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package eu.dnetlib.data.mapreduce.hbase.statsExport.utils;
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import com.google.common.collect.Multimap;
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import eu.dnetlib.data.mapreduce.util.LicenseComparator;
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import eu.dnetlib.data.proto.DatasourceProtos.Datasource;
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import eu.dnetlib.data.proto.DatasourceProtos.Datasource.Metadata;
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import eu.dnetlib.data.proto.FieldTypeProtos;
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import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
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import eu.dnetlib.data.proto.FieldTypeProtos.StringField;
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import eu.dnetlib.data.proto.FieldTypeProtos.StructuredProperty;
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import eu.dnetlib.data.proto.OafProtos.Oaf;
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import eu.dnetlib.data.proto.OafProtos.OafEntity;
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import eu.dnetlib.data.proto.OafProtos.OafRel;
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import eu.dnetlib.data.proto.OrganizationProtos.Organization;
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import eu.dnetlib.data.proto.ProjectProtos.Project;
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import eu.dnetlib.data.proto.RelTypeProtos.RelType;
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import eu.dnetlib.data.proto.ResultProtos.Result;
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import eu.dnetlib.data.proto.ResultProtos.Result.Instance;
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import org.apache.log4j.Logger;
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import java.text.DateFormat;
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import java.text.ParseException;
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import java.text.SimpleDateFormat;
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import java.util.Date;
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import java.util.List;
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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 com.sun.org.apache.xerces.internal.parsers.DOMParser;
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import org.w3c.dom.Document;
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/**
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* @author eri Simple serializer that parses input Oaf Protos and prepares them
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* for sqoop
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*/
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public class Serializer {
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private static Logger logger = Logger.getLogger(Serializer.class);
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private String DELIM;
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private String ENCLOSING;
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public Serializer(String DELIM, String ENCLOSING) {
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this.DELIM = DELIM;
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this.ENCLOSING = ENCLOSING;
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}
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public String serialize(Oaf oaf) {
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switch (oaf.getKind()) {
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case entity:
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OafEntity valueEntity = oaf.getEntity();
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switch (valueEntity.getType()) {
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case datasource:
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return buildDatasource(oaf);
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case organization:
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return buildOrganization(oaf);
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case project:
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return buildProject(oaf);
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case result:
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return buildResult(oaf);
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default:
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break;
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}
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break;
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case relation:
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return buildRel(oaf.getRel());
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}
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return null;
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}
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public String serialize(OafRel oaf) {
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switch (oaf.getRelType()) {
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case resultProject:
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return getResultProject(oaf);
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default:
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return buildRel(oaf);
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}
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}
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private String buildRel(OafRel Rel) {
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return cleanId(Rel.getTarget()) + DELIM;
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}
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public void extractRelations(Oaf oaf, Multimap<String, String> relations) {
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OafEntity valueEntity = oaf.getEntity();
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getOriginalId(valueEntity, relations);
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switch (valueEntity.getType()) {
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case datasource:
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getDatasourceLanguages(valueEntity, relations);
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case result:
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getResultTopics(valueEntity, relations);
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getResultLanguages(valueEntity, relations);
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getResultClassifications(valueEntity, relations);
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getResultDatasources(valueEntity, relations);
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getResultConcepts(valueEntity, relations);
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getResultDois(valueEntity, relations);
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getResultCitations(valueEntity, relations);
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case project:
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getProjectKeywords(valueEntity, relations);
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getProjectSubjects(valueEntity, relations);
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default:
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}
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}
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private void getOriginalId(OafEntity oafEntity, Multimap<String, String> relations) {
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String relName = oafEntity.getType().toString().toLowerCase() + "Oid";
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for (String oid : oafEntity.getOriginalIdList()) {
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relations.put(relName, cleanId(oid));
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}
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}
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private void getProjectKeywords(OafEntity oafEntity, Multimap<String, String> relations) {
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relations.put("projectKeyword", getStringField(oafEntity.getProject().getMetadata().getKeywords().getValue()));
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}
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private void getProjectSubjects(OafEntity oafEntity, Multimap<String, String> relations) {
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for (StructuredProperty subj : oafEntity.getProject().getMetadata().getSubjectsList()) {
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relations.put("projectSubject", getStringField(subj.getValue()));
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}
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}
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private String getResultProject(OafRel oaf) {
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StringBuilder buff = new StringBuilder();
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buff.append(cleanId(oaf.getTarget())).append(DELIM);
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// is declared as int!!!
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long diff = DATEDIFF(oaf.getResultProject().getOutcome().getRelMetadata().getEnddate(), oaf.getResultProject().getOutcome().getRelMetadata().getStartdate());
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if (diff < 0) {
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diff = 0;
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}
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buff.append(getNumericField(String.valueOf(diff)));
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return buff.toString();
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}
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private void getDatasourceLanguages(OafEntity valueEntity, Multimap<String, String> rels) {
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Datasource d = valueEntity.getDatasource();
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Metadata metadata = d.getMetadata();
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for (StringField lang : metadata.getOdlanguagesList()) {
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rels.put("datasourceLanguage", getStringField(lang.getValue()));
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}
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}
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private void getResultLanguages(OafEntity valueEntity, Multimap<String, String> rels) {
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Result d = valueEntity.getResult();
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Result.Metadata metadata = d.getMetadata();
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if (metadata.getLanguage().getClassname() != null && !metadata.getLanguage().getClassname().isEmpty()) {
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rels.put("resultLanguage", getStringField(metadata.getLanguage().getClassname()));
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}
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}
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private void getResultDois(OafEntity valueEntity, Multimap<String, String> rels) {
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for (StructuredProperty pid : valueEntity.getPidList()) {
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rels.put("resultPid", getStringField(pid.getQualifier().getClassname()) + getStringField(pid.getValue()));
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}
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}
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private void getResultClassifications(OafEntity valueEntity, Multimap<String, String> rels) {
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Result result = valueEntity.getResult();
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for (Instance instance : (result.getInstanceList())) {
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String classification = instance.getInstancetype().getClassname();
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if (classification != null && !classification.isEmpty()) {
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rels.put("resultClassification", getStringField(instance.getInstancetype().getClassname()));
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}
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}
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}
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private void getResultConcepts(OafEntity valueEntity, Multimap<String, String> rels) {
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Result result = valueEntity.getResult();
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for (Result.Context context : result.getMetadata().getContextList()) {
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rels.put("resultConcept", cleanId(context.getId()));
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}
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}
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private void getResultDatasources(OafEntity valueEntity, Multimap<String, String> rels) {
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Result result = valueEntity.getResult();
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// hosted by
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for (Instance instance : (result.getInstanceList())) {
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String hostedBy = instance.getHostedby().getKey();
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if (hostedBy != null && !hostedBy.isEmpty()) {
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rels.put("resultDatasource", cleanId(hostedBy) + DELIM);
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}
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}
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// collected from
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for (FieldTypeProtos.KeyValue collectedFromValue : (valueEntity.getCollectedfromList())) {
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String collectedFrom = collectedFromValue.getKey();
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if (collectedFrom != null && !collectedFrom.isEmpty()) {
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rels.put("resultDatasource", cleanId(collectedFrom) + DELIM);
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}
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}
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}
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private void getResultTopics(OafEntity valueEntity, Multimap<String, String> rels) {
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Result d = valueEntity.getResult();
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Result.Metadata metadata = d.getMetadata();
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List<StructuredProperty> Topics = metadata.getSubjectList();
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for (StructuredProperty topic : Topics) {
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rels.put("resultTopic", getStringField(topic.getValue()));
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}
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}
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private void getResultCitations(OafEntity oafEntity, Multimap<String, String> rels) {
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for (FieldTypeProtos.ExtraInfo extraInfo : oafEntity.getExtraInfoList()) {
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if (extraInfo.getName().equals("result citations")) {
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DOMParser parser = new DOMParser();
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try {
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parser.parse(new InputSource(new java.io.StringReader(extraInfo.getValue())));
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Document doc = parser.getDocument();
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doc.getDocumentElement().normalize();
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NodeList citations = doc.getElementsByTagName("citation");
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for (int temp = 0; temp < citations.getLength(); temp++) {
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Element citation = (Element) citations.item(temp);
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NodeList ids = citation.getElementsByTagName("id");
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for(int temp1 = 0; temp1 < ids.getLength(); temp1++){
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Element id = (Element) ids.item(temp1);
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if(id.getAttribute("type").equals("openaire")){
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//System.out.println(id.getAttribute("value"));
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rels.put("resultCitation", id.getAttribute("value"));
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}
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}
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}
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} catch (Exception e) {
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logger.error("Error getting result citations", e);
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}
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}
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}
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}
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private String buildDatasource(Oaf oaf) {
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Metadata metadata = oaf.getEntity().getDatasource().getMetadata();
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StringBuilder buff = new StringBuilder();
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// name
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if (metadata.getOfficialname().getValue().equalsIgnoreCase("unknown")) {
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buff.append(getStringField("Unknown Repository"));
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} else {
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buff.append(getStringField(metadata.getOfficialname().getValue()));
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}
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// type
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if (metadata.hasDatasourcetype()) {
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buff.append(getStringField(metadata.getDatasourcetype().getClassname().replaceFirst(".*::", "")));
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}
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// compatibility,
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buff.append(getStringField(metadata.getOpenairecompatibility().getClassname()));
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// latitude
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buff.append(getLatLongField(metadata.getLatitude().getValue()));
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// longtitude
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buff.append(getLatLongField(metadata.getLongitude().getValue()));
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// dateofvalidation,
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buff.append(getStringDateField(metadata.getDateofvalidation().getValue()));
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// yearofvalidation,
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buff.append(getYearInt(metadata.getDateofvalidation().getValue()));
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//harvested
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buff.append(getStringField("false"));
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//piwik_id
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String piwik_id = "";
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for (String oid : oaf.getEntity().getOriginalIdList()) {
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if (oid.contains("piwik")) {
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piwik_id = oid.split(":")[1];
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break;
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}
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}
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buff.append(getStringField(cleanNumber(piwik_id)));
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return buff.toString();
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}
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private String buildOrganization(Oaf oaf) {
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StringBuilder buff = new StringBuilder();
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Organization.Metadata metadata = oaf.getEntity().getOrganization().getMetadata();
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// `name`,
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buff.append(getStringField(metadata.getLegalname().getValue()));
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// `country`,
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buff.append(getStringField(metadata.getCountry().getClassid()));
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return buff.toString();
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}
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private String buildResult(Oaf oaf) {
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StringBuilder buff = new StringBuilder();
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Result.Metadata metadata = oaf.getEntity().getResult().getMetadata();
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String titleString = "";
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if (metadata.getTitleList().size() > 0) {
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StructuredProperty title = metadata.getTitleList().get(0);
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titleString = title.getValue().replaceAll("\\s+", " ");
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titleString = titleString.replaceAll("\n", " ");
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}
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// pubtitle
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buff.append(getStringField(titleString));
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// publisher
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buff.append(getStringField(metadata.getPublisher().getValue()));
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// journal
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buff.append(getStringField(metadata.getJournal().getName())); //#null#!
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// year
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buff.append(getYearInt(metadata.getDateofacceptance().getValue()));
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// date
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buff.append(getStringDateField(metadata.getDateofacceptance().getValue()));
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// bestlicense
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buff.append(getStringField(getBestLicense(oaf.getEntity().getResult())));
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// type
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buff.append(getStringField(metadata.getResulttype().getClassname()));
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// embargo_end_date
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buff.append(getStringDateField(metadata.getEmbargoenddate().getValue()));
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// `authors`,
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int authors = metadata.getAuthorCount();
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String delayed = "no";
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for (OafRel rel : oaf.getEntity().getCachedRelList()) {
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if (rel.getRelType().equals(RelType.resultProject))
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// remember : in result Project, first id is project, second is result.
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{
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String daysfromend = getYearDifferenceInteger(rel.getResultProject().getOutcome().getRelMetadata().getEnddate(),
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rel.getResultProject().getOutcome().getRelMetadata().getStartdate());
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if (Integer.parseInt(daysfromend) > 0) {
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delayed = "yes";
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}
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}
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}
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// `delayed`,
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buff.append(getStringField(delayed));
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//authors
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buff.append(getNumericField(String.valueOf(authors)));
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384
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385
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String sources = "";
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386
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387
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388
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for (Instance instance : (oaf.getEntity().getResult().getInstanceList())) {
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List<String> urls = instance.getUrlList();
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for (String url : urls) {
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sources += cleanUrl(url) + " ;";
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}
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}
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394
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395
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//sources
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sources = ENCLOSING + sources + ENCLOSING + DELIM;
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397
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398
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buff.append(sources);
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399
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400
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return buff.toString();
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401
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|
402
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}
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403
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|
404
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private String getBestLicense(Result result) {
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405
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Qualifier bestLicense = null;
|
406
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LicenseComparator lc = new LicenseComparator();
|
407
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for (Instance instance : (result.getInstanceList())) {
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408
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if (lc.compare(bestLicense, instance.getAccessright()) > 0) {
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409
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bestLicense = instance.getAccessright();
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}
|
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}
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if (bestLicense != null) {
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return bestLicense.getClassname();
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} else {
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return "";
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}
|
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}
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418
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private String buildProject(Oaf oaf) {
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420
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|
421
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FundingParser fundingParser = new FundingParser(DELIM, ENCLOSING);
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StringBuilder buff = new StringBuilder();
|
423
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Project.Metadata metadata = oaf.getEntity().getProject().getMetadata();
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424
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// `acronym`,
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String acronym = metadata.getAcronym().getValue();
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427
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if (acronym.equalsIgnoreCase("UNKNOWN")) {
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428
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acronym = metadata.getTitle().getValue();
|
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}
|
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buff.append(getStringField(acronym));
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431
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432
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//title
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433
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buff.append(getStringField(metadata.getTitle().getValue()));
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434
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435
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//funding_lvl
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436
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List<StringField> fundList = metadata.getFundingtreeList();
|
437
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if (!fundList.isEmpty()) // `funding_lvl0`,
|
438
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{
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439
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//funder + 3 funding levels
|
440
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buff.append(fundingParser.getFundingInfo(fundList.get(0).getValue()));
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441
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} else {
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442
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buff.append(fundingParser.getFundingInfo(""));
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443
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}
|
444
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|
445
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//sc39
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String sc39 = metadata.getEcsc39().getValue();
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447
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if (sc39.equalsIgnoreCase("true") || sc39.equalsIgnoreCase("t") || sc39.contains("yes")) {
|
448
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sc39 = "yes";
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449
|
} else if (sc39.equalsIgnoreCase("false") || sc39.equalsIgnoreCase("f") || sc39.contains("no")) {
|
450
|
sc39 = "no";
|
451
|
}
|
452
|
buff.append(getStringField(sc39));
|
453
|
|
454
|
//project_type
|
455
|
buff.append(getStringField(metadata.getContracttype().getClassid()));
|
456
|
|
457
|
// start_year
|
458
|
buff.append(getYearInt(metadata.getStartdate().getValue()));
|
459
|
|
460
|
// end_year
|
461
|
buff.append(getYearInt(metadata.getEnddate().getValue()));
|
462
|
|
463
|
// duration enddate-startdate
|
464
|
buff.append(getYearDifferenceInteger(metadata.getEnddate().getValue(), metadata.getStartdate().getValue()));
|
465
|
|
466
|
// haspubs
|
467
|
buff.append(getStringField("no"));
|
468
|
|
469
|
// numpubs
|
470
|
buff.append(getNumericField("0"));
|
471
|
|
472
|
// enddate
|
473
|
buff.append(getStringDateField(metadata.getEnddate().getValue()));
|
474
|
|
475
|
// startdate
|
476
|
buff.append(getStringDateField(metadata.getStartdate().getValue()));
|
477
|
|
478
|
// `daysforlastpub`,
|
479
|
buff.append(getNumericField(""));
|
480
|
|
481
|
// `delayedpubs`,
|
482
|
buff.append(getNumericField(""));
|
483
|
|
484
|
//call identifier
|
485
|
buff.append(getStringField(metadata.getCallidentifier().getValue()));
|
486
|
|
487
|
//code
|
488
|
buff.append(getStringField(metadata.getCode().getValue()));
|
489
|
|
490
|
return buff.toString();
|
491
|
}
|
492
|
|
493
|
|
494
|
private String getYearDifferenceInteger(String enddate, String startdate) {
|
495
|
|
496
|
if (enddate != null && !enddate.isEmpty() && startdate != null && !startdate.isEmpty()) {
|
497
|
|
498
|
String[] split = startdate.split("-");
|
499
|
|
500
|
if (split.length == 0) {
|
501
|
return ENCLOSING + "0" + ENCLOSING + DELIM;
|
502
|
}
|
503
|
|
504
|
int Startdate = Integer.parseInt(split[0]);
|
505
|
|
506
|
split = enddate.split("-");
|
507
|
|
508
|
if (split.length == 0) {
|
509
|
return ENCLOSING + "0" + ENCLOSING + DELIM;
|
510
|
}
|
511
|
|
512
|
int Enddate = Integer.parseInt(split[0]);
|
513
|
|
514
|
int diff = Enddate - Startdate;
|
515
|
|
516
|
return ENCLOSING + diff + ENCLOSING + DELIM;
|
517
|
|
518
|
}
|
519
|
|
520
|
return ENCLOSING + "0" + ENCLOSING + DELIM;
|
521
|
}
|
522
|
|
523
|
private String getYearInt(String data) {
|
524
|
if (data == null || data.isEmpty() || data.equals("-1")) {
|
525
|
return ENCLOSING + "0" + ENCLOSING + DELIM;
|
526
|
}
|
527
|
|
528
|
String[] split = data.split("-");
|
529
|
|
530
|
if (split.length == 0) {
|
531
|
return ENCLOSING + "0" + ENCLOSING + DELIM;
|
532
|
}
|
533
|
|
534
|
String year = split[0];
|
535
|
|
536
|
year = cleanNumber(year);
|
537
|
|
538
|
if (year == null || year.isEmpty()) year = "0";
|
539
|
|
540
|
return ENCLOSING + year + ENCLOSING + DELIM;
|
541
|
|
542
|
}
|
543
|
|
544
|
private String cleanNumber(String number) {
|
545
|
number = number.replaceAll("[^A-Za-z0-9:,_]", "");
|
546
|
return number;
|
547
|
}
|
548
|
|
549
|
private String getLatLongField(String data) {
|
550
|
|
551
|
if (data == null || data.isEmpty())
|
552
|
return ENCLOSING + "null" + ENCLOSING + DELIM;
|
553
|
|
554
|
return ENCLOSING + data.replaceAll("[^-0-9.]+", "") + ENCLOSING + DELIM;
|
555
|
|
556
|
}
|
557
|
|
558
|
private String getStringField(String data) {
|
559
|
|
560
|
if (data == null || data.isEmpty())
|
561
|
return ENCLOSING + "null" + ENCLOSING + DELIM;
|
562
|
|
563
|
return ENCLOSING + clean(data) + ENCLOSING + DELIM;
|
564
|
|
565
|
}
|
566
|
|
567
|
private String getStringDateField(String data) {
|
568
|
if (data == null || data.isEmpty() || data.equals("-1")) {
|
569
|
return ENCLOSING + "0" + ENCLOSING + DELIM;
|
570
|
} else {
|
571
|
data = data.replace(DELIM, " ");
|
572
|
data = data.replace(ENCLOSING, " ");
|
573
|
data = data.replaceAll("\\r\\n|\\r|\\n", "");
|
574
|
try {
|
575
|
DateFormat format = new SimpleDateFormat("yyyy-MM-dd");
|
576
|
data = format.format(format.parse(data));
|
577
|
return ENCLOSING + data + ENCLOSING + DELIM;
|
578
|
} catch (ParseException e) {
|
579
|
return ENCLOSING + "0" + ENCLOSING + DELIM;
|
580
|
}
|
581
|
}
|
582
|
}
|
583
|
|
584
|
private String getNumericField(String data) {
|
585
|
if (data == null || data.isEmpty()) {
|
586
|
return ENCLOSING + "0" + ENCLOSING + DELIM;
|
587
|
} else {
|
588
|
return ENCLOSING + data + ENCLOSING + DELIM;
|
589
|
}
|
590
|
}
|
591
|
|
592
|
public String getId(Oaf oaf) {
|
593
|
switch (oaf.getKind()) {
|
594
|
case entity:
|
595
|
return cleanId(oaf.getEntity().getId());
|
596
|
case relation:
|
597
|
return cleanId(oaf.getRel().getSource());
|
598
|
|
599
|
}
|
600
|
return null;
|
601
|
|
602
|
}
|
603
|
|
604
|
public String getId(OafRel relOaf) {
|
605
|
return cleanId(relOaf.getSource());
|
606
|
}
|
607
|
|
608
|
private String clean(String value) {
|
609
|
if (value != null) {
|
610
|
|
611
|
value = value.replaceAll("[\"\\r\\\\;]", "");
|
612
|
value = value.replace(DELIM, " ");
|
613
|
value = value.replace(ENCLOSING, " ");
|
614
|
value = value.replaceAll("\\r\\n|\\r|\\n", " ");
|
615
|
|
616
|
return value;
|
617
|
} else {
|
618
|
return "";
|
619
|
}
|
620
|
|
621
|
}
|
622
|
|
623
|
private String cleanId(String value) {
|
624
|
if (value != null) {
|
625
|
// DO NOT CHANGE THIS: IT REMOVES ID PREFIX ( "5|datacite____::" to "datacite____::")
|
626
|
// AND REPLACES OCCURRENCES OF DELIM CHARS IN DATA
|
627
|
value = value.replaceFirst(".*\\|", "");
|
628
|
value = value.replace("\n", "");
|
629
|
value = value.replace(ENCLOSING, "");
|
630
|
value = value.replace(DELIM, "");
|
631
|
value = value.replace("\"", "");
|
632
|
value = value.replace("«", " ");
|
633
|
value = value.replace("»", " ");
|
634
|
}
|
635
|
|
636
|
return ENCLOSING + value + ENCLOSING;
|
637
|
}
|
638
|
|
639
|
private String cleanUrl(String value) {
|
640
|
value = value.replace(DELIM, " ");
|
641
|
value = value.replace(ENCLOSING, " ");
|
642
|
value = value.replace(" ", "");
|
643
|
value = value.replace("\n", "");
|
644
|
return value;
|
645
|
}
|
646
|
|
647
|
private long DATEDIFF(String startDate, String endDate) {
|
648
|
long MILLISECS_PER_DAY = 24 * 60 * 60 * 1000L;
|
649
|
long days;
|
650
|
SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd"); // "dd/MM/yyyy HH:mm:ss");
|
651
|
// <startdate>2011-09-01</startdate>
|
652
|
// <enddate>2015-08-31</enddate>
|
653
|
Date dateIni;
|
654
|
Date dateFin;
|
655
|
|
656
|
if (startDate == null || startDate.isEmpty() || endDate == null || endDate.isEmpty()) {
|
657
|
return 0;
|
658
|
}
|
659
|
try {
|
660
|
dateIni = format.parse(startDate);
|
661
|
dateFin = format.parse(endDate);
|
662
|
days = (dateFin.getTime() - dateIni.getTime()) / MILLISECS_PER_DAY;
|
663
|
} catch (Exception e) {
|
664
|
|
665
|
return 0;
|
666
|
}
|
667
|
|
668
|
return days;
|
669
|
}
|
670
|
}
|