recert file SparkDedupTest.java

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;
@@ -26,13 +27,7 @@ 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.BeforeAll;
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.MethodOrderer;
-import org.junit.jupiter.api.Order;
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.api.TestMethodOrder;
+import org.junit.jupiter.api.*;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Mock;
 import org.mockito.Mockito;
@@ -102,7 +97,8 @@ public class SparkDedupTest implements Serializable {
 				IOUtils
 					.toString(
 						SparkDedupTest.class
-							.getResourceAsStream("/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
+							.getResourceAsStream(
+								"/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml")));
 
 		lenient()
 			.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("organization")))
@@ -110,7 +106,8 @@ public class SparkDedupTest implements Serializable {
 				IOUtils
 					.toString(
 						SparkDedupTest.class
-							.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
+							.getResourceAsStream(
+								"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
 
 		lenient()
 			.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
@@ -118,7 +115,8 @@ public class SparkDedupTest implements Serializable {
 				IOUtils
 					.toString(
 						SparkDedupTest.class
-							.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
+							.getResourceAsStream(
+								"/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
 
 		lenient()
 			.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
@@ -126,7 +124,8 @@ public class SparkDedupTest implements Serializable {
 				IOUtils
 					.toString(
 						SparkDedupTest.class
-							.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
+							.getResourceAsStream(
+								"/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
 
 		lenient()
 			.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("dataset")))
@@ -134,7 +133,8 @@ public class SparkDedupTest implements Serializable {
 				IOUtils
 					.toString(
 						SparkDedupTest.class
-							.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json")));
+							.getResourceAsStream(
+								"/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json")));
 
 		lenient()
 			.when(isLookUpService.getResourceProfileByQuery(Mockito.contains("otherresearchproduct")))
@@ -142,51 +142,54 @@ public class SparkDedupTest implements Serializable {
 				IOUtils
 					.toString(
 						SparkDedupTest.class
-							.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json")));
+							.getResourceAsStream(
+								"/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json")));
 	}
 
 	@Test
 	@Order(1)
 	public void createSimRelsTest() throws Exception {
 
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+		ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
 				.toString(
 					SparkCreateSimRels.class
-						.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json")));
 
 		parser
-			.parseArgument(new String[] {
-				"-i", testGraphBasePath,
-				"-asi", testActionSetId,
-				"-la", "lookupurl",
-				"-w", testOutputBasePath,
-				"-np", "50"
-			});
+			.parseArgument(
+				new String[] {
+					"-i", testGraphBasePath,
+					"-asi", testActionSetId,
+					"-la", "lookupurl",
+					"-w", testOutputBasePath,
+					"-np", "50"
+				});
 
 		new SparkCreateSimRels(parser, spark).run(isLookUpService);
 
-		final long orgs_simrel = spark
+		long orgs_simrel = spark
 			.read()
 			.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
 			.count();
 
-		final long pubs_simrel = spark
+		long pubs_simrel = spark
 			.read()
 			.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "publication"))
 			.count();
 
-		final long sw_simrel = spark
+		long sw_simrel = spark
 			.read()
 			.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "software"))
 			.count();
 
-		final long ds_simrel = spark
+		long ds_simrel = spark
 			.read()
 			.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "dataset"))
 			.count();
 
-		final long orp_simrel = spark
+		long orp_simrel = spark
 			.read()
 			.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct"))
 			.count();
@@ -202,29 +205,31 @@ public class SparkDedupTest implements Serializable {
 	@Order(2)
 	public void cutMergeRelsTest() throws Exception {
 
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+		ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
 				.toString(
 					SparkCreateMergeRels.class
-						.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
 
 		parser
-			.parseArgument(new String[] {
-				"-i",
-				testGraphBasePath,
-				"-asi",
-				testActionSetId,
-				"-la",
-				"lookupurl",
-				"-w",
-				testOutputBasePath,
-				"-cc",
-				"3"
-			});
+			.parseArgument(
+				new String[] {
+					"-i",
+					testGraphBasePath,
+					"-asi",
+					testActionSetId,
+					"-la",
+					"lookupurl",
+					"-w",
+					testOutputBasePath,
+					"-cc",
+					"3"
+				});
 
 		new SparkCreateMergeRels(parser, spark).run(isLookUpService);
 
-		final long orgs_mergerel = spark
+		long orgs_mergerel = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
 			.as(Encoders.bean(Relation.class))
@@ -235,7 +240,7 @@ public class SparkDedupTest implements Serializable {
 			.where("cnt > 3")
 			.count();
 
-		final long pubs_mergerel = spark
+		long pubs_mergerel = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
 			.as(Encoders.bean(Relation.class))
@@ -245,7 +250,7 @@ public class SparkDedupTest implements Serializable {
 			.select("source", "cnt")
 			.where("cnt > 3")
 			.count();
-		final long sw_mergerel = spark
+		long sw_mergerel = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
 			.as(Encoders.bean(Relation.class))
@@ -256,7 +261,7 @@ public class SparkDedupTest implements Serializable {
 			.where("cnt > 3")
 			.count();
 
-		final long ds_mergerel = spark
+		long ds_mergerel = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
 			.as(Encoders.bean(Relation.class))
@@ -267,7 +272,7 @@ public class SparkDedupTest implements Serializable {
 			.where("cnt > 3")
 			.count();
 
-		final long orp_mergerel = spark
+		long orp_mergerel = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
 			.as(Encoders.bean(Relation.class))
@@ -296,44 +301,46 @@ public class SparkDedupTest implements Serializable {
 	@Order(3)
 	public void createMergeRelsTest() throws Exception {
 
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+		ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
 				.toString(
 					SparkCreateMergeRels.class
-						.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
 
 		parser
-			.parseArgument(new String[] {
-				"-i",
-				testGraphBasePath,
-				"-asi",
-				testActionSetId,
-				"-la",
-				"lookupurl",
-				"-w",
-				testOutputBasePath
-			});
+			.parseArgument(
+				new String[] {
+					"-i",
+					testGraphBasePath,
+					"-asi",
+					testActionSetId,
+					"-la",
+					"lookupurl",
+					"-w",
+					testOutputBasePath
+				});
 
 		new SparkCreateMergeRels(parser, spark).run(isLookUpService);
 
-		final long orgs_mergerel = spark
+		long orgs_mergerel = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
 			.count();
-		final long pubs_mergerel = spark
+		long pubs_mergerel = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
 			.count();
-		final long sw_mergerel = spark
+		long sw_mergerel = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
 			.count();
-		final long ds_mergerel = spark
+		long ds_mergerel = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
 			.count();
 
-		final long orp_mergerel = spark
+		long orp_mergerel = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
 			.count();
@@ -350,39 +357,40 @@ public class SparkDedupTest implements Serializable {
 	@Order(4)
 	public void createDedupRecordTest() throws Exception {
 
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+		ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
 				.toString(
 					SparkCreateDedupRecord.class
-						.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/dedup/createDedupRecord_parameters.json")));
 		parser
-			.parseArgument(new String[] {
-				"-i",
-				testGraphBasePath,
-				"-asi",
-				testActionSetId,
-				"-la",
-				"lookupurl",
-				"-w",
-				testOutputBasePath
-			});
+			.parseArgument(
+				new String[] {
+					"-i",
+					testGraphBasePath,
+					"-asi",
+					testActionSetId,
+					"-la",
+					"lookupurl",
+					"-w",
+					testOutputBasePath
+				});
 
 		new SparkCreateDedupRecord(parser, spark).run(isLookUpService);
 
-		final long orgs_deduprecord = jsc
+		long orgs_deduprecord = jsc
 			.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord")
 			.count();
-		final long pubs_deduprecord = jsc
+		long pubs_deduprecord = jsc
 			.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord")
 			.count();
-		final long sw_deduprecord = jsc
+		long sw_deduprecord = jsc
 			.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord")
 			.count();
-		final long ds_deduprecord = jsc
-			.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_deduprecord")
-			.count();
-		final long orp_deduprecord = jsc
-			.textFile(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord")
+		long ds_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_deduprecord").count();
+		long orp_deduprecord = jsc
+			.textFile(
+				testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord")
 			.count();
 
 		assertEquals(85, orgs_deduprecord);
@@ -396,27 +404,29 @@ public class SparkDedupTest implements Serializable {
 	@Order(5)
 	public void updateEntityTest() throws Exception {
 
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+		ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
 				.toString(
 					SparkUpdateEntity.class
-						.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
 		parser
-			.parseArgument(new String[] {
-				"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
-			});
+			.parseArgument(
+				new String[] {
+					"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
+				});
 
 		new SparkUpdateEntity(parser, spark).run(isLookUpService);
 
-		final long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
-		final long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
-		final long projects = jsc.textFile(testDedupGraphBasePath + "/project").count();
-		final long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count();
-		final long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count();
-		final long dataset = jsc.textFile(testDedupGraphBasePath + "/dataset").count();
-		final long otherresearchproduct = jsc.textFile(testDedupGraphBasePath + "/otherresearchproduct").count();
+		long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
+		long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
+		long projects = jsc.textFile(testDedupGraphBasePath + "/project").count();
+		long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count();
+		long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count();
+		long dataset = jsc.textFile(testDedupGraphBasePath + "/dataset").count();
+		long otherresearchproduct = jsc.textFile(testDedupGraphBasePath + "/otherresearchproduct").count();
 
-		final long mergedOrgs = spark
+		long mergedOrgs = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
 			.as(Encoders.bean(Relation.class))
@@ -426,7 +436,7 @@ public class SparkDedupTest implements Serializable {
 			.distinct()
 			.count();
 
-		final long mergedPubs = spark
+		long mergedPubs = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
 			.as(Encoders.bean(Relation.class))
@@ -436,7 +446,7 @@ public class SparkDedupTest implements Serializable {
 			.distinct()
 			.count();
 
-		final long mergedSw = spark
+		long mergedSw = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
 			.as(Encoders.bean(Relation.class))
@@ -446,7 +456,7 @@ public class SparkDedupTest implements Serializable {
 			.distinct()
 			.count();
 
-		final long mergedDs = spark
+		long mergedDs = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
 			.as(Encoders.bean(Relation.class))
@@ -456,7 +466,7 @@ public class SparkDedupTest implements Serializable {
 			.distinct()
 			.count();
 
-		final long mergedOrp = spark
+		long mergedOrp = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
 			.as(Encoders.bean(Relation.class))
@@ -474,27 +484,27 @@ public class SparkDedupTest implements Serializable {
 		assertEquals(389, dataset);
 		assertEquals(517, otherresearchproduct);
 
-		final long deletedOrgs = jsc
+		long deletedOrgs = jsc
 			.textFile(testDedupGraphBasePath + "/organization")
 			.filter(this::isDeletedByInference)
 			.count();
 
-		final long deletedPubs = jsc
+		long deletedPubs = jsc
 			.textFile(testDedupGraphBasePath + "/publication")
 			.filter(this::isDeletedByInference)
 			.count();
 
-		final long deletedSw = jsc
+		long deletedSw = jsc
 			.textFile(testDedupGraphBasePath + "/software")
 			.filter(this::isDeletedByInference)
 			.count();
 
-		final long deletedDs = jsc
+		long deletedDs = jsc
 			.textFile(testDedupGraphBasePath + "/dataset")
 			.filter(this::isDeletedByInference)
 			.count();
 
-		final long deletedOrp = jsc
+		long deletedOrp = jsc
 			.textFile(testDedupGraphBasePath + "/otherresearchproduct")
 			.filter(this::isDeletedByInference)
 			.count();
@@ -510,19 +520,21 @@ public class SparkDedupTest implements Serializable {
 	@Order(6)
 	public void propagateRelationTest() throws Exception {
 
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+		ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
 				.toString(
 					SparkPropagateRelation.class
-						.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json")));
 		parser
-			.parseArgument(new String[] {
-				"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
-			});
+			.parseArgument(
+				new String[] {
+					"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
+				});
 
 		new SparkPropagateRelation(parser, spark).run(isLookUpService);
 
-		final long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
+		long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
 
 		assertEquals(4862, relations);
 
@@ -536,9 +548,10 @@ public class SparkDedupTest implements Serializable {
 			.select(mergeRels.col("target"))
 			.distinct()
 			.toJavaRDD()
-			.mapToPair((PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));
+			.mapToPair(
+				(PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
 
-		final JavaRDD<String> toCheck = jsc
+		JavaRDD<String> toCheck = jsc
 			.textFile(testDedupGraphBasePath + "/relation")
 			.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json))
 			.join(mergedIds)
@@ -547,8 +560,8 @@ public class SparkDedupTest implements Serializable {
 			.join(mergedIds)
 			.map(t -> t._2()._1());
 
-		final long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
-		final long updated = toCheck.count();
+		long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
+		long updated = toCheck.count();
 
 		assertEquals(updated, deletedbyinference);
 	}
@@ -560,8 +573,8 @@ public class SparkDedupTest implements Serializable {
 		testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2);
 	}
 
-	private void testUniqueness(final String path, final int expected_total, final int expected_unique) {
-		final Dataset<Relation> rel = spark
+	private void testUniqueness(String path, int expected_total, int expected_unique) {
+		Dataset<Relation> rel = spark
 			.read()
 			.textFile(getClass().getResource(path).getPath())
 			.map(
@@ -578,8 +591,7 @@ public class SparkDedupTest implements Serializable {
 		FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
 	}
 
-	public boolean isDeletedByInference(final String s) {
+	public boolean isDeletedByInference(String s) {
 		return s.contains("\"deletedbyinference\":true");
 	}
-
 }