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package eu.dnetlib.data.mdstore.plugins;
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import java.io.StringReader;
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import java.util.Map;
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import java.util.Set;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import java.util.stream.Collectors;
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import org.apache.commons.lang3.math.NumberUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.dom4j.Document;
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import org.dom4j.DocumentException;
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import org.dom4j.Element;
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import org.dom4j.Node;
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import org.dom4j.QName;
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import org.dom4j.io.SAXReader;
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import org.springframework.beans.factory.annotation.Autowired;
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import com.mongodb.BasicDBObject;
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import com.mongodb.DBObject;
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import com.mongodb.client.MongoCollection;
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import eu.dnetlib.data.db.AffiliationsDao;
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import eu.dnetlib.data.db.Group;
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import eu.dnetlib.data.db.Person;
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import eu.dnetlib.data.mdstore.modular.mongodb.MongoMDStore;
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import eu.dnetlib.rmi.data.MDStoreServiceException;
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public class EnrichLabsPluginNEW extends AbstractIstiMDStorePlugin {
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private static final Log log = LogFactory.getLog(EnrichLabsPluginNEW.class);
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@Autowired
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private AffiliationsDao affilationDao;
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@SuppressWarnings("unchecked")
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@Override
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public void process(final MongoMDStore store, final Map<String, String> params) throws MDStoreServiceException {
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log.warn("********************************************");
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log.warn("* ENRICH LABS");
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log.warn("********************************************");
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// CODE -> year -> Lab
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final Map<String, Person> affiliations = affilationDao.listPersonsWithAffiliations()
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.stream()
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.collect(Collectors.toMap(Person::getId, a -> a));
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final MongoCollection<DBObject> pubsCollection = store.getCollection();
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for (final DBObject obj : pubsCollection.find()) {
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final String id = obj.get("id").toString();
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log.debug("**********************************************");
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log.debug("Record " + id);
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try {
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final Document doc = (new SAXReader()).read(new StringReader(obj.get("body").toString()));
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resetAffiliations(doc);
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final Integer publicationYear = NumberUtils.toInt(doc.valueOf("//*[local-name()='date' and @dateType='Accepted']"), 0);
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for (final Object o : doc.selectNodes("//*[local-name()='person']")) {
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final Element node = (Element) o;
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final String infoId = node.valueOf("./*[local-name()='infoId']");
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final Pattern pattern = Pattern.compile("info:cnr-pdr\\/author\\/(.+)\\/(.+)\\/(.+)");
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final Matcher matcher = pattern.matcher(infoId);
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if (matcher.find()) {
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final String code = matcher.group(1);
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final Person p = affiliations.get(code);
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if (p != null) {
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final Set<Group> groups = p.getAffiliations().get(publicationYear);
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if (groups != null) {
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node.selectSingleNode("./*[local-name() = 'personName']").setText(p.getName());
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for (final Group g : groups) {
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final Element affNode = node.addElement(new QName("affiliation", node.getNamespace()));
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affNode.setText("ISTI-CNR");
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affNode.addAttribute("code", code);
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affNode.addAttribute("groupAcronym", g.getId());
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affNode.addAttribute("group", g.getName());
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affNode.addAttribute("type", g.getType());
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}
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} else {
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log.info("Affilition for year " + publicationYear + " not found, person: " + infoId);
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}
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} else {
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log.info("Person not found: " + infoId);
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}
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} else {
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log.warn("Invalid infoId: " + infoId);
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}
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}
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pubsCollection.updateOne(new BasicDBObject("id", id), new BasicDBObject("$set", new BasicDBObject("body", doc.asXML())));
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} catch (final DocumentException e) {
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log.warn("Problem parsing a mdstore record");
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}
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}
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}
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private void resetAffiliations(final Document doc) {
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for (final Object n : doc.selectNodes("//*[local-name() = 'person']/*[local-name() = 'affiliation']")) {
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((Node) n).detach();
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}
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}
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}
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