Merge pull request 'Add a "CleanRelation" action after the PropagateRelation to filter out all relations that have been deleted by inference or that are pointing to dangling entities' (#328) from cleanup_relations_after_dedup into beta

Reviewed-on: D-Net/dnet-hadoop#328

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

@@ -0,0 +1,78 @@
+package eu.dnetlib.dhp.oa.dedup
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser
+import eu.dnetlib.dhp.common.HdfsSupport
+import eu.dnetlib.dhp.schema.oaf.Relation
+import eu.dnetlib.dhp.utils.ISLookupClientFactory
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService
+import org.apache.commons.io.IOUtils
+import org.apache.spark.SparkConf
+import org.apache.spark.sql._
+import org.apache.spark.sql.functions.col
+import org.apache.spark.sql.types.{DataTypes, StructField, StructType}
+import org.slf4j.LoggerFactory
+
+object SparkCleanRelation {
+  private val log = LoggerFactory.getLogger(classOf[SparkCleanRelation])
+
+  @throws[Exception]
+  def main(args: Array[String]): Unit = {
+    val parser = new ArgumentApplicationParser(
+      IOUtils.toString(
+        classOf[SparkCleanRelation].getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json")
+      )
+    )
+    parser.parseArgument(args)
+    val conf = new SparkConf
+
+    new SparkCleanRelation(parser, AbstractSparkAction.getSparkSession(conf))
+      .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")))
+  }
+}
+
+class SparkCleanRelation(parser: ArgumentApplicationParser, spark: SparkSession)
+    extends AbstractSparkAction(parser, spark) {
+  override def run(isLookUpService: ISLookUpService): Unit = {
+    val graphBasePath = parser.get("graphBasePath")
+    val inputPath = parser.get("inputPath")
+    val outputPath = parser.get("outputPath")
+
+    SparkCleanRelation.log.info("graphBasePath: '{}'", graphBasePath)
+    SparkCleanRelation.log.info("inputPath: '{}'", inputPath)
+    SparkCleanRelation.log.info("outputPath: '{}'", outputPath)
+
+    AbstractSparkAction.removeOutputDir(spark, outputPath)
+
+    val entities =
+      Seq("datasource", "project", "organization", "publication", "dataset", "software", "otherresearchproduct")
+
+    val idsSchema = StructType.fromDDL("`id` STRING, `dataInfo` STRUCT<`deletedbyinference`:BOOLEAN,`invisible`:BOOLEAN>")
+
+    val emptyIds = spark.createDataFrame(spark.sparkContext.emptyRDD[Row].setName("empty"),
+      idsSchema)
+
+    val ids = entities
+      .foldLeft(emptyIds)((ds, entity) => {
+        val entityPath = graphBasePath + '/' + entity
+        if (HdfsSupport.exists(entityPath, spark.sparkContext.hadoopConfiguration)) {
+          ds.union(spark.read.schema(idsSchema).json(entityPath))
+        } else {
+          ds
+        }
+      })
+      .filter("dataInfo.deletedbyinference != true AND dataInfo.invisible != true")
+      .select("id")
+      .distinct()
+
+    val relations = spark.read.schema(Encoders.bean(classOf[Relation]).schema).json(inputPath)
+      .filter("dataInfo.deletedbyinference != true AND dataInfo.invisible != true")
+
+    AbstractSparkAction.save(
+      relations
+        .join(ids, col("source") === ids("id"), "leftsemi")
+        .join(ids, col("target") === ids("id"), "leftsemi"),
+      outputPath,
+      SaveMode.Overwrite
+    )
+  }
+}

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json

@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "i",
+    "paramLongName": "graphBasePath",
+    "paramDescription": "the base path of raw graph",
+    "paramRequired": true
+  },
+  {
+    "paramName": "w",
+    "paramLongName": "inputPath",
+    "paramDescription": "the path to the input relation to cleanup",
+    "paramRequired": true
+  },
+  {
+    "paramName": "o",
+    "paramLongName": "outputPath",
+    "paramDescription": "the path of the output relation cleaned",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml

@@ -92,9 +92,34 @@
                 --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--o</arg><arg>${graphOutputPath}</arg>
+            <arg>--outputPath</arg><arg>${workingPath}/propagaterelation/</arg>
             <arg>--workingPath</arg><arg>${workingPath}</arg>
         </spark>
+        <ok to="CleanRelation"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="CleanRelation">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Clean Relations</name>
+            <class>eu.dnetlib.dhp.oa.dedup.SparkCleanRelation</class>
+            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=15000
+            </spark-opts>
+            <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
+            <arg>--inputPath</arg><arg>${workingPath}/propagaterelation/relation</arg>
+            <arg>--outputPath</arg><arg>${graphOutputPath}/relation</arg>
+        </spark>
         <ok to="group_entities"/>
         <error to="Kill"/>
     </action>

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

@@ -1,11 +1,32 @@
 
 package eu.dnetlib.dhp.oa.dedup;
 
-import static java.nio.file.Files.createTempDirectory;
-
-import static org.apache.spark.sql.functions.count;
-import static org.junit.jupiter.api.Assertions.*;
-import static org.mockito.Mockito.lenient;
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Sets;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import eu.dnetlib.pace.util.MapDocumentUtil;
+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.FilterFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.PairFunction;
+import org.apache.spark.sql.*;
+import org.apache.spark.sql.Dataset;
+import org.junit.jupiter.api.*;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.Mock;
+import org.mockito.Mockito;
+import org.mockito.junit.jupiter.MockitoExtension;
+import scala.Tuple2;
 
 import java.io.File;
 import java.io.FileReader;
@@ -19,36 +40,11 @@ import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
 
-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.FilterFunction;
-import org.apache.spark.api.java.function.MapFunction;
-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;
-import org.apache.spark.sql.SparkSession;
-import org.junit.jupiter.api.*;
-import org.junit.jupiter.api.extension.ExtendWith;
-import org.mockito.Mock;
-import org.mockito.Mockito;
-import org.mockito.junit.jupiter.MockitoExtension;
-
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.google.common.collect.Sets;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.*;
-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;
+import static java.nio.file.Files.createTempDirectory;
+import static org.apache.spark.sql.functions.col;
+import static org.apache.spark.sql.functions.count;
+import static org.junit.jupiter.api.Assertions.*;
+import static org.mockito.Mockito.lenient;
 
 @ExtendWith(MockitoExtension.class)
 @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
@@ -681,15 +677,16 @@ public class SparkDedupTest implements Serializable {
 
 		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", testDedupGraphBasePath
+					"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", outputRelPath
 				});
 
 		new SparkPropagateRelation(parser, spark).run(isLookUpService);
 
-		long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
+		long relations = jsc.textFile(outputRelPath + "/relation").count();
 
 //		assertEquals(4860, relations);
 		System.out.println("relations = " + relations);
@@ -708,7 +705,7 @@ public class SparkDedupTest implements Serializable {
 				(PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
 
 		JavaRDD<String> toCheck = jsc
-			.textFile(testDedupGraphBasePath + "/relation")
+			.textFile(outputRelPath + "/relation")
 			.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json))
 			.join(mergedIds)
 			.map(t -> t._2()._1())
@@ -724,6 +721,65 @@ public class SparkDedupTest implements Serializable {
 
 	@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
+		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);
+
+		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");
+
+		assertNotEquals(df_before.count(), df_after.count());
+		assertEquals(0, df_after.count());
+	}
+
+	@Test
+	@Order(10)
 	void testRelations() throws Exception {
 		testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_1.json", 12, 10);
 		testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2);