258 lines
8.9 KiB
Java
258 lines
8.9 KiB
Java
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package eu.dnetlib.dhp.oa.graph.dump.skgif;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import org.apache.commons.io.FileUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.ForeachFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.EmitPerManifestation;
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import eu.dnetlib.dhp.skgif.model.Persons;
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import eu.dnetlib.dhp.skgif.model.Topic;
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//@Disabled
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public class EmitFromEntitiesJobTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static SparkSession spark;
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private static Path workingDir;
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private static final Logger log = LoggerFactory.getLogger(EmitFromEntitiesJobTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(EmitFromEntitiesJobTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(EmitFromEntitiesJobTest.class.getSimpleName());
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conf.setMaster("local[*]");
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conf.set("spark.driver.host", "localhost");
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conf.set("hive.metastore.local", "true");
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conf.set("spark.ui.enabled", "false");
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conf.set("spark.sql.warehouse.dir", workingDir.toString());
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conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
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spark = SparkSession
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.builder()
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.appName(EmitFromEntitiesJobTest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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}
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@AfterAll
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public static void afterAll() throws IOException {
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FileUtils.deleteDirectory(workingDir.toFile());
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spark.stop();
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}
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@Test
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public void testEmitFromResult() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graph/")
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.getPath();
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EmitFromEntities
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath", sourcePath,
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"-outputPath", workingDir.toString() + "/result/",
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"-workingDir", workingDir.toString() + "/"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Persons> persons = sc
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.textFile(workingDir.toString() + "/result/Persons")
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.map(item -> OBJECT_MAPPER.readValue(item, Persons.class));
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JavaRDD<Topic> topics = sc
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.textFile(workingDir.toString() + "/result/Topic")
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.map(item -> OBJECT_MAPPER.readValue(item, Topic.class));
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JavaRDD<EmitPerManifestation> manifestation = sc
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.textFile(workingDir.toString() + "/publication/manifestation")
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.map(item -> OBJECT_MAPPER.readValue(item, EmitPerManifestation.class));
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org.apache.spark.sql.Dataset<Persons> personsDataset = spark
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.createDataset(persons.rdd(), Encoders.bean(Persons.class));
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personsDataset.show(false);
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Persons claudiaBorer = personsDataset
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.filter(
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(FilterFunction<Persons>) p -> p
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.getLocal_identifier()
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.equalsIgnoreCase("temp_person_::2c1eea261f7d9a97ab7ca8c4200781db"))
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.first();
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Assertions
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.assertEquals(
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2,
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personsDataset
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.filter(
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(FilterFunction<Persons>) p -> p.getGiven_name().equalsIgnoreCase("claudia")
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&& p.getFamily_name().equalsIgnoreCase("borer"))
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.count());
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Assertions
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.assertEquals(
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1,
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personsDataset
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.filter(
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(FilterFunction<Persons>) p -> p.getGiven_name().equalsIgnoreCase("claudia")
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&& p.getFamily_name().equalsIgnoreCase("borer")
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&& !p
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.getLocal_identifier()
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.equalsIgnoreCase("temp_person_::2c1eea261f7d9a97ab7ca8c4200781db"))
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.count());
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Assertions.assertEquals("claudia", claudiaBorer.getGiven_name().toLowerCase());
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Assertions.assertEquals("borer", claudiaBorer.getFamily_name().toLowerCase());
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Assertions
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.assertEquals(
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2,
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personsDataset
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.filter((FilterFunction<Persons>) p -> p.getLocal_identifier().startsWith("person"))
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.count());
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Assertions
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.assertEquals(
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1,
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personsDataset
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.filter(
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(FilterFunction<Persons>) p -> p.getLocal_identifier().startsWith("person")
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&& p.getIdentifiers().get(0).getValue().equals("0000-0002-5597-4916"))
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.count());
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Persons orcidPerson = personsDataset
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.filter(
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(FilterFunction<Persons>) p -> p.getLocal_identifier().startsWith("person")
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&& p.getIdentifiers().get(0).getValue().equals("0000-0002-5597-4916"))
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.first();
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Assertions.assertEquals("M.", orcidPerson.getGiven_name());
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Assertions.assertEquals("Kooi", orcidPerson.getFamily_name());
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Assertions.assertEquals(1, orcidPerson.getIdentifiers().size());
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Assertions.assertEquals("orcid", orcidPerson.getIdentifiers().get(0).getScheme());
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Assertions.assertEquals("0000-0002-5597-4916", orcidPerson.getIdentifiers().get(0).getValue());
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Dataset<EmitPerManifestation> manifestationDataset = spark
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.createDataset(manifestation.rdd(), Encoders.bean(EmitPerManifestation.class));
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manifestationDataset.show(false);
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Assertions.assertEquals(5, manifestationDataset.count());
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Dataset<Topic> topicDataset = spark
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.createDataset(topics.rdd(), Encoders.bean(Topic.class));
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Assertions.assertEquals(0, topicDataset.count());
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}
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@Test
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public void testEmitFromResultComplete() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graph_complete_entities/")
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.getPath();
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EmitFromEntities
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath", sourcePath,
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"-outputPath", workingDir.toString() + "/result/",
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"-workingDir", workingDir.toString() + "/"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Persons> persons = sc
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.textFile(workingDir.toString() + "/result/Persons")
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.map(item -> OBJECT_MAPPER.readValue(item, Persons.class));
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org.apache.spark.sql.Dataset<Persons> personsDataset = spark
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.createDataset(persons.rdd(), Encoders.bean(Persons.class));
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personsDataset.foreach((ForeachFunction<Persons>) p -> System.out.println(OBJECT_MAPPER.writeValueAsString(p)));
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JavaRDD<Topic> topics = sc
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.textFile(workingDir.toString() + "/result/Topic")
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.map(item -> OBJECT_MAPPER.readValue(item, Topic.class));
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Dataset<Topic> topicDataset = spark
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.createDataset(topics.rdd(), Encoders.bean(Topic.class));
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Assertions.assertEquals(3, topicDataset.count());
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topicDataset.foreach((ForeachFunction<Topic>) t -> System.out.println(OBJECT_MAPPER.writeValueAsString(t)));
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JavaRDD<EmitPerManifestation> manifestation = sc
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.textFile(workingDir.toString() + "/publication/manifestation")
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.map(item -> OBJECT_MAPPER.readValue(item, EmitPerManifestation.class));
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Dataset<EmitPerManifestation> manifestationDataset = spark
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.createDataset(manifestation.rdd(), Encoders.bean(EmitPerManifestation.class));
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manifestationDataset.show(false);
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}
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@Test
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public void testEmitFromResultApiSubset() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graphForAPIExample/")
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.getPath();
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EmitFromEntities
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath", sourcePath,
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"-outputPath", workingDir.toString() + "/result/",
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"-workingDir", workingDir.toString() + "/"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Persons> persons = sc
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.textFile(workingDir.toString() + "/result/Persons")
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.map(item -> OBJECT_MAPPER.readValue(item, Persons.class));
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org.apache.spark.sql.Dataset<Persons> personsDataset = spark
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.createDataset(persons.rdd(), Encoders.bean(Persons.class));
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personsDataset.foreach((ForeachFunction<Persons>) p -> System.out.println(OBJECT_MAPPER.writeValueAsString(p)));
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JavaRDD<Topic> topics = sc
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.textFile(workingDir.toString() + "/result/Topic")
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.map(item -> OBJECT_MAPPER.readValue(item, Topic.class));
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Dataset<Topic> topicDataset = spark
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.createDataset(topics.rdd(), Encoders.bean(Topic.class));
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// Assertions.assertEquals(3, topicDataset.count());
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topicDataset.foreach((ForeachFunction<Topic>) t -> System.out.println(OBJECT_MAPPER.writeValueAsString(t)));
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JavaRDD<EmitPerManifestation> manifestation = sc
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.textFile(workingDir.toString() + "/publication/manifestation")
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.map(item -> OBJECT_MAPPER.readValue(item, EmitPerManifestation.class));
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Dataset<EmitPerManifestation> manifestationDataset = spark
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.createDataset(manifestation.rdd(), Encoders.bean(EmitPerManifestation.class));
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manifestation.foreach(m-> System.out.println(OBJECT_MAPPER.writeValueAsString(m)));
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}
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}
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