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package eu.dnetlib.data.mapreduce.hbase.dataimport;
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import com.google.gson.Gson;
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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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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.*;
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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 org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import java.io.IOException;
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import java.io.InputStream;
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import java.util.*;
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import java.util.concurrent.atomic.AtomicInteger;
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import java.util.function.Function;
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import java.util.stream.Collectors;
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import static eu.dnetlib.data.mapreduce.hbase.dataimport.DumpToActionsUtility.*;
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import static eu.dnetlib.data.proto.ResultOrganizationProtos.ResultOrganization;
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public class DOIBoostToActions {
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private static Map<String, Pair<String, String>> datasources = new HashMap<String, Pair<String, String>>() {{
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put("MAG", new Pair<>("Microsoft Academic Graph", "openaire____::microsoft"));
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put("ORCID", new Pair<>("ORCID", "openaire____::orcid"));
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put("CrossRef", new Pair<>("Crossref", "openaire____::crossref"));
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put("UnpayWall", new Pair<>("UnpayWall", "openaire____::unpaywall"));
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}};
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private static Map<String, FieldTypeProtos.Qualifier> affiliationPIDType = new HashMap<String, FieldTypeProtos.Qualifier>() {{
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put("MAG", FieldTypeProtos.Qualifier.newBuilder().setClassid("mag_id" ).setClassname("Microsoft Academic Graph Identifier").setSchemename("dnet:pid_types").setSchemeid("dnet:pid_types").build());
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put("grid.ac", getQualifier("grid", "dnet:pid_types"));
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put("wikpedia", getQualifier("urn", "dnet:pid_types"));
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}};
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static Map<String, Map<String, String>> typologiesMapping;
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static {
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try {
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final InputStream is = DOIBoostToActions.class.getResourceAsStream("/eu/dnetlib/data/mapreduce/hbase/dataimport/mapping_typologies.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 (IOException e) {
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e.printStackTrace();
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}
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}
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final static String doiBoostNSPREFIX ="doiboost____";
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public static List<AtomicAction> generatePublicationActionsFromDump(final JsonObject rootElement, final ActionFactory factory, final String setName, final Agent agent, boolean invisible,
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final boolean onlyOrganization) {
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//Create OAF Proto
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final OafProtos.Oaf.Builder oaf = OafProtos.Oaf.newBuilder();
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//Add Data Info
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oaf.setDataInfo(FieldTypeProtos.DataInfo.newBuilder()
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.setInvisible(invisible)
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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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//Adding Kind
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oaf.setKind(KindProtos.Kind.entity);
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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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entity.setDateofcollection("2018-10-10");
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if (rootElement.has("collectedFrom") && rootElement.get("collectedFrom").isJsonArray()){
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StreamUtils.toStream(rootElement.getAsJsonArray("collectedFrom").iterator())
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.map(JsonElement::getAsString)
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.forEach(cf ->
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{
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final String id =datasources.get(cf).getValue();
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final String name =datasources.get(cf).getKey();
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if (StringUtils.isNotBlank(id) && StringUtils.isNotBlank(name)) {
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final FieldTypeProtos.KeyValue collectedFrom = FieldTypeProtos.KeyValue.newBuilder()
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.setValue(name)
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.setKey("10|openaire____::" + AbstractDNetXsltFunctions.md5(StringUtils.substringAfter(id, "::")))
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.build();
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entity.addCollectedfrom(collectedFrom);
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}
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}
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);
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}
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//Adding identifier
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final String doi = getStringValue(rootElement, "doi");
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if (doi == null)
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return null;
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final String sourceId = String.format("50|%s::%s", doiBoostNSPREFIX, AbstractDNetXsltFunctions.md5(doi));
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entity.setId(sourceId);
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entity.addPid(FieldTypeProtos.StructuredProperty.newBuilder()
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.setValue(doi)
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.setQualifier(getQualifier("doi", "dnet:pid_types"))
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.build());
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//Create Result Field
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ResultProtos.Result.Builder result = ResultProtos.Result.newBuilder();
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final String type = getStringValue(rootElement,"type");
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if (!typologiesMapping.containsKey(type))
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return null;
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//Adding Instances
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final String typeValue = typologiesMapping.get(type).get("value");
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final String cobjValue = typologiesMapping.get(type).get("cobj");
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getArrayObjects(rootElement, "instances").stream().map(it ->
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{
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ResultProtos.Result.Instance.Builder instance= ResultProtos.Result.Instance.newBuilder();
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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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instance.setHostedby(FieldTypeProtos.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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final String acc_class_id =it.get("access-rights").getAsString();
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String acc_class_value;
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switch (acc_class_id){
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case "OPEN": {
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acc_class_value = "open access";
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break;
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}
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case "CLOSED": {
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acc_class_value = "closed access";
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break;
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}
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default: {
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acc_class_value = "not available";
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}
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}
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instance.addUrl(it.get("url").getAsString());
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instance.setAccessright(FieldTypeProtos.Qualifier.newBuilder()
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.setClassid(acc_class_id)
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.setClassname(acc_class_value)
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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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final String id =datasources.get(it.get("provenance").getAsString()).getValue();
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final String name =datasources.get(it.get("provenance").getAsString()).getKey();
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if (StringUtils.isNotBlank(id) && StringUtils.isNotBlank(name)) {
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final FieldTypeProtos.KeyValue collectedFrom = FieldTypeProtos.KeyValue.newBuilder()
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.setValue(name)
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.setKey("10|openaire____::" + AbstractDNetXsltFunctions.md5(StringUtils.substringAfter(id, "::")))
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.build();
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instance.setCollectedfrom(collectedFrom);
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}
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return instance.build();
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}).forEach(result::addInstance);
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//Adding DOI URL as Instance
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final String doiURL = getStringValue(rootElement, "doi-url");
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if (StringUtils.isNotBlank(doiURL)) {
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final ResultProtos.Result.Instance.Builder instance = ResultProtos.Result.Instance.newBuilder();
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instance.addUrl(doiURL);
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instance.setAccessright(FieldTypeProtos.Qualifier.newBuilder()
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.setClassid("CLOSED")
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.setClassname("Closed Access")
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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.setCollectedfrom(FieldTypeProtos.KeyValue.newBuilder()
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.setValue("CrossRef")
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.setKey("10|openaire____::" + AbstractDNetXsltFunctions.md5("crossref"))
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.build());
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result.addInstance(instance);
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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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Pair<List<FieldTypeProtos.Author>, Collection<OafProtos.Oaf>> authorsOrganizations = createAuthorsOrganization(rootElement);
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if (authorsOrganizations.getKey().size() > 0) {
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metadata.addAllAuthor(authorsOrganizations.getKey());
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}
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else {
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return null;
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}
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//adding Language
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metadata.setLanguage(FieldTypeProtos.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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//Adding subjects
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List<String> subjects =getArrayValues(rootElement, "subject");
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subjects.forEach(s-> metadata.addSubject(FieldTypeProtos.StructuredProperty.newBuilder()
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.setValue(s)
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.setQualifier(getQualifier("keyword", "dnet:subject"))
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.build()));
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List<String>titles =getArrayValues(rootElement, "title");
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titles.forEach(t->
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metadata.addTitle(FieldTypeProtos.StructuredProperty.newBuilder()
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.setValue(t)
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.setQualifier(getQualifier("main title", "dnet:dataCite_title"))
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.build()));
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settingRelevantDate(rootElement, metadata, "issued", "issued", true);
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settingRelevantDate(rootElement, metadata, "accepted", "accepted", false);
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settingRelevantDate(rootElement, metadata, "published-online", "published-online", false);
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settingRelevantDate(rootElement, metadata, "published-print", "published-print", false);
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getArrayObjects(rootElement, "abstract").forEach(d -> metadata.addDescription(FieldTypeProtos.StringField.newBuilder().setValue(d.get("value").getAsString()).build()));
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//Adding Journal
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final String publisher = getStringValue(rootElement,"publisher");
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if (StringUtils.isNotBlank(publisher)){
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final ResultProtos.Result.Journal.Builder journal = ResultProtos.Result.Journal.newBuilder().setName(publisher);
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if (hasJSONArrayField(rootElement,"issn" )){
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StreamUtils.toStream(rootElement.getAsJsonArray("issn").iterator())
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.map(JsonElement::getAsJsonObject)
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.forEach(it -> {
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final String issntype = getStringValue(it, "type");
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final String value = getStringValue(it, "value");
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if("electronic".equals(issntype)){
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journal.setIssnOnline(value);
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}
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if ("print".equals(issntype))
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journal.setIssnPrinted(value);
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});
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}
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metadata.setJournal(journal.build());
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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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System.out.println(JsonFormat.printToString(oaf.build()));
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final List<AtomicAction> actionList = new ArrayList<>();
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if (!onlyOrganization)
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actionList.add(factory.createAtomicAction(setName, agent, oaf.getEntity().getId(), "result", "body", oaf.build().toByteArray()));
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if (!authorsOrganizations.getValue().isEmpty()) {
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authorsOrganizations.getValue().forEach(o ->
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{
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actionList.add(factory.createAtomicAction(setName, agent, o.getEntity().getId(), "organization", "body", o.toByteArray()));
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if (!onlyOrganization)
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actionList.addAll(createPublicationOrganizationRelation(oaf.build(), o, factory, setName, agent));
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final String gridOrganization = getSimilarGridOrganization(o.getEntity());
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if (gridOrganization!= null) {
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actionList.add(factory.createAtomicAction(setName, agent, o.getEntity().getId(), "organizationOrganization_dedupSimilarity_isSimilarTo", gridOrganization, "".getBytes()));
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actionList.add(factory.createAtomicAction(setName, agent, gridOrganization, "organizationOrganization_dedupSimilarity_isSimilarTo", o.getEntity().getId(), "".getBytes()));
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}
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});
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}
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return actionList;
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288
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}
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290
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291
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292
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private static String getSimilarGridOrganization(final OafProtos.OafEntity organization) {
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293
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294
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final List<FieldTypeProtos.StructuredProperty> pidList = organization.getPidList();
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if (pidList!= null ) {
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for (FieldTypeProtos.StructuredProperty p: pidList) {
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if (p.getQualifier().getClassname().equals("grid")){
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return "20|grid________::"+AbstractDNetXsltFunctions.md5(p.getValue());
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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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return null;
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303
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304
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}
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305
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private static List<AtomicAction> createPublicationOrganizationRelation(final OafProtos.Oaf publication, final OafProtos.Oaf organization, final ActionFactory factory, final String setName, final Agent agent) {
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307
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308
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List<AtomicAction> result = new ArrayList<>();
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309
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310
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final OafProtos.Oaf.Builder roaf = OafProtos.Oaf.newBuilder();
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311
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roaf.setKind(KindProtos.Kind.relation);
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312
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313
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roaf.setDataInfo(FieldTypeProtos.DataInfo.newBuilder()
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314
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.setInvisible(false)
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315
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.setDeletedbyinference(false)
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316
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.setInferred(false)
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317
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.setTrust("0.9")
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318
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.setProvenanceaction(getQualifier("sysimport:actionset", "dnet:provenanceActions"))
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319
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.build());
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320
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321
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322
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final OafProtos.OafRel.Builder rel = OafProtos.OafRel.newBuilder();
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323
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324
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rel.setRelType(RelTypeProtos.RelType.resultOrganization);
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325
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rel.setSubRelType(RelTypeProtos.SubRelType.affiliation);
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326
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327
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//Create a relation Result --> Organization
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rel.setSource(publication.getEntity().getId());
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rel.setTarget(organization.getEntity().getId());
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rel.setRelClass(ResultOrganization.Affiliation.RelName.hasAuthorInstitution.toString());
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331
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332
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final ResultOrganization.Builder rel_instance = ResultOrganization.newBuilder();
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333
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334
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final ResultOrganization.Affiliation.Builder affiliationRel = ResultOrganization.Affiliation.newBuilder();
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335
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affiliationRel.setRelMetadata(RelMetadataProtos.RelMetadata.newBuilder()
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336
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.setSemantics(getQualifier("hasAuthorInstitution", "dnet:result_organization_relations"))
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337
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.build());
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338
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rel_instance.setAffiliation(affiliationRel.build());
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339
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rel.setResultOrganization(rel_instance.build());
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340
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341
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rel.addCollectedfrom(FieldTypeProtos.KeyValue.newBuilder()
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342
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.setValue(datasources.get("MAG").getKey())
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343
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.setKey("10|openaire____::" + AbstractDNetXsltFunctions.md5(StringUtils.substringAfter(datasources.get("MAG").getValue(), "::")))
|
|
344
|
.build());
|
|
345
|
|
|
346
|
|
|
347
|
|
|
348
|
rel.setChild(false);
|
|
349
|
roaf.setRel(rel.build());
|
|
350
|
|
|
351
|
result.add(factory.createAtomicAction(setName, agent, publication.getEntity().getId(), "resultOrganization_affiliation_hasAuthorInstitution", organization.getEntity().getId(), roaf.build().toByteArray() ));
|
|
352
|
|
|
353
|
|
|
354
|
//Create a relation Organization --> Result
|
|
355
|
rel.setTarget(publication.getEntity().getId());
|
|
356
|
rel.setSource(organization.getEntity().getId());
|
|
357
|
rel.setRelClass(ResultOrganization.Affiliation.RelName.isAuthorInstitutionOf.toString());
|
|
358
|
|
|
359
|
|
|
360
|
affiliationRel.setRelMetadata(RelMetadataProtos.RelMetadata.newBuilder()
|
|
361
|
.setSemantics(getQualifier("isAuthorInstitutionOf", "dnet:result_organization_relations"))
|
|
362
|
.build());
|
|
363
|
rel_instance.setAffiliation(affiliationRel.build());
|
|
364
|
rel.setResultOrganization(rel_instance.build());
|
|
365
|
roaf.setRel(rel.build());
|
|
366
|
result.add(factory.createAtomicAction(setName, agent, organization.getEntity().getId(), "resultOrganization_affiliation_isAuthorInstitutionOf", publication.getEntity().getId(), roaf.build().toByteArray()));
|
|
367
|
|
|
368
|
return result;
|
|
369
|
|
|
370
|
}
|
|
371
|
|
|
372
|
private static boolean hasJSONArrayField(final JsonObject root, final String key) {
|
|
373
|
return root.has(key) && root.get(key).isJsonArray();
|
|
374
|
}
|
|
375
|
|
|
376
|
private static void settingRelevantDate(JsonObject rootElement, ResultProtos.Result.Metadata.Builder metadata , final String jsonKey, final String dictionaryKey, final boolean addToDateOfAcceptance) {
|
|
377
|
//Adding date
|
|
378
|
String date = getStringValue(rootElement,jsonKey);
|
|
379
|
if (date == null)
|
|
380
|
return;
|
|
381
|
if (date.length() == 4) {
|
|
382
|
date += "-01-01";
|
|
383
|
}
|
|
384
|
if (isValidDate(date)) {
|
|
385
|
if (addToDateOfAcceptance)
|
|
386
|
metadata.setDateofacceptance(FieldTypeProtos.StringField.newBuilder().setValue(date).build());
|
|
387
|
metadata.addRelevantdate(FieldTypeProtos.StructuredProperty.newBuilder()
|
|
388
|
.setValue(date)
|
|
389
|
.setQualifier(getQualifier(dictionaryKey,"dnet:dataCite_date"))
|
|
390
|
.build());
|
|
391
|
}
|
|
392
|
}
|
|
393
|
|
|
394
|
|
|
395
|
public static FieldTypeProtos.KeyValue extractIdentifier(final String value) {
|
|
396
|
FieldTypeProtos.KeyValue.Builder pid = FieldTypeProtos.KeyValue.newBuilder();
|
|
397
|
if (StringUtils.contains(value, "orcid.org")){
|
|
398
|
return pid.setValue(value)
|
|
399
|
.setKey("ORCID").build();
|
|
400
|
}
|
|
401
|
if (StringUtils.contains(value, "academic.microsoft.com/#/detail")){
|
|
402
|
return pid.setValue(value)
|
|
403
|
.setKey("MAG Identifier").build();
|
|
404
|
}
|
|
405
|
return pid.setValue(value)
|
|
406
|
.setKey("URL").build();
|
|
407
|
}
|
|
408
|
|
|
409
|
|
|
410
|
public static OafProtos.Oaf createOrganizationFromJSON(final JsonObject affiliation) {
|
|
411
|
final Map<String, FieldTypeProtos.Qualifier> affiliationIdentifiers = new HashMap<>();
|
|
412
|
final List<String> magId = new ArrayList<>();
|
|
413
|
getArrayObjects(affiliation, "identifiers").forEach(it -> {
|
|
414
|
if (StringUtils.contains(it.get("value").getAsString(), "academic.microsoft.com")) {
|
|
415
|
affiliationIdentifiers.put(it.get("value").getAsString(), affiliationPIDType.get("MAG"));
|
|
416
|
magId.add(it.get("value").getAsString());
|
|
417
|
}
|
|
418
|
else
|
|
419
|
affiliationIdentifiers.put( it.get("value").getAsString(), affiliationPIDType.get(it.get("schema").getAsString()));
|
|
420
|
});
|
|
421
|
if (magId.size() > 0) {
|
|
422
|
final String microsoftID = magId.get(0);
|
|
423
|
OafProtos.Oaf.Builder oaf = OafProtos.Oaf.newBuilder();
|
|
424
|
oaf.setKind(KindProtos.Kind.entity);
|
|
425
|
OafProtos.OafEntity.Builder entity = OafProtos.OafEntity.newBuilder();
|
|
426
|
entity.setType(TypeProtos.Type.organization);
|
|
427
|
entity.setId("20|microsoft___::"+AbstractDNetXsltFunctions.md5(microsoftID));
|
|
428
|
final String id =datasources.get(affiliation.get("provenance").getAsString()).getValue();
|
|
429
|
final String name =datasources.get(affiliation.get("provenance").getAsString()).getKey();
|
|
430
|
if (StringUtils.isNotBlank(id) && StringUtils.isNotBlank(name)) {
|
|
431
|
final FieldTypeProtos.KeyValue collectedFrom = FieldTypeProtos.KeyValue.newBuilder()
|
|
432
|
.setValue(name)
|
|
433
|
.setKey("10|openaire____::" + AbstractDNetXsltFunctions.md5(StringUtils.substringAfter(id, "::")))
|
|
434
|
.build();
|
|
435
|
entity.addCollectedfrom(collectedFrom);
|
|
436
|
} else {
|
|
437
|
return null;
|
|
438
|
}
|
|
439
|
entity.addOriginalId(microsoftID);
|
|
440
|
|
|
441
|
affiliationIdentifiers.forEach((key, value) -> entity.addPid(
|
|
442
|
FieldTypeProtos.StructuredProperty.newBuilder()
|
|
443
|
.setQualifier(value)
|
|
444
|
.setValue(key)
|
|
445
|
.build()));
|
|
446
|
|
|
447
|
final OrganizationProtos.Organization.Builder organization = OrganizationProtos.Organization.newBuilder();
|
|
448
|
organization.setMetadata(OrganizationProtos.Organization.Metadata.newBuilder()
|
|
449
|
.setWebsiteurl(FieldTypeProtos.StringField.newBuilder().setValue(affiliation.get("official-page").getAsString()).build())
|
|
450
|
.setLegalname(FieldTypeProtos.StringField.newBuilder().setValue(affiliation.get("value").getAsString()).build())
|
|
451
|
.build());
|
|
452
|
|
|
453
|
entity.setOrganization(organization);
|
|
454
|
oaf.setEntity(entity);
|
|
455
|
oaf.setDataInfo(FieldTypeProtos.DataInfo.newBuilder()
|
|
456
|
.setInvisible(false)
|
|
457
|
.setDeletedbyinference(false)
|
|
458
|
.setInferred(false)
|
|
459
|
.setTrust("0.9")
|
|
460
|
.setProvenanceaction(getQualifier("sysimport:actionset", "dnet:provenanceActions"))
|
|
461
|
.build());
|
|
462
|
return oaf.build();
|
|
463
|
}
|
|
464
|
return null;
|
|
465
|
}
|
|
466
|
|
|
467
|
public static Pair<List<FieldTypeProtos.Author>, Collection<OafProtos.Oaf>> createAuthorsOrganization(final JsonObject root) {
|
|
468
|
|
|
469
|
final Map<String, OafProtos.Oaf> affiliations = new HashMap<>();
|
|
470
|
|
|
471
|
List<JsonObject> authors = getArrayObjects(root, "authors");
|
|
472
|
|
|
473
|
final AtomicInteger counter = new AtomicInteger();
|
|
474
|
|
|
475
|
List<FieldTypeProtos.Author> collect = authors.stream().map(author -> {
|
|
476
|
final String given = getStringValue(author, "given");
|
|
477
|
final String family = getStringValue(author, "family");
|
|
478
|
String fullname = getStringValue(author, "fullname");
|
|
479
|
|
|
480
|
if (StringUtils.isBlank(fullname) && StringUtils.isNotBlank(given) && StringUtils.isNotBlank(family)) {
|
|
481
|
fullname = String.format("%s %s", given, family);
|
|
482
|
}
|
|
483
|
|
|
484
|
if (StringUtils.isBlank(fullname)){
|
|
485
|
return null;
|
|
486
|
|
|
487
|
}
|
|
488
|
final FieldTypeProtos.Author.Builder abuilder = FieldTypeProtos.Author.newBuilder();
|
|
489
|
|
|
490
|
if (StringUtils.isNotBlank(given))
|
|
491
|
abuilder.setName(given);
|
|
492
|
if (StringUtils.isNotBlank(family))
|
|
493
|
abuilder.setSurname(family);
|
|
494
|
if (StringUtils.isNotBlank(fullname))
|
|
495
|
abuilder.setFullname(fullname);
|
|
496
|
|
|
497
|
final List<JsonObject> identifiers = getArrayObjects(author, "identifiers");
|
|
498
|
final List<JsonObject> authorAffiliation = getArrayObjects(author, "affiliations");
|
|
499
|
|
|
500
|
authorAffiliation.forEach(it ->
|
|
501
|
{
|
|
502
|
OafProtos.Oaf org = createOrganizationFromJSON(it);
|
|
503
|
if (org != null) {
|
|
504
|
affiliations.put(org.getEntity().getId(), org);
|
|
505
|
abuilder.addAffiliation(org.getEntity().getOrganization().getMetadata().getLegalname());
|
|
506
|
}
|
|
507
|
});
|
|
508
|
identifiers.stream().map(id -> {
|
|
509
|
final String value = id.get("value").getAsString();
|
|
510
|
return extractIdentifier(value);
|
|
511
|
}).collect(
|
|
512
|
Collectors.toMap(
|
|
513
|
FieldTypeProtos.KeyValue::getKey,
|
|
514
|
Function.identity(),
|
|
515
|
(a,b) -> a
|
|
516
|
)).values().forEach(abuilder::addPid);
|
|
517
|
abuilder.setRank(counter.getAndIncrement());
|
|
518
|
|
|
519
|
return abuilder.build();
|
|
520
|
|
|
521
|
}).filter(Objects::nonNull).collect(Collectors.toList());
|
|
522
|
|
|
523
|
return new Pair<> ( collect,affiliations.values() );
|
|
524
|
}
|
|
525
|
|
|
526
|
|
|
527
|
|
|
528
|
|
|
529
|
|
|
530
|
|
|
531
|
}
|