
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import eu.etaxonomy.cdm.common.URI;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.Map;
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import org.apache.commons.lang3.StringUtils;
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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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/*
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*NomenclaturalTypeDesignations>
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*<abcd21:NomenclaturalTypeDesignation>
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*<abcd21:TypeStatus>epitype</abcd21:TypeStatus>
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*</abcd21:NomenclaturalTypeDesignation>
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*</abcd21:NomenclaturalTypeDesignations>
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*/
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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.getStatusList().add(getSpecimenTypeDesignationStatusByKey(type));
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typeFound=true;
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// path = ntd.item(n).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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if (dataHolder.getStatusList() != null){
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dataHolder.getStatusList().add(null);
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}else{
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dataHolder.setStatusList(new ArrayList<SpecimenTypeDesignationStatus>());
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}
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}
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}
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} catch (NullPointerException e) {
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dataHolder.setStatusList(new ArrayList<SpecimenTypeDesignationStatus>());
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}
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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 getPreparation(Node result) {
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if (DEBUG) {
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logger.info("GetPreparation");
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}
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NodeList results, preps, ntds, ntd;
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String prep;
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String item;
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results = result.getChildNodes();
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try {
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for (int k = 0; k < results.getLength(); k++) {
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if (results.item(k).getNodeName()
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.equals(prefix + "SpecimenUnit")) {
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preps = results.item(k).getChildNodes();
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for (int l = 0; l < preps.getLength(); l++) {
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if (preps.item(l).getNodeName().equals(prefix+ "Preparations")) {
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ntds = preps.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+ "preparation")) {
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ntd = ntds.item(m).getChildNodes();
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prep = "";
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for (int n = 0; n < ntd.getLength(); n++) {
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//Fix me: now only the type or the agent is imported because it is overwritten
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if (ntd.item(n).getNodeName().equals(prefix + "preparationType"))
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{
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item = ntd.item(n).getTextContent().trim();
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prep += " Preparation Type: "+item +System.lineSeparator();
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if(DEBUG) {
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logger.info("ADD "+prep);
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}
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dataHolder.setUnitNotes(prep);
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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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if (ntd.item(n).getNodeName().equals(prefix + "preparationAgent"))
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{
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item = ntd.item(n).getTextContent().trim();
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prep += " Preparation Agent: "+item;
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if(DEBUG) {
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logger.info("ADD "+prep);
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}
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dataHolder.setUnitNotes(prep);
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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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}
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} catch (NullPointerException e) {
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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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String preferredFlag = null;
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String identifierStr = null;
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String dateStr = null;
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String modifierStr = null;
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//TODO: add the identifier!!
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// abcd:Identification>
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// <abcd:Result>
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// <abcd:TaxonIdentified>
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// <abcd:ScientificName>
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// <abcd:FullScientificNameString>Melosira varians C. Agardh</abcd:FullScientificNameString>
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// <abcd:NameAtomised><abcd:Botanical><abcd:GenusOrMonomial>Melosira</abcd:GenusOrMonomial><abcd:FirstEpithet>varians</abcd:FirstEpithet><abcd:Rank>sp.</abcd:Rank><abcd:AuthorTeam>C.Agardh</abcd:AuthorTeam></abcd:Botanical></abcd:NameAtomised>
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// </abcd:ScientificName>
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// </abcd:TaxonIdentified>
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// </abcd:Result>
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// <abcd:PreferredFlag>true</abcd:PreferredFlag>
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// <abcd:Identifiers>
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// <abcd:Identifier>
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// <abcd:PersonName><abcd:FullName>W.-H. Kusber</abcd:FullName></abcd:PersonName>
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// </abcd:Identifier>
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// </abcd:Identifiers>
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// <abcd:Date>
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// <abcd:DateText>2014-07-11T00:00:00</abcd:DateText></abcd:Date>
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// </abcd:Identification>
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// TODO:here we need to get the informations about the higher taxa to get the info about the nomenclatural code!!
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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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if (tmpName.contains("cf.")){
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modifierStr = "cf.";
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tmpName = tmpName.replace("cf.", "");
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}
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if (tmpName.contains("aff.")){
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modifierStr = "aff.";
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tmpName = tmpName.replace("aff.", "");
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}
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logger.info("TMP NAME " + tmpName);
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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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preferredFlag = identifications.item(m).getTextContent();
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// if (dataHolder.getNomenclatureCode() != null&& dataHolder.getNomenclatureCode() != "") {
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// // logger.info("TMP NAME P" + tmpName);
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//
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// dataHolder.getIdentificationList().add(new Identification(tmpName, preferredFlag, dataHolder.getNomenclatureCode(), null));
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// } else {
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// dataHolder.getIdentificationList().add(new Identification(tmpName, preferredFlag));
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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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} else if (identifications.item(m).getNodeName().equals(prefix + "Identifiers")){
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identifierStr = this.getIdentifiers(identifications.item(m));
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}else if (identifications.item(m).getNodeName().equals(prefix +"Date")){
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dateStr = this.getDateIdentified(identifications.item(m));
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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 (StringUtils.isNoneBlank(dataHolder.getNomenclatureCode())) {
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// logger.info("TMP NAME P" + tmpName);
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dataHolder.getIdentificationList().add(new Identification(tmpName, preferredFlag, dataHolder.getNomenclatureCode(), identifierStr, dateStr, modifierStr));
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} else {
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dataHolder.getIdentificationList().add(new Identification(tmpName, preferredFlag,identifierStr, dateStr, modifierStr));
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}
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}
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}
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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.setNomenclatureCode("");
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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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261
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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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265
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// if (identifications.item(m).getNodeName()
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// .equals(prefix + "PreferredFlag")) {
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267
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// hasPref = true;
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268
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// }
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269
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// }
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270
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// if (!hasPref && tmpName != null) {
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// if (dataHolder.getNomenclatureCode() != null
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272
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// && dataHolder.getNomenclatureCode() != "") {
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273
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// dataHolder.getIdentificationList().add(new Identification(tmpName, "0", dataHolder.getNomenclatureCode(), null, dateStr));
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274
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// } else {
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275
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// dataHolder.getIdentificationList().add(new Identification(tmpName, "0", null, dateStr));
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276
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// }
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277
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// }
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278
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// }
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279
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// }
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280
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}
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281
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282
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/**
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283
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* @param item
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284
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* @return
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285
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*/
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286
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private String getDateIdentified(Node item) {
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287
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NodeList results, dateNode, dateTextNode;
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288
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results = item.getChildNodes();
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289
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boolean identifierFound = false;
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290
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291
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for (int k = 0; k < results.getLength(); k++) {
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292
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if (results.item(k).getNodeName().equals(prefix + "DateText")) {
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293
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return results.item(k).getTextContent();
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294
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}
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295
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296
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297
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}
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298
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return null;
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299
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300
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}
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301
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302
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303
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/**
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304
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* @param item
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305
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*/
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306
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private String getIdentifiers(Node item) {
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307
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NodeList results, identifier, personName;
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308
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results = item.getChildNodes();
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309
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boolean identifierFound = false;
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310
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311
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for (int k = 0; k < results.getLength(); k++) {
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312
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if (results.item(k).getNodeName().equals(prefix + "Identifier")) {
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313
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/*
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314
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* <abcd21:Identifiers>
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315
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* <abcd21:Identifier>
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316
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* <abcd21:PersonName>
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317
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* <abcd21:FullName>R. Jahn</abcd21:FullName>
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318
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* </abcd21:PersonName>
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319
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* </abcd21:Identifier>
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320
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* </abcd21:Identifiers>
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321
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*/
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322
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identifier = results.item(k).getChildNodes();
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323
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for (int l = 0; l < identifier.getLength(); l++) {
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324
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if (identifier.item(l).getNodeName().equals(prefix + "PersonName")) {
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325
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identifierFound = true;
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326
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Node identifierPersonName = identifier.item(l);
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327
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personName = identifierPersonName.getChildNodes();
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328
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for (int m = 0; m < personName.getLength(); m++) {
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329
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if (personName.item(m).getNodeName().equals(prefix + "FullName")) {
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330
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return personName.item(m).getTextContent();
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331
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}
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332
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}
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333
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334
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}
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335
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336
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}
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337
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338
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}
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339
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}
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340
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return null;
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|
341
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342
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}
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|
343
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344
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|
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345
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/**
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346
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* getScientificName : get the list of scientific names
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347
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* @param result
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348
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* @return
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|
349
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*/
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|
350
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private String getScientificName(Node result) {
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|
351
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// logger.info("IN getScientificName " + dataHolder.nomenclatureCode);
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352
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NodeList taxonsIdentified, scnames, atomised;
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|
353
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String tmpName = "";
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354
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taxonsIdentified = result.getChildNodes();
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355
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for (int l = 0; l < taxonsIdentified.getLength(); l++) {
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356
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357
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if (taxonsIdentified.item(l).getNodeName().equals(prefix + "ScientificName")) {
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358
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scnames = taxonsIdentified.item(l).getChildNodes();
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359
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for (int n = 0; n < scnames.getLength(); n++) {
|
|
360
|
|
|
361
|
if (scnames.item(n).getNodeName().equals(prefix + "FullScientificNameString")) {
|
|
362
|
path = scnames.item(n).getNodeName();
|
|
363
|
tmpName = scnames.item(n).getTextContent();
|
|
364
|
getHierarchie(scnames.item(n));
|
|
365
|
dataHolder.knownABCDelements.add(path);
|
|
366
|
path = "";
|
|
367
|
}
|
|
368
|
else if (scnames.item(n).getNodeName().equals(prefix + "NameAtomised")) {
|
|
369
|
Node nameAtomised = scnames.item(n);
|
|
370
|
try {
|
|
371
|
if (nameAtomised.hasChildNodes()) {
|
|
372
|
NodeList children = nameAtomised.getChildNodes();
|
|
373
|
String tmp = children.item(1).getNodeName();
|
|
374
|
|
|
375
|
if (tmp.indexOf(prefix) != -1 && prefix.length() > 0) {
|
|
376
|
dataHolder.setNomenclatureCode(tmp.split(prefix)[1]);
|
|
377
|
}
|
|
378
|
else {
|
|
379
|
dataHolder.setNomenclatureCode(scnames.item(n).getChildNodes().item(1).getNodeName());
|
|
380
|
}
|
|
381
|
|
|
382
|
Node child = children.item(0);
|
|
383
|
|
|
384
|
dataHolder.getAtomisedIdentificationList().add(this.getAtomisedNames(dataHolder.getNomenclatureCode(),children));
|
|
385
|
}
|
|
386
|
} catch (Exception e) {
|
|
387
|
if(DEBUG) {
|
|
388
|
logger.warn("PB nomenclaturecode");
|
|
389
|
}
|
|
390
|
dataHolder.setNomenclatureCode("");
|
|
391
|
}
|
|
392
|
|
|
393
|
|
|
394
|
}
|
|
395
|
}
|
|
396
|
}
|
|
397
|
}
|
|
398
|
return tmpName;
|
|
399
|
}
|
|
400
|
|
|
401
|
/**
|
|
402
|
* getRerences : get the reference and citations
|
|
403
|
* @param result
|
|
404
|
* @return
|
|
405
|
*/
|
|
406
|
protected boolean getReferences(Node result) {
|
|
407
|
// logger.info("GET REFERENCE");
|
|
408
|
NodeList results, reference;
|
|
409
|
results = result.getChildNodes();
|
|
410
|
boolean referencefound = false;
|
|
411
|
String[] refDetails =new String[3];
|
|
412
|
|
|
413
|
for (int k = 0; k < results.getLength(); k++) {
|
|
414
|
if (results.item(k).getNodeName().equals(prefix + "SourceReference")) {
|
|
415
|
reference = results.item(k).getChildNodes();
|
|
416
|
for (int l = 0; l < reference.getLength(); l++) {
|
|
417
|
if (reference.item(l).getNodeName().equals(prefix + "TitleCitation")) {
|
|
418
|
path = reference.item(l).getNodeName();
|
|
419
|
refDetails[0]=reference.item(l).getTextContent();
|
|
420
|
getHierarchie(reference.item(l));
|
|
421
|
dataHolder.knownABCDelements.add(path);
|
|
422
|
path = "";
|
|
423
|
referencefound = true;
|
|
424
|
}
|
|
425
|
if (reference.item(l).getNodeName().equals(prefix + "CitationDetail")) {
|
|
426
|
path = reference.item(l).getNodeName();
|
|
427
|
refDetails[1]=reference.item(l).getTextContent();
|
|
428
|
getHierarchie(reference.item(l));
|
|
429
|
dataHolder.knownABCDelements.add(path);
|
|
430
|
path = "";
|
|
431
|
referencefound = true;
|
|
432
|
}
|
|
433
|
if (reference.item(l).getNodeName().equals(prefix + "URI")) {
|
|
434
|
path = reference.item(l).getNodeName();
|
|
435
|
refDetails[2]=reference.item(l).getTextContent();
|
|
436
|
getHierarchie(reference.item(l));
|
|
437
|
dataHolder.knownABCDelements.add(path);
|
|
438
|
path = "";
|
|
439
|
referencefound = true;
|
|
440
|
}
|
|
441
|
}
|
|
442
|
if (refDetails!=null){
|
|
443
|
for (int i=0;i<3;i++) {
|
|
444
|
if (refDetails[i]==null) {
|
|
445
|
refDetails[i]="";
|
|
446
|
}
|
|
447
|
}
|
|
448
|
dataHolder.getReferenceList().add(refDetails);
|
|
449
|
refDetails =new String[3];
|
|
450
|
}
|
|
451
|
}
|
|
452
|
}
|
|
453
|
return referencefound;
|
|
454
|
}
|
|
455
|
|
|
456
|
/**
|
|
457
|
* Traverses the tree for compareABCDtoCDM
|
|
458
|
*
|
|
459
|
* @param node
|
|
460
|
* @param dataHolder
|
|
461
|
*/
|
|
462
|
protected void traverse(Node node) {
|
|
463
|
// Extract node info:
|
|
464
|
String test = node.getTextContent();
|
|
465
|
|
|
466
|
// Print and continue traversing.
|
|
467
|
if (test != null && test != "#text" && node.getNodeName() != "#text"&& test.split("\n").length == 1 && test.length() > 0) {
|
|
468
|
path = node.getNodeName();
|
|
469
|
getHierarchie(node);
|
|
470
|
dataHolder.allABCDelements.put(path, test);
|
|
471
|
path = "";
|
|
472
|
}
|
|
473
|
// Now traverse the rest of the tree in depth-first order.
|
|
474
|
if (node.hasChildNodes()) {
|
|
475
|
// Get the children in a list.
|
|
476
|
NodeList nl = node.getChildNodes();
|
|
477
|
// How many of them?
|
|
478
|
int size = nl.getLength();
|
|
479
|
for (int i = 0; i < size; i++) {
|
|
480
|
// Recursively traverse each of the children.
|
|
481
|
traverse(nl.item(i));
|
|
482
|
}
|
|
483
|
}
|
|
484
|
}
|
|
485
|
|
|
486
|
|
|
487
|
|
|
488
|
/*
|
|
489
|
* (non-Javadoc)
|
|
490
|
*
|
|
491
|
* @see eu.etaxonomy.cdm.io.common.mapping.IInputTransformer#
|
|
492
|
* getSpecimenTypeDesignationStatusByKey(java.lang.String)
|
|
493
|
*/
|
|
494
|
private SpecimenTypeDesignationStatus getSpecimenTypeDesignationStatusByKey(
|
|
495
|
String key) {
|
|
496
|
if (key == null) {
|
|
497
|
return null;
|
|
498
|
} else if (key.matches("(?i)(T|Type)")) {
|
|
499
|
return SpecimenTypeDesignationStatus.TYPE();
|
|
500
|
} else if (key.matches("(?i)(HT|Holotype)")) {
|
|
501
|
return SpecimenTypeDesignationStatus.HOLOTYPE();
|
|
502
|
} else if (key.matches("(?i)(LT|Lectotype)")) {
|
|
503
|
return SpecimenTypeDesignationStatus.LECTOTYPE();
|
|
504
|
} else if (key.matches("(?i)(NT|Neotype)")) {
|
|
505
|
return SpecimenTypeDesignationStatus.NEOTYPE();
|
|
506
|
} else if (key.matches("(?i)(ST|Syntype)")) {
|
|
507
|
return SpecimenTypeDesignationStatus.SYNTYPE();
|
|
508
|
} else if (key.matches("(?i)(ET|Epitype)")) {
|
|
509
|
return SpecimenTypeDesignationStatus.EPITYPE();
|
|
510
|
} else if (key.matches("(?i)(IT|Isotype)")) {
|
|
511
|
return SpecimenTypeDesignationStatus.ISOTYPE();
|
|
512
|
} else if (key.matches("(?i)(ILT|Isolectotype)")) {
|
|
513
|
return SpecimenTypeDesignationStatus.ISOLECTOTYPE();
|
|
514
|
} else if (key.matches("(?i)(INT|Isoneotype)")) {
|
|
515
|
return SpecimenTypeDesignationStatus.ISONEOTYPE();
|
|
516
|
} else if (key.matches("(?i)(IET|Isoepitype)")) {
|
|
517
|
return SpecimenTypeDesignationStatus.ISOEPITYPE();
|
|
518
|
} else if (key.matches("(?i)(PT|Paratype)")) {
|
|
519
|
return SpecimenTypeDesignationStatus.PARATYPE();
|
|
520
|
} else if (key.matches("(?i)(PLT|Paralectotype)")) {
|
|
521
|
return SpecimenTypeDesignationStatus.PARALECTOTYPE();
|
|
522
|
} else if (key.matches("(?i)(PNT|Paraneotype)")) {
|
|
523
|
return SpecimenTypeDesignationStatus.PARANEOTYPE();
|
|
524
|
} else if (key.matches("(?i)(unsp.|Unspecified)")) {
|
|
525
|
return SpecimenTypeDesignationStatus.UNSPECIFIC();
|
|
526
|
} else if (key.matches("(?i)(2LT|Second Step Lectotype)")) {
|
|
527
|
return SpecimenTypeDesignationStatus.SECOND_STEP_LECTOTYPE();
|
|
528
|
} else if (key.matches("(?i)(2NT|Second Step Neotype)")) {
|
|
529
|
return SpecimenTypeDesignationStatus.SECOND_STEP_NEOTYPE();
|
|
530
|
} else if (key.matches("(?i)(OM|Original Material)")) {
|
|
531
|
return SpecimenTypeDesignationStatus.ORIGINAL_MATERIAL();
|
|
532
|
} else if (key.matches("(?i)(IcT|Iconotype)")) {
|
|
533
|
return SpecimenTypeDesignationStatus.ICONOTYPE();
|
|
534
|
} else if (key.matches("(?i)(PT|Phototype)")) {
|
|
535
|
return SpecimenTypeDesignationStatus.PHOTOTYPE();
|
|
536
|
} else if (key.matches("(?i)(IST|Isosyntype)")) {
|
|
537
|
return SpecimenTypeDesignationStatus.ISOSYNTYPE();
|
|
538
|
} else {
|
|
539
|
return null;
|
|
540
|
}
|
|
541
|
}
|
|
542
|
|
|
543
|
/**
|
|
544
|
* getHierarchie : get the whole path
|
|
545
|
* @param node
|
|
546
|
*/
|
|
547
|
private void getHierarchie(Node node) {
|
|
548
|
// logger.info("getHierarchie");
|
|
549
|
while (node != null && node.getNodeName() != prefix + "DataSets" && node.getParentNode() != null) {
|
|
550
|
// logger.info("nodeparent "+node.getParentNode().getNodeName());
|
|
551
|
path = node.getParentNode().getNodeName() + "/" + path;
|
|
552
|
node = node.getParentNode();
|
|
553
|
}
|
|
554
|
// logger.info("path gethierarchie: "+path);
|
|
555
|
}
|
|
556
|
|
|
557
|
|
|
558
|
/**
|
|
559
|
* getIDs : get the source institution id, source id...
|
|
560
|
* @param root
|
|
561
|
*/
|
|
562
|
protected void getIDs(Element root) {
|
|
563
|
NodeList group;
|
|
564
|
try {
|
|
565
|
group = root.getElementsByTagName(prefix + "SourceInstitutionID");
|
|
566
|
path = group.item(0).getNodeName();
|
|
567
|
getHierarchie(group.item(0));
|
|
568
|
dataHolder.knownABCDelements.add(path);
|
|
569
|
path = "";
|
|
570
|
dataHolder.institutionCode = group.item(0).getTextContent();
|
|
571
|
} catch (NullPointerException e) {
|
|
572
|
dataHolder.institutionCode = "";
|
|
573
|
}
|
|
574
|
try {
|
|
575
|
group = root.getElementsByTagName(prefix + "SourceID");
|
|
576
|
path = group.item(0).getNodeName();
|
|
577
|
getHierarchie(group.item(0));
|
|
578
|
dataHolder.knownABCDelements.add(path);
|
|
579
|
path = "";
|
|
580
|
dataHolder.collectionCode = group.item(0).getTextContent();
|
|
581
|
} catch (NullPointerException e) {
|
|
582
|
dataHolder.collectionCode = "";
|
|
583
|
}
|
|
584
|
try {
|
|
585
|
group = root.getElementsByTagName(prefix + "UnitID");
|
|
586
|
path = group.item(0).getNodeName();
|
|
587
|
getHierarchie(group.item(0));
|
|
588
|
dataHolder.knownABCDelements.add(path);
|
|
589
|
path = "";
|
|
590
|
dataHolder.setUnitID(group.item(0).getTextContent());
|
|
591
|
} catch (NullPointerException e) {
|
|
592
|
dataHolder.setUnitID("");
|
|
593
|
}
|
|
594
|
try {
|
|
595
|
group = root.getElementsByTagName(prefix + "UnitGUID");
|
|
596
|
path = group.item(0).getNodeName();
|
|
597
|
getHierarchie(group.item(0));
|
|
598
|
dataHolder.knownABCDelements.add(path);
|
|
599
|
path = "";
|
|
600
|
try{
|
|
601
|
dataHolder.setPreferredStableUri(URI.create(group.item(0).getTextContent()));
|
|
602
|
}catch(IllegalArgumentException e){
|
|
603
|
dataHolder.setPreferredStableUri(null);
|
|
604
|
}
|
|
605
|
} catch (NullPointerException e) {
|
|
606
|
dataHolder.setPreferredStableUri(null);
|
|
607
|
}
|
|
608
|
}
|
|
609
|
|
|
610
|
/**
|
|
611
|
* getRecordBasis : extract the recordBasis out of the ABCD document
|
|
612
|
* @param root
|
|
613
|
*/
|
|
614
|
protected void getRecordBasis(Element root) {
|
|
615
|
NodeList group;
|
|
616
|
try {
|
|
617
|
group = root.getElementsByTagName(prefix + "RecordBasis");
|
|
618
|
path = group.item(0).getNodeName();
|
|
619
|
getHierarchie(group.item(0));
|
|
620
|
dataHolder.knownABCDelements.add(path);
|
|
621
|
path = "";
|
|
622
|
dataHolder.setRecordBasis(group.item(0).getTextContent()) ;
|
|
623
|
} catch (NullPointerException e) {
|
|
624
|
dataHolder.setRecordBasis("") ;
|
|
625
|
}
|
|
626
|
}
|
|
627
|
|
|
628
|
protected void getKindOfUnit(Element root) {
|
|
629
|
NodeList group;
|
|
630
|
try {
|
|
631
|
group = root.getElementsByTagName(prefix + "KindOfUnit");
|
|
632
|
path = group.item(0).getNodeName();
|
|
633
|
getHierarchie(group.item(0));
|
|
634
|
dataHolder.knownABCDelements.add(path);
|
|
635
|
path = "";
|
|
636
|
dataHolder.setKindOfUnit(group.item(0).getTextContent());
|
|
637
|
} catch (NullPointerException e) {
|
|
638
|
dataHolder.setKindOfUnit("");
|
|
639
|
}
|
|
640
|
}
|
|
641
|
|
|
642
|
/**
|
|
643
|
* getNumbers : getAccessionNumber, collector number ...
|
|
644
|
* @param root
|
|
645
|
*/
|
|
646
|
protected void getNumbers(Element root) {
|
|
647
|
NodeList group;
|
|
648
|
try {
|
|
649
|
group = root.getElementsByTagName(prefix + "AccessionNumber");
|
|
650
|
path = group.item(0).getNodeName();
|
|
651
|
getHierarchie(group.item(0));
|
|
652
|
dataHolder.knownABCDelements.add(path);
|
|
653
|
path = "";
|
|
654
|
dataHolder.accessionNumber = group.item(0).getTextContent();
|
|
655
|
} catch (NullPointerException e) {
|
|
656
|
dataHolder.accessionNumber = "";
|
|
657
|
}
|
|
658
|
try {
|
|
659
|
group = root.getElementsByTagName(prefix + "CollectorsFieldNumber");
|
|
660
|
path = group.item(0).getNodeName();
|
|
661
|
getHierarchie(group.item(0));
|
|
662
|
dataHolder.knownABCDelements.add(path);
|
|
663
|
path = "";
|
|
664
|
String collectorsFieldNumber = group.item(0).getTextContent();
|
|
665
|
dataHolder.setFieldNumber(collectorsFieldNumber);
|
|
666
|
} catch (NullPointerException e) {
|
|
667
|
dataHolder.setFieldNumber("");
|
|
668
|
}
|
|
669
|
|
|
670
|
//try {
|
|
671
|
//group = root.getElementsByTagName(prefix + "AccessionNumber");
|
|
672
|
//path = group.item(0).getNodeName();
|
|
673
|
//getHierarchie(group.item(0));
|
|
674
|
//dataHolder.knownABCDelements.add(path);
|
|
675
|
//path = "";
|
|
676
|
//dataHolder.accessionNumber = group.item(0).getTextContent();
|
|
677
|
//} catch (NullPointerException e) {
|
|
678
|
//dataHolder.accessionNumber = "";
|
|
679
|
//}
|
|
680
|
}
|
|
681
|
|
|
682
|
/**
|
|
683
|
* getGeolocation : get locality
|
|
684
|
* @param root
|
|
685
|
* @param state
|
|
686
|
*/
|
|
687
|
protected void getGeolocation(Element root, Abcd206ImportState state) {
|
|
688
|
NodeList group, childs;
|
|
689
|
try {
|
|
690
|
group = root.getElementsByTagName(prefix + "LocalityText");
|
|
691
|
path = group.item(0).getNodeName();
|
|
692
|
getHierarchie(group.item(0));
|
|
693
|
dataHolder.knownABCDelements.add(path);
|
|
694
|
path = "";
|
|
695
|
dataHolder.locality = group.item(0).getTextContent();
|
|
696
|
if (group.item(0).hasAttributes()) {
|
|
697
|
if (group.item(0).getAttributes().getNamedItem("lang") != null) {
|
|
698
|
dataHolder.languageIso = group.item(0).getAttributes().getNamedItem("lang").getTextContent();
|
|
699
|
}
|
|
700
|
}
|
|
701
|
} catch (NullPointerException e) {
|
|
702
|
dataHolder.locality = "";
|
|
703
|
}
|
|
704
|
try {
|
|
705
|
group = root.getElementsByTagName(prefix + "LongitudeDecimal");
|
|
706
|
path = group.item(0).getNodeName();
|
|
707
|
getHierarchie(group.item(0));
|
|
708
|
dataHolder.knownABCDelements.add(path);
|
|
709
|
path = "";
|
|
710
|
Node node = group.item(0);
|
|
711
|
dataHolder.longitude = Double.valueOf(group.item(0).getTextContent());
|
|
712
|
} catch (NullPointerException e) {
|
|
713
|
dataHolder.longitude = null;
|
|
714
|
}
|
|
715
|
try {
|
|
716
|
group = root.getElementsByTagName(prefix + "LatitudeDecimal");
|
|
717
|
path = group.item(0).getNodeName();
|
|
718
|
getHierarchie(group.item(0));
|
|
719
|
dataHolder.knownABCDelements.add(path);
|
|
720
|
path = "";
|
|
721
|
dataHolder.latitude = Double.valueOf(group.item(0).getTextContent());
|
|
722
|
} catch (NullPointerException e) {
|
|
723
|
dataHolder.latitude = null;
|
|
724
|
}
|
|
725
|
try {
|
|
726
|
group = root.getElementsByTagName(prefix + "CoordinateErrorDistanceInMeters");
|
|
727
|
path = group.item(0).getNodeName();
|
|
728
|
getHierarchie(group.item(0));
|
|
729
|
dataHolder.knownABCDelements.add(path);
|
|
730
|
path = "";
|
|
731
|
dataHolder.setGatheringCoordinateErrorMethod(group.item(0).getTextContent());
|
|
732
|
} catch (NullPointerException e) {
|
|
733
|
dataHolder.setGatheringCoordinateErrorMethod(null);
|
|
734
|
}
|
|
735
|
try {
|
|
736
|
group = root.getElementsByTagName(prefix + "Country");
|
|
737
|
childs = group.item(0).getChildNodes();
|
|
738
|
for (int i = 0; i < childs.getLength(); i++) {
|
|
739
|
if (childs.item(i).getNodeName().contains("Name")) {
|
|
740
|
path = childs.item(i).getNodeName();
|
|
741
|
getHierarchie(childs.item(i));
|
|
742
|
dataHolder.knownABCDelements.add(path);
|
|
743
|
path = "";
|
|
744
|
dataHolder.country = childs.item(i).getTextContent();
|
|
745
|
}
|
|
746
|
}
|
|
747
|
} catch (NullPointerException e) {
|
|
748
|
dataHolder.country = "";
|
|
749
|
}
|
|
750
|
try {
|
|
751
|
group = root.getElementsByTagName(prefix + "Country");
|
|
752
|
childs = group.item(0).getChildNodes();
|
|
753
|
for (int i = 0; i < childs.getLength(); i++) {
|
|
754
|
if (childs.item(i).getNodeName().contains("ISO3166Code")) {
|
|
755
|
path = childs.item(i).getNodeName();
|
|
756
|
getHierarchie(childs.item(i));
|
|
757
|
dataHolder.knownABCDelements.add(path);
|
|
758
|
path = "";
|
|
759
|
dataHolder.isocountry = childs.item(i).getTextContent();
|
|
760
|
}
|
|
761
|
}
|
|
762
|
} catch (NullPointerException e) {
|
|
763
|
dataHolder.isocountry = "";
|
|
764
|
}
|
|
765
|
try {
|
|
766
|
group = root.getElementsByTagName(prefix + "Altitude");
|
|
767
|
for (int i = 0; i < group.getLength(); i++) {
|
|
768
|
childs = group.item(i).getChildNodes();
|
|
769
|
for (int j = 0; j < childs.getLength(); j++) {
|
|
770
|
if (childs.item(j).getNodeName().equals(prefix + "MeasurementOrFactText")) {
|
|
771
|
path = childs.item(j).getNodeName();
|
|
772
|
getHierarchie(childs.item(j));
|
|
773
|
dataHolder.knownABCDelements.add(path);
|
|
774
|
path = "";
|
|
775
|
dataHolder.altitude = Integer.valueOf(childs.item(j).getTextContent());
|
|
776
|
}
|
|
777
|
}
|
|
778
|
}
|
|
779
|
} catch (NullPointerException e) {
|
|
780
|
dataHolder.altitude = -9999;
|
|
781
|
}
|
|
782
|
|
|
783
|
getGatheringDepth(root);
|
|
784
|
|
|
785
|
try {
|
|
786
|
group = root.getElementsByTagName(prefix + "NamedArea");
|
|
787
|
dataHolder.setNamedAreaList(new HashMap<String, String>());
|
|
788
|
for (int i = 0; i < group.getLength(); i++) {
|
|
789
|
childs = group.item(i).getChildNodes();
|
|
790
|
String currentArea = null;
|
|
791
|
for (int j = 0; j < childs.getLength(); j++) {
|
|
792
|
if (childs.item(j).getNodeName() .equals(prefix + "AreaName")) {
|
|
793
|
path = childs.item(j).getNodeName();
|
|
794
|
getHierarchie(childs.item(j));
|
|
795
|
dataHolder.knownABCDelements.add(path);
|
|
796
|
path = "";
|
|
797
|
currentArea = childs.item(j).getTextContent();
|
|
798
|
dataHolder.getNamedAreaList().put(currentArea, null);
|
|
799
|
}
|
|
800
|
}
|
|
801
|
if(currentArea!=null){
|
|
802
|
for (int j = 0; j < childs.getLength(); j++) {
|
|
803
|
if (childs.item(j).getNodeName() .equals(prefix + "AreaClass")) {
|
|
804
|
path = childs.item(j).getNodeName();
|
|
805
|
getHierarchie(childs.item(j));
|
|
806
|
dataHolder.knownABCDelements.add(path);
|
|
807
|
path = "";
|
|
808
|
dataHolder.getNamedAreaList().put(currentArea, childs.item(j).getTextContent());
|
|
809
|
}
|
|
810
|
}
|
|
811
|
}
|
|
812
|
}
|
|
813
|
} catch (NullPointerException e) {
|
|
814
|
dataHolder.setNamedAreaList(new HashMap<String, String>());
|
|
815
|
}
|
|
816
|
|
|
817
|
if(state.getConfig().isRemoveCountryFromLocalityText()){
|
|
818
|
if(dataHolder.locality.startsWith(dataHolder.country)){
|
|
819
|
dataHolder.locality = dataHolder.locality.replaceFirst(dataHolder.country+"[\\W]", "");
|
|
820
|
}
|
|
821
|
for (String namedArea : ((HashMap<String, String>) dataHolder.getNamedAreaList()).keySet()) {
|
|
822
|
if(dataHolder.locality.startsWith(namedArea)){
|
|
823
|
dataHolder.locality = dataHolder.locality.replaceFirst(namedArea+"[\\W]", "");
|
|
824
|
}
|
|
825
|
}
|
|
826
|
}
|
|
827
|
}
|
|
828
|
|
|
829
|
|
|
830
|
/**
|
|
831
|
* @param root
|
|
832
|
*/
|
|
833
|
private void getGatheringDepth(Element root) {
|
|
834
|
NodeList group;
|
|
835
|
try {
|
|
836
|
group = root.getElementsByTagName(prefix + "Gathering");
|
|
837
|
for (int i = 0; i < group.getLength(); i++) {
|
|
838
|
NodeList children = group.item(i).getChildNodes();
|
|
839
|
for (int j = 0; j < children.getLength(); j++) {
|
|
840
|
if (children.item(j).getNodeName().equals(prefix + "Depth")) {
|
|
841
|
NodeList altitudes = children.item(j).getChildNodes();
|
|
842
|
for (int k = 0; k < altitudes.getLength(); k++) {
|
|
843
|
if (altitudes.item(k).getNodeName().equals(prefix + "MeasurementOrFactText")) {
|
|
844
|
path = altitudes.item(k).getNodeName();
|
|
845
|
getHierarchie(altitudes.item(k));
|
|
846
|
dataHolder.knownABCDelements.add(path);
|
|
847
|
path = "";
|
|
848
|
try{
|
|
849
|
dataHolder.setGatheringDepthText(altitudes.item(k).getTextContent());
|
|
850
|
}catch(NumberFormatException e){
|
|
851
|
logger.debug("Gathering depth value is not parsable to double: " + altitudes.item(k).getTextContent());
|
|
852
|
}
|
|
853
|
}
|
|
854
|
}
|
|
855
|
}
|
|
856
|
}
|
|
857
|
}
|
|
858
|
} catch (NullPointerException e) {
|
|
859
|
dataHolder.setDepth( -9999.0);
|
|
860
|
}
|
|
861
|
if(dataHolder.getDepth()==null){
|
|
862
|
group = root.getElementsByTagName(prefix + "Gathering");
|
|
863
|
for (int i = 0; i < group.getLength(); i++) {
|
|
864
|
NodeList children = group.item(i).getChildNodes();
|
|
865
|
for (int j = 0; j < children.getLength(); j++) {
|
|
866
|
if (children.item(j).getNodeName().equals(prefix + "Depth")) {
|
|
867
|
NodeList altitudes = children.item(j).getChildNodes();
|
|
868
|
for (int k = 0; k < altitudes.getLength(); k++) {
|
|
869
|
if (altitudes.item(k).getNodeName().equals(prefix + "MeasurementOrFactAtomised")) {
|
|
870
|
NodeList facts = altitudes.item(k).getChildNodes();
|
|
871
|
for (int l = 0; l < facts.getLength(); l++) {
|
|
872
|
if (facts.item(l).getNodeName().equalsIgnoreCase(prefix + "LowerValue")) {
|
|
873
|
path = facts.item(l).getNodeName();
|
|
874
|
getHierarchie(facts.item(l));
|
|
875
|
dataHolder.knownABCDelements.add(path);
|
|
876
|
path = "";
|
|
877
|
try{
|
|
878
|
dataHolder.setGatheringDepthMin(Double.parseDouble(facts.item(l).getTextContent()));
|
|
879
|
} catch(NumberFormatException e){
|
|
880
|
logger.debug("Gathering depth min is not numeric. " + facts.item(l).getTextContent());
|
|
881
|
}
|
|
882
|
}
|
|
883
|
else if (facts.item(l).getNodeName().equalsIgnoreCase(prefix + "UpperValue")) {
|
|
884
|
path = facts.item(l).getNodeName();
|
|
885
|
getHierarchie(facts.item(l));
|
|
886
|
dataHolder.knownABCDelements.add(path);
|
|
887
|
path = "";
|
|
888
|
try{
|
|
889
|
dataHolder.setGatheringDepthMax(Double.parseDouble(facts.item(l).getTextContent()));
|
|
890
|
}catch(NumberFormatException e){
|
|
891
|
logger.debug("Gathering depth max is not numeric. " + facts.item(l).getTextContent());
|
|
892
|
}
|
|
893
|
}
|
|
894
|
else if (facts.item(l).getNodeName().equals(prefix + "UnitOfMeasurement")) {
|
|
895
|
path = facts.item(l).getNodeName();
|
|
896
|
getHierarchie(facts.item(l));
|
|
897
|
dataHolder.knownABCDelements.add(path);
|
|
898
|
path = "";
|
|
899
|
dataHolder.setGatheringDepthUnit(facts.item(l).getTextContent());
|
|
900
|
}
|
|
901
|
}
|
|
902
|
}
|
|
903
|
}
|
|
904
|
}
|
|
905
|
}
|
|
906
|
}
|
|
907
|
}
|
|
908
|
}
|
|
909
|
|
|
910
|
/**
|
|
911
|
* getMultimedia: get the FileURI objects
|
|
912
|
* @param root
|
|
913
|
*/
|
|
914
|
protected void getMultimedia(Element root) {
|
|
915
|
NodeList group, multimedias, multimedia, creators, creator, copyRightNodes, iprNodes, textNodes, licenceNodes, licences, copyrights;
|
|
916
|
try {
|
|
917
|
group = root.getElementsByTagName(prefix + "MultiMediaObjects");
|
|
918
|
for (int i = 0; i < group.getLength(); i++) {
|
|
919
|
multimedias = group.item(i).getChildNodes();
|
|
920
|
|
|
921
|
for (int j = 0; j < multimedias.getLength(); j++) {
|
|
922
|
if (multimedias.item(j).getNodeName().equals(prefix + "MultiMediaObject")) {
|
|
923
|
multimedia = multimedias.item(j).getChildNodes();
|
|
924
|
Map<String,String> mediaObjectMap = new HashMap<String, String>();
|
|
925
|
|
|
926
|
String fileUri = extractMediaInformation(multimedia, mediaObjectMap);
|
|
927
|
if (fileUri != ""){
|
|
928
|
dataHolder.putMultiMediaObject(fileUri,mediaObjectMap);
|
|
929
|
}
|
|
930
|
}
|
|
931
|
}
|
|
932
|
}
|
|
933
|
} catch (NullPointerException e) {
|
|
934
|
logger.info(e);
|
|
935
|
|
|
936
|
e.printStackTrace();
|
|
937
|
}
|
|
938
|
}
|
|
939
|
|
|
940
|
|
|
941
|
/**
|
|
942
|
* @param multimedia
|
|
943
|
* @param mediaObjectMap
|
|
944
|
* @param fileUri
|
|
945
|
* @return
|
|
946
|
*/
|
|
947
|
private String extractMediaInformation(NodeList multimedia, Map<String, String> mediaObjectMap) {
|
|
948
|
NodeList creators;
|
|
949
|
NodeList copyRightNodes;
|
|
950
|
NodeList iprNodes;
|
|
951
|
NodeList licenceNodes;
|
|
952
|
NodeList license;
|
|
953
|
NodeList copyrights;
|
|
954
|
|
|
955
|
String fileUri = "";
|
|
956
|
for (int k = 0; k < multimedia.getLength(); k++) {
|
|
957
|
if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "fileURI")) {
|
|
958
|
fileUri = multimedia.item(k).getTextContent();
|
|
959
|
mediaObjectMap.put("fileUri", fileUri);
|
|
960
|
path = multimedia.item(k).getNodeName();
|
|
961
|
getHierarchie(multimedia.item(k));
|
|
962
|
dataHolder.knownABCDelements.add(path);
|
|
963
|
path = "";
|
|
964
|
} else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "context")) {
|
|
965
|
mediaObjectMap.put("Context", multimedia.item(k).getTextContent());
|
|
966
|
} else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "createDate")) {
|
|
967
|
mediaObjectMap.put("CreateDate", multimedia.item(k).getTextContent());
|
|
968
|
}else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "Creators")){
|
|
969
|
String creatorString = "";
|
|
970
|
creators = multimedia.item(k).getChildNodes();
|
|
971
|
for (int l = 0; l < creators.getLength(); l++) {
|
|
972
|
|
|
973
|
if (creators.item(l).getNodeName().equalsIgnoreCase(prefix + "Creator")){
|
|
974
|
if (creatorString != ""){
|
|
975
|
creatorString += ", ";
|
|
976
|
}
|
|
977
|
creatorString += creators.item(l).getTextContent();
|
|
978
|
}
|
|
979
|
}
|
|
980
|
mediaObjectMap.put("Creators",creatorString);
|
|
981
|
} else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "Creator")){
|
|
982
|
mediaObjectMap.put("Creators",multimedia.item(k).getTextContent());
|
|
983
|
} else if (multimedia.item(k).getNodeName().equals("CreatedDate")){
|
|
984
|
mediaObjectMap.put("CreatedDate",multimedia.item(k).getTextContent());
|
|
985
|
} else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "comment")){
|
|
986
|
mediaObjectMap.put("Comment",multimedia.item(k).getTextContent());
|
|
987
|
} else if (multimedia.item(k).getNodeName().equalsIgnoreCase(prefix + "IPR")){
|
|
988
|
String copyRightString = "";
|
|
989
|
iprNodes = multimedia.item(k).getChildNodes();
|
|
990
|
for (int l = 0; l < iprNodes.getLength(); l++) {
|
|
991
|
if (iprNodes.item(l).getNodeName().equalsIgnoreCase(prefix + "Copyrights")){
|
|
992
|
copyRightNodes = iprNodes.item(l).getChildNodes();
|
|
993
|
for (int m = 0; m < copyRightNodes.getLength(); m++) {
|
|
994
|
if (copyRightNodes.item(m).getNodeName().equalsIgnoreCase(prefix + "Copyright")){
|
|
995
|
copyrights = copyRightNodes.item(m).getChildNodes();
|
|
996
|
for (int n = 0; n < copyrights.getLength(); n++){
|
|
997
|
if (copyrights.item(n).getNodeName().equalsIgnoreCase(prefix + "text")){
|
|
998
|
mediaObjectMap.put("Copyright", copyrights.item(n).getTextContent());
|
|
999
|
}
|
|
1000
|
}
|
|
1001
|
}
|
|
1002
|
}
|
|
1003
|
} else if (iprNodes.item(l).getNodeName().equalsIgnoreCase(prefix + "Licenses")){
|
|
1004
|
licenceNodes = iprNodes.item(l).getChildNodes();
|
|
1005
|
for (int m = 0; m < licenceNodes.getLength(); m++) {
|
|
1006
|
if (licenceNodes.item(m).getNodeName().equalsIgnoreCase(prefix + "License")){
|
|
1007
|
license = licenceNodes.item(m).getChildNodes();
|
|
1008
|
for (int n = 0; n < license.getLength(); n++){
|
|
1009
|
if (license.item(n).getNodeName().equalsIgnoreCase(prefix + "Text")){
|
|
1010
|
mediaObjectMap.put("License", license.item(n).getTextContent());
|
|
1011
|
}else{
|
|
1012
|
Node node = license.item(n);
|
|
1013
|
NodeList children = node.getChildNodes();
|
|
1014
|
for (int o = 0; o < children.getLength(); o++){
|
|
1015
|
if (children.item(o).getNodeName().equalsIgnoreCase(prefix + "Text")){
|
|
1016
|
mediaObjectMap.put("License", children.item(n).getTextContent());
|
|
1017
|
}
|
|
1018
|
|
|
1019
|
}
|
|
1020
|
}
|
|
1021
|
}
|
|
1022
|
}
|
|
1023
|
}
|
|
1024
|
}else{
|
|
1025
|
//System.err.println(iprNodes.item(l).getNodeName());
|
|
1026
|
}
|
|
1027
|
|
|
1028
|
}
|
|
1029
|
|
|
1030
|
} else{
|
|
1031
|
// System.err.println(multimedia.item(k).getNodeName());
|
|
1032
|
}
|
|
1033
|
|
|
1034
|
}
|
|
1035
|
return fileUri;
|
|
1036
|
}
|
|
1037
|
|
|
1038
|
protected void getAssociatedUnitIds(Element root) {
|
|
1039
|
NodeList associations, childrenAssociations, childrenUnitAssociations;
|
|
1040
|
try {
|
|
1041
|
associations = root.getElementsByTagName(prefix + "Associations");
|
|
1042
|
for (int i = 0; i < associations.getLength(); i++) {
|
|
1043
|
childrenAssociations = associations.item(i).getChildNodes();
|
|
1044
|
for (int j = 0; j < childrenAssociations.getLength(); j++) {
|
|
1045
|
if (childrenAssociations.item(j).getNodeName().equals(prefix + "UnitAssociation")) {
|
|
1046
|
childrenUnitAssociations = childrenAssociations.item(j).getChildNodes();
|
|
1047
|
String[] associatedUnitId = new String[2];
|
|
1048
|
for (int k = 0; k < childrenUnitAssociations.getLength(); k++) {
|
|
1049
|
if (childrenUnitAssociations.item(k).getNodeName().equals(prefix + "UnitID")) {
|
|
1050
|
associatedUnitId[0]= childrenUnitAssociations.item(k).getTextContent();
|
|
1051
|
|
|
1052
|
path = childrenUnitAssociations.item(k).getNodeName();
|
|
1053
|
getHierarchie(childrenUnitAssociations.item(k));
|
|
1054
|
dataHolder.knownABCDelements.add(path);
|
|
1055
|
path = "";
|
|
1056
|
}
|
|
1057
|
if (childrenUnitAssociations.item(k).getNodeName().equals(prefix +"DatasetAccessPoint")){
|
|
1058
|
associatedUnitId[1]= childrenUnitAssociations.item(k).getTextContent();
|
|
1059
|
}
|
|
1060
|
}
|
|
1061
|
dataHolder.addAssociatedUnitId(associatedUnitId);
|
|
1062
|
}
|
|
1063
|
}
|
|
1064
|
}
|
|
1065
|
} catch (NullPointerException e) {
|
|
1066
|
logger.info(e);
|
|
1067
|
}
|
|
1068
|
}
|
|
1069
|
|
|
1070
|
protected void getUnitNotes(Element root) {
|
|
1071
|
NodeList childNodes = root.getChildNodes();
|
|
1072
|
for (int i = 0; i < childNodes.getLength(); i++) {
|
|
1073
|
if(childNodes.item(i).getNodeName().equals(prefix + "Notes")){
|
|
1074
|
dataHolder.setUnitNotes(childNodes.item(i).getTextContent());
|
|
1075
|
path = childNodes.item(i).getNodeName();
|
|
1076
|
getHierarchie(childNodes.item(i));
|
|
1077
|
dataHolder.knownABCDelements.add(path);
|
|
1078
|
path = "";
|
|
1079
|
}
|
|
1080
|
}
|
|
1081
|
}
|
|
1082
|
|
|
1083
|
//Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLong/SpatialDatum ../CoordinateErrorMethod
|
|
1084
|
protected void getGatheringSpatialDatum(Element root) {
|
|
1085
|
NodeList group = root.getElementsByTagName(prefix + "Gathering");
|
|
1086
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1087
|
NodeList spatialDatum = ((Element) group.item(i)).getElementsByTagName(prefix + "SpatialDatum");
|
|
1088
|
dataHolder.setGatheringSpatialDatum(AbcdParseUtility.parseFirstTextContent(spatialDatum));
|
|
1089
|
}
|
|
1090
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1091
|
NodeList coordinateMethod = ((Element) group.item(i)).getElementsByTagName(prefix + "CoordinateErrorMethod");
|
|
1092
|
dataHolder.setGatheringCoordinateErrorMethod(AbcdParseUtility.parseFirstTextContent(coordinateMethod));
|
|
1093
|
}
|
|
1094
|
}
|
|
1095
|
|
|
1096
|
protected void getGatheringElevation(Element root) {
|
|
1097
|
try {
|
|
1098
|
//check for freetext elevation
|
|
1099
|
NodeList group = root.getElementsByTagName(prefix + "Gathering");
|
|
1100
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1101
|
NodeList children = group.item(i).getChildNodes();
|
|
1102
|
for (int j = 0; j < children.getLength(); j++) {
|
|
1103
|
if (children.item(j).getNodeName().equals(prefix + "Altitude")) {
|
|
1104
|
NodeList altitudes = children.item(j).getChildNodes();
|
|
1105
|
for (int k = 0; k < altitudes.getLength(); k++) {
|
|
1106
|
if (altitudes.item(k).getNodeName().equals(prefix + "MeasurementOrFactText")) {
|
|
1107
|
path = altitudes.item(k).getNodeName();
|
|
1108
|
getHierarchie(altitudes.item(k));
|
|
1109
|
dataHolder.knownABCDelements.add(path);
|
|
1110
|
path = "";
|
|
1111
|
dataHolder.setGatheringElevationText(altitudes.item(k).getTextContent());
|
|
1112
|
}
|
|
1113
|
}
|
|
1114
|
}
|
|
1115
|
|
|
1116
|
}
|
|
1117
|
}
|
|
1118
|
|
|
1119
|
} catch (NullPointerException e) {
|
|
1120
|
dataHolder.setGatheringElevationText(null);
|
|
1121
|
}
|
|
1122
|
|
|
1123
|
try{
|
|
1124
|
//check for atomised elevation
|
|
1125
|
if(dataHolder.getGatheringElevationText()==null){
|
|
1126
|
NodeList group = root.getElementsByTagName(prefix + "Gathering");
|
|
1127
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1128
|
NodeList children = group.item(i).getChildNodes();
|
|
1129
|
for (int j = 0; j < children.getLength(); j++) {
|
|
1130
|
if (children.item(j).getNodeName().equals(prefix + "Altitude")) {
|
|
1131
|
NodeList altitudes = children.item(j).getChildNodes();
|
|
1132
|
for (int k = 0; k < altitudes.getLength(); k++) {
|
|
1133
|
if (altitudes.item(k).getNodeName().equals(prefix + "MeasurementOrFactAtomised")) {
|
|
1134
|
NodeList facts = altitudes.item(k).getChildNodes();
|
|
1135
|
for (int l = 0; l < facts.getLength(); l++) {
|
|
1136
|
if (facts.item(l).getNodeName().equals(prefix + "LowerValue")) {
|
|
1137
|
path = facts.item(l).getNodeName();
|
|
1138
|
getHierarchie(facts.item(l));
|
|
1139
|
dataHolder.knownABCDelements.add(path);
|
|
1140
|
path = "";
|
|
1141
|
dataHolder.setGatheringElevationMin(facts.item(l).getTextContent());
|
|
1142
|
}
|
|
1143
|
else if (facts.item(l).getNodeName().equals(prefix + "UpperValue")) {
|
|
1144
|
path = facts.item(l).getNodeName();
|
|
1145
|
getHierarchie(facts.item(l));
|
|
1146
|
dataHolder.knownABCDelements.add(path);
|
|
1147
|
path = "";
|
|
1148
|
dataHolder.setGatheringElevationMax(facts.item(l).getTextContent());
|
|
1149
|
}
|
|
1150
|
else if (facts.item(l).getNodeName().equals(prefix + "UnitOfMeasurement")) {
|
|
1151
|
path = facts.item(l).getNodeName();
|
|
1152
|
getHierarchie(facts.item(l));
|
|
1153
|
dataHolder.knownABCDelements.add(path);
|
|
1154
|
path = "";
|
|
1155
|
dataHolder.setGatheringElevationUnit(facts.item(l).getTextContent());
|
|
1156
|
}
|
|
1157
|
}
|
|
1158
|
}
|
|
1159
|
}
|
|
1160
|
}
|
|
1161
|
}
|
|
1162
|
}
|
|
1163
|
}
|
|
1164
|
} catch (NullPointerException e) {
|
|
1165
|
dataHolder.setGatheringElevationText(null);
|
|
1166
|
}
|
|
1167
|
}
|
|
1168
|
|
|
1169
|
protected void getGatheringNotes(Element root) {
|
|
1170
|
try {
|
|
1171
|
NodeList group = root.getElementsByTagName(prefix + "Gathering");
|
|
1172
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1173
|
NodeList children = group.item(i).getChildNodes();
|
|
1174
|
for (int j = 0; j < children.getLength(); j++) {
|
|
1175
|
if (children.item(j).getNodeName().equals(prefix + "Notes")) {
|
|
1176
|
path = children.item(j).getNodeName();
|
|
1177
|
getHierarchie(children.item(j));
|
|
1178
|
dataHolder.knownABCDelements.add(path);
|
|
1179
|
path = "";
|
|
1180
|
dataHolder.setGatheringNotes(children.item(j).getTextContent());
|
|
1181
|
}
|
|
1182
|
}
|
|
1183
|
}
|
|
1184
|
|
|
1185
|
|
|
1186
|
} catch (NullPointerException e) {
|
|
1187
|
dataHolder.setGatheringElevationText(null);
|
|
1188
|
}
|
|
1189
|
|
|
1190
|
}
|
|
1191
|
|
|
1192
|
protected void getGatheringDate(Element root) {
|
|
1193
|
try {
|
|
1194
|
NodeList group = root.getElementsByTagName(prefix + "Gathering");
|
|
1195
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1196
|
NodeList children = group.item(i).getChildNodes();
|
|
1197
|
for (int j = 0; j < children.getLength(); j++) {
|
|
1198
|
if (children.item(j).getNodeName().equals(prefix + "DateTime")) {
|
|
1199
|
NodeList dateTimes = children.item(j).getChildNodes();
|
|
1200
|
for (int k = 0; k < dateTimes.getLength(); k++) {
|
|
1201
|
if (dateTimes.item(k).getNodeName().equals(prefix + "ISODateTimeBegin")) {
|
|
1202
|
path = dateTimes.item(k).getNodeName();
|
|
1203
|
getHierarchie(dateTimes.item(k));
|
|
1204
|
dataHolder.knownABCDelements.add(path);
|
|
1205
|
path = "";
|
|
1206
|
dataHolder.setGatheringDateText(dateTimes.item(k).getTextContent());
|
|
1207
|
}
|
|
1208
|
}
|
|
1209
|
|
|
1210
|
for (int k = 0; k < dateTimes.getLength(); k++) {
|
|
1211
|
if (dateTimes.item(k).getNodeName().equals(prefix + "DateText")) {
|
|
1212
|
path = dateTimes.item(k).getNodeName();
|
|
1213
|
getHierarchie(dateTimes.item(k));
|
|
1214
|
dataHolder.knownABCDelements.add(path);
|
|
1215
|
path = "";
|
|
1216
|
dataHolder.setGatheringDateText(dateTimes.item(k).getTextContent());
|
|
1217
|
}
|
|
1218
|
}
|
|
1219
|
}
|
|
1220
|
|
|
1221
|
}
|
|
1222
|
}
|
|
1223
|
|
|
1224
|
} catch (NullPointerException e) {
|
|
1225
|
dataHolder.setGatheringDateText(null);
|
|
1226
|
}
|
|
1227
|
}
|
|
1228
|
|
|
1229
|
protected void getGatheringMethod(Element root) {
|
|
1230
|
try {
|
|
1231
|
NodeList group = root.getElementsByTagName(prefix + "Gathering");
|
|
1232
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1233
|
NodeList children = group.item(i).getChildNodes();
|
|
1234
|
for (int j = 0; j < children.getLength(); j++) {
|
|
1235
|
if (children.item(j).getNodeName().equalsIgnoreCase(prefix + "Method")) {
|
|
1236
|
NodeList methods = children.item(j).getChildNodes();
|
|
1237
|
for (int k = 0; k < methods.getLength(); k++) {
|
|
1238
|
dataHolder.setGatheringMethod(methods.item(k).getTextContent());
|
|
1239
|
}
|
|
1240
|
}
|
|
1241
|
|
|
1242
|
}
|
|
1243
|
}
|
|
1244
|
|
|
1245
|
} catch (NullPointerException e) {
|
|
1246
|
dataHolder.setGatheringDateText(null);
|
|
1247
|
}
|
|
1248
|
}
|
|
1249
|
|
|
1250
|
|
|
1251
|
/**
|
|
1252
|
* getGatheringPeople : get GatheringAgent with fullname
|
|
1253
|
* @param root
|
|
1254
|
*/
|
|
1255
|
protected void getGatheringPeople(Element root) {
|
|
1256
|
try {
|
|
1257
|
dataHolder.gatheringAgentsText = "";
|
|
1258
|
dataHolder.gatheringAgentsList = new ArrayList<String>();
|
|
1259
|
|
|
1260
|
NodeList group = root.getElementsByTagName(prefix + "GatheringAgent");
|
|
1261
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1262
|
NodeList children = group.item(i).getChildNodes();
|
|
1263
|
for (int j = 0; j < children.getLength(); j++) {
|
|
1264
|
if (children.item(j).getNodeName().equals(prefix + "Person")) {
|
|
1265
|
NodeList persons = children.item(j).getChildNodes();
|
|
1266
|
for (int k = 0; k < persons.getLength(); k++) {
|
|
1267
|
if (persons.item(k).getNodeName().equals(prefix + "FullName")) {
|
|
1268
|
path = persons.item(k).getNodeName();
|
|
1269
|
getHierarchie(persons.item(k));
|
|
1270
|
dataHolder.knownABCDelements.add(path);
|
|
1271
|
path = "";
|
|
1272
|
if (!persons.item(k).getTextContent().trim().equalsIgnoreCase("none")) {
|
|
1273
|
|
|
1274
|
dataHolder.gatheringAgentsList.add(persons.item(k).getTextContent());
|
|
1275
|
}
|
|
1276
|
}
|
|
1277
|
}
|
|
1278
|
}
|
|
1279
|
|
|
1280
|
if (children.item(j).getNodeName().equals(prefix + "AgentText")){
|
|
1281
|
if (!children.item(j).getTextContent().trim().equalsIgnoreCase("none")) {
|
|
1282
|
dataHolder.gatheringAgentsText=children.item(j).getTextContent();
|
|
1283
|
}
|
|
1284
|
|
|
1285
|
|
|
1286
|
}
|
|
1287
|
|
|
1288
|
}
|
|
1289
|
}
|
|
1290
|
|
|
1291
|
group = root.getElementsByTagName(prefix + "Gathering");
|
|
1292
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1293
|
NodeList children = group.item(i).getChildNodes();
|
|
1294
|
for (int j = 0; j < children.getLength(); j++) {
|
|
1295
|
if (children.item(j).getNodeName().equals(prefix + "Agents")) {
|
|
1296
|
NodeList persons = children.item(j).getChildNodes();
|
|
1297
|
for (int k = 0; k < persons.getLength(); k++) {
|
|
1298
|
if (persons.item(k).getNodeName().equals(prefix + "GatheringAgentsText") ) {
|
|
1299
|
path = persons.item(k).getNodeName();
|
|
1300
|
getHierarchie(persons.item(k));
|
|
1301
|
dataHolder.knownABCDelements.add(path);
|
|
1302
|
path = "";
|
|
1303
|
if (!persons.item(k).getTextContent().trim().equalsIgnoreCase("none")) {
|
|
1304
|
dataHolder.gatheringAgentsText=persons.item(k).getTextContent();
|
|
1305
|
}
|
|
1306
|
}
|
|
1307
|
|
|
1308
|
|
|
1309
|
|
|
1310
|
}
|
|
1311
|
}
|
|
1312
|
|
|
1313
|
}
|
|
1314
|
}
|
|
1315
|
|
|
1316
|
} catch (NullPointerException e) {
|
|
1317
|
if (StringUtils.isBlank(dataHolder.gatheringAgentsText) && dataHolder.gatheringAgentsList == null){
|
|
1318
|
dataHolder.gatheringAgentsText = "";
|
|
1319
|
dataHolder.gatheringAgentsList = new ArrayList<String>();
|
|
1320
|
}
|
|
1321
|
}
|
|
1322
|
|
|
1323
|
}
|
|
1324
|
|
|
1325
|
/*PARSING METHODS*/
|
|
1326
|
|
|
1327
|
private HashMap<String, String> getAtomisedNames(String code,NodeList atomised) {
|
|
1328
|
if (DEBUG) {
|
|
1329
|
logger.info("code getatomised " + code);
|
|
1330
|
}
|
|
1331
|
if (code.indexOf("Botanical") != -1) {
|
|
1332
|
return this.getAtomisedBotanical(atomised);
|
|
1333
|
}
|
|
1334
|
if (code.indexOf("Bacterial") != -1) {
|
|
1335
|
return this.getAtomisedBacterial(atomised);
|
|
1336
|
}
|
|
1337
|
if (code.indexOf("Viral") != -1) {
|
|
1338
|
return this.getAtomisedViral(atomised);
|
|
1339
|
}
|
|
1340
|
if (code.indexOf("Zoological") != -1) {
|
|
1341
|
return this.getAtomisedZoological(atomised);
|
|
1342
|
}
|
|
1343
|
return new HashMap<String, String>();
|
|
1344
|
}
|
|
1345
|
|
|
1346
|
private HashMap<String, String> getAtomisedZoological(NodeList atomised) {
|
|
1347
|
if(DEBUG) {
|
|
1348
|
logger.info("getAtomisedZoo");
|
|
1349
|
}
|
|
1350
|
HashMap<String, String> atomisedMap = new HashMap<String, String>();
|
|
1351
|
|
|
1352
|
for (int i = 0; i < atomised.getLength(); i++) {
|
|
1353
|
if (atomised.item(i).getNodeName().equals(prefix + "GenusOrMonomial")) {
|
|
1354
|
atomisedMap.put("Genus", atomised.item(i).getTextContent());
|
|
1355
|
path = atomised.item(i).getNodeName();
|
|
1356
|
getHierarchie(atomised.item(i));
|
|
1357
|
dataHolder.knownABCDelements.add(path);
|
|
1358
|
path = "";
|
|
1359
|
}
|
|
1360
|
else if (atomised.item(i).getNodeName().equals(prefix + "Subgenus")) {
|
|
1361
|
atomisedMap.put("Subgenus", atomised.item(i).getTextContent());
|
|
1362
|
path = atomised.item(i).getNodeName();
|
|
1363
|
getHierarchie(atomised.item(i));
|
|
1364
|
dataHolder.knownABCDelements.add(path);
|
|
1365
|
path = "";
|
|
1366
|
}
|
|
1367
|
else if (atomised.item(i).getNodeName().equals(prefix + "SpeciesEpithet")) {
|
|
1368
|
atomisedMap.put("SpeciesEpithet", atomised.item(i).getTextContent());
|
|
1369
|
path = atomised.item(i).getNodeName();
|
|
1370
|
getHierarchie(atomised.item(i));
|
|
1371
|
dataHolder.knownABCDelements.add(path);
|
|
1372
|
path = "";
|
|
1373
|
}
|
|
1374
|
else if (atomised.item(i).getNodeName().equals(prefix + "SubspeciesEpithet")) {
|
|
1375
|
atomisedMap.put("SubspeciesEpithet", atomised.item(i).getTextContent());
|
|
1376
|
path = atomised.item(i).getNodeName();
|
|
1377
|
getHierarchie(atomised.item(i));
|
|
1378
|
dataHolder.knownABCDelements.add(path);
|
|
1379
|
path = "";
|
|
1380
|
}
|
|
1381
|
else if (atomised.item(i).getNodeName().equals(prefix + "AuthorTeamOriginalAndYear")) {
|
|
1382
|
atomisedMap.put("AuthorTeamOriginalAndYear", atomised.item(i).getTextContent());
|
|
1383
|
path = atomised.item(i).getNodeName();
|
|
1384
|
getHierarchie(atomised.item(i));
|
|
1385
|
dataHolder.knownABCDelements.add(path);
|
|
1386
|
path = "";
|
|
1387
|
}
|
|
1388
|
else if (atomised.item(i).getNodeName().equals(prefix + "AuthorTeamParenthesisAndYear")) {
|
|
1389
|
atomisedMap.put("AuthorTeamParenthesisAndYear", atomised.item(i).getTextContent());
|
|
1390
|
path = atomised.item(i).getNodeName();
|
|
1391
|
getHierarchie(atomised.item(i));
|
|
1392
|
dataHolder.knownABCDelements.add(path);
|
|
1393
|
path = "";
|
|
1394
|
}
|
|
1395
|
else if (atomised.item(i).getNodeName().equals(prefix + "CombinationAuthorTeamAndYear")) {
|
|
1396
|
atomisedMap.put("CombinationAuthorTeamAndYear", atomised.item(i).getTextContent());
|
|
1397
|
path = atomised.item(i).getNodeName();
|
|
1398
|
getHierarchie(atomised.item(i));
|
|
1399
|
dataHolder.knownABCDelements.add(path);
|
|
1400
|
path = "";
|
|
1401
|
}
|
|
1402
|
else if (atomised.item(i).getNodeName().equals(prefix + "Breed")) {
|
|
1403
|
atomisedMap.put("Breed", atomised.item(i).getTextContent());
|
|
1404
|
path = atomised.item(i).getNodeName();
|
|
1405
|
getHierarchie(atomised.item(i));
|
|
1406
|
dataHolder.knownABCDelements.add(path);
|
|
1407
|
path = "";
|
|
1408
|
}
|
|
1409
|
else if (atomised.item(i).getNodeName().equals(prefix + "NamedIndividual")) {
|
|
1410
|
atomisedMap.put("NamedIndividual", atomised.item(i).getTextContent());
|
|
1411
|
path = atomised.item(i).getNodeName();
|
|
1412
|
getHierarchie(atomised.item(i));
|
|
1413
|
dataHolder.knownABCDelements.add(path);
|
|
1414
|
path = "";
|
|
1415
|
}
|
|
1416
|
}
|
|
1417
|
return atomisedMap;
|
|
1418
|
}
|
|
1419
|
|
|
1420
|
private HashMap<String, String> getAtomisedViral(NodeList atomised) {
|
|
1421
|
HashMap<String, String> atomisedMap = new HashMap<String, String>();
|
|
1422
|
for (int i = 0; i < atomised.getLength(); i++) {
|
|
1423
|
if (atomised.item(i).getNodeName().equals(prefix + "GenusOrMonomial")) {
|
|
1424
|
atomisedMap.put("Genus", atomised.item(i).getTextContent());
|
|
1425
|
path = atomised.item(i).getNodeName();
|
|
1426
|
getHierarchie(atomised.item(i));
|
|
1427
|
dataHolder.knownABCDelements.add(path);
|
|
1428
|
path = "";
|
|
1429
|
}
|
|
1430
|
if (atomised.item(i).getNodeName().equals(prefix + "ViralSpeciesDesignation")) {
|
|
1431
|
atomisedMap.put("ViralSpeciesDesignation", atomised.item(i).getTextContent());
|
|
1432
|
path = atomised.item(i).getNodeName();
|
|
1433
|
getHierarchie(atomised.item(i));
|
|
1434
|
dataHolder.knownABCDelements.add(path);
|
|
1435
|
path = "";
|
|
1436
|
}
|
|
1437
|
if (atomised.item(i).getNodeName().equals(prefix + "Acronym")) {
|
|
1438
|
atomisedMap.put("Acronym", atomised.item(i).getTextContent());
|
|
1439
|
path = atomised.item(i).getNodeName();
|
|
1440
|
getHierarchie(atomised.item(i));
|
|
1441
|
dataHolder.knownABCDelements.add(path);
|
|
1442
|
path = "";
|
|
1443
|
}
|
|
1444
|
}
|
|
1445
|
return atomisedMap;
|
|
1446
|
}
|
|
1447
|
|
|
1448
|
private HashMap<String, String> getAtomisedBotanical(NodeList atomised) {
|
|
1449
|
HashMap<String, String> atomisedMap = new HashMap<String, String>();
|
|
1450
|
for (int i = 0; i < atomised.getLength(); i++) {
|
|
1451
|
if (atomised.item(i).getNodeName().equals(prefix + "GenusOrMonomial")) {
|
|
1452
|
atomisedMap.put("Genus", atomised.item(i).getTextContent());
|
|
1453
|
path = atomised.item(i).getNodeName();
|
|
1454
|
getHierarchie(atomised.item(i));
|
|
1455
|
dataHolder.knownABCDelements.add(path);
|
|
1456
|
path = "";
|
|
1457
|
}
|
|
1458
|
if (atomised.item(i).getNodeName().equals(prefix + "FirstEpithet")) {
|
|
1459
|
atomisedMap.put("FirstEpithet", atomised.item(i).getTextContent());
|
|
1460
|
path = atomised.item(i).getNodeName();
|
|
1461
|
getHierarchie(atomised.item(i));
|
|
1462
|
dataHolder.knownABCDelements.add(path);
|
|
1463
|
path = "";
|
|
1464
|
}
|
|
1465
|
if (atomised.item(i).getNodeName()
|
|
1466
|
.equals(prefix + "InfraspecificEpithet")) {
|
|
1467
|
atomisedMap.put("InfraSpeEpithet", atomised.item(i).getTextContent());
|
|
1468
|
path = atomised.item(i).getNodeName();
|
|
1469
|
getHierarchie(atomised.item(i));
|
|
1470
|
dataHolder.knownABCDelements.add(path);
|
|
1471
|
path = "";
|
|
1472
|
}
|
|
1473
|
if (atomised.item(i).getNodeName().equals(prefix + "Rank")) {
|
|
1474
|
atomisedMap.put("Rank", atomised.item(i).getTextContent());
|
|
1475
|
path = atomised.item(i).getNodeName();
|
|
1476
|
getHierarchie(atomised.item(i));
|
|
1477
|
dataHolder.knownABCDelements.add(path);
|
|
1478
|
path = "";
|
|
1479
|
}
|
|
1480
|
if (atomised.item(i).getNodeName().equals(prefix + "HybridFlag")) {
|
|
1481
|
atomisedMap.put("HybridFlag", atomised.item(i).getTextContent());
|
|
1482
|
path = atomised.item(i).getNodeName();
|
|
1483
|
getHierarchie(atomised.item(i));
|
|
1484
|
dataHolder.knownABCDelements.add(path);
|
|
1485
|
path = "";
|
|
1486
|
}
|
|
1487
|
if (atomised.item(i).getNodeName()
|
|
1488
|
.equals(prefix + "AuthorTeamParenthesis")) {
|
|
1489
|
atomisedMap.put("AuthorTeamParenthesis", atomised.item(i).getTextContent());
|
|
1490
|
path = atomised.item(i).getNodeName();
|
|
1491
|
getHierarchie(atomised.item(i));
|
|
1492
|
dataHolder.knownABCDelements.add(path);
|
|
1493
|
path = "";
|
|
1494
|
}
|
|
1495
|
if (atomised.item(i).getNodeName().equals(prefix + "AuthorTeam")) {
|
|
1496
|
atomisedMap.put("AuthorTeam", atomised.item(i).getTextContent());
|
|
1497
|
path = atomised.item(i).getNodeName();
|
|
1498
|
getHierarchie(atomised.item(i));
|
|
1499
|
dataHolder.knownABCDelements.add(path);
|
|
1500
|
path = "";
|
|
1501
|
}
|
|
1502
|
if (atomised.item(i).getNodeName().equals(prefix + "CultivarGroupName")) {
|
|
1503
|
atomisedMap.put("CultivarGroupName", atomised.item(i).getTextContent());
|
|
1504
|
path = atomised.item(i).getNodeName();
|
|
1505
|
getHierarchie(atomised.item(i));
|
|
1506
|
dataHolder.knownABCDelements.add(path);
|
|
1507
|
path = "";
|
|
1508
|
}
|
|
1509
|
if (atomised.item(i).getNodeName().equals(prefix + "CultivarName")) {
|
|
1510
|
atomisedMap.put("CultivarName", atomised.item(i).getTextContent());
|
|
1511
|
path = atomised.item(i).getNodeName();
|
|
1512
|
getHierarchie(atomised.item(i));
|
|
1513
|
dataHolder.knownABCDelements.add(path);
|
|
1514
|
path = "";
|
|
1515
|
}
|
|
1516
|
if (atomised.item(i).getNodeName().equals(prefix + "TradeDesignationNames")) {
|
|
1517
|
atomisedMap.put("Trade", atomised.item(i).getTextContent());
|
|
1518
|
path = atomised.item(i).getNodeName();
|
|
1519
|
getHierarchie(atomised.item(i));
|
|
1520
|
dataHolder.knownABCDelements.add(path);
|
|
1521
|
path = "";
|
|
1522
|
}
|
|
1523
|
}
|
|
1524
|
return atomisedMap;
|
|
1525
|
}
|
|
1526
|
|
|
1527
|
private HashMap<String, String> getAtomisedBacterial(NodeList atomised) {
|
|
1528
|
HashMap<String, String> atomisedMap = new HashMap<String, String>();
|
|
1529
|
for (int i = 0; i < atomised.getLength(); i++) {
|
|
1530
|
if (atomised.item(i).getNodeName().equals(prefix + "GenusOrMonomial")) {
|
|
1531
|
atomisedMap.put("Genus", atomised.item(i).getTextContent());
|
|
1532
|
path = atomised.item(i).getNodeName();
|
|
1533
|
getHierarchie(atomised.item(i));
|
|
1534
|
dataHolder.knownABCDelements.add(path);
|
|
1535
|
path = "";
|
|
1536
|
}
|
|
1537
|
if (atomised.item(i).getNodeName().equals(prefix + "Subgenus")) {
|
|
1538
|
atomisedMap.put("SubGenus", atomised.item(i).getTextContent());
|
|
1539
|
path = atomised.item(i).getNodeName();
|
|
1540
|
getHierarchie(atomised.item(i));
|
|
1541
|
dataHolder.knownABCDelements.add(path);
|
|
1542
|
path = "";
|
|
1543
|
}
|
|
1544
|
if (atomised.item(i).getNodeName().equals(prefix + "SubgenusAuthorAndYear")) {
|
|
1545
|
atomisedMap.put("SubgenusAuthorAndYear", atomised.item(i).getTextContent());
|
|
1546
|
path = atomised.item(i).getNodeName();
|
|
1547
|
getHierarchie(atomised.item(i));
|
|
1548
|
dataHolder.knownABCDelements.add(path);
|
|
1549
|
path = "";
|
|
1550
|
}
|
|
1551
|
if (atomised.item(i).getNodeName().equals(prefix + "SpeciesEpithet")) {
|
|
1552
|
atomisedMap.put("SpeciesEpithet", atomised.item(i).getTextContent());
|
|
1553
|
path = atomised.item(i).getNodeName();
|
|
1554
|
getHierarchie(atomised.item(i));
|
|
1555
|
dataHolder.knownABCDelements.add(path);
|
|
1556
|
path = "";
|
|
1557
|
}
|
|
1558
|
if (atomised.item(i).getNodeName().equals(prefix + "SubspeciesEpithet")) {
|
|
1559
|
atomisedMap.put("SubspeciesEpithet", atomised.item(i).getTextContent());
|
|
1560
|
path = atomised.item(i).getNodeName();
|
|
1561
|
getHierarchie(atomised.item(i));
|
|
1562
|
dataHolder.knownABCDelements.add(path);
|
|
1563
|
path = "";
|
|
1564
|
}
|
|
1565
|
if (atomised.item(i).getNodeName().equals(prefix + "ParentheticalAuthorTeamAndYear")) {
|
|
1566
|
atomisedMap.put("ParentheticalAuthorTeamAndYear", atomised.item(i).getTextContent());
|
|
1567
|
path = atomised.item(i).getNodeName();
|
|
1568
|
getHierarchie(atomised.item(i));
|
|
1569
|
dataHolder.knownABCDelements.add(path);
|
|
1570
|
path = "";
|
|
1571
|
}
|
|
1572
|
if (atomised.item(i).getNodeName().equals(prefix + "AuthorTeamAndYear")) {
|
|
1573
|
atomisedMap.put("AuthorTeamAndYear", atomised.item(i).getTextContent());
|
|
1574
|
path = atomised.item(i).getNodeName();
|
|
1575
|
getHierarchie(atomised.item(i));
|
|
1576
|
dataHolder.knownABCDelements.add(path);
|
|
1577
|
path = "";
|
|
1578
|
}
|
|
1579
|
if (atomised.item(i).getNodeName().equals(prefix + "NameApprobation")) {
|
|
1580
|
atomisedMap.put("NameApprobation", atomised.item(i).getTextContent());
|
|
1581
|
path = atomised.item(i).getNodeName();
|
|
1582
|
getHierarchie(atomised.item(i));
|
|
1583
|
dataHolder.knownABCDelements.add(path);
|
|
1584
|
path = "";
|
|
1585
|
}
|
|
1586
|
}
|
|
1587
|
return atomisedMap;
|
|
1588
|
}
|
|
1589
|
|
|
1590
|
|
|
1591
|
/**
|
|
1592
|
* @param root
|
|
1593
|
*/
|
|
1594
|
public void getGatheringImages(Element root) {
|
|
1595
|
NodeList group, multimedias, multimedia, creators, creator;
|
|
1596
|
try {
|
|
1597
|
group = root.getElementsByTagName(prefix + "SiteImages");
|
|
1598
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1599
|
multimedias = group.item(i).getChildNodes();
|
|
1600
|
for (int j = 0; j < multimedias.getLength(); j++) {
|
|
1601
|
if (multimedias.item(j).getNodeName().equals(prefix + "SiteImage")) {
|
|
1602
|
multimedia = multimedias.item(j).getChildNodes();
|
|
1603
|
Map<String,String> mediaObjectMap = new HashMap<String, String>();
|
|
1604
|
String fileUri = extractMediaInformation(multimedia, mediaObjectMap);
|
|
1605
|
|
|
1606
|
if (fileUri != ""){
|
|
1607
|
dataHolder.putGatheringMultiMediaObject(fileUri,mediaObjectMap);
|
|
1608
|
}
|
|
1609
|
}
|
|
1610
|
}
|
|
1611
|
}
|
|
1612
|
} catch (NullPointerException e) {
|
|
1613
|
logger.info(e);
|
|
1614
|
}
|
|
1615
|
|
|
1616
|
}
|
|
1617
|
|
|
1618
|
}
|