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package eu.dnetlib.data.transform.xml;
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import java.util.List;
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import com.google.common.collect.Lists;
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import com.google.protobuf.Descriptors.FieldDescriptor;
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import com.google.protobuf.Message.Builder;
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import eu.dnetlib.data.mapreduce.util.OafRowKeyDecoder;
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import eu.dnetlib.data.proto.DatasourceOrganizationProtos.DatasourceOrganization;
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import eu.dnetlib.data.proto.DatasourceOrganizationProtos.DatasourceOrganization.Provision;
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import eu.dnetlib.data.proto.DatasourceProtos.Datasource;
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import eu.dnetlib.data.proto.FieldTypeProtos.DataInfo;
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import eu.dnetlib.data.proto.FieldTypeProtos.KeyValue;
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import eu.dnetlib.data.proto.OafProtos.Oaf;
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import eu.dnetlib.data.proto.OafProtos.OafEntity;
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import eu.dnetlib.data.proto.OafProtos.OafRel;
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import eu.dnetlib.data.proto.OrganizationProtos.Organization;
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import eu.dnetlib.data.proto.PersonProtos.Person;
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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.ProjectOrganizationProtos.ProjectOrganization;
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import eu.dnetlib.data.proto.ProjectOrganizationProtos.ProjectOrganization.Participation;
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import eu.dnetlib.data.proto.ProjectPersonProtos.ProjectPerson;
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import eu.dnetlib.data.proto.ProjectPersonProtos.ProjectPerson.ContactPerson;
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import eu.dnetlib.data.proto.ProjectProtos.Project;
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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.ResultOrganizationProtos.ResultOrganization;
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import eu.dnetlib.data.proto.ResultOrganizationProtos.ResultOrganization.Affiliation;
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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.Instance;
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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.Node;
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import org.w3c.dom.NodeList;
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public class DbmfToHbaseXsltFunctions extends CommonDNetXsltFunctions {
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public static String oafEntity(final String type,
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final String id,
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final String collectedFromId,
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final String collectedFromName,
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final NodeList identities,
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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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final String entityId = OafRowKeyDecoder.decode(id).getKey();
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List<String> ids = Lists.newArrayList();
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for(int i = 0; i < identities.getLength(); i++){
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Node n = identities.item(i);
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String s = n.getTextContent();
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ids.add(s);
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}
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switch (Type.valueOf(type)) {
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case datasource:
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return serializeOafEntity(nodeList, Type.datasource, entityId, getKV(collectedFromId, collectedFromName), ids, dateOfCollection,
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dateOfTransformation, Datasource.newBuilder());
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case organization:
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return serializeOafEntity(nodeList, Type.organization, entityId, getKV(collectedFromId, collectedFromName), ids, dateOfCollection,
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dateOfTransformation, Organization.newBuilder());
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case person:
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return serializeOafEntity(nodeList, Type.person, entityId, getKV(collectedFromId, collectedFromName), ids, dateOfCollection,
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dateOfTransformation, Person.newBuilder());
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case project:
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return serializeOafEntity(nodeList, Type.project, entityId, getKV(collectedFromId, collectedFromName), ids, dateOfCollection,
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dateOfTransformation, Project.newBuilder());
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case result:
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return serializeOafEntity(nodeList, Type.result, entityId, getKV(collectedFromId, collectedFromName), ids, dateOfCollection,
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dateOfTransformation ,Result.newBuilder());
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default:
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throw new IllegalArgumentException("Invalid entity type: " + type);
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}
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}
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public static String oafRel(final String relationType,
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final String source,
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final String target,
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final NodeList nodeList,
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final String relClass,
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final String relScheme) {
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return oafRel(relationType, source, target, nodeList, relClass, relScheme, null, null);
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}
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public static String oafRel(final String relationType,
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final String source,
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final String target,
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final NodeList nodeList,
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final String relClass,
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final String relScheme,
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final String collectedFromId,
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final String collectedFromName) {
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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 RelType relType = RelType.valueOf(relationType);
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switch (relType) {
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case datasourceOrganization:
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Provision.Builder provision = Provision.newBuilder().setRelMetadata(
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RelMetadata.newBuilder().setSemantics(getSimpleQualifier(Provision.RelName.valueOf(relClass).toString(), relScheme)));
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DatasourceOrganization.Builder dorg = DatasourceOrganization.newBuilder().setProvision(provision);
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return serializeOafRel(nodeList, eSource, eTarget, relType, SubRelType.provision, relClass, collectedFromId, collectedFromName, false, dorg, provision);
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case personResult:
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Authorship.Builder auth = Authorship.newBuilder().setRelMetadata(
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RelMetadata.newBuilder().setSemantics(getSimpleQualifier(Authorship.RelName.valueOf(relClass).toString(), relScheme)));
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PersonResult.Builder personResult = PersonResult.newBuilder().setAuthorship(auth);
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return serializeOafRel(nodeList, eSource, eTarget, relType, SubRelType.authorship, relClass, collectedFromId, collectedFromName, false, personResult, auth);
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case projectPerson:
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ContactPerson.Builder contact = ContactPerson.newBuilder().setRelMetadata(
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RelMetadata.newBuilder().setSemantics(getSimpleQualifier(ContactPerson.RelName.valueOf(relClass).toString(), relScheme)));
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ProjectPerson.Builder projectPerson = ProjectPerson.newBuilder().setContactPerson(contact);
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return serializeOafRel(nodeList, eSource, eTarget, relType, SubRelType.contactPerson, relClass, collectedFromId, collectedFromName, false, projectPerson, contact);
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case projectOrganization:
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Participation.Builder participant = Participation.newBuilder().setRelMetadata(
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RelMetadata.newBuilder().setSemantics(getSimpleQualifier(Participation.RelName.valueOf(relClass).toString(), relScheme)));
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ProjectOrganization.Builder projectOrganization = ProjectOrganization.newBuilder().setParticipation(participant);
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return serializeOafRel(nodeList, eSource, eTarget, relType, SubRelType.participation, relClass, collectedFromId, collectedFromName, false, projectOrganization, participant);
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case resultProject:
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Outcome.Builder outcome = Outcome.newBuilder().setRelMetadata(
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RelMetadata.newBuilder().setSemantics(getSimpleQualifier(Outcome.RelName.valueOf(relClass).toString(), relScheme)));
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ResultProject.Builder resultProject = ResultProject.newBuilder().setOutcome(outcome);
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return serializeOafRel(nodeList, eSource, eTarget, relType, SubRelType.outcome, relClass, collectedFromId, collectedFromName, false, resultProject, outcome);
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case resultOrganization:
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Affiliation.Builder affiliation = Affiliation.newBuilder().setRelMetadata(
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RelMetadata.newBuilder().setSemantics(getSimpleQualifier(Affiliation.RelName.valueOf(relClass).toString(), relScheme)));
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ResultOrganization.Builder resultOrganization = ResultOrganization.newBuilder().setAffiliation(affiliation);
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return serializeOafRel(nodeList, eSource, eTarget, relType, SubRelType.affiliation, relClass, collectedFromId, collectedFromName, false, resultOrganization, affiliation);
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default:
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throw new IllegalArgumentException("unhandled relType: " + relationType);
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}
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}
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// ////////////////////////////////////////////////////////
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protected static String serializeOafEntity(final NodeList nodelist,
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final Type type,
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final String id,
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final KeyValue collectedFrom,
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final List<String> identities,
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final String dateOfCollection,
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final String dateOfTransformation,
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final Builder entity) {
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try {
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final FieldDescriptor md = entity.getDescriptorForType().findFieldByName("metadata");
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final OafEntity.Builder parent = getEntity(type, id, collectedFrom, identities, dateOfCollection, dateOfTransformation, null);
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final Builder metadata = entity.newBuilderForField(md);
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final DataInfo.Builder dataInfo = DataInfo.newBuilder();
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if (type.equals(Type.result)) {
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final Instance.Builder instance = Instance.newBuilder();
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parseNodelist(nodelist, instance);
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FieldDescriptor instanceDescriptor = Result.getDescriptor().findFieldByName(Instance.getDescriptor().getName());
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if (instanceDescriptor != null) {
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entity.setField(instanceDescriptor, instance);
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}
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}
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parseNodelist(nodelist, parent, entity, metadata, dataInfo);
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final FieldDescriptor entityDescriptor = OafEntity.getDescriptor().findFieldByName(type.toString());
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final Oaf build = getOaf(parent.setField(entityDescriptor, entity.setField(md, metadata.build()).build()), dataInfo);
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return base64(build.toByteArray());
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} catch (Exception e) {
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e.printStackTrace(System.err);
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throw new RuntimeException(e);
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}
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}
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protected static String serializeOafRel(final NodeList nodeList,
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final String sourceId,
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final String targetId,
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final RelType relType,
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final SubRelType subRelType,
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final String relClass,
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final String collectedFromId,
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final String collectedFromName,
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final boolean isChild,
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final Builder rel,
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final Builder subRel) {
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try {
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final DataInfo.Builder dataInfo = DataInfo.newBuilder();
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parseNodelist(nodeList, rel, subRel, dataInfo);
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OafRel.Builder builder = getRel(sourceId, targetId, relType, subRelType, relClass, collectedFromId, collectedFromName, isChild);
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FieldDescriptor subRelDescriptor = rel.getDescriptorForType().findFieldByName(subRelType.toString());
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rel.setField(subRelDescriptor, subRel.build());
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FieldDescriptor relDescriptor = OafRel.getDescriptor().findFieldByName(relType.toString());
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builder.setField(relDescriptor, rel.build());
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Oaf build = getOaf(builder, dataInfo);
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return base64(build.toByteArray());
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} catch (Exception e) {
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e.printStackTrace(System.err);
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throw new RuntimeException(e);
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}
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}
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private static void parseNodelist(final NodeList nodeList, final Builder... builders) {
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for (int i = 0; i < nodeList.getLength(); i++) {
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final Node fieldNode = nodeList.item(i);
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final Node attr = fieldNode.getAttributes().getNamedItem("name");
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final String fieldName = attr.getNodeValue();
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final NodeList children = fieldNode.getChildNodes();
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for (int j = 0; j < children.getLength(); j++) {
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final Node child = children.item(j);
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final String childName = child.getLocalName();
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if ("ITEM".equals(childName) || StringUtils.isBlank(childName)) {
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for (Builder builder : builders) {
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FieldDescriptor desc = builder.getDescriptorForType().findFieldByName(fieldName);
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if (desc != null) {
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String text = getText((StringUtils.isBlank(childName)) ? fieldNode : child);
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if (!StringUtils.isBlank(text)) {
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addField(builder, desc, text);
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}
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}
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}
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}
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}
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}
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}
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private static String getText(final Node node) {
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StringBuffer result = new StringBuffer();
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if (!node.hasChildNodes()) { return ""; }
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NodeList list = node.getChildNodes();
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for (int i = 0; i < list.getLength(); i++) {
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Node subnode = list.item(i);
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if (subnode.getNodeType() == Node.TEXT_NODE) {
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result.append(subnode.getNodeValue());
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} else if (subnode.getNodeType() == Node.CDATA_SECTION_NODE) {
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result.append(subnode.getNodeValue());
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} else if (subnode.getNodeType() == Node.ENTITY_REFERENCE_NODE) {
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result.append(getText(subnode));
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}
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}
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return result.toString().trim();
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}
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260
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}
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