428 lines
19 KiB
Java
428 lines
19 KiB
Java
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package eu.dnetlib.doiboost.orcidnodoi.proto;
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public class ProtoWriter {
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}
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//
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//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getArrayValues;
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//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getDefaultResulttype;
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//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getQualifier;
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//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.getStringValue;
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//import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.isValidDate;
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//
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//import java.io.IOException;
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//import java.io.InputStream;
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//import java.util.ArrayList;
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//import java.util.HashMap;
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//import java.util.List;
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//import java.util.Map;
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//
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//import org.apache.commons.io.IOUtils;
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//import org.apache.commons.lang3.StringUtils;
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//
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//import com.google.gson.Gson;
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//import com.google.gson.JsonArray;
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//import com.google.gson.JsonElement;
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//import com.google.gson.JsonObject;
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//import com.googlecode.protobuf.format.JsonFormat;
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//
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//import eu.dnetlib.actionmanager.actions.ActionFactory;
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//import eu.dnetlib.actionmanager.actions.AtomicAction;
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//import eu.dnetlib.actionmanager.common.Agent;
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//import eu.dnetlib.data.mapreduce.hbase.Reporter;
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//import eu.dnetlib.data.mapreduce.util.StreamUtils;
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//import eu.dnetlib.data.proto.FieldTypeProtos;
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//import eu.dnetlib.data.proto.FieldTypeProtos.Author;
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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.FieldTypeProtos.Qualifier;
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//import eu.dnetlib.data.proto.FieldTypeProtos.StringField;
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//import eu.dnetlib.data.proto.FieldTypeProtos.StructuredProperty;
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//import eu.dnetlib.data.proto.KindProtos;
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//import eu.dnetlib.data.proto.OafProtos;
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//import eu.dnetlib.data.proto.ResultProtos;
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//import eu.dnetlib.data.proto.TypeProtos;
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//import eu.dnetlib.data.transform.xml.AbstractDNetXsltFunctions;
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//import eu.dnetlib.miscutils.collections.Pair;
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//import eu.dnetlib.miscutils.datetime.DateUtils;
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//import eu.dnetlib.pace.model.Person;
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//
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//public class ProtoWriter {
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//
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// public static final String ORCID = "ORCID";
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// public final static String orcidPREFIX = "orcid_______";
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// public static final String OPENAIRE_PREFIX = "openaire____";
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// public static final String SEPARATOR = "::";
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//
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// private static Map<String, Pair<String, String>> datasources = new HashMap<String, Pair<String, String>>() {
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//
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// {
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// put(ORCID.toLowerCase(), new Pair<>(ORCID, OPENAIRE_PREFIX + SEPARATOR + "orcid"));
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//
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// }
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// };
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//
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// // json external id will be mapped to oaf:pid/@classid Map to oaf:pid/@classname
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// private static Map<String, Pair<String, String>> externalIds = new HashMap<String, Pair<String, String>>() {
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//
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// {
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// put("ark".toLowerCase(), new Pair<>("ark", "ark"));
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// put("arxiv".toLowerCase(), new Pair<>("arxiv", "arXiv"));
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// put("pmc".toLowerCase(), new Pair<>("pmc", "pmc"));
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// put("pmid".toLowerCase(), new Pair<>("pmid", "pmid"));
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// put("source-work-id".toLowerCase(), new Pair<>("orcidworkid", "orcidworkid"));
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// put("urn".toLowerCase(), new Pair<>("urn", "urn"));
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// }
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// };
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//
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// static Map<String, Map<String, String>> typologiesMapping;
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//
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// static {
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// try {
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// final InputStream is = OrcidToActions.class.getResourceAsStream("/eu/dnetlib/data/mapreduce/hbase/dataimport/mapping_typologies_orcid.json");
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// final String tt = IOUtils.toString(is);
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// typologiesMapping = new Gson().fromJson(tt, Map.class);
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// } catch (final IOException e) {
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// e.printStackTrace();
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// }
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// }
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//
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// public static final String PID_TYPES = "dnet:pid_types";
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//
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// public static List<AtomicAction> generatePublicationActionsFromDump(final JsonObject rootElement,
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// final ActionFactory factory,
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// final String setName,
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// final Agent agent,
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// final Reporter context) {
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//
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// if (!isValid(rootElement, context)) { return null; }
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//
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// // Create OAF proto
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//
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// final OafProtos.Oaf.Builder oaf = OafProtos.Oaf.newBuilder();
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//
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// oaf.setDataInfo(
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// DataInfo.newBuilder()
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// .setDeletedbyinference(false)
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// .setInferred(false)
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// .setTrust("0.9")
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// .setProvenanceaction(getQualifier("sysimport:actionset:orcidworks-no-doi", "dnet:provenanceActions"))
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// .build());
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//
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// // Adding kind
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// oaf.setKind(KindProtos.Kind.entity);
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//
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// oaf.setLastupdatetimestamp(DateUtils.now());
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//
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// // creating result proto
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// final OafProtos.OafEntity.Builder entity = OafProtos.OafEntity.newBuilder().setType(TypeProtos.Type.result);
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//
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// entity.setDateofcollection("2018-10-22");
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// entity.setDateoftransformation(DateUtils.now_ISO8601());
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//
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// // Adding external ids
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// StreamUtils.toStream(externalIds.keySet().iterator())
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// .forEach(jsonExtId -> {
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// final String classid = externalIds.get(jsonExtId.toLowerCase()).getValue();
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// final String classname = externalIds.get(jsonExtId.toLowerCase()).getKey();
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// final String extId = getStringValue(rootElement, jsonExtId);
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// if (StringUtils.isNotBlank(extId)) {
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// entity.addPid(StructuredProperty.newBuilder()
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// .setValue(extId)
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// .setQualifier(Qualifier.newBuilder().setClassid(classid).setClassname(classname).setSchemeid("dnet:pid_types")
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// .setSchemename("dnet:pid_types").build())
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// .build());
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// }
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// });
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//
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// // Create result field
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// final ResultProtos.Result.Builder result = ResultProtos.Result.newBuilder();
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//
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// // Create metadata proto
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// final ResultProtos.Result.Metadata.Builder metadata = ResultProtos.Result.Metadata.newBuilder();
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//
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// // Adding source
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// final String source = getStringValue(rootElement, "source");
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// if (StringUtils.isNotBlank(source)) {
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// metadata.addSource(StringField.newBuilder().setValue(source).build());
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// }
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//
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// // Adding title
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// final String title = createRepeatedField(rootElement, "titles");
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// if (StringUtils.isBlank(title)) {
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// context.incrementCounter("filtered", "title_not_found", 1);
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// return null;
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// }
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// metadata.addTitle(FieldTypeProtos.StructuredProperty.newBuilder()
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// .setValue(title)
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// .setQualifier(getQualifier("main title", "dnet:dataCite_title"))
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// .build());
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//
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// // Adding identifier
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// final String id = getStringValue(rootElement, "id");
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// String sourceId = null;
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// if (id != null) {
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// entity.addOriginalId(id);
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// sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, AbstractDNetXsltFunctions.md5(id));
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// } else {
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// sourceId = String.format("50|%s" + SEPARATOR + "%s", orcidPREFIX, AbstractDNetXsltFunctions.md5(title));
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// }
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// entity.setId(sourceId);
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//
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// // Adding relevant date
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// settingRelevantDate(rootElement, metadata, "publication_date", "issued", true);
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//
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// // Adding collectedfrom
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// final FieldTypeProtos.KeyValue collectedFrom = FieldTypeProtos.KeyValue.newBuilder()
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// .setValue(ORCID)
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// .setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a")
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// .build();
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// entity.addCollectedfrom(collectedFrom);
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//
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// // Adding type
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// final String type = getStringValue(rootElement, "type");
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// String cobjValue = "";
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// if (StringUtils.isNotBlank(type)) {
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//
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// metadata.setResourcetype(FieldTypeProtos.Qualifier.newBuilder()
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// .setClassid(type)
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// .setClassname(type)
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// .setSchemeid("dnet:dataCite_resource")
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// .setSchemename("dnet:dataCite_resource")
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// .build());
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//
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// final String typeValue = typologiesMapping.get(type).get("value");
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// cobjValue = typologiesMapping.get(type).get("cobj");
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// final ResultProtos.Result.Instance.Builder instance = ResultProtos.Result.Instance.newBuilder();
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//
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// // Adding hostedby
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// instance.setHostedby(FieldTypeProtos.KeyValue.newBuilder()
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// .setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "55045bd2a65019fd8e6741a755395c8c")
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// .setValue("Unknown Repository")
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// .build());
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//
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// // Adding url
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// final String url = createRepeatedField(rootElement, "urls");
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// if (StringUtils.isNotBlank(url)) {
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// instance.addUrl(url);
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// }
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//
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// final String pubDate = getPublicationDate(rootElement, "publication_date");
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// if (StringUtils.isNotBlank(pubDate)) {
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// instance.setDateofacceptance(FieldTypeProtos.StringField.newBuilder().setValue(pubDate).build());
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// }
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//
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// instance.setCollectedfrom(collectedFrom);
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//
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// // Adding accessright
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// instance.setAccessright(FieldTypeProtos.Qualifier.newBuilder()
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// .setClassid("UNKNOWN")
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// .setClassname("UNKNOWN")
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// .setSchemeid("dnet:access_modes")
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// .setSchemename("dnet:access_modes")
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// .build());
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//
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// // Adding type
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// instance.setInstancetype(FieldTypeProtos.Qualifier.newBuilder()
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// .setClassid(cobjValue)
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// .setClassname(typeValue)
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// .setSchemeid("dnet:publication_resource")
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// .setSchemename("dnet:publication_resource")
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// .build());
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//
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// result.addInstance(instance);
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// } else {
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// context.incrementCounter("filtered", "type_not_found", 1);
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// return null;
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// }
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//
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// // Adding authors
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// final List<Author> authors = createAuthors(rootElement);
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// if (authors != null && authors.size() > 0) {
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// metadata.addAllAuthor(authors);
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// } else {
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// context.incrementCounter("filtered", "author_not_found", 1);
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// return null;
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// }
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//
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// metadata.setResulttype(getQualifier(getDefaultResulttype(cobjValue), "dnet:result_typologies"));
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// result.setMetadata(metadata.build());
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// entity.setResult(result.build());
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// oaf.setEntity(entity.build());
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//
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// final List<AtomicAction> actionList = new ArrayList<>();
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//
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// actionList.add(factory.createAtomicAction(setName, agent, oaf.getEntity().getId(), "result", "body", oaf.build().toByteArray()));
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//
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//// System.out.println(JsonFormat.printToString(oaf.build()));
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// return actionList;
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//
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// }
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//
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// public static List<Author> createAuthors(final JsonObject root) {
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//
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// final String authorsJSONFieldName = "authors";
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//
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// if (root.has(authorsJSONFieldName) && root.get(authorsJSONFieldName).isJsonArray()) {
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//
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// final List<Author> authors = new ArrayList<>();
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// final JsonArray jsonAuthors = root.getAsJsonArray(authorsJSONFieldName);
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// int firstCounter = 0;
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// int defaultCounter = 0;
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// int rank = 1;
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// int currentRank = 0;
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//
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// for (final JsonElement item : jsonAuthors) {
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// final JsonObject author = item.getAsJsonObject();
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// final Author.Builder result = Author.newBuilder();
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// if (item.isJsonObject()) {
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// final String surname = getStringValue(author, "surname");
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// final String name = getStringValue(author, "name");
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// final String oid = getStringValue(author, "oid");
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// final String seq = getStringValue(author, "seq");
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// if (StringUtils.isNotBlank(seq)) {
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// if (seq.equals("first")) {
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// firstCounter += 1;
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// rank = firstCounter;
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//
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// } else if (seq.equals("additional")) {
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// rank = currentRank + 1;
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// } else {
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// defaultCounter += 1;
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// rank = defaultCounter;
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// }
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// }
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//
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// if (StringUtils.isNotBlank(oid)) {
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// result.addPid(KeyValue.newBuilder()
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// .setValue(oid)
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// .setKey("ORCID")
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// .build());
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// result.setFullname(name + " " + surname);
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// if (StringUtils.isNotBlank(name)) {
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// result.setName(name);
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// }
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// if (StringUtils.isNotBlank(surname)) {
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// result.setSurname(surname);
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// }
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// } else {
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// String fullname = "";
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// if (StringUtils.isNotBlank(name)) {
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// fullname = name;
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// } else {
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// if (StringUtils.isNotBlank(surname)) {
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// fullname = surname;
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// }
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// }
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// Person p = new Person(fullname, false);
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// if (p.isAccurate()) {
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// result.setName(p.getNormalisedFirstName());
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// result.setSurname(p.getNormalisedSurname());
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// result.setFullname(p.getNormalisedFullname());
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// }
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// else {
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// result.setFullname(fullname);
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// }
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// }
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// }
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// result.setRank(rank);
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// authors.add(result.build());
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// currentRank = rank;
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// }
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// return authors;
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//
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// }
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// return null;
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// }
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//
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// private static String createRepeatedField(final JsonObject rootElement, final String fieldName) {
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// String field = "";
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// if (!rootElement.has(fieldName)) { return null; }
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// if (rootElement.has(fieldName) && rootElement.get(fieldName).isJsonNull()) { return null; }
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// if (rootElement.get(fieldName).isJsonArray()) {
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// if (!isValidJsonArray(rootElement, fieldName)) { return null; }
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// final StringBuilder ttl = new StringBuilder();
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// getArrayValues(rootElement, fieldName).forEach(ttl::append);
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// field = ttl.toString();
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// } else {
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// field = getStringValue(rootElement, fieldName);
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// }
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//
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// if (field != null && !field.isEmpty() && field.charAt(0) == '"' && field.charAt(field.length() - 1) == '"') {
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// field = field.substring(1, field.length() - 1);
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// }
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// return field;
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// }
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//
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// private static void settingRelevantDate(final JsonObject rootElement,
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// final ResultProtos.Result.Metadata.Builder metadata,
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// final String jsonKey,
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// final String dictionaryKey,
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// final boolean addToDateOfAcceptance) {
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//
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// final String pubDate = getPublicationDate(rootElement, "publication_date");
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// if (StringUtils.isNotBlank(pubDate)) {
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// if (addToDateOfAcceptance) {
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// metadata.setDateofacceptance(FieldTypeProtos.StringField.newBuilder().setValue(pubDate).build());
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// }
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// metadata.addRelevantdate(FieldTypeProtos.StructuredProperty.newBuilder()
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// .setValue(pubDate)
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// .setQualifier(getQualifier(dictionaryKey, "dnet:dataCite_date"))
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// .build());
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// }
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// }
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//
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// private static String getPublicationDate(final JsonObject rootElement,
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// final String jsonKey) {
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//
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// final JsonObject pubDateJson = rootElement.getAsJsonObject(jsonKey);
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// if (pubDateJson == null) { return null; }
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// final String year = getStringValue(pubDateJson, "year");
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// final String month = getStringValue(pubDateJson, "month");
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// final String day = getStringValue(pubDateJson, "day");
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//
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// if (StringUtils.isBlank(year)) { return null; }
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// String pubDate = "".concat(year);
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// if (StringUtils.isNotBlank(month)) {
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// pubDate = pubDate.concat("-" + month);
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// if (StringUtils.isNotBlank(day)) {
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// pubDate = pubDate.concat("-" + day);
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// } else {
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// pubDate += "-01";
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// }
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// } else {
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// pubDate += "-01-01";
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// }
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// if (isValidDate(pubDate)) { return pubDate; }
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// return null;
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// }
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//
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// protected static boolean isValid(final JsonObject rootElement, final Reporter context) {
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//
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// final String type = getStringValue(rootElement, "type");
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// if (!typologiesMapping.containsKey(type)) {
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// context.incrementCounter("filtered", "unknowntype_" + type, 1);
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// return false;
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// }
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//
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// if (!isValidJsonArray(rootElement, "titles")) {
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// context.incrementCounter("filtered", "invalid_title", 1);
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// return false;
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// }
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// return true;
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// }
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//
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// private static boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) {
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// if (!rootElement.has(fieldName)) { return false; }
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// final JsonElement jsonElement = rootElement.get(fieldName);
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// if (jsonElement.isJsonNull()) { return false; }
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// if (jsonElement.isJsonArray()) {
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// final JsonArray jsonArray = jsonElement.getAsJsonArray();
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// if (jsonArray.isJsonNull()) { return false; }
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// if (jsonArray.get(0).isJsonNull()) { return false; }
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// }
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// return true;
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// }
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//}
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