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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 org.apache.commons.lang.StringUtils;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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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.OAIProvenance;
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import eu.dnetlib.data.proto.FieldTypeProtos.OAIProvenance.OriginDescription;
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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.PersonPersonProtos.PersonPerson;
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import eu.dnetlib.data.proto.PersonPersonProtos.PersonPerson.CoAuthorship;
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import eu.dnetlib.data.proto.PersonProtos.Person;
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import eu.dnetlib.data.proto.PersonProtos.Person.CoAuthor;
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import eu.dnetlib.data.proto.PersonResultProtos.PersonResult;
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import eu.dnetlib.data.proto.PersonResultProtos.PersonResult.Authorship;
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import eu.dnetlib.data.proto.RelMetadataProtos.RelMetadata;
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import eu.dnetlib.data.proto.RelTypeProtos.RelType;
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import eu.dnetlib.data.proto.RelTypeProtos.SubRelType;
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import eu.dnetlib.data.proto.ResultProjectProtos.ResultProject;
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import eu.dnetlib.data.proto.ResultProjectProtos.ResultProject.Outcome;
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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.ResultResultProtos.ResultResult;
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import eu.dnetlib.data.proto.ResultResultProtos.ResultResult.PublicationDataset;
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import eu.dnetlib.data.proto.TypeProtos.Type;
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public class DmfToHbaseXsltFunctions extends AbstractDNetOafXsltFunctions {
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private static final int MAX_COAUTHORS = 50;
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// dnet:oafPersonResultFromDMF($resultId, $oafPerson, position(), "sysimport:crosswalk:repository", "0.9")
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public static String oafPersonResult_Authorship_FromDMF(final String source,
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final String target,
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final int rank,
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final String relClass,
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final String provenanceAction,
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final String trust,
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final NodeList about) {
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try {
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final String eSource = OafRowKeyDecoder.decode(source).getKey();
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final String eTarget = OafRowKeyDecoder.decode(target).getKey();
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final Authorship.Builder auth = Authorship.newBuilder().setRanking("" + rank)
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.setRelMetadata(RelMetadata.newBuilder().setSemantics(getSimpleQualifier(relClass, "dnet:personroles")));
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final OafRel.Builder rel = getRel(eSource, eTarget, RelType.personResult, SubRelType.authorship, relClass, false).setPersonResult(
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PersonResult.newBuilder().setAuthorship(auth));
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return base64(getOaf(rel, getDataInfo(about, provenanceAction, trust, false, false)).toByteArray());
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} catch (final Throwable e) {
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System.err.println("source: " + source);
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System.err.println("target: " + target);
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System.err.println("provenanceAction: " + provenanceAction);
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System.err.println("trust: " + trust);
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System.err.println("rank: " + rank);
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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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// dnet:oafPersonPersonFromMDStore($personId, $coauthorId)
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public static String oafPersonPerson_CoAuthorship_FromDMF(final String source,
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final String target,
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final String relClass,
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final String provenanceAction,
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final String trust,
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final NodeList about) {
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try {
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final String eSource = OafRowKeyDecoder.decode(source).getKey();
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final String eTarget = OafRowKeyDecoder.decode(target).getKey();
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final PersonPerson.Builder pp = PersonPerson.newBuilder();
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final CoAuthorship.Builder coauth = CoAuthorship.newBuilder().setRelMetadata(
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RelMetadata.newBuilder().setSemantics(getSimpleQualifier(relClass, "dnet:personroles")));
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final OafRel.Builder rel = getRel(eSource, eTarget, RelType.personPerson, SubRelType.coauthorship, relClass, false).setPersonPerson(
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pp.setCoauthorship(coauth));
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return base64(getOaf(rel, getDataInfo(about, provenanceAction, trust, false, false)).toByteArray());
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} catch (final Throwable e) {
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System.err.println("source: " + source);
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System.err.println("target: " + target);
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System.err.println("provenanceAction: " + provenanceAction);
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System.err.println("trust: " + trust);
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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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// dnet:oafPersonFromDMF($personId, ., "sysimport:crosswalk:repository", "0.9")
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// collectedFromId, collectedFromName, originalId, dateOfCollection
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public static String oafPerson_FromDMF(final String personId,
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final String fullname,
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final NodeList authors,
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final String namespaceprefix,
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final String objIdentifier,
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final Map<String, Object> map,
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final String provenanceAction,
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final String trust,
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final NodeList about,
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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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try {
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final String entityId = OafRowKeyDecoder.decode(personId).getKey();
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final Person.Builder person = Person.newBuilder();
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final Person.Metadata.Builder metadata = getMetadata(fullname);
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if (authors != null) {
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for (int i = 0; (i < authors.getLength()) && (i < MAX_COAUTHORS); i++) {
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final Node node = authors.item(i);
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final String name = StringUtils.trim(node.getTextContent());
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if (!name.equals(fullname)) {
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final CoAuthor.Builder coAuthor = CoAuthor.newBuilder();
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coAuthor.setId(oafPersonId("person", namespaceprefix, objIdentifier, name, map));
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coAuthor.setMetadata(getMetadata(name));
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person.addCoauthor(coAuthor);
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}
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}
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}
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// metadata.setNationality(getSimpleQualifier("UNKNOWN", "dnet:countries"));
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final List<StructuredProperty> pids = Lists.newArrayList(getStructuredProperty(originalId, "oai", "oai", "dnet:pid_types", "dnet:pid_types"));
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final OafEntity.Builder entity = getEntity(Type.person, entityId, getKV(collectedFromId, collectedFromName), originalId, dateOfCollection, pids)
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.setPerson(person.setMetadata(metadata));
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final Oaf oaf = getOaf(entity, getDataInfo(about, provenanceAction, trust, false, false));
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return base64(oaf.toByteArray());
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} catch (final Throwable e) {
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System.err.println("personId: " + personId);
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System.err.println("fullname: " + fullname);
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System.err.println("provenanceAction: " + provenanceAction);
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System.err.println("trust: " + trust);
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System.err.println("collectedFromId: " + collectedFromId);
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System.err.println("collectedFromName: " + collectedFromName);
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System.err.println("originalId: " + originalId);
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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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private static Person.Metadata.Builder getMetadata(final String fullname) {
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final Person.Metadata.Builder metadata = Person.Metadata.newBuilder();
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metadata.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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metadata.setFirstname(sf(p.getNormalisedFirstName()));
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metadata.clearSecondnames().addSecondnames(sf(p.getNormalisedSurname()));
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// metadata.setFullname(sf(p.getNormalisedFullname()));
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}
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return metadata;
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}
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// dnet:oafResultProjectFromDMF($resultId, $projectId, "sysimport:crosswalk:repository", "0.9")
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public static String oafResultProject_Outcome_FromDMF(final String source,
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final String target,
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final String relClass,
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final String provenanceAction,
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final String trust,
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final NodeList about) {
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try {
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final String eSource = OafRowKeyDecoder.decode(source).getKey();
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final String eTarget = OafRowKeyDecoder.decode(target).getKey();
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final Outcome.Builder outcome = Outcome.newBuilder().setRelMetadata(
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RelMetadata.newBuilder().setSemantics(getSimpleQualifier(relClass, "dnet:result_project_relations")));
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final ResultProject.Builder rp = ResultProject.newBuilder().setOutcome(outcome);
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final OafRel.Builder rel = getRel(eSource, eTarget, RelType.resultProject, SubRelType.outcome, relClass, false).setResultProject(rp);
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195
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return base64(getOaf(rel, getDataInfo(about, provenanceAction, trust, false, false)).toByteArray());
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} catch (final Throwable e) {
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System.err.println("source: " + source);
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198
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System.err.println("target: " + target);
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System.err.println("provenanceAction: " + provenanceAction);
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200
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System.err.println("trust: " + trust);
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201
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202
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e.printStackTrace();
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203
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throw new RuntimeException(e);
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}
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}
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// dnet:oafResultProjectFromDMF($resultId, $projectId, "sysimport:crosswalk:repository", "0.9")
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public static String oafResultProject_Outcome_FromDMF(final String source,
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final String target,
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final String relClass,
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final String provenanceAction,
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final String trust) {
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return oafResultProject_Outcome_FromDMF(source, target, relClass, provenanceAction, trust, null);
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}
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215
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216
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public static String oafResultResult_PublicationDataset_FromDMF(final String source,
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final String target,
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218
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final String relClass,
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219
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final String provenanceAction,
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220
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final String trust) {
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221
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return oafResultResult_PublicationDataset_FromDMF(source, target, relClass, provenanceAction, trust, null);
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222
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}
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223
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224
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public static String oafResultResult_PublicationDataset_FromDMF(final String source,
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225
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final String target,
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226
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final String relClass,
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227
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final String provenanceAction,
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228
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final String trust,
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229
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final NodeList about) {
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230
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try {
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231
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final String eSource = OafRowKeyDecoder.decode(source).getKey();
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232
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final String eTarget = OafRowKeyDecoder.decode(target).getKey();
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233
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234
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final PublicationDataset.Builder pd = PublicationDataset.newBuilder().setRelMetadata(
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235
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RelMetadata.newBuilder().setSemantics(getSimpleQualifier(relClass, "dnet:result_result_relations")));
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236
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237
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final ResultResult.Builder rr = ResultResult.newBuilder().setPublicationDataset(pd);
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238
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239
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final OafRel.Builder rel = getRel(eSource, eTarget, RelType.resultResult, SubRelType.publicationDataset, relClass, false).setResultResult(rr);
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240
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241
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return base64(getOaf(rel, getDataInfo(about, provenanceAction, trust, false, false)).toByteArray());
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242
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} catch (final Throwable e) {
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243
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System.err.println("source: " + source);
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244
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System.err.println("target: " + target);
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245
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System.err.println("provenanceAction: " + provenanceAction);
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246
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System.err.println("trust: " + trust);
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247
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248
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e.printStackTrace();
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249
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throw new RuntimeException(e);
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250
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}
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251
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}
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252
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253
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public static String oafResult_FromDMF(final String resultId,
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254
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final String provenanceAction,
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255
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final String trust,
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256
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final NodeList about,
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257
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final String hostedbyId,
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258
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final String hostedbyName,
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259
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final String collectedFromId,
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260
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final String collectedFromName,
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261
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final String originalId,
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262
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final String dateOfCollection,
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263
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final NodeList nodelist) {
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264
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try {
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265
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final String entityId = OafRowKeyDecoder.decode(resultId).getKey();
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266
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267
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final Result.Builder result = Result.newBuilder();
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268
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269
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final ValueMap values = ValueMap.parseNodeList(nodelist);
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270
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271
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final Result.Metadata.Builder metadata = Result.Metadata.newBuilder();
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272
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final Descriptor mDesc = Result.Metadata.getDescriptor();
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273
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274
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if (values.get("creator") != null) {
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275
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for (final String fullname : Iterables.limit(values.get("creator").listValues(), 10)) {
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276
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277
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final Person.Metadata.Builder authorMetadata = Person.Metadata.newBuilder();
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278
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279
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authorMetadata.setFullname(sf(fullname));
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280
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281
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final eu.dnetlib.pace.model.Person p = new eu.dnetlib.pace.model.Person(fullname, false);
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282
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if (p.isAccurate()) {
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283
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authorMetadata.setFirstname(sf(p.getNormalisedFirstName()));
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284
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authorMetadata.clearSecondnames().addSecondnames(sf(p.getNormalisedSurname()));
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285
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authorMetadata.setFullname(sf(p.getNormalisedFullname()));
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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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result.addAuthor(Person.newBuilder().setMetadata(authorMetadata));
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289
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}
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|
290
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}
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291
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292
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addStructuredProps(metadata, mDesc.findFieldByName("subject"), values.get("subject").listValues(), "keyword", "dnet:result_subject");
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293
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addStructuredProps(metadata, mDesc.findFieldByName("title"), values.get("title").listValues(), "main title", "dnet:dataCite_title");
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294
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295
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for (final String fieldname : Lists.newArrayList("description", "source")) {
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296
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if (values.get(fieldname) != null) {
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297
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for (final String s : values.get(fieldname).listValues()) {
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298
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addField(metadata, mDesc.findFieldByName(fieldname), s);
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299
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}
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|
300
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}
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301
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}
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302
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303
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addField(metadata, mDesc.findFieldByName("language"), setQualifier(getDefaultQualifier("dnet:languages"), values.get("language").listValues()));
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304
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addField(metadata, mDesc.findFieldByName("dateofacceptance"), values.get("dateaccepted").listValues());
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305
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addField(metadata, mDesc.findFieldByName("publisher"), values.get("publisher").listValues());
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306
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addField(metadata, mDesc.findFieldByName("embargoenddate"), values.get("embargoenddate").listValues());
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307
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addField(metadata, mDesc.findFieldByName("storagedate"), values.get("storagedate").listValues());
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308
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309
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addField(metadata, mDesc.findFieldByName("resulttype"), getSimpleQualifier("publication", "dnet:result_typologies"));
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310
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311
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addField(metadata, mDesc.findFieldByName("fulltext"), values.get("fulltext").listValues());
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312
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addField(metadata, mDesc.findFieldByName("format"), values.get("format").listValues());
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313
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314
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// addField(metadata, Result.Metadata.getDescriptor().findFieldByName("provenanceaction"),
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315
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// getSimpleQualifier("sysimport:crosswalk:repository", "dnet:provenanceActions").build());
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316
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317
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if (values.get("concept") != null) {
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318
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for (final Element e : values.get("concept")) {
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319
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final String id = e.getAttributes().get("id");
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320
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if (StringUtils.isBlank(id)) throw new IllegalArgumentException("Context id cannot be blank");
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321
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metadata.addContext(Context.newBuilder().setId(id));
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322
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}
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|
323
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}
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324
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|
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325
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if (values.get("journal") != null) {
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326
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for (final Element e : values.get("journal")) {
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|
327
|
|
|
328
|
final Journal.Builder journal = Journal.newBuilder();
|
|
329
|
if (e.getText() != null) {
|
|
330
|
journal.setName(e.getText());
|
|
331
|
}
|
|
332
|
|
|
333
|
final Map<String, String> attr = e.getAttributes();
|
|
334
|
if (attr != null) {
|
|
335
|
if (attr.get("issn") != null) {
|
|
336
|
journal.setIssnPrinted(attr.get("issn"));
|
|
337
|
}
|
|
338
|
if (attr.get("eissn") != null) {
|
|
339
|
journal.setIssnOnline(attr.get("eissn"));
|
|
340
|
}
|
|
341
|
if (attr.get("lissn") != null) {
|
|
342
|
journal.setIssnLinking(attr.get("lissn"));
|
|
343
|
}
|
|
344
|
}
|
|
345
|
metadata.setJournal(journal.build());
|
|
346
|
}
|
|
347
|
}
|
|
348
|
|
|
349
|
final Instance.Builder instance = Instance.newBuilder().setHostedby(getKV(hostedbyId, hostedbyName));
|
|
350
|
|
|
351
|
addField(instance, Instance.getDescriptor().findFieldByName("licence"),
|
|
352
|
setQualifier(getDefaultQualifier("dnet:access_modes"), values.get("accessrights").listValues()));
|
|
353
|
addField(instance, Instance.getDescriptor().findFieldByName("instancetype"),
|
|
354
|
setQualifier(getDefaultQualifier("dnet:publication_resource"), values.get("cobjcategory").listValues()));
|
|
355
|
|
|
356
|
if (values.get("identifier") != null) {
|
|
357
|
addField(instance, Instance.getDescriptor().findFieldByName("url"),
|
|
358
|
Lists.newArrayList(Iterables.filter(values.get("identifier").listValues(), urlFilter)));
|
|
359
|
}
|
|
360
|
|
|
361
|
result.addInstance(instance);
|
|
362
|
|
|
363
|
final List<Element> extrefs = values.get("reference");
|
|
364
|
if (!extrefs.isEmpty()) {
|
|
365
|
final Descriptor extDesc = ExternalReference.getDescriptor();
|
|
366
|
for (final Element element : extrefs) {
|
|
367
|
final ExternalReference.Builder extref = ExternalReference.newBuilder();
|
|
368
|
addField(extref, extDesc.findFieldByName("url"), element.getText());
|
|
369
|
addField(extref, extDesc.findFieldByName("sitename"), element.getAttributes().get("source"));
|
|
370
|
addField(extref, extDesc.findFieldByName("refidentifier"), element.getAttributes().get("identifier"));
|
|
371
|
addField(extref, extDesc.findFieldByName("label"), element.getAttributes().get("title"));
|
|
372
|
addField(extref, extDesc.findFieldByName("query"), element.getAttributes().get("query"));
|
|
373
|
addField(extref, extDesc.findFieldByName("qualifier"),
|
|
374
|
setQualifier(getDefaultQualifier("dnet:externalReference_typologies"), Lists.newArrayList(element.getAttributes().get("type")))
|
|
375
|
.build());
|
|
376
|
|
|
377
|
result.addExternalReference(extref);
|
|
378
|
}
|
|
379
|
}
|
|
380
|
|
|
381
|
final List<StructuredProperty> pids = Lists.newArrayList();
|
|
382
|
pids.addAll(parsePids(nodelist));
|
|
383
|
pids.add(getStructuredProperty(originalId, "oai", getClassName("oai"), "dnet:pid_types", "dnet:pid_types"));
|
|
384
|
|
|
385
|
final OafEntity.Builder entity = getEntity(Type.result, entityId, getKV(collectedFromId, collectedFromName), originalId, dateOfCollection, pids)
|
|
386
|
.setResult(result.setMetadata(metadata));
|
|
387
|
|
|
388
|
entity.setOaiprovenance(getOAIProvenance(about));
|
|
389
|
|
|
390
|
final Oaf oaf = getOaf(entity, getDataInfo(about, provenanceAction, trust, false, false));
|
|
391
|
return base64(oaf.toByteArray());
|
|
392
|
} catch (final Throwable e) {
|
|
393
|
System.err.println("resultId: " + resultId);
|
|
394
|
System.err.println("hostedbyId: " + hostedbyId);
|
|
395
|
System.err.println("hostedbyName: " + hostedbyName);
|
|
396
|
System.err.println("provenanceAction: " + provenanceAction);
|
|
397
|
System.err.println("trust: " + trust);
|
|
398
|
System.err.println("collectedFromId: " + collectedFromId);
|
|
399
|
System.err.println("collectedFromName: " + collectedFromName);
|
|
400
|
System.err.println("originalId: " + originalId);
|
|
401
|
System.err.println("dateOfCollection: " + dateOfCollection);
|
|
402
|
e.printStackTrace();
|
|
403
|
throw new RuntimeException(e);
|
|
404
|
}
|
|
405
|
}
|
|
406
|
|
|
407
|
private static OAIProvenance getOAIProvenance(final NodeList about) {
|
|
408
|
|
|
409
|
OAIProvenance.Builder oaiProv = OAIProvenance.newBuilder();
|
|
410
|
|
|
411
|
if (((about != null) && (about.getLength() > 0))) {
|
|
412
|
|
|
413
|
final org.w3c.dom.Element provenance = getDirectChild((org.w3c.dom.Element) about.item(0), "provenance");
|
|
414
|
|
|
415
|
if (provenance != null) {
|
|
416
|
final org.w3c.dom.Element origDesc = getDirectChild(provenance, "originDescription");
|
|
417
|
oaiProv.setOriginDescription(buildOriginDescription(origDesc, OriginDescription.newBuilder()));
|
|
418
|
}
|
|
419
|
}
|
|
420
|
|
|
421
|
return oaiProv.build();
|
|
422
|
}
|
|
423
|
|
|
424
|
private static OriginDescription buildOriginDescription(final org.w3c.dom.Element origDesc, final OriginDescription.Builder od) {
|
|
425
|
od.setHarvestDate(origDesc.getAttribute("harvestDate")).setAltered(Boolean.valueOf(origDesc.getAttribute("altered")));
|
|
426
|
|
|
427
|
org.w3c.dom.Element elem = getDirectChild(origDesc, "baseURL");
|
|
428
|
od.setBaseURL(elem != null ? elem.getTextContent() : "");
|
|
429
|
|
|
430
|
elem = getDirectChild(origDesc, "identifier");
|
|
431
|
od.setIdentifier(elem != null ? elem.getTextContent() : "");
|
|
432
|
|
|
433
|
elem = getDirectChild(origDesc, "datestamp");
|
|
434
|
od.setDatestamp(elem != null ? elem.getTextContent() : "");
|
|
435
|
|
|
436
|
elem = getDirectChild(origDesc, "metadataNamespace");
|
|
437
|
od.setMetadataNamespace(elem != null ? elem.getTextContent() : "");
|
|
438
|
|
|
439
|
elem = getDirectChild(origDesc, "originDescription");
|
|
440
|
|
|
441
|
if (elem != null) {
|
|
442
|
|
|
443
|
od.setOriginDescription(buildOriginDescription(elem, OriginDescription.newBuilder()));
|
|
444
|
}
|
|
445
|
|
|
446
|
return od.build();
|
|
447
|
}
|
|
448
|
|
|
449
|
}
|