Merge remote-tracking branch 'origin/stable_ids' into stable_ids

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java

@@ -22,6 +22,7 @@ import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import scala.Tuple2;
+import scala.Tuple3;
 
 public class SparkPropagateRelation extends AbstractSparkAction {
 
@@ -85,13 +86,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 
 		Dataset<Relation> rels = spark.read().textFile(relationPath).map(patchRelFn(), Encoders.bean(Relation.class));
 
-		Dataset<Relation> newRels = processDataset(
+		Dataset<Relation> newRels = createNewRels(rels, mergedIds, getFixRelFn());
-			processDataset(rels, mergedIds, FieldType.SOURCE, getFixRelFn(FieldType.SOURCE)),
-			mergedIds,
-			FieldType.TARGET,
-			getFixRelFn(FieldType.TARGET))
-				.filter(SparkPropagateRelation::containsDedup)
-				.distinct();
 
 		Dataset<Relation> updated = processDataset(
 			processDataset(rels, mergedIds, FieldType.SOURCE, getDeletedFn()),
@@ -120,6 +115,29 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 			.map((MapFunction<Tuple2<String, Relation>, Relation>) t -> t._2(), Encoders.bean(Relation.class));
 	}
 
+	private static Dataset<Relation> createNewRels(
+		Dataset<Relation> rels,
+		Dataset<Tuple2<String, String>> mergedIds,
+		MapFunction<Tuple2<Tuple2<Tuple3<String, Relation, String>, Tuple2<String, String>>, Tuple2<String, String>>, Relation> mapRel) {
+
+		Dataset<Tuple3<String, Relation, String>> mapped = rels
+			.map(
+				(MapFunction<Relation, Tuple3<String, Relation, String>>) r -> new Tuple3<>(getId(r, FieldType.SOURCE),
+					r, getId(r, FieldType.TARGET)),
+				Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class), Encoders.STRING()));
+
+		Dataset<Tuple2<Tuple3<String, Relation, String>, Tuple2<String, String>>> relSource = mapped
+			.joinWith(mergedIds, mapped.col("_1").equalTo(mergedIds.col("_1")), "left_outer");
+
+		return relSource
+			.joinWith(mergedIds, relSource.col("_1._3").equalTo(mergedIds.col("_2")), "left_outer")
+			.filter(
+				(FilterFunction<Tuple2<Tuple2<Tuple3<String, Relation, String>, Tuple2<String, String>>, Tuple2<String, String>>>) r -> r
+					._2() != null || r._1() != null)
+			.map(mapRel, Encoders.bean(Relation.class))
+			.distinct();
+	}
+
 	private static Dataset<Relation> processDataset(
 		Dataset<Relation> rels,
 		Dataset<Tuple2<String, String>> mergedIds,
@@ -153,28 +171,25 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 		}
 	}
 
-	private static MapFunction<Tuple2<Tuple2<String, Relation>, Tuple2<String, String>>, Relation> getFixRelFn(
+	private static MapFunction<Tuple2<Tuple2<Tuple3<String, Relation, String>, Tuple2<String, String>>, Tuple2<String, String>>, Relation> getFixRelFn() {
-		FieldType type) {
 		return value -> {
-			if (value._2() != null) {
+
-				Relation r = value._1()._2();
+			Relation r = value._1()._1()._2();
-				String id = value._2()._2();
+			String newSource = value._1()._2() != null ? value._1()._2()._2() : null;
-				if (r.getDataInfo() == null) {
+			String newTarget = value._2() != null ? value._2()._2() : null;
-					r.setDataInfo(new DataInfo());
+
-				}
+			if (r.getDataInfo() == null) {
-				r.getDataInfo().setDeletedbyinference(false);
+				r.setDataInfo(new DataInfo());
-				switch (type) {
-					case SOURCE:
-						r.setSource(id);
-						return r;
-					case TARGET:
-						r.setTarget(id);
-						return r;
-					default:
-						throw new IllegalArgumentException("");
-				}
 			}
-			return value._1()._2();
+			r.getDataInfo().setDeletedbyinference(false);
+
+			if (newSource != null)
+				r.setSource(newSource);
+
+			if (newTarget != null)
+				r.setTarget(newTarget);
+
+			return r;
 		};
 	}
 
@@ -192,8 +207,4 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 		};
 	}
 
-	private static boolean containsDedup(final Relation r) {
-		return r.getSource().toLowerCase().contains(ModelConstants.DEDUP)
-			|| r.getTarget().toLowerCase().contains(ModelConstants.DEDUP);
-	}
 }

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java

@@ -12,6 +12,7 @@ import java.io.IOException;
 import java.io.Serializable;
 import java.net.URISyntaxException;
 import java.nio.file.Paths;
+import java.util.List;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
@@ -66,6 +67,7 @@ public class SparkDedupTest implements Serializable {
 		testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
 			.toAbsolutePath()
 			.toString();
+
 		testDedupGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
 			.toAbsolutePath()
 			.toString();
@@ -534,7 +536,7 @@ public class SparkDedupTest implements Serializable {
 
 		long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
 
-		assertEquals(4862, relations);
+		assertEquals(4718, relations);
 
 		// check deletedbyinference
 		final Dataset<Relation> mergeRels = spark