diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java index d442d73a89..c46464ffdd 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java @@ -11,8 +11,6 @@ import eu.dnetlib.pace.config.DedupConfig; import java.io.IOException; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.dom4j.DocumentException; @@ -72,12 +70,9 @@ public class SparkCreateDedupRecord extends AbstractSparkAction { Class clazz = ModelSupport.entityTypes.get(EntityType.valueOf(subEntity)); DedupRecordFactory.createDedupRecord(spark, mergeRelPath, entityPath, clazz) - .map( - (MapFunction) - value -> OBJECT_MAPPER.writeValueAsString(value), - Encoders.STRING()) .write() .mode(SaveMode.Overwrite) + .option("compression", "gzip") .json(outputPath); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java index fde5dd75f8..ee13eff6b4 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkUpdateEntity.java @@ -33,7 +33,7 @@ public class SparkUpdateEntity extends AbstractSparkAction { private static final Logger log = LoggerFactory.getLogger(SparkUpdateEntity.class); - final String IDJSONPATH = "$.id"; + private static final String IDJSONPATH = "$.id"; public SparkUpdateEntity(ArgumentApplicationParser parser, SparkSession spark) { super(parser, spark); @@ -65,27 +65,25 @@ public class SparkUpdateEntity extends AbstractSparkAction { log.info("workingPath: '{}'", workingPath); log.info("dedupGraphPath: '{}'", dedupGraphPath); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); // for each entity ModelSupport.entityTypes.forEach( - (entity, clazz) -> { - final String outputPath = dedupGraphPath + "/" + entity; + (type, clazz) -> { + final String outputPath = dedupGraphPath + "/" + type; removeOutputDir(spark, outputPath); JavaRDD sourceEntity = sc.textFile( - DedupUtility.createEntityPath( - graphBasePath, entity.toString())); + DedupUtility.createEntityPath(graphBasePath, type.toString())); - if (mergeRelExists(workingPath, entity.toString())) { + if (mergeRelExists(workingPath, type.toString())) { final String mergeRelPath = - DedupUtility.createMergeRelPath( - workingPath, "*", entity.toString()); + DedupUtility.createMergeRelPath(workingPath, "*", type.toString()); final String dedupRecordPath = DedupUtility.createDedupRecordPath( - workingPath, "*", entity.toString()); + workingPath, "*", type.toString()); final Dataset rel = spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class)); @@ -107,7 +105,6 @@ public class SparkUpdateEntity extends AbstractSparkAction { MapDocumentUtil.getJPathString( IDJSONPATH, s), s)); - JavaRDD map = entitiesWithId .leftOuterJoin(mergedIds) diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index 695498a6e9..5979fc9b70 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -72,7 +72,7 @@ public class SparkDedupTest implements Serializable { spark = SparkSession.builder() - .appName(SparkCreateSimRels.class.getSimpleName()) + .appName(SparkDedupTest.class.getSimpleName()) .master("local[*]") .config(new SparkConf()) .getOrCreate(); @@ -300,8 +300,8 @@ public class SparkDedupTest implements Serializable { long deletedSw = jsc.textFile(testDedupGraphBasePath + "/software") - .filter(this::isDeletedByInference) - .count(); + .filter(this::isDeletedByInference) + .count(); assertEquals(mergedOrgs, deletedOrgs); assertEquals(mergedPubs, deletedPubs); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource index f54cbf0716..1230623650 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource +++ 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