333 lines
13 KiB
Java
333 lines
13 KiB
Java
package eu.dnetlib.dhp.bypassactionset;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.bypassactionset.model.FOSDataModel;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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import eu.dnetlib.dhp.countrypropagation.CountryPropagationJobTest;
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import org.apache.commons.io.FileUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.LocalFileSystem;
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import java.nio.file.Path;
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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.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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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 java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.nio.file.Files;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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public class GetFOSTest {
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private static final Logger log = LoggerFactory.getLogger(GetFOSTest.class);
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private static Path workingDir;
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private static SparkSession spark;
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private static LocalFileSystem fs;
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(CountryPropagationJobTest.class.getSimpleName());
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fs = FileSystem.getLocal(new Configuration());
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log.info("using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(GetFOSTest.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(CountryPropagationJobTest.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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void getFOSFileTest() throws CollectorException, IOException, ClassNotFoundException {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/fos/h2020_fos_sbs.csv")
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.getPath();
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final String outputPath = workingDir.toString() + "/fos.json";
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new GetFOSData()
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.doRewrite(sourcePath, outputPath, "eu.dnetlib.dhp.bypassactionset.FOSDataModel", '\t',fs );
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BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
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String line;
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int count = 0;
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while ((line = in.readLine()) != null) {
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FOSDataModel fos = new ObjectMapper().readValue(line, FOSDataModel.class);
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System.out.println(new ObjectMapper().writeValueAsString(fos));
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count += 1;
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}
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assertEquals(38, count);
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}
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@Test
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void distributeDoiTest() throws Exception{
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/fos/fos.json")
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.getPath();
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DistributeFOSSparkJob
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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() + "/distribute"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<FOSDataModel> tmp = sc
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.textFile(workingDir.toString() + "/distribute")
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.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
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assertEquals(50, tmp.count());
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assertEquals(1, tmp.filter(row -> row.getDoi().equals("10.3390/s18072310")).count());
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assertEquals("engineering and technology", tmp.filter(r -> r.getDoi().equals("10.3390/s18072310")).collect().get(0).getLevel1());
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assertEquals("nano-technology", tmp.filter(r -> r.getDoi().equals("10.3390/s18072310")).collect().get(0).getLevel2());
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assertEquals("nanoscience & nanotechnology", tmp.filter(r -> r.getDoi().equals("10.3390/s18072310")).collect().get(0).getLevel3());
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assertEquals(1, tmp.filter(row -> row.getDoi().equals("10.1111/1365-2656.12831")).count());
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assertEquals("social sciences", tmp.filter(r -> r.getDoi().equals("10.1111/1365-2656.12831")).collect().get(0).getLevel1());
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assertEquals("psychology and cognitive sciences", tmp.filter(r -> r.getDoi().equals("10.1111/1365-2656.12831")).collect().get(0).getLevel2());
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assertEquals("NULL", tmp.filter(r -> r.getDoi().equals("10.1111/1365-2656.12831")).collect().get(0).getLevel3());
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// {"doi":"10.1111/1365-2656.12831\u000210.17863/cam.24369","level1":"social sciences","level2":"psychology and cognitive sciences","level3":"NULL"}
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}
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/**
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* @Test
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* void testCountryPropagationSoftware() throws Exception {
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* final String sourcePath = getClass()
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* .getResource("/eu/dnetlib/dhp/countrypropagation/sample/software")
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* .getPath();
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* final String preparedInfoPath = getClass()
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* .getResource("/eu/dnetlib/dhp/countrypropagation/preparedInfo")
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* .getPath();
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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", sourcePath,
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* "-saveGraph", "true",
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* "-resultTableName", Software.class.getCanonicalName(),
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* "-outputPath", workingDir.toString() + "/software",
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* "-preparedInfoPath", preparedInfoPath
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* });
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*
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* final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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*
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* JavaRDD<Software> tmp = sc
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* .textFile(workingDir.toString() + "/software")
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* .map(item -> OBJECT_MAPPER.readValue(item, Software.class));
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*
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* // tmp.map(s -> new Gson().toJson(s)).foreach(s -> System.out.println(s));
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*
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* Assertions.assertEquals(10, tmp.count());
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*
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* Dataset<Software> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Software.class));
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*
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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());
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* Assertions.assertEquals(3, verificationDs.filter("size(country) = 2").count());
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* Assertions.assertEquals(0, verificationDs.filter("size(country) > 2").count());
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*
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* Dataset<String> countryExploded = verificationDs
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* .flatMap(
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* (FlatMapFunction<Software, Country>) row -> row.getCountry().iterator(), Encoders.bean(Country.class))
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* .map((MapFunction<Country, String>) Qualifier::getClassid, Encoders.STRING());
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*
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* Assertions.assertEquals(9, countryExploded.count());
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*
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* Assertions.assertEquals(1, countryExploded.filter("value = 'FR'").count());
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* Assertions.assertEquals(1, countryExploded.filter("value = 'TR'").count());
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* Assertions.assertEquals(2, countryExploded.filter("value = 'IT'").count());
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* Assertions.assertEquals(1, countryExploded.filter("value = 'US'").count());
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* Assertions.assertEquals(1, countryExploded.filter("value = 'MX'").count());
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* Assertions.assertEquals(1, countryExploded.filter("value = 'CH'").count());
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* Assertions.assertEquals(2, countryExploded.filter("value = 'JP'").count());
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*
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* Dataset<Tuple2<String, String>> countryExplodedWithCountryclassid = verificationDs
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* .flatMap((FlatMapFunction<Software, Tuple2<String, String>>) row -> {
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* List<Tuple2<String, String>> prova = new ArrayList<>();
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* List<Country> countryList = row.getCountry();
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* countryList
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* .forEach(
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* c -> prova
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* .add(
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* new Tuple2<>(
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* row.getId(), c.getClassid())));
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* return prova.iterator();
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* }, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
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*
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* Assertions.assertEquals(9, countryExplodedWithCountryclassid.count());
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*
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* countryExplodedWithCountryclassid.show(false);
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* Assertions
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* .assertEquals(
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* 1,
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* countryExplodedWithCountryclassid
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* .filter(
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* "_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'FR' ")
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* .count());
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* Assertions
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* .assertEquals(
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* 1,
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* countryExplodedWithCountryclassid
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* .filter(
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* "_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'TR' ")
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* .count());
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* Assertions
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* .assertEquals(
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* 2,
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* countryExplodedWithCountryclassid
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* .filter(
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* "_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'IT' or _2 = 'MX') ")
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* .count());
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* Assertions
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* .assertEquals(
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* 2,
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* countryExplodedWithCountryclassid
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* .filter(
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* "_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'IT' or _2 = 'US') ")
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* .count());
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* Assertions
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* .assertEquals(
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* 1,
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* countryExplodedWithCountryclassid
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* .filter(
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* "_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'JP'")
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* .count());
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* Assertions
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* .assertEquals(
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* 2,
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* countryExplodedWithCountryclassid
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* .filter(
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* "_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'CH' or _2 = 'JP') ")
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* .count());
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*
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* Dataset<Tuple2<String, String>> countryExplodedWithCountryclassname = verificationDs
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* .flatMap(
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* (FlatMapFunction<Software, Tuple2<String, String>>) row -> {
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* List<Tuple2<String, String>> prova = new ArrayList<>();
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* List<Country> countryList = row.getCountry();
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* countryList
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* .forEach(
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* c -> prova
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* .add(
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* new Tuple2<>(
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* row.getId(),
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* c.getClassname())));
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* return prova.iterator();
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* },
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* Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
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*
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* countryExplodedWithCountryclassname.show(false);
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* Assertions
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* .assertEquals(
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* 1,
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* countryExplodedWithCountryclassname
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* .filter(
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* "_1 = '50|od______1582::6e7a9b21a2feef45673890432af34244' and _2 = 'France' ")
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* .count());
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* Assertions
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* .assertEquals(
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* 1,
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* countryExplodedWithCountryclassname
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* .filter(
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* "_1 = '50|dedup_wf_001::40ea2f24181f6ae77b866ebcbffba523' and _2 = 'Turkey' ")
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* .count());
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* Assertions
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* .assertEquals(
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* 2,
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* countryExplodedWithCountryclassname
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* .filter(
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* "_1 = '50|od______1106::2b7ca9726230be8e862be224fd463ac4' and (_2 = 'Italy' or _2 = 'Mexico') ")
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* .count());
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* Assertions
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* .assertEquals(
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* 2,
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* countryExplodedWithCountryclassname
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* .filter(
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* "_1 = '50|od_______935::46a0ad9964171c3dd13373f5427b9a1c' and (_2 = 'Italy' or _2 = 'United States') ")
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* .count());
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* Assertions
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* .assertEquals(
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* 1,
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* countryExplodedWithCountryclassname
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* .filter(
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* "_1 = '50|dedup_wf_001::b67bc915603fc01e445f2b5888ba7218' and _2 = 'Japan' ")
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* .count());
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* Assertions
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* .assertEquals(
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* 2,
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* countryExplodedWithCountryclassname
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* .filter(
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* "_1 = '50|od_______109::f375befa62a741e9250e55bcfa88f9a6' and (_2 = 'Switzerland' or _2 = 'Japan') ")
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* .count());
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*
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* Dataset<Tuple2<String, String>> countryExplodedWithCountryProvenance = verificationDs
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* .flatMap(
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* (FlatMapFunction<Software, Tuple2<String, String>>) row -> {
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* List<Tuple2<String, String>> prova = new ArrayList<>();
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* List<Country> countryList = row.getCountry();
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* countryList
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* .forEach(
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* c -> prova
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* .add(
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* new Tuple2<>(
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* row.getId(),
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* c
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* .getDataInfo()
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* .getInferenceprovenance())));
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* return prova.iterator();
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* },
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* Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
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*
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* Assertions
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* .assertEquals(
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* 7, countryExplodedWithCountryProvenance.filter("_2 = 'propagation'").count());
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* }
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*/
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}
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