forked from D-Net/dnet-hadoop
635 lines
30 KiB
Java
635 lines
30 KiB
Java
package eu.dnetlib.dhp.countrypropagation;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.countrypropagation.pojo.DatasourceCountry;
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import eu.dnetlib.dhp.countrypropagation.pojo.ResultCountrySet;
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import eu.dnetlib.dhp.schema.oaf.Country;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Software;
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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.FlatMapFunction;
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import org.apache.spark.api.java.function.MapFunction;
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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 scala.Tuple2;
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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 java.util.ArrayList;
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import java.util.List;
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/**
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* @author miriam.baglioni
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* @Date 23/11/22
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*/
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public class CountryPropagationAllStepsTest {
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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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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(DatasourceCountryPreparationTest.class.getSimpleName());
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SparkConf conf = new SparkConf();
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conf.setAppName(DatasourceCountryPreparationTest.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(DatasourceCountryPreparationTest.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 allStepsTest() throws Exception {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/countrypropagation/graph")
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.getPath();
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PrepareDatasourceCountryAssociation
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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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"--workingPath", workingDir.toString() + "/country",
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"--allowedtypes", "pubsrepository::institutional",
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"--whitelist",
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"10|openaire____::3795d6478e30e2c9f787d427ff160944;10|opendoar____::16e6a3326dd7d868cbc926602a61e4d0;10|eurocrisdris::fe4903425d9040f680d8610d9079ea14;10|openaire____::5b76240cc27a58c6f7ceef7d8c36660e;10|openaire____::172bbccecf8fca44ab6a6653e84cb92a;10|openaire____::149c6590f8a06b46314eed77bfca693f;10|eurocrisdris::a6026877c1a174d60f81fd71f62df1c1;10|openaire____::4692342f0992d91f9e705c26959f09e0;10|openaire____::8d529dbb05ec0284662b391789e8ae2a;10|openaire____::345c9d171ef3c5d706d08041d506428c;10|opendoar____::1c1d4df596d01da60385f0bb17a4a9e0;10|opendoar____::7a614fd06c325499f1680b9896beedeb;10|opendoar____::1ee3dfcd8a0645a25a35977997223d22;10|opendoar____::d296c101daa88a51f6ca8cfc1ac79b50;10|opendoar____::798ed7d4ee7138d49b8828958048130a;10|openaire____::c9d2209ecc4d45ba7b4ca7597acb88a2;10|eurocrisdris::c49e0fe4b9ba7b7fab717d1f0f0a674d;10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539;10|eurocrisdris::432ca599953ff50cd4eeffe22faf3e48"
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});
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sc.textFile(
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getClass()
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.getResource("/eu/dnetlib/dhp/countrypropagation/graph/publication")
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.getPath()).saveAsTextFile(workingDir.toString() + "/source/publication");
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sc
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.textFile(
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getClass()
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.getResource("/eu/dnetlib/dhp/countrypropagation/graph/software")
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.getPath()).saveAsTextFile(workingDir.toString() + "/source/software");
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verifyDatasourceCountry();
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PrepareResultCountrySet
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--workingPath", workingDir.toString() + "/country",
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"--sourcePath", workingDir.toString() + "/source/publication",
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"--resultTableName", Publication.class.getCanonicalName()
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});
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verifyResultCountrySet();
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PrepareResultCountrySet
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--workingPath", workingDir.toString() + "/country",
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"--sourcePath", workingDir.toString() + "/source/software",
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"--resultTableName", Software.class.getCanonicalName()
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});
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SparkCountryPropagationJob
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--sourcePath",workingDir.toString() + "/source/publication",
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"-resultTableName", Publication.class.getCanonicalName(),
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"-workingPath", workingDir.toString() +"/country"
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});
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verifyPropagationPublication();
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SparkCountryPropagationJob
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--sourcePath",workingDir.toString() + "/source/software",
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"-resultTableName", Software.class.getCanonicalName(),
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"-workingPath", workingDir.toString() + "/country"
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});
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verifyPropagationSoftware();
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}
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void verifyDatasourceCountry(){
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<DatasourceCountry> tmp = sc
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.textFile(workingDir.toString() + "/country/datasourceCountry")
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.map(item -> OBJECT_MAPPER.readValue(item, DatasourceCountry.class));
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Assertions.assertEquals(3, tmp.count());
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Assertions
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.assertEquals(
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1, tmp
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.filter(
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dsc -> dsc
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.getDataSourceId()
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.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14"))
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.count());
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Assertions
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.assertEquals(
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1, tmp
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.filter(
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dsc -> dsc
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.getDataSourceId()
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.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280"))
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.count());
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Assertions
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.assertEquals(
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1, tmp
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.filter(
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dsc -> dsc
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.getDataSourceId()
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.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539"))
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.count());
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Assertions
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.assertEquals(
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"NL", tmp
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.filter(
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dsc -> dsc
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.getDataSourceId()
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.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14"))
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.collect()
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.get(0)
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.getCountry()
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.getClassid());
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Assertions
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.assertEquals(
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"Netherlands", tmp
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.filter(
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dsc -> dsc
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.getDataSourceId()
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.equals("10|eurocrisdris::fe4903425d9040f680d8610d9079ea14"))
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.collect()
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.get(0)
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.getCountry()
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.getClassname());
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Assertions
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.assertEquals(
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"IT", tmp
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.filter(
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dsc -> dsc
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.getDataSourceId()
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.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280"))
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.collect()
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.get(0)
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.getCountry()
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.getClassid());
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Assertions
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.assertEquals(
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"Italy", tmp
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.filter(
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dsc -> dsc
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.getDataSourceId()
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.equals("10|opendoar____::f0dd4a99fba6075a9494772b58f95280"))
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.collect()
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.get(0)
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.getCountry()
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.getClassname());
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Assertions
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.assertEquals(
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"FR", tmp
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.filter(
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dsc -> dsc
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.getDataSourceId()
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.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539"))
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.collect()
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.get(0)
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.getCountry()
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.getClassid());
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Assertions
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.assertEquals(
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"France", tmp
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.filter(
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dsc -> dsc
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.getDataSourceId()
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.equals("10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539"))
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.collect()
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.get(0)
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.getCountry()
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.getClassname());
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tmp.foreach(e -> System.out.println(OBJECT_MAPPER.writeValueAsString(e)));
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}
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void verifyResultCountrySet(){
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<ResultCountrySet> tmp = sc
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.textFile(workingDir.toString() + "/country/preparedInfo/publication")
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.map(item -> OBJECT_MAPPER.readValue(item, ResultCountrySet.class));
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Assertions.assertEquals(5, tmp.count());
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ResultCountrySet rc = tmp
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.filter(r -> r.getResultId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072"))
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.collect()
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.get(0);
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Assertions.assertEquals(1, rc.getCountrySet().size());
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Assertions.assertEquals("NL", rc.getCountrySet().get(0).getClassid());
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Assertions.assertEquals("Netherlands", rc.getCountrySet().get(0).getClassname());
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rc = tmp
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.filter(r -> r.getResultId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b"))
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.collect()
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.get(0);
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Assertions.assertEquals(1, rc.getCountrySet().size());
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Assertions.assertEquals("NL", rc.getCountrySet().get(0).getClassid());
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Assertions.assertEquals("Netherlands", rc.getCountrySet().get(0).getClassname());
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rc = tmp
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.filter(r -> r.getResultId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6"))
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.collect()
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.get(0);
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Assertions.assertEquals(2, rc.getCountrySet().size());
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Assertions
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.assertTrue(
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rc
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.getCountrySet()
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.stream()
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.anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
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Assertions
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.assertTrue(
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rc
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.getCountrySet()
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.stream()
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.anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
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rc = tmp
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.filter(r -> r.getResultId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df"))
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.collect()
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.get(0);
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Assertions.assertEquals(2, rc.getCountrySet().size());
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Assertions
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.assertTrue(
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rc
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.getCountrySet()
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.stream()
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.anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
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Assertions
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.assertTrue(
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rc
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.getCountrySet()
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.stream()
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.anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands")));
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rc = tmp
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.filter(r -> r.getResultId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088"))
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.collect()
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.get(0);
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Assertions.assertEquals(2, rc.getCountrySet().size());
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Assertions
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.assertTrue(
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rc
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.getCountrySet()
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.stream()
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.anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
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Assertions
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.assertTrue(
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rc
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.getCountrySet()
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.stream()
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.anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
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}
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void verifyPropagationPublication(){
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Publication> tmp = sc
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.textFile(workingDir.toString() + "/country/publication")
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.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
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Assertions.assertEquals(12, tmp.count());
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Assertions.assertEquals(5, tmp.filter(r -> r.getCountry().size() > 0).count());
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tmp
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.foreach(
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r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemeid())));
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tmp
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.foreach(
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r -> r
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.getCountry()
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.stream()
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.forEach(c -> Assertions.assertEquals("dnet:countries", c.getSchemename())));
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tmp
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.foreach(
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r -> r
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.getCountry()
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.stream()
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.forEach(c -> Assertions.assertFalse(c.getDataInfo().getDeletedbyinference())));
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tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertFalse(c.getDataInfo().getInvisible())));
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tmp.foreach(r -> r.getCountry().stream().forEach(c -> Assertions.assertTrue(c.getDataInfo().getInferred())));
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tmp
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.foreach(
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r -> r.getCountry().stream().forEach(c -> Assertions.assertEquals("0.85", c.getDataInfo().getTrust())));
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tmp
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.foreach(
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r -> r
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.getCountry()
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.stream()
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.forEach(c -> Assertions.assertEquals("propagation", c.getDataInfo().getInferenceprovenance())));
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tmp
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.foreach(
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r -> r
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.getCountry()
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.stream()
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.forEach(
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c -> Assertions
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.assertEquals("country:instrepos", c.getDataInfo().getProvenanceaction().getClassid())));
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tmp
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.foreach(
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r -> r
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.getCountry()
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.stream()
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.forEach(
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c -> Assertions
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.assertEquals(
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"dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemeid())));
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tmp
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.foreach(
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r -> r
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.getCountry()
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.stream()
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.forEach(
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c -> Assertions
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.assertEquals(
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"dnet:provenanceActions", c.getDataInfo().getProvenanceaction().getSchemename())));
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List<Country> countries = tmp
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.filter(r -> r.getId().equals("50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072"))
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.collect()
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.get(0)
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.getCountry();
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Assertions.assertEquals(1, countries.size());
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Assertions.assertEquals("NL", countries.get(0).getClassid());
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Assertions.assertEquals("Netherlands", countries.get(0).getClassname());
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countries = tmp
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.filter(r -> r.getId().equals("50|07b5c0ccd4fe::e7f5459cc97865f2af6e3da964c1250b"))
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.collect()
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.get(0)
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.getCountry();
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Assertions.assertEquals(1, countries.size());
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Assertions.assertEquals("NL", countries.get(0).getClassid());
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Assertions.assertEquals("Netherlands", countries.get(0).getClassname());
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countries = tmp
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.filter(r -> r.getId().equals("50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6"))
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.collect()
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.get(0)
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.getCountry();
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Assertions.assertEquals(2, countries.size());
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Assertions
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.assertTrue(
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countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
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Assertions
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.assertTrue(
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countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
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countries = tmp
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.filter(r -> r.getId().equals("50|355e65625b88::74009c567c81b4aa55c813db658734df"))
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.collect()
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.get(0)
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.getCountry();
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Assertions.assertEquals(2, countries.size());
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Assertions
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.assertTrue(
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countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
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Assertions
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.assertTrue(
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countries
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.stream()
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.anyMatch(cs -> cs.getClassid().equals("NL") && cs.getClassname().equals("Netherlands")));
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countries = tmp
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.filter(r -> r.getId().equals("50|355e65625b88::54a1c76f520bb2c8da27d12e42891088"))
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.collect()
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.get(0)
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.getCountry();
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Assertions.assertEquals(2, countries.size());
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Assertions
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.assertTrue(
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countries.stream().anyMatch(cs -> cs.getClassid().equals("IT") && cs.getClassname().equals("Italy")));
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Assertions
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.assertTrue(
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countries.stream().anyMatch(cs -> cs.getClassid().equals("FR") && cs.getClassname().equals("France")));
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}
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void verifyPropagationSoftware(){
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Software> tmp = sc
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.textFile(workingDir.toString() + "/source/software")
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.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
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Assertions.assertEquals(10, tmp.count());
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Dataset<Software> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class));
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Assertions.assertEquals(6, verificationDs.filter("size(country) > 0").count());
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Assertions.assertEquals(3, verificationDs.filter("size(country) = 1").count());
|
|
Assertions.assertEquals(3, verificationDs.filter("size(country) = 2").count());
|
|
Assertions.assertEquals(0, verificationDs.filter("size(country) > 2").count());
|
|
|
|
Dataset<String> countryExploded = verificationDs
|
|
.flatMap(
|
|
(FlatMapFunction<Software, Country>) row -> row.getCountry().iterator(), Encoders.bean(Country.class))
|
|
.map((MapFunction<Country, String>) Qualifier::getClassid, Encoders.STRING());
|
|
|
|
Assertions.assertEquals(9, countryExploded.count());
|
|
|
|
Assertions.assertEquals(1, countryExploded.filter("value = 'FR'").count());
|
|
Assertions.assertEquals(1, countryExploded.filter("value = 'TR'").count());
|
|
Assertions.assertEquals(2, countryExploded.filter("value = 'IT'").count());
|
|
Assertions.assertEquals(1, countryExploded.filter("value = 'US'").count());
|
|
Assertions.assertEquals(1, countryExploded.filter("value = 'MX'").count());
|
|
Assertions.assertEquals(1, countryExploded.filter("value = 'CH'").count());
|
|
Assertions.assertEquals(2, countryExploded.filter("value = 'JP'").count());
|
|
|
|
Dataset<Tuple2<String, String>> countryExplodedWithCountryclassid = verificationDs
|
|
.flatMap((FlatMapFunction<Software, Tuple2<String, String>>) row -> {
|
|
List<Tuple2<String, String>> prova = new ArrayList<>();
|
|
List<Country> countryList = row.getCountry();
|
|
countryList
|
|
.forEach(
|
|
c -> prova
|
|
.add(
|
|
new Tuple2<>(
|
|
row.getId(), c.getClassid())));
|
|
return prova.iterator();
|
|
}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
|
|
|
Assertions.assertEquals(9, countryExplodedWithCountryclassid.count());
|
|
|
|
//countryExplodedWithCountryclassid.show(false);
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
countryExplodedWithCountryclassid
|
|
.filter(
|
|
"_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'FR' ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
countryExplodedWithCountryclassid
|
|
.filter(
|
|
"_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'TR' ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
2,
|
|
countryExplodedWithCountryclassid
|
|
.filter(
|
|
"_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'IT' or _2 = 'MX') ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
2,
|
|
countryExplodedWithCountryclassid
|
|
.filter(
|
|
"_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'IT' or _2 = 'US') ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
countryExplodedWithCountryclassid
|
|
.filter(
|
|
"_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'JP'")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
2,
|
|
countryExplodedWithCountryclassid
|
|
.filter(
|
|
"_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'CH' or _2 = 'JP') ")
|
|
.count());
|
|
|
|
Dataset<Tuple2<String, String>> countryExplodedWithCountryclassname = verificationDs
|
|
.flatMap(
|
|
(FlatMapFunction<Software, Tuple2<String, String>>) row -> {
|
|
List<Tuple2<String, String>> prova = new ArrayList<>();
|
|
List<Country> countryList = row.getCountry();
|
|
countryList
|
|
.forEach(
|
|
c -> prova
|
|
.add(
|
|
new Tuple2<>(
|
|
row.getId(),
|
|
c.getClassname())));
|
|
return prova.iterator();
|
|
},
|
|
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
|
|
|
//countryExplodedWithCountryclassname.show(false);
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
countryExplodedWithCountryclassname
|
|
.filter(
|
|
"_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'France' ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
countryExplodedWithCountryclassname
|
|
.filter(
|
|
"_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'Turkey' ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
2,
|
|
countryExplodedWithCountryclassname
|
|
.filter(
|
|
"_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'Italy' or _2 = 'Mexico') ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
2,
|
|
countryExplodedWithCountryclassname
|
|
.filter(
|
|
"_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'Italy' or _2 = 'United States') ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
1,
|
|
countryExplodedWithCountryclassname
|
|
.filter(
|
|
"_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'Japan' ")
|
|
.count());
|
|
Assertions
|
|
.assertEquals(
|
|
2,
|
|
countryExplodedWithCountryclassname
|
|
.filter(
|
|
"_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'Switzerland' or _2 = 'Japan') ")
|
|
.count());
|
|
|
|
Dataset<Tuple2<String, String>> countryExplodedWithCountryProvenance = verificationDs
|
|
.flatMap(
|
|
(FlatMapFunction<Software, Tuple2<String, String>>) row -> {
|
|
List<Tuple2<String, String>> prova = new ArrayList<>();
|
|
List<Country> countryList = row.getCountry();
|
|
countryList
|
|
.forEach(
|
|
c -> prova
|
|
.add(
|
|
new Tuple2<>(
|
|
row.getId(),
|
|
c
|
|
.getDataInfo()
|
|
.getInferenceprovenance())));
|
|
return prova.iterator();
|
|
},
|
|
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count());
|
|
}
|
|
}
|