forked from D-Net/dnet-hadoop
Include SparkCleanRelation logic in SparkPropagateRelation
SparkPropagateRelation includes merge relations Revised tests for SparkPropagateRelation
This commit is contained in:
parent
488d9a1cea
commit
2caaaec42d
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@ -1,57 +0,0 @@
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package eu.dnetlib.dhp.oa.dedup;
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import java.util.Objects;
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import org.apache.spark.sql.Encoder;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.expressions.Aggregator;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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public class RelationAggregator extends Aggregator<Relation, Relation, Relation> {
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private static final Relation ZERO = new Relation();
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@Override
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public Relation zero() {
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return ZERO;
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}
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@Override
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public Relation reduce(Relation b, Relation a) {
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return mergeRel(b, a);
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}
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@Override
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public Relation merge(Relation b, Relation a) {
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return mergeRel(b, a);
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}
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@Override
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public Relation finish(Relation r) {
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return r;
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}
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private Relation mergeRel(Relation b, Relation a) {
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if (Objects.equals(b, ZERO)) {
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return a;
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}
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if (Objects.equals(a, ZERO)) {
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return b;
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}
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b.mergeFrom(a);
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return b;
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}
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@Override
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public Encoder<Relation> bufferEncoder() {
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return Encoders.kryo(Relation.class);
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}
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@Override
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public Encoder<Relation> outputEncoder() {
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return Encoders.kryo(Relation.class);
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}
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}
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@ -1,78 +0,0 @@
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package eu.dnetlib.dhp.oa.dedup
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.common.HdfsSupport
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import eu.dnetlib.dhp.schema.oaf.Relation
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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 org.apache.commons.io.IOUtils
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import org.apache.spark.SparkConf
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import org.apache.spark.sql._
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import org.apache.spark.sql.functions.col
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import org.apache.spark.sql.types.{DataTypes, StructField, StructType}
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import org.slf4j.LoggerFactory
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object SparkCleanRelation {
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private val log = LoggerFactory.getLogger(classOf[SparkCleanRelation])
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@throws[Exception]
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def main(args: Array[String]): Unit = {
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val parser = new ArgumentApplicationParser(
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IOUtils.toString(
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classOf[SparkCleanRelation].getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json")
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)
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)
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parser.parseArgument(args)
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val conf = new SparkConf
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new SparkCleanRelation(parser, AbstractSparkAction.getSparkSession(conf))
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.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")))
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}
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}
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class SparkCleanRelation(parser: ArgumentApplicationParser, spark: SparkSession)
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extends AbstractSparkAction(parser, spark) {
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override def run(isLookUpService: ISLookUpService): Unit = {
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val graphBasePath = parser.get("graphBasePath")
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val inputPath = parser.get("inputPath")
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val outputPath = parser.get("outputPath")
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SparkCleanRelation.log.info("graphBasePath: '{}'", graphBasePath)
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SparkCleanRelation.log.info("inputPath: '{}'", inputPath)
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SparkCleanRelation.log.info("outputPath: '{}'", outputPath)
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AbstractSparkAction.removeOutputDir(spark, outputPath)
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val entities =
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Seq("datasource", "project", "organization", "publication", "dataset", "software", "otherresearchproduct")
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val idsSchema = StructType.fromDDL("`id` STRING, `dataInfo` STRUCT<`deletedbyinference`:BOOLEAN,`invisible`:BOOLEAN>")
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val emptyIds = spark.createDataFrame(spark.sparkContext.emptyRDD[Row].setName("empty"),
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idsSchema)
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val ids = entities
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.foldLeft(emptyIds)((ds, entity) => {
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val entityPath = graphBasePath + '/' + entity
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if (HdfsSupport.exists(entityPath, spark.sparkContext.hadoopConfiguration)) {
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ds.union(spark.read.schema(idsSchema).json(entityPath))
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} else {
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ds
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}
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})
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.filter("dataInfo.deletedbyinference != true AND dataInfo.invisible != true")
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.select("id")
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.distinct()
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val relations = spark.read.schema(Encoders.bean(classOf[Relation]).schema).json(inputPath)
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.filter("dataInfo.deletedbyinference != true AND dataInfo.invisible != true")
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AbstractSparkAction.save(
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relations
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.join(ids, col("source") === ids("id"), "leftsemi")
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.join(ids, col("target") === ids("id"), "leftsemi"),
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outputPath,
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SaveMode.Overwrite
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)
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}
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}
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@ -3,23 +3,19 @@ package eu.dnetlib.dhp.oa.dedup;
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import static org.apache.spark.sql.functions.col;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.Iterator;
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import java.util.Objects;
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import org.apache.commons.beanutils.BeanUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import 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.ReduceFunction;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.catalyst.encoders.RowEncoder;
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import org.apache.spark.sql.types.StructType;
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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.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.common.EntityType;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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@ -70,73 +66,63 @@ public class SparkPropagateRelation extends AbstractSparkAction {
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log.info("workingPath: '{}'", workingPath);
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log.info("graphOutputPath: '{}'", graphOutputPath);
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final String outputRelationPath = DedupUtility.createEntityPath(graphOutputPath, "relation");
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removeOutputDir(spark, outputRelationPath);
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Dataset<Relation> mergeRels = spark
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.read()
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.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
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.as(REL_BEAN_ENC);
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.read()
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.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
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.as(REL_BEAN_ENC);
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// <mergedObjectID, dedupID>
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Dataset<Row> mergedIds = mergeRels
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.where(col("relClass").equalTo(ModelConstants.MERGES))
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.select(col("source").as("dedupID"), col("target").as("mergedObjectID"))
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.distinct()
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.cache();
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Dataset<Row> idsToMerge = mergeRels
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.where(col("relClass").equalTo(ModelConstants.MERGES))
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.select(col("source").as("dedupID"), col("target").as("mergedObjectID"))
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.distinct();
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Dataset<Row> allRels = spark
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.read()
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.schema(REL_BEAN_ENC.schema())
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.json(DedupUtility.createEntityPath(graphBasePath, "relation"));
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.read()
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.schema(REL_BEAN_ENC.schema())
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.json(graphBasePath + "/relation");
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Dataset<Relation> dedupedRels = allRels
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.joinWith(mergedIds, allRels.col("source").equalTo(mergedIds.col("mergedObjectID")), "left_outer")
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.joinWith(mergedIds, col("_1.target").equalTo(mergedIds.col("mergedObjectID")), "left_outer")
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.select("_1._1", "_1._2.dedupID", "_2.dedupID")
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.as(Encoders.tuple(REL_BEAN_ENC, Encoders.STRING(), Encoders.STRING()))
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.flatMap(SparkPropagateRelation::addInferredRelations, REL_KRYO_ENC);
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.joinWith(idsToMerge, allRels.col("source").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
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.joinWith(idsToMerge, col("_1.target").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
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.select("_1._1", "_1._2.dedupID", "_2.dedupID")
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.as(Encoders.tuple(REL_BEAN_ENC, Encoders.STRING(), Encoders.STRING()))
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.map((MapFunction<Tuple3<Relation, String, String>, Relation>) t -> {
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Relation rel = t._1();
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String newSource = t._2();
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String newTarget = t._3();
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Dataset<Relation> processedRelations = distinctRelations(
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dedupedRels.union(mergeRels.map((MapFunction<Relation, Relation>) r -> r, REL_KRYO_ENC)))
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.filter((FilterFunction<Relation>) r -> !Objects.equals(r.getSource(), r.getTarget()));
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if (rel.getDataInfo() == null) {
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rel.setDataInfo(new DataInfo());
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}
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save(processedRelations, outputRelationPath, SaveMode.Overwrite);
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}
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if (newSource != null || newTarget != null) {
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rel.getDataInfo().setDeletedbyinference(false);
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private static Iterator<Relation> addInferredRelations(Tuple3<Relation, String, String> t) throws Exception {
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Relation existingRel = t._1();
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String newSource = t._2();
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String newTarget = t._3();
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if (newSource != null)
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rel.setSource(newSource);
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if (newSource == null && newTarget == null) {
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return Collections.singleton(t._1()).iterator();
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}
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if (newTarget != null)
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rel.setTarget(newTarget);
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}
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// update existing relation
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if (existingRel.getDataInfo() == null) {
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existingRel.setDataInfo(new DataInfo());
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}
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existingRel.getDataInfo().setDeletedbyinference(true);
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return rel;
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}, REL_BEAN_ENC);
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// Create new relation inferred by dedupIDs
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Relation inferredRel = (Relation) BeanUtils.cloneBean(existingRel);
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// ids of records that are both not deletedbyinference and not invisible
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Dataset<Row> ids = validIds(spark, graphBasePath);
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inferredRel.setDataInfo((DataInfo) BeanUtils.cloneBean(existingRel.getDataInfo()));
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inferredRel.getDataInfo().setDeletedbyinference(false);
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// filter relations that point to valid records, can force them to be visible
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Dataset<Relation> cleanedRels = dedupedRels
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.join(ids, col("source").equalTo(ids.col("id")), "leftsemi")
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.join(ids, col("target").equalTo(ids.col("id")), "leftsemi")
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.as(REL_BEAN_ENC)
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.map((MapFunction<Relation, Relation>) r -> {
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r.getDataInfo().setInvisible(false);
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return r;
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}, REL_KRYO_ENC);
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if (newSource != null)
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inferredRel.setSource(newSource);
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if (newTarget != null)
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inferredRel.setTarget(newTarget);
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return Arrays.asList(existingRel, inferredRel).iterator();
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}
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private Dataset<Relation> distinctRelations(Dataset<Relation> rels) {
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return rels
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.filter(getRelationFilterFunction())
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Dataset<Relation> distinctRels = cleanedRels
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.groupByKey(
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(MapFunction<Relation, String>) r -> String
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.join(" ", r.getSource(), r.getTarget(), r.getRelType(), r.getSubRelType(), r.getRelClass()),
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@ -146,13 +132,33 @@ public class SparkPropagateRelation extends AbstractSparkAction {
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return b;
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})
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.map((MapFunction<Tuple2<String, Relation>, Relation>) Tuple2::_2, REL_BEAN_ENC);
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final String outputRelationPath = graphOutputPath + "/relation";
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removeOutputDir(spark, outputRelationPath);
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save(
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distinctRels
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.union(mergeRels)
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.filter("source != target AND dataInfo.deletedbyinference != true AND dataInfo.invisible != true"),
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outputRelationPath,
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SaveMode.Overwrite);
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}
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private FilterFunction<Relation> getRelationFilterFunction() {
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return r -> StringUtils.isNotBlank(r.getSource()) ||
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StringUtils.isNotBlank(r.getTarget()) ||
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StringUtils.isNotBlank(r.getRelType()) ||
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StringUtils.isNotBlank(r.getSubRelType()) ||
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StringUtils.isNotBlank(r.getRelClass());
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static Dataset<Row> validIds(SparkSession spark, String graphBasePath) {
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StructType idsSchema = StructType
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.fromDDL("`id` STRING, `dataInfo` STRUCT<`deletedbyinference`:BOOLEAN,`invisible`:BOOLEAN>");
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Dataset<Row> allIds = spark.emptyDataset(RowEncoder.apply(idsSchema));
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for (EntityType entityType : ModelSupport.entityTypes.keySet()) {
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String entityPath = graphBasePath + '/' + entityType.name();
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if (HdfsSupport.exists(entityPath, spark.sparkContext().hadoopConfiguration())) {
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allIds = allIds.union(spark.read().schema(idsSchema).json(entityPath));
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}
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}
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return allIds
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.filter("dataInfo.deletedbyinference != true AND dataInfo.invisible != true")
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.select("id")
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.distinct();
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}
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}
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@ -1,20 +0,0 @@
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[
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{
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"paramName": "i",
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"paramLongName": "graphBasePath",
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"paramDescription": "the base path of raw graph",
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"paramRequired": true
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},
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{
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"paramName": "w",
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"paramLongName": "inputPath",
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"paramDescription": "the path to the input relation to cleanup",
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"paramRequired": true
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},
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{
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"paramName": "o",
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"paramLongName": "outputPath",
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"paramDescription": "the path of the output relation cleaned",
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"paramRequired": true
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}
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]
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@ -100,35 +100,9 @@
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--conf spark.sql.shuffle.partitions=15000
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</spark-opts>
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<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
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<arg>--graphOutputPath</arg><arg>${workingPath}/propagaterelation/</arg>
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<arg>--graphOutputPath</arg><arg>${graphOutputPath}</arg>
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<arg>--workingPath</arg><arg>${workingPath}</arg>
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</spark>
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<ok to="CleanRelation"/>
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<error to="Kill"/>
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</action>
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<action name="CleanRelation">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Clean Relations</name>
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<class>eu.dnetlib.dhp.oa.dedup.SparkCleanRelation</class>
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<jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--conf spark.executor.memoryOverhead=${sparkExecutorMemoryOverhead}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=15000
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</spark-opts>
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<arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
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<arg>--inputPath</arg><arg>${workingPath}/propagaterelation/relation</arg>
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<arg>--outputPath</arg><arg>${graphOutputPath}/relation</arg>
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</spark>
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<ok to="group_entities"/>
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<error to="Kill"/>
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</action>
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@ -3,7 +3,6 @@ package eu.dnetlib.dhp.oa.dedup;
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import static java.nio.file.Files.createTempDirectory;
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import static org.apache.spark.sql.functions.col;
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import static org.apache.spark.sql.functions.count;
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import static org.junit.jupiter.api.Assertions.*;
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import static org.mockito.Mockito.lenient;
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@ -23,14 +22,13 @@ import java.util.stream.Collectors;
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import org.apache.commons.io.FileUtils;
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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.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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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.PairFunction;
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import org.apache.spark.sql.*;
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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.Row;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.*;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.Mock;
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@ -46,8 +44,6 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import eu.dnetlib.pace.util.MapDocumentUtil;
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import scala.Tuple2;
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@ExtendWith(MockitoExtension.class)
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@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
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@ -62,6 +58,8 @@ public class SparkDedupTest implements Serializable {
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private static String testGraphBasePath;
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private static String testOutputBasePath;
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private static String testDedupGraphBasePath;
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private static String testConsistencyGraphBasePath;
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||||
|
||||
private static final String testActionSetId = "test-orchestrator";
|
||||
private static String whitelistPath;
|
||||
private static List<String> whiteList;
|
||||
|
|
@ -75,6 +73,7 @@ public class SparkDedupTest implements Serializable {
|
|||
.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI())
|
||||
.toFile()
|
||||
.getAbsolutePath();
|
||||
|
||||
testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
|
||||
.toAbsolutePath()
|
||||
.toString();
|
||||
|
|
@ -83,6 +82,10 @@ public class SparkDedupTest implements Serializable {
|
|||
.toAbsolutePath()
|
||||
.toString();
|
||||
|
||||
testConsistencyGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
|
||||
.toAbsolutePath()
|
||||
.toString();
|
||||
|
||||
whitelistPath = Paths
|
||||
.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/whitelist.simrels.txt").toURI())
|
||||
.toFile()
|
||||
|
|
@ -674,22 +677,45 @@ public class SparkDedupTest implements Serializable {
|
|||
assertEquals(mergedOrp, deletedOrp);
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(6)
|
||||
void copyRelationsNoOpenorgsTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCopyRelationsNoOpenorgs.class
|
||||
.getResourceAsStream(
|
||||
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
|
||||
});
|
||||
|
||||
new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService);
|
||||
|
||||
final Dataset<Row> outputRels = spark.read().text(testDedupGraphBasePath + "/relation");
|
||||
|
||||
System.out.println(outputRels.count());
|
||||
// assertEquals(2382, outputRels.count());
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(7)
|
||||
void propagateRelationTest() throws Exception {
|
||||
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"));
|
||||
String outputRelPath = testDedupGraphBasePath + "/propagaterelation";
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", outputRelPath
|
||||
"-i", testDedupGraphBasePath, "-w", testOutputBasePath, "-o", testConsistencyGraphBasePath
|
||||
});
|
||||
|
||||
new SparkPropagateRelation(parser, spark).run(isLookUpService);
|
||||
|
||||
long relations = jsc.textFile(outputRelPath + "/relation").count();
|
||||
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
|
||||
|
||||
// assertEquals(4860, relations);
|
||||
System.out.println("relations = " + relations);
|
||||
|
|
@ -699,95 +725,52 @@ public class SparkDedupTest implements Serializable {
|
|||
.read()
|
||||
.load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*"))
|
||||
.as(Encoders.bean(Relation.class));
|
||||
final JavaPairRDD<String, String> mergedIds = mergeRels
|
||||
.where("relClass == 'merges'")
|
||||
.select(mergeRels.col("target"))
|
||||
.distinct()
|
||||
.toJavaRDD()
|
||||
.mapToPair(
|
||||
(PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
|
||||
|
||||
JavaRDD<String> toCheck = jsc
|
||||
.textFile(outputRelPath + "/relation")
|
||||
.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json))
|
||||
.join(mergedIds)
|
||||
.map(t -> t._2()._1())
|
||||
.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json))
|
||||
.join(mergedIds)
|
||||
.map(t -> t._2()._1());
|
||||
Dataset<Row> inputRels = spark
|
||||
.read()
|
||||
.json(testDedupGraphBasePath + "/relation");
|
||||
|
||||
long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
|
||||
long updated = toCheck.count();
|
||||
Dataset<Row> outputRels = spark
|
||||
.read()
|
||||
.json(testConsistencyGraphBasePath + "/relation");
|
||||
|
||||
assertEquals(updated, deletedbyinference);
|
||||
assertEquals(
|
||||
0, outputRels
|
||||
.filter("dataInfo.deletedbyinference == true OR dataInfo.invisible == true")
|
||||
.count());
|
||||
|
||||
assertEquals(
|
||||
5, outputRels
|
||||
.filter("relClass NOT IN ('merges', 'isMergedIn')")
|
||||
.count());
|
||||
|
||||
assertEquals(5 + mergeRels.count(), outputRels.count());
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(8)
|
||||
void testCleanBaseRelations() throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
|
||||
|
||||
// append dangling relations to be cleaned up
|
||||
void testCleanedPropagatedRelations() throws Exception {
|
||||
Dataset<Row> df_before = spark
|
||||
.read()
|
||||
.schema(Encoders.bean(Relation.class).schema())
|
||||
.json(testGraphBasePath + "/relation");
|
||||
Dataset<Row> df_input = df_before
|
||||
.unionByName(df_before.drop("source").withColumn("source", functions.lit("n/a")))
|
||||
.unionByName(df_before.drop("target").withColumn("target", functions.lit("n/a")));
|
||||
df_input.write().mode(SaveMode.Overwrite).json(testOutputBasePath + "_tmp");
|
||||
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"--graphBasePath", testGraphBasePath,
|
||||
"--inputPath", testGraphBasePath + "/relation",
|
||||
"--outputPath", testDedupGraphBasePath + "/relation"
|
||||
});
|
||||
|
||||
new SparkCleanRelation(parser, spark).run(isLookUpService);
|
||||
.json(testDedupGraphBasePath + "/relation");
|
||||
|
||||
Dataset<Row> df_after = spark
|
||||
.read()
|
||||
.schema(Encoders.bean(Relation.class).schema())
|
||||
.json(testDedupGraphBasePath + "/relation");
|
||||
|
||||
assertNotEquals(df_before.count(), df_input.count());
|
||||
assertNotEquals(df_input.count(), df_after.count());
|
||||
assertEquals(5, df_after.count());
|
||||
}
|
||||
|
||||
@Test
|
||||
@Order(9)
|
||||
void testCleanDedupedRelations() throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
|
||||
|
||||
String inputRelPath = testDedupGraphBasePath + "/propagaterelation/relation";
|
||||
|
||||
// append dangling relations to be cleaned up
|
||||
Dataset<Row> df_before = spark.read().schema(Encoders.bean(Relation.class).schema()).json(inputRelPath);
|
||||
|
||||
df_before.filter(col("dataInfo.deletedbyinference").notEqual(true)).show(50, false);
|
||||
|
||||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"--graphBasePath", testGraphBasePath,
|
||||
"--inputPath", inputRelPath,
|
||||
"--outputPath", testDedupGraphBasePath + "/relation"
|
||||
});
|
||||
|
||||
new SparkCleanRelation(parser, spark).run(isLookUpService);
|
||||
|
||||
Dataset<Row> df_after = spark
|
||||
.read()
|
||||
.schema(Encoders.bean(Relation.class).schema())
|
||||
.json(testDedupGraphBasePath + "/relation");
|
||||
.json(testConsistencyGraphBasePath + "/relation");
|
||||
|
||||
assertNotEquals(df_before.count(), df_after.count());
|
||||
assertEquals(0, df_after.count());
|
||||
|
||||
assertEquals(
|
||||
0, df_after
|
||||
.filter("dataInfo.deletedbyinference == true OR dataInfo.invisible == true")
|
||||
.count());
|
||||
|
||||
assertEquals(
|
||||
5, df_after
|
||||
.filter("relClass NOT IN ('merges', 'isMergedIn')")
|
||||
.count());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -813,6 +796,7 @@ public class SparkDedupTest implements Serializable {
|
|||
public static void finalCleanUp() throws IOException {
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath));
|
||||
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
|
||||
FileUtils.deleteDirectory(new File(testConsistencyGraphBasePath));
|
||||
}
|
||||
|
||||
public boolean isDeletedByInference(String s) {
|
||||
|
|
|
|||
|
|
@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.dedup;
|
|||
|
||||
import static java.nio.file.Files.createTempDirectory;
|
||||
|
||||
import static org.apache.spark.sql.functions.col;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.mockito.Mockito.lenient;
|
||||
|
||||
|
|
@ -15,10 +16,6 @@ import java.nio.file.Paths;
|
|||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaPairRDD;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.PairFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
|
|
@ -33,8 +30,6 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||
import scala.Tuple2;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
|
||||
|
|
@ -44,11 +39,11 @@ public class SparkOpenorgsProvisionTest implements Serializable {
|
|||
ISLookUpService isLookUpService;
|
||||
|
||||
private static SparkSession spark;
|
||||
private static JavaSparkContext jsc;
|
||||
|
||||
private static String testGraphBasePath;
|
||||
private static String testOutputBasePath;
|
||||
private static String testDedupGraphBasePath;
|
||||
private static String testConsistencyGraphBasePath;
|
||||
private static final String testActionSetId = "test-orchestrator";
|
||||
|
||||
@BeforeAll
|
||||
|
|
@ -64,6 +59,9 @@ public class SparkOpenorgsProvisionTest implements Serializable {
|
|||
testDedupGraphBasePath = createTempDirectory(SparkOpenorgsProvisionTest.class.getSimpleName() + "-")
|
||||
.toAbsolutePath()
|
||||
.toString();
|
||||
testConsistencyGraphBasePath = createTempDirectory(SparkOpenorgsProvisionTest.class.getSimpleName() + "-")
|
||||
.toAbsolutePath()
|
||||
.toString();
|
||||
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath));
|
||||
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
|
||||
|
|
@ -76,8 +74,13 @@ public class SparkOpenorgsProvisionTest implements Serializable {
|
|||
.master("local[*]")
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
@AfterAll
|
||||
public static void finalCleanUp() throws IOException {
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath));
|
||||
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
|
||||
FileUtils.deleteDirectory(new File(testConsistencyGraphBasePath));
|
||||
}
|
||||
|
||||
@BeforeEach
|
||||
|
|
@ -186,26 +189,21 @@ public class SparkOpenorgsProvisionTest implements Serializable {
|
|||
|
||||
new SparkUpdateEntity(parser, spark).run(isLookUpService);
|
||||
|
||||
long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
|
||||
Dataset<Row> organizations = spark.read().json(testDedupGraphBasePath + "/organization");
|
||||
|
||||
long mergedOrgs = spark
|
||||
Dataset<Row> mergedOrgs = spark
|
||||
.read()
|
||||
.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.where("relClass=='merges'")
|
||||
.javaRDD()
|
||||
.map(Relation::getTarget)
|
||||
.distinct()
|
||||
.count();
|
||||
.select("target")
|
||||
.distinct();
|
||||
|
||||
assertEquals(80, organizations);
|
||||
assertEquals(80, organizations.count());
|
||||
|
||||
long deletedOrgs = jsc
|
||||
.textFile(testDedupGraphBasePath + "/organization")
|
||||
.filter(this::isDeletedByInference)
|
||||
.count();
|
||||
Dataset<Row> deletedOrgs = organizations
|
||||
.filter("dataInfo.deletedbyinference = TRUE");
|
||||
|
||||
assertEquals(mergedOrgs, deletedOrgs);
|
||||
assertEquals(mergedOrgs.count(), deletedOrgs.count());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -226,10 +224,9 @@ public class SparkOpenorgsProvisionTest implements Serializable {
|
|||
|
||||
new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService);
|
||||
|
||||
final JavaRDD<String> rels = jsc.textFile(testDedupGraphBasePath + "/relation");
|
||||
|
||||
assertEquals(2382, rels.count());
|
||||
final Dataset<Row> outputRels = spark.read().text(testDedupGraphBasePath + "/relation");
|
||||
|
||||
assertEquals(2382, outputRels.count());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -244,51 +241,41 @@ public class SparkOpenorgsProvisionTest implements Serializable {
|
|||
parser
|
||||
.parseArgument(
|
||||
new String[] {
|
||||
"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
|
||||
"-i", testDedupGraphBasePath, "-w", testOutputBasePath, "-o", testConsistencyGraphBasePath
|
||||
});
|
||||
|
||||
new SparkPropagateRelation(parser, spark).run(isLookUpService);
|
||||
|
||||
long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
|
||||
|
||||
assertEquals(4896, relations);
|
||||
|
||||
// check deletedbyinference
|
||||
final Dataset<Relation> mergeRels = spark
|
||||
.read()
|
||||
.load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*"))
|
||||
.as(Encoders.bean(Relation.class));
|
||||
final JavaPairRDD<String, String> mergedIds = mergeRels
|
||||
|
||||
Dataset<Row> inputRels = spark
|
||||
.read()
|
||||
.json(testDedupGraphBasePath + "/relation");
|
||||
|
||||
Dataset<Row> outputRels = spark
|
||||
.read()
|
||||
.json(testConsistencyGraphBasePath + "/relation");
|
||||
|
||||
final Dataset<Row> mergedIds = mergeRels
|
||||
.where("relClass == 'merges'")
|
||||
.select(mergeRels.col("target"))
|
||||
.distinct()
|
||||
.toJavaRDD()
|
||||
.mapToPair(
|
||||
(PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
|
||||
.select(col("target").as("id"))
|
||||
.distinct();
|
||||
|
||||
JavaRDD<String> toCheck = jsc
|
||||
.textFile(testDedupGraphBasePath + "/relation")
|
||||
.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json))
|
||||
.join(mergedIds)
|
||||
.map(t -> t._2()._1())
|
||||
.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json))
|
||||
.join(mergedIds)
|
||||
.map(t -> t._2()._1());
|
||||
Dataset<Row> toUpdateRels = inputRels
|
||||
.as("rel")
|
||||
.join(mergedIds.as("s"), col("rel.source").equalTo(col("s.id")), "left_outer")
|
||||
.join(mergedIds.as("t"), col("rel.target").equalTo(col("t.id")), "left_outer")
|
||||
.filter("s.id IS NOT NULL OR t.id IS NOT NULL")
|
||||
.distinct();
|
||||
|
||||
long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
|
||||
long updated = toCheck.count();
|
||||
Dataset<Row> updatedRels = inputRels
|
||||
.select("source", "target", "relClass")
|
||||
.except(outputRels.select("source", "target", "relClass"));
|
||||
|
||||
assertEquals(updated, deletedbyinference);
|
||||
assertEquals(toUpdateRels.count(), updatedRels.count());
|
||||
assertEquals(140, outputRels.count());
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void finalCleanUp() throws IOException {
|
||||
FileUtils.deleteDirectory(new File(testOutputBasePath));
|
||||
FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
|
||||
}
|
||||
|
||||
public boolean isDeletedByInference(String s) {
|
||||
return s.contains("\"deletedbyinference\":true");
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue