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package eu.dnetlib.data.transform.xml;
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import java.util.List;
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import java.util.Map;
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import com.google.common.collect.Iterables;
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import com.google.common.collect.Lists;
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import com.google.protobuf.Descriptors.Descriptor;
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import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder;
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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.PersonProtos.Person;
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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.ExternalReference;
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import eu.dnetlib.data.proto.ResultProtos.Result.Instance;
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import eu.dnetlib.data.proto.ResultProtos.Result.Journal;
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import eu.dnetlib.data.proto.TypeProtos.Type;
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import org.apache.commons.lang.StringUtils;
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import org.w3c.dom.NodeList;
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public class OafToHbaseXsltFunctions extends CommonDNetXsltFunctions {
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public static String oafResult(
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final String resultId,
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final String provenance,
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final String trust,
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final NodeList about,
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final String hostedbyId,
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final String hostedbyName,
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final String collectedFromId,
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final String collectedFromName,
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final String originalId,
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final String dateOfCollection,
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final String dateOfTransformation,
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final NodeList nodelist) {
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try {
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final String entityId = OafRowKeyDecoder.decode(resultId).getKey();
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final ValueMap values = ValueMap.parseNodeList(nodelist);
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final Descriptor mDesc = Result.Metadata.getDescriptor();
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final Result.Metadata.Builder metadata = buildMetadata(values, mDesc);
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final Result.Builder result = buildResult(metadata, values, mDesc, hostedbyId, hostedbyName);
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final OafEntity.Builder entity = buildOafEntity(result, entityId, nodelist, getKV(collectedFromId, collectedFromName), originalId);
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entity.setDateofcollection(dateOfCollection)
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.setDateoftransformation(dateOfTransformation).setOaiprovenance(getOAIProvenance(about));
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final Oaf oaf = getOaf(entity, getDataInfo(about, provenance, trust, false, false));
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return base64(oaf.toByteArray());
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} catch (final Throwable e) {
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handleException(e, resultId, hostedbyId, hostedbyName, provenance, trust, collectedFromId, collectedFromName, originalId, dateOfCollection);
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}
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return null;
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}
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public static String oafResultUpdate(final String resultId,
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final String provenance,
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final String trust,
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final NodeList nodelist,
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final String hostedbyId,
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final String hostedbyName) {
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try {
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final String entityId = OafRowKeyDecoder.decode(resultId).getKey();
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final ValueMap values = ValueMap.parseNodeList(nodelist);
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final Descriptor mDesc = Result.Metadata.getDescriptor();
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final Result.Metadata.Builder metadata = buildMetadata(values, mDesc);
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final Result.Builder result = buildResult(metadata, values, mDesc, hostedbyId, hostedbyName);
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final OafEntity.Builder entity = buildOafEntity(result, entityId, nodelist, null, null);
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final Oaf oaf = getOaf(entity, null);
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return base64(oaf.toByteArray());
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} catch (final Throwable e) {
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handleException(e, resultId, hostedbyId, hostedbyName, provenance, trust, null, null, null, null);
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}
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return null;
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}
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private static OafEntity.Builder buildOafEntity(final Result.Builder result,
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final String entityId,
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final NodeList nodelist,
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KeyValue collectedFrom,
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String originalId) {
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final List<StructuredProperty> pids = Lists.newArrayList();
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pids.addAll(parsePids(nodelist));
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final OafEntity.Builder entity =
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getEntity(Type.result, entityId, collectedFrom, StringUtils.isBlank(originalId) ? null : Lists.newArrayList(originalId), null, null, pids)
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.setResult(result);
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return entity;
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}
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private static Result.Metadata.Builder buildMetadata(final ValueMap values, final Descriptor mDesc) {
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final Result.Metadata.Builder metadata = Result.Metadata.newBuilder();
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addStructuredProps(metadata, mDesc.findFieldByName("subject"), values.get("subject"), "keyword", "dnet:subject_classification_typologies");
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addStructuredProps(metadata, mDesc.findFieldByName("title"), values.get("title"), "main title", "dnet:dataCite_title");
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for (final String fieldname : Lists.newArrayList("description", "source", "contributor")) {
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if (values.get(fieldname) != null) {
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for (final String s : values.get(fieldname).listValues()) {
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addField(metadata, mDesc.findFieldByName(fieldname), s);
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}
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}
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}
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addField(metadata, mDesc.findFieldByName("language"), setQualifier(getDefaultQualifier("dnet:languages"), values.get("language").listValues()));
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addField(metadata, mDesc.findFieldByName("dateofacceptance"), values.get("dateaccepted").listValues());
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addField(metadata, mDesc.findFieldByName("publisher"), values.get("publisher").listValues());
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addField(metadata, mDesc.findFieldByName("embargoenddate"), values.get("embargoenddate").listValues());
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addField(metadata, mDesc.findFieldByName("storagedate"), values.get("storagedate").listValues());
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final String cobjcategoryCode = values.get("cobjcategory").stream()
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.map(e -> e.getText())
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.map(s -> s != null && !s.isEmpty() ? s : "0000")
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.findFirst()
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.orElse("0000");
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String resulttype = "";
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switch (cobjcategoryCode) {
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// add here the code to be excluded from the default mapping as 'publication'
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/*
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case "0029":
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resulttype = "software";
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break;
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*/
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case "0021":
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resulttype = "dataset";
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break;
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default:
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resulttype = "publication";
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}
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addField(metadata, mDesc.findFieldByName("resulttype"), getSimpleQualifier(resulttype, "dnet:result_typologies"));
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addField(metadata, mDesc.findFieldByName("fulltext"), values.get("fulltext").listValues());
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addField(metadata, mDesc.findFieldByName("format"), values.get("format").listValues());
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if (values.get("concept") != null) {
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for (final Element e : values.get("concept")) {
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final String id = e.getAttributes().get("id");
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if (StringUtils.isBlank(id)) throw new IllegalArgumentException("Context id cannot be blank");
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metadata.addContext(Context.newBuilder().setId(id));
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}
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}
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if (values.get("journal") != null) {
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for (final Element e : values.get("journal")) {
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final Journal.Builder journal = Journal.newBuilder();
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if (e.getText() != null) {
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journal.setName(e.getText());
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}
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final Map<String, String> attr = e.getAttributes();
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if (attr != null) {
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if (attr.get("issn") != null) {
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journal.setIssnPrinted(attr.get("issn"));
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}
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if (attr.get("eissn") != null) {
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journal.setIssnOnline(attr.get("eissn"));
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}
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if (attr.get("lissn") != null) {
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journal.setIssnLinking(attr.get("lissn"));
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}
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}
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metadata.setJournal(journal.build());
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}
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}
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return metadata;
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}
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private static Result.Builder buildResult(final Result.Metadata.Builder metadata,
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final ValueMap values,
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final Descriptor mDesc,
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final String hostedbyId,
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final String hostedbyName) {
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final Result.Builder result = Result.newBuilder();
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if (values.get("creator") != null) {
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for (final String fullname : Iterables.limit(values.get("creator").listValues(), 10)) {
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final Person.Metadata.Builder authorMetadata = Person.Metadata.newBuilder();
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authorMetadata.setFullname(sf(fullname));
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final eu.dnetlib.pace.model.Person p = new eu.dnetlib.pace.model.Person(fullname, false);
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if (p.isAccurate()) {
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authorMetadata.setFirstname(sf(p.getNormalisedFirstName()));
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authorMetadata.clearSecondnames().addSecondnames(sf(p.getNormalisedSurname()));
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authorMetadata.setFullname(sf(p.getNormalisedFullname()));
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}
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result.addAuthor(Person.newBuilder().setMetadata(authorMetadata));
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}
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}
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final Instance.Builder instance = Instance.newBuilder().setHostedby(getKV(hostedbyId, hostedbyName));
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addField(instance, Instance.getDescriptor().findFieldByName("licence"),
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setQualifier(getDefaultQualifier("dnet:access_modes"), values.get("accessrights").listValues()));
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addField(instance, Instance.getDescriptor().findFieldByName("instancetype"),
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setQualifier(getDefaultQualifier("dnet:publication_resource"), values.get("cobjcategory").listValues()));
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if (values.get("identifier") != null) {
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addField(instance, Instance.getDescriptor().findFieldByName("url"),
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Lists.newArrayList(Iterables.filter(values.get("identifier").listValues(), urlFilter)));
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}
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result.addInstance(instance);
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final List<Element> extrefs = values.get("reference");
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if (!extrefs.isEmpty()) {
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final Descriptor extDesc = ExternalReference.getDescriptor();
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for (final Element element : extrefs) {
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final ExternalReference.Builder extref = ExternalReference.newBuilder();
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addField(extref, extDesc.findFieldByName("url"), element.getText());
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addField(extref, extDesc.findFieldByName("sitename"), element.getAttributes().get("source"));
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addField(extref, extDesc.findFieldByName("refidentifier"), element.getAttributes().get("identifier"));
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addField(extref, extDesc.findFieldByName("label"), element.getAttributes().get("title"));
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addField(extref, extDesc.findFieldByName("query"), element.getAttributes().get("query"));
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addField(extref, extDesc.findFieldByName("qualifier"),
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setQualifier(getDefaultQualifier("dnet:externalReference_typologies"), Lists.newArrayList(element.getAttributes().get("type")))
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.build());
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result.addExternalReference(extref);
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}
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}
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return result.setMetadata(metadata);
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}
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private static void handleException(Throwable e, final String resultId, final String hostedbyId, final String hostedbyName,
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final String provenance, final String trust, final String collectedFromId, final String collectedFromName,
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final String originalId, final String dateOfCollection) {
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System.err.println("resultId: " + resultId);
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if (StringUtils.isNotBlank(hostedbyId)) System.err.println("hostedbyId: " + hostedbyId);
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if (StringUtils.isNotBlank(hostedbyName)) System.err.println("hostedbyName: " + hostedbyName);
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if (StringUtils.isNotBlank(provenance)) System.err.println("provenance: " + provenance);
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if (StringUtils.isNotBlank(trust)) System.err.println("trust: " + trust);
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if (StringUtils.isNotBlank(collectedFromId)) System.err.println("collectedFromId: " + collectedFromId);
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if (StringUtils.isNotBlank(collectedFromName)) System.err.println("collectedFromName: " + collectedFromName);
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if (StringUtils.isNotBlank(originalId)) System.err.println("originalId: " + originalId);
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if (StringUtils.isNotBlank(dateOfCollection)) System.err.println("dateOfCollection: " + dateOfCollection);
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e.printStackTrace();
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throw new RuntimeException(e);
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}
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}
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