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

@@ -2,14 +2,13 @@
 package eu.dnetlib.dhp.oa.dedup;
 
 import java.util.*;
+import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import org.apache.commons.beanutils.BeanUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.FlatMapGroupsFunction;
 import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.api.java.function.ReduceFunction;
 import org.apache.spark.sql.*;
 
 import eu.dnetlib.dhp.oa.dedup.model.Identifier;
@@ -107,6 +106,8 @@ public class DedupRecordFactory {
 
 					final HashSet<String> acceptanceDate = new HashSet<>();
 
+					boolean isVisible = false;
+
 					while (it.hasNext()) {
 						Tuple3<String, String, OafEntity> t = it.next();
 						OafEntity entity = t._3();
@@ -114,6 +115,7 @@ public class DedupRecordFactory {
 						if (entity == null) {
 							aliases.add(t._2());
 						} else {
+							isVisible = isVisible || !entity.getDataInfo().getInvisible();
 							cliques.add(entity);
 
 							if (acceptanceDate.size() < MAX_ACCEPTANCE_DATE) {
@@ -129,13 +131,20 @@ public class DedupRecordFactory {
 
 					}
 
-					if (acceptanceDate.size() >= MAX_ACCEPTANCE_DATE || cliques.isEmpty()) {
+					if (!isVisible || acceptanceDate.size() >= MAX_ACCEPTANCE_DATE || cliques.isEmpty()) {
 						return Collections.emptyIterator();
 					}
 
 					OafEntity mergedEntity = MergeUtils.mergeGroup(dedupId, cliques.iterator());
 					// dedup records do not have date of transformation attribute
 					mergedEntity.setDateoftransformation(null);
+					mergedEntity
+						.setMergedIds(
+							Stream
+								.concat(cliques.stream().map(OafEntity::getId), aliases.stream())
+								.distinct()
+								.sorted()
+								.collect(Collectors.toList()));
 
 					return Stream
 						.concat(

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

@@ -5,11 +5,11 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTION
 import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVENANCE_DEDUP;
 
 import java.io.IOException;
+import java.util.Arrays;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
-import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.*;
-import org.apache.spark.sql.SparkSession;
 import org.dom4j.DocumentException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -17,6 +17,7 @@ import org.xml.sax.SAXException;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.common.EntityType;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.DataInfo;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
@@ -25,6 +26,7 @@ import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import eu.dnetlib.pace.config.DedupConfig;
+import scala.collection.JavaConverters;
 
 public class SparkCreateDedupRecord extends AbstractSparkAction {
 
@@ -85,6 +87,36 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
 				.mode(SaveMode.Overwrite)
 				.option("compression", "gzip")
 				.json(outputPath);
+
+			log.info("Updating mergerels for: '{}'", subEntity);
+			final Dataset<Row> dedupIds = spark
+				.read()
+				.schema("`id` STRING, `mergedIds` ARRAY<STRING>")
+				.json(outputPath)
+				.selectExpr("id as source", "explode(mergedIds) as target");
+			spark
+				.read()
+				.load(mergeRelPath)
+				.where("relClass == 'merges'")
+				.join(dedupIds, JavaConverters.asScalaBuffer(Arrays.asList("source", "target")).toSeq(), "left_semi")
+				.write()
+				.mode(SaveMode.Overwrite)
+				.option("compression", "gzip")
+				.save(workingPath + "/mergerel_filtered");
+
+			final Dataset<Row> validRels = spark.read().load(workingPath + "/mergerel_filtered");
+
+			final Dataset<Row> filteredMergeRels = validRels
+				.union(
+					validRels
+						.withColumnRenamed("source", "source_tmp")
+						.withColumnRenamed("target", "target_tmp")
+						.withColumn("relClass", functions.lit(ModelConstants.IS_MERGED_IN))
+						.withColumnRenamed("target_tmp", "source")
+						.withColumnRenamed("source_tmp", "target"));
+
+			saveParquet(filteredMergeRels, mergeRelPath, SaveMode.Overwrite);
+			removeOutputDir(spark, workingPath + "/mergerel_filtered");
 		}
 	}
 

pom.xml

@@ -937,7 +937,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[8.0.1]</dhp-schemas.version>
+        <dhp-schemas.version>[9.0.0]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>