251 lines
8.0 KiB
Java
251 lines
8.0 KiB
Java
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package eu.dnetlib.dhp.bypassactionset;
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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.List;
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import java.util.stream.Collectors;
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import eu.dnetlib.dhp.schema.oaf.Author;
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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 org.apache.neethi.Assertion;
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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.bypassactionset.bipfinder.PrepareBipFinder;
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import eu.dnetlib.dhp.bypassactionset.bipfinder.SparkUpdateBip;
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import eu.dnetlib.dhp.bypassactionset.model.BipScore;
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import eu.dnetlib.dhp.countrypropagation.CountryPropagationJobTest;
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import eu.dnetlib.dhp.schema.oaf.Measure;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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public class BipTest {
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private static final Logger log = LoggerFactory.getLogger(FOSTest.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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private static final String ID_PREFIX = "50|doi_________";
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(BipTest.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(FOSTest.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 prepareBipTest() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/bip/bip.json")
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.getPath();
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PrepareBipFinder
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--inputPath", sourcePath,
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"--outputPath", workingDir.toString() + "/remapDoi"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<BipScore> tmp = sc
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.textFile(workingDir.toString() + "/remapDoi")
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.map(item -> OBJECT_MAPPER.readValue(item, BipScore.class));
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Assertions.assertEquals(86, tmp.count());
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// tmp.foreach(v -> System.out.println(OBJECT_MAPPER.writeValueAsString(v)));
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String doi1 = ID_PREFIX +
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IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.0000/096020199389707"));
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Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).count());
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Assertions.assertEquals(3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getScoreList().size());
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Assertions
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.assertEquals(
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"6.34596412687e-09", tmp
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.filter(r -> r.getId().equals(doi1))
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.collect()
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.get(0)
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.getScoreList()
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.stream()
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.filter(sl -> sl.getId().equals("influence"))
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.collect(Collectors.toList())
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.get(0)
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.getUnit()
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.get(0)
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.getValue());
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Assertions
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.assertEquals(
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"0.641151896994", tmp
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.filter(r -> r.getId().equals(doi1))
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.collect()
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.get(0)
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.getScoreList()
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.stream()
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.filter(sl -> sl.getId().equals("popularity_alt"))
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.collect(Collectors.toList())
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.get(0)
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.getUnit()
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.get(0)
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.getValue());
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Assertions
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.assertEquals(
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"2.33375102921e-09", tmp
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.filter(r -> r.getId().equals(doi1))
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.collect()
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.get(0)
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.getScoreList()
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.stream()
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.filter(sl -> sl.getId().equals("popularity"))
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.collect(Collectors.toList())
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.get(0)
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.getUnit()
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.get(0)
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.getValue());
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}
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@Test
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void updateResult() throws Exception {
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final String bipScorePath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/bip/preparedbip.json")
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.getPath();
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final String inputPath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/bip/publicationnomatch.json")
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.getPath();
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SparkUpdateBip
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--bipScorePath", bipScorePath,
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"--inputPath", inputPath,
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"--outputPath", workingDir.toString() + "/publication",
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"--resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication"
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});
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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() + "/publication/bip")
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.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
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Assertions.assertEquals(6, tmp.count());
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Assertions.assertEquals(0, tmp.filter(r -> r.getMeasures() != null).count());
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tmp.foreach(r -> Assertions.assertEquals("publication", r.getResulttype().getClassid()));
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}
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@Test
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void updateResultMatchCheckMeasures() throws Exception {
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final String bipScorePath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/bip/preparedbip.json")
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.getPath();
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final String inputPath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/bip/publicationmatch.json")
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.getPath();
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SparkUpdateBip
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--bipScorePath", bipScorePath,
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"--inputPath", inputPath,
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"--outputPath", workingDir.toString() + "/publication",
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"--resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication"
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});
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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() + "/publication/bip")
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.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
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Assertions.assertEquals(6, tmp.count());
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Assertions.assertEquals(1, tmp.filter(r -> r.getMeasures() != null).count());
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Assertions
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.assertEquals(
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1, tmp.filter(r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f")).count());
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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(
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r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f")
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&& r.getMeasures() != null)
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.count());
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Assertions.assertEquals(3, tmp
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.filter(r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f"))
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.collect()
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.get(0)
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.getMeasures().size());
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Assertions.assertEquals("5.91019644836e-09",
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tmp.filter(r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f"))
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.collect()
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.get(0).getMeasures().stream().filter(m -> m.getId().equals("influence")).collect(Collectors.toList()).get(0).getUnit().get(0).getValue());
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Assertions.assertEquals("0.0",
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tmp.filter(r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f"))
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.collect()
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.get(0).getMeasures().stream().filter(m -> m.getId().equals("popularity_alt")).collect(Collectors.toList()).get(0).getUnit().get(0).getValue());
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Assertions.assertEquals("9.88840807598e-09",
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tmp.filter(r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f"))
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.collect()
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.get(0).getMeasures().stream().filter(m -> m.getId().equals("popularity")).collect(Collectors.toList()).get(0).getUnit().get(0).getValue());
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tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
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}
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}
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