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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 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.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.ExternalReference;
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import eu.dnetlib.data.proto.ResultProtos.Result.Instance;
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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.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 boolean invisible,
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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 originalId,
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final String dateOfCollection,
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final String dateOfTransformation,
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final NodeList metadata) {
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ValueMap values = null;
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try {
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final String entityId = OafRowKeyDecoder.decode(resultId).getKey();
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values = ValueMap.parseNodeList(metadata);
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final Descriptor mDesc = Result.Metadata.getDescriptor();
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final List<KeyValue> collectedFrom = getKeyValues(values, "collectedfrom", Type.datasource);
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final List<KeyValue> hostedBy = getKeyValues(values, "hostedby", Type.datasource);
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final Result.Metadata.Builder metadataBuilder = buildMetadata(values, mDesc);
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final Result.Builder result = buildResult(metadataBuilder, values, collectedFrom, hostedBy);
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final OafEntity.Builder entity = buildOafEntity(result, entityId, metadata, collectedFrom, 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(invisible, 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, values);
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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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ValueMap values = null;
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try {
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final String entityId = OafRowKeyDecoder.decode(resultId).getKey();
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values = ValueMap.parseNodeList(nodelist);
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final List<KeyValue> hostedBy = getKeyValues(values, "hostedby", Type.datasource);
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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, null, hostedBy);
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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, values);
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}
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return null;
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}
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private static OafEntity.Builder buildOafEntity(
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final Result.Builder result,
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final String entityId,
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final NodeList nodelist,
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final List<KeyValue> collectedFrom,
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final 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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if (values.get("creator") != null) {
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for (final Element e : values.get("creator")) {
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final Author.Builder author = Author.newBuilder();
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final String fullname = e.getText();
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author.setFullname(fullname);
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author.setRank(Integer.valueOf(e.getAttributeValue(ValueMap.IDX_ATTRIBUTE)));
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final String nameIdentifier = e.getAttributeValue("nameIdentifier");
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final String nameIdentifierScheme = e.getAttributeValue("nameIdentifierScheme");
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if (StringUtils.isNotBlank(nameIdentifier) && StringUtils.isNotBlank(nameIdentifierScheme)) {
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author.addPid(getKV(nameIdentifierScheme, nameIdentifier));
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}
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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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author.setName(p.getNormalisedFirstName());
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author.setSurname(p.getNormalisedSurname());
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}
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metadata.addAuthor(author);
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}
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}
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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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String resulttype = getResultType(values);
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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.isNotBlank(id)) {
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metadata.addContext(Context.newBuilder().setId(id));
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}
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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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addJournal(metadata, e);
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}
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}
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return metadata;
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}
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private static String getResultType(final ValueMap values) {
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final Element cobjcategory = values.get("cobjcategory").stream()
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.map(e -> StringUtils.isNotBlank(e.getText()) ? e : new Element("0000", e.getAttributes()))
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.findFirst()
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.orElse(new Element("0000", new HashMap<>()));
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final String resulttype = cobjcategory.getAttributeValue("type");
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if (StringUtils.isNotBlank(resulttype)) {
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return resulttype;
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}
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return getDefaultResulttype(cobjcategory);
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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 List<KeyValue> collectedFrom,
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final List<KeyValue> hostedBy) {
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final Result.Builder result = Result.newBuilder();
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final Instance.Builder instance = Instance.newBuilder();
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addField(instance, Instance.getDescriptor().findFieldByName("license"), values.get("license").listValues());
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addField(instance, Instance.getDescriptor().findFieldByName("accessright"),
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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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addField(instance, Instance.getDescriptor().findFieldByName("hostedby"), hostedBy);
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addField(instance, Instance.getDescriptor().findFieldByName("collectedfrom"), collectedFrom);
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addField(instance, Instance.getDescriptor().findFieldByName("dateofacceptance"), values.get("dateaccepted").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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if (values.get("refereed") != null) {
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addField(instance, Instance.getDescriptor().findFieldByName("refereed"), values.get("refereed").listValues());
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}
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final ElementList pcs = values.get("processingchargeamount");
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if (pcs != null && !pcs.isEmpty()) {
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addField(instance, Instance.getDescriptor().findFieldByName("processingchargeamount"), pcs.listValues());
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final String currency = pcs.get(0).getAttributeValue("currency");
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if (StringUtils.isNotBlank(currency)) {
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addField(instance, Instance.getDescriptor().findFieldByName("processingchargecurrency"), currency);
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}
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}
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// #4468: processingchargeamount - implementatio to clarify: result vs instance. Single value vs repeatable
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// if (values.get("processingchargeamount") != null) {
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// ElementList processingchargeamount = values.get("processingchargeamount");
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// for(Element pc : processingchargeamount) {
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// addField(instance, Instance.getDescriptor().findFieldByName("processingchargeamount"), pc.getText());
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// addField(instance, Instance.getDescriptor().findFieldByName("processingchargecurrency"), pc.getAttributeValue("processingchargecurrency"));
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// }
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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 ValueMap values) {
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System.err.println("resultId: " + resultId);
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if (values != null) {
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System.err.println("values: " + values);
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}
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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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