[DUMP CSV] test and resources for the result dumps
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package eu.dnetlib.dhp.oa.graph.dump.csv;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.utils.DHPUtils;
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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.JavaSparkContext;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Row;
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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 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.HashMap;
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import java.util.Optional;
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import static org.apache.commons.lang3.StringUtils.split;
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/**
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* @author miriam.baglioni
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* @Date 11/05/23
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*/
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public class DumpResultTest {
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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
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.getLogger(DumpResultTest.class);
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private static HashMap<String, String> map = new HashMap<>();
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files
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.createTempDirectory(DumpResultTest.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(DumpResultTest.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(DumpResultTest.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 testDumpResult() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/input/")
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.getPath();
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spark.read().text(getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/working/resultIds")
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.getPath())
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.write()
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.text(workingDir.toString() + "/working/resultIds/");
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SparkDumpResults.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/output",
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"-workingPath", workingDir.toString() + "/working",
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"-resultType", "publication",
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-sourcePath", sourcePath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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Dataset<Row> tmp = spark.read().option("header", "true").option("delimiter", Constants.SEP)
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.csv(workingDir.toString() + "/working/publication/result");
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Assertions.assertEquals(3, tmp.count());
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Row row = tmp
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.where("id = '50|DansKnawCris::0224aae28af558f21768dbc6439c7a95'")
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.first();
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Assertions.assertEquals(ModelConstants.OPEN_ACCESS_RIGHT().getClassid(),row.getAs("accessright"));
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Assertions.assertEquals("FI" ,row.getAs("country"));
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Assertions.assertEquals("Lit.opg., bijl." ,row.getAs("description"));
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Assertions.assertEquals(3 ,split(row.getAs("keywords"), ", ").length);
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Assertions.assertTrue(row.getAs("keywords").toString().contains("archeologie"));
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Assertions.assertTrue(row.getAs("keywords").toString().contains("prospectie"));
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Assertions.assertTrue(row.getAs("keywords").toString().contains("archaeology"));
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Assertions.assertEquals("nl", row.getAs("language"));
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Assertions.assertEquals("2007-01-01", row.getAs("publication_date"));
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Assertions.assertEquals("FakePublisher1", row.getAs("publisher"));
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Assertions.assertEquals("Inventariserend veldonderzoek d.m.v. boringen (karterende fase) : Raadhuisstraat te Dirkshorn, gemeente Harenkarspel", row.getAs("title"));
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Assertions.assertEquals("publication", row.getAs("type"));
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row = tmp
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.where("id = '50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9'")
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.first();
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Assertions.assertEquals(ModelConstants.OPEN_ACCESS_RIGHT().getClassid(),row.getAs("accessright"));
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Assertions.assertEquals(2 ,split(row.getAs("country"), ", ").length);
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Assertions.assertNull(row.getAs("description"));
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Assertions.assertEquals(2 ,split(row.getAs("keywords"), ", ").length);
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Assertions.assertTrue(row.getAs("keywords").toString().contains("archeologie"));
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Assertions.assertTrue(row.getAs("keywords").toString().contains("archaeology"));
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Assertions.assertEquals("UNKNOWN", row.getAs("language"));
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Assertions.assertNull( row.getAs("publication_date"));
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Assertions.assertNull( row.getAs("publisher"));
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Assertions.assertEquals("None", row.getAs("title"));
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Assertions.assertEquals("publication", row.getAs("type"));
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row = tmp
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.where("id = '50|DansKnawCris::26780065282e607306372abd0d808245'")
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.first();
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Assertions.assertEquals(ModelConstants.OPEN_ACCESS_RIGHT().getClassid(),row.getAs("accessright"));
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Assertions.assertNull(row.getAs("country"));
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Assertions.assertNull(row.getAs("description"));
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Assertions.assertEquals(2 ,split(row.getAs("keywords"), ", ").length);
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Assertions.assertTrue(row.getAs("keywords").toString().contains("archeologie"));
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Assertions.assertTrue(row.getAs("keywords").toString().contains("archaeology"));
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Assertions.assertEquals("UNKNOWN", row.getAs("language"));
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Assertions.assertNull( row.getAs("publication_date"));
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Assertions.assertNull( row.getAs("publisher"));
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Assertions.assertEquals("None", row.getAs("title"));
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Assertions.assertEquals("publication", row.getAs("type"));
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}
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@Test
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public void testDumpAuthor() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/input/")
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.getPath();
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spark.read().text(getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/working/resultIds")
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.getPath())
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.write()
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.text(workingDir.toString() + "/working/resultIds/");
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SparkDumpResults.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/output",
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"-workingPath", workingDir.toString() + "/working",
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"-resultType", "publication",
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-sourcePath", sourcePath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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Dataset<Row> tmp = spark.read().option("header", "true").option("delimiter", Constants.SEP)
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.csv(workingDir.toString() + "/working/publication/author");
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Assertions.assertEquals(5, tmp.count());
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Assertions.assertEquals(1,tmp.where("firstName == 'Maryam'").count());
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Assertions.assertEquals(DHPUtils.md5("50|DansKnawCris::0224aae28af558f21768dbc6439c7a951"),tmp.where("firstName == 'Maryam'").first().getAs("id"));
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Assertions.assertEquals(DHPUtils.md5("0000-0003-2914-2734"),tmp.where("firstName == 'Michael'").first().getAs("id"));
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Assertions.assertEquals(DHPUtils.md5("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d92"),tmp.where("firstName == 'Mikhail'").first().getAs("id"));
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}
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@Test
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public void testDumpResultAuthorRelations() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/input/")
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.getPath();
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spark.read().text(getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/working/resultIds")
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.getPath())
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.write()
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.text(workingDir.toString() + "/working/resultIds/");
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SparkDumpResults.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/output",
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"-workingPath", workingDir.toString() + "/working",
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"-resultType", "publication",
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-sourcePath", sourcePath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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Dataset<Row> tmp = spark.read().option("header", "true").option("delimiter", Constants.SEP)
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.csv(workingDir.toString() + "/working/publication/result_author");
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Assertions.assertEquals(6, tmp.count());
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Assertions.assertEquals(2, tmp.where("author_id == '" + DHPUtils.md5("0000-0003-2914-2734") + "'").count());
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Assertions.assertEquals(1, tmp.where("author_id == '" + DHPUtils.md5("0000-0003-2914-2734") + "'")
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.where("result_id == '50|DansKnawCris::0224aae28af558f21768dbc6439c7a95'").count());
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Assertions.assertEquals(1, tmp.where("author_id == '" + DHPUtils.md5("0000-0003-2914-2734") + "'")
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.where("result_id == '50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9'").count());
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}
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@Test
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public void testDumpResultPid() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/input/")
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.getPath();
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spark.read().text(getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/working/resultIds")
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.getPath())
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.write()
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.text(workingDir.toString() + "/working/resultIds/");
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SparkDumpResults.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/output",
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"-workingPath", workingDir.toString() + "/working",
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"-resultType", "publication",
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-sourcePath", sourcePath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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Dataset<Row> tmp = spark.read().option("header", "true").option("delimiter", Constants.SEP)
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.csv(workingDir.toString() + "/working/publication/result_pid");
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tmp.show(false);
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Assertions.assertEquals(4, tmp.count());
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Assertions.assertEquals(2, tmp.where("result_id == '50|DansKnawCris::0224aae28af558f21768dbc6439c7a95'").count());
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Assertions.assertEquals("10.1023/fakedoi", tmp.where("result_id == '50|DansKnawCris::0224aae28af558f21768dbc6439c7a95' and type == 'doi'").first().getAs("pid"));
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}
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}
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