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57029
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argiro.kok
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package eu.dnetlib.data.claims.parser;
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katerina.i
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argiro.kok
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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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argiro.kok
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import org.apache.log4j.Logger;
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41200
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katerina.i
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import org.w3c.dom.Document;
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katerina.i
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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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katerina.i
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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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konstantin
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import java.util.ArrayList;
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41200
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katerina.i
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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 = Logger.getLogger(OafParser.class);
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public static Result oaf2Result(String oaf) throws ParserConfigurationException, IOException, SAXException, XPathExpressionException, TransformerException {
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katerina.i
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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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katerina.i
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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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| 162 |
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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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| 165 |
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if (nl.getLength() > 0) {
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| 166 |
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for (int i = 0; i < nl.getLength(); i++) {
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| 167 |
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String ranking = ((Element)(nl.item(i).getParentNode())).getAttribute("rank");
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| 168 |
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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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katerina.i
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}
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DOMSource domSource = new DOMSource(document);
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| 175 |
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StringWriter writer = new StringWriter();
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| 176 |
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StreamResult streamResult = new StreamResult(writer);
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| 177 |
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TransformerFactory tf = TransformerFactory.newInstance();
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| 178 |
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Transformer transformer = tf.newTransformer();
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| 179 |
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transformer.transform(domSource, streamResult);
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| 180 |
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result.setMetadataRecord(writer.toString());
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katerina.i
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result.setCollectedFrom(ClaimUtils.COLLECTED_FROM_OPENAIRE);
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| 182 |
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result.setRecordFormat(ClaimUtils.FORMAT_XML);
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// result.setFound(true);
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katerina.i
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}
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| 186 |
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return result;
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| 187 |
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}
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| 188 |
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| 189 |
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| 190 |
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katerina.i
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public static Project oaf2Project(String oaf) throws Exception {
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| 191 |
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katerina.i
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Project project = null;
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| 192 |
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if(oaf == null ){
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| 193 |
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return null;
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katerina.i
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| 195 |
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}
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| 196 |
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katerina.i
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DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
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| 197 |
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DocumentBuilder dBuilder = null;
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| 198 |
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try {
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| 199 |
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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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| 205 |
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XPath xpath = xPathfactory.newXPath();
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| 206 |
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| 207 |
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String size = null;
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| 208 |
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NodeList nl = (NodeList) xpath.compile("/response/header/total/text()").evaluate(document, XPathConstants.NODESET);
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| 209 |
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if (nl.getLength() > 0) {
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| 210 |
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size= nl.item(0).getNodeValue();
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| 211 |
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}
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| 212 |
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if(size!=null && Integer.parseInt(size)>0){
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| 213 |
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project = new Project();
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| 214 |
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nl = (NodeList) xpath.compile("//objIdentifier/text()").evaluate(document, XPathConstants.NODESET);
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| 215 |
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if (nl.getLength() > 0) {
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| 216 |
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project.setOpenaireId(nl.item(0).getNodeValue());
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| 217 |
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}
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| 218 |
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nl = (NodeList) xpath.compile("//title/text()").evaluate(document, XPathConstants.NODESET);
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| 219 |
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if (nl.getLength() > 0) {
|
| 220 |
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project.setName(nl.item(0).getNodeValue());
|
| 221 |
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}
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| 222 |
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nl = (NodeList) xpath.compile("//acronym/text()").evaluate(document, XPathConstants.NODESET);
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| 223 |
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if (nl.getLength() > 0) {
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| 224 |
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project.setAcronym(nl.item(0).getNodeValue());
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| 225 |
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}
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| 226 |
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nl = (NodeList) xpath.compile("//funder/name/text()").evaluate(document, XPathConstants.NODESET);
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| 227 |
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if (nl.getLength() > 0) {
|
| 228 |
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project.setFunderName(nl.item(0).getNodeValue());
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| 229 |
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}
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| 230 |
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nl = (NodeList) xpath.compile("//funder/shortname/text()").evaluate(document, XPathConstants.NODESET);
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| 231 |
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if (nl.getLength() > 0) {
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| 232 |
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project.setFunderShortName(nl.item(0).getNodeValue());
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| 233 |
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}
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| 234 |
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nl = (NodeList) xpath.compile("//funder/id/text()").evaluate(document, XPathConstants.NODESET);
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| 235 |
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if (nl.getLength() > 0) {
|
| 236 |
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project.setFunderId(nl.item(0).getNodeValue());
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| 237 |
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}
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| 238 |
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| 239 |
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nl = (NodeList) xpath.compile("//funding_level_0/text()").evaluate(document, XPathConstants.NODESET);
|
| 240 |
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if (nl.getLength() > 0) {
|
| 241 |
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project.setFundingStreamLevel0(nl.item(0).getNodeValue());
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| 242 |
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}
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| 243 |
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| 244 |
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nl = (NodeList) xpath.compile("//code/text()").evaluate(document, XPathConstants.NODESET);
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| 245 |
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if (nl.getLength() > 0) {
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| 246 |
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project.setCode(nl.item(0).getNodeValue());
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| 247 |
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}
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| 248 |
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| 249 |
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nl = (NodeList) xpath.compile("//rels/rel/to[@class='hasContact']").evaluate(document, XPathConstants.NODESET);
|
| 250 |
|
|
if (nl.getLength() > 0) {
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| 251 |
46884
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konstantin
|
project.setContactEmails(new ArrayList<String>());
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| 252 |
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katerina.i
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for (int i = 0; i < nl.getLength(); i++) {
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| 253 |
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if(((Element)(nl.item(i).getParentNode())).getElementsByTagName("email").getLength() > 0) {
|
| 254 |
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String email = ((Element) (nl.item(i).getParentNode())).getElementsByTagName("email").item(0).getTextContent();
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| 255 |
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project.getContactEmails().add(email);
|
| 256 |
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}
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| 257 |
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katerina.i
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}
|
| 258 |
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}
|
| 259 |
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| 260 |
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// project.setFound(true);
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| 261 |
41200
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katerina.i
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| 262 |
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}
|
| 263 |
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} catch (Exception e) {
|
| 264 |
47219
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argiro.kok
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logger.error("Error while parsing project",e);
|
| 265 |
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throw new Exception(e);
|
| 266 |
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}
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| 267 |
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katerina.i
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| 268 |
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return project;
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| 269 |
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|
| 270 |
|
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}
|
| 271 |
49865
|
argiro.kok
|
public static Result oaf2Software(String oaf) throws ParserConfigurationException, IOException, SAXException, XPathExpressionException, TransformerException {
|
| 272 |
|
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Result result = null;
|
| 273 |
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|
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
|
| 274 |
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|
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
|
| 275 |
|
|
InputSource is = new InputSource(new StringReader(oaf));
|
| 276 |
|
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Document document= dBuilder.parse(is);
|
| 277 |
|
|
XPathFactory xPathfactory= XPathFactory.newInstance();
|
| 278 |
|
|
XPath xpath = xPathfactory.newXPath();
|
| 279 |
41200
|
katerina.i
|
|
| 280 |
49865
|
argiro.kok
|
String size = null;
|
| 281 |
|
|
NodeList nl = (NodeList) xpath.compile("/response/header/total/text()").evaluate(document, XPathConstants.NODESET);
|
| 282 |
|
|
if (nl.getLength() > 0) {
|
| 283 |
|
|
size= nl.item(0).getNodeValue();
|
| 284 |
|
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}
|
| 285 |
|
|
System.out.println("size:"+size);
|
| 286 |
|
|
if(size!=null && Integer.parseInt(size)>0){
|
| 287 |
|
|
result = new Result();
|
| 288 |
|
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nl = (NodeList) xpath.compile("//field[@name = \"resultId\"]/@value").evaluate(document, XPathConstants.NODESET);
|
| 289 |
|
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if (nl.getLength() > 0) {
|
| 290 |
|
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result.setOpenaireId(nl.item(0).getNodeValue());
|
| 291 |
|
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}
|
| 292 |
|
|
nl = (NodeList) xpath.compile("//field[@name = \"resulttypeid\"]/@value").evaluate(document, XPathConstants.NODESET);
|
| 293 |
|
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if (nl.getLength() > 0) {
|
| 294 |
|
|
result.setResultType(nl.item(0).getNodeValue());
|
| 295 |
|
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}
|
| 296 |
|
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nl = (NodeList) xpath.compile("//field[@name = \"bestaccessright\"]/@value").evaluate(document, XPathConstants.NODESET);
|
| 297 |
|
|
if (nl.getLength() > 0) {
|
| 298 |
|
|
result.setBestLicense(nl.item(0).getNodeValue());
|
| 299 |
|
|
}
|
| 300 |
|
|
nl = (NodeList) xpath.compile("//field[@name = \"embargoenddate\"]/@value").evaluate(document, XPathConstants.NODESET);
|
| 301 |
|
|
if (nl.getLength() > 0) {
|
| 302 |
|
|
result.setEmbargoEndDate(nl.item(0).getNodeValue());
|
| 303 |
|
|
}
|
| 304 |
|
|
nl = (NodeList) xpath.compile("//field[@name = \"title\"]/@value").evaluate(document, XPathConstants.NODESET);
|
| 305 |
|
|
if (nl.getLength() > 0) {
|
| 306 |
|
|
result.setTitle(nl.item(0).getNodeValue());
|
| 307 |
|
|
}
|
| 308 |
|
|
//
|
| 309 |
|
|
nl = (NodeList) xpath.compile("//field[@name = \"pid\"]").evaluate(document, XPathConstants.NODESET);
|
| 310 |
|
|
System.out.println("size: pid"+nl.getLength());
|
| 311 |
|
|
if (nl.getLength() > 0) {
|
| 312 |
|
|
for (int i = 0; i < nl.getLength(); i++) {
|
| 313 |
|
|
NodeList list = (NodeList) xpath.compile("./field[@name = \"classid\"]/@value").evaluate(nl.item(i), XPathConstants.NODESET);
|
| 314 |
|
|
System.out.println("size: classid"+list.getLength());
|
| 315 |
|
|
|
| 316 |
|
|
if (list.getLength() > 0 && list.item(0).getNodeValue() !=null ) {
|
| 317 |
|
|
|
| 318 |
|
|
if (list.item(0).getNodeValue().equals("doi")) {
|
| 319 |
|
|
list = (NodeList) xpath.compile("./field[@name = \"value\"]/@value").evaluate(nl.item(i), XPathConstants.NODESET);
|
| 320 |
|
|
result.setDoi(list.item(0).getNodeValue());
|
| 321 |
|
|
result.setExternalUrl("http://dx.doi.org/" + result.getDoi());
|
| 322 |
|
|
|
| 323 |
|
|
|
| 324 |
|
|
} else if (list.item(0).getNodeValue().equals("pmc")) {
|
| 325 |
|
|
list = (NodeList) xpath.compile("./field[@name = \"value\"]/@value").evaluate(nl.item(i), XPathConstants.NODESET);
|
| 326 |
|
|
result.setDoi(list.item(0).getNodeValue());
|
| 327 |
|
|
result.setExternalUrl("http://dx.doi.org/" + result.getDoi());
|
| 328 |
|
|
|
| 329 |
|
|
|
| 330 |
|
|
}else if (list.item(0).getNodeValue().equals("orcidworkid")) {
|
| 331 |
|
|
list = (NodeList) xpath.compile("./field[@name = \"value\"]/@value").evaluate(nl.item(i), XPathConstants.NODESET);
|
| 332 |
|
|
result.setDoi(list.item(0).getNodeValue());
|
| 333 |
|
|
result.setExternalUrl("http://dx.doi.org/" + result.getDoi());
|
| 334 |
|
|
|
| 335 |
|
|
|
| 336 |
|
|
}else if (list.item(0).getNodeValue().equals("oai")) {
|
| 337 |
|
|
list = (NodeList) xpath.compile("./field[@name = \"value\"]/@value").evaluate(nl.item(i), XPathConstants.NODESET);
|
| 338 |
|
|
result.setDoi(list.item(0).getNodeValue());
|
| 339 |
|
|
result.setExternalUrl("http://dx.doi.org/" + result.getDoi());
|
| 340 |
|
|
|
| 341 |
|
|
|
| 342 |
|
|
}
|
| 343 |
|
|
}
|
| 344 |
|
|
}
|
| 345 |
|
|
}
|
| 346 |
|
|
nl = (NodeList) xpath.compile("//rels/rel/to[@class='hasAuthor']").evaluate(document, XPathConstants.NODESET);
|
| 347 |
|
|
if (nl.getLength() > 0) {
|
| 348 |
|
|
for (int i = 0; i < nl.getLength(); i++) {
|
| 349 |
|
|
String ranking = ((Element)(nl.item(i).getParentNode())).getElementsByTagName("ranking").item(0).getTextContent();
|
| 350 |
|
|
String fullname = (((Element)(nl.item(i).getParentNode())).getElementsByTagName("fullname").item(0).getTextContent().replace(",", " "));
|
| 351 |
|
|
result.getAuthors().put(ranking,fullname);
|
| 352 |
|
|
}
|
| 353 |
|
|
|
| 354 |
|
|
}
|
| 355 |
|
|
if(result.getExternalUrl()==null){
|
| 356 |
|
|
// nl = (NodeList) xpath.compile("//webresource/url/text()").evaluate(document, XPathConstants.NODESET);
|
| 357 |
|
|
// if (nl.getLength() > 0) {
|
| 358 |
|
|
// result.setExternalUrl(nl.item(0).getNodeValue());
|
| 359 |
|
|
// }
|
| 360 |
|
|
nl = (NodeList) xpath.compile("//children/instance/licence[@classid='OPEN']").evaluate(document, XPathConstants.NODESET);
|
| 361 |
|
|
if (nl.getLength() > 0) {
|
| 362 |
|
|
NodeList list = (NodeList) xpath.compile("./webresource/url/text()").evaluate(nl.item(0).getParentNode(), XPathConstants.NODESET);
|
| 363 |
|
|
if (list.getLength() > 0) {
|
| 364 |
|
|
result.setExternalUrl(list.item(0).getNodeValue());
|
| 365 |
|
|
}
|
| 366 |
|
|
}else{
|
| 367 |
|
|
nl = (NodeList) xpath.compile("//children/instance/licence[@classid='EMBARGO']").evaluate(document, XPathConstants.NODESET);
|
| 368 |
|
|
if (nl.getLength() > 0) {
|
| 369 |
|
|
NodeList list = (NodeList) xpath.compile("./webresource/url/text()").evaluate(nl.item(0).getParentNode(), XPathConstants.NODESET);
|
| 370 |
|
|
if (list.getLength() > 0) {
|
| 371 |
|
|
result.setExternalUrl(list.item(0).getNodeValue());
|
| 372 |
|
|
}
|
| 373 |
|
|
}else{
|
| 374 |
|
|
nl = (NodeList) xpath.compile("//children/instance/licence[@classid='CLOSED']").evaluate(document, XPathConstants.NODESET);
|
| 375 |
|
|
if (nl.getLength() > 0) {
|
| 376 |
|
|
NodeList list = (NodeList) xpath.compile("./webresource/url/text()").evaluate(nl.item(0).getParentNode(), XPathConstants.NODESET);
|
| 377 |
|
|
if (list.getLength() > 0) {
|
| 378 |
|
|
result.setExternalUrl(list.item(0).getNodeValue());
|
| 379 |
|
|
}
|
| 380 |
|
|
}
|
| 381 |
|
|
}
|
| 382 |
|
|
}
|
| 383 |
|
|
}
|
| 384 |
|
|
|
| 385 |
|
|
|
| 386 |
|
|
nl = (NodeList) xpath.compile("//response/header").evaluate(document, XPathConstants.NODESET);
|
| 387 |
|
|
if(nl.getLength()>0){
|
| 388 |
|
|
nl.item(0).getParentNode().removeChild(nl.item(0));
|
| 389 |
|
|
}
|
| 390 |
|
|
|
| 391 |
|
|
|
| 392 |
|
|
|
| 393 |
|
|
DOMSource domSource = new DOMSource(document);
|
| 394 |
|
|
StringWriter writer = new StringWriter();
|
| 395 |
|
|
StreamResult streamResult = new StreamResult(writer);
|
| 396 |
|
|
TransformerFactory tf = TransformerFactory.newInstance();
|
| 397 |
|
|
Transformer transformer = tf.newTransformer();
|
| 398 |
|
|
transformer.transform(domSource, streamResult);
|
| 399 |
|
|
result.setMetadataRecord(writer.toString());
|
| 400 |
|
|
result.setCollectedFrom(ClaimUtils.COLLECTED_FROM_OPENAIRE);
|
| 401 |
|
|
result.setRecordFormat(ClaimUtils.FORMAT_XML);
|
| 402 |
|
|
// result.setFound(true);
|
| 403 |
|
|
|
| 404 |
|
|
}
|
| 405 |
|
|
return result;
|
| 406 |
|
|
}
|
| 407 |
|
|
|
| 408 |
|
|
|
| 409 |
41200
|
katerina.i
|
}
|