forked from D-Net/dnet-hadoop
Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop
This commit is contained in:
commit
4b9fb2ffb8
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@ -11,6 +11,8 @@ import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.time.DateUtils;
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import eu.dnetlib.broker.objects.OaBrokerMainEntity;
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import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
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import eu.dnetlib.dhp.broker.oa.util.BrokerConstants;
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import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
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public class EventFactory {
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@ -52,9 +54,11 @@ public class EventFactory {
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final OaBrokerMainEntity source = updateInfo.getSource();
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final OaBrokerMainEntity target = updateInfo.getTarget();
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map.setTargetDatasourceId(target.getCollectedFromId());
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map.setTargetDatasourceName(target.getCollectedFromName());
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map.setTargetDatasourceType(target.getCollectedFromType());
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final OaBrokerRelatedDatasource targetDs = updateInfo.getTargetDs();
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map.setTargetDatasourceId(targetDs.getOpenaireId());
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map.setTargetDatasourceName(targetDs.getName());
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map.setTargetDatasourceType(targetDs.getType());
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map.setTargetResultId(target.getOpenaireId());
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@ -73,11 +77,19 @@ public class EventFactory {
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// PROVENANCE INFO
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map.setTrust(updateInfo.getTrust());
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map.setProvenanceDatasourceId(source.getCollectedFromId());
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map.setProvenanceDatasourceName(source.getCollectedFromName());
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map.setProvenanceDatasourceType(source.getCollectedFromType());
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map.setProvenanceResultId(source.getOpenaireId());
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source
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.getDatasources()
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.stream()
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.filter(ds -> ds.getRelType().equals(BrokerConstants.COLLECTED_FROM_REL))
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.findFirst()
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.ifPresent(ds -> {
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map.setProvenanceDatasourceId(ds.getOpenaireId());
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map.setProvenanceDatasourceName(ds.getName());
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map.setProvenanceDatasourceType(ds.getType());
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});
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return map;
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}
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@ -17,8 +17,8 @@ import org.slf4j.LoggerFactory;
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import eu.dnetlib.broker.objects.OaBrokerMainEntity;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
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import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.AddDatasourceTypeAggregator;
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import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.SimpleDatasourceInfo;
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import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDatasource;
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import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDatasourceAggregator;
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import scala.Tuple2;
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public class JoinStep0Job {
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@ -45,33 +45,33 @@ public class JoinStep0Job {
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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 = workingPath + "/joinedEntities_step0";
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log.info("outputPath: {}", outputPath);
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final String joinedEntitiesPath = workingPath + "/joinedEntities_step0";
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log.info("joinedEntitiesPath: {}", joinedEntitiesPath);
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final SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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ClusterUtils.removeDir(spark, outputPath);
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ClusterUtils.removeDir(spark, joinedEntitiesPath);
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final LongAccumulator total = spark.sparkContext().longAccumulator("total_entities");
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final Dataset<OaBrokerMainEntity> sources = ClusterUtils
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.readPath(spark, workingPath + "/simpleEntities", OaBrokerMainEntity.class);
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final Dataset<SimpleDatasourceInfo> datasources = ClusterUtils
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.readPath(spark, workingPath + "/datasources", SimpleDatasourceInfo.class);
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final Dataset<RelatedDatasource> typedRels = ClusterUtils
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.readPath(spark, workingPath + "/relatedDatasources", RelatedDatasource.class);
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final TypedColumn<Tuple2<OaBrokerMainEntity, SimpleDatasourceInfo>, OaBrokerMainEntity> aggr = new AddDatasourceTypeAggregator()
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final TypedColumn<Tuple2<OaBrokerMainEntity, RelatedDatasource>, OaBrokerMainEntity> aggr = new RelatedDatasourceAggregator()
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.toColumn();
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final Dataset<OaBrokerMainEntity> dataset = sources
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.joinWith(datasources, sources.col("collectedFromId").equalTo(datasources.col("id")), "inner")
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.joinWith(typedRels, sources.col("openaireId").equalTo(typedRels.col("source")), "left_outer")
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.groupByKey(t -> t._1.getOpenaireId(), Encoders.STRING())
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.agg(aggr)
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.map(t -> t._2, Encoders.bean(OaBrokerMainEntity.class));
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ClusterUtils.save(dataset, outputPath, OaBrokerMainEntity.class, total);
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ClusterUtils.save(dataset, joinedEntitiesPath, OaBrokerMainEntity.class, total);
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});
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@ -9,14 +9,23 @@ import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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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.SparkSession;
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import org.apache.spark.util.LongAccumulator;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.broker.oa.util.ClusterUtils;
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import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.SimpleDatasourceInfo;
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import eu.dnetlib.dhp.broker.oa.util.ConversionUtils;
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import eu.dnetlib.dhp.broker.oa.util.DatasourceRelationsAccumulator;
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import eu.dnetlib.dhp.broker.oa.util.aggregators.withRels.RelatedDatasource;
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import eu.dnetlib.dhp.schema.oaf.Datasource;
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import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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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 scala.Tuple3;
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public class PrepareRelatedDatasourcesJob {
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@ -42,7 +51,7 @@ public class PrepareRelatedDatasourcesJob {
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final String workingPath = parser.get("workingPath");
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log.info("workingPath: {}", workingPath);
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final String relsPath = workingPath + "/datasources";
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final String relsPath = workingPath + "/relatedDatasources";
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log.info("relsPath: {}", relsPath);
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final SparkConf conf = new SparkConf();
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@ -53,16 +62,46 @@ public class PrepareRelatedDatasourcesJob {
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final LongAccumulator total = spark.sparkContext().longAccumulator("total_datasources");
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final Dataset<SimpleDatasourceInfo> dataset = ClusterUtils
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.readPath(spark, graphPath + "/datasource", Datasource.class)
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.map(
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ds -> new SimpleDatasourceInfo(ds.getId(), ds.getDatasourcetype().getClassid()),
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Encoders.bean(SimpleDatasourceInfo.class));
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final Dataset<Tuple3<String, String, String>> rels = prepareResultTuples(
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spark, graphPath, Publication.class)
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.union(prepareResultTuples(spark, graphPath, eu.dnetlib.dhp.schema.oaf.Dataset.class))
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.union(prepareResultTuples(spark, graphPath, Software.class))
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.union(prepareResultTuples(spark, graphPath, OtherResearchProduct.class));
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ClusterUtils.save(dataset, relsPath, SimpleDatasourceInfo.class, total);
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final Dataset<OaBrokerRelatedDatasource> datasources = ClusterUtils
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.readPath(spark, graphPath + "/datasource", Datasource.class)
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.map(ConversionUtils::oafDatasourceToBrokerDatasource, Encoders.bean(OaBrokerRelatedDatasource.class));
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final Dataset<RelatedDatasource> dataset = rels
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.joinWith(datasources, datasources.col("openaireId").equalTo(rels.col("_2")), "inner")
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.map(t -> {
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final RelatedDatasource r = new RelatedDatasource();
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r.setSource(t._1._1());
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r.setRelDatasource(t._2);
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r.getRelDatasource().setRelType(t._1._3());
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return r;
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}, Encoders.bean(RelatedDatasource.class));
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ClusterUtils.save(dataset, relsPath, RelatedDatasource.class, total);
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});
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}
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private static final Dataset<Tuple3<String, String, String>> prepareResultTuples(final SparkSession spark,
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final String graphPath,
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final Class<? extends Result> sourceClass) {
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return ClusterUtils
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.readPath(spark, graphPath + "/" + sourceClass.getSimpleName().toLowerCase(), sourceClass)
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.filter(r -> !ClusterUtils.isDedupRoot(r.getId()))
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.filter(r -> r.getDataInfo().getDeletedbyinference())
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.map(
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r -> DatasourceRelationsAccumulator.calculateTuples(r),
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Encoders.bean(DatasourceRelationsAccumulator.class))
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.flatMap(
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acc -> acc.getRels().iterator(),
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Encoders.tuple(Encoders.STRING(), Encoders.STRING(), Encoders.STRING()));
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}
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}
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|
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@ -15,6 +15,7 @@ import org.apache.commons.lang3.StringUtils;
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import org.apache.spark.util.LongAccumulator;
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import eu.dnetlib.broker.objects.OaBrokerMainEntity;
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import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
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import eu.dnetlib.dhp.broker.model.Topic;
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import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
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@ -34,18 +35,19 @@ public abstract class UpdateMatcher<T> {
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this.highlightToStringFunction = highlightToStringFunction;
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}
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public Collection<UpdateInfo<T>> searchUpdatesForRecord(final OaBrokerMainEntity res,
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public Collection<UpdateInfo<T>> searchUpdatesForRecord(final OaBrokerMainEntity target,
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final OaBrokerRelatedDatasource targetDs,
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final Collection<OaBrokerMainEntity> others,
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final Map<String, LongAccumulator> accumulators) {
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final Map<String, UpdateInfo<T>> infoMap = new HashMap<>();
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for (final OaBrokerMainEntity source : others) {
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if (source != res) {
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for (final T hl : findDifferences(source, res)) {
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if (source != target) {
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for (final T hl : findDifferences(source, target)) {
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final Topic topic = getTopicFunction().apply(hl);
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if (topic != null) {
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final UpdateInfo<T> info = new UpdateInfo<>(topic, hl, source, res,
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final UpdateInfo<T> info = new UpdateInfo<>(topic, hl, source, target, targetDs,
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getCompileHighlightFunction(),
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getHighlightToStringFunction());
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|
|
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@ -14,6 +14,10 @@ public class BrokerConstants {
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public static final String OPEN_ACCESS = "OPEN";
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public static final String IS_MERGED_IN_CLASS = "isMergedIn";
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public static final String COLLECTED_FROM_REL = "collectedFrom";
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public static final String HOSTED_BY_REL = "hostedBy";
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public static final float MIN_TRUST = 0.25f;
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public static final float MAX_TRUST = 1.00f;
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|
|
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|
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@ -22,11 +22,13 @@ import eu.dnetlib.broker.objects.OaBrokerJournal;
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import eu.dnetlib.broker.objects.OaBrokerMainEntity;
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import eu.dnetlib.broker.objects.OaBrokerProject;
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import eu.dnetlib.broker.objects.OaBrokerRelatedDataset;
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import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
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import eu.dnetlib.broker.objects.OaBrokerRelatedPublication;
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import eu.dnetlib.broker.objects.OaBrokerRelatedSoftware;
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import eu.dnetlib.broker.objects.OaBrokerTypedValue;
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import eu.dnetlib.dhp.schema.oaf.Author;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
|
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import eu.dnetlib.dhp.schema.oaf.Datasource;
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import eu.dnetlib.dhp.schema.oaf.ExternalReference;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.Instance;
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|
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@ -119,8 +121,6 @@ public class ConversionUtils {
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res
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.setJournal(
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result instanceof Publication ? oafJournalToBrokerJournal(((Publication) result).getJournal()) : null);
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res.setCollectedFromId(mappedFirst(result.getCollectedfrom(), KeyValue::getKey));
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res.setCollectedFromName(mappedFirst(result.getCollectedfrom(), KeyValue::getValue));
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||||
res.setPids(mappedList(result.getPid(), ConversionUtils::oafPidToBrokerPid));
|
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res.setInstances(flatMappedList(result.getInstance(), ConversionUtils::oafInstanceToBrokerInstances));
|
||||
res
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||||
|
|
@ -223,6 +223,18 @@ public class ConversionUtils {
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|||
return res;
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}
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|
||||
public static final OaBrokerRelatedDatasource oafDatasourceToBrokerDatasource(final Datasource ds) {
|
||||
if (ds == null) {
|
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return null;
|
||||
}
|
||||
|
||||
final OaBrokerRelatedDatasource res = new OaBrokerRelatedDatasource();
|
||||
res.setName(StringUtils.defaultIfBlank(fieldValue(ds.getOfficialname()), fieldValue(ds.getEnglishname())));
|
||||
res.setOpenaireId(ds.getId());
|
||||
res.setType(classId(ds.getDatasourcetype()));
|
||||
return res;
|
||||
}
|
||||
|
||||
private static String first(final List<String> list) {
|
||||
return list != null && list.size() > 0 ? list.get(0) : null;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,68 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.Objects;
|
||||
import java.util.Set;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import scala.Tuple3;
|
||||
|
||||
public class DatasourceRelationsAccumulator implements Serializable {
|
||||
|
||||
/**
|
||||
*
|
||||
*/
|
||||
private static final long serialVersionUID = 3256220670651218957L;
|
||||
|
||||
private List<Tuple3<String, String, String>> rels = new ArrayList<>();
|
||||
|
||||
public List<Tuple3<String, String, String>> getRels() {
|
||||
return rels;
|
||||
}
|
||||
|
||||
public void setRels(final List<Tuple3<String, String, String>> rels) {
|
||||
this.rels = rels;
|
||||
}
|
||||
|
||||
protected void addTuple(final Tuple3<String, String, String> t) {
|
||||
rels.add(t);
|
||||
}
|
||||
|
||||
public static final DatasourceRelationsAccumulator calculateTuples(final Result r) {
|
||||
|
||||
final Set<String> collectedFromSet = r
|
||||
.getCollectedfrom()
|
||||
.stream()
|
||||
.map(kv -> kv.getKey())
|
||||
.filter(StringUtils::isNotBlank)
|
||||
.distinct()
|
||||
.collect(Collectors.toSet());
|
||||
|
||||
final Set<String> hostedBySet = r
|
||||
.getInstance()
|
||||
.stream()
|
||||
.map(i -> i.getHostedby())
|
||||
.filter(Objects::nonNull)
|
||||
.filter(kv -> !StringUtils.equalsIgnoreCase(kv.getValue(), "Unknown Repository"))
|
||||
.map(kv -> kv.getKey())
|
||||
.filter(StringUtils::isNotBlank)
|
||||
.distinct()
|
||||
.filter(id -> !collectedFromSet.contains(id))
|
||||
.collect(Collectors.toSet());
|
||||
|
||||
final DatasourceRelationsAccumulator res = new DatasourceRelationsAccumulator();
|
||||
collectedFromSet
|
||||
.stream()
|
||||
.map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.COLLECTED_FROM_REL))
|
||||
.forEach(res::addTuple);
|
||||
hostedBySet.stream().map(s -> new Tuple3<>(r.getId(), s, BrokerConstants.HOSTED_BY_REL)).forEach(res::addTuple);
|
||||
return res;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -11,6 +11,7 @@ import org.slf4j.Logger;
|
|||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
|
||||
import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
|
||||
import eu.dnetlib.dhp.broker.model.EventFactory;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.UpdateMatcher;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets.EnrichMissingDatasetIsReferencedBy;
|
||||
|
|
@ -80,9 +81,11 @@ public class EventFinder {
|
|||
final List<UpdateInfo<?>> list = new ArrayList<>();
|
||||
|
||||
for (final OaBrokerMainEntity target : results.getData()) {
|
||||
if (verifyTarget(target, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) {
|
||||
for (final UpdateMatcher<?> matcher : matchers) {
|
||||
list.addAll(matcher.searchUpdatesForRecord(target, results.getData(), accumulators));
|
||||
for (final OaBrokerRelatedDatasource targetDs : target.getDatasources()) {
|
||||
if (verifyTarget(targetDs, dsIdWhitelist, dsIdBlacklist, dsTypeWhitelist)) {
|
||||
for (final UpdateMatcher<?> matcher : matchers) {
|
||||
list.addAll(matcher.searchUpdatesForRecord(target, targetDs, results.getData(), accumulators));
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -90,17 +93,17 @@ public class EventFinder {
|
|||
return asEventGroup(list);
|
||||
}
|
||||
|
||||
private static boolean verifyTarget(final OaBrokerMainEntity target,
|
||||
private static boolean verifyTarget(final OaBrokerRelatedDatasource target,
|
||||
final Set<String> dsIdWhitelist,
|
||||
final Set<String> dsIdBlacklist,
|
||||
final Set<String> dsTypeWhitelist) {
|
||||
|
||||
if (dsIdWhitelist.contains(target.getCollectedFromId())) {
|
||||
if (dsIdWhitelist.contains(target.getOpenaireId())) {
|
||||
return true;
|
||||
} else if (dsIdBlacklist.contains(target.getCollectedFromId())) {
|
||||
} else if (dsIdBlacklist.contains(target.getOpenaireId())) {
|
||||
return false;
|
||||
} else {
|
||||
return dsTypeWhitelist.contains(target.getCollectedFromType());
|
||||
return dsTypeWhitelist.contains(target.getType());
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -8,6 +8,7 @@ import eu.dnetlib.broker.objects.OaBrokerEventPayload;
|
|||
import eu.dnetlib.broker.objects.OaBrokerInstance;
|
||||
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
|
||||
import eu.dnetlib.broker.objects.OaBrokerProvenance;
|
||||
import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
|
||||
public final class UpdateInfo<T> {
|
||||
|
|
@ -20,6 +21,8 @@ public final class UpdateInfo<T> {
|
|||
|
||||
private final OaBrokerMainEntity target;
|
||||
|
||||
private final OaBrokerRelatedDatasource targetDs;
|
||||
|
||||
private final BiConsumer<OaBrokerMainEntity, T> compileHighlight;
|
||||
|
||||
private final Function<T, String> highlightToString;
|
||||
|
|
@ -28,12 +31,14 @@ public final class UpdateInfo<T> {
|
|||
|
||||
public UpdateInfo(final Topic topic, final T highlightValue, final OaBrokerMainEntity source,
|
||||
final OaBrokerMainEntity target,
|
||||
final OaBrokerRelatedDatasource targetDs,
|
||||
final BiConsumer<OaBrokerMainEntity, T> compileHighlight,
|
||||
final Function<T, String> highlightToString) {
|
||||
this.topic = topic;
|
||||
this.highlightValue = highlightValue;
|
||||
this.source = source;
|
||||
this.target = target;
|
||||
this.targetDs = targetDs;
|
||||
this.compileHighlight = compileHighlight;
|
||||
this.highlightToString = highlightToString;
|
||||
this.trust = TrustUtils.calculateTrust(source, target);
|
||||
|
|
@ -51,6 +56,10 @@ public final class UpdateInfo<T> {
|
|||
return target;
|
||||
}
|
||||
|
||||
public OaBrokerRelatedDatasource getTargetDs() {
|
||||
return targetDs;
|
||||
}
|
||||
|
||||
protected Topic getTopic() {
|
||||
return topic;
|
||||
}
|
||||
|
|
@ -75,8 +84,20 @@ public final class UpdateInfo<T> {
|
|||
compileHighlight.accept(hl, getHighlightValue());
|
||||
|
||||
final String provId = getSource().getOpenaireId();
|
||||
final String provRepo = getSource().getCollectedFromName();
|
||||
final String provType = getSource().getCollectedFromType();
|
||||
final String provRepo = getSource()
|
||||
.getDatasources()
|
||||
.stream()
|
||||
.filter(ds -> ds.getRelType().equals(BrokerConstants.COLLECTED_FROM_REL))
|
||||
.map(ds -> ds.getName())
|
||||
.findFirst()
|
||||
.orElse("");
|
||||
final String provType = getSource()
|
||||
.getDatasources()
|
||||
.stream()
|
||||
.filter(ds -> ds.getRelType().equals(BrokerConstants.COLLECTED_FROM_REL))
|
||||
.map(ds -> ds.getType())
|
||||
.findFirst()
|
||||
.orElse("");
|
||||
|
||||
final String provUrl = getSource()
|
||||
.getInstances()
|
||||
|
|
|
|||
|
|
@ -0,0 +1,42 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
|
||||
|
||||
public class RelatedDatasource implements Serializable {
|
||||
|
||||
/**
|
||||
*
|
||||
*/
|
||||
private static final long serialVersionUID = 3015550240920424010L;
|
||||
|
||||
private String source;
|
||||
private OaBrokerRelatedDatasource relDatasource;
|
||||
|
||||
public RelatedDatasource() {
|
||||
}
|
||||
|
||||
public RelatedDatasource(final String source, final OaBrokerRelatedDatasource relDatasource) {
|
||||
this.source = source;
|
||||
this.relDatasource = relDatasource;
|
||||
}
|
||||
|
||||
public String getSource() {
|
||||
return source;
|
||||
}
|
||||
|
||||
public void setSource(final String source) {
|
||||
this.source = source;
|
||||
}
|
||||
|
||||
public OaBrokerRelatedDatasource getRelDatasource() {
|
||||
return relDatasource;
|
||||
}
|
||||
|
||||
public void setRelDatasource(final OaBrokerRelatedDatasource relDatasource) {
|
||||
this.relDatasource = relDatasource;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -7,15 +7,16 @@ import org.apache.spark.sql.Encoders;
|
|||
import org.apache.spark.sql.expressions.Aggregator;
|
||||
|
||||
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
|
||||
import eu.dnetlib.dhp.broker.oa.util.BrokerConstants;
|
||||
import scala.Tuple2;
|
||||
|
||||
public class AddDatasourceTypeAggregator
|
||||
extends Aggregator<Tuple2<OaBrokerMainEntity, SimpleDatasourceInfo>, OaBrokerMainEntity, OaBrokerMainEntity> {
|
||||
public class RelatedDatasourceAggregator
|
||||
extends Aggregator<Tuple2<OaBrokerMainEntity, RelatedDatasource>, OaBrokerMainEntity, OaBrokerMainEntity> {
|
||||
|
||||
/**
|
||||
*
|
||||
*/
|
||||
private static final long serialVersionUID = 8788588975496014728L;
|
||||
private static final long serialVersionUID = -7212121913834713672L;
|
||||
|
||||
@Override
|
||||
public OaBrokerMainEntity zero() {
|
||||
|
|
@ -29,10 +30,10 @@ public class AddDatasourceTypeAggregator
|
|||
|
||||
@Override
|
||||
public OaBrokerMainEntity reduce(final OaBrokerMainEntity g,
|
||||
final Tuple2<OaBrokerMainEntity, SimpleDatasourceInfo> t) {
|
||||
final Tuple2<OaBrokerMainEntity, RelatedDatasource> t) {
|
||||
final OaBrokerMainEntity res = StringUtils.isNotBlank(g.getOpenaireId()) ? g : t._1;
|
||||
if (t._2 != null && StringUtils.isNotBlank(t._2.getType())) {
|
||||
res.setCollectedFromType(t._2.getType());
|
||||
if (t._2 != null && res.getDatasources().size() < BrokerConstants.MAX_NUMBER_OF_RELS) {
|
||||
res.getDatasources().add(t._2.getRelDatasource());
|
||||
}
|
||||
return res;
|
||||
|
||||
|
|
@ -40,7 +41,15 @@ public class AddDatasourceTypeAggregator
|
|||
|
||||
@Override
|
||||
public OaBrokerMainEntity merge(final OaBrokerMainEntity g1, final OaBrokerMainEntity g2) {
|
||||
if (StringUtils.isNotBlank(g1.getOpenaireId()) && StringUtils.isNotBlank(g1.getCollectedFromType())) {
|
||||
if (StringUtils.isNotBlank(g1.getOpenaireId())) {
|
||||
final int availables = BrokerConstants.MAX_NUMBER_OF_RELS - g1.getDatasources().size();
|
||||
if (availables > 0) {
|
||||
if (g2.getDatasources().size() <= availables) {
|
||||
g1.getDatasources().addAll(g2.getDatasources());
|
||||
} else {
|
||||
g1.getDatasources().addAll(g2.getDatasources().subList(0, availables));
|
||||
}
|
||||
}
|
||||
return g1;
|
||||
} else {
|
||||
return g2;
|
||||
|
|
@ -56,4 +65,5 @@ public class AddDatasourceTypeAggregator
|
|||
public Encoder<OaBrokerMainEntity> outputEncoder() {
|
||||
return Encoders.bean(OaBrokerMainEntity.class);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,40 +0,0 @@
|
|||
|
||||
package eu.dnetlib.dhp.broker.oa.util.aggregators.withRels;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class SimpleDatasourceInfo implements Serializable {
|
||||
|
||||
/**
|
||||
*
|
||||
*/
|
||||
private static final long serialVersionUID = 2996609859416024734L;
|
||||
|
||||
private String id;
|
||||
private String type;
|
||||
|
||||
public SimpleDatasourceInfo() {
|
||||
}
|
||||
|
||||
public SimpleDatasourceInfo(final String id, final String type) {
|
||||
this.id = id;
|
||||
this.type = type;
|
||||
}
|
||||
|
||||
public String getId() {
|
||||
return id;
|
||||
}
|
||||
|
||||
public void setId(final String id) {
|
||||
this.id = id;
|
||||
}
|
||||
|
||||
public String getType() {
|
||||
return type;
|
||||
}
|
||||
|
||||
public void setType(final String type) {
|
||||
this.type = type;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -448,6 +448,30 @@
|
|||
<arg>--index</arg><arg>${esIndexName}</arg>
|
||||
<arg>--esHost</arg><arg>${esIndexHost}</arg>
|
||||
</spark>
|
||||
<ok to="stats"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="stats">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>GenerateStatsJob</name>
|
||||
<class>eu.dnetlib.dhp.broker.oa.GenerateStatsJob</class>
|
||||
<jar>dhp-broker-events-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
|
|
|||
|
|
@ -64,14 +64,209 @@
|
|||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="stats"/>
|
||||
<start to="join_entities_step0"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
|
||||
<action name="stats">
|
||||
<action name="join_entities_step0">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>JoinStep0</name>
|
||||
<class>eu.dnetlib.dhp.broker.oa.JoinStep0Job</class>
|
||||
<jar>dhp-broker-events-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
</spark>
|
||||
<ok to="join_entities_step1"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="join_entities_step1">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>JoinStep1</name>
|
||||
<class>eu.dnetlib.dhp.broker.oa.JoinStep1Job</class>
|
||||
<jar>dhp-broker-events-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
</spark>
|
||||
<ok to="join_entities_step2"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="join_entities_step2">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>JoinStep2</name>
|
||||
<class>eu.dnetlib.dhp.broker.oa.JoinStep2Job</class>
|
||||
<jar>dhp-broker-events-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
</spark>
|
||||
<ok to="join_entities_step3"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="join_entities_step3">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>JoinStep3</name>
|
||||
<class>eu.dnetlib.dhp.broker.oa.JoinStep3Job</class>
|
||||
<jar>dhp-broker-events-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
</spark>
|
||||
<ok to="join_entities_step4"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="join_entities_step4">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>JoinStep4</name>
|
||||
<class>eu.dnetlib.dhp.broker.oa.JoinStep4Job</class>
|
||||
<jar>dhp-broker-events-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
</spark>
|
||||
<ok to="prepare_groups"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="prepare_groups">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>PrepareGroupsJob</name>
|
||||
<class>eu.dnetlib.dhp.broker.oa.PrepareGroupsJob</class>
|
||||
<jar>dhp-broker-events-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--graphPath</arg><arg>${graphInputPath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
</spark>
|
||||
<ok to="generate_events"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="generate_events">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>GenerateEventsJob</name>
|
||||
<class>eu.dnetlib.dhp.broker.oa.GenerateEventsJob</class>
|
||||
<jar>dhp-broker-events-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--datasourceIdWhitelist</arg><arg>${datasourceIdWhitelist}</arg>
|
||||
<arg>--datasourceTypeWhitelist</arg><arg>${datasourceTypeWhitelist}</arg>
|
||||
<arg>--datasourceIdBlacklist</arg><arg>${datasourceIdBlacklist}</arg>
|
||||
</spark>
|
||||
<ok to="index_es"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="index_es">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>IndexOnESJob</name>
|
||||
<class>eu.dnetlib.dhp.broker.oa.IndexOnESJob</class>
|
||||
<jar>dhp-broker-events-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.dynamicAllocation.maxExecutors="8"
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--index</arg><arg>${esIndexName}</arg>
|
||||
<arg>--esHost</arg><arg>${esIndexHost}</arg>
|
||||
</spark>
|
||||
<ok to="stats"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="stats">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
|
|
|
|||
|
|
@ -8,15 +8,23 @@ import java.util.Collection;
|
|||
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.ExtendWith;
|
||||
import org.mockito.Mock;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import eu.dnetlib.broker.objects.OaBrokerMainEntity;
|
||||
import eu.dnetlib.broker.objects.OaBrokerRelatedDatasource;
|
||||
import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPublicationDate;
|
||||
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
class UpdateMatcherTest {
|
||||
|
||||
UpdateMatcher<String> matcher = new EnrichMissingPublicationDate();
|
||||
|
||||
@Mock
|
||||
private OaBrokerRelatedDatasource targetDs;
|
||||
|
||||
@BeforeEach
|
||||
void setUp() throws Exception {
|
||||
}
|
||||
|
|
@ -30,7 +38,7 @@ class UpdateMatcherTest {
|
|||
final OaBrokerMainEntity p4 = new OaBrokerMainEntity();
|
||||
|
||||
final Collection<UpdateInfo<String>> list = matcher
|
||||
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
|
||||
.searchUpdatesForRecord(res, targetDs, Arrays.asList(p1, p2, p3, p4), null);
|
||||
|
||||
assertTrue(list.isEmpty());
|
||||
}
|
||||
|
|
@ -46,7 +54,7 @@ class UpdateMatcherTest {
|
|||
res.setPublicationdate("2018");
|
||||
|
||||
final Collection<UpdateInfo<String>> list = matcher
|
||||
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
|
||||
.searchUpdatesForRecord(res, targetDs, Arrays.asList(p1, p2, p3, p4), null);
|
||||
|
||||
assertTrue(list.isEmpty());
|
||||
}
|
||||
|
|
@ -62,7 +70,7 @@ class UpdateMatcherTest {
|
|||
p2.setPublicationdate("2018");
|
||||
|
||||
final Collection<UpdateInfo<String>> list = matcher
|
||||
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
|
||||
.searchUpdatesForRecord(res, targetDs, Arrays.asList(p1, p2, p3, p4), null);
|
||||
|
||||
assertTrue(list.size() == 1);
|
||||
}
|
||||
|
|
@ -79,7 +87,7 @@ class UpdateMatcherTest {
|
|||
p2.setPublicationdate("2018");
|
||||
|
||||
final Collection<UpdateInfo<String>> list = matcher
|
||||
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
|
||||
.searchUpdatesForRecord(res, targetDs, Arrays.asList(p1, p2, p3, p4), null);
|
||||
|
||||
assertTrue(list.isEmpty());
|
||||
}
|
||||
|
|
@ -98,7 +106,7 @@ class UpdateMatcherTest {
|
|||
p4.setPublicationdate("2018");
|
||||
|
||||
final Collection<UpdateInfo<String>> list = matcher
|
||||
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
|
||||
.searchUpdatesForRecord(res, targetDs, Arrays.asList(p1, p2, p3, p4), null);
|
||||
|
||||
assertTrue(list.isEmpty());
|
||||
}
|
||||
|
|
@ -117,7 +125,7 @@ class UpdateMatcherTest {
|
|||
p4.setPublicationdate("2018");
|
||||
|
||||
final Collection<UpdateInfo<String>> list = matcher
|
||||
.searchUpdatesForRecord(res, Arrays.asList(p1, p2, p3, p4), null);
|
||||
.searchUpdatesForRecord(res, targetDs, Arrays.asList(p1, p2, p3, p4), null);
|
||||
|
||||
assertTrue(list.size() == 1);
|
||||
}
|
||||
|
|
|
|||
2
pom.xml
2
pom.xml
|
|
@ -624,6 +624,6 @@
|
|||
<mockito-core.version>3.3.3</mockito-core.version>
|
||||
<mongodb.driver.version>3.4.2</mongodb.driver.version>
|
||||
<vtd.version>[2.12,3.0)</vtd.version>
|
||||
<dnet.openaire.broker.common>3.0.0</dnet.openaire.broker.common>
|
||||
<dnet.openaire.broker.common>3.1.0</dnet.openaire.broker.common>
|
||||
</properties>
|
||||
</project>
|
||||
|
|
|
|||
Loading…
Reference in New Issue