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package eu.dnetlib.data.mapreduce.hbase.dataimport;
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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 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.util.StreamUtils;
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import eu.dnetlib.data.proto.RelMetadataProtos;
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import eu.dnetlib.data.proto.RelTypeProtos;
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import eu.dnetlib.data.transform.xml.AbstractDNetXsltFunctions;
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import org.apache.commons.lang3.StringUtils;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Map;
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import java.util.Objects;
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import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.*;
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import static eu.dnetlib.data.proto.FieldTypeProtos.*;
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import static eu.dnetlib.data.proto.KindProtos.Kind;
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import static eu.dnetlib.data.proto.OafProtos.*;
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import static eu.dnetlib.data.proto.ResultProtos.Result;
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import static eu.dnetlib.data.proto.ResultProtos.Result.*;
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import static eu.dnetlib.data.proto.ResultResultProtos.ResultResult;
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import static eu.dnetlib.data.proto.TypeProtos.Type;
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public class ScholixToActions {
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public static List<AtomicAction> generateActionsFromScholix(final JsonObject rootElement, final Map<String, ScholExplorerConfiguration> conf,
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final String setName, final Agent agent, ActionFactory factory, String nsPrefix, final String dsName,
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final String dsId, String dateOfCollection) {
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final List<AtomicAction> actions = new ArrayList<>();
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final String typology = getStringValue(rootElement, "typology");
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final List<String> publisher = getArrayValues(rootElement, "publisher");
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final String abstractValue = getStringValue(rootElement, "abstract");
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final List<String> authors = getArrayValues(rootElement, "author");
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final List<String> dates = getArrayValues(rootElement, "date");
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final JsonArray localIdentifiers = rootElement.getAsJsonArray("localIdentifier");
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final String dnetId = getStringValue(rootElement, "id").substring(17);
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String title = "";
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if (rootElement.has("title") && rootElement.get("title").isJsonArray()) {
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StringBuilder ttl = new StringBuilder();
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getArrayValues(rootElement, "title").forEach(ttl::append);
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title = ttl.toString();
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} else {
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title = getStringValue(rootElement, "title");
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}
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if ("\"".equals(title) || title == null || StringUtils.isEmpty(title))
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return actions;
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if (title != null && title.charAt(0) == '"' && title.charAt(title.length() - 1) == '"' ) {
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title = title.substring(1, title.length() - 1);
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}
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final Oaf.Builder oafBuilder = Oaf.newBuilder();
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final boolean isVisible = StringUtils.isNotBlank(title) && StreamUtils.toStream(localIdentifiers.iterator())
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.map(JsonElement::getAsJsonObject)
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.anyMatch(o -> {
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final String type = getStringValue(o, "type");
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return StringUtils.isNotBlank(type) && conf.containsKey(type) && conf.get(type).isVisible();
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});
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oafBuilder.setDataInfo(
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DataInfo.newBuilder()
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.setInvisible(!isVisible)
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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", "dnet:provenanceActions"))
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.build());
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oafBuilder.setKind(Kind.entity);
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final String sourceId = String.format("50|%s::%s", nsPrefix, dnetId);
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final KeyValue collectedFrom = KeyValue.newBuilder()
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.setValue(dsName)
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.setKey("10|openaire____::" + AbstractDNetXsltFunctions.md5(dsId))
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.build();
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final OafEntity.Builder oafEntityBuilder = OafEntity.newBuilder()
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.setType(Type.result)
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.setDateofcollection(dateOfCollection)
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.addCollectedfrom(collectedFrom)
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.setId(sourceId);
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StreamUtils.toStream(localIdentifiers.iterator())
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.map(JsonElement::getAsJsonObject)
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.map(localIdentifier -> getPid(localIdentifier, conf))
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.filter(Objects::nonNull)
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.forEach(oafEntityBuilder::addPid);
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final Result.Builder result = Result.newBuilder();
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final Metadata.Builder metadata = Metadata.newBuilder()
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.setResulttype(getQualifier(typology, "dnet:result_typologies"))
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.setLanguage(Qualifier.newBuilder()
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.setClassid("und")
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.setClassname("Undetermined")
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.setSchemeid("dent:languages")
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.setSchemename("dent:languages")
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.build());
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if (StringUtils.isNotBlank(title)) {
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metadata.addTitle(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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if (publisher.size() > 0)
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metadata.setPublisher(StringField.newBuilder().setValue(publisher.get(0)).build());
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if (StringUtils.isNotEmpty(abstractValue)) {
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metadata.addDescription(StringField.newBuilder().setValue(abstractValue).build());
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}
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dates.stream()
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.map(d -> {
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if (d.length() == 4 && StringUtils.isNumeric(d)) {
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return d + "-01-01";
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} else {
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return d;
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}
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}).filter(d -> isValidDate(d))
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.forEach(d -> metadata.addRelevantdate(StructuredProperty.newBuilder()
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.setValue(d)
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.setQualifier(getQualifier("dnet:date", "dnet:date"))
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.build()));
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if (rootElement.has("subject") && !rootElement.get("subject").isJsonNull()) {
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JsonArray subject = rootElement.getAsJsonArray("subject");
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subject.forEach(it -> {
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final JsonObject item = it.getAsJsonObject();
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final String scheme = getStringValue(item, "scheme");
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metadata.addSubject(StructuredProperty.newBuilder()
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.setValue(Objects.requireNonNull(getStringValue(item, "value")))
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.setQualifier(getQualifier(scheme, "dnet:subject"))
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.build());
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}
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);
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}
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int i = 1;
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for (String it : authors) {
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metadata.addAuthor(Author.newBuilder()
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.setFullname(it)
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.setRank(i++)
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.build());
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}
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result.setMetadata(metadata.build());
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localIdentifiers.forEach(it -> {
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final JsonObject localIdentifier = it.getAsJsonObject();
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final String pidType = getStringValue(localIdentifier, "type");
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final ScholExplorerConfiguration currentConf = conf.get(pidType);
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if (currentConf.getGeneratedUrl() != null) {
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final Instance.Builder instance = Instance.newBuilder();
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final String pidValue = getStringValue(localIdentifier, "id");
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instance.addUrl(String.format(currentConf.getGeneratedUrl(), pidValue));
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instance.setAccessright(Qualifier.newBuilder()
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.setClassid("UNKNOWN")
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.setClassname("not available")
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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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instance.setInstancetype(Qualifier.newBuilder()
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.setClassid("0000")
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.setClassname("Unknown")
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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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instance.setHostedby(KeyValue.newBuilder()
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.setKey("10|openaire____::55045bd2a65019fd8e6741a755395c8c")
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.setValue("Unknown Repository")
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.build());
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instance.setCollectedfrom(collectedFrom);
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result.addInstance(instance);
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}
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});
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generateExternalReference(extractRelations(rootElement, "externalRels"))
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.forEach(result::addExternalReference);
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oafEntityBuilder.setResult(result.build());
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oafBuilder.setEntity(oafEntityBuilder.build());
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//System.out.println(JsonFormat.printToString(oafBuilder.build()));
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actions.add(factory.createAtomicAction(setName, agent, oafEntityBuilder.getId(), "result", "body", oafBuilder.build().toByteArray()));
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final List<JsonObject> doiRels = extractRelations(rootElement, "doiRels");
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doiRels.stream().map(it -> convertDoiRelations(it, factory, sourceId, nsPrefix, collectedFrom, setName, agent)).forEach(actions::addAll);
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return actions;
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}
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private static AtomicAction createResultResultRelation(final String source, final String target,
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final KeyValue collectedFrom, final ResultResult resultResultRel, final String relClass, final String cfRelation, final ActionFactory factory, final String setName, final Agent agent) {
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final Oaf.Builder oaf = Oaf.newBuilder();
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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", "dnet:provenanceActions"))
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.build());
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oaf.setKind(Kind.relation);
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final OafRel.Builder relation = OafRel.newBuilder();
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relation.setSource(source);
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relation.setTarget(target);
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relation.setRelType(RelTypeProtos.RelType.resultResult);
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if (StringUtils.contains(relClass.toLowerCase(), "supplement")) {
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relation.setSubRelType(RelTypeProtos.SubRelType.supplement);
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} else {
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relation.setSubRelType(RelTypeProtos.SubRelType.publicationDataset);
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}
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relation.setChild(false);
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relation.setResultResult(resultResultRel);
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relation.setRelClass(relClass);
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relation.addCollectedfrom(collectedFrom);
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oaf.setRel(relation.build());
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//System.out.println(JsonFormat.printToString(oaf.build()));
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return factory.createAtomicAction(setName, agent, source, cfRelation, target, oaf.build().toByteArray());
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}
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private static List<AtomicAction> convertDoiRelations(final JsonObject doiRel, final ActionFactory factory, final String sourceId, final String nsPrefix, final KeyValue collectedFrom, final String setName, final Agent agent) {
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final String target = Objects.requireNonNull(getStringValue(doiRel, "dnetId")).substring(17);
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final String targetId = String.format("50|%s::%s", nsPrefix, target);
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final String relationSemantic = getStringValue(doiRel, "relationSemantic");
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String cfRelation;
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String cfInverseRelation;
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ResultResult.Builder resultRel = ResultResult.newBuilder();
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ResultResult.Builder resultInverseRel = ResultResult.newBuilder();
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String relClass;
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String inverseRelClass;
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switch (relationSemantic) {
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case "isSupplementedBy": {
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cfRelation = "resultResult_supplement_isSupplementedBy";
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cfInverseRelation = "resultResult_supplement_isSupplementTo";
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relClass = ResultResult.Supplement.RelName.isSupplementedBy.toString();
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inverseRelClass = ResultResult.Supplement.RelName.isSupplementTo.toString();
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resultRel.setSupplement(ResultResult.Supplement.newBuilder()
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.setRelMetadata(RelMetadataProtos.RelMetadata.newBuilder()
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.setSemantics(getQualifier(relClass, "dnet:result_result_relations"))
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.build())
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.build());
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resultInverseRel.setSupplement(ResultResult.Supplement.newBuilder()
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.setRelMetadata(RelMetadataProtos.RelMetadata.newBuilder()
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.setSemantics(getQualifier(inverseRelClass, "dnet:result_result_relations"))
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.build())
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.build());
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break;
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}
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case "isSupplementTo": {
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cfRelation = "resultResult_supplement_isSupplementTo";
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cfInverseRelation = "resultResult_supplement_isSupplementedBy";
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inverseRelClass = ResultResult.Supplement.RelName.isSupplementedBy.toString();
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relClass = ResultResult.Supplement.RelName.isSupplementTo.toString();
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resultInverseRel.setSupplement(ResultResult.Supplement.newBuilder()
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.setRelMetadata(RelMetadataProtos.RelMetadata.newBuilder()
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.setSemantics(getQualifier(inverseRelClass, "dnet:result_result_relations"))
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.build())
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.build());
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resultRel.setSupplement(ResultResult.Supplement.newBuilder()
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.setRelMetadata(RelMetadataProtos.RelMetadata.newBuilder()
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.setSemantics(getQualifier(relClass, "dnet:result_result_relations"))
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.build())
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.build());
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break;
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}
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default: {
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cfRelation = "resultResult_publicationDataset_isRelatedTo";
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cfInverseRelation = "resultResult_publicationDataset_isRelatedTo";
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relClass = ResultResult.PublicationDataset.RelName.isRelatedTo.toString();
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inverseRelClass = relClass;
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resultInverseRel.setPublicationDataset(ResultResult.PublicationDataset.newBuilder()
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.setRelMetadata(RelMetadataProtos.RelMetadata.newBuilder()
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.setSemantics(getQualifier(relClass, "dnet:result_result_relations"))
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.build())
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.build());
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resultRel = resultInverseRel;
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}
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}
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290
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291
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final List<AtomicAction> actions = new ArrayList<>();
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actions.add(createResultResultRelation(sourceId, targetId, collectedFrom, resultRel.build(), relClass, cfRelation, factory, setName, agent));
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actions.add(createResultResultRelation(targetId, sourceId, collectedFrom, resultInverseRel.build(), inverseRelClass, cfInverseRelation, factory, setName, agent));
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294
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return actions;
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}
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297
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298
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private static List<ExternalReference> generateExternalReference(final List<JsonObject> jsonRels) {
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final List<ExternalReference> result = new ArrayList<>();
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300
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301
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jsonRels.forEach(it -> {
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ExternalReference.Builder builder = ExternalReference.newBuilder();
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if("url".equals(getStringValue(it.getAsJsonObject("id"), "schema"))) {
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builder.setUrl(Objects.requireNonNull(getStringValue(it.getAsJsonObject("id"), "identifier")));
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}
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result.add(builder
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.setRefidentifier(Objects.requireNonNull(getStringValue(it.getAsJsonObject("id"), "identifier")))
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.setSitename(Objects.requireNonNull(getStringValue(it, "collectedFrom")))
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.setQualifier(Qualifier.newBuilder()
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.setClassid(Objects.requireNonNull(getStringValue(it.getAsJsonObject("id"), "schema")))
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.setClassname(Objects.requireNonNull(getStringValue(it.getAsJsonObject("id"), "schema")))
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.setSchemename("dnet:externalReference_typologies")
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.setSchemeid("dnet:externalReference_typologies")
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.build())
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.build());
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});
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return result;
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}
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319
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320
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private static List<JsonObject> extractRelations(final JsonObject rootElement, final String fieldType) {
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321
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final List<JsonObject> result = new ArrayList<>();
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322
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if (rootElement.has(fieldType) && rootElement.get(fieldType).isJsonArray()) {
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final JsonArray asJsonArray = rootElement.getAsJsonArray(fieldType);
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asJsonArray.forEach(it -> result.add(it.getAsJsonObject()));
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}
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return result;
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327
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}
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328
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}
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