forked from D-Net/dnet-hadoop
355 lines
18 KiB
Java
355 lines
18 KiB
Java
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package eu.dnetlib.dhp.broker.oa;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.List;
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import java.util.Map;
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import java.util.Optional;
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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.commons.lang3.tuple.Pair;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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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.apache.spark.sql.TypedColumn;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.broker.model.Event;
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import eu.dnetlib.dhp.broker.model.EventFactory;
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import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsReferencedBy;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsRelatedTo;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsSupplementedBy;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsSupplementedTo;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetReferences;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedProjects.EnrichMissingProject;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedProjects.EnrichMoreProject;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsReferencedBy;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsRelatedTo;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsSupplementedBy;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationIsSupplementedTo;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedPublications.EnrichMissingPublicationReferences;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedSoftware.EnrichMissingSoftware;
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import eu.dnetlib.dhp.broker.oa.matchers.relatedSoftware.EnrichMoreSoftware;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingAbstract;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingAuthorOrcid;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingOpenAccess;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPid;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPublicationDate;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingSubject;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreOpenAccess;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMorePid;
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import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMoreSubject;
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import eu.dnetlib.dhp.broker.oa.util.BrokerConstants;
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import eu.dnetlib.dhp.broker.oa.util.EventGroup;
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import eu.dnetlib.dhp.broker.oa.util.ResultAggregator;
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import eu.dnetlib.dhp.broker.oa.util.ResultGroup;
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import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.oaf.OafEntity;
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import eu.dnetlib.dhp.schema.oaf.Project;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.Software;
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import eu.dnetlib.dhp.utils.ISLookupClientFactory;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.pace.config.DedupConfig;
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import scala.Tuple2;
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public class GenerateEventsApplication {
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private static final Logger log = LoggerFactory.getLogger(GenerateEventsApplication.class);
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// Simple Matchers
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private static final UpdateMatcher<Result, ?> enrichMissingAbstract = new EnrichMissingAbstract();
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private static final UpdateMatcher<Result, ?> enrichMissingAuthorOrcid = new EnrichMissingAuthorOrcid();
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private static final UpdateMatcher<Result, ?> enrichMissingOpenAccess = new EnrichMissingOpenAccess();
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private static final UpdateMatcher<Result, ?> enrichMissingPid = new EnrichMissingPid();
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private static final UpdateMatcher<Result, ?> enrichMissingPublicationDate = new EnrichMissingPublicationDate();
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private static final UpdateMatcher<Result, ?> enrichMissingSubject = new EnrichMissingSubject();
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private static final UpdateMatcher<Result, ?> enrichMoreOpenAccess = new EnrichMoreOpenAccess();
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private static final UpdateMatcher<Result, ?> enrichMorePid = new EnrichMorePid();
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private static final UpdateMatcher<Result, ?> enrichMoreSubject = new EnrichMoreSubject();
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// Advanced matchers
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private static final UpdateMatcher<Pair<Result, List<Project>>, ?> enrichMissingProject = new EnrichMissingProject();
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private static final UpdateMatcher<Pair<Result, List<Project>>, ?> enrichMoreProject = new EnrichMoreProject();
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private static final UpdateMatcher<Pair<Result, List<Software>>, ?> enrichMissingSoftware = new EnrichMissingSoftware();
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private static final UpdateMatcher<Pair<Result, List<Software>>, ?> enrichMoreSoftware = new EnrichMoreSoftware();
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private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMisissingPublicationIsRelatedTo = new EnrichMissingPublicationIsRelatedTo();
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private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsReferencedBy =
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new EnrichMissingPublicationIsReferencedBy();
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private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationReferences = new EnrichMissingPublicationReferences();
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private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsSupplementedTo =
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new EnrichMissingPublicationIsSupplementedTo();
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private static final UpdateMatcher<Pair<Result, List<Publication>>, ?> enrichMissingPublicationIsSupplementedBy =
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new EnrichMissingPublicationIsSupplementedBy();
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private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMisissingDatasetIsRelatedTo =
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new EnrichMissingDatasetIsRelatedTo();
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private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsReferencedBy =
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new EnrichMissingDatasetIsReferencedBy();
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private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetReferences =
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new EnrichMissingDatasetReferences();
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private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsSupplementedTo =
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new EnrichMissingDatasetIsSupplementedTo();
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private static final UpdateMatcher<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>, ?> enrichMissingDatasetIsSupplementedBy =
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new EnrichMissingDatasetIsSupplementedBy();
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// Aggregators
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private static final TypedColumn<Tuple2<Result, Relation>, ResultGroup> resultAggrTypedColumn = new ResultAggregator().toColumn();
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(GenerateEventsApplication.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/merge_claims_parameters.json")));
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parser.parseArgument(args);
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final 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 graphPath = parser.get("graphPath");
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log.info("graphPath: {}", graphPath);
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final String eventsPath = parser.get("eventsPath");
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log.info("eventsPath: {}", eventsPath);
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final String isLookupUrl = parser.get("isLookupUrl");
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log.info("isLookupUrl: {}", isLookupUrl);
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final String dedupConfigProfileId = parser.get("dedupConfProfile");
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log.info("dedupConfigProfileId: {}", dedupConfigProfileId);
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final SparkConf conf = new SparkConf();
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final DedupConfig dedupConfig = loadDedupConfig(isLookupUrl, dedupConfigProfileId);
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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removeOutputDir(spark, eventsPath);
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final Dataset<Event> all = spark.emptyDataset(Encoders.kryo(Event.class));
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for (final Class<? extends Result> r1 : BrokerConstants.RESULT_CLASSES) {
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all.union(generateSimpleEvents(spark, graphPath, r1, dedupConfig));
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for (final Class<? extends Result> r2 : BrokerConstants.RESULT_CLASSES) {
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all.union(generateRelationEvents(spark, graphPath, r1, r2, dedupConfig));
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}
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}
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all.write().mode(SaveMode.Overwrite).json(eventsPath);
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});
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}
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private static void removeOutputDir(final SparkSession spark, final String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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private static <R extends Result> Dataset<Event> generateSimpleEvents(final SparkSession spark,
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final String graphPath,
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final Class<R> resultClazz,
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final DedupConfig dedupConfig) {
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final Dataset<Result> results = readPath(spark, graphPath + "/" + resultClazz.getSimpleName().toLowerCase(), Result.class)
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.filter(r -> r.getDataInfo().getDeletedbyinference());
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final Dataset<Relation> mergedRels = readPath(spark, graphPath + "/relation", Relation.class)
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.filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
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return results.joinWith(mergedRels, results.col("id").equalTo(mergedRels.col("source")), "inner")
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.groupByKey((MapFunction<Tuple2<Result, Relation>, String>) t -> t._2.getTarget(), Encoders.STRING())
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.agg(resultAggrTypedColumn)
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.map((MapFunction<Tuple2<String, ResultGroup>, ResultGroup>) t -> t._2, Encoders.kryo(ResultGroup.class))
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.filter(ResultGroup::isValid)
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.map((MapFunction<ResultGroup, EventGroup>) g -> GenerateEventsApplication.generateSimpleEvents(g, dedupConfig), Encoders.kryo(EventGroup.class))
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.flatMap(group -> group.getData().iterator(), Encoders.kryo(Event.class));
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}
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private static EventGroup generateSimpleEvents(final ResultGroup results, final DedupConfig dedupConfig) {
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final List<UpdateInfo<?>> list = new ArrayList<>();
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for (final Result target : results.getData()) {
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list.addAll(enrichMissingAbstract.searchUpdatesForRecord(target, results.getData(), dedupConfig));
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list.addAll(enrichMissingAuthorOrcid.searchUpdatesForRecord(target, results.getData(), dedupConfig));
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list.addAll(enrichMissingOpenAccess.searchUpdatesForRecord(target, results.getData(), dedupConfig));
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list.addAll(enrichMissingPid.searchUpdatesForRecord(target, results.getData(), dedupConfig));
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list.addAll(enrichMissingPublicationDate.searchUpdatesForRecord(target, results.getData(), dedupConfig));
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list.addAll(enrichMissingSubject.searchUpdatesForRecord(target, results.getData(), dedupConfig));
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list.addAll(enrichMoreOpenAccess.searchUpdatesForRecord(target, results.getData(), dedupConfig));
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list.addAll(enrichMorePid.searchUpdatesForRecord(target, results.getData(), dedupConfig));
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list.addAll(enrichMoreSubject.searchUpdatesForRecord(target, results.getData(), dedupConfig));
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}
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final EventGroup events = new EventGroup();
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list.stream().map(EventFactory::newBrokerEvent).forEach(events::addElement);
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return events;
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}
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private static <SRC extends Result, TRG extends OafEntity> Dataset<Event> generateRelationEvents(final SparkSession spark,
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final String graphPath,
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final Class<SRC> sourceClass,
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final Class<TRG> targetClass,
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final DedupConfig dedupConfig) {
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final Dataset<Result> sources = readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), Result.class)
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.filter(r -> r.getDataInfo().getDeletedbyinference());
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final Dataset<TRG> targets = readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), targetClass);
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final Dataset<Relation> mergedRels = readPath(spark, graphPath + "/relation", Relation.class)
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.filter(r -> r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
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final Dataset<Relation> rels = readPath(spark, graphPath + "/relation", Relation.class)
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.filter(r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS));
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final Dataset<ResultGroup> duplicates = sources.joinWith(mergedRels, sources.col("id").equalTo(rels.col("source")), "inner")
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.groupByKey((MapFunction<Tuple2<Result, Relation>, String>) t -> t._2.getTarget(), Encoders.STRING())
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.agg(resultAggrTypedColumn)
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.map((MapFunction<Tuple2<String, ResultGroup>, ResultGroup>) t -> t._2, Encoders.kryo(ResultGroup.class))
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.filter(ResultGroup::isValid);
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if (targetClass == Project.class) {
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// TODO join using: generateProjectsEvents
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} else if (targetClass == Software.class) {
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// TODO join using: generateSoftwareEvents
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} else if (targetClass == Publication.class) {
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// TODO join using: generatePublicationRelatedEvents
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} else if (targetClass == eu.dnetlib.dhp.schema.oaf.Dataset.class) {
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// TODO join using: generateDatasetRelatedEvents
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}
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return null;
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}
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private List<Event> generateProjectsEvents(final Collection<Pair<Result, List<Project>>> childrenWithProjects, final DedupConfig dedupConfig) {
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final List<UpdateInfo<?>> list = new ArrayList<>();
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for (final Pair<Result, List<Project>> target : childrenWithProjects) {
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list.addAll(enrichMissingProject.searchUpdatesForRecord(target, childrenWithProjects, dedupConfig));
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list.addAll(enrichMoreProject.searchUpdatesForRecord(target, childrenWithProjects, dedupConfig));
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}
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return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
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}
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private List<Event> generateSoftwareEvents(final Collection<Pair<Result, List<Software>>> childrenWithSoftwares, final DedupConfig dedupConfig) {
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final List<UpdateInfo<?>> list = new ArrayList<>();
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for (final Pair<Result, List<Software>> target : childrenWithSoftwares) {
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list.addAll(enrichMissingSoftware.searchUpdatesForRecord(target, childrenWithSoftwares, dedupConfig));
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list.addAll(enrichMoreSoftware.searchUpdatesForRecord(target, childrenWithSoftwares, dedupConfig));
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}
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return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
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}
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private List<Event> generatePublicationRelatedEvents(final String relType,
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final Collection<Pair<Result, Map<String, List<Publication>>>> childrenWithRels,
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final DedupConfig dedupConfig) {
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final List<UpdateInfo<?>> list = new ArrayList<>();
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final List<Pair<Result, List<Publication>>> cleanedChildrens = childrenWithRels
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.stream()
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.filter(p -> p.getRight().containsKey(relType))
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.map(p -> Pair.of(p.getLeft(), p.getRight().get(relType)))
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.filter(p -> p.getRight().size() > 0)
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.collect(Collectors.toList());
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for (final Pair<Result, List<Publication>> target : cleanedChildrens) {
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if (relType.equals("isRelatedTo")) {
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list.addAll(enrichMisissingPublicationIsRelatedTo.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig));
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} else if (relType.equals("references")) {
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list.addAll(enrichMissingPublicationReferences.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig));
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} else if (relType.equals("isReferencedBy")) {
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list.addAll(enrichMissingPublicationIsReferencedBy.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig));
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} else if (relType.equals("isSupplementedTo")) {
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list.addAll(enrichMissingPublicationIsSupplementedTo.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig));
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} else if (relType.equals("isSupplementedBy")) {
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list.addAll(enrichMissingPublicationIsSupplementedBy.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig));
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}
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}
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return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
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}
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private List<Event> generateDatasetRelatedEvents(final String relType,
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final Collection<Pair<Result, Map<String, List<eu.dnetlib.dhp.schema.oaf.Dataset>>>> childrenWithRels,
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final DedupConfig dedupConfig) {
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final List<UpdateInfo<?>> list = new ArrayList<>();
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final List<Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>>> cleanedChildrens = childrenWithRels
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.stream()
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.filter(p -> p.getRight().containsKey(relType))
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.map(p -> Pair.of(p.getLeft(), p.getRight().get(relType)))
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.filter(p -> p.getRight().size() > 0)
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.collect(Collectors.toList());
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for (final Pair<Result, List<eu.dnetlib.dhp.schema.oaf.Dataset>> target : cleanedChildrens) {
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if (relType.equals("isRelatedTo")) {
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list.addAll(enrichMisissingDatasetIsRelatedTo.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig));
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} else if (relType.equals("references")) {
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list.addAll(enrichMissingDatasetReferences.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig));
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} else if (relType.equals("isReferencedBy")) {
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list.addAll(enrichMissingDatasetIsReferencedBy.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig));
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} else if (relType.equals("isSupplementedTo")) {
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list.addAll(enrichMissingDatasetIsSupplementedTo.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig));
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} else if (relType.equals("isSupplementedBy")) {
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list.addAll(enrichMissingDatasetIsSupplementedBy.searchUpdatesForRecord(target, cleanedChildrens, dedupConfig));
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}
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}
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return list.stream().map(EventFactory::newBrokerEvent).collect(Collectors.toList());
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}
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public static <R> Dataset<R> readPath(
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final SparkSession spark,
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final String inputPath,
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final Class<R> clazz) {
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return spark
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.read()
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.textFile(inputPath)
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.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
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}
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private static DedupConfig loadDedupConfig(final String isLookupUrl, final String profId) throws Exception {
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final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl);
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final String conf = isLookUpService.getResourceProfileByQuery(String
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.format("for $x in /RESOURCE_PROFILE[.//RESOURCE_IDENTIFIER/@value = '%s'] return $x//DEDUPLICATION/text()", profId));
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final DedupConfig dedupConfig = new ObjectMapper().readValue(conf, DedupConfig.class);
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dedupConfig.getPace().initModel();
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dedupConfig.getPace().initTranslationMap();
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// dedupConfig.getWf().setConfigurationId("???");
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return dedupConfig;
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}
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}
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