Merge branch 'master' of code-repo.d4science.org:D-Net/dnet-hadoop

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase2.java

@@ -19,7 +19,6 @@ import org.apache.spark.sql.expressions.Aggregator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.collect.Lists;
 
@@ -28,8 +27,6 @@ import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
 import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
 import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
-import eu.dnetlib.dhp.oa.provision.model.TypedRow;
-import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 import scala.Tuple2;
@@ -305,20 +302,6 @@ public class CreateRelatedEntitiesJob_phase2 {
 
 	private static FilterFunction<JoinedEntity> filterEmptyEntityFn() {
 		return (FilterFunction<JoinedEntity>) v -> Objects.nonNull(v.getEntity());
-		/*
-		 * return (FilterFunction<JoinedEntity>) v -> Optional .ofNullable(v.getEntity()) .map(e ->
-		 * StringUtils.isNotBlank(e.getId())) .orElse(false);
-		 */
-	}
-
-	private static TypedRow getTypedRow(String type, OafEntity entity)
-		throws JsonProcessingException {
-		TypedRow t = new TypedRow();
-		t.setType(type);
-		t.setDeleted(entity.getDataInfo().getDeletedbyinference());
-		t.setId(entity.getId());
-		t.setOaf(OBJECT_MAPPER.writeValueAsString(entity));
-		return t;
 	}
 
 	private static void removeOutputDir(SparkSession spark, String path) {

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java

@@ -3,28 +3,33 @@ package eu.dnetlib.dhp.oa.provision;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
-import java.util.HashSet;
+import java.util.*;
-import java.util.Optional;
+import java.util.function.Supplier;
-import java.util.Set;
+import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.Function;
+import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.rdd.RDD;
-import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.*;
-import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.expressions.Aggregator;
-import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.base.Splitter;
 import com.google.common.collect.Iterables;
+import com.google.common.collect.Maps;
 import com.google.common.collect.Sets;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
 import eu.dnetlib.dhp.oa.provision.model.SortableRelationKey;
 import eu.dnetlib.dhp.oa.provision.utils.RelationPartitioner;
 import eu.dnetlib.dhp.schema.oaf.Relation;
@@ -102,6 +107,8 @@ public class PrepareRelationsJob {
 		log.info("maxRelations: {}", maxRelations);
 
 		SparkConf conf = new SparkConf();
+		conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
+		conf.registerKryoClasses(ProvisionModelSupport.getModelClasses());
 
 		runWithSparkSession(
 			conf,
@@ -125,9 +132,8 @@ public class PrepareRelationsJob {
 	 * @param maxRelations maximum number of allowed outgoing edges
 	 * @param relPartitions number of partitions for the output RDD
 	 */
-	private static void prepareRelationsRDD(
+	private static void prepareRelationsRDD(SparkSession spark, String inputRelationsPath, String outputPath,
-		SparkSession spark, String inputRelationsPath, String outputPath, Set<String> relationFilter, int maxRelations,
+		Set<String> relationFilter, int maxRelations, int relPartitions) {
-		int relPartitions) {
 
 		// group by SOURCE and apply limit
 		RDD<Relation> bySource = readPathRelationRDD(spark, inputRelationsPath)
@@ -142,27 +148,95 @@ public class PrepareRelationsJob {
 			.map(Tuple2::_2)
 			.rdd();
 
-		// group by TARGET and apply limit
-		RDD<Relation> byTarget = readPathRelationRDD(spark, inputRelationsPath)
-			.filter(rel -> rel.getDataInfo().getDeletedbyinference() == false)
-			.filter(rel -> relationFilter.contains(rel.getRelClass()) == false)
-			.mapToPair(r -> new Tuple2<>(SortableRelationKey.create(r, r.getTarget()), r))
-			.repartitionAndSortWithinPartitions(new RelationPartitioner(relPartitions))
-			.groupBy(Tuple2::_1)
-			.map(Tuple2::_2)
-			.map(t -> Iterables.limit(t, maxRelations))
-			.flatMap(Iterable::iterator)
-			.map(Tuple2::_2)
-			.rdd();
-
 		spark
-			.createDataset(bySource.union(byTarget), Encoders.bean(Relation.class))
+			.createDataset(bySource, Encoders.bean(Relation.class))
 			.repartition(relPartitions)
 			.write()
 			.mode(SaveMode.Overwrite)
 			.parquet(outputPath);
 	}
 
+	private static void prepareRelationsDataset(
+		SparkSession spark, String inputRelationsPath, String outputPath, Set<String> relationFilter, int maxRelations,
+		int relPartitions) {
+		spark
+			.read()
+			.textFile(inputRelationsPath)
+			.repartition(relPartitions)
+			.map(
+				(MapFunction<String, Relation>) s -> OBJECT_MAPPER.readValue(s, Relation.class),
+				Encoders.kryo(Relation.class))
+			.filter((FilterFunction<Relation>) rel -> rel.getDataInfo().getDeletedbyinference() == false)
+			.filter((FilterFunction<Relation>) rel -> relationFilter.contains(rel.getRelClass()) == false)
+			.groupByKey(
+				(MapFunction<Relation, String>) Relation::getSource,
+				Encoders.STRING())
+			.agg(new RelationAggregator(maxRelations).toColumn())
+			.flatMap(
+				(FlatMapFunction<Tuple2<String, RelationList>, Relation>) t -> Iterables
+					.limit(t._2().getRelations(), maxRelations)
+					.iterator(),
+				Encoders.bean(Relation.class))
+			.repartition(relPartitions)
+			.write()
+			.mode(SaveMode.Overwrite)
+			.parquet(outputPath);
+	}
+
+	public static class RelationAggregator
+		extends Aggregator<Relation, RelationList, RelationList> {
+
+		private int maxRelations;
+
+		public RelationAggregator(int maxRelations) {
+			this.maxRelations = maxRelations;
+		}
+
+		@Override
+		public RelationList zero() {
+			return new RelationList();
+		}
+
+		@Override
+		public RelationList reduce(RelationList b, Relation a) {
+			b.getRelations().add(a);
+			return getSortableRelationList(b);
+		}
+
+		@Override
+		public RelationList merge(RelationList b1, RelationList b2) {
+			b1.getRelations().addAll(b2.getRelations());
+			return getSortableRelationList(b1);
+		}
+
+		@Override
+		public RelationList finish(RelationList r) {
+			return getSortableRelationList(r);
+		}
+
+		private RelationList getSortableRelationList(RelationList b1) {
+			RelationList sr = new RelationList();
+			sr
+				.setRelations(
+					b1
+						.getRelations()
+						.stream()
+						.limit(maxRelations)
+						.collect(Collectors.toCollection(() -> new PriorityQueue<>(new RelationComparator()))));
+			return sr;
+		}
+
+		@Override
+		public Encoder<RelationList> bufferEncoder() {
+			return Encoders.kryo(RelationList.class);
+		}
+
+		@Override
+		public Encoder<RelationList> outputEncoder() {
+			return Encoders.kryo(RelationList.class);
+		}
+	}
+
 	/**
 	 * Reads a JavaRDD of eu.dnetlib.dhp.oa.provision.model.SortableRelation objects from a newline delimited json text
 	 * file,

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationComparator.java

@@ -0,0 +1,43 @@
+
+package eu.dnetlib.dhp.oa.provision;
+
+import java.util.Comparator;
+import java.util.Map;
+import java.util.Optional;
+
+import com.google.common.collect.ComparisonChain;
+import com.google.common.collect.Maps;
+
+import eu.dnetlib.dhp.schema.oaf.Relation;
+
+public class RelationComparator implements Comparator<Relation> {
+
+	private static final Map<String, Integer> weights = Maps.newHashMap();
+
+	static {
+		weights.put("outcome", 0);
+		weights.put("supplement", 1);
+		weights.put("review", 2);
+		weights.put("citation", 3);
+		weights.put("affiliation", 4);
+		weights.put("relationship", 5);
+		weights.put("publicationDataset", 6);
+		weights.put("similarity", 7);
+
+		weights.put("provision", 8);
+		weights.put("participation", 9);
+		weights.put("dedup", 10);
+	}
+
+	private Integer getWeight(Relation o) {
+		return Optional.ofNullable(weights.get(o.getSubRelType())).orElse(Integer.MAX_VALUE);
+	}
+
+	@Override
+	public int compare(Relation o1, Relation o2) {
+		return ComparisonChain
+			.start()
+			.compare(getWeight(o1), getWeight(o2))
+			.result();
+	}
+}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/RelationList.java

@@ -0,0 +1,25 @@
+
+package eu.dnetlib.dhp.oa.provision;
+
+import java.io.Serializable;
+import java.util.PriorityQueue;
+import java.util.Queue;
+
+import eu.dnetlib.dhp.schema.oaf.Relation;
+
+public class RelationList implements Serializable {
+
+	private Queue<Relation> relations;
+
+	public RelationList() {
+		this.relations = new PriorityQueue<>(new RelationComparator());
+	}
+
+	public Queue<Relation> getRelations() {
+		return relations;
+	}
+
+	public void setRelations(Queue<Relation> relations) {
+		this.relations = relations;
+	}
+}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SortableRelation.java

@@ -0,0 +1,80 @@
+
+package eu.dnetlib.dhp.oa.provision;
+
+import java.io.Serializable;
+import java.util.Map;
+import java.util.Optional;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.google.common.collect.ComparisonChain;
+import com.google.common.collect.Maps;
+
+import eu.dnetlib.dhp.schema.oaf.Relation;
+
+public class SortableRelation extends Relation implements Comparable<SortableRelation>, Serializable {
+
+	private static final Map<String, Integer> weights = Maps.newHashMap();
+
+	static {
+		weights.put("outcome", 0);
+		weights.put("supplement", 1);
+		weights.put("review", 2);
+		weights.put("citation", 3);
+		weights.put("affiliation", 4);
+		weights.put("relationship", 5);
+		weights.put("publicationDataset", 6);
+		weights.put("similarity", 7);
+
+		weights.put("provision", 8);
+		weights.put("participation", 9);
+		weights.put("dedup", 10);
+	}
+
+	private static final long serialVersionUID = 34753984579L;
+
+	private String groupingKey;
+
+	public static SortableRelation create(Relation r, String groupingKey) {
+		SortableRelation sr = new SortableRelation();
+		sr.setGroupingKey(groupingKey);
+		sr.setSource(r.getSource());
+		sr.setTarget(r.getTarget());
+		sr.setRelType(r.getRelType());
+		sr.setSubRelType(r.getSubRelType());
+		sr.setRelClass(r.getRelClass());
+		sr.setDataInfo(r.getDataInfo());
+		sr.setCollectedfrom(r.getCollectedfrom());
+		sr.setLastupdatetimestamp(r.getLastupdatetimestamp());
+		sr.setProperties(r.getProperties());
+		sr.setValidated(r.getValidated());
+		sr.setValidationDate(r.getValidationDate());
+
+		return sr;
+	}
+
+	@JsonIgnore
+	public Relation asRelation() {
+		return this;
+	}
+
+	@Override
+	public int compareTo(SortableRelation o) {
+		return ComparisonChain
+			.start()
+			.compare(getGroupingKey(), o.getGroupingKey())
+			.compare(getWeight(this), getWeight(o))
+			.result();
+	}
+
+	private Integer getWeight(SortableRelation o) {
+		return Optional.ofNullable(weights.get(o.getSubRelType())).orElse(Integer.MAX_VALUE);
+	}
+
+	public String getGroupingKey() {
+		return groupingKey;
+	}
+
+	public void setGroupingKey(String groupingKey) {
+		this.groupingKey = groupingKey;
+	}
+}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java

@@ -5,6 +5,8 @@ import java.util.List;
 
 import com.google.common.collect.Lists;
 
+import eu.dnetlib.dhp.oa.provision.RelationList;
+import eu.dnetlib.dhp.oa.provision.SortableRelation;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 
 public class ProvisionModelSupport {
@@ -15,11 +17,12 @@ public class ProvisionModelSupport {
 			.addAll(
 				Lists
 					.newArrayList(
-						TypedRow.class,
 						RelatedEntityWrapper.class,
 						JoinedEntity.class,
 						RelatedEntity.class,
-						SortableRelationKey.class));
+						SortableRelationKey.class,
+						SortableRelation.class,
+						RelationList.class));
 		return modelClasses.toArray(new Class[] {});
 	}
 }

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntityWrapper.java

@@ -16,10 +16,6 @@ public class RelatedEntityWrapper implements Serializable {
 	}
 
 	public RelatedEntityWrapper(Relation relation, RelatedEntity target) {
-		this(null, relation, target);
-	}
-
-	public RelatedEntityWrapper(TypedRow entity, Relation relation, RelatedEntity target) {
 		this.relation = relation;
 		this.target = target;
 	}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/TypedRow.java

@@ -1,64 +0,0 @@
-
-package eu.dnetlib.dhp.oa.provision.model;
-
-import java.io.Serializable;
-
-import com.google.common.base.Objects;
-
-public class TypedRow implements Serializable {
-
-	private String id;
-
-	private Boolean deleted;
-
-	private String type;
-
-	private String oaf;
-
-	public String getId() {
-		return id;
-	}
-
-	public void setId(String id) {
-		this.id = id;
-	}
-
-	public Boolean getDeleted() {
-		return deleted;
-	}
-
-	public void setDeleted(Boolean deleted) {
-		this.deleted = deleted;
-	}
-
-	public String getType() {
-		return type;
-	}
-
-	public void setType(String type) {
-		this.type = type;
-	}
-
-	public String getOaf() {
-		return oaf;
-	}
-
-	public void setOaf(String oaf) {
-		this.oaf = oaf;
-	}
-
-	@Override
-	public boolean equals(Object o) {
-		if (this == o)
-			return true;
-		if (o == null || getClass() != o.getClass())
-			return false;
-		TypedRow typedRow2 = (TypedRow) o;
-		return Objects.equal(id, typedRow2.id);
-	}
-
-	@Override
-	public int hashCode() {
-		return Objects.hashCode(id);
-	}
-}

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java

@@ -121,10 +121,6 @@ public class XmlRecordFactory implements Serializable {
 		}
 	}
 
-	private static OafEntity toOafEntity(TypedRow typedRow) {
-		return parseOaf(typedRow.getOaf(), typedRow.getType());
-	}
-
 	private static OafEntity parseOaf(final String json, final String type) {
 		try {
 			switch (EntityType.valueOf(type)) {

dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml

@@ -133,6 +133,7 @@
             </spark-opts>
             <arg>--inputRelationsPath</arg><arg>${inputGraphRootPath}/relation</arg>
             <arg>--outputPath</arg><arg>${workingDir}/relation</arg>
+            <arg>--maxRelations</arg><arg>${maxRelations}</arg>
             <arg>--relPartitions</arg><arg>5000</arg>
         </spark>
         <ok to="fork_join_related_entities"/>

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJobTest.java

@@ -0,0 +1,93 @@
+
+package eu.dnetlib.dhp.oa.provision;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import org.apache.commons.io.FileUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+public class PrepareRelationsJobTest {
+
+	private static final Logger log = LoggerFactory.getLogger(PrepareRelationsJobTest.class);
+
+	public static final String SUBRELTYPE = "subRelType";
+	public static final String OUTCOME = "outcome";
+	public static final String SUPPLEMENT = "supplement";
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+
+	@BeforeAll
+	public static void setUp() throws IOException {
+		workingDir = Files.createTempDirectory(PrepareRelationsJobTest.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+
+		conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
+		conf.registerKryoClasses(ProvisionModelSupport.getModelClasses());
+
+		spark = SparkSession
+			.builder()
+			.appName(PrepareRelationsJobTest.class.getSimpleName())
+			.master("local[*]")
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	public void testRunPrepareRelationsJob(@TempDir Path testPath) throws Exception {
+
+		final int maxRelations = 10;
+		PrepareRelationsJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-inputRelationsPath", getClass().getResource("relations.gz").getPath(),
+					"-outputPath", testPath.toString(),
+					"-relPartitions", "10",
+					"-relationFilter", "asd",
+					"-maxRelations", String.valueOf(maxRelations)
+				});
+
+		Dataset<Relation> out = spark.read()
+				.parquet(testPath.toString())
+				.as(Encoders.bean(Relation.class))
+				.cache();
+
+		Assertions.assertEquals(10, out.count());
+
+		Dataset<Row> freq = out.toDF().cube(SUBRELTYPE).count().filter((FilterFunction<Row>) value -> !value.isNullAt(0));
+		long outcome = freq.filter(freq.col(SUBRELTYPE).equalTo(OUTCOME)).collectAsList().get(0).getAs("count");
+		long supplement = freq.filter(freq.col(SUBRELTYPE).equalTo(SUPPLEMENT)).collectAsList().get(0).getAs("count");
+
+		Assertions.assertTrue(outcome > supplement);
+		Assertions.assertEquals(7, outcome);
+		Assertions.assertEquals(3, supplement);
+	}
+
+}

dhp-workflows/dhp-graph-provision/src/test/resources/log4j.properties

@@ -0,0 +1,11 @@
+# Set root logger level to DEBUG and its only appender to A1.
+log4j.rootLogger=INFO, A1
+
+# A1 is set to be a ConsoleAppender.
+log4j.appender.A1=org.apache.log4j.ConsoleAppender
+
+# A1 uses PatternLayout.
+log4j.logger.org = ERROR
+log4j.logger.eu.dnetlib = DEBUG
+log4j.appender.A1.layout=org.apache.log4j.PatternLayout
+log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n