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package eu.dnetlib.data.claimsDemo;
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//import eu.dnetlib.data.claims.migration.Claim;
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import eu.dnetlib.data.claims.migration.*;
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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.Node;
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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.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.XPathExpression;
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import javax.xml.xpath.XPathFactory;
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import java.io.*;
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import java.net.HttpURLConnection;
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import java.net.URL;
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import java.sql.Timestamp;
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import java.util.Date;
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/**
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* Created by argirok on 20/11/2015.
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*/
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/*
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Parsing xml from claims DB
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* DMF xml
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* Relation XML
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*/
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public class ParsingClaimUtils {
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private DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
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private DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
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private InputSource inputSource;
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private Document document;
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private XPathFactory xPathfactory;
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private XPath xpath;
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private String relationType;
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private SearchUtils searchUtils= new SearchUtils();
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/*ParsingClaimUtils(String xml) throws ParserConfigurationException, IOException, SAXException {
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inputSource = new InputSource(new StringReader(xml));
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document = dBuilder.parse(inputSource);
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relationType=getAttributeFromRel2ActionsXML("type");
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}*/
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ParsingClaimUtils(String uri, boolean search) throws ParserConfigurationException, IOException, SAXException{
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document = dBuilder.parse(uri);
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xPathfactory = XPathFactory.newInstance();
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xpath = xPathfactory.newXPath();
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}
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public String getValueFromXMLAtrribute(String elementName) {
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return getValueFromElement("field", elementName);
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}
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private String getValueFromElement(String element, String elementName) {
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XPathExpression expr = null;
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try {
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expr = xpath.compile(String.format("//%s[@name=\"%s\"]", element, elementName));
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NodeList nl = (NodeList) expr.evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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Node nNode = nl.item(0);
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if (nNode.getNodeType() == Node.ELEMENT_NODE) {
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Element eElement = (Element) nNode;
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return eElement.getAttribute("value");
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}
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}
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return null;
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} catch (Exception e) {
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e.printStackTrace();
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return null;
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}
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}
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private String getResultsSize() {
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XPathExpression expr = null;
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try {
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expr = xpath.compile("//total/text()");
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NodeList nl = (NodeList) expr.evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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return nl.item(0).getNodeValue();
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}
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return null;
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} catch (Exception e) {
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e.printStackTrace();
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return null;
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}
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}
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/*
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Get the type of the target of an annotation /
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Get the type of the source of a claim /
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*/
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static public String getTargetType(String relationType) {
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String sourceType = ClaimUtils.PUBLICATION;
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if (relationType.equals("resultResult_publicationpublication_isRelatedTo")) {
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sourceType = ClaimUtils.PUBLICATION;
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} else if (relationType.equals("resultResult_publicationdataset_isRelatedTo")) {
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sourceType = ClaimUtils.PUBLICATION;
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} else if (relationType.equals("resultProject")) {
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sourceType = ClaimUtils.PUBLICATION;
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//could be a dataset too
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} else if (relationType.equals("resultResult_datasetpublication_isRelatedTo")) {
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sourceType = ClaimUtils.DATASET;
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} else if (relationType.equals("resultResult_datasetdataset_isRelatedTo")) {
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sourceType = ClaimUtils.DATASET;
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}
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return sourceType;
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}
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/*
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Get the type of the body of an annotation /
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Get the type of the target of a claim /
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*/
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public static String getBodyType(String relationType) {
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String sourceType = ClaimUtils.PUBLICATION;
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if (relationType.equals("resultResult_publicationpublication_isRelatedTo")) {
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sourceType = ClaimUtils.PUBLICATION;
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} else if (relationType.equals("resultResult_publicationdataset_isRelatedTo")) {
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sourceType = ClaimUtils.DATASET;
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} else if (relationType.equals("resultProject")) {
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sourceType = ClaimUtils.PROJECT;
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//could be a dataset too
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} else if (relationType.equals("resultResult_datasetpublication_isRelatedTo")) {
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sourceType = ClaimUtils.PUBLICATION;
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} else if (relationType.equals("resultResult_datasetdataset_isRelatedTo")) {
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sourceType = ClaimUtils.DATASET;
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}
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return sourceType;
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}
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static public Result getResultFromDMF(String xml) throws ParserConfigurationException, IOException, SAXException {
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Result r=new Result();
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r.setXml(xml);
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DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
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DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
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InputSource inputSource= new InputSource(new StringReader(xml));
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Document document=dBuilder.parse(inputSource);
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XPathFactory xPathfactory= XPathFactory.newInstance();
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XPath xpath = xPathfactory.newXPath();
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try {
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NodeList nl = (NodeList) xpath.compile("//*[local-name()=\"identifier\"][@identifierType='doi']/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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r.setDoi(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//*[local-name()=\"identifier\"][@identifierType='orcidworkid']/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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r.setOrcidworkid(nl.item(0).getNodeValue());
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}
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// DON'T DELETE following lines for orcidworkid!!
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// @identiferType typo is made on purpose -> there are dmf xml with this typo.
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if(r.getXml().contains("@identiferType='orcidworkid'")) {
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r.setXml(r.getXml().replace("@identiferType='orcidworkid'","@identifierType='orcidworkid'"));
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nl = (NodeList) xpath.compile("//*[local-name()=\"identifier\"][@identiferType='orcidworkid']/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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r.setOrcidworkid(nl.item(0).getNodeValue());
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}
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}
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nl = (NodeList) xpath.compile("//*[local-name()='objIdentifier']/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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r.setOpenaireId(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//*[local-name()='identifier']/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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r.setExternal_url(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//*[local-name()='accessrights']/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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r.setAccessRights(nl.item(0).getNodeValue());
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}
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// <oaf:accessrights>EMBARGO</oaf:accessrights>
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//<oaf:embargoenddate>2015-03-01</oaf:embargoenddate>
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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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r.setEmbargoEndDate(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//*[local-name()='title']/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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r.setTitle(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//*[local-name()='collectedFrom']/@id").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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r.setCollectedFrom(nl.item(0).getNodeValue());
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}
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} catch (Exception e) {
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e.printStackTrace();
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return null;
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}
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return r;
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}
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static public void getClaimFromConceptDMF(Claim claim, String xml) {
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Result r=new Result();
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Context context =new Context();
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try {
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DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
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DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
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InputSource inputSource= new InputSource(new StringReader(xml));
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Document document=dBuilder.parse(inputSource);
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XPathFactory xPathfactory= XPathFactory.newInstance();
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XPath xpath = xPathfactory.newXPath();
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NodeList nl = (NodeList) xpath.compile("//*[local-name()='recordIdentifier']/text()").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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r.setOpenaireId(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//*[local-name()='concept']/@id").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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context.setOpenaireId(nl.item(0).getNodeValue());
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}
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} catch (Exception e) {
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e.printStackTrace();
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}
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claim.setTarget(buildResult(r.getOpenaireId(), null,claim.getId(),ClaimUtils.USEAPIRESULTS));
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buildContext(context);
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claim.setSource(context);
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}
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static public void getRelationClaim(Claim claim, String xml) throws IOException, SAXException, ParserConfigurationException {
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String relationType="";
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String sourceId=""; //Annotation source
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String targetId=""; //Annotation target
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// //<RELATION type='resultProject' source='50|od______1266::af81022e9c489007a8f9ab27c2c725cb' target='40|fct_________::0432268334291febec6d0dbc1f8bae5d' />
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try {
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DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
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DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
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InputSource inputSource= new InputSource(new StringReader(xml));
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Document document=dBuilder.parse(inputSource);
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XPathFactory xPathfactory= XPathFactory.newInstance();
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XPath xpath = xPathfactory.newXPath();
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NodeList nl = (NodeList) xpath.compile("//RELATION/@type").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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relationType=(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//RELATION/@source").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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targetId=(nl.item(0).getNodeValue());
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}
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nl = (NodeList) xpath.compile("//RELATION/@target").evaluate(document, XPathConstants.NODESET);
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if (nl.getLength() > 0) {
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sourceId=(nl.item(0).getNodeValue());
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}
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} catch (Exception e) {
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e.printStackTrace();
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}
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claim.setTarget(buildResult(targetId, getTargetType(relationType),claim.getId(),ClaimUtils.USEAPIRESULTS));
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String bodyType=getBodyType(relationType);
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if (bodyType.equals(ClaimUtils.PROJECT)) {
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claim.setSource(buildProject(sourceId, claim.getId(),ClaimUtils.USEAPIPROJECTS));
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} else {
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claim.setSource(buildResult(sourceId, bodyType,claim.getId(),ClaimUtils.USEAPIRESULTS));
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bodyType=((Result)claim.getSource()).getResultType();
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}
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claim.setTargetType(((Result) claim.getTarget()).getResultType());
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claim.setSourceType(bodyType);
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}
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static public void buildContext(Context context){
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269
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if(context!=null&&context.getOpenaireId()!=null){
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try {
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context.setTitle(ContextUtils.extractEgiLabel(context.getOpenaireId()));
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}catch (Exception e){
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e.printStackTrace();
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System.err.println("ContextUtils: Couldn't get Egi label for id "+context.getId());
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275
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}
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276
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}
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277
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}
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static Result buildResult(String id, String type,String claimId,boolean useApi) {
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Result body= new Result();
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280
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if (id.contains("|")) {
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id = id.split("\\|")[1];
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}
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body.setOpenaireId(id);
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284
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body.setResultType(type);
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285
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if(useApi){
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286
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//look for a publication
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287
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getResultFromAPI(body, claimId,true);
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288
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String openaireId=body.getOpenaireId();
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289
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String objId=getObjIdentifierFromSearch(openaireId);
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290
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if(!body.isFound()){
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291
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if(objId!=null&&!openaireId.equals(objId)){
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292
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// not found! look for a publication with objId
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293
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//if result not found in API with openaireId, search for it with objIdentifier
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294
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body.setOpenaireId(objId);
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295
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getResultFromAPI(body, claimId,true);
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296
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body.setOpenaireId(openaireId);
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297
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//TODO check which one of the ids we should keep!!!!
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298
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}
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299
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if(!body.isFound()){
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300
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//if still not found search for Dataset with the id
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301
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getResultFromAPI(body, claimId, false);
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302
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if (!body.isFound() && (objId = getObjIdentifierFromSearch(openaireId)) != null && !openaireId.equals(objId)) {
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303
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// still not found!! search for Dataset with the onjId
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//if result not found in API with openaireId, search for it with objIdentifier
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body.setOpenaireId(objId);
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getResultFromAPI(body, claimId, false);
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body.setOpenaireId(openaireId);
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//TODO check which one of the ids we should keep!!!!
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}
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}
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}
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312
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//TODO check if it is a dataset
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313
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if(!body.isFound()) {
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314
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try {
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PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter("results_not_found.txt", true)));
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316
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Date date = new java.util.Date();
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out.println(new Timestamp(date.getTime()) + " - Result Not Found: " + body.getOpenaireId() + " (API) in claim " + claimId);
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out.close();
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} catch (IOException e) {
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320
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e.printStackTrace();
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321
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System.err.println("Couldn't write to file " + "results_not_found.txt");
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322
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}
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323
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}
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324
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}else {
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325
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getResultFromSearch(body, claimId);
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326
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}
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return body;
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328
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}
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|
329
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330
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private static void getResultFromSearch(Result r,String claimId){
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331
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SearchUtils searchUtils= new SearchUtils();
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332
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String searchUri=searchUtils.getResultSearchUrl(r.getOpenaireId());
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|
333
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if(searchUri==null){
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334
|
return ;
|
|
335
|
}
|
|
336
|
System.out.println("Result query: "+searchUri);
|
|
337
|
try {
|
|
338
|
String size=null;
|
|
339
|
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
|
|
340
|
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
|
|
341
|
Document document=dBuilder.parse(searchUri);
|
|
342
|
XPathFactory xPathfactory= XPathFactory.newInstance();
|
|
343
|
XPath xpath = xPathfactory.newXPath();
|
|
344
|
NodeList nl = (NodeList) xpath.compile("//total/text()").evaluate(document, XPathConstants.NODESET);
|
|
345
|
if (nl.getLength() > 0) {
|
|
346
|
size= nl.item(0).getNodeValue();
|
|
347
|
}
|
|
348
|
if(size!=null && Integer.parseInt(size)>0){
|
|
349
|
nl = (NodeList) xpath.compile("//field[@name='resulttypename']/@value").evaluate(document, XPathConstants.NODESET);
|
|
350
|
if (nl.getLength() > 0) {
|
|
351
|
r.setResultType(nl.item(0).getNodeValue());
|
|
352
|
}
|
|
353
|
nl = (NodeList) xpath.compile("//field[@name='bestlicense']/@value").evaluate(document, XPathConstants.NODESET);
|
|
354
|
if (nl.getLength() > 0) {
|
|
355
|
r.setBestLicense(nl.item(0).getNodeValue());
|
|
356
|
}
|
|
357
|
nl = (NodeList) xpath.compile("//field[@name='collectedfrom']/@value").evaluate(document, XPathConstants.NODESET);
|
|
358
|
if (nl.getLength() > 0) {
|
|
359
|
r.setCollectedFrom(nl.item(0).getNodeValue());
|
|
360
|
}
|
|
361
|
nl = (NodeList) xpath.compile("//field[@name='title']/@value").evaluate(document, XPathConstants.NODESET);
|
|
362
|
if (nl.getLength() > 0) {
|
|
363
|
r.setTitle(nl.item(0).getNodeValue());
|
|
364
|
}
|
|
365
|
nl = (NodeList) xpath.compile("//field[@name='pid']").evaluate(document, XPathConstants.NODESET);
|
|
366
|
for(int i=0; i<nl.getLength();i++){
|
|
367
|
String id="";
|
|
368
|
String type="";
|
|
369
|
int count;
|
|
370
|
|
|
371
|
|
|
372
|
NodeList valueNodes = (NodeList) xpath.compile("//field[@name='value']/@value").evaluate(nl.item(i), XPathConstants.NODESET);
|
|
373
|
if (valueNodes.getLength() > 0) {
|
|
374
|
id = valueNodes.item(i).getNodeValue();
|
|
375
|
}
|
|
376
|
NodeList classNodes = (NodeList) xpath.compile("//field[@name='classid']/@value").evaluate(nl.item(i), XPathConstants.NODESET);
|
|
377
|
if (classNodes.getLength() > 0) {
|
|
378
|
type = classNodes.item(i).getNodeValue();
|
|
379
|
}
|
|
380
|
if (type.equals("doi") && id != null) {
|
|
381
|
r.setDoi(id);
|
|
382
|
r.setExternal_url("http://dx.doi.org/"+r.getDoi());
|
|
383
|
|
|
384
|
}else if(type.equals("pmc") && id != null) {
|
|
385
|
r.setPmcid(id);
|
|
386
|
}
|
|
387
|
|
|
388
|
}
|
|
389
|
|
|
390
|
|
|
391
|
}else{
|
|
392
|
try{
|
|
393
|
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter("results_not_found.txt", true)));
|
|
394
|
Date date= new java.util.Date();
|
|
395
|
out.println(new Timestamp(date.getTime())+" - Result Not Found: "+r.getOpenaireId()+ " in claim "+claimId);
|
|
396
|
out.close();
|
|
397
|
}catch (IOException e) {
|
|
398
|
e.printStackTrace();
|
|
399
|
System.err.println("Couldn't write to file " + "results_not_found.txt");
|
|
400
|
}
|
|
401
|
//System.err.println("Result Not Found " + r.getOpenaireId());
|
|
402
|
r.setFound(false);
|
|
403
|
}
|
|
404
|
|
|
405
|
} catch (Exception e) {
|
|
406
|
e.printStackTrace();
|
|
407
|
return ;
|
|
408
|
}
|
|
409
|
}
|
|
410
|
public static String getObjIdentifierFromSearch(String id){
|
|
411
|
SearchUtils searchUtils= new SearchUtils();
|
|
412
|
String searchUri=searchUtils.getResultSearchUrl(id);
|
|
413
|
String objIdentifier=null;
|
|
414
|
if(searchUri==null){
|
|
415
|
return null;
|
|
416
|
}
|
|
417
|
System.out.println("Result query: "+searchUri);
|
|
418
|
try {
|
|
419
|
String size=null;
|
|
420
|
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
|
|
421
|
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
|
|
422
|
Document document=dBuilder.parse(searchUri);
|
|
423
|
XPathFactory xPathfactory= XPathFactory.newInstance();
|
|
424
|
XPath xpath = xPathfactory.newXPath();
|
|
425
|
NodeList nl = (NodeList) xpath.compile("//total/text()").evaluate(document, XPathConstants.NODESET);
|
|
426
|
if (nl.getLength() > 0) {
|
|
427
|
size= nl.item(0).getNodeValue();
|
|
428
|
}
|
|
429
|
if(size!=null && Integer.parseInt(size)>0){
|
|
430
|
//indexId="objIdentifier"
|
|
431
|
//<field name="resultId" multiplicity="false" indexId="objIdentifier" label="Object id" value="dedup_wf_001::7832a296929028bbe447d66398a0c43a"/>
|
|
432
|
nl = (NodeList) xpath.compile("//field[@indexId='objIdentifier']/@value").evaluate(document, XPathConstants.NODESET);
|
|
433
|
if (nl.getLength() > 0) {
|
|
434
|
objIdentifier=nl.item(0).getNodeValue();
|
|
435
|
}
|
|
436
|
|
|
437
|
|
|
438
|
}
|
|
439
|
} catch (Exception e) {
|
|
440
|
e.printStackTrace();
|
|
441
|
return null;
|
|
442
|
}
|
|
443
|
return objIdentifier;
|
|
444
|
}
|
|
445
|
private static void getResultFromAPI(Result r,String claimId, boolean isPublication){
|
|
446
|
SearchUtils searchUtils= new SearchUtils();
|
|
447
|
String searchUri;
|
|
448
|
if(isPublication) {
|
|
449
|
searchUri = searchUtils.getPublicationApiUrl(r.getOpenaireId());
|
|
450
|
}else{
|
|
451
|
searchUri = searchUtils.getDatasetApiUrl(r.getOpenaireId());
|
|
452
|
}
|
|
453
|
if(searchUri==null){
|
|
454
|
return;
|
|
455
|
}
|
|
456
|
System.out.println("Result query: "+searchUri);
|
|
457
|
try {
|
|
458
|
URL obj =obj = new URL(searchUri);
|
|
459
|
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
|
|
460
|
int responseCode = con.getResponseCode();
|
|
461
|
BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()));
|
|
462
|
StringBuffer response = new StringBuffer();
|
|
463
|
String inputLine;
|
|
464
|
while ((inputLine = in.readLine()) != null) {
|
|
465
|
response.append(inputLine+"\n");
|
|
466
|
}
|
|
467
|
in.close();
|
|
468
|
String xml = response.toString();
|
|
469
|
String size=null;
|
|
470
|
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
|
|
471
|
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
|
|
472
|
//Document document=dBuilder.parse(searchUri);
|
|
473
|
InputSource is = new InputSource(new StringReader(xml));
|
|
474
|
Document document= document=dBuilder.parse(is);
|
|
475
|
XPathFactory xPathfactory= XPathFactory.newInstance();
|
|
476
|
XPath xpath = xPathfactory.newXPath();
|
|
477
|
|
|
478
|
|
|
479
|
NodeList nl = (NodeList) xpath.compile("/response/header/total/text()").evaluate(document, XPathConstants.NODESET);
|
|
480
|
if (nl.getLength() > 0) {
|
|
481
|
size= nl.item(0).getNodeValue();
|
|
482
|
}
|
|
483
|
if(size!=null && Integer.parseInt(size)>0){
|
|
484
|
nl = (NodeList) xpath.compile("//resulttype/@classid").evaluate(document, XPathConstants.NODESET);
|
|
485
|
if (nl.getLength() > 0) {
|
|
486
|
r.setResultType(nl.item(0).getNodeValue());
|
|
487
|
}
|
|
488
|
nl = (NodeList) xpath.compile("//bestlicense/@classid").evaluate(document, XPathConstants.NODESET);
|
|
489
|
if (nl.getLength() > 0) {
|
|
490
|
r.setBestLicense(nl.item(0).getNodeValue());
|
|
491
|
}
|
|
492
|
//TODO check this
|
|
493
|
/* nl = (NodeList) xpath.compile("//collectedfrom/@id").evaluate(document, XPathConstants.NODESET);
|
|
494
|
r.setCollectedFrom(ClaimUtils.COLLECTED_FROM_OPENAIRE);
|
|
495
|
for(int i=0;i<nl.getLength();i++) {
|
|
496
|
String datasourceId=nl.item(i).getNodeValue();
|
|
497
|
if (datasourceId.equals(ClaimUtils.DATASOURCE_ID__ORCID)) {
|
|
498
|
r.setCollectedFrom(ClaimUtils.COLLECTED_FROM_ORCID);
|
|
499
|
}else if (datasourceId.equals(ClaimUtils.DATASOURCE_ID_CROSSREF)) {
|
|
500
|
r.setCollectedFrom(ClaimUtils.COLLECTED_FROM_CROSSREF);
|
|
501
|
}else if (datasourceId.equals(ClaimUtils.DATASOURCE_ID_DATACTE)) {
|
|
502
|
r.setCollectedFrom(ClaimUtils.COLLECTED_FROM_DATACITE);
|
|
503
|
}else if (datasourceId.equals(ClaimUtils.DATASOURCE_ID__ORCID)) {
|
|
504
|
r.setCollectedFrom(ClaimUtils.COLLECTED_FROM_ORCID);
|
|
505
|
}
|
|
506
|
}*/
|
|
507
|
// if (nl.getLength() > 0) {
|
|
508
|
// r.setCollectedFrom(nl.item(0).getNodeValue());
|
|
509
|
// }
|
|
510
|
nl = (NodeList) xpath.compile("//title/text()").evaluate(document, XPathConstants.NODESET);
|
|
511
|
if (nl.getLength() > 0) {
|
|
512
|
r.setTitle(nl.item(0).getNodeValue());
|
|
513
|
}
|
|
514
|
nl = (NodeList) xpath.compile("//pid[@classid='doi']/text()").evaluate(document, XPathConstants.NODESET);
|
|
515
|
if (nl.getLength() > 0) {
|
|
516
|
r.setDoi(nl.item(0).getNodeValue());
|
|
517
|
r.setExternal_url("http://dx.doi.org/"+r.getDoi());
|
|
518
|
}
|
|
519
|
nl = (NodeList) xpath.compile("//pid[@classid='pmc']/text()").evaluate(document, XPathConstants.NODESET);
|
|
520
|
if (nl.getLength() > 0) {
|
|
521
|
r.setPmcid(nl.item(0).getNodeValue());
|
|
522
|
|
|
523
|
}
|
|
524
|
r.setXml(xml);
|
|
525
|
r.setCollectedFrom(ClaimUtils.COLLECTED_FROM_OPENAIRE);
|
|
526
|
r.setFound(true);
|
|
527
|
|
|
528
|
}else{
|
|
529
|
r.setFound(false);
|
|
530
|
}
|
|
531
|
|
|
532
|
} catch (Exception e) {
|
|
533
|
e.printStackTrace();
|
|
534
|
}
|
|
535
|
}
|
|
536
|
public static void getXmlfromDatacite(Result r){
|
|
537
|
r.setResultType(ClaimUtils.DATASET);
|
|
538
|
SearchUtils searchUtils= new SearchUtils();
|
|
539
|
if(r!=null&&r.getDoi()==null){
|
|
540
|
return ;
|
|
541
|
}
|
|
542
|
String xml =searchUtils.getDataciteXmlRecord(r.getDoi());
|
|
543
|
if(xml==null){
|
|
544
|
return ;
|
|
545
|
}
|
|
546
|
try {
|
|
547
|
String size=null;
|
|
548
|
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
|
|
549
|
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
|
|
550
|
InputSource is = new InputSource(new StringReader(xml));
|
|
551
|
Document document= document=dBuilder.parse(is);
|
|
552
|
XPathFactory xPathfactory= XPathFactory.newInstance();
|
|
553
|
XPath xpath = xPathfactory.newXPath();
|
|
554
|
NodeList nl ;
|
|
555
|
|
|
556
|
nl = (NodeList) xpath.compile("//j.0:title/text()").evaluate(document, XPathConstants.NODESET);
|
|
557
|
if (nl.getLength() > 0) {
|
|
558
|
r.setTitle(nl.item(0).getNodeValue());
|
|
559
|
}
|
|
560
|
nl = (NodeList) xpath.compile("//j.0:identifier/text()").evaluate(document, XPathConstants.NODESET);
|
|
561
|
if (nl.getLength() > 0) {
|
|
562
|
r.setDoi(nl.item(0).getNodeValue());
|
|
563
|
r.setExternal_url("http://dx.doi.org/"+r.getDoi());
|
|
564
|
}
|
|
565
|
r.setXml(xml);
|
|
566
|
r.setCollectedFrom(ClaimUtils.COLLECTED_FROM_DATACITE);
|
|
567
|
r.setFound(true);
|
|
568
|
} catch (Exception e) {
|
|
569
|
e.printStackTrace();
|
|
570
|
}
|
|
571
|
}
|
|
572
|
public static void getJsonfromCrossref(Result r){
|
|
573
|
SearchUtils searchUtils= new SearchUtils();
|
|
574
|
if(r!=null&&r.getDoi()==null){
|
|
575
|
return ;
|
|
576
|
}
|
|
577
|
String xml =searchUtils.getCrossrefJsonRecord(r.getDoi());
|
|
578
|
if(xml!=null){
|
|
579
|
r.setXml(xml);
|
|
580
|
r.setCollectedFrom(ClaimUtils.COLLECTED_FROM_CROSSREF);
|
|
581
|
}
|
|
582
|
}
|
|
583
|
public static void getXmlfromOrcid(Result r){
|
|
584
|
r.setResultType(ClaimUtils.PUBLICATION);
|
|
585
|
SearchUtils searchUtils= new SearchUtils();
|
|
586
|
if(r!=null&&r.getOrcidworkid()==null){
|
|
587
|
return ;
|
|
588
|
}
|
|
589
|
System.out.println("OWI: " + r.getOrcidworkid());
|
|
590
|
String orcid=r.getOrcidworkid().substring(0,19);
|
|
591
|
String orcidworkid=r.getOrcidworkid().substring(20,r.getOrcidworkid().length());
|
|
592
|
//0000-0003-5000-0001
|
|
593
|
System.out.println("orcid: "+orcid);
|
|
594
|
System.out.println("OWI: "+orcidworkid);
|
|
595
|
String xml =searchUtils.getOrcidXmlRecord(orcid);
|
|
596
|
if(xml==null){
|
|
597
|
return ;
|
|
598
|
}
|
|
599
|
try {
|
|
600
|
String size=null;
|
|
601
|
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
|
|
602
|
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
|
|
603
|
InputSource is = new InputSource(new StringReader(xml));
|
|
604
|
Document document= document=dBuilder.parse(is);
|
|
605
|
XPathFactory xPathfactory= XPathFactory.newInstance();
|
|
606
|
XPath xpath = xPathfactory.newXPath();
|
|
607
|
NodeList nl ;
|
|
608
|
// getParent().toXML()
|
|
609
|
// <orcid-work put-code="19500531" visibility="public">
|
|
610
|
String s = (String) xpath.compile("//orcid-work[@put-code="+orcidworkid+"]").evaluate(document, XPathConstants.STRING);
|
|
611
|
System.out.println("Here: "+s);
|
|
612
|
|
|
613
|
|
|
614
|
NodeList worknl = (NodeList) xpath.compile("//orcid-work[@put-code="+orcidworkid+"]").evaluate(document,XPathConstants.NODESET);
|
|
615
|
if (worknl.getLength() > 0) {
|
|
616
|
|
|
617
|
nl = (NodeList) xpath.compile("//orcid-work").evaluate(document, XPathConstants.NODESET);
|
|
618
|
for (int i = 0; i < nl.getLength(); i++) {
|
|
619
|
if(!worknl.item(0).isEqualNode(nl.item(i))) {
|
|
620
|
nl.item(i).getParentNode().removeChild(nl.item(i));
|
|
621
|
}
|
|
622
|
}
|
|
623
|
|
|
624
|
|
|
625
|
DOMSource domSource = new DOMSource(document);
|
|
626
|
StringWriter writer = new StringWriter();
|
|
627
|
StreamResult result = new StreamResult(writer);
|
|
628
|
TransformerFactory tf = TransformerFactory.newInstance();
|
|
629
|
Transformer transformer = tf.newTransformer();
|
|
630
|
transformer.transform(domSource, result);
|
|
631
|
System.out.println("XML IN String format is: \n" + writer.toString());
|
|
632
|
r.setXml(xml);
|
|
633
|
r.setCollectedFrom(ClaimUtils.COLLECTED_FROM_ORCID);
|
|
634
|
r.setFound(true);
|
|
635
|
}
|
|
636
|
nl = (NodeList) xpath.compile("//j.0:identifier/text()").evaluate(document, XPathConstants.NODESET);
|
|
637
|
if (nl.getLength() > 0) {
|
|
638
|
r.setDoi(nl.item(0).getNodeValue());
|
|
639
|
r.setExternal_url("http://dx.doi.org/"+r.getDoi());
|
|
640
|
}
|
|
641
|
} catch (Exception e) {
|
|
642
|
e.printStackTrace();
|
|
643
|
}
|
|
644
|
}
|
|
645
|
public static Project buildProject(String id, String claimId, boolean useAPI){
|
|
646
|
Project body=new Project();
|
|
647
|
if (id.contains("|")) {
|
|
648
|
id = id.split("\\|")[1];
|
|
649
|
}
|
|
650
|
body.setOpenaireId(id);
|
|
651
|
if(useAPI){
|
|
652
|
getProjectFromAPI(body,claimId);
|
|
653
|
return body;
|
|
654
|
}else{
|
|
655
|
getProjectFromSearch(body, claimId);
|
|
656
|
return body;
|
|
657
|
}
|
|
658
|
|
|
659
|
|
|
660
|
}
|
|
661
|
|
|
662
|
private static void getProjectFromSearch(Project project, String claimId){
|
|
663
|
SearchUtils s=new SearchUtils();
|
|
664
|
String searchUri=s.getProjectSearchUrl(project.getOpenaireId());
|
|
665
|
if(searchUri==null){
|
|
666
|
return ;
|
|
667
|
}
|
|
668
|
System.out.println("Project query: "+searchUri);
|
|
669
|
try {
|
|
670
|
String size=null;
|
|
671
|
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
|
|
672
|
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
|
|
673
|
Document document=dBuilder.parse(searchUri);
|
|
674
|
XPathFactory xPathfactory= XPathFactory.newInstance();
|
|
675
|
XPath xpath = xPathfactory.newXPath();
|
|
676
|
NodeList nl = (NodeList) xpath.compile("//total/text()").evaluate(document, XPathConstants.NODESET);
|
|
677
|
if (nl.getLength() > 0) {
|
|
678
|
size= nl.item(0).getNodeValue();
|
|
679
|
}
|
|
680
|
if(size!=null && Integer.parseInt(size)>0){
|
|
681
|
/*
|
|
682
|
<field name="name" indexId="projectacronym" multiplicity="true" label=colle value="OPENAIRE"/><field name="code" indexId="projectcode" multiplicity="true" label="Project code" value="246686"/><field name="title" indexId="projecttitle" multiplicity="true" label="Title" value="Open Access Infrastructure for Research in Europe"/>
|
|
683
|
*/
|
|
684
|
nl = (NodeList) xpath.compile("//field[@name='title']/@value").evaluate(document, XPathConstants.NODESET);
|
|
685
|
if (nl.getLength() > 0) {
|
|
686
|
project.setName(nl.item(0).getNodeValue());
|
|
687
|
}
|
|
688
|
nl = (NodeList) xpath.compile("//field[@name='name']/@value").evaluate(document, XPathConstants.NODESET);
|
|
689
|
if (nl.getLength() > 0) {
|
|
690
|
project.setAcronym(nl.item(0).getNodeValue());
|
|
691
|
}
|
|
692
|
/*
|
|
693
|
<test/><field name="funder" multiplicity="true"><field name="funderid" indexId="funderid" label="" value="ec__________::EC"/><field name="fundershortname" indexId="fundershortname" label="" value="EC"/><field name="fundername" indexId="fundername" label="" value="European Commission"/></field>
|
|
694
|
*/
|
|
695
|
|
|
696
|
nl = (NodeList) xpath.compile("//field[@name='fundername']/@value").evaluate(document, XPathConstants.NODESET);
|
|
697
|
if (nl.getLength() > 0) {
|
|
698
|
project.setFunderName(nl.item(0).getNodeValue());
|
|
699
|
}
|
|
700
|
nl = (NodeList) xpath.compile("//field[@name='funderid']/@value").evaluate(document, XPathConstants.NODESET);
|
|
701
|
if (nl.getLength() > 0) {
|
|
702
|
project.setFunderId(nl.item(0).getNodeValue());
|
|
703
|
}
|
|
704
|
|
|
705
|
}else{
|
|
706
|
try{
|
|
707
|
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter("projects_not_found.txt", true)));
|
|
708
|
Date date= new java.util.Date();
|
|
709
|
out.println(new Timestamp(date.getTime())+" - Projects Not Found: "+project.getOpenaireId()+ " in claim "+claimId);
|
|
710
|
out.close();
|
|
711
|
}catch (IOException e) {
|
|
712
|
e.printStackTrace();
|
|
713
|
System.err.println("Couldn't write to file " + "projects_not_found.txt");
|
|
714
|
}
|
|
715
|
//System.err.println("PROJECT Not Found " + project.getOpenaireId());
|
|
716
|
project.setFound(false);
|
|
717
|
|
|
718
|
}
|
|
719
|
|
|
720
|
} catch (Exception e) {
|
|
721
|
}
|
|
722
|
}
|
|
723
|
private static void getProjectFromAPI(Project project, String claimId){
|
|
724
|
|
|
725
|
|
|
726
|
SearchUtils s=new SearchUtils();
|
|
727
|
String searchUri=s.getProjectApiUrl(project.getOpenaireId());
|
|
728
|
searchUri="http://api.openaire.eu/search//projects?format=xml&openaireParticipantID=dedup_wf_001::82c87f641bb6219626a0ceca81e0d434";
|
|
729
|
if(searchUri==null){
|
|
730
|
return ;
|
|
731
|
}
|
|
732
|
//TODO the parsing from API
|
|
733
|
System.out.println("Project query: "+searchUri);
|
|
734
|
try {
|
|
735
|
URL obj =obj = new URL(searchUri);
|
|
736
|
HttpURLConnection con = (HttpURLConnection) obj.openConnection();
|
|
737
|
int responseCode = con.getResponseCode();
|
|
738
|
BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()));
|
|
739
|
StringBuffer response = new StringBuffer();
|
|
740
|
String inputLine;
|
|
741
|
while ((inputLine = in.readLine()) != null) {
|
|
742
|
response.append(inputLine);
|
|
743
|
}
|
|
744
|
in.close();
|
|
745
|
String xml = response.toString();
|
|
746
|
String size=null;
|
|
747
|
DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
|
|
748
|
DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
|
|
749
|
//Document document=dBuilder.parse(searchUri);
|
|
750
|
InputSource is = new InputSource(new StringReader(xml));
|
|
751
|
Document document= document=dBuilder.parse(is);
|
|
752
|
XPathFactory xPathfactory= XPathFactory.newInstance();
|
|
753
|
XPath xpath = xPathfactory.newXPath();
|
|
754
|
|
|
755
|
|
|
756
|
NodeList nl = (NodeList) xpath.compile("/response/header/total/text()").evaluate(document, XPathConstants.NODESET);
|
|
757
|
if (nl.getLength() > 0) {
|
|
758
|
size= nl.item(0).getNodeValue();
|
|
759
|
}
|
|
760
|
if(size!=null && Integer.parseInt(size)>0){
|
|
761
|
|
|
762
|
nl = (NodeList) xpath.compile("//title/text()").evaluate(document, XPathConstants.NODESET);
|
|
763
|
if (nl.getLength() > 0) {
|
|
764
|
project.setName(nl.item(0).getNodeValue());
|
|
765
|
}
|
|
766
|
nl = (NodeList) xpath.compile("//acronym/text()").evaluate(document, XPathConstants.NODESET);
|
|
767
|
if (nl.getLength() > 0) {
|
|
768
|
project.setAcronym(nl.item(0).getNodeValue());
|
|
769
|
}
|
|
770
|
nl = (NodeList) xpath.compile("//funder/name/text()").evaluate(document, XPathConstants.NODESET);
|
|
771
|
if (nl.getLength() > 0) {
|
|
772
|
project.setFunderName(nl.item(0).getNodeValue());
|
|
773
|
}
|
|
774
|
nl = (NodeList) xpath.compile("//funder/id/text()").evaluate(document, XPathConstants.NODESET);
|
|
775
|
if (nl.getLength() > 0) {
|
|
776
|
project.setFunderId(nl.item(0).getNodeValue());
|
|
777
|
}
|
|
778
|
|
|
779
|
project.setFound(true);
|
|
780
|
|
|
781
|
}else{
|
|
782
|
try{
|
|
783
|
PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter("projects_not_found.txt", true)));
|
|
784
|
Date date= new java.util.Date();
|
|
785
|
out.println(new Timestamp(date.getTime())+" - Projects Not Found: "+project.getOpenaireId()+ " in claim "+claimId);
|
|
786
|
out.close();
|
|
787
|
}catch (IOException e) {
|
|
788
|
e.printStackTrace();
|
|
789
|
System.err.println("Couldn't write to file " + "projects_not_found.txt");
|
|
790
|
}
|
|
791
|
//System.err.println("PROJECT Not Found " + project.getOpenaireId());
|
|
792
|
project.setFound(false);
|
|
793
|
}
|
|
794
|
|
|
795
|
} catch (Exception e) {
|
|
796
|
e.printStackTrace();
|
|
797
|
}
|
|
798
|
}
|
|
799
|
}
|