245 lines
8.2 KiB
Java
245 lines
8.2 KiB
Java
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package eu.dnetlib.dhp.oa.graph.dump.eosc;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.*;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.MapGroupsFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.eosc.model.Affiliation;
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import eu.dnetlib.dhp.eosc.model.Country;
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import eu.dnetlib.dhp.eosc.model.OrganizationPid;
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import eu.dnetlib.dhp.eosc.model.Result;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Organization;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import scala.Tuple2;
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/**
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* @author miriam.baglioni
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* @Date 27/07/22
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*/
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public class ExtendEoscResultWithOrganizationStep2 implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(ExtendEoscResultWithOrganizationStep2.class);
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private final static String UNKNOWN = "UNKNOWN";
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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ExtendEoscResultWithOrganizationStep2.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/eosc_extend_result_with_organization_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String workingPath = parser.get("workingPath");
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log.info("workingPath: {}", workingPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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Utils.removeOutputDir(spark, workingPath + "publicationextendedaffiliation");
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addOrganizations(spark, inputPath, workingPath, outputPath);
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});
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}
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private static void addOrganizations(SparkSession spark, String inputPath, String workingPath, String outputPath) {
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Dataset<Result> results = Utils
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.readPath(spark, workingPath + "publication", Result.class);
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Dataset<Relation> relations = Utils
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.readPath(spark, inputPath + "/relation", Relation.class)
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.filter(
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(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
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!r.getDataInfo().getInvisible() && r.getSubRelType().equalsIgnoreCase(ModelConstants.AFFILIATION));
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Dataset<Organization> organizations = Utils.readPath(spark, inputPath + "/organization", Organization.class);
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Dataset<ResultOrganizations> resultOrganization = relations
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.joinWith(organizations, relations.col("source").equalTo(organizations.col("id")), "left")
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.map((MapFunction<Tuple2<Relation, Organization>, ResultOrganizations>) t2 -> {
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if (t2._2() != null) {
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ResultOrganizations rOrg = new ResultOrganizations();
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rOrg.setResultId(t2._1().getTarget());
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Affiliation org = new Affiliation();
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org.setId(t2._2().getId());
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if (Optional.ofNullable(t2._2().getLegalname()).isPresent()) {
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org.setName(t2._2().getLegalname().getValue());
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} else {
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org.setName("");
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}
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HashMap<String, Set<String>> organizationPids = new HashMap<>();
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if (Optional.ofNullable(t2._2().getPid()).isPresent())
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t2._2().getPid().forEach(p -> {
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if (!organizationPids.containsKey(p.getQualifier().getClassid()))
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organizationPids.put(p.getQualifier().getClassid(), new HashSet<>());
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organizationPids.get(p.getQualifier().getClassid()).add(p.getValue());
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});
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List<OrganizationPid> pids = new ArrayList<>();
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for (String key : organizationPids.keySet()) {
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for (String value : organizationPids.get(key)) {
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OrganizationPid pid = new OrganizationPid();
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pid.setValue(value);
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pid.setType(key);
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pids.add(pid);
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}
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}
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org.setPid(pids);
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rOrg.setAffiliation(org);
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return rOrg;
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}
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return null;
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}, Encoders.bean(ResultOrganizations.class))
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.filter(Objects::nonNull);
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results
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.joinWith(resultOrganization, results.col("id").equalTo(resultOrganization.col("resultId")), "left")
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.groupByKey(
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(MapFunction<Tuple2<Result, ResultOrganizations>, String>) t2 -> t2._1().getId(), Encoders.STRING())
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.mapGroups(
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(MapGroupsFunction<String, Tuple2<Result, ResultOrganizations>, Result>) (s, it) -> {
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Tuple2<Result, ResultOrganizations> first = it.next();
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if (first._2() == null) {
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return first._1();
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}
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Result ret = first._1();
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List<Affiliation> affiliation = new ArrayList<>();
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Set<String> alreadyInsertedAffiliations = new HashSet<>();
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affiliation.add(first._2().getAffiliation());
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alreadyInsertedAffiliations.add(first._2().getAffiliation().getId());
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it.forEachRemaining(res -> {
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if (!alreadyInsertedAffiliations.contains(res._2().getAffiliation().getId())) {
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affiliation.add(res._2().getAffiliation());
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alreadyInsertedAffiliations.add(res._2().getAffiliation().getId());
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}
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});
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ret.setAffiliation(affiliation);
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return ret;
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}, Encoders.bean(Result.class))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(workingPath + "publicationextendedaffiliation");
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relations
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.joinWith(organizations, relations.col("source").equalTo(organizations.col("id")))
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.map(
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(MapFunction<Tuple2<Relation, Organization>, eu.dnetlib.dhp.eosc.model.Organization>) t2 -> mapOrganization(
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t2._2()),
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Encoders.bean(eu.dnetlib.dhp.eosc.model.Organization.class))
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.filter(Objects::nonNull)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + "organization");
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relations
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.joinWith(organizations, relations.col("source").equalTo(organizations.col("id")))
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.map(
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(MapFunction<Tuple2<Relation, Organization>, eu.dnetlib.dhp.eosc.model.Relation>) t2 -> eu.dnetlib.dhp.eosc.model.Relation
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.newInstance(t2._1().getSource(), t2._1().getTarget()),
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Encoders.bean(eu.dnetlib.dhp.eosc.model.Relation.class))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + "resultOrganization");
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}
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private static eu.dnetlib.dhp.eosc.model.Organization mapOrganization(Organization org) {
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if (Boolean.TRUE.equals(org.getDataInfo().getDeletedbyinference()))
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return null;
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if (!Optional.ofNullable(org.getLegalname()).isPresent()
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&& !Optional.ofNullable(org.getLegalshortname()).isPresent())
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return null;
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eu.dnetlib.dhp.eosc.model.Organization organization = new eu.dnetlib.dhp.eosc.model.Organization();
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Optional
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.ofNullable(org.getLegalshortname())
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.ifPresent(value -> organization.setLegalshortname(value.getValue()));
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Optional
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.ofNullable(org.getLegalname())
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.ifPresent(value -> organization.setLegalname(value.getValue()));
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Optional
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.ofNullable(org.getWebsiteurl())
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.ifPresent(value -> organization.setWebsiteurl(value.getValue()));
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Optional
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.ofNullable(org.getAlternativeNames())
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.ifPresent(
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value -> organization
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.setAlternativenames(
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value
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.stream()
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.map(v -> v.getValue())
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.collect(Collectors.toList())));
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Optional
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.ofNullable(org.getCountry())
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.ifPresent(
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value -> {
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if (!value.getClassid().equals(UNKNOWN)) {
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organization
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.setCountry(
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Country.newInstance(value.getClassid(), value.getClassname()));
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}
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});
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Optional
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.ofNullable(org.getId())
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.ifPresent(value -> organization.setId(value));
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Optional
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.ofNullable(org.getPid())
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.ifPresent(
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value -> organization
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.setPid(
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value
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.stream()
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.map(p -> OrganizationPid.newInstance(p.getQualifier().getClassid(), p.getValue()))
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.collect(Collectors.toList())));
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return organization;
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}
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}
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