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package eu.dnetlib.data.transform.xml;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Maps;
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import com.google.common.collect.Sets;
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import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder;
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import eu.dnetlib.data.proto.FieldTypeProtos.Author;
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import eu.dnetlib.data.proto.FieldTypeProtos.KeyValue;
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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.ResultProtos.Result;
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import eu.dnetlib.data.proto.ResultProtos.Result.Context;
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import eu.dnetlib.data.proto.ResultProtos.Result.Instance;
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import eu.dnetlib.data.proto.ResultProtos.Result.Metadata.Builder;
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import eu.dnetlib.data.proto.TypeProtos.Type;
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import org.apache.commons.lang3.StringUtils;
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import org.w3c.dom.Element;
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import org.w3c.dom.NamedNodeMap;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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public class OdfToHbaseXsltFunctions extends CommonDNetXsltFunctions {
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private static Map<String, String> mappingAccess = Maps.newHashMap();
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static {
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mappingAccess.put("info:eu-repo/semantics/openAccess", "OPEN");
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mappingAccess.put("info:eu-repo/semantics/closedAccess", "CLOSED");
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mappingAccess.put("info:eu-repo/semantics/restrictedAccess", "RESTRICTED");
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mappingAccess.put("info:eu-repo/semantics/embargoedAccess", "EMBARGO");
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// Transformator now maps the access rights into proper values, not sure if it does for all datasets.
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mappingAccess.put("OPEN", "OPEN");
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mappingAccess.put("CLOSED", "CLOSED");
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mappingAccess.put("RESTRICTED", "RESTRICTED");
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mappingAccess.put("EMBARGO", "EMBARGO");
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mappingAccess.put("OPEN SOURCE", "OPEN SOURCE");
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}
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public static String odfResult(
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final String resultId,
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final boolean invisible,
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final NodeList about,
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final NodeList metadata,
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final NodeList titles,
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final NodeList creators,
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final NodeList subjects,
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final NodeList publisher,
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final NodeList descriptions,
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final NodeList dates,
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final NodeList dateaccepted,
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final NodeList resourceTypes,
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final NodeList formats,
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final NodeList sizes,
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final NodeList languages,
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final NodeList cobjcategory,
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final NodeList contributors,
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final NodeList rights,
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final NodeList license,
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final NodeList version,
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final NodeList pidList,
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final String provenance,
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final String trust,
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final NodeList hostedby,
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final NodeList collectedfrom,
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final NodeList originalIds,
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final String instanceUri,
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final String landingPage,
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final NodeList distributionlocation,
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final NodeList documentationUrl,
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final String dateOfCollection,
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final String dateOfTransformation) {
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try {
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final String entityId = OafRowKeyDecoder.decode(resultId).getKey();
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final Result.Builder result = Result.newBuilder();
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Result.Metadata.Builder metadataProto = Result.Metadata.newBuilder();
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// subject
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for (int i = 0; i < subjects.getLength(); i++) {
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Node currentNode = subjects.item(i);
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NodeList childNodes = currentNode.getChildNodes();
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if (childNodes.getLength() > 0) {
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String subjectValue = childNodes.item(0).getNodeValue();
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String schemeName = "keyword";
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String schemeURI ="keyword";
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if (currentNode.hasAttributes()) {
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NamedNodeMap attributes = currentNode.getAttributes();
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Node schemeNameNode = attributes.getNamedItem("subjectScheme");
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Node schemeURINode = attributes.getNamedItem("schemeURI");
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if(schemeNameNode != null) schemeName = schemeNameNode.getTextContent();
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if(schemeURINode != null) schemeURI = schemeURINode.getTextContent();
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if(schemeNameNode != null && schemeURINode == null) schemeURI = schemeName;
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if(schemeURINode != null && schemeNameNode == null) schemeName = schemeURI;
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}
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("subject"),
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getStructuredProperty(subjectValue, schemeURI, schemeName, "dnet:subject_classification_typologies", "dnet:subject_classification_typologies"));
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}
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}
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// title
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for (int i = 0; i < titles.getLength(); i++) {
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Node currentNode = titles.item(i);
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NodeList childNodes = currentNode.getChildNodes();
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if (childNodes.getLength() > 0) {
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String titleValue = childNodes.item(0).getNodeValue();
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String classname = "main title";
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String classid = "main title";
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if (currentNode.hasAttributes()) {
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NamedNodeMap attributes = currentNode.getAttributes();
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Node titleType = attributes.getNamedItem("titleType");
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if (titleType != null && titleType.getNodeValue().equals("AlternativeTitle")) {
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classname = "alternative title";
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classid = "alternative title";
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}
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if (titleType != null && titleType.getNodeValue().equals("Subtitle")) {
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classname = "subtitle";
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classid = "subtitle";
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}
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if (titleType != null && titleType.getNodeValue().equals("TranslatedTitle")) {
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classname = "translated title";
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classid = "translated title";
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}
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}
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("title"),
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getStructuredProperty(titleValue, classname, classid, "dnet:dataCite_title", "dnet:dataCite_title"));
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}
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}
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// creators
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for (int i = 0; i < creators.getLength(); i++) {
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final Element creator = (Element) creators.item(i);
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if (creator != null && creator.hasChildNodes()) {
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final NodeList creatorNames = creator.getElementsByTagName("creatorName");
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if (creatorNames.getLength() > 0) {
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createAuthor(metadataProto, i, creator, creatorNames);
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} else{
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//handle authors with namespaceprefix
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final NodeList creatorNamesNs = creator.getElementsByTagNameNS("http://datacite.org/schema/kernel-4", "creatorName");
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if (creatorNamesNs.getLength() > 0) {
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createAuthor(metadataProto, i, creator, creatorNamesNs);
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}
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}
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}
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}
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// description
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for (int i = 0; i < descriptions.getLength(); i++) {
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Element currentNode = (Element) descriptions.item(i);
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if (currentNode != null && currentNode.hasChildNodes()) {
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String descriptionValue = currentNode.getChildNodes().item(0).getNodeValue();
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final String descriptionType = currentNode.getAttribute("descriptionType");
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if (StringUtils.isNotBlank(descriptionType)) {
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switch (descriptionType) {
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case "TechnicalInfo":
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("tool"), descriptionValue);
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break;
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case "Abstract":
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("description"), descriptionValue);
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break;
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case "DistributionForm":
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("format"), descriptionValue);
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break;
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}
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} else {
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("description"), descriptionValue);
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}
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}
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}
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// contributors
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for (int i = 0; i < contributors.getLength(); i++) {
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final Element contributor = (Element) contributors.item(i);
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if (contributor != null && contributor.hasChildNodes()) {
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NodeList contributorNames = contributor.getElementsByTagName("contributorName");
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if (contributorNames != null) {
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Element contributorName = (Element) contributorNames.item(0);
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if (contributorName != null) {
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final String contributorValue = contributorName.getTextContent();
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final String contributorType = contributor.getAttribute("contributorType");
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if (StringUtils.isNotBlank(contributorType)) {
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switch (contributorType) {
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case "ContactPerson":
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("contactperson"), contributorValue);
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break;
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case "ContactGroup":
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("contactgroup"), contributorValue);
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break;
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}
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} else {
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("contributor"), contributorValue);
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}
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}
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}
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}
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}
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// publisher
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("publisher"), getFirstItem(publisher));
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216
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// dates
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for (int i = 0; i < dates.getLength(); i++) {
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Node currentNode = dates.item(i);
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if (currentNode != null && currentNode.hasAttributes() && currentNode.hasChildNodes()) {
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final NamedNodeMap attributes = currentNode.getAttributes();
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final Node dateType = attributes.getNamedItem("dateType") == null ? attributes.getNamedItem("datetype") : null;
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if (dateType != null) {
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String dateAttribute = dateType.getNodeValue();
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String dateValue = currentNode.getChildNodes().item(0).getNodeValue();
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String protoAttribute = "relevantdate";
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if ("Accepted".equals(dateAttribute)) {
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protoAttribute = "dateofacceptance";
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} else if ("Issued".equals(dateAttribute)) {
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protoAttribute = "storagedate";
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} else if ("Updated".equals(dateAttribute)) {
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protoAttribute = "lastmetadataupdate";
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} else if ("Available".equals(dateAttribute)) {
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protoAttribute = "embargoenddate";
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}
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239
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if (protoAttribute.equals("relevantdate") == false) {
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName(protoAttribute), dateValue);
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} else {
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242
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName(protoAttribute),
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getStructuredProperty(dateValue, "UNKNOWN", "UNKNOWN", "dnet:dataCite_date", "dnet:dataCite_date"));
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}
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245
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}
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246
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}
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247
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}
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248
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249
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//license
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250
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("license"), getFirstItem(license));
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251
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// dateofacceptance
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("dateofacceptance"), getFirstItem(dateaccepted));
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253
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254
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// size
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255
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("size"), getFirstItem(sizes));
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256
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257
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// version
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258
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("version"), getFirstItem(version));
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259
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260
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// language
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261
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("language"),
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262
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setQualifier(getDefaultQualifier("dnet:languages"), Lists.newArrayList(getFirstItem(languages))));
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263
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264
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// resource type
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265
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("resourcetype"),
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266
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setQualifier(getDefaultQualifier("dnet:dataCite_resource"), Lists.newArrayList(getFirstItem(resourceTypes))));
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267
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268
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// resultType
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269
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final String cobjcategoryCode = getFirstItem(cobjcategory);
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270
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final String resulttype = getResultType(cobjcategory);
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271
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("resulttype"), getSimpleQualifier(resulttype, "dnet:result_typologies"));
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272
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273
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switch (resulttype) {
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274
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case "software" :
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275
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// format
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276
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("programmingLanguage"),
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277
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getSimpleQualifier(getFirstItem(formats), "dnet:programming_languages"));
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278
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break;
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279
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case "dataset":
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280
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for (int i = 0; i < formats.getLength(); i++) {
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281
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Node currentNode = formats.item(i);
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282
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NodeList childNodes = currentNode.getChildNodes();
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283
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if (childNodes.getLength() > 0) {
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284
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String formatValue = childNodes.item(0).getNodeValue();
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285
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("format"), formatValue);
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286
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}
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287
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}
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288
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break;
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289
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case "other":
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290
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291
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break;
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292
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}
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293
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294
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// documentationUrl
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295
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for (int i = 0; i < documentationUrl.getLength(); i++) {
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296
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final Element docUrl = (Element) documentationUrl.item(i);
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297
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if (docUrl != null && docUrl.hasChildNodes()) {
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298
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final String value = docUrl.getTextContent();
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299
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if (StringUtils.isNotBlank(value)) {
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300
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addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("documentationUrl"), value);
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301
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}
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302
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}
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303
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}
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304
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305
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ValueMap values = ValueMap.parseNodeList(metadata);
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306
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// contexts
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307
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if (values.get("concept") != null) {
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308
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for (final eu.dnetlib.data.transform.xml.Element e : values.get("concept")) {
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309
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final String id = e.getAttributes().get("id");
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310
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if (StringUtils.isBlank(id)) throw new IllegalArgumentException("Context id cannot be blank");
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311
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metadataProto.addContext(Context.newBuilder().setId(id));
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312
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}
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313
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}
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314
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315
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//journal
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316
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if (values.containsKey("journal")) {
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317
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for (final eu.dnetlib.data.transform.xml.Element journal : values.get("journal")) {
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318
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addJournal(metadataProto, journal);
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319
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|
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320
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}
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321
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}
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322
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323
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final List<KeyValue> hostedBys = getKeyValues(ValueMap.parseNodeList(hostedby), "hostedby", Type.datasource);
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324
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final List<KeyValue> collectedFroms = getKeyValues(ValueMap.parseNodeList(collectedfrom), "collectedfrom", Type.datasource);
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325
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326
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final Instance.Builder instance = Instance.newBuilder();
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327
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328
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String tmpRigths = "UNKNOWN";
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329
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final String firstRight = getFirstItem(rights);
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330
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if (mappingAccess.containsKey(firstRight)) {
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331
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tmpRigths = mappingAccess.get(firstRight);
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332
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}
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333
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334
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addField(instance, Instance.getDescriptor().findFieldByName("license"), getFirstItem(license));
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335
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addField(instance, Instance.getDescriptor().findFieldByName("hostedby"), hostedBys);
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336
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337
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addField(instance, Instance.getDescriptor().findFieldByName("accessright"),
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338
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setQualifier(getDefaultQualifier("dnet:access_modes"), Lists.newArrayList(tmpRigths)));
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339
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340
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addField(instance, Instance.getDescriptor().findFieldByName("instancetype"),
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341
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setQualifier(getDefaultQualifier("dnet:dataCite_resource"), Lists.newArrayList(cobjcategoryCode)));
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|
342
|
|
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343
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if (StringUtils.isNotBlank(landingPage)) {
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344
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addField(instance, Instance.getDescriptor().findFieldByName("url"), landingPage);
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345
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}
|
|
346
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//sometimes the instanceUri is blank...
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347
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if (StringUtils.isNotBlank(instanceUri)) {
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348
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addField(instance, Instance.getDescriptor().findFieldByName("url"), instanceUri);
|
|
349
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}
|
|
350
|
|
|
351
|
addField(instance, Instance.getDescriptor().findFieldByName("distributionlocation"), getFirstItem(distributionlocation));
|
|
352
|
|
|
353
|
addField(instance, Instance.getDescriptor().findFieldByName("collectedfrom"), collectedFroms);
|
|
354
|
addField(instance, Instance.getDescriptor().findFieldByName("dateofacceptance"), getFirstItem(dateaccepted));
|
|
355
|
if (values.get("refereed") != null) {
|
|
356
|
addField(instance, Instance.getDescriptor().findFieldByName("refereed"), values.get("refereed").listValues());
|
|
357
|
}
|
|
358
|
|
|
359
|
result.addInstance(instance);
|
|
360
|
|
|
361
|
List<StructuredProperty> pids = parsePids(pidList);
|
|
362
|
|
|
363
|
// original ids
|
|
364
|
final Set<String> originalIdList = Sets.newHashSet();
|
|
365
|
for (int i = 0; i < originalIds.getLength(); i++) {
|
|
366
|
Node currentNode = originalIds.item(i);
|
|
367
|
if (currentNode != null && currentNode.hasChildNodes()) {
|
|
368
|
originalIdList.add(currentNode.getChildNodes().item(0).getNodeValue());
|
|
369
|
}
|
|
370
|
}
|
|
371
|
|
|
372
|
OafEntity.Builder entity =
|
|
373
|
getEntity(Type.result, entityId, collectedFroms, originalIdList, dateOfCollection, dateOfTransformation, pids).setResult(
|
|
374
|
result.setMetadata(metadataProto));
|
|
375
|
|
|
376
|
entity.setOaiprovenance(getOAIProvenance(about));
|
|
377
|
|
|
378
|
Oaf oaf = getOaf(entity, getDataInfo(invisible, about, provenance, trust, false, false));
|
|
379
|
return base64(oaf.toByteArray());
|
|
380
|
} catch (Exception e) {
|
|
381
|
e.printStackTrace(System.err);
|
|
382
|
throw new RuntimeException(e);
|
|
383
|
}
|
|
384
|
|
|
385
|
}
|
|
386
|
|
|
387
|
private static void createAuthor(final Builder metadataProto, final int i, final Element creator, final NodeList creatorNames) {
|
|
388
|
final Element creatorName = (Element) creatorNames.item(0);
|
|
389
|
|
|
390
|
final Author.Builder author = Author.newBuilder();
|
|
391
|
author.setRank(i+1);
|
|
392
|
final String fullname = StringUtils.trim(creatorName.getTextContent());
|
|
393
|
|
|
394
|
author.setFullname(fullname);
|
|
395
|
|
|
396
|
final eu.dnetlib.pace.model.Person p = new eu.dnetlib.pace.model.Person(fullname, false);
|
|
397
|
if (p.isAccurate()) {
|
|
398
|
author.setName(p.getNormalisedFirstName());
|
|
399
|
author.setSurname(p.getNormalisedSurname());
|
|
400
|
}
|
|
401
|
final NodeList nameIdentifiers = creator.getElementsByTagName("nameIdentifier");
|
|
402
|
if (nameIdentifiers.getLength() > 0) {
|
|
403
|
final Element nameIdentifier = (Element) nameIdentifiers.item(0);
|
|
404
|
final String nameIdentifierScheme = nameIdentifier.getAttribute("nameIdentifierScheme");
|
|
405
|
final String id = StringUtils.trim(nameIdentifier.getTextContent());
|
|
406
|
if (StringUtils.isNotBlank(id) && StringUtils.isNotBlank(nameIdentifierScheme)) {
|
|
407
|
author.addPid(getKV(nameIdentifierScheme, id));
|
|
408
|
}
|
|
409
|
}
|
|
410
|
|
|
411
|
addField(metadataProto, Result.Metadata.getDescriptor().findFieldByName("author"), author);
|
|
412
|
}
|
|
413
|
|
|
414
|
private static String getResultType(final NodeList cobjcategoryNode) {
|
|
415
|
|
|
416
|
final ValueMap values = ValueMap.parseNodeList(cobjcategoryNode);
|
|
417
|
|
|
418
|
final eu.dnetlib.data.transform.xml.Element cobjcategory = values.get("cobjcategory").stream()
|
|
419
|
.map(e -> StringUtils.isNotBlank(e.getText()) ? e : new eu.dnetlib.data.transform.xml.Element("0000", e.getAttributes()))
|
|
420
|
.findFirst()
|
|
421
|
.orElse(new eu.dnetlib.data.transform.xml.Element("0000", new HashMap<>()));
|
|
422
|
|
|
423
|
final String resulttype = cobjcategory.getAttributeValue("type");
|
|
424
|
if (StringUtils.isNotBlank(resulttype)) {
|
|
425
|
return resulttype;
|
|
426
|
}
|
|
427
|
|
|
428
|
return getDefaultResulttype(cobjcategory);
|
|
429
|
}
|
|
430
|
|
|
431
|
public static String getFirstItem(final NodeList list) {
|
|
432
|
String out = "";
|
|
433
|
if (list != null) {
|
|
434
|
|
|
435
|
if (list.getLength() > 0 && list.item(0).getChildNodes() != null && list.item(0).getChildNodes().getLength() > 0) {
|
|
436
|
out = list.item(0).getChildNodes().item(0).getNodeValue();
|
|
437
|
}
|
|
438
|
}
|
|
439
|
return out;
|
|
440
|
}
|
|
441
|
|
|
442
|
}
|