Add test class for ingesting DBLP data

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/dblp/PrepareDblpActionSets.java

@@ -36,7 +36,7 @@ import scala.Tuple2;
  */
 public class PrepareDblpActionSets implements Serializable {
 
-	private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelations.class);
+	private static final Logger log = LoggerFactory.getLogger(PrepareDblpActionSets.class);
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 	private static final String ID_PREFIX = "50|doi_________::";
 	public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
@@ -47,7 +47,7 @@ public class PrepareDblpActionSets implements Serializable {
 
 		String jsonConfiguration = IOUtils
 			.toString(
-				PrepareAffiliationRelations.class
+					PrepareDblpActionSets.class
 					.getResourceAsStream(
 						"/eu/dnetlib/dhp/actionmanager/dblp/input_actionset_parameter.json"));
 
@@ -79,7 +79,7 @@ public class PrepareDblpActionSets implements Serializable {
 
 				dblpData
 					.saveAsHadoopFile(
-						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
 
 			});
 	}
@@ -88,6 +88,8 @@ public class PrepareDblpActionSets implements Serializable {
 		String inputPath,
 		List<KeyValue> collectedFrom) {
 
+		log.info("Reading DBLP XML data");
+//
 //		TODO: load DBLP data into a Dataset
 		Dataset<Row> df = spark
 			.read()

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/dblp/PrepareDblpActionSetsTest.java

@@ -0,0 +1,202 @@
+
+package eu.dnetlib.dhp.actionmanager.dblp;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import javax.xml.crypto.Data;
+
+import eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob;
+import eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJobTest;
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+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.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Project;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+public class PrepareDblpActionSetsTest {
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+
+	private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJobTest.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files
+				.createTempDirectory(SparkAtomicActionScoreJobTest.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(SparkAtomicActionScoreJobTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+				.builder()
+				.appName(SparkAtomicActionScoreJobTest.class.getSimpleName())
+				.config(conf)
+				.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	private void runJob(String dblpInputPath, String outputPath) throws Exception {
+		PrepareDblpActionSets
+				.main(
+						new String[] {
+								"-isSparkSessionManaged", Boolean.FALSE.toString(),
+								"-dblpInputPath", dblpInputPath,
+								"-outputPath", outputPath,
+						});
+	}
+
+	@Test
+	void testXmlParsing() throws Exception {
+
+		String dblpInputPath = getClass()
+				.getResource("/eu/dnetlib/dhp/actionmanager/dblp/dblp_dump_sample.xml")
+				.getPath();
+
+		String outputPath = workingDir.toString() + "/actionSet";
+
+		// execute the job to generate the action sets for result scores
+		runJob(dblpInputPath, outputPath);
+
+//		TODO: use the data written in `outputPath` to perform tests
+
+//		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+//
+//		JavaRDD<OafEntity> tmp = sc
+//				.sequenceFile(outputPath, Text.class, Text.class)
+//				.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+//				.map(aa -> ((OafEntity) aa.getPayload()));
+//
+//		assertEquals(8, tmp.count());
+//
+//		Dataset<OafEntity> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(OafEntity.class));
+//		verificationDataset.createOrReplaceTempView("result");
+//
+//		Dataset<Row> testDataset = spark
+//				.sql(
+//						"Select p.id oaid, mes.id, mUnit.value from result p " +
+//								"lateral view explode(measures) m as mes " +
+//								"lateral view explode(mes.unit) u as mUnit ");
+//
+//		Assertions.assertEquals(28, testDataset.count());
+//
+//		assertResultImpactScores(testDataset);
+//		assertProjectImpactScores(testDataset);
+
+	}
+
+	void assertResultImpactScores(Dataset<Row> testDataset) {
+		Assertions
+				.assertEquals(
+						"6.63451994567e-09", testDataset
+								.filter(
+										"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
+												"and id = 'influence'")
+								.select("value")
+								.collectAsList()
+								.get(0)
+								.getString(0));
+		Assertions
+				.assertEquals(
+						"0.348694533145", testDataset
+								.filter(
+										"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
+												"and id = 'popularity_alt'")
+								.select("value")
+								.collectAsList()
+								.get(0)
+								.getString(0));
+		Assertions
+				.assertEquals(
+						"2.16094680115e-09", testDataset
+								.filter(
+										"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
+												"and id = 'popularity'")
+								.select("value")
+								.collectAsList()
+								.get(0)
+								.getString(0));
+	}
+
+	void assertProjectImpactScores(Dataset<Row> testDataset) throws Exception {
+
+		Assertions
+				.assertEquals(
+						"0", testDataset
+								.filter(
+										"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
+												"and id = 'numOfInfluentialResults'")
+								.select("value")
+								.collectAsList()
+								.get(0)
+								.getString(0));
+		Assertions
+				.assertEquals(
+						"1", testDataset
+								.filter(
+										"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
+												"and id = 'numOfPopularResults'")
+								.select("value")
+								.collectAsList()
+								.get(0)
+								.getString(0));
+		Assertions
+				.assertEquals(
+						"25", testDataset
+								.filter(
+										"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
+												"and id = 'totalImpulse'")
+								.select("value")
+								.collectAsList()
+								.get(0)
+								.getString(0));
+		Assertions
+				.assertEquals(
+						"43", testDataset
+								.filter(
+										"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
+												"and id = 'totalCitationCount'")
+								.select("value")
+								.collectAsList()
+								.get(0)
+								.getString(0));
+	}
+}