package eu.dnetlib.dhp.actionmanager.bipfinder; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.List; import java.util.stream.Collectors; import org.apache.commons.io.FileUtils; import org.apache.hadoop.io.Text; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; 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.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; 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.*; import eu.dnetlib.dhp.schema.oaf.KeyValue; import scala.Tuple2; public class SparkAtomicActionScoreJobTest { 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(); } @Test public void matchOne() throws Exception { String bipScoresPath = getClass() .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") .getPath(); String inputPath = getClass() .getResource( "/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json") .getPath(); SparkAtomicActionScoreJob .main( new String[] { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-inputPath", inputPath, "-bipScorePath", bipScoresPath, "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", "-outputPath", workingDir.toString() + "/actionSet" }); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); JavaRDD tmp = sc .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) .map(aa -> ((Publication) aa.getPayload())); Assertions.assertTrue(tmp.count() == 1); Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); verificationDataset.createOrReplaceTempView("publication"); Dataset execVerification = spark .sql( "Select p.id oaid, mes.id, mUnit.value from publication p " + "lateral view explode(measures) m as mes " + "lateral view explode(mes.unit) u as mUnit "); Assertions.assertEquals(2, execVerification.count()); Assertions .assertEquals( "50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", execVerification.select("oaid").collectAsList().get(0).getString(0)); Assertions .assertEquals( "1.47565045883e-08", execVerification.filter("id = 'influence'").select("value").collectAsList().get(0).getString(0)); Assertions .assertEquals( "0.227515392", execVerification.filter("id = 'popularity'").select("value").collectAsList().get(0).getString(0)); } @Test public void matchOneWithTwo() throws Exception { String bipScoresPath = getClass() .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") .getPath(); String inputPath = getClass() .getResource( "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json") .getPath(); SparkAtomicActionScoreJob .main( new String[] { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-inputPath", inputPath, "-bipScorePath", bipScoresPath, "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", "-outputPath", workingDir.toString() + "/actionSet" }); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); JavaRDD tmp = sc .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) .map(aa -> ((Publication) aa.getPayload())); Assertions.assertTrue(tmp.count() == 1); Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); verificationDataset.createOrReplaceTempView("publication"); Dataset execVerification = spark .sql( "Select p.id oaid, mes.id, mUnit.value from publication p " + "lateral view explode(measures) m as mes " + "lateral view explode(mes.unit) u as mUnit "); Assertions.assertEquals(4, execVerification.count()); Assertions .assertEquals( "50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb", execVerification.select("oaid").collectAsList().get(0).getString(0)); Assertions .assertEquals( 2, execVerification.filter("id = 'influence'").count()); Assertions .assertEquals( 2, execVerification.filter("id = 'popularity'").count()); List tmp_ds = execVerification.filter("id = 'influence'").select("value").collectAsList(); String tmp_influence = tmp_ds.get(0).getString(0); Assertions .assertTrue( "1.47565045883e-08".equals(tmp_influence) || "1.98956540239e-08".equals(tmp_influence)); tmp_influence = tmp_ds.get(1).getString(0); Assertions .assertTrue( "1.47565045883e-08".equals(tmp_influence) || "1.98956540239e-08".equals(tmp_influence)); Assertions.assertTrue(!tmp_ds.get(0).getString(0).equals(tmp_ds.get(1).getString(0))); } @Test public void matchTwo() throws Exception { String bipScoresPath = getClass() .getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json") .getPath(); String inputPath = getClass() .getResource( "/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json") .getPath(); SparkAtomicActionScoreJob .main( new String[] { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-inputPath", inputPath, "-bipScorePath", bipScoresPath, "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", "-outputPath", workingDir.toString() + "/actionSet" }); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); JavaRDD tmp = sc .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) .map(aa -> ((Publication) aa.getPayload())); Assertions.assertTrue(tmp.count() == 2); Dataset verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class)); verificationDataset.createOrReplaceTempView("publication"); Dataset execVerification = spark .sql( "Select p.id oaid, mes.id, mUnit.value from publication p " + "lateral view explode(measures) m as mes " + "lateral view explode(mes.unit) u as mUnit "); Assertions.assertEquals(4, execVerification.count()); Assertions .assertEquals( 2, execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb'").count()); Assertions .assertEquals( 2, execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09'").count()); Assertions .assertEquals( 2, execVerification.filter("id = 'influence'").count()); Assertions .assertEquals( 2, execVerification.filter("id = 'popularity'").count()); Assertions .assertEquals( "1.47565045883e-08", execVerification .filter( "oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + "and id = 'influence'") .select("value") .collectAsList() .get(0) .getString(0)); Assertions .assertEquals( "1.98956540239e-08", execVerification .filter( "oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + "and id = 'influence'") .select("value") .collectAsList() .get(0) .getString(0)); Assertions .assertEquals( "0.282046161584", execVerification .filter( "oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " + "and id = 'popularity'") .select("value") .collectAsList() .get(0) .getString(0)); Assertions .assertEquals( "0.227515392", execVerification .filter( "oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " + "and id = 'popularity'") .select("value") .collectAsList() .get(0) .getString(0)); } }