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package eu.dnetlib.data.claims.parser;
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import eu.dnetlib.data.claims.entity.Project;
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import eu.dnetlib.data.claims.entity.Result;
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import eu.dnetlib.data.claims.utils.ClaimUtils;
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import org.apache.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import org.w3c.dom.Document;
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import org.w3c.dom.Element;
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import org.w3c.dom.NodeList;
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import org.xml.sax.InputSource;
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import org.xml.sax.SAXException;
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import javax.xml.parsers.DocumentBuilder;
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import javax.xml.parsers.DocumentBuilderFactory;
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import javax.xml.parsers.ParserConfigurationException;
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import javax.xml.transform.Transformer;
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import javax.xml.transform.TransformerException;
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import javax.xml.transform.TransformerFactory;
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import javax.xml.transform.dom.DOMSource;
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import javax.xml.transform.stream.StreamResult;
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import javax.xml.xpath.XPath;
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import javax.xml.xpath.XPathConstants;
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import javax.xml.xpath.XPathExpressionException;
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import javax.xml.xpath.XPathFactory;
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import java.io.IOException;
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import java.io.StringReader;
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import java.io.StringWriter;
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import java.util.ArrayList;
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/**
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* Created by kiatrop on 5/2/2016.
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*/
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public class OafParser {
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/**
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* For external url: returns http://dx.doi.org/ +doi else the first url from websource
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*
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* @param oaf
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* @return
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* @throws ParserConfigurationException
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* @throws IOException
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* @throws SAXException
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* @throws XPathExpressionException
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* @throws TransformerException
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*/
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private static final Logger logger = LogManager.getLogger(OafParser.class);
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public static Result oaf2Result(String oaf) throws ParserConfigurationException, IOException, SAXException, XPathExpressionException, TransformerException {
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Result result = null;
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DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
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DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
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InputSource is = new InputSource(new StringReader(oaf));
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Document document= dBuilder.parse(is);
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XPathFactory xPathfactory= XPathFactory.newInstance();
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XPath xpath = xPathfactory.newXPath();
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String size = null;
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NodeList nl = (NodeList) xpath.compile("/response/header/total/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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size= nl.item(0).getNodeValue();
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}else{
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nl = (NodeList) xpath.compile("//objIdentifier/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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// result.setOpenaireId(nl.item(0).getNodeValue());
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size="1";
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}
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}
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if(size!=null && Integer.parseInt(size)>0){
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result = new Result();
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nl = (NodeList) xpath.compile("//objIdentifier/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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result.setOpenaireId(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//resulttype/@classid").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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result.setResultType(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//bestlicense/@classid").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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result.setBestLicense(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//bestaccessright/@classid").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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result.setBestLicense(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//embargoenddate/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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result.setEmbargoEndDate(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//title/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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result.setTitle(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//pid[@classid='doi']/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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result.setDoi(nl.item(0).getNodeValue());
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result.setExternalUrl("http://dx.doi.org/" + result.getDoi());
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}
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if(result.getExternalUrl()==null){
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// nl = (NodeList) xpath.compile("//webresource/url/text()").evaluate(document, XPathConstants.NODESET);
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// if (nl.getLength() > 0) {
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// result.setExternalUrl(nl.item(0).getNodeValue());
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// }
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nl = (NodeList) xpath.compile("//children/instance/licence[@classid='OPEN']").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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NodeList list = (NodeList) xpath.compile("./webresource/url/text()").evaluate(nl.item(0).getParentNode(), XPathConstants.NODESET);
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if (list.getLength() > 0) {
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result.setExternalUrl(list.item(0).getNodeValue());
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}
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}else{
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nl = (NodeList) xpath.compile("//children/instance/licence[@classid='EMBARGO']").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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NodeList list = (NodeList) xpath.compile("./webresource/url/text()").evaluate(nl.item(0).getParentNode(), XPathConstants.NODESET);
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if (list.getLength() > 0) {
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result.setExternalUrl(list.item(0).getNodeValue());
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}
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}else{
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nl = (NodeList) xpath.compile("//children/instance/licence[@classid='CLOSED']").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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NodeList list = (NodeList) xpath.compile("./webresource/url/text()").evaluate(nl.item(0).getParentNode(), XPathConstants.NODESET);
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if (list.getLength() > 0) {
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result.setExternalUrl(list.item(0).getNodeValue());
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}
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}
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}
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}
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}
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nl = (NodeList) xpath.compile("//pid[@classid='pmc']/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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result.setPmcid(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//pid[@classid='orcidworkid']/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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result.setOrcidworkid(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//pid[@classid='oai']/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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result.setOai(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//provenanceaction[@classid='user:claim:datacite']/@classid").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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result.setProvenanceaction(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//response/header").evaluate(document, XPathConstants.NODESET);
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if(nl.getLength()>0){
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nl.item(0).getParentNode().removeChild(nl.item(0));
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}
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nl = (NodeList) xpath.compile("//rel[@class='hasAuthor']").evaluate(document, XPathConstants.NODESET);
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System.out.println("Author length"+nl.getLength());
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if (nl.getLength() > 0) {
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for (int i = 0; i < nl.getLength(); i++) {
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String ranking = ((Element)(nl.item(i).getParentNode())).getElementsByTagName("ranking").item(0).getTextContent();
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String fullname = (((Element)(nl.item(i).getParentNode())).getElementsByTagName("fullname").item(0).getTextContent().replace(",", " "));
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result.getAuthors().put(ranking,fullname);
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}
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}
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nl = (NodeList) xpath.compile("//creator/text()").evaluate(document, XPathConstants.NODESET);
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System.out.println("Creator length"+nl.getLength());
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if (nl.getLength() > 0) {
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for (int i = 0; i < nl.getLength(); i++) {
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String ranking = ((Element)(nl.item(i).getParentNode())).getAttribute("rank");
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String fullname = (((Element)(nl.item(i).getParentNode())).getTextContent().replace(",", " "));
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result.getAuthors().put(ranking,fullname);
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}
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}
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DOMSource domSource = new DOMSource(document);
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StringWriter writer = new StringWriter();
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StreamResult streamResult = new StreamResult(writer);
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TransformerFactory tf = TransformerFactory.newInstance();
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Transformer transformer = tf.newTransformer();
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transformer.transform(domSource, streamResult);
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result.setMetadataRecord(writer.toString());
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result.setCollectedFrom(ClaimUtils.COLLECTED_FROM_OPENAIRE);
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result.setRecordFormat(ClaimUtils.FORMAT_XML);
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// result.setFound(true);
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}
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return result;
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}
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public static Project oaf2Project(String oaf) throws Exception {
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Project project = null;
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if(oaf == null ){
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return null;
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}
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DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
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DocumentBuilder dBuilder = null;
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try {
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dBuilder = dbFactory.newDocumentBuilder();
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InputSource is = new InputSource(new StringReader(oaf));
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Document document = dBuilder.parse(is);
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XPathFactory xPathfactory= XPathFactory.newInstance();
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XPath xpath = xPathfactory.newXPath();
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String size = null;
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NodeList nl = (NodeList) xpath.compile("/response/header/total/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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size= nl.item(0).getNodeValue();
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}
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if(size!=null && Integer.parseInt(size)>0){
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project = new Project();
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nl = (NodeList) xpath.compile("//objIdentifier/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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project.setOpenaireId(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//title/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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project.setName(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//acronym/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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project.setAcronym(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//funder/name/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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project.setFunderName(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//funder/shortname/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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project.setFunderShortName(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//funder/id/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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project.setFunderId(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//funding_level_0/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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project.setFundingStreamLevel0(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//code/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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project.setCode(nl.item(0).getNodeValue());
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}
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249
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nl = (NodeList) xpath.compile("//rels/rel/to[@class='hasContact']").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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project.setContactEmails(new ArrayList<String>());
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for (int i = 0; i < nl.getLength(); i++) {
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if(((Element)(nl.item(i).getParentNode())).getElementsByTagName("email").getLength() > 0) {
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String email = ((Element) (nl.item(i).getParentNode())).getElementsByTagName("email").item(0).getTextContent();
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project.getContactEmails().add(email);
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}
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258
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}
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259
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}
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260
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261
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// project.setFound(true);
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262
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263
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}
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264
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} catch (Exception e) {
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265
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logger.error("Error while parsing project",e);
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266
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throw new Exception(e);
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267
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}
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268
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269
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return project;
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270
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271
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}
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public static Result oaf2Software(String oaf) throws ParserConfigurationException, IOException, SAXException, XPathExpressionException, TransformerException {
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273
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Result result = null;
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274
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DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
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275
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DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
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276
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InputSource is = new InputSource(new StringReader(oaf));
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277
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Document document= dBuilder.parse(is);
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278
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XPathFactory xPathfactory= XPathFactory.newInstance();
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279
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XPath xpath = xPathfactory.newXPath();
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280
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281
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String size = null;
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282
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NodeList nl = (NodeList) xpath.compile("/response/header/total/text()").evaluate(document, XPathConstants.NODESET);
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283
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if (nl.getLength() > 0) {
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284
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size= nl.item(0).getNodeValue();
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285
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}
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286
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System.out.println("size:"+size);
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287
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if(size!=null && Integer.parseInt(size)>0){
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288
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result = new Result();
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289
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nl = (NodeList) xpath.compile("//field[@name = \"resultId\"]/@value").evaluate(document, XPathConstants.NODESET);
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290
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if (nl.getLength() > 0) {
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291
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result.setOpenaireId(nl.item(0).getNodeValue());
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292
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}
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293
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nl = (NodeList) xpath.compile("//field[@name = \"resulttypeid\"]/@value").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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result.setResultType(nl.item(0).getNodeValue());
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296
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}
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297
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nl = (NodeList) xpath.compile("//field[@name = \"bestaccessright\"]/@value").evaluate(document, XPathConstants.NODESET);
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298
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if (nl.getLength() > 0) {
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299
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result.setBestLicense(nl.item(0).getNodeValue());
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300
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}
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301
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nl = (NodeList) xpath.compile("//field[@name = \"embargoenddate\"]/@value").evaluate(document, XPathConstants.NODESET);
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302
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if (nl.getLength() > 0) {
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result.setEmbargoEndDate(nl.item(0).getNodeValue());
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304
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}
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305
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nl = (NodeList) xpath.compile("//field[@name = \"title\"]/@value").evaluate(document, XPathConstants.NODESET);
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306
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if (nl.getLength() > 0) {
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result.setTitle(nl.item(0).getNodeValue());
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308
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}
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309
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//
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310
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nl = (NodeList) xpath.compile("//field[@name = \"pid\"]").evaluate(document, XPathConstants.NODESET);
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311
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System.out.println("size: pid"+nl.getLength());
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312
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if (nl.getLength() > 0) {
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313
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for (int i = 0; i < nl.getLength(); i++) {
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314
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NodeList list = (NodeList) xpath.compile("./field[@name = \"classid\"]/@value").evaluate(nl.item(i), XPathConstants.NODESET);
|
|
315
|
System.out.println("size: classid"+list.getLength());
|
|
316
|
|
|
317
|
if (list.getLength() > 0 && list.item(0).getNodeValue() !=null ) {
|
|
318
|
|
|
319
|
if (list.item(0).getNodeValue().equals("doi")) {
|
|
320
|
list = (NodeList) xpath.compile("./field[@name = \"value\"]/@value").evaluate(nl.item(i), XPathConstants.NODESET);
|
|
321
|
result.setDoi(list.item(0).getNodeValue());
|
|
322
|
result.setExternalUrl("http://dx.doi.org/" + result.getDoi());
|
|
323
|
|
|
324
|
|
|
325
|
} else if (list.item(0).getNodeValue().equals("pmc")) {
|
|
326
|
list = (NodeList) xpath.compile("./field[@name = \"value\"]/@value").evaluate(nl.item(i), XPathConstants.NODESET);
|
|
327
|
result.setDoi(list.item(0).getNodeValue());
|
|
328
|
result.setExternalUrl("http://dx.doi.org/" + result.getDoi());
|
|
329
|
|
|
330
|
|
|
331
|
}else if (list.item(0).getNodeValue().equals("orcidworkid")) {
|
|
332
|
list = (NodeList) xpath.compile("./field[@name = \"value\"]/@value").evaluate(nl.item(i), XPathConstants.NODESET);
|
|
333
|
result.setDoi(list.item(0).getNodeValue());
|
|
334
|
result.setExternalUrl("http://dx.doi.org/" + result.getDoi());
|
|
335
|
|
|
336
|
|
|
337
|
}else if (list.item(0).getNodeValue().equals("oai")) {
|
|
338
|
list = (NodeList) xpath.compile("./field[@name = \"value\"]/@value").evaluate(nl.item(i), XPathConstants.NODESET);
|
|
339
|
result.setDoi(list.item(0).getNodeValue());
|
|
340
|
result.setExternalUrl("http://dx.doi.org/" + result.getDoi());
|
|
341
|
|
|
342
|
|
|
343
|
}
|
|
344
|
}
|
|
345
|
}
|
|
346
|
}
|
|
347
|
nl = (NodeList) xpath.compile("//rels/rel/to[@class='hasAuthor']").evaluate(document, XPathConstants.NODESET);
|
|
348
|
if (nl.getLength() > 0) {
|
|
349
|
for (int i = 0; i < nl.getLength(); i++) {
|
|
350
|
String ranking = ((Element)(nl.item(i).getParentNode())).getElementsByTagName("ranking").item(0).getTextContent();
|
|
351
|
String fullname = (((Element)(nl.item(i).getParentNode())).getElementsByTagName("fullname").item(0).getTextContent().replace(",", " "));
|
|
352
|
result.getAuthors().put(ranking,fullname);
|
|
353
|
}
|
|
354
|
|
|
355
|
}
|
|
356
|
if(result.getExternalUrl()==null){
|
|
357
|
// nl = (NodeList) xpath.compile("//webresource/url/text()").evaluate(document, XPathConstants.NODESET);
|
|
358
|
// if (nl.getLength() > 0) {
|
|
359
|
// result.setExternalUrl(nl.item(0).getNodeValue());
|
|
360
|
// }
|
|
361
|
nl = (NodeList) xpath.compile("//children/instance/licence[@classid='OPEN']").evaluate(document, XPathConstants.NODESET);
|
|
362
|
if (nl.getLength() > 0) {
|
|
363
|
NodeList list = (NodeList) xpath.compile("./webresource/url/text()").evaluate(nl.item(0).getParentNode(), XPathConstants.NODESET);
|
|
364
|
if (list.getLength() > 0) {
|
|
365
|
result.setExternalUrl(list.item(0).getNodeValue());
|
|
366
|
}
|
|
367
|
}else{
|
|
368
|
nl = (NodeList) xpath.compile("//children/instance/licence[@classid='EMBARGO']").evaluate(document, XPathConstants.NODESET);
|
|
369
|
if (nl.getLength() > 0) {
|
|
370
|
NodeList list = (NodeList) xpath.compile("./webresource/url/text()").evaluate(nl.item(0).getParentNode(), XPathConstants.NODESET);
|
|
371
|
if (list.getLength() > 0) {
|
|
372
|
result.setExternalUrl(list.item(0).getNodeValue());
|
|
373
|
}
|
|
374
|
}else{
|
|
375
|
nl = (NodeList) xpath.compile("//children/instance/licence[@classid='CLOSED']").evaluate(document, XPathConstants.NODESET);
|
|
376
|
if (nl.getLength() > 0) {
|
|
377
|
NodeList list = (NodeList) xpath.compile("./webresource/url/text()").evaluate(nl.item(0).getParentNode(), XPathConstants.NODESET);
|
|
378
|
if (list.getLength() > 0) {
|
|
379
|
result.setExternalUrl(list.item(0).getNodeValue());
|
|
380
|
}
|
|
381
|
}
|
|
382
|
}
|
|
383
|
}
|
|
384
|
}
|
|
385
|
|
|
386
|
|
|
387
|
nl = (NodeList) xpath.compile("//response/header").evaluate(document, XPathConstants.NODESET);
|
|
388
|
if(nl.getLength()>0){
|
|
389
|
nl.item(0).getParentNode().removeChild(nl.item(0));
|
|
390
|
}
|
|
391
|
|
|
392
|
|
|
393
|
|
|
394
|
DOMSource domSource = new DOMSource(document);
|
|
395
|
StringWriter writer = new StringWriter();
|
|
396
|
StreamResult streamResult = new StreamResult(writer);
|
|
397
|
TransformerFactory tf = TransformerFactory.newInstance();
|
|
398
|
Transformer transformer = tf.newTransformer();
|
|
399
|
transformer.transform(domSource, streamResult);
|
|
400
|
result.setMetadataRecord(writer.toString());
|
|
401
|
result.setCollectedFrom(ClaimUtils.COLLECTED_FROM_OPENAIRE);
|
|
402
|
result.setRecordFormat(ClaimUtils.FORMAT_XML);
|
|
403
|
// result.setFound(true);
|
|
404
|
|
|
405
|
}
|
|
406
|
return result;
|
|
407
|
}
|
|
408
|
|
|
409
|
|
|
410
|
}
|