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package eu.etaxonomy.cdm.io.taxonx2013;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.w3c.dom.NamedNodeMap;
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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.common.DOI;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.reference.ReferenceType;
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import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
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public class TaxonXModsExtractor extends TaxonXExtractor{
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private final Map<String,UUID> personMap = new HashMap<String, UUID>();
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private final Logger logger = Logger.getLogger(getClass());
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private final String AUTHOR = "author";
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private final String EDITOR = "editor";
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/**
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* @param agentService
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*/
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public TaxonXModsExtractor(TaxonXImport importer) {
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this.importer = importer;
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}
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public Reference<?> extractMods(Node node){
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//TODO needed? currently only filled but never read
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Map<String, String> modsMap = new HashMap<String, String>();
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NodeList children = node.getChildNodes();
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List<String> roleList = new ArrayList<String>();
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String content="";
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Reference<?> ref = tryMakeReferenceByClassification(children);
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if (ref == null){
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// int reftype = askQuestion("What kind of reference is it?\n 1: Generic\n 2: Book\n 3: Article\n" +
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// " 4 : BookSection\n 5 : Journal\n 6 : Printseries\n 7: Thesis ");
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int reftype=1;
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ref = getReferenceWithType(reftype);
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}
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handleModsNames(children, ref);
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for (int i=0; i<children.getLength();i++){
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Node modsChildNode = children.item(i);
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String modsChildNodeName = modsChildNode.getNodeName();
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if (modsChildNodeName.equalsIgnoreCase("mods:titleinfo")){
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NodeList tmp = modsChildNode.getChildNodes();
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for (int j=0;j<tmp.getLength();j++){
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if (tmp.item(j).getNodeName().equalsIgnoreCase("mods:title")) {
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content=tmp.item(j).getTextContent().trim();
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if (!content.isEmpty()) {
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modsMap.put("mainTitle",content);
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// ref.setTitleCache(content,true);
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ref.setTitle(content);
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// ref.generateTitle();
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}
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}
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}
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}else if (modsChildNodeName.equalsIgnoreCase("mods:name")){
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//handled separately
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}else if (modsChildNodeName.equalsIgnoreCase("mods:typeofresource")){
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content = modsChildNode.getTextContent().trim();
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if (!content.isEmpty()) {
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modsMap.put("typeofresource",content);
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}
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}else if (modsChildNodeName.equalsIgnoreCase("mods:identifier")){
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content = modsChildNode.getTextContent().trim();
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if (!content.isEmpty()) {
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modsMap.put(modsChildNode.getAttributes().getNamedItem("type").getNodeValue(),content);
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if (modsChildNode.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("isbn")) {
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ref.setIsbn(content);
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}else if (modsChildNode.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("issn")) {
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ref.setIssn(content);
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}else if (modsChildNode.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("DOI")) {
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try {
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ref.setDoi(DOI.fromString(content));
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} catch (IllegalArgumentException e) {
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logger.warn(content + " is not a vaild DOI");
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}
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}else if (modsChildNode.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("GenericHash")) {
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ref.setIssn("GenericHash: "+content);
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try {
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ref.setUri(new URI("http://plazi.cs.umb.edu/GgServer/search?MODS.ModsDocID="+content));
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} catch (URISyntaxException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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}else{
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logger.info("identifier " + modsChildNode.getAttributes().getNamedItem("type").getNodeValue() + " not yet handled.");
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}
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}
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}else if (modsChildNodeName.equalsIgnoreCase("mods:location")){
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NodeList tmp = modsChildNode.getChildNodes();
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for (int j=0;j<tmp.getLength();j++){
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// System.out.println("Child of mods:location: "+tmp.item(j).getNodeName());
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if (tmp.item(j).getNodeName().equalsIgnoreCase("mods:url")) {
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content = tmp.item(j).getTextContent().trim();
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if (!content.isEmpty() && (content != "http://un.availab.le")) {
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modsMap.put("url",content);
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ref.setUri(URI.create(content));
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}
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}
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}
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}
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else if (modsChildNodeName.equalsIgnoreCase("mods:relatedItem")){
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addRelatedMods(modsChildNode, modsMap, ref);
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}else if (modsChildNodeName.equalsIgnoreCase("mods:classification")){
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//already handled before
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}else if (modsChildNodeName.equalsIgnoreCase("#text") && modsChildNode.getTextContent().matches("\\s*")){
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//already handled before
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}else{
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logger.warn("mods item not recognized yet: " + modsChildNodeName);
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}
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}
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modsMap.put("people",StringUtils.join(roleList.toArray(),SPLITTER));
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List<Reference> references = importer.getReferenceService().list(Reference.class, 0, 0, null, null);
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for(Reference<?> refe:references){
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if (refe.getCitation().equalsIgnoreCase(ref.getCitation())) {
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ref=refe;
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}
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}
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// System.out.println(modsMap);
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//
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// System.out.println("REFERENCE "+ref.getCitation());
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// System.out.println("REFERENCE "+ref.getTitle());
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// System.out.println("REFERENCE "+ref.getTitleCache());
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return ref;
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}
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private void handleModsNames(NodeList children, Reference<?> ref) {
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List<String> roleList = new ArrayList<String>();
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List<Person> persons = new ArrayList<Person>();
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List<String> editors= new ArrayList<String>();
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//handle all mods:name
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for ( int i = 0; i<children.getLength(); i++){
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if (children.item(i).getNodeName().equalsIgnoreCase("mods:name")){
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NamedNodeMap attributeMap = children.item(i).getAttributes();
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if ((attributeMap.getNamedItem("type") != null) && attributeMap.getNamedItem("type").getNodeValue().equalsIgnoreCase("personal")) {
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handleNameTypePersonal(children.item(i), roleList, persons, editors);
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} else if (attributeMap.getNamedItem("type") == null){
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logger.warn("mods:name attribute 'type' is missing. Name not handled");
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}else {
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logger.warn("mods:name 'type' " + attributeMap.getNamedItem("type").getNodeValue() + " not yet supported");
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}
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}
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}
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//evaluate authors and editors
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if (persons.size()>0){
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if (ref == null){
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logger.warn("mods:name exists but reference is null");
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}else if (persons.size()==1){
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ref.setAuthorship(persons.get(0));
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}
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else{
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Team authorship = Team.NewInstance();
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for (Person pers:persons){
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authorship.addTeamMember(pers);
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}
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if (!personMap.containsKey(authorship.getTitleCache()) && (authorship.getTeamMembers().size()>0)){
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UUID uuid = importer.getAgentService().saveOrUpdate(authorship);
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personMap.put(authorship.getTitleCache(),uuid);
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}else{
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if(authorship.getTeamMembers().size()>1) {
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UUID uuid = personMap.get(authorship.getTitleCache());
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authorship = (Team) importer.getAgentService().find(uuid);
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}
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}
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ref.setAuthorship(authorship);
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}
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if (editors.size()>0) {
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ref.setEditor(StringUtils.join(editors,", "));
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}
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}
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}
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/**
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* Extracts the reference with correct type from mods:classification.
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* Incomplete implementation. Will be filled whenever new cases show up
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* @param children list of all children of mods:mods
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* @return
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*/
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//http://www.loc.gov/standards/mods/userguide/classification.html
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private Reference<?> tryMakeReferenceByClassification(NodeList children) {
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for (int i=0; i<children.getLength();i++){
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if (children.item(i).getNodeName().equalsIgnoreCase("mods:classification")){
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Node classificationNode = children.item(i);
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String text = classificationNode.getTextContent();
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if ("journal article".equals(text)){
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return ReferenceFactory.newArticle();
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}else if ("book".equals(text)){
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return ReferenceFactory.newBook();
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}else{
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if (StringUtils.isNotBlank(text)){
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logger.warn("mods:classification could not be recognized: " + text);
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}else{
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logger.warn("mods:classification has not text. ");
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}
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}
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}
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}
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return null;
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}
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231
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232
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private void handleNameTypePersonal(Node node, List<String> roleList, List<Person> persons, List<String> editors) {
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boolean newRole=false;
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String content="";
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236
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String role =null;
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237
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238
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List<String> nameParts = new ArrayList<String>();
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240
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NodeList tmp = node.getChildNodes();
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for (int j=0;j<tmp.getLength();j++){
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if (tmp.item(j).getNodeName().equalsIgnoreCase("mods:namePart")) {
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content=tmp.item(j).getTextContent().trim();
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if (! content.isEmpty()) {
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nameParts.add(content);
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}
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} else if (tmp.item(j).getNodeName().equalsIgnoreCase("mods:role")) {
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NodeList roleChildren = tmp.item(j).getChildNodes();
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for (int k=0; k< roleChildren.getLength();k++){
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if (roleChildren.item(k).getNodeName().equalsIgnoreCase("mods:roleTerm")){
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content = roleChildren.item(k).getTextContent().trim();
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if (!content.isEmpty()) {
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roleList.add(content);
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// p.setNomenclaturalTitle(content);
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if (content.equalsIgnoreCase(EDITOR)) {
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role=EDITOR;
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}
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else if (content.equalsIgnoreCase(AUTHOR)) {
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role=AUTHOR;
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}
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262
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newRole=true;
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263
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}
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}
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265
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}
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266
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}
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267
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268
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}
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269
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270
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Person p=null;
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271
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if (! nameParts.isEmpty()){
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p = Person.NewInstance();
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p.setTitleCache(StringUtils.join(nameParts.toArray(), " "), true);
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274
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}
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275
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276
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if (newRole){
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277
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if ((p!=null) && role.equals(AUTHOR)) {
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278
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UUID uuid = null;
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279
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if (!personMap.containsKey(p.getTitleCache())){
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uuid = importer.getAgentService().saveOrUpdate(p);
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281
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p = (Person) importer.getAgentService().find(uuid);
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282
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personMap.put(p.getTitleCache(),uuid);
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283
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}else{
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284
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uuid = personMap.get(p.getTitleCache());
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285
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p = (Person) importer.getAgentService().find(uuid);
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286
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}
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287
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// logger.info("ADD PERSON "+p);
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288
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persons.add(p);
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289
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}
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290
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else if ((p!=null) && role.equals(EDITOR)) {
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291
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editors.add(p.getTitleCache());
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292
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}
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293
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}
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294
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}
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295
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296
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/**
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297
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* @param item
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298
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* @param modsMap
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299
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*/
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300
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private void addRelatedMods(Node node, Map<String, String> modsMap, Reference<?> ref) {
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301
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NodeList tmp =node.getChildNodes();
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302
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NodeList partNodes = null;
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303
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NodeList children = null;
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304
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305
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List<String> originInfo = null;
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306
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List<String> partList = null;
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307
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308
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TimePeriod date;
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309
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310
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String publisher="";
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311
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String publishplace="";
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312
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String pstart="";
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313
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String pend="";
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314
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315
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Map<String,String> mapmap=null;
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316
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317
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Map<String, String> relatedInfoMap = new HashMap<String, String>();
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318
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List<String> roleList = new ArrayList<String>();
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319
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String content="";
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320
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321
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relatedInfoMap.put("type",node.getAttributes().getNamedItem("type").getNodeValue());
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322
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323
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324
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Reference<?> inRef = null;
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325
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for (int j=0;j<tmp.getLength();j++){
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326
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Node childNode = tmp.item(j);
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327
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String childNodeName = childNode.getNodeName();
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328
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if (childNodeName.equalsIgnoreCase("#text") && childNode.getTextContent().matches("\\s*")){
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329
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//do nothing
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330
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} else if (childNodeName.equalsIgnoreCase("mods:titleInfo")) {
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331
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content=childNode.getTextContent().trim();
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332
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if (!content.isEmpty()) {
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333
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relatedInfoMap.put("titleInfo",content);
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334
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if (node.getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("host")){
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335
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List<Reference> references = importer.getReferenceService().list(Reference.class, 0, 0, null, null);
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336
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boolean refFound = false;
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337
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for (Reference<?> tmpRef:references){
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338
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if(tmpRef.getTitleCache().equalsIgnoreCase(content)){
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339
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refFound = true;
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340
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inRef= tmpRef;
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|
341
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}
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|
342
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}
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343
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if (!refFound){
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344
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inRef = getBestInreference(ref);
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|
345
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if (inRef == null){
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346
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inRef = ReferenceFactory.newGeneric();
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347
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}
|
|
348
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|
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349
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//book.setTitleCache(content,true);
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|
350
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inRef.setTitle(content);
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|
351
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}
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352
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if ((ref.getInReference() == null) || !ref.getInReference().equals(inRef)) {
|
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353
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ref.setInReference(inRef);
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|
354
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}else{
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355
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//TODO
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|
356
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}
|
|
357
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}
|
|
358
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}
|
|
359
|
} else if (childNodeName.equalsIgnoreCase("mods:originInfo")) {
|
|
360
|
children = childNode.getChildNodes();
|
|
361
|
originInfo = new ArrayList<String>();
|
|
362
|
for (int i=0;i<children.getLength();i++){
|
|
363
|
content=children.item(i).getTextContent().trim();
|
|
364
|
if (!content.isEmpty()) {
|
|
365
|
originInfo.add(children.item(i).getNodeName()+":"+content);
|
|
366
|
if (children.item(i).getNodeName().contains("dateIssued")) {
|
|
367
|
ref.setDatePublished(TimePeriodParser.parseString(content));
|
|
368
|
}
|
|
369
|
}
|
|
370
|
publisher="";
|
|
371
|
publishplace="";
|
|
372
|
if (children.item(i).getNodeName().contains("publisher")) {
|
|
373
|
try{
|
|
374
|
publisher=children.item(i).getChildNodes().item(0).getTextContent().trim();
|
|
375
|
// System.out.println("PUBLISHER "+publisher);
|
|
376
|
}catch(Exception e){System.out.println("oups "+e);}
|
|
377
|
}
|
|
378
|
if (children.item(i).getNodeName().contains("place")) {
|
|
379
|
try{
|
|
380
|
publishplace=children.item(i).getTextContent().trim();
|
|
381
|
// System.out.println("PUBLISHED "+publishplace);
|
|
382
|
}catch(Exception e){System.out.println("oups "+e);}
|
|
383
|
}
|
|
384
|
if (publishplace.isEmpty() && !publisher.isEmpty()) {
|
|
385
|
ref.setPublisher(publisher);
|
|
386
|
}
|
|
387
|
if (!publishplace.isEmpty() && !publisher.isEmpty()) {
|
|
388
|
ref.setPublisher(publisher, publishplace);
|
|
389
|
}
|
|
390
|
}
|
|
391
|
relatedInfoMap.put("originInfo", StringUtils.join(originInfo.toArray(),SPLITTER));
|
|
392
|
} else if (childNodeName.equalsIgnoreCase("mods:name")){
|
|
393
|
//handled later
|
|
394
|
} else if (childNodeName.equalsIgnoreCase("mods:part")){
|
|
395
|
children = childNode.getChildNodes();
|
|
396
|
partList = new ArrayList<String>();
|
|
397
|
for (int i=0;i<children.getLength();i++){
|
|
398
|
mapmap = new HashMap<String, String>();
|
|
399
|
// System.out.println(children.item(i).getNodeName());
|
|
400
|
|
|
401
|
if (children.item(i).getNodeName().equalsIgnoreCase("#text") && children.item(i).getTextContent().matches("\\s*")){
|
|
402
|
//do nothing
|
|
403
|
} else if (children.item(i).getNodeName().equalsIgnoreCase("mods:date")){
|
|
404
|
content = children.item(i).getTextContent().trim();
|
|
405
|
if (!content.isEmpty()){
|
|
406
|
date = TimePeriodParser.parseString(content);
|
|
407
|
//TODO need to check if date belongs to ref or inref
|
|
408
|
ref.setDatePublished(date);
|
|
409
|
}
|
|
410
|
} else if (children.item(i).getNodeName().equalsIgnoreCase("mods:detail") &&
|
|
411
|
children.item(i).getAttributes().getNamedItem("type").getNodeValue().equalsIgnoreCase("volume")){
|
|
412
|
partNodes = children.item(i).getChildNodes();
|
|
413
|
for (int k=0; k<partNodes.getLength();k++){
|
|
414
|
if (partNodes.item(k).getNodeName().equalsIgnoreCase("mods:number")) {
|
|
415
|
content = partNodes.item(k).getTextContent().trim();
|
|
416
|
if (!content.isEmpty()) {
|
|
417
|
ref.setVolume(content);
|
|
418
|
}
|
|
419
|
}
|
|
420
|
}
|
|
421
|
} else if (children.item(i).getNodeName().equalsIgnoreCase("mods:extent")) {
|
|
422
|
mapmap.put("unit", children.item(i).getAttributes().getNamedItem("unit").getNodeValue());
|
|
423
|
partNodes = children.item(i).getChildNodes();
|
|
424
|
pstart="";
|
|
425
|
pend="";
|
|
426
|
for (int k=0; k<partNodes.getLength();k++){
|
|
427
|
if (partNodes.item(k).getNodeName().equalsIgnoreCase("mods:start")) {
|
|
428
|
content = partNodes.item(k).getTextContent().trim();
|
|
429
|
if (!content.isEmpty()) {
|
|
430
|
mapmap.put("start",content);
|
|
431
|
pstart=content;
|
|
432
|
}
|
|
433
|
}
|
|
434
|
if (partNodes.item(k).getNodeName().equalsIgnoreCase("mods:end")) {
|
|
435
|
content = partNodes.item(k).getTextContent().trim();
|
|
436
|
if (!content.isEmpty()) {
|
|
437
|
mapmap.put("end",content);
|
|
438
|
pend=content;
|
|
439
|
}
|
|
440
|
}
|
|
441
|
}
|
|
442
|
// System.out.println("SET PAGES "+pstart+"-"+pend);
|
|
443
|
ref.setPages(pstart+"-"+pend);
|
|
444
|
}else{
|
|
445
|
logger.warn("mods:part not yet supported: " + children.item(i).getNodeName());
|
|
446
|
}
|
|
447
|
partList.add(mapmap.toString());
|
|
448
|
}
|
|
449
|
modsMap.put("part",StringUtils.join(partList.toArray(),SPLITTER));
|
|
450
|
}else{
|
|
451
|
logger.warn("relatedItem child not yet supported: " + childNodeName);
|
|
452
|
}
|
|
453
|
}
|
|
454
|
|
|
455
|
|
|
456
|
handleModsNames(children, inRef);
|
|
457
|
|
|
458
|
relatedInfoMap.put("relatedRoles", StringUtils.join(roleList.toArray(),SPLITTER));
|
|
459
|
modsMap.put("relatedInfo",relatedInfoMap.toString());
|
|
460
|
}
|
|
461
|
|
|
462
|
|
|
463
|
/**
|
|
464
|
* Returns empty reference which best fits to the given ref as in-reference.
|
|
465
|
* TODO move to {@link ReferenceType} or {@link ReferenceFactory}
|
|
466
|
* @param ref
|
|
467
|
* @return
|
|
468
|
*/
|
|
469
|
private Reference<?> getBestInreference(Reference<?> ref) {
|
|
470
|
if (ref.getType().equals(ReferenceType.Article)){
|
|
471
|
return ReferenceFactory.newJournal();
|
|
472
|
}else if (ref.getType().equals(ReferenceType.BookSection)){
|
|
473
|
return ReferenceFactory.newBook();
|
|
474
|
}else{
|
|
475
|
//TODO support more types
|
|
476
|
logger.warn("In-Reference type not yet supported for :" + ref.getType());
|
|
477
|
|
|
478
|
}
|
|
479
|
return null;
|
|
480
|
}
|
|
481
|
|
|
482
|
}
|