334 lines
11 KiB
Java
334 lines
11 KiB
Java
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package eu.dnetlib.dhp.oa.graph.dump.eosc;
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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.List;
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import java.util.Optional;
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import org.apache.commons.io.FileUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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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.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.eosc.model.Indicator;
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import eu.dnetlib.dhp.eosc.model.Organization;
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import eu.dnetlib.dhp.eosc.model.Result;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import scala.Tuple2;
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/**
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* @author miriam.baglioni
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* @Date 21/09/22
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*/
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public class SelectEoscResultTest {
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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(SelectEoscResultTest.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(SelectEoscResultTest.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(SelectEoscResultTest.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(SelectEoscResultTest.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 selectEoscResults() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/eosc/input/publication")
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.getPath();
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final String cmp = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
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.getPath();
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final String mdp = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/eosc/working/masterduplicate")
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.getPath();
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SelectEoscResultsJobStep1.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/publication",
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"-sourcePath", sourcePath,
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-communityMapPath", cmp,
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"-eoscDatasourceIdsPath", mdp
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Result> tmp = sc
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.textFile(workingDir.toString() + "/publication")
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.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
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Assertions.assertEquals(3, tmp.count());
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Assertions
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.assertEquals(
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0,
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tmp
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.filter(r -> Optional.ofNullable(r.getAffiliation()).isPresent() && r.getAffiliation().size() > 0)
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.count());
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tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
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}
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// "source":"20|13811704aa70::51a6ade52065e3b371d1ae822e07f1ff","subRelType":"affiliation","target":"50|06cdd3ff4700::93859bd27121c3ee7c6ee4bfb1790cba"
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// legalname = Doris Engineering (France)
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// pid =
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// [(pidtype:"GRID","value":"grid.432986.2"),("classid":"ROR","value":"https://ror.org/03nd0ms94"),("classid":"GRID","value":"grid.432986.2"),("classid":"ROR","value":"https://ror.org/03nd0ms94")]
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// sono replicate e ci dovrebbero essere uniche nel dump
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// "source":"20|MetisRadboud::b58bdbe8ae5acead04fc76777d2f8017","subRelType":"affiliation","target":"50|06cdd3ff4700::93859bd27121c3ee7c6ee4bfb1790cba"
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// legalname = RENNES METROPOLE
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// pid = [(PIC, 892062829)]
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// "source":"20|____________::d1b0ee22411434cf905692d0fac25749","subRelType":"affiliation","target":"50|06cdd3ff4700::cd7711c65d518859f1d87056e2c45d98"
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// legalname = MIKARE RESEARCH
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// pid = []
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// for 50|06cdd3ff4700::ff21e3c55d527fa7db171137c5fd1f1f no affiliation relation is provided
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@Test
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public void ExtendEoscResultWithOrganizationTest() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/eosc/input")
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.getPath();
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final String cmp = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
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.getPath();
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String resultPath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/eosc/working/publication")
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.getPath();
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ExtendEoscResultWithOrganizationStep2.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/publication",
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"-sourcePath", sourcePath,
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// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-resultPath", resultPath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Result> tmp = sc
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.textFile(workingDir.toString() + "/publication")
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.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
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Assertions.assertEquals(3, tmp.count());
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Assertions
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.assertEquals(
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2,
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tmp
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.filter(r -> Optional.ofNullable(r.getAffiliation()).isPresent() && r.getAffiliation().size() > 0)
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.count());
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Assertions
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.assertEquals(
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2,
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tmp
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.filter(r -> r.getId().equalsIgnoreCase("50|06cdd3ff4700::93859bd27121c3ee7c6ee4bfb1790cba"))
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.first()
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.getAffiliation()
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.size());
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List<Organization> affiliations = tmp
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.filter(r -> r.getId().equalsIgnoreCase("50|06cdd3ff4700::93859bd27121c3ee7c6ee4bfb1790cba"))
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.first()
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.getAffiliation();
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Assertions
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.assertTrue(
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affiliations.stream().anyMatch(a -> a.getName().equalsIgnoreCase("Doris Engineering (France)")));
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Assertions.assertTrue(affiliations.stream().anyMatch(a -> a.getName().equalsIgnoreCase("RENNES METROPOLE")));
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Organization organization = affiliations
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.stream()
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.filter(a -> a.getId().equalsIgnoreCase("20|13811704aa70::51a6ade52065e3b371d1ae822e07f1ff"))
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.findFirst()
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.get();
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Assertions.assertEquals("Doris Engineering (France)", organization.getName());
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Assertions
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.assertTrue(
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organization
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.getPid()
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.stream()
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.anyMatch(
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p -> p.getValue().equalsIgnoreCase("grid.432986.2") && p.getType().equalsIgnoreCase("grid")));
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Assertions
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.assertTrue(
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organization
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.getPid()
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.stream()
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.anyMatch(
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p -> p.getValue().equalsIgnoreCase("https://ror.org/03nd0ms94")
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&& p.getType().equalsIgnoreCase("ror")));
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Assertions.assertEquals(2, organization.getPid().size());
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organization = affiliations
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.stream()
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.filter(a -> a.getId().equalsIgnoreCase("20|MetisRadboud::b58bdbe8ae5acead04fc76777d2f8017"))
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.findFirst()
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.get();
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Assertions.assertEquals("RENNES METROPOLE", organization.getName());
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Assertions.assertEquals(1, organization.getPid().size());
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Assertions
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.assertTrue(
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organization.getPid().get(0).getValue().equalsIgnoreCase("892062829")
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&& organization.getPid().get(0).getType().equalsIgnoreCase("pic"));
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Assertions
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.assertEquals(
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1,
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tmp
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.filter(r -> r.getId().equalsIgnoreCase("50|06cdd3ff4700::cd7711c65d518859f1d87056e2c45d98"))
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.first()
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.getAffiliation()
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.size());
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Assertions
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.assertEquals(
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"MIKARE RESEARCH",
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tmp
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.filter(r -> r.getId().equalsIgnoreCase("50|06cdd3ff4700::cd7711c65d518859f1d87056e2c45d98"))
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.first()
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.getAffiliation()
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.get(0)
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.getName());
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Assertions
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.assertEquals(
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0,
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tmp
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.filter(r -> r.getId().equalsIgnoreCase("50|06cdd3ff4700::cd7711c65d518859f1d87056e2c45d98"))
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.first()
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.getAffiliation()
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.get(0)
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.getPid()
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.size());
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Assertions
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.assertFalse(
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Optional
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.ofNullable(
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tmp
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.filter(
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r -> r.getId().equalsIgnoreCase("50|06cdd3ff4700::ff21e3c55d527fa7db171137c5fd1f1f"))
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.first()
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.getAffiliation())
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.isPresent());
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}
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@Test
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public void verifyIndicatorsTest() throws Exception {
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// 50|06cdd3ff4700::93859bd27121c3ee7c6ee4bfb1790cba
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// 50|06cdd3ff4700::ff21e3c55d527fa7db171137c5fd1f1f
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final String resultPath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/eosc/working/publication")
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.getPath();
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final String actionSetPath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/eosc/input/actionset")
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.getPath();
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Utils
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.readPath(spark, actionSetPath, eu.dnetlib.dhp.schema.oaf.Result.class)
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.toJavaRDD()
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.map(p -> new AtomicAction(p.getClass(), p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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.saveAsHadoopFile(
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workingDir.toString() + "/actionSet", Text.class, Text.class, SequenceFileOutputFormat.class);
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ExtendWithUsageCounts.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/publication",
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"-actionSetPath", workingDir.toString() + "/actionSet",
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"-resultPath", resultPath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Result> tmp = sc
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.textFile(workingDir.toString() + "/publication")
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.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
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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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x -> x.getId().equals("50|06cdd3ff4700::93859bd27121c3ee7c6ee4bfb1790cba") &&
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Optional.ofNullable(x.getIndicator()).isPresent())
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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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x -> x.getId().equals("50|06cdd3ff4700::ff21e3c55d527fa7db171137c5fd1f1f") &&
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Optional.ofNullable(x.getIndicator()).isPresent())
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.count());
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Indicator indicators = tmp
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.filter(x -> x.getId().equals("50|06cdd3ff4700::93859bd27121c3ee7c6ee4bfb1790cba"))
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.first()
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.getIndicator();
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Assertions.assertEquals(79, Integer.valueOf(indicators.getUsageCounts().getDownloads()));
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Assertions.assertEquals(94, Integer.valueOf(indicators.getUsageCounts().getViews()));
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indicators = tmp
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.filter(x -> x.getId().equals("50|06cdd3ff4700::ff21e3c55d527fa7db171137c5fd1f1f"))
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.first()
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.getIndicator();
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Assertions.assertEquals(0, Integer.valueOf(indicators.getUsageCounts().getDownloads()));
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Assertions.assertEquals(1, Integer.valueOf(indicators.getUsageCounts().getViews()));
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Assertions.assertEquals(1, tmp.filter(r -> !Optional.ofNullable(r.getIndicator()).isPresent()).count());
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}
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}
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